southern school on computational chemistry 6...

Organizing Committee

Steven Davis University of Mississippi

Glake Hill, Jr. Jackson State University

Cynthia Hudley University of California at Santa Barbara

Jerzy Leszczynski (Chairman) Jackson State University

David H. Magers Mississippi College

Svein Saebo Mississippi State University

Staff

Shonda Allen Jackson State University

Olexandr Isayev Jackson State University

Yevgeniy Podolyan Jackson State University

Sponsors

National Science Foundation (EPSCoR) National Science Foundation (CREST)

University of California at Santa Barbara Army High Performance Computing Research Center

Department of Defense through the Engineer Research and Development Center (ERDC)

6 th Southern School on Computational Chemistry 3

Schedule of Events

Friday, April 7, 2006

Registration 12:00 noon – 2:00 p.m. 4:00 p.m. – 5:00 p.m.

Lunch 12:30 p.m. – 1:55 p.m.

Opening Remarks (Jerzy Leszczynski)

1:55 p.m. – 2:00 p.m.

Dušanka Janeži 2:00 p.m. – 3:00 p.m. Jane Murray 3:00 p.m. – 3:20 p.m. Anna Kaczmarek 3:20 p.m. – 3:40 p.m.

1st Session

Peter Politzer 3:40 p.m. – 4:00 p.m.

Coffee Break 4:00 p.m. – 4:30 p.m.

Ras Pandey 4:30 p.m. – 4:50 p.m. Jian-Ge Zhou 4:50 p.m. – 5:10 p.m. Andrea Michalkova 5:10 p.m. – 5:30 p.m.

2nd Session

Andrzej Wierzbicki 5:30 p.m. – 5:50 p.m.

Dinner 6:30 p.m. – 8:00 p.m.

Poster Session 8:00 p.m. – 10:00 p.m.

6 th Southern School on Computational Chemistry4

Saturday, April 8, 2006

Breakfast(provided by hotel)

8:00 a.m. – 9:00 a.m.

Registration 8:00 a.m. – 9:00 a.m. 10:30 a.m. – 11:30 p.m.

Kevin W. Plaxco 9:00 a.m. – 10:00 a.m. Dinadayalane Tandabany 10:00 a.m. – 10:20 a.m. 3rd Session Andrzej Sygula 10:20 a.m. – 10:40 a.m.

Coffee Break 10:40 a.m. – 11:10 a.m.

Manoj Shukla 11:10 a.m. – 11:30 a.m. David Close 11:30 a.m. – 11:50 a.m. Leonid Gorb 11:50 a.m. – 12:10 p.m.

4th Session

Devashis Majumdar 12:10 p.m. – 12:30 p.m.

Lunch 1:00 p.m. – 2:30 p.m.

Edyta Dyguda 2:30 p.m. – 2:50 p.m. David Magers 2:50 p.m. – 3:10 p.m. 5th Session Mohammad Qasim 3:10 p.m. – 3:30 p.m.

Coffee Break 3:30 p.m. – 4:00 p.m.

Bridgit Crews 4:00 p.m. – 4:20 p.m. Yinghong Sheng 4:20 p.m. – 4:40 p.m. Reeshemah Allen 4:40 p.m. – 5:00 p.m.

6th Session

Edmund Moses Ndip 5:00 p.m. – 5:20 p.m.

Dinner 6:00 p.m. – 8:00 p.m.


Oral Presentations

1st Session Session Chairman: Fillmore FreemanUniversity of California, Irvine

Dušanka JanežiNational Institute of Chemistry, Slovenia

Molecular modeling - a new approach

Jane MurrayUniversity of New Orleans

Molecular surface electrostatic potentials and anesthetic activity

Anna KaczmarekNicolaus Copernicus University

Interaction-induced properties through symmetry-adapted perturbation theory

Peter PolitzerUniversity of New Orleans

The reaction force

2nd Session Session Chairman: John WattsJackson State University

Ras Pandey University of Southern Mississippi

Computational modeling of film growth and tethered membrane

Jian-Ge Zhou Jackson State University

Does methanethiol adsorb on the Au(111) surface dissociate?

Andrea MichalkovaJackson State University

Theoretical study of adsorption of sarin and soman on edge clay mineral fragments

Andrzej WierzbickiUniversity of South Alabama

Novel aspects of molecular recognition and binding of antifreeze proteins at the water-ice interface

3rd Session Session Chairman: Mark JackFlorida A&M University

Kevin W. PlaxcoUniversity of California

My protein folds faster than yours: an experimentalist's view of a protein folding theory

Dinadayalane TandabanyJackson State University

Modeling of (5,5) armchair SWNT: Stone-Wales defect formation and physisorption of linear hydrocarbon inside the tube

Andrzej SygulaMississippi State University

Conformational studies of molecular clips and tweezers with bowl-shaped corannulene subunits


4th Session Session Chairman: Yevgeniy PodolyanJackson State University

Manoj ShuklaJackson State University

Excited state structures, interactions and proton transfer in guanine

David CloseEast Tennessee State University

Calculations on one-electron oxidation and one-electron reduction of nucleotides

Leonid GorbEngineer Research and Development Center

Conventional ab initio and molecular dynamics calculations: prediction of physical properties and chemical reactivity of DNA bases and nitro-compounds

Devashis Majumdar Jackson State University

Probing the acetylcholinesterase inhibition of sarin: A comparative interaction study of the inhibitor and acetylcholine with a model enzyme cavity

5th Session Session Chairman: Frances HillArmy High Performance Computing Research Center

Edyta Dyguda-KazimierowiczWroclaw University of Technology

Hazardous organophosphates: computational insight into gas phase alkaline hydrolysis of phosphorus-ester bonds

David Magers Mississippi College

Exploring the many uses of homodesmotic reactions

Mohammad QasimEngineer Research and Development Center

Comparison of structural reactivities of nitroaromatics, heterocyclic nitramines and cage heterocyclic nitramines under selected reaction conditions

6th Session Session Chairman: Jesse EdwardsFlorida A&M University

Bridgit Crews University of California

IR spectroscopy of gas phase clusters of biological molecules

Yinghong ShengJackson State University

Theoretical study of the photochemistry of spiropyrans

Reeshemah AllenJackson State University

Computational study of antioxidants: uric acid and ascorbic acid

Edmund Moses NdipHampton University

A comparative theoretical study of furan, pyrrole, and thiophene - based organic semiconductors


Table of Contents

15 Computational Studies of Substituted 2-Aminomaleimides Formation Dmytro Afanasyev, Sergiy Chepyshev, and Alexander Prosyanik

17 Computational Study of Antioxidants: Uric Acid and Ascorbic Acid Reeshemah Allen, M.K. Shukla and Jerzy Leszczynski

18 The DFT(BP86) Study of Bonding Mechanism in Transition-Metal Carbonyl Neutrals and CationsV. I. Bolshakov, V. V. Rossikhin, E. O. Voronkov, S. I. Okovytyy, and Jerzy Leszczynski

20 The Investigation of Electrooxidation of Water in HBF4 Solutions L.V.Borshchevich and V.F.Vargaljuk

22 Active-Site Inhibitor Modeling Using a Customized HIV-Protease Peptide Deborah J. Bryan, John West, Jesse Edwards, Reginald Parker, Ben M. Dunn

23 Conventional Strain Energy in Isomers of Dimethylcyclobutadiene Qianyi Cheng and David H. Magers

24 Calculations on One-Electron Oxidation and One-Electron Reduction of Nucleotides David M. Close

26 IR Spectroscopy of Gas Phase Clusters of Biological Molecules Bridgit Crews, Mattanjah S. de Vries

27 Size Dependence Emission Quenching Properties of Modified DNA Capped Gold Nanoparticles Gopal Darbha, Angela Fortner, Jelani Griffin and Paresh Chandra Ray

28 Modeling of (5,5) Armchair SWNT: Stone-Wales Defect Formation and Physisorption of Linear Hydrocarbon Inside the Tube T. C. Dinadayalane and Jerzy Leszczynski

29 Theoretical Comparison of Cisplatin and Cisplatin Analogs Using DFT Calculations LaTanya Dixon, Glake Hill, Jerzy Leszczynski

30 Hazardous Organophosphates: Computational Insight into Gas Phase Alkaline Hydrolysis of Phosphorus-Ester Bonds Edyta Dyguda-Kazimierowicz, W. Andrzej Sokalski, and Jerzy Leszczy ski

32 Excitation of Surface Dipole and Solenoidal Modes on Toroidal NanostructuresM. Encinosa and M. Jack

33 C—H, S—H, and S—C Insertion Reactions, 1,2-Rearrangements (Thia-Wolff), and Singlet-Triplet Gaps of Disulfinylcarbenes: A Computational Study Fillmore Freeman, Quan M. Kha, Thang X. Nguyen, Tarang Safi, and Norman E. Sebastian

34 Conventional ab Initio and Molecular Dynamics Calculations: Prediction of Physical Properties and Chemical Reactivity of DNA Bases and Nitro-Compounds Leonid Gorb


35 Causes of Rare Tautomer Forms Stabilization of Bases are in Single- and Double-Stranded DNA under Dimers Formation H. A. Grebneva

39 Computational Studies of a Series of Gluccocorticoid Steroid Derivatives Jessica Hardaway, M. Omar. F. Khan, Zhengqing You, Henry J. Lee, and Jesse Edwards

40 Effect of Benzene and Strained Bicyclo[2.1.1] Hexene Annelation on Li+- Interaction Ayorinde Hassan, T. C. Dinadayalane and Jerzy Leszczynski

41 Ab Initio Studies of the Tautomerization of 3,7-dihydro-1H-purine-2,6-dione Tiffani Holmes, Glake Hill, Jerzy Lesczcynski

42 A Density Functional Study of the Reaction of Perfluorooctanoic Acid with Sulfur Containing Amino Acids Tiffani Holmes, Carmen Robinson, Glake Hill, Jerzy Leszczynski

43 Ab Initio Studies of Inclusion Complexes of Cyclodextrins with Polycyclic Aromatic HydrocarbonsMing-Ju Huang

44 The Initial Chemical Events in CL-20 under Extreme Condition: An ab Initio Molecular Dynamics Study Olexandr Isayev, Yana Kholod, Leonid Gorb, M. Qasim, J. Furey, H. Fredrickson and Jerzy Leszczynski

45 Molecular Modeling - A New Approach Dušanka Janeži

46 Interaction-Induced Properties through Symmetry-Adapted Perturbation Theory Anna Kaczmarek, Bart omiej Skwara, Andrzej J. Sadlej and Jerzy Leszczynski

47 The Mechanism of Alkenes Epoxidation with Potassium Peroxymonosulfate. Ab Initio StudyY. Kholod, M. Belov, S. Okovytyy, J. Leszczynski

48 The Mechanism of Alkaline Hydrolysis of the Cyclic Nitramines: RDX, HMX and CL-20. A DFT Study Y. Kholod, S. Okovytyy, L. Gorb M. Qasim, J. Furey, H. Fredrickson and J. Leszczynski

49 Kinetic Model of Cytosine Bimolecular Tautomerization Dmytro Kosenkov, Leonid Gorb, Oleg V. Shishkin and Jerzy Leszczynski

51 Quantum-Chemical Research of Reaction Mechanism V. Kukueva

54 Quantum Mechanical Calculations of Molecular Structure and Vibrational Spectra of CH3-NClnSiF3 (N = 0-3) Compounds G.M. Kuramshina, S.V .Syn’ko, Yu.A. Pentin

58 DFT Calculations of Substituted Anilines G.M. Kuramshina, S.F. Makhmutova, S.V. Pikhtovnikov, S.M. Usmanov

61 Assessment of the Performance of Density-Functional Methods for Calculations on Iron Porphyrins and Related Compounds Meng-Sheng Liao, John D. Watts, and Ming-Ju Huang


62 Understanding the Unique Architecture of Scx@C82 (x=1, 2 and 3) by Use of the 4n+2 RuleDan Liu and Frank Hagelberg

63 Conventional Strain Energy in Boracycloproane, Diboracyclopropane, Boracyclobutane and Diboracyclobutane Brandon Magers, Harley McAlexander, and David H. Magers

64 Exploring the Many Uses of Homodesmotic Reactions David H. Magers

65 Probing the Acetylcholinesterase Inhibition of Sarin: A Comparative Interaction Study of the Inhibitor and Acetylcholine with a Model Enzyme Cavity D. Majumdar, Szczepan Roszak, and Jerzy Leszczynski

66 Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of Carbon and Silicon Harley McAlexander, Brandon Magers, Crystal B. Coghlan, and David H. Magers

67 Adsorption of Sarin on Platinum and Palladium (001) and (111) Surfaces: An Ab Initio StudyA. Michalkova, D. Majumdar, and J. Leszczynski

69 Theoretical Study of Adsorption of Sarin and Soman on Edge Clay Mineral Fragments A. Michalkova, J. Martinez, O. A. Zhikol, L. Gorb, O. V. Shishkin, J. Leszczynski

71 Molecular Surface Electrostatic Potentials and Anesthetic Activity Jane S. Murray

72 The Quantum-Chemical Investigation of Heterocyclization Process for Amines of the Endo-5-aminomethyl-exo-2,3-epoxybicyclo[2.2.1]heptane Row Okovytyy S.I., Tokar A.V., Kasyan L.I.

74 Computational Modeling of Film Growth and Tethered Membrane R.B. Pandey

75 Generalized Kinetic Model for the Molecular Architecture of Polymer Systems R. Parker, J. Edwards, A. S. Abhiraman, M. J. Realff and D. A. Ling

76 Computational Studies of Solvated Sevelamar Hydrochloride R. Parker, J. Edwards, Y. Woodard, A. A. Odukale, C. Batich, and E. Ross

77 Theoretical Study of the Adsorption of VX on Calcium Oxide Y. Paukku, A. Michalkova, and J. Leszczynski

79 Computational DFT Study of the Mechanism of the Acid-Catalyzed Aminolysis of Succinic AnhydrideT. Petrova, S. Okovytyy, L. Gorb, J. Leszczynski

81 To the Problem of Calculation of Unstable Fluoro-Complexes Sublimation Heats V.N. Plakhotnyk, K.S.Gavrichev, V.V. Rossikhin, E.I.Kustov, S.I. Okovytyy, J. Leszczynski

83 The Reaction Force Peter Politzer

84 Comparison of Structural Reactivities of Nitroaromatics, Heterocyclic Nitramines and Cage Heterocyclic Nitramines under Selected Reaction Conditions Mohammad Qasim, Jerzy Leszczynski, Leonid Gorb, Herbert Fredrickson


86 My Protein Folds Faster than Yours: An Experimentalist's View of a Protein Folding TheoryKevin W. Plaxco

87 Quantitative Structure-Activity Relationship Study on Estrogenic Activity of Terpenoids Isolated from Ferula Plants B.F. Rasulev, A.I. Saidkhodzhaev, S.S. Nazrullaev, K.S. Akhmedkhodzhaeva, Z.A. Khushbaktova, J. Leszczynski

88 Docking and Molecular Simulations of a Series of Estradiol Derivative Selective Estrogen Modulators J. Robinson, J. S. Cooperwood, J. Edwards, D. Simmons, M. Musa, R. Parker

89 Theoretical Study of Adsorption of Selected Nucleic Acids on Dickite T. L. Robinson, A. Michalkova, L. Gorb, and J. Leszczynski

91 Molecular Dynamic Studies of Several HIV-1 Protease Modified Peptide Inhibitors Christina Russell, Jesse Edwards, John West, Reginald Parker, Ben M. Dunn

92 Electron Impact Ionization of Ions with q > 2 B. C. Saha, A. K. Basak and M. A. Uddin

95 Understanding Strong Two-Photon Absorption in Porphyrin Monomer and Dimers Zuhail Sainudeen and Paresh Chandra Ray

96 Towards the Quantum Computing.Theoretical Studies of Si/Ge Microclusters Julia Saloni, Szczepan Roszak, and Jerzy Leszczynski

97 The Quantum-Chemical Analysis of the Influence of Glycine Ligand on the Electroreduction of Cr3+/2+ Ions V.A. Seredjuk, V.F. Vargaljuk

99 Theoretical Study of the Photochemistry of Spiropyrans Yinghong Sheng and Jerzy Leszczynski

100 Excited State Structures, Interactions and Proton Transfer in Guanine M.K. Shukla and Jerzy Leszczynski

103 Comparative QSAR Study of the Anti-inflammatory Activity of Some Sesquiterpene Lactones: GA-PLS versus GA-MLRA Methods Talibah Smith, Bakhtiyor Rasulev and Jerzy Leszczynski

104 Side-chain Mobility and Binding Selectivity of Naphthylquinoline Derivatives: Correlation of Conformational Energetics with Thermodynamic Binding Energies Angela Sood, M. Jeanann Lovell, G. Reid Bishop, and David H. Magers

106 Enthalpies of Formation of TNT Derivatives by Homodesmotic Reactions Amika Sood, Patricia Honea, and David H. Magers

107 The Quantum-Chemical Calculations of Reduction-Oxidation Potentials for Cuz+/Cu0

SystemsO.S. Stets, V.F. Vargaljuk, V.A. Polonskiy, V.A. Seredjuk

109 Conformational Studies of Molecular Clips and Tweezers with Bowl-Shaped Corannulene SubunitsAndrzej Sygula


111 Theoretical Studies on Oxygen Proton Bound Systems Jaroslaw J. Szymczak, Szczepan Roszak, and Jerzy Leszczynski

112 Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of Carbon and Germanium Lyssa A. Taylor and David H. Magers

113 Investigations of the Molecular Interactions of CNT, Lignin and Epon 862 E. Whitby, J. Edwards, R. Parker, Q. Liu, W. Johnson, J. Willis, D. Thomas and D. Ryan

114 Novel Aspects of Molecular Recognition and Binding of Antifreeze Proteins at the Water-Ice Interface Andrzej Wierzbicki

115 Comparative Investigation of Three Dimensional Si Clusters on Graphite and Diamond SubstratesJianhua Wu and Frank Hagelberg

116 Film Formation with Hydrophobic and Polar Groups in Reactive Evaporating Aqueous Solution: A Bond-Fluctuating Simulation Model Shihai Yang, Sam Bateman, Ras Pandey, Marek Urban

117 Computational Molecular Electronics / Biochip Design Ilya Yanov, Yana Kholod and Jerzy Leszczynski

118 The Origin of Surface Localized Ionic Clusters during Film Formation; Spectroscopic Studies and ab Initio Calculations M. Yu, Y. Sheng, J. Leszczynski, and M. W. Urban

119 Does Methanethiol Adsorb on the Au(111) Surface Dissociate? Jian-Ge Zhou and Frank Hagelberg

120 Anomalous Receptivity of Timber-Based Materials With Respect to Gasoline as a Consequence of Intermolecular Interaction in the Cellulose – Aromatic Hydrocarbons SystemR. Zhu, M. Soroka, Yu. Zelenko, V. Rossikhin, V. Plakhotnyk, S.I. Okovytyy, J. Leszczynski

6th Southern School on Computational Chemistry 15

Computational Studies of Substituted 2-Aminomaleimides Formation

Dmytro Afanasyev, Sergiy Chepyshev, and Alexander Prosyanik

Laboratory of Biologically Active Compounds, Ukrainian State Chemical Technology University, Gagarin ave., 8, Dnepropetrovsk, 49005

Substituted 2-aminomaleimides are of great interest because of their use as agricultural chemicals, pharmaceuticals and their synthetic intermediates [1]. A method for the treatment of conditions associated with a need for inhibition of GSK-3, such as diabetes, dementias such as Alzheimer’s disease and manic depression, comprising administration of pharmaceutically effective forms of 2-aminomaleimides has been proposed recently [2]. The present report is devoted to computational studies of N-alkyl-2-alkylaminomaleimides formation. It has been discovered in our laboratory [3] and takes place in the reaction between Z-2-amino-3-ethoxycarbonylacrylic acid alkylamides and primary aliphatic amines. According to our opinion, there are two possible routes of the reaction:

NH2

CONHREtO2C

N

NH2

O O

R

RNH2

NH2EtO2C

CONHR

N

NHR

O O

R

RNH 2

EtO2C NHR

CONHR

NH2

H

H

In order to determine energetically favorable pathway of the reaction quantum-chemical calculations for the addition of methylamine to Z-2-amino-3-ethoxycarbonylacrylic acid methylamide have been carried out. Structures of transition state, prereaction complex and product of the addition reaction have been located on the PES. As a theoretical method, PBE density-functional [4] was chosen along with TZ2P basis set and Coulomb fitting techniques. All calculations have been conducted with fast RI-DFT code incorporated into PRIRODA 2.02+ program package written by D. Laikov [5]. Results of the calculations are presented on the potential energy diagram below.

6th Southern School on Computational Chemistry16

Interaction between molecules in prereaction complex seems to be weak and increased integration accuracy is needed to locate the minimum corresponding to the complex. Transition state lays 48.8 kcal/mol higher than prereaction complex and has a closed-shell character.

Calculations for the rotation pathway are in progress.

References:

[1] Pat. JP58055455, Cl. C07D207/456.- Publ. 1983-04-01; Pat. JP58088359, Cl. C07D207/456.- Publ. 1983-05-26.[2] Pat. WO 00/21927, Cl. C07D207/44, 403/04, 401/04.- Publ. 20.04.00. [3] a) S.V. Chepyshev, I.V. Chernyj, K.V. Yanova, V.A. Alexenko, A.V. Prosyanik, Ukrainian Journal of Chemistry (in preparation);

b) Thesis of International Conference on Heterocyclic Compounds Chemistry - Kost-2005, 17-21 Oct, 2005, Moscow.[4] J.P.Perdew, K.Burke, M.Ernzerhof, Phys. Rev. Lett., 77 (1996) 3865-3868. [5] D.N. Laikov, Chem. Phys. Lett., 1997, 281,151.

Acknowledgements:

Generous support of Prof. Jerzy Leszczynski is gratefully acknowledged. Sincere thanks are also to Dr. Dmitri Laikov for the use of his PRIRODA program.

References.


Computational Study of Antioxidants: Uric Acid and Ascorbic Acid

Reeshemah Allen, M.K. Shukla and Jerzy Leszczynski

Computational Center for Molecular Structure and Interactions Department of Chemistry, Jackson State University

1400 J.R. Lynch Street, Jackson, MS 39217

In biological systems, antioxidants posses the ability to intervene in oxidation-reduction reactions by decreasing the rate in which free radicals react with vital cellular components such as lipid membranes, proteins, or DNA. The body provides a defense against such mutagens, carcinogen and other oxidative damage through the use of naturally occurring antioxidants, such as uric acid (UA) and ascorbic acid (AA) or Vitamin C. Uric acid, the end product of purine catabolism in human is widely known as an endogenous water soluble antioxidant. L-ascorbic acid (vitamin C) is a naturally occurring water soluble antioxidant that exists in the pure form as a white crystalline solid. Ascorbic acid is an extremely interesting molecule that possesses many important biochemical properties. However, primates and guinea pigs lack the ability to synthesis ascorbate from glucose and are therefore dependent on dietary intake.

A comprehensive and extensive study on the structures and properties of uric and ascorbic acid were performed employing B3LYP and MP2 levels of theories. The structure of different tautomers, anions, and different radical species of uric and ascorbic acid were closely analyzed. The effect of aqueous solvation on the relative stability of the neutral, anionic, and radical species of uric acid was investigated using Tomasi’s polarized continuum model. The preferred tautomer of uric acid was the all keto structure, while the most stable anion of urate occurs due to the deprotonation at the N3 site, and the most stable radical anion is UAN3

•N9¯ with the spin

density located at the C5 position. The effects of aqueous solution on ascorbic acid were evaluated by using the CPCM and PCM solvation models. The investigation of ascorbate revealed that the most stable structure for asorbate was that deprotonated at the O3 site, the most stable radical anion is AAO3

•O2¯ with the spin density located within the ring. The computed

hyperfine coupling constants of the ascorbate radical anion were found to be in good agreement with the corresponding experimental data.

A theoretical DFT study using the B3LYP functional was also performed to investigate the interaction of urate and ascorbate with Li+, Na+, K+, Be2+, Mg2+, and Ca2+ metal cations. The results show that the calculated metal cations will form bicoordination complexes with urate and ascorbate agreeing with the corresponding experimental data. The monovalent metal cations energetically preferred the N3 and O2 sites of the urate, furthermore the divalent metal cations will interact through the N7 and O6 sites of urate in the gas phase. In water solution the interaction of monovalent metal cations with urate exuded the same trend in the gas phase. The divalent cations containing complexes, on the other hand, were found to be stabilized significantly in the water solution. This suggests that several divalent metal complexes will be present in the water solution. The study involving the metal complexes with ascorbic acid were revealed equally interesting. The investigation of the interaction of the monovalent metals Li+,Na+, and K+ cations suggested that these metal are incline to bicoordinate with the AAO3

- anion at O2 and O3 sites, furthermore the divalent cations Be2+, Mg2+, and Ca2+ would prefer to bicoordinate with the AAO3

- anion at the O1 and O2 sites. Typically, the interaction of studied metal cations with ascorbate in the bulk water solution was similar to that in the gas phase.


