计算机模拟技术在表面活性剂研究中的应用

根据表面活性剂溶液行为的模拟所需的时间和空间尺度,介绍了三种主要的计算机模拟方法:原子模拟、粗粒模拟和介观模拟.综述了这些模拟方法在表面活性剂单体、缔合体系及与聚合物相互作用等研究中的应用.指出了用计算机模拟方法研究表面活性剂体系的发展前景.     

微波化学温度模拟研究进展

在微波化学研究中,通过数学模拟分析微波作用在化学体系的温度分布及变化,有助于控制微波加热过程,了解微波与物质之间的相互作用机理.本文针对微波化学数值模拟的特点,系统介绍了各种方法及模拟过程,对数值模拟分析中的关键问题进行了讨论,综述了近年来数值模拟温度分布在微波化学中的应用,提出了目前的研究难点,并展望了发展趋势.     

流体熵相关性质的Monte Carlo模拟新方法

提出了用于计算实际体系熵相关性质的Monte Carlo多级取样分子模拟方法. 应用这一方法, 对硬球流体的化学势及Helmholtz自由能进行了估算, 得到了满意的结果. 计算化学势时, 不存在通常试验粒子方法所遇到的高密度问题. 该方法特别适合规律性的系统研究, 较之普通模拟方法要有效得多. 模拟得到的硬球体系无限稀释组份的超额化学势与对比直径的关系, 在相变区域为一条双凹曲线; 无论是在相变区还是在单相区, Carnahan-Starling公式对这一关系的描述均有较大偏差.     

超临界水的分子动力学模拟

采用分子动力学(MD)模拟的方法对超临界条件下水的结构及扩散性质进行了研究.模拟结果表明超临界条件下水分子之间的氢键作用明显减弱,分子极性大大降低.扩散性质与常温下相比,其大小约上升了两个数量级.     

流体熵相关性质的Monte Carlo模拟新方法

提出了用于计算实际体系熵相关性质的Monte Carlo 多级取样分子模拟方法.应用这一方法,对硬球流体的化学势及Helmholtz 自由能进行了估算,得到了满意的结果.计算化学势时,不存在通常试验粒子方法所遇到的高密度问题.该方法特别适合规律性的系统研究,较之普通模拟方法要有效得多.模拟得到的硬球体系无限稀释组份的超额化学势与对比直径的关系,在相变区域为一条双凹曲线;无论是在相变区还是在单相区,Carnahan-Starling 公式对这一关系的描述均有较大偏差.     

表面电荷及外电场对液固界面热阻的影响

采用非平衡分子动力学方法模拟了外电场及固体表面电荷对水与固体间界面热阻的影响. 结果表明,外加电场平行于界面时, 其对界面热阻几乎没有影响, 而垂直于界面时, 界面热阻将随着电场强度的增大而减小. 壁面带正电荷或负电荷都将使得界面热阻减小. 界面热阻与表面电荷密度及电场强度均满足二次函数关系. 模拟结果表明施加外电场和表面电荷是控制液固界面热阻的有效方法.     

ABEEMσπ和OPLS-AA力场对蛋白质GA88/GB88的分子动力学模拟

将原子与键电负性均衡方法融入分子力学方法,即利用ABEEMσπ浮动电荷力场与ABEEM-7P水模型相结合的方法及OPLS-AA固定电荷力场方法,对GA88和GB88蛋白进行了水溶液(温度295 K)和真空中的分子动力学模拟.比较两种方法得到的两个蛋白质的结构与实验结构的均方根偏差,分析了两种方法得到的两个蛋白质的回旋半径、氢键分布、径向分布及电荷分布情况.结果表明,ABEEMσπ和OPLS-AA力场均能正确模拟蛋白质结构,得到的各项偏差值接近,但从各偏差的波动大小可见,ABEEMσπ力场的模拟更稳定;回旋半径模拟很好地体现了蛋白质的"电致紧缩"现象;氢键分布、径向分布及电荷分布表明,与OPLS-AA固定电荷力场相比,ABEEMσπ浮动电荷力场能更好地体现蛋白质和周围水分子的极化效应.     

