气体在无定型聚异戊二烯中扩散的分子动力学模拟

采用分子动力学模拟方法研究了多个温度下氧气、氮气及甲烷在无定型顺式1,4-聚异戊二烯中的扩散系数。在模拟过程中,使用COMPASS力场作为分子力场。应用COMPASS力场的势能函数,聚合物的密度及玻璃化转变温度的计算结果与实验值有较好吻合。在278-378 K的温度范围内,通过3或1.5 ns时长的正则系综动力学模拟,计算了不同温度下氧气、氮气及甲烷的扩散系数。结果表明,根据爱因斯坦关系式计算得到的扩散系数与实验结果比较接近。对气体扩散系数与温度的关系进一步研究,发现在278-378 K温度范围内,甲烷的扩散系数随温度变化的半对数曲线图是非线性的,而氧气和氮气的扩散系数随温度变化的半对数曲线图是线性的。本文研究结果有助于理解温度对气体扩散的影响机制,并为高温下气体在天然橡胶中扩散系数的测定及天然橡胶热氧老化建模分析提供依据。     

Molecular dynamics simulations of formamide interaction with hydrocyanic acid on a catalytic surface TiO2

The behavior of water—formamide and hydrocyanic acid—formamide solutions on an anatase surface have been studied using molecular dynamics (MD) simulation method. The interaction activation energies have been estimated for the temperature range from 250 up to 400 K. The diffusion coefficients and structural radial distribution functions have been calculated for the formamide, water and hydrocyanic acid on an anatase surface. The calculated activation energies of the water—formamide—anatase and hydrocyanic acid—formamide—anatase systems were analyzed and compared. A comparative analysis of the systems under investigation was performed and a possible correlation between the obtained MD results and the molecular mechanism involving the formamide’s interaction with dioxide titan adsorbing surface were discussed.     

Limiting diffusion coefficients of ionic liquids in water and methanol: a combined experimental and molecular dynamics study

Mutual diffusion coefficients D(12) of the ionic liquids 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C(2)MIM][NTf(2)]) and [C(4)MIM][NTf(2)] in highly diluted solutions of water and methanol have been measured at different temperatures between 288 K and 313 K using the Taylor dispersion technique. Tracer diffusion coefficients of the two cations [C(2)MIM](+) and [C(4)MIM](+) as well as the anion [NTf(2)](-) in these solutions have been obtained by molecular dynamics (MD) simulations. For our simulations we used well established force fields for the solvents water and methanol and a recently developed force field for imidazolium-based ionic liquid [C(n)MIM][NTf(2)]. Mutual diffusion coefficients D(12) have been calculated from the tracer diffusion coefficients using the Nernst-Hartley equation strictly valid only at low ionic concentration. The agreement between the diffusion coefficients reported in the literature, the experimental data obtained in this work and the MD results is excellent.     

The Influence of Temperature on Ethene Diffusion in H[Al]ZSM-5 Studied by Molecular Dynamics

Molecular dynamics(MD) simulation of ethene diffusion in the lattice of H[Al]ZSM-5 was performed at the temperature ranging from 300 K to 700 K. The calculated diffusion coefficients increase with the temperature from 2.60×10-9 m2/s at 300 K to 12.78×10-9 m2/s at 700 K. The Arrhenius plot gives an activation energy of 6.31 kJ/mol. The anisotropy of the diffusion process was examined.     

Molecular dynamics study of tryptophylglycine: a dipeptide nanotube with confined water

To investigate the mechanism of structural changes of a peptide nanotube and water confined inside the channel, the helical peptide tryptophylglycine monohydrate (WG.H2O) was studied by molecular dynamics (MD) simulations using the three-dimension parallel MD program ddgmq (software package) and a consistent force field. Simulations were performed on both the water-containing system and a model system without water molecules. The details of the structural behavior with temperature are investigated for the entire simulated temperature range. Phase transitions were obtained at 115, 245, 270, 310, and 385 K, due to the contributions of both the peptide and the confined water subsystems. The crystalline, amorphous, liquidlike, liquid, and superheated phases of water were observed in the temperature ranges 40-115, 115-245, 245-310, 310-385, and >385 K, respectively. At 300 K, the diffusion constant of the confined water is 0.46 x 10-5 cm2 s-1, a value comparable to that of other peptide nanotubes. The empty peptide system melts at 440 K. Mechanisms of the negative thermal expansion (NTE) along the tube axis were investigated for different temperature ranges. The contraction of the crystalline water (or amorphous water) draws also the tube walls in and leads to NTE below 245 K. The other NTEs appear to be connected to the collapse of the ice network or the solid peptide network between 245 K and room temperature or from 310 to 440 K, respectively.     

