分子模拟方法在聚合物性质研究中的应用

综述了四种常用的分子模拟方法:即量子力学方法、分子力学方法、蒙特卡洛方法和分子动力学方法在聚合物性质研究中的应用。四种方法各有优势,共同与计算机模拟成为密不可分的组成部分。     

并行计算在分子模拟中的应用

简要介绍了并行计算机的发展背景,结合网络中心搭建的Linux cluster并行机说明了此类并行机的基本架 构。对三款常用的并行分子模拟软件进行了评述,比较了不同架构并行机的运行效率。对其中一款软件在此并行 机上进行了实测,并对并行机和分子模拟软件的发展进行了合理的预测。     

分子模拟在聚合物膜研究中的应用

简要回顾了近15年来分子模拟在各种聚合物膜研究中的应用,分析了它为宏观实验现象提供的新解释以及给聚合物膜的改性和设计研究工作带来的新思路,同时也对当前计算条件下模拟中存在的问题进行了探讨。     

分子模拟技术在气体膜分离研究中的应用

回顾了分子模拟技术在气体膜分离领域的应用，介绍了各种模拟方法的特点，阐述了具体的应用范围、存在的问题及发展趋势。表明分子模拟在定性分析气体与膜材料的亲和性、预测渗透系数和分离因子方面有一定价值，但离定量预测和分析还有一定距离，非平衡分子动力学是适用于气体膜分离研究的方法，其研究还处于初期阶段。     

定量构效关系在化合物性质研究中的应用

概述了定量构效关系（QSPR/QSAR）的基本原理以及定量构效关系在化合物性质研究中的应用,重点介绍了定量构效关系在化合物毒性、水溶性和LogPow等方面的应用。     

分子模拟参数在三维定量构效关系（3D—QSAR）中的应用

分子是否相似,这在很早以前已成为设计生物活性物质及考虑结构变化时的一个重要依据。以天然物质及现有的活性化合物为先导物,从中寻求新的类似物,此即为众所周知并广泛应用的模拟合成。“相似的化合物显示相似的活性”,以此为前提进行新化合物的合成亦取得不少成果。然而在这里,认识生物体分子及其类似性则至关重要,人们从结构式所设想的类似性往往并非一致。从传统的生物等价性(bioisosterism)考虑,由对生物方面相似性的认识而积累的有关经验来指导医药、农药的合成无疑是一个方向,但还难以达到定性的标准。     

分子模拟在化工应用中的若干问题及思考

随着高技术学科的飞速进步,化工学科在多年来已形成的理论和实验研究之外,又产生了一种完全独立而新颖的研究手段——分子模拟.目前化学工业受关注的新技术涉及聚合物、电解质等复杂物质,临界、超临界等复杂状态,界面、膜、溶液等复杂现象.实现化学工业从产品到过程设计完全自动化,在这些方面除了准确的物性数据外,更要对各种复杂现象的机理有深刻了解.分子模拟被认为是实现这一目标的关键技术之一.本文以分子动力学为主,结合计算量子化学,对分子模拟在化工应用中的若干问题进行讨论.     

分子模拟技术在分子筛的吸附扩散研究中的应用

二分子模拟是近年发展起来的一门新兴计算化学技术.简要介绍了分子模拟技术的基本原理及其优点和缺点,重点阐述了分子模拟中的Monte Carlo分子模拟和分子动力学模拟两种方法及其在分子筛的吸附扩散研究中的应用.同时介绍了这两种组合方法的应用,最后展望了分子模拟技术的发展方向.     

分子模拟在纳米材料改性聚合物中的应用

介绍了近年来国内外分子模拟研究纳米改性聚合物材料的部分工作,主要包括纳米材料的结构模拟,力学性能的模拟,改性剂相互作用的模拟以及聚合物基纳米复合材料界面作用的模拟。     

分子模拟在分子印迹技术中的应用

分子模拟是近年来发展起来的一门新兴的计算化学技术.它在辅助物质设计和分子结构理解方面取得的显著成绩使得它在其他领域中有着越来越广泛的应用.综述了分子模拟在分子印迹技术中的应用.     

