Crystal structure, vibrational and optic properties of 2-N-methylamino-3-methylpyridine N-oxide - Its X-ray and spectroscopic studies as well as DFT quantum chemical calculations.

The crystal and molecular structure and physicochemical properties of 2-N-methylamino-3-methylpyridine N-oxide (MA3MPO) have been studied. MA3MPO was synthesized from 2-amino-3-methylpyridine by several steps to form colorless crystals suitable for crystallographic analysis. The data reveal that MA3MPO crystallizes in the monoclinic space group P21/n. The studied compound contains a nearly flat triply substituted pyridine skeleton whose structure is stabilized by an intramolecular N-H⋅⋅⋅O hydrogen bond. The N-oxide molecules are connected together by weak C-H⋯O hydrogen bonds, an acceptor of which is the oxygen atom from the N-oxide group. This leads to creation of two-dimensional network of hydrogen bonds. Its IR, Raman, UV-Vis and luminescence spectra have been measured and analyzed on the basis of DFT and NBO quantum chemical calculations in which the B3LYP/6-311++G(d,p) approach was applied. The distribution of the electron levels in the studied compound has been analyzed in terms of the possibility of its participation in the ligand-to-lanthanide ion energy transfer.

Conformation of the azo bond and its influence on the molecular and crystal structures, IR and Raman spectra, and electron properties of 6-methyl-3,5-dinitro-2-[(E)-phenyldiazenyl]pyridine - Quantum chemical DFT calculations.

The crystal and molecular structures of 6-methyl-3,5-dinitro-2-[(E)-phenyldiazenyl]pyridine have been determined by X-ray diffraction and quantum chemical DFT calculations. The crystal is monoclinic, space group Cc (No. 9) with Z=4 with the unit cell parameters: a=12.083(7), b=12.881(6), c=8.134(3) Å and ß=97.09(5)°. The azo-bridge appears in the trans conformation in which C2-N2-N2'-C1' torsion angle takes a value -178.6(3)°, whereas the dihedral angle between the planes of the phenyl and pyridine rings is 3.5(2)°. The IR and Raman spectra measured in the temperature range 80-350K and quantum chemical calculations with the use of B3LYP/6-311G(2d,2p) approach confirmed the trans configuration of the azo-bridge as the most stable energetically and allowed determination of the energy other virtual structures. The observed effects were used in the discussion of vibrational dynamics of the studied compound. The energy gap between cis and trans conformers equals to 1.054eV (0.03873 Hartree). The electron absorption and emission spectra have been measured and analyzed on the basis of DFT calculations. The life time of the excited state is 12µs and the Stokes shift is close to 5470cm-1.

The hydrazo-bond in 4,4'-dimethyl-3,3'-dinitro-2,2'-hydrazobipyridine - crystal structure, conformation and vibrational characteristics.

The crystal and molecular structure of 4,4'-dimethyl-3,3'-dinitro-2,2'-hydrazobipyridine have been determined by X-ray diffraction and quantum chemical DFT analysis. The title compound crystallizes in P1¯ space group, with one-half molecule in the asymmetric unit. The molecular structure is stabilized by intramolecular NH···O hydrogen bonds. The molecules are linked by a combination of weak intermolecular CH⋯O interactions and also aromatic π-π stacking. The molecular structure of the studied compound has been determined using the DFT B3LYP/6-311G(2d,2p) approach and compared to that derived from X-ray studies. The IR and Raman wavenumbers have been calculated for the optimized geometry of a possible monomer structural model. The structural and vibrational properties of the intramolecular NH···O interaction are described.

The role of hydrogen bonds in the crystals of 2-amino-4-methyl-5-nitropyridinium trifluoroacetate monohydrate and 4-hydroxybenzenesulfonate - X-ray and spectroscopic studies.

