Exploring the influence of metal cations on individual hydrogen bonds in Watson-Crick guanine-cytosine DNA base pair: An interacting quantum atoms analysis.

This study delves into the nature of individual hydrogen bonds and the relationship between metal cations and hydrogen bonding in the Watson-Crick guanine-cytosine (GC) base pair and its alkali and alkaline earth cation-containing complexes (Mn+-GC). The findings reveal how metal cations affect the nature and strength of individual hydrogen bonds. The study employs interacting quantum atoms (IQA) analysis to comprehensively understand three individual hydrogen bonds within the GC base pair and its cationic derivatives. These analyses unveil the nature and strength of hydrogen bonds and serve as a valuable reference for exploring the impact of cations (and other factors) on each hydrogen bond. All the H ⋯ $$ \cdots $$ D interactions (H is hydrogen and D is oxygen or nitrogen) in the GC base pair are primarily electrostatic in nature, with the charge transfer component playing a substantial role. Introducing a metal cation perturbs all H ⋯ $$ \cdots $$ D interatomic interactions in the system, weakening the nearest hydrogen bond to the cation (indicated by a) and reinforcing the other (b and c) interactions. Notably, the interaction a, the strongest H ⋯ $$ \cdots $$ D interaction in the GC base pair, becomes the weakest in the Mn+-GC complexes. A broader perspective on the stability of GC and Mn+-GC complexes is provided through interacting quantum fragments (IQF) analysis. This approach considers all pairwise interactions between fragments and intra-fragment components, offering a complete view of the factors that stabilize and destabilize GC and Mn+-GC complexes. The IQF analysis underscores the importance of electron sharing, with the dominant contribution arising from the inter-fragment exchange-correlation term, in shaping and sustaining GC and Mn+-GC complexes. From this point of view, alkaline and alkaline earth cations have distinct effects, with alkaline cations generally weakening inter-fragment interactions and alkaline earth cations strengthening them. In addition, IQA and IQF calculations demonstrate that the hydration of cations led to small changes in the hydrogen bonding network. Finally, the IQA interatomic energies associated with the hydrogen bonds and also inter-fragment interaction energies provide robust indicators for characterizing hydrogen bonds and complex stability, showing a strong correlation with total interaction energies.

Pnicogen bonds: a theoretical study based on the Laplacian of electron density.

Although, most of the authors classify the pnicogen bonds as σ-hole bonding, there are some evidence that show they do not require any positive electrostatic potential around interacting molecules. In this work, the Laplacian of electron density is used to study pnicogen bonds in different dimer and trimer complexes. It is shown that the noncovalent P···P, P···N, and N···N bonds can be categorized as lump-hole interactions; a region of charge depletion and excess kinetics energy (hole) in the valence shell charge concentration (VSCC) of pnicogen atom combines with a region of charge concentration and excess potential energy (lump) in the VSCC of another molecule and form a pnicogen bond. In fact, since the full quantum potential (according to the local statement of virial theorem) has been used in the definition of the Laplacian, the lump-hole concept is more useful than the σ-hole in which the electrostatic part of potential is only considered. It is shown that the existence of hole in the VSCC of pnicogen atom is responsible for formation and (in the absence of other interactions) geometry of pnicogen bonded complexes. Because there is (at least) one hole in their VSCC, the pnicogen atoms in PH3, PH2F, H2C═PH, H2C═PF, and NH2F can engage in direct pnicogen-pnicogen interactions. However, the VSCC of nitrogen atom in the NH3 is devoid of hole and hence cannot act as an electron acceptor in pnicogen-bonded complexes.

Characteristics of beryllium bonds; a QTAIM study.

The nature of beryllium bonds formed between BeX2 (X is H, F and Cl) and some Lewis bases have been investigated. The distribution of the Laplacian of electron density shows that there is a region of charge depletion around the Be atom, which, according to Laplacian complementary principal, can interact with a region of charge concentration of an atom in the base and form a beryllium bond. The molecular graphs of the investigated complexes indicate that beryllium in BeH2 and BeF2 can form "beryllium bonds" with O, N and P atoms but not with halogens. In addition, eight criteria based on QTAIM properties, including the values of electron density and its Laplacian at the BCP, penetration of beryllium and acceptor atom, charge, energy, volume and first atomic moment of beryllium atom, have been considered and compared with the corresponding ones in conventional hydrogen bonds. These bonds share many common features with very strong hydrogen bonds, however,some differences have also been observed.