Towards more realistic computational modeling of homogenous catalysis by density functional theory: combined QM/MM and ab initio molecular dynamics

The combined quantum mechanics/molecular mechanics (QM/MM) and the ab initio molecular dynamics methods (AIMD) are fast emerging as viable computational molecular modeling tools. Both methods allow for the incorporation of effects that are often ignored in high level calculations, but may be critical to the real chemistry of the simulated system. In the combined QM/MM method part of the system, say the active site, is treated quantum mechanically whereas the remainder of the system is treated with a faster molecular mechanics force field. This allows high level calculations to be performed where the effects of the environment are incorporated in a computationally tractable manner. With the ab initio molecular dynamics methods, the system is simulated at a finite temperature with no empirical force field. Rather, the forces at each time step are determined with a full electronic structure calculation at the density functional level. Thus, simulations of chemical reactions can be performed where finite temperature effects are realistically represented. In this paper a brief introduction to both methods is given. The methods are further demonstrated with specific applications to modeling homogenous catalytic processes at the molecular level. These applications are our latest efforts to build more realistic computational models of catalytic systems at the density functional level.     

基于分子动力学的橡胶聚合物计算机辅助设计方法

聚合物分子设计的关键步骤是得到能够满足多种性质要求的重复单元结构。作为化学产品工程中的新型发展手段，计算机辅助分子设计(CAMD)技术可以通过基团贡献法生成满足约束条件的聚合物重复单元结构，分子动力学(MD)技术则可以在微观层面上进行计算机实验模拟系统性质。建立了聚合物的CAMD-MD通用设计方法，并进行轮胎橡胶聚合物的分子设计，首先基于基团贡献法进行重复单元的设计；其次，利用层次分析法确定多性质权重排名，并基于分子动力学方法探究候选结构的性质；最后将方法应用于实际橡胶结构中，模拟得到聚能密度、密度、玻璃化转换温度和热导率性质，验证了方法的可行性。     

基于分子动力学模拟的轮胎橡胶催化热解制氢机理

采用分子动力学模拟方法,选取Ni、ZSM-5以及Ni/ZSM-5催化剂,对轮胎橡胶热解制氢的机理进行探究,并同时与前人做过的实验研究进行对比验证模拟计算。文中利用Material Studio建立轮胎橡胶模型,DMol3模块对生成氢气路径进行过渡态搜索,CULP模块对其加入Ni催化剂的热解过程进行模拟。模拟结果表明,制氢催化效果顺序为Ni>Ni/ZSM-5>ZSM-5。催化热解大致分为两个阶段：①低温阶段长链裂解成单体化合物,单体主要是异戊二烯、苯乙烯以及1,3-丁二烯;②高温阶段自由基攻击单体生成小分子物质。加入Ni催化剂后降低了热解终止温度。催化剂的加入在低温阶段主要表现在加快热解进程,增加低温阶段时单体数量。在高温阶段主要表现在改变了气体产物分布,Ni的加入降低了轮胎热解温度,并且使氢比例增加。     

Effects of decabromodiphenyl ethane flame retardant on the combustion behavior and physical-mechanical properties of chloroprene rubber: Experimental and molecular dynamic simulation

Herein, a molecular dynamics simulation method was used to predict the compatibility of chloroprene rubber (CR) and decabromodiphenyl ethane (DBDPE) and to investigate the mechanical properties of CR-based composites. The limiting oxygen index and cone calorimeter measurement values indicated that the addition of DBDPE was beneficial for reducing the peak heat release rate during combustion and facilitating the formation of compact and strong char layers for carbon black-filled CR composites, resulting in efficient reduction of flammability and fire risk. Incorporation of DBDPE obviously delayed the dehydrochlorination of the CR matrix. Moreover, adding 50 phr DBDPE had little effect on the tensile strength and elongation at the break, and increased the modulus at 100% elongation by 64.3% in contrast to CR without DBDPE. However, the cold properties of CR vulcanizates decreased slightly with an increase in the DBDPE content.     

