Serine/Threonine Protein Kinases as Attractive Targets for Anti-Cancer Drugs-An Innovative Approach to Ligand Tuning Using Combined Quantum Chemical Calculations, Molecular Docking, Molecular Dynamic Simulations, and Network-like Similarity Graphs.

Serine/threonine protein kinases (CK2, PIM-1, RIO1) are constitutively active, highly conserved, pleiotropic, and multifunctional kinases, which control several signaling pathways and regulate many cellular functions, such as cell activity, survival, proliferation, and apoptosis. Over the past decades, they have gained increasing attention as potential therapeutic targets, ranging from various cancers and neurological, inflammation, and autoimmune disorders to viral diseases, including COVID-19. Despite the accumulation of a vast amount of experimental data, there is still no "recipe" that would facilitate the search for new effective kinase inhibitors. The aim of our study was to develop an effective screening method that would be useful for this purpose. A combination of Density Functional Theory calculations and molecular docking, supplemented with newly developed quantitative methods for the comparison of the binding modes, provided deep insight into the set of desirable properties responsible for their inhibition. The mathematical metrics helped assess the distance between the binding modes, while heatmaps revealed the locations in the ligand that should be modified according to binding site requirements. The Structure-Binding Affinity Index and Structural-Binding Affinity Landscape proposed in this paper helped to measure the extent to which binding affinity is gained or lost in response to a relatively small change in the ligand's structure. The combination of the physico-chemical profile with the aforementioned factors enabled the identification of both "dead" and "promising" search directions. Tests carried out on experimental data have validated and demonstrated the high efficiency of the proposed innovative approach. Our method for quantifying differences between the ligands and their binding capabilities holds promise for guiding future research on new anti-cancer agents.

Butterfly Effect in Cytarabine: Combined NMR-NQR Experiment, Solid-State Computational Modeling, Quantitative Structure-Property Relationships and Molecular Docking Study.

Cytarabine (Ara-C) is a synthetic isomer of cytidine that differs from cytidine and deoxycytidine only in the sugar. The use of arabinose instead of deoxyribose hinders the formation of phosphodiester linkages between pentoses, preventing the DNA chain from elongation and interrupting the DNA synthesis. The minor structural alteration (the inversion of hydroxyl at the 2' positions of the sugar) leads to change of the biological activity from anti-depressant and DNA/RNA block builder to powerful anti-cancer. Our study aimed to determine the molecular nature of this phenomenon. Three 1H-14N NMR-NQR experimental techniques, followed by solid-state computational modelling (Quantum Theory of Atoms in Molecules, Reduced Density Gradient and 3D Hirshfeld surfaces), Quantitative Structure-Property Relationships, Spackman's Hirshfeld surfaces and Molecular Docking were used. Multifaceted analysis-combining experiments, computational modeling and molecular docking-provides deep insight into three-dimensional packing at the atomic and molecular levels, but is challenging. A spectrum with nine lines indicating the existence of three chemically inequivalent nitrogen sites in the Ara-C molecule was recorded, and the lines were assigned to them. The influence of the structural alteration on the NQR parameters was modeled in the solid (GGA/RPBE). For the comprehensive description of the nature of these interactions several factors were considered, including relative reactivity and the involvement of heavy atoms in various non-covalent interactions. The binding modes in the solid state and complex with dCK were investigated using the novel approaches: radial plots, heatmaps and root-mean-square deviation of the binding mode. We identified the intramolecular OH···O hydrogen bond as the key factor responsible for forcing the glycone conformation and strengthening NH···O bonds with Gln97, Asp133 and Ara128, and stacking with Phe137. The titular butterfly effect is associated with both the inversion and the presence of this intramolecular hydrogen bond. Our study elucidates the differences in the binding modes of Ara-C and cytidine, which should guide the design of more potent anti-cancer and anti-viral analogues.

Favipiravir Analogues as Inhibitors of SARS-CoV-2 RNA-Dependent RNA Polymerase, Combined Quantum Chemical Modeling, Quantitative Structure-Property Relationship, and Molecular Docking Study.

Our study was motivated by the urgent need to develop or improve antivirals for effective therapy targeting RNA viruses. We hypothesized that analogues of favipiravir (FVP), an inhibitor of RNA-dependent RNA polymerase (RdRp), could provide more effective nucleic acid recognition and binding processes while reducing side effects such as cardiotoxicity, hepatotoxicity, teratogenicity, and embryotoxicity. We proposed a set of FVP analogues together with their forms of triphosphate as new SARS-CoV-2 RdRp inhibitors. The main aim of our study was to investigate changes in the mechanism and binding capacity resulting from these modifications. Using three different approaches, QTAIM, QSPR, and MD, the differences in the reactivity, toxicity, binding efficiency, and ability to be incorporated by RdRp were assessed. Two new quantum chemical reactivity descriptors, the relative electro-donating and electro-accepting power, were defined and successfully applied. Moreover, a new quantitative method for comparing binding modes was developed based on mathematical metrics and an atypical radar plot. These methods provide deep insight into the set of desirable properties responsible for inhibiting RdRp, allowing ligands to be conveniently screened. The proposed modification of the FVP structure seems to improve its binding ability and enhance the productive mode of binding. In particular, two of the FVP analogues (the trifluoro- and cyano-) bind very strongly to the RNA template, RNA primer, cofactors, and RdRp, and thus may constitute a very good alternative to FVP.

