适用于TATB,RDX,HMX含能材料的全原子力场的建立与验证

报道一个适用于三种常见的含能材料分子三硝基三氨基苯(TATB),环三亚甲基三硝胺(RDX),环四亚甲基四硝胺(HMX)的全原子力场.力场采用广泛使用的力场函数形式,其中键参数通过拟合量子化学密度泛函计算的数据获得,电荷参数和范德华参数通过拟合相应的分子晶体的物理性质(密度和升华焓)优化得到.通过计算分子和分子晶体的性质显示该力场可以用来准确地预测分子结构、分子振动频率和分子晶体的晶胞参数、密度和升华焓.进一步的验证显示该力场可用来较为准确地预测分子晶体的状态方程和机械模量.     

GEMC和GDI方法计算流体气液相平衡的比较

考察采用TraPPE联合原子和OPLS全原子力场两种分子力场, Gibbs系综蒙特卡罗(GEMC)方法和Gibbs-Duhem积分(GDI)方法计算流体气液相平衡的适用性、计算速度、计算精度等问题. 结果表明, 在采用全原子力场情况下, GDI方法比GEMC方法极大地节省了计算时间. 从计算结果来看, 两种方法各有适用范围, 在使用时可互为补充. 在给定力场的前提下, 两种方法所得到的液相密度、蒸发焓、临界温度和临界密度相差不大, 而当力场中的缺陷导致蒸发焓的计算不够准确时, 两种计算方法得到的气体的压力和密度明显不同,进而导致预测的临界压力也明显不同.     

乙醇醛的分子动态结构

以量子化学计算作为起点, 为最简单的糖类分子——乙醇醛开发了两套分子力学力场参数: 基于肽类的力场和基于醛类的力场. 分子动力学模拟结果表明, 所开发的类醛力场参数能够较好地描述乙醇醛分子在水中的结构以及水分子在其周围的分布. 通过瞬时简正模式分析, 得到了3N-6个模式的瞬时振动频率和振动跃迁偶极矩等振动光谱参数的统计分布及其相关性. 结合量子化学计算和分子动力学模拟对生物分子体系的多元振动光谱参数进行预测和评估, 为从化学键水平出发模拟宽带飞秒二维红外相关光谱提供了一个新方法.     

应用ABEEM/MM蛋白质力场模型研究半胱氨酸二肽构象的性质

ABEEM/MM蛋白质力场模型是应用于蛋白质体系的原子-键电负性均衡方法(ABEEM)与力场(MM)相结合的浮动电荷模型.该模型能够准确地描述分子在环境变化时的静电极化,并能快速计算气态和溶液多肽的结构和能量.首次应用ABEEM/MM蛋白质力场模型研究半胱氨酸二肽构象的性质,如构象能、氢键等.此外,应用从头计算HF/6-31G**方法对其性质进行计算.ABEEM/MM蛋白质力场模型可以快速准确地得到半胱氨酸二肽分子不同稳定构象的性质,其结果可以和从头计算相媲美.以上研究有助于加深对半胱氨酸二肽构象性质的了解,从而也为进一步验证ABEEM/MM蛋白质力场模型的正确性以及参数的合理性提供可靠的依据.     

硝胺及其甲基衍生物的从头计算研究 3: 甲硝胺及其同位素衍生物的谐性力场和振动光谱

用TEXAS从头计算程序,取STO-4-21G基组,计算了甲硝胺的谐性力场和振动光谱.直接理论计算的谐性力场经由其他分子转移来的经验校正因子校正后,提供了甲硝胺振动基频的预测.预测值和甲硝胺分子在气相中的振动光谱实验值之间的平均偏差为31cm^-1.为了获得更合适的气相甲硝胺振动力场和预测它的同位素衍生物的振动光谱,我们优化了一组新的校正因子,使理论值和实验值的平均偏差减为8.9cm^-1.用这组校正因子得到的力场预测了三个同位素衍生物的振动光谱,其同位素位移的理论预测值和实验值符合良好.     

硝胺及其甲基衍生物的从头计算研究 3: 甲硝胺及其同位素衍生物的谐性力场和振动光谱

用TEXAS从头计算程序,取STO-4-21G基组,计算了甲硝胺的谐性力场和振动光谱.直接理论计算的谐性力场经由其他分子转移来的经验校正因子校正后,提供了甲硝胺振动基频的预测.预测值和甲硝胺分子在气相中的振动光谱实验值之间的平均偏差为31cm^-1.为了获得更合适的气相甲硝胺振动力场和预测它的同位素衍生物的振动光谱,我们优化了一组新的校正因子,使理论值和实验值的平均偏差减为8.9cm^-1.用这组校正因子得到的力场预测了三个同位素衍生物的振动光谱,其同位素位移的理论预测值和实验值符合良好.     

