Molecular dynamics simulation study on zwitterionic structure to maintain the normal conformations of Glutathione

Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD, conformational flexibility and dihedral distribution were performed. The re- sults showed that zwitterionic structure maintains the normal conformations of GSH to a better extent, which should be a first good proof of the hypothesis of "maintain of normal structure".     

Molecular simulation study on the self-assembly behaviors of zwitterionic heterogemini surfactant in aqueous solution

The self-assembly behaviors of a series of zwitterionic heterogemini surfactants C_mH_2m+1-PO^4–(CH₂)₂-N⁺(CH₃)₂-C_nH_2n+1, abbreviated as C_m-P-N-C_n (m, n?=?9, 9; 9, 12; 9, 15; 9, 18; 12, 12; 12, 15; 12, 18; 15, 15; 15, 18; 18, 18), have been investigated in aqueous solution by the dissipative particle dynamics (DPD) method. Morphologies such as sphere (S), rod (R), planar grid (PG), lamella (L), honeycomb (H), one-, two-, and three-dimensional tunnels (1DT, 2DT, and 3DT) have been observed showing more diversities than those of the corresponding symmetric gemini surfactants C_m-N-N-C_m (m?=?9, 12, 15, 18). With the increase of surfactant concentration in the aqueous solution, a distinct transition path ‘‘S—R—PG—3DT—L—2DT—1DT’’ is proved to be common for all the C_m-P-N-C_n systems. Besides, the hydrophobic chain length has a significant influence on the self-assembly behaviors in the case of m?≠?n. Radial distribution function is an effective method to quantitatively evaluate the interaction and relationship between each functional group in the surfactant molecule and water. Results can provide a new insight into the self-assembly behaviors of zwitterionic heterogemini surfactants and the corresponding applications.     

甲烷水合物导热机理的分子动力学模拟

甲烷水合物导热系数是甲烷水合物勘探、开采、储运以及其他应用过程中一个十分重要的物理参数.我们采用平衡分子动力学（EMD）方法Green-Kubo理论计算温度203.15～263.15K、压力范围3～100MPa、晶穴占有率为0～1的sI甲烷水合物的导热系数,采用的水分子模型包括TIP4P、TIP4P-Ew、TIP4P-FQ、TIP4P/2005、TIP4P/Ice.研究了主客体分子、外界温压条件等对甲烷水合物导热性能的影响.研究结果显示甲烷水合物的低导热性能由主体分子构建的sI笼型结构决定,而客体分子进入笼型结构后,使得笼型结构导热性能增强,同时进入笼型结构的客体分子越多,甲烷水合物导热性能越强.研究结果还显示在高温区域（T〉TDebye/3）内不同温度作用下,所有sI水合物具有相似的导热规律.压力对导热系数有一定影响,尤其是在较高压力条件下,压力越高,导热系数越大.而在不同温度和不同压力作用过程中,密度的改变对导热系数的增大或减小几乎没有影响.     

Molecular dynamics simulation in the grand canonical ensemble

An extended system Hamiltonian is proposed to perform molecular dynamics (MD) simulation in the grand canonical ensemble. The Hamiltonian is similar to the one proposed by Lynch and Pettitt (Lynch and Pettitt, J Chem Phys 1997, 107, 8594), which consists of the kinetic and potential energies for real and fractional particles as well as the kinetic and potential energy terms for material and heat reservoirs interacting with the system. We perform a nonlinear scaling of the potential energy parameters of the fractional particle, as well as its mass to vary the number of particles dynamically. On the basis of the equations of motion derived from this Hamiltonian, an algorithm has been proposed for MD simulation at constant chemical potential. The algorithm has been tested for the ideal gas, for the Lennard-Jones fluid over a wide range of temperatures and densities, and for water. The results for the low-density Lennard-Jones fluid are compared with the predictions from a truncated virial equation of state. In the case of the dense Lennard-Jones fluid and water our predicted results are compared with the results reported using other available methods for the calculation of the chemical potential. The method is also applied to the case of vapor-liquid coexistence point predictions.     