分子模拟方法在渗透汽化膜研究中的应用进展

综述了分子模拟在渗透汽化无机膜、聚合物膜及有机-无机复合膜研究中的应用。分析了对宏观实验现象提供的微观解释。探讨了模拟研究中存在的问题,并对分子模拟在渗透汽化膜研究中的前景进行了展望。     

醇类有机物热传导的分子动力学模拟及微观机理研究

传热是化工生产的基本问题之一,热导率是化工产品生产工艺设计中一类重要的热力学数据。通过非平衡分子动力学方法模拟了8种液态醇类有机物在不同温度下的导热过程。热导率计算值与实验值的平均相对偏差为3.77%。通过对热流的分解发现,分子动能、分子间库仑相互作用和分子内的二面角对醇类有机物的热传导影响较大。同时随着分子链增长,通过分子内相互作用进行的热传导逐渐占主导作用,表明醇类有机物的热能传输机理与分子结构有显著关系。此外,随着温度的升高,通过分子的动能、分子间库仑作用和分子内键角、键伸缩作用项传输的热流增大,表明温度对液态醇类有机物的热传导也有一定影响。本工作从微观分子间和分子内作用分析了液态醇类有机物结构和温度对热导率的影响,为液态有机物的热传导研究提供了微观依据。     

Molecular dynamics simulation and mechanism study on thermal conductivity of alcohols

Heat transfer is one of the basic issues in chemical production, and thermal conductivity is an important thermodynamic data in the design of chemical product production processes. In this paper, nonequilibrium molecular dynamics methods are used to simulate the heat transfer of liquid alcohols at four different temperatures, and the thermal conductivity of the corresponding conditions is obtained. The average relative deviation between the calculated value and the experimental value was 3.77%. Through the decomposition of heat flux, it was found that molecular kinetic energy, Coulomb interaction and intramolecular dihedral angle contribute the most to the heat conduction of alcohols. At the same time, as the molecular volume increases, the thermal conduction pathway of the intramolecular interaction term gradually dominates, indicating that the thermal conduction mechanism of alcohols has a significant relationship with the molecular structure. In addition, as the temperature elevates, the heat flux transmitted through the molecular kinetic energy, intermolecular Coulomb interaction, and the intramolecular angle bending and bond stretching term increases, while the heat flux transmitted through the molecular potential energy decreases significantly. This work provides a microscopic explanation for the effects of the structure and temperature of liquid alcohols on thermal conductivity, and provides a micro foundation for the study of heat conduction of liquid alcohols.     

Evolution of Ceftriaxone Resistance of Penicillin-Binding Proteins 2 Revealed by Molecular Modeling

Penicillin-binding proteins 2 (PBP2) are critically important enzymes in the formation of the bacterial cell wall. Inhibition of PBP2 is utilized in the treatment of various diseases, including gonorrhea. Ceftriaxone is the only drug used to treat gonorrhea currently, and recent growth in PBP2 resistance to this antibiotic is a serious threat to human health. Our study reveals mechanistic aspects of the inhibition reaction of PBP2 from the wild-type FA19 strain and mutant 35/02 and H041 strains of Neisseria Gonorrhoeae by ceftriaxone. QM(PBE0-D3/6-31G**)/MM MD simulations show that the reaction mechanism for the wild-type PBP2 consists of three elementary steps including nucleophilic attack, C–N bond cleavage in the β-lactam ring and elimination of the leaving group in ceftriaxone. In PBP2 from the mutant strains, the second and third steps occur simultaneously. For all considered systems, the acylation rate is determined by the energy barrier of the first step that increases in the order of PBP2 from FA19, 35/02 and H041 strains. Dynamic behavior of ES complexes is analyzed using geometry and electron density features including Fukui electrophilicity index and Laplacian of electron density maps. It reveals that more efficient activation of the carbonyl group of the antibiotic leads to the lower energy barrier of nucleophilic attack and larger stabilization of the first reaction intermediate. Dynamical network analysis of MD trajectories explains the differences in ceftriaxone binding affinity: in PBP2 from the wild-type strain, the β₃-β₄ loop conformation facilitates substrate binding, whereas in PBP2 from the mutant strains, it exists in the conformation that is unfavorable for complex formation. Thus, we clarify that the experimentally observed decrease in the second-order rate constant of acylation (k₂/K_S) in PBP2 from the mutant strains is due to both a decrease in the acylation rate constant k₂ and an increase in the dissociation constant K_S.