咪唑醋酸离子液体热力学性质的理论研究

咪唑醋酸离子液体在催化、电化学、萃取等领域具有潜在的应用价值,对其热力学性质的深入研究将为其应用提供理论依据。本文采用密度泛函理论(DFT)方法和Born-Fajans-Haber (BFH)循环法对咪唑醋酸离子液体[C_nmim][OAc] (n=1-6)进行热力学性质的理论研究。计算其相变过程中的解离焓、汽化焓、熔化焓、晶格焓、溶解焓等,并与已有实验值进行比较。利用Gaussian 09程序在B3LYP/6-311+G(d, p)和M062X/TZVP两种水平下计算解离焓值,同时通过计算得到分子体积和总气相能的焓修正值,借助Matlab计算软件拟合得到汽化焓值,取得与已有实验值很好的一致性。使用Jenkins公式求得晶格能,计算得到晶格焓,最后利用BFH循环计算得到溶解焓。     

丙酮酸分子结构与振动光谱的密度泛函理论研究

用密度泛函方法BLYP、B3LYP和从头算Hartree-Fock(HF)方法在6-31G*基组水平上对丙酮酸分子的几何结构（甲基的重叠式和交错式两种构象）和振动光谱分别进行了优化和计算,并给出了各种频率所对应的红外强度及拉曼活性,对光谱进行了指认。结果表明：在丙酮酸分子的两种构象中,重叠式比较稳定*B3LYP计算得到的构型参数与实验结果比较一致;在振动频率的计算中,BLYP未标度力场所计算的非CH3伸缩振动基频预测值和实验值的平均绝对偏差为10.4cm-1;而HF标度力场的平均绝对偏差为17.9cm-1。说明两者的结果与实验观测频率比较吻合,但B3LYP的频率计算值偏差（38.3cm-1）较大。根据振动频率的势能分布和红外光谱强度对此分子的振动基频进行了理论归属。     

硝胺及其甲基衍生物的从头计算研究 Ⅲ.甲硝胺及其同位素衍生物的谐性力场和振动光谱

用TEXAS从头计算程序,取STO-4-21G基组,计算了甲硝胺的谐性力场和振动光谱.直接理论计算的谐性力场经由其他分子转移来的经验校正因子校正后,提供了甲硝胺振动基频的预测.预测值和甲硝胺分子在气相中的振动光谱实验值之间的平均偏差为31cm~(-1).为了获得更合适的气相甲硝胺振动力场和预测它的同位素衍生物的振动光谱,我们优化了一组新的校正因子,使理论值和实验值的平均偏差减为8.9cm~(-1).用这组校正因子得到的力场预测了三个同位素衍生物的振动光谱,其同位素位移的理论预测值和实验值符合良好.     

咪唑基离子液体的物理化学性质估算及预测(英文)

根据经验和半经验方程及空隙模型理论,可以估算及预测离子液体在298.15K的物理化学性质.本文讨论了离子液体的分子体积,密度,标准熵,晶格能,表面张力,等张比容,摩尔蒸发焓,空隙体积,空隙率和热膨胀系数.通过实验测得的三种离子液体1-乙基-3-甲基咪唑硫酸乙酯([C2mim][EtSO4)]),1-丁基-3-甲基咪唑硫酸辛酯([C4mim][OcSO4])和1-乙基-3-甲基咪唑双三氟甲磺酰亚胺盐([C2mim][NTf2])的密度和表面张力估算了它们的其它物理化学性质.由这三种离子液体的分子体积及等张比容预测了同系列中其它离子液体[Cnmim][EtSO4],[Cnmim][OcSO4]和[Cnmim][NTf2](n=1-6)的分子体积及等张比容,由此计算出它们的密度及表面张力.进而预测了它们的物理化学性质.将预测的离子液体[C4mim][NTf2]和[C2mim][OcSO4]的密度值与文献报导的实验值进行比较,其偏差在实验误差范围内.最后,将由Kabo经验方程计算的七个离子液体[C2mim][EtSO4]、[C4mim][OcSO4]、[C2mim][NTf2]、[C4mim][NTf2]、丁基三甲基铵双三氟甲磺酰亚胺盐([N4111][NTf2])、甲基三辛基铵双三氟甲磺酰亚胺盐([N8881][NTf2])和1-辛基-3-甲基吡啶四氟硼酸盐([m3opy][BF4])的摩尔蒸发焓与由Verevkin简单规则预测的摩尔蒸发焓进行比较,发现两者符合很好.因此,在缺乏密度和表面张力实验数据的情况下,可以用Verevkin简单规则来预测离子液体的摩尔蒸发焓.     

