Ab initio molecular dynamics investigation of the structure and the noncollinear magnetism in liquid oxygen: occurrence of O4 molecular units

We modeled liquid oxygen using ab initio molecular dynamics in which both the atomic structure and the noncollinear magnetic structure evolve without constraints. The atomic structure shows preference for parallel alignment of first-neighbor molecules and is supported by an excellent agreement between theoretical and experimental nuclear structure factors. The magnetic structure shows short-range antiferromagnetic correlations in agreement with spin-polarized neutron diffraction data. The observed correlations primarily result from appropriate trajectories of colliding O2 molecules. The simulation provides evidence for the occurrence of long-living O4 molecular units.     

Changes in protein structure and dynamics as a function of hydration from (1)H second moments

We report the proton second moment obtained directly from the Free Induction Decay (FID) of the NMR signal of variously hydrated bovine serum albumin (BSA) and hen egg white lysozyme (HEWL) and from the width of the NMR Z-spectrum of the cross-linked protein gels of different concentrations. The second moment of the proteins decreases in a continuous stepwise way as a function of increasing water content, which suggests that the structural and dynamical changes occur in small incremental steps. Although the second moment is dominated by the short range distances of nearest neighbors, the changes in the second moment show that the protein structure becomes more open with increasing hydration level. A difference between the apparent liquid content of the sample as found from decomposition of the FID and the analytically determined water content demonstrates that water absorbed in the early stages of hydration is motionally immobilized and magnetically indistinguishable from rigid protein protons while at high hydration levels some protein side-chain protons move rapidly contributing to liquid-like component of the NMR signal.     

Effects of co-solutes on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution: a molecular dynamics simulations study

The effects of trimethylamine-N-oxide (TMAO), urea and tetramethyl urea (TMU) on the hydrogen bonding structure and dynamics of aqueous solution of N-methylacetamide (NMA) are investigated by classical molecular dynamics simulations. The modification of the water's hydrogen bonding structure and interactions is calculated in presence of these co-solutes. It is observed that the number of four-hydrogen-bonded water molecules in the solution decreases significantly in the presence of TMAO rather than urea and TMU. The lifetime and structural relaxation time of water–water and NMA–water hydrogen bonds show a strong increase with the addition of TMAO and TMU in the solution, whereas the change is nominal in case of urea solution. It is also found that the translational and rotational dynamics of water and NMA slowdown with increasing the concentration of these osmolytes. The slower dynamics of water and NMA is more pronounced in case of TMAO and TMU solution, as these co-solutes strengthen the average hydrogen bond energies between water–water and NMA–water, whereas urea has a little effect on the hydrogen bonding structure and dynamics of aqueous NMA solution. The calculated self-diffusion coefficient values for water and these co-solutes are in similar pattern with experimental observations.     

Effect of a monomeric sequence on the structure of hydrated Nafion in the sandwich model and solvent dynamics in nano-channels: a molecular dynamic study

Molecular dynamics simulations are performed to obtain insight into the structural properties of hydrated Nafion using the sandwich model of the polymer membrane. It is shown that a larger distance between the sulfonate groups of a chain leads to the polymer forming a better inverted micelles structure. Water– and hydronium–polymer interfaces are investigated. Comparing our results with others indicates that, from the perspective of distance, the formation of shells of water and hydronium ions is independent of the model and monomer type, but depends on both if the coordination number is considered. The behaviour of water molecules and hydronium ions is also studied dynamically. Our survey shows that there is an increasing jump in the diffusion coefficient of water at a certain distance between the sulfonate groups of a chain, which then tends to change slightly. Such behaviour is discussed on the basis of density, the available space, as well as the loss of one translational degree of freedom of the water molecules at larger distances. The diffusion coefficient for the hydronium ions was also determined to be much smaller than that for water (by 3.5–6.1 times). The diffusion coefficient of the hydronium ions shows a declining jump at a certain distance between the sulfonate groups of a chain, but the jump is not significant as that for the water molecules.     

Effect of grain boundary sliding on the toughness of ultrafine grain structure steel: A molecular dynamics simulation study

Molecular dynamics simulations are carried out to investigate the mechanisms of low-temperature impact toughness of the ultrafine grain structure steel. The simulation results suggest that the sliding of the {001}/{110} type and {110}/{111} type grain boundary can improve the impact toughness. Then, the mechanism of grain boundary sliding is studied and it is found that the motion of dislocations along the grain boundary is the underlying cause of the grain boundary sliding. Finally, the sliding of the grain boundary is analyzed from the standpoint of the energy. We conclude that the measures which can increase the quantity of the {001}/{110} type and {110}/{111} type grain boundary and elongate the free gliding distance of dislocations along these grain boundaries will improve the low-temperature impact toughness of the ultrafine grain structure steel.     

