A CC2 dielectric continuum model and a CC2 molecular mechanics model

In this paper we present theory and applications for the second-order approximate singles and doubles coupled cluster (CC2) electronic structure method coupled to either a dielectric continuum (the CC2/DC model) or a molecular mechanical intermolecular force field (the CC2/MM model). Calculations of the interaction energy, solvation energy, electric dipole moment and electric quadrupole moment of liquid water are presented using the correlated CC2 approach. The results are compared to the corresponding results using the uncorrelated Hartree-Fock (HF) and the correlated coupled cluster singles and doubles (CCSD) methods. Also, a hierarchy in the coupling between the quantum mechanical (QM) and the molecular mechanical (MM) part of the system is investigated in the QM/MM model for the three different electronic structure methods.     

Hydrogen bonding in liquid water: An ab initio QM/MM MD simulation study

Pattern and dynamics of hydrogen bonds in liquid water were investigated by a quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulation at Hartree–Fock (HF) level of theory. A large subregion of the whole system comprising two complete coordination shells was treated quantum mechanically in order to include all polarization and charge transfer effects and to obtain accurate data about structure and dynamics of the intermolecular bonds. The results of this investigation are in agreement with recent experimental findings and suggest that in liquid water every molecule forms in average 2.8, but almost as a rule less than four intermolecular hydrogen bonds.     

QM/MM study of hydrolysis of arginine catalysed by arginase

ABSTRACT

In this paper, we have investigated the catalytic mechanism of rat liver arginase using a quantum mechanics/molecular mechanics (QM/MM) approach. The enzyme catalyses the hydrolysis of L-arginine (L-Arg) to generate L-ornithine and urea. The reaction mechanism proposed by the previous experimental studies is well reproduced by the QM/MM computations. The explicit treatment of the protein environment suggests that Glu277 fulfil its role in stabilising and orienting L-Arg before nucleophilic attack by the bridging hydroxide in the first step. We have also found that the proton transfer step involving a hydrogen bond switch is the rate-limiting step. The activation energy is computed to be 9.0 and 5.9 kcal/mol at the UB3LYP-D3/CHARMM22 and UBHandHLYP-D3/CHARMM22 levels, which are comparable to the observed activation barrier of 7.2 kcal/mol.     

Investigation of dodecylammonium adsorption on mica,albite and quartz surfaces by QM/MM simulation

The absorption mechanisms of collector and mineral surface structures play important roles in studies of lepidolite flotation. In this work, quantum mechanics (QM) and hybrid quantum mechanics/molecular mechanics (MM) methods were implemented to investigate the flotation mechanisms of lepidolite from muscovite, quartz and albite. The crystal structures, electron density distributions, bonds and the densities of states of lepidolite were calculated and compared with those of muscovite. The adsorption structures and energies of monomer dodecylammonium (DDA) on the three different minerals were also calculated. The headgroup of the DDA cation was found to adsorb on the surface of minerals, with its hydrophobic tail stretching into the vacuum slab, approximately perpendicular to the surface. Simulation results indicate that the purity of fine lepidolite is limited by the existence of muscovite, due to their similarities in surficial structure and properties. Other gangues were found to be removed efficiently with the use of acidic conditions. The results are in good agreement with other experiments. Compared with simple MM simulations, the use of the QM/MM methods to investigate the adsorption on minerals without specific forcefield parameters was concluded to be a more accurate method to attain monomer surfactant–mineral adsorption energies.     

基于参考势的从头算量子力学/分子力学混合方法研究Parvalbumin B蛋白结合钙、镁离子的选择性

蛋白的离子选择性与蛋白的功能密切相关,而离子选择性本质上来源于蛋白分子与离子结合自由能的差别. 尽管近几十年来分子力场在描述蛋白体系相互作用方面取得了长足的进步,由于缺乏对静电极化和电荷转移效应显式的描述,传统的分子力场依然难以精确地描述金属蛋白体系中蛋白质与金属离子的相互作用. 量子化学方法非常适合于蛋白质与金属离子之间相互作用的描述. 但是在分子模拟中采用量子化学方法则太昂贵了. 近年来发展起来的参考势方法在保证计算精度的前提下兼顾效率,可以有效地解决这个窘境. 在这个方法中,动力学模拟的轨迹是在分子力场的精度下获得的. 随后,通过从分子力场到量子化学方法的矫正,从而获得在量子化学势函数级别下的自由能信息. 本文采用参考势函数方法研究了Parvalbumin B蛋白的结合口袋对钙、镁离子的选择性. 计算结果表明电荷转移效应非常重要,而量子化学方法可以比较精确地预测离子的选择性. 并且,量子化学区域的选择对于结果的可靠性也是非常重要的.     

