A Path Integral Molecular Dynamics Simulation of a Harpoon-Type Redox Reaction in a Helium Nanodroplet

We present path integral molecular dynamics (PIMD) calculations of an electron transfer from a heliophobic Cs2 dimer in its (3Σu) state, located on the surface of a He droplet, to a heliophilic, fully immersed C60 molecule. Supported by electron ionization mass spectroscopy measurements (Renzler et al., J. Chem. Phys. 2016, 145, 181101), this spatially quenched reaction was characterized as a harpoon-type or long-range electron transfer in a previous high-level ab initio study (de Lara-Castells et al., J. Phys. Chem. Lett. 2017, 8, 4284). To go beyond the static approach, classical and quantum PIMD simulations are performed at 2 K, slightly below the critical temperature for helium superfluidity (2.172 K). Calculations are executed in the NVT ensemble as well as the NVE ensemble to provide insights into real-time dynamics. A droplet size of 2090 atoms is assumed to study the impact of spatial hindrance on reactivity. By changing the number of beads in the PIMD simulations, the impact of quantization can be studied in greater detail and without an implicit assumption of superfluidity. We find that the reaction probability increases with higher levels of quantization. Our findings confirm earlier, static predictions of a rotational motion of the Cs2 dimer upon reacting with the fullerene, involving a substantial displacement of helium. However, it also raises the new question of whether the interacting species are driven out-of-equilibrium after impurity uptake, since reactivity is strongly quenched if a full thermal equilibration is assumed. More generally, our work points towards a novel mechanism for long-range electron transfer through an interplay between nuclear quantum delocalization within the confining medium and delocalized electronic dispersion forces acting on the two reactants.     

核糖核酸酶Sa表面水和尿素分子的分布和动力学行为的分子动力学模拟

利用分子动力学模拟研究了在不同尿素浓度下,核糖核酸酶Sa(RNase Sa)表面水和尿素分子的分布和动力学行为。 结果表明,尿素分子可与RNase Sa酶形成较强的相互作用,并取代其表面的水分子而富集在蛋白质表面。 尿素分子更倾向与RNase Sa酶的疏水残基作用,与RNase Sa酶主链形成氢键的能力更强。 尿素分子的平动和转动远远慢于水分子的平动和转动。 RNase Sa酶表面水分子的平动和转动随着尿素浓度增加而逐渐变慢,但RNase Sa酶表面尿素分子的动力学并不依赖于尿素浓度变化。 本研究中明晰的RNase Sa酶表面水和尿素分子分布和动力学有助于理解水和尿素分子对蛋白质稳定性的影响。     

Molecular Dynamics Simulations of Energetic Solids

A continuing objective in the area of energetic materials is to reduce sensitivity toward impact and shock. One approach is to develop a better understanding of how factors related to the crystal lattice, e.g., defects, influence the initiation and propagation of detonation. Molecular dynamics is a useful tool for this purpose. This paper presents an overview of molecular dynamics treatments of energetic solids. Some of these have simulated initiation and propagation in idealized systems; others have focused on developing a satisfactory procedure for describing molecular crystals of practical significance. Our emphasis in this discussion is on the progress that has been made along the second lines.     

Properties of Polyvinyl Alcohol Oligomers: A Molecular Dynamics Study

MD studies of liquid isopropyl alcohol and melts of short poly(vinyl alcohol) (PVA) oligomers are described. The specific volume was found to depend inversely on the number N of repeat units. If the chain length is enhanced, the viscosity of the PVA melt increases and the peaks in the radial distribution function become sharper. Additional peaks that appear in melts of PVA chains are of pure intramolecular origin. The calculated radius of gyration was found to depend on the number of formula units via . The orientation correlation functions showed that all molecular vectors of PVA melts with chain lengths N = 1, 2, 3 relax completely within a few nanoseconds. The relaxation times for the O H bond vector as obtained via the Kohlrausch‐Williams‐Watts expression showed an exponential dependence on the number of repeat units.