Initial growth of single-walled carbon nanotubes on supported iron clusters: a molecular dynamics study

Molecular dynamics simulations were used to study the initial growth of single-walled carbon nanotubes (SWNTs) on a supported iron cluster (Fe₅₀). Statistical analysis shows that the growth direction of SWNTs becomes more perpendicular to the substrate over time due to the weak interaction between carbon nanotube and the substrate. The diameter of the nanotube also increases with the simulation time and approaches the size of the supported iron cluster.     

Si60团簇的结构及其与Si(111)面间碰撞的分子动力学模拟

利用紧束缚分子动力学退火方法模拟研究了Si60团簇的稳定结构和基态能量,结果表明Si60团簇为具有T对称性的截顶二十面体的富勒烯结构,平均键长为0236nm,直径为0933nm,原子结合能为4.45eVatom,JahnTeller效应对Si60团簇的结构有很大影响.通过对Si60分子和Si(111)面碰撞机理的粒子数、体积和能量不变分子动力学模拟,发现Si60分子吸附在Si(111)面所需要的垂直入射动能为40eV,Si60分子远不如C60分子稳定 关键词： 紧束缚 JahnTeller效应 碰撞     

Role of oxygen functional groups for structure and dynamics of interfacial water on low rank coal surface: a molecular dynamics simulation

Molecular dynamics simulations were employed to study the effects of oxygen functional groups for structure and dynamics properties of interfacial water molecules on the subbituminous coal surface. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of subbituminous coal according to XPS results, and the composing proportion for hydroxyl, carbonyl and carboxyl is 25:3:5. The hydration energy with ?386.28 kJ/mol means that the adsorption process between water and coal surface is spontaneous. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxyl and carbonyl is similar.     

Effects of wettability and interfacial nanobubbles on flow through structured nanochannels: an investigation of molecular dynamics

Solid–fluid boundary conditions are strongly influenced by a number of factors, including the intrinsic properties of the solid/fluid materials, surface roughness, wettability, and the presence of interfacial nanobubbles (INBs). The interconnected nature of these factors means that they should be considered jointly. This paper employs molecular dynamics (MD) simulation in a series of studies aimed at elucidating the influence of wettability in boundary behaviour and the accumulation of interfacial gas. Specifically, we examined the relationship between effective slip length, the morphology of nanobubbles, and wettability. Two methods were employed for the promotion of hydrophobicity between two structured substrates with similar intrinsic contact angles. We also compared anisotropic and isotropic atomic arrangements in the form of graphite and Si(100), respectively. A physical method was employed to deal with variations in surface roughness, whereas a chemical method was used to adjust the wall–fluid interaction energy (?_wf). We first compared the characteristic properties of wettability, including contact angle and fluid density within the cavity. We then investigated the means by which variations in solid–fluid interfacial wettability affect interfacial gas molecules. Our results reveal that the morphology of INB on a patterned substrate is determined by wettability as well as the methods employed for the promotion of hydrophobicity. The present study also illustrates the means by which the multiple effects of the atomic arrangement of solids, surface roughness, wettability and INB influence effective slip length.     

Effect of nanostructures on evaporation and explosive boiling of thin liquid films: a molecular dynamics study

Molecular dynamics simulations have been employed to investigate the boiling phenomena of thin liquid films adsorbed on a nanostructured solid surface. The molecular system was comprised of the following: solid platinum wall, liquid argon, and argon vapor. A few layers of the liquid argon were placed on the nanoposts decorated solid surface. The nanoposts height was varied keeping the liquid film thickness constant to capture three scenarios: (i) liquid-film thickness is higher than the height of the nanoposts, (ii) liquid-film and nanoposts are of same height, and (iii) liquid-film thickness is less than the height of the nanoposts. The rest of the simulation box was filled with argon vapor. The simulation was started from its initial configuration, and once the equilibrium of the three phase system was established, the wall was suddenly heated to a higher temperature which resembles an ultrafast laser heating. Two different jump temperatures were selected: a few degrees above the boiling point to initiate normal evaporation and far above the critical point to initiate explosive boiling. Simulation results indicate nanostructures play a significant role in both cases: Argon responds very quickly for the nanostructured surface, the transition from liquid to vapor becomes more gradual, and the evaporation rate increases with the nanoposts height.     