Combined multi-level quantum mechanics theories and molecular mechanics study of water-induced transition state of OH~- + CO_2 reaction in aqueous solution

The presence of a solvent interacting with a system brings about qualitative changes from the corresponding gasphase reactions. A solvent can not only change the energetics along the reaction pathway, but also radically alter the reaction mechanism. Here, we investigated the water-induced transition state of the OH~- + CO_2→ HCO_3~- reaction using a multi-level quantum mechanics and molecular mechanics method with an explicit water model. The solvent energy contribution along the reaction pathway has a maximum value which induces the highest energy point on the potential of mean force. The charge transfer from OH~- to CO_2 results in the breaking of the OH~- solvation shell and the forming of the CO_2 solvation shell. The loss of hydrogen bonds in the OH~-solvation shell without being compensated by the formation of hydrogen bonds in the CO_2 solvation shell induces the transition state in the aqueous solution. The calculated free energy reaction barrier at the CCSD(T)/MM level of theory, 11.8 kcal/mol, agrees very well with the experimental value, 12.1 kcal/mol.     

Parallelization of the polarizable embedding scheme for higher-order response functions

We present a parallel implementation of the Polarizable Embedding (PE) method, an advanced quantum mechanics/molecular mechanics (QM/MM) approach, for Hartree–Fock (PE-HF) and density functional theory (PE-DFT). The parallelization includes calculations of energies and linear, quadratic, and cubic response functions. The couplings to the QM system due to the polarizable embedding potential have been implemented using a master/slave approach. The implementation shows good scaling behaviour, demonstrated through calculations on a small (a water molecule in a bulk of water molecules) and a larger system (Green Fluorescent Protein (GFP)).     

有序分子系统的线性与非线性光谱学的简化描述

通过对有序分子系统的线性与非线性光谱学的简化描述 ,帮助对有序分子体系光谱学进行研究的实验学家建立明确的物理图像和定量的研究工具 .这一描述是从最近对二阶非线性光学界面研究技术 ,即光学二次谐波 (SHG)和和频偏振振动光谱 (SFG VPS)的定量取向和偏振处理中推广出来的 .这一处理的方法关键在于简化线性和非线性光学中的有效极化率 ,构造出一个通用的取向泛函 ,并能通过实验参数清晰地计算出取向泛函的取向和强度因子 .同时还讨论了相干光谱技术在准确测量有序分子体系的取向和序的相比于非相干光谱方法的优点 .     

Freezing of water confined at the nanoscale

Freezing of water in hydrophilic nanopores (D=1.2 nm) is probed at the microscopic scale using x-ray diffraction, Raman spectroscopy, and molecular simulation. A freezing scenario, which has not been observed previously, is reported; while the pore surface induces orientational order of water in contact with it, water does not crystallize at temperatures as low as 173?K. Crystallization at the surface is suppressed as the number of hydrogen bonds formed is insufficient (even when including hydrogen bonds with the surface), while crystallization in the pore center is hindered as the curvature prevents the formation of a network of tetrahedrally coordinated molecules. This sheds light on the concept of an ubiquitous unfreezable water layer by showing that the latter has a rigid (i.e., glassy) liquidlike structure, but can exhibit orientational order.     

Thermal behavior of hydrogen atom intercalated between two layers of C150H30 graphite plane: MD simulation

For investigation of thermal behaviors of hydrogen (H) atom in a graphite intercalated compound (GIC), the molecular dynamic (MD) procedure at the molecular mechanics 2 (MM2) level was applied to a hydrogen terminated cluster model composed of two layers of C₁₅₀H₃₀ plane. On the basis of the optimized structure, one intercalated H atom was stabilized at the mass center of the cluster model. According to the trajectory of the intercalated H atom, the diffusion is initiated at 100 K towards lower potential energy area in the periphery of the cluster model. The diffusion rate increased with the increase in the simulation temperature from 100 to 500 K. According to the extended Hückel calculation, the band gap of graphite is broadened by 0.1 eV with the intercalation. Thus, the present MD simulation proposed that the semiconductivity of GIC is promoted due to the development of the ionic conductivity. However, H atom adsorbed on the surface of C₁₅₀H₃₀ plane formed the stable covalent bond with a host carbon atom and made little contribution to the conductivity.     

