The quest for the best nonpolarizable water model from the adaptive force matching method

The recently introduced adaptive force matching (AFM) method is used to develop a significantly improved pair‐wise nonpolarizable potential for water. A rigid version of the potential is also presented to enable larger time steps for biological simulations. In this work, it is demonstrated that the AFM method can be used to systematically assess the importance of each functional term during the construction of a force field. For a water potential, it is established that a single off‐atom charge center (M) in the plane of water outperforms two out‐of‐plane charge sites for reproducing intermolecular forces. The four‐site pair‐wise nonpolarizable force field developed in this work rivals some of the most sophisticated polarizable models in terms of reproducing accurate ab initio forces. The force fields are parameterized to perform best in the temperature range from 0 to 40°C. Equilibrium and dynamical properties calculated with the flexible and rigid force fields are in good agreement with experimental results. For the flexible model, the agreement improves when path integral simulation is performed. These force fields provide high‐quality results at a very low computational cost and are thus well suited to atomistic scale biological simulations. The AFM method provides a mechanism for selecting important terms in force field expressions and is a very promising tool for producing accurate force fields in condensed phases. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

大学基础化学教学中分子间作用力与范德华力的概念辨析

探讨了分子间作用力和范德华力这两个概念的差异,从作用力的物理模型上厘清了这两个在大学基础化学教学中易混淆的基本概念。     

A Molecular Theory of the Hydration Force in an Electrolyte Solution

A model, consisting of a pair of large macroions in a dipolar hard sphere-point ion electrolyte, is considered in order to evaluate the hydration force (solvent-mediated) contribution to the force between colloidal particles, which is missing in the DLVO theory. Using the mean spherical approximation (MSA), an explicit expression for this force is obtained. It is shown that the force consists of the hard-core exclusion term that was proposed recently by Henderson and Lozada-Cassou (HLC) [J. Colloid Interface Sci.121, 486 (1988)], and a dipole alignment contribution that originates from the orientational ordering of the solvent molecules near the colloidal particles. The long-range asymptotic form of the total force is given by a Coulomb contribution and is described by the Poisson–Boltzmann or Derjaguin–Landau–Verwey–Overbeek (DLVO) result. The hydration force is short-ranged and extends about ten solvent layers and is responsible for the oscillations of the total force. The total force that we obtain is similar to the semiempirical result of HLC. The comparison with the experimental results for a 10⁻³M KCl electrolyte solution is discussed.     

Calculation of optimum geometries and force fields by the CNDO/force method

CNDO/Force calculations have been performed on a series of molecules, H₂CO, F₂CO, CF₄, CHF₃, CH₂F₂ and CH₃F. The optimum geometries and force fields are reported. It is found that the method can successfully predict the geometries of polyatomic molecules. The bending force constants and interaction force constants are, in general, comparable with experimental values both with respect to sign and magnitude. The stretching force constants have higher values than the experimental force constants. However, the trend in stretching force constants of a series of molecules is comparable with that of the corresponding experimental values.     

Friction force microscopy of self-assembled monolayers: probing molecular organisation at the nanometre scale

The basic principles behind friction force microscopy are described. Applications of friction force microscopy to self-assembled monolayers are reviewed. Work in the author’s laboratory on the frictional properties of self-assembled monolayers is described, and the findings applied in the characterisation of a much more complex material, plasma-treated polyester. Friction force microscopy is found to be a powerful tool for the analysis of the chemical composition and molecular organisation of molecular materials at the nanometre scale.     

采用超低场生物力谱技术研究核酸适配体与凝血酶蛋白的相互作用

蛋白质和核酸是构成生命体最为重要的两类生物大分子,它们之间的相互作用是分子生物学研究的中心问题之一,也是许多生命活动的重要组成部分。本文基于一种全新的超低场生物力谱技术,以凝血酶蛋白为研究对象,考察了凝血酶与其对应的核酸适配体之间的相互作用。结果表明,凝血酶蛋白与核酸适配体之间的结合力大小约为80 p N。同时,在分子水平上获得了凝血酶蛋白与核酸适配体之间的解离动力学信息。     

Automatic molecular structure perception for the universal force field

The Universal Force Field (UFF) is a classical force field applicable to almost all atom types of the periodic table. Such a flexibility makes this force field a potential good candidate for simulations involving a large spectrum of systems and, indeed, UFF has been applied to various families of molecules. Unfortunately, initializing UFF, that is, performing molecular structure perception to determine which parameters should be used to compute the UFF energy and forces, appears to be a difficult problem. Although many perception methods exist, they mostly focus on organic molecules, and are thus not well‐adapted to the diversity of systems potentially considered with UFF. In this article, we propose an automatic perception method for initializing UFF that includes the identification of the system's connectivity, the assignment of bond orders as well as UFF atom types. This perception scheme is proposed as a self‐contained UFF implementation integrated in a new module for the SAMSON software platform for computational nanoscience ( http://www.samson-connect.net ). We validate both the automatic perception method and the UFF implementation on a series of benchmarks.     

