金属晶体间微观静摩擦特性的分子动力学模拟研究

以光滑干摩擦接触平面为对象,利用金属晶体间的强体积效应特征,建立了简化计算静摩擦力的界面势能模型.根据第一性原理的方法模拟得出界面分子势能的变化,通过界面分子势能计算出静摩擦力大小,并将数据结果通过通用黏附能量函数计算出的静摩擦力大小进行验证,也将计算结果与超高真空原子力显微镜试验结果进行对比.最后拟合出最大静摩擦力与法向载荷的线性函数关系,得出摩擦力的数值为真实接触面积的函数,并与法向载荷成正比的结论.从微观上对同种金属材料间库伦摩擦定律进行验证与研究.     

Internal dynamics of a globular protein under external force field

The inelastic neutron-scattering experiment of a small globular protein in powder form can present the density of states as a function of the frequency. This characterizes the internal dynamics of the protein, which (especially in the case of low-frequency internal dynamics, < 200 cm^?1) is required for an improved understanding of protein function. The theoretical frequency distributions of the internal dynamics of a protein have only been calculated in vacuo using the normal mode analysis. Here we show that frequency distributions of the internal motions of a protein in different environments can be provided by changing the magnitude of external force fields acting on the protein. Our test case is bovine pancreatic trypsin inhibitor (BPTI), consisting of 58 amino acid residues. To mimic the effect of intermolecular contacts in powders, external force fields formed by surrounding water molecules are forced to act on the protein. The neutron-derived density of states of BPTI in powders is shown to be reproduced by the external force fields. In addition, the densities of states, shifted to low frequencies, are suggested to represent that of BPTI in solution. © 1994 by John Wiley & Sons, Inc.     

Estimating and modeling charge transfer from the SAPT induction energy

Recent studies using quantum mechanics energy decomposition methods, for example, SAPT and ALMO, have revealed that the charge transfer energy may play an important role in short ranged inter‐molecular interactions, and have a different distance dependence comparing with the polarization energy. However, the charge transfer energy component has been ignored in most current polarizable or non‐polarizable force fields. In this work, first, we proposed an empirical decomposition of SAPT induction energy into charge transfer and polarization energy that mimics the regularized SAPT method (ED‐SAPT). This empirical decomposition is free of the divergence issue, hence providing a good reference for force field development. Then, we further extended this concept in the context of AMOEBA polarizable force field, proposed a consistent approach to treat the charge transfer phenomenon. Current results show a promising application of this charge transfer model in future force field development. © 2017 Wiley Periodicals, Inc.     

Comparing polarizable force fields to ab initio calculations reveals nonclassical effects in condensed phases

In a recent work [Giese and York J. Chem. Phys. 120, 9903 (2004)] showed that many-body force field models based solely on pairwise Coulomb screening cannot simultaneously reproduce both gas-phase and condensed-phase polarizability limits. In particular, polarizable force fields applied to bifurcated water chains have been demonstrated to be overpolarized with respect to ab initio methods. This behavior was ascribed to the neglect of coupling between many-body exchange and polarization. In the present article we reproduce those results using different ab initio levels of theory and a polarizable model based on the chemical-potential equalization principle. Moreover we show that, when hydrogen-bond (H-bond) forming systems are considered, an additional nonclassical effect, i.e., intermolecular charge transfer, must be taken into account. Such effect, contrarily to that of coupling between many-body exchange and polarization, makes classical polarizable force fields underpolarized. In the case of water at standard conditions, being H-bonded geometries much more probable than the bifurcated ones, intermolecular charge transfer is the dominant effect.     

转动传能中的量子干涉: 干涉角和相对速度的关系

考虑一级含时波恩近似和长程相互作用势, Sun提出了转动传能中的量子干涉模型.在静态池中CO A1Π～ e 3Σ-和He碰撞的实验已经成功模拟.为了从实验中直接获得碰撞速度和干涉角的关系, Sha提出了利用分子束和离子速度成像技术的实验.作为理论研究干涉角和碰撞速度的关系,计算了不同速度下的干涉角,同时获得了变化的趋势.对在分子束条件下(通过控制碰撞速度来控制干涉角)实验具有指导意义.     

How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP,TP2 and ONEG?