端羟基聚丁二烯/增塑剂共混物相容性的分子动力学模拟和介观模拟

应用分子动力学(MD)和介观动力学(MesoDyn)模拟方法对固体推进剂中端羟基聚丁二烯(HTPB)与增塑剂癸二酸二辛酯(DOS)、硝化甘油(NG)的相容性进行了研究. 采用MD模拟方法在COMPASS力场下, 对纯物质、HTPB/增塑剂共混物的密度、内聚能密度、溶度参数和共混物分子间的Flory-Huggins作用参数及结合能等进行了模拟计算, 通过比较溶度参数差值(Δδ)的大小、模拟前后体系密度变化情况均可以预测HTPB与增塑剂的相容性, 结合能的分析揭示了HTPB/增塑剂共混物组分间的相互作用及本质. 将Flory-Huggins作用参数转化为MesoDyn模拟的输入参数, 采用MesoDyn模拟方法对HTPB/增塑剂共混体系的介观形貌与动力学演变过程进行了研究, 通过模拟得到的等密度图、自由能密度和有序度参数等可以判断共混体系的相容性. MD和MesoDyn模拟结果均表明: HTPB/DOS属于相容体系, 而HTPB/NG属于不相容体系, 其结论与实验结果一致.     

一种基于电洗脱的核酸纯化回收芯片的设计及优化

提出了一种基于电洗脱原理的核酸纯化回收芯片, 通过对芯片上电极进行适当的切换操作, 可一次完成核酸样品分离和纯化回收. 同时采用数值模拟的方法对纯化回收芯片管道的几何形状及电场分布进行了优化设计, 并进行了实验验证. 实验结果与模拟分析非常吻合, 证明优化设计达到了预期的效果.     

端羟基聚丁二烯/增塑剂共混物相容性的分子动力学模拟

固体推进剂和炸药的力学性能在很大程度上依赖于配方中高分子粘结剂与增塑剂的相容性. 本文对相容和非相容两种体系进行了分子动力学(MD)模拟, 以考察分子模拟方法的实用性. 为预测固体推进剂中端羟基聚丁二烯(HTPB)与增塑剂癸二酸二辛酯(DOS)、硝化甘油(NG)的相容性, 采用MD模拟方法在COMPASS力场下, 对HTPB、DOS、NG和共混物HTPB/DOS、HTPB/NG的密度、内聚能密度及溶度参数等进行了模拟计算. 通过比较溶度参数差值(△δ)的大小、分子间径向分布函数和模拟前后体系密度变化情况均可以预测HTPB/DOS属于相容体系,而HTPB/NG属于不相容体系, 与实验结果一致. 径向分布函数分析同时揭示了HTPB/增塑剂组分之间的相互作用及本质. 本文的模拟方法可以作为预测聚合物与增塑剂相容性的有利工具, 也可以为固体推进剂和炸药的配方设计提供理论指导.     

Free energy perturbation study of water dimer dissociation kinetics

An efficient approach is described for using accurate ab initio calculations to determine the rates of elementary condensation and evaporation processes that lead to nucleation of aqueous aerosols. The feasibility of the method is demonstrated in an application to evaporation rates of water dimer at 230 K. The method, known as ABC-FEP (ab initio/classical free energy perturbation), begins with a calculation of the potential of mean force for the dissociation (evaporation) of small water clusters using a molecular dynamics (MD) simulation with a model potential. The free energy perturbation is used to calculate how changing from the model potential to a potential calculated from ab initio methods would alter the potential of mean force. The difference in free energy is the Boltzmann-weighted average of the difference between the ab initio and classical potential energies, with the average taken over a sample of configurations from the MD simulation. In principle, the method does not require a highly accurate model potential, though more accurate potentials require fewer configurations to achieve a small sampling error in the free energy perturbation step. To test the feasibility of obtaining accurate potentials of mean force from ab initio calculations at a modest number of configurations, the free energy perturbation method has been used to correct the errors when some standard models for bulk water (SPC, TIP4P, and TIP4PFQ) are applied to water dimer. To allow a thorough exploration of sampling issues, a highly accurate fit to results of accurate ab initio calculations, known as SAPT-5s, as been used a proxy for the ab initio calculations. It is shown that accurate values for a point on the potential of mean force can be obtained from any of the water models using ab initio calculations at only 50 configurations. Thus, this method allows accurate simulations of small clusters without the need to develop water models specifically for clusters.     