Elucidating the Role of Noncovalent Interactions in Favipiravir, a Drug Active against Various Human RNA Viruses; a 1H-14N NQDR/Periodic DFT/QTAIM/RDS/3D Hirshfeld Surfaces Combined Study.

Favipiravir (6-fluoro-3-hydroxypyrazine-2-carboxamide, FPV), an active pharmaceutical component of the drug discovered and registered in March 2014 in Japan under the name Avigan, with an indication for pandemic influenza, has been studied. The study of this compound was prompted by the idea that effective processes of recognition and binding of FPV to the nucleic acid are affected predominantly by the propensity to form intra- and intermolecular interactions. Three nuclear quadrupole resonance experimental techniques, namely 1H-14N cross-relaxation, multiple frequency sweeps, and two-frequency irradiation, followed by solid-state computational modelling (density functional theory supplemented by the quantum theory of atoms in molecules, 3D Hirshfeld Surfaces, and reduced density gradient) approaches were applied. The complete NQR spectrum consisting of nine lines indicating the presence of three chemically inequivalent nitrogen sites in the FPV molecule was detected, and the assignment of lines to particular sites was performed. The description of the nearest vicinity of all three nitrogen atoms was used to characterize the nature of the intermolecular interactions from the perspective of the local single atoms and to draw some conclusions on the nature of the interactions required for effective recognition and binding. The propensity to form the electrostatic N-H···O, N-H···N, and C-H···O intermolecular hydrogen bonds competitive with two intramolecular hydrogen bonds, strong O-H···O and very weak N-H···N, closing the 5-member ring and stiffening the structure, as well as π···π and F···F dispersive interactions, were analysed in detail. The hypothesis regarding the similarity of the interaction pattern in the solid and the RNA template was verified. It was discovered that the -NH2 group in the crystal participates in intermolecular hydrogen bonds N-H···N and N-H···O, in the precatalytic state only in N-H···O, while in the active state in N-H···N and N-H···O hydrogen bonds, which is of importance to link FVP to the RNA template. Our study elucidates the binding modes of FVP (in crystal, precatalytic, and active forms) in detail and should guide the design of more potent analogues targeting SARS-CoV-2. Strong direct binding of FVP-RTP to both the active site and cofactor discovered by us suggests a possible alternative, allosteric mechanism of FVP action, which may explain the scattering of the results of clinical trials or the synergistic effect observed in combined treatment against SARS-CoV-2.

Synthesis and Crystal Structure of Adamantylated 4,5,6,7-Tetrahalogeno-1H-benzimidazoles Novel Multi-Target Ligands (Potential CK2, M2 and SARS-CoV-2 Inhibitors); X-ray/DFT/QTAIM/Hirshfeld Surfaces/Molecular Docking Study.

A series of new congeners, 1-[2-(1-adamantyl)ethyl]-1H-benzimidazole (AB) and 1-[2-(1-adamantyl)ethyl]-4,5,6,7-tetrahalogeno-1H-benzimidazole (Hal=Cl, Br, I; tClAB, tBrAB, tIAB), have been synthesized and studied. These novel multi-target ligands combine a benzimidazole ring known to show antitumor activity and an adamantyl moiety showing anti-influenza activity. Their crystal structures were determined by X-ray, while intermolecular interactions were studied using topological Bader's Quantum Theory of Atoms in Molecules, Hirshfeld Surfaces, CLP and PIXEL approaches. The newly synthesized compounds crystallize within two different space groups, P-1 (AB and tIAB) and P21/c (tClAB and tBrAB). A number of intramolecular hydrogen bonds, C-H⋯Hal (Hal=Cl, Br, I), were found in all halogen-containing congeners studied, but the intermolecular C-H⋯N hydrogen bond was detected only in AB and tIAB, while C-Hal⋯π only in tClAB and tBrAB. The interplay between C-H⋯N and C-H⋯Hal hydrogen bonds and a shift from the strong (C-H⋯Cl) to the very weak (C-H⋯I) attractive interactions upon Hal exchange, supplemented with Hal⋯Hal overlapping, determines the differences in the symmetry of crystalline packing and is crucial from the biological point of view. The hypothesis about the potential dual inhibitor role of the newly synthesized congeners was verified using molecular docking and the congeners were found to be pharmaceutically attractive as Human Casein Kinase 2, CK2, inhibitors, Membrane Matrix 2 Protein, M2, blockers and Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2, inhibitors. The addition of adamantyl moiety seems to broaden and modify the therapeutic indices of the 4,5,6,7-tetrahalogeno-1H-benzimidazoles.

