Hydration of GABA and of the GABA·ZN2+ complex: A Monte Carlo simulation study

With empirical and theoretical atom–atom potentials the GABA·nH₂O, n = 25, 192 and GABA·Zn²⁺ · nH₂O, n = 25, 50, 100 complexes are simulated at 298.15 K by the Monte Carlo technique. The results show that the carboxyl group of GABA coordinates six water molecules. Two geometries of the GABA·Zn²⁺ complex, corresponding to the “direct” and “through-water” interaction of Zn²⁺ with the carboxyl group of GABA were found. For the latter interaction a GABA·Zn²⁺ · 6H₂O complex was found whereas the hydration of the former interaction leads to a GABA·Zn²⁺ · 5H₂O complex. Here the carboxyl group of GABA displaces only one water molecule in the first hydration shell of Zn²⁺. Energetically the “direct” and “through-water” geometries seem to be competitive, the former being slightly favored.     

Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions

Intermolecular potential functions have been developed for use in computer simulations of substituted benzenes. Previously reported optimized potentials for liquid simulations (OPLS) for benzene and organic functional groups were merged and tested by computing free energies of hydration for toluene, p-xylene, phenol, anisole, benzonitrile, p-cresol, hydroquinone, and p-dicyanobenzene. The calculations featured Monte Carlo simulations at 25°C and 1 atm with statistical perturbation theory. The average difference between the computed results and experimental data for the absolute free energies of hydration is 0.5 kcal/mol. The AM1-SM2 method is also found to perform well in predicting the free energies of hydration for the substituted benzenes. In addition, the Monte Carlo simulations provided details on the hydration of the substituted benzenes, in particular for the solute–water hydrogen bonding. © 1993 John Wiley & Sons, Inc.     

A rapidly convergent simulation method: Mixed Monte Carlo/stochastic dynamics

Although Monte Carlo and molecular dynamics are the primary methods used for free energy simulations of molecular systems, their application to molecules that have multiple conformations separated by energy barriers of ≥ 3 kcal/mol is problematic because of slow rates of convergence. In this article we introduce a hybrid simulation method termed MC-SD which mixes Monte Carlo (MC) and stochastic dynamics (SD). This new method generates a canonical ensemble via alternating MC and SD steps and combines the local exploration strengths of dynamics with the barrier-crossing ability of large-step Monte Carlo. Using calculations on double-well potentials and long simulations (10⁸ steps of MC and 1 μs of SD) of the simple, conformationally flexible molecule n-pentane, we find that MC-SD simulations converage faster than either MC or SD alone and generate ensembles which are equivalent to those created by classical MC or SD. Using pure SD at 300 K, the conformational populations of n-pentane are shown to be poorly converged even after a full microsecond of simulation. © 1994 by John Wiley & Sons, Inc.     

Nuclear magnetic resonance studies of methyl-5, 6-dicarboxy-2-norbornene derivatives

A simple procedure is provided for the quantitative analysis of Diels-Alder adduct prepared from commercial methylcyclopentadiene and maleic anhydride by NMR spectra without further separation of its components. The adduct is considered as a mixture of endo norbornene derivatives (C_n), (D_n), (E) and (F_n) which are obtained from 1-, 2- and 5-methylcyclopentadiene and cyclopentadiene, respectively. The quantitative analysis of the adduct can be made on a basis of the ratio of the signal intensities of the olefinic protons in the adduct. The result shows that the adduct prepared under mild conditions mainly consists of three norbornene derivatives (C_n), (D_n) and (F_n), with a negligibly small amount of (E). When the adduct prepared under mild conditions is heated, it contains the exo isomers (Cx), (Dx) and (Fx). The ratio of the endo and the exo norbornene derivatives, i.e. ((C_n) + (D_n) + (F_n)):((C_x) + (D_x) + (F_x)), may be estimated from the signal intensities of the 5- and 6-protons. As the result of the analyses of the adducts which are obtained by heating at different temperatures the adduct prepared under mild conditions, the mole fraction of 2-methyl isomers (D_n) and (D_x), which is found to be 58 % in the adduct prepared at ? 15°C, keeps on increasing with rising temperature and shows almost the same value, ～86%, when heated above 150°C. Therefore, the equilibrium between 1-methyl and 2-methyl isomers does not change above 150°C. On the other hand, the isomerization from endo to exo isomers is not found below 110°C, and then exo isomers keep on increasing above 140°C.     

