Journal of Computational Chemistry
1096-987X
0192-8651
Mỹ
Cơ quản chủ quản: John Wiley & Sons Inc. , WILEY
Lĩnh vực:
Chemistry (miscellaneous)Computational Mathematics
Phân tích ảnh hưởng
Thông tin về tạp chí
This distinguished journal publishes articles concerned with all aspects of computational chemistry: analytical, biological, inorganic, organic, physical, and materials. The Journal of Computational Chemistry presents original research, contemporary developments in theory and methodology, and state-of-the-art applications. Computational areas that are featured in the journal include ab initio and semiempirical quantum mechanics, density functional theory, molecular mechanics, molecular dynamics, statistical mechanics, cheminformatics, biomolecular structure prediction, molecular design, and bioinformatics.
Các bài báo tiêu biểu
<sup>13</sup>C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models Abstract Precise theoretical predictions of NMR parameters are helpful for the spectroscopic identification of complicated biological molecules, especially for the carbon shielding tensors in amino acids. The 13 C shielding tensors of various crystalline amino acids and peptides have been calculated using the gauge‐including projector augmented wave (GIPAW) method based on two different periodic structure models, namely that deduced from available crystallographic data and that from theoretically optimized structures. The incorporation of surrounding lattice effects is found to be crucial in obtaining reliable predictions of 13 C shielding tensors that are comparable to the experimental data. This is accomplished by refining the experimental crystallographic data of the amino acids and peptides at the GGA/PBE level by which more accurate intramolecular CH bond lengths and intermolecular hydrogen‐bonding interactions are obtained. Accordingly, more accurate predictions of 13 C shielding tensors comparable to the experimental results (within a maximum deviation of ±10 ppm) were achieved, rendering more explicit 13 C shielding tensors assignments for solid biological systems particularly for amino acids with multiple carboxyl carbons, such as asparagine, glutamine, and glutamic acid. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Tập 30 Số 2 - Trang 222-235 - 2009
Application of semiempirical long‐range dispersion corrections to periodic systems in density functional theory Abstract Ewald summation is used to apply semiempirical long‐range dispersion corrections (Grimme, J Comput Chem 2006, 27, 1787; 2004, 25, 1463) to periodic systems in density functional theory. Using the parameters determined before for molecules and the Perdew‐Burke‐Ernzerhof functional, structure parameters and binding energies for solid methane, graphite, and vanadium pentoxide are determined in close agreement with observed values. For methane, a lattice constant a of 580 pm and a sublimation energy of 11 kJ mol−1 are calculated. For the layered solids graphite and vanadia, the interlayer distances are 320 pm and 450 pm, respectively, whereas the graphite interlayer energy is −5.5 kJ mol−1 per carbon atom and layer. Only when adding the semiempirical dispersion corrections, realistic values are obtained for the energies of adsorption of C4 alkenes in microporous silica (−66 to −73 kJ mol−1 ) and the adsorption and chemisorption (alkoxide formation) of isobutene on acidic sites in the micropores of zeolite ferrierite (−78 to −94 kJ mol−1 ). As expected, errors due to missing self‐interaction correction as in the energy for the proton transfer from the acidic site to the alkene forming a carbenium ion are not affected by the dispersion term. The adsorption and reaction energies are compared with the results from Møller‐Plesset second‐order perturbation theory with basis set extrapolation. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008
Tập 29 Số 13 - Trang 2088-2097 - 2008
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 Abstract Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1656–1676, 2004
Tập 25 Số 13 - Trang 1656-1676 - 2004
Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation Abstract We present the first global parameterization and validation of a novel charge model, called AM1‐BCC, which quickly and efficiently generates high‐quality atomic charges for computer simulations of organic molecules in polar media. The goal of the charge model is to produce atomic charges that emulate the HF/6‐31G* electrostatic potential (ESP) of a molecule. Underlying electronic structure features, including formal charge and electron delocalization, are first captured by AM1 population charges; simple additive bond charge corrections (BCCs) are then applied to these AM1 atomic charges to produce the AM1‐BCC charges. The parameterization of BCCs was carried out by fitting to the HF/6‐31G* ESP of a training set of >2700 molecules. Most organic functional groups and their combinations were sampled, as well as an extensive variety of cyclic and fused bicyclic heteroaryl systems. The resulting BCC parameters allow the AM1‐BCC charging scheme to handle virtually all types of organic compounds listed in The Merck Index and the NCI Database. Validation of the model was done through comparisons of hydrogen‐bonded dimer energies and relative free energies of solvation using AM1‐BCC charges in conjunction with the 1994 Cornell et al. forcefield for AMBER.13 Homo‐ and hetero‐dimer hydrogen‐bond energies of a diverse set of organic molecules were reproduced to within 0.95 kcal/mol RMS deviation from the ab initio values, and for DNA dimers the energies were within 0.9 kcal/mol RMS deviation from ab initio values. The calculated relative free energies of solvation for a diverse set of monofunctional isosteres were reproduced to within 0.69 kcal/mol of experiment. In all these validation tests, AMBER with the AM1‐BCC charge model maintained a correlation coefficient above 0.96. Thus, the parameters presented here for use with the AM1‐BCC method present a fast, accurate, and robust alternative to HF/6‐31G* ESP‐fit charges for general use with the AMBER force field in computer simulations involving organic small molecules. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1623–1641, 2002
Tập 23 Số 16 - Trang 1623-1641 - 2002
Implementing dimer metadynamics using gromacs We develop a Gromacs implementation of dimer metadynamics (DM) (JCTC 13, 425 [2017]) for enhanced sampling through artificial delocalization effects. This implementation is based entirely on a Plumed collective variable developed for this purpose, the fine tuning of Gromacs input parameters, modified forcefields and custom nonbonded interactions. We demonstrate this implementation on alanine dipeptide in vacuum and in water, and on the 12‐residue alanine polypeptide in water and compare the results with a standard multiple‐replica technique such as parallel tempering. In all the considered cases, this comparison is consistent and the results with DM are smoother and require shorter simulations, thus proving the consistency and effectiveness of this Gromacs implementation. © 2018 Wiley Periodicals, Inc.
