Molecular-dynamics simulation for the characterization of liquid chromatographic stationary phase: effect of temperature.

The influence of temperature on the surface structure of the octadecylsilica (ODS) bonded phase was investigated with a molecular dynamics (MD) simulation. The MD simulation was applied to a molecular model consisting of three parts: amorphous silica base, dimethyloctadecylsilyl ligands and n-hexane as a mobile phase solvent. More detailed information on the effect of temperature was obtained at the low temperature region than that reported in our previous study. The motion of ODS ligands could be estimated by the mean square displacement (MSD) of the terminal carbon atoms of ODS ligands. The gauche fraction in the ODS ligand conformation can also be estimated to obtain the ligand conformation for each simulation condition in detail. It can be seen that an elevated temperature induced the more bent ligand conformation. The trend has a good agreement to that of the results experimentally observed by using various spectroscopic techniques such as nuclear magnetic resonance (NMR), Fourier-transform infrared spectroscopy (FT-IR), and Raman spectroscopy.     

Characterization of the microscopic surface structure of the octadecylsilica stationary phase using a molecular-dynamics simulation.

The influence of the mobile-phase composition and temperature on the surface structure of the octadecylsilica (ODS) stationary-phase was investigated by applying a molecular-dynamics (MD) simulation. The molecular model to which the MD simulation was applied consisted of three parts: an amorphous silica base, dimethyloctadecylsilyl ligands and mobile-phase solvents. More detailed information on the effect of the mobile-phase composition was obtained by constructing larger molecular models than those used in our previous study. The thickness of the hydrocarbon layer of the stationary phase could be estimated based on the distance between the carbon atom located at the terminal end of the ODS ligand and the silica gel surface. The structural information obtained by the calculation showed good consistency with the experimentally observed values. The gauche fraction in the ODS ligand conformation could be also estimated to obtain a more detailed ligand conformation for each molecular model. It was found that as the temperature increased, the ligand conformation collapsed more. This trend was the same as the experimentally observed trends obtained by NMR, FT-IR, and Raman spectroscopic techniques.     

Molecular Dynamics Simulation of Glass Transition Behavior of Polyimide Ensemble

The prediction of glass transition temperature from chemical structure has a great significance to select and design new high-properties materials. However, for the estimation and correlation methods, the deficiency of parameters for newer groups will lead to invalidity of Tg prediction or greater deviation from experiment. In the present work, we predicted Tg for a polyimide (PI) ensemble with rigid moieties, and analyzed structural factor that regards to the rotation barrier of the bridging…     

HTPB/增塑剂玻璃化转变温度及力学性能的分子动力学模拟

为了预测高分子粘结剂端羟基聚丁二烯(HTPB)与增塑剂癸二酸二辛酯(DOS)、硝化甘油(NG)的相容性及HTPB/增塑剂共混物的玻璃化转变温度(Tg)和力学性能,在COMPASS力场条件下采用分子动力学(MD)模拟方法对相容体系(HTPB-DOS)和不相容体系(HTPB-NG)进行了研究.结果表明,通过比较溶度参数差值(Δδ)的大小可以预测HTPB与增塑剂的相容性,即HTPB与DOS属于相容体系,而HTPB与NG不相容.通过温度-比容曲线可以得到HTPB、HTPB/DOS与HTPB/NG的Tg分别为197.54,176.30和200.03K.力学性能分析结果表明,添加DOS增塑剂后使HTPB的弹性模量(E),体积模量(K)和剪切模量(G)下降,材料刚性减弱,柔性增强,力学性能得到改善.本模拟方法可以作为预测聚合物/增塑剂共混物性能的有利工具,也可以为固体推进剂和高聚物粘结炸药的配方设计提供理论指导.     

Anomalous mixing behavior of polyisobutylene/polypropylene blends: molecular dynamics simulation study

The unusual mixing behavior of polyisobutylene (PIB) with head-to-head (hhPP) and head-to-tail polypropylene (PP) is studied using large-scale molecular dynamics (MD). The heats of mixing and Flory chi parameters were computed from MD simulations of both blends using a united atom model. The chi parameters from the simulations were estimated from the structure factors using the random phase approximation in analogy with neutron scattering (SANS) experiments. MD simulations for syndiotactic hhPP/PIB predicted a lower critical solution temperature with a chi parameter in very good agreement with SANS experiments on the atactic hhPP/PIB blend. MD simulations also predicted that the isotactic PP/PIB blend was immiscible at high molecular weight in qualitative agreement with cloud point measurements on atactic PP/PIB.     