Comparison of the Possibilities of Environmental Usage of Sewage Sludge from Treatment Plants Operating with MBR and SBR Technology.

Sewage sludge from sewage treatment plants has soil-forming and fertilising properties. However, sewage sludge cannot always be used in nature, including agriculture. One of the main reasons is the concentration of heavy metals. Sludge from wastewater treatment plants operating in MBR (membrane biological reactor) and SBR (sequential batch reactor) systems was analysed. Studies comparing the risk analysis of the natural use of sludge from MBR and SBR treatment plants were performed for the first time, due to the fact that more and more MBR plants, which are a BAT technology, are being developed in Poland, displacing the classical SBR plants. MBR technology uses a combination of activated sludge and filtration with microfiltration membranes. Wastewater treated in these reactors meets the highest quality standards, both in terms of physicochemical and microbiological aspects. This paper presents studies on the mobility of heavy metals in sewage sludge carried out using the BCR sequential extraction method. Geo-accumulation index (GAI), potential environmental risk index (ER), risk assessment code (RAC), and environmental risk determinant (ERD) were calculated. Heavy metals dominated the stable fractions in all cases. Furthermore, an increased content of copper and cadmium was observed in the MBR sludge. This fact is favourable in view of the efforts to eliminate heavy metals in the environment.

The Influence of Sewage Sludge Content and Sintering Temperature on Selected Properties of Lightweight Expanded Clay Aggregate.

Wastewater treatment processes produce sewage sludge (SS), which, in line with environmental sustainability principles, can be a valuable source of matter in the production of lightweight expanded clay aggregate (LECA). The literature on the influence of SS content and sintering temperature on the properties of LECA is scarce. This paper aims to statistically evaluate the effects of SS content and sintering temperature on LECA physical properties. Total porosity, pore volume, and apparent density were determined with the use of a density analyzer. A helium pycnometer was utilized to determine the specific density. Closed porosity was calculated. The test results demonstrated a statistically significant influence of the SS content on the specific density and water absorption of LECA. The sintering temperature had a significant effect on the specific density, apparent density, total porosity, closed porosity, total volume of pores, and water absorption. It was proved that a broad range of the SS content is admissible in the raw material mass for the production of LECA.

Polymorphism and disorder in natural active ingredients. Low and high-temperature phases of anhydrous caffeine: Spectroscopic ((1)H-(14)N NMR-NQR/(14)N NQR) and solid-state computational modelling (DFT/QTAIM/RDS) study.

The polymorphism of anhydrous caffeine (1,3,7-trimethylxanthine; 1,3,7-trimethyl-1H-purine-2,6-(3H,7H)-dione) has been studied by (1)H-(14)N NMR-NQR (Nuclear Magnetic Resonance-Nuclear Quadrupole Resonance) double resonance and pure (14)N NQR (Nuclear Quadrupole Resonance) followed by computational modelling (Density Functional Theory, supplemented Quantum Theory of Atoms in Molecules with Reduced Density Gradient) in solid state. For two stable (phase II, form ß) and metastable (phase I, form α) polymorphs the complete NQR spectra consisting of 12 lines were recorded. The assignment of signals detected in experiment to particular nitrogen sites was verified with the help of DFT. The shifts of the NQR frequencies, quadrupole coupling constants and asymmetry parameters at each nitrogen site due to polymorphic transition were evaluated. The strongest shifts were observed at N(3) site, while the smallest at N(9) site. The commercial pharmaceutical sample was found to contain approximately 20-25% of phase I and 75-80% of phase II. The orientational disorder in phase II with a local molecular arrangement mimics that in phase I. Substantial differences in the intermolecular interaction phases I and II of caffeine were analysed using computational (DFT/QTAIM/RDS) approach. The analysis of local environment of each nitrogen nucleus permitted drawing some conclusions on the topology of interactions in both polymorphs. For the most stable orientations in phase I and phase II the maps of the principal component qz of EFG tensor and its asymmetry parameter at each point of the molecular system were calculated and visualized. The relevant maps calculated for both phases I and II indicates small variation in electrostatic potential upon phase change. Small differences between packings in phases slightly disturb the neighbourhood of the N(1) and N(7) nitrogens, thus are meaningless from the biological point of view. The composition of two phases in pharmaceutical material should not be any obstacle, which is relevant from the pharmaceutical industry point of view.

