Theoretical understanding of the ABC persistent structure in strongly H-bonded systems: Computational analysis of phosphonic and bis-(heptafluoropropyl) phosphonic acid dimers in gas phase

Abstract

Hydrogen bonds (HBs) that involve direct interaction with fluorine have been the subject of considerable research; however, the indirect influence of fluorine on the dynamics of the strongly hydrogen bonded systems as well as on neighboring donor and acceptor molecules remains inadequately understood and challenging to anticipate. In this paper, we present a theoretical analysis of the infrared absorption spectra of two different phosphinic acids in the gaseous state, R${}_2$POOH, namely the phosphinic acid (where R = H${}_2$ ) and the bis-(heptafluoropropyl) phosphonic acid (where R = C${}_3$F${}_7$). within the spectral range 750–3500 cm${}^{-1}$ at a temperature domain of 345–500 K (Aslin et al., 2002). The equilibrium between the dimers and monomers, giving rise to the stability of the recorded spectra, is experimentally obtained at T =500 K. The resulting band has the characteristic of an ABC structure (Hadzi structure), which is typical to the spectra of structures characterized by exceptionally strong hydrogen bonds in solution and in crystal phase. The experimental spectra is contrasted with the one computationally determined using a theoretical model that congregates, Fermi resonances, Davydov coupling, the theory of strong anharmonic coupling and the effect of the reversible action of the medium on the anharmonic vibrational modes altogether with the same approach dealing with Kubo’s linear response theory. A satisfactory superimposition between the numerically generated spectra and the experimental infrared absorption spectra is elucidated. The theoretical analysis is performed through the examination of the effect of the commonly employed theories and approximations in order to illuminate how to numerically simulate the ABC structure. The method offers a clear explanation for the Hadzi structure’s formation by demonstrating that the BC diad is produced by the Fermi resonance mechanism, while the peak A is caused by the Davydov coupling mechanism. The clarification of the dynamics and the function of fluorine in hydrogen bonding could signify a notable progress in creating a comprehensive simulation tool designed to forecast the infrared absorption bands of compounds exhibiting strong and very strong hydrogen bonds, along with their interactions and affinity with DNA polymerase. This tool might make it possible to conduct methodical research on the intricate relationship between fluorine’s direct and indirect effects on the properties of physiologically active compounds and how they interact with drug-like targets.