计算化学和计算材料学项目式实验设计:锂离子电池有机电解液分子动力学模拟

分子动力学模拟已在化学、材料等科研领域得到广泛应用,但在本科化学、材料学实验中鲜有涉及。为培养学生化学、材料计算设计思维,同时帮助学生充分掌握分子动力学模拟方法,基于锂离子电池有机电解液研究案例设计了一个分子动力学模拟综合实验。本实验设计包括分子和溶液结构建模、结构优化、模拟退火、热浴平衡、后处理性质计算等操作步骤,帮助学生初步掌握分子动力学模拟的基本原理、流程和分析方法,实现理论方法水平和软件操作技能的双重提升。     

分子及团簇的分子动力学模拟——介绍一个计算化学实验

分子动力学方法在化学及相关学科研究中的重要地位日趋凸显,但在本科化学实验中鲜有涉及,现有计算化学实验多侧重量子化学方法对分子性质的计算。为普及分子动力学模拟这一有力工具,同时帮助学生理解分子的动态行为,本文以丙氨酸二肽模型分子为例设计了一个简单的分子动力学模拟实验。通过本实验学生能初步掌握分子动力学模拟的基本原理、流程和分析方法,同时加深对物理化学中势能面等抽象概念的理解。本实验即可作为单独设课的计算化学实验的内容,亦可在物理化学实验中作为拓展实验开设。     

室温离子液体的分子动力学模拟

室温离子液体作为一种新型的反应介质正在受到人们的关注,近十年来成为了化学领域的研究热点。随着人们对离子液体结构与性质研究的不断深入和计算方法的快速发展,分子模拟已是研究离子液体的结构和性质的有力工具。本文介绍了分子动力学(molecular dynamics,MD)的基本原理,分子力场的种类,以及离子液体分子动力学模拟一般采用的AMBER、OPLS和CHARMM三种力场的构建形式。综述了近年来纯组分离子液体、混合组分离子液体分子动力学模拟方法研究取得的成果和最新进展,并分析了主要存在的问题。展望了离子液体分子动力学模拟的研究方向和前景,同时还提出了包含极化作用和静电远程作用的离子液体分子动力学模拟研究的基本思路。     

计算(机)化学学科进展(2011-2013)

计算(机)化学已成为化学学科的重要组成部分,在理论计算、分子模拟、数据挖掘以及复杂体系分析中发挥了重要作用。本文总结了近年来化学信息学的研究进展,包括化学信息学方法、软件及数据库技术以及化学信息学在结构、性质、相互作用、反应机理,蛋白质及功能材料的性能研究,复杂体系化学数据分析中的应用。共引用参考文献78篇。     

甲烷化反应机理的蒙特卡罗模拟

甲烷化反应机理的蒙特卡罗模拟郭向云，李永旺，王琴，罗庆云，钟炳（中国科学院山西煤炭化学研究所太原０３０００１）关键词蒙特卡罗方法，模拟，甲烷化机理催化反应机理可用普通动力学模型研究，也可用蒙特卡罗（ＭＣ）模型研究。对于一些比较复杂的催化反应，其动力学...     

改进的半经典动力学模拟二苯乙烯光致顺反异构化反应

发展了一种改进的半经典动力学模拟方法, 并将其程序化用于气相二苯乙烯光致顺反异构化反应的机理研究.新的方法不仅采用e 指数模型改进了原有Zhu-Nakamura 理论中计算电子非绝热跃迁几率的计算方法, 而且将约束哈密顿方法用于限制性分子动力学模拟过程中. 计算结果表明, 采用此方法得到的统计平均的量子产率及反应机理与以前的实验与理论结果吻合较好, 从而可以应用于全量子动力学方法无法进行的大分子体系的动力学研究.     

