Combined analysis of chemical bonding in a CuIIdimer using QTAIM, Voronoi tessellation and Hirshfeld surface approaches

Ligand-Receptor Interactions of Lamivudine: A View from Charge Density Study and QM/MM Calculations

The nature and strength of interactions for an anti-HIV drug, Lamivudine, were studied in a pure crystal form of the drug and the ligand–receptor complexes. High-resolution single-crystal X-ray diffraction studies of the tetragonal polymorph allowed the drug’s experimental charge density distribution in the solid state to be obtained. The QM/MM calculations were performed for a simplified model of the Lamivudine complex with deoxycytidine kinase (two complexes with different binding modes) to reconstruct the theoretical charge density distribution. The peculiarities of intramolecular interactions were compared with previously reported data for an isolated molecule. Intermolecular interactions were revealed within the quantum theory of ‘Atoms in Molecules’, and their contributions to the total crystal energy or ligand–receptor binding energy were evaluated. It was demonstrated that the crystal field effect weakened the intramolecular interactions. Overall, the energies of intermolecular interactions in ligand–receptor complexes (320.1–394.8 kJ/mol) were higher than the energies of interactions in the crystal (276.9 kJ/mol) due to the larger number of hydrophilic interactions. In contrast, the sum of the energies of hydrophobic interactions was found to be unchanged. It was demonstrated by means of the Voronoi tessellation that molecular volume remained constant for different molecular conformations (250(13) Å3) and increased up to 399 Å3 and 521(30) Å3 for the Lamivudine phosphate and triphosphate.

Charge density analysis of abiraterone acetate

A high-resolution single-crystal X-ray diffraction study of abiraterone acetate (1) has been carried out. The charge density distribution in the crystal of this anticancer drug is reconstructed from experimental data. The nature and the contributions of various intermolecular interactions to the total crystal energy are studied by means of the quantum theory `Atoms-in-Molecules', a non-covalent interactions method and energy framework plots. In general, dispersion C-H...H-C and C-H...π interactions play the main role in crystal packing of 1. The Voronoi tessellation analysis of 1 confirmed that contribution of hydrophobic and hydrophilic interactions to the molecular surface is close to their contribution to the total crystal energy. Similar analysis of abiraterone complexes with the cytochrome P450 family demonstrated that contribution of the C-H...H-C and C-H...π interactions to the molecular surface of the drug remains unchanged to fit the binding pocket, despite the presence of water and heme molecules, and hydrophilic groups within the pocket.

Coordination Affinity of Cu(II)-Based Silsesquioxanes toward N,N-Ligands and Associated Skeletal Rearrangements: Cage and Ionic Products Exhibiting a High Catalytic Activity in Oxidation Reactions

An unusual skeletal rearrangement of piperazine into ethylenediamine has been observed for the first time as a result of an attempt to synthesize a piperazine-linked metal-organic framework (MOF) using cage Cu(II),Na-phenylsilsequixane as a potential building block. Instead of the expected "metallasilsesquioxane-based MOF", a Cu₆ complex 1 coordinated both by silsesquioxane and ethylenediamine ligands was isolated. An effort to reproduce this result via direct interaction of Cu-phenylsilsequioxane and ethylenediamine surprisingly afforded two other types of complexes, copper-sodium 2 and copper 3 ionic products. Cationic components in both products 2 and 3 are represented by (i) copper and sodium ions (in the case of 2) or (ii) copper ions exclusively (in the case of 3) coordinated by ethylenediamine ligands. Both complexes 2 and 3 include Si₆-based condensed silsesquioxane fragments serving as anionic components of the products. Symptomatically, the types of the Si₆-frameworks in 2 and 3 are drastically different. More specifically, the Si₆ unit in 2 is an unprecedented distorted silsesquioxane skeleton consisting of two condensed tetramembered rings. Structural features of compounds 1-3 were established by single crystal X-ray diffraction. Compound 2 was found to catalyze the oxidation of cyclohexane to cyclohexanol and cyclohexanone with H₂O₂ (a mixture of these products was obtained after adding PPh₃ to the reaction solution) as well as the transformation of cyclohexanol to cyclohexanone under the action of tert-butyl hydroperoxide.

Peculiarities of Br⋯Br bonding in crystal structures of polybromides and bromine solvates

Analysis of supramolecular associates formed by Br⋯Br interactions in crystals of 204 polybromide and bromine-containing compounds has been carried out.

Solid-State Photoinitiated Cycloaddition Reaction of 4,4′-(Ethene-1,2-diyl)bis(pyridinium) Dinitrate: Charge-Density Perspective on Initial Stage of the Reaction

Solid-state photoinitiated [2 + 2] cycloaddition reaction 2(H2bpe)(NO3)2 → (H4tpcb)(NO3)4 (bpe = 1,2-bis(pyrid-4-yl)ethylene; tpcb = 1,2,3,4-tetrakis(pyrid-4-yl)cyclobutane) was carried out in a single-crystal-to-single-crystal manner. The reaction product was characterized by means of X-ray diffraction and 1H NMR spectroscopy. Only the rctt-isomer of tpcb was found as the reaction product. Intermolecular interactions in a single crystal of (H2bpe)(NO3)2 were studied within the QTAIM approach. Although sum energy of strong and weak hydrogen bonds dominates in total packing energy, contribution of π…π stacking interactions to the packing energy is also prominent. At solid (H2bpe)(NO3)2, stacking of photoreactive H2bpe2+ cations is realized via N…C, C…C and C–H…C bonding, although no four-membered cycles formed by these bond paths was found in molecular graph representation. Reduced density gradient (RDG) surfaces and molecular Voronoi surfaces clearly demonstrate accumulation of charge density between olefin groups prone to take part in photoinitiated cycloaddition reactions. Good correlation between description of hydrogen bonding in terms of QTAIM and Voronoi approaches was demonstrated. The Voronoi approach confirmed that during the photoreaction the system of hydrogen bonds remained almost unchanged.

Towards understanding π-stacking interactions between non-aromatic rings

The first systematic study of π interactions between non-aromatic rings, based on the authors' own results from an experimental X-ray charge-density analysis assisted by quantum chemical calculations, is presented. The landmark (non-aromatic) examples include quinoid rings, planar radicals and metal-chelate rings. The results can be summarized as: (i) non-aromatic planar polyenic rings can be stacked, (ii) interactions are more pronounced between systems or rings with little or no π-electron delocalization (e.g. quinones) than those involving delocalized systems (e.g. aromatics), and (iii) the main component of the interaction is electrostatic/multipolar between closed-shell rings, whereas (iv) interactions between radicals involve a significant covalent contribution (multicentric bonding). Thus, stacking covers a wide range of interactions and energies, ranging from weak dispersion to unlocalized two-electron multicentric covalent bonding ('pancake bonding'), allowing a face-to-face stacking arrangement in some chemical species (quinone anions). The predominant interaction in a particular stacked system modulates the physical properties and defines a strategy for crystal engineering of functional materials.