Parametrization of macrolide antibiotics using the force field toolkit

Macrolides are an important class of antibiotics that target the bacterial ribosome. Computer simulations of macrolides are limited as specific force field parameters have not been previously developed for them. Here, we determine CHARMM‐compatible force field parameters for erythromycin, azithromycin, and telithromycin, using the force field toolkit (ffTK) plugin in VMD. Because of their large size, novel approaches for parametrizing them had to be developed. Two methods for determining partial atomic charges, from interactions with TIP3P water and from the electrostatic potential, as well as several approaches for fitting the dihedral parameters were tested. The performance of the different parameter sets was evaluated by molecular dynamics simulations of the macrolides in ribosome, with a distinct improvement in maintenance of key interactions observed after refinement of the initial parameters. Based on the results of the macrolide tests, recommended procedures for parametrizing very large molecules using ffTK are given. © 2015 Wiley Periodicals, Inc.     

原子力显微镜在多糖结构研究中的进展

简述了原子力显微镜(AFM)的工作原理和特点,以及在多糖,特别是在淀粉结构研究中的进展。     

Effects of denaturation and association of collagen on adsorption behavior: two-dimensional nanostructure and its property

Effects of denaturation and association of collagen on adsorption behavior were studied in various pH and temperature T by a quartz crystal microbalance QCM. The surface nanostructure, the adhesion force F _ad, and the local frictional coefficient μ of collagen were studied by an atomic force microscope AFM and a lateral force microscope LFM. Adsorptions of collagen were Langmuir type in the regions of pH 3.0–5.8 and T = 25–50 °C. With increasing pH and T, adsorption mass Γ increased, and adsorbed fibrils increased in width. At interface, the association of collagen molecules in solution enhanced the formation of fibrils. The results of F _ad in the solution of pH 3.0 increased with increasing Γ and T but decreased in pH 5.8. The results of μ increased with increasing Γ and T, and those in pH 3.0, were much greater than those in pH 5.8. From comparing them with the results of bovine serum albumin and sodium hyaluronate monolayer, we concluded that nonelectrostatic interactions and the softness of collagen layer contribute primarily to F _ad and μ.     

Recent progress in measurements of oscillatory forces and liquid properties under confinement

The present review paper focuses on direct measurements of oscillatory forces. Beside the surface forces apparatus (SFA), atomic force microscopy (AFM) has emerged as the most commonly used technique to measure surface forces. Recent instrumental advances of both methods are highlighted in the review. Different systems, showing oscillatory forces are classified. Principle distinction is made between 1-component liquids (water, organic liquids and liquid crystals), pseudo 1-component liquids (ionic liquids and microemulsions) and 2-component liquids (dispersions containing polyelectrolytes, micelles or nanoparticles). In the last few years, the oscillatory force studies address particle characterisation, synergistic effects in multicomponent systems, the introduction of ‘switchable’ forces, and resolving liquid properties under confinement. Last but not least, the ability of AFM and SFA to measure oscillatory forces is discussed.     

Effect of cooperativity on the O-H stretching force constant in associated water species

CNDO/force calculations have been employed to calculate the O-H stretching force constants for various structures of associated water species such as water-dimethylether, water-acetonitrile, water-lithium fluoride, linear and cyclic water polymers. The variation in the O-H stretching force constant in A_m… O-H… D_n species where A_m and D_n represent, respectively,m number of electron-acceptor andn number of electron-donor molecules, is explained on the basis of the cooperativity effect. With increasing electron-acceptor power of A and electron-donor power of D, the hydrogen-bonded O-H stretching force constant is significantly reduced. The results obtained in these studies are in general agreement with experimental observations reported earlier.     

Study of the effect of atorvastatin on the interaction between ICAM-1 and CD11b by live-cell single-molecule force spectroscopy

The interaction between the cell adhesion molecule CD11b and its ligand ICAM-1 plays an important role in inflammatory responses in the disease of atherosclerosis. Atorvastatin is a commonly prescribed statin drug which has been considered as one of the most potent therapeutic agents for atherosclerosis due to its lipid-lowering effect. Recently, there is a growing body of evidence that atorvastatin has anti-inflammatory effect. We have applied the advanced method of live-cell single-molecule force spectros...     

Peptide free‐energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95

The C96 and AMBER95 force fields were compared with small model peptides Ac‐(Ala)_n‐NMe (Ac = CH₃CO, NMe = NHCH₃, n=2 and 3) in vacuo and in TIP3P water by computing the free‐energy profiles using multicanonical molecular dynamics method. The C96 force field is a modified version of the AMBER95 force field, which was adjusted to reproduce the energy difference between extended β‐ and constrained α‐helical energies for the alanine tetrapeptide, obtained by the high level ab initio MO method. The slight modification resulted in a large difference in the free energy profiles. The C96 force field prefers relatively extended conformers, whereas the AMBER95 force field favors turn conformations. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 748–762, 2000     

The importance of the three-particle correlation function in the theory of monatomic classical liquids like argon

The present study was motivated by the work of Fortov et al. (2008) on the use of experimental methods of analysis of spatial correlation of dust particles in plasma. Here, we therefore focus on the importance of the three-particle correlation function g ₃ in the theory of monatomic classical liquids like argon, in the framework of two-body central forces. We cover (i) the asymptotic relation of g ₃ to the Ornstein–Zernike direct correlation function c(r); (ii) the use of g ₃ to determine the specific heat difference c _P ? c _V ; and (iii) g ₃ related to the pressure dependence of the pair correlation function.     

