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Title: Non-planar amino groups: Protein structure database analysis and ab initio quantum chemical studies on model systems
Authors: Bhattacharyya, Dhananjay
Sen, Kakali
Mukherjee, Shayantani
Issue Date: Jan-2006
Publisher: NISCAIR-CSIR, India
Abstract: Hydrogen bond is one of the most important interactions in bio-molecular stability and recognition. Amino groups of nucleotides or amino acid residues act as important hydrogen bond donors in such interactions. The positions of the hydrogen atoms, which determine the directionality of the hydrogen bonds, are generally not available in the PDB entries. Although, such positions are reported in a few crystal structures, analysis of their geometry indicates that in most of them the positions are not thoroughly refined. The pyramidal nature of a few well-refined amino groups, however, indicates that a strong correlation exists between the non-planarity of the amide and the peptide torsion angles. The pyramidal nature of the amino groups might arise due to effect of lone pair electrons at the central nitrogen atoms, which do not take part in extended conjugation. In order to establish the above hypothesis, we have also studied a few amino group containing model systems by ab initio quantum chemical methods, which donate one of their lone pair electrons from nitrogen atoms during photo-induced electron transfer processes. The amino group of the excited state complex, geometry optimized by MCSCF/6-31 G** basis set, is found to have twisted planar geometry and the pyramidal nature is completely lost. This further supports the effect of lone-pair electrons in the vicinity of a conjugated system in amino group non-planarity.
Page(s): 58-67
ISSN: 0975-0975(Online); 0376-4710(Print)
Appears in Collections: IJC-A Vol.45A(01) [January 2006]

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