Solvent effects and potential of mean force study of the S_N2 reaction of CH_3F+CN~- in water

We used a combined quantum mechanics and molecular mechanics(QM/MM) method to investigate the solvent effects and potential of mean force of the CH_3F+CN~- reaction in water. Comparing to gas phase, the water solution substantially affects the structures of the stationary points along the reaction path. We quantitatively obtained the solvent effects' contributions to the reaction: 1.7 kcal/mol to the activation barrier and -26.0 kcal/mol to the reaction free energy.The potential mean of force calculated with the density functional theory/MM theory has a barrier height at 19.7 kcal/mol,consistent with the experimental result at 23.0 kcal/mol; the calculated reaction free energy at -43.5 kcal/mol is also consistent with the one estimated based on the gas-phase data at -39.7 kcal/mol.     

Torsional mechanics of single walled carbon nanotubes with hydrogen for energy storage and fuel cell applications

Torsional mechanics of single walled carbon nanotubes(SWCNTs) encapsulated with hydrogen molecules was investigated in this study, using the molecular dynamics(MD) simulation approach. The torsional properties of hydrogen stored SWCNTs were crucial for determining the durability and lifetime of SWNCTs-based energy storage and proton exchange membrane fuel cell(PEMFC) applications. The influence of hydrogen storage concentration, SWCNT geometry, vacancy defects, temperature variation and varying boundaries of rotated as well as fixed groups on the torsional mechanics of SWCNT was investigated. The results and conclusions provide an insight into the torsional properties of SWCNTs with hydrogen storage that could be used for the development of SWCNTs-based hydrogen storage devices and PEMFC applications.     

Theory of chemical bonds in metalloenzymes XIX: labile manganese oxygen bonds of the CaMn4O5 cluster in oxygen evolving complex of photosystem II

Spin polarisation effects of labile manganese–oxygen bonds in the X-ray diffraction structure of the oxygen-evolving complex (OEC) of photosystem II (PSII) at 1.9 Å resolution have been investigated by the UB3LYP computations on the basis of three different theoretical models with and without hydrogen bonds: quantum-mechanical (QM) Model I, QM(Model II)/MM and QM Model III. The spin densities on the manganese and oxygen atoms of the CaMn₄O₅ cluster revealed by these computations have elucidated internal, semi-internal and external reductions of high-valent manganese ions in the CaMn₄O₅ cluster in OEC of PSII. The internal reduction of Mn(IV) ions by the back charge transfer from oxygen dianions is remarkable in the small QM Model I, whereas it is significantly reduced in the case of more realistic QM Model III including hydrogen bonding stabilisations of oxygen dianions. However, semi-internal reduction of the CaMn₄O₅ cluster with remote amino acid residues such as Asp61 anion occurs even in QM Model III, indicating the necessity of large QM parts for redox-active systems such as OEC of PSII. The computational results have clearly demonstrated important roles of confinement effects of the CaMn₄O₅ cluster with labile Mn–O bonds with protein. These computational results have been applied to molecular design of artificial robust catalysts for water oxidation by use of sunlight.     

Small silver clusters at paramagnetic defects of silica surfaces: A density functional embedded-cluster study

We studied the interaction of small Ag_n clusters (n = 1–4) with paramagnetic defect centers of a dehydroxylated silica surface using an all-electron scalar relativistic density functional method. The surface and adsorption complexes on it were modeled with an accurate quantum mechanics/molecular mechanics (QM/MM) scheme of embedding QM clusters in an elastic polarizable environment, described at the molecular mechanics level (MM). We analyzed two types of frequent point defects as sites for trapping and growing of Ag clusters: a silicon atom with a dangling bond (E′ center), ≡ Si?, and a non-bridging oxygen center (NBO), ≡ Si–O?. The Ag clusters interact with these paramagnetic centers forming strong covalent metal-defect bonds. The high adsorption energy allows one to consider the NBO and E′ sites as traps of single Ag atoms and as centers of cluster growth. We also explored the effect of adsorption on observable electronic properties of the silver clusters and of the defects of the silica surface.     

