Hydrogen-Bonded (H2O·X)2 [X=Cl–, Br–] Clusters in 1-Phenacyl-4-(Dimethylamino)Pyridinium Halide Monohydrates

The synthesis, and X-ray crystal and molecular structures, of 1-phenacyl-4-(dimethylamino)pyridinium chloride and bromide monohydrates are described.

Cation tautomerism, twinning and disorder in the triclinic and monoclinic forms of 4-amino-5-chloro-2,6-dimethylpyrimidinium 5-chloro-2-hydroxybenzoate and a new disordered refinement of 2-amino-4,6-dimethoxypyrimidin-1-ium thiophene-2-carboxylate

Pyrimidines are important compounds in biology and medicine, and the aminopyrimidine fragment can be identified in three of the four bases in DNA. The targeted drug action of pharmaceuticals containing this functionality is likely to depend heavily on molecular recognition processes involving hydrogen bonding. Crystallization of an equimolar mixture of 4-amino-5-chloro-2,6-dimethylpyrimidine and 5-chloro-2-hydroxybenzoic acid yielded two forms of the 1:1 salt, C₆H₉ClN₃⁺·C₇H₄ClO₃^-, each containing a different tautomeric form of the cation. 6-Amino-5-chloro-2,4-dimethylpyrimidin-1-ium 5-chloro-2-hydroxybenzoate, (I), crystallizes in the space group P-1, with Z' = 2, and all of the component ions are fully ordered. 4-Amino-5-chloro-2,6-dimethylpyrimidin-1-ium 5-chloro-2-hydroxybenzoate, (II), also crystallizes with Z' = 2, but in the space group P2₁/c and as a merohedral twin which closely mimics an orthorhombic unit cell. In (II), one of the cations and one of the anions is disordered, each over two sets of atomic sites having occupancies of 0.836 (2) and 0.164 (2), and 0.834 (2) and 0.166 (2). The bond lengths in the cations of (I) and (II) provide evidence for o-quinonoid and p-quinonoid bond fixation, respectively. A combination of six N-H...O hydrogen bonds links the component ions of (I) into two independent four-ion aggregates, but the ions in (II) are linked by a combination of four N-H...O and two N-H...N hydrogen bonds to form a three-dimensional framework structure. The recently reported structure of 2-amino-4,6-dimethoxypyrimidin-1-ium thiophene-2-carboxylate, C₆H₁₀N₃O₂⁺·C₅H₃O₂S^-, (III), has been rerefined, using the original data set, to show that the anion is disordered over two sets of atomic sites, approximately related by a 180° rotation about the exocyclic C-C bond, and having occupancies of 0.8687 (19) and 0.1313 (19).

Crystal structure of 2-amino-pyridinium 6-chloro-nicotinate

In the title salt, C5H7N(+)·C6H3ClNO(-), the 2-amino-pyri-din-ium cation inter-acts with the carboxyl-ate group of the 6-chloro-nicotinate anion through a pair of independent N-H⋯O hydrogen bonds, forming an R 2 (2)(8) ring motif. In the crystal, these dimeric units are connected further via N-H⋯O hydrogen bonds, forming chains along [001]. In addition, weak C-H⋯N and C-H⋯O hydrogen bonds, together with weak π-π inter-actions, with centroid-centroid distances of 3.6560 (5) and 3.6295 (5) Å, connect the chains, forming a two-dimensional network parallel to (100).

Vibrational spectra (experimental and theoretical), molecular structure, natural bond orbital, HOMO-LUMO energy, Mulliken charge and thermodynamic analysis of N'-hydroxy-pyrimidine-2-carboximidamide by DFT approach

The FT-IR, FT-Raman, (1)H, (13)C NMR and UV-Visible spectral measurements of N'-hydroxy-pyrimidine-2-carboximidamide (HPCI) and complete analysis of the observed spectra have been proposed. DFT calculation has been performed and the structural parameters of the compound was determined from the optimized geometry with 6-311+G(d,p) basis set and giving energies, harmonic vibrational frequencies and force constants. The results of the optimized molecular structure are presented and compared with the experimental. The geometric parameters, harmonic vibrational frequencies and chemical shifts were compared with the experimental data of the molecule. The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15)°. The crystal structure is also stabilized by intermolecular N-H⋯O, N-H⋯N, O-H⋯N, C-H⋯O hydrogen bond and offset π-π stacking interactions. The influences of hydroxy and carboximidamide groups on the skeletal modes and proton chemical shifts have been investigated. Moreover, we have not only simulated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) but also determined the transition state and band gap. The kinetic, thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intermolecular electronic interactions and their stabilization energy. The thermodynamic properties like entropies and their correlations with temperatures were also obtained from the harmonic frequencies of the optimized structure.

