Scaling Function Between the Exponential-6 and the Generalized Lennard-Jones Potential Functions

The van der Waals forces for non-bonded interaction can be expressed either by the Exponential-6 or by the Lennard-Jones(m-n) potential functions, whereby m > n. Hitherto a relationship exists between the Exponential-6 and the Lennard-Jones(12-6) potential functions, with a scaling factor = 13.772 at or near the equilibrium and = 12.0 for long range interaction. This paper attempts to develop relationships between Exponential-6 and a more generalized Lennard-Jones(m-n). Analysis reveals that the relationship exists only when n = 6 and that two sets of scaling factors (as functions of index m) applies for the relationship between Exponential-6 and the Lennard-Jones(m-6), whereby m > 6.     

Relationships Among Potential-Energy Functions

We analyse recently proposed connection formulas between potential-energy functions for bond stretching, bond bending and molecular interactions, and propose more convenient and practical expressions. For example, our mathematical relationships between Morse and Murrel—Mottram potential parameters yield much closer agreement between such potential-energy functions.     

On the Applicability of Mathematical Constants and Sequences in Intermolecular Potential Energy Functions

Six intermolecular potential energy functions incorporating mathematical functions such as the Golden ratio, Euler number and Pi, and three consecutive numbers in the Half Square, Lucas and Fibonacci sequences are proposed herein. It is shown that the Lucas potential function exhibits reasonable agreement with the Lennard-Jones(12-10) function, whilst the Golden ratio potential function describes the argon gas potential energy and the Lennard-Jones(14-7) function excellently. Both the Euler and Pi potential functions agree well with the Lennard-Jones(12-6) function, whilst the Fibonacci potential function exhibits very good correlation with the Lennard-Jones(9-6) function. The relatedness of the mathematical constants and sequences examined in this paper with application to intermolecular potential functions suggests their additional significance in the field of chemistry.     

Mathematical Relationships Between Bond-Bending Force Fields

Molecular mechanics softwares adopt various set of force field functions. In some cases, reliable data from one set of force field parameters cannot be used in a software that adopts another set of force field. Using mathematical approach, exact relationships between parameters from three bond-bending force fields, namely the (i) harmonic cosine angle, (ii) polynomial series, and (iii) Fourier series, are herein developed. Parameters from these three potential functions are further related to the approximate form, the harmonic angle function, which is valid for small change in chemical bond angle.     

New out-of-plane angle and bond angle internal coordinates and related potential energy functions for molecular mechanics and dynamics simulations

With currently used definitions of out-of-plane angle and bond angle internal coordinates, Cartesian derivatives have singularities, at ±π/2 in the former case and π in the latter. If either of these occur during molecular mechanics or dynamics simulations, the forces are not well defined. To avoid such difficulties, we provide new out-of-plane and bond angle coordinates and associated potential energy functions that inherently avoid these singularities. The application of these coordinates is illustrated by ab initio calculations on ammonia, water, and carbon dioxide. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1067–1084, 1999     

Generation of Molecular Fields, Quantum Similarity Measures and Related Questions

A straightforward discussion on how to generate molecular fields is developed within the postulates of quantum mechanics. The theoretical formalism points towards the generalization and extension of the well-known molecular field forms, associated to density function and electrostatic molecular potential (EMP), including another category of fields associated to quantum molecular similarity measures. The results show that the new formalism can be easily applied to obtain an unlimited number of new information about molecular behavior.     

分子力场进展

分子力学（简称ＭＭ）是近年来化学家常用的一种计算方法。与量子力学从头计算和半经验方法相比，用分子力学处理大分子可以大大节省计算时间，而且，在大多数情况下，用分子力学方法计算得到的分子几何构型参数与实验值之间的差值可在实验误差范围之内。所以，分子力学是研究生物化学体系的有效和可行的手段。分子力学的核心是分子力场。本文介绍了分子力场的量子力学背景、分子力场和光谱力场之间的关系。分子力场的一般形式、分力     

键函数对ArCl-相互作用势理论计算结果的影响

近年来, 在体系间弱相互作用势函数的研究领域中, 理论及实验两个方面都取得很大的进展. 对于闭壳层体系间相互作用(中性原子与分子的相互作用)研究得比较清楚[1,2]. 然而, 开壳层与闭壳层体系的相互作用, 特别是中性原子与离子的研究成为当前的一个重要研究方向.     

Comparison of Force Fields on the Basis of Various Model Approaches—How To Design the Best Model for the [CnMIM][NTf2] Family of Ionic Liquids

In this contribution, we present two new united‐atom force fields (UA‐FFs) for 1‐alkyl‐3‐methylimidazolium bis(trifluoromethylsulfonyl)imide [C_nMIM][NTf₂] (n=1, 2, 4, 6, 8) ionic liquids (ILs). One is parametrized manually, and the other is developed with the gradient‐based optimization workflow (GROW). By doing so, we wanted to perform a hard test to determine how researchers could benefit from semiautomated optimization procedures. As with our already published all‐atom force field (AA‐FF) for [C_nMIM][NTf₂] (T. Köddermann, D. Paschek, R. Ludwig, ChemPhysChem­ 2007, 8, 2464 ), the new force fields were derived to fit experimental densities, self‐diffusion coefficients, and NMR rotational correlation times for the IL cation and for water molecules dissolved in [C₂MIM][NTf₂]. In the manual force field, the alkyl chains of the cation and the CF₃ groups of the anion were treated as united atoms. In the GROW force field, only the alkyl chains of the cation were united. All other parts of the structures of the ions remained unchanged to prevent any loss of physical information. Structural, dynamic, and thermodynamic properties such as viscosity, cation rotational correlation times, and heats of vaporization calculated with the new force fields were compared with values simulated with the previous AA‐FF and the experimental data. All simulated properties were in excellent agreement with the experimental values. Altogether, the UA‐FFs are slightly superior for speed‐up reasons. The UA‐FF speeds up the simulation by about 100 % and reduces the demanded disk space by about 78 %. More importantly, real time and efforts to generate force fields could be significantly reduced by utilizing GROW. The real time for the GROW parametrization in this work was 2 months. Manual parametrization, in contrast, may take up to 12 months, and this is, therefore, a significant increase in speed, though it is difficult to estimate the duration of manual parametrization.     

Chain Conformations in the Crystalline Field of Syndiotactic Vinyl Polymers Deriving from 1,3‐Diene Monomers. Analysis by Molecular Mechanics

Summary: Conformational energy calculations on the chain conformation in the crystalline field have been performed for various syndiotactic vinyl polymers deriving from 1,3‐diene monomers. Energy maps as a function of the independent torsion angles have evidenced for all the polymers minima corresponding to highly extended and to helical chains. Energy minimizations as a function of all the internal parameters for the s(2/1)2 and t cm symmetries have allowed the evaluation of the energy differences between chains having the two symmetries and the prediction of the values of the conformational parameters for each polymer. The results have been compared with the experimental data reported in the literature for some of the studied polymers.

Conformational energy map of sPBD12.     

Electrostatic potentials and fields from density expansions of deformed atoms in molecules

The exact representation of the molecular density by means of atomic expansions, consisting in spherical harmonics times analytical radial factors, is employed for the calculation of electrostatic potentials, fields, and forces. The resulting procedure is equivalent to an atomic multipolar expansion in the long-range regions, but works with similar efficiency and accuracy in the short-range region, where multipolar expansions are not valid. The performances of this procedure are tested on the calculation of the electrostatic potential contour maps and electrostatic field flux lines of water and nitrobenzene, computed from high-quality molecular electron densities obtained with Slater basis sets.     

