表面活性剂溶液行为的粗粒化模拟

分子动力学模拟技术目前已经成为了研究表面活性剂有序聚集体的不可或缺的工具之一。近几年来,粗粒化模拟方法克服了传统的介观模拟和精细力场模拟的缺点,既能够重现自组装体系的热力学或者结构方面的信息,又极大地拓展了模拟体系所能达到的空间和时间尺度,逐渐成为了计算领域的一个热点。本文综述了近几年来表面活性剂粗粒化分子动力学模拟的最新发展状况,分别就不同粗粒化模型的建模策略、作用势能表达、参数拟合和模型评价等问题作了详细的介绍,并通过实例说明了粗粒化力场对表面活性剂体系的适用性。在此基础上,指出了发展粗粒化力场过程中所面临的一些关键性问题,这对于表面活性剂溶液行为的粗粒化模拟具有重要的意义。     

Aggregation Behavior of Trisiloxane-Tailed Surface Active Ionic Liquids in Aqueous Solution: Coarse-Grained Molecular Dynamics Study

The aggregation behaviors of two trisiloxane-tailed surface active ionic liquids in water have been investigated by coarse-grained (CG) molecular dynamics simulation on the basis of MARTINI force field. The new CG model is developed from the optimized molecule computed by using density functional theory. Direct comparison of angles and bonds obtained from all-atom (AA) simulations with those calculated from the CG model has been conducted to validate the latter model. Excellent agreement between AA and CG demonstrates that the potential of the new CG model can represent the complex system well. The long time CG simulation has been performed to understand the formation process of micelles when dissolving ionic liquids in water. Vesicles were observed at the final stage of the simulation and their partially truncated views and density profiles were obtained to describe the structure in detail.     

Molecular Dynamics Simulations of Cellulose Oligomers: Conformational Analysis

Summary: The results of classical molecular simulations of cellulose oligomers are presented here. The conformations of the chains in the high temperature melt, room temperature quenched melt and gas phase are compared with respect to various geometrical parameters including square end‐to‐end distances, glycosidic link torsion correlations, ring puckering and hydrogen bonding. The cellulose oligomer melts were relaxed at 800 K with molecular dynamics, and then cooled down in three different ways to obtain dense amorphous systems at 500 K and at room temperature. The sample resulting from the quench (step) shows too much similarity with the melt at 800 K. The two other cooling schemes (ramp, 2ramps) give very similar results for all quantities investigated. The relevance of previous single molecule calculations with respect to the dense amorphous systems is called into question. Comparisons between the chains in the dense systems and those in the gas phase reveal that, even for these relatively short stiff chains, differences exist in the preferred conformations. At high temperatures, where both systems are in equilibrium, the distribution of square end‐to‐end distances are both fairly smooth, but the gas phase clearly prefers more compact conformations. At 300 K, the differences are exacerbated as the equilibrium distribution for the gas phase shows a high proportion of folded conformers, whereas the nonequilibrium quenched systems necessarily retain the extended envelope of the higher temperature. Differences are also evident in the puckering, the rotation of the hydroxymethyl groups and the pattern of hydrogen bonds.

The probability density distribution for the square end‐to‐end distance for octaose in the gas phase (light line) and in the dense phase (dark line) at 300 K.     

Formation of the Interphase of a Cured Epoxy Resin Near a Metal Surface: Reactive Coarse-Grained Molecular Dynamics Simulations

Mesoscale molecular dynamics simulations are performed to analyze the curing process of an epoxy resin with polyfunctional amines on a generic surface. The coarse grained potentials were derived from all-atomistic molecular dynamics simulations using iterative Boltzmann inversion. The reactive scheme incorporates cross-linking between an epoxy resin and an amine, as well as amine adsorption on the surface. The structure of the cured network is examined and compared with equilibrium properties of the uncured system. Special attention has been paid on the implications of the surface that is believed to play a crucial role in the performance of epoxy systems.     

Dissipative Particle Dynamics Simulations of Polymer Brushes: Comparison with Molecular Dynamics Simulations

Summary: The structure of polymer brushes is investigated by dissipative particle dynamics (DPD) simulations that include explicit solvent particles. With an appropriate choice of the DPD interaction parameters , we obtain good agreement with previous molecular dynamics (MD) results where the good solvent behavior has been modeled by an effective Lennard–Jones potential. The present results confirm that DPD simulation techniques can be applied for large length scale simulations of polymer brushes. A relation between the different length scales and is established.

Polymer brush at a solid–liquid interface.     

