The Use of the GSAM Approach for the Structural Investigation of Low-Lying Isomers of Molecular Clusters from Density-Functional-Theory-Based Potential Energy Surfaces: The Structures of Microhydrated Nucleic Acid Bases

Abstract

This study presents structural properties of microhydrated nucleic acid bases (NABs) - uracil (U), thymine (T), guanine (G), adenine (A), and cytosine (C) - investigated by theoretical computations at the B3LYP level of theory. To obtain the different representations of these microhydrated species, we applied the GSAM procedure: the most stable conformers labeled X,nH2O (X = U, T, G, A and n = 1...5) for which the Boltzmann population is higher than 2% at 298K are calculated at the B3LYP and B3LYP-D levels of theory. At the B3LYP level, our calculated geometries are compared with those obtained in the literature. New physically relevant isomers are found with the GSAM algorithm, especially for the tetra- and pentahydrated species. The use of DFT-D functional does not strongly modify the relative energies of the isomers for the monohydrated species. When the number of water molecules increases, the results become extremely sensitive to the consideration of dispersion contributions.

Microhydration Effects on the Ultrafast Photodynamics of Cytosine: Evidences for a Possible Hydration‐Site Dependence

“…In general, our computation results are consistent with previous studies regarding the stability order among Cy•H 2 Oi somers. [8,23,24,[32][33][34][35][36][37][38][39] TheG 4MP2 energies agree very well with the more accurate CCSD(T) results.H owever,w ef ound that wB97XD fails to predict the correct stability order of the keto and enol forms of Cy monomer (see the Supporting Information), and therefore, wB97XD results should be considered only for binding-site isomers of the same Cy tautomers.…”

“…Thew ater binding sites are denoted as A, B, and C,f ollowing the labeling conventions used by other authors. [32][33][34] Fork eto-Cy, site A is at the sugar edge, whereas sites B and C are along the Watson-Crick edge. In general, our computation results are consistent with previous studies regarding the stability order among Cy•H 2 Oi somers.…”

Quantum chemical MP2 results on some hydrates of cytosine: binding sites, energies and the first hydration shell

“…DFT calculations give a larger difference, roughly between 1.0-1.5 kcal mol À1 . 8,13,20 As noted above, the new B3LYP-D fails here, giving a virtually zero…”

“…Two sets of literature results are included in Table 2 for comparison: traditional B3LYP/DZP++ calculations by Kim and Schaefer 13 and an intriguing recent study by Thicoipe et al 20 The latter authors used a global search algorithm (GSAM) to find the microhydrated forms, with up to five water molecules (and for all the five nucleic acid bases). The QC method they used was DFT (B3LYP and B3LYP-D, with the 6-311+G(d,p) basis set).…”

Microhydration Effects on the Ultrafast Photodynamics of Cytosine: Evidences for a Possible Hydration‐Site Dependence

“…A more thorough list of Cy⋅H 2 O isomers are given in the Supporting Information. The water binding sites are denoted as A , B , and C , following the labeling conventions used by other authors 32–34. For keto‐Cy, site A is at the sugar edge, whereas sites B and C are along the Watson–Crick edge.…”