Effect of branching architecture on glass transition behavior of hyperbranched copolystyrenes: the experiment and simulation studies

By controlling the feed ratio of CMS/styrene and the polymerization time, a series of hyperbranched copolystyrenes(HBCPS) were synthesized with comparable weight-averaged molecular weights(Mw) but different degree of branching(DB) through atom transfer radical self-condensing vinyl copolymerization(ATR-SCVCP) with Cu Br/2,2?-bipyridyl as the catalyst. The resulting HBCPS samples were used to investigate the effect of branching architecture on their glass transition behavior. With the DB increased, the glass transition temperatures(Tg) of HBCPS samples measured by DMA and DSC both decreased. Their spin-lattice relaxation times(1H T1r) of protons displayed the same downtrend with increasing DB. Besides, a correlation between the Tgs and the DB was well established by all-atom molecular dynamics(MD) simulations. The values of MD-determined Tgs are little higher than the corresponding experimental ones. However, the dependence of Tgs on DB is in good agreement with the experimental results, i.e., Tg decreases both in experiments and simulations with increasing DB.     

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 mobility of the paracetamol amorphous form

The purpose of this paper is to study the molecular mobility of paracetamol molecules in their amorphous state below the glass transition temperature (Tg) in order to evaluate the thermodynamic driving force which allows the amorphous form to recrystallize under different polymorphic modifications. Samples were aged at temperatures of -15, 0, 6, and 12 degrees C for periods of time from 1 h to a maximum of 360 h. The extent of physical aging was measured by a DSC study of enthalpy recovery in the glass transition region. The onset temperature of glass transition was also determined (Tg). Enthalpy recovery (deltaH) and change in heat capacity (deltaCp) were used to calculate the mean molecular relaxation time constant (tau) using the empirical Kohlausch-Williams-Watts (KWW) equation. Enthalpy recovery and onset glass transition temperature increased gradually with aging and aging temperatures. Structural equilibrium was reached experimentally only at an aging temperature of 12 degrees C (Tg-10 degrees C), according to the deltaH(infinity) results. The experimental model used is appropriate only at lower aging temperatures, while at higher ones the complexity of the system increases and molecular polymorphic arrangement could be involved. When structural equilibrium is experimentally reached, molecules can be arranged in their lowest energy state, and the polymorphic form I formation is the one preferred.     

Glycerol revisited molecular dynamic simulations of structural,dynamical, and thermodynamic properties

We performed molecular dynamics simulations to investigate the properties of glycerol for a wide range of temperatures at standard pressure. We calculated structural (radial distribution functions and pair potential of mean force), dynamical (mean square displacement and transport properties), and thermodynamic (density, thermal expansion, and Hildebrand solubility parameter) properties of glycerol. The results of structural properties showed that the correlation between glycerol atoms weakens as temperature increases. The values of mean square displacement showed that changing temperature has a strong influence on mobility of glycerol atoms. The values of diffusion coefficient and viscosity are remarkably close to the experimental values over the whole range of temperatures studied. The simulation results provide a reasonable estimation of density with percent error of 0.40 %. The simulated values of Hildebrand solubility parameter of glycerol decrease with raising temperature because the cohesive forces weaken. To the best of our knowledge, this work for the first time calculates the potential of mean force, viscosity, and Hildebrand solubility parameter of glycerol by MD simulation.     