Molecular force field for ionic liquids IV: trialkylimidazolium and alkoxycarbonyl-imidazolium cations; alkylsulfonate and alkylsulfate anions

This is the fourth article of a series that describes the parametrization of a force field for the molecular simulation of common ionic liquids within the framework of statistical mechanics. The force field was developed in the spirit of the OPLS-AA model and is thus oriented toward the calculation of equilibrium thermodynamic and structural properties in the condensed (liquid) phase. The ions modeled in the present paper are cations of the 1,2,3-trialkylimidazolium and alkoxycarbonyl imidazolium families and alkylsulfate and alkylsulfonate anions. As in previous publications, the force field is built in a stepwise manner that allows, for example, the construction of models for an entire family of cations or anions, with alkyl side chains of different length. Because of the transferability of the present force field, the ions studied here can be combined with those reported in our three previous publications to create a large variety of ionic liquids that can be studied by molecular simulation. The extension of the force field was validated by comparison of simulation results with the corresponding crystal structure and liquid density experimental data.     

Effective force field for liquid hydrogen fluoride from ab initio molecular dynamics simulation using the force-matching method

A recently developed force-matching method for obtaining effective force fields for condensed matter systems from ab initio molecular dynamics (MD) simulations has been applied to fit a simple nonpolarizable two-site pairwise force field for liquid hydrogen fluoride. The ab initio MD in this case was a Car-Parrinello (CP) MD simulation of 64 HF molecules at nearly ambient conditions within the Becke-Lee-Yang-Parr approximation to the electronic density functional theory. The force-matching procedure included a fit of short-ranged nonbonded forces, bonded forces, and atomic partial charges. The performance of the force-match potential was examined for the gas-phase dimer and for the liquid phase at various temperatures. The model was able to reproduce correctly the bent structure and energetics of the gas-phase dimer, while the results for the structural properties, self-diffusion, vibrational spectra, density, and thermodynamic properties of liquid HF were compared to both experiment and the CP MD simulation. The force-matching model performs well in reproducing nearly all of the liquid properties as well as the aggregation behavior at different temperatures. The model is computationally cheap and compares favorably to many more computationally expensive potential energy functions for liquid HF.     

Computer simulation of solid and liquid benzene with an atomistic interaction potential derived from ab initio calculations

Molecular dynamics atomistic simulations of solid and liquid benzene have been performed, employing a model intermolecular potential derived from quantum mechanical calculations. The ab initio database includes approximately 200 geometries of the benzene dimer with interaction energies computed at the MP2 level of theory. The accuracy of the modeled force field results is satisfactory. The thermodynamic and structural properties, calculated in the condensed phases, are compared with experimental data and previous simulation results. Single particle and collective dynamical properties are also investigated through the calculation of translational and rotational diffusion coefficients, reorientational dynamics, and viscosities. The agreement of these data with experimental measurements confirms the reliability of the proposed force field.     

Gas‐phase and liquid‐state properties of esters,nitriles, and nitro compounds with the OPLS‐AA force field

Nonbonded and torsional parameters for carboxylate esters, nitriles, and nitro compounds have been developed for the OPLS‐AA force field. In addition, torsional parameters for alkanes have been updated. These parameters were fit to reproduce ab initio gas‐phase structures and conformational energetics, experimental condensed‐phase structural and thermodynamic properties, and experimental free energies of hydration. The computed densities, heats of vaporization, and heat capacities for fifteen liquids are in excellent agreement with experimental values. The new parameters permit accurate molecular modeling of compounds containing a wider variety of functional groups, which are common in organic molecules and drugs. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1340–1352, 2001     

A transferable ab initio based force field for aqueous ions

We present a new polarizable force field for aqueous ions (Li(+), Na(+), K(+), Rb(+), Cs(+), Mg(2 +), Ca(2 +), Sr(2 +), and Cl(-)) derived from condensed phase ab initio calculations. We use maximally localized Wannier functions together with a generalized force and dipole-matching procedure to determine the whole set of parameters. Experimental data are then used only for validation purposes and a good agreement is obtained for structural, dynamic, and thermodynamic properties. The same procedure applied to crystalline phases allows to parametrize the interaction between cations and the chloride anion. Finally, we illustrate the good transferability of the force field to other thermodynamic conditions by investigating concentrated solutions.     

A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols

In this work, parameters are optimized for a charge‐on‐spring based polarizable force field for linear alcohols. We show that parameter transferability can be obtained using a systematic approach in which the effects of parameter changes on physico‐chemical properties calculated from simulation are predicted. Our previously described QM/MM calculations are used to attribute condensed‐phase polarizabilities, and starting from the non‐polarizable GROMOS 53A5/53A6 parameter set, van der Waals and Coulomb interaction parameters are optimized to reproduce pure‐liquid (thermodynamic, dielectric, and transport) properties, as well as hydration free energies. For a large set of models, which were obtained by combining small perturbations of 10 distinct parameters, values for pure‐liquid properties of the series methanol to butanol were close to experiment. From this large set of models, we selected 34 models without special repulsive van der Waals parameters to distinguish between hydrogen‐bonding and non‐hydrogen‐bonding atom pairs, to make the force field simple and transparent. © 2017 Wiley Periodicals, Inc.     