Impact of structural differences in carcinopreventive agents indole-3-carbinol and 3,3'-diindolylmethane on biological activity. An X-ray, ¹H-¹4N NQDR, ¹³C CP/MAS NMR, and periodic hybrid DFT study.

Three experimental techniques (1)H-(14)N NQDR, (13)C CP/MAS NMR and X-ray and Density Functional Theory (GGA/BLYP with PBC) and Hirshfeld surfaces were applied for the structure-activity oriented studies of two phyto-antioxidants and anticarcinogens: indole-3-carbinol, I3C, and 3,3'-diindolylmethane, DIM, (its bioactive metabolite). One set of (14)N NQR frequencies for DIM (2.310, 2.200 and 0.110 MHz at 295K) and I3C (2.315, 1.985 and 0.330 MHz at 160K) was recorded. The multiplicity of NQR lines recorded at RT revealed high symmetry (chemical and physical equivalence) of both methyl indazole rings of DIM. Carbonyl (13)C CSA tensor components were calculated from the (13)C CP/MAS solid state NMR spectrum of I3C recorded under fast and slow spinning. At room temperature the crystal structure of I3C is orthorhombic: space group Pca21, Z=4, a=5.78922(16), b=15.6434(7) and c=8.4405(2)Å. The I3C molecules are aggregated into ribbons stacked along [001]. The oxygen atomsare disorderedbetween the two sites of different occupancy factors. It implies that the crystal is built of about 70% trans and 30% gauche conformers, and apart from the weak OH⋯O hydrogen bonds (O⋯O=3.106Å) the formation of alternative O'H⋯O bonds (O'⋯O=2.785Å) is possible within the 1D ribbons. The adjacent ribbons are further stabilised by O'H⋯O bonds (O'⋯O=2.951Å). The analysis of spectra and intermolecular interactions pattern by experimental techniques was supported by solid (periodic) DFT calculations. The knowledge of the topology and competition of the interactions in crystalline state shed some light on the preferred conformations of CH2OH in I3C and steric hindrance of methyl indole rings in DIM. A comparison of the local environment in gas phase and solid permitted drawing some conclusions on the nature of the interactions required for effective processes of recognition and binding of a given anticarcinogen to the protein or nucleic acid.

Unusual case of desmotropy. Combined spectroscopy (¹H-¹4N NQDR) and quantum chemistry (periodic hybrid DFT/QTAIM and Hirshfeld surface-based) study of solid dacarbazine (anti-neoplastic).

Antineoplastic chemo-therapeutic drug 5-(3,3-dimethyl-1-triazenyl)imidazole-4-carboxamide (Dacarbazine, DTIC), has been studied experimentally in solid state by ¹H-¹4N NQDR double resonance at 295 K and theoretically by the Density Functional Theory (DFT)/Quantum Theory of Atoms in Molecules (QTAIM) and Hirshfeld surfaces analysis. Only one set of eighteen resonance frequencies was found in the experiment. This indicates the presence of six inequivalent nitrogen sites: -N(CH3), -NH2, -NH- and three -N= (of which one is a ring, two are from triazene) in the DTIC molecule. This contradicts the X-ray data which revealed the multiplication of nitrogen sites due to unusual desmotropism. The averaging of NQR frequencies caused by the fast in NQR time-scale exchange of protons in a double-well potential combined with the oscillations of twisted supramolecular synthons was proposed as a potential mechanism responsible for this apparent contradiction. An effective improvement in the quality of the spectrum reproduction was achieved when the calculations were performed assuming the periodic boundary conditions, BLYP functional, the DNP basis set and taking the 3×3×3 k-point separation. The ordering of the nitrogen sites according to the increasing quadrupole coupling constant (QCC): N(3)

Conformational stability and thermal pathways of relaxation in triclosan (antibacterial/excipient/contaminant) in solid-state: combined spectroscopic ((1)H NMR) and computational (periodic DFT) study.

The mechanism of molecular dynamics in the antibacterial/antifungal agent, triclosan (5-chloro-2-(2',4'-dichlorophenoxy)-phenol), in solid state was studied by (1)H NMR spectroscopy and periodic density functional theory (DFT) calculations. Temperature dependencies of the proton spin-lattice relaxation time (T1) in the ranges 86-293 and 90-250 K (at 15 and 24.667 MHz, respectively) and the second moment (M2) of the (1)H NMR resonant line in the range 103-300 K were measured. Two minima in the temperature dependence of T1 revealed a classical Arrhenius governed activation processes. The low temperature shallow minimum T1(T) of 71 s at 115 K, 15 MHz, which shifts with frequency, was assigned to classical hindered jumps of hydroxyl group around OC axis and with respect to a 5-chloro-2-phenol ring. The activation energy of this motion estimated on the basis of the fit of the theoretical model to the experimental points is 9.68 kJ/mol. The pointed high temperature minimum T1(T) of 59 s at 190 K, 15 MHz, which also shifts with frequency, was assigned to the small angle librations by Θlib= ± 9° between two positions of equilibrium differing in energy by 7.42 kJ/mol. The activation energy of this motion estimated on the basis of the fit of the theoretical model to the experimental points is 31.1 kJ/mol. Both motions result in a negligible reduction in the (1)H NMR line second moment, thus the second moment delivers an irrelevant description of the molecular motions in triclosan.

