𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Energy decomposition in molecular complexes: Implications for the treatment of polarization in molecular simulations

✍ Scribed by Carles Curutchet; Josep María Bofill; Begoña Hernández; Modesto Orozco; F. Javier Luque


Publisher
John Wiley and Sons
Year
2003
Tongue
English
Weight
154 KB
Volume
24
Category
Article
ISSN
0192-8651

No coin nor oath required. For personal study only.

✦ Synopsis


Abstract

This study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura–Morokuma (KM) energy decomposition analysis at the HF/6‐31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1263–1275, 2003


📜 SIMILAR VOLUMES


Study of the electrostatics treatment in
✍ Robert Garemyr; Arne Elofsson 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 355 KB 👁 3 views

This article considers the treatment of long-range interactions in molecular dynamics simulations. We investigate the effects of using different cutoff distances, constant versus distancedependent dielectric, and different smoothing methods. In contrast to findings of earlier studies, we find that i

Simulated folding in polypeptides of div
✍ Vibin Ramakrishnan; Ranjit Ranbhor; Susheel Durani 📂 Article 📅 2005 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 393 KB 👁 1 views

## Abstract Stereochemistry could be a powerful variable for conformational tune up of polypeptides for de novo design. It may be also useful probe of possible role of interamide energetics in selection and stabilization of conformation. The homopolypeptides Ac–Xxx~30~–NHMe, with Xxx = Ala, Val, an

Variation in the nrDNA ITS of Pinus Subs
✍ David S. Gernandt; Aaron Liston; Daniel Piñero 📂 Article 📅 2001 🏛 Elsevier Science 🌐 English ⚖ 215 KB

The pinyon pines (Pinus subsection Cembroides), distributed in semiarid regions of the western United States and Mexico, include a mixture of relictual and more recently evolved taxa. To investigate relationships among the pinyons, we screened and partially sequenced 3000-bp clones of the nuclear ri