聚乙烯在石墨表面结晶的分子动力学模拟

采用分子动力学方法模拟了聚乙烯在石墨(001)表面的吸附和结晶过程;直观的给出了聚乙烯链被石墨(001)面吸附并诱导形成有序的片层晶体的过程;发现结晶温度对得到的有序结构中的聚乙烯链相对石墨表面的特定取向有影响(300 K和600 K时的取向方向不同);表面覆盖率影响聚乙烯吸附层的厚度,对取向的方向无影响.     

Molecular dynamics study on the influence of C-terminal sugar substitution on dynamics and conformation of vancomycin derivatives

Computational investigations were performed to examine the effects of the addition of 2-acetamido-2-deoxy-β-D-galactopyranosylamine or 1-amino-1-deoxy-D-glucitol connected to the C-terminus of vancomycin with different linkers. The purpose of this modification was to find more effective vancomycin derivatives by providing alternative interactions between vancomycin moiety and the peptidoglycan precursor. Each prepared vancomycin–peptidoglycan complex was optimized and submitted to the molecular dynamics study and analysis. The analysis of overall root mean square deviation, changes in position and interactions involving modified part of vancomycin as well as cluster analysis were carried out. One of the proposed vancomycin analogues seems to be efficient vancomycin substitute.     

Molecular dynamics simulation on influence of temperature effect on electro-coalescence behavior of nano-droplets

In electric dehydration of crude oil, the dewatering efficiency can be improved by raising emulsion temperature properly which reduces the viscosity of crude oil. However, it should be noticed that the emulsion temperature does not only affect the emulsion viscosity but also nano-droplets dynamics behavior which impacts the coalescence efficiency either. Therefore the influence of temperature effect on the electro-coalescence of nano-droplets is studied by a molecular dynamics method. The results show that the temperature presents an active or negative effect, depending on the competitive relation between electrostatic interaction and thermal motion. Two stages are distinguished according to the dominant mechanism. During stage I, governed by the electrostatic interaction, lower temperature promotes the polarization and leads to an acceleration of the droplets coalescence, but higher temperature restrains the coalescence process due to molecules thermal motion breaking the polarization process. During stage II, governed by the thermal motion, lower temperature improves the coalescence because of a diffusion effect, but higher temperature deteriorates electro-coalescence because of a violent molecular thermal motion. Additionally, hydrogen bond and radial distribution functions are obtained by statistics to describe droplets micromorphology, which explains the reason why the droplet forms longer chain structure at the critical electric field.     

分子动力学模拟研究荧光分子芘在磺基甜菜碱胶束中的增溶

采用分子动力学模拟研究了荧光分子芘在磺基甜菜碱两性表面活性剂聚集体中的增溶现象．结果表明,芘分子自发地自溶液中增溶进入胶束疏水内核的栅栏层区域．当胶束溶液中芘分子的局部浓度增大时,两个芘分子可以同时增溶进胶束的栅栏层区域,此时两个芘分子形成π-π共轭堆积的激发态络合物．但是由于荧光分子之间的弱兀．兀相互作用,激发态络合物在胶束中是不稳定的,表现为两个芘分子的多次结合和分离．模拟表明,分子动力学方法可以在分子水平上研究荧光探针分子在表面活性剂胶束中的增溶位点,解释荧光分子在胶束中的动力学现象．     

Molecular dynamics simulation of structure H clathrate-hydrates of binary guest molecules

Molecular dynamics (MD) simulations are performed to study the stability of structure H clathrate-hydrates of methane+large-molecule guest substance (LMGS) at temperatures of 270, 273, 278 and 280 K under canonical (NVT-) ensemble condition in a 3×3×3 structure H unit cell replica with 918 TIP4P water molecules. The studied LMGS are 2-methylbutane (2-MB), 2,3-dimethylbutane (2,3-DMB), neohexane (NH), methylcyclohexane (MCH), adamantane and tert-butyl methyl ether (TBME). In the process of MD simulation, achieving equilibrium of the studied system is recognized by stability in calculated pressure for NVT-ensemble. So, for the accuracy of MD simulations, the obtained pressures are compared with the experimental phase diagrams. Therefore, the obtained equilibrium pressures by MD simulations are presented for studying the structure H clathrate-hydrates. The results show that the calculated temperature and pressure conditions by MD simulations are consistent with the experimental phase diagrams. Also, the radial distribution functions (RDFs) of host-host, host-guest and guest-guest molecules are used to analysis the characteristic configurations of the structure H clathrate-hydrate.     

