Crystal structures of 4-phenyl-piperazin-1-ium 6-chloro-5-ethyl-2,4-dioxopyrimidin-1-ide and 4-phenyl-piperazin-1-ium 6-chloro-5-isopropyl-2,4-dioxopyrimidin-1-ide.

The title mol-ecular salts, C10H15N2 (+)·C6H6ClN2O2 (-), (I), and C10H15N2 (+)·C7H8ClN2O2 (-), (II), consist of 4-phenyl-piperazin-1-ium cations with a 6-chloro-5-ethyl-2,4-dioxopyrimidin-1-ide anion in (I) and a 6-chloro-5-isopropyl-2,4-dioxopyrimidin-1-ide anion in (II). Salt (I) crystallizes with two independent cations and anions in the asymmetric unit. In the crystal structures of both salts, the ions are linked via N-H⋯O and N-H⋯N hydrogen bonds, forming sheets which are parallel to (100) in (I) and to (001) in (II). In (I), the sheets are linked via C-H⋯Cl hydrogen bonds, forming a three-dimensional framework.

Spectroscopic investigation (FT-IR and FT-Raman), vibrational assignments, HOMO-LUMO, NBO, MEP analysis and molecular docking study of 2-[(4-chlorobenzyl)sulfanyl]-4-(2-methylpropyl)-6-(phenylsulfanyl)-pyrimidine-5-carbonitrile, a potential chemotherapeutic agent.

Vibrational spectral analysis of 2-[(4-chlorobenzyl)sulfanyl]-4-(2-methylpropyl)-6-(phenylsulfanyl)-pyrimidine-5-carbonitrile was carried out using FT-IR and FT-Raman spectroscopic techniques. The equilibrium geometry and vibrational wave numbers have been computed using density functional B3LYP method with 6-311++G(d,p)(5D,7F) as basis set. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using NBO analysis. The nonlinear optical behavior of the title compound is also theoretically predicted. From the MEP, it is evident that the negative charge covers the C≡N group and the positive region is over the phenyl and the pyrimidine rings. From the potential energy scan it is clear that the lone pairs of the sulfur atom prefer to point away from the pyrimidine ring and the C≡N group resulting with two possible minimum conformations at the N4C8S1C25 angle equal nearly 0° or 150°. Molecular docking results suggest that the compound might exhibit inhibitory activity against GPb and may act as potential anti-diabetic compound.

Vibrational spectroscopic and molecular docking study of 2-Benzylsulfanyl-4-[(4-methylphenyl)-sulfanyl]-6-pentylpyrimidine-5-carbonitrile, a potential chemotherapeutic agent.

FT-IR and FT-Raman spectra of 2-Benzylsulfanyl-4-[(4-methylphenyl)-sulfanyl]-6-pentylpyrimidine-5-carbonitrile were recorded and analyzed. The structure of the molecule has been optimized and the structural characteristics have been determined by density functional theory. The geometrical parameters (DFT) are in agreement with the XRD results. HOMO and LUMO and other chemical properties are reported. Nonlinear optical properties are reported. A detailed molecular picture of the title compound and its interactions were obtained from NBO analysis. The negative (red and yellow) regions of the MEP are related to electrophilic reactivity and the positive (blue) regions to nucleophilic reactivity, as shown in the MEP plot and the title compound has several possible sites, CN, N atom of pyrimidine ring and sulfur atoms for electrophilic attack. From the molecular docking studies it is clear that the title compound binds at the catalytic site of the substrate by weak non-covalent interactions most prominent of which are H-bonding, π-π, alkyl-π, and amide-π interactions.

Vibrational spectra, NBO analysis, HOMO-LUMO and first hyperpolarizability of 2-{[(2-Methylprop-2-en-1-yl)oxy]methyl}-6-phenyl-2,3,4,5-tetrahydro-1,2,4-triazine-3,5-dione, a potential chemotherapeutic agent based on density functional theory calculations.

The experimental FT-IR and FT-Raman spectra of 2-{[(2-Methylprop-2-en-1-yl)oxy]methyl}-6-phenyl-2,3,4,5-tetrahydro-1,2,4-triazine-3,5-dione were recorded. The optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of the compound have been examined by means of density functional theory. Reliable vibrational assignments and molecular orbital have been investigated by the potential energy distribution and natural bonding orbital analyses, respectively. The calculated first hyperpolarizability of the title compound is 2.82×10(-30) esu which is 21.69 times that of the standard NLO material urea. MEP was performed by the B3LYP level and the predicted infrared intensities and Raman activities have also been reported. Quantum chemical parameters were arrived from the frontier molecular orbital theory. The calculated geometrical parameters are in agreement with experimental results. From the MEP it is evident that the negative charge covers the CO groups and the positive region is over the rings and NH group.

