Publications

The investigated co-crystal of 3-chloro-N-methyl­pyridinium iodide with tetra­bromo­quinone (3-Cl-N-MePy⋅I⋅Br₄Q) reveals a π-hole interaction between an iodide anion and a quinoid ring involving an n → π* charge transfer. The quinoid ring has a partial negative charge (estimated to be in the range 0.08–0.11e) and a partial radical character, which is related to the black colour of the crystals (crystals of neutral tetra­bromo­quinone are yellow). A detailed X-ray charge density study revealed two symmetry-independent bond critical points between the iodide anions and carbon atoms of the ring. Their maximum electron density of 0.065eÅ⁻3 was reproduced by quantum chemical modelling. The energy of the interaction is estimated to be -11.16kcalmol⁻1, which is comparable to the strength of moderate hydrogen bonding (about -10kcalmol⁻1); it is dominantly electrostatic in nature, with a considerable dispersion component.

The mutual penetration of electron densities between two interacting molecules complicates the computation of an accurate electrostatic interaction energy based on a pseudo-atom representation of electron densities. The numerical exact potential and multipole moment (nEP/MM) method is time-consuming since it performs a 3D integration to obtain the electrostatic energy at short interaction distances. Nguyen et al. [(2018), Acta Cryst. A 74, 524–536] recently reported a fully analytical computation of the electrostatic interaction energy (aEP/MM). This method performs much faster than nEP/MM (up to two orders of magnitude) and remains highly accurate. A new program library, Charger, contains an implementation of the aEP/MM method. Charger has been incorporated into the MoProViewer software. Benchmark tests on a series of small molecules containing only C, H, N and O atoms show the efficiency of Charger in terms of execution time and accuracy. Charger is also powerful in a study of electrostatic symbiosis between a protein and a ligand. It determines reliable protein–ligand interaction energies even when both contain S atoms. It easily estimates the individual contribution of every residue to the total protein–ligand electrostatic binding energy. Glutathione transferase (GST) in complex with a benzophenone ligand was studied due to the availability of both structural and thermodynamic data. The resulting analysis highlights not only the residues that stabilize the ligand but also those that hinder ligand binding from an electrostatic point of view. This offers new perspectives in the search for mutations to improve the interaction between the two partners. A proposed mutation would improve ligand binding to GST by removing an electrostatic obstacle, rather than by the traditional increase in the number of favourable contacts.

The crystal structure of lithium 2,5-dihydroxyquinonate dihydrate bis­(dimethyl sulfoxide) solvate (Li2DHQ­(H2O)2(DMSO)2) reveals a close contact between the lone pair on the electropositive S atom of DMSO and the dianionic quinoid ring. This contact, resembling a π-hole interaction involving a dianion as an acceptor, was studied in detail by a combination of X-ray charge density and quantum chemical modeling. The topology of electron density reveals a bond path and a (3, −1) critical point between the S atom of the DMSO and a C atom of the quinoid ring, while an analysis of the electrostatic potential indicates that the interaction between these two atoms is repulsive. However, the global electrostatic interaction between the DMSO and the dihydroxyquinonate moieties is attractive (−19.1 kJ/mol), as well as the total in vacuo interaction energy (−42.8 kJ/mol).

The complex trans-[RuNO(NH₃)₄F]SiF₆ was synthesized in quantitative yield and the structure was characterized by X-ray diffraction and spectroscopic methods. The complex crystallizes in the non-centrosymmetric space group Pn. Hirshfeld surface analysis revealed that the dominant intermolecular inter­actions are of types H⋯F and F⋯O, which are likely to be responsible for the packing of the molecules in a non-centrosymmetric structure. Irradiation with blue light leads to the formation of Ru–ON (metastable state MS1) and Ru–η²-(NO) (metastable state MS2) bond isomers, as shown by IR and UV–Vis spectroscopy. The structural features of the MS1 isomer were elucidated by photocrystallography. The complex exhibits exceptionally good thermal stability of the metastable state MS1, such that it can be populated by light at 290–300K, which is important for potential applications. The second harmonic (SH) emission can be generated by femtosecond-pulsed irradiation of the complex. The generated SH is rather efficient and stable under long-term exposure. Finally, since both metastable states and harmonic generation can be generated at room temperature, an attempt to drive the SH response by photoisomerization of the nitro­syl ligand was made and is discussed.

Herein, we present a detailed X-ray charge density study of the electron delocalization in five species of chloranilic acid: neutral molecule, mono- and dianion, and two chelating modes: bidendate and (bis)­bidentate. The experiments provide the electron density at the bond critical points, which yields an accurate measure of bond order (and therefore electron delocalization), and complement previous literature and our data on bond lengths extracted from crystal structures and infrared spectra. Mapping of the electrostatic potential indicates electron-rich and electron-poor areas in the molecule, corresponding to single (electron-poor), double, and delocalized bonds (electron-rich) that can explain stacking interactions of quinoid rings in crystal packing.

Even with decades of research, purine nucleoside phosphorylases (PNPs) are enzymes whose mechanism is yet to be fully understood. This is especially true in the case of hexameric PNPs, and is probably, in part, due to their complex oligomeric nature and a whole spectrum of active site conformations related to interactions with different ligands. Here we report an extensive structural characterization of the apo forms of hexameric PNP from Helicobacter pylori (HpPNP), as well as its complexes with phosphate (Pi) and an inhibitor, formycin A (FA), together with kinetic, binding, docking and molecular dynamics studies. X-ray structures show previously unseen distributions of open and closed active sites. Microscale thermophoresis results indicate that a two-site model describes Pi binding, while a three-site model is needed to characterize FA binding, irrespective of Pi presence. The latter may be related to the newly found nonstandard mode of FA binding. The ternary complex of the enzyme with Pi and FA shows, however, that Pi binding stabilizes the standard mode of FA binding. Surprisingly, HpPNP has low affinity towards the natural substrate adenosine. Molecular dynamics simulations show that Pi moves out of most active sites, in accordance with its weak binding. Conformational changes between nonstandard and standard binding modes of nucleoside are observed during the simulations. Altogether, these findings show some unique features of HpPNP and provide new insights into the functioning of the active sites, with implications for understanding the complex mechanism of catalysis of this enzyme. Databases The atomic coordinates and structure factors have been deposited in the Protein Data Bank: with accession codes 6F52 (HpPNPapo_1), 6F5A (HpPNPapo_2), 6F5I (HpPNPapo_3), 5LU0 (HpPNP_PO4), 6F4W (HpPNP_FA) and 6F4X (HpPNP_PO4_FA). Enzymes Purine nucleoside orthophosphate ribosyl transferase, EC2.4.2.1, UniProtID: P56463

Cancer research pointed to the importance of genes involved in replication and reestablishment of chromatin in oncogenesis. Gene dysfunction in tumours is often associated with epigenetic changes. The aim of this study was to analyse DNA methylation of regulatory regions of genes GMNN and EZH2 in diffuse large B-cell lymphoma subtypes. Methylation assays were developed for the analysis of those regions at single CpG site resolution. Primers for PCR-amplification of bisulfite treated DNA fragments were designed. PCR conditions were optimized for the amplification of three and four fragments of regulatory region of GMNN and EZH2, respectively. Subsequently, optimal conditions for pyrosequencing were determined. Finally, one assay per gene was created. Newly developed assays were used in the analysis of diffuse large B-cell lymphoma subtypes. The results showed no statistically significant difference between the subtypes. Since the analysis covered only a small part of the regulatory regions of GMNN and EZH2, the study should be expanded to additional CpG sites and repeated on a larger group of patients.