Abstract
Various methods (Hartree–Fock methods, semi-empirical methods, Density Functional Theory, Molecular Mechanics) used to optimize a molecule structure feature the same basic approach but differ in the mathematical approximations used. The geometry optimization procedure calculates the energy at an initial geometry of a molecule and then proceeds to search a new geometry with a lower energy. Using the 3D structures collected from the PubChem database, 20 amino acid geometry optimization calculations were performed with several methods. The purpose of the study was to analyze these methods (39) to find the relationship between them and to determine which to use under different circumstances. Cluster analysis and principal component analysis were performed to evaluate the similarities between the different methods. The results after the analysis can classified into three main groups and can be selected accordingly to solve different types of problems.
Highlights
Theory, Molecular Mechanics) used to optimize a molecule structure feature the same basic approach but differ in the mathematical approximations used
A basis set is essentially a finite number of atomic-like functions, over which the molecular orbital is formed via linear combination of atomic orbitals (LCAO)
Some recommendations we found in the articles studied and by consulting Gaussian tutorials are: A large basis set is not always the best
Summary
Theory, Molecular Mechanics) used to optimize a molecule structure feature the same basic approach but differ in the mathematical approximations used. The geometry optimization procedure calculates the energy at an initial geometry of a molecule and proceeds to search a new geometry with a lower energy. Using the 3D structures collected from the PubChem database, 20 amino acid geometry optimization calculations were performed with several methods. The purpose of the study was to analyze these methods (39) to find the relationship between them and to determine which to use under different circumstances. Cluster analysis and principal component analysis were performed to evaluate the similarities between the different methods. The results after the analysis can classified into three main groups and can be selected to solve different types of problems
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