Vibrational spectrum at a water surface: a hybrid quantum mechanics/molecular mechanics molecular dynamics approach

A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.     

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.     

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.     

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.     

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)).     

Optical properties of pyridine and methyl-pyridinium in water using DFT/MM

Molecular properties such as excitation energies, polarisabilities and two-photon absorption cross-sections of pyridine and N-methyl-pyridinium embedded in a solvent of water are studied using density functional theory/molecular mechanics (DFT/MM) calculations. The purpose of this study is to study how well the differences between a cationic and a neutral specie can be predicted with water as the solvent. In order to answer this question, the DFT/MM method used is benchmarked in terms of convergence profiles, e.g. how many calculations are needed in order to obtain a statistically converged result. Quantification of for example how many water molecules needs to be included in the quantum mechanics system in the calculations before a converged molecular property is obtained which is also benchmarked. The latter will serve as valuable information in further calculations of larger organic molecules, where more experimental data are available. In this work, the calculated excitation energies are compared to experimentally determined ultraviolet/visible (UV/VIS) spectra of both pyridine and N-methyl-pyridinium and a reasonable agreement is found.     

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.     

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.     

Molecular mechanics modeling of the adsorption of methionine on graphite

In this study we were modeling the adsorption of the amino acid methionine on a graphite surface using molecular mechanics calculations. We were employing two different force fields, namely MM+ and AMBER, and considering the molecule in its non-ionic and zwitterionic form. The surface was modeled as a single sheet of graphite. We found that each of the force fields delivers qualitative consistency with experimental results, but the AMBER force field with the parameter set of AMBER3 leads to the best quantitative agreement regarding adsorption energy, bonding energies and distances.     

The rotating Morse potential energy eigenvalues solved by using the analytical transfer matrix method

We study the eigenvalues of the rotating Morse potential by using the quantization condition from the analytical transfer matrix(ATM) method.A hierarchy of supersymmetric partner potentials is obtained with Pekeris approximation,which can be used to calculate the energies of higher rotational states from the energies of lower states.The energies of rotational states of the hydrogen molecule are calculated by the ATM condition,and comparison of the results with those from the hypervirial perturbation method reveals that the accuracy of the approximate expression of Pekeris for the eigenvalues of the rotating Morse potential can be improved substantially in the framework of supersymmetric quantum mechanics.     

Quantum mechanics simulation and experimental study of adhesive interaction and aggregation of carbon-silicate nanoparticles—reinforcing fillers of polymer composites

Nanoparticles are widely used as polymer composite-reinforcing additives—fillers. Understanding the interaction mechanisms and regularities responsible for nanoparticle aggregation is of great significance for elucidating the nature of reinforcing of polymer composites. The paper reports on quantum mechanics calculations and full-scale experimental study of adhesive interaction of carbon and silicate adsorption complexes (nanomodels of active filler particles of polymer composites). The quantum mechanics approach allowed describing the adhesive properties of particle aggregates reasoning from nanoscopic structure of their surface. The quantum mechanics data were checked for adequacy on schungite—a natural mineral containing carbon and silicate. Schungite microparticles were milled to nanosizes by colloidal grinding in various disperse liquid media (alcohol, acetone, water) and the structure and properties of aggregated schungite micro- and nanoparticles were studied; fractal analysis of their surface was performed. It is found that smaller aggregates of silicate and carbon particles with higher surface fractal dimension are formed in colloidal grinding with small molecular sizes of disperse media (in our case, ethanol or methanol) and this agrees with the data predicted by quantum mechanics calculations.     

NO对未燃尽炭吸附汞影响的机理研究

本文应用量子化学密度泛函理论B3PW91方法,研究了NO对飞灰中未燃尽炭吸附汞的影响机理。建立了含有NO的未燃尽炭固体表面簇模型,计算得到了单质汞在含有NO的未燃尽炭表面的不同吸附位、吸附构型和吸附能。不同吸附方式中,NO平行吸附在未燃尽炭表面时最稳定。NO对单质汞在飞灰未燃尽炭表面的吸附的影响机理比较复杂,与烟气中NO的含量有关。研究结果表明量子化学的理论计算是揭示汞等痕量元素的吸附机理的一种有效方法。     

Calculations of <Superscript>31</Superscript>P Magnetic Shielding Constants of Derivatives of Betaine and Phosphine Molecules Dissolved in Different Solvents by Using Supermolecular Model and Combined Methods of Quantum Chemistry and Molecular Mechanics

Spatial structures of molecular clusters modeling a solvate shell around phosphorus-containing methyl- and butyl-derivatives of phosphine and betaine molecules dissolved in different solvents (acetone, toluene, formamide) have been calculated by using different variants of density functional theory (unrestricted Becke three-parameter Lee–Yang–Parr [UB3LYP], Perdew–Burke–Ernzerhof [PBE], optimized exchange functional [OPTX] developed by Handy and Cohen in conjunction with Lee–Yang–Parr [LYP] correlational functional [OLYP]) with 6-31G(d,p) and 6-31G++(d,p) basis sets. The ³¹P magnetic shielding constants for the structures are calculated with the usage of gauge-including atomic orbitals in UB3LYP/6-31G(d,p) and 6-31G++(d,p) methods. The modeling of molecular clusters is done by using the supermolecular model, the molecular mechanics method and the combination of quantum chemistry and molecular mechanics methods (QM/MM). The own N-layered integrated molecular orbital method (ONIOM) has been applied for modeling and calculating of isotropic ³¹P nucleus magnetic shielding of clusters of trimethylphosphine and trimethylbetaine molecules dissolved in acetone using combinations of UB3LYP/6-31G(d,p) (higher level) and unrestricted Hartree–Fock (UHF)/6-31G(d,p) (lower level) methods. Applicability of the ONIOM approach and different ways of modeling to the calculation of ³¹P nucleus magnetic shielding constants is studied. A comparison of the results obtained by the density functional theory, ONIOM and MM methods is given.     

