Literature DB >> 21562655

Practical methods for including torsional anharmonicity in thermochemical calculations on complex molecules: the internal-coordinate multi-structural approximation.

Jingjing Zheng1, Tao Yu, Ewa Papajak, I M Alecu, Steven L Mielke, Donald G Truhlar.   

Abstract

Many methods for correcting harmonic partition functions for the presence of torsional motions employ some form of one-dimensional torsional treatment to replace the harmonic contribution of a specific normal mode. However, torsions are often strongly coupled to other degrees of freedom, especially other torsions and low-frequency bending motions, and this coupling can make assigning torsions to specific normal modes problematic. Here, we present a new class of methods, called multi-structural (MS) methods, that circumvents the need for such assignments by instead adjusting the harmonic results by torsional correction factors that are determined using internal coordinates. We present three versions of the MS method: (i) MS-AS based on including all structures (AS), i.e., all conformers generated by internal rotations; (ii) MS-ASCB based on all structures augmented with explicit conformational barrier (CB) information, i.e., including explicit calculations of all barrier heights for internal-rotation barriers between the conformers; and (iii) MS-RS based on including all conformers generated from a reference structure (RS) by independent torsions. In the MS-AS scheme, one has two options for obtaining the local periodicity parameters, one based on consideration of the nearly separable limit and one based on strongly coupled torsions. The latter involves assigning the local periodicities on the basis of Voronoi volumes. The methods are illustrated with calculations for ethanol, 1-butanol, and 1-pentyl radical as well as two one-dimensional torsional potentials. The MS-AS method is particularly interesting because it does not require any information about conformational barriers or about the paths that connect the various structures.

Entities:  

Year:  2011        PMID: 21562655     DOI: 10.1039/c0cp02644a

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  12 in total

1.  Conformational analysis of a polyconjugated protein-binding ligand by joint quantum chemistry and polarizable molecular mechanics. Addressing the issues of anisotropy, conjugation, polarization, and multipole transferability.

Authors:  Elodie Goldwaser; Benoit de Courcy; Luc Demange; Christiane Garbay; Françoise Raynaud; Reda Hadj-Slimane; Jean-Philip Piquemal; Nohad Gresh
Journal:  J Mol Model       Date:  2014-11-01       Impact factor: 1.810

2.  Computational Kinetics by Variational Transition-State Theory with Semiclassical Multidimensional Tunneling: Direct Dynamics Rate Constants for the Abstraction of H from CH3OH by Triplet Oxygen Atoms.

Authors:  Rubén Meana-Pañeda; Xuefei Xu; He Ma; Donald G Truhlar
Journal:  J Phys Chem A       Date:  2017-02-15       Impact factor: 2.781

3.  Unimolecular reaction of acetone oxide and its reaction with water in the atmosphere.

Authors:  Bo Long; Junwei Lucas Bao; Donald G Truhlar
Journal:  Proc Natl Acad Sci U S A       Date:  2018-05-29       Impact factor: 11.205

4.  Application of one-dimensional semiclassical transition state theory to the CH3OH + H ⇌ CH2OH/CH3O + H2 reactions.

Authors:  Xiao Shan; David C Clary
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2018-03-13       Impact factor: 4.226

5.  Investigation on the Thermal Dissociation of Vinyl Nitrite with a Saddle Point Involved.

Authors:  Yulei Guan; Junpeng Lou; Haixia Ma; Jirong Song
Journal:  ACS Omega       Date:  2019-09-16

6.  Anharmonic kinetics of the cyclopentane reaction with hydroxyl radical.

Authors:  Junjun Wu; Lu Gem Gao; Wei Ren; Donald G Truhlar
Journal:  Chem Sci       Date:  2020-01-25       Impact factor: 9.825

7.  Fully anharmonic IR and Raman spectra of medium-size molecular systems: accuracy and interpretation.

Authors:  Vincenzo Barone; Malgorzata Biczysko; Julien Bloino
Journal:  Phys Chem Chem Phys       Date:  2014-02-07       Impact factor: 3.676

8.  Accurate structure, thermodynamic and spectroscopic parameters from CC and CC/DFT schemes: the challenge of the conformational equilibrium in glycine.

Authors:  Vincenzo Barone; Malgorzata Biczysko; Julien Bloino; Cristina Puzzarini
Journal:  Phys Chem Chem Phys       Date:  2013-04-19       Impact factor: 3.676

9.  Calculation of absolute molecular entropies and heat capacities made simple.

Authors:  Philipp Pracht; Stefan Grimme
Journal:  Chem Sci       Date:  2021-03-25       Impact factor: 9.825

10.  Multi-path variational transition state theory for chiral molecules: the site-dependent kinetics for abstraction of hydrogen from 2-butanol by hydroperoxyl radical, analysis of hydrogen bonding in the transition state, and dramatic temperature dependence of the activation energy.

Authors:  Junwei Lucas Bao; Rubén Meana-Pañeda; Donald G Truhlar
Journal:  Chem Sci       Date:  2015-06-16       Impact factor: 9.825

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