Understanding the conformational ensembles of intrinsically disordered proteins and peptides (IDPs) in their various biological environments is essential for understanding their mechanisms and functional roles in the proteome, leading to a greater knowledge of, and potential treatments for, a broad range of diseases. To determine whether molecular simulation is able to generate accurate conformational ensembles of IDPs, we explore the structural landscape of the PLP peptide (an intrinsically disordered region of the proteolipid membrane protein) in aqueous and membrane-mimicking solvents, using replica exchange with solute scaling (REST2), and examine the ability of four force fields (ff14SB, ff14IDPSFF, CHARMM36 and CHARMM36m) to reproduce literature circular dichroism (CD) data. Results from variable temperature (VT) ¹H and Rotating frame Overhauser Effect SpectroscopY (ROESY) nuclear magnetic resonance (NMR) experiments are also presented and are consistent with the structural observations obtained from the simulations and CD. We also apply the optimum simulation protocol to TP2 and ONEG (a cell-penetrating peptide (CPP) and a negative control peptide, respectively) to gain insight into the structural differences that may account for the observed difference in their membrane-penetrating abilities. Of the tested force fields, we find that CHARMM36 and CHARMM36m are best suited to the study of IDPs, and accurately predict a disordered to helical conformational transition of the PLP peptide accompanying the change from aqueous to membrane-mimicking solvents. We also identify an α-helical structure of TP2 in the membrane-mimicking solvents and provide a discussion of the mechanistic implications of this observation with reference to the previous literature on the peptide. From these results, we recommend the use of CHARMM36m with the REST2 protocol for the study of environment-specific IDP conformations. We believe that the simulation protocol will allow the study of a broad range of IDPs that undergo conformational transitions in different biological environments.

A protocol for simulating intrinsically disordered peptides in aqueous and hydrophobic solvents is proposed. Results from four force fields are compared with experiment. CHARMM36m performs the best for the simulated IDPs in all environments.     

Deriving effective mesoscale potentials from atomistic simulations

We demonstrate how an iterative method for potential inversion from distribution functions developed for simple liquid systems can be generalized to polymer systems. It uses the differences in the potentials of mean force between the distribution functions generated from a guessed potential and the true distribution functions to improve the effective potential successively. The optimization algorithm is very powerful: convergence is reached for every trial function in few iterations. As an extensive test case we coarse-grained an atomistic all-atom model of polyisoprene (PI) using a 13:1 reduction of the degrees of freedom. This procedure was performed for PI solutions as well as for a PI melt. Comparisons of the obtained force fields are drawn. They prove that it is not possible to use a single force field for different concentration regimes.     

Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues

The hydration free energies of amino acid side chains are an important determinant of processes that involve partitioning between different environments, including protein folding, protein complex formation, and protein-membrane interactions. Several recent papers have shown that calculated hydration free energies for polar and aromatic residues (Trp, His, Tyr, Asn, Gln, Asp, Glu) in several common molecular dynamics force fields differ significantly from experimentally measured values. We have attempted to improve the hydration energies for these residues by modifying the partial charges of the OPLS-AA force field based on natural population analysis of density functional theory calculations. The resulting differences between calculated hydration free energies and experimental results for the seven side chain analogs are less than 0.1 kcal/mol. Simulations of the synthetic Trp-rich peptide Trpzip2 show that the new charges lead to significantly improved geometries for interacting Trp-side chains. We also investigated an off-plane charge model for aromatic rings that more closely mimics their electronic configuration. This model results in an improved free energy of hydration for Trp and a somewhat altered benzene-sodium potential of mean force with a more favorable energy for direct benzene-sodium contact.     

Empirical force fields for complex hydrated calcio-silicate layered materials

The use of empirical force fields is now a standard approach in predicting the properties of hydrated oxides which are omnipresent in both natural and engineering applications. Transferability of force fields to analogous hydrated oxides without rigorous investigations may result in misleading property predictions. Herein, we focus on two common empirical force fields, the simple point charge ClayFF potential and the core-shell potential to study tobermorite minerals, the most prominent family of Calcium-Silicate-Hydrates that are complex hydrated oxides. We benchmark the predictive capabilities of these force fields against first principles results. While the structural information seem to be in close agreement with DFT results, we find that for higher order properties such as elastic constants, the core-shell potential quantitatively improves upon the simple point charge model, and shows a larger degree of transferability to complex materials. In return, to remedy the deficiencies of the simple point charge potential for hydrated calcio-silicates, we suggest using both structural data and elasticity data for potential calibration, a new force field potential, CSH-FF. This re-parameterized version of ClayFF is then applied to simulating an atomistic model of cement (Pellenq et al., PNAS, 2009). We demonstrate that this force field improves the predictive capabilities of ClayFF, being considerably less computational intensive than the core-shell model.     

PAPQMD parametrization of molecular systems with cyclopropyl rings: Conformational study of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid

The suitability of ab initio, semiempirical and density functional methods as sources of stretching and bending parameters has been explored using the PAPQMD (Program for Approximate Parametrization from Quantum Mechanical Data) strategy. Results show that semiempirical methods provide parameters comparable to those compiled on empirical force fields. In this respect the AM1 method seems to be a good method to obtain parameters at a minimum computational cost. On the other hand, harmonic force fields initially developed for proteins and DNA have been extended to include compounds containing highly strained three-membered rings, like 1-aminocyclopropane-1-carboxylic acid. For this purpose the cyclopropyl ring has been explicitly parametrized at the AM1 level considering different chemical environments. Finally, the new set of parameters has been used to investigate the conformational preferences of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid. Results indicate that such compounds tend to adopt a helical conformation stabilized by intramolecular hydrogen bonds between residues i and i+3. This conformation allows the arrangement of the cyclic side chains without steric clashes.     

