The Distance between Minima of Electron Density and Electrostatic Potential as a Measure of Halogen Bond Strength

Dynamics of non-covalent interactions during the P-O bond cleavage reaction by ribonuclease A

In this work, an atomistic-scale investigation of the phosphodiester P-O bond cleavage reaction by the enzyme ribonuclease A was carried out using computer simulation techniques. It is shown that during the reaction the network of non-covalent interactions in the active center of the ribonuclease changes significantly, while the role of these non-covalent interactions is different: coordination of the corresponding groups, electron density transfer, and ligand holding in the active center. It is shown that the process of proton transfer from Asp121 to His119 is the first stage of this reaction; at the same time, the hydrogen bond between the phosphate ligand and the imino group of Arg39 is broken, which, although keeping the ligand in the active center, does not allow the ligand to orient itself more conveniently for subsequent proton transfers. Furthermore, the key step of this reaction occurs: proton transfer with the participation of imidazole rings His12 and His119, in which the guiding role is played by several hydrogen bonds with the participation of Phe120, and the role of an electron density carrier is played by the pnictogen bond between the oxygen of the phosphate ligand and the pyridine-like nitrogen of the imidazole ring His119, which was detected for the first time.

Unveiling the electronic structure peculiarities of phosphine selenides as NMR probes for non-covalent interactions: an experimental and theoretical study

In this work, R3PSe (R = Me, Et, n-Bu, t-Bu and Ph) were studied experimentally using NMR spectroscopy in solution and the solid-state in combinaton with quantum chemical methods. The study shows that the NMR parameters of these phosphine selenides, such as δP, δSe, and 1JPSe, are sensitive to subtle changes in the electronic environment of the P and Se atoms. Consequently, phosphine selenides R3PSe can serve as promising spectral probes for the detection and quantitative investigation of various non-covalent interactions. Additionally, the variations of R in phosphine selenides influence the observed NMR spectral parameters, primarily through effects such as π-backdonation and hyperconjugation, which have been observed experimentally and confirmed theoretically.

Mutual influence of non-covalent interactions formed by imidazole: A systematic quantum-chemical study

Imidazole is a five-membered heterocycle that is part of a number of biologically important molecules such as the amino acid histidine and the hormone histamine. Imidazole has a unique ability to participate in a variety of non-covalent interactions involving the NH group, the pyridine-like nitrogen atom or the π-system. For many biologically active compounds containing the imidazole moiety, its participation in formation of hydrogen bond NH⋯O/N and following proton transfer is the key step of mechanism of their action. In this work a systematic study of the mutual influence of various paired combinations of non-covalent interactions (e.g., hydrogen bonds and π-interactions) involving the imidazole moiety was performed by means of quantum chemistry (PW6B95-GD3/def2-QZVPD) for a series of model systems constructed based on analysis of available x-ray data. It is shown that for considered complexes formation of additional non-covalent interactions can only enhance the proton-donating ability of imidazole. At the same time, its proton-accepting ability can be both enhanced and weakened, depending on what additional interactions are added to a given system. The mutual influence of non-covalent interactions involving imidazole can be classified as weak geometric and strong energetic cooperativity-a small change in the length of non-covalent interaction formed by imidazole can strongly influence its strength. The latter can be used to develop methods for controlling the rate and selectivity of chemical reactions involving the imidazole fragment in larger systems. It is shown that the strong mutual influence of non-covalent interactions involving imidazole is due to the unique ability of the imidazole ring to effectively redistribute electron density in non-covalently bound systems with its participation.

Can We Merge the Weak and Strong Tetrel Bonds? Electronic Features of Tetrahedral Molecules Interacted with Halide Anions

Using the orbital-free quantum crystallography approach, we have disclosed the quantitative trends in electronic features for bonds of different strengths formed by tetrel (Tt) atoms in stable molecular complexes consisting of electrically neutral tetrahedral molecules and halide anions. We have revealed the role of the electrostatic and exchange-correlation components of the total one-electron static potential that are determined by the equilibrium atomic structure and by kinetic Pauli potential, which reflects the spin-dependent electron motion features of the weak and strong bonds. The gap between the extreme positions in the electrostatic and total static potentials along the line linking the Tt atom and halide anion is wide for weak bonds and narrow for strong ones. It is in very good agreement with the number of minima in the Pauli potential between the bounded atoms. This gap exponentially correlates with the exchange-correlation potential in various series with a fixed nucleophilic fragment. A criterion for categorizing the noncovalent tetrel bonds (TtB) based on the potential features is suggested.