     

双层铜金属薄膜纳米压痕机械性能的分子动力学模拟

多层金属薄膜的机械性质在纳米组件的设计上是非常重要的.目前,纳米尺度材料的机械性质测量的最主要方法为纳米压痕检测技术.本文应用分子动力学理论对双层铜金属薄膜界面的结构形态与特性进行分析探讨.选用FCC结构单晶铜的(100)面,(110)面和双层铜金属薄膜作为探讨界面性质的材料,进而探讨了单晶铜及双层铜金属薄膜的纳米压痕变形性质.     

Molecular Dynamics Simulation of the Fracture in Polymer‐Exfoliated Layered Silicate Nanocomposites

Summary: The MD technique was used to investigate the fracture behavior in fully exfoliated layered silicate (nanoplatelet)‐polymer nanocomposites. MD results reveal that the addition of the nanoplatelets can improve the fracture strength of polymers. The interactions between the surface of the nanoplatelets and the segments of the polymer, and the relaxation time of polymer chains have significant influences on the fracture strength of the polymer. For polymers with T_g below room temperature, such as polyurethane, or close to room temperature, such as nylon, the nanoplatelets are always working for the enhancement of the mechanical properties. However, for polymers with T_g above room temperature, such as epoxy and polystyrene, the addition of the nanoplatelets is not working well for toughening these polymers. If the nanoplatelets are to enhance the mechanical properties of these polymers, it is necessary to build up a stress relaxation interface between the polymer and the nanoplatelet in order to reduce the effect of the difference between the relaxation time of nanofillers and that of polymers.

Force per area versus distance curves as a function of the difference of the relaxation times of the nanoplatelets and polymer chains.     

Thermally Induced Phase Transition of Crystalline Syndiotactic Polystyrene Studied by Molecular Dynamics Simulation

The structural phase transition between the polymorphs of syndiotactic polystyrene has been studied by means of molecular dynamics simulation. It was found that the initial δ_e form of the crystal structure was completely transformed into the γ form by thermal treatment. Not only the crystal structure but also the transition path are investigated at the molecular level for the first time.     

Molecular Dynamics Simulation of the Binding Interaction between Hormone Glucagon Protein and Self-Assembled Monolayer Molecules

Restrained molecular dynamics simulations were performed to study the binding affinity of the peptide with alkanethiols of different tail-groups, S（CH2）7CH3, S（CH2）7OH and S（CH2）7COOH, which self-assembled on Au（111） surface in the presence of water molecules. The curves of binding affinity were calculated by fixing the center of mass of the peptide at various distances from the assembling surface. Simulation results show that the binding affin- ity is in the order as COOH-SAMs〉OH-SAMs〉CH3-SAMs, while 100% COOH-SAMs〉5% COOH-SAMS in concentration. The effects on binding affinity by different tail-groups were also studied. Results show that the binding affinity between COOH-SAMs and the peptide is bigger than those of the others and increasing the acidity of COOH-SAMs will result in stronger attractive power.     

诺氟沙星-DNA复合物的分子动力学模拟

采用分子模建的方法构建了诺氟沙星-DNA复合物的初始结构, 通过2 ns的分子动力学(MD)模拟研究表明: 诺氟沙星能够和双螺旋d[ATATCGATAT]₂形成稳定的复合物, 药物分子可紧密结合在DNA的小沟区域, 并且能够与DNA的鸟嘌呤碱基形成两个稳定的氢键. 在分子水平上提供了诺氟沙星直接与双螺旋DNA相互作用的结构及复合物的动态变化情况.     

Structure of Polymer Brushes in Cylindrical Tubes: A Molecular Dynamics Simulation

Summary: Molecular dynamics simulations of a coarse‐grained bead‐spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length N and grafting density σ are varied over a wide range and the crossover from “mushroom” to “brush” behavior is studied for three pore diameters. The monomer density profile and the distribution of the free chain ends are computed and compared to the corresponding model of polymer brushes at flat substrates. It is found that there exists a regime of N and σ for large enough pore diameter where the brush height in the pore exceeds the brush height on the flat substrate, while for large enough N and σ (and small enough pore diameters) the opposite behavior occurs, i.e. the brush is compressed by confinement. These findings are used to discuss the corresponding theories on polymer brushes at concave substrates.

