béla viskolcz university of szeged department of chemical informatics

Molecular EvolutionEarth as a molecular printer?

Béla ViskolczUniversity of Szeged

Department of Chemical Informatics

University of Szeged, Department of Chemical Informatics

Prebiotic molecular evolution

COMPLEXITY

VARIABILTY


Molecular evolution basic level

COMPLEXITY


Overview Atom Molecule

o Glycineo Pyridine o Glycerin aldehyde

Molecular Network Topic of Summerschool


Ancient atmosphere


Change in atmosphere

Oxidation conditions: Carbon: -4 to +4 Nitrogen: -3 to 0

Atom Molecules



Number of molecules Known Molecules

Organic: ~ 15 x 106

Inorganic: ~ 1 x 106

Virtual Molecules?Organic: > 1012 or 1060

COMPLEXITY

VARIABILTY


Motivation I.

Molecular Informatics More Money for Applied Science


Molecules by graph

CO

O

N HH

C HH

H


Runable input

(.com)

Terminated output

(.log)

Output with Error output

Output with

no error termination

Normal term.

Conv. Crit.

Freq

Calculation and

collection of molecular properties

Database

Manipulation of the

input

(By hand)

Modified input

Initial input

(.pdb,…)

Normal

termination?

Input preparation

Com2Chem: Computational Combinatorial Chemistry

Computational

Know How

Chemical

Know How

Methodology Know How

Regeneration of inputx2

Workflow of the Com2Chem


Highest stability


Complexes


Reactions

N1


Reactions


More properties…


Pyrimidine- Formula C4H4N2

- Guinness Molecule - Wide occurrence in nature as substituted and ring fused compounds.- Derivatives of pyrimidine are present in nucleotides, this are ADN structure.



Reverse Entropy Funnel

HCNxC2H2xHCN


HC

NxC

2 H2 x

HC

N


The most stable structures


Glyceraldehyde

- Formula C3H6O3

- Organic molecule present in several biological process.

- Important during the prebiotic stage of the Earth.



Details of computations

Isomers and spatial conformations-Glyceraldehyde: 277 com files on gas phase and 277 in aqueous phase.-Pyrimidine: 7983 com files on gas phase and 7983 in aqueous phase.

- Spatial conformations makes reference to the generation of some species that are exactly the same but the orientation in space (relative Cartesian coordinates of the entire specie) is different, which leads to different electronic/atomic interactions.


Details of computations

Gaussian 09 Calculation on G09 were made under G3MP2B3 method:

Optimization, frequency, QCISD(T) and MP2 calculation.Each calculation used 8 processors from the cluster.

For the Gas Phase Glyceraldehyde isomers calculation took:

49 days, 9 hours, 59 minutes and 50 seconds CPU time 6 days, 4 hours, 14 minutes and 59 seconds clock time

For the Gas Phase Pyrimidine isomers calculation took:1131 days, 16 hours, 23 minutes and 47.1 seconds CPU time 141 days, 11 hours, 3 minutes and 23.4 seconds, clock time


http://www.lapszemle.ro/2011/08/07/a-cukor-nem-olvad-hanem-szetbomlik/

C1-6H0-14O0-6

Stochiometry Σ267 258

17 121 162

C6H12O611 constitutional isomers!

Calculation Matrix




http://kbond4.wordpress.com/

X=F,Cl,Br,I

C+N+O+S+F+Cl+Br+I=Y

S valence (connectivity) 2, 4, 6

N valence (connectivity) 3, 5

Mr (g/mol) Σ(Y=5) Σ(Y=6)1-75 26 398 378

76-100 153 058 928 593

101-125 235 070 7 731 832

126-150 160 848 10 924 887

151-175 29 932 4 917 433

176-200 18 266 1 697 180

201-225 28 781 1 025 626

226-250 8 462 825 300

251-275 1 383 589 487

275-300 968 106 103

663 166Σ= 28 746 819

C1Y H0(2Y+2) X0Y O0YS0YN0Y

http://kbond4.wordpress.com/

Molecular Network



The email-Network


Network


Moelcular Network

Elements of Molecular Network



N(isomer) Stochiometry

934 C1_H0_N0_O2_F0_S345 C2_H4_N0_O3_F0_S043 C2_H6_N0_O3_F0_S041 C3_H2_N0_O2_F0_S0129 C3_H2_N0_O3_F0_S077 C3_H4_N0_O2_F0_S0255 C3_H4_N0_O3_F0_S077 C3_H6_N0_O2_F0_S0277 C3_H6_N0_O3_F0_S054 C3_H8_N0_O2_F0_S0191 C3_H8_N0_O3_F0_S0

From atom to molecules

CH

ON

SC3H6O3

C2H4O3

C2H6O3


Network elements I.

C3H6O3

C3H8O2

C3H8O3

C3H6O2

C3H4O3

C3H4O2

C3H2O2

C2H4O2

C2H6O3

± CO

±CH2O

CH

ON

S

±CH4


Network elements I.

C3H6O3

C3H8O2

C3H8O3

C3H6O2

C3H4O3

C3H4O2

C3H2O2

C2H4O2

C2H6O3

± CO

±CH2O

CH

ON

S±(C/ ̶ H2O)

±(CO/-2H2O)

±(C/-H2)


Network elements II.

C3H6O3

C3H8O2

C3H8O3

C3H6O2

C3H4O3

C3H4O2

C3H2O2

±H2

±H2

±H2

±H2

±H2

±H2O

±H2O

±H2O

C2H4O2

C2H6O3

CH

ON

S


Individual projectsNo. Name University N(isomer) Stochiometry

12 Dhiraj Sinha University of South-Bohemia 934 C1_H0_N0_O2_F0_S36 Bedard Joe University of Ryerson 45 C2_H4_N0_O3_F0_S0

10 Park Hyemin University of Toronto 43 C2_H6_N0_O3_F0_S09 Ramkissoon Chaitnandanie University of Toronto 41 C3_H2_N0_O2_F0_S04 Ying Lu University of Toronto 129 C3_H2_N0_O3_F0_S05 Lee Kyungseop University of Toronto 77 C3_H4_N0_O2_F0_S03 Yu Peiqi University of Toronto 255 C3_H4_N0_O3_F0_S08 Xu Xuan Ting University of Toronto 77 C3_H6_N0_O2_F0_S01 Li Jian Bin University of Toronto 277 C3_H6_N0_O3_F0_S02 Wang Daniel Yunwen University of Toronto 54 C3_H8_N0_O2_F0_S07 Chen Keyue University of Toronto 191 C3_H8_N0_O3_F0_S0

Köszönöm megtisztelő figyelmüket!

THANK YOU FOR YOUR ATTENTION

Financial support TÁMOP 4.2.2-A: New functional

materials … TÁMOP 4.2.2-C: Supercomputer a

national virtual laboratory


References Szori Milan, Jojart Balazs, Izsak Robert, Szori Kornel, Csizmadia

Imre G, Viskolcz Bela: Chemical evolution of biomolecule building blocks. Can thermodynamics explain the accumulation of glycine in the prebiotic ocean? PHYSICAL CHEMISTRY CHEMICAL PHYSICS 13:(16) pp. 7449-7458. (2011)

Franco Cimino, Milán Szőri,Claudio A. Morgado and Béla Viskolcz, Relative Stability of C4H4N2 isomers and complexes – Pyrimidine as a Guiness molecule. in preparation


Thermodynamics Given number of electrons Relative energy,

enthalpy etc.

béla viskolcz university of szeged department of chemical informatics

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