自组装的分子动力学模拟

简要回顾了近年来国内外分子动力学模拟自组装的研究,对已报道的建模方法、可视化表现以及相关应用略作概述,并以此为基础对自组装过程的分子动力学模拟研究所面临的问题和尚需深入的内容进行了讨论。基于自组装、相变和涨落的固有联系,提出了以研究波动为手段,和以频率相关热容为研究对象的探索方向。希望能够为分子动力学模拟推动自组装研究提供有益的参考。     

基于ReaxFF力场的对硝基苯酚臭氧氧化分子动力学模拟

本文采用基于ReaxFF反应力场的分子动力学方法(ReaxFF MD),利用自主研发的国际首个基于GPU加速的ReaxFF MD程序系统GMD-Reax和独特的化学反应分析工具VARx MD,探索臭氧氧化对硝基苯酚的反应机理。通过模拟考察了300 K恒温条件下臭氧氧化水中对硝基苯酚的行为,获得了酚结构开环、CO_2生成、主要自由基(·OH、·O_2、·O)及团簇型自由基的数量演变趋势,并可定性描述六元环开环和CO_2生成均遵循伪一级反应动力学规律。反应机理分析表明酚类分子在水溶液中被臭氧氧化的路径主要经过攫氢、六元环开环、碳链的氧化分解三个阶段,也揭示了自由基和团簇型自由基在臭氧降解对硝基苯酚时所发挥的重要作用。本工作是应用ReaxFF MD分子模拟方法对常温水环境下臭氧降解酚类污染物反应机理研究的一个尝试,可为深入认识该机理及相关的实验、理论研究提供一定的参考。     

抚顺油页岩干酪根热解反应性分子动力学-量子力学模拟

采用MS（Materials Studio 2017）软件中Forcite模块,对自主构建的抚顺油页岩干酪根二维结构模型进行能量最小化分子动力学模拟,通过能量最优化过程得到干酪根初始优化结构。在此基础上进行分子动力学退火模拟,获得全局能量最优化构型,即油页岩干酪根分子三维结构模型。基于密度泛函理论的量子力学模拟方法,计算分析干酪根三维结构模型的动力学、键能、键级、电荷密度等参数,分析化学活性位点,探讨了干酪根热解微观化学演化机理,进而预测了反应性。     

离子液体的分子模拟与量化计算

分子模拟方法是研究离子液体结构与性质关系非常有效的方法,可以从分子间相互作用出发研究离子液体的微观结构、热力学和动力学性质;量子化学计算则在分子、电子水平上对离子液体的结构、性能及催化机理进行理论研究。本文综述了分子模拟方法应用于离子液体体系的研究进展,重点介绍了利用分子动力学模拟和量子化学计算方法对不同离子液体进行研究,获得离子液体的结构性质、光谱性质(红外光谱、拉曼光谱)及离子液体催化反应机理等,为探讨离子液体结构-性质的关系、离子对的作用方式、催化反应活性中心、反应途径、反应活化能、振动模式和频率以及设计功能性离子液体提供理论导向。     

Molecular simulation of thermophysical properties of aromatic polymers containing oxetane ring in the main chain

Molecular simulation techniques have been applied to newly synthesized aromatic polymers, containing oxetane rings in the main chain, to characterize the shape of rod‐like macromolecules. Single chains and periodic unit cells of a series of aromatic polymers with degree of polymerization 15 were used in the simulations, in accordance with the experimentally obtained one. The total potential energy was minimized and then NVE and NPT molecular dynamics simulations were performed for 1,000 ps at 11 temperatures between 10 and 1,000 K. The coefficient of asymmetry was calculated from the computer‐generated structures. The predictive capability of the NPT molecular dynamics simulation and Polymer Properties modules of Cerius² were used to estimate the orientational properties (order parameter), glass transition temperature, cohesive energy, and decomposition temperature of the polymers simulated. In general, there is a good‐to‐excellent agreement between simulated results and available experimental data of the above investigated properties. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 2334–2352, 1999     

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations

Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used.     

Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study

Using quantum chemistry plus ab initio molecular dynamics and classical molecular dynamics methods, we address the relationship between molecular conformation and the biomedical function of arylamide polymers. Specifically, we have developed new torsional parameters for a class of these polymers and applied them in a study of the interaction between a representative arylamide and one of its biomedical targets, the anticoagulant drug heparin. Our main finding is that the torsional barrier of a C(aromatic)-C(carbonyl) bond increases significantly upon addition of an o-OCH2CH2NH3+ substituent on the benzene ring. Our molecular dynamics studies that are based on the original general AMBER force field (GAFF) and GAFF modified to include our newly developed torsional parameters show that the binding mechanism between the arylamide and heparin is very sensitive to the choice of torsional potentials. Ab initio molecular dynamics simulation of the arylamide independently confirms the degree of flexibility we obtain by classical molecular dynamics when newly developed torsional potentials are used.     

High-temperature decomposition of the cellulose molecule: a stochastic molecular dynamics study

The kinetics and products of cellulose pyrolysis can be studied using large-scale molecular dynamics simulations at high temperatures, where the reaction rates are high enough to make the simulation times practical. We carried out molecular dynamics simulations employing the ReaxFF reactive force field to study the initial step of the thermal decomposition process. We gathered statistics of simulated reactive events at temperatures ranging from 1400 to 2200 K, considering cellulose molecules with different molecular weights and initial conformations. Our simulations suggest that, in gas-phase conditions at these high temperatures, the decomposition occurs primarily through random cleavage of the β(1 → 4)-glycosidic bonds, for which we obtained an activation energy of (171 ± 2) kJ mol^?1 and a frequency factor of \(\left( {1.07 \pm 0.12} \right) \times 10^{15}\) s^?1. We did not observe dependency of the kinetic parameters on the molecular weight or initial conformation. Some of the decomposition reactions involved the release of low-molecular-weight products. Excluding radicals, the most commonly observed species were glycolaldehyde, water, formaldehyde and formic acid. Many of our observations are supported by the existing experimental and theoretical knowledge. We did not, however, observe the formation of levoglucosan, which is the dominant product in conventional pyrolysis experiments at much lower temperatures. This is understandable, since the high temperatures can force the dominance of radical reactions over pericyclic reactions. Nevertheless, our results support further use of ReaxFF-based molecular dynamics simulations in the study of cellulose pyrolysis.     

Polychlorinated polyamides—III. Synthesis and characterization of polyamides derived from perchloroterephthaloyl dichloride

Six new polyamides have been prepared either by polymerization in solution or by interfacial polymerization by reacting perchloroterephthaloyl dichloride with aromatic diamines. The polymers were characterized by i.r. spectroscopy, elemental analysis, DSC, and TGA. The glass transition temperature, the melting temperature, and the thermal decomposition temperature have been determined. In order to estimate the molecular weights, intrinsic viscosities were determined. Some of the polymers showed high thermal stability.     

The Soret effect in dilute polymer solutions: influence of chain length, chain stiffness, and solvent quality

Thermal diffusion in dilute polymer solutions is studied by reverse nonequilibrium molecular dynamics. The polymers are represented by a generic bead-spring model. The influence of the solvent quality on the Soret coefficient is investigated. At constant temperature and monomer fraction, a better solvent quality causes a higher affinity for the polymer to the cold region. This may even go to thermal-diffusion-induced phase separation. The sign of the Soret coefficient changes in a symmetric nonideal binary Lennard-Jones solution when the solvent quality switches from good to poor. The known independence of the thermal diffusion coefficients of the molecular weight is reproduced for three groups of polymers with different chain stiffnesses. The thermal diffusion coefficients reach constant values at chain lengths of around two to three times the persistence length. Moreover, rigid polymers have higher Soret coefficients and thermal diffusion coefficients than more flexible polymers.     

