Literature DB >> 12868110

Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds.

Norman L Allinger1, Kuo-Hsiang Chen, Jenn-Huei Lii, Kathleen A Durkin.   

Abstract

Simple alcohols and ethers have been studied with the MM4 force field. The structures of 13 molecules have been well fit using the MM4 force field. Moments of inertia have been fit with rms percentage errors as indicated: 18 moments for ethers, 0.28%; 21 moments for alcohols, 0.22%. Rotational barriers and conformational equilibria have also been examined, and the experimental and ab initio results are reproduced substantially better with MM4 than they were with MM3. Much of the improvement comes from the use of additional interaction terms in the force constant matrix, of which the torsion-bend and torsion-torsion are particularly important. Induced dipoles are included in the calculation, and dipole moments are reasonably well fit. It has been possible for the first time to fit conformational energetic data for both open chain and cyclic alcohols (e.g., propanol and cyclohexanol) with the same parameter set. For vibrational spectra, over a total of 82 frequencies, the rms error is 27 cm(-1), as opposed to 38 cm(-1) with MM3. Both the alpha and beta bond shortening resulting from the presence of the electronegative oxygen atom in the molecule are well reproduced. The electronegativity of the oxygen is sufficient that one must also include not only the alpha and beta electronegativity effects on bond lengths, but also on angle distortions, if structures are to be well reproduced. The heats of formation of 32 alcohols and ethers were fit overall to within experimental error (weighted standard deviation error 0.26 kcal/mol). Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1447-1472, 2003

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Year:  2003        PMID: 12868110     DOI: 10.1002/jcc.10268

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  17 in total

1.  An improved theoretical approach to the empirical corrections of density functional theory.

Authors:  Jenn-Huei Lii; Ching-Han Hu
Journal:  J Comput Aided Mol Des       Date:  2011-12-24       Impact factor: 3.686

2.  Selenoglycosides in silico: ab initio-derived reparameterization of MM4, conformational analysis using histo-blood group ABH antigens and lectin docking as indication for potential of bioactivity.

Authors:  Francesco Strino; Jenn-Huei Lii; Chaitanya A K Koppisetty; Per-Georg Nyholm; Hans-Joachim Gabius
Journal:  J Comput Aided Mol Des       Date:  2010-10-26       Impact factor: 3.686

Review 3.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

4.  Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model.

Authors:  Victor M Anisimov; Igor V Vorobyov; Benoît Roux; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2007       Impact factor: 6.006

Review 5.  Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?

Authors:  Pnina Dauber-Osguthorpe; A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

Review 6.  CHARMM additive and polarizable force fields for biophysics and computer-aided drug design.

Authors:  K Vanommeslaeghe; A D MacKerell
Journal:  Biochim Biophys Acta       Date:  2014-08-19

7.  Nonadditive empirical force fields for short-chain linear alcohols: methanol to butanol. Hydration free energetics and Kirkwood-Buff analysis using charge equilibration models.

Authors:  Yang Zhong; Sandeep Patel
Journal:  J Phys Chem B       Date:  2010-09-02       Impact factor: 2.991

8.  Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.

Authors:  K Vanommeslaeghe; E Prabhu Raman; A D MacKerell
Journal:  J Chem Inf Model       Date:  2012-11-28       Impact factor: 4.956

9.  CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

Authors:  K Vanommeslaeghe; E Hatcher; C Acharya; S Kundu; S Zhong; J Shim; E Darian; O Guvench; P Lopes; I Vorobyov; A D Mackerell
Journal:  J Comput Chem       Date:  2010-03       Impact factor: 3.376

10.  Conformational analysis of thioglycoside derivatives of histo-blood group ABH antigens using an ab initio-derived reparameterization of MM4: implications for design of non-hydrolysable mimetics.

Authors:  Francesco Strino; Jenn-Huei Lii; Hans-Joachim Gabius; Per-Georg Nyholm
Journal:  J Comput Aided Mol Des       Date:  2009-09-15       Impact factor: 3.686

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