Efficient formalism for large-scale ab initio molecular dynamics based on time-dependent density functional theory

A new "on the fly" method to perform Born-Oppenheimer ab initio molecular dynamics (AIMD) simulations is presented. Inspired by Ehrenfest dynamics in time-dependent density functional theory, the electronic orbitals are evolved by a Schr?dinger-like equation, where the orbital time derivative is multiplied by a parameter. This parameter controls the time scale of the fictitious electronic motion and speeds up the calculations with respect to standard Ehrenfest dynamics. In contrast with other methods, wave function orthogonality needs not be imposed as it is automatically preserved, which is of paramount relevance for large-scale AIMD simulations.     

Hydration characteristics of Ca2+ and Mg2+: a density functional theory,polarized continuum model and molecular dynamics investigation

In this work, density functional theory, Møller–Plesset second-order perturbation theory, and ab initio molecular dynamics (AIMD) were used to investigate hydrated characteristics of Mg²⁺ and Ca²⁺ as a function of coordination number in the first hydration shell (CN) and cluster size. It is generally accepted that the CNs of Mg²⁺ and Ca²⁺ are both six. Calculations show that the hydration of Mg²⁺ generally prefers six-coordinated structures, whereas the CN value of Ca²⁺ varies from 6 to 8 as the hydration proceeds. Moreover, the first hydration of Ca²⁺ is found to be more flexible than that of Mg²⁺, as indicated by the results of transition state calculations and AIMD simulations. In addition, the constraint of Mg²⁺ on the first hydration shell is obviously stronger than that of Ca²⁺, while the constraint on the inner hydration shells fades slightly faster for Mg²⁺ than Ca²⁺. It is also found that the charge transfer from central cation to water molecules is affected only by the first hydration shell for Mg²⁺, whereas by the first and second hydration shells for Ca²⁺. Based on hydration characteristics, approximatively saturated ion hydration shells for the hydration of Mg²⁺ and Ca²⁺ were proposed.     

小碳团簇结构的从头算分子动力学模拟

引入第一原理密度泛函理论, 即赝势密度泛函在实空间的有限差分方法和朗之万分子动力学退火技术, 对碳团簇Cn(n=2-8)的基态结构进行了理论计算, 所得结果与其他作者的计算结果及实验数据吻合较好.     

钴和铁熔体短程序的分子动力学模拟

通过分子动力学模拟研究了金属钴和铁熔体从普通液态到过冷液态普通微观结构的性质.所计算两体分布函数与可获得的实验结果基本一致,从普通液态到过冷液态的局域结构中的原子配位数为11和12的分布几率随着温度的降低而变小,而原子的配位数大于12的分布几率反而增加,角分布函数位于55.有一个明显的峰,位于110°有一个宽展的峰,位于150°有一个肩膀,表明金属钴和铁熔体的微观局域结构要比规则的二十面体团簇的结构复杂得多.我们的模拟结果表明金属熔体中的二十面体短程序随着温度的降低而增加,并在过冷液态中而占优势.     

采用密度泛函理论与分子动力学对聚甲基丙烯酸甲酯双折射性的理论计算

双折射性是各种光学材料的重要性能之一,具有高双折射率的光学材料在诸多研究及工业领域的应用越来越广泛.然而,作为常用的光学薄膜及光波导材料之一的聚合物材料的双折射性通常却很弱,只能通过实验对其双折射率进行大致的表征,缺乏对其双折射率的系统性理论计算,从而限制了提高聚合物双折射性的研究.本文建立了从聚合物的单体分子结构到多分子链的系统性的双折射率理论计算方法,并借助此方法研究了导致聚合物弱双折射性的限制因素.以聚甲基丙烯酸甲酯(PMMA)为研究对象,运用密度泛函理论研究了其本征双折射率,这里的本征双折射率是指分子链完全取向时其单体单元的双折射率.计算结果表明其本征双折射率高达0.0738左右,并且通过计算给出了PMMA单体单元的平均双折射率色散曲线.采用分子动力学方法研究了该聚合物(包含20个分子链)的材料双折射率.理论计算结果表明,尽管该聚合物具有较大的本征双折射率,但是由于聚合物中分子链取向度极低,聚合物材料最终表现出来的双折射率只有0.00052.本文建立的研究方法及研究结果为研究增强聚合物材料双折射性提供了理论依据.     

Hydration and translocation of an excess proton in water clusters: Anab initio molecular dynamics study

The hydration structure and translocation of an excess proton in hydrogen bonded water clusters of two different sizes are investigated by means of finite temperature quantum simulations. The simulations are performed by employing the method of Car-Parrinello molecular dynamics where the forces on the nuclei are obtained directly from ‘on the fly’ quantum electronic structure calculations. Since no predefined interaction potentials are used in this scheme, it is ideally suited to study proton translocation processes which proceed through breaking and formation of chemical bonds. The coordination number of the hydrated proton and the index of oxygen to which the excess proton is attached are calculated along the simulation trajectories for both the clusters.     

