Geometrical Optimization of Glycine Molecule Sequence using GAMESS Computational Software

1. 90◦ ? Structure sequence during Optimization GLYCINE Molecule Geometrical Optimization by GAMESS Computational SOFTWARE at http://www.webmo.net Hartree-Fock SCF Method, STO3G basis set Proton Transfer STRUCTURE SEQUENCE as Obtained at iterative steps till Convergence are EXAMINED for the possible inferences from the Intermediate steps Optimization procedures started with Nonionic form of this alpha amino acid, results in converging with the nonionic structure. When the Zwitterionic Form is the input structure, convergence occurs with the nonionic form as the final stabilized form. In this particular instance convergence required 45 iterative steps. And, the iterative stage is indicated by the step numbers The Consequences are illustrated with the Calculation of NMR spectra for the intermediate structures and monitor for the spectral changes corresponding to the step wise structural changes. A detailed image of this result for display S Aravamudhan WMBS NEHU 25-29 Oct 2010

2. 0 5 7 10 input 32 14 22 Illustrative Movie of this structure sequence output S Aravamudhan WMBS NEHU 25-29 Oct 2010

3. ZWITTER ION Non ionic form GLYCINE A detail S Aravamudhan WMBS NEHU 25-29 Oct 2010

4. Particularly take note of the Proton No 8 and its NMR peak location; does proton 8 turn out to be typical amide proton and why not any of the other two attached to the nitrogen? An Illustration of the possibility of calculating NMR chemical shifts for Glycine and the full assignment of the peak position to the proton location in the molecule. Thus the upfield-down field changes can be associated with the variation in the geometry and the molecular electronic structure S Aravamudhan WMBS NEHU 25-29 Oct 2010

5. Proton 8 An example of Experimental 13C NMR Spectra The CMR image enlarged view S Aravamudhan WMBS NEHU 25-29 Oct 2010

6. Is it possible to identify these NMR spectra as belonging to any of the spectra obtainable for GLYCINE in several of the variable conditions in a BIOLOGICAL environment? This question again has to be first of all addressed to the chemical conditions like pH and solvent nature to find out whether it is possible to get a set of spectra in the same sequence as it occurs in the isolated molecule geometry optimization. Since such experimental spectra would have to be acquired under variety of conditions (mostly in low concentration solution of glycine), it may not be immediate that a conclusion for generalizing can be found. The spectral data from the currently available NMR data base are not adequate and it is necessary to alter the experimental conditions with the specific target of obtaining a particular spectral pattern as obtained by the theoretical calculation. A typical data base documentation of Experimental PMR spectrum of Glycine A correlation of the theoretical scales and experimental scales for chemical shifts Computed and Experimental 13C NMR spectra S Aravamudhan WMBS NEHU 25-29 Oct 2010