Euclidean inverses for the characterization of three-dimensional molecular structures

Balasubramanian, K.; Sun, Hongmei

doi:10.1016/s0009-2614(96)01316-4

Cited by 2 publications

(4 citation statements)

References 18 publications

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“…For this reason, Katzer and Sax decided to first identify the bonds in which torsions are possible (free bonds, i.e., single bonds that are not part of a ring). They appeal to topological symmetry, which is the invariance of molecular connectivity under the permutation of atoms (i.e., the topological symmetry does not change due to molecular vibrations) 38,39 . The topology of a molecule is retrieved by its graph.…”

Section: How To Identify and Characterize A Hindered Rotor?mentioning

confidence: 99%

“…They appeal to topological symmetry, which is the invariance of molecular connectivity under the permutation of atoms (i.e., the topological symmetry does not change due to molecular vibrations). 38,39 The topology of a molecule is retrieved by its graph. The atoms and bonds correspond to the vertices, V , and edges, E, of the graph, respectively, and the bond lengths represent the interatomic distances.…”

Section: How To Identify and Characterize A Hindered Rotor?mentioning

confidence: 99%

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The hindered rotor theory: A review

Dzib

Merino

2021

WIREs Comput Mol Sci

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Hindered rotations are common in nature and can greatly affect thermodynamic properties. Typically, the standard rigid-rotor harmonic-oscillator approximation is used to compute thermodynamic properties; however, it often leads to serious errors, particularly for molecules with hindered rotations. Hence, to reach accurate thermodynamic predictions for such cases, the hindered rotor approximation must be applied. Different methods to compute thermodynamic properties for molecules with hindered rotations are available. Herein, we review the theoretical basis of different methods, their accuracy, and applicability. We also present the different algorithms to identify hindered rotors and obtain the input parameters for the hindered rotor model, and the software available to compute thermodynamic properties under this scheme.

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Section: How To Identify and Characterize A Hindered Rotor?mentioning

confidence: 99%

Section: How To Identify and Characterize A Hindered Rotor?mentioning

confidence: 99%

The hindered rotor theory: A review

Dzib

Merino

2021

WIREs Comput Mol Sci

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“…Geometrical symmetry is defined by invariance of the rigid molecular structure with respect to geometrical operations. Similarly, topological symmetry is defined as the invariance of molecular connectivity with respect to atom permutation 13, 14. Molecular connectivity may be represented by chemical graphs.…”

Section: Symmetrymentioning

confidence: 99%

“…It should be pointed out that the principal eigenvalue algorithm can also be applied to the metric matrix (distance matrix), in which case equivalence classes based on geometrical symmetry are obtained 14, 16, 17. Due to the continuous character of the metric matrix, accidental degeneracy appears very unlikely.…”

Section: Symmetrymentioning

confidence: 99%

Identification and thermodynamic treatment of several types of large‐amplitude motions

Katzer¹,

Sax²

2005

J Comput Chem

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We present a partially automated method for the thermodynamic treatment of large-amplitude motions. Starting from the molecular geometry and the Hessian matrix, we evaluate anharmonic partition functions for selected vibrational degrees of freedom. Supported anharmonic vibration types are internal rotation and inversion (oscillation in a double-well potential). By heuristic algorithms, we identify internal rotations in most cases automatically from the Hessian eigenvectors, and we also estimate the parameters of anharmonic partition functions (e.g., potential barrier, periodicity, and symmetry number) with thermodynamically sufficient precision. We demonstrate the validity of our schemes by comparison to pointwise calculated ab initio potential curves.

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Euclidean inverses for the characterization of three-dimensional molecular structures

Cited by 2 publications

References 18 publications

The hindered rotor theory: A review

The hindered rotor theory: A review

Identification and thermodynamic treatment of several types of large‐amplitude motions

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