The DFT(BP86) Study of Bonding Mechanism in Transition-Metal Carbonyl Neutrals and Cations

V. I. Bolshakov,1 V. V. Rossikhin,1 E. O. Voronkov,2 S. I. Okovytyy,3,4

and Jerzy Leszczynski4

1Pridneprovs’ka State Academy of Civil Engineering and Architecture, 49635, Ukraine, 2Dnepropetrovsk National Technical University, Dnepropetrovsk, 49010, Ukraine,

3Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine, 4Computational Center for Molecular Structure and Interactions, Department of Chemistry,

Jackson State University, Jackson, Mississippi 39217 USA

Results of calculations of structure and oscillatory spectra of neutral and positively charged carbonyls of transition metals within the frame of a method of the density functional theory are presented at exchange-correlation functional BP86 [1, 2]. The specified parameters for V(CO)6,Cr(CO)6, Ni(CO)4 , Mo(CO)6 , W(CO)6 molecules and corresponding cations were calculated using recently developed 6-31G## basis set [3, 4] and modified using similarly procedure pseudo-potential CEP-31G##basic set. It should be note, that 6-31G## basic set does not cover atoms of molybdenum and tungsten. For Carbon and Oxygen atoms a standard 6-31G* basic set has been used. Obtained by Gaussian 03 [5] results of calculations (see Table 1) show, that proposed for atoms of metals basis sets allow to receive bond lengths and oscillatory frequencies in the consent with experiment [6, 7]. It, in turn, enables the quantitative description of mutual importance - and - bonding on strength of M-CO bonds.

Table 1 Calculated bond lengths (Å) and frequencies ( -1) of metalcarbonyl compounds

Compound Bondlength,frequency

6-31g##/6-31g*

CEP-31g##/6-31g*

M-C(Å),

M-C(%) Expt.

V-C 2.004 2.000 - 2.0156

C-O 1.164 1.164 - 1.1386

V-C 612 614 - - V(CO)6

C-O1966(IR)1984(RS)

1967(IR)1985(RS) - 19867

V-C 2.066 2.062 0.062 - C-O 1.151 1.151 - -

V-C 536 537 12.4;12.5 - V(CO) 6

C-O 2058.5(IR) 2060.6(IR) - - Cr-C 1.913 1.908 - 1.9206

C-O 1.164 1.164 - 1.1606

Cr-C 686 680 - - Cr(CO)6

C-O1995.2(IR)2014.8(RS)

1996.6(IR)2015.8(RS) - 2002.967

Cr(CO) 6 Cr-C 1.987 1.984 0.0740.076 Cr-C ~0.148


C-O 1.151 1.151 - - Cr-C 591 587 13.8;13.7 ~15.08

C-O 2058.9(IR) 2061.3(IR) - - Ni-C 1.826 1.820 - 1.8386

C-O 1.160 1.161 - 1.1416

Ni-C 447 447 - - Ni(CO)4

C-O2039.2(IR.RS)

2033.8(IR.RS) - 2061.37

Ni-C 1.900 1.899 0.0740.079 -

C-O 1.145 1.146 - - Ni-C 417 410 6.7 ;8.3 -

Ni(CO) 4

C-O2130.3{IR)2167.0(RS)

2127.0{IR)2163.7(RS) - 2176.27

Mo-C - 2.064 - 2.0636

C-O - 1.164 - 1.1456

Mo-C - 598 - - Mo(CO)6

C-O - 1988.4(IR)2010.5(RS) - 2005.497

Mo-C - 2.124 0.060 - C-O - 1.152 - -

Mo-C - 547 8.5 - Mo(CO) 6

C-O - 2062.8(IR) - - W-C - 2.064 - 2.0596

C-O - 1.165 - 1.1496

W-C - 581 - - W(CO)6

C-O - 1981.3(IR)2003.3(RS) - 2000.367

W-C - 2.115 0.051 W-C ~ 0.108

C-O - 1.153 - - W-C - 545 7.2 ~10.08W(CO) 6

C-O - 2044.8(IR) - -

References:

1. A.D. Becke, Phys. Rev. A, 38, 3098 ,1988.2. J. P. Perdew, Phys. Rev. B, 33, 8822, 1986. 3. Rossikhin V.V., Kuz'menko V.V., Voronkov E.O., Zaslavskaya L.I. J. Phys. Chem., 100,19801, 1996. 4.Okovytyy S.I., Rossikhin V.V., Voronkov E.O., Leszczynski J., J. Phys. Chem., 108, 4930, 2004.5. M. J. Frisch, G. W. Trucks, H. B. Schlegel, at al., Gaussian, Inc., Wallingford CT, 2004. 6. CRC Handbook of Chemistry and Physics, David R. Lide, ed., CRC Press, Boca Raton, FL, 2005.7. M.Shou, L.Andrews, Charles W. Bauschlicher, Jr. Chem. Rev., 101, 1931, 2001.8. Hubbard, D.L.Lichtenberger. J. Am. Chem.Soc., 104, 2132, 1982


The Investigation of Electrooxidation of Water in HBF4 Solutions

L.V. Borshchevich and V.F. Vargaljuk

Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine

The reaction of electrochemical oxidation of water on metal-oxide electrodes is one of the reactions, which are accompanying to many anodic processes. Kinetics and mechanism of this process have been subjects of many investigations. However, the mechanism of the reaction 2

2 + 2 + has not been cleared up yet. Through that there is not convincing interpretation of experimentally measured anomalous positive values of reaction order on hydrogen-cations ( ( +) = + 0,5) for examined reaction, inspite of attempts to take into account the features of the oxide film [1].

We have carried out the quantum chemical modeling of cluster structures, which are generated in mineral acids and their salts solutions (hydrated cations, anions and their associats) and considered the energetics of electron transfer process. Quantum chemical calculations were carried out using GAMESS program [2] at Hartree-Fock level [3]. The double valence-split basis 6-31G(d) has been chosen for all of the atoms. The calculations of the oxidized cluster forms, containing unpaired electron, have been done with spin unrestricted approach UHF [4]. Influence of solvation effects was taken into account with the polarizing continuum model , which was developed by Tomassi and co-workers [5]. The structure of the first ions hydrate shell was being studied with supermolecular approximation. Interaction with other solvent molecules was taken into account over the range of macroscopic approximation at = 80. The calculation results are collected in the table.

As can be seen from the table, the ionization of water molecules, which are located outside of appreciable influence of ions, is the most endothermic reaction. The easiest water electrooxidation process occurs in the close to anions region (casters 2-5). Smaller e values correspond to cation-anionic associates (clusters 6-10); however it is enough for effective catalysis.

Since kinetic measuring denotes appreciable influence of cations on dynamics of electrochemical oxygen formation reaction, we can conclude, that water molecules are oxidized by two parallel pathways:

1. in structure of anions clusters

( 2 ) e ( 2 )+( 2 ) 1

( )( 2 ) 1e ( +)( 2 ) 1 ( )( 2 ) 1 ( )

2. in structure of cations clusters

Kat+(H2O)yA e Kat+(H2O)y 1(H2O+)A Kat+(H2O)y 1(OH)A e

Kat+(H2O)y 1(OH+)A Kat+(H2O)y 1(O)A ( )


Table. The energies of electron extraction reaction from hydrate clusters ( e, kcal/mol)

Reaction e1 (H2O)6 e- = (H2O+)(H2O)5 233,332 (ClO4 )(H2O)2 e- = (ClO4 )(H2O+)(H2O) 119,443 (SO4

2 )(H2O)6 – e- = (SO42 )(H2O+)(H2O)5 119,64

4 ( SO4 )(H2O)4 e- = (H2SO4 )(H2O+)(H2O)3 121,385 (BF4 )(H2O)5 e- = (BF4 )(H2O+)(H2O)4 142,576 (H3O+)(ClO4 )(H2O)3 e- = (H3O+)(ClO4 )(H2O+)(H2O)2 200,787 (Li+)(ClO4 )(H2O)4 e- = (Li+)(ClO4 )(H2O+)(H2 )3 02,50 8 (Na+)(ClO4 )(H2O)6 – e- = (Na+)(ClO4 )(H2O+)(H2O)5 199,129 (H3O+)(HSO4

+)(H2O)5 e- = (H3O+)ClO4 )(H2O+)(H2O)4 213,8210 (Li+)(HSO4

+)(H2O)6 e- = (Li+)(HSO4 )(H2O+)(H2 )5 196,9911 (Na+)(HSO4

+)(H2O)8 e- = (Na+)(HSO4 )(H2O+)(H2O)7 193,9312 (H3O+)(BF4 )(H2O)3 e- = (H3O+)BF4 )(H2O+)(H2O)2 226,8613 (Li+)(BF4 )(H2O)3 e- = (Li+)(BF4 )(H2O+)(H2O)2 222,0414 (Na+)(BF4 )(H2O)5 e- = (Na+)(BF4 )(H2O+)(H2O)4 227,96

This case, obviously, makes ( +) defining impossible, because changing of [H+] is compensated with corresponding amount of alkaline metals ions for supporting of the constancy of the solution ionic force.

Essentially different picture is observed in the case of HBF4 electrolytes. Cation-anionic clusters have practically identical energetic characteristics for electron extraction reaction as individual water molecules here, whereas reactionary ability of anionic clusters remains high: decreasing of e in (BF4 )(H2O)5-clusters achieves 91 kcal/mol. Also, that is especially important, efficiency of influence of 3

+ and Na+ ions in tetrafluorineborate solutions on anodic process is virtually the same: e is 226.86 kcal/mol for ( 3

+)(BF4 )(H2O)3-clusters and 227,96 kcal/mol for (Na+)(BF4 )(H2O)5-clusters. It let us choose Na+-ion as a cation which can replace 3

+-ion, and define p(H+) in composition of HBF4 and NaBF4 solutions. The found ( +) value is 0,82 here, that is reasonable value which is in good corresponding with the

reaction model ( ).The electrooxidation of water molecules reaction order on sodium-ions, in the range of its

concentration which corresponds to insignificant changes of 3+-ions concentration is equals to

+0.1. It confirms an assumption, which we made on the base of quantum chemical calculations, that cation-anionic clusters do not play appreciable role in electrode reaction in HBF4 solutions in contrast to HClO4 solutions.

References1.Birss V.I. Damjanovic A. A Study of the transition from oxide growth to O2 evolution at Pt electrodes in acide solutios // J. Electrochem. Soc. – 1983. – V.130, 8. – P. 1688–1694. 2.Schmidt M.W., Baldridge K.K., Boatz J.A. et al. General Atomic and Molecular Electronic Structur System // J. Comput. Chem, - 1993. – Vol.14. – P.1347–1363. 3.Roothan C.C. New Developments in Molecular Orbital Theory // Rev. Mod. Phys. – 1951. – Vol.23. – P.69–74.4.Pople J.A., Nesbet R.K. Self–Consistent Orbitals for Radicals // J. Chem. Phys. – 1954. – Vol.22. – P.571 – 578. 5.Miertus S., Scrocco E., Tomasi J. Electrostatic Interaction of a Solute With a Continuum. A Direct Utilization of ab initio Molecular Potentials for the Prevision of Solvent Effects // J. Chem. Phys. – 1981. – Vol.55. – P. 117–124.


Active-Site Inhibitor ModelingUsing a Customized HIV-Protease Peptide

Deborah J. Bryan* (I), John West (I), Jesse Edwards (I), Reginald Parker (II),Ben M. Dunn (III)

I. Department of Chemistry/AHPCRC, Florida A&M University Tallahassee, Florida, 32307 II. Department of Molecular Biology and Biochemistry, University of Florida, Gainesville,

Florida, 32608 III. Florida A&M/Florida State University College of Engineering, Tallahassee, Florida, 32307

In an effort to develop unique HIV protease inhibitors Dunn et. al. have synthesized a series of customized peptide inhibitors potentially capable of adapting to mutations in the HIV protease through the introduction of flexibility and bulky side chain groups. Flexibility was introduced to the candidate inhibitor, XI5, through the reduction of the carbonyl group at the core of the peptide. To determine the presence and degree of flexibility molecular dynamic simulations of both XI5 and a non-reduced version of the peptide, XI5co2, were carried out in vacuum and in water at 300K for 400 ps to 1 ns for NVT and NPT ensembles. A reduction of the carbonyl group in the middle of the XI5 peptide chain was found to have introduced flexibility as evidenced by the fluctuation of the Omega torsion angle of residue four (Omega four) in both the vacuum and water-solvated system. In the vacuum system, the Omega four angle of XI5 exhibited a wide fluctuation centering around –140 degrees, while the normal amide bond angles exhibited an average torsion of 180 degrees. In the water-solvated system, Omega four had two distinct angles present throughout the simulation, either +140 degrees or –140 degrees, while the Omega four angle of the non-reduced XI5co2 exhibited the 180 degree torsion expected of a normal amide bond. The Phi-Psi plot of XI5 revealed little fluctuation along the main chain in the vacuum system; however, greater fluctuation existed in the water system. The Chi plots of XI5 in the water system indicated that the transition of the smaller, Ethyl, side chain was both more abrupt and frequent when compared to that of the larger, Methylnaphthalene, side chain. The end-to-end distance fluctuated in a similar range for both peptides. The most notable difference in flexibility between the two peptides was observed in the Omega angle of residue four. Also, Monte Carlo simulations were used to examine volume and radius of gyration of these compounds in order to compare them with known substrates of the HIV Protease.


Conventional Strain Energy in Isomers of Dimethylcyclobutadiene

Qianyi Cheng and David H. Magers

Computational Chemistry Group Department of Chemistry & Biochemistry, Mississippi College

The conventional strain energies for 1,2-dimethylcyclobutadiene (Figure 1.), 1,3-dimethylcyclobutadiene (Figure 2.), and 1,4-dimethylcyclobutadiene (Figure 3.), are

determined within the isodesmic, homodesmotic, and hyperhomodesmotic models to see if reduction of strain might correlate with the stabilizing effect these different dimethyl substitutions have on cyclobutadiene. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory (MP2), and density functional theory. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. Two basis sets, both of triple zeta quality on valence electrons, are employed: 6-311G(d,p) and 6-311+G(2df,2pd). Finally, computed bond angles are also examined for correlation with the relative stability and the relative strain energies of the different isomers. We gratefully acknowledge support from NSF EPSCoR (EPS-0132618).

Figure 1: 1,2-dimethylcyclobutadiene Figure 2: 1,3-dimethylcyclobutadiene

Figure 3: 1,4-dimethylcyclobutadiene


Calculations on One-Electron Oxidation and One-Electron Reduction of Nucleotides

David M. Close

East Tennessee State University, Dept. of Physics, Johnson City, TN

A recent paper by Schaefer et al.1 outlines calculations on 2’-deoxyadenosine-5’-phosphate (5’-dAMP). Since the phosphate is left with a net negative charge, optimizations on the anion show a tendency of the phosphate to move towards the base. Calculations on the one-electron oxidation product of 5’-dAMP show that the “last” electron seems to be removed from both the base and the phosphate moiety. The authors suggest this oxidation step may lead to cleavage of the C5’-O5’ bond in DNA (which would represent a single strand break).

SOMO of one-electron oxidized 5’-dAMP

One has to look at several aspects of these calculations. First of all the authors are using their calibrated B3LYP/DZP++ approach. One has to be careful in using diffuse functions as they tend to spread out the unpaired electron. Also it is important to consider the situation in DNA where the charge on the phosphoryl group is shielded by counterions and water molecules. This has the effect of increasing the ionization potential and means that the site of oxidation will likely shift to the adenine base. Finally one has to remember that the adenine cation is strongly acidic (pKa <1)2. This means that there is a strong driving force for deprotonation of the cation which is independent of environmental conditions. Results will be presented to show that all three points here are valid concerns.

A second paper by Schaefer et al.3 concerns one electron reduction of 2’-deoxycytidine-3’-phosphate (3’-dCMP) and looks at calculations begun by Simons et al.4 on the attachment of low energy electrons which initiate cleavage of the C3’-O3’ bond. The authors show that small changes in the phosphodiester torsion angle can lead to shifts from a base centered radical to a phosphate centered radical. Actually it is possible to show a geometry of 3’-dCMP with unpaired spin density on both ends of the molecule.


SOMO of one-electron oxidized 3’-dCMP

Again one has to look at several aspects of these calculations. In the figure above the phosphate has rotated to form an intramolecular H-bond. Rotating back to the geometry found in DNA favors the base centered cytosine anion. The cytosine anion is a strong base (pKa >13), and therefore is expected to protonate rapidly (most likely at N3) in solution2. After protonation of the cytosine anion, all of the spin density is on the base. Also one can show the effects that counterions and water molecules have on shielding the phosphoryl group. The combination of these effects leads to the conclusion that reduction of 3’-dCMP most likely leads to the cytosine base anion, which will rapidly protonate, localizing the site of spin density on the base.

1) R. Hou, J. Gu, Y. Xie, Y. Xi, H.F. Schaefer, J. Phys. Chem. B 109, 22053 (2005) 2) S. Steenken, Free Radical Res. Comm. 16, 349 (1992). 3) J. Gu, Y. Xie, H.F. Schaefer, J. Am. Chem. Soc, 128, 1250 (2006). 4) J. Berdys, I. Anusiewicz, P. Skurski, and J. Simons, J. Am. Chem. Soc, 126, 6441 (2004).


IR Spectroscopy of Gas Phase Clusters of Biological Molecules

Bridgit Crews, Mattanjah S. de Vries

Department of Chemistry and Biochemistry, University of California Santa Barbara

Our research combines a number of techniques for a novel approach to the study of individual molecules and their clusters. A main focus of our research looks at the effects of hydration on peptides, and of clustering on the bases which make up DNA. We use short laser pulses to bring these molecules into the gas phase with very little fragmentation (laser desorption) and rapidly cool them in a supersonic expansion. The molecules are subsequently photo ionized by several more tunable lasers and detected in a time of flight mass spectrometer. Recent measurements taken in our lab on the nucleobase Guanine and its cluster with various amino acids will be presented along with data on isolated Enkephalin and its cluster with water.


Size Dependence Emission Quenching Properties of Modified DNA Capped Gold Nanoparticles

Gopal Darbha, Angela Fortner, Jelani Griffin and Paresh Chandra Ray

Department of Chemistry, Jackson State University, Jackson, MS 39217, USA

Particles with sizes in the range of 1-100 nm have been demonstrated to exhibit size dependant physical properties that differ from bulk materials. Here we present theoretical and experimental results on dye fluorescence quenching induced by gold nanoparticles having different sizes. Gold nanoparticles strongly quench the fluorescence when it adsorbed on nanoparticle surfaces, through an energy-transfer mechanism. Fluorescence spectra clearly show that the quenching efficiency decreases with increasing size of the gold nanoparticles and increasing the distance between dye and nanoparticles. This suggests that the quenching is a result of electron transfer rather than long-range (Forster-type) energy transfer processes


Modeling of (5,5) Armchair SWNT: Stone-Wales Defect Formation and Physisorption of Linear Hydrocarbon Inside the Tube

T. C. Dinadayalane and Jerzy Leszczynski*

Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 JR Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA

Hartree-Fock, MP2 and B3LYP calculations have been performed to investigate the formation energy of single Stone-Wales defect at different locations considering two different orientations in the (5,5) single-walled carbon nanotube (SWNT). The effect of nanotube length on the formation energy was examined. The structures and reactivities of the nanotubes with a single Stone-Wales defect are compared with the corresponding defect-free single-walled carbon nanotube. The computed formation energies at the B3LYP/6-31G(d) are in good agreement with those obtained at the MP2/6-31G(d) level. Our results reveal that the SWNTs with Stone-Wales defect occurring at the edge of the nanotube or near the center of the nanotube are lower or comparable in energy to the SWNTs with the defect at the center of the tube. The computed pyramidalization angles for the carbon atoms of the perfect nanotube and the Stone-Wales defect region were critically analyzed to correlate the reactivity of the sites and the local curvature. Band gap values obtained for the defect and defect-free nanotubes were compared. Second part of the presentation will be devoted to the stabilization of the linear hydrocarbon chain inside the (5,5) armchair SWNT. The origin for this non-bonding stabilization will be addressed.

Scheme 1


Theoretical Comparison of Cisplatin and Cisplatin AnalogsUsing DFT Calculations

LaTanya Dixon, Glake Hill, Jerzy Leszczynski

Computational Center for Molecular Structure and InteractionsDepartment of Chemistry, Jackson State University, Jackson, MS 39217

There have been many developments in the use of platinum metal compounds as chemotherapeutic agents since the discovery of cis-diamminedichloroplatinum (II) (cisplatin) in the late 1960s. Cisplatin, an intravenously administered drug, exhibits antitumor activity in testicular, head and neck, ovarian and non-small cell lung cancer. However, cisplatin’s success in tumor apoptosis cannot outweigh its major drawbacks. During cisplatin chemotherapy cell resistance and cellular death of normal cells occurs. Therefore, analogs of cisplatin have been developed to decrease toxicity, cell resistance and discomfort in drug administration.

Unfortunately, the mechanism of cisplatin and its analog has still been elusive to date. We believe the mechanism could be better understood by supporting previous platinum drug research with an energetic and structural comparison of cisplatin and the analogs in the gas and solvated phase. This research consists of three active and approved analogs: carboplatin, nedaplatin and oxaliplatin. The analogs vary in ammine carrier groups and labile leaving groups in comparison to the original parent compound. Optimizations and single point calculations were done using the B3LYP level of theory and 6-311++G (2df,2pd) basis set. The Stuttgart-Dresden pseudopotential was applied for the platinum and chlorine atoms. A thorough comparison of cisplatin and its analogs will be discussed.


Hazardous Organophosphates: Computational Insight into Gas Phase Alkaline Hydrolysis of Phosphorus-Ester Bonds

Edyta Dyguda-Kazimierowicz,1 W. Andrzej Sokalski,1 and Jerzy Leszczy ski2

1 Institute of Physical & Theoretical Chemistry, Department of Chemistry, Wroc aw University of Technology, Wyb. Wyspia skiego 27, 50-370 Wroc aw, Poland

2 Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1325 Lynch St., Jackson, MS 39217-0510, USA

Severe toxicity of trisubstituted phosphoryl derivatives, directed not only toward a crop protection but also raising a threat of being used as chemical warfare agents, resulted in a pressing need to develop safe and efficient decontamination methods. Consequently, there is a growing interest in the fundamental mechanisms of organophosphates hydrolysis. The nonharmful transformation of such toxic chemicals could also be attained by enzymatic biodegradation and the factors determining selection of leading enzyme candidates include both the efficiency of biocatalysis and the ability to act on a broad spectrum of substrates. From this perspective bacterial phosphotriesterase, PTE, constitutes the most promising target, as it has been shown to cleave a variety of phosphorus-ester bonds (i.e., phosphorus-fluoride, phosphorus-oxygen, and phosphorus-sulphur) and to approach for such processes the limits of diffusion in case of its best known substrate.

The ability to control an enzyme action and to introduce mutations leading to some novel activities in a rational way requires the detailed knowledge of catalytic mechanism. Despite an increasing amount of experimental data on PTE-catalyzed hydrolysis of organophosphates, its molecular mechanism has not yet been elucidated. Among the questions that remained unanswered is the relationship between the wide range of substrates accepted by PTE, that is the possibility that their hydrolysis may or may not share some common characteristics that allow all of them to be facilitated by the same PTE active site.

Our project is directed toward a deeper understanding of PTE mechanism of action that could further be applied in the rational, computer-aided catalytic activity control. With this goal in mind, systematic ab initio study of possible gas phase mechanisms of the alkaline PTE substrates hydrolysis was performed. In this contribution the possible strategies of P-O (paraoxon, parathion), P-F (DFP, sarin), P-S (acephate, demeton-S) and P-CN (tabun) bonds breakage will be discussed. Since experimental evidences suggest the significant similarity between alkaline and enzymatic hydrolysis of phosphorus-ester bond, our results can subsequently be employed as a starting point for further simulation of PTE-catalyzed process.

Acknowledgement: This project is funded by DoD through ERDC grant #W912MZ-04-2-0002.


Figure 1. HF/6-31+G(d) energy profile and variation in the selected interatomic distances for the alkaline hydrolysis of a model compound, O,O-dimethyl phosphorofluoridate.


Excitation of Surface Dipole and Solenoidal Modes on Toroidal Nanostructures

M. Encinosa and M. Jack

Department of Physics, Florida A&M University, Tallahassee, Florida, 32307, USA

The time-dependent Schrodinger equation inclusive of curvature effects is developed for a spinless electron constrained to motion on a toroidal surface and subjected to circularly and linearly polarized waves in the microwave regime. Typical nanotori major radii studied here are 50 nm with circularly symmetric cross sections. A seven-state basis set is employed with the goal of determining the character of the surface currents as the system is driven at a resonance frequency that selects for a solenoidal mode. Trajectory methods are used as a means of visualizing the character of the induced surface currents. Optical transitions into solenoidal modes of excitation can be observed. The magnetic moment which is induced by surface currents on the torus shows an expected dipole component parallel to the toroidal central symmetry axis together with additional components in radial and/or azimuthal direction. Size and relative magnitude of the different components can be steered by adjusting magnitude, polarization, and phase information of the electromagnetic field of a single linear or circular polarized microwave or of the field created by the interference of two equally polarized waves.

a b

Figure: Magnetic moment (t) of T2 surface currents for a) single linearly polarized wave and b) interference of incoming and reflected linearly polarized wave. From top to bottom: Components in direction of ez , e , and e .