Topology of the interactions pattern in pharmaceutically relevant polymorphs of methylxanthines (caffeine, theobromine, and theophiline): combined experimental (¹H-¹4N nuclear quadrupole double resonance) and computational (DFT and Hirshfeld-based) study.

Three anhydrous methylxanthines: caffeine (1,3,7-trimethylxanthine; 1,3,7-trimethyl-1H-purine-2,6-(3H,7H)-dione) and its two metabolites theophylline (1,3-dimethylxanthine; 1,3-dimethyl-7H-purine-2,6-dione) and theobromine (3,7-dimethyl-xanthine; 3,7-dimethyl-7H-purine-2,6-dione), which reveal multifaceted therapeutic potential, have been studied experimentally in solid state by (1)H-(14)N NMR-NQR (nuclear magnetic resonance-nuclear quadrupole resonance) double resonance (NQDR). For each compound the complete NQR spectrum consisting of 12 lines was recorded. The multiplicity of NQR lines indicates the presence of a stable ß form of anhydrous caffeine at 233 K and stable form II of anhydrous theobromine at 213 K. The assignment of signals detected in NQR experiment to particular nitrogen atoms was made on the basis of quantum chemistry calculations performed for monomer, cluster, and solid at the DFT/GGA/BLYP/DPD level. The shifts due to crystal packing interactions were evaluated, and the multiplets detected by NQR were assigned to N(9) in theobromine and N(1) and N(9) in caffeine. The ordering theobromine > theophylline > caffeine site and theophylline < theobromine < caffeine according to increasing electric field gradient (EFG) at the N(1) and N(7) sites, respectively, reflects the changes in biological activity profile of compounds from the methylxanthines series (different pharmacological effects). This difference is elucidated on the basis of the ability to form intra- and intermolecular interactions (hydrogen bonds and π···π stacking interactions). The introduction of methyl groups to xanthine restricts the ability of nitrogen atoms to participate in strong hydrogen bonds; as a result, the dominating effect shifts from hydrogen bond (theobromine) to π···π stacking (caffeine). Substantial differences in the intermolecular interactions in stable forms of methylxanthines differing in methylation (site or number) were analyzed within the Hirshfeld surface-based approach. The analysis of local environment of the nitrogen nucleus permitted drawing some conclusions on the nature of the interactions required for effective processes of recognition and binding of a given methylxanthine to A1-A(2A) receptor (target for caffeine in the brain). Although the interactions responsible for linking neighboring methylxanthines molecules in crystals and methylxanthines with targets in the human organism can differ significantly, the knowledge of the topology of interactions provides reliable preliminary information about the nature of this binding.

An insight into prototropism and supramolecular motifs in solid-state structures of allopurinol, hypoxanthine, xanthine, and uric acid. A ¹H-¹4N NQDR spectroscopy, hybrid DFT/QTAIM, and Hirshfeld surface-based study.

Allopurinol (1,5-dihydro-4H-pyrazolo [3,4-d]pyrimidin-4-one), the active pharmaceutical ingredient (API) of the drugs applied for the treatment of gout and tumor lysis syndrome, recently discovered to have multifaceted therapeutic potential, and hypoxanthine which is a naturally occurring purine have been studied experimentally in the solid state by (1)H-(14)N NMR-NQR double resonance. Twelve (14)N resonance frequencies have been detected at 295 K and assigned to two pairs of two kinds of nitrogen sites (-N═ and -NH) in each compound. The experimental results are supported by and interpreted with the help of quantum theory of atoms in molecules (QTAIM)/density functional theory (DFT) calculations. The factors, such as the substituent effect, in particular the shift of nitrogen from position 7 (as in hypoxanthine) to position 8 (as in allopurinol), hybridization, possible prototropic tautomerism, and the pattern of intermolecular bonding, have been taken into account in (1)H-(14)N NMR-NQR spectra interpretation. This study demonstrates the advantages of combining NQR, DFT/QTAIM, and Hirshfeld surface analysis to extract detailed information on electron density distribution and complex H-bonding networks in crystals of purinic type heterocycles, relevant in pharmacological processes. In the absence of X-ray data for xanthine, the NQR parameters supported by DFT/QTAIM calculations and Hirshfeld surface analysis were proved to be valuable tools for clarifying the details of crystalline packing and predicting an unsolved crystalline structure of xanthine. The influence of a decrease in purine ring conjugation level upon oxidation on the biological activity of allopurinol, a xanthine oxidase (XO) enzyme inhibitor, which blocks the conversion of hypoxanthine to xanthine and subsequently xanthine to uric acid, is also discussed.

