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用于高效准确的量子力学/分子力学分子动力学、自由能和激发态性质的CHARMM-TURBOMOLE接口。

The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties.

作者信息

Riahi Saleh, Rowley Christopher N

机构信息

Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland, A1B 3X7, Canada.

出版信息

J Comput Chem. 2014 Oct 30;35(28):2076-86. doi: 10.1002/jcc.23716. Epub 2014 Sep 1.

Abstract

The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM-TURBOMOLE is well-suited for extended QM/MM MD simulations using first principles methods with large (triple-ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg(2+) (aq), where the MM outer sphere water molecules are represented using the SWM4-NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg(2+) and Zn(2+) were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time-averaged solution absorption spectrum of indole, the emission spectrum of the indole 1La excited state, and the electronic circular dichroism spectrum of an oxacepham.

摘要

描述了哈佛大学分子力学(CHARMM)中的化学与TURBOMOLE之间的量子力学(QM)/分子力学(MM)接口。CHARMM提供了一系列广泛的模拟算法,如分子动力学(MD)和自由能微扰,并支持成熟的非极化和德鲁德极化力场。TURBOMOLE使用密度泛函理论或波函数方法以及激发态性质进行快速QM计算。CHARMM-TURBOMOLE非常适合使用具有大(三重ζ)基组的第一性原理方法进行扩展QM/MM MD模拟。我们通过对Mg(2+)(水溶液)的QM/MM模拟展示了这些能力,其中MM外层水分子使用SWM4-NDP德鲁德极化力场表示,离子和内配位球使用QM PBE、PBE0和MP2方法表示。使用热力学积分计算了Mg(2+)和Zn(2+)的相对溶剂化自由能。我们还展示了激发态性质的特征。我们计算了吲哚的时间平均溶液吸收光谱、吲哚1La激发态的发射光谱以及氧头孢菌素的电子圆二色光谱。

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