✦ LIBER ✦

Multipole electrostatics in hydration free energy calculations

✍ Scribed by Yue Shi; Chuanjie Wu; Jay W. Ponder; Pengyu Ren

Publisher: John Wiley and Sons
Year: 2010
Tongue: English
Weight: 241 KB
Volume: 32
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.21681

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

Hydration free energy (HFE) is generally used for evaluating molecular solubility, which is an important property for pharmaceutical and chemical engineering processes. Accurately predicting HFE is also recognized as one fundamental capability of molecular mechanics force field. Here, we present a systematic investigation on HFE calculations with AMOEBA polarizable force field at various parameterization and simulation conditions. The HFEs of seven small organic molecules have been obtained alchemically using the Bennett Acceptance Ratio method. We have compared two approaches to derive the atomic multipoles from quantum mechanical calculations: one directly from the new distributed multipole analysis and the other involving fitting to the electrostatic potential around the molecules. Wave functions solved at the MP2 level with four basis sets (6‐311G*, 6‐311++G(2d,2p), cc‐pVTZ, and aug‐cc‐pVTZ) are used to derive the atomic multipoles. HFEs from all four basis sets show a reasonable agreement with experimental data (root mean square error 0.63 kcal/mol for aug‐cc‐pVTZ). We conclude that aug‐cc‐pVTZ gives the best performance when used with AMOEBA, and 6‐311++G(2d,2p) is comparable but more efficient for larger systems. The results suggest that the inclusion of diffuse basis functions is important for capturing intermolecular interactions. The effect of long‐range correction to van der Waals interaction on the hydration free energies is about 0.1 kcal/mol when the cutoff is 12Å, and increases linearly with the number of atoms in the solute/ligand. In addition, we also discussed the results from a hybrid approach that combines polarizable solute with fixed‐charge water in the HFE calculation. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

📜 SIMILAR VOLUMES

Hydration free energy calculations by th

Hydration free energy calculations by the acceptance ratio method

✍ Minoru Saito; Haruki Nakamura 📂 Article 📅 1990 🏛 John Wiley and Sons 🌐 English ⚖ 514 KB

The hydration energy difference between the alanine and glycine zwitter ions was calculated by both the free energy perturbation method and the acceptance ratio method. The calculations were carried out by using different increments of the mutation parameter A , A h = -0.05, -0.10, and -0.20. The fr

Generalized linear response method: Appl

Generalized linear response method: Application to hydration free energy calculations

✍ Chen, Xin; Tropsha, Alexander 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 210 KB 👁 1 views

A generalized linear response GLR method was developed and applied to hydration free energy calculations. According to this method, the atomic hydration can be described as a two-step process. In the first step a point particle is introduced into water, which, according to the scaled particle theory

Gaussian multipoles in practice: Electro

Gaussian multipoles in practice: Electrostatic energies for intermolecular potentials

✍ Richard J. Wheatley; John B. O. Mitchell 📂 Article 📅 1994 🏛 John Wiley and Sons 🌐 English ⚖ 974 KB

## Abstract A method is presented for calculating the total electrostatic interaction energies between molecules from __ab initio__ monomer wave functions. This approach differs from existing methods, such as Stone's distributed multipole analysis (DMA), in including the short‐range penetration ene

Free energies of hydration using restrai

Free energies of hydration using restrained electrostatic potential derived charges via free energy perturbations and linear response

✍ Henchman, Richard H.; Essex, Jonathan W. 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 205 KB 👁 1 views

To determine the reliability of the restrained electrostatic potential Ž . derived REPD charge method described in a companion article, the free energies of hydration of 22 simple organic molecules were calculated using free energy perturbations and linear response theory. Of the four charge sets ex

Calculation of electrostatic interaction

Calculation of electrostatic interaction energies in molecular dimers from atomic multipole moments obtained by different methods of electron density partitioning

✍ Anatoliy Volkov; Philip Coppens 📂 Article 📅 2004 🏛 John Wiley and Sons 🌐 English ⚖ 695 KB

## Abstract Accurate and fast evaluation of electrostatic interactions in molecular systems is still one of the most challenging tasks in the rapidly advancing field of macromolecular chemistry, including molecular recognition, protein modeling and drug design. One of the most convenient and accura

Free energy calculations involving NH4+

Free energy calculations involving NH4+ in water

✍ Stéphane Boudon; Georges Wipff 📂 Article 📅 1991 🏛 John Wiley and Sons 🌐 English ⚖ 845 KB

The analysis of the hydration of NH4+ and the estimation of relative or absolute free energies of hydration by means of Monte Carlo computer simulations using different 1-6-12 potential fcnctions is reported. Two electrostatic representations of NH,+ (used respectively by W. L. Jorgensen and P. A. K