Comparative Antibacterial Analysis of the Anthraquinone Compounds Based on the AIM Theory and Molecular Docking Analysis

Hydroxyanthraquinones and anthraquinone glucoside derivatives are always considered as the active antibacterial components. In the present text, a comprehensive comparison and analysis of these compounds were performed for their structure characteristics and antibacterial effect by applying quantum chemical calculations, atoms in molecules theory and molecular docking procedure. The molecular geometric configuration, electrostatic potential, the frontier orbital energies and topological properties were analyzed. Once glucose ring is introduced into the hydroxyanthraquinone rings, almost all of the positive molecular potentials are distributed among the hydroxyl hydrogen atoms of the glucose rings. The anthraquinone glucoside compounds have generally higher intermolecular binding energies than the corresponding aglycones due to the strong interaction between the glucose rings and the surrounding amino acids. Once glucoside ring is introduced into the emodin, low electron density ρ(r) and positive Laplacian value of the O-H bond are the evidences of the highly polarized and covalently decreased bonding interactions. The type of carboxyl, hydroxyl, hydroxylmethyl groups on phenyl ring and the substituent glucose rings are important to the interactions with the topoisomerase type II enzyme DNA gyrase B.

Weak Interactions in the Structures of Newly Synthesized (–)-Cytisine Amino Acid Derivatives

Eight new (–)-(N-[(AA)-(N-phtaloyl)]cytisines (where AA is amino acid: glycine, β-alanine, D,L-valine, L-valine, L-isoleucine, L-leucine, D-leucine and D,L-phenyloalanine), were synthesized and fully spectroscopically characterized (NMR, FTIR and MS). For two of these compounds, N-[glycine-(N-phtaloyl)]cytisine and N-[L-isoleucine-(N-phtaloyl)]cytisine, X-ray crystal structures were obtained and used as the basis for an in-depth analysis of intermolecular interactions and packing energies. The structural geometrical data (weak hydrogen bonds, π···π interactions, etc.) were compared with the energies of interactions and the topological characteristics (electron density, Laplacian at the appropriate critical point) based on the atoms-in-molecules theory. The results suggest that there is no straightforward connection between the geometry of point-to-point interactions and the molecule-to-molecule energies. Additionally, the usefulness of the transfer of multipolar parameters in estimating of critical points’ characteristics have been confirmed.

Experimental and Theoretical Study on the Interaction of P-Aminophenol Hydrochloride with H2O

UV-Vis absorption spectra, cyclic voltammetry and 1H nuclear magnetic resonance (1H NMR) spectra were applied to explore the hydrogen bond interactions of p-aminophenol hydrochloride (PAH) with H2O. The results indicated the hydrogen bonds were formed in PAH–H2O system. The anodic/cathodic peak potentials and UV-Vis absorption bands of PAH in H2O could be affected due to the interactions. The results of density functional theory, atoms in molecules theory and natural bond orbital analyses further confirmed the existence of hydrogen bonds between the phenolic hydroxyl, –NH3+ protons and Cl− of PAH and H2O. Furthermore, the π-π stacking was suggested between PAH benzene rings from the 1H NMR spectra at higher concentrations.

Short is strong: experimental electron density in a very short N···I halogen bond

2,3,5,6-Tetrafluoro-1,4-diiodobenzene and 4-(dimethylamino)pyridine co-crystallize in 1:2 stoichiometry. A diffraction experiment at standard resolution was already conducted in 2010 and revealed one of the shortest N···I contacts ever reported. We collected X-ray intensities at 100 K up to a very high resolution of 1.23 Å−1. These experimental data allowed to refine a structure model based on atom-centered multipoles according to the Hansen-Coppens approach and provided an experimental electron density. A subsequent analysis with the help of Bader’s atoms in molecules theory showed a strong interaction between the pyridine N atom and the σ hole of its closest iodine neighbor on the halogenated benzene. This contact is characterized by a distance of 2.6622(4) Å and associated with a remarkably large electron density of 0.359(5) e⋅Å−3 in the (3, −1) critical point, unprecedented for a secondary interaction. This bona fide shortest halogen bond ever investigated by an experimental charge density study is associated with a significantly negative total energy density in the bond critical point and thus can reliably be classified as strong. Both the electron density and the position of the bond critical point suggest to compare the short N···I contact to coordinative or covalent bonds rather than to σ hole interactions.

Atomic decomposition of conceptual DFT descriptors: application to proton transfer reactions

We present an atomic decomposition of the molecular energy, reaction force and reaction flux, which is based on Bader's atoms-in-molecules theory.