An online parameter and property database for the TraPPE force field

Eggimann, Becky L.; Sunnarborg, Amara J.; Stern, Hudson D.; Bliss, Andrew P.; Siepmann, J. Ilja

doi:10.1080/08927022.2013.842994

Cited by 135 publications

(134 citation statements)

References 42 publications

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“…Condensed-phase force fields such as CHARMM [5][6][7][8][9][10][11][12][13][14][15] , AMBER [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31] , OPLS 32-44 , TraPPE [45][46][47][48][49][50][51][52] and GROMOS [53][54][55][56][57][58][59][60][61][62][63][64][65][66][67][68] mainly aim at the description of solids, liquids and solutions, including solvated biomolecules as a particularly relevant special case. ...…”

Section: Introductionmentioning

confidence: 99%

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Horta

Merz

Fuchs

et al. 2016

J. Chem. Theory Comput.

147

287

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This article reports on the calibration and validation of a new GROMOS-compatible parameter set 2016H66 for small organic molecules in the condensed phase. The calibration is 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. For 57 organic compounds, the calibration targets are the experimental pure-liquid density ρliq and the vaporization enthalpy ΔHvap, as well as the hydration free energy ΔGwat and the solvation free energy ΔGche in cyclohexane, at atmospheric pressure and at (or close to) room temperature. The final root-mean-square deviations (RMSD) for these four quantities over the set of compounds are 32.4 kg m(-3), 3.5 kJ mol(-1), 4.1 kJ mol(-1), and 2.1 kJ mol(-1), respectively, and the corresponding average deviations (AVED) are 1.0 kg m(-3), 0.2 kJ mol(-1), 2.6 kJ mol(-1), and 1.0 kJ mol(-1), respectively. For the five nucleic-acid bases, the parametrization is performed by transferring the final 2016H66 parameters from analogous organic compounds followed by a slight readjustment of the charges to reproduce the experimental water-to-chloroform transfer free energies ΔGtrn. The final RMSD for this quantity over the five bases is 1.7 kJ mol(-1), and the corresponding AVED is 0.8 kJ mol(-1). As an initial validation of the 2016H66 set, seven additional thermodynamic, transport, and dielectric properties are calculated for the 57 organic compounds in the liquid phase. The agreement with experiment in terms of these additional properties is found to be reasonable, with significant deviations typically affecting either a specific chemical function or a specific molecule. This suggests that in most cases, a classical force-field description along with a careful parametrization against ρliq, ΔHvap, ΔGwat, and ΔGche results in a model that appropriately describes the liquid in terms of a wide spectrum of its physical properties.

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Section: Introductionmentioning

confidence: 99%

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Horta

Merz

Fuchs

et al. 2016

J. Chem. Theory Comput.

147

287

View full text Add to dashboard Cite

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“…Some of the simplest aldehydes, as formaldehyde (metanal, HCHO, one carbon atom), acetaldehyde (etanal, CH 3 CHO, two carbon atoms), and butyraldehyde (butanal, CH 3 CH 2 CH 2 CHO, four carbon atoms), are produced by the chemical industry on the scale of million tons/year . Related also to their industrial importance, their thermodynamic properties have been frequently targeted by investigations based on computer simulations in the 21st century …”

Section: Introductionmentioning

confidence: 99%

X‐Ray Diffraction and Computer Simulation Studies of the Structure of Liquid Aliphatic Aldehydes: From Propanal to Nonanal

Pethes

Temleitner

Tomšič

et al. 2018

Physica Status Solidi (b)

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Synchrotron X‐ray diffraction experiments and molecular dynamics (MD) simulations have been performed on simple aliphatic aldehydes, from propanal to nonanal. The performance of the OPLS (Optimized Potentials for Liquid Simulations) all‐atom interaction potential model for aldehydes has been assessed via direct comparison of simulated and experimental total scattering structure factors. In general, MD results reproduce the experimental data at least semi‐quantitatively. However, a slight mismatch can be observed between the two datasets in terms of the position of the main diffraction maxima. Partial radial distribution functions have also been calculated from the simulation results. Clear differences can be detected between the various OH partial radial distribution functions, depending on whether the H atom is attached to the carbon atom that is doubly bonded to the oxygen atom of the aldehyde group or not.

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“…Less than 3 decades ago, the state of the art was embodied by the first direct simulations of phase equilibria for simple fluids such as argon . Today, chemical engineers routinely apply molecular simulation to study challenging problems related to drug design and formulation; biomolecular crowding; protein folding and aggregation; wetting phenomena and hydration thermodynamics; nucleation and growth processes; the thermophysical properties of complex fluids such as ionic liquids and liquid crystals; the phase behavior of polymeric, colloidal, and self‐assembled systems; and the synthesis, design and characterization of advanced materials for applications ranging from adsorption‐separation processes to energy conversion and storage …”

Section: Introductionmentioning

confidence: 99%