Two new organic-organic salts, 2-amino-4-methyl-5-nitropyridinium trifluoroacetate monohydrate (AMNP-TFA), and 2-amino-4-methyl-5-nitropyridinium 4-hydroxybenzenesulfonate (AMNP-HBS), were obtained and characterized by means of FT-IR, FT-Raman and single crystal X-ray crystallography. In the former crystal, the cations, anions and water molecules are linked into layers by three types of hydrogen bonds, NPH⋯O, NAH⋯O and OH⋯O. These layers are connected by weaker CH⋯O hydrogen bonds. In the latter crystal, the cations and anions form one-dimensional structure through a number of hydrogen-bonding interactions involving the OH, NH(+) and NH2 groups as donors. In this case the NPH⋯O and NAH⋯O hydrogen bonds are formed. The combination of interactions between cations and anions results in the formation of columns. Additionally, there are π-π stacking interactions between the columns. The obtained X-ray structural data are related to the vibrational spectra of the studied crystals.

Comprehensive physicochemical studies of a new hybrid material: 2-amino-4-methyl-3-nitropyridinium hydrogen oxalate.

A new organic-organic salt, 2-amino-4-methyl-3-nitropyridinium hydrogen oxalate (AMNPO), and its deuterium analogue have been synthesized and characterized by means of FT-IR, FT-Raman, DSC and single crystal X-ray studies. The DSC measurements and temperature dependence of the IR and Raman spectra in the range 4-295 K show that it undergoes a reversible phase transition at ~240 K. At room temperature it crystallizes in noncentrosymmetric space group P21. The unit-cell is built of the 2-amino-4-methyl-3-nitropyridinium cations and oxalate monoanions which are connected via the N-H···O and O-H···O hydrogen bonds. The geometrical and hydrogen bond parameters are similar for non-deuterated (at 120 and 293 K) and deuterated compounds (at 90K). The phase transition is probably a consequence of order-disorder transition inside of hydrogen network. The 6-311G(2d,2p) basis set with B3LYP functional have been used to discuss the structure and vibrational spectra of the studied compound.

Vibrational spectra, crystal structure, DFT quantum chemical calculations and conformation of the hydrazo-bond in 6-methyl-3-nitro-2-(2-phenylhydrazinyl)pyridine.

The crystal and molecular structures of 6-methyl-3-nitro-2-(2-phenylhydrazinyl)pyridine (6-methyl-3-nitro-2-phenylhydrazopyridine) have been determined by X-ray diffraction and quantum chemical DFT analysis. The crystal is monoclinic, space group C2/c, with Z=8 formula units in the elementary unit cell of dimensions a=16.791(4), b=6.635(2), c=21.704(7)Å, ß=100.54(3)°. The molecule consists of two nearly planar pyridine subunits. A conformation of the linking hydrazo-bridge CNHNHC is bend and the dihedral angle between the planes of the phenyl and pyridine rings is 88.2(5)°. The hydrogen bonding of the type NH···N and possibly also CH···O favors a dimer formation in the crystal structure. The dimers are further linked by a NH···O hydrogen bond, so forming a layer parallel to the ab plane. The molecular structure of the studied compound has been determined using the DFT B3LYP/6-311G(2d,2p) approach and compared to that derived from X-ray studies. The IR and Raman wavenumbers have been calculated for the optimized geometry of a possible monomer structural model but the possibility of the dimer formation through the NH···N hydrogen bond has also been considered. The structural and vibrational properties of the intra-molecular NH···O interaction are described.

Molecular and crystal structures, vibrational studies and quantum chemical calculations of 3 and 5-nitroderivatives of 2-amino-4-methylpyridine.