黑芥子苷生物合成中酶催化机理的QM/MM研究

黑芥子苷作为植物中硫代葡萄糖苷最为主要且丰富的类型,在促进健康和昆虫防御方面具有潜在的功能. 黑芥子苷核心结构生物合成的最后一步在硫代葡萄糖苷化合物中具有高度的代表性. 这一步是在硫转移酶的催化作用下,从3-(甲基硫代)丙基脱硫葡萄糖苷转化为3-(甲基硫代)丙基葡萄糖苷的过程. 由于硫转移酶与3-(甲基硫代)丙基葡萄糖苷复合物的晶体结构还未见报道,因此一直以来人们对该磺化反应的细节知之甚少. 幸运的是,黑芥子苷与3-(甲基硫代)丙基葡萄糖苷的结构十分相似,而且结合有黑芥子苷的拟南芥硫转移酶18的晶体结构已经确定. 为了了解此酶的作用机理,本文采用分子动力学模拟以及组合的量子力学和分子力学方法研究了拟南芥硫转移酶18催化脱硫-黑芥子苷转化为黑芥子苷的过程. 计算结果表明,该反应是通过协同解离机理发生的,而且在反应过程中,赖氨酸93、苏氨酸96、苏氨酸97、酪氨酸130、组氨酸155和酶的两条肽链(脯氨酸92-赖氨酸93肽链和谷氨酰胺95-苏氨酸96-苏氨酸97肽链)稳定了过渡态的结构,在定位底物和促进催化反应中发挥了重要的作用,其中,组氨酸155在反应过程中充当催化碱,赖氨酸93充当催化酸. 目前提出的协同解离机理解释了拟南芥硫转移酶18在黑芥子苷生物合成中的作用,并对其他硫转移酶催化葡萄糖苷生物合成的研究具有指导意义.     

Molecular Dynamics Simulation of 4-N-Hexyl-4'-Cyanobiphenyl Adsorbed at the Air-Water Interface

The interfacial behavior of 4-n-hexyl-4'-cyanobiphenyl(6CB) molecules at the air-water interface is investigated by full atomistic molecular dynamics simulations. To understand the morphology and the structure of adsorbed 6CB molecules in detail, the snapshots and mass density profiles of the simulation system are generated. The average tilt angles between the interface normal and various vectors defined in the rigid and alkyl parts of 6CB are in good agreement with the experimental data available. The interfacial thickness and monolayer width are obtained from the mass density profiles of water and 6CB phase, respectively. The second and fourth rank orientational order parameters of cyanobiphenyl core are found to be larger than those of an elastic alkyl chain.Bond order parameters for 6CB are also calculated. The calculated oxygen-oxygen radial distribution function and hydrogen bonding statistics for bulk water are compared with those for the interfacial region. The surface tensions of the systems are calculated. All simulation results are compared with the available literature data.     

Investigation of hydrogen bond effects on the hyperpolarizability of 2-Aminopyridinium maleate (2APM) complex and determining the non-linear optical susceptibility of the molecular crystal of 2APM

2-Aminopyridinium maleate (2APM) is a recently discovered organic acid-base complex that crystallizes in a non-centrosymmetric space group Pc and hence has a nonzero second-order optical susceptibility. In 2APM the cation (aminopyridinium ion) is connected to the anion (maleate ion) through hydrogen bonds (N1-H10–O2 and N2-H12–O1), we have calculated the molecular properties of 2APM for varying strength of these hydrogen bonds. It is observed that the molecular hyperpolarizabilty varies for varying strength of these hydrogen bonds. These observations are interpreted in terms of the change in nature of the hydrogen bond interaction as its strength is varied. Macropscopic second-order optical susceptibility (d ₀) of 2APM is obtained using the calculated value of molecular hyperpolarizability and the reported crystal structure of 2APM. In order to study the influence of molecular packing on the macroscopic non-linear optical property of the crystal, susceptibility calculations are repeated for 2-methyl-4nitroaniline (MNA) crystal, which is a very well known non-linear optical organic crystal with an exceptionally high value of second-order optical susceptibility. A comparison between the non-linear optical property of 2APM and MNA crystals is given. Comparing the values of d ₀ of 2APM crystals with that of urea shows that the nonlinear optical response of 2APM crystals will be nearly 10 times that of a urea crystal.     

The UV-vis absorption spectrum of the flavonol quercetin in methanolic solution: A theoretical investigation

The UV-vis absorption spectrum of the solvated quercetin molecule in methanol was investigated theoretically by means of an elegant type of QM/MM scheme better known as sequential Monte Carlo/quantum mechanics (S-MC/QM) methodology. A set of 125 uncorrelated Monte Carlo molecular liquid structures were properly selected through the autocorrelation function of the energy in order to be used in the quantum mechanical calculations. These molecular liquid structures were obtained by means of the radial and minimum distance distribution functions. A detailed account of the pattern of hydrogen bond structures obtained in this study is also available. The computed results obtained here were directly compared with the available experimental data in order to validate our theoretical model and through this comparison a very good conformity between theoretical and available experimental results was found.