Modelling a nematic liquid crystal

The bulk phase liquid crystalline behaviour of a cyclic siloxane with a pentamethylcyclosiloxane core and biphenyl-4-allyloxybenzoate mesogens (BCS) was studied using molecular dynamics (MD) and wide angle X-ray analysis. This material exhibits partial crystallinity at room temperature and liquid crystalline behaviour above 120° C. For the MD simulations an ensemble of 27 molecules with 135 mesogenic units was simulated and a molecular mechanics force field was used to model the structural anisotropy of the siloxane molecules. Simulations were carried out both at room temperature and at an elevated temperature (425 K). Room temperature simulations showed that, contrary to our initial assumptions, the low energy molecular conformations were not cylindrical but splayed in shape. During the simulation a smectic-like, tilted layer structure was found to evolve for the cluster when full atom potentials were used, while no such development was observed when electrostatic interactions were neglected. The presence of a tilted layered structure was also suggested by the X-ray data. These results indicate that long range electrostatic interactions are significant for the molecular system under study. In order to calculate the orientational order parameter, the orientation of the molecular axis had to be determined. This was achieved by describing the mesogen shapes to be ellipsoidal and defining the principal axis of the ellipsoids to be the molecular directors. By sampling over 200 ps of simulation at 425 K, the time averaged order parameter (S) was calculated. The calculated S of 0.36 was comparable to the value of 0.4-0.45 found from the experimental data. Apart from providing insight into the relative importance of the various competing forces in the formation of the liquid crystalline phase, these simulations are also expected to be useful in predicting the mesophase behaviour of liquid crystalline systems.     

不同结晶度的乙二醇及其水溶液玻璃化转变与焓松弛

为了考察晶体成分对无定形成分玻璃化转变和结构松弛行为的影响,利用差示扫描量热法(DSC),结合低温显微技术,研究了乙二醇(EG)及其50％水溶液在不同结晶度时的玻璃化转变和焓松弛行为.采用等温结晶方法控制骤冷的部分结晶玻璃体中的晶体份额.DSC结果表明,对于部分结晶的EG,只有单一的玻璃化转变过程,而对于50％EG,当结晶度不同时,不同程度地表现出两次玻璃化转变（无定形相Ⅰ和无定形相Ⅱ）.相Ⅰ的玻璃化转变温度和完全无定形态的含水EG的玻璃化转变温度相一致;相Ⅱ的玻璃化转变温度要比此温度约高6 ℃.低温显微观察结果印证了DSC实验结果.DSC等温退火的实验和KWW(Kohlrausch-Williams-Watts)衰变函数分析结果表明,EG无定形和50％EG中的两种无定形有不同的焓松弛行为.     

Polymer-clay nanocomposites: a multiscale molecular modeling approach

A hierarchical procedure bridging the gap between atomistic and mesoscopic simulation for polymer-clay nanocomposite (PCN) design is presented. The dissipative particle dynamics (DPD) is adopted as the mesoscopic simulation technique, and the interaction parameters of the mesoscopic model are estimated by mapping the corresponding energy values obtained from atomistic molecular dynamics (MD) simulations. The predicted structure of the nylon 6 PCN system considered is in excellent agreement with previous experimental and atomistic simulation results.     

Diffusion coefficients of small gas molecules in amorphous cis-1,4-polybutadiene estimated by molecular dynamics simulations

Molecular dynamics (MD) simulations were employed to estimate the diffusion coefficients of small gas molecules (Ar, O2, N2, CO2, and CH4) in amorphous cis-1,4-polybutadiene in the temperature range of 250-400 K. The VT diagram and solubility parameter of the amorphous polymer have been successfully reproduced using a full atomistic potential. Diffusion coefficients were calculated from long NPT MD runs (up to 3 ns) at temperature ranging from 250 up to 400 K. Calculated diffusion coefficients compare well with experimental data as well as previous published work, though a systematic overestimation is found due to the finite-size effect of the model. The influence of various physical and computational parameters on the results is discussed. The diffusion mechanism is examined at the different temperatures of study.     

不同构型聚丙烯的玻璃化转变温度的分子模拟

应用分子力学和分子动力学的方法对3种不同构型聚丙烯高分子的玻璃化转变温度进行了模拟.用NPT(等温等压)分子动力学模拟获得聚丙烯(PP)在不同温度下的特征体积,通过对模拟得到的V-T做图,求得玻璃化转变温度,其结果与实验值吻合较好.并分析了聚丙烯主链柔顺性和立构规整度对高分子玻璃化转变的影响.     