A Refined Intermolecular Interaction Potential for Methane: Spectral Analysis and Molecular Dynamics Simulations

The previously constructed methane interaction potential energy surface calculated at the second‐order Møller‐Plesset (MP2) perturbation theory has been significantly improved in two aspects. First, all ab initio potential energy data are calculated by the supermolecule counterpoise corrected coupled cluster with single and double and perturbative triple excitations [CCSD(T)] method with Dunning’s correlation‐consistent aug‐cc‐pVXZ, X=D, T, Q, 5, basis sets and extrapolated to the complete basis set (CBS) limits with a convergence precision of 0.01 kcal/mol. Second, instead of the simple 4‐site model proposed in the previous study, a 5‐site model has been used to represent the ab initio potential data. The simulated infrared spectrum using the potential energy surface seems to be broadly in line with the spectral features observed in experiments. Molecular dynamics simulations using the ab initio force field show quantitative agreements with experiments. The properties examined in this paper include the atom‐to‐atom radial distribution functions in liquid and supercritical phases and the self‐diffusion coefficients over a wide range of thermodynamic conditions. It is shown that the refined ab initio force field can be applied to study fluid properties in different phases.     

Protein-Protein Interactions: Insight from Molecular Dynamics Simulations and Nanoparticle Tracking Analysis

Protein-protein interaction plays an essential role in almost all cellular processes and biological functions. Coupling molecular dynamics (MD) simulations and nanoparticle tracking analysis (NTA) assay offered a simple, rapid, and direct approach in monitoring the protein-protein binding process and predicting the binding affinity. Our case study of designed ankyrin repeats proteins (DARPins)—AnkGAG1D4 and the single point mutated AnkGAG1D4-Y56A for HIV-1 capsid protein (CA) were investigated. As reported, AnkGAG1D4 bound with CA for inhibitory activity; however, it lost its inhibitory strength when tyrosine at residue 56 AnkGAG1D4, the most key residue was replaced by alanine (AnkGAG1D4-Y56A). Through NTA, the binding of DARPins and CA was measured by monitoring the increment of the hydrodynamic radius of the AnkGAG1D4-gold conjugated nanoparticles (AnkGAG1D4-GNP) and AnkGAG1D4-Y56A-GNP upon interaction with CA in buffer solution. The size of the AnkGAG1D4-GNP increased when it interacted with CA but not AnkGAG1D4-Y56A-GNP. In addition, a much higher binding free energy (∆GB) of AnkGAG1D4-Y56A (−31 kcal/mol) obtained from MD further suggested affinity for CA completely reduced compared to AnkGAG1D4 (−60 kcal/mol). The possible mechanism of the protein-protein binding was explored in detail by decomposing the binding free energy for crucial residues identification and hydrogen bond analysis.     

Coupling Effects of Electrostatic Interactions and Salt Concentration Gradient in Polymer Translocation through a Nanopore: A Coarse-Grained Molecular Dynamics Simulations Study

We study the influence of polymer pore interactions and focus on the role played by the concentration gradient of salt in the translocation of polyelectrolytes (PE) through nanopores explicitly using coarse-grained Langevin dynamics simulations. The mean translocation time is calculated by varying the applied voltage, the pH, and the salt concentration gradient. Changing the pH can alter the electrostatic interaction between the protein pore and the polyelectrolyte chain. The polymer pore interaction is weakened by the increase in the strength of the externally applied electric field that drives translocation. Additionally, the screening effect of the salt can reduce the strong charge-charge repulsion between the PE beads which can make translocation faster. The simulation results show there can be antagonistic or synergistic coupling between the salt concentration-induced screening effect and the drift force originating from the salt concentration gradient thereby affecting the translocation time. Our simulation results are explained qualitatively with free energy calculations.     

表面活性剂界面自组装的分子动力学模拟

主要介绍了表面活性剂在液／液、气／液和固／液界面的自组装,详细讨论了分子动力学模拟在表面活性剂界面自组装体系的应用,指出了近年来该领域的发展现状及应用前景。     

基于粗粒化模型对有机溶剂的分子动力学模拟

在基于Boltzmann分布对四种基本构象进行Monte Carlo取样后, 通过与全原子模型的范德华势比较得到了Gay-Berne (GB)参数. 又在对用量化计算得到的分子体系的电势进行电荷、偶极矩和四极矩的拟合后, 得到了电多极展开势(EMP)参数. 利用得到的粗粒化参数, 基于粗粒化模型, 对CHCl₃及四氢呋喃(THF)两种有机溶剂进行了分子动力学模拟(MDS), 并将结果同全原子模拟进行了比较. 计算结果表明用粗粒化模型从整体上能重复全原子模型的模拟结果, 但在某些细节的计算与全原子模型有偏差, 其原因可能是目前工作仅考虑了单位点情况, 为此今后在对具有复杂结构的分子进行粗粒化模拟时还应考虑合理放置及增加相互作用位点.     