On the characteristic properties of oxidation of sulfide minerals exposed to nanosecond electromagnetic pulses

High-power nanosecond electromagnetic pulses cause changes in the chemical and phase surface composition of sulfide minerals (pyrrhotite and pentlandite) and their sorption, flotation, and chemical activities. The influence of the conditions and parameters of the electric-pulse effect on the change in the amount of elemental sulfur and iron oxide on the surface of mineral particles, as well as the concentration of iron and sulfoxide ions in the aqueous mineral suspension, has been studied. The parameters of preliminary pulsed treatment of pyrrhotite and pentlandite that lead to improvement of flotation separation of minerals have been determined.     

东升庙硫多金属矿床氧化微粒的XRD,FTIR和XPS分析

利用XRD,FTIR和XPS现代分析测试技术对东升庙硫多金属矿床氧化微粒的物质组成、相结构和表面元素状态进行了表征以及转化机理研究。结果表明,样品主要由石膏、方解石、石英、白云母、针铁矿、有机质等组成,深部氧化带原生矿石主要发生了氧化、水解、脱水和碳酸化作用,且氧化过程、氧化条件不及地表氧化带复杂,未发现新的矿物,少见西北干旱和极端干旱气候条件下地表氧化带极其发育的硫酸盐类矿物。研究结果不仅可以用于该类型矿床氧化微粒矿物鉴定方面,而且对于这部分矿体的找矿勘探、采矿、选矿等方面具有重要意义。     

CO methanation on Ni(1 1 1) and modified Ni3Al(1 1 1) surfaces: A first-principle study

The adsorption energies of intermediates in CO methanation on the modified Ni₃Al(1 1 1) surface and the Ni(1 1 1) surface are calculated using density functional theory. A microkinetic analysis based on the calculated adsorption energies is performed to explain the different kinetics of CO methanation catalyzed by Ni₃Al and Ni powders. The electronic structures of different atoms on the modified Ni₃Al surface are also presented, and correlate well with the adsorption energies and geometries.     

红外拟合光谱分析微波对重晶石浮选的影响机理

目前浮选提高重晶石品位的方法通常采用新型浮选药剂从低品位重晶石矿中进行分选,采用微波加热预处理矿物可提高浮选回收率,但微波对浮选药剂与矿物的作用机理还不清楚。微波加热技术近年来用于矿物加工、冶金与材料制备等领域,具有反应速度快、产品指标高等优点。以油酸钠为捕收剂,对微波预处理后的重晶石纯矿物进行浮选,并对不同微波作用时间下的重晶石浮选样品进行红外光谱检测,通过红外拟合平滑光谱和二阶导数光谱计算分析,研究微波对重晶石浮选的影响机理。浮选试验结果表明,未经微波预处理的重晶石,在油酸钠用量为55 mg·L-1、pH值为8.0的条件下,浮选指标最佳,回收率为91.41%;而对比之下,经微波作用后的重晶石进行浮选,随着微波处理时间的增加浮选指标逐渐提高,且在微波作用60s时的回收率最高,达95.27%。基于浮选试验的红外光谱分析表明,重晶石未经微波预处理进行浮选,与油酸钠作用,在波数为3 004 cm-1处-CH₂-的对称伸缩振动峰、2 953 cm-1处-CH₃的反对称伸缩振动峰、1 119和1 077 cm-1处SO2-₄的非对称伸缩振动峰均发生了红移,说明油酸钠在重晶石表面发生化学吸附;而经微波预处理后的重晶石浮选时,在波数为2 853 cm-1处-CH₂-对称伸缩振动峰、2 923 cm-1处-CH₂-反对称伸缩振动峰、2 958 cm-1处-CH₃反对称伸缩振动峰、1 181,1 122和1 086 cm-1处SO2-₄非对称伸缩振动峰、982 cm-1处SO2-₄对称伸缩振动峰、635和610 cm-1处SO2-₄弯曲振动峰,其峰位并未发生红移,但峰强随着微波作用时间的增加明显加强,且微波作用60 s时其峰强增加最明显;对微波处理后的红外光谱进行拟合平滑光谱和二阶导数光谱计算发现,在波数为2 958,2 923,2 853,1 181,1 122,1 086,982,635和610 cm-1处峰面积均有不同程度的增加,且在微波作用60s时峰面积分别增加了1.84%,259.12%,761.15%,235.72%,145.61%,198.50%,641.16%,549.67%和744.97%,表明微波预处理并未诱发重晶石表面发生化学反应,但强化了捕收剂油酸钠与重晶石矿之间的化学吸附,使其与重晶石表面的化学吸附更加致密,吸附量增加,因此重晶石回收率增加,浮选指标提高。