烷烃在丝光沸石型分子筛中吸附和扩散行为

采用巨正则系综蒙特卡罗(grand canonical Monte Carlo, GCMC)与分子动力学(molecular dynamics, MD)相结合的方法, 研究烷烃分子在丝光沸石(MOR)型分子筛中的吸附和扩散性质. 采用GCMC 方法研究温度为300 K、330 K时, MOR型分子筛中甲烷、乙烷、丙烷、丁烷的吸附. 研究表明, 随着压力的增加吸附量增加, 随温度的升高吸附量有所降低. 饱和吸附量从大到小依次为: 甲烷>乙烷>丙烷>丁烷. 由模拟所得到的单组分吸附等温线, 通过理想吸附溶液理论(IAST)计算二元混合物的吸附平衡相图, 模拟结果与计算结果一致. 采用分子动力学方法, 研究乙烷、丙烷在MOR分子筛上的扩散性质, 结果表明各个方向上的扩散系数不同, z方向上的扩散系数最大.     

Mutual diffusion coefficients of heptane isomers in nitrogen: a molecular dynamics study

The accurate knowledge of transport properties of pure and mixture fluids is essential for the design of various chemical and mechanical systems that include fluxes of mass, momentum, and energy. In this study we determine the mutual diffusion coefficients of mixtures composed of heptane isomers and nitrogen using molecular dynamics (MD) simulations with fully atomistic intermolecular potential parameters, in conjunction with the Green-Kubo formula. The computed results were compared with the values obtained using the Chapman-Enskog (C-E) equation with Lennard-Jones (LJ) potential parameters derived from the correlations of state values: MD simulations predict a maximum difference of 6% among isomers while the C-E equation presents that of 3% in the mutual diffusion coefficients in the temperature range 500-1000 K. The comparison of two approaches implies that the corresponding state principle can be applied to the models, which are only weakly affected by the anisotropy of the interaction potentials and the large uncertainty will be included in its application for complex polyatomic molecules. The MD simulations successfully address the pure effects of molecular structure among isomers on mutual diffusion coefficients by revealing that the differences of the total mutual diffusion coefficients for the six mixtures are caused mainly by heptane isomers. The cross interaction potential parameters, collision diameter σ(12), and potential energy well depth ?(12) of heptane isomers and nitrogen mixtures were also computed from the mutual diffusion coefficients.     

A new high-temperature multinuclear-magnetic-resonance probe and the self-diffusion of light and heavy water in sub- and supercritical conditions

A high-resolution nuclear-magnetic-resonance probe (500 MHz for 1H) has been developed for multinuclear pulsed-field-gradient spin-echo diffusion measurements at high temperatures up to 400 degrees C. The convection effect on the self-diffusion measurement is minimized by achieving the homogeneous temperature distributions of +/-1 and +/-2 degrees C, respectively, at 250 and 400 degrees C. The high temperature homogeneity is attained by using the solid-state heating system composed of a ceramic (AlN) with high thermal conductivity comparable with that of metal aluminium. The self-diffusion coefficients D for light (1H2O) and heavy (2H2O) water are distinguishably measured at subcritical temperatures of 30-350 degrees C with intervals of 10-25 degrees C on the liquid-vapor coexisting curve and at a supercritical temperature of 400 degrees C as a function of water density between 0.071 and 0.251 gcm3. The D value obtained for 1H2O is 10%-20% smaller than those previously reported because of the absence of the convection effect. At 400 degrees C, the D value for 1H2O is increased by a factor of 3.7 as the water density is reduced from 0.251 to 0.071 gcm3. The isotope ratio D(1H2O)D(2H2O) decreases from 1.23 to approximately 1.0 as the temperature increases from 30 to 400 degrees C. The linear hydrodynamic relationship between the self-diffusion coefficient divided by the temperature and the inverse viscosity does not hold. The effective hydrodynamic radius of water is not constant but increases with the temperature elevation in subcritical water.     

