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Illustrating an Elementary Approach by Cluster Calculations for
Structure, Dynamics and Reactions

S.Aravamudhan and Amarta Kr. Pal
Department of Chemistry
North Eastern Hill University
SHILLONG 793022 Meghalaya

                                                                 There has been much interest in studying the structures and
                                                                 spectroscopy of solvent-solute clusters, consisting of ions (either
                                                                 cations or anions) or neutral species, which are solvated by neutral
                                                                 molecules (usually water) or rare gas atoms. It is hoped that these
                                                                 studies will enable a better understanding of the fundamentals of
                                                                 structure, dynamics and reactions of ions and molecules in bulk

As it stands stated in the above excerpt, there have been several efforts(2) to study the systems of cluster by quantum chemical calculations of structures and energies. These efforts have been mostly to obtain the optimized, end-structure-parameters and energies. Starting with the given input structure of the cluster, structure sequences are generated during the optimization procedures at various steps till the end. And enquiring into the structural details and the sequences of structures obtained during the Geometry Optimization can be providing indications to the various pathways of interactions of cluster components. This approach is a much simpler approach for beginners to inquire about the mechanistic aspects of reactions than a potential energy surface calculations and trying to relate to reaction coordinates.

  In this abstract this approach is reported as a feasible methodology. An illustrative set of calculations using computational chemistry tools are the basis for such conclusion and in particular a calculation on the isolated molecule alpha amino acid [Glycine] substantiates a remark made on the acid base characteristics of such amino acids elegantly bringing out the intra-molecular proton transfer from one of the equilibrium structure to result in another. The roles of water molecules present in the neighborhood can be shown to influence this intra molecular transfer to become water mediated inter molecular transfer of protons. The importance of hydronium ion ([H3O]+ ) formation is also evidenced. The equilibrium characteristics of zwitterions form and the unionized form of the amino acid also could be well discerned and such results seem to be indicating details which were not thought of as possibilities for study by such simple calculations.

  An effort also would be made to provide references of previous related studies when the results are discussed(2).

             1.   “Atomic and Molecular Clusters”, Roy L. Johnston, Taylor Francis (Year 2002), Sec.3.5, p73.

Abstract as submitted for participation in CRSI 13th NSC (
Registration & Submisssion of Abstract on 16th Dec. 2010  Receipt from the organizers; received for Payment of Registration Fee
uploaded & submitted MSWORD document of the Abstract.
For reorts on the efforts cited in Abstract above view the contents of this author's webdirectory at URL:
The initial draft of the poster display sheets


Theoretically Possible Structures and the Averaging;
Calculated Chemical Shifts and Simulated NMR Spectra:
And, Comparison with Experimental Spectra.

Department of Chemistry
North Eastern Hill University
PO NEHU Campus SHILLONG 793022

This contribution would have reference to this author’s previous contributions (1) to the Annual Meetings of the Indian Biophysics Society. The effort had been to illustrate the kind of averaging techniques useful for averaging the chemical shift values corresponding to the confirmation changes during a fluctuation of a given structure. As per what is now known, the advantages of the NMR technique in comparison with Xray technique are that the solution structures can be determined by NMR. However, it is also necessary to consider the determination of the Macromolecular structure in Solution by NMR methods entails obtaining the several contributing structures for a given Biological macromolecule while the x-Ray method would be resulting in a single conformation as the structural investigation.

If a given solution structure obtained by NMR is a superposition of several structures, then each contributing structure must be recognized as a MEAN structure exhibiting fluctuations from the mean thus each of the contributing structure must be subjected to fluctuation characteristics while processing.

Thus when a molecule is having several confirmations in equilibrium, arriving at the effective structure accounting for the experimental NMR features would depend upon the appropriate characteristic times, and it may either require summing the experimental spectra or averaging the chemical shift values and then constructing a single spectrum corresponding to the experimental spectrum.
It does not simple enough to envisage how the theoretically calculated chemical shifts corresponding to contributing structures can be used to average the theoretical (optimized / can there be more than one?) structures, average the calculated chemical shifts and simulate the spectrum to be compared with the experimental spectra. This calculation and simulation results would be discussed in the presentation.

  1.)     a)