AM1 studies on the potential energy surface for the proton transfer in protonated water clusters,H+(H2O)n

The potential energy surfaces for the proton transfer processes in H⁺(H₂O)_n with n=2 ～ 11 have been studied using the semiempirical AM1 method. Two model systems were adopted: branched and linear systems. The branched system showed a tendency to form a bulk cluster, while the linear system showed a tendency toward a constant barrier height with increasing number of water molecules in the model system. The potential energy surfaces were discussed using Marcus theory. In the case of H⁺ (H₂O)_n with n=10 and 11, the intrinsic barrier to the proton transfer was found to be around 1.0 kcal/mol.     

The Morphology of Symmetric Triblock Copolymer Melts Confined in a Slit: A Monte Carlo Simulation

Monte Carlo simulations based on a modified bond‐fluctuation and vacancy‐diffusion algorithm on a simple cubic lattice were employed to examine the morphology of thin films of the symmetric A_mB_2nA_m triblock copolymer confined between two hard homogeneous parallel walls. The walls preferred either segment A or segment B. Parallel lamellae, parallel cylinders and perpendicular cylinders morphologies, dependent on the composition, film thickness and interaction energies, were identified in these simulations, in agreement with the experimental observations of several researchers.     

低聚1,4-苯乙烯撑及其衍生物的结构和吸收光谱的理论研究

用B3LYP/6-31G对低聚物(PV)_n (PV＝1,4-phenylene vinylene, n＝2～8)和(PVSD)_n (PVSD＝2-(1,4-phenylene vinylene)-10-vinylene-spirocyclohexane-1,6-dibenzo[d,f](1,3)dioxepin, n＝1～4)体系进行了全优化并分析其结构特点, (PV)_n (n＝2～8)体系的结构中所有相邻C原子间形成的二面角均小于1°, 即所有原子有共面的趋势. 而在(PVSD)_n (n＝1～4)体系中低聚物的七元环处有较大的二面角, 约38°, 即在此处结构存在较大的扭曲. 这种扭曲结构对其光谱性质有较大的影响. 在优化结构的基础上分析了两系列低聚物的HOMO-LUMO能隙随n递增的变化规律和对光谱性质的影响, 推断高聚物的发光性质. 同时用ZINDO, TD-DFT方法计算这两系列低聚物的能隙和吸收光谱, 并将低聚物的这些性质与链长的倒数作图外推得到相应的高聚物的能带隙和吸收光谱最大吸收波长. 根据外推能带的曲线估算了聚合物的有效共轭链长. 结果说明, 在(PVSD)_n (n＝∞)中的扭曲结构特点导致其相对(PV)_n (n＝∞)的有效共轭链长变短, 能带隙变宽, 吸收光谱蓝移.     

Solubility of N2 in poly(α‐n‐hexyl‐β,L‐aspartate): Temperature and force‐field dependence

The solubility of N₂ in poly(α‐n‐hexyl‐β,L ‐aspartate), a stereoregular poly(β‐peptide), was investigated with atomistic Monte Carlo simulations. The structure of this material is intermediate between that of polymers able to form a three‐dimensional crystal lattice and that of liquid‐crystalline polymers with a biphasic distribution. The dependence of the calculated solubility coefficients on both the parameters of the force field and the temperature was examined. The results are compared with recently reported experimental data. Furthermore, the motion of the penetrant molecules within the polymer matrix was analyzed. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2928–2936, 2003     

Quantum Monte Carlo investigation of the H-shift and O2-loss channels of cis-2-butene-1-peroxy radical

Owing to importance in combustion processes, O₂-loss and 1, 6-H-shift in cis-2-butene-1-peroxy radical have been investigated. Energies for these processes and the barrier height of the latter are computed using the diffusion Monte Carlo (DMC) method. The DMC energy for the 1, 6-H-shift was determined to be 4.56 ± 0.19 kcal/mol with barrier height of 26.79 ± 0.20 kcal/mol. The energy for O₂-loss was found to be 14.93 ± 0.24 kcal/mol. Quantitative differences between the findings of the present study and previous CBS-QB3 results indicate a discrepancy between high-level methods for the resonance-stabilized radicals. Further study is needed to identify the origin of these differences.     

Kinetics of radiation-induced grafting reactions. III. Poly(isobutylene oxide)—styrene systems

Graft polymerization of styrene onto preirradiated poly(isobutylene oxide) was carried out at 25°C. The concentration of active sites for grafting was estimated by means of ESR and by the activation analysis of bromine atoms bound to the chain ends. Kinetic data such as differential amount of active sites (DACT), growth rate (GR), and average lifetime (τ) were obtained to calculate the molecular weight distribution of graft chains by the Monte Carlo simulation method. The number-average molecular weight of the graft chain was calculated from the equation, M _n = 2GRτ (mw), which agreed well with the observed value.     

