Accelerating the Calculation of Solute-Solvent Interaction Energies through Systematic Molecular Fragmentation

Collins Michael A.; Ho Junmin

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Accelerating the Calculation of Solute-Solvent Interaction Energies through Systematic Molecular Fragmentation

机译：通过系统分子破碎加速溶质溶剂相互作用能量的计算

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The method of systematic molecular fragmentation by annihilation (SMFA) is modified to apply to the interaction energy between a solute and solvent, where the solute is a pair of reacting molecules. For NH3 + CH3Cl as the solute, it is shown that SMFA can estimate (to chemical accuracy) the average binding energy of the solute in large water clusters containing up to 160 water molecules, at an appropriate level of electronic structure theory. The SMFA calculation can be carried out in a computation time that makes it feasible to estimate the solvation contribution to free energies of activation and reaction by ensemble averaging.

机译：通过湮灭（SMFA）进行系统分子破碎的方法，以适用于溶质和溶剂之间的相互作用能量，其中溶质是一对反应分子。对于NH 3 + CH3CL作为溶质，表明SMFA可以在适当的电子结构理论的适当水平的电子结构理论中估计（化学精度）估计（化学精度）在含有高达160个水分子的大型水簇中溶质的平均结合能。 SMFA计算可以在计算时间中进行，这使得可以通过集合平均来估计对激活和反应的自由能量的溶剂化贡献。

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《The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory》 |2019年第39期|共9页
作者
Collins Michael A.; Ho Junmin;
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Australian Natl Univ Res Sch Chem Canberra ACT 2601 Australia;

Univ New South Wales Sch Chem Sydney NSW 2052 Australia;

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正文语种 eng
中图分类物理化学（理论化学）、化学物理学;
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1. Accelerating the Calculation of Solute-Solvent Interaction Energies through Systematic Molecular Fragmentation [J] . Collins Michael A., Ho Junmin The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory . 2019,第39期

机译：通过系统分子破碎加速溶质溶剂相互作用能量的计算
2. Identifying the Interaction of Vancomycin With Novel pH-Responsive Lipids as Antibacterial Biomaterials Via Accelerated Molecular Dynamics and Binding Free Energy Calculations [J] . Shaimaa Ahmed, Suresh B. Vepuri, Mahantesh Jadhav, Cell biochemistry and biophysics . 2018,第1a2期

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3. Computational study on the interaction between CCR5 and HIV-1 entry inhibitor maraviroc: insight from accelerated molecular dynamics simulation and free energy calculation [J] . Qifeng Bai, Yang Zhang, Xiaomeng Li Physical chemistry chemical physics: PCCP . 2014,第44期

机译：CCR5和HIV-1进入抑制剂Maraviroc之间相互作用的计算研究：加速分子动力学模拟和自由能计算的洞察
4. Analysis of the Interactions between the N-terminal Peptide of gp41 and T20 Using Molecular Dynamics and Free Energy Calculations [C] . Jian Jun Tan, Ming Li, Zhang Xiao Yi, The 3rd International Conference on Bioinformatics and Biomedical Engineering(iCBBE 2009)(第三届生物信息与生物医学工程国际会议）论文集 . 2009

机译：使用分子动力学和自由能计算分析gp41 N末端肽与T20之间的相互作用
5. Improvements and Applications of Alchemical Free Energy, Constant pH and Accelerated Molecular Dynamics Calculations in the AMBER Molecular Dynamics Suite [D] . Mermelstein, Daniel Janson. 2018

机译：AMBER分子动力学套件中的炼金术自由能，恒定pH和加速分子动力学计算的改进和应用
6. Molecular Recognition in a Diverse Set of Protein-Ligand Interactions Studied with Molecular Dynamics Simulations and End-Point Free Energy Calculations [O] . Bo Wang, Liwei Li, Thomas D. Hurley, -1

机译：用分子动力学模拟和终点自由能计算研究蛋白质-配体相互作用的不同集合中的分子识别
7. Accurate treatment of nonbonded interactions within systematic molecular fragmentation [O] . Matthew A. Addicoat, Michael A. Collins 2009

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Accelerating the Calculation of Solute-Solvent Interaction Energies through Systematic Molecular Fragmentation

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