Investigation of the dissociative adsorption for cyclopropane on the copper surface by density functional theory and quantum chemical molecular dynamics method

The dissociative adsorption of cyclopropane on the copper surface was studied using quantum chemical molecular dynamics method with “Colors-Excite” code and density functional theory by Amsterdam Density Functional program (ADF2000). The excited state of cyclopropane was used as adsorbate to simulate the dissociated adsorption under an irradiation energy of ca. 10 eV. One of the C-C bonds in cyclopropane was broken and the two new bonds between cyclopropane and copper surface were formed. The electrons transferred from the copper atoms to cyclopropane with a value of about 0.2e. The shorter distances between the carbons and surface copper atoms showed the existence of strong interaction. Consistently, the results indicated metallacyclopentane was the most possible intermediate species in dissociative adsorption by ADF2000 and “Colors-Excite” method.     

Ionic solvation and association in LiCl aqueous solution: a density functional theory,polarised continuum model and molecular dynamics investigation

In this work, the ionic solvation and association behaviours in the LiCl aqueous solution were investigated using density functional theory (DFT), a polarised continuum model and classical molecular dynamics simulations. DFT calculations of LiCl(H₂O)_1–6,8 clusters show that contact ion pair (CIP) and solvent-shared ion pair (SSIP) conformers of LiCl(H₂O)_n (n ≥ 4) clusters are generally energetic both in the gas phase and in the aqueous solution. Some SSIP conformers may be slightly more stable than their CIP isomers when at least eight water molecules are incorporated in the inner hydration shells of LiCl hydrates. The transformation between CIP and SSIP conformers is easy by overcoming a small energy barrier, which mainly results from the hydration shell reorganisation of Li⁺. Molecular dynamics simulations show that ion pairs or ion clusters can be found in the LiCl aqueous solution, and the probability of CIP conformers or ion clusters presented in the LiCl solution generally increases with rise in temperature. However, the presentation of ion pairs or ion clusters in the LiCl aqueous solution does not inevitably lead to the nucleation of LiCl crystallisation.     

Role of oxygen functional groups for structure and dynamics of interfacial water on low rank coal surface: a molecular dynamics simulation

Molecular dynamics simulations were employed to study the effects of oxygen functional groups for structure and dynamics properties of interfacial water molecules on the subbituminous coal surface. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of subbituminous coal according to XPS results, and the composing proportion for hydroxyl, carbonyl and carboxyl is 25:3:5. The hydration energy with ?386.28 kJ/mol means that the adsorption process between water and coal surface is spontaneous. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxyl and carbonyl is similar.     

NaAlH4 表面Ti催化空间构型和X射线吸收光谱: Car-Parrinello分子动力学和密度泛函理论研究

通过采用Car-Parrinello分子动力学方法对掺杂Ti前后的NaAlH₄(001)2×2×1超晶胞表面晶体在333 K(60 ℃)温度条件催化脱氢的空间构型做了理论研究,发现掺杂Ti的合金中AlH₄团的其中两个Al—H键长分别从约1.64 (1 =0.1 nm)增大至1.74和1.93 ,而未掺杂合金表面中AlH₄团的4个Al—H键长基本不变,这意味着掺杂Ti相对未掺杂的合金更易于放氢.但在模拟温度条件下并未发现Ti-Al成键趋     

Molecular structure,NMR and vibrational spectral analysis of 2,4‐difluorophenol by ab initio HF and density functional theory

Quantum chemical calculations of energies, geometries and vibrational wavenumbers of 2,4‐difluorophenol (2,4‐DFP) were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6‐311G(d,p) as basis set. The optimized geometrical parameters obtained by HF and DFT calculations are in good agreement with related molecules. The best level of theory in order to reproduce the experimental wavenumbers is the B3LYP method with the 6‐311G(d,p) basis set. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of 2,4‐DFP is also reported. The entropy of the title compound was also performed at HF/6‐311G(d,p) and B3LYP/6‐311G(d,p) levels of theory. The isotropic chemical shift computed by ¹H, ¹³C NMR analyses also shows good agreement with experimental observations. The theoretical spectrograms for FT‐IR and FT‐Raman spectra of the title molecule have been constructed. Copyright © 2009 John Wiley & Sons, Ltd.     