Computer simulation of the structure of the hydration shells of calcium and calcium-water-zeolite a

A potential function is suggested to describe the interaction of the calcium ion with the water molecule using the tetrahedral model of the water molecule. Monte Carlo simulations of small clusters Ca(H₂O)_n (n≤20) and analyses of the resulting F-structures showed that the coordination number of Ca is 8. The structure of water adsorbed in the α-cavity of zeolite CaA depends predominantly on interactions with Ca²⁺ ions. The water molecule forms one hydrogen bond with an oxygen atom of the framework; the molecules are not hydrogen-bonded with each other. In this respect the structure of water in the Ca form of zeolite A resembles that in the Na form but differs from that in the K form. Institute of Physical Chemistry, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 1, pp. 88–97, January–February, 1996 Translated by L. Smolina     

Translocation of a protein-like chain through an interacting channel

The effect of channel-protein interaction on the translocation of a protein-like chain through a finite channel under certain electric field was studied by using dynamical Monte Carlo simulations.The interior behavior of chain conformation under different interactions was investigated,such as the number of monomers outside of channel n_out,monomers inside of channel n_m,mean-square radius of gyration〈S²〉and the average energy〈U〉.It shows that with strong attractive interaction,the translocation is more difficult than moderate interaction.At the same time,the dependence of translocation time with different interactions shows that moderate repulsive interaction(ε_cp= 0.5) accelerates the translocation.Although the waiting time for successful translocation ofε_cp = 1.0 is the longest,the average translocation time is not very large.It is far smaller than that ofε_cp=-1.0.The probability distributions of translocation time p（t’） and the probability distributions of three duration times p（t₁’）,p（t₂’） and p（t₃’） were all discussed.Log-normal distributions are found.All these findings will strengthen the understanding of protein translocation.     

Effect of the Intramolecular Chain Transfer to Polymer on PLP/SEC Experiments of Alkyl Acrylates

Pulsed‐laser polymerization (PLP) has been adopted by IUPAC as the method of choice for the determination of propagation rate constants (k_p). However, the method has failed in the polymerization of alkyl acrylates at temperatures above 30 °C. In this work, the PLP experiments were analyzed by simulation using a Monte Carlo algorithm. It was found that the experimental difficulties encountered to accurately determine k_p at temperatures above 30 °C were caused by extensive intramolecular chain transfer. This mechanism is not operative at lower temperatures because of its high activation energy.

Pulsed‐laser polymerization of BA in bulk at temperatures between −41 and +40 °C: Simulated MWD trace.     

Living cationic polymerization of 2‐adamantyl vinyl ether

Living cationic polymerization of 2‐adamantyl vinyl ether (2‐vinyloxytricyclo[3.3.1.1]^3,7decane; 2‐AdVE) was achieved with the CH₃CH(OiBu)OCOCH₃/ethylaluminum sesquichloride/ethyl acetate [CH₃CH(OiBu)OCOCH₃/Et_1.5AlCl_1.5/CH₃COOEt] initiating system in toluene at 0 °C. The number‐average molecular weights (M_n's) of the obtained poly(2‐AdVE)s increased in direct proportion to monomer conversion and produced the polymers with narrow molecular weight distributions (MWDs) (M_w/M_n = ～1.1). When a second monomer feed was added to the almost polymerized reaction mixture, the added monomer was completely consumed and the M_n's of the polymers showed a direct increase against conversion of the added monomer. Block and statistical copolymerization of 2‐AdVE with n‐butyl vinyl ether (CH₂?CH? O? CH₂ CH₂CH₂CH₃; NBVE) were possible via living process based on the same initiating system to give the corresponding copolymers with narrow MWDs. Grass transition temperature (T_g) and thermal decomposition temperature (T_d) of the poly(2‐AdVE) (e.g., M_n = 22,000, M_w/M_n = 1.17) were 178 and 323 °C, respectively. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1629–1637, 2008     

Hydrogen storage in porous structures of adamantane‐based nitrogen‐heterocyclic ring with diamond‐like structure

Using the density functional theory and molecular mechanics methods, we calculated the binding energy and parameters about the primitive cell designed by us with the adamantane and the nitrogen heterocyclic ring, the vibrational frequencies about the small complexes. Grand canonical Monte Carlo simulations were performed to predict the capacities for the hydrogen storage and adsorption isotherms. The results show the positive effects of bigger specific surface area and pore volume on hydrogen storage and isosteric heat. The gravimetric hydrogen uptake of adamantane‐based nitrogen‐heterocyclic ring of quaterpyridyl can reach 9.02 wt % at room temperature and 100 bar. But the volumetric H₂ capacities of the four materials are low at T = 298 K because of weak interaction between the materials and H₂ molecule. © 2014 Wiley Periodicals, Inc.     

