An efficient simulation technique for electrostatic free energies with applications to azurin

We present an efficient technique for Monte Carlo simulation of electrostatic free energy changes in biomolecular systems. It is a development of a recent method for the study of the influence of electrostatic interactions on the ion binding properties and redox potentials of biomolecules. The electrolyte solution is described by the primitive model, in which ions are treated as hard charged spheres and the solvent is replaced by a structureless continuum. The protein is kept fixed in the center of a spherical simulation cell, and the dielectric constant has the solvent value throughout the cell. By a multiparticle perturbation approach, it is possible to obtain a number of free energy changes within one simulation only. The usefulness of the method is illustrated with a study of the copper binding electron-transport protein azurin (from Alcaligenes denitrificans). The change in acidity of the histidine residues upon changing the redox state of the copper ion is calculated. The theoretical predictions agree well with available experiments. © 1995 by John Wiley & Sons, Inc.     

Spatially adaptive lattice coarse-grained Monte Carlo simulations for diffusion of interacting molecules

While lattice kinetic Monte Carlo (KMC) methods provide insight into numerous complex physical systems governed by interatomic interactions, they are limited to relatively short length and time scales. Recently introduced coarse-grained Monte Carlo (CGMC) simulations can reach much larger length and time scales at considerably lower computational cost. In this paper we extend the CGMC methods to spatially adaptive meshes for the case of surface diffusion (canonical ensemble). We introduce a systematic methodology to derive the transition probabilities for the coarse-grained diffusion process that ensure the correct dynamics and noise, give the correct continuum mesoscopic equations, and satisfy detailed balance. Substantial savings in CPU time are demonstrated compared to microscopic KMC while retaining high accuracy.     

Electrodeposition of copper on a Pt(111) electrode in sulfuric acid containing poly(ethylene glycol) and chloride ions as probed by in situ STM

This study employed real-time in situ STM imaging to examine the adsorption of PEG molecules on Pt(111) modified by a monolayer of copper adatoms and the subsequent bulk Cu deposition in 1 M H(2)SO(4) + 1 mM CuSO(4)+ 1 mM KCl + 88 μM PEG. At the end of Cu underpotential deposition (~0.35 V vs Ag/AgCl), a highly ordered Pt(111)-(√3 × √7)-Cu + HSO(4)(-) structure was observed in 1 M H(2)SO(4) + 1 mM CuSO(4). This adlattice restructured upon the introduction of poly(ethylene glycol) (PEG, molecular weight 200) and chloride anions. At the onset potential for bulk Cu deposition (~0 V), a Pt(111)-(√3 × √3)R30°-Cu + Cl(-) structure was imaged with a tunneling current of 0.5 nA and a bias voltage of 100 mV. Lowering the tunneling current to 0.2 nA yielded a (4 × 4) structure, presumably because of adsorbed PEG200 molecules. The subsequent nucleation and deposition processes of Cu in solution containing PEG and Cl(-) were examined, revealing the nucleation of 2- to 3-nm-wide CuCl clusters on an atomically smooth Pt(111) surface at overpotentials of less than 50 mV. With larger overpotential (η > 150 mV), Cu deposition seemed to bypass the production of CuCl species, leading to layered Cu deposition, starting preferentially at step defects, followed by lateral growth to cover the entire Pt electrode surface. These processes were observed with both PEG200 and 4000, although the former tended to produce more CuCl nanoclusters. Raising [H(2)SO(4)] to 1 M substantiates the suppressing effect of PEG on Cu deposition. This STM study provided atomic- or molecular-level insight into the effect of PEG additives on the deposition of Cu.     

Asymmetric dinuclear copper(I) complexes of bis-(2-(2-pyridyl)ethyl)-2-(N-toluenesulfonylamino)ethylamine with short copper-copper distances

Addition of two equivalents of CuCl to deprotonated bis-(2-(2-pyridyl)ethyl)-2-(N-toluenesulfonylamino)ethylamine (PETAEA) and its derivatives yielded new types of dinuclear Cu(I) complexes, Cu(mu-PETAEA)CuCl, Cu(mu-PEMAEA)CuCl, and Cu(mu-PENAEA)CuCl (PEMAEA is the 4-methoxyphenyl derivative of PETAEA and PENAEA is the 4-nitrophenyl derivative), exhibiting a four coordinate N(4)Cu center, a two coordinate NCuCl center, and a metal-metal distance within the range of 2.6572(8) to 2.6903(3) A. Analysis of the covalent radii for four coordinate and two coordinate copper(I), the acute copper-nitrogen-copper angles, and density functional theory (DFT) calculations suggest a weak attraction between the two copper atoms. The complexes apparently formed in a two-step process with the formation of the tetracoordinate mononuclear complex preceding the coordination of a second equivalent of CuCl to the lone pair of the sulfonamidate ligand.     