Comparison of Ethene Diffusion Characteristics in H[Al]ZSM‐5 at 300 K and 400 K by Molecular Dynamics

The ethene diffusion characteristics in the framework of H[Al]ZSM‐5 at 300 K and 400 K have been studied by molecular dynamics (MD) simulation. The data have been obtained for the molecular kinetic, potential and total energies, mean square displacement and self‐diffusion coefficient, interaction and beat of adsorption. The dependence of molecular diffusion on temperature has been explored.     

Diffusion dynamics of the Li+ ion on a model surface of amorphous carbon: a direct molecular orbital dynamics study

Diffusion processes of the Li+ ion on a model surface of amorphous carbon (Li+C96H24 system) have been investigated by means of the direct molecular orbital (MO) dynamics method at the semiempirical AM1 level. The total energy and energy gradient on the full-dimensional AM1 potential energy surface were calculated at each time step in the dynamics calculation. The optimized structure, where Li+ is located in the center of the cluster, was used as the initial structure at time zero. The dynamics calculation was carried out in the temperature range 100-1000 K. The calculations showed that the Li+ ion vibrates around the equilibrium point below 200 K, while the Li+ ion moves on the surface above 250 K. At intermediate temperatures (300 K < T < 400 K), the ion moves on the surface and falls in the edge regions of the cluster. At higher temperatures (600 K < T), the Li+ ion transfers freely on the surface and edge regions. The diffusion pathway of the Li+ ion was discussed on the basis of theoretical results.     

HTPB与Al不同晶面结合能和力学性能的分子动力学模拟

采用分子力学(MM)和分子动力学(MD)方法, 在250、300、350、400、450 K, 对固体推进剂端羟基聚丁二烯(HTPB)和铝晶胞不同晶面结构所组成的层模型在COMPASS力场下, 进行模拟计算, 求得结合能和静态力学性能(弹性系数、模量和泊松比). 模拟结果表明, 在400 K时HTPB与Al(011)面的结合能最大, 从综合力学性能优劣上看, 各个面从优到劣的排序为(011)>(221)>(001), HTPB与Al的结合能与力学性能具有对应关系, 结合能大的力学性能优异, 结合能小的力学性能较差.     

Kinetics and mechanism of the beta-alanine + OH gas phase reaction: a quantum mechanical approach

The OH hydrogen abstraction reaction from beta-alanine has been studied using the BHandHLYP hybrid HF-density functional and 6-311G(d,p) basis sets. The energies have been improved by single point calculations at the CCSD(T)/6-311G(d,p) level of theory. The structures of the different stationary points are discussed. Reaction profiles are modeled including the formation of pre-reactive and product complexes. Negative net activation energy is obtained for the overall reaction. A complex mechanism is proposed, and the rate coefficients are calculated using transition state theory over the temperature range of 250-400 K. The rate coefficients are proposed for the first time and it was found that in the gas phase the hydrogen abstraction occurs mainly from the CH(2) group next to the amino end. The following expressions, in cm(3) mol(-1) s(-1), are obtained for the overall rate constants, at 250-400 and 290-310 K, respectively: k(250-400)= 2.36 x 10(-12) exp(340/T), and k(290-310)= 1.296 x 10(-12) exp(743/T). The three parameter expression that best describes the studied reaction is k(250-400)= 1.01 x 10(-21)T(3.09) exp(1374/T). The beta-alanine + OH reaction was found to be 1.5 times faster than the alpha-alanine + OH reaction.     