C—H, S—H, and S—C Insertion Reactions, 1,2-Rearrangements (Thia-Wolff), and Singlet-Triplet Gaps of Disulfinylcarbenes:

A Computational Study

Fillmore Freeman, Quan M. Kha, Thang X. Nguyen, Tarang Safi,and Norman E. Sebastian

Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025

HF, B3LYP, MP2, CCD, CCSD, and QCISD with the 6-31G(d), 6-31+G(d,p), 6-311+G(d,p), 6-311+G(3d,2p), 6-311++G(3d,2p), cc-pVDZ, and cc-pVTZ basis sets have been used to investigate the mechanisms of intramolecular C—H, S—H, and S—C insertions, intermolecular C—H insertions, and 1,2-rearrangements (Thia-Wolff) of bis(hydrogensulfinyl)carbene (1) and bis(methanesulfinyl)carbene (2).

O

S

S

O

HH

HH SS

O

O

S-1 T-1

O

H

S S

H

H

H

O

H

H

H

H

H

H

H

H

S

O

S

O

S-2 T-2


Conventional ab Initio and Molecular Dynamics Calculations: Prediction of Physical Properties and Chemical Reactivity

of DNA Bases and Nitro-Compounds

Leonid Gorb

US Army ERDC, Vicksburg, Mississippi, 39180, USA Computational Center for Molecular Structure and Interactions,

Jackson State University, Jackson, Mississippi, 39217, USA.

The similarity and differences of the results of conventional ab initio approach (solution of time-independent Schrödinger equation) and molecular dynamic approach (ab initio solution of Konh and Sham equations to generate the forces acting on the nuclei followed by solution of Newtonian equations to generate trajectories) are presented and analyzed for selected examples of physical properties (rigidity of heterocyclic ring in DNA bases and aromatic ring in nitro-compounds) and chemical reactivity (decomposition of cyclic nitroamines).


Causes of Rare Tautomer Forms Stabilization of Bases are in Single- and Double-Stranded DNA under Dimers Formation

H. A. Grebneva

Donetsk Physical and Technical Institute, NAS of Ukraine 83114 Donetsk, Ukraine E-mail: [email protected]

Features of UV-mutagenesis

After the ultraviolet (UV)-irradiation, photoproducts are formed in a DNA molecule. In most cases these are cyclobutane pyrimidine dimers and (6-4) adducts. By “dimers” we’ll mean cyclobutane pyrimidine dimers, as well as (6-4)-adducts. Usually mutations occur opposite the dimers at SOS-replication, reparation or transcription. Such mutagenesis is termed targeted. Sometimes mutations are formed in a small neighborhood of dimer, this is the untargeted mutagenesis [1].

Generally accepted paradigm of the UV-mutagenesis

A mechanism of the formation of base-substitution mutations at synthesis of DNA containing pyrimidine dimers has been proposed. It is assumed that the mutations arise because the DNA-polymerase sometimes incorporates uncomplementar nucleotides opposite the dimers. In other words, it is considered that from the point of view of mutagenesis all the dimers are identical, and the only reason is that the operation of DNA-polymerases is imperfect. Now, such point of view is standard [2, 3]. Models of spontaneous and ultraviolet mutagenesis [4], as well as the model of spontaneous untargeted mutagenesis [2, 3] are proposed. They are based on the fact that in E. coli there are polymerases IV and V the both of low synthesis accuracy [5].

No doubt, this approach describes some cases and features of the mutagenesis. As known, DNA polymerases IV and V are, as a rule, in action when the DNA polymerase III E. coli has a defective subunit [2, 3, 5]. However, it is the DNA polymerase III with perfect proof-reading functions of 53 -exonucleases (subunit of full value) results in majority of mutations upon the induction of SOS system when the “sliding clamp” mechanism is on [6]. Hence, the generally accepted paradigm describes a small part of mutagenesis in E. coli. Moreover, the approach is restricted as it ignores the structure of DNA damage.

There is a number of experimental facts which contradict the standard hypothesis [1]. Moreover, it can not explain some phenomena. In particular, the mechanism of complex mutations formation, physicochemical causes of replicating instabilities, why guanine – cytosine pairs mutate much more often than the others, why there are hot and cold spots of UV-mutagenesis, why (6-4) adducts are much more mutable than the cyclobutane pyrimidine dimers, etc. This shows that the classical model of mutagenesis [2, 4] is narrow and a more profound study of both the photodamages structure and details of the synthesis of DNA containing such photodamages is necessary.

Changes in tautomeric states of bases during dimers formation as a potential cause of UV-mutagenesis

Watson and Crick supposed that the reason for a spontaneous mutagenesis could be the ability of the DNA bases to be in various tautomeric forms [7]. It is shown that under the


formation of dimers, the tautomeric state of the constituent bases may be changed [1]. New probable tautomeric states have originated under the formation of thymine dimers [1].

Fig. 1. Adenine (A) – thymine (T) pair: a) the Watson-Crick’s adenine (A) – thymine (T) pair; b) – h) possible new tautomeric states of adenine and thymine resulting from the formation of thymine dimers.

Numerous experimental and theoretical data testify that the bases of DNA can be in various tautomeric forms, the tautomeric state of bases may change under the UV-irradiation [8], and the double-proton phototautomerisation may occur [9].

A mechanism of changes in the tautomeric state of bases has been worked out for the case of ultraviolet quantum absorption by DNA molecule [1]. Fig. 1 shows the obtained possible rare tautomeric states of the A-T pair [1]. And not only the base, which is a component of dimer, changes its tautomeric state.


Terminology problems

There exit a terminology problem. Physicists and experts in quantum chemistry consider the bases with lost or added (as compared to canonic bases) one or several hydrogen atoms to be bases in rare tautomeric forms. They make no difference between intra- and intermolecular processes which gave such a result.

Specialists in organic chemistry treat the problem in more detail. In their opinion the tautomerisation is an intramolecular displacement of the proton, in contrast to salt formation – the intermolecular displacement of the proton and complex state change. Within this terminology, the T1*-A1* pair the both bases are in rare tautomeric forms, the rest four forms are salt with bases playing the part of base and acid in turn. In this connection, for simplicity, we’ll call the states shown in Fig. 1 as those in rare tautomeric forms.

Causes of stability of the rare tautomeric forms of bases in double-stranded DNA

All rare tautomeric forms of bases will be stable as upon dimer formation the DNA strand becomes curved resulting in the elongation or breakage of hydrogen bonds between the bases [10]. In the case of elongation the shape of potential curve changes. The second minimum becomes deeper [11]. That’s why, the hydrogen atom will come to the partner in hydrogen bond, as a result of processes described in [1], and the new tautomeric state will be stable at a small elongation of the hydrogen bond. Of course, such rare tautomeric states will be stable in the case of broken hydrogen bonds.

Reasons of stability of the rare tautomeric forms of bases in the active centres of enzymes during DNA synthesis

An important stage for increasing the accuracy of DNA synthesis is that of identification of nucleotides and nucleotide pairs. The identifying ability of polymerases is improved, in particular, by removing water from enzyme’s active center [12, 13]. The enzyme molecule is as a rule, very large, it as if protects substrate’s molecule, getting at the active center of the enzyme, under the influence of the medium. That’s why, enzyme’s molecule can be at a time treated as a medium, a catalyst and a template whose characteristics vary during the reaction. The absence of water at the active centers of polymerases provides the conservation of tautomeric states of bases participating in DNA synthesis,. when the DNA molecule is single-stranded.

Reasons of stability of the rare tautomeric forms of bases in single-stranded DNA during the SOS synthesis

It is not excluded that when different enzymes are active the DNA molecule will for a time exist in the form of one strand. Let us estimate a possibility, for the bases in rare tautomeric forms, of transformation to canonical tautomeric states because of the contact with water molecules. The experiment shows that the lifetime of “free” guanine, i. e. the time till it links a water molecule, makes 0,1 to 10 s and even 1000 s [14], where the meant are guanine molecules that are in water medium. For guanine present in NA strand the time is much higher. Different DNA polymerases synthesize nucleotides at a rate of 10 to 1000 per a second [2-5]. Let during DNA synthesis the DNA strand be (in the single-stranded form). The time for which there will be no enzyme protection is defined by the rate of enzyme activity. For the DNA polymerase V it will be not higher than 0,1 second. As the time for the base to link water molecule and to change the tautomeric state is higher than 0,1 s, we see that the process is low-probable.


Acknowledgment. This work was facilitated by The State Fund for Fundamental Research of Ukraine. (Grant No F7/208-2004).

1. H. A. Grebneva, J. Mol. Struct. 645 (2003) 133-143.2. M. Tang, P. Pham, X. Shen, J.-S. Taylor, M. O’Donnell, R. Woodgate, M. Goodman, Nature 404 (2000) 1014 -1018.3. A. Maor-Shoshani, N.B. Reuven, G. Tomer, Z. Livneh, Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 565-570.4. M. Ruiz-Rubio, B.A. Bridges, Mol. Gen. Genet. 208 (1987) 542-548.5. M. Tang, X. Shen, E.G. Frank, M. O’Donnell, R. Woodgate, M.F. Goodman, Proc. Natl. Acad. Sci. U.S.A. 96 (1999) 8919-8924.6. I.J. Fijalkowska, R.M. Schaaper, Proc. Natl. Acad. Sci. USA. 93 (1996) 2856-2861.7. J. D. Watson, F. H. C. Crick, Cold Spring Harbor Symp Quant Biol 18 (1953) 123-131. 8. N.I. Ostapenko, Yu.A. Skryshevskii, A.K. Kadashchuk, Yu.V. Rubin, Izvestia of Acad. Sci. USSR 54 (1990) 445-449.9. C.A. Taylor, M.A. El-Bayoumi, M. Kasha, Proc. Natl. Acad. Sci. USA. 63 (1969) 253-260.10. G. Raghunathan, T. Kieber-Emmons, R. Rein, J. L. Alderfer, J. Biomol. Struct. and Dyn. 7(1990) 899.11. H. A. Grebneva, J. Struct. Chem. 38 (1997) 422-430. 12. N.C. Seeman, J.M. Rosenberg, A. Rich, Proc. Natl. Acad. Sci. USA. 73 (1976) 804-808. 13. J. Petruska, M. F. Goodman, M. S. Boosalis, L. C. Sowers, C. Cheong, I.. Jr. Tinoco, Proc. Natl. Acad. Sci. USA. 85 (1988) 6252-6256.14. L. Gorb, Y. Podolyan, J. Leszczynski, W. Siebrand, Biopolymers (Nucl. Acid. Sci.) 61 (2002) 77-91.


Computational Studies of a Series of Gluccocorticoid Steroid Derivatives

Jessica Hardaway1, M. Omar. F. Khan2, Zhengqing You2, Henry J. Lee2,and Jesse Edwards1

1Department of Chemistry 2College of Pharmacy and Pharmaceutical Sciences

Florida A&M University Tallahassee, Florida 32307

A series of gluccocorticoid steroid receptors have been synthesized by the H. J. Lee group in an attempt to develop pharmaceuticals in the area of anti-inflammatory research. The activities (IC50) range from 10nm to greater than 10000 nM. The Sparc On-line calculator developed by the Environmental Protection Agency was used to predict the macroscopic and microscopic pka’s, and relative concentrations of species at various pH levels. The level of correlation between activity and pka will be determined in this work. Also, the potential existence of different ionized species at in the blood plasma range of pH will be explored and discussed.


Effect of Benzene and Strained Bicyclo[2.1.1] Hexene Annelation on Li+- Interaction

Ayorinde Hassan, T. C. Dinadayalane and Jerzy Leszczynski*

Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 JR Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA

E-mail: [email protected]

Effect of annelation to the benzene ring on the cation- interaction, particularly binding Li+

has been investigated at the B3LYP, MPW1B95 and MP2 methods using 6-31G(d,p) basis set. The deviation of the interaction energies among the three levels is less than 2 kcal/mol. The binding of Li+ ion with benzene is significantly increased by tri-annelation of benzene or highly strained bicyclo[2.1.1]hexene ring. The sequential replacement of benzene in triphenylene by bicyclo[2.1.1]hexene gradually increases the Li+ binding to central benzene ring of the organic fragment. Substantial increase of interaction energy by bicyclo[2.1.1]hexene ring annelation may be attributed to the weak C-H…Li+ interaction along with the Li+- interaction. Bicyclo[2.1.1]hexene ring tri-annelated benzene appears as a good receptor for cation binding.

=

or

Scheme 1: Li+- interaction


Ab Initio Studies of the Tautomerization of3,7-dihydro-1H-purine-2,6-dione

Tiffani Holmes, Glake Hill , Jerzy Lesczcynski

CCMSI 1400 J.R. Lynch St. P.O. Box 17910 Jackson State University, Jackson MS 39217

Xanthine composes a group of alkaloids that are used as bronchodialators and is used to treat symptoms of asthma. Some methylated xanthines include caffeine and a theobromine, a component of chocolate. Studies have shown that xanthine undergoes keto/enol tautomerization and can form fourteen different conformations. The present study investigates the tautomerization of 3,7-dihydro-1H-purine-2,6-dione (xanthine) through quantum chemical ab initio calculations.

Initial geometry optimizations were performed using Hartree Fock’s self consistent field method with a 6-31G* basis set. Secondary optimizations were done using the second order Moller-Plesset level of theory with the 6-31+G** basis set. These calculations confirmed that the lowest energy isomer is a diketo form with –H occupying the N3 and N7 sites. An energetic scheme of xanthine’s tautomerization has been devised and will be presented.


A Density Functional Study of the Reaction of Perfluorooctanoic Acid with Sulfur Containing Amino Acids

Tiffani Holmes, Carmen Robinson, Glake Hill, Jerzy Leszczynski

Jackson State University, Jackson MS 39217

The physical and chemical properties of the carbon fluorine bond make fluorochemicals resistant to biodegradation. The stability of these compounds has caused widespread concern because of pollution due to the inability of these chemicals to break down in the environment and within the body. Previous studies suggest that the peroxisome proliferator chemical, perfluorooctanoic acid, is circulated throughout the body by way of sulfur containing amino acids. This reaction occurs by way of mechanism where the sulfur of the amino acid covalently attaches to the oxygen of the –OH group of the fluorinated fatty acid.

The reaction of perfluorooctanoic acid with the amino acids cysteine and methionine was investigated using density functional theory. Preliminary calculations were performed using density functional theory’s hybrid method B3LYP electron correlation method with a 6-31G(d) basis set. Preliminary calculations resulted in the discovery of two low energy conformers of equal energy that differ by way of the COOH dihedral angle. Interaction energies have been calculated and will be presented.


Ab Initio Studies of Inclusion Complexes of Cyclodextrins with Polycyclic Aromatic Hydrocarbons

Ming-Ju Huang

Department of Chemistry, Jackson State University, Jackson, MS 39217

Hartree-Fock (HF/6-31G) calculations have been performed on a family of Heptakis(methyl)- -Cyclodextrin and Heptakis(2-O-hydroxypropyl)- -Cyclodextrin isomers derived from the 2-, 3-, and 6-hydroxyl positions and their inclusion complexes with polycyclic aromatic hydrocarbons such as pyrene, benzo[a]pyrene, 1-hydroxypyrene, 1-nitropyrene, 1-bromo-pyrene, and 1-azapyrene. From the stabilization energies of the 66 inclusion complexes, we found that 1-hydroxypyrene is the best guest to form the inclusion complexes (11 out of 12 are stable complexes). 3HP CD with 1-nitropyrene with head-first has the largest stabilization energy (-12.67 kcal/mol) for heptakis(2-O-hydroxypropyl)- -cyclodextrin. 6mcd with 1-hydroxypyrene with tail-first has the largest stabilization energy (-14.15 kcal/mol) for methyl- -cyclodextrin.


The Initial Chemical Events in CL-20 under Extreme Condition: An ab Initio Molecular Dynamics Study

Olexandr Isayeva, Yana Kholoda,b, Leonid Gorba,c, M. Qasim,c J. Furey,cH. Fredricksonc and Jerzy Leszczynskia

aComputational Center of Molecular Structure and Interactions, Jackson State University, Jackson, MS 39217, USA

bDnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine cUS Army ERDC, Vicksburg, MS, 39180, USA

CL-20 (Octahydro-1,3,4,7,8,10-hexanitro-5,2,6-(iminomethenimino)-1H-imidazo[4,5-b]-pyrazin) is one of the most important high energetic nitramines which are used as explosives and propellants. The decomposition of CL-20 is very complicated and involves hundreds of elementary reactions. Accurate knowledge of these reactions and predictions of their kinetic parameters are important for modeling these complex processes in combustion and explosion. However, due to the energetic nature of these materials and the rapid rates of the intermediate reactions, it is difficult to monitor these individual reactions experimentally. Recent advances in first principles modeling have led to enormous progress toward understanding complex condensed phase chemical phenomena. Theoretical methods, especially accurate ab initiomolecular dynamics method, provide a viable alternative to study the dynamics of these reactions.

Electronic properties and the dynamics of the initial thermal decomposition step of gas- and -crystal phases of CL-20 are investigated using the Car-Parrinello molecular dynamics (CPMD)

approach. The lengths of the simulations were about 10 ps, temperatures are 1500 and 3000 K. At the high temperature, the NO2 fission channel is found to be dominant; this step is followed by the skeleton decay. The difference in the reaction pathways between gas- and crystal phases has been accounted for the strong intermolecular interaction into crystal lattice. By the preliminary analysis thermal rate constants at 3000K have been estimated.

a) b)

Sample snapshots from the trajectory (T=3000 K): a) = 0.0 ps, b) = 0.5 ps.


Molecular Modeling - A New Approach

Dušanka Janeži

National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia

Molecular modeling is indispensable in theoretical research in chemistry, molecular physics, structural biology, new materials development, and other fields. To productively use molecular modeling methods, their theoretical basis must be understood and the appropriate method must be chosen for solving a given problem. Computer simulation methods have been developed primarily in the direction of increasing the simulation lengths and the size of modeled systems, that allows a greater understanding of the relationship between the structure and function in biological macromolecules. The length of simulations has to exceed the nanosecond scale to correspond to the time scale of the chemically and biologically interesting processes, which occur on the microsecond scale.

Among the main theoretical methods of investigation of the dynamic properties of molecular systems are computer simulations and quantum chemical computations. Molecular dynamics is obviously a powerful tool for simulating molecular motion. A complementary computational method to examine molecular behaviour is the normal mode analysis that examines motion in the harmonic limit.

In this contribution I will present the survey of our past and current endeavor on molecular modeling algorithm development. In particular, I will describe new symplectic integration algorithms for the numerical solution of molecular dynamics equations and methods for the determination of vibrational frequencies and normal modes of large systems.

We propose an analytical treatment of the internal high-frequency molecular vibrations in the molecular dynamics simulations using a new form of the classical Liouville propagator. The essence of the work lays in the construction of the second-order integrating algorithm that is useful for all-atom molecular dynamics simulations of molecular systems described by flexible models. We apply this algorithm to the molecular dynamics simulations of liquid water providing the evidence about its superior numerical characteristics over the standard approach. The accuracy of the method was confirmed, in particular, by computing the IR spectrum of water in which no blue shifting of the stretching normal mode frequencies is observed as occurs with the standard method.

We have also developed a computer program for molecular dynamics simulation that implements the split integration symplectic method and is designed to run on specialized parallel computers. The molecular dynamics integration is performed by the new integration method, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. We study the computational performance of simulation on specialized computers and provide a comparison to standard personal computers. The combination of the new integration method with two specialized parallel computers is an effective way to significantly increase the speed of molecular dynamics simulations.


Interaction-Induced Propertiesthrough Symmetry-Adapted Perturbation Theory

Anna Kaczmarek,†,‡ Bart omiej Skwara,§ Andrzej J. Sadlej†,‡

and Jerzy Leszczynski‡

†Institute of Chemistry, Nicolaus Copernicus University, Toru , POLAND §Institute of Physical and Theoretical Chemistry, Wroc aw University of Technology, Wroc aw,

POLAND‡ CCMSI, Department of Chemistry, Jackson State University, Jackson, MS

First-order symmetry adapted perturbation theory (SAPT) is used to obtain components of the interaction energy. The terms arising from the inaccuracy of monomer description are identified and referred to as the basis set truncation contributions (BSTE). The elimination of the main part of BSTE is achieved by using the dimer centered basis set (DCBS). The remaining part of the interaction energy is still not fully BSTE-free and contains the BSTE terms arising from the multiple-exchanges of the electron labels between subsystems. However, the use of DCBS ensures proper balance between the quality of the dimer and monomers description.

On the basis of the earlier studies on the interaction energy, the analysis of the interaction-induced dipole moments for model systems has been carried out. The total induced dipole moments are decomposed into electrostatic, exchange, and BSTE components.


The Mechanism of Alkenes Epoxidation with Potassium Peroxymonosulfate. Ab Initio Study

Y. Kholod,1,2 M. Belov,1 S. Okovytyy,1,2 J. Leszczynski2

1Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine 2Computational Center for Molecular Structure and Interactions,

Jackson State University, Jackson, Mississippi, 39217, USA

Epoxides are not only useful precursors for organic chemists but also the frequent structures in natural products in relation to their biological activities. Efficient methods have been developed for their synthesis from olefins, and many of them use transition-metal catalysts. In recent years, much effort has been devoted to the development of metal-free epoxidation procedures. One of the most interesting of metal-free epoxidation techniques is based on usage of Caro's acid potassium salt (KHSO5) as an oxidation agent. The process (1) usually is carried out in aqueous solutions:

CH2CH2 CH2

O

CH2(1)

+H2SO5

-H2SO4

Despite significant interest of many researches to this technique, the inner mechanism of the process still remains unknown. Thus, in present work we have used quantum-chemical calculations at UB3LYP/6-31G(d) and CASSCF(6,6)/6-31G(d) levels of theory to explore the potential energy surfaces (PES) of ethylene epoxidation with potassium peroxymonosulfate, to compare activation barriers of both processes.

Analysis of PES at the UB3LYP/6-31G(d) level of theory has shown that the reaction (1) has revealed the closed-shell transition state (TS1) with symmetrical character. In contrast, the diradical transition state (TS2) which has an unsymmetrical open chain structure has been located at CASSCF(6,6)/6-31G(d) level of theory.


The Mechanism of Alkaline Hydrolysis of the Cyclic Nitramines: RDX, HMX and CL-20. A DFT study

Y. Kholod,a,b S. Okovytyy,a,b L. Gorb a,c M. Qasim,c J. Furey,c H. Fredricksonc

and J. Leszczynskia

aComputational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi, 39217, USA

bDnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine cUS Army ERDC, Vicksburg, Mississippi, 39180, USA

Explosives, such as the cyclic nitramines: RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine),HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) and CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazatetracyclo[5.5.0.05,9.03,11]dodecane), are high toxic compounds to various terrestrial and aquatic receptors.

N

NO2

NNO2

NO2N

N

O2N

NH2N NO2

N N

NNN

N N

NO2

NO2O2N NO2O2N

O2N NO2

RDX HMX CL-20

The decomposition of them through alkaline hydrolysis is one possible technique for utilization of those contaminants. A number of investigations have been devoted to kinetics of alkaline hydrolysis of the cyclic nitramines.

Kinetics studies reveal than the first NO2-group elimination seems to be the limitation stage of degradation process. In the current work the B3LYP/6-31G(d,p) level of theory have been used to explore the potential energy surfaces of alkaline hydrolysis of the studied nitramines according to two possible mechanisms:

N N

N

N

NN

O

O

OO

O

O

N N

N

N

NN

O

O

OO

O

O

OH-OH-

N N

N

N

NN

O

O

OO

O

O

N N

N

N

OHN

O

O

O

O

OH-

N N

N

N

NN

O

O

OO

O

O

H

N N

N

N

N

OH

OH

OH

OHSN2

E2

-NO2-

-H2O -NO2-

According to the results of performed calculations, the bimolecular elimination (E2) of nitro group coupled with OH-group attack of a proton to form C=N double bond is more preferable. The nucleophilic substitution of a nitrogen atom of cycle with hydroxyl anion (SN2) is complicated by a nitrogen lone pair.


Kinetic Model of Cytosine Bimolecular Tautomerization

Dmytro Kosenkov,1 Leonid Gorb1,2 , Oleg V. Shishkin3 and Jerzy Leszczynski1

1Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217

2Institute of Molecular Biology and Genetics, National Academy of Sciences, Kiev, Ukraine 03143

3Institute for Scintillation Materials, National Academy of Sciences of Ukraine, Kharkiv 61072, Ukraine

The observations suggest that tautomeric forms of cytosine are not detected by any of available experimental technique when cytosine forms the solid state (crystal) [1]. (Fig.1). However, the presence of those tautomers in gas-phase is also well known. Typically, to transfer cytosine molecules from solid state to gas phase the laser initiated desorption is used [2]. Therefore the question on the mechanism of tautomers appearance arises.

The observation of cytosine tautomers could not be explained by unimolecular mechanism due to high activation energy of tautomerization. The biomolecular mechanism [3] is more favorable. We assume that the tautomerization proceeds during the evaporation of the cytosine crystal. In the current work the kinetic model of such evaporation that is accompanied by bimolecular tautomerization of cytosine is proposed.

Our model consists of the system of four ordinary linear differential equations that describe the evaporation and tautomerization of the cytosine. The forward and reverse transitions between canonic and tautomeric forms along with evaporation of cytosine have been considered. There is substantial dependence of the tautomer concentration in gas-phase on the temperature and evaporation rate of the cytosine crystal. The rate constants of tautomerization have been estimated on the basis of DFT calculations and used as the parameters in kinetic equations.

