核糖核酸酶Sa表面水和尿素分子的分布和动力学行为的分子动力学模拟

利用分子动力学模拟研究了在不同尿素浓度下,核糖核酸酶Sa(RNase Sa)表面水和尿素分子的分布和动力学行为。 结果表明,尿素分子可与RNase Sa酶形成较强的相互作用,并取代其表面的水分子而富集在蛋白质表面。 尿素分子更倾向与RNase Sa酶的疏水残基作用,与RNase Sa酶主链形成氢键的能力更强。 尿素分子的平动和转动远远慢于水分子的平动和转动。 RNase Sa酶表面水分子的平动和转动随着尿素浓度增加而逐渐变慢,但RNase Sa酶表面尿素分子的动力学并不依赖于尿素浓度变化。 本研究中明晰的RNase Sa酶表面水和尿素分子分布和动力学有助于理解水和尿素分子对蛋白质稳定性的影响。     

分子动力学模拟极端嗜热核糖结合蛋白的热力学稳定性

采用分子动力学模拟方法研究极端嗜热性核糖结合蛋白(tteRBP)的嗜热机理.在常温(300 K)和最佳活性温度(375 K)时,分别对tteRBP分子进行动力学模拟,结果表明,整体分子均保持结构稳定,但分子内部的协调运动不同.在375 K时蛋白整体柔性显著提高,使分子能够局部调整构象以适应极端高温.蛋白结构变化的分析也确认了高温时构象局部微调对蛋白极端高温稳定性的关键作用.     

软胶体粒子形成束晶的动力学模拟

利用广义指数模型描述软胶体粒子, 结合分子动力学模拟研究软胶体粒子形成束晶的动力学过程. 通过等温压缩和等密度降温2个不同的过程, 研究了束晶形成过程中结构变化特征和动力学路径对结构的影响规律. 研究发现, 与蒙特卡洛模拟结果相比, 分子动力学模拟得到的结构随着密度的变化有明显的迟滞现象, 这是由于考虑了真实的动力学因素引起的差异. 此外, 在相同温度和压力下通过不同的动力学路径得到的相结构不完全相同, 这是由于动力学形成过程会对相结构产生很大的影响.     

耗散粒子动力学与可极化ABEEM力场结合模拟嵌段共聚物自组装形态调控

本文采用介观尺度上的耗散粒子动力学与基于ABEEM可极化力场的全原子分子动力学相结合的方式,从理论上探究了嵌段共聚物结构、对称性、分子组成及温度等对嵌段共聚物最终自组装结构形态的影响.模拟结果表明,这些因素均会对嵌段共聚物在选择性溶剂中的最终自组装结构产生一定影响.这一理论研究为实现可控操纵自组装结构,提供了有意义的参考.     

分子模拟在纳米载药材料中的应用研究进展

纳米载药系统因其可改善药代动力学特性、降低毒性、控制溶出,还具有靶向性,已成为近年来生物医学领域的研究热点。分子模拟是一种新颖的节省资源的预测方法,可用于模拟研究在不同条件下纳米粒子的形成、行为和结构变化的相关信息,其计算结果有助于预测实验所需材料。本综述介绍了不同尺度的模拟方法,包括全原子分子动力学(AAMD)、蒙特卡洛(MC)、粗粒分子动力学(CGMD)和耗散粒子动力学(DPD)方法,并对其理论基础及最新模拟进展进行了阐述。     

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。     

乙二胺-三乙烯二胺/甲胺-三乙烯二胺高氯酸盐共晶含能材料的制备和理论计算研究

制备并解析了有机胺高氯酸盐共晶SY(乙二胺-三乙烯二胺高氯酸盐)和MT(甲胺-三乙烯二胺高氯酸盐),实验方法研究表明SY和MT中含有大量分子内和分子间氢键,形成多元环状结构,保证了晶体结构的稳定;采用分子动力学模拟的方法利用COMPASS力场分析了SY和MT在不同温度(213K-513K)下的动力学行为,研究结果表明SY和MT中N-H键L_(ave)和L_(max)变化量超过0. 07,判定其为SY和MT的引发键;在外电场作用下,C-N和N-H键键长均有所增加,而Cl-O键键长缩短,说明电场对不同键的影响不一致;在高温下(275K-515K)的分子动力学研究表明,SY和MT的能隙均变小,说明共晶的感度随温度的升高而变高。     