A graph-theoretical kinetic Monte Carlo framework for on-lattice chemical kinetics

Existing kinetic Monte Carlo (KMC) frameworks for the simulation of adsorption, desorption, diffusion, and reaction on a lattice often assume that each participating species occupies a single site and represent elementary events involving a maximum of two sites. However, these assumptions may be inadequate, especially in the case of complex chemistries, involving multidentate species or complex coverage and neighboring patterns between several lattice sites. We have developed a novel approach that employs graph-theoretical ideas to overcome these challenges and treat easily complex chemistries. As a benchmark, the Ziff-Gulari-Barshad system is simulated and comparisons of the computational times of the graph-theoretical KMC and a simpler KMC approach are made. Further, to demonstrate the capabilities of our framework, the water-gas shift chemistry on Pt(111) is simulated.     

Method for computing protein binding affinity

A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo move, which allows transitions between the unbound and bound states. Provided that an accurate protein structure is given, that the protein-ligand binding site is known, and that an accurate chemical force field together with a continuum solvation model is used, this method provides a quantitative estimate of the free energy of binding.     

Detection of binuclear copper-caffeine complexes under electrospray ionization condition

A number of copper salts, Cu(OOCCH(3))(2), Cu(ClO(4))(2), Cu(NO(3))(2), CuCl(2) and CuSO(4) have been tested for their ability to form binuclear copper-caffeine complexes. The electrospray ionization (ESI) mass spectra of methanol solution containing caffeine and CuCl(2) or CuSO(4) show signals of two copper atom containing ions, so the signals correspond to binuclear complexes: [2Caf + Cu(2)SO(4)](+), [2Caf + Cu(2)](+), [2Caf + Cu(2)Cl](+), [2Caf + Cu(2)Cl(2)](+) and [2Caf + Cu(2)Cl(3)](+). Sulfate and chloride anion are characterized by charge densities higher than those of the carboxylate, nitrate and perchlorate anion. Thus, due to the electrostatic forces, the binuclear complexes containing SO(4)(2-) or Cl(-) can survive the transfer from solution to the gas phase and then can successfully be observed on ESI mass spectra. The ion [2Caf + Cu(2)Cl(3)](+) is present in solution and could be detected when using methanol/chloroform as solvent. The ions [2Caf + Cu(2)](+), [2Caf + Cu(2)Cl](+) and [2Caf + Cu(2)Cl(2)](+) are formed from the [2Caf + Cu(2)Cl(3)](+) ion (by subsequent loss of Cl atoms) on transfer from the solution to the gas phase or in the gas phase. The ion [2Caf + Cu(2)](+) does not contain a bridging agent, thus it is reasonable to assume that it contains a Cu-Cu bond.     

Comparison of kinetic Monte Carlo and molecular dynamics simulations of diffusion in a model glass former

We present results from kinetic Monte Carlo (KMC) simulations of diffusion in a model glass former. We find that the diffusion constants obtained from KMC simulations have Arrhenius temperature dependence, while the correct behavior, obtained from molecular dynamics simulations, can be super-Arrhenius. We conclude that the discrepancy is due to undersampling of higher-lying local minima in the KMC runs. We suggest that the relevant connectivity of minima on the potential energy surface is proportional to the energy density of the local minima, which determines the "inherent structure entropy." The changing connectivity with potential energy may produce a correlation between dynamics and thermodynamics.     

芘在玻璃基片表面的单层组装及其对有机铜盐的选择性传感

将多环芳烃芘经含三乙基四胺结构的连接臂化学单层组装于玻璃基质表面, 制备了一种荧光薄膜材料. 荧光测量结果表明, 醋酸铜、酒石酸铜、柠檬酸铜等有机铜盐可以显著猝灭薄膜荧光, 而且猝灭过程可逆; 硫酸铜、氯化铜、硝酸铜等无机铜盐对薄膜荧光影响不大; 醋酸锌、醋酸铅、醋酸钴、醋酸镍等其它醋酸盐对有机铜盐的检测影响轻微. 荧光寿命测定表明, 醋酸铜对上述薄膜荧光的猝灭遵循静态猝灭机制.     