The cytosine tetramer is used as a model of solid cytosine. The geometry optimization has been performed at the B3LYP/6-31++G(d,p) level of theory with Gaussian03 program. The Gibbs free energies and the rate constants were evaluated from the frequency calculations at the level of optimization.

Fig. 1 The unit cell of the cytosine crystal only canonic form of the cytosine is observed. The curved arrows denote directions of proton transfer during the formation of ‘rare’ tautomeric forms observed in gas-phase experiments. The dashed lines denote intermolecular hydrogen bonds.


References 1. D.L. Barker, R.E. Marsh, Acta Crystallogr., 1964, 17, 1581. 2. E. Nir, M.Muller, L.I. Grace, M.S. de Vries, Chem phys. Lett., 2002, 355, 593. Z. Yang, M.t. Rodgers, Phys. Chem. Chem. Phys., 2004, 6, 2749


Quantum-Chemical Research of Reaction Mechanism

V.Kukueva

Fire Safety Institute, Onoprienko str. 8, Cherkassy, Ukraine, 18034

The development of theoretical tools to describe and understand adsorption and reactions at surfaces has been quite parallel to the experimental one. A number of useful concepts have been introduced to describe the electronic structure, the interaction energies and the dynamics of adsorbents on surfaces. It is now possible to describe at a semi-quantitative level the electronic structure and energetic of adsorption on metal surfaces.

What determines the catalytic activity of a given surface for a given chemical reaction? One of the aspects about solid surfaces that have the largest fundamental and technical importance is the way in which chemical reactions are affected by the presence of a surface. Many catalytic reactions are structure sensitive, meaning that the rate depends on the geometrical structure of the surface. Almost all of them proceed with rates that are much larger at a surface than in the gas or liquid phase. For reactions with more than one possible product the presence of a surface can change the selectivity [1]. On the other side, the poisoning and promoting effect that co-adsorbates can have on the rate of a reaction for a fixed surface structure of the catalyst is ascribed to an electronic factor [2]. These principles are used extensively in all industrial production of chemicals.

At the most general level the role of the surface can often be regarded as a means of stabilizing intermediates in the reaction. Such effects are all demonstrations of a dependence of the potential energy surface (PES) on which the catalytic reaction proceeds on the position and kind of atoms in the surroundings. The potential energy surface is given by the electronic structure of the system and even differences in activity between different facets of same metal are due to differences in the electronic structure of the system and are thus electronic in nature. The starting point is the understanding is much larger for metal surfaces than for oxides, so even though oxides are at least as important catalysts as metal, the present paper will be restricted to deal with metallic surfaces almost exclusively. The chemisorption of a gas atom like H, O, C, or N on a metal surface is accompanied by the formation of very strong bonds. For H results for the 4d and 5d series have been described [2], and it is seen that the trend is exactly the same as for 3d’s. It is clear that the number of d-electrons of the surface is more important in determining the binding energy that other factors such as lattice constant or whether the d-electrons are 3d, 4d, or 5d. The synthesis of NH3 directly from N2 and H2, for instance, is extremely slow in the gas phase because it requires a prohibitively large energy to break the N-N bond. At a metal surface the N atoms are stabilized by the chemisorption bond to the surface and this means that the reactions can proceed with a reasonable activation energy [1].

The quantum-chemical calculation has been provided to illustrate the possibilities of theoretical interpretation and prediction of catalytic reaction pathway. As an object of research the oxidation of NH3 on the Fe surface have been choosed. We will the kinetics developed for the ammonia oxidation to explain: if the molecular either atomic oxygen co-adsorption more preferable for this reaction. The calculation of elementary interaction of ammonium molecule with atomic and molecular oxygen in presence ferrum atom by quantum-chemical method MNDO have been provided in this paper. The model of ammonia with clear Fe surface interaction has been investigated at first. Ammonia on the Fe forms the one layer adsorption region, where the binding power can be increased at the co-adsorption with atomic and molecular oxygen. Then the research has been devoted to calculation of the ammonia on the Fe


in presence atomic and molecular oxygen accordingly. The activation energy barrier and total energy have been presented for each stage.

The collision complexes: Fe…NH3, Fe…O2, Fe…O have been calculated for evidence of the first stage of catalytic transformation, namely – particles adsorption on the metal surface. The Fe

… NH3 collision complex has been calculated at the distance between particles from 1 till 3.20

.The calculation of ammonium molecule on the clear Fe shows the insignificant interaction. We

can see it by small energy minima at the distance equal to R = 1.90

(fig. 1 a). We also presented the Lennard-Jones [3] potential curve of interaction two particles for comparison (fig. 1b). As we can see the calculation results almost repeat the shape of classic potential curve.

1.00 1.50 2.00 2.50 3.00

. .

-12.00

-8.00

-4.00

0.00

E , eV

R, A

0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 a bFig. 1 a. The calculated the interaction potential of collision complex NH3…Fe by the MNDO method. b. Schematic picture of the potential a simple gas atom feels outside a metal.

The activation energy of this interaction not high Eact= 4,03 e . This is can be explained by the presence of vacant d- rbitals of Fe and ammonia electron pair. The adsorption energy [4] equal to ds= 1 + el, where 1 – one electron energy, el – electrostatic interaction energy of interatomic interaction. Specifically for this calculation the absolute energy value corresponds to total interaction energy, which coincides with potential energy minimum. The collision complexes between Fe and atomic and between Fe and molecular oxygen have been calculated. It is interesting to note that there is potential minimum at the almost the same distances between Fe atom and both particles. It can be interpreted as equal interaction probabilities for all investigated particles. But the comparison activation energy shows that the less barrier is for ammonia and molecular oxygen adsorption ( ct = 4,03 eV and ct = 4,45 eV, accordingly). For atomic oxygen adsorption the activation energy has some more value ct = 6,74 eV. It is necessary to note, that there is attraction between atomic oxygen and Fe. According to calculation results we have classical potential curve, to evidence even molecule formation. It gives us right to suppose that atomic oxygen influents not at the ammonia oxidation but at the catalyst oxidation. The activation energy analysis of investigated adsorption complexes (table 1)

shows that almost at the same distance between particles (R = 1,9 0

) the activation barrier of Fe…O complex some exceed the analogical values for other interacting components. Therefore at the adsorption stage in the competition between particles the molecular oxygen is predominating. It is coincide with experiments [5]. It is also agreed with suggested explanation


of molecular oxygen participation in the formation complexes at the surface due to particularities of it electronic structure (the triplet ground state with two unpaired electrons).

Results of MNDO calculations of the processes on the Fe catalyst during ammonia oxidation.

Table 1.

The next research stage is calculation of ammonia with Fe interaction at the presence molecular or atomic oxygen. As for as NH3…O…Fe collision complex shows considerable

interaction and energy minimum at R = 1.80

. According to electronic density distribution analysis we can see that oxygen atom almost “seat” on the d-orbitals of iron. There is weak overlapping between ammonia molecular orbitals and oxygen atomic orbitals. Besides, there is significant interaction of the oxygen p-orbitals and iron d-orbitals. It can be explained by more strong influence atomic oxygen on the Fe, than on the NH3. The deep potential minimum had confirmed this supposition. As mentioned above the chemisorption’s analyses have demonstrated the same conclusion. But the calculation of all collision complexes confirmed significantly deep interaction between ammonia and atomic oxygen at the presence of Fe catalyst. The potential curve of the NH3…O2…Fe has small energy minimum, in spite of the activation energy much less, then for atomic oxygen. Therefore it is necessary to admit that atomic oxygen can be more active in the ammonia oxidation on the Fe surface. It is agreed with traditional point of view on the ammonia oxidation mechanism. But we can’t underestimate the molecular oxygen presence, because as experiments have showed [5] and our calculations confirmed, the molecular oxygen has formed the complexes on the catalyst surface. It is probable would be useful to use ferrum oxide and catalysis could be carried out in the molecular oxygen presence.

So, the calculated activation energies and potential curves analysis allows say about predominant flowing one or another stage of complicated chemical transformation in the catalytic reaction process. It was proofed, that atomic oxygen has more influence on the catalyst surface, than on the ammonium oxidation process. The predicted formation of adsorbed complexes between molecular oxygen and catalyst surface to be obtained by experiments has been confirmed by our calculations. Accordingly calculation results the participation of atomic oxygen in the ammonia oxidation is substantially too.

References

1. Theretical aspects of surface reactions, J.K.Norskov and P.Stolze. Surface Science, 189/190, 91-105 (1987) 2. North-Holland, Amsterdam, J.K.Norskov, Progress in Surface Science, V. 38, 2, 1991 3. S.Holloway and J.K.Norskov, Surface science lecture notes, 1991, Liverpool University press 4. Van Santen Rutger A, and Neurock, Catal. Rev.-sci.eng., 1995, 37 (4), 557-698 5. C.T.Au and M.W.Roberts, Nature, 319, 206 (1986)

Collision complexes NH3…Fe O2…Fe O…Fe Fe…O2…NH3 Fe...O...NH3Total energy, tot eV -350,689 -745,635 -427,04 -989,23 -668,7 Heat of formation 0

298,kcal/mol

164,77 72,00 29,216 211,19 219,94

Dist. betw. particles andFe, R, Å

1,9 1,95 1,9 2,05 1,75

The activation energy, Eact

4,03 4,45 6,74 1,16 4,2


Quantum Mechanical Calculations of Molecular Structure and Vibrational Spectra of CH3-NClnSiF3 (N = 0-3) Compounds

G.M. Kuramshina, S.V .Syn’ko, Yu.A. Pentin

Faculty of Chemistry, Moscow State University (M.V.Lomonosov), Moscow 119992, Russia

The relatively simple halogen substituted methylsilane derivatives CX2Y-SiZ3 or CX3-SiY2Z(X,Y,Z = H, F, Cl Br, I) are attracted an attention of investigators not only due to their very important technological application but also due to the special place of silicon containing compounds in the theory of molecular structure. The replacement of one of ethane carbon atoms by silicon one leads to the very specific changes in structure, force fields and vibrational spectra of methylsilanes. Investigated in the present work the fluorosylilderivatives are of special interest due to the fluorination. Earlier we have investigated the ir and Raman spectra of methyl and chloromethyltrifluorosilanes [1-4] and the assignment was proposed on a base of normal coordinate analysis using the empirical force field obtained for the related compounds [5-7]. These investigations have allowed us to identify some trends in molecular structure, vibrational spectra and molecular force fields of these compounds. The conclusion was made that the introducing the electronegative substitute both to carbon or silicon atoms significantly results on the position of some vibrational frequencies especially on the C-Si stretching. However, to our knowledge, complete vibrational studies of the titled compounds have not been reported and no quantum mechanical predictions of the vibrational spectra of these compounds have been carried out.

The goal of this work is the benchmark quantum mechanical calculations at the different theoretical levels for methyltrifluorosilane CH3SIF3 (I) and three chloromethyltrifluorosilanes CH2ClSiF3 (II), CHCl2SiF3 (III) CCl3SiF3 (IV). On a base of calculations the new assignment of I-IV vibrational spectra was proposed and the molecular force fields of these compounds were analyzed.

Ab initio calculations were carried out using the Gaussian 03 package (Revision .2) within HF and MP2 approaches. The quantum mechanical calculations were done using the B3LYP and BLYP functionals. The next four basis sets were used in all calculations: 6-31G*, 6-311++G**, aug-cc-pVDZ and aug-cc-pVTZ. The minima of the potential surface were found by relaxing the geometric parameters with the standard optimization methods. Analytical force constants were derived and harmonic vibrational frequencies as well as Raman activities were calculated using investigated theoretical levels. All calculations have been done without any symmetry restrictions on the structures. Addtionally, the barriers to hindered internal rotation around the C-Si bond were calculated.

Earlier the similar calculations were carried out for the chlorosubstituted methylsilanes [8] and the B3LYP/aug-cc-pVDZ level was shown as the most cost/effective one for the predictions of structure and molecular spectra of these compounds. Initially, in this work the same level of theory was chosen as a basic for the CH3-nClnSiF3 (n=0-3) compounds. But the detailed analysis of theoretical date and comparison with experimental ir and Raman data have showed that the B3LYP/aug-cc-pVDZ level results in significantly understated values of frequencies and the more expanded basis set is necessary for the correct description of observed data. So the Dunning’s triple zeta correlation consistent basis set with augmenting diffuse functions with B3LYP functional was chosen as a basic for the quantum mechanical calculations of I-IV.


The optimized equilibrium geometries of I-IV are presented in Table 1. The revised interpretation of vibrational spectra of I-IV on a base of the B3LYP/aug-cc-pVTZ results is performed in Tables 2 and 3,

Table 1. Optimized B3LYP/aug-cc-pVDZ and B3LYP/aug-cc-pVTZ geometry parameters of I-IV (distances in Å, bond angles in degrees).

CH3SiF3a CH2ClSiF3 CHCl2SiF3 CCl3SiF3

1b 2c 1b 2c 1b 2c 1b 2c

R(C-Si) 1.842 1.837 1.865 1.858 1.884 1.876 1.899 1.891 R(C-H) 1.098 1.090 1.096 1.088 1.094 1.085 R(C-Cl) 1.813 1.808 1.803 1.797 1.800 1.794 R(Si-F) 1.626 1.594 1.619 1.586 1.618 1.585 1.613 1.581 R(Si-F)s 1.624 1.591 1.613 1.581

CSiF 112.27 111.97 111.94 111.85 109.95 109.82 110.26 110.00 CSiF s 109.99 109.18 111.94 111.37 SiCH 110.18 110.42 109.91 111.19 111.76 112.29 HCCl 107.59 107.63 106.50 106.72 HCH 108.76 108.47 108.87 108.46 FSiF 106.46 106.87 106.93 108.26 108.69 108.94 FSiF s 107.43 107.77 ClCCl 112.14 112.09 109.88 109.97

a MW data: R(C-Si)=1.812Å; R(CH)=1.081Å; R(SiF)=1.574Å; SiCH=111.01°; CSiF=112.20° (Durig J.R., Li Y.S., Tong C.C. J. Mol. Struct., 1972. vol 14 (2), 255). b1 - B3LYP/aug-cc-pVDZ c2 - B3LYP/aug-cc-pVTZ

Table 2. Experimental and theoretical (B3LYP/aug-cc-pVTZ) frequencies (cm-1) of CH3SiF3 and CCl3SiF3 molecules (the potential energy distribution in % is given in parentheses)

CH3SiF3 CCl3SiF3No Sym. mode Exp. [2] calculation Exp. [2] calculation

12345

A1 (CX3)(CX3)(SiF3)(Si )(SiF3)

2925 1286 902 701 390

3045 (100 CH) 1314(50HCH,47SiCH) 886 (61SiF,31SiC) 681 (60SiC, 42SiF) 373 (50FSiF,42CSiF)

393 217 818 941 474

372 (38CCl,18FSiF,17CSiF,13SiCCl) 202 (24ClCCl,29SiC,24SiCCl) 794 (75SiF) 960 (49SiC,20SiF) 461 (13SiC,42CCl)

6 A2 140 125 (100 ) 44 48 (100 )789101112

E (CX3) (CX3)(SiF3) (CX3) (SiF3) (SiF3)

2993 1412 982 783 331 232

3119 (100CH) 1457 (95HCH) 959 (84SiF) 802 (75SiCH,15SiF) 316 (82FSiF,12CSiF) 213 (78CSiF,15FSiF)

757 280 1014 119 352 217

703 (82CCl,12ClCCl) 269 (57ClCCl,14CCl,21FSiF) 985 (97SiF) 110 (70SiCCl,30CSiF) 339 (50FSiF,21CSiF) 202 (47CSiF,32ClCCl,14FSiF)


Table 3. Experimental and theoretical (B3LYP/aug-cc-pVTZ) frequencies (cm-1) of CH2ClSiF3and CHCl2SiF3 molecules (the potential energy distribution in % is given in parentheses)

CH2ClSiF3 CHCl2SiF3

No.

Sym mode Exp. [4]

calculated mode exp [5]

calculated

1234567891011

A’ (CH) (CH2)(CH2)(SiF3)(SiF3)(CCl)(Si-C) (SiF3)(SiF3)(SiF3)(CCl)

2955 1397 1199 990 900 767 664 403 337 238 123

3080(100CH) 1438 (82HCH) 1220 (56ClCH,40SiCH) 960(93SiF) 884(59SiF, 28SiC) 746(57CCl,15CSi) 648(37SiC,32CCl) 391(42FSiF,40CSiF) 327(66FSiF,20CSiF) 230(38CSiF,31FSiF 113(39SiCCl,39CSiF)

(CH) (CH) (SiF3)(SiF3)(CCl)(Si-C) (SiF3)(SiF3)(SiF3)(CCl2)(CCl2)

2981 1193 1003 913 792 624 428 340 300 212 150

3127 (100CH) 1187 (51SiCH,40HCCl) 985(90SiF3)896 (47SiF,31SiC) 768 (47SiF,15CSi,29CCl)615 (31CCl,22SiC) 414 (35FSiF,37CSiF) 324 (46FSiF,18CSiF) 290 (52FSiF,26ClCCl) 202 (34ClCCl,12CSi) 136 (50CSiF,27SiCCl)

12131415161718

A (CH) (SiF3) (CH2)(SiF3)(CH2)(SiF3)

3003 1112 990 767 337 200 65

3133(100CH) 1128 (72ClCH,25SiCH) 972 (90SiF3)745 (64SiCH,21ClCH) 310 (86FSiF) 206 (82CSiF,11FSiF) 57 (100 )

(SiF3) (CH) (SiF3) (CCl2)(SiF3)(CCl2)

1003 1173 743 347 239 123 53

970 (97SiF3)1210 (100HCCl) 701 (97CCl) 336 (69FSiF,18CSiF) 221 (44CSiF,30FSiF) 109 (69SiCCl,34CSiF) 40 (98 )

These assignments of I-IV vibrational spectra are differed from proposed in [1-4]. The most interesting is the behavior of the C-Si stretching in I-IV series. The C-Si stretching theoretical frequency monotonically decreases in the I-III series (681, 648, 615 cm-1, correspondingly) but for IV it is significantly increases (up to 960 cm-1) and it is totally different from what can be expected. Similar picture for shifts of C-Si frequencies of I-IV is observed at all other calculations at all investigated levels of theory including HF and MP2. B3LYP/aug-cc-pVDZ frequency is equal to 951 cm-1 , B3LYP/6-311++G** one is equal to 957 cm-1 ). Earlier the band near 623 cm-1 was assigned to C-Si stretching of IV based on the assumption that the increasing the number of chlorine atoms in methyl group should lead to the lowering the C-Si frequency. If the quantum mechanical calculations reflect the real picture of intramolecular dynamics of I-IV the empirical assignment must be revised. In the ir spectrum of IV there is observed the weak band near 941 cm-1 that could be assigned to C-Si stretching of IV.

References

1. S.V.Syn’ko, G.M.Kuramshina , Yu.A.Pentin, G.S.Gol’din. Structure and vibrational spectra of chloromethylsilanes. Rev. informarmation series “Hetero-organic compounds and their application”, Moscow, NIITEKHIM, 1989. 2. S.V.Syn’ko, G.M.Kuramshina, E.M.Protasov, et.al. Mosc. Univ. Bull, 2, Chemistry, 1983, vol. 24(5), 449. 3. S.V.Syn’ko, Yu.A.Pentin, G.M.Kuramshina, et.al. Mosc. Univ. Bull., Chemistry, 1984, vol. 25(6), 548. 4. S.V.Syn’ko, Yu.A.Pentin, G.S.Gol’din, et.al. Mosc. Univ. Bull., Chemistry, 1985, vol.26(2), 131.


5. S.V.Syn’ko, Yu.A.Pentin, G.M.Kuramshina, et.al. Mosc. Univ. Bull., Chemistry, 1985, vol. 26(3), 280. 6. I.V.Kochikov, G.M.Kuramshina, S.V.Syn’ko, Yu.A.Pentin. J. Mol. Struct. 1988, vol. 172, P.299.7. I.V.Kochikov, G.M.Kuramshina, S.V.Syn’ko, et.al. Mosc. Univ. Bull., Chemistry, 1986, vol. 27(1), 25.8. G.M.Kuramshina, Yu.A.Pentin, S.V.Syn’ko. Russ. J. Phys. Chem., 2003, vol. 77(2), 298.

Acknowledgement. The RFBR grants No 05-03-32135 and 05-07-98001-r_ob’ are gratefully acknowledged for the partial financial support.


DFT Calculations of Substituted Anilines

G.M. Kuramshinaa, S.F. Makhmutovab, S.V. Pikhtovnikovb, S.M. Usmanovb

aFaculty of Chemistry, Moscow State University (M.V.Lomonosov), Moscow 119992, Russia Birsk State Social Pedagogical Academy, Birsk, 452453, Russia

The structures and molecular properties of aniline and its derivatives are the subject of considerable interest and several studies of these compounds have been done during the last decades both experimentally and experimentally. The goal of the present investigation is the modern theoretical study of the structure, vibrational spectra and molecular force fields of aniline and three fluoroanilines (orto-, meta-, para-). Fluoroanilines are characterized by the specific chemical properties, in particularly in ionization processes so it is important to have the good quality theoretical data for the ground states of these compounds.

The performance of different theoretical approaches for the aniline molecule was comparatively studied elsewhere [1-3] and conclusion was made that DFT methods were the most cost/effective ones for the predicting its geometry and vibrational spectrum. There were also several studies of resonant spectra of aniline derivatives.

In the present study molecular orbital calculations were carried out using the Gaussian 03 program package (Rev.C.02). The fully optimized geometries of aniline (I) and o- (II), m- (III), and p- (IV) fluoroanilines were calculated using Dunning’s double and triple zeta correlationconsistent basis sets with augmenting diffuse functions (aug-cc-pVDZ and aug-cc-pVTZ) at the DFT (B3LYP) level of theory. The minima of the potential surface were found by relaxing the geometric parameters with the standard optimization methods. Analytical force constants were derived and harmonic vibrational frequencies were calculated at investigated theoretical levels.

One of the goals of this work is to find the trends in geometry parameters and vibrational spectra of II-IV which depend on the orto-, meta- and para-fluorosubstitution. The geometry of amino-group can be characterized by the inversion and tilt angles (Fig.2), the optimized values of these parameters are performed in Table 1. The inversion angle can be used as a measure of pyramidalization of the amino-group.

N7 C1

C2

C6

C3

C5

C4

F8 H9

H14

H10

H11H12

H13

X1X2

Figure 1. Definition of and angles: = C1X1N7, = X2C1N7 (X1 and X2 are centers of H…H and C…C lines, correspondingly)

The B3LYP/aug-cc-pVTZ optimized conformations of I-IV are shown in Figure 1.


1.3961.399

1.388

1.3911.077

Q1Q2

Q3

Q4Q5

Q6

NC1

C2C3

C4

C5C6

1.396

1.392

1.389

1.3881.377

1.006

1.007

1.398

1.390

C1

C2N

F

C3

C4

C5C6

1.362

aniline (I) o-fluoroaniline (II)

1.381

1.387

1.391

1.392

1.383

1.4011.006

C1

C2N

C6

F

C5

C3

C4

1.3541.396 1.389

1.3821.399

1.3991.007

C1N

C2

C6C5

C3

C4 F1.357

m-fluoroaniline (III) p-fluoroaniline (IV)

Figure 2. Optimized B3LYP/aug-cc-pVTZ structures of investigated molecules.

Microwave spectroscopic studies have shown that II in the ground state had a non-planar structure with the hydrogen atoms of amino-group bent out of the aromatic plane by ~ 36.7 and that C-F bond was slightly tilted towards the NH2-group. The last can be considered as indication of intramolecular hydrogen bonding. The observable bent is in good correspondence with theoretical prediction (Table 1).

Theoretical data of II demonstrate rather large difference in the dihedral angles C2-C1-N7-H14 and C6C1N7H13 (equal to 20.5° and 26.2°, correspondingly) indicating the twisting of amino-group toward the fluorine-substituent. As a result we have that in II the F…H14 distance is equal to 2.364 Å while the F…H9 distance is equal to 2.584Å. For instance in III the distances F…H8 and F…H10 are equal to 2.562 Å and 2.594 Å, correspondingly, and for IV the intramolecular distance F…H9 is equal to 2.584Å. The shortening of F…H14 indicates the possibility of a weak intramolecular hydrogen bonding in II. The optimized force fields of I-IVwere transformed from Cartesian coordinates to the redundant system of 49 internal coordinates using the SPECTRUM package and potential energy distributions on vibrations of I-IV were calculated. A part of molecular force constants related to the bond stretchings are presented in Table 1. The trends in vibrational frequencies of I-IV were analyzed and finger print regions are considered.


Table 1. Optimized B3LYP/aug-cc-pVTZ values of the angles and (in degrees) and force constants of the skeleton valence bonds in mdyn/Å (optimized geometries are presented in Fig.1)

CN Q1 Q2 Q3 Q4 Q5 Q6 CF I 2.83 44.74 6.143 5.007 5.254 5.159 5.149 5.254 5.007 - II 2.78 42.81 6.400 5.147 5.401 5.133 5.170 5.221 5.040 5.767 III 2.73 42.75 6.286 5.034 5.361 5.259 5.150 5.276 4.968 5.959 IV 3.01 46.0 6.105 5.017 5.239 5.278 5.278 5.239 5.017 5.914

Acknowledgement. The RFBR grants No 05-03-32135 and 05-01-97928-r_agidel’ are gratefully acknowledged for the partial financial support.

