Density Functional Theory Study of Cyanoetheneselenol: A Molecule of Astrobiological Interest.

The interstellar medium has a rich chemistry which involves a wide variety of molecules. Of particular interest are molecules that have a link to prebiotic chemistry which hold the key to understanding of our origins. On the basis of suggestions that selenium may have been involved in the origin and evolution of life, we have studied the selenium analogue of cyanoethenethiol, namely the novel cyanoetheneselenol. Cyanoetheneselenol exhibits conformational and geometrical isomerism. This theoretical work deals with the study of four forms of cyanoetheneselenol in terms of their structural, spectroscopic and thermodynamic parameters. All computations were performed using density functional theory method with the B3LYP functional and the Pople basis set, 6-311 + G(d,p), for all atoms. The relative stability of the four isomers of cyanoetheneselenol was obtained and interpreted. The infrared spectra were generated and assignment of the normal modes of vibration was performed. Probable regions of detection, proposed on the basis of parameters obtained from this study for the four isomers, include comets, the molecular cloud: Sagittarius B2(N), and planetary atmospheres. The molecular and spectroscopic parameters should be useful for future identification of the astrobiological molecule cyanoetheneselenol and the development of the Square Kilometre Array. Graphical Abstract E and Z isomers of cyanoetheneselenol.

Infrared spectrum, structural and optical properties and molecular docking study of 3-(4-fluorophenyl)-5-phenyl-4,5-dihydro-1H-pyrazole-1-carbaldehyde.

The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of 3-(4-fluorophenyl)-5-phenyl-4,5-dihydro-1H-pyrazole-1-carbaldehyde have been investigated experimentally and theoretically. The title compound was optimized using at HF and DFT levels of calculations. The B3LYP/6-311++G(d,p) (5D,7F) results and in agreement with experimental infrared bands. The normal modes are assigned using potential energy distribution. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using natural bonding orbital analysis. The frontