Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field

The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results are compared with experimental data and equivalent simulations performed with the GAFF pairwise‐additive force field. Although AMOEBA results give mean errors close to “chemical accuracy,” GAFF performs surprisingly well, with statistically significantly more accurate results than AMOEBA in some solvents. However, for both models, free energies calculated in chloroform show worst agreement to experiment and individual solutes are consistently poor performers, suggesting non‐potential‐specific errors also contribute to inaccuracy. Scope for the improvement of both potentials remains limited by the lack of high quality experimental data across multiple solvents, particularly those of high dielectric constant. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

A method for calculating atomic charges in large molecules

A simple electronegativity method is used to calculate atomic charges for molecules of interest to biochemistry. These include purines, pyrimidines, and amino acids. Results are compared to those obtained from other theoretical methods (ab initio and semiempirical) as well as to nuclear magnetic resonance (NMR) data. Correlation is fair with CNDO results but very good for ab initio, DelRe, and other electronegativity methods. Good correlation was also achieved with NMR data. It is shown that a correction factor may be required in some cases and that important resonance effects need to be taken into account. Because of the small amount of calculational effort involved, these results suggest that this method could be quite useful in this field.     

计算受体和配体结合自由能的新方法

利用ABEEMσπ浮动电荷力场与连续介质模型相结合的方法,计算了受体和配体的结合自由能.将结合自由能分解为真空中的力场作用项、溶剂化能量以及熵效应.由于ABEEMσπ/MM方法充分考虑了外界环境发生变化引起的体系中各个位点之间的电荷极化,因而极大地提高了结合自由能的计算精度.利用该方法计算的2个复合物的结合自由能与实验值的偏差均小于0.5kJ/mol.     

A molecular mechanics force field for conformational analysis of aliphatic acyclic amines

An improved molecular mechanics force field for conformational and vibrational studies of aliphatic acyclic amines is developed. The resulting force field reproduces molecular structures adequately and provides a good fit for energy differences between conformers and barriers to internal rotation for a large number of amines. In addition, vibrational frequencies are calculated in good agreement with available experimental data. When compared with existent force fields for amines, the present force field is considerably more simple and gives rise to calculated properties in closer agreement with experiment.     

Mean field theory of charged dendrimer molecules

Using self-consistent field theory (SCFT), we study the conformational properties of polyelectrolyte dendrimers. We compare results for three different models of charge distributions on the polyelectrolytes: (1) a smeared, quenched charge distribution characteristic of strong polyelectrolytes; (2) a smeared, annealed charge distribution characteristic of weak polyelectrolytes; and (3) an implicit counterion model with Debye-Huckel interactions between the charged groups. Our results indicate that an explicit treatment of counterions is crucial for the accurate characterization of the conformations of polyelectrolyte dendrimers. In comparing the quenched and annealed models of charge distributions, annealed dendrimers were observed to modulate their charges in response to the density of polymer monomers, counterions, and salt ions. Such phenomena is not accommodated within the quenched model of dendrimers and is shown to lead to significant differences between the predictions of quenched and annealed model of dendrimers. In this regard, our results indicate that the average dissociated charge α inside the dendrimer serves as a useful parameter to map the effects of different parametric conditions and models onto each other. We also present comparisons to the scaling results proposed to explain the behavior of polyelectrolyte dendrimers. Inspired by the trends indicated by our results, we develop a strong segregation theory model whose predictions are shown to be in very good agreement with the numerical SCFT calculations.     

A simple method for calculating reliable atomic charges in large molecules

Modifications are made to a previously developed scheme for calculating atomic charge which uses orbital electronegativity and which requires minimal calculational effort. The introduced changes are a result of deficiencies noted in the earlier method which were due to an inadequate accounting of effects from neighboring atom charges. Results obtained using the modified scheme for both model compounds as well as larger molecules of interest to biochemistry are compared to previous results and also to several levels of ab initio calculations. It is shown that a definite improvement is obtained and that the present method gives very good correlations with each calculational level. Comparisons are also made with other methods that use electronegativity theory. It is shown that the present scheme represents a definite improvement over alternate orbital electronegativity methods and is roughly comparable to a higher level scheme that utilizes atomic electronegativity values. A discussion comparing the latter method with the present one is included. Because of the small amount of calculational effort involved, the results indicate that the present method could be quite useful in providing reliable atomic charges for large molecular systems.     

Prediction of adsorption of small molecules in porous materials based on ab initio force field method

Computational prediction of adsorption of small molecules in porous materials has great impact on the basic and applied research in chemical engineering and material sciences. In this work,we report an approach based on grand canonical ensemble Monte Carlo(GCMC) simulations and ab initio force fields. We calculated the adsorption curves of ammonia in ZSM-5 zeolite and hydrogen in MOF-5(a metal-organic-framework material). The predictions agree well with experimental data. Because the predictions are based on the first principle force fields,this approach can be used for the adsorption prediction of new molecules or materials without experimental data as guidance.     

Counterpoise orbital basis in SCF computations of conformational energies of molecules

The functional counterpoise idea of Boys and Bernardi is extended to SCF computations, to improve the accuracy of computed values of conformational energies of molecules. It consists of using the same orbital basis to obtain the SCF energies for different molecular conformations. The procedure is found to be effective for two examples discussed in the paper.     

Improved method for calculating vibronic spectra of complex molecules

The previously suggested approximate method for calculating the overlap integrals of vibrational wave functions is considerably improved for the purpose of maximally accurate calculation of excitation-induced mixing of normal coordinates. A general formula is obtained for all types of overlap integrals as a finite power series of the potential surface shift parameters; the coefficients are derivatives of the corresponding generating Junctions represented as polynomials of the shift vector elements of the normal coordinates and the mixing matrix. The spectra of model molecules of decatetraene and tetra- and hexadecaheptaene were calculated using the expressions derived in this work and a semiempirical parametric method for determination of excitation-induced changes in the potential surface of molecules. The calculations confirmed the high efficiency of both the parametric method and the new technique. Translated fromZhumal Strukturnoi Khimii, Vol. 38, No. 2, pp. 240–247, March–April, 1997.     

An improved force field for conformational analysis of sulfated polysaccharides

A force field to be used in molecular mechanics studies of sulfated polysaccharides with explicit account of water and counterion interactions was derived from the analysis of six crystal structures of sulfated monosaccharide salts. The force field is based on Allinger's MM2, and was developed starting from the parameters used in previous studies of heparin and related oligosaccharides. While the novel parameters have been derived empirically, use of the atomic charge distribution obtained from ab initio quantum-mechanical computations, at the 6–31 + G^** level, improves the quality of structural fitting significantly. The overall discrepancy between the positions of the nonhydrogen atoms determined by X-ray diffractometry and those corresponding to the minimum-energy structure is 0.21 Å. While most geometrical features of both carbohydrate and sulfate moieties are reproduced satisfactorily, in some cases (particularly in the case of the Na⁺ salt of α-methyl-4-O-sulfogalactopyranoside) the hydrogen bond pattern is altered by energy minimization, probably due to errors in the balance of the strong electrostatic forces. © 1997 by John Wiley & Sons, Inc.     

A rapid method for calculating derivatives of solvent accessible surface areas of molecules

A novel method to calculate the derivatives of solvent accessible surface areas is presented. Unlike earlier analytic methods, which require the molecular topology and the use of global Gauss-Bonnet theorem, this method requires only the fractional accessibilities of surface arcs. We developed an efficient numerical algorithm to calculate the surface arcs by creating a uniform set of points on the circles of intersection between surface atoms. A hierarchical point density doubling scheme led to a logarithmic dependence of Central Processing Unit (CPU) time on the number of points used. This algorithm calculated area derivatives for a 1000-atom protein in 1.5 s on an SGI INDIGO² which were within 2% of the analytic area derivatives calculated with the program ANAREA. This algorithm scales linearly with the number of atoms for large molecules and is easily parallelizable. © 1995 by John Wiley & Sons, Inc.     

Generalization of Dewar's half-electron method for calculating energies of open-shell electronic states

Dewar's “half-electron” model for calculating electronic energies of certain open-shell doublet and triplet states is extended so as to be applicable to the lowest-energy open-shell state of any given symmetry and multiplicity.