References

1. M.A. Palafox,, L.L.Néñez, M.Gil, J. Mol. Struct. (Theochem) 2002, vol. 593, 101. 2. M.A. Palafox, F.J.Meléndez, J. Mol. Struct. (Theochem) 1999, vol. 493, 171. 3. W. B. Tzeng, K. Narayanan, C. Y. Hsieh and C. C. Tung, J. Chem. Soc., Far. Trans.,1997, vol. 93, 2981.


Assessment of the Performance of Density-Functional Methods for Calculations on Iron Porphyrins and Related Compounds

Meng-Sheng Liao, John D. Watts, and Ming-Ju Huang

Department of Chemistry P.O. Box 17910

Jackson State University Jackson, MS 39217

The behaviors of a large number of GGA, meta-GGA, and hybrid-GGA density functionals in describing the spin-state energetics of iron porphyrins and related compounds have been investigated. There is a large variation in performance between the various functionals for the calculations of the high-spin state relative energies. Most GGA and meta-GGA functionals are biased toward lower-spin states and so fail to give the correct ground state for the high-spin systems, for which the meta-GGA functionals show more or less improvement over the GGA ones. The GGA functionals that use the OPTX correction for exchange show remarkably high performance for calculating the high-spin state energetics, but their results for the intermediate-spin states are somewhat questionable. A heavily parameterized GGA functional, HCTH/407, provides results which are in qualitative agreement with the experimental findings for the iron porphyrins [FeP, FeP(Cl), FeP(THF)2], but its relative energies for the high-spin states are probably somewhat too low. The high-spin state relative energies are then even more underestimated by the corresponding meta-GGA functional -HCTH. For the hybrid-GGA functionals, the Hartree-Fock (HF)-type (or exact) exchange contribution strongly stabilizes the high-spin states, and so the performance of such functionals is largely dependent upon the amount of the HF exchange admixture in them. The B3LYP, B97, B97-1, and -HCTH-hybfunctionals are able to provide a satisfactory description of the energetics of all the systems considered.


Understanding the Unique Architecture of Scx@C82 (x=1, 2 and 3)by Use of the 4n+2 Rule

Dan Liu and Frank Hagelberg

Computational Center for Molecular Structure and Interactions Department of Physics, Atmospheric Sciences and General Science,

Jackson State University, Jackson, MS, 39217

Metallofullerenes have attracted considerable attention due to their pivotal role for the understanding of endohedral clusters as well as their potential applications in nanotechnology.1The C82 species exhibits a unique variety of metal encapsulation modes. So far, one, two and three Sc-encapsulated C82 (labeled Sc2+@C82

2-, Sc24+@C82

4- and Sc36+@C82

6-), as well as La3+@C82

3-, Gd3+@C823- etc., have been reported. On the other hand, the isomeric structures of

encaged fullerene cage are quite distinct from each other. The most stable isomer of C82 has C2symmetry while the fullerene cages of Sc@C82 and Sc2@C82 share C2v symmetry, and C3vsymmetry has been found for the cage of Sc3@C82. In short, C82 (C2v) is stabilized by accepting two, three or four electrons, while six electrons stabilize the C82 (C3v) isomer. For comparison, two or four electrons are typically transferred to C84 and three or six electrons to C80. Relying on the quantum calculations in combination with orbital analysis and the 4n+2 rule, this project aims at defining the architectural principles that give rise the unique variety of metal-encapsulated C82 clusters.

ReferenceEndofullerenes: A New Family of Carbon Clusters; Akasaka, T., Nagase, S., Eds.; Kluwer

Academic Publisher: Dordrecht, The Netherlands, 2002; p. 1-297.


Conventional Strain Energy in Boracycloproane, Diboracyclopropane, Boracyclobutane and Diboracyclobutane

Brandon Magers, Harley McAlexander, and David H. Magers


The conventional strain energies for boracyclopropane, diboracyclopropane,boracyclobutane, 1,2-diboracyclobutane, and 1,3-diboracyclobutane are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory (MP2), and density functional theory. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. Two basis sets, both of triple zeta quality on valence electrons, are employed: 6-311G (d,p) and 6-311+G(2df,2pd). Results are compared to the conventional strain energies of cyclopropane and cyclobutane to determine what effect boron substitution has on the conventional strain energies of these prototypical homocycles. We gratefully acknowledge support from NSF EPSCoR (EPS-0132618).


Exploring the Many Uses of Homodesmotic Reactions

David H. Magers


A homodesmotic reaction is any reaction in which bond number, bond type, and bonding environments are all conserved. In the past, we have utilized homodesmotic reactions primarily for computing the conventional strain energies for small cyclic systems. More recently, we have utilized them to compute standard enthalpies of formation. The computed enthalpy for most molecular systems will greatly differ from that same system’s standard enthalpy of formation because the reference state is different. Current models for computing standard enthalpies of formation have to account for these different reference states. However, in a homodesmotic reaction where bonding environment is conserved, a computed enthalpy of reaction can be almost identical to the enthalpy of the reaction computed from standard enthalpies of formation. The effect from the differing reference states is essentially cancelled. By choosing a homodesmotic reaction in which reference values for standard enthalpies of formation for all of the products and reactants can be found except for the system of interest, the standard enthalpy of formation for this system can be determined from the computed enthalpy of the reaction. Results of this method are presented for certain benzene derivatives and for certain alkanes and sulfides for comparison with reference data to validate the method. For larger systems, often several different homodesmotic reactions can be devised for the same molecule. Our results from these different reactions yield quite similar results further validating the method. Finally, we are currently attempting to use homodesmotic reactions to compute resonance stabilization energies for models systems such as benzene and 1,3-butadiene. Preliminary results are promising. We gratefully acknowledge support from NSF EPSCoR (EPS-0132618).


Probing the Acetylcholinesterase Inhibition of Sarin:A Comparative Interaction Study of the Inhibitor and Acetylcholine

with a Model Enzyme Cavity

D. Majumdar,a Szczepan Roszak,b and Jerzy Leszczynskia

Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS 39217, and Institute of Physical and Theoretical

Chemistry, Wroclaw University of Technology, Wybrze e Wyspia skiego 27, 50-370 Wroclaw, Poland

Interaction energies have been estimated between sarin and a model enzyme cavity of acetylcholinesterase (ACHE) using density functional (DFT) and Møller-Plesset second order perturbation (MP2) level of theories. The calculated interaction energies have been compared with those of acetylcholine and the same model ACHE cavity. The ACHE…Sarin and ACHE…Ach structures have been optimized using DFT based two-layer ONIOM hybrid calculations. The nature of interactions has been investigated in detail using an interaction energy partitioning technique. The effects of solvation on the interaction energies have also been taken into account. An inhibition mechanism during the uptake of sarin inside the ACHE cavity has been proposed from the comparison of the energetics of the ACHE…Sarin and ACHE…Ach complexes.


Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of Carbon and Silicon

Harley McAlexander, Brandon Magers, Crystal B. Coghlan, and David H. Magers


The conventional strain energies for three- and four-membered heterocycles of carbon and silicon are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. These include silacyclopropane, disilacyclopropane, silacyclobutane, 1,2-disilacyclobutane, 1,3-disilacyclobutane, and trisilacyclobutane. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory (MP2), and density functional theory. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. Two basis sets, both of triple zeta quality on valence electrons, are employed: 6-311G (d,p) and 6-311+G(2df,2pd). Additionally, single-point fourth-order perturbation theory and coupled-clustered calculations using the larger of the two basis sets at the optimized MP2 geometries were used to investigate the effects of higher-order electron correlation. Cross-sections of the electron density in the plane of the ring for each of the three-membered rings were plotted to observe how the electron density is distributed in the sigma bonds of the different systems.

Results indicate that silicon substitution reduces the conventional strain energy of cyclobutane, but increases the conventional strain energy in cyclopropane by destroying the stabilizing factor of sigma delocalization. Electron-density plots show that only in cyclopropane is the electron density thoroughly delocalized in the sigma bonds of the ring. We gratefully acknowledge support from NSF EPSCoR (EPS-0132618).


Adsorption of Sarin on Platinum and Palladium (001) and (111) Surfaces: An Ab Initio Study

A. Michalkova, D. Majumdar, and J. Leszczynski

Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P. O. Box 17910, Jackson, MS 39217, USA

Platinum and palladium with their extraordinary sorption properties make them catalysts that are most commonly employed in industrial processes. These properties are so unique that platinum may be presented as one of the most versatile, all-purpose, heterogenous metal catalysts. They can have some applications as catalysts for organophosphorus compounds decomposition. Sarin (GB), isopropyl methylphosphonofluoridate, is a very toxic organophosphorus compound. This substance has become known as a nerve agent due to its effects on the disruption of nerve impulses in living organisms. This study of Sarin adsorption on the Pt and Pd clusters should result in a better understanding of how organophosphorus compounds interact with these surfaces of transition metals. This work can lead to designing a better system for their catalytic decomposition.

Quantum chemical calculations employing the density functional theory (DFT) and second order Møller-Plesset perturbation theory (MP2) were performed to investigate the adsorption of Sarin on the platinum and palladium (001) and (111) surface. These methods were used in conjunction with the LANDL2DZ basis set which uses an effective core potential on all Pt and Pd atoms. This basis set was augmented by the polarization functions for all the main atoms. Several representative cluster models of the platinum and palladium (001) and (111) surfaces were chosen with different sizes. The Pt-Pt and Pd-Pd bond distances were fixed at the bulk value of 2.77 Å and 2.75 Å. The geometry of Sarin was fully optimized while the geometry of the metal fragment was kept frozen.

Figure 1. The optimized structure of Sarin adsorbed on the Pt7 cluster obtained at the B3LYP/6-31G(d) level of theory

The results this study reveal that GB is chemisorbed on all selected models by the formation of a chemical bond between the oxygen atom of GB and the surface (see Figure 1. that illustrates the optimized structure of Sarin adsorbed on the Pt7 cluster obtained at the B3LYP/6-31G(d)


level of theory). The O1…Pt distance of this bond amounts from 2.1 to 2.4 Å and the O1…Pd amounts from 2.1 to 2.2 Å according to the size of the metal fragment. Sarin is differently stabilized on the Pt and Pd fragments (the interaction energies amount from -8 to -22 kcal/mol). One can see that the size and type of the surface affect significantly the value of the interaction energy. These changes are proportional to the strength of formed intermolecular interactions. On the other hand, the size of the model mimicking the metal surface does not affect the character of the intermolecular interactions in studied systems.


Theoretical Study of Adsorption of Sarin and Soman onEdge Clay Mineral Fragments

A. Michalkovaa, J. Martinezb, O. A. Zhikolc, L. Gorba,d,O. V. Shishkinc, J. Leszczynskia

a Computational Center of Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P. O. Box 17910, Jackson, MS 39217, USA b Department of Cemistry and Physics, Faculty of Chemistry, Pontific Catholic University of

Chile, Santiago, Chile c Institute for Scintillation Materials, National Academy of Sciences of Ukraine, 60 Lenina ave.,

61001 Kharkov, Ukraine dU.S. Army Engineer Research and Development Center (ERDC), Vicksburg, MS 39180

This study provides details of the structure and interactions of Sarin and Soman with edge tetrahedral fragments of clay minerals. The adsorption mechanism of Sarin and Soman on these mineral fragments containing the Si4+ and Al3+ central cations was investigated. The calculations were performed using the B3LYP and MP2 levels of theory in conjunction with the 6-31G(d) basis set. The studied systems were fully optimized. Optimized geometries, adsorption energies and Gibbs free energies of Sarin and Soman adsorption complexes were computed. The number and strength of formed intermolecular interactions have been analyzed using the AIM theory. The charge of the systems and a termination of the mineral fragment are the main contributing factors on the formation of intermolecular interactions in the studied systems. In the neutral complexes Sarin and Soman is physadsorbed on these mineral fragments due to the formation of C-H…O, and O-H…O hydrogen bonds. The chemical bond is formed between a phosphorus atom of Sarin and Soman and an oxygen atom of the -2 charged clusters containing an Al3+

central cation (see Figure 1a.) and -1 charged complex containing a Si4+ central cation (chemisorption). Sarin and Soman interact mostly in the same way with the same terminated edge mineral fragments containing different central cations. However, the interaction energies of the complexes with an Al3+ central cation are larger than these values for the Si4+ complexes. The interaction enthalpies of all studied systems corrected for the basis set superposition error were found to be negative. However, based on the Gibbs free energy values only strongly interacting complexes containing charged edge mineral fragment with an Al3+ central cation are stable at a room temperature. We can conclude that Sarin and Soman will be adsorbed preferably on this type of edge mineral surfaces. Moreover, based on the character of these edge surfaces tetrahedral edge mineral fragment can provide effective centers for the dissociation.

The interactions between Sarin and Soman and differently terminated edge octahedral mineral fragments containing the Mg2+ central cation have been investigated. The DFT(B3LYP) and MP2 levels of theory in conjunction with the 6-31G(d) basis set have been used to study the adsorption complexes. The intermolecular hydrogen bond interactions have been analyzed applying Atoms in Molecules (AIM) approach. Because of steric factors Sarin is oriented differently towards the mineral fragment than Soman. It is the reason why Sarin and Soman interact in a different way with the same mineral fragments. Sarin forms the Mg-O chemical bond with the (1+) charged fragment. The systems are mostly stabilized by the formation of relatively strong multiple O-H…O and F…H-O hydrogen bonds and additionally stabilized by weaker C-H…O hydrogen bonds. The interactions of Sarin and Soman with the systems containing differently terminated fragment were found to be different (this is in contrast with the conclusion of the study of Sarin and Soman adsorption on the edge tetrahedral mineral fragments


where the stability of the system was mainly influenced by the charge of the system). Interaction energies corrected by the basis set superposition error, along with the Hint and Gint values were also calculated and analyzed. It was found that target molecules interact the most preferably with (2+) charged edge octahedral mineral fragment containing 6 water molecules (see Figure 1b.).

a) GB-[AlO(OH)3]2- b) GB-[Mg(H2O)6]2+

Figure 1. The optimized structure of Sarin adsorbed on the tetrahedral [AlO(OH)3]2- and the octahedral [Mg(H2O)6]2+ mineral fragments obtained at the B3LYP/6-31G(d) level of theory.


Molecular Surface Electrostatic Potentials and Anesthetic Activity

Jane S. Murray

Department of Chemistry University of New Orleans

New Orleans, LA 70148

General anesthetics apparently act through weak, noncovalent and reversible interactions with certain sites in appropriate brain proteins. As a means of gaining insight into the factors underlying anesthetic potency, we have analyzed the computed electrostatic potentials VS(r) on the surfaces of 20 molecules having activities varying between zero and high. Our results are fully consistent with, and help to interpret, what has been observed experimentally. We find that an intermediate level of internal charge separation is required; this is measured by , the average absolute deviation of VS(r), and the approximate window is 7 < < 13 kcal/mole. This fits in well with the fact that anesthetics need to be lipid soluble, but also to have some degree of hydrophilicity. We further show that polyhalogenated alkanes and ethers, which include the most powerful known anesthetics, have strong positive potentials, VS,max, associated with their hydrogens, chlorines and bromines (but not fluorines). These positive sites may impede the functioning of key brain proteins, for example by disrupting their normal hydrogen bond patterns. It has indeed been recognized for some time that the most active polyhalogenated alkanes and ethers contain hydrogens usually in combination with chlorines and/or bromines.


The Quantum-Chemical Investigation of Heterocyclization Process for Amines of the

Endo-5-aminomethyl-exo-2,3-epoxybicyclo[2.2.1]heptane Row

Okovytyy S.I., Tokar A.V., Kasyan L.I.

Dnepropetrovsk National University 13 Nauchnaya str., Dnepropetrovsk, 49050

From experimental works it have been known that the N-carboxamides of endo-5-aminomethyl-exo-2,3-epoxybicyclo[2.2.1]heptane row are not subjected to intramolecular heterocyclization under conditions of oxidation with peroxyacids. N-carboxamides are the final products of this reaction. At the same time they have easily formed the tricycle azabrendanes under conditions of reduction with lithium aluminum hydride. We have been investigated this last process using DFT-method BHandHLYP/6-31G(d) in gas phase and in solution of ether and tetrahydrofuran mixture (single-point calculations with gas phase geometry in Onzager’s model). The computational model considers the influence of aluminum hydride as electrophilic activator of epoxidic oxygen atom. The structures of initial epoxynorbornane amines (I) as reductive forms of corresponding N-carboxamides as well as the structures of transition states (II) and final tricycle azabrendanes (III) have been established.

HN

CH2R

OH3Al

N

CH2R

OH3Al

HN

CH2R

OH3Al

H

1,98 A 1,88 A 1,81 A12

3 4 5

6

7

I II III

R=CH3 (Ia), CF3 (Ib), C6H5 (Ic), p-CH3C6H4 (Id), p-ClC6H4 (Ie), o-ClC6H4 (If).

The received data have allowed to investigate the main parameters of transition state’s geometries, which are reported in Table 1.


Table 1. The main geometric parameters of transition states of formation azabrendanes systems reaction (Å, degrees) and corresponding values of activation energy (kJ/mol), computing with BHandHLYP/6-31G(d)-method

Bond lengths, Å Angles, degrees Eact, kJ/mol

Comp AlO OC3 C3N OC3N OC2C3 OC2C3N Gas phase Solution( 5,83)

Ia 1,889 1,894 2,272 156,36 82,74 159,40 60,04 41,72 Ib 1,878 1,976 2,199 155,88 86,93 157,94 74,47 58,13 Ic 1,884 1,904 2,272 157,35 83,10 159,05 59,99 50,17 Id 1,884 1,904 2,275 157,19 83,15 159,10 59,32 44,44 Ie 1,885 1,909 2,267 157,17 83,41 158,74 62,61 45,96 If 1,883 1,908 2,280 157,23 83,36 158,86 59,28 54,75

The consideration of transition state’s geometry have revealed their earlier character (r(OC3)<r(C3N)) and SN2-like structures (it could seen from the values of the valence angles OC3N). For each of (I-III) it have shown the formation of Al–O-bonds. The lengths of these bonds are about 1,88 Å in transition states. The study of electron density distribution as well as charges in molecules of epoxides (I) has exposed the influence of R-substituent character on nucleophilic properties of attacking nitrogen atom: for molecules with R-donors these properties are higher then with R-acceptors. The received values of activation energy (in solution) have allowed to arrange the compounds (Ia-If) in the row:

Ib > If > Ic >Ie >Id >Ia, which is in agreement with accepted notions about the nature of substituents near the nucleophilic nitrogen atom.


Computational Modeling of Film Growth and Tethered Membrane

R.B. Pandey

Department of Physics and Astronomy University of Southern Mississippi, Hattiesburg, MS 39406-5046

In order to design soft materials and predict their physical properties, it is important to characterize their constituents via appropriate coarse-grained description. Basic constituents may vary in size, shape, molecular weight, and interactions. However, most of these diverse elements can be constructed from particles (smallest unit) with appropriate characteristics and fabrication process. Using particles as basic building block, we study the growth of a thin film from a mixture of multi-component hydrophobic and polar particles in evaporating aqueous solution. The second example deals with designing of a tethered membrane, i.e., a sheet from particles tethered together by covalent bonds. Conformation and dynamics of the tethered membrane are examined in effective solvent media. Multi-scale dynamics and structural evolution will be discussed.


Generalized Kinetic Model for the Molecular Architecture of Polymer Systems

R. Parker,1 J. Edwards,2 A. S. Abhiraman,1 M. J. Realff1 and D. A. Ling1

1Florida Advanced Center for Composite Technologies,FAMU-FSU College of Engineering, Tallahassee, Florida, 32310, USA

2Department of Chemistry, Florida Agricultural and Mechanical University, Tallahassee, Florida, 32307, USA

3Hindustan Lever, Unilever, India 4 Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology,

Atlanta, Georgia 30332

The quality of a polymer product is a function of its inputs and the process used to manufacture the product. A well-defined process can reproducibly yield a product with specified end-use properties. Industry employs process models that make adjustments to compensate for the fluctuations from external factors. These models are usually based on the experience a manufacturer has with a specific product and its associated process. As a consequence, advances on polymer technology from industry have been incremental. Employment of a more fundamental understanding of the relationships between the chemical kinetics and the resulting physical structure can produce revolutionary advances in coatings and fibers, nano-structured and bulk systems, and for various polymerization kinetics and processes.

A comprehensive kinetic model for polymerization is proposed. For a polymer system with functionality = n, the model requires n - 1 kinetic rate constants and an intramolecular rate constant. The model will use rate balances on the degree of substitution (reacted state) of monomers and Monte Carlo methods to construct the inter-connections of the monomer units for a given conversion and distribution of reacted states of monomers. Various measures will be calculated from the molecular architecture which will include the distribution of branches sizes, the total number of branches in a polymer system, the number of monomer units for various degrees of substitution involved in a cycle, the distribution the sizes (in terms of monomer units) of cycles, the total number of cycles, the distribution (and averages) of the molecular weight, and the radius of gyration.

In general, previous research yielded kinetic models that were quantitatively valid for bi-functional systems. The results of this research will offer a model for higher functionality systems with varying degrees of intramolecular reactions and differing configurations for monomer units. The efficacy and potential for the proposed model was demonstrated in previous research of the reaction kinetics and polymer structure of silica sol-gel systems which were validated through comparison of experimental data where possible. This research outlines a generalized kinetic model for the development of the molecular architecture for homo-polymerization systems.


Computational Studies of Solvated Sevelamar Hydrochloride

R. Parker,1 J. Edwards,2 Y. Woodard,1 A. A. Odukale3, C. Batich3, and E. Ross4



3Hindustan Lever, Unilever, India 4Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology,

Atlanta, Georgia 30332

Sevelamar hydrochloride is a crosslinked poly(allylamine hydrochloride) that binds phosphates by ionic interactions between protonated amide groups along the polymer backbone.

One current application is in the pharmaceutical, Renagel®. Renagel® is used to reduce the level of phosphates in the body. High phosphate levels results in end-state renal disease (ERSD). Other methods used to reduce phosphate levels involve the use of calcium and aluminum salts. This results in a build up of aluminum and calcium in the body, another deleterious health effect.

Another application is the use of sevelamar hydrochloride as a phosphate detector. Embedding the polymer within a conductive resin allows the ionic exchanges which causes a measurable voltage differential. The voltage differences for differing levels of phosphates can be used to calibrate the sensor. Current research is being performed to understand accuracy of these systems which includes their ability.

In both applications, understanding the binding mechanisms of phosphates to sevelamar hydrochloride is important in developing optimized devices. Further, it is important to understand the governing mechanism in order to accurately value them. For example, if the binding for phosphates is permanent, then the phosphate sensor has a limited lifespan. As such, it’s pricing can be greatly differentiated.

Current simulation shows no differences in the capture mechanism between a fully solvated system and unsolvated systems with low and dielectric constants. As such, it is hypothesized that Van der Waals forces control the binding mechanism through the development of a cage. Further, it has been shown that once the phosphate ions are captured that the average volume of the polymer swells. These computational investigations allow a great understanding an eventual engineering material for sensor and pharmaceutical use.


Theoretical Study of the Adsorption of VX on Calcium Oxide

Y. Paukku, A. Michalkova, and J. Leszczynski

Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS

The VX nerve agent (O-Ethyl-S-[2(diisopropylamino)ethyl] methylphosphonothioate) is the most well-known of the V-series of nerve agents. It has a high persistence in the environment. That makes it especially dangerous. It is odorless and tasteless, and can be distributed as a liquid or, through evaporation, into small amounts of vapor. It works as a nerve agent by blocking the function of the enzyme, acetylcholinesterase. Normally, an electric nerve pulse would cause the release of acetylcholine over a synapse that would touch the post-synaptic neuron. This continues the transmission of a nerve signal over the synapse. The excess acetylcholine is then hydrolyzed to non-reactive substances (acetic acid and choline). VX blocks the diffusing properties of acetylcholinesterase, thus causing nerves to fire continuously resulting in contractions of all the "involuntary" muscles in the body.

Metal oxides have been considered as “destructive adsorbents” of such harmful compounds as VX (metal oxides surfaces can adsorb and break chemical bonds in the hazardous adsorbate). This method is based on ultrahigh surface area of metal oxides with very reactive surfaces. For example, calcium oxide (CaO) has unique adsorption ability due to considerably high surface area, high capacity and fast kinetics. Therefore, this work is devoted to the study of the adsorption of VX on calcium oxide that will result to a better understanding of the interactions of nerve agents with metal oxides. So, it could lead to finding of remediation techniques and technologies for the decomposition of nerve agents.

Figure 1. The initial structure of VX adsorbed on the surface of the non-hydroxylated CaO fragment.

We have prepared several models of the adsorption of VX on calcium oxide. One of such models is illustrated in Figure 1 (the initial structure of VX adsorbed on a small non-hydroxylated Ca4O4 fragment of calcium oxide). The adsorption of VX on the small representative cluster models of calcium oxide is investigated at the B3LYP/6-31G(d) and


MP2/6-31G(d) levels of theory. The geometry of VX is fully optimized while the geometry of the oxide fragment is kept frozen. We have investigated the structure, interactions and interaction energy (corrected by the basis set superposition error) of the adsorption systems. We have analyzed the changes in the geometry and the charges of VX and the CaO fragment caused by the adsorption.


Computational DFT Study of the Mechanism of the Acid-Catalyzed Aminolysis of Succinic Anhydride

T. Petrova, a,b S. Okovytyy, a,b L. Gorb, a J. Leszczynski a

aDepartment of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University

1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217-0510, USA bDepartment of Organic Chemistry, Dnepropetrovsk National University, Dnepropetrovsk

49625, Ukraine

The reaction of primary amines with anhydrides is a common and practical approach to the formation of amides. The reaction can also be viewed as a model for the formation of peptide bonds. The wide amount of available experimental data forms a basis for studying the mechanism of this reaction:

CH2 C

CH2 C

O

O

O

CH2 C

CH2 C

O

OH

O

NHRNH2R

+

.As it follows from the scheme above, a primary amine reacts readily with a cyclic anhydride

to produce compounds with both amide and carboxylic groups. The reaction may also be subject to general-acid catalysis and this catalysis is associated with proton-transfer process.

In the present work a quantum-chemical investigation of the potential energy surface for the aminolysis reaction between succinic anhydride and methylamine with acetic acid as catalyst has been carried out. The theoretical calculations have been performed at the B3LYP/6-31G(d) level of theory using the Gaussian 98 program.


CH2 C

CH2 C

O

O

O

NCH3

H

H

O CH CH3

OCH2 C

CH2 C

O

O

O

NHCH3

H

CH2 C

CH2 C

O

O

O

CH2 C

CH2 C

O

O

O

O CH3H CO

NHCH3

HCH3COOH

CH3COOH

CH3COOH

CH2 C

CH2 C

O

O

O

OCH3

H

CO

NHCH3

HCH2 C

CH2 C

O

O

O

NCH3

HH

OC

HCH3

OCH2 C

CH2 C

O

O

O

NHCH3

H CH3COOH

CH2 C

CH2 C

O

OH

O

NHR

CH3COOH

==

NH2CH3+

+

+

+

==

+

pathway 1

pathway 2

-

The research examines the stepwise mechanism of acid-catalyzed anhydride aminolysis in gas phase. In fact, a stepwise pathway for the aminolysis of succinic anhydride is an addition/elimination mechanism, where the addition and elimination steps are coupled with proton transfer to maintain neutrality in the tetrahedral intermediate formed. The role of the acid in the process is to facilitate the proton transfer lowering the proton-transfer energy barrier. Two possible pathways of the catalysis for the stepwise mechanism were considered. We have found that the mechanism of the proton transfer is different in these two cases (see pathway 1 and pathway 2 on the scheme above).

We have revealed that according to our predictions in the case of pathway 1 the first stage of reaction is rate-determining (18.76 kcal/mol). In contrast, calculations predict that activation barrier for the second stage of the pathway 2 (10.76 kcal/mol) is higher than one for the first stage of reaction (6.45 kcal/mol). It is also necessary to highlight that eight-membered rings formed in the transition state structures for the pathway 2 of acid-catalyzed process are more stable than six-membered rings in the case of the aminolysis by the pathway 1. This explains the lowering of energy barriers along the reaction path of the catalyzed process taking place in a gas phase.


To the Problem of Calculation of Unstable Fluoro-Complexes Sublimation Heats*

V.N. Plakhotnyk,1 K.S.Gavrichev,2 V.V. Rossikhin,1 E.I.Kustov,1S.I. Okovytyy,3,4 J. Leszczynski4

1Dnepropetrovsk National University of Railway Transport, Dnepropetrovsk, 49010, Ukraine 2 Institute of General and Inorganic Chemistry named after N.S. Kurnakova, RAS, Russia

3Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine 4Computational Center for Molecular Structure and Interactions,

Jackson State University, Jackson, Mississippi, 39217, USA

Complex fluorides are wide-used in some important fields of industry, for example in qualitative metallurgy, welding and soldering, atomic and rocket technique, etc. [1, 2]. Last years demand for durable and power-consuming power sources is increased. Lithium accumulators and supercondensers are the most hopeful power sources which allow successive solving of problems of flight safety, photo- and video-technique, information processing, ecology and medicine [3-5]. Calculations of thermodynamic parameters of reactions of their synthesis and transformations often include necessity of involving of enthalpies and Gibbs energies of sublimation processes Qc into corresponding thermochemical cycles.

However, experimental determination of these values faces the necessity to deal with complex and expensive experimental equipment. Furthermore, thermal stability of objects significantly decreases if radii of external cations decrease and their charges increase. This phenomenon leads to impossibility to experimental determination of Qc for these cases. The reason for this phenomenon is that sublimation temperatures of those compounds lie significant higher than their thermodynamical dissociation temperatures. These dissociation processes lead to formation of simple fluorides and volatile Lewis acids. In the current work we have calculated Qc values for complex fluorides B(III), P(V) and As(V) with Li+ in the external coordination sphere (LiEFx). Building of thermochemical cycles, including thermolysis enthalpies of solid

H LiEFx and gaseous H* LiEFx fluoro-complexes, energies of fluoro-complex lattices WLi Fx

and lithium fluoride WLiF, sublimation heats Qc Li Fx and Qc LiF as well as enthalpies of ionic association in gas phase H Li Fx and H LiF. have been a base of calculations.

It is clear, using calculated ab initio thermolysis enthalpies of gaseous fluoro-complexes enthalpies of their and LiF ionic association it is possible to calculate sublimation heats of


thermally unstable fluoro-complexes, as well as their thermolysis enthalpies in solid state. These values have significant practical importance.

We have used the experimental value Qc LiF as a test value for choice of a calculation method. The mentioned value has been determined by a number of scientists and is a reference data [6]. The best agreement between calculated (Qs LiF = 66.2 kcal/mol) and experimentally obtained data (Qs LiF = 66.4kcal/mol) has been obtained at the BP86/6-31+G* level of theory using Gaussian03 package of programs [7]. The “embedding effect” of a Li+ ion into fluoro-complex anions, which amount to ~15% have been considered in summation of ionic radii during lattice energies calculation according to Kapustinskiy-Yatsimirskiy [8].

*This work is facilitated by Ukrainian Scientific-Technology Center, the project Gr-83j.

References:

1. N. Isikava. The novel in technology of fluore compounds. 1984 , Moscow, 592 p. 2. N. Isikava, E. Kobayasi. Fluor. Chemistry and usage.1982 ,Moscow, 280 p. 3. G-A Nazri, G. Pistoria.Litium Baateries.Science and Technology.2004,Kluwer Academic Publishers, Boston, p.708. 4. W.A. Schalkwijk, B. Scrosati. Advances in Lithium-Ion Batteries.2002,Kluwer Academic Plenum Publishers, New York, p.513. 5. Y.M. Volfkovich, T.M. Serdyuk. Electrochemical energetics. 2, 3,136, 2002. 6. P. Galkin. The major properties of inorganic fluorides.1976, Moscow, 400 p. 7. M.J. Frisch, G.W. Trucks, H.B. Schlegel, et al.,Gaussian,Inc.,Wallingford CT,2004. 8. K. B. Yatsimirskiy. Thermochemisry of complex compounds .1951, Moscow, 251 p.


The Reaction Force

Peter Politzer

Department of Chemistry University of New Orleans

New Orleans, LA 70148 USA

The concept of the reaction force will be presented and discussed in detail. For typical processes with energy barriers, it has a universal form which defines three key points along an intrinsic reaction coordinate: the force minimum, zero and maximum. We suggest that the resulting four zones be interpreted as involving preparation of reactants in the first, transition to products in the second and third, and relaxation in the fourth. This general picture is supported by the distinctive patterns of the variations in relevant electronic properties. Two important points that are brought out by the reaction force are (a) that the traditional activation energy is comprised of two separate contributions, and (b) that the transition state corresponds to a balance between the driving and retarding forces.


Comparison of Structural Reactivities of Nitroaromatics, Heterocyclic Nitramines and Cage Heterocyclic Nitramines

under Selected Reaction Conditions

Mohammad Qasim1, Jerzy Leszczynski2, Leonid Gorb1, Herbert Fredrickson1

1ERDC-EL, Vicksburg, MS; 2Computational Center for Molecular Structure and Interactions, Jackson State University, MS

HypothesisPreferred transformation pathways are determined by molecular structure. This hypothesis

was examined in regard to the nitroaromatic, 2,4,6-trinitrotoluene (TNT); cyclic nitramines, hexahydro-1,3,5-trinitro-,3,5-triazine (RDX) and octahydro-1,3,5,7—tetranitro-1,3,5,7-tetrazocine (HMX); and cage nitramine, 2,4,6,8,10,12-hexanitrohexaazoisowurtzitane (CL-20).

ApproachTo correlate reaction rates and mechanisms to molecular structure, structural reactivity

relationships of these compounds were examined through; i) Computational prediction (Semiempirical—all energetic compounds plus DFT—TNT and

CL-20) of transformation mechanisms of the mentioned energetics; ii) Spectroscopic verification using various sodium hydroxide (OH-) concentrations (alkaline

hydrolysis) and dark Fenton and photo-induced free radicals.iii) CL-20 reactions with disodium disulfite (possibly a free radical generator as well as a

reductive) were also examined Both hypothesis and computational predictions were verified and supported

spectroscopically. All rates of reaction were followed via stopped flow (SF); free radical reactions utilized Fenton and photo-induced (via monochromatic irradiation) free radicals, the latter obtained through irradiation at wavelengths of maximum absorption and also at maxima of reaction-generated wavelengths. Initial and selected subsequent steps of reactions were followed through changes in UV/VIS spectra. CL-20 reactions, also, were followed via SF.

Results: Due to its aromatic planar structure, free radical reactions with TNT, using dark Fenton

reagents and irradiation at 233 nm (wavelength of maximum absorption) did not produce significant spectral changes.

Irradiation, alone, of TNT at 233 nm produced no change whatsoever. Irradiation, alone, of CL-20 at 236 nm (wavelength of maximum absorption) produced

dramatic change: complete disappearance of its UV spectra; formation of a short-lived intermediate at 280 nm as well as a non-aromatic product at

210 nm that had high molar absorptivity; appearance of a sharp, high intensity peak at lower wavelength—characteristic of low

molecular weight compounds, and appearing identical to the spectra of a standard imidazole sample.

A similar peak appeared upon irradiation of RDX. Irradiation of CL-20 photo-induced free radical reactions at the 370 nm band, where the

conjugated pi system of the aromatic intermediate absorbs. Disappearance of the band indicates degradation by photo-induced free-radical reactions


Upon irradiation of CL-20 at 420 nm, at low concentration of sodium hydroxide (NaOH), the peak disappears. If irradiated at 420 nm at high concentration of NaOH, the peak shifts back to 370 nm.

Upon further addition of OH-, to CL-20, the spectra shifts back to a shorter wavelength, The backwards shift of the peaks indicates formation of a smaller molecule. possibly due to the removal of an imidazole ring to form a two-ring aromatic compound.

RDX and HMX required high concentrations of OH- to effect transformation. Transformation of HMX via OH- is slower than that of RDX due to RDX being a smaller

compound. With all compounds, UV spectral changes due to dark Fenton reactions were not as significant

as reactions through irradiation.

Conclusions For maximum robustness and lowest toxicity, chemical transformation techniques must be

selected according to the molecular structure of the compound to be transformed. For example, transformation of CL-20 via high OH- concentrations leads to toxic pyrazine,

whereas transformation via photo-induced free radical reactions at 236 nm leads to formation of a peak of high absorptivity at a wavelength lower than that of the parent—indicating an alternative CL-20 transformation mechanism.

Experimental findings correlated well with computational predictions—suggesting that prediction of transformation mechanisms plus lab verification as to feasibility, followed by computational analysis of total results, constitutes an excellent tool for investigating transformation.

References M. Qasim, J. Furey, H. Fredrickson, J. Szecsody, C. McGrath, R. Bajpai, “Semi empirical

Predictions of Chemical Degradation Reaction Mechanisms of CL-20 as Related to Molecular Structure,” Struct Chem., Vol. 15, No. 5, 10/04.

R. Bajpai, D. Parekh, S. Herrmann, M. Popovi , J. Paca, M. Qasim; “A kinetic model of aqueous-phase alkali hydrolysis of 2,4,6-trinitrotoluene,” J. Haz.Materials 106B (2004) 55-66.

M. Qasim, H. Fredrickson, C. McGrath, J. Furey, R. Bajpai; “Theoretical Predictions of Chemical Degradation Reaction Mechanisms of RDX and Other Cyclic Nitramines Derived from Their Molecular Structures,” SAR/QSAR JEnviron Res, Vol. 16, No. 3, 2005, 1-17.

S. Okovytyy, Y. Kholod, M. Qasim, H. Frederickson, J. Leszczynski “The Mechanism of Unimolecular Decomposition of CL-20 (2,4,6,8,10,12 Hexanitro-2,4,6,8,10,12-Hexaazaisowurtzitane). A Computational DFT Study,” J. Phys. Chem. A , 2005, 109, 2964-2970.

M. Qasim, H. Fredrickson, J. Furey, P. Honea, J. Leszczynski, S. Okovytyy, J. Szecsody, “Prediction of CL-20 Chemical Degradation Pathways, Theoretical and Experimental Evidence for Dependence on Competing Modes of Reaction,” SAR and QSAR, 03/11/05.

M. Qasim, H. Fredrickson, P. Honea, J. Furey, J. Leszczynski, S. Okovytyy, J. Szecsody, Y. Kholod; “Prediction of CL-20 Chemical Degradation Pathways, Theoretical and Experimental Evidence for Dependence on Competing Modes of Reaction,” SAR and QSAR in Environmental Research, accepted and in press.


My Protein Folds Faster than Yours: An Experimentalist's View of a Protein Folding Theory

Kevin W. Plaxco

Department of Chemistry and Biochemistry and Program in BioMolecular Science and Engineering, University of California, Santa Barbara CA 93106

Across the universe of simple, single domain proteins, the fastest folds a million times more rapidly than the slowest. What accounts for this dramatic range of kinetic behaviors? In this talk I cast an experimentalist's critical eye on recent theories of protein folding kinetics that address this fundamental biophysical issue.


Quantitative Structure-Activity Relationship Study on Estrogenic Activity of Terpenoids Isolated from Ferula Plants

B.F. Rasulev 1,2,*, A.I. Saidkhodzhaev2, S.S. Nazrullaev2,K.S. Akhmedkhodzhaeva2, Z.A. Khushbaktova2, J. Leszczynski1

1Computational Center for Molecular Structure and Interactions, Jackson State University,1325 J. R. Lynch Street, P.O. Box 17910, Jackson, Mississippi 39217-0510 USA

2Institute of the Chemistry of Plant substances, Academy of Sciences, Tashkent, Uzbekistan, fax (99871) 1206475, *Email: [email protected]

The relationship between chemical structure and estrogenic activity in series of terpenoid esters with aromatic and aliphatic acid's substituents, isolated from Ferula plants is studied. The fragments of terpenoid’s structure potentially responsible for estrogenic activity are revealed. The quantitative structure-estrogenic activity study have been carried out by QSAR approach with use of data derived from quantum-chemical calculations, as well as data generated from the three-dimensional structure of terpenoids. A number of molecular descriptors was obtained from the density functional theory (DFT) at B3LYP/6-31G(d, p) level calculations. The variable selection Genetic Algorithm used for the best fitting and it has allowed to determine structural and physico-chemical parameters of the terpenoids responsible for estrogenic activity. The significant QSAR model was obtained with r value of 0.950 and q2 (cross-validation r2) value of 0.852. The resulting model showed a reliable dependence of estrogenic activity of the terpenoids on such parameters as molecular shape, number of phenolic groups, surface polarity and energy of highest occupied molecular orbital.

Figure: Schematic representation of receptor-ligand interaction: with estradiol (thin line) and with ferutinin (volume representation).


Docking and Molecular Simulations of a Series of Estradiol Derivative Selective Estrogen Modulators

J. Robinson1, J. S. Cooperwood2, J. Edwards1, D. Simmons2, M. Musa2, R. Parker3

1Chemistry Department, and 2Pharmacy and Pharmaceutical Sciences, 3Florida A&M Univerisity/Florida State University, College of Engineering,

Florida A&M University, Tallahassee, Florida 32307

Breast cancer is one of the leading causes of death in women between the ages of 35 and 55 years of age. This work will also focus on a unique class of selective estrogen positive receptive modulators. Three classes of selective estrogen receptor modulators (SERM’s) will be discussed in this work. Current treatments focus on the estrogen responsive population. Therefore, this work will focus on a unique class of selective estrogen positive receptive modulators. Three classes of estrogen will be discussed in this work. These compounds were synthesized and tested for bioactivity by Dr. John Cooperwood’s group. We used the Sybyl6.9 suite of programs to perform FlexX and Cscore series of docking calculations to determine the binding energies of these ligands in the estrogen active site. Using the docking results and molecular dynamics simulations, we are able to provide evidence of intermolecular interactions between the estrogen active site and ligands of two of the classes of compounds being studied. In particular, we used the structure of the ligand, 4-Hydroxytamoxifen a currently used pharmaceutical, bound in the active site of the PDB crystal structure 3ERT, as the reference molecule. Using the results of the docking calculations we were able to determine that scoring functions containing free energy expressions with hydrogen bonding terms provided the lowest free energy of binding on a consistent basis and exhibited the highest correlation with the experimentally determined bioactivities. In the case of the estradiol and 17-ethynyl estradiol derivatives the correlation (R2)between activity and the ChemScore (part of Cscore series) scoring functions were 0.86 and 0.89, respectively. There was only one exception, the morpholinyl derivatives received high docking scores but had the lowest bioactivities. These results suggest hydrogen bonding played an essential role in the activity of these compounds just as in the case of the crystal structure of 4-Hydroxytamoxifen. We will also, present the molecular dynamic simulations of these molecules in order to examine the motion of these systems in solvent, along with Monte Carlo simulations to calculate potential changes in volume within the active site.


Theoretical Study of Adsorption of Selected Nucleic Acids on Dickite

T. L. Robinson, A. Michalkova, L. Gorb, and J. Leszczynski

Computational Center of Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 JR Lynch Street, Jackson, MS 39217

Molecules which store genetic information (e.g. RNA and DNA) are central to all life on earth. They are polymers. Their monomer units are nucleotides. Each nucleotide consists of a 5-carbon sugar (deoxyribose), a nitrogen containing base attached to the sugar, and a phosphate group. There are four different types of nucleotides found in DNA, differing only in the nitrogenous base. Adenine (A) and guanine (G) represent the purine bases. The pyrimidine bases are thymine (T) and cytosine (C) which are commonly found in DNA. Uracil is one of the four major RNA nucleobases, and replaces the DNA base thymine.

Clay minerals refers to a group of hydrous aluminosilicates that predominate the clay-sized (<2 |xm) fraction of soils. Many authors have hypothesized the involvement of surface chemistry on clays in the prebiotic chemical evolution that culminated in the origin of life. Clay minerals could have bound organic molecules from the surrounding water, concentrating them many times and providing naturally occurring environments for the assembly. In recent years, numerous observations have reinforced the hypothesis of a surface-mediated origin of life. The chemical and molecular structure of nucleic acids as well as clay’s properties may influence their adsorption on mineral surfaces. Therefore, this study is devoted to investigate the interactions of selected RNA and DNA bases on the specific clay mineral surfaces. It can lead to a better understanding and prediction of the sorption and catalytic ability of clay minerals with regards to the nucleic bases.

Particularly, we have performed the study of the adsorption of thymine and uracil on tetrahedral and octahedral non-hydrated and hydrated surface of dickite (1:1 dioctahedral clay mineral of the kaolinite group). The density functional theory (DFT) using the B3LYP functional and 6-31G(d) basis set were applied for the calculations. We have studied the structure, interactions, charge distribution, and the interaction energies corrected by the basis set superposition error of these complexes.

The results reveal that thymine and uracil are placed in the same way on the non-hydrated tetrahedral and octahedral surface of dickite (a perpendicular orientation towards the tetrahedral surface and planar towards the octahedral surface, for example see Figure 1. that illustrates the optimized structure of thymine adsorbed on non-hydrated octahedral surface of dickite obtained at the B3LYP/6-31G(d) level of theory). These bases posses almost the same interactions with the surface (mostly hydrogen bonds formed between the N-H groups and oxygen atoms of thymine and uracil and the oxygen atoms and hydroxyl groups of the mineral surface). Small differences were found only in the strength of these intermolecular interactions. The adsorption leads to the geometrical changes and modifications in the charge distribution. Hydration of the tetrahedral surface has a significant effect on the orientation of the target molecule (the molecule is placed planar towards the surface). In the case of the octahedral surface the hydration affects only slightly the bases position. Studied bases interact much more strongly with the octahedral than with the tetrahedral surface of dickite. Hydration of the surface leads to a much better stabilization of thymine and uracil on both studied surfaces of dickite.


Figure 1. The optimized structure of thymine adsorbed on non-hydrated octahedral surface of dickite obtained at the B3LYP/6-31G(d) level of theory.


Molecular Dynamic Studies ofSeveral HIV-1 Protease Modified Peptide Inhibitors

Christina Russell (I),* Jesse Edwards (I), John West (I), Reginald Parker (II),Ben M. Dunn (III)

I. Department of Chemistry/AHPCRC, Florida A&M University Tallahassee, Florida, 32307 II. Department of Molecular Biology and Biochemistry, University of Florida,

Gainesville, Florida, 32608 III. Florida A&M/Florida State University College of Engineering, Tallahassee, Florida, 32307.

One of the major targets in anti-HIV therapeutics is protease inhibition. In an attempt to develop anti-HIV protease inhibitors, Dunn et. al. synthesized a series of unique peptides. In a previous computational work using molecular dynamics Bryan et. al showed the flexibility of one of Dunn’s seven unit peptides, XI5. The flexibility was induced by the reduction of the central carbonyl in the peptide chain. In this work, we present the dynamic simulations of 5 different peptide inhibitors of HIV-1 Protease. The flexibility of these compounds will be discussed along with the volumes and their radius of gyration. Monte Carlo simulations were used to determine the volumes and radius of gyration.


Electron Impact Ionization of Ions with q > 2

B. C. Saha, A. K. Basak * and M. A. Uddin*

Department of Physics,Florida A&M University, Tallahassee, FL-32307

*Department of Physics The University of Rajshahi, Rajshahi, Banglades

The study of electron impact ionization (EII) of atoms and ions plays a vital role for the basic understanding of collision physics and the cross-sections are very useful for numerous applications in plasma kinetics problems, mass spectrometry, gas lasers, astrophysics, atmospheric physics, radiation science and semiconductor physics. Because of the formidable experimental difficulties, the situation concerning the quantitative knowledge of the EII cross-sections is still far beyond the need for many areas of application. The void in the experimental cross-sections has to be filled in through generation of high quality data by accurate theoretical methods. With the advent of fast computers, several quantal methods have been developed [1-5] in recent years. However, quantum calculations are arduous and expensive with the supercomputers. One can produce cross-section data just for some selected targets at some discrete energy grids using the quantal theories just alike the experimental tools. Practical applications indeed require a quick estimation of a large number of reasonably precise cross-section data often over a wide range of impact energies and target species, which neither experiments nor any rigorous method can generate easily. Therefore, a simple to use either the semi-empirical or semi-classical methods are essential.

Reviews on the various theoretical studies on EII are available now [6-8]. The most simple and widely used empirical formula for the calculations of the EII cross-section was given by Lotz [9]. However, Bernshtam [10] proposed a more accurate empirical formula (BRY) valid for ions with charge $q > 1. Thomson [11], Elwert [12] and Gryzinski [13] have formulated semi-classical models. The formulae of Thomson and Elwert are parameter-free and ignore the motion of the target electron. The semi-classical results of both Thomson and Elwert show large deviations with the experimental data; their findings disagree with both the theoretical predictions and experimental measurements at the high-energy region. Deutsch and Mark [14] have developed a semi-classical (DM) model by combining the binary-encounter approximation of Gryzinski with the Born-Bethe [15] theory. The Gryzinski model contains a number of parameters and assumes a continuous velocity distribution of the target electron. The DM model works for the neutral atoms (q = 0) and also contains a number of parameters which have been generalized somewhat. Kim and Rudd [16] presented the binary-encounter dipole (BED) model by coupling the modified form of Mott cross-section [17] with the dipole interaction of Born-Bethe theory. The simplest version of the BED model is the binary-encounter Bethe (BEB) model. Both of the models have a common scaling factor involving the Burgess denominator (T+U+I) with T as the kinetic energy of the incident electron, and U and I as the kinetic and binding energies of the target electron, respectively. The plausible argument to replace T, as in the original Mott [17] and Bethe [15] theories, with (T+U+I) or its reduced form (t+u+1), where t=T/I and u=U/I, goes as follows: Owing to the correlation of the colliding electrons, the effective kinetic energy as seen by the incident electron should include the potential energy U+I of the target electron. Since U+I is comparable to T in the threshold region, T+U+I (or, t+u+1) is more effective to reduce the cross-sections in this region, while at large incident energies the effect is predominantly due to T. This trend is what is exactly demanded by the behavior of the experimental data. The BEB model has generated reliable cross-sections for some molecular


targets [18-22] while most ab initio theories overestimate the cross-sections from the threshold to peak region. So far as the incident electron is concerned, the BED-BEB models make no distinction between the collisions with a neutral and an ionic target. The differences, between description of the target electron in neutrals and that in ions, are accounted for via I, U, and the differential continuum oscillator strength, df/dw. The Coulomb field of the ionic targets distorts the charge cloud of the incident electron throughout its entire path of motion, whereas the neutral target does so only in the vicinity of the target. Qualitatively, the charge distribution of the incident electron is attracted towards the target ion, thus increasing the overlap between the charge distributions of the incident and target electrons and producing ionic enhancement of cross-sections. This increase in cross-sections is accounted for by scaling of the Burgess denominator. Most models for the computation of EII cross-section as a function of the electron energy T involve many empirical parameters. The most successful and widely used among such models is the DM model. The BED model was originally formulated without any empirical parameters. However, it was necessary to introduce one empirical parameter to obtain satisfactory results for molecules that contain atom-like orbitals with the principal quantum number n with the replacement of (t+u+1) with (t+(u+1)/n. Likewise, a similar but non-parametric adjustment was found necessary for monopositive (q = 1) ions with the replacement of [t+u+1] with [t+(u+1)/2].