Comparison of the glass transition temperature and fragility parameter of isomalto-olygomer predicted by molecular dynamics simulations with those measured by differential scanning calorimetry

The purpose of this study is to examine whether molecular dynamics (MD) simulations using a commercially available software for personal computers can estimate the glass transition temperature (Tg) of amorphous systems containing pharmaceutically-relevant excipients. MD simulations were carried out with an amorphous matrix model constructed from isomaltoheptaose, and the Tg estimated from the calculated density versus temperature profile was compared with the Tg measured by differential scanning calorimetry (DSC) for freeze-dried isomalto-oligomer having an average molecular weight close to that of isomaltoheptaose. The Tg values determined by DSC were lower by 10 to 20 K than those extrapolated from the Tg values estimated by MD simulation. Fragility parameter was estimated to be 56 and 51 from MD simulation and from DSC measurement, respectively. Thus, the results suggest that MD simulation can provide approximate estimates for the Tg and fragility parameter of amorphous formulations. However, a reduction of the cooling rate, achievable by sufficiently elongating the simulation duration, is necessary for more accurate estimation.     

Temperature and structural changes of water clusters in vacuum due to evaporation

This paper presents a study on evaporation of pure water clusters. Molecular dynamics simulations between 20 ns and 3 micros of clusters ranging from 125 to 4096 molecules in vacuum were performed. Three different models (SPC, TIP4P, and TIP5P) were used to simulate water, starting at temperatures of 250, 275, and 300 K. We monitored the temperature, the number of hydrogen bonds, the tetrahedral order, the evaporation, the radial distribution functions, and the diffusion coefficients. The three models behave very similarly as far as temperature and evaporation are concerned. Clusters starting at a higher temperature show a higher initial evaporation rate and therefore reach the point where evaporation stop (around 240 K) sooner. The radius of the clusters is decreased by 0.16-0.22 nm after 0.5 micros (larger clusters tend to decrease their radius slightly more), which corresponds to around one evaporated molecule per nm(2). The cluster temperature seems to converge towards 215 K independent of cluster size, when starting at 275 K. We observe only small structural changes, but the clusters modeled by TIP5P show a larger percentage of molecules with low diffusion coefficient as t-->infinity, than those using the two other water models. TIP4P seems to be more structured and more hydrogen bonds are formed than in the other models as the temperature falls. The cooling rates are in good agreement with experimental results, and evaporation rates agree well with a phenomenological expression based on experimental observations.     

Molecular dynamics simulations of triflic acid and triflate ion/water mixtures: a proton conducting electrolytic component in fuel cells

Triflic acid is a functional group of perflourosulfonated polymer electrolyte membranes where the sulfonate group is responsible for proton conduction. However, even at extremely low hydration, triflic acid exists as a triflate ion. In this work, we have developed a force-field for triflic acid and triflate ion by deriving force-field parameters using ab initio calculations and incorporated these parameters with the Optimized Potentials for Liquid Simulations - All Atom (OPLS-AA) force-field. We have employed classical molecular dynamics (MD) simulations with the developed force field to characterize structural and dynamical properties of triflic acid (270-450 K) and triflate ion/water mixtures (300 K). The radial distribution functions (RDFs) show the hydrophobic nature of CF(3) group and presence of strong hydrogen bonding in triflic acid and temperature has an insignificant effect. Results from our MD simulations show that the diffusion of triflic acid increases with temperature. The RDFs from triflate ion/water mixtures shows that increasing hydration causes water molecules to orient around the SO(3)(-) group of triflate ions, solvate the hydronium ions, and other water molecules. The diffusion of triflate ions, hydronium ion, and water molecules shows an increase with hydration. At λ = 1, the diffusion of triflate ion is 30 times lower than the diffusion of triflic acid due to the formation of stable triflate ion-hydronium ion complex. With increasing hydration, water molecules break the stability of triflate ion-hydronium ion complex leading to enhanced diffusion. The RDFs and diffusion coefficients of triflate ions, hydronium ions and water molecules resemble qualitatively the previous findings using per-fluorosulfonated membranes.     

Modelling of solid polymers in chemical detail - gases in amorphous polymers

The diffusion of gases in dense polymers, above and below the glass-transition temperature, is described with a new Transition State Theory model that is based on the concept that the dynamics of small molecules dissolved in dense polymers is separated from the structural relaxation of the dense polymers. The model is used to study the dynamics of rare gases dissolved in atomistic micro-structures of four polymers at 300 K: poly(dimethylsiloxane), poly(isobutylene), atactic poly(vinylchloride) and the polycarbonate of 4,4′-isopropylidenediphenol (bisphenol-A). Short-time-scale MD runs (5 ps) are used to characterize the elastic thermal motion of the host matrix; this information on mobility is then used for a stochastic simulation of solute dynamics up to ca. 1ms. All dissolved molecules show similar behavior by displaying three time regimes: a short-time, high-mobility domain, an intermediate time domain of anomalous diffusion, and a diffusive regime at long times. From the long-time data diffusion coefficients are estimated; comparison with experimental data results in good agreement.     

