An Electron Density Source‐Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States^†

Abstract

The source function (SF) decomposes the electron density at any point into contributions from all other points in the molecule, complex, or crystal. The SF "illuminates" those regions in a molecule that most contribute to the electron density at a point of reference. When this point of reference is the bond critical point (BCP), a commonly used surrogate of chemical bonding, then the SF analysis at an atomic resolution within the framework of Bader's Quantum Theory of Atoms in Molecules returns the contribution of each atom in the system to the electron density at that BCP. The SF is used to locate the important regions that control the hydrogen bonds in both Watson-Crick (WC) DNA dimers (adenine:thymine (AT) and guanine:cytosine (GC)) which are studied in their neutral and their singly ionized (radical cationic and anionic) ground states. The atomic contributions to the electron density at the BCPs of the hydrogen bonds in the two dimers are found to be delocalized to various extents. Surprisingly, gaining or loosing an electron has similar net effects on some hydrogen bonds concealing subtle compensations traced to atomic sources contributions. Coarser levels of resolutions (groups, rings, and/or monomers-in-dimers) reveal that distant groups and rings often have non-negligible effects especially on the weaker hydrogen bonds such as the third weak CH⋅⋅⋅O hydrogen bond in AT. Interestingly, neither the purine nor the pyrimidine in the neutral or ionized forms dominate any given hydrogen bond despite that the former has more atoms that can act as source or sink for the density at its BCP. © 2018 Wiley Periodicals, Inc.

Novel Tautomerisation Mechanisms of the Biologically Important Conformers of the Reverse Löwdin, Hoogsteen, and Reverse Hoogsteen G*·C* DNA Base Pairs via Proton Transfer: A Quantum-Mechanical Survey

“…All calculations of the geometries and harmonic vibrational frequencies of the considered base mispairs and transition states of their conversion have been conducted using Gaussian'09 package (Frisch et al, 2010) at the DFT B3LYP/6-311++G(d,p) level of theory (Lee et al, 1988; Parr and Yang, 1989; Tirado-Rives and Jorgensen, 2008), that has been already applied for analogous systems and approved to give accurate geometrical structures, normal mode frequencies, barrier heights, and characteristics of intermolecular H-bonds (Matta, 2010; Arabi and Matta, 2018; Gatti et al, 2018). We have used a scaling factor equal to 0.9668 in order to correct harmonic frequencies for the investigated base pairs (Brovarets' and Hovorun, 2010, 2015f; Brovarets', 2013a,b; Palafox, 2014; El-Sayed et al, 2015; Brovarets' et al, 2018a,b,c,d,e,f; Brovarets' and Tsiupa, 2019).…”

When does a hydrogen bond become avan der Waalsinteraction? a topological answer

“…The value of SF%( AHD ) is used to describe the strength of H‐bond according to Gatti and coworkers . A similar procedure was subsequently performed for the θ ( D − H ⋯ A ) bond angle.…”

Occurrences of protonated base triples in RNA are determined by their cooperative binding energies and specific functional requirements

“…Such a strategy has been shown to reduce the compu-tational cost, without affecting the essential chemical interactions involved. 75 GaussView 76 package has been used to perform the modeling and editing of the initial structures.…”