Physicochemical characterization of nicergoline and cabergoline in its amorphous state

Formulation of poorly water-soluble crystalline drugs into their more soluble amorphous form is a common approach for improving their bioavailability. In this study, the amorphous forms of nicergoline (NIC) and cabergoline (CAB) were obtained by different methods (melting and precipitation under solvent evaporation). The physicochemical characteristics of the samples were determined by HPLC, differential scanning calorimetry (DSC), thermogravimetry, and X-ray powder diffractometry. The physical stability of the amorphous forms was investigated by DSC by considering how the onset temperature and the enthalpy content at the glass transition vary with aging time and temperature. Using the Kohlrausch–Williams–Watts equation on the data obtained from the experiments, the “mean molecular relaxation time constant” (τ) was estimated. This parameter was used to understand the stability of NIC and CAB in their glassy state at different temperatures, and results showed that their stability is adequate to enable the formulation of these drugs into solid dosage forms.     

Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent

Replica exchange methods (REMs) are increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. However, despite having been shown to be very effective on model systems, the application of REM in complex systems such as for the simulation of protein and peptide folding in explicit solvent has not been objectively tested in detail. Here we present a comparison of conventional MD and temperature replica exchange MD (T-REMD) simulations of a beta-heptapeptide in explicit solvent. This system has previously been shown to undergo reversible folding on the time scales accessible to MD simulation and thus allows a direct one-to-one comparison of efficiency. The primary properties compared are the free energy of folding and the relative populations of different conformers as a function of temperature. It is found that to achieve a similar degree of precision T-REMD simulations starting from a random set of initial configurations were approximately an order of magnitude more computationally efficient than a single 800 ns conventional MD simulation for this system at the lowest temperature investigated (275 K). However, whereas it was found that T-REMD simulations are more than four times more efficient than multiple independent MD simulations at one temperature (300 K) the actual increase in conformation sampling was only twofold. The overall gain in efficiency using REMD resulted primarily from the ordering of different conformational states over temperature, as opposed to a large increase of conformational sampling. It is also shown that in this system exchanges are accepted primarily based on (random) fluctuations within the solvent and are not strongly correlated with the instantaneous peptide conformation raising questions in regard to the efficiency of T-REMD in larger systems.     

丙三醇浓溶液Tg附近协同松弛的量热研究

利用差示扫描量热法测量了丙三醇水溶液Tg前后的比热容. 通过曲线拟合获得AGF模型参数. 研究结果表明, 该模型很好地预测了(Tg+20 K)以下体系的结构松弛时间. 协同重排活化能(Δμ')和协同重排域尺寸(z*)的分析结果表明, 只有选择比聚合物大得多的某一协同重排位形数, 用AGF方法得到的z*才具有物理意义. 作为材料常数的Δμ' 随体系水含量的增加而逐渐降低. 用Donth方法得到的丙三醇水溶液的协同重排域长度尺度(ξCRR)随着水含量的增加逐渐降低, 且其变化趋势可与Δμ'的分析结果相符. 但用AGF方法和Donth方法得到的协同重排域尺寸不能统一.     

Conformational analysis of six- and twelve-membered ring compounds by molecular dynamics

A molecular dynamics (MD)-based conformational analysis has been performed on a number of cycloalkanes in order to demonstrate the reliability and generality of MD as a tool for conformational analysis. MD simulations on cyclohexane and a series of methyl-substituted cyclohexanes were performed at temperatures between 400 and 1200 K. Depending on the simulation temperature, different types of interconversions (twist-boat–twist-boat, twist- boat–chair and chair–chair) could be observed, and the MD simulations demonstrated the expected correlation between simulation temperature and ring inversion barriers. A series of methyl-substituted 1,3- dioxanes were investigated at 1000 K, and the number of chair–chair interconversions could be quantitatively correlated to the experimentally determined ring inversion barrier. Similarly, the distribution of sampled minimum-energy conformations correlated with the energy-derived Boltzmann distribution. The macrocyclic ring system cyclododecane was subjected to an MD simulation at 1000 K and 71 different conformations could be sampled. These conformations were compared with the results of previously reported conformational analyses using stochastic search methods, and the MD method provided 19 out of the 20 most stable conformations found in the MM2 force field. Finally, the general performance of the MD method for conformational analysis is discussed.