Surface-integral QSPR models: local energy properties

Surface-integral models based on AM1 semiempirical molecular orbital calculations are presented for the free energies of solvation in water, n-octanol, and chloroform and for the enthalpy of solvation in water. A parametrized function of four local properties calculated at the isodensity surface (the molecular electrostatic potential, local ionization energy, electron affinity, and polarizability) is integrated over the triangulated surface area to obtain the target quantity. The resulting models give results only slightly less accurate than those reported for parametrized generalized Born/polar surface area models despite relying only on gas-phase calculations. The water and octanol free-energy models were validated by calculating the water-octanol partition coefficient for a test set of organic compounds with moderate success. The models lead to a local solvation energy, which can be projected onto the molecular isodensity surface and provides insight into "hot" areas for solvation in water or the other solvents.     

Energetics of proton transfer in liquid water. I. Ab initio study for origin of many-body interaction and potential energy surfaces

The energetics of proton transfer in liquid water investigated by using ab initio calculation. The molecular electronic interaction of hydrated proton clusters in classified into many-body interaction elements by a new energy decomposition method. It is found that up to three-body molecular interaction is essential to describe the potential energy surface. The three-body effect mainly arises from the (non-classical) charge transfer and strongly depends on their configuration. Higher than three-body effects are small enough to be neglected. To simulate the liquid state reactions, two cluster models including all water molecules up to the second shell in the proton transfer reactions are employed. It is shown that these proton transfer reactions only involve small potential energy barriers of a few kcal/mol or less when structural rearrangement of the solvent is induced along the proton movement.     

Multiscale approach to explore the potential energy surface of water clusters (H2O)nn <or= 8

We propose a multiscale method to explore the energy landscape of water clusters. An asynchronous genetic algorithm is employed to explore the potential energy surface (PES) of OSS2 and TTM2.1-F models. Local minimum structures are collected on the fly, and the ultrafast shape recognition algorithm was used to remove duplicate structures. These structures are then refined at the B3LYP/6-31+G* level. The number of distinct local minima we found (21, 76, 369, 1443, and 3563 isomers for n = 4-8, respectively) reflects the complexity of the PES of water clusters.     

Free energy of liquid water from a computer simulation via cell theory

A method to calculate the free energy of water from computer simulation is presented. Based on cell theory, it approximates the potential energy surface sampled in the simulation by an anisotropic six-dimensional harmonic potential to model the three hindered translations and three hindered rotations of a single rigid water molecule. The potential is parametrized from the magnitude of the forces and torques measured in the simulation. The entropy of these six harmonic oscillators is calculated and summed with a conformational term to give the total entropy. Combining this with the simulation enthalpy yields the free energy. The six water models examined are TIP3P, SPC, TIP4P, SPC/E, TIP5P, and TIP4P-Ew. The results reproduce experiment well: free energies for all models are within 1.6 kJ mol(-1) and entropies are within 3.6 J K(-1) mol(-1). Approximately two-thirds of the entropy comes from translation, a third from rotation, and 5% from conformation. Vibrational frequencies match those in the experimental infrared spectrum and assist in their assignment. Intermolecular quantum effects are found to be small, with free energies for the classical oscillator lying 0.5-0.7 kJ mol(-1) higher than in the quantum case. Molecular displacements and vibrational and zero point energies are also calculated. Altogether, these results validate the harmonic oscillator as a quantitative model for the liquid state.     