Can Water Clusters Ionize HCl under the Conditions of Arctic Stratosphere? 2. Mechanism of Cluster Dissociation

Pseudopotential model described in the preceding communication is used to simulate the H₃O⁺(H₂O) _n Cl^– clusters at room and stratospheric temperatures by the Monte Carlo method. Two thermodynamically stable states of the cluster were observed at finite temperatures. The first state corresponds to the bound and the second, to the dissociated states of HCl molecule. Both states are separated by a very high potential barrier ( k _B T). The formation of the second minimum of the mean force potential of ion–ion interaction is related to the reorganization of a cluster as a whole that qualitatively distinguishes this mechanism from the formation of relatively stable dissociated states in aqueous bulk solution.     

GPGPU for orbital function evaluation with a new updating scheme

We have accelerated an ab initio quantum Monte Carlo electronic structure calculation using general purpose computing on graphical processing units (GPGPU). The part of the code causing the bottleneck for extended systems is replaced by Compute Unified Device Architecture‐GPGPU subroutine kernels which build up spline basis set expansions of electronic orbital functions at each Monte Carlo step. We have achieved a speedup of a factor of 30 for the bottleneck for a simulation of solid TiO₂ with 1536 electrons. To improve the performance with GPGPU we propose a new updating scheme for Monte Carlo sampling, quasi‐simultaneous updating, which is intermediate between configuration‐by‐configuration updating and the widely used particle‐by‐particle updating. The error in the energy due to by the single precision treatment and the new updating scheme is found to be within the required accuracy of ～10^?3 hartree per primitive cell. © 2012 Wiley Periodicals, Inc.     

Properties of block and graft copolymers of polybutadiene with small complexed poly(4-vinylpyridine) segments

Various diblocks, triblocks and a graft copolymer of butadiene with 4-vinylpyridine short blocks have been prepared. They were complexed with ZnCl₂ to give ionomer-like materials. For all copolymers, the T_g of the elastomeric block (?84°C to ?91°C) was unchanged by complexation. For all diblocks and triblocks with short blocks (DP _n ～ 3) the storage modulus was only slightly increased by comparison with uncomplexed materials. For the graft copolymer even with short blocks the material is less sensitive to temperature after complexation. For triblocks, when the DP _n of the vinylpyridine blocks was high enough (15 units), complexes were associated in multiplets of large size and the elastomeric properties were retained up to 200°C.     

Activation energy of hydrogen migration by relay in the O2/Pt19/SnO2/H2 + n H2O system

In the framework of investigation of active and stable electrocatalysts for fuel cells, the hydrogen migration by relay with the consecutive formation of H₂O molecules in the O₂/Pt₁₉/SnO₂/H₂·nH₂O → O/Pt₁₉/SnO₂·nH₂O + H₂O system was simulated. The simulations were performed by the density functional theory (DFT) method with the generalized gradient adjustment (GGA=PBE) under periodic boundary conditions in the projector augmented plane wave (PAW) basis set with a pseudo-potential using the VASP program package. At the cathode on the platinum cluster surface, the oxygen molecules without a barrier form peroxide complexes that dissociate with an energy decrease. The protons transferred via the proton-conducting channels from the anode to cathode form first OH groups bound to the platinum cluster and then H₂O molecules that are easily separated from the cluster (～0.2 eV). The proton transfer process proceeds by relay and involves several water molecules.     

Untersuchungen im System LaI2/H2: Phasenverhältnisse und Fehlordnung

Investigation of the LaI₂/H₂ System: Phase Relations and Stacking Disorder Heating of LaI₂ under 1 bar hydrogen pressure to 650 °C leads to light gray LaI₂H_0.95(3), accompanied by a structural change from tetragonal to hexagonal. Sharp reflections in the XRD pattern can be indexed in P6₃/mmc with a = 4.2158(7)Å and c = 15.508(3)Å, however, diffuse reflections indicate the presence of stacking faults in the structure, which correspond to a polytypic intergrowth of MoS₂ and NbS₂ type structural fragments. Increasing the reaction temperature to 730 °C results in a better defined diffraction pattern with the peak positions close to those of the 2H‐NbS₂ structure type. An X‐ray powder study of the samples LaI₂H_n proved the miscibility gap between LaI₂ and LaI₂H_n (0 ≤ n ≤ 0.5) in agreement with previous results. With decreasing H‐content of the homogeneous phase the lattice parameters change in opposite direction, a increasing to 4.236(1)Å and c decreasing to 15.39(2)Å for the lower limit.