2-氨基-2-咪唑啉异构化和质子迁移溶剂效应的密度泛函计算和Monte Carlo模拟

采用密度泛函理论和MonteCarlo模拟方法研究了2-氨基-2-咪唑啉在气相和水中的异构现象和质子迁移反应.考虑了直接迁移和水助催化迁移等两种质子迁移途径.气相中稳定点的几何结构和热力学性质是在B3LYP/6-311+G^**理论水平上计算得到的.溶剂效应的研究结果表明,水作为溶剂可降低直接迁移途径的速率,有利于水助催化反应途径的进行.     

Monte Carlo simulation of phase separation kinetics in a concentrated polymer solution

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Solvent effect on K to Na ion mutation: a Monte Carlo simulation study

Monte Carlo simulation studies of statistical perturbation theory (SPT) have been carried out to investigate the solvent effects on the relative free energies of solvation and the difference in partition coefficients (log P) for K⁺ to Na⁺ ion mutation in the several solvents. We compared the relative free energies for interconversion of K⁺ to Na⁺, in H₂O (TIP4P) in this study with those published works, that in H₂O (TIP4P) is −16.55 kcal/mol in this study, those of the published works are −17.6, −17.3 and −17.31 kcal/mol and that of the experiment is −17.6 kcal/mol, respectively. Comparing the relative free energies for interconversion of K⁺ to Na⁺, in CH₃OH in this study with those published works, that in CH₃OH is −18.08±0.28 kcal/mol in this study, that of molecular dynamic simulation is −19.6±0.4 kcal/mol and that of the experimental work is −17.3 kcal/mol, respectively. There is good agreement among the several studies if we consider both methods of obtaining the solvation (or hydration) free energies and the standard deviations. For the present K⁺ and Na⁺ ions, the relative free energies of solvation vs Born's function of solvents are decreased with increasing Born's function of solvent except for CH₃OH, THF and MEOME. There is also good agreement between the calculated structural properties in this study and the computer simulation, ab initio and experimental works.     

Monte Carlo simulation of the local ordering of water molecules. I. Binary spatial correlations

The pair distribution functions (DFs) of the oxygen and hydrogen atoms over space around one of the water molecules were calculated during Monte Carlo simulation (Metropolis procedure for the NVT ensemble at normal density and 300 K). An analysis of the isosurfaces of the DF_OO and DF_OH constructed around the selected water molecule for several fixed values of local density allowed us to obtain detailed information about the most probable localization of water molecules in the second and third coordination spheres.     

Monte Carlo simulation of the structure of mono- and bidisperse polyethylene nanocomposites

The structure of bidisperse polyethylene(PE) nanocomposite mixtures of 50:50(by mole) of long and short chains of C160H322/C80H162 and C160H322/C40H82 filled with spherical nanoparticles were investigated by a coarse-grained, on lattice Monte Carlo method using rotational isomeric state theory for short-range and Lennard-Jones for long-range energetic interactions. Simulations were performed to evaluate the effect of wall-to-wall distance between fillers(D), polymer-filler interaction(w) and polydispersity(number of short chains in the mixture) on the behavior of the long PE chains. The results indicate that long chain conformation statistics remain Gaussian regardless of the effects of confinement, interaction strength and polydispersity. The various long PE subchain structures(bridges, dangling ends, trains, and loops) are influenced strongly by confinement whereas monomer-filler interaction and polydispersity did not have any impact. In addition, the average number of subchain segments per filler in bidisperse PE nanocomposites decreased by about 50% compared to the nanocomposite system with monodisperse PE chains. The presence of short PE chains in the polymer matrix leads to a reduction of the repeat unit density of long PE chains at the interface suggesting that the interface is preferentially populated by short chains.     

A Monte Carlo simulation study of the aqueous hydration of d(CGCGCG) in Z form

Summary Monte Carlo computer simulation is described for the hexamer d(CGCGCG) in the Z form together with 910 water molecules at an environmental density of 1 gm/cc in a cubic cell under periodic boundary conditions. Water-water interactions were treated using the TIP4P potential and the solute water interactions by TIP4P spliced with the non-bonded interactions from the AMBER 3.0 force field. The simulation was subjected to proximity analysis to obtain solute coordination numbers and pair interaction energies for each solute atom. Hydration density distributions partitioned into contributions from the major groove, the minor groove, and the sugar-phosphate backbone were examined, and the probabilities of occurrence for one- and two-water bridges in the simulation were enumerated. The results are compared with observations of crystallographic ordered water sites from the X-ray diffraction studies.     