Dimerization of thymol blue in solution: Theoretical evidence

The possibility of dimerization of thymol blue was addressed by ab initio and force field calculations. In agreement with experimental information, a dimer forming symmetrical chemical environments for hydrogen bond formation was determined. This dimer is stable in vacuum and aqueous media and corresponds to the same protonated state proposed by the experiment. A comparison of the CVFF and MM3 force fields and ab initio results shows the suitability of CVFF to qualitatively describe this system.     

Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy

Four commonly used molecular mechanics force fields, CHARMM22, OPLS, CVFF, and GROMOS87, are compared for their ability to reproduce experimental free energies of hydration (ΔG_hydr) from molecular dynamics (MD) simulations for a set of small nonpolar and polar organic molecules: propane, cyclopropane, dimethylether, and acetone. ΔG_hydr values were calculated by multiconfiguration thermodynamic integration for each of the different force fields with three different sets of partial atomic charges: full charges from an electrostatic potential fit (ESP), and ESP charges scaled by 0.8 and 0.6. All force fields, except for GROMOS87, give reasonable results for ΔG_hydr · if partial atomic charges of appropriate magnitude are assigned. For GROMOS87, the agreement with experiment for hydrocarbons (propane and ethane) was improved considerably by modifying the repulsive part of the carbon-water oxygen Lennard-Jones potential. The small molecules studied are related to the chemical moieties constituting camphor (C₁₀H_l6O). By invoking force-field transferability, we calculated the ΔG_hydr for camphor. With the modified GROMOS force field, a ΔG_hydr within 4 kJ/mol of the experimental value of −14.8 kJ/mol was obtained. Camphor is one of the largest molecules for which an absolute hydration free energy has been calculated by molecular simulation. The accuracy and reliability of the thermodynamic integration calculations were analyzed in detail and we found that, for ΔG_hydr calculations for the set of small molecules in aqueous solution, molecular dynamics simulations of 0.8–1.0 ns in length give an upper statistical error bound of 1.5 kJ/mol, whereas shorter simulations of 0.25 nm in length given an upper statistical error bound of 3.5 kJ/mol. © 1997 by John Wiley & Sons, Inc.     

Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields

An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol.     

Investigating the relationship between infrared spectra of shared protons in different chemical environments: a comparison of protonated diglyme and protonated water dimer

The energetics, dynamics, and infrared spectroscopy of the shared proton in different chemical environments is investigated using molecular dynamics simulations. A three-dimensional potential energy surface (PES) suitable for describing proton transfer between an acceptor and a donor oxygen atom is combined with an all-atom force field to carry out reactive molecular dynamics simulations. The construction of the fully dimensional PES is inspired from the established mixed quantum mechanics/molecular mechanics treatment of larger systems. The "morphing potential" method is used to transform the generic PES for proton transfer along an O...H+...O motif into a three-dimensional PES for proton transfer in protonated diglyme. Using molecular dynamics simulations at finite temperature, the gas phase infrared spectra are calculated for both species from the Fourier transform of the dipole moment autocorrelation function. For protonated diglyme the modes involving the H+ motion are strongly mixed with other degrees of freedom. At low temperature, the O...H+...O asymmetric stretching vibration is found at 870 cm-1, whereas for H5O2+ this band is at 724 cm-1. As expected, the vibrational bands of protonated diglyme show no temperature dependence whereas for H5O2+ at T = 100 K the proton transfer mode is found at 830 cm-1, in good agreement with 861 cm-1 from very recent molecular dynamics simulations.     

Photoprocesses of excited molecules in confined liquid environments: An overview

The photoprocesses like excited state proton transfer (ESPT), intramolecular charge transfer (ICT), fluorescence energy transfer (FET), occurring in the excited molecules find ample applications in the chemical and biochemical fields. These photoprocesses are markedly affected by the introduction of biomimicking liquid confining environments like micelles, reverse micelles, cyclodextrins, proteins, etc. The local polarity, viscosity and pH, induced by the confined environments have a significant role in modifying the photoprocesses. In this review we have presented a comprehensive report of the recent progress in the study of these photoprocesses in photoexcited molecules in different confined liquid environments. Mostly, recent works have been reviewed in this article to acquire information about progress in the photophysical and photochemical reactions in different confined environments.