Journal ArticleDOI
Application of a Universal Force Field to Organic Molecules
TLDR
In this article, the Universal Force Field (UFF) was used to predict the structures of a variety of organic molecules, including unstrained and uncongested hydrocarbons, silanes, alkenes, saturated amines, saturated ethers and phosphines.Abstract:
The application of a Universal force field (UFF) to the treatment of organic molecules is described. The ability of the force field to predict the structures of a variety of organic molecules is examined, and the results are compared with the MM2 or MM3 force fields. UFF correctly predicts the structures of unstrained and uncongested hydrocarbons, silanes, alkenes, saturated amines, saturated ethers and phosphines, aromatic systems, and simple unconjugated multiple bond containing compounds such as nitriles, ketones, and imines wellread more
Citations
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Journal ArticleDOI
UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations
TL;DR: In this article, the Universal force field (UFF) is described, where the force field parameters are estimated using general rules based only on the element, its hybridization, and its connectivity.
Book ChapterDOI
QM/MM Methods for Biological Systems
Hans Martin Senn,Walter Thiel +1 more
TL;DR: In this article, the state of the art of combined quantum-mechanics/molecular mechanics (QM/MM) methods with a focus on biomolecular systems is reviewed.
Journal ArticleDOI
Metal Ion Modeling Using Classical Mechanics
Pengfei Li,Kenneth M. Merz +1 more
TL;DR: This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models, and valence bond-based models.
Journal ArticleDOI
Binding site of activators of the cystic fibrosis transmembrane conductance regulator in the nucleotide binding domains
TL;DR: Comparison of theoretical binding free energy estimates in the model to free energy estimated from the apparent dissociation constants, KD, resulted in a remarkably good correlation coefficient for one of the putative binding sites, located in the interface between NBD1 and NBD2.
Journal ArticleDOI
A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set
Bruno A. C. Horta,Bruno A. C. Horta,Pascal T. Merz,Patrick F.J. Fuchs,Jozica Dolenc,Sereina Riniker,Philippe H. Hünenberger +6 more
TL;DR: This article reports on the calibration and validation of a new GROMOS-compatible parameter set 2016H66 for small organic molecules in the condensed phase, based on 62 organic molecules spanning the chemical functions alcohol, ether, aldehyde, ketone, carboxylic acid, ester, amine, amide, thiol, sulfide, and disulfide, as well as aromatic compounds and nucleic-acid bases.
References
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Journal ArticleDOI
Application of a universal force field to organic molecules
TL;DR: In this paper, the Universal Force Field (UFF) was used to predict the structures of a variety of organic molecules, including unstrained and uncongested hydrocarbons, silanes, alkenes, saturated amines, saturated ethers and phosphines.
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