Snapshot picture of a brush grafted inside of a cylinder, for , , displaying different chains in distinct colors in order to be able to distinguish them. Top shows a side view of the cylinder, and the lower part a view of the cross‐section. Note that the particles forming the cylindrical wall are not displayed.     

水化镁基蒙脱石的分子动力学模拟

利用分子动力学(MD)模拟了300 K时镁基蒙脱石(粘土)层间水和镁离子的结构和动力学性质.模拟结果显示水在粘土层间分为二层,只有一小部分水被粘土表面吸附,与粘土结构中的羟基形成氢键,不同分布位置的水处于动态平衡.层间水分子氢键配位数比普通水少24%左右,水在粘土中自扩散系数D＝5.355×10^-10 m²·s^-1,约为主体相水的1/4.镁离子在粘土层间形成一层,其与水分子配位数约为6.进一步讨论了温度对粘土层中水的结构和动力学性质的影响.随着温度升高,水层的局部密度ρ(z)降低,水在XY方向的扩散系数不断增大.当温度达到600 K后,层间水分子间的氢键断裂,与超临界状态下水的结构相似,层间水的扩散系数达最大值,温度进一步升至700 K时,其值基本无变化.     

RbCl熔解的分子动力学模拟研究

采用等压分子动力学模拟方法，研究了从晶相到液相不同温度下ＲｂＣｌ体系的结构和性质，等压模拟咄等容怀致的平衡性质和结构特征，键序参数计算，不计及导热过程情形下，体系在振荡驰豫时间量级内完成熔化过程，由于不需要密度数据，等压模拟有望发展成为材料设计中的一种手段。     

Virtual Screening and Molecular Dynamics Simulation Study of Influenza Polymerase PB2 Inhibitors

Influenza A virus is the main cause of worldwide epidemics and annual influenza outbreaks in humans. In this study, a virtual screen was performed to identify compounds that interact with the PB2 cap-binding domain (CBD) of influenza A polymerase. A virtual screening workflow based on Glide docking was used to screen an internal database containing 8417 molecules, and then the output compounds were selected based on solubility, absorbance, and structural fingerprints. Of the 16 compounds selected for biological evaluation, six compounds were identified that rescued cells from H1N1 virus-mediated death at non-cytotoxic concentrations, with EC50 values ranging from 2.5–55.43 μM, and that could bind to the PB2 CBD of H1N1, with Kd values ranging from 0.081–1.53 μM. Molecular dynamics (MD) simulations of the docking complexes of our active compounds revealed that each compound had its own binding characteristics that differed from those of VX-787. Our active compounds have novel structures and unique binding modes with PB2 proteins, and are suitable to serve as lead compounds for the development of PB2 inhibitors. An analysis of the MD simulation also helped us to identify the dominant amino acid residues that play a key role in binding the ligand to PB2, suggesting that we should focus on increasing and enhancing the interaction between inhibitors and these major amino acids during lead compound optimization to obtain more active PB2 inhibitors.     

Molecular Dynamic Simulation of Side-Chain Liquid Crystalline Elastomer

Summary: Molecular dynamic simulation of side chain liquid crystalline elastomer has been carried out. As an initial state a flexible polymer network in a low molecular liquid-crystal (LC) solvent was used. The LC solvent comprises of anisotropic rod-like semiflexible linear molecules (mesogens) composed of particles bonded into the chain by FENE potential. Rigidity of LC molecules was induced by a bending potential. All interactions between nonbonded particles are described by a repulsive Lennard-Jones potential. For the systems with different values of density and order parameter obtained after sufficiently long trajectory the attachment of ends of mesogens to the polymer network was simulated. The kinetic of the process of mesogens attachment to network was studied as well as morphology of attachment. The structural and dynamical behaviour of side chain LC elastomer was studied and compared with systems of polymer network in low molecular LC solvent.     

