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.

Elucidating the Role of Noncovalent Interactions in Favipiravir, a Drug Active against Various Human RNA Viruses; a H-N 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 H-N 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.

A rapid determination of nuclear quadrupole resonance frequencies using field-cycling magnetic resonance and frequency modulated RF excitations.

A modification of Slusher-Hahn's double resonance technique is described and experimentally tested. It is based on application of multiple frequency sweeps and can be used for a rapid location of nuclear quadrupole resonance (NQR) frequencies. The resolution of the present technique is relatively low but, when the NQR frequencies are located, it is easy to use either the Slusher-Hahn's technique or pulse NQR to determine the NQR frequencies with a higher precision.

N NQR spectroscopy reveals the proton position in N-HN bonds: a case study with proton sponges.

The position of protons in hydrogen bonds is often uncertain to some degree, as the technique most often used for structure determination, X-ray diffraction, is sensitive to electron density, which is not particularly abundant around protons. In hydrogen bonds, protons introduce an additional problem: the potential for proton motion is inherently anharmonic and thus requires the consideration of nuclear quantum effects (NQEs). Here, we demonstrate that 14N NQR spectroscopy is able to rather accurately determine proton positions in N-HN bonds, in certain cases with an accuracy comparable to that of X-ray and neutron diffraction at room temperature.

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 β) 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.

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.

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.

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 β form of anhydrous caffeine at 233 K and stable form II of anhydrous theobromine at 213 K.

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.

Hydrogen bonding and proton transfer in cocrystals of 4,4'-bipyridyl and organic acids studied using nuclear quadrupole resonance.

Cocrystals of 4,4'-bipyridyl and several carboxylic acids were grown from the methanol solution of the cocrystal formers. Complete (14)N NQR spectra of these cocrystals have been measured using (1)H-(14)N nuclear quadrupole double resonance. The principal values of the quadrupole coupling tensor are calculated from the (14)N NQR frequencies.

¹⁴N nuclear quadrupole resonance study of polymorphism in famotidine.

(14)N nuclear quadrupole resonance (NQR) in two known polymorphs of famotidine was measured. At room temperature, seven quadrupolar sets of transition frequencies (ν(+), ν(-), and ν(0)) corresponding to seven different nitrogen sites in the crystal structure of each of the two polymorphs were found. This confirms the expected ability of NQR to distinguish polymorph B from its analog A.

Nuclear quadrupole resonance investigation of hydrogen bonding in some cocrystals of 2,3,5,6-tetramethylpyrazine and carboxylic acids.

Cocrystals of 2,3,5,6-tetramethylpyrazine and several carboxylic acids have been prepared, and the complete (14)N nuclear quadrupole resonance spectra have been measured. The (14)N nuclear quadrupole resonance spectra have been used to check whether the cocrystals are indeed formed and to investigate the hydrogen bonding scheme of 2,3,5,6-tetramethylpyrazine molecules. Since a 2,3,5,6-tetramethylpyrazine molecule has two hydrogen bond acceptors, it may form either 1:1 or 1:2 cocrystals with carbocylic acids.

Hydrogen bonds in cocrystals and salts of 2-amino-4,6-dimethylpyrimidine and carboxylic acids studied by nuclear quadrupole resonance.

(14)N and (17)O nuclear quadrupole resonance frequencies have been measured in 1:1 cocrystals and salts of 2-amino-4,6-dimethylpyrimidine and several carboxylic acids. A systematic decrease of the (17)O quadrupole coupling constant on increasing strength of the hydrogen bond is observed in cocrystals bound by O-H···N hydrogen bonds. The O-H distances deduced from the line widths of the (17)O NQR lines show that the hydrogen atom is in a hydrogen bond formed by a carboxylic groups for about 0.

Tautomerism and possible polymorphism in solid hydroxypyridines and pyridones studied by 14N NQR.

(14)N nuclear quadrupole resonance frequencies have been measured in solid 2-pyridone, 3-hydroxypyridine, and 4-pyridone by (1)H-(14)N nuclear quadrupole double resonance. Two slightly nonequivalent nitrogen positions are observed in solid 3-hydroxypyridine, whereas only one nitrogen position has been observed in 2-pyridone and 4-pyridone within the experimental resolution. Rather low (14)N quadrupole coupling constants in pyridones are the consequence of the delocalization of the nitrogen lone pair electrons in the aromatic rings.

Phase transition and ring-puckering motion in a metal-organic perovskite [(CH2)3NH2][Zn(HCOO)3].

Phase transitions in a metal-organic perovskite with an azetidinium cation, which exhibits giant polarizability, were investigated using differential scanning calorimetry (DSC) and (1)H nuclear magnetic resonance (NMR) measurements. The DSC results indicated successive phase transitions at 254 and 299 K. The temperature dependence of the spin-lattice relaxation time T(1) determined by NMR indicated that the activation energy for cation ring-puckering motion was 25 kJ mol(-1) in phase I (T > 299 K).