Ab initio rigid water: effect on water structure, ion hydration, and thermodynamics

We investigate the liquid structure, ion hydration, and some thermodynamic properties associated with the rigid geometry approximation to water by applying ab initio molecular dynamics simulations (AIMD) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional at T = 320 K. We vary the rigid water geometry in order to locate a class of practical water models that yield reasonable liquid structure and dynamics, and to examine the progression of AIMD-predicted water behavior as the OH bond length varies. Water constrained at the optimal PBE gas phase geometry yields reasonable pair correlation functions. The predicted liquid phase pressure, however, is large ( approximately 8.0 kbar). Although the O-H bond in water should elongate when transferred from gas to the condensed phase, when it is constrained to 0.02, or even just 0.01 A longer than the optimal gas phase value, liquid water is predicted to be substantially overstructured compared to experiments. Zero temperature calculations of the thermodynamic properties of cubic ice underscore the sensitivity toward small variations in the O-H bond length. We examine the hydration structures of potassium, chloride, and formate ions in one rigid PBE water model. The results are in reasonable agreement with unconstrained AIMD simulations.     

Assessment of performance of the general purpose polarizable force field QMPFF3 in condensed phase

The recently introduced force field (FF) QMPFF3 is thoroughly validated in gas, liquid, and solid phases. For the first time, it is demonstrated that a physically well-grounded general purpose FF fitted exclusively to a comprehensive set of high level vacuum quantum mechanical data applied as it is to simulation of condensed phase provides high transferability for a wide range of chemical compounds. QMPFF3 demonstrates accuracy comparable with that of the FFs explicitly fitted to condensed phase data, but due to high transferability it is expected to be successful in simulating large molecular complexes.     

Understanding the dielectric properties of liquid amides from a polarizable force field

The role played by electronic polarization in the dielectric properties of liquid N-methyl acetamide (NMA) is examined using molecular dynamics simulations with a polarizable force field based on classical Drude oscillators. The model presented is the first force field shown to reproduce the anomalously large dielectric constant of liquid NMA. Details of the molecular polarizability are found to be important. For instance, all elements of the polarizability tensor, rather then just the trace, impact on the condensed phase properties. Two factors related to electronic polarizability are found to contribute to this large dielectric constant. First is the significant enhancement of the mean amide molecular dipole magnitude, which is 50% larger in the liquid than in the gas phase. Second is the consequent strong hydrogen bonding between molecular neighbors that enhances the orientational alignment of the molecular dipoles. Polarizable models of amide compounds that have two (acetamide) and zero (N,N-dimethyl acetamide) polar hydrogen-bond donor atoms are also investigated. Experimentally, the neat liquid dielectric constants at 373 K are 100 for NMA, 66 for acetamide and 26 for N,N-dimethyl acetamide. The polarizable models replicate this trend, predicting a dielectric constant of 92+/-5 for NMA, 66+/-3 for acetamide and 23+/-1 for N,N-dimethyl acetamide.     

Polarizable empirical force field for sulfur‐containing compounds based on the classical Drude oscillator model

Condensed‐phase computational studies of molecules using molecular mechanics approaches require the use of force fields to describe the energetics of the systems as a function of structure. The advantage of polarizable force fields over nonpolarizable (or additive) models lies in their ability to vary their electronic distribution as a function of the environment. Toward development of a polarizable force field for biological molecules, parameters for a series of sulfur‐containing molecules are presented. Parameter optimization was performed to reproduce quantum mechanical and experimental data for gas phase properties including geometries, conformational energies, vibrational spectra, and dipole moments as well as for condensed phase properties such as heats of vaporization, molecular volumes, and free energies of hydration. Compounds in the training set include methanethiol, ethanethiol, propanethiol, ethyl methyl sulfide, and dimethyl disulfide. The molecular volumes and heats of vaporization are in good accordance with experimental values, with the polarizable model performing better than the CHARMM22 nonpolarizable force field. Improvements with the polarizable model were also obtained for molecular dipole moments and in the treatment of intermolecular interactions as a function of orientation, in part due to the presence of lone pairs and anisotropic atomic polarizability on the sulfur atoms. Significant advantage of the polarizable model was reflected in calculation of the dielectric constants, a property that CHARMM22 systematically underestimates. The ability of this polarizable model to accurately describe a range of gas and condensed phase properties paves the way for more accurate simulation studies of sulfur‐containing molecules including cysteine and methionine residues in proteins. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010