Atomic-level investigation of Al and Ni thin film growth on Ni(1 1 1) surface: Molecular dynamics simulation

Using molecular dynamics (MD) simulation, the structural characteristics of Al and Ni thin film growth on Ni(1 1 1) substrate according to the incident energy of adatoms were investigated. In case of Al on Ni(1 1 1), Al adatoms were grown basically through the layer-by-layer growth mode. On the other hand, Ni thin films on Ni(1 1 1) surface at low incident energy were shown to favor island growth. The steering effect due to atomic attraction, which results in rougher surface, was significantly observed at low incident energy. The growth mode of Ni film was, however, changed to follow layer-by-layer growth mode for the incident energy of 6 eV. The different aspects of surface morphology between Al and Ni deposition on Ni(1 1 1) surface could be successfully explained by the surface diffusion and impact cascade diffusion.     

氦泡在bcc钨中晶界处成核长大的分子动力学模拟

钨(W)是潜在的聚变堆面向等离子体材料.聚变反应中产生的氦(He)不溶于金属W,并在其中易聚集形成He泡,使W基体发生脆化,从而导致W基体的性能发生退化.在前人工作的基础上,本文采用分子动力学研究了He泡在单晶bcc-W中以及bcc-W中∑3[211](110)和∑9[110](411)晶界处He泡形核长大初期的演化过程.结果发现,晶界处He泡的长大机制和单晶W中有所不同.单晶W中He泡通过挤出位错环促进长大.而He泡在∑3[211](110)晶界处的长大机制为:首先挤出并发射少量自间隙W原子,而后挤出1/2⟨111⟩位错线,随后,该位错线会沿晶界面上[111]方向迁移出去;在∑9[110](411)晶界处,He泡在我们的模拟时间尺度范围内没有观察到W自间隙子的发射和位错的挤出.     

界面氢键对受限水结构和动态特性的影响

应用反应力场分子动力学方法, 模拟了水限制在全羟基化二氧化硅晶体表面间的弛豫过程, 研究了基底表面与水形成的界面氢键, 及其对受限水结构和动态特性行为的影响. 当基底表面硅醇固定时, 靠近基底表面水分子中的氧原子与基底表面的氢原子形成强氢键, 这使得靠近表面水分子中的氧原子比对应的氢原子更靠近基底表面, 从而水分子的偶极矩远离表面. 当基底表面硅醇可动时, 靠近基底表面水分子与基底表面原子形成两种强氢键, 一种是水分子中的氧原子与表面的氢原子形成的强氢键, 数量较少, 另一种是水分子中的氢原子与表面的氧原子形成的强氢键, 数量较多, 这使得靠近表面水分子中的氢原子比对应的氧原子更靠近表面, 从而水分子的偶极矩指向表面. 在相同几何间距下, 当基底表面硅醇可动时, 表面的活动性使得几何限制作用减弱, 导致了受限水分层现象没有固定表面限制下的明显. 此外, 固定表面比可动表面与水形成的界面氢键作用较强, 数量较多, 导致了可动表面限制下水的运动更为剧烈.     

Diffusion and growth of nickel,iron and magnesium adatoms on the aluminum truncated octahedron: A molecular dynamics simulation

The structure of nickel (Ni), iron (Fe), and magnesium (Mg) adatoms on the aluminum (Al) truncated octahedron is studied using molecular dynamics and the analytic embedded atom method. First, the energy barriers of several typical diffusion processes of Ni, Fe, and Mg adatoms on the Al truncated octahedral cluster were calculated using the nudged elastic band method. The calculated energy barriers were found to be related to the surface energy and atomic radius of the adatom and substrate atom. The result shows that the incorporation of Ni and Fe atoms into Al core easily occurs, and the Mg atom should segregate at the surface of the Al cluster. Thus, the growth of Ni, Fe and Mg on the Al truncated octahedron with 1289 atoms was simulated at several temperatures. In the Ni–Al and Fe–Al cases, the core-shell structure was not obtained. For the Mg–Al system, a good Mg shell on the Al core was found at lower temperatures, and an almost perfect truncated octahedron with more Al shells emerged with an increase in temperature.     

Entropy and enthalpy calculations from perturbation and integration thermodynamics methods using molecular dynamics simulations: applications to the calculation of hydration and association thermodynamic properties

Calculation of association thermodynamic properties using molecular simulation is essential in computational chemistry. In the case of good agreement with the experimental thermodynamic binding properties, this type of calculation may complement experimental works by providing a microscopic view of the association process. Whereas the calculation of the free energy of association is nowadays well controlled, the calculation of the enthalpy and entropy of association remains difficult in most cases, especially as the association involves hosts and guests of biological interest. A novel method for calculating the entropy change from a molecular dynamics simulation is described. Within the theoretical framework, we discuss the different approximations leading to the final stage of the operational expressions of ΔG and ΔH in the NpT ensemble and we establish an expression for ΔS using the Free Energy Perturbation (FEP) formalism in this statistical ensemble. Finally, we illustrate the theoretical considerations by calculations of the hydration entropy changes between cations of different masses and charges. We extend the study by calculating the changes in the thermodynamic properties of association of inorganic cations with a macrocycle of biological interest.     