柔性金属—有机骨架材料中已烷的扩散研究

本工作将MM3力场进行了扩展,使其可用于描述其它IRMOF材料的柔韧性;在此基础上,我们采用分子动力学模拟研究了柔性IRMOF-1和-16材料中已烷的扩散。 本文重点研究了温度和分子数对己烷自扩散系数、扩散机理,以及骨架柔性的影响。结果表明,分子数是影响扩散路径的重要因素。其次,IRMOF-16的柔性强于IRMOF-1。 工作的结论有助于进一步研究链状分子在柔性MOF材料中的扩散。     

交联SU-8光刻胶与Ni基底结合性的分子动力学模拟

应用分子动力学模拟软件Materials Studio构建SU-8光刻胶与Ni基底的界面结构,研究后烘温度对界面结合性的影响.结合工艺中所采用的后烘温度,模拟计算了338～368K时Ni基底上SU-8胶的交联反应,在经过反复的能量最小化和分子动力学模拟后,对最终得到的平衡结构进行了界面结合能的计算.计算结果表明界面结合能随着后烘温度的升高而增大,在368K时结合能达到最大值,说明此时界面结合最好.对分子体系进行了能量分析,结果表明界面分子间的范德华力作用能是影响界面结合的主要因素.对体系界面原子间进行了径向分布函数分析,发现范德华力作用范围内(0.31～0.60nm)出现两组Ni—O的强峰,也证实了上述结论。     

分子在纯硅β分子筛内扩散的随机行走模型

建立了一个β分子筛上分子扩散的模型. 该模型中, 分子在β分子筛中运动是在不同吸附点位上作无规行走. β孔道的拓扑结构和在两种孔道吸附位上不同的跃迁几率导致分子沿两个主轴方向扩散, 扩散系数存在一个关联关系; 分子动力学对不同温度下苯分子在β分子筛上扩散模拟证实了这一关联关系. 氩原子在不同作用半径下的动力学模拟表明, 分子作用半径大小是满足随机行走假设的重要条件, 即该模型要求扩散分子作用半径足够大, 与分子筛孔径相近.     

Mechanisms of double ionization in strong laser field from simulation with Coupled Coherent States: Beyond reduced dimensionality models

The recently developed Coupled Coherent States method for solution of the time-dependent Schrödinger equation is used to simulate the strong laser field double ionization of a helium atom in six spatial dimensions. The calculated double ionization yield, as a function of laser intensity, reproduces the “shoulder”, attributable to electron recollisions. The method, which employs a Coherent State representation guided by classical trajectories also provides physical insight into the ionization mechanism. The appearance of the ‘shoulder’, is seen by analysis of the guiding trajectories to arise predominantly from sequential excitation of one electron into a highly excited orbit, followed by an electron–electron collision leading to correlated escape of the two electrons. A second little known mechanism involves recollisions resulting in ionization of the secondary electron, leaving the first in a highly excited state, from which it is later ionized by the laser field.     

利用基于直接动力学的轨线面跳跃方法处理非绝热过程

势能面交叉引起的非绝热过程广泛存在于光化学和光物理中。对这一过程进行描述是理论化学的重要挑战之一。非绝热过程涉及原子核与电子之间的耦合运动,因此量子化学的基本假设之一"玻恩-奥本海默"近似被打破,所以对其进行描述需要发展新的动力学理论方法。在这些方法中,Tully发展的最少轨线面跳跃方法凭借易于程序化、便于计算等优点已经发展成为处理非绝热问题的主要动力学方法之一。其中原子核以经典的方式在单一势能面上进行演化,电子以量子的方式沿着同一轨线进行演化。在整个演化过程中,非绝热跃迁通过轨线在不同势能面间的跃迁来描述,其中跳跃发生的几率与电子的演化有关。如果将该方法与从头算直接动力学相结合,可以在全原子水平上研究实际分子体系的非绝热动力学,给出其激发态寿命、非绝热动力学中分子的主要运动方式、反应通道以及分支比等重要信息。本文旨在讨论最少面跳跃直接动力学方法研究非绝热问题的一些进展,包括动力学基本理论,特别关注将最少面跳跃方法和直接动力学结合的数值实现细节,同时讨论该方法在研究实际体系当中的一些应用,并对轨线面跳跃方法下一步发展的一些方向进行合理的展望。     

多原子体系非绝热动力学的近似理论方法

非绝热动力学普遍存在于光物理和光化学过程中。描述非绝热跃迁需要处理电子-原子核间的相互耦合运动。由于计算量随体系尺度增大剧烈增长,准确的量子动力学计算目前只适用于描述小分子体系。为了研究多原子分子体系的非绝热过程,近年来发展了一些基于量子-经典动力学近似方法。本文将对典型的这类方法包括经典Ehrenfest方法、面跳跃方法、基于Wigner表示的混合量子-经典方法进行简要的介绍,并讨论如何将量子-经典动力学方法与电子结构从头算手段相结合,模拟非绝热过程。重点阐明各种方法的基本思想和优缺点,并对该领域的发展进行展望。     

Ultrafast Electron Transfer with Symmetrical Quasi-classical Dynamics based on Mapping Hamiltonian and Quantum Dynamics based on ML-MCTDH

Symmetrical quasi-classical (SQC) method based on mapping Hamiltonian is an efficient approach that is potentially useful to treat the nonadiabatic dynamics of very large systems. We try to evaluate the performance of this method in the ultrafast electron transfer processes involving a few of electronic states and a large number of vibrational modes. The multilayer multiconfigurational time-dependent Hartree (ML-MCTDH) method was used to get the accurate dynamical results for benchmark. Although the population dynamics in the longtime limit show differences in the ML-MCTDH and SQC calculations, the SQC method gives acceptable results.     

Choline Chloride as a Nano-Crowder Protects HP-36 from Urea-Induced Denaturation: Insights from Solvent Dynamics and Protein-Solvent Interactions

Urea at sufficiently high concentration unfolds the secondary structure of proteins leading to denaturation. In contrast, choline chloride (ChCl) and urea, in 1 : 2 molar ratio, form a deep eutectic mixture, a liquid at room temperature, protecting proteins from denaturation. In order to get a microscopic picture of this phenomenon, we perform extensive all-atom molecular dynamics simulations on a model protein, HP-36. Based on our calculation of Kirkwood-Buff integrals, we analyze the relative accumulation of urea and ChCl around the protein. Additional insights are drawn from the translational and rotational dynamics of solvent molecules and hydrogen bond auto-correlation functions. In the presence of urea, water shows slow subdiffusive dynamics around the protein owing to a strong interaction of water with the backbone atoms. Urea also shows subdiffusive motion. The addition of ChCl further slows down the dynamics of urea, restricting its accumulation around the protein backbone. Adding to this, choline cations in the first solvation shell of the protein show the strongest subdiffusive behavior. In other words, ChCl acts as a nano-crowder by excluding urea from the protein backbone and thereby slowing down the dynamics of water around the protein. This prevents the protein from denaturation and makes it structurally rigid, which is supported by the smaller radius of gyration and root mean square deviation values of HP-36.     

Computer simulation studies of the miscibility of poly(3-hydroxybutyrate)-based blends

By means of the molecular dynamics simulation method, the miscibility of poly(3-hydroxybutyrate)/polyethylene (PHB/PE) blend has been investigated. Two glass transition temperatures of the PHB/PE are found by scrutinizing its volume-temperature curve, and this result is qualitatively in agreement with the experimental results. To further analyze the miscibility of poly(3-hydroxybutyrate)-based blends, the Flory-Huggins parameters of PHB/PE, poly(3-hydroxybutyrate)/poly(ethylene oxide) (PHB/PEO), poly(ethylene oxide)/polyethylene (PEO/PE) have been calculated via a Monte Carlo scheme, and the morphology of the PHB/PEO and the PHB/PE blend has been simulated using dissipative particle dynamics method. The time evolution of dividing interface for PHB/PEO/PE blend shows a dynamic phase separation process. All these results indicate that PHB and PEO tend to mix together, whereas PE aggregates to form PE-rich domains in the PHB/PE and PHB/PEO/PE blends.     

Effect of Size and Temperature on Water Dynamics inside Carbon Nano-Tubes Studied by Molecular Dynamics Simulation

Water transport inside carbon nano-tubes (CNTs) has attracted considerable attention due to its nano-fluidic properties, its importance in nonporous systems, and the wide range of applications in membrane desalination and biological medicine. Recent studies show an enhancement of water diffusion inside nano-channels depending on the size of the nano-confinement. However, the underlying mechanism of this enhancement is not well understood yet. In this study, we performed Molecular Dynamics (MD) simulations to study water flow inside CNT systems. The length of CNTs considered in this study is 20 nm, but their diameters vary from 1 to 10 nm. The simulations are conducted at temperatures ranging from 260 K to 320 K. We observe that water molecules are arranged into coaxial water tubular sheets. The number of these tubular sheets depends on the CNT size. Further analysis reveals that the diffusion of water molecules along the CNT axis deviates from the Arrhenius temperature dependence. The non-Arrhenius relationship results from a fragile liquid-like water component persisting at low temperatures with fragility higher than that of the bulk water.     

LINCS: A linear constraint solver for molecular simulations

In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1463–1472, 1997