Derivation of class II force fields: V. Quantum force field for amides,peptides, and related compounds

As the field of biomolecular structure advances, there is an ever-growing need for accurate modeling of molecular energy surfaces to simulate and predict the properties of these important systems. To address this need, a second generation amide force field for use in simulations of small organics as well as proteins and peptides has been derived. The critical question of what accuracy can be expected from calculations in general, and with this class II force field in particular, is addressed for structural, dynamic, and energetic properties. The force field is derived from a recent methodology we have developed that involves the systematic use of quantum mechanical observables. Systematic ab initio calculations were carried out for numerous configurations of 17 amide and related compounds. Relative energies and first and second derivatives of the energy of 638 structures of these compounds resulted in 140,970 ab initio quantum mechanical observables. The class II peptide quantum mechanical force field (QMFF), containing 732 force constants and reference values, was parameterized against these observables. A major objective of this work is to help establish the role of anharmonicity and coupling in improving the accuracy of molecular force fields, as these terms have not yet become an agreed upon standard in the ever more extensive simulations being used to probe biomolecular properties. This has been addressed by deriving a class I harmonic diagonal force field (HDFF), which was fit to the same energy surface as the QMFF, thus providing an opportunity to quantify the effects of these coupling and anharmonic contributions. Both force field representations are assessed in terms of their ability to fit the observables. They have also been tested by calculating the properties of 11 stationary states of these amide molecules. Optimized structures, vibrational frequencies, and conformational energies obtained from the quantum calculations and from both the QMFF and the HDFF are compared. Several strained and derivatized compounds including urea, formylformamide, and butyrolactam are included in these tests to assess the range of applicability (transferability) of the force fields. It was found that the class II coupled anharmonic force field reproduced the structures, energies, and vibrational frequencies significantly more faithfully than the class I harmonic diagonal force field. An important measure, rms energy deviation, was found to be 1.06 kcal/mol with the class II force field, and 2.30 kcal/mol with the harmonic diagonal force field. These deviations represent the error in relative configurational energy differences for strained and distorted structures calculated with the force fields compared with quantum mechanics. This provides a measure of the accuracy that might be expected in applications where strain may be important such as calculating the energy of a system as it approaches a (rotational) barrier, in ligand binding to a protein, or effects of introducing substituents into a molecule that may induce strain. Similar results were found for structural properties. Protein dynamics is becoming of ever-increasing interest, and, to simulate dynamic properties accurately, the dynamic behavior of model compounds needs to be well accounted for. To this end, the ability of the class I and class II force fields to reproduce the vibrational frequencies obtained from the quantum energy surface was assessed. An rms deviation of 43 cm⁻¹ was achieved with the coupled anharmonic force field, as compared to 105 cm⁻¹ with the harmonic diagonal force field. Thus, the analysis presented here of the class II force field for the amide functional group demonstrates that the incorporation of anharmonicity and coupling terms in the force field significantly improves the accuracy and transferability with regard to the simulation of structural, energetic, and dynamic properties of amides. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 430–458, 1998     

Classical Reactive Molecular Dynamics Implementations: State of the Art

Reactive molecular dynamics (RMD) implementations equipped with force field approaches to simulate both the time evolution as well as chemical reactions of a broad class of materials are reviewed herein. We subdivide the RMD approaches developed during the last decade as well as older ones already reviewed in 1995 by Srivastava and Garrison and in 2000 by Brenner into two classes. The methods in the first RMD class rely on the use of a reaction cutoff distance and employ a sudden transition from the educts to the products. Due to their simplicity these methods are well suited to generate equilibrated atomistic or material‐specific coarse‐grained polymer structures. In connection with generic models they offer useful qualitative insight into polymerization reactions. The methods in the second RMD class are based on empirical reactive force fields and implement a smooth and continuous transition from the educts to the products. In this RMD class, the reactive potentials are based on many‐body or bond‐order force fields as well as on empirical standard force fields, such as CHARMM, AMBER or MM3 that are modified to become reactive. The aim with the more sophisticated implementations of the second RMD class is the investigation of the reaction kinetics and mechanisms as well as the evaluation of transition state geometries. Pure or hybrid ab initio, density functional, semi‐empirical, molecular mechanics, and Monte Carlo methods for which no time evolution of the chemical systems is achieved are excluded from the present review. So are molecular dynamics techniques coupled with quantum chemical methods for the treatment of the reactive regions, such as Car–Parinello molecular dynamics.     