The crystal structures of 2-amino-4-methyl-3-nitropyridine (I), 2-amino-4-methyl-3,5-dinitropyridine (II) and 2-amino-4-methyl-5-nitropyridine (III) have been determined. The compounds crystallize in the monoclinic P2(1)/n, triclinic P-1 and monoclinic C2/c space groups, respectively. These structures are stabilized by a combination of N-H···N and N-H···O hydrogen bonds and exhibit layered arrangement with a dimeric N-H···N motif in which the molecular units are related by inversion centre. The molecular structures of the studied compounds have been determined using the DFT B3LYP/6-311G(2d,2p) approach and compared to those derived from X-ray studies. The IR and Raman wavenumbers have been calculated from the optimized geometry of monomers and dimers formed in the unit cell and compared to the experimental values obtained from the spectra.

Elucidation of structural restraints for phosphate residues with different hydrogen bonding and ionization states.

Solid state NMR spectroscopy and gauge including atomic orbital (GIAO) theoretical calculations were employed to establish structural restraints (ionization, hydrogen bonding, spatial arrangement) for O-phosphorylated l-threonine derivatives in different ionization states and hydrogen bonding strengths. These structural restraints are invaluable in molecular modeling and docking procedures for biological species containing phosphoryl groups. Both the experimental and the GIAO approach show that 31P delta ii chemical shift tensor parameters are very sensitive to the ionization state. The negative values found for the skew kappa are typical for -2 phosphates. The distinct span Omega values reflect the change of strength of hydrogen bonding. For species in the -1 ionization state, engaged in very strong hydrogen bonds, Omega is smaller than for a phosphate group involved in weak hydrogen bonding. For phosphates in the -2 ionization state, Omega is significantly smaller compared to -1 species, although the kappa for -1 samples never reaches negative values. For -1 phosphate residues, in the case when 1H one pulse and/or combined rotation and multiple pulse spectroscopy (CRAMPS) sequences fail and assignment of proton chemical shift is ambiguous, a combination of 1H-(13)C and 1H-(31)P 2D heteronuclear correlation (HETCOR) correlations is found to be an excellent tool for the elucidation of 1H isotropic chemical shifts. In addition, a 2D strategy using 1H-(1)H double quantum filter (DQF) correlations [a back-to-back (BABA) sequence in this work] is useful for analyzing the topology of hydrogen bonding. In the case of a multicenter phosphorus domain, 2D 31P-(31)P proton driven spin diffusion experiments give information about the spatial arrangement of the phosphate residues.

Combined effect of the DeltaPhe or DeltaAla residue and the p-nitroanilide group on a didehydropeptides conformation.

Two series of dehydropeptides of the general formulae Boc-Gly-X-Phe-p-NA, Boc-Gly-Gly-X-Phe-p-NA, Gly-X-Gly-Phe-p-NA.TFA, and Boc-Gly-X-Gly-Phe-p-NA, with X = Delta(Z)Phe and DeltaAla, were studied with NMR in DMSO and CDCl(3)-DMSO, and with CD in MeOH, MeCN, and TFE. The NMR spectra measured in DMSO suggest that peptides with the DeltaPhe residue next to Phe are folded whereas peptides with Gly between DeltaPhe and Phe are less ordered. NMR spectra of DeltaAla-containing peptides indicate that these peptides are flexible and their conformational equilibria are populated by many different conformations. The CD spectra show that conformational properties of the peptides studied are distinctly influenced by a mutual position of the dehydroamino acid residue and the p-NA group. They indicate that all dehydropeptides with the DeltaPhe residue, Boc-Gly-DeltaAla-Phe-p-NA, and Boc-Gly-Gly-DeltaAla-Phe-p-NA adopt ordered conformations in all solvents studied, presumably of the beta-turn type. The last two peptides exhibit surprising chiroptical properties. Their spectra show exciton coupling-like couplets in the region of the p-NA group absorption. This shape of CD spectra suggests a rigid, chiral conformation with a fixed disposition of the p-NA group. The CD spectra indicate that Boc-Gly-DeltaAla-Gly-Phe-p-NA and Gly-DeltaAla-Gly-Phe-p-NA.TFA are unordered, independently of the solvent.