Quantum-chemical insight into structure-reactivity relationship in 4,5,6,7-tetrahalogeno-1H-benzimidazoles: a combined X-ray, DSC, DFT/QTAIM, Hirshfeld surface-based, and molecular docking approach.

The weak interaction patterns in 4,5,6,7-tetrahalogeno-1H-benzimidazoles, protein kinase CK2 inhibitors, in solid state are studied by the X-ray method and quantum chemistry calculations. The crystal structures of 4,5,6,7-tetrachloro- and 4,5,6,7-tetrabromo-1H-benzimidazole are determined by X-ray diffraction and refined to a final R-factor of 3.07 and 3.03%, respectively, at room temperature. The compound 4,5,6,7-tetrabromo-1H-benzimidazole, which crystallizes in the I41/a space group, is found to be isostructural with previously studied 4,5,6,7-tetraiodo-1H-benzimidazole in contrast to 4,5,6,7-tetrachloro-1H-benzimidazole, which crystallizes as triclinic P1̅ with 4 molecules in elementary unit. For 4,5,6,7-tetrachloro-1H-benzimidazole, differential scanning calorimetry (DSC) revealed a second order glassy phase transition at Tg = 95°/106° (heating/cooling), an indication of frozen disorder. The lack of 3D isostructurality found in all 4,5,6,7-tetrahalogeno-1H-benzimidazoles is elucidated on the basis of the intra- and intermolecular interactions (hydrogen bonding, van der Waals contacts, and C-H···π interactions). The topological Bader's Quantum Theory of Atoms in Molecules (QTAIM) and Spackman's Hirshfeld surface-based approaches reveal equilibration of electrostatic matching and dispersion van der Waals interactions between molecules consistent with the crystal site-symmetry. The weakening of van der Waals forces accompanied by increasing strength of the hydrogen bond (N-H···N) result in a decrease in the crystal site-symmetry and a change in molecular packing in the crystalline state. Crystal packing motifs were investigated with the aid of Hirshfeld surface fingerprint plots. The ordering 4,5,6,7-tetraiodo > 4,5,6,7-tetrabromo > 4,5,6,7-tetrachloro > 4,5,6,7-tetrafluoro reflects not only a decrease in crystal symmetry but also increase in chemical reactivity (electronic activation), which could explain some changes in biological activity of compounds from the 4,5,6,7-tetrahalogeno-1H-benzimidazole series. The ability of formation of a given type of bonds by 4,5,6,7-tetrahalogeno-1H-benzimidazole molecules is the same in the crystal and in CK2. Analysis of the interactions in the crystal permits drawing conclusions on the character (the way) of connections between a given 4,5,6,7-tetrahalogeno-1H-benzimidazole as a ligand with CK2 protein to make a protein-ligand complex.

Complex mechanism of relaxation in solid chloroxylenol (antibacterial/antifungal agent) studied by ¹H NMR spectroscopy and density functional theory calculations.

Molecular relaxation in antibacterial/antifungal agent: chloroxylenol (4-chloro-3,5-dimethylphenol, PCMX) in the solid state was studied by the (1)H NMR and quantum chemistry calculations. The temperature dependencies of the proton spin-lattice relaxation time (T1) in the ranges 15-273 K (at 24.667 MHz), 77-295 K (at 15 MHz), and 112-291 K at 90 MHz and the second moment (M2) of (1)H NMR resonant line in the range 106-380 K were measured. The two minima in the temperature dependence of T1 revealed two activation processes, whereas the M2 dependence in the studied range was quite flat and revealed the only significant reduction at 380 K. The low temperature part of T1(T) dependence indicated the occurrence of two processes characteristic of methyl bearing solids; the quantum mechanics governed incoherent tunneling (responsible for the low temperature flattening of T1) and the classical Arrhenius dependence governed hindered rotation (related to the wide low temperature minimum of 0.066 s at 57 K, 24.667 MHz). The 2D potential energy surface obtained using DFT/B3LYP/6-311++G(2d,p) calculations revealed the inequivalence of methyl groups and the lack of their interplay/coupling. The activation energies of classical hindered rotation are 3.35 and 2.5 kJ/mol, whereas temperatures at which the proton tunneling T(tun) finally ceases are 52 and 63 K, for inequivalent methyl groups. C(p)(T) required for the estimation of T(tun) was calculated purely theoretically on the basis of the Einstein and Debye models of specific heat and 51 modes of atomic vibrations, 4 internal rotations, and 3 torsions calculated by DFT. The -CH3 motion (tunneling and classical) results in the reduction in the (1)H NMR line second moment from 17.3 G(2) (rigid) to approximately 11.05 G(2). The pointed high temperature minimum T1(T) of 0.109 s at 89 K, 24.667 MHz, which shifts with frequency, was assigned to small-angle libration jumps, by the Θ2 = ±15° between two positions of equilibrium. The activation energy of this motion estimated on the basis of the fit of the theoretical model to the experimental points is 10.5 kJ/mol. The reduction in the (1)H NMR line second moment assigned to this motion is much lower (due to order parameter s = 0.64) and equal to 1.6 G(2). The high temperature reduction from 9.6 G(2) to 0.9 G(2) at 380 K is a result of the phase transition connected with melting (385-389 K).

