SMALL MOLECULE COMPUTATIONAL CHEMISTRY for COMPUTATIONAL BIOLOGY and MACROMOLECULAR MODELING

Friday, April 21, 2023 1S.Aravamudhan Workshop

July 25-30,2011

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Organizer’s acceptance for participation

Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems

AbstractRecent years have witnessed an explosion in computational power, leading to attempts to model ever more complex systems. Nevertheless, there remain cases for which the use of brute-force computer simulations is clearly not the solution. In such cases, great benefit can be obtained from the use of physically sound simplifications……………….

Annu. Rev. Phys. Chem. 2011. 62:41–64

Computer modeling of the function of macromolecules and related systems presents a problem of enormous complexity. Although available computer power has increased rapidly, there are, nevertheless, still many cases for which the use of brute-force simulations is clearly not the best approach. Furthermore, there exist many systems whose nature was correctly elucidated even before the emergence of the current level of computing power…………... …………………………….Obviously, this has enormous difficulties. However, there also exist far less dramatic examples of cases in which one cannot (and perhaps should not) progress without the use of a simplified model, and, in fact, recent years have witnessed a growing appreciation of the fact that the simulation of complex systems, and, in particular, the modeling of biological function, can greatly benefit from physically sound simplifications.

1. INTRODUCTION Workshop on Modeling Biological Systems

Friday, April 21, 2023 2S.Aravamudhan Workshop July 25-30,2011

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H2N CHR COOH, the nonionic neutral form does not find much mention: Can there be equilibrium between zwitterion and the nonionic form at neutral pH?

Acidic Alkaline

Why only the zwitterions is a dipolar ion and not the other ions?

Neutral water molecule has a permanent dipole moment and water is a polar solvent

Beginning with the contents of TEXTBOOK on ORGANIC CHEMISTRY by Morrison and Boyd………..

Friday, April 21, 2023 3S.Aravamudhan Workshop July 25-30,2011

+- - +

| μ | = qdSign convention for dipole

has been reversed

All atoms are neutral.

Atoms covalently bonded in molecules are considered have the full share of the one of electron of the shared pair of electron hence such atoms are also neutral

Partially covalent bonds between atoms cause partial charges to be located and these can give rise to dipole moments; Polar bondsFriday, April 21, 2023 4S.Aravamudhan Workshop

July 25-30,2011

Links below are or getting clarifications on the conventions

http://www.youtube.com/user/aram1121944/#p/u/8/LctfaPFRjJ8 http://www.av8n.com/physics/electric-dipole.htmhttp://en.wikipedia.org/wiki/Dipole http://hyperphysics.phy-astr.gsu.edu/hbase/electric/dipole.htmlhttp://www.youtube.com/watch?v=513aIefo6QA

Nearly same energetic structures but widely varying dipole moment characteristics. Does this have a significance at any stage in modeling systems?

To know the orientation of dipole moment of water molecule is simple enough but as the glycine molecule finds itself in varying environments it would not be all that simple to estimate its dipole moment.

Friday, April 21, 2023 5S.Aravamudhan Workshop July 25-30,2011

Maximum difference of 6.5 Kcals mole-1

Zwitterion/neutNonionic/neut

Zwitter ion is a case in which a full unit of positive charge and negative charge are located at different ends of the molecule and hence special reference as dipolar ion.

Other categories are cation, anion or polar molecule where partial charges are created.

Difference of about -79.55 KCals per Mole

Friday, April 21, 2023 6S.Aravamudhan Workshop July 25-30,2011

The nonionic form is more stable. But in neutral pH, the zwitterionic form predominates. Indicates the importance of the stabilization by water medium.

Click for computed results

Since the two neutral forms of the amino acid (Glycine) have small energy difference, if an input structure corresponds to the guessed structure for zwitter ionic form, using an abinitio QM method with STO 3G basis set, a ge4ometrical optimization invariably results in the nonionic neutral form.

http://www.ugc-inno-nehu.com/DBIBT/0_1_Gly_Movie_2.gif

http://www.ugc-inno-nehu.com/DBIBT/0_2_MV_0_45.JPG

In all these what is the importance of Energy? And, When the structures are nearly of same energy, can electric dipole moment, be of any consideration?

A few model situations for exemplifying the above consequences are included in the next slide.

Friday, April 21, 2023 7S.Aravamudhan Workshop July 25-30,2011

http://www.ugc-inno-nehu.com/DBIBT/0_3_glyw_opt_movie.gif

Glycine neutral nonionic str-3 & WaterNote the dipole moment characteristics of these two molecules.

When these two molecules are placed juxtaposed and subjected to optimization, what would be the consequence?

During this process how would have the energy varied?

http://www.ugc-inno-nehu.com/DBIBT/0_3_glyw_opt_movie.jpg

The above optimization structure sequence displayed at a faster time scale

http://www.ugc-inno-nehu.com/DBIBT/0_3_glyw_opt_movie_faster.gif

http://www.ugc-inno-nehu.com/DBIBT/0_3_glyw_opt_movie_Wrotated.gif

Hydrophilic?