System size and trajectory length dependence of the static structure factor and the diffusion coefficient as calculated from molecular dynamics simulations: The case of SPC/E water

The effect of the applied trajectory length on the convergence of the self-diffusion coefficient was examined for the SPC/E water model in the NVT ensemble with different system sizes at 293 K. Temperature dependence and isotope effects, via using D₂O instead of H₂O, were also investigated. A simulation for the polarizable SWM4-DP model was also carried out to compare the effect of different potential models. Radial distribution functions and the neutron weighted structure factor were also calculated; they were found to be insensitive to changing the system size in the range of 216 to 16,000 molecules. On the other hand, the diffusion coefficient is rather sensitive to the applied trajectory length, system size and the method of calculation. The diffusion coefficient is therefore not appropriate for assessing, and distinguishing between, potential models of water, whereas the structure factor could serve as a more stable measure.     

Adsorption behaviour of NaCl solution on the surface of MgO: a molecular dynamics study

Magnesium alloy is one of the most promising biomaterials in vascular clogging and bone injury. But it still has some defects to overcome and the key task is to control the degradation velocity. In this study, the reaction between NaCl solution and MgO is simplified as the first stage of the degradation of magnesium alloy stent, and the adsorption properties of NaCl solution on the MgO surface are investigated by MD simulation. The distribution of each component of the solution perpendicular to the MgO surface is analysed and the diffusion coefficient is calculated. Besides, a parameterised analysis is carried out. The results show that there is a solution layer formed at the surface of the MgO, and the existence of metal oxide restricts the diffusion of the solution. The adsorption capacity and the diffuse rate have an opposite variation tendency with the change of temperature, concentration and velocity. The self-diffusion coefficient of the solution increases with the increase in temperature as well as velocity, inversely adsorption capacity decreases with the increase in velocity. Besides, the influence of temperature on the adsorption capacity is small. What is more, the diffusion coefficient decreases while the adsorption capacity increases with the increase in concentration.     

Local hydrated structure of an Fe2+/Fe3+ aqueous solution: an investigation using a combination of molecular dynamics and X-ray absorption fine structure methods

The hydrated shell of both Fe2+ and Fe3+ aqueous solutions are investigated by using the molecular dynamics (MD) and X-ray absorption structure (XAS) methods. The MD simulations show that the first hydrated shells of both Fe2+ and Fe3+ are characterized by a regular octahedron with an Fe-O distance of 2.08 for Fe2+ and 1.96 for Fe3+, and rule out the occurrence of a Jahn-Teller distortion in the hydrated shell of an Fe2+ aqueous solution. The corresponding X-ray absorption near edge fine structure (XANES) calculation successfully reproduces all features in the XANES spectra in Fe2+ and Fe3+ aqueous solution. A feature that is located at energy 1 eV higher than the white line (WL) in an Fe3+ aqueous solution may be assigned to the contribution of the charge transfer.     

Overstretching of a 30 bp DNA duplex studied with steered molecular dynamics simulation: Effects of structural defects on structure and force-extension relation

Single-molecule experiments on polymeric DNA show that the molecule can be overstretched at nearly constant force by about 70% beyond its relaxed contour length. In this publication we use steered molecular dynamics (MD) simulation to study the effect of structural defects on force-extension curves and structures at high elongation in a 30 base pair duplex pulled by its torsionally unconstrained 5' -5' ends. The defect-free duplex shows a plateau in the force-extension curve at 120pN in which large segments with inclined and paired bases (“S-DNA”) near both ends of the duplex coexist with a central B-type segment separated from the former by small denaturation bubbles. In the presence of a base mismatch or a nick, force-extension curves are very similar to the ones of the defect-free duplex. For the duplex with a base mismatch, S-type segments with highly inclined base pairs are not observed; rather, the overstretched duplex consists of B-type segments separated by denaturation bubbles. The nicked duplex evolves, via a two-step transition, into a two-domain structure characterized by a large S-type segment coexisting with several short S-type segments which are separated by short denaturation bubbles. Our results suggest that in the presence of nicks the force-extension curve of highly elongated duplex DNA might reflect locally highly inhomogeneous stretching.