A thermal decomposition study of polymers by tunable synchrotron vacuum ultraviolet photoionization mass spectrometry

The thermal decomposition of polymers (poly(vinyl chloride) (PVC) and polystyrene (PS)) has been studied with synchrotron VUV photoionization mass spectrometry at low pressure. Pyrolysis products formed at different temperatures have been identified by the measurement of photoionization mass spectra at different photon energies. The experimental results demonstrate the variation of the pyrolysis product pool of PVC at different temperatures, dividing the thermal decomposition process into two stages: the low‐temperature stage to form HCl and benzene, and the high‐temperature stage to form numerous large aromatic hydrocarbons. For the thermal decomposition of PS, four reaction categories are determined. This work reports a new application of synchrotron VUV photoionization mass spectrometry in the study of the thermal decomposition of polymers, and demonstrates its good performance in product analysis, which is expected to help understand the thermal decomposition mechanism of PVC, PS and other synthesized polymers. Copyright © 2009 John Wiley & Sons, Ltd.     

Modelling of solid polymers in chemical detail - gases in amorphous polymers

The diffusion of gases in dense polymers, above and below the glass-transition temperature, is described with a new Transition State Theory model that is based on the concept that the dynamics of small molecules dissolved in dense polymers is separated from the structural relaxation of the dense polymers. The model is used to study the dynamics of rare gases dissolved in atomistic micro-structures of four polymers at 300 K: poly(dimethylsiloxane), poly(isobutylene), atactic poly(vinylchloride) and the polycarbonate of 4,4′-isopropylidenediphenol (bisphenol-A). Short-time-scale MD runs (5 ps) are used to characterize the elastic thermal motion of the host matrix; this information on mobility is then used for a stochastic simulation of solute dynamics up to ca. 1ms. All dissolved molecules show similar behavior by displaying three time regimes: a short-time, high-mobility domain, an intermediate time domain of anomalous diffusion, and a diffusive regime at long times. From the long-time data diffusion coefficients are estimated; comparison with experimental data results in good agreement.     

八硝基立方烷高温热分解分子动力学模拟

随着对高能量密度材料的性能要求不断提高,新型高能量密度材料成为近期研究热点,其中八硝基立方烷(ONC)由于其优越的性能成为其中典型的代表,然而关于八硝基立方烷热分解的动力学机理研究比较少。本文采用ReaxFF反应力场模拟高温条件下凝聚相八硝基立方烷初始热分解过程。研究发现热分解过程中八硝基立方烷笼状骨架结构中C-C键最先发生断裂,并逐步破坏形成八硝基环辛烯等,随后出现NO₂和O等,计算结果表明笼状骨架结构的破坏存在三种不同路径。八硝基立方烷在高温条件下热分解的主要产物有NO₂、O₂、CO₂、N₂、NO₃、NO、CNO以及CO等,其中N₂和CO₂是终态产物,不同温度对产物均产生不同程度的影响。     

RDX及其衍生物高温热解的反应分子动力学模拟

本文采用ReaxFF反应分子动力学方法,研究了RDX及其衍生物晶体在高温条件下(2000、2500和3000 K)的热分解机理以及主要产物随时间的变化情况。结果表明:RDX及其衍生物晶体热解的第一步反应均为N―NO_2键断裂生成NO_2分子,随后反应由于六元环上和侧链基团的不同导致侧链脱除或开环反应的顺序不同。在这四种单胞体系热解中,NO_2和NO分子为共同的中间产物,形成之后迅速发生次级反应并最终生成N_2。各体系热解终产物一致,均为N_2、H_2O和CO_2,其中N_2分子数最多,大于20个。由于原始分子结构和组成中C/N比、H/O比的不同,各体系热解后H_2O和CO_2分子数目相差较大。不同温度下,各单胞体系热分解生成的最大含碳团簇中C原子数均较小。在进一步超胞体系的模拟中,RDX和RDX-D2体系生成的含碳团簇中C原子数分别达到约30和16个,远高于单胞模拟,且受温度影响较大;而RDX-D1和RDX-D3单胞或超胞模拟结果相近,均未生成含碳团簇,仅存在小分子含碳碎片。因此,初始分子的结构和元素比对含碳团簇的生成有明显影响。