The biomolecule, 2-[(2-methoxyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile: FT-IR, Laser-Raman spectra and DFT.

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized potential chemotherapeutic agent namely, 2-[(2-methoxyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile have been investigated. The experimental FT-IR (4000-400cm(-1)) and Laser-Raman spectra (4000-100cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with the results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations.

Structural and spectroscopic characterization of a novel potential anti-inflammatory agent 3-(adamantan-1-yl)-4-ethyl-1H-1,2,4-triazole-5(4H)thione by first principle calculations.

A comprehensive investigation on the molecular structure, electronic properties and vibrational spectra of the 3-(adamantan-1-yl)-4-ethyl-1H-1,2,4-triazole-5(4H)thione, a novel potential anti-inflammatory agent has been done with the hope that the results of present study may be helpful in the prediction of its mechanism of biological activity. The experimentally observed spectral data (FT-IR and FT-Raman) of the title compound was compared with the spectral data obtained by DFT/B3LYP method. The (1)H nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge Including Atomic Orbital method and compared with experimental results. The molecular properties like dipole moment, polarizability, first static hyperpolarizability, the molecular electrostatic potential surface, contour map have been calculated to get a better insight of the properties of the title molecule. Natural bond orbital (NBO) analysis has been applied to study stability of the molecule arising from charge delocalization. UV-Vis spectrum of the title compound was also recorded and the electronic properties, such as Frontier orbitals and band gap energies were calculated by TD-DFT approach. Global and local reactivity descriptors have been computed to predict reactivity and reactive sites on the molecule.

Experimental FT-IR, Laser-Raman and DFT spectroscopic analysis of a potential chemotherapeutic agent 6-(2-methylpropyl)-4-oxo-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carbonitrile.

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized potential chemotherapeutic agent namely, 6-(2-methylpropyl)-4-oxo-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carbonitrile have been investigated. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09 W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with the results in the literature. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and depicted.

5-(Adamantan-1-yl)-3-anilinomethyl-2,3-di-hydro-1,3,4-oxa-diazole-2-thione.

In the title compound, C19H23N3OS, the oxa-diazole and benzene rings are inclined at a dihedral angle of 50.30 (11)°, with the major twist between them occurring at the ring-methyl-ene N-C bond [N-N-C-N torsion angle = -101.2 (2)°]. In the crystal, helical supra-molecular chains along [010] are sustained by N-H⋯S hydrogen bonds. These are linked into layers lying parallel to (-101) by methyl-ene-phenyl C-H⋯π inter-actions.

2-Benzyl-sulfanyl-4-[(4-methyl-phen-yl)sulfan-yl]-6-pentyl-pyrimidine-5-carbonitrile.

In the title compound, C(24)H(25)N(3)S(2), the S-bound benzene rings have orthogonal [dihedral angle = 85.31 (9)°] and splayed [67.92 (11)°] orientations with respect to the pyrimidine ring; the dihedral angle between the benzene rings is 48.18 (12)°. The pentyl group has an extended all-trans conformation and lies to one side of the pyrimidine ring [the N(py)-C(py)-C(p)-C(p) torsion angle = -85.7 (2)°; py = pyrimidine and p = pent-yl].

2-[(4-Chloro-benz-yl)sulfan-yl]-4-(2-methyl-prop-yl)-6-(phenyl-sulfan-yl)pyrimidine-5-carbonitrile.

In the title compound, C(22)H(20)ClN(3)S(2), the S-bound benzene rings are inclined [dihedral angles = 78.13 (10) and 36.70 (9)°] with respect to the pyrimidine ring. The methyl-propyl group occupies a position normal to the pyrimidine ring [N-C-C-C torsion angle = 92.3 (2)°]. In the crystal, supra-molecular layers are formed in the bc plane, being consolidated by C-H⋯π and π-π inter-actions, the latter between the pyrimidine and S-bound benzene rings [inter-centroid distance = 3.7683 (12) Å].