Interpretation of 1H and 2H spin–lattice relaxation dispersions: Insights from molecular dynamics simulations of polymer melts

We demonstrate that molecular dynamics simulations are a versatile tool to ascertain the interpretation of spin–lattice relaxation data. For ¹H, our simulation approach allows us to separate and to compare intra- and inter-molecular contributions to spin–lattice relaxation dispersions. Dealing with the important example of polymer melts, we show that the intramolecular parts of ¹H spectral densities and correlation functions are governed by rotational motion, while their inter-molecular counterparts provide access to translational motion, in particular, to mean-squared displacements and self-diffusion coefficients. Exploiting that the full microscopic information is available from molecular dynamics simulations, we determine the range of validity of experimental approaches, which often assume Gaussian dynamics, and we provide guidelines for the determination of free parameters required in experimental analyses. For ²H, we examine the traditional methodology to extract correlation times of complex dynamics from relaxation data. Furthermore, based on knowledge from our computational study, it is shown that measurement of ²H spin–lattice relaxation dispersions allows one to disentangle the intra- and inter-molecular contributions to the corresponding ¹H data in experimental work. Altogether, our simulation results yield a solid basis for future ¹H and ²H spin–lattice relaxation analysis.     

The structure,dynamics and solvation mechanisms of ions in water from long time molecular dynamics simulations: a case study of CaCl2 (aq) aqueous solutions

Systematic long time (5–20 ns) molecular dynamics (MD) simulations have been carried out to study the structural and dynamical properties of CaCl₂ aqueous solutions over a wide range of concentrations (≤9.26 m) in this study. Our simulations reveal totally different structural characteristics of those yielded from short time (≤1 ns) MD simulations [A.A. Chialvo and J.M. Simonson, J. Chem. Phys. 119, 8052 (2003); T. Megyes, I. Bako, S. Balint, T. Grosz, and T. Radnai, J. Mol. Liq. 129, 63 (2006)]. An apparent discontinuity was found at 4–5 m of CaCl₂ in various properties including ion–water coordination number and self-diffusion coefficient of ions, which were first noticed by Phutela and Pitzer in their thermodynamic modelling [R.C. Phutela and K.S. Pitzer, J. Sol. Chem. 12, 201 (1983)]. In this study, residence time was first taken into consideration in the study of Ca²⁺–Cl^? ion pairing, and it was found that contact ion pair and solvent-sharing ion pair start to form at the CaCl₂(aq) concentrations of about 4.5 and 4 m, respectively, which may be responsible for the apparent discontinuity. In addition, the residence time of water molecules around Ca²⁺ or Cl^? showed that the hydration structures of Ca²⁺ and Cl^? are flexible with short residence time (<1 ns). It needs to be pointed out that it takes much longer simulation time for the CaCl₂–H₂O system to reach equilibrium than what was assumed in previous studies.     

基于密度泛函理论下O和Na掺杂单层h-BN的电子结构性质和光学效应的分析

基于密度泛函理论的第一性原理方法研究了O、Na单掺杂及O和Na共掺杂单层h-BN的形成能、电子结构和光学性质.结果表明:单掺杂体系中,O掺杂N位置、Na掺杂B位置时,掺杂形成能最低;共掺杂体系中,O和Na邻位掺杂,掺杂形成能最低.与单层h-BN相比,引入杂质原子后的体系禁带宽度均减小,其中O掺杂为n型掺杂,Na掺杂为p型掺杂,而O和Na共掺h-BN体系为直接带隙材料,有利于提高载流子的迁移率.在光学性质方面,Na掺杂h-BN体系与O和Na共掺h-BN的静介电常数均增大,在低能区介电虚部和光吸收峰均发生红移,其中Na掺杂体系红移最为显著,极化能力最强.因此Na单掺和O和Na共掺有望增强单层h-BN的光催化能力,可扩展其在催化材料、光电器件等领域的应用.     

聚酰亚胺/钽铌酸钾纳米颗粒复合材料结构与机械性能分子动力学模拟

利用多尺度建模方法构建了聚酰亚胺/钽铌酸钾纳米颗粒复合物模型, 通过分子动力学模拟研究了不同尺寸钽铌酸钾纳米颗粒(5.5, 8.0, 9.4, 10.5, 11.5 Å)对复合材料的结构、弹性模量和相互作用能的影响规律, 并通过计算纳米颗粒表面原子键能和单位表面积原子数目探究了复合物机械性能提高的内部机理. 聚酰亚胺和聚酰亚胺/钽铌酸钾复合材料的杨氏模量分别为2.91和3.17 GPa, 泊松比分别为0.37和0.35, 钽铌酸钾纳米颗粒的引入可以显著改善聚酰亚胺的机械性能. 纳米颗粒表面原子的键能为8.62-54.37 kJ·mol^-1, 表明颗粒与基体主要通过范德华力作用结合且有氢键存在. 计算结果表明, 相同掺杂比例下, 纳米颗粒尺寸越小, 纳米颗粒表面原子数目越大, 颗粒与基体作用更强, 杨氏模量的提高幅度越大, 尺寸效应越显著. 因此, 掺杂小尺寸纳米颗粒是提高聚酰亚胺机械性能的有效途径.     

