Efficient solvent boundary potential for hybrid potential simulations.
نویسندگان
چکیده
A common challenge in computational biophysics is to obtain statistical properties similar to those of an infinite bulk system from simulations of a system of finite size. In this work we describe a computationally efficient algorithm for performing hybrid quantum chemical/molecular mechanical (QC/MM) calculations with a solvent boundary potential. The system is partitioned into a QC region within which catalytic reactions occur, a spherical region with explicit solvent that envelops the quantum region and is treated with a MM model, and the surrounding bulk solvent that is treated implicitly by the boundary potential. The latter is constructed to reproduce the solvation free energy of a finite number of atoms embedded inside a low-dielectric sphere with variable radius, and takes into account electrostatic and van der Waals interactions between the implicit solvent and the QC and MM atoms in the central region. The method was implemented in the simulation program pDynamo and tested by examining elementary steps in the reaction mechanisms of two enzymes, citrate synthase and lactate dehydrogenase. Good agreement is found for the energies and geometries of the species along the reaction profiles calculated with the method and those obtained by previous experimental and computational studies. Directions in which the utility of the method can be further improved are discussed.
منابع مشابه
Energy Study at Different Temperatures for Active Site of Azurin in Water, Ethanol, Methanol and Gas Phase by Monte Carlo Simulations
The interaction between the solute and the solsent molecules play a crucial role in understanding the various molecular processes involved in chemistry and biochemistry, so in this work the potential energy of active site of azurin have been calculated in solvent by the Monte Carlo simulation. In this paper we present quantitative results of Monte Carlo calculations of potential energies of ...
متن کاملFinite representation of an infinite bulk system: Solvent boundary potential for computer simulations
An approach is developed to obtain statistical properties similar to those of an infinite bulk system from computer simulations of a finite cluster. A rigorous theoretical formulation is given for the solvent boundary potential which takes the influence of the surrounding bulk into account. The solvent boundary potential is the configuration-dependent solvation free energy of an effective clust...
متن کاملStructure of a tethered polymer under flow using molecular dynamics and hybrid molecular-continuum simulations
We analyse the structure of a single polymer tethered to a solid surface undergoing a Couette flow. We study the problem using molecular dynamics (MD) and hybrid MD-continuum simulations, wherein the polymer and the surrounding solvent are treated via standard MD, and the solvent flow farther away from the polymer is solved by continuum fluid dynamics (CFD). The polymer represents a freely join...
متن کاملOne-pot Synthesis of Amidoalkyl Naphthol Derivatives as Potential Nucleoside Antibiotics and HIV Protease Inhibitors using Nano-SnO2 as an Efficient Catalyst
An efficient three-component one-pot synthesis of 1-amidoalkyl-2-naphthols from 2-naphthol, aldehydes, and acetamide using nano-SnO2as catalyst is described. The reactions were carried out at 80oC under water-solvent media. The structures of the compounds were characterized by IR, 1HNMR, 13C-NMR, and Mass spectra and by elemental analysis. The advantages of the effective meth...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Physical chemistry chemical physics : PCCP
دوره 13 22 شماره
صفحات -
تاریخ انتشار 2011