TGSA: A molecular superposition program based on topo-geometrical considerations

A theoretical approach to the solvation of brassinosteroids

“…Then a molecular alignment approach with the most relevant local minima obtained by the MMH method in the case of association with one water molecule was performed. This molecular alignment procedure called Topo-Geometrical Superposition Approach (TGSA) [19] allows us to obtain the set of relevant semiempirical local minima, which is later refined using a density functional theory method (DFT), B3LYP with the 6-31G and the 6-31+G* basis set [20]. The PCM method [21,22] has been used to calculate bulk solvent effects.…”

“…Then we used a molecular alignment procedure with the most relevant local minima obtained by the MMH method in the case of association with one water molecule (n = 1). This procedure, called TopoGeometrical Superposition Approach (TGSA) [19], is only based on comparisons of atom types and interatomic distances. Hence, the procedure can handle large molecular sets within affordable computational costs.…”

“…Hence, the procedure can handle large molecular sets within affordable computational costs. This algorithm performs the molecular superposition within a molecular set in two ways: (1) calculating all pairwise alignments; and (2) choosing a molecule as a template [19]. Then we calculate all pairwise alignments between the most important configurations of each brassinosteroids with one molecule of water, to be absolutely sure that no redundant degenerate clusters were obtained for further analysis.…”

“…TGSA [19] is an algorithm that only requires the atomic numbers and coordinates of the molecules to be superposed, it considers the molecules as rigid bodies [39]. In these cases the quality of the superposition, evaluated by the Carbó index [40] is quite high.…”

“…This is in disagreement with our requirements since we need clusters with different configuration and with an important contribution to the partition function. The problem is that as we are applying TGSA [19] to the most important configurations given as a result of the MMH procedure, the solute is the same. Therefore, it is the part of the system that superposes almost entirely and then the only feature that differentiates each configuration from another is the position of the solvent.…”