Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairsстатья
Информация о цитировании статьи получена из
Web of Science,
Scopus
Статья опубликована в журнале из списка Web of Science и/или Scopus
Дата последнего поиска статьи во внешних источниках: 4 марта 2022 г.
Аннотация:The model of Regularized Quantum Mechanical Force Field (RQMFF) was applied to the jointtreatment of ab initio and experimental vibrational data of the four primary nucleobases using a newalgorithm based on the scaling procedure in Cartesian coordinates. The matrix of scaling factorsin Cartesian coordinates for the considered molecules includes diagonal elements for all atoms ofthe molecule and off-diagonal elements for bonded atoms and for some non-bonded atoms (1–3and some 1–4 interactions). The choice of the model is based on the results of the second-orderperturbation analysis of the Fock matrix for uncoupled interactions using the Natural Bond Orbital(NBO) analysis. The scaling factors obtained within this model as a result of solving the inverseproblem (regularized Cartesian scale factors) of adenine, cytosine, guanine, and thymine moleculeswere used to correct the Hessians of the canonical base pairs: adenine–thymine and cytosine–guanine.The proposed procedure is based on the block structure of the scaling matrix for molecular entitieswith non-covalent interactions, as in the case of DNA base pairs. It allows avoiding introducinginternal coordinates (or coordinates of symmetry, local symmetry, etc.) when scaling the force field ofa compound of a complex structure with non-covalent H-bonds.