Spherical and Aspherical Intermolecular Force Fields for Sulfur Allotropes

Abraha, Aron; Williams, Donald E.

doi:10.1021/ic990573g

Cited by 20 publications

(11 citation statements)

References 29 publications

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“…In general, agreement with the experimental crystal structures is somewhat worse than for other compounds. Abraha and Williams,81 who considered a set of crystal structures of elemental sulfur (S n ), presented evidence that the bonded sulfur atom in these structures is not spherical and that an aspherical van der Waals model was necessary to achieve acceptable agreement with the experimental data. Implementation of such aspherical model may also increase accuracy of the potential for other sulfur‐containing molecules albeit at a higher computational cost.…”

Section: Resultsmentioning

confidence: 99%

Development of a new physics‐based internal coordinate mechanics force field and its application to protein loop modeling

2010

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We report the development of ICMFF, new force field parameterized using a combination of experimental data for crystals of small molecules and quantum mechanics calculations. The main features of ICMFF include: (a) parameterization for the dielectric constant relevant to the condensed state (ε=2) instead of vacuum; (b) an improved description of hydrogen-bond interactions using duplicate sets of van der Waals parameters for heavy atom-hydrogen interactions; and (c) improved backbone covalent geometry and energetics achieved using novel backbone torsional potentials and inclusion of the bond angles at the C α atoms into the internal variable set. The performance of ICMFF was evaluated through loop modeling simulations for 4-13 residue loops. ICMFF was combined with a solvent-accessible surface area solvation model optimized using a large set of loop decoys. Conformational sampling was carried out using the Biased Probability Monte Carlo method. Average/median backbone root-mean-square deviations of the lowest energy conformations from the native structures were 0.25/0.21 Å for 4 residues loops, 0.84/0.46 Å for 8 residue loops, and 1.16/0.73 Å for 12 residue loops. To our knowledge, these results are significantly better than or comparable to those reported to date for any loop modeling method that does not take crystal packing into account. Moreover, the accuracy of our method is on par with the best previously reported results obtained considering the crystal environment. We attribute this success to the high accuracy of the new ICM force field achieved by meticulous parameterization, to the optimized solvent model, and the efficiency of the search method.

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Section: Resultsmentioning

confidence: 99%

Development of a new physics‐based internal coordinate mechanics force field and its application to protein loop modeling

2010

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“…The repulsion-dispersion interactions, in both Stages 3 and 4, are calculated using the Buckingham potential under the pairwise additivity assumption. In contrast to C, N (Williams & Cox, 1984), O (Cox et al, 1981) and H (Williams & Cox, 1984;Coombes et al, 1996), for which transferable parameters for the Buckingham potential exist, parameters for sulfur are available only for specific sulfur/sulfur non-bonded interactions: the C-S-C bonding pattern (Lommerse et al, 2000), the S n pattern (Abraha & Williams, 1999), and the SO 2 Cpattern (Motherwell et al, 2002). Given ROY's molecular Rigid fragment definition for the ROY molecule, ensuring that the length of the intramolecular hydrogen bond (shown as dashed line) remains constant during the global search.…”

Section: Stage 2 -Choice Of Computational Modelmentioning

confidence: 99%

The polymorphs of ROY: application of a systematic crystal structure prediction technique

Vasileiadis

Kazantsev

Karamertzanis

et al. 2012

Acta Crystallogr Sect B

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We investigate the ability of current ab initio crystal structure prediction techniques to identify the polymorphs of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, also known as ROY because of the red, orange and yellow colours of its polymorphs. We use a methodology combining the generation of a large number of structures based on a computationally inexpensive model using the CrystalPredictor global search algorithm, and the further minimization of the most promising of these structures using the CrystalOptimizer local minimization algorithm which employs an accurate, yet efficiently constructed, model based on isolated-molecule quantum-mechanical calculations. We demonstrate that this approach successfully predicts the seven experimentally resolved structures of ROY as lattice-energy minima, with five of these structures being within the 12 lowest energy structures predicted. Some of the other low-energy structures identified are likely candidates for the still unresolved polymorphs of this molecule. The relative stability of the predicted structures only partially matches that of the experimentally resolved polymorphs. The worst case is that of polymorph ON, whose relative energy with respect to Y is overestimated by 6.65 kJ mol(-1). This highlights the need for further developments in the accuracy of the energy calculations.

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“…The optimized parameters for sulphur interactions are further compared with two additional sets of parameters, namely those by No et al 70 (denoted as S-No) and by Abraha et al 71 (denoted as S-Ab). These alternative parameter sets are presented in Table 6.…”

Section: Optimized Parametersmentioning

confidence: 99%

Repulsion–dispersion parameters for the modelling of organic molecular crystals containing N, O, S and Cl

2018

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In lattice energy models that combine ab initio and empirical components, it is important to ensure consistency between these components so that meaningful quantitative results are obtained. A method for deriving parameters of atom-atom repulsion dispersion potentials for crystals, tailored to different ab initio models, is presented. It is based on minimization of the sum of squared deviations between experimental and calculated structures and energies. The solution algorithm is designed to avoid convergence to local minima in the parameter space by combining a deterministic low-discrepancy sequence for the generation of multiple initial parameter guesses with an efficient local minimization algorithm. The proposed approach is applied to derive transferable exp-6 potential parameters suitable for use in conjunction with a distributed multipole electrostatics model derived from isolated molecule charge densities calculated at the M06/6-31G(d,p) level of theory. Data for hydrocarbons, azahydrocarbons, oxohydrocarbons, organosulphur compounds and chlorohydrocarbons are used for the estimation. A good fit is achieved for the new set of parameters with a mean absolute error in sublimation enthalpies of 4.1 kJ mol À1 and an average rmsd 15 of 0.31Å. The parameters are found to perform well on a separate cross-validation set of 39 compounds.

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Spherical and Aspherical Intermolecular Force Fields for Sulfur Allotropes

Cited by 20 publications

References 29 publications

Development of a new physics‐based internal coordinate mechanics force field and its application to protein loop modeling

Development of a new physics‐based internal coordinate mechanics force field and its application to protein loop modeling

The polymorphs of ROY: application of a systematic crystal structure prediction technique

Repulsion–dispersion parameters for the modelling of organic molecular crystals containing N, O, S and Cl

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