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides

We present an extension of the coarse-grained MARTINI model for proteins and apply this extension to amyloid- and elastin-like peptides. Atomistic simulations of tetrapeptides, octapeptides, and longer peptides in solution are used as a reference to parametrize a set of pseudodihedral potentials that describe the internal flexibility of MARTINI peptides. We assess the performance of the resulting model in reproducing various structural properties computed from atomistic trajectories of peptides in water. The addition of new dihedral angle potentials improves agreement with the contact maps computed from atomistic simulations significantly. We also address the question of which parameters derived from atomistic trajectories are transferable between different lengths of peptides. The modified coarse-grained model shows reasonable transferability of parameters for the amyloid- and elastin-like peptides. In addition, the improved coarse-grained model is also applied to investigate the self-assembly of β-sheet forming peptides on the microsecond time scale. The octapeptides SNNFGAIL and (GV)(4) are used to examine peptide aggregation in different environments, in water, and at the water-octane interface. At the interface, peptide adsorption occurs rapidly, and peptides spontaneously aggregate in favor of stretched conformers resembling β-strands.     

CaF2熔化温度的分子动力学模拟

The molecular dynamics method has been applied to simulate the melting temperatures of CaF 2 at elevated temperature and high pressure and to calculate the P～V equation of state of CaF 2 up to 100 GPa at 300 K. The interatomic potential was taken to be the sum of pairwise additive Coulomb, van der Waals attractions, and repulsive interactions. In addition, the shell model was used in molecular dynamics simulation. The pressure dependence of the melting temperature of CaF 2 was predicted up to 4 GPa. However, in order to account for the superheating melting of the molecular dynamic simulation, the simulated melting temperatures of CaF 2 were corrected by the modern theory of melting. Consequently, the melting temperatures of CaF 2 were accurately obtained at elevated temperature and high pressure. Therefore, it is shown that shell model molecular dynamics simulation at constant pressure indeed provides a useful tool for studying the melting temperatures of other materials under high pressures.     

Capturing the Polarization Response of Solvated Proteins under Constant Electric Fields in Molecular Dynamics Simulations

We capture and compare the polarization response of a solvated globular protein ubiquitin to static electric (E-fields) using atomistic molecular dynamics simulations. We collectively follow E-field induced changes, electrical and structural, occurring across multiple trajectories using the magnitude of the protein dipole vector ( P _p ). E-fields antiparallel to P _p induce faster structural changes and more facile protein unfolding relative to parallel fields of the same strength. While weak E-fields (0.1–0.5 V/nm) do not unfold ubiquitin and produce a reversible polarization, strong E-fields (1–2 V/nm) unfold the protein through a pathway wherein the helix:β-strand interactions rupture before those for the β1-β5 clamp. Independent of E-field direction, high E-field induced structural changes are also reversible if the field is switched off before P _p exceeds 2 times its equilibrium value. We critically examine the dependence of water properties, protein rotational diffusion and E-field induced protein unfolding pathways on the thermostat/barostat parameters used in our simulations.     

Molecular Dynamics Simulations and Steered Molecular Dynamics Simulations of Glabridin Bound to Wild Type and V30A Mutant Transthyretin: Ligand-linked Perturbation of Tertiary Conformation

Transthyretin(TTR), as a tetrameric protein, functions as a neuroprotector. The native TTR homotetramer dissociates into dimers and monomers. Dimers and monomers self-assemble into amyloid fibrils, and this process can lead to some diseases. Native TTR homotetramer is a widely accepted model for TTR amyloid formation. In this study, simulations using molecular dynamics(MD) and steered MD(SMD) were performed to explore the mechanisms for glabridin(Glab), a specific inhibitor for TTR binding, for V30A mutant and wild-type(WT) TTR. MD simulation results indicate that, compared with Glab binding to WT and V30A mutant, the WT TTR could lead to the collapse of β-strands from Ser52 to His56 at chain A. This phenomenon facilitated the easy dissociation of chains A and C. Calculations of the binding free energy between the two chains showed that the V30A-Glab TTR complex displayed a lower binding energy than other systems(WT TTR and WT-Glab TTR). Then, SMD simulation was performed to explore the unbinding pathway for Glab through the WT and V30A mutant TTR. The results show that Lys15(chain A) produced a hydrogen bond with Glab at the force peak via the WT TTR tunnel. Meanwhile, in the V30A TTR mutant, the hydrogen bond between Lys15(chain A) and Glab was broken at the force peak. This condition was beneficial for Glab to be taken off from the protein. Our theoretical results will be useful in designing a new specific inhibitor of TTR protein to control the TTR homotetramer dissociation.     

On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.