Molecular dynamics simulation study on the inhibitory effects of choline-O-sulfate on hIAPP protofibrilation

Type 2 diabetes mellitus (T2Dm) is a neurodegenerative disease, which occurs due to the self-association of human islet amyloid polypeptide (hIAPP), also known as human amylin. It was reported experimentally that choline-O-sulfate (COS), a small organic molecule having a tertiary amino group and sulfate group, can prevent the aggregation of human amylin without providing the mechanism of the action of COS in the inhibition process. In this work, we investigate the influence of COS on the full-length hIAPP peptide by performing 500 ns classical molecular dynamics simulations. From pure water simulation (without COS), we have identified the residues 11–20 and 23–36 that mainly participate in the fibril formation, but in the presence of 1.07 M COS these residues become totally free of β-sheet conformation. Our results also show that the sulfate oxygen of COS directly interacts with the peptide backbone, which leads to the local disruption of peptide–peptide interaction. Moreover, the presence of favorable peptide-COS vdW interaction energy and high coordination number of COS molecules in the first solvation shell of the peptide indicates the hydrophobic solvation of the peptide residues by COS molecules, which also play a crucial role in the prevention of β-sheet formation. Finally, from the potential of mean force (PMFs) calculations, we observe that the free energy between two peptides is more negative in the absence of COS and with increasing concentration of COS, it becomes unfavorable significantly indicating that the peptide dimer formation is most stable in pure water, which becomes less favorable in the presence of COS. © 2019 Wiley Periodicals, Inc.     

Molecular dynamics simulation study of the structural features and inclusion capacities of cucurbit[6]uril derivatives in aqueous solutions

Molecular dynamics (MD) simulations were performed for cucurbit[6]uril (CB6) methyl and cyclohexyl derivatives in aqueous solutions. Furthermore, MD simulations have been conducted to study the inclusion complexes between each CB6 derivative with α,ω-pentane diammonium ion (NH₃⁺(CH₂)₅NH₃⁺) to estimate the binding free energies, the complex geometries and the intermolecular forces responsible for complex formation. Results show a complete inclusion of the guest molecule in the cavity of the host for all complexes. Results also indicate that the guest dynamics inside the cavity of the substituted host is similar to that for the unsubstituted host. This demonstrates that the molecular recognition of the host is not affected by the alkyl substitution at the equator. Also, there is an insignificant conformational change of the macrocyclic structure upon inclusion of the guest. Molecular mechanics/Poisson Boltzmann surface area method was used to estimate the binding free energy of each complex. Results indicate that host–guest electrostatic interactions make the largest contribution to the complex binding free energy. Moreover, van der Waals interactions add significantly to the complex stability. The guest molecules show more or less similar binding free energies with the substituted CB6 that exhibits slightly more negative values than unsubstituted CB6 which is proved also by umbrella sampling.     

Essential dynamics for the study of microstructures in liquids

Essential Dynamics (ED) is a powerful tool for analyzing molecular dynamics (MD) simulations and it is widely adopted for conformational analysis of large molecular systems such as, for example, proteins and nucleic acids. In this study, we extend the use of ED to the study of clusters of arbitrary size constituted by weakly interacting particles, for example, atomic clusters and supramolecular systems. The key feature of the method we present is the identification of the relevant atomic‐molecular clusters to be analyzed by ED for extracting the information of interest. The application of this computational approach allows a straightforward and unbiased conformational study of the local microstructures in liquids, as emerged from semiclassical MD simulations. The good performance of the method is demonstrated by calculating typical observables of liquid water, that is, NMR, NEXAFS O1s, and IR spectra, known to be rather sensitive both to the presence and to the conformational features of hydrogen‐bonded clusters. © 2014 Wiley Periodicals, Inc.     

