Literature DB >> 17048945

Conformation of alkanes in the gas phase and pure liquids.

Laura L Thomas1, Theodore J Christakis, William L Jorgensen.   

Abstract

Monte Carlo (MC) statistical mechanics simulations have been carried out for the homologous alkane series of n-butane through n-dodecane in the gas phase and for the pure liquids at 298 K and 1 atm using the OPLS-AA force field. The study addresses potential cumulative deviations of computed properties and potential conformational differences between the gas phase and pure liquids, for example, from self-solvation in the gas phase. The average errors in comparison with experimental data for the computed densities and heats of vaporization are modest at 0.7% and 6.9%, respectively. Also, the invariant gas and liquid-phase results for average end-to-end distances and percentages of trans conformations for each nonterminal C-C bond assert that the conformer populations are not altered upon transfer from the gas phase to the pure liquid for the n-alkanes in this size range. Average end-to-end distances were also computed from the results of conformational searches and corroborated the MC findings. Quantitatively, the OPLS-AA result for the trans population of the C3-C4 bond in n-undecane is in close agreement with the findings from (13)C NMR experiments. Finally, previous work on determining the shortest n-alkane that does not have an all-trans global energy minimum has been extended. The smallest n-alkane with a hairpin geometry that is lower in energy than the all-trans conformer occurs for C(22)H(46) with OPLS-AA, though with a correction for GG sequences, the true turning point is likely in the C(16)-C(18) range.

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Year:  2006        PMID: 17048945     DOI: 10.1021/jp064811m

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  15 in total

1.  Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field.

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Journal:  J Comput Aided Mol Des       Date:  2011-12-21       Impact factor: 3.686

2.  Gas-liquid transfer data used to analyze hydrophobic hydration and find the nature of the Kauzmann-Tanford hydrophobic factor.

Authors:  Robert L Baldwin
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-23       Impact factor: 11.205

3.  A new AMBER-compatible force field parameter set for alkanes.

Authors:  Alexei M Nikitin; Yury V Milchevskiy; Alexander P Lyubartsev
Journal:  J Mol Model       Date:  2014-02-19       Impact factor: 1.810

4.  Understanding the factors affecting the activation of alkane by Cp'Rh(CO)2 (Cp' = Cp or Cp*).

Authors:  Michael W George; Michael B Hall; Omar S Jina; Peter Portius; Xue-Zhong Sun; Michael Towrie; Hong Wu; Xinzheng Yang; Snezana D Zaric
Journal:  Proc Natl Acad Sci U S A       Date:  2010-11-03       Impact factor: 11.205

5.  Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field.

Authors:  Oliver Beckstein; Anaïs Fourrier; Bogdan I Iorga
Journal:  J Comput Aided Mol Des       Date:  2014-02-21       Impact factor: 3.686

6.  Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field.

Authors:  Ian M Kenney; Oliver Beckstein; Bogdan I Iorga
Journal:  J Comput Aided Mol Des       Date:  2016-08-31       Impact factor: 3.686

7.  Chemical probes that selectively recognize the earliest Aβ oligomers in complex mixtures.

Authors:  Ashley A Reinke; Peter M U Ung; Jerome J Quintero; Heather A Carlson; Jason E Gestwicki
Journal:  J Am Chem Soc       Date:  2010-11-24       Impact factor: 15.419

8.  Effect of varying the 1-4 intramolecular scaling factor in atomistic simulations of long-chain N-alkanes with the OPLS-AA model.

Authors:  Xianggui Ye; Shengting Cui; Valmor F de Almeida; Bamin Khomami
Journal:  J Mol Model       Date:  2012-11-20       Impact factor: 1.810

9.  Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design.

Authors:  Daniel J Cole; Julian Tirado-Rives; William L Jorgensen
Journal:  Biochim Biophys Acta       Date:  2014-09-06

10.  Characterization of 1,2-Distearoyl-sn-glycero-3-phosphoethanolamine-N-[Methoxy(polyethylene glycerol)-2000] and Its Complex with Doxorubicin Using Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics.

Authors:  Weidong Hu; Allen Mao; Patty Wong; Adrien Larsen; Paul J Yazaki; Jeffrey Y C Wong; John E Shively
Journal:  Bioconjug Chem       Date:  2017-06-09       Impact factor: 4.774

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