Monte Carlo simulation of polarizable systems: Early rejection scheme for improving the performance of adiabatic nuclear and electronic sampling Monte Carlo simulations

An early rejection scheme for trial moves in adiabatic nuclear and electronic sampling Monte Carlo simulation (ANES-MC) of polarizable intermolecular potential models is presented. The proposed algorithm is based on Swendsen–Wang filter functions for prediction of success or failure of trial moves in Monte Carlo simulations. The goal was to reduce the amount of calculations involved in ANES-MC electronic moves, by foreseeing the success of an attempt before making those moves. The new method was employed in Gibbs ensemble Monte Carlo (GEMC) simulations of the polarizable simple point charge-fluctuating charge (SPC-FQ) model of water. The overall improvement in GEMC depends on the number of swap attempts (transfer molecules between phases) in one Monte Carlo cycle. The proposed method allows this number to increase, enhancing the chemical potential equalization. For a system with 300 SPC-FQ water molecules, for example, the fractions of early rejected transfers were about 0.9998 and 0.9994 at 373 and 423 K, respectively. This means that the transfer moves consume only a very small part of the overall computing effort, making GEMC almost equivalent to a simulation in the canonical ensemble.     

Monte Carlo simulation of salt effect on water structure through 3D mechanistic potentials

Highly concentrated electrolyte solutions were studied through a Monte Carlo-based simulator, developed to consider the water molecules not a homogeneous dielectric as usual, but as dipoles that can move and rotate within a 3D lattice. This approach allowed fast calculations of detailed interactions between the particles, which were described from mechanistic potentials including dipole–dipole, ion–dipole, ion–ion, and hydrogen bonding (HB) interactions. A good agreement was found between experimental data and simulated results. The study also provides new insights about the balance of the different interactions in systems with or without electrolytes, and the effects of the electrolytes addition on the original water structure. The proposed model was also compared with previous explicit models.     

2-羟基咪唑在气相和水中的异构平衡和质子迁移的从头算计算和Monte Carlo模拟

采用从头算方法在MP2/6-31＋G^*水平上研究了2-羟基咪唑分子在孤立分子和一水合物的异构体的相对稳定性和可能的质子迁移反应, 分析了一个水分子的参与对2-羟基咪唑分子异构体的相对稳定性和质子迁移速率的影响, 采用Monte Carlo模拟方法研究了反应体系在水溶液中反应的溶剂化效应. 结果表明: 2-羟基咪唑分子的孤立分子和一水合物的最稳定异构体相同, 都为酮式. 直接质子迁移反应在水溶液中活化能垒有轻微增加, 但产物能量得到降低; 水助催化质子迁移反应在水溶液中的活化能垒和产物能量都得到明显降低. 综合气相和水相的计算结果, 2-羟基咪唑水助催化的质子迁移反应较易进行, 且在水溶液中进行容易, 可以很容易被实验观察到.     

Kinetic analysis of the cross reaction between dithioester and alkoxyamine by a Monte Carlo simulation

A model reaction of dithioester and alkoxyamine is proposed to probe the reversible addition–fragmentation chain transfer (RAFT) process. The kinetics of the model reaction is analyzed and compared with that of pure alkoxyamine homolysis with a Monte Carlo simulation. Although the pure alkoxyamine obeys the law of persistent radical effect, the model reaction results in higher concentration of the persistent radical during the main period of the reaction. However, for a very fast RAFT process or a very low addition rate constant, the time dependence of the persistent radical concentration is quite close to that of pure alkoxyamine. Furthermore, the cross termination between the intermediate and alkyl radicals causes a retardation effect for the model reaction when the intermediate is relatively long‐lived. The Monte Carlo simulation indicates that it is feasible to measure the individual rate constants of the RAFT process, such as the rate constant of addition, with a large excess of alkoxyamine. In addition, the special feature of the system with different leaving groups in the alkoxyamine and dithioester is also discussed. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 374–387, 2007     

A DFT study on proton transfers in hydrolysis reactions of phosphate dianion and sulfate monoanion

B3LYP calculations were carried out on hydrolysis reactions of monosubstituted(R) phosphate dianion and sulfate monoanion. In the reacting system, water clusters (H₂O)₂₂ and (H₂O)₃₅ are included to trace reaction paths. For both P and S substrates with R = methyl group, elementary processes were calculated. While the phosphate undergoes the substitution at the phosphorus, the sulfate does at the methyl carbon. For the S substrate with R = neopentyl group, the product tert‐amyl alcohol was found to be formed via a dyotropic rearrangement from the neopentyl alcohol intermediate. For R = aryl groups, transition‐state geometries were calculated to be similar between P and S substrates. Calculated activation energies are in good agreement with experimental values. After the rate‐determining transition state of the substitution, the hydronium ion H₃O⁺ is formed at the third water molecule. It was suggested that alkyl and aryl substrates are of the different reactivity of the hydrolysis. © 2014 Wiley Periodicals, Inc.     