Nuclear quadrupole resonance characterization of carbamazepine cocrystals.

Nuclear quadrupole resonance (NQR) is used as a method for the characterization of cocrystals and crystal polymorphs. (14)N NQR spectra of several cocrystals of carbamazepine have been measured together with the (14)N NQR spectra of cocrystal formers. The results show that the (14)N NQR spectrum of a cocrystal and the (14)N NQR spectra of cocrystal formers differ well outside the experimental resolution.

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.

Unusual electron charge density in carboxylic acid. 17O quadrupole coupling in cis-cyclobutane-1,2-dicarboxylic acid.

The (17)O NQR frequencies have been measured in cis-cyclobutane-1,2-dicarboxylic acid and the quadrupole coupling tensors have been determined at various temperatures. Two O···H oxygen positions and two O-H oxygen positions are observed, showing the presence of two different types of O-H···O hydrogen bonds in the unit cell. The quadrupole coupling constants at the O-H oxygen positions are approximately 30% lower than the lowest quadrupole coupling constants experimentally observed at the C-O-H positions in other carboxylic acids with either ordered or disordered hydrogen bonds.

An innovative method for the non-destructive identification of photodegradation products in solid state: 1H-14N NMR-NQR and DFT/QTAIM study of photodegradation of nifedipine (anti-hypertensive) to nitrosonifedipine (potential anti-oxidative).

Stability of the antihypertensive drug nifedipine (NIF) has been studied experimentally in solid state by (1)H-(14)N NMR-NQR double resonance (NQDR) and theoretically by the Density Functional Theory (DFT). Photodegradation of NIF to its metabolite in vivo nitrosonifedipine, NO-NIF (antioxidative agent) upon long term daylight exposure was detected and the changes in the molecular structure of NIF were analysed. The photoconversion of NIF to NO-NIF in solid was found to be accompanied with the electron density redistribution at nitrogen sites (NH to N and NO(2) to NO) and proved to be successfully detected with identification of photoproducts by (1)H-(14)N NQDR and DFT methods.

Conformations and intermolecular interactions pattern in solid chloroxylenol and triclosan (API of anti-infective agents and drugs). A (35)Cl NQR, (1)H-(14)N NQDR, X-ray and DFT/QTAIM study.

Two antibacterial and antifungal agents, chloroxylenol (4-chloro-3,5-dimethyl-phenol) and triclosan (5-chloro-2-(2',4'-dichlorophenoxy)-phenol), were studied experimentally in solid state with an X-ray, (35)Cl-nuclear quadrupole resonance (NQR) and (17)O-nuclear quadrupole double resonance (NQDR) spectroscopies and, theoretically, with the density functional theory/quantum theory of atoms in molecules (DFT/QTAIM). The crystallographic structure of triclosan, which crystallises in space group P31 with one molecule in the asymmetric unit [a = 12.64100(10), b = 12.

Nature of isomerism of solid isothiourea salts, inhibitors of nitric oxide synthases, as studied by 1H-14N nuclear quadrupole double resonance, X-ray, and density functional theory/quantum theory of atoms in molecules.

Isothioureas, inhibitors of nitric oxide synthases, have been studied experimentally in solid state by nuclear quadrupole double resonance (NQDR) and X-ray methods and theoretically by the quantum theory of atoms in molecules/density functional theory. Resonance frequencies on (14)N have been detected and assigned to particular nitrogen sites in each molecule. The crystal packings of (S)-3,4-dichlorobenzyl-N-methylisothiouronium chloride with the disordered chlorine positions in benzene ring and (S)-butyloisothiouronium bromide have been resolved in X-ray diffraction studies.

Phonon-driven proton transfer in 3,5-pyridine dicarboxylic acid studied by 2H, 14N, and 17O nuclear quadrupole resonance.

Hydrogen bonding in crystalline 3,5-pyridine dicarboxylic acid has been studied by (2)H, (14)N, and (17)O nuclear quadrupole resonance. The (2)H and (17)O data show the presence of two distinct hydrogen bonds, a "normal" O-H···O bond and a short, strong N···H···O bond, with significantly different NQR parameters. In the latter, the temperature variation of the (14)N nuclear quadrupole resonance (NQR) parameters is related to the phonon-driven proton transfer in the N···H···O hydrogen bond.

A 14N nuclear quadrupole resonance study of phase transitions and molecular dynamics in hydrogen bonded organic antiferroelectrics 55DMBP-H2ca and 1,5-NPD-H2ca.

The temperature dependence of the (14)N NQR frequencies has been measured in antiferroelectric and paraelectric 55DMBP-H(2)ca and 1,5-NPD-H(2)ca. In both compounds we observe two non-equivalent nitrogen positions (N(+)-H···O(-) and N···H-O) in the antiferroelectric phase. The two nitrogen positions become equivalent (N···H···O) in the paraelectric phase.

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.