2-[(4-Chloro-benz-yl)sulfanyl]-4-(2-methyl-prop-yl)-6-[3-(trifluoro-meth-yl)anilino]-pyrimidine-5-carbonitrile.

Three independent mol-ecules comprise the asymmetric unit of the title compound, C(23)H(20)ClF(3)N(4)S. The conformations of the mol-ecules are similar with the chloro-benzene and CF(3)-benzene rings almost perpendicular to, and almost co-planar with, the pyrimidinyl ring [range of dihedral angles = 80.36 (13)-88.07 (14) and 11.89 (14)-23.30 (14)°, respectively]; the benzene rings are roughly orthogonal to each other [64.81 (16)-72.16 (15)°]. In the crystal, two of the independent mol-ecules associate via weak N-H⋯N(cyano) hydrogen bonds and 12-membered {⋯HNC(3)N}(2) synthons; the third independent mol-ecule self-associates similarly but about a centre of inversion. The sample studied was found to be a non-merohedral twin and the minor twin component refined to 47.16 (7)%.

2-[(2-Meth-oxy-eth-yl)sulfan-yl]-4-(2-methyl-prop-yl)-6-oxo-1,6-dihydro-pyrimidine-5-carbonitrile.

In the title compound, C(12)H(17)N(3)O(2)S, the 4-methyl-2-methyl-sulfanyl-6-oxo-1,6-dihydro-pyrimidine-5-carbonitrile part of the mol-ecule is almost planar (r.m.s deviation = 0.062 Å). In the crystal, mol-ecules form centrosymmetric dimers via pairs of N-H⋯O hydrogen bonds.

(E)-1-(1,3-Benzodioxol-5-yl)-4,4-di-methyl-pent-1-en-3-one.

In the mol-ecule of the title compound, C(14)H(16)O(3), all non-H atoms except for one methyl C atom lie on a crystallographic mirror plane. The conformation with respect to the C=C bond [1.3465 (12) Å] is trans. In the crystal, mol-ecules are linked via C-H⋯O hydrogen bonds into C(5) chains propagating along [100].

6-(2-Methyl-prop-yl)-4-oxo-2-sulfanyl-idene-1,2,3,4-tetra-hydro-pyrimidine-5-carbonitrile.

The title thio-uracil derivative, C(9)H(11)N(3)OS, exists in the thione form. The six atoms comprising the ring are almost coplanar [r.m.s. deviation = 0.015 Å] and the 2-methyl-propyl group lies approximately perpendicular to this plane [the N-C-C-C torsion angle is 72.88 (14)°]. Linear supra-molecular chains along [001] sustained by N-H⋯O and N-H⋯S hydrogen bonding feature in the crystal packing.

6-(3,5-Dimethyl-benz-yl)-5-ethyl-1-[(3-phenyl-prop-oxy)meth-yl]-1,2,3,4-tetra-hydro-pyrimidine-2,4-dione.

The pyrimidine ring of the title compound, C(25)H(30)N(2)O(3), is approximately planar (r.m.s. deviation = 0.003 Å); the C atom at the 5-position deviates by 0.012 (3) Šfrom the mean plane and the C atom at the 6-position by 0.038 (3) Å. In the mol-ecule, the pyrimidine ring is oriented at 86.72 (9) and 59.75 (9)° with respect to the two benzene rings, and the two benzene rings are inclined to each other at 58.35 (9)°. In the crystal, the amino group is hydrogen-bond donor to the exocyclic O atom at the 4-position of an adjacent mol-ecule, the hydrogen bond generating an inversion dimer.

2-Eth-oxy-methyl-6-ethyl-2,3,4,5-tetra-hydro-1,2,4-triazine-3,5-dione.

The 1,2,4-triazine ring of the title compound, C(8)H(13)N(3)O(3), is nearly planar (r.m.s. deviation = 0.019 Å). The imino group is hydrogen-bond donor to the exocyclic O atom at the 5-position of an adjacent mol-ecule, the N-H⋯O hydrogen bond generating a chain parallel to the b axis.

1-[(Cyclo-propyl-meth-oxy)meth-yl]-5-ethyl-6-(4-methyl-benzyl)-1,2,3,4-tetra-hydro-pyrimidine-2,4-dione.