The multiscale coarse-graining method. IX. A general method for construction of three body coarse-grained force fields

The multiscale coarse-graining (MS-CG) method is a method for constructing a coarse-grained (CG) model of a system using data obtained from molecular dynamics simulations of the corresponding atomically detailed model. The formal statistical mechanical derivation of the method shows that the potential energy function extracted from an MS-CG calculation is a variational approximation for the true potential of mean force of the CG sites, one that becomes exact in the limit that a complete basis set is used in the variational calculation if enough data are obtained from the atomistic simulations. Most applications of the MS-CG method have employed a representation for the nonbonded part of the CG potential that is a sum of all possible pair interactions. This approach, despite being quite successful for some CG models, is inadequate for some others. Here we propose a systematic method for including three body terms as well as two body terms in the nonbonded part of the CG potential energy. The current method is more general than a previous version presented in a recent paper of this series [L. Larini, L. Lu, and G. A. Voth, J. Chem. Phys. 132, 164107 (2010)], in the sense that it does not make any restrictive choices for the functional form of the three body potential. We use hierarchical multiresolution functions that are similar to wavelets to develop very flexible basis function expansions with both two and three body basis functions. The variational problem is solved by a numerical technique that is capable of automatically selecting an appropriate subset of basis functions from a large initial set. We apply the method to two very different coarse-grained models: a solvent free model of a two component solution made of identical Lennard-Jones particles and a one site model of SPC/E water where a site is placed at the center of mass of each water molecule. These calculations show that the inclusion of three body terms in the nonbonded CG potential can lead to significant improvement in the accuracy of CG potentials and hence of CG simulations.     

Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations

The free energy landscapes of peptide conformations were calibrated by ab initio quantum chemical calculations, after the enhanced conformational diversity search using the multicanonical molecular dynamics simulations. Three different potentials of mean force for an isolated dipeptide were individually obtained by the multicanonical molecular dynamics simulations using the conventional force fields, AMBER parm94, AMBER parm96, and CHARMm22. Each potential of mean force was then calibrated based upon the umbrella sampling algorithm from the adiabatic energy map that was calculated separately by the ab initio molecular orbital method, and all of the calibrated potentials of mean force coincided well. The calibration method was also applied to the simulations of a peptide dimer in explicit water models, and it was shown that the calibrated free energy landscapes did not depend on the force field used in the classical simulations, as far as the conformational space was sampled well. The current calibration method fuses the classical free energy calculation with the quantum chemical calculation, and it should generally make simulations for biomolecular systems much more reliable when combining with enhanced conformational sampling.     

水分子团簇分子力场方法的比较研究

采用传统水分子力场模型(SPC, TIPnP(n=3-5))和极化模型(POL3, AMOEBA, SPC-FQ, TIP4P-FQ)对水分子二聚体团簇性质进行了比较和研究. 以从头计算和实验数据为依据, 分析水分子在外场作用下体系的静电极化, 电荷转移和分子结构变化. 通过水分子二聚体结合能和各分解能量项评价极化静电势能在双分子结合能中的地位和作用, 以及各水分子力场的适用性. 通过水分子团簇多体相互作用能的计算,展示不同极化水分子力场定量计算极化能量的实际能力. 通过对力场模型结果的对比和分析, 为进一步发展极化力场模型, 并应用到其他体系提供借鉴和依据.     

Global search for minimum energy (H2O)n clusters, n = 3-5

The Gaussian-3 (G3) model chemistry method has been used to calculate the relative deltaG(o) values for all possible conformers of neutral clusters of water, (H2O)n, where n = 3-5. A complete 12-fold conformational search around each hydrogen bond produced 144, 1728, and 20,736 initial starting structures of the water trimer, tetramer, and pentamer. These structures were optimized with PM3, followed by HF/6-31G* optimization, and then with the G3 model chemistry. Only two trimers are present on the G3 potential energy hypersurface. We identified 5 tetramers and 10 pentamers on the potential energy and free-energy hypersurfaces at 298 K. None of these 17 structures were linear; all linear starting models folded into cyclic or three-dimensional structures. The cyclic pentamer is the most stable isomer at 298 K. On the basis of this and previous studies, we expect the cyclic tetramers and pentamers to be the most significant cyclic water clusters in the atmosphere.