温度及深度对钛中氦泡释放过程影响的分子动力学研究

利用分子动力学模拟方法对温度及He泡深度给金属Ti内He泡的体积、压强和释放过程等带来的影响进行了研究. 首先, 通过研究室温下He泡在金属Ti内不同深度处的状态, 得到He泡的形状、压强、体积等物理量随其深度的变化规律. 发现He泡压强随其深度增加逐渐变大, 体积则逐渐减小, 但当He泡深度增大到2.6 nm时, 二者均维持在某个固定值附近. 然后对包含有He泡的Ti体系在温度作用下的演化过程进行了模拟, 发现不同深度处He泡从金属Ti内释放出来所需要的临界温度有很大差别, 总体来看He泡越深, 释放所需的临界温度越高. 但不同温度下He原子的释放速率没有明显差别, 释放过程几乎均为瞬间完成. 最后通过对He泡内部压强和其上方金属Ti薄层的抗张强度进行统计对比, 阐述了金属Ti 体内He泡的释放机制: 当He泡内部压强大于其上方Ti薄层抗张强度时, He泡就会将Ti 薄层撕裂, 从而使He原子得到释放.     

基于密度泛函理论的外电场下盐交联聚乙烯分子的结构及其特性

交联聚乙烯是主要的高压电缆绝缘材料.为了研究外电场对盐交联分子结构的影响,本文对Zn原子使用def2-TZVP基组, C, H, O原子使用6-31G(d)基组,运用明尼苏达密度泛函(M06-2X)对交联聚乙烯分子进行优化得到了它的稳定结构.并研究了不同外电场(0—0.020 a.u., 1 a.u.=5.142×10~(11)V/m)作用下盐交联聚乙烯分子结构和能量变化,外电场对前线轨道的能级和成分的影响,原子之间的键级、断键和红光光谱的变化.研究结果表明:随着电场的增大,交联聚乙烯分子从空间网状结构逐渐变成线性结构,总能量降低,但势能增大,偶极矩和极化率升高,交联聚乙烯分子的稳定性随着电场的增大而降低;最高占据轨道能级持续增大,最低空轨道能级从0.011 a.u.电场开始持续降低,能隙持续降低,临界击穿场强为11.16 GV/m;沿电场方向聚乙烯链端表现出亲核反应活性,它的C—C键更容易断裂,形成甲基碳负离子,逆电场方向聚乙烯链端表现出亲电反应活性,它的C—H键更容易断裂形成H正离子;分子红外光谱高频区吸收峰明显红移,低频区吸收峰既有红移又有蓝移.     

Analysis of structure and vibrational spectra of 2,5‐dihydroxybenzoicacid based on density functional theory calculations

The spectra of 2,5‐dihydroxybenzoic acid (DHBA) have been recorded using Fourier transform‐infrared spectroscopy (FT‐IR) and FT‐Raman measurements. The total energy calculations of DHBA were evaluated for various possible conformers. The spectra were interpreted with the help of normal coordinate analysis based on density functional theory (DFT) using standard B3LYP/6–31G* method for the most optimized geometry. The effect of intramolecular hydrogen bonding was discussed. Normal coordinate calculations were performed with the DFT force field corrected by a recommended set of scaling factors, yielding fairly good agreement between observed and calculated frequencies. On the basis of the comparison between calculated and experimental results, assignments of fundamental modes were examined. Copyright © 2009 John Wiley & Sons, Ltd.     

Density functional theory and molecular dynamics simulation study on corrosion inhibition performance of mild steel by mercapto-quinoline Schiff base corrosion inhibitor

Corrosion inhibition mechanism of two mercapto-quinoline Schiff bases, eg., 3-((phenylimino)methyl)quinoline-2-thiol (PMQ) and 3-((5-methylthiazol-2-ylimino)methyl) quinoline-2-thiol (MMQT) on mild steel surface is investigated by quantum chemical calculation and molecular dynamics simulation. Quantum chemical parameters such as E_HOMO, E_LUMO, energy gap (ΔE), dipolemoment (µ), electronegativity (χ), global hardness (η) and fraction of electron transfers from the inhibitor molecule to the metallic atom surface (ΔN) have been studied to investigate their relative corrosion inhibition performance. Parameters like local reactive sites of the present molecule have been analyzed through Fukui indices. Moreover, adsorption behavior of the inhibitor molecules on Fe (1 1 0) surface have been analyzed using molecular dynamics simulation. The binding strength of the concerned inhibitor molecules on mild steel surface follows the order MMQT>PMQ, which is in good agreement with the experimentally determined inhibition efficiencies. In view of the above, our approach will be helpful for quick prediction of a potential inhibitor from a lot of similar inhibitors and subsequently in their rational designed synthesis for corrosion inhibition application following a wet chemical synthetic route.