Automated handling of complex chemical structures in Z-matrix coordinates-The chemcoord library.
J Comput Chem
; 44(5): 710-726, 2023 Feb 15.
Article
em En
| MEDLINE
| ID: mdl-36541725
ABSTRACT
In this work, we present a fully automated method for the construction of chemically meaningful sets of hierarchical nonredundant internal coordinates (ICs; also commonly denoted as Z-matrices) from the Cartesian coordinates of a molecular system. Particular focus is placed on avoiding ill-definitions of angles and dihedrals due to linear arrangements of atoms, to consistently guarantee a well-defined transformation to Cartesian coordinates, even after structural changes. The representations thus obtained are particularly well suited for pathway construction in double-ended methods for transition state search and optimizations with nonlinear constraints. Analytical gradients for the transformation between the coordinate systems were derived for analytical geometry optimizations purely in Z-matrix coordinates. The geometry optimization was coupled with a Symbolic Algebra package to support arbitrary nonlinear constraints in Z-matrix coordinates, while retaining analytical energy gradient conversion. The difference to the commonly used nonhierarchical IC transformations is discussed. Sample applications are provided for a number of common chemical reactions and illustrative examples.
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01-internacional
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MEDLINE
Assunto principal:
Matemática
Idioma:
En
Ano de publicação:
2023
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Article