Molecular modeling of organic and biomolecular systems using <i>BOSS</i> and <i>MCPRO</i>

Jorgensen, William L.; Tirado‐Rives, Julian

doi:10.1002/jcc.20297

Cited by 407 publications

(517 citation statements)

References 57 publications

(75 reference statements)

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“…Two types of movements were attempted in every step with equal likelihood: single particle displacements, and intact monomer rotations or translations. A monomer is defined as the set of particles including and surrounding an oxygen nucleus within 1.2 Å. Spatial steps are adjusted to obtain acceptance probabilities of ∼40% as recommended elsewhere [31]. Low temperatures (T = 1 K) are chosen to accelerate annealing and multiple starting configurations and higher temperatures are attempted in larger clusters.…”

Section: Monte Carlo Simulationsmentioning

confidence: 99%

Lewis-inspired representation of dissociable water in clusters and Grotthuss chains

et al. 2011

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Proton transfer to and from water is critical to the function of water in many settings. However, it has been challenging to model. Here, we present proof-of-principle for an efficient yet robust model based on Lewis-inspired submolecular particles with interactions that deviate from Coulombic at short distances to take quantum effects into account. This "LEWIS" model provides excellent correspondence with experimental structures for water molecules and water clusters in their neutral, protonated and deprotonated forms, reasonable values for the proton affinities of water and hydroxide, a good value for the strength of the hydrogen bond in the water dimer, the correct order of magnitude for the stretch and bend force constants of water, and the expected time course for Grotthuss transport in water chains.

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Section: Monte Carlo Simulationsmentioning

confidence: 99%

Lewis-inspired representation of dissociable water in clusters and Grotthuss chains

et al. 2011

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“…16 Complete energy minimizations were carried out with the BOSS program 22 except that the internal geometry of the water molecule is fixed in the TIP4P model, r(OH) = 0.9572 Å and ∠HOH = 104.52°. Notably, in the reported OPLS-AA model for para-substituted benzenes, the net charge on the substituent plus attached benzene carbon atom is zero.…”

Section: Computational Detailsmentioning

confidence: 99%

Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion

Jorgensen

Jensen

Alexandrova

2007

J. Chem. Theory Comput.

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101

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Variations in hydrogen-bond strengths are investigated for complexes of nine para-substituted phenols (XPhOH) with a water molecule and chloride ion. Results from ab initio HF/6-311+G(d, p) and MP2/6-311+G(d, p)//HF/6-311+G(d, p) calculations are compared with those from the OPLS-AA and OPLS/CM1A force fields. In the OPLS-AA model, the partial charges on the hydroxyl group of phenol are not affected by the choice of para substituent, while the use of CM1A charges in the OPLS/CM1A approach does provide charge redistribution. The ab initio calculations reveal a 2.0-kcal/mol range in hydrogen-bond strengths for the XPhOH⋯OH 2 complexes in the order X = NO 2 > CN > CF 3 > Cl > F > H >OH >CH 3 > NH 2 . The pattern is not well-reproduced with OPLS-AA, which also compresses the variation to 0.7 kcal/mol. However, the OPLS/CM1A results are in good accord with the ab initio findings for both the ordering and range, 2.3 kcal/mol. The hydrogen bonding is, of course, weaker with XPhOH as acceptor, the order for X is largely inverted, and the range is reduced to ca. 1.0 kcal/mol. The substituent effects are found to be much greater for the chloride ion complexes with a range of 11 kcal/mol. For quantitative treatment of such strong ion-molecule interactions the need for fully polarizable force fields is demonstrated.

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“…AM1 [4] [5] partial atomic charges scaled by 1.14 for the solute and solvent were used in the MC simulations. A more detailed description of the MC move and the atomic charge partitioning scheme can be found in [1].…”

Section: Monte Carlo Simulation Setup and Proceduresmentioning

confidence: 99%

Contribution of a Solute's Chiral Solvent Imprint to Optical Rotation

et al. 2007

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Molecular modeling of organic and biomolecular systems using BOSS and MCPRO

Abstract: An overview is provided of the capabilities for the current versions of the BOSS and MCPRO programs for molecular modeling of organic and biomolecular systems. Recent applications are noted, particularly for QM/MM studies of organic and enzymatic reactions and for protein-ligand binding.

Cited by 407 publications

References 57 publications

Lewis-inspired representation of dissociable water in clusters and Grotthuss chains

Lewis-inspired representation of dissociable water in clusters and Grotthuss chains

Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion

Contribution of a Solute's Chiral Solvent Imprint to Optical Rotation

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