Molecular dynamics study of ferrocene topology under various temperatures

We present the first quantum mechanical Atom-Centered Density-Matrix Propagation molecular dynamic (MD) study to investigate ferrocene (Fc) conformation in gas phase. The MD simulations were performed at several temperatures (7, 18, 80, 120, 180, 293, and 500 K) for a period of 10 ps. It is found that, at very low temperatures (≤18 K), ferrocene prefers eclipsed-like conformation. At higher temperatures (>18 K), the cyclopentadienyl rings (Cp) of ferrocene exhibit apparent fluxional rotations, leading to configurations with the rotational angle δ distributing within a range of 0° (eclipsed) to 18° (approximately half of 36° for the staggered conformation), accompanied by the cyclopentadienyl ring tilt up to approximately 12° at 500 K. The simulated mean inferred (IR) spectrum of ferrocene at 7 K is clearly dominant by a doublet-splitting band of eclipsed-like Fc features in the region of 400 to 600 cm⁻¹, in agreement with previous IR studies. The animation obtained from the MD simulations indicates that, at room temperature, the Fe-C distances in ferrocene are in fact not strictly congruent but 2:2:1-fold.     

Theoretical studies of solid bicyclo-HMX: effects of hydrostatic pressure and temperature

On the basis of density functional theory (DFT) and molecular dynamics (MD), the structural, electronic, and mechanical properties of the energetic material bicyclo-HMX have been studied. The crystal structure optimized by the LDA/CA-PZ method compares well with the experimental data. Band structure and density of states calculations indicate that bicyclo-HMX is an insulator with the band gap of ca. 3.4 eV and the N-NO(2) bond is the reaction center. The pressure effect on the bulk structure and properties has been investigated in the range of 0-400 GPa. The crystal structure and electronic character change slightly as the pressure increases from 0 to 10 GPa; when the pressure is over 10 GPa, further increment of the pressure determines significant changes of the structures and large broadening of the electronic bands together with the band gap decreasing sharply. There is a larger compression along the c-axis than along the a- and b-axes. To investigate the influence of temperature on the bulk structure and properties, isothermal-isobaric MD simulations are performed on bicyclo-HMX in the temperature range of 5-400 K. It is found that the increase of temperature does not significantly change the crystal structure. The thermal expansion coefficients calculated for the model indicate anisotropic behavior with slightly larger expansion along the a- and c-axes than along the b-axis.     

Molecular dynamics simulations of a poly(ethylene oxide) surface

Potentials developed earlier for crystalline and amorphous bulk PEO systems have been used for the MD simulation of a PEO surface model. The surface comprises the outer region of a 122 Å-thick sheet of PEO in which the PEO, -(CH₂-CH₂-O)_n- chains run obliquely across the cell, and are terminated by C₂H₅ ethyl groups. The atoms on one side of the sheet are tethered to facilitate a satisfactory Ewald summation. The sheet expands from its ‘crystalline’ width of 122 Å to 128 Å in the simulated model. Simulations were performed at three temperatures: 300 K, 400 K and 500 K. Different behaviour in the surface layer was found compared to that in the bulk. The structural and dynamical properties of the surface were analyzed at each temperature.     

Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient

In this work, we have evaluated how well the general assisted model building with energy refinement (AMBER) force field performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, five organic compounds in aqueous solutions, four proteins in aqueous solutions, and nine organic compounds in nonaqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned errors and the root mean square errors are 0.137 and 0.171 × 10(-5) cm(-2) s(-1), respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for eight organic solvents with experimental data (R(2) = 0.784), four proteins in aqueous solutions (R(2) = 0.996), and nine organic compounds in nonaqueous solutions (R(2) = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide, and cyclohexane have been studied. The major molecular dynamics (MD) settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution.