Abstract
In this work, we introduce TorsiFlex, a user-friendly software written in Python 3 and designed to find all the torsional conformers of flexible acyclic molecules in an automatic fashion. For the mapping of the torsional potential energy surface, the algorithm implemented in TorsiFlex combines two searching strategies: preconditioned and stochastic. The former is a type of systematic search based on chemical knowledge and should be carried out before the stochastic (random) search. The algorithm applies several validation tests to accelerate the exploration of the torsional space. For instance, the optimized structures are stored and this information is used to prevent revisiting these points and their surroundings in future iterations. TorsiFlex operates with a dual-level strategy by which the initial search is carried out at an inexpensive electronic structure level of theory and the located conformers are reoptimized at a higher level. Additionally, the program takes advantage of conformational enantiomerism, when possible. As a case study, and in order to exemplify the effectiveness and capabilities of this program, we have employed TorsiFlex to locate the conformers of the twenty proteinogenic amino acids in their neutral canonical form. TorsiFlex has produced a number of conformers that roughly doubles the amount of the most complete work to date.Graphical
Highlights
Flexible molecules are prone to adopt different geometries due to the internal rotation about single bonds
This section summarizes the results for the twenty proteinogenic amino acids
If the summation of Eq 16 is restricted to the conformers associated with the stochastic search, χst, we find that at T = 300 K this contribution is generally small, with the exception of two amino acids, Trp, and Met, for which the contribution is larger than 5%, but none of the cases reached 10%
Summary
Flexible molecules are prone to adopt different geometries due to the internal rotation about single bonds. Each of these equilibrium structures is represented by a unique spatial configuration, that is, a conformational isomer. The search and location of equilibrium structures in flexible molecules with multiple internal rotations demands an efficient sampling of the torsional potential energy surface (PES). For systems of more modest size and for the location of the lowenergy conformers, it is possible to adopt semiempirical tight-binding [20], or a combination of low-level quantum mechanics (QM) and molecular mechanics methods (MM) [21]
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