Synthesis, crystal structure and theoretical studies of a Schiff base 2-[4-hydroxy benzylidene]-amino naphthalene

The molecular structure of a new Schiff base, 2-[4-hydroxy benzylidene]-amino naphthalene (HBAN) has been examined by HF and B3LYP/6-311++G(d,p) calculations. The X-ray structure was determined in order to establish the conformation of the molecule. The compound, C17H13NO, crystallizes in the orthorhombic, P212121 space group with the cell dimension, a=6.2867(2), b=10.2108(3), c=19.2950(6) Å, α=β=γ=90° and z=4. The asymmetric unit contains a molecule of a Schiff base. A strong intermolecular O-H⋯N and a weak C-H⋯O hydrogen bonds stabilized the crystal structure. The vibrational spectra of HBAN have been calculated using density functional theoretical computation and compared with the experimental. The study is extended to the HOMO-LUMO analysis to calculate the energy gap (Δ), Ionization potential (I), Electron Affinity (A), Global Hardness (η), Chemical Potential (μ) and Global Electrophilicity (w). The calculated HOMO and LUMO energy reveals that the charge transfer occurs within the molecule.

1, 5-Bis (2-hydroxyacetophenone)thiocarbohydrazone: a novel colorimetric and fluorescent dual-mode chemosensor for the recognition of fluoride

1,5-Bis (2-hydroxyacetophenone)thiocarbohydrazone (H4L) has been synthesized and characterized by means of spectroscopic and single crystal X-ray diffraction methods. Interactions of the H4L with a variety of anions were investigated using a combination of UV-visible and fluorescence spectroscopic methods in a biological competing solvent DMSO. The H4L has a high degree of selectivity for fluoride over other anions. (1)H NMR titration experiments indicate that a deprotonation process is involved in the chemo sensing process.

N-[1-(5-Acetamido-3-acetyl-2-methyl-2,3-dihydro-1,3,4-thia-diazol-2-yl)-2-phenyl-ethyl]acetamide

In the title compound, C(17)H(22)N(4)O(3)S, the dihedral angle between the planes of the thia-diazole and phenyl rings is 63.47 (7)°. The dihedral angle between the thia-diazole ring and the acetamide side chain is 7.72 (9)°. Mol-ecules related by a 2(1) screw axis along the a axis are linked by inter-molecular N-H⋯O hydrogen bonds generating a supra-molecular chain.

Aminopyrimidine-carboxyl(ate) interactions in trimethoprim maleate, an antifolate drug

In the title cocrystal, trimethoprim maleate [2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidin-1-ium maleate], C(14)H(19)N(4)O(3)(+).C(4)H(3)O(4)(-), the trimethoprim molecule is protonated at N1. The carboxyl group of the maleate ion makes a specific double hydrogen bond of type N-H.O with the 2-amino group and the protonated N1 atom of the trimethoprim cation which is similar to the carboxylate-trimethoprim cation interaction observed in the complex of dihydrofolate reductase with trimethoprim. The pyrimidine moieties of trimethoprim cations are centrosymmetrically paired through a pair of N-H.N hydrogen bonds involving the 4-amino group and the pyridinium N3 atom of a symmetry-related molecule. One of the O atoms at the maleate carboxylate group bridges the 2-amino and 4-amino groups on either side of the paired trimethoprim cations. The other O atom of the carboxylate group forms an intramolecular O-H.O hydrogen bond with the carboxyl group. These characteristic hydrogen bonds result in infinite two-dimensional aggregation of rings into a supramolecular ladder, which is further crosslinked through weak C-H.O interactions with methoxy groups of neighbouring trimethoprim molecules to form a layered structure.

8-Hydroxy-7-nitroquinoline-5-sulfonic acid monohydrate

The title compound, C9H6N2O6S.H2O, is zwitterionic (i.e. 8-hydroxy-7-nitroquinolinium-5-sulfonate monohydrate) with a deprotonated sulfonic group and a protonated quinoline N atom which interacts with the hydroxy O atom. The H atom of the hydroxy group is distal to the N atom and is involved in an interaction with an O atom of the nitro group, which is oriented at 32.2(1) degrees with respect to the quinoline ring system.