Temperature variation of ultralow frequency modes and mean square displacements in solid lasamide (diuretic drug) studied by 35Cl-NQR, X-ray and DFT/QTAIM.

The application of combined (35)Cl-NQR/X-ray/DFT/QTAIM methods to study the temperature variation of anisotropic displacement parameters and ultralow frequency modes of anharmonic torsional vibrations in the solid state is illustrated on the example of 2,4-dichloro-5-sulfamolybenzoic acid (lasamide, DSBA) which is a diuretic and an intermediate in the synthesis of furosemide and thus its common impurity. The crystallographic structure of lasamide is solved by X-ray diffraction and refined to a final R-factor of 3.06% at room temperature. Lasamide is found to crystallize in the triclinic space group P-1, with two equivalent molecules in the unit cell a = 7.5984(3) Å, b = 8.3158(3) Å, c = 8.6892(3) Å; α = 81.212(3)°, ß = 73.799(3)°, γ = 67.599(3)°. Its molecules form symmetric dimers linked by two short and linear intermolecular hydrogen bonds O-H···O (O-H···O = 2.648 Å and ∠OHO = 171.5°), which are further linked by weaker and longer intermolecular hydrogen bonds N-H···O (N-H···O = 2.965 Å and ∠NHO = 166.4°). Two (35)Cl-NQR resonance frequencies, 36.899 and 37.129 MHz, revealed at room temperature are assigned to chlorine sites at the ortho and para positions, relative to the carboxyl functional group, respectively. The difference in C-Cl(1) and C-Cl(2) bond lengths only slightly affects the value of (35)Cl-NQR frequencies, which results mainly from chemical inequivalence of chlorine atoms but also involvement in different intermolecular interactions pattern. The smooth decrease in both (35)Cl-NQR frequencies with increasing temperature in the range of 77-300 K testifies to the averaging of EFG tensor at each chlorine site due to anharmonic torsional vibrations. Lasamide is thermally stable; no temperature-induced release of chlorine or decomposition of this compound is detected. The temperature dependence of ultralow frequency modes of anharmonic small-angle internal torsional vibrations averaging EFG tensor and mean square angle displacements at both chlorine sites is derived from the (35)Cl-NQR temperature dependence. The frequencies of torsional vibrations higher for the para site than the ortho site are in good agreement with those obtained from thermal parameters obtained from X-ray studies. The mean square angle displacements are in good agreement with those estimated from X-ray data with the use of the TLS model. The detailed DFT/QTAIM analysis suggests that the interplay between different hydrogen bonds in adjacent molecules forming dimers is responsible for the differences in flexibility of the carboxyl and sulphonamide substituents as well as both C-Cl(1) and C-Cl(2) bonds. Three ultralow wavenumber modes of internal vibrations in Raman and IR spectra obtained at the B3LYP/6-311++G(d,p) level close to those obtained within the TLS model suggest that internal and external modes of vibrations are not well separated.

Electron configuration and hydrogen-bonding pattern in several thymine and uracil analogues studied by 1H-14N NQDR and DFT/QTAIM.

