Santos LA, da Cunha EFF, Freitas MP, Ramalho TC. Hydrophobic noncovalent interactions of inosine-phenylalanine: a theoretical model for investigating the molecular recognition of nucleobases.
J Phys Chem A 2014;
118:5808-17. [PMID:
24814712 DOI:
10.1021/jp411230w]
[Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Understanding the molecular recognition process of nucleobases is one of the greatest challenges for both computational chemistry and biophysics fields. In fact, our results point out that it is a hard task to take into account the hydrophobic interactions, such as π-π and T-stacking interactions, by theoretical calculations using conventional force fields due to quantum effects of hyperconjugation and electronic correlation. In this line, our findings put in evidence that simple modifications in the Lennard-Jones potential can improve theoretical predictions in scenarios where hydrophobic interactions can drive the molecular recognition.
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