The pyrimidine ring in the title compound, C(19)H(24)N(2)O(3), is nearly planar (r.m.s. deviation = 0.008 Å); the C atom at the 5-position deviates by 0.054 (3) Šfrom the mean plane and the C atom at the 6-position by 0.006 (3) Šin the opposite direction. The benzene ring is approximately perpendicular to the pyrimidine ring [dihedral angle = 83.90 (10)°]. The amino group is hydrogen-bond donor to the exocyclic O atom at the 2-position of an adjacent mol-ecule, the hydrogen bond generating an inversion dimer. The cyclo-propyl ring is disordered over two sets of sites with the major component having 71.5 (4)% occupancy.

1-[(Cyclo-propyl-meth-oxy)meth-yl]-6-(3,4-dimeth-oxy-benzyl)-5-ethyl-1,2,3,4-tetra-hydro-pyrimidine-2,4-dione ethanol hemisolvate.

The asymmetric unit of the compound, C(20)H(26)N(2)O(5)·0.5C(2)H(5)OH, consists of two tetra-hydro-pyrimidine-2,4-dione mol-ecules and an ethanol mol-ecule. The pyrimidine rings are nearly planar (r.m.s. deviation = 0.006 Šin one mol-ecule and 0.009 Šin the other); the C atom at the 5-position deviates by 0.083 (3) Š[0.064 (3) Šin the second mol-ecule] from the mean plane and the C atom at the 6-position by 0.034 (3) Š[0.082 (3) Šin the second mol-ecule]. In each mol-ecule, the benzene ring is nearly perpendicular to the pyrimidine ring, the dihedral angle is 88.51 (8)° in one mol-ecule and 84.70 (8)° in the other. The amino group of each tetra-hydro-pyrimidine-2,4-dione mol-ecule is a hydrogen-bond donor to the exocyclic O atom at the 2-position of an adjacent mol-ecule, the hydrogen bond generating an inversion dimer in each case. The ethanol mol-ecule forms a hydrogen bond to the meth-oxy O atom of one of two independent mol-ecules.

Synthesis of novel 6-phenyl-2,4-disubstituted pyrimidine-5-carbonitriles as potential antimicrobial agents.

New series of 6-phenyl-2,4-disubstituted pyrimidine-5-carbonitriles namely, 2-substitued thio-6-phenyl-3,4-dihydro-4-oxopyrimidine-5-carbonitriles (5a-d, 6, 7a-d, 8), 2-(4-chlorobenzylthio)-4-chloro-6-phenylpyrimidine-5-carbonitrile (9), 2-(4-chlorobenzylthio)-4-arylthio-6-phenylpyrimidine-5-carbonitriles (10a-d) and 2-(4-chlorobenzylthio)-4-arylamino-6-phenylpyrimidine-5-carbonitriles (11a-d) was synthesized and tested for in vitro activities against a panel of Gram-positive and Gram-negative bacteria and the yeast-like pathogenic fungus Candida albicans. Compounds 5b, 5c, 6, 7a, 7b, 7c, 9 and 11a displayed marked antibacterial activity particularly against the tested Gram-positive bacteria, while compounds 6, 7c, 7d and 9 were moderately or weakly active against C. albicans.

Synthesis and antimicrobial activity of some novel 5-alkyl-6-substituted uracils and related derivatives.

6-chloro-5-ethyl-, n-propyl- and isopropyluracils 5a-c were efficiently prepared from the corresponding 5-alkybarbituric acids 3a-c via treatment with phosphorus oxychloride and N,N-dimethylaniline to yield the corresponding 5-alkyl-2,4,6-trichloro-pyrimidines 4a-c, which were selectively hydrolyzed by heating in 10% aqueous sodium hydroxide for 30 minutes. The reaction of compounds 5a-c with 1-substituted piperazines yielded the corresponding 5-alkyl-6-(4-substituted-1-piperazinyl)uracils 6a-j. The target 8-alkyltetrazolo[1,5-f]pyrimidine-5,7(3H,6H)-diones 7a-c were prepared via the reaction of 5a-c with sodium azide. Compounds 6a-j and 7a-c were tested for in vitro activities against a panel of Gram-positive and Gram-negative bacteria and the yeast-like pathogenic fungus Candida albicans. Compound 6h displayed potent broad-spectrum antibacterial activity, while compound 6b showed moderate activity against the Gram-positive bacteria. All the tested compounds were practically inactive against Candida albicans.