A few sample cases are shown in Figs. 1 and 2. In Fig.1, our results are compared with various experimental findings.

The agreement is excellent. In Fig. 2, we have shown our results for C4+ ionic target with other theoretical findings as well as available experimental values. Here again our MBED results give the best description of the experimental cross sections.


References

[1] Younger, S.M. J Quant Spectrosc Radiat Transfer 1981, 26, 329. [2] Jacubowicz, H.; Moores, D.L. 1981 J Phys B 1981, 14, 3733. [3] Bray, I.; Stelbovics, A.T. Phys Rev Lett 1992, 69, 53. [4] Mitnik, D.M.; Pindzola, M.S.; Griffin, D.C.; Badnell, N.R. J Phys B 1999, 32, L479. [5] Riahi, A.; Laghdas, K.; Reidf, R.H.G.; Rachafi, S.; Joachain, C.J.; Defrance, P.2001 J Phys B 2001, 34, 175. [6] Moores, D.L.; Reed, K.J. Adv Atm Mol Opt Phys 1994, 34, 301. [7] Deutsch, H.; Becker, K.; Matt, S.; M\"{a}rk, T.D. 2000 Int J Mass Spectrom 2000, 197, 37. [8] Younger, S. M. et. al :Electron Impact Ionization, Springer-Verlag, Berlin, 1985 p.24. [9] Lotz, W. Z Phys 1968, 216, 241. [10] Bernshtam, V.A.; Ralchenko, Y.V.; Maron, Y. J Phys B 2000, 33, 5025.[11] Thomson, J.J. Phil Mag 1912, 23, 449. [12] Elwert, G. Z Naturforsch. 1952, 7a, 432. [13] Gryzinski, M. Phys Rev 1965, 138, 336. [14] Deutsch, H.; M\"{a}rk, T.D. Int J Mass Spect Ion Proc 1987, 79, R1. [15] Bethe, H. Ann Phys 1930, 5, 325. [16] Kim, Y.-K.; Rudd, M.E. Phys Rev A 1994, 50, 3954. [17] Mott, N.F. Proc Roy Soc (London) A 1930, 126, 259. [18] Hwang, W.; Kim, Y.-K.; Rudd, M.E. J Chem Phys 1996, 104, 2956. [19] Kim, Y.-K.; Hwang, W.; Weinberger, N.M.; Ali, M.A.; Rudd, M.E.J Chem Phys 1997, 106, 1026.[20] Ali, M.A.; Kim, Y.-K.; Hwang, W.; Weinberger, N.M.; Rudd, M.E. J Chem Phys 1997, 106, 9602. [21] Nishimura, H.; Huo, W.M.; Ali, M.A.; Kim,Y.-K. J Chem Phys 1999, 110, 3811. [22] Kim, Y.-K.; Rudd, M.E. Comments At Mol Phys 1999, 34, 309.


Understanding Strong Two-Photon Absorption in Porphyrin Monomer and Dimers

Zuhail Sainudeen and Paresh Chandra Ray

Department of Chemistry, Jackson State University, Jackson, MS 39217, USA

We present a quantum-chemical analysis of the two-photon absorption properties of directly meso-meso-linked porphyrin arrays with a particular attention to their dependence upon the conjugation length and dihedral angle between the neighboring porphyrins. The molecular geometries are obtained via BL3YP/6-31G (d,p) level optimization including the SCRF/PCM approach, while the dynamic NLO and two-photon absorption properties are calculated with the ZINDO/CV method including solvent effects. The effects of donor or acceptor substitution and elongation of the conjugation path length are established to demonstrate the engineering guidelines for enhancing two-photon absorption cross section and molecular optical nonlinearities. Our result indicate that control of the dihedral angle of the directly linked meso-meso diporphyrins can offer a fine-tuning of electronic interactions between the two porphyrin units. We also compare our theoretical findings with the experimental results wherever available in the literature.


Towards the Quantum Computing. Theoretical Studies of Si/Ge Microclusters

Julia Saloni,a,b Szczepan Roszak,a,band Jerzy Leszczynskia

aComputational Centre for Molecular Structure and Interactions, Jackson State University, Jackson, MS 39217,

bInstitute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wybrze eWyspia skiego 27, 50-370 Wroclaw, Poland.

The past fifty years show incredibly great development in computer’s technology area.

Computers become very powerful as their basic element, the transistor, has decreased its

dimensions. Although future minimalization, and at the same time preservation the properties of

the transistor became impossible. The new solution for computation is required – a “quantum

solution”. The transistor may be replaced by nanoelectronic device, which will employ the

quantum mechanical phenomena (crucial when the size become sufficiently small). The binary

information can be described by two state quantum systems such as two spin direction of an

electron. A single bit of information in this form is known as a “qubit”. This studies focus on the

possible use of Si/Ge based materials (e.g. quantum dots) working as qubits in future quantum

computers. The research presents the theoretical investigation of the molecular structure and

thermodynamics of small Si/Ge clusters, followed by analysis of the nature of chemical bonds

and evaluation of their electronic properties.

Figure 1. Example of Si/Ge complex


The Quantum-Chemical Analysis of the Influence of Glycine Ligand on the Electroreduction of Cr3+/2+ Ions

V.A. Seredjuk, V.F. Vargaljuk


The results of the analysis of possible mechanism of aquo- and composed monoglycineaquocomplexes electroreduction in a neutral and alkalescent environment based on the quantum-chemical modeling of charge transfer reaction in a polar medium are given. Modeling was carried out using GAMESS program by spin-unrestricted Hartree-Fock method. Stuttgart RSC 1997 ECP basis set has been used for central atom Chromium and 6-311G basis set for atoms of ligands. The influence of the hydratation effect has been considered by means of the Kirkwood-Onsager model.

Since comparing of electronic energy of various structures could be possible only for systems with the same number and quantity of atoms we have examined clusters with different geometry of the first shell with the following structures:

[Crz+(H2O)n]aq·(H2O)m aq, and

[Crz+(gl)(H2O)n]aq·(H2O)m aqThe most energetically favorable structure of cluster with the minimal sum of energy of

hydrated complexes [Crz+(H2O)n]aq or [Crz+(gl)(H2O)n]aq and energy of m molecules of water in external shell where (n+m)=const. was considered.

Fig.1. Structure of octahedral (a) and four coordinating (b) aquocomplexes.

According to the calculations for aquocomplexes with +3 and +2 oxidation degree the most stable configuration is octahedral (Fig 1a), which is in line with the experimental data. While for the intermediate aquocomplexes Cr+ four coordinating complex squared flat structure is more energetically stable (Fig 1b).

In neutral medium glycin acts as monoligand and coordinates to Chromium atom by Oxygen atom of carboxylic group. Complexes Cr+3 and Cr+2 the most stable configuration is octahedral (Fig 2a). For monoglycineaquocomplex Cr+ the most favorable complex has four coordinating squared structures (Fig 2b).


Fig. 2 Structure of octahedral (a) and four coordinating (b) monoglycineaquocomplexes in neutral medium

In the case alkalescent medium glycin coordinates with Chromium atom by Oxygen and Nitrogen atoms, occupying two coordination places. In the case of monoglycineaquocomplex of Cr+2 the octahedral and four coordinating squared coordinating structures have virtually the same energy (Fig 3a, 3b). For monoglycineaquocomplex Cr+ the most favorable complex has three coordinating triangle structures (Fig 3c).

Fig. 3 Structure of a - octahedral (a), four coordinating (b) and three coordinating(c) monoglycineaquocomplex in alkalescent medium.

It has been shown, that both octahedral complexes of Cr3+ (Fig. 1a, 2a, 3a) can receive one electron relatively easy in both of the systems and can be reduced to a Cr2+ without any essential inner reconstruction. Addition of electron to octahedral complexes of Cr2+ leads to significant increasing of energy of the system. In order to add an electron octahedral complexes of Cr2+ have to be transformed to form coordinating states shown in the Fig. 1b, 2b, 3b. This transformation requires a great energy consumption. Thus, such a reconstruction as

Cr2+ 6H2Oaq Cr2+ 4H2Oaq +2H2Oaq

requires energy to increase by 68 kJ/mol. The presence of glycine molecule as a ligand in neutral medium in the system decreases this energy to 45 kJ/mol and to 33 kJ/mol in alkalescent medium.

The transfer of the third electron does not require pre-reconstruction of the complexes of Cr+

and it occurs like barrierless process. Thus, the transfer of the second electron is the limiting stage of the electroreduction of

complexes of Cr3+. The main discharging states in this stage are the flat four coordinated structures (Fig 1b, 2b, 3b) where the glycine’s participation decreases the required intrasphere energy of the transformation of the initial octahedral systems.


Theoretical Study of the Photochemistry of Spiropyrans

Yinghong Sheng and Jerzy Leszczynski

The Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P. O. Box 17910, 1400 J. R. Lynch Street, Jackson, Mississippi 39217

A comprehensive theoretical study of the reaction mechanisms for the conversion between spiropyrans (SPs) and the open-form of merocyanines (MCs) has been conducted by theoretical calculations. Two possible reaction mechanisms for the thermal conversion between SPs to MCs were found on the ground state PES. In addition, the reaction mechanisms of spiropyran merocyanine conversion on the triplet and the lowest excited singlet potential energy surfaces were also studied; several possible reaction mechanisms on the excited state PESs were proposed. A comprehensive mechanistic view of the ultrafast photochemistry of spiropyrans was revealed and interpreted in terms of the strengths of substituents and the polarity of solvents.

N OX

YNX

O NX

O

Closed form open form

UV

Vis

Y Y

Sheng, Y.; Leszczynski, L.; Garcia, A. A.; Rosario, R.; Gust, D.; Springer, J. J. Phys. Chem. B 2004, 108, 16233.


Excited State Structures, Interactions and Proton Transfer in Guanine

M.K. Shukla and Jerzy Leszczynski

Computational Centre for Molecular Structure and Interactions Department of Chemistry, Jackson State University

Jackson, Ms 39217

The genetic information is stored in the form of specific sequence of hydrogen bonding patters formed between purine and pyrimidine bases in deoxyribo nucleic acid (DNA). Change in the hydrogen bonding sequence due to the external or internal environment can lead to genetic deformation or dangerous diseases, if left unrepaired. Nucleic acid bases, purines (adenine and guanine) and pyrimidines (thymine and cytosine) absorb ultraviolet (UV) radiation efficiently. It is well known that we are exposed to different kind of radiation. The amount of UV radiation reaching on the earth is unevenly distributed throughout the continent and its amount is increasing due to the depletion of ozone in the upper atmosphere. Excited purine and pyrimidine bases due to the absorption of UV radiation can come to the respective ground state through radiative or nonradiative decay or it may undergo to some excited state reaction. Purine and pyrimidine bases deactivate very efficiently (in sub picosecond time scale) through the process of internal conversion. On the other hand, UV radiation can photostimulate the DNA with the formation of pyrimidine dimmers. It appears that the selection of purine (adenine and guanine) and pyrimidines (thymine and cytosine) bases as genetic material by nature was based on the unique photostable properties of these molecules. However, the exact mechanism of internal conversion in these systems is not yet known. It is well known that high energy radiations are very dangerous to living system. They ionize the molecules and therefore, are responsible for the production of highly reactive species known as radicals. They can cause mutations, cancers and several other fatal diseases by ionizing nucleic acid bases and sugar group in DNA. Hydrogen bonding is ubiquitous. Depending upon hydrogen bond energies, hydrogen-bonds may be classified as strong, moderate and weak. It is well known that the DNA in vivo is heavily hydrated and water molecules play an important role towards the formation of the three dimensional structure of the DNA.


(a)(b)

(c)(d)

(e) (f)

Figure: Geometry of guanine and hydrated guanine: (a) guanine in the ground (S0), (b) G in S1( *), (c) G+6W in S0, (d) G+6W in S1( *). Transition state corresponding to the keto-enol proton transfer reaction in the S1( *) state: (e) in isolated guanine, (f) in monohydrated guanine.

Ab initio computational study was performed to study the ground and excited state proton transfer in guanine, effect of explicit hydration and different base pairing on the ground and excited state geometries of guanine. Ground state geometries were optimized at the HF and DFT-B3LYP levels while for excited state calculation CIS and TDDFT methods were used. The TD-B3LYP computed transition energies are found to be generally in good agreement with the corresponding experimental data. The ground state proton transfer reaction barrier is very high, but the inclusion of a water molecule in the proton transfer reaction path significantly decreases the barrier height. It was found that the singlet electronic excitation of guanine may not facilitate the excited state proton transfer corresponding to the tautomerization of the keto to the enol form. Geometries of the hydrated transition states in the ground and lowest singlet * excited states were found to be zwitterionic form in which water molecule in the form of hydronium

1

2

3

4

5

6 7

8

9

W11.1631.305

1.2271.108

1.1851.275

1.2841.193

1.3431.357

1.3601.3331.306

1.327

1.3361.333

1.3521.411

1.3801.344

1.2731.300

1.3841.349

1.3771.472

1.3641.383

1.4061.400

1.2521.265

1

2

3

4

5

6 7

8

9

1.3241.282

1.2731.307

1.3351.347

1.3131.335

1.3341.332

1.3521.409

1.3811.342

1.2721.300

1.3841.350

1.3941.3931.251

1.255

1.3581.396

1.3381.468

N1

C2

N3

C4

C5

C6N7

C8

N9

O6

N2

H21

H22

H1

H9

H8


cation (H3O+) and guanine is in the anionic form, except for the N9H form in the excited state where water molecule is in the hydroxyl anionic form (OH-) and the guanine is in the cationic form. Geometry of guanine in the lowest singlet * excited state is non-planar in the isolated and hydrated environment. The structural nonplanarity is localized in the six-membered part of the ring. Significant change in the hydration structure is revealed in the excited state as compared to that in the ground state. However, the structural deformation of the guanine in the excited state was different in the penta and hexahydrated complexes as compared to that in the isolated and mono- and trihydrated complexes. It appears that the first solvation shell of guanine will accommodate only six-water molecule.


Comparative QSAR Study of the Anti-inflammatory Activity of Some Sesquiterpene Lactones: GA-PLS versus GA-MLRA Methods

Talibah Smith, Bakhtiyor Rasulev and Jerzy Leszczynski

Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS

Quantitative structure-activity relationship (QSAR) analysis has been performed on a series of sesquiterpene lactone austricine derivatives. Sesquiterpene lactones have been applied in Eastern folk medicine owing to a wide spectrum of their therapeutic actions including anti-tumoral, anti-viral, anti-inflammatory etc.

A QSAR between the 3D structures and anti-inflammatory activity has been performed for a series of 18 sesquiterpene lactones. Modeling of the anti-inflammatory activity of these compounds as a function of the theoretically derived descriptors was established by multiple linear regression (MLR) and partial least squares (PLS) regression. The genetic algorithm (GA) was used for the selection of the variables that resulted in the best-fitted models. A number of molecular descriptors were obtained from the density functional theory (DFT) B3LYP/6-31(d, p) level optimized geometries (quantum-chemical descriptors).

This study shows that the compounds' activity correlates reasonably well with the selected descriptors encoding the chemical structures. A number of QSAR models with additive and quantum-chemical descriptors have been obtained and discussed in terms of their relativity to the mode of anti-inflammatory action exhibited by sesquiterpene lactones.

A comparative analysis of the two regression methods, PLS and MLR analysis, used in this study and the strength and weaknesses of both methods are discussed.


Side-chain Mobility and Binding Selectivity of Naphthylquinoline Derivatives: Correlation of Conformational Energetics with

Thermodynamic Binding Energies

Angela Sood, M. Jeanann Lovell, G. Reid Bishop, and David H. Magers

Department of Chemistry & Biochemistry, Mississippi College

A library of naphthylquinoline derivatives satisfying hypothesized structural criteria for triplex DNA selectivity have been designed and synthesized by Dr. Lucjan Strekowski of Georgia State University. Proposed structural characteristic criteria promoting intercalation between bases of triplex DNA include a large aromatic surface area, an unfused flexible ring system, and a crescent shape. High-throughput competition dialysis experiments among fourteen of these test compounds demonstrated that the replacement of the secondary amine function found in LS8 (Figure 1.) with an ether oxygen producing MHQ12 (Figure 2.) greatly increased selectivity towards triplex DNA over the more common duplex DNA. Preliminary semi-empirical studies showed a correlation of enhanced triplex DNA selectivity with an increase in rotational flexibility of the side chain of the derivative compound.

The binding study has been extended to include two additional compounds, OZ121 (Figure 3.) and G106 (Figure 4.). OZ121 is identical to the highly selective MHQ12 except that a sulfur atom replaces the ether oxygen. G106 contains an amide linkage between the naphthylquinoline and the side chain. Here we present results from computational studies designed to examine the dynamic flexibility of the naphthylquinoline side-chain for the four compounds containing amine, ether, thiol, or amide linkages. Calculations are performed to determine the energy of each compound with varying dihedral angles between the side chain and the naphthylquinoline. Beginning from optimized geometries, the specific dihedral angle is frozen at 5-degree increments for values between 0 and 360 degrees and the rest of the structure is reoptimized to yield the energy barrier of the side-chain rotation and the approximate dihedral angle at which the top of the barrier lies. Calculations are performed using SCF theory and density functional theory with various basis sets. Results from these computational studies of all four derivatives are coupled with results from thermodynamic binding studies to determine if any informative correlations can be made. We gratefully acknowledge the support of NSF EPSCoR (EPS-0132618).

Figure 1: LS8 – amine linkage Figure 2: MHQ12 – ether linkage


Figure 3: OZ121 – thiol linkage Figure 4: G106 – amide linkage


Enthalpies of Formation of TNT Derivatives byHomodesmotic Reactions

Amika Sood, Patricia Honea, and David H. Magers


TNT (2,4,6-trinitrotoluene) is a well known and widely used explosive. In the current study, we focus on the computation of the standard enthalpy of formation of TNT and similar aromatic compounds by homodesmotic reactions. In homodesmotic reactions the number and types of bonds and the bonding environment of each atom are conserved. We first computed standard enthalpies of formation for certain smaller aromatics whose enthalpies are known to validate our method. We obtained excellent results for these systems with the exception of 3-nitroaniline for which our computed enthalpy was almost 3 kcal/mol too high. We then used different homodesmotic reactions to compute the standard enthalpies of formation of the TNT derivatives. Results are consistent with the exception of those obtained from reactions that utilize the experimental enthalpy value for 3-nitroaniline. Better convergence is obtained with our theoretical value for this system, leading us to believe that the reference value is incorrect. We gratefully acknowledge support from NSF EPSCoR (EPS-0132618).


The Quantum-Chemical Calculations of Reduction-Oxidation Potentials for Cuz+/Cu0 Systems

O.S. Stets, V.F. Vargaljuk, V.A. Polonskiy, V.A. Seredjuk


The copper ions (charge z = +1, +2, +3) in surrounding of n water molecules were the object of modeling. Modeling was carried out using GAMESS program [1] by spin-unrestricted Hartree-Fock method [2]. Stuttgart RSC 1997 ECP basis set has been used for central atoms and 6-31G basis set for atoms of ligands. The energy of optimized metal aqua complexes surrounded by the first solvation shell has been calculated and then improved taking into account solvation effects. Cavitation range for the particle was accepted as Cu – H medium range with addition of hydrogen atom range (1.2 Å).

We have investigated [Cuz+(H2O)n]aq·(H2O)m aq clusters (n – the number of water moleculs in internal shell, m – the number of water moleculs in external shell, (n + m) = const) for calculation of energies of complexes with different geometry of the first solvation shell. We chose value (n + m) = 6, because it is not typical for copper cations to combine into aqua complexes with coordination number higher than six.

Calculations of energies of complexes were improved by taking into account correlation effects using DFT theory and 6-311G basis set (for atoms of ligands). The results are collected in the table.

Table. The energies of copper aqua complexes

Centralatom

Internal coordination shell Multiplicity ([Cuz+(H2O)n]aq·(H2O)m aq),

hartree

Cu+ 2H2O 1 -655,9149

Cu2+ 6H2O 2 -655,7129

Cu3+ 6H2O 3 -655,3856

We calculated energy changes ( E) for Cu3+ + Cu2+ and Cu2+ + Cu+ processes using values of the energies of copper aqua complexes. Then according to equation 0 = a + b· E/n we have computed normal reduction-oxidation potentials. The coefficients a and b equal to -4.747 V and 0.00832 V/(kJ/mol) for Cu3+/Cu2+ system, and -4.88 V and 0.00936 V/(kJ/mol) for Cu2+/Cu+ system. Potential values equal to

0 (Cu3+/Cu2+) = +2.407 B (+2.400 ),0 (Cu2+/Cu+) = +0.087 B (+0.158 ).

The experimantal reference values of potentials shown in parentheses for comparison [3]. We have used value of the energy of copper atom in metal phase for the calculation of 0

(Cu+/Cu0). Energy of copper atom in vacuum was calculated with afore-described methodology. Then the energy of copper atom in metal phase (Cu0s) was determined by equation (Cu0s) =


(Cu0g) – v ( v – experimantal reference value of copper vaporization energy {337.6 kJ/mol [3]}).

Potential value for Cu+ + Cu0 process equals to +0.533 V (experimantal reference value is +0.522 V [3]).

In summury we can conclude that used in this work methodology of calculations is accurate enough for modeling of possible pathways of electrochemical processess with participation of copper ions.

References1. Schmidt M.W., Baldridge K.K., Boatz J.A., Elbert S.T., Gordon M.S., Jensen J.H., Koseki S., Matsunaga N., Nguyen K.A., Su S., Windus T.L., Dupuis M., Montgomery J.A.// J.Comput.Chem. – 1993. – Vol. 14. – P. 1347-1363. 2. Pople J.A., Nesbet R.K.// Self-Consistent Orbitals for Radicals// J. Chem. Phys. – 1954. – Vol. 22. – P. 571-578. 3. Debosh D. Electrochemical constants. – Moscow, 1980. – 232 p.


Conformational Studies of Molecular Clips and Tweezers withBowl-Shaped Corannulene Subunits

Andrzej Sygula

Department of Chemistry, Mississippi State University, Mail Stop 9573, Mississippi State, MS 39762

Nonpyrolytic methodologies for synthesis of curved-surface Polycyclic Aromatic Hydrocarbons (Buckybowls) have recently become available due in part to the progress made in our laboratory.1 It is now possible to synthesize novel molecular architectures with embedded corannulene (1) subunits which could serve as molecular clips and tweezers.

1

The bowl-shape of corannulene in connection with its relatively low inversion barrier introduces structural flexibility which leads to several possible conformations of the molecular assembly with significantly different voids and porosities of the resulting solids. We have employed molecular modeling for some of the medium-sized systems already synthesized2 or planned to be synthesized in our laboratory (e.g. 2-5) in order to predict the preferred, lowest energy conformations of these exciting hydrocarbons. Synthetic methods developed by us will briefly be outlined and the results of Becke3LYP/6-31G(d) calculations will be presented and discussed in relation to the potential complexation abilities of the system studied.


RR

R = -COOMe

2

R

R

R = -COOMe

3

54

1 For the recent review see: Sygula, A.; Rabideau, P. W. in “ Carbon Rich Compounds: Molecules to Materials”, Haley, M., Tykwinsky, R. Eds. Willey-VCH, 2006; Chapter 12, p. 529. 2 (a) Sygula, A.; Sygula, R.; Ellern, A.; Rabideau, P. W. Org. Lett. 2003, 5, 2595. (b) Sygula, A.; Sygula, R.; Rabideau, P. W. Tetrahedron Lett. 2005, 46, 1189. (c) Sygula, A.; Sygula, R.; Rabideau, P. W. Org. Lett. 2005, 7, 4999.


Theoretical Studies on Oxygen Proton Bound Systems

Jaroslaw J. Szymczak,1,2 Szczepan Roszak,1,2 and Jerzy Leszczynski1

1Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, Jackson, MS 39217, USA

2Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27 50-370 Wroclaw, Poland

The clusters have been studied using density functional and Møller-Plesset (MP2) second order perturbation theories. The effect of dynamic correlation on the structures has been further studied on smaller clusters using complete active space self-consistent field followed by the multiconfigurational MP2 calculations. Calculations were performed for complexes resulting from coupling of interacting species to the highest possible spin momentum. The results show that the consecutive attachment of O2 molecules stabilizes one of the two O-H+ bonds of the core with the simultaneous destabilization of the other. As the cluster grows the structure of the complexes changes from a symmetric OH+O core to a significantly asymmetric O2H+O2(O2)5cation with the OH+O bridge displaying the geometry of the conventional hydrogen bond.

a) b)

The spin ( - ) electron difference density. The isodensity contours were plotted for 0.01 (a) and 0.1 (b) electron/bohr3.


Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of Carbon and Germanium

Lyssa A. Taylor and David H. Magers


The conventional strain energies for three- and four-membered heterocycles of carbon and germanium are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. These include germacyclopropane, digermacyclopropane, germacyclobutane, 1,2-digermacyclobutane, 1,3-digermacyclobutane, and trigermacyclobutane. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory (MP2), and density functional theory. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. Two basis sets, both of triple zeta quality on valence electrons, are employed: 6-311G(d,p) and 6-311+G(2df,2pd). Additionally, single-point fourth-order perturbation theory and coupled-clustered calculations using the larger of the two basis sets at the optimized MP2 geometries were used to investigate the effects of higher-order electron correlation. Cross-sections of the electron density in the plane of the ring for each of the three-membered rings were plotted to observe how the electron density is distributed in the sigma bonds of the different systems.

Results are compared to those obtained for heterocycles of carbon and silicon to determine if germanium has the same effect on the conventional strain energy of cyclopropane and cyclobutane as silicon which reduces the conventional strain energy of cyclobutane, but increases the conventional strain energy in cyclopropane. We gratefully acknowledge support from NSF EPSCoR (EPS-0132618).


Investigations of the Molecular Interactions ofCNT, Lignin and Epon 862

E. Whitby,1 J. Edwards,2 R. Parker,1 Q. Liu1, W. Johnson,1 J. Willis,1D. Thomas2 and D. Ryan2



CNT has the promise as a component of organic materials to integrate well into these composites and to provide increased functionality. Florida Advanced Center for Composite Technologies and others utilize sonication and surfactant to disperse CNT in many polymer materials to increase properties such as mechanical strength, thermal conductivity and electrical conductivity amongst others. Success has been achieved with regard to many applications in this regard. A current project is examining the impact of including lignin in the composite structure. It is postulated that lignin can helped to enhance the properties of a CNT/ Epon 862 nanocomposite as it is a natural surfactant and binder. Additionally, photoconductivity was a recently discovered property of lignin.

A lignin enhanced CNT/ Epon 862 composite has the potential to increase dispersion and mechanical strength. Dispersion is a requisite step into unlocking the multi-functional properties. Dispersion for nanoparticles in this case is defined by systems equally distributed in terms of their particle size and spatial location. Pictures of molecular models and SEM micrographs demonstrates how well distributed the lignin/ CNT/ Epon 862 composite system. Analysis of molecular modeling and dynamic mechanical analysis demonstrates the resulting improvement in mechanical strength.

From these analyses, we will drive the degree and mechanisms of interaction of a lignin/ CNT/ Epon 862 composite model. Currently, mechanical strength for the lignin/ CNT/ Epon 862 composite has increased 50 to 100% above the CNT/ Epon 862 composite. Further, the CNT/ Epon 862 composite mechanical strength is 700% increase above the neat resin. It is important to note that the concentration of CNT in the lignin/ CNT/ Epon 862 composite system is 50% of the CNT/ Epon 862 composite system. With such a mechanical strength improvement, the interactions of the lignin/ CNT/ Epon 862 composite system appear to be substantially high. Consequently, further study via molecular modeling and SEM will help to elucidate the details associated with these molecular mechanisms. These details can provide the keys to materials with enhanced functionality.


Novel Aspects of Molecular Recognition and Binding of Antifreeze Proteins at the Water-Ice Interface

Andrzej Wierzbicki

Department of Chemistry University of South Alabama

Mobile, Alabama 36688

Following a series of Antifreeze Protein (AFP) mutation experiments in the late nineties in which selective residues were replaced on both hydrophilic and hydrophobic sides of the AFPs, it became obvious that the original ice-binding and recognition hypothesis reliant upon AFPs hydrogen-bonding capability is incomplete. A new hypothesis was forwarded emphasizing the importance of highly-conserved, alanine-rich hydrophobic faces of AFPs.

In this study we will analyze the alternative mechanisms, which do not rely on hydrogen-bonding capability of AFPs, that are responsible for recognition and accumulation of AFP molecules at the water/ice interface necessary for their antifreeze activity.


Comparative Investigation of Three Dimensional Si Clusters on Graphite and Diamond Substrates

Jianhua Wu and Frank Hagelberg

Computational Center for Molecular Structure and Interactions Department of Physics, Atmospheric Sciences, and General Science

Jackson State University, Jackson, MS 39217

The structure and electronic properties of three-dimensional Sin (n=5-7) clusters adsorbed on the graphite and diamond surfaces are studied by Density Functional Theory and within periodic boundary conditions. A three-layer graphite slab is used to represent the graphite substrate, where the atoms of all the layers are relaxed to adopt their optimized positions. An eight-layer diamond slab is used to represent the diamond substrate with two bottom layers being fixed to the bulk values. In order to avoid the interaction between neighboring clusters, a 12.23 Å×12.72 Å surface cell is used for the graphite substrate. The graphite surface model used in this contribution comprises a total of 180 carbon atoms. A p(8×4) surface cell is employed for the diamond substrate. In this case, the supercell contains 256 carbon atoms. The calculations have been performed using the Vienna ab initio Simulation Package (VASP).

Various cases of adsorption are considered. For the graphite substrate, the most stable one consists in Si atom adsorption on the site above the graphite surface. The silicon clusters “float” above the graphite surface which is separated from the clusters by approximately 3.1 Å. The adsorption energy is about 0.4 eV. In the case of a diamond substrate, the most stable adsorption involves bridge site attachment of the Si clusters on the reconstructed diamond surface. A covalent bond between Si and C atoms on the surface is identified in most cases. The structure of the gas phase Si cluster is modified as a result of the strong interaction between Si atoms and the diamond surface. The adsorption energy exceeds that found for Si clusters on the graphite substrate by one order of magnitude. For both systems Density of states (DOS) distributions are computed. In case of a graphite substrate, the DOS distributions display distinct substructures that can be uniquely ascribed to Si clusters. The energy gaps of Si clusters are changed as a consequence of the weak interaction between them and the graphite substrate. No distinct features of the DOS for diamond adsorption can be associated with the attached Si clusters. Therefore, it is hard to evaluate their energy gaps in the latter adsorption case.


Film Formation with Hydrophobic and Polar Groups in Reactive Evaporating Aqueous Solution: A Bond-Fluctuating Simulation

Model

Shihai Yang1, Sam Bateman, Ras Pandey1, Marek Urban2

1Department of Physics and Astronomy 2School of Polymers and High Performance Materials

The University of Southern Mississippi Hattiesburg, MS 39406

Using a Monte Carlo simulation model, we study film formation with reactive hydrophobic (H) and hydrophilic (P) components in aqueous (A) solution to understand the polyurethane film growth in laboratory. Each component is represented by particles with their appropriate characteristics on a 3D lattice Lx×Ly×Lz with an adsorbing substrate. These particles interact with a short range interaction and execute their stochastic motion by the Metropolis algorithm and may precipitate due to their molecular weights. A is allowed to evaporate only from the top while H and P react with each other by forming fluctuating covalent bonds proceeding from the substrate with probability PB. Covalent bonds may also be formed between H and A particles when A is considered reactive, leading to a modified hydrophobic group H* which is capable of further reactions. Particle A vanishes from the film after it reacts with H. The number of reactive functional groups of each H, P, A and H* particles is 3, 2, 1 and 3, respectively. Growth of the film thickness (h) and its surface roughness (W) are studied at a range of temperature (T). With non-reactive A particles, the saturated film thickness (hs) and roughness (Ws) increase on raising the temperature. With reactive A particles, film thickness (hs) increases on raising the temperature while film roughness (Ws) has a non-monotonic dependence with temperature.


Computational Molecular Electronics / Biochip Design

Ilya Yanov, Yana Kholod and Jerzy Leszczynski

Computational Center for Molecular Structure and Interactions (CCMSI) Jackson State University

Recent developments in nanotechnology open the possibility for production of nanoscale electronic devices and sensors. The main feature of electronic devices is the fact that they are open systems with respect to electron flow. A theoretical consideration of such devices should be done in terms of statistically mixed states which address the problem to quantum kinetic theory [1].

A review of contemporary developments in the computational approach to quantum transport theory is presented.

An application of ab initio, semiempirical and model schemes to C60, adenine-thymine DNA base pair and prospective porphyrin-based biosensor device is discussed.

1. Frensley, W. R. Quantum Transport; Academic

Press: San Diego, 1994; Chapter 2.


The Origin of Surface Localized Ionic Clusters during Film Formation; Spectroscopic Studies and ab Initio Calculations

M. Yu,1 Y. Sheng,2 J. Leszczynski,2 and M. W. Urban1

1 School of Polymers and High Performance Materials, Shelby F. Thames Polymer Science Research Center,The University of Southern Mississippi, Hattiesburg, MS, 39406

2 Computational Center for Molecular Structure and Interactions,Jackson State University, Jackson, MS, 39217

Recently, we explored film formation processes of colloidal particles that are stabilized by biologically active and surface stabilizing phospholipids. These studies showed that colloid particle morphologies have a significant impact on the film formation and particularly, on the film-air (F-A) and film-substrate (F-S) interfaces. Specifically, it is possible to obtain surface rafts which exhibit stimuli-responsive characteristics controlled by particle-phospholipid interactions as well as a chemical makeup of phospholipids. Their chemical makeup and stability are inherently related to ionic interactions, referred to as surface localized ionic clusters (SLICs). Using attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy, X-ray diffraction, combined with ab initio calculations, we identified structural features of SLICs and their formation. Since their structural features and interactions are important for further studies, molecular level interactions between SLICs components are also examined.


Does Methanethiol Adsorb on the Au(111) Surface Dissociate?

Jian-Ge Zhou and Frank Hagelberg

Computational Center for Molecular Structure and Interactions Jackson State University

Jackson, MS 39217

The interaction of methanethiol molecules with the Au(111) surface is investigated using Density Functional Theory within three-dimensional boundary conditions. It is found for the first time that the S-H bond remains intact when the methanethiol molecules are adsorbed on the regular Au(111) surface. However, it breaks if defects are present in the Au(111) surface. At low coverage, the fcc region is favored for S atom adsorption, but at saturated coverage the adsorption energies at various site are almost iso-energetic. The presented calculations show that a methanethiol layer on the regular Au(111) surface does not dimerize. The S-H bond breaking mechanism is identified, which solves the controversial problem if bond cleavage occurs at low or room temperature [1].

[1] I. Rzeznicka, J. Lee, P. Maksymovych, and J. Yates, Jr., J. Phys. Chem. B 109, 15992 (2005).


Anomalous Receptivity of Timber-Based Materials With Respect to Gasoline as a Consequence of Intermolecular Interaction in the

Cellulose – Aromatic Hydrocarbons System

R. Zhu,1 M. Soroka,1 Yu. Zelenko,1 V. Rossikhin,1 V.Plakhotnyk,1 S.I. Okovytyy,2,3 J. Leszczynski3

1Dnepropetrovsk National University of Railway Transport, Dnepropetrovsk, 49010, Ukraine 2Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine

3Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi, 39217, USA

It was shown earlier that in the technology of elimination of the ecological consequences of transport accidents with petroleum products it is expedient to use sorption processes with solid-absorbent and consequent utilization of the absorption products [1, 2].

The most effective absorbents are timber-based materials such as shavings, sawdust and other byproducts of woodworking industry. The briquetting of these materials improve its technological characteristics. It is interesting that the nature of the petroleum product is important. Namely the receptivity of the absorbent to gasoline (A-76) is 2-3 times higher and has value of 200-250% in comparison to diesel oil. At the same time the rate of the absorption increased too.

The calculations of electronic and spatial structure of cellulose molecule (the constituent of wood fiber) and the o-xylene molecule arranged in immediate vicinity of the cellulose have been done to reveal the nature of this anomalous absorption behavior.

The thermodynamic parameters of the o-xylene interaction with the cellulose fragment have been calculated. The size of the fragment we constrained to chain of 18 carbon atom length. The calculations have been done at PM3 semiempirical level by Gaussian03 software [3]. The spatial arrangement of these molecules that correspond to minimal energy of the system is shown bellow.

According to the results of calculations the enthalpy and Gibb’s free energy of the interaction between the fragment of cellulose and o-xylene molecules are H 298 = - 52 kJ/mol and G 298 =- 3 kJ/mol and show weak dependence on the hydrocarbon isomer type. Thus anomalous receptivity of timber-based materials with respect to gasoline (A-76) that contains a great amount of o-xylene, toluol and benzene can be explained by a noticeable intermolecular interaction


between cellulose molecules and aromatic hydrocarbons. The mechanism of that interaction probably includes partial transfer of -electronic density of aromatic rings to empty orbitals of hydrogen atoms of cellulose. The effective electric charges on the cellulose hydrogen atoms sometimes reached values from +0.18 up to +0.23.

References: 1. V. Plakhotnyk, Yu. Zelenko, J. “Scientific Israel – Technological Advantages”, 2004, v.6,

1-2, 197. 2. V.N. Plahotnyk, L.A. Yaryshkina, V.I. Sirakov, V.T. Tanshin, T.L. Savina, A.N. Boichenko, Environmental activity at railway transport of Ukraine: problems and solutions, 2001, Ed. Transport Ukrainy, Kiev, p. 244. 3. M.J.Frisch, G.W.Trucks, H.B.Schlegel, et al., Gaussian, Inc., Wallingford CT, 2004.

6th Southern School on Computational Chemistry List of Participants 125

Dmytro Afanasyev Ukrainian State Chemical Technology University Dnepropetrovsk, Ukraine 49005 Tel: +38(0562)929475 Email: [email protected]

Lovell Agwaramgbo 27 Olympic Ct New Orleans, LA 70131 Tel: 504-391-1742 Fax: 504-391-1742 Email: [email protected]

Reeshemah Allen Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601 979-3979 Fax: 601 979-7823 Email: [email protected]

Shonda Allen Hill Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-3723 Fax: 601-979-6865 Email: [email protected]

Maxym Belov Dnepropetrovsk National University Chemistry Dept. 13 Naukova St. Dnepropetrovsk, Ukraine 49050 Email: [email protected]

Larisa Borshchevich Dnepropetrovsk National University Naukova street, 13 Dnepropetrovsk , Ukraine 49050 Tel: +380 562 460095 Fax: +380 56 7765833 Email: [email protected]

Deborah Bryan 219 Jones Hall Chemistry Department Florida A&M University Tallahassee, Florida 32307 Tel: 850-599-3638 Fax: 850-561-2388 Email: [email protected]

Louis Carlacci AHPCRC/Network CS 1425 Porter Street Frederick, MD 21702 Tel: 301-619-6732 Email: [email protected]

Qianyi Cheng Box 4036 Department of Chemistry & BiochemistryMississippi College Clinton, MS 39058 Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected]

David Close East Tennessee State University Physics Dept. Box 70652 Johnson City, TN 37614 Tel: 423-439-5646 Fax: 423-439-6907 Email: [email protected]

Bridgit Crews Department of Chemistry and Biochemistry 9510 University of California Santa Barbara, Ca 93106-9510 Tel: (805) 893 4720 Email: [email protected]

Gopala Darbha c/o Dr.Paresh.C.Ray Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-919-6619 Email: [email protected]

LaTanya Dixon Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601 979 3723 Fax: 601 979 6865 Email: [email protected]

Edyta Dyguda-Kazimierowicz Institute of Physical and Theoretical ChemistryWroclaw University of Technology Wyb. Wyspianskiego 27 Wroclaw, Poland 50-370 Tel: +48 (71) 320 3200 Fax: +48 (71) 320 3364 Email: [email protected]

List of Participants 6th Southern School on Computational Chemistry126

Jesse Edwards 219 Jones Hall Chemistry Department Florida A&M University Tallahassee, Florida 32307 Tel: 850-412-5329 Fax: 850-561-2388 Email: [email protected]

Jason Ford-Green Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 850-443-9233 Email: [email protected]

Ryan Fortenberry Box 4036 Department of Chemistry & BiochemistryMississippi College Clinton, MS 39058 Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected]

Fillmore Freeman Department of Chemistry University of California, Irvine Irvine, CA 92697-2025 Tel: 9498246501 Fax: 9498242210 Email: [email protected]

Alona Furmanchuk Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-9796544 Fax: 601-979-7823 Email: [email protected]

Leonid Gorb Engineer Research and Development Center3909 Halls Ferry Rd Viksburg, MS 39180 Tel: 601-634-3863 Email: [email protected]

Helen Grebneva Donetsk Physical and Technical Institute NAN Ukraine 83114 Donetsk, st. P. Lucsemburg, 72 Donetsk, Ukraine 83114 Tel: +38 062 3048121 Email: [email protected]

Frank Hagelberg Jackson State University Department of Physics 1325 J.R. Lynch St Jackson, MS 39217 Tel: 601 979 3633 Fax: 601 979 3630 Email: [email protected]

Jessica Hardaway 219 Jones Hall Chemistry Department Florida A&M University Tallahassee, Florida 32307 Tel: 850-599-3638 Fax: 850-561-2388 Email: [email protected]

Ayroinde Hassan Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-7824 Email: [email protected]

Frances Hill Network Computing Services, Inc/AHPCRC 1200 Washington Ave S Minneapolis, MN 55415 Tel: 612-337-3569 Fax: 612-337-3483 Email: [email protected]

Tiffani Holmes Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 228 623 0673 Email: [email protected]

Ming-Ju Huang Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-3492 Email: [email protected]

Olexandr Isayev Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-1134 Fax: 601-979-7823 Email: [email protected]


Mark Jack Florida A&M University Dept. of Physics 205 Jones Hall 1530 Martin-Luther King Jr. Blvd. Tallahassee, FL 32307 Tel: 8505998457 Fax: 8505993577 Email: [email protected]

Dusanka Janezic Center for Molecular Modeling National Institute of Chemistry Hajdrihova 19 Ljubljana, SLOVENIA 10000 Tel: +386 1 476 0321 Fax: +386 1 476 0300 Email: [email protected]

Anna Kaczmarek Institute of Chemistry N. Copernicus University 7, Gagarin St. Toru , Poland 87-100 Tel: +48 56 611 4413 Fax: +48 56 654 2477 Email: [email protected]

Yana Kholod Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: (601) 979 3979 Fax: (601) 979 7823 Email: [email protected]

Dmytro Kosenkov Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: (601)9793979 Fax: (601)9797823 Email: [email protected]

Vitalina Kukueva Onoprienko, 8, Fire Safety Institute Cherkassy, Ukraine 18034 Tel: (80472) 55-09-62 Fax: (80472) 55-09-71 Email: [email protected]

Gulnara Kuramshina Lab. of Molec. Spectroscopy Dept. of Phys. Chem., Faculty of Chemistry, Moscow State University (M.V.Lomonosov) Moscow, Russia 119992 Tel: 7(495)939-2950 Fax: 7(495)932-8846 Email: [email protected]

Christopher Lee Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: (601) 9327471 Email: [email protected]

Danuta Leszczynska FAMU-FSU College of Engineering Department of Civil Engineering 2525 Pottsdamer Str Tallahassee, FL 32310 Tel: 904-487-6137 Fax: 904-487-6142 Email: [email protected]

Jerzy Leszczynski Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-3482 Fax: 601-979-7823 Email: [email protected]

Meng-Sheng Liao Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: (601)979-3714 Fax: (601)979-3674 Email: [email protected]

Dan Liu Jackson State University Department of Physics 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601 979 3640 Email: [email protected]

Brandon Magers Box 4036 Department of Chemistry & BiochemistryMississippi College Clinton, MS 39058 Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected]

David Magers Box 4036 Department of Chemistry & BiochemistryMississippi College Clinton, MS 39058 Tel: 601-925-3851 Fax: 601-925-3933 Email: [email protected]


Devashis Majumdar Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-7824 Email: [email protected]

Harley McAlexander Box 4036 Department of Chemistry & BiochemistryMississippi College Clinton, MS 39058 Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected]

Andrea Michalkova Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-9791041 Fax: 601-9797823 Email: [email protected]

Jane Murray Department of Chemistry University of New Orleans New Orleans, LA 70148 Tel: 202-351-1554 Email: [email protected]

Edmund Moses Ndip Hampton University Hampton, VA 23668 Tel: 757 727 5043 Fax: 757 727 5604 Email: [email protected]

Sergiy Okovytyy Nauchny St. 13 Dnepropetrovsk National University Dnepropetrovsk, Ukraine 49625 Tel: +(38056)7764608 Fax: +(38056)7765833 Email: [email protected]

Ras Pandey Physics & Astronomy University of Southern Mississippi Box 5046 Hattiesburg, MS 39306-5046 Tel: 601 266 4485 Fax: 601 266 5149 Email: [email protected]

Reginald Parker 2525 Pottsdamer Drive, B317 Tallahassee, Florida 32310 Tel: 850-410-6378 Fax: 850-410-6342 Email: [email protected]

Yuliya Paukku Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 6019797824 Fax: 6019797823 Email: [email protected]

Tetyana Petrova Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-3979 Email: [email protected]

Kevin W Plaxco University of California Department of Chemistry and Biochemistry Santa Barbara, CA 93106 Tel: (805) 893-5558 Fax: (805) 893-4120 Email: [email protected]

Yevgeniy Podolyan Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-4114 Fax: 601-979-7823 Email: [email protected]

Peter Politzer Department of Chemistry University of New Orleans New Orleans, LA 70148 Tel: 202-351-1555 Email: [email protected]

Mohammad Qasim USACE- ERDC (Environmental Laboratory)3909 HAlls Ferry Road Vicksburg, MS 39180 Tel: (601) 634 3422 Fax: (601) 634 2742 Email: [email protected]


Bakhtiyor Rasulev Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-7824 Fax: 601-979-7823 Email: [email protected]

Jamar Robinson 219 Jones Hall Chemistry Department Florida A&M University Tallahassee, Florida 32307 Tel: 850-599-3638 Fax: 850-561-2388 Email: [email protected]

Teri Robinson Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-3981 Fax: 601-979-7823 Email: [email protected]

Christina Russell 219 Jones Hall Chemistry Department Florida A&M University Tallahassee, Florida 32307 Tel: 850-599-3638 Fax: 850-561-2388 Email: [email protected]

Zuhail Sainudeen Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601 940 3390 Email: [email protected]

Julia Saloni Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-3979 Email: [email protected]

Vladimir Seredjuk Dnepropetrovsk National University Naukova street, 13 Dnepropetrovsk, Ukraine 49050 Tel: +380 562 460095 Fax: +380 56 7765833 Email: [email protected]

Yinghong Sheng Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 6019791219 Fax: 6019797823 Email: [email protected]

Manoj Shukla Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-1136 Fax: 601-979-7823 Email: [email protected]

Tomekia Simeon Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Email: [email protected]

Talibah Smith Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: (601) 979-7824 Email: [email protected]

Amika Sood Box 4036 Department of Chemistry & BiochemistryMississippi College Clinton, MS 39058 Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected]

Angela Sood Box 4036 Department of Chemistry & BiochemistryMississippi College Clinton, MS 39058 Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected]

Olga Stets Dnepropetrovsk National University Naukova street, 13 Dnepropetrovsk, Ukraine 49050 Tel: +380 562 460095 Fax: +380 56 7765833 Email: [email protected]


Andrzej Sygula Mississippi State University Department of Chemistry Mail Stop 9573 Mississippi State, MS 39762 Tel: 662-325-7612 Fax: 662-325-1618 Email: [email protected]

Jaroslaw Szymczak Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 6019791632 Fax: 6019797823 Email: [email protected]

Dinadayalane Tandabany Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-7824 Fax: 601-979-7823 Email: [email protected]

Lyssa Taylor Box 4036 Department of Chemistry & BiochemistryMississippi College Clinton, MS 39058 Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected]

Tamara Taylor Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-454-0052 Email: [email protected]

Jing Wang Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-1159 Fax: 601-979-7823 Email: [email protected]

John Watts Jackson State University Department of Chemistry 1325 Lynch St. Jackson, MS 39217-0510 Tel: 601-979-3488 Fax: 601-979-3674 Email: [email protected]

Edgar Whitby 2855 Apalachee Parkway Tallahassee, Florida 32301 Tel: 850-294-8480 Fax: 850-4106342 Email: [email protected]

Andrzej Wierzbicki Department of Chemistry University of South Alabama Mobile, AL 36688 Tel: 251 4607436 Fax: 251 4607359 Email: [email protected]

Jianhua Wu Jackson State University Jackson, MS 39217 Tel: 601-979-3640 Fax: 601-979-3630 Email: [email protected]

Shihai Yang University of Southern Mississippi Hattiesburg, MS 39401 Tel: 601-297-5459 Email: [email protected]

Ilya Yanov Jackson State University Department of Chemistry 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-4136 Fax: 601-979-7823 Email: [email protected]

Min Yu university of southern mississippi P.O.Box 10076 hattiesburg, ms 39406 Tel: 6012666724 Fax: 6012666178 Email: [email protected]

Jian-Ge Zhou Jackson State University Department of Physics 1325 J.R. Lynch St Jackson, MS 39217-0510 Tel: 601-979-3640 Fax: 601-979-3630 Email: [email protected]

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