Predictors of Cavitation in Glassy Polymers under Tensile Strain: A Coarse‐Grained Molecular Dynamics Investigation

The nucleation of cavities in a homogeneous polymer under tensile strain is studied in a coarse‐grained MD simulation. To establish a causal relation between local microstructure and the onset of cavitation, a detailed analysis of some local properties is presented. In contrast to common assumptions, the nucleation of a cavity is neither correlated to a local loss of density nor to stress at the atomic scale or the chain‐end density in the nondeformed state. Instead, a cavity in glassy polymers nucleates in regions that display a low bulk elastic modulus. Even if the localization of a cavity is not directly predictable from the initial configuration, the elastically weak zones identified in the initial state emerge as favorite spots for cavity formation.

     

Influence of Solid-liquid Interaction and Temperature on the Dynamic Dewetting of a Thin Polymer Film:A Molecular Dynamics Study

Coarse-grained molecular dynamics simulations were carried out to investigate the dewetting behavior of a polymer thin film on partial wetting solid surface at the early stage of the dewetting process. Spontaneous dewetting is initiated by removing a band of strip from both the ends of the liquid polymer film which has achieved equilibrium. The solid-liquid interaction and temperature were varied to show their influence on the dewetting dynamics during dewetting as well as the shape evolution of the liquid ...     

Effect of Size and Temperature on Water Dynamics inside Carbon Nano-Tubes Studied by Molecular Dynamics Simulation

Water transport inside carbon nano-tubes (CNTs) has attracted considerable attention due to its nano-fluidic properties, its importance in nonporous systems, and the wide range of applications in membrane desalination and biological medicine. Recent studies show an enhancement of water diffusion inside nano-channels depending on the size of the nano-confinement. However, the underlying mechanism of this enhancement is not well understood yet. In this study, we performed Molecular Dynamics (MD) simulations to study water flow inside CNT systems. The length of CNTs considered in this study is 20 nm, but their diameters vary from 1 to 10 nm. The simulations are conducted at temperatures ranging from 260 K to 320 K. We observe that water molecules are arranged into coaxial water tubular sheets. The number of these tubular sheets depends on the CNT size. Further analysis reveals that the diffusion of water molecules along the CNT axis deviates from the Arrhenius temperature dependence. The non-Arrhenius relationship results from a fragile liquid-like water component persisting at low temperatures with fragility higher than that of the bulk water.     

不同构型聚α-烯烃分子润滑性的分子动力学模拟

采用分子动力学方法研究不同构型的直链和支链化润滑油聚α-烯烃(PAO)在剪切铁板间的黏度、 摩擦性以及油膜内PAO分子的聚集行为, 从微观角度解释了PAO分子结构与润滑油膜稳定性的关系. 模拟结果表明, 相比于直链PAO, 支链化PAO润滑油剪切黏度受剪切速率影响较小; 支链化PAO剪切摩擦系数小于直链PAO润滑油; 对比直链PAO分子, 支链化PAO分子由于侧链的存在, 可在润滑体系内多层吸附层间形成复杂的网状结构, 降低PAO分子在剪切力作用下的移动. 这种网状结构有利于润滑油膜的稳定, 延长了润滑油的使用寿命.     

Trianglimine-Mediated Selective Sieving of Cis Isomer from the Mixture of Dihaloethenes: A Combined Molecular Dynamics and DFT Investigation

The manufacture of alkenyl halides on a larger scale often results in the formation of a mixture of isomers, each having individual significant applications while their separation from each other is a strenuous task. Since most of the conventional distillation techniques are known to be intricate, energy consuming and expensive, the quest for an alternative separation strategies is still continuing. In this context, the recently reported trianglimine macrocycle - a new class of intrinsically porous material, is promising in discerning cis isomer from a mixture of cis and trans dichloroethene. Herein, an attempt has been made to apprehend the host-guest inclusion phenomenon accountable for the selectivity of cis over the trans isomers of 1,2-dihaloethene (F, Cl and Br) using molecular dynamics simulation and density functional calculations at ω-B97xd/6-311G+(d,p) level of theory. The average binding energy of selected snapshots has been calculated at different loadings, temperatures and pressures from molecular dynamics simulation. Our results show that trianglimine can stabilise the cis isomers of the dihaloethenes inside its cavity forming complexes with high interaction energies and the rationale behind the recyclability of the host molecule has been clarified. The outcomes of the calculations bring out the potential utility of this new host architecture to produce highly pure value added chemicals in industries.