Formation of diclofenac molecular ions as the effect of Cu(2+)-π interaction under electrospray ionization mass spectrometry conditions

Solutions containing diclofenac (M) and a copper salt [CuCl2, Cu(ClO4)2, Cu(NO3)2, CuSO4) were analysed by electrospray ionisation mass spectrometry (ESI-MS). Because of the cation-pi interactions in diclofenac-Cu(II) complexes, the diclofenac molecular ion M+* at m/z 295 was formed. It was found that the solvent composition (methanol versus water/methanol) and counter ion strongly affect the M+* ion formation. Formation pathways of ion M+* are discussed.     

The influence of defects on the morphology of Si (111) etched in NH4F

We have implemented a kinetic Monte Carlo (KMC) simulation to study the effects of wafer miscut and wafer defects on the morphologies of Si (111) surfaces etched in NH4F. Although a conventional KMC simulation reproduced previously published results, it failed to produce the morphologies observed in our experiments. By introducing both dopant sites and lattice defect sites into the model, we are able to simulate samples having different dopant elements and densities as well as different defect concentrations. Using the modified KMC simulation, the simulated surface morphologies agree well with the morphologies observed in our experiments. The enhanced model also gives insights to the formation mechanism for multiple level stacking pits, a notable morphology on the etched surfaces of samples with very small miscut angles.     

分散法制备的CuCl/MCM-41上C3H6选择催化还原NO反应的研究

研究了由分散法制备的两种CuCl/MCM-41催化剂上丙烯在过量氧存在下选择催化还原NO反应, 发现所制备的CuCl/AlMCM-41催化剂的反应活性明显高于CuCl/SiMCM-41. XRD, IR, TPR及ESR的研究结果表明, CuCl/AlMCM-41催化剂上的主要活性中心是与骨架铝配位的铜离子(Cu2+/Cu+).     

分散体系中任意形状的胶粒模型与相互作用能——Ⅲ. 园柱体型颗粒

在分散体系的研究中,也经常遇到园柱体型胶粒,例如蛋白质分子,海泡石和凸凹棒石粘土颗粒,它们都能用带电的园柱体型采近似处理。这种类型的颗粒以往研究不多,其原因大约有二,一是处理这类颗粒时,数学上的困难很大;二是这类颗粒之间的相互作用,和它们之间的取向有关。Sparnaay首先用Derjaguin法得出园柱体型颗粒处于平行和垂直位置时,相互排斥能的近似表达式。Brenner和McQuarrie(BM)对颗粒外的电位分布采     

Absolute Helmholtz free energy of highly anharmonic crystals: theory vs Monte Carlo

We discuss the problem of the quantitative theoretical prediction of the absolute free energy for classical highly anharmonic solids. Helmholtz free energy of the Lennard-Jones (LJ) crystal is calculated accurately while accounting for both the anharmonicity of atomic vibrations and the pair and triple correlations in displacements of the atoms from their lattice sites. The comparison with most precise computer simulation data on sublimation and melting lines revealed that theoretical predictions are in excellent agreement with Monte Carlo simulation data in the whole range of temperatures and densities studied.     

CuCl2和CuSO4的核磁共振系数、粘度系数及其与水分子结构的关系

测定了较低浓度范围内CuCl2、CuSO4水溶液的粘度系数(B)、核磁共振(NMR)系数(B')及其对水17O NMR化学位移的影响, 进一步计算了Cu2+、Cl-、SO2-40的粘度系数及核磁共振系数, 并与文献值进行了比较. 利用17O NMR化学位移、粘度系数和核磁共振系数与水团簇结构和水分子缔合的关系, 分析了CuCl2、CuSO4对水结构的影响. 结果表明, CuCl2和CuSO4均具有促进水分子缔合, 使水团簇加大的作用, 且CuSO4对水的缔合作用大于CuCl2, Cl-对水缔合的破坏作用大于SO2-40 . Cu2+作为顺磁离子, 在核磁共振弛豫过程中, 具有明显的缩短水中质子的自旋-晶格弛豫时间, 使谱线变宽的作用.     