Molecular simulation of structure formation and rheological properties of mixtures of telechelic and monofunctional associating polymer

We study the phase behavior, the characteristic times, and the rheological properties under the steady shear flow of the mixtures consisting of telechelic and monofunctional associating polymers by a coarse‐grained molecular dynamics simulation. The mixtures form the transient networks, the closely packed spherical micelles, and the wormlike micelles. We confirm the molecular origins of the several characteristic times of the mixtures. The dependencies of the characteristic times on the composition ratio between telechelic and monofunctional associating polymers show good agreement with reported experimental results. Under the steady shear flow, the mixtures show the shear thinning induced by the change of the spatial configuration of the micelles. The telechelic associating polymers especially play an important role in connecting the micelles at the shear thinning regime and enhance the steady shear viscosity. Furthermore, at the wormlike micellar region, the mixtures show the second shear thinning initiated by the transformation of the association conformation of the telechelic associating polymers.     

熔融ZnCl2结构的分子动力学模拟研究

熔融ZnCl2作为一种离子性共价性参半的典型熔盐, 其近邻结构在实验测量和分子动力学模拟方面均作过一些研究。本文依据新近EXAFS实验结果, 比较了不同的有效势下模拟得到的径向分布函数,表明KDR势可作为一种实用势。并进一步在KDR势模拟产生的瞬态构型基础上, 使用键序参数方法研究了晶态和熔融态ZnCl2中的近邻结构。结果表明, 和晶态ZnCl2一样, 在熔融ZnCl2中存在稳定的Zn/Cl正四面体结构, 但熔态和晶态Zn/Cl近邻结构热波方差σ不同。计算表明300K晶态σ=5.0℃, 613K熔融态σ=12.2℃。也对熔融ZnCl2的网络状结构和宏观输运性质进行了讨论。     

Molecular dynamics simulations of the hexagonal structure of crystals with long methylene sequences

An unconstrained polymethylene crystal, consisting of 9600 CH₂ groups, in which each CH₂ is permitted to carry out stretching, bending, and torsional motion, has been studied at various temperatures using molecular dynamics simulations. Information about the atomistic details of the dynamics and structure of these crystals is presented. A significant disorder exists at tempratures well below the melting point. Close to melting, the disordered crystals have about 2% of gauche bonds that are distributed mainly at positions close to the surface of the crystal. The major disorder consists, however, of a collective twisting of the chains leading to a hexagonal crystal structure. The hexagonal structure of the symmetric motifs is caused by a dynamic multidomain arrangement of the chains. © 1993 John Wiley & Sons, Inc.     

Molecular dynamics simulation study of association in trifluoroethanol/water mixtures

Mixtures of Trifluoroethanol (TFE) and water with different proportions are studied using molecular dynamics simulations. The radial and spatial distribution functions, as well as the size distribution of TFE clusters are obtained from the trajectories. The variation of radial and spatial distribution functions with composition show that the addition of TFE enhances the water structure, but the hydrogen bonds between TFE molecules are broken as TFE is diluted with water. The TFE‐rich solutions have stronger TFE–water hydrogen bonds. The clustering of TFE molecules in low concentration region is attributed to the hydrophobic interactions between CF₃ groups. The distribution of cluster sizes in solution supports these conclusions. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Revisiting the structure and dynamics of hydrated Cd2+ in aqueous solutions: Insights from the RI-SCS-MP2/MM molecular dynamics simulation

The spin component scale MP2/molecular mechanics molecular dynamics simulation investigated the hydration shell formation and hydrated Cd²⁺ dynamics in the water environment. At the first hydration shell, six water molecules with 2.27 Å for the average distance between water and Cd²⁺. Dynamical properties were analyzed by computing the water molecule's mean residence time (MRT) in its first and second hydration shells. The MRT of each shell was determined to be 31.8 and 1.92 ps, suggesting the strong influence of Cd²⁺ in the first hydration shell. The second shell was labile, with an average number of water molecules being 18. Despite the strong interaction between Cd²⁺ and water molecules in the first shell, the influence of ions in the second hydration shell remained weak.