Some thio- and aza-derivatives of natural nucleobases uracil and thymine: 2-thiouracil, 4-thiouracil, 6-methyl-2-thiouracil, 6-azauracil, and 6-aza-2-thiothymine have been studied experimentally in solid state by (1)H-(14)N NMR-NQR double resonance (NQDR) and theoretically by the Density Functional Theory (DFT)/Quantum Theory of Atoms in Molecules (QTAIM). The (14)N resonance frequencies have been measured at 173 and 295 K and assigned to particular nitrogen sites (-N═ and -NH-). The temperature factor has been found negligible. The changes in the molecular skeletons, electric charge distribution, intermolecular interactions pattern, and molecular aggregations caused by oxygen replacement with sulfur and carbon replacement with nitrogen are discussed in detail. Correlations between all the principal components of the (14)N quadrupole coupling tensor have been found helpful in the search for the experimental (14)N NQR frequencies, their assignment to a particular nitrogen positions and estimation of the strength of the inter- and intramolecular interactions. The variation in the NQR parameters have been mainly related to the variation in the population of π-electron orbital. For thiouracil derivatives a general trend is that the stronger the hydrogen bond is, the lower is the asymmetry parameter, while for thymine and 6-aza-2-thiotymine, the opposite relation holds. Differences in correlations of the principal components of the (14)N quadrupole coupling tensor at the amino and iminonitrogen positions in heterocyclic rings are discussed. The effect of C→H and C→N substitution at the amino nitrogen position and C→N substitution at the iminonitrogen position on the quadrupole coupling tensor is analyzed. This study also demonstrates the advantages of combining NQR and DFT/QTAIM to predict an unsolved crystalline structure of 4-thiouracil.

A comparative study of the hydrogen-bonding patterns and prototropism in solid 2-thiocytosine (potential antileukemic agent) and cytosine, as studied by 1H-14N NQDR and QTAIM/ DFT.

A potential antileukemic and anticancer agent, 2-thiocytosine (2-TC), has been studied experimentally in the solid state by (1)H-(14)N NMR-NQR double resonance (NQDR) and theoretically by the quantum theory of atoms in molecules (QTAIM)/density functional theory (DFT). Eighteen resonance frequencies on (14)N were detected at 180 K and assigned to particular nitrogen sites (-NH(2), -N=, and -NH-) in 2-thiocytosine. Factors such as the nonequivalence of molecules (connected to the duplication of sites) and possible prototropic tautomerism (capable of modifying the type of site due to proton transfer) were taken into account during frequency assignment. The result of replacing oxygen with sulfur, which leads to changes in the intermolecular interaction pattern and molecular aggregation, is discussed. This study demonstrates the advantages of combining NQDR and DFT to extract detailed information on the H-bonding properties of crystals with complex H-bonding networks. Solid-state properties were found to have a profound impact on the stabilities and reactivities of both compounds.

Supramolecular synthon pattern in solid clioquinol and cloxiquine (APIs of antibacterial, antifungal, antiaging and antituberculosis drugs) studied by ³5Cl NQR, ¹H-¹7O and ¹H-¹4N NQDR and DFT/QTAIM.

The quinolinol derivatives clioquinol (5-chloro-7-iodo-8-quinolinol, Quinoform) and cloxiquine (5-chloro-8-quinolinol) were studied experimentally in the solid state via ³5Cl NQR, ¹H-¹7O and ¹H-¹4N NQDR spectroscopies, and theoretically by density functional theory (DFT). The supramolecular synthon pattern of O-H···N hydrogen bonds linking dimers and π-π stacking interactions were described within the QTAIM (quantum theory of atoms in molecules) /DFT (density functional theory) formalism. Both proton donor and acceptor sites in O-H···N bonds were characterized using ¹H-¹7O and ¹H-¹4N NQDR spectroscopies and QTAIM. The possibility of the existence of O-H···H-O dihydrogen bonds was excluded. The weak intermolecular interactions in the crystals of clioquinol and cloxiquine were detected and examined. The results obtained in this work suggest that considerable differences in the NQR parameters for the planar and twisted supramolecular synthons permit differentiation between specific polymorphic forms, and indicate that the more planar supramolecular synthons are accompanied by a greater number of weaker hydrogen bonds linking them and stronger π···π stacking interactions.

(14)N NQR, (1)H NMR and DFT/QTAIM study of hydrogen bonding and polymorphism in selected solid 1,3,4-thiadiazole derivatives.

The 1,3,4-thiadiazole derivatives (2-amino-1,3,4-thiadiazole, acetazolamide, sulfamethizole) have been studied experimentally in the solid state by (1)H-(14)N NQDR spectroscopy and theoretically by Density Functional Theory (DFT). The specific pattern of the intra and intermolecular interactions in 1,3,4-thiadiazole derivatives is described within the QTAIM (Quantum Theory of Atoms in Molecules)/DFT formalism. The results obtained in this work suggest that considerable differences in the NQR parameters permit differentiation even between specific pure association polymorphic forms and indicate that the stronger hydrogen bonds are accompanied by the larger η and smaller ν(-) and e(2)Qq/h values. The degree of π-electron delocalization within the 1,3,4-thiadiazole ring and hydrogen bonds is a result of the interplay between the substituents and can be easily observed as a change in NQR parameters at N atoms. In the absence of X-ray data NQR parameters can clarify the details of crystallographic structure revealing information on intermolecular interactions.