Efficient Implementation of Cluster Expansion Models in Surface Kinetic Monte Carlo Simulations with Lateral Interactions: Subtraction Schemes,Supersites, and the Supercluster Contraction

While lateral interaction models for reactions at surfaces have steadily gained popularity and grown in terms of complexity, their use in chemical kinetics has been impeded by the low performance of current kinetic Monte Carlo (KMC) algorithms. The origins of the additional computational cost in KMC simulations with lateral interactions are traced back to the more elaborate cluster expansion Hamiltonian, the more extensive rate updating, and to the impracticality of rate-catalog-based algorithms for interacting adsorbate systems. Favoring instead site-based algorithms, we propose three ways to reduce the cost of KMC simulations: (1) representing the lattice energy by a smaller Supercluster Hamiltonian without loss of accuracy, (2) employing the subtraction schemes for updating key quantities in the simulation that undergo only small, local changes during a reaction event, and (3) applying efficient search algorithms from a set of established methods (supersite approach). The cost of the resulting algorithm is fixed with respect to the number of lattice sites for practical lattice sizes and scales with the square of the range of lateral interactions. The overall added cost of including a complex lateral interaction model amounts to less than a factor 3. Practical issues in implementation due to finite numerical accuracy are discussed in detail, and further suggestions for treating long-range lateral interactions are made. We conclude that, while KMC simulations with complex lateral interaction models are challenging, these challenges can be overcome by modifying the established variable step-size method by employing the supercluster, subtraction, and supersite algorithms (SSS-VSSM). © 2019 Wiley Periodicals, Inc.     

单晶表面上水-气转移反应动力学及可逆吸附的作用—─Monte Carlo 模拟研究

用二元方格网络表示Ｃｕ（１１１）单晶表面上吸附活性位构型，建立了一个水－气转移反应的蒙特卡罗模型；对水－气转移反应的动力学进行了模拟，并研究了可逆吸附在表面反应中的重要作用．当水的解离吸附为反应的决速步骤时，模拟得到的ＣＯ和Ｈ２Ｏ的反应级数与Ｃａｍｐｂｅｌ等的单晶实验结果一致．模拟研究还表明，可逆吸附不仅可以抑制催化剂表面同种吸附物种ｃｌｕｓｔｅｒ的形成，而且可以不断提供新的吸附活性位，从而使表面反应稳定进行得以维持．     

Complexation between the fungicide tebuconazole and copper(II) probed by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) is used to probe the complex formation between tebuconazole (1) and copper(II) salts, which both are commonly used fungicides in agriculture. Experiments with model solutions containing 1 and CuCl(2) reveal the initial formation of the copper(II) species [(1)CuCl](+) and [(1)(2)CuCl](+) which undergo reduction to the corresponding copper(I) ions [(1)Cu](+) and [(1)(2)Cu](+) under more drastic ionization conditions in the ESI source. In additional experiments, copper/tebuconazole complexes were also detected in samples made from soil solutions of various origin and different amount of mineralization. The direct sampling of such solutions via ESI-MS is thus potentially useful for understanding of the interactions between copper(II) salts and tebuconazole in environmental samples.     

A new technique for metropolis Monte Carlo simulation to capture aggregate structures of fine particles: Cluster-moving Monte Carlo algorithm

We present a new Monte Carlo simulation procedure which is capable of capturing aggregate structures in a suspension where fine particles are dispersed. The algorithm we call the “cluster-moving” Monte Carlo algorithm involves moving aggregates (clusters) as unitary particles at every certain Monte Carlo step. We discuss here the theoretical background of the cluster-moving Monte Carlo algorithm and the availability of the algorithm for simulations of systems where fine particles aggregate. The results of simulations for two model systems, magnetic fluids and colloidal dispersions, have shown that the new algorithm produces much more rapid convergence than the conventional one for unstable dispersion systems and reproduces physically reasonable aggregate structures of fine particles.     

Atomistic Simulation Study of Cu0.327Ni0.673 Alloys: from Solid Solution to Phase Segregation

We present a combined Monte‐Carlo/molecular dynamics study of a Cu_0.327Ni_0.673 alloy system. On the basis of nearest‐neighbor coordination number analyses atomic clustering and phase segregation is explored. Along this line, free energy profiles are calculated and separated into entropic and energetic contributions. The competition of both terms was found in accordance to the experimental phase diagrams (phase separation of the solid solution below about 600 Kelvin). Two independent simulation runs were performed. At 1000 Kelvin the observed configurations correspond to solid solutions exhibiting a weak tendency to cluster atoms of identical species. At room temperature the energetic favoring of atomic separation is clearly dominant and leads to the formation of Ni‐rich and Cu‐rich domains. The latter are separated by interfacial regions whose width ranges from 0.5 to 1 nanometers.