Solvation model induced structural changes in peptides. A quantum chemical study on Ramachandran surfaces and conformers of alanine diamide using the polarizable continuum model

Journal of Computational Chemistry
Ilona HudákyAndrás Perczel

Abstract

Potential energy surfaces of the model peptide HCO-L-Ala-NH2 were calculated using polarizable continuum model (PCM) for the description of aqueous solution at RHF/3-21G, RHF/6-31+G(d), and B3LYP/6-31+G(d) levels of theory. Energy minima were optimized at all three levels as well as at B3LYP/PCM/6-311++G(d,p) level of theory. Results were correlated to experimental data of protein structures retrieved from PDB SELECT. It is concluded that alanine residues of proteins are modeled better by PCM results than by gas-phase calculations on the alanine diamide model (frequently called alanine dipeptide model). The currently available version of the PCM model implemented in Gaussian 03 provides a reasonable alternative to anticipate solvation effects without the computational costs of introducing explicit solvent molecules into the model system. Frequencies calculated at RHF/PCM/6-31+G(d) and B3LYP/PCM/6-31+G(d) levels of theory show high correlation; thus, RHF results have their own merit.

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Citations

May 11, 2006·Chemical Reviews·Ninad Prabhu, Kim Sharp
Dec 23, 2015·Journal of Chemical Theory and Computation·Jakub Kaminsky, Frank Jensen
Sep 27, 2007·Proteins·Ilona Hudáky, András Perczel
Oct 13, 2011·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Giuseppe LanzaGianluigi Broggini
Feb 14, 2012·Biopolymers·Aneta BuczekMałgorzata A Broda
Nov 18, 2017·Journal of Computer-aided Molecular Design·Michio IwaokaHiroshi Hirota
Nov 28, 2009·Journal of Computer-aided Molecular Design·Asmund RinnanSøren Balling Engelsen
Apr 12, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Ilia A Solov'yovWalter Greiner
Sep 1, 2007·Journal of Chemical Theory and Computation·Jakub Kaminský, Frank Jensen
Jan 8, 2011·The Journal of Physical Chemistry. B·Guillem Revilla-LópezCarlos Alemán
Jul 21, 2006·The Journal of Physical Chemistry. B·Michio IwaokaNaoki Kimura
Oct 13, 2006·Inorganic Chemistry·Eva-Stina Riihimäki, Lars Kloo

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