A Molecular Mechanics Model for Flavins

Flavin containing molecules form a group of important cofactors that assist a wide range of enzymatic reactions. Flavins use the redox-active isoalloxazine system, which is capable of one- and two-electron transfer reactions and can exist in several protonation states. In this work, molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field were derived for biologically important flavins, including riboflavin, flavin mononucleotide, and flavin adenine dinucleotide. The model was developed for important protonation and redox states of the isoalloxazine group. The partial charges were derived using the CHARMM force field parametrization strategy, where quantum mechanics water–solute interactions are used to target optimization. In addition to monohydrate energies and geometries, electrostatic potential around the compound was used to provide additional restraints during the charge optimization. Taking into account the importance of flavin-containing molecules special attention was given to the quality of bonded terms. All bonded terms, including stiff terms and torsion angle parameters, were parametrized using exhaustive potential energy surface scans. In particular, the model reproduces well the butterfly motion of isoalloxazine in the oxidized and reduced forms as predicted by quantum mechanics in gas phase. The model quality is illustrated by simulations of four flavoproteins. Overall, the presented molecular mechanics model will be of utility to model flavin cofactors in different redox states. © 2019 Wiley Periodicals, Inc.     

A Molecular Mechanics Energy Partitioning Software for Biomolecular Systems

The partitioning of the molecular mechanics (MM) energy in calculations involving biomolecular systems is important to identify the source of major stabilizing interactions, e.g., in ligand–protein interactions, or to identify residues with considerable contributions in hybrid multiscale calculations, i.e., quantum mechanics/molecular mechanics (QM/MM). Here, we describe Energy Split, a software program to calculate MM energy partitioning considering the AMBER Hamiltonian and parameters. Energy Split includes a graphical interface plugin for VMD to facilitate the selection of atoms and molecules belonging to each part of the system. Energy Split is freely available at or can be easily installed through the VMD Store.     

量子力学和分子力学组合方法

量子力学和分子力学(QM/MM)组合方法结合了量子力学的精确性和分子力学的高效性,在研究凝聚态中的化学反应及生物大分子的结构和活性等方面发挥着重要作用。本文主要介绍了QM/MM组合方法的基本原理及国内外有关QM/MM组合方法的研究进展。     

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules

An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 ?. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.     

聚合物银纹化的分子机理

本文综述了近年来有关聚合物银纹化分子机理方面研究的进展情况。内容包括银纹的起源、生长、断裂过程以及各种结构关系对银纹的影响，并对几种典型的聚合物银纹形态进行了描述。     

Molecular Mechanics Study of Organophosphorus Compounds

Abstract

Molecular Mechanics calculation (Allinger's force field and MM2 1985 program) was successfully applied for the structure-reactivity studies of organophosphorus compounds in our laboratory.     

Molecular Mechanics Study on Asymmetry Catalysis

Theasymmetrycatalysisisanimportantchemicalreactionwidelyusedinbiology,pharmacyalldagriculture.Itispreferredtoenantioselectivehydrogenationofmethylpyruvate(MP)oversuppoFtedplatiniumnanoclusters.Cinchonidine(CD)isamodifier,aco-catalysttothereaction.Withoutthemodifier,therewouldbenoenantioselectivitytothehydrogenationofpyruvate.Inordertoobtainbetterunderstandingofthemechanismofthereaction,especiallytheroleofthemoditler,thepresentstudybymolecularmodelinghasbeenperformedandtheresultsarereportedhe…     

分子力学计算的参数化过程

介绍了如何通过设计模型分子构造参数的方法和过程：首先设计模型分子；在平衡位置附近选择几个点，对模型分子进行分子力学和量子化学的计算；计算出量子化学能量Eqm和分子力学能量Emm的差值；然后对结构参数（健长，键角，二面角）和能量差值进行拟合，得拟合曲线的方程，从方程的系数可求出参数．文章给出了一些实例．     

A Study of a Molecular Mechanics Field Used in Simulating Enantiorecognition

Enantiorecognitionisameasureofthediscriminationabilitybetweenenantiomericmolecules.Itisoffundamentalsignificanceinmanyareasofthechemicalandbiologicalsciences,italsoplaysanimportantroleinseparationofenantiomersbychromatography.Althoughtheintermolecularforces(hydrogenbonding,multipolarassociation,dispersionforces,chargetransfercomplexation,hydrophobicassociation.etc.)havebeenthoroughlystudiedandarewelldocumented,buthowtheseforcespreciselyworkinconcerttopromoteintermolecularactionisnotclearyet'.T…     

一种非西他滨的合成方法

非西他滨(Fiacitabine,FIAC)是一种嘧啶核苷类似物,具有抗各种疱疹病毒的活性。本文以2-脱氧-2-氟-三苯甲酰基-α-D-阿拉伯呋喃糖为原料,常温条件下,经过溴化氢醋酸溶液溴化得到2-脱氧-2-氟-三苯甲酰基-α-D-溴化阿拉伯呋喃糖(4);再以胞嘧啶为原料经过碘化、Bz-保护得到N-(5-碘-2-氧代-1,2-二氢嘧啶-4-基)苯甲酰胺(5),最后中间体4和5反应后脱保护基得到非西他滨。整条路线反应原料廉价,反应步骤少,选择性高,总收率高达43%。     

A New Method for Studying Foaminess

A new method is proposed for studying the foaminess of surfactant solutions. The method is based on the determination of the stability of the foam monolayer in contact with the solution surface. Data on the foaminess of an aqueous sodium dodecyl sulfate solution are reported.     

香豆素类化合物的一种新合成方法

香豆素类化合物是一类重要的有生物活性的天然产物,也可用作香料、阻凝剂和三线态光敏剂。用 Meldrum 酸合成该类化合物,已有一些报道。我们在研究 Meldrum 酸系列     

Quantum Mechanics/Molecular Mechanics Simulations Show Saccharide Distortion is Required for Reaction in Hen Egg-White Lysozyme

Hybrid quantum mechanics/molecular mechanics (QM/MM) calculations on lysozyme show significant distortion of the bound saccharide is required to facilitate the catalytic reaction.     

杯芳烃构象的分子力学研究

杯芳烃是对位取代的苯酚与甲醛反应得到的环状缩合物,由于其独特的结构和易于衍生化的特点而受到广泛的关注［１］．杯芳烃中苯酚单元由亚甲基相连,由于酚羟基端可经杯中央翻转而产生多种构象异构体．杯［４］芳烃有４种典型构象：杯式、部分杯式、１,２－交替式和１,...     

分子力学在有机化学中的应用

本文评述了近年来分子力学在有机化学中的应用,特别是在有机化学反应和核磁共振中的应用。     

一种推求双原子分子电子谱项的方法

本文在原子光谱项确定的基础上 ,提出了一种简洁、系统的推求双原子分子电子谱项的方法