Comparison of methods for deriving atomic charges from the electrostatic potential and momentsSigfridsson, Emma; Ryde, Ulf
doi: 10.1002/(SICI)1096-987X(199803)19:4<377::AID-JCC1>3.0.CO;2-Ppmid: N/A
Four methods for deriving partial atomic charges from the quantum chemical electrostatic potential (CHELP, CHELPG, Merz‐Kollman, and RESP) have been compared and critically evaluated. It is shown the charges strongly depend on how and where the potential points are selected. Two alternative methods are suggested to avoid the arbitrariness in the point‐selection schemes and van der Waals exclusion radii: CHELP‐BOW, which also estimates the charges from the electrostatic potential, but with potential points that are Boltzmann‐weighted after their occurrence in actual simulations using the energy function of the program in which the charges will be used, and CHELMO, which estimates the charges directly from the electrostatic multipole moments. Different criteria for the quality of the charges are discussed. The CHELMO method gives the best multipole moments for small and medium‐sized polar systems, whereas the CHELP‐BOW charges reproduce best the total interaction energy in actual simulations. Among the standard methods, the Merz‐Kollman charges give the best moments and potentials, but they show an appreciable dependence on the orientation of the molecule. We have also examined the recent warning that charges derived by a least‐squares fit to the electrostatic potential normally are not statistically valid. It is shown that no rank‐deficiency problems are encountered for molecules with up to 84 atoms if the least‐squares fit is performed using pseudoinverses calculated by singular value decomposition and if constraints are treated by elimination. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 377–395, 1998
Monte‐Carlo model for the hydrogenation of alkenes on metal catalystDuca, Dario; Baranyai, Péter; Vidóczy, Tamás
doi: 10.1002/(SICI)1096-987X(199803)19:4<396::AID-JCC2>3.0.CO;2-Npmid: N/A
A Monte‐Carlo model for the simulation of alkene hydrogenation on metallic catalysts has been developed and implemented in Fortran language. We describe the model employed for ethylene hydrogenation on platinum and show the flow chart of the program. Computational characteristics such as number of necessary calculations to reach steady state, running times on different platforms, and effect of the size of the catalyst matrix, are presented. Good correlation between simulated and experimental data was observed. A subroutine allows for visual observation of the reaction. This approach is very useful for obtaining a personal impression of the important factors governing the reaction. By using this example the advantages of Monte‐Carlo simulation to test the level of understanding of catalytic phenomena are discussed. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 396–403, 1998
Implementation and validation of the Lacks‐Gordon exchange functional in conventional density functional and adiabatic connection methodsAdamo, Carlo; Barone, Vincenzo
doi: 10.1002/(SICI)1096-987X(199803)19:4<418::AID-JCC4>3.0.CO;2-Vpmid: N/A
We present an analysis of the numerical performances of the exchange functional proposed by Lacks and Gordon, which we have implemented in the Gaussian series of programs. This functional has been built with the double aim of respecting most of the known scaling and asymptotic properties and of giving good numerical performances, especially as concerns noncovalent interactions. We have found that the coupling of the Lacks‐Gordon exchange and Lee‐Yang‐Parr correlation functionals provides a reliable conventional density functional approach. The corresponding parameter‐free adiabatic connection model, in which the ratio between Hartree‐Fock and Lacks‐Gordon exchange is determined a priori from purely theoretical considerations, allows us to obtain remarkable results for both covalent and noncovalent interactions in a satisfactory theoretical scheme, encompassing the free electron gas limit and most of the known scaling conditions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 418–429, 1998
Derivation of class II force fields: V. Quantum force field for amides, peptides, and related compoundsMaple, J. R.; Hwang, M.‐J.; Jalkanen, K. J.; Stockfisch, T. P.; Hagler, A. T.
doi: 10.1002/(SICI)1096-987X(199803)19:4<430::AID-JCC5>3.0.CO;2-Tpmid: N/A
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
Crystal structure predictions for acetic acidMooij, Wijnand T. M.; van Eijck, Bouke P.; Price, Sarah L.; Verwer, Paul; Kroon, Jan
doi: 10.1002/(SICI)1096-987X(199803)19:4<459::AID-JCC6>3.0.CO;2-Rpmid: N/A
Possible crystal structures of acetic acid were generated, considering eight space groups and assuming one molecule in the asymmetric unit. Our grid‐search method was compared with a Monte Carlo approach as implemented in the Biosym/MSI Polymorph Predictor. This revealed no sampling deficiencies. A large number of possible crystal structures were found (∼100 within only 5 kJ/mol), including the experimental structure. Energy minimizations were done with a united‐atoms force field (GROMOS), an all‐atoms force field (AMBER), and a potential that describes the electrostatic interactions with distributed multipoles (DMA). In all cases, the experimental structure had a low lattice energy. The number of hypothetical crystal structures was reduced considerably by removing space‐group symmetry constraints, or by a primitive molecular dynamics shake‐up. Nevertheless, sufficient structures of equal or lower energy compared with the experimental structure remained to suggest that other factors need to be considered for genuine structure prediction. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 459–474, 1998