Studies of Adjacent Re‐Entry Folds of Chains of Syndiotactic l,2‐Poly(1,3‐butadiene) by Molecular Mechanics Calculations

The mode of packing and the adjacent re‐entry folds of chains of syndiotactic 1,2‐poly(1,3‐butadiene) have been studied by molecular mechanics calculations with the use of various sets of potential functions. The results of the packing analysis indicate that the crystal grows preferentially along the [100] and [110] directions. Models of fold have been built up on an infinite ab surface completely covered by adjacent re‐entry folds in the (100) and (110) planes. The results of energy minimizations show that several almost isoenergetic folds, constituted by four monomeric units, can be realized in the (100) planes, while the fold in the (110) planes has higher energy. The calculated value of the work of fold is in satisfactory agreement with that derived by crystallization kinetics reported in literature.

     

PdYH分子的结构与势能函数

用密度泛函理论的B3LYP方法, 对钯和钇原子采用SDD收缩价基函数, 氢原子采用6-311＋＋G**全电子基函数, 对PdY和PdYH体系的结构进行优化. 计算表明: PdY分子的几何构型为C_∞v, 其基态为X²Σ^＋态, 键长R＝0.24168 nm, 离解能为D_e＝2.8261 eV, 谐振频率ω_e＝254.0656 cm^－1, 并拟合得到Murrell-Sorbie势能函数; PdYH分子最稳态为C_s构型, 电子组态为¹A', 平衡核间距R_PdY＝0.24281 nm, R_YH＝0.19824 nm, 键角∠PdYH＝116.7157°, 离解能D_e＝5.6146 eV, 基态简正振动频率: 对称伸缩振动频率ν₁ (a')＝348.2909 cm^－1, 弯曲振动频率ν₂ (a')＝243.3382 cm^－1, 反对称伸缩振动频率ν₃ (a')＝1442.2695 cm^－1. 由微观过程的可逆性原理分析了分子的可能离解极限. 并用多体项展式理论方法分别导出基态PdY和PdYH分子的势能函数, 其等值势能面图准确地再现了PdY和PdYH分子的结构特征和离解能, 由此讨论了Pd＋Y＋H分子反应的势能面静态特征.     

Influence of the Temperature on the Crystal Structure of Poly(p‐phenylene sulfide): A Study by X‐Ray Measurements and Molecular Mechanics

The crystal structure of poly(p‐phenylene sulfide) (PPS) has been investigated by X‐ray analysis on fiber samples and by molecular mechanics calculations over a wide range of temperatures, from 0 K to 548 K, showing that all the structural parameters remain substantially constant. The thermal expansion coefficients of the a and b axes have been evaluated. Structural parameters experimentally obtained at the various temperatures have been used in calculations by molecular mechanics. The crystal structures calculated by various methods and using several potential functions are in very good agreement. New parameters are proposed for the nonbonded terms of the potential functions.     

Models of Adjacent Re‐Entry Folds in the β Form of Syndiotactic Polystyrene. Conformational and Packing Analysis by Molecular Mechanics

The adjacent re‐entry folds of chains of syndiotactic polystyrene crystallized in the β form have been investigated by molecular mechanics. Various models of fold of chains along bilayers have been found. The results are in agreement with the literature experimental data indicating that the fold surface is irregular. Both the conformational and the packing energy of folded chains have been minimized by various techniques using several set of potential functions. A theoretical prediction of the work of fold is given.     

Combination of pi and Golden Ratio in Lennard–Jones-Type and Morse-Type Potential Energy Functions

This paper tests the validity of a Lennard–Jones-type and Morse-type potential functions, consisting a combination of pi and golden ratio constants, for describing intermolecular and interatomic interaction energy. The adjustable parameter, n, can be obtained based on experimental data near the minimum well-depth or by parametric conversion from other established potential functions. The remarkably good correlation of the proposed potential functions with experimental data and other potential functions reveal an intriguing property of the relationship between pi and golden ratio within the context of chemistry.     

Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: diffusion, free energy of hydration, and structural properties

In this article we compare different force fields that are widely used (Gromacs, Charmm-22/x-Plor, Charmm-27, Amber-1999, OPLS-AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic parameters of, in particular, sodium, and, to a lesser extent, chloride, translate into large differences in the computed radial-distribution functions. This uncertainty reflect the incomplete experimental knowledge of the structural properties of ionic aqueous solutions at finite molarity. We discuss possible implications on the computation of potential of mean force and effective potentials.