Hydrophobic?

Friday, April 21, 2023 8S.Aravamudhan Workshop July 25-30,2011

Water dipole rotated by 180 degrees.

Note the similar process sequentially when a zwitterion is placed with water molecule for a geometry optimization

http://www.ugc-inno-nehu.com/DBIBT/0_4_glyzw-w.-opt-mov.gif

Corresponding trends of variation in energy for the above sequence of structures

http://www.ugc-inno-nehu.com/DBIBT/0_4_glyzw-w-opt-mov.jpg

Friday, April 21, 2023 9S.Aravamudhan Workshop July 25-30,2011

The way the theoretical calculations display the movement of water molecule in presence of glycine, could be the way a drug molecule moves towards the target macromolecule governed by electrical forces. If the small molecule moves so in a biological fluid medium, this would be similar to the way a ship would b e moving in water current and gets docked at the port. Hence small molecule gets docked on the macromolecule for favorable interaction. This word has been used also while virtual computer aided screening and positioning the small molecule in the binding site

Spectroscopy can distinguish the cation, anion, neutral nonionic form and the neutral zwitter ionic forms.

Computational (Quantum Chemical) softwares provide for calculations of these spectra theoretically and to compare with experimental results. A typical calculated results is displayable from the link below:

http://www.ugc-inno-nehu.com/DBIBT/0_5_sapDnmr-ni-zw-persp.JPG

Even if experimentally the spectra cannot be obtained for the variety of structures, calculated pattern and the partial charge distributions can give valuable information on the trends of electronic structure variations due to the interactions. This can be helpful in modeling the system appropriately for reaching an optimal solutions without too much of search.

Friday, April 21, 2023 10S.Aravamudhan Workshop July 25-30,2011

The link below is a reproduction from a book on Biological NMR. The experimental spectral trends have been reported.

http://www.ugc-inno-nehu.com/DBIBT/0_6_exptal_spectral_trends.JPG

http://www.ugc-inno-nehu.com/DBIBT/0_7_variation_NMR_forGOsequence.JPG

A similar trend as above from computational software

http://www.ugc-inno-nehu.com/DBIBT/0_8_glycine-isomers-water-GO-60pc.JPG

http://www.ugc-inno-nehu.com/DBIBT/0_9_File3.pdf

After this much of introduction to theoretical methods for spectroscopic manifestations during geometrical structure variations…………………

Getting more information from cluster calculations

Friday, April 21, 2023 11S.Aravamudhan Workshop July 25-30,2011

On the role of water there are several publications from Theoretical Biologists who have investigated using quantum chemical methods. Some of these date back to 1960-70s. These can be reviewed in the current scenario of Computational Chemistry……….

Friday, April 21, 2023 S.Aravamudhan Workshop July 25-30,2011 12

Intermediate Results in Computational

Biology: Can they be the Realities during

Biological Processes?S. Aravamudhan

Department of ChemistryNorth Eastern Hill University

SHILLONG 793022Meghalaya: INDIA

This topic has been inspired by the current BIOLOGICAL applications of Magnetic Resonance Techniques (NMR in particular)

and the advances in Computational Chemistry

Context of my Contributions to IBS Meetings

Abstract: Workshop on Modeling Biological Systems

Friday, April 21, 2023 S.Aravamudhan Workshop July 25-30,2011 13

http://www.ugc-inno-nehu.com/WMBS/0_Introduction\0_introduction.ppt

http://www.ugc-inno-nehu.com/WMBS\1_Glycine_GO_NMR\0_Glycine_GO_NMR.ppt

http://www.ugc-inno-nehu.com/WMBS/2_HydroniumIon/000_Gly_GO_seq_structure.ppt

http://www.ugc-inno-nehu.com/WMBS/3_Specific_Water_interct_Amino/0_specific.ppt

http://www.ugc-inno-nehu.com/DBIBT/1_1_File2.pdf

http://www.ugc-inno-nehu.com/DBIBT/1_2_File1.pdf

http://www.ugc-inno-nehu.com/DBIBT/1_3_File5.pdf

http://www.ugc-inno-nehu.com/DBIBT/1_4_File4.pdf

If any problems are encountered while downloading the PowerPoint files, type in the URL: http://www.ugc-inno-nehu.com/WMBS/ in the browser address bar and find the appropriate web folders and files.

Friday, April 21, 2023 S.Aravamudhan Workshop July 25-30,2011 14

Questions ; Comments ; Remarks Prof.S.Aravamudhan Phone:0364 272 2615Department of Chemistry Mobile: 9862053872North Eastern Hill University Email: inboxnehu_sa@yahoo.com

Shillong 793003 Meghalaya URL: http://aravamudhan-s.ucoz.com

A link to the facsimile of the participation certificate