Dynamic Monte Carlo simulation of chain growth polymerization and its concentration effect

Polymerization kinetics and chain configuration are two of lasting hotspots in Polymer Science. As these problems are concerned, computer experiment affords a very useful method besides theoretical and experi-mental investigations. The conventional Monte …     

A DFT study of proton transfers for the reaction of phenol and hydroxyl radical leading to dihydroxybenzene and H2O in the water cluster

Reactions of phenol and hydroxyl radical were studied under the aqueous environment to investigate the antioxidant characters of phenolic compounds. M06‐2X/6‐311 + G(d,p) calculations were carried out, where proton transfers via water molecules were examined carefully. Stepwise paths from phenol + OH^• + (H₂O)_n (n = 3, 7, and 12) to the phenoxyl radical (Ph O^•) via dihydroxycyclohexadienyl radicals (ipso, ortho, meta, and para OH‐adducts) were obtained. In those paths, the water dimer was computed to participate in the bond interchange along hydrogen bonds. The concerted path corresponding to the hydrogen atom transfer (HAT, apparently Ph OH + OH^• → Ph O^• + H₂O) was found. In the path, the hydroxyl radical located on the ipso carbon undergoes the charge transfer to prompt the proton (not hydrogen) transfer. While the present new mechanism is similar to the sequential proton loss electron transfer (SPLET) one, the former is of the concerted character. Tautomerization reactions of ortho or para (OH)C₆H₅=O + (H₂O)_n → C₆H₄(OH)₂(H₂O)_n were traced with n = 2, 3, 4, and 14. The n = 3 (and n = 14) model of ortho and para was calculated to be most likely by the strain‐less hydrogen‐bond circuit.     

Monte Carlo模拟研究高分子单链在基体中扩散的拓扑效应

高分子流体的性质同高分子的链结构及其动力学行为密切相关. 在高分子共混物中,共混组分的性质不仅依赖于自身的拓扑结构,还受到其它组分分子拓扑的影响. 本文中采用基于格子模型的Monte Carlo模拟方法研究了在高分子基体中扩散的4种不同拓扑组合（环形或线形高分子链）体系中目标单链的静态和动态性质. 结果发现,环形目标单链的性质受基体分子拓扑结构的影响要大于线形目标单链;其中环/线这一拓扑组合中目标单链的扩散机理相比其本体已经发生了较大改变,链末端在其中起了重要作用. 此外,我们对引起这一现象出现的可能原因做了分析.     

Homogenization process caused by competition between phase separation and ester‐interchange reactions in immiscible polyester blends: A Monte Carlo simulation

The homogenization process caused by competition between phase separation and ester‐interchange reactions in immiscible polyester blends was investigated via the Monte Carlo simulation method. Phase separation and ester‐interchange reactions were performed simultaneously with the one‐site bond fluctuation model on a homogeneous blend of immiscible polyesters. Three different values of the repulsive pair‐interaction energy (E_AB) between segments A and B and two trial ratios of phase separation to ester‐interchange reactions at a given E_AB were introduced to examine the competition between them. Phase separation was monitored by the calculation of the collective structure factor, and copolymerization was traced by the calculation of the degree of randomness (DR). In all cases, as the homogenization proceeded, the maximum intensity of the collective structure factor initially increased, reached a maximum, and finally decreased, whereas the peak position where the structure factor had a maximum shifted downward in the early stage and then remained unchanged after the intensity of the collective structure factor reached the maximum. This indicates that during the homogenization process, the domain size did not change significantly after phase‐separated structures were developed distinctly. In this simulation, phase‐separated structures were traced until the DR was above 0.8. This result indicates that homogenization can be accomplished via homogeneous ester‐interchange reactions over most of the polyester chains because copolyesters resulting from ester‐interchange reactions do not act as an efficient compatibilizer. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 590–598, 2000     

Monte Carlo模拟负载型Au团簇的熔化行为

采用Monte Carlo方法研究了石墨负载Au团簇的熔化行为,着重考察了载体对负载型团簇结构的影响。建立了一个正二十面体的Au团簇和AB堆积的石墨载体,通过记录每一个状态的结构来研究团簇的熔化过程。模拟结果表明,随着温度的升高,Au原子从外到内,逐层熔化,形成二维岛状结构。Au与石墨载体之间的相互作用使得Au原子单层分散在石墨表面,相互作用越强,金属原子越靠近载体。     

Effect of the reactivity of a crosslinking agent on the microphase separation in sequential IPNs: A Monte Carlo simulation study

The effects of the reactivity of a crosslinking agent on the microphase‐separated structure of sequential interpenetrating polymer networks are analyzed with a Monte Carlo simulation technique. The simulation results showed that the maximum structure factor decreases with an increasing crosslinking rate. However, the maximum structure factor increases when the crosslinking rate is increased further. This behavior is explained by a competition between the phase separation and the restriction of chain mobility due to the increase in molecular weight. In addition, there exists a chain length where the chain motion is the most restricted when crosslinks are formed. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 1005–1012, 2000     

超临界流体中CO和H2吸附过程的Monte Carlo模拟

利用Monte Carlo (MC) 方法,研究了一氧化碳和氢气在不同密度正己烷中的等温吸附情况.模型考虑了正己烷密度对一氧化碳和氢气在催化剂表面吸附量与吸附速率的影响.结果表明,主要有三个因素会影响溶质的吸附量:当溶剂密度低于其临界密度时,体系压力是影响溶质吸附量的主要因素；当体系处于超临界区时,超临界溶剂的溶解能力以及溶质和溶剂之间的竞争吸附是影响溶质吸附量的主要因素.在一定范围内增加溶剂的密度（压力）可以提高溶质在催化剂表面的吸附速率.