An efficient method for calculating atomic charges of peptides and proteins from electronic populations.

The Journal of Physical Chemistry. B
Young Kee Kang, Harold A Scheraga

Abstract

An efficient method is presented to calculate atomic charges of peptides and proteins derived from Mulliken electronic populations for terminally blocked amino acids (Ac-X-NHMe, X = any neutral or charged residue) calculated at the B3LYP/6-31G(d,p)//HF/6-31G(d,p) level of theory. This electronic population-derived atomic charges (EPAC) method is based on the geometry-dependent atomic charge (GDAC) method proposed by Cho et al. (J. Phys. Chem. B 2001, 105, 3624), in which atomic charges are calculated by using the partial equalization of atomic electronegativities with electronegativity parameters and damping factors given by interatomic distances between covalently bonded atoms in a molecule. The overall mean absolute difference (mad) and root-mean-square deviation (rmsd) between dipole moments micro(EPAC) and micro(B3LYP), obtained from EPAC charges and from B3LYP/6-31G(d,p) level calculations, respectively, for Ac-X-NHMe are estimated to be 0.38 and 0.59 D, respectively, for 26 representative conformations in the training set, and 0.54 and 0.79 D, respectively, for 172 representative conformations not used for parametrization. For Ac-(Ala)(n)-NHMe (n = 2-6), the EPAC method reasonably predicts the increase of the dipole momen...Continue Reading

References

Feb 1, 1995·Journal of Computer-aided Molecular Design·J W StorerD G Truhlar
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus
Jul 1, 2006·Journal of Chemical Theory and Computation·Qingyi Yang, Kim A Sharp
Jul 1, 2007·Journal of Chemical Theory and Computation·Zhong-Zhi Yang, Bao-Qiu Cui
Apr 1, 1986·Journal of Computational Chemistry·Scott J WeinerDavid A Case

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Citations

Jan 1, 2010·International Journal of Molecular Sciences·Zhiwei YangLijun Zhou
Jul 19, 2012·Biopolymers·Young Kee Kang, Byung Jin Byun
Jul 6, 2018·European Biophysics Journal : EBJ·Khair BuxSyed Tarique Moin
Apr 27, 2018·ACS Omega·Pietro G A AronicaChandra S Verma

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