Direct measurement of hydrophobic particle–bubble interactions in aqueous solutions by atomic force microscopy: Effect of particle hydrophobicity

Direct measurements of the interaction forces between a spherical silica particle and a small air bubble have been conducted in aqueous electrolyte solutions by using an atomic force microscope (AFM). The silica particle was hydrophobized with a silanating reagent, and the interaction forces were measured by using several particles with different surface hydrophobicities. In the measured force curves, a repulsive force was observed at large separation distances as the particle moved towards the bubble. The origin of the repulsive force was attributed to an electrostatic double-layer force because both the particle and bubble were negatively charged. After the repulsive force, an extremely long-range attractive force acted between the surfaces. These results indicate that the intervening thin water film between the particle and bubble rapidly collapsed, resulting in the particle penetrating the bubble.

The instability of the thin water film between the surfaces suggests the existence of an additional attractive force. By comparing the repulsive forces of the obtained force curves with the DLVO theory, the rupture thickness was estimated. The hydrophobicity of the particle did not significantly change the rupture thickness, whereas the pH of the solution is considered to be a critical factor.     

运用功能化修饰的碳纳米管针尖测量配体-受体的作用力

电弧法自制碳纳米管原子力显微镜针尖,对其末端进行功能化修饰,然后测量配体-受体之间的作用力。运用没有功能化修饰的碳纳米管针尖与修饰有亲和素分子的基底进行接触测量时,没有粘滞力出现;而运用末端修饰生物素分子的碳纳米管针尖测量时,有粘滞力产生。功能化的碳纳米管针尖直接测得的粘滞力均大约200pN,此值符合一对配体生物素和受体亲和素之间的作用力。这一结果很难用传统的针尖获得,功能化修饰的碳纳米管针尖能够克服传统针尖在力测量中的局限,在生物学和化学领域有着广泛的应用前景。     

Au(111)/咪唑基离子液体界面结构研究：阳离子侧链长度的影响

本文结合电化学方法与原子力显微镜力曲线技术,研究了两种烷基侧链长度不同的离子液体BMITFSA和OMITFSA在Au(111)电极表面附近的层状结构的数目和耐受力对电位的依赖性,探究了烷基侧链长度变化对界面层状结构的影响. 研究表明,不同烷基侧链长度的离子液体体系力-电位曲线形状基本相似. 在零电荷电位（the potential of zero charge,PZC）附近时,力值最小,因为此时电极表面荷电量较小,层状结构不稳定;电位偏离PZC的过程中,第一层层状结构力值呈现先增大后减小的趋势. 受到烷基侧链所处的不同位置影响,在PZC电位以负,短侧链离子液体的层状结构稳定性较好,而PZC电位以正,长侧链离子液体的稳定性较好.     

Effects of Various Forces on Particle Distribution and Thermal Features of Suspensions Containing Alumina Nanoparticles

The two-phase Euler-Lagrange method has been used in order to investigate the effects of various forces on particle distribution and thermal characteristics of the water-based Al₂O₃ nanofluid flow inside a pipe under uniform wall heat flux. In the Euler-Lagrange approach, the particles are individually tracked in Lagrangian frame, while the fluid is evaluated in Eulerian frame. Brownian, thermophoretic, drag, lift, and virtual mass forces have been considered. Moreover, experimental data from various researchers were used to analyze the results. Concentration distribution is nonuniform at cross section of the pipe which increasing each parameters of Reynolds number, mean concentration and particles size will intensify its nonuniformity. This nonuniformity will make velocity profile flatter. The Brownian force makes the particle distribution more uniform, whereas the thermophoretic force enhances nonuniformity of the particle distribution. The effects of not considering the Brownian and thermophoretic forces on heat transfer are more significant for finer particles and higher concentrations. Furthermore, at lower Reynolds number, the Brownian force incorporates a more significant role especially in farther distances from entrance.      

Modelling the vibrational behaviour of the cyclic carboxylic acid dimer. SQM force field of the formic acid dimer

The vibrational behaviour of the cyclic carboxylic acid dimer is modelled through the scaled quantum mechanical (SQM) force field of the cyclic formic acid dimer. The results indicate that the SQM force field technique is very well applicable to hydrogen bonded molecules. The frequency shifts observed on hydrogen bonding can be related to the shifts observed on lowering the temperature. This study also confirms that a clear distinction between cyclic carboxylic acid dimers and catamers can be made through the difference between infrared and Raman frequencies, and it is proved here that these conditions are also valid for weaker hydrogen bonded cyclic carboxylic acid dimers.