Tập 39 Số 25 - Trang 2126-2132 - 2018
Electronic structure, chemical bonding, and finite‐temperature magnetic properties of full Heusler alloys Abstract The electronic structure, chemical bonding, and magnetic properties of 15 full Heusler alloys X2 MnZ have been studied on the basis of density‐functional theory using the TB‐LMTO‐ASA approach and the local‐density (LDA), as well as the generalized‐gradient approximation (GGA). Correlations between the chemical bondings derived from crystal orbital Hamilton population (COHP) analysis and magnetic phenomena are obvious, and different mechanisms leading to spin polarization and ferromagnetism are derived. As long as a magnetically active metal atom X is present, antibonding XX and XMn interactions at the Fermi level drive the systems into the ferromagnetic ground state; only if X is nonmagnetic (such as in Cu2 MnZ), antibonding MnMn interactions arise, which again lead to ferromagnetism. Finite‐temperature effects (Curie temperatures) are analyzed using a mean‐field description, and a surprisingly simple (or, trivial) relationship between structural properties (MnMn interatomic distances) and T C is found, being of semiquantitative use for the prediction of the latter. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 90–102, 2006
Tập 27 Số 1 - Trang 90-102 - 2006
Optimization of equilibrium geometries and transition structures Abstract A modified conjugate gradient algorithm for geometry optimization is outlined for use with ab initio MO methods. Since the computation time for analytical energy gradients is approximately the same as for the energy, the optimization algorithm evaluates and utilizes the gradients each time the energy is computed. The second derivative matrix, rather than its inverse, is updated employing the gradients. At each step, a one‐dimensional minimization using a quartic polynomial is carried out, followed by an n ‐dimensional search using the second derivative matrix. By suitably controlling the number of negative eigenvalues of the second derivative matrix, the algorithm can also be used to locate transition structures. Representative timing data for optimizations of equilibrium geometries and transition structures are reported for ab initio SCF –MO calculations.
Tập 3 Số 2 - Trang 214-218 - 1982
Energies, structures, and electronic properties of molecules in solution with the C‐PCM solvation model Abstract The conductor‐like solvation model, as developed in the framework of the polarizable continuum model (PCM), has been reformulated and newly implemented in order to compute energies, geometric structures, harmonic frequencies, and electronic properties in solution for any chemical system that can be studied in vacuo. Particular attention is devoted to large systems requiring suitable iterative algorithms to compute the solvation charges: the fast multipole method (FMM) has been extensively used to ensure a linear scaling of the computational times with the size of the solute. A number of test applications are presented to evaluate the performances of the method. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 669–681, 2003
Tập 24 Số 6 - Trang 669-681 - 2003
6‐31G* basis set for third‐row atoms Abstract Medium basis sets based upon contractions of Gaussian primitives are developed for the third‐row elements Ga through Kr. The basis functions generalize the 6‐31G and 6‐31G* sets commonly used for atoms up to Ar. A reexamination of the 6‐31G* basis set for K and Ca developed earlier leads to the inclusion of 3d orbitals into the valence space for these atoms. Now the 6‐31G basis for the whole third‐row K through Kr has six primitive Gaussians for 1s, 2s, 2p, 3s, and 3p orbitals, and a split‐valence pair of three and one primitives for valence orbitals, which are 4s, 4p, and 3d. The nature of the polarization functions for third‐row atoms is reexamined as well. The polarization functions for K, Ca, and Ga through Kr are single set of Cartesian d‐type primitives. The polarization functions for transition metals are defined to be a single 7f set of uncontracted primitives. Comparison with experimental data shows good agreement with bond lengths and angles for representative vapor‐phase metal complexes. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 976–984, 2001
Tập 22 Số 9 - Trang 976-984 - 2001
Compact contracted basis sets for third‐row atoms: Ga–Kr Abstract The (14s 11p 5d ) primitive basis set of Dunning for the third‐row main group atoms Ga‐Kr has been contracted [6s 4p 1d ]. The core functions have been relatively highly contracted while those which represent the valence region have been left uncontracted to maintain flexibility. Calculations with the [6s 4p 1d ] contraction are reported for a variety of molecules involving third‐row atoms. This basis set is found to satisfactorily reproduce experimental properties such as geometric configurations, dipole moments, and vibrational frequencies for a range of molecules. Comparisons are made with the performance of the uncontracted basis set. Polarization functions for the contracted basis set are reported and performance of the basis set with and without polarization functions is examined. A relaxation of the [6s 4p 1d ] contraction to [9s 6p 2d ] for higher level evergy calculations is also presented.
Tập 11 Số 10 - Trang 1206-1216 - 1990