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Frank Jensen

Comprehensive Analysis of Energy Minima of the 20 Natural Amino Acids

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  • Yongna Yuan, University of Manchester, United Kingdom
  • Matthew J. L. Mills, University of Manchester, United Kingdom
  • Paul L. A. Popelier, University of Manchester, United Kingdom
  • Frank Jensen
Energy minima of the 20 natural amino acids (capped by a peptide bond at both the N and the C termini, CH3-C(=O)-N(H)-(H)C-alpha(R)-C(=O)-N(H)-CH3), were obtained by ab initio geometry optimization. Starting with a large number of minima, quickly generated by MarvinView, geometry optimization at the HF/6-31G(d,p) level of theory reduced the number of minima, followed by further optimization at the B3LYP/apc-1 and MP2/cc-pVDZ levels, which caused some minima to disappear and some stable minima to migrate on the Ramachandran map. There is a relation between the number of minima and the size and the flexibility of the side chain. The energy minima of the 20 amino acids are mainly located in the regions of beta(L), gamma(L), delta(L), and ?L of the Ramachandran map. Multipole moments of atoms occurring in the fragment [-NH-C-alpha-C(=O)-] common to all 20 amino acids were calculated at the three levels of theory mentioned above. The near parallelism in behavior of these moments between levels of theory is beneficial toward estimating moments with the more expensive B3LYP and MP2 methods from data calculated with the cheaper HF method. Finally, we explored the transferability of properties between different amino acids: the bond length and angles of the common fragment [-NH-C-alpha(H alpha C beta)-C'(=O)-] in all amino acids except Gly and Pro. All bond lengths are highly transferable between different amino acids, and the standard deviations are small.
Original languageEnglish
JournalJournal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory
Volume118
Issue36
Pages (from-to)7876-7891
Number of pages16
ISSN1089-5639
DOIs
Publication statusPublished - Sep 2014

    Research areas

  • ATOMS-IN-MOLECULES, POLARIZABLE MULTIPOLAR ELECTROSTATICS, FULL CONFORMATIONAL SPACE, SIDE-CHAIN CONFORMATIONS, GAS-PHASE CONFORMATIONS, EXPLORATORY AB-INITIO, PEPTIDE MODELS, N-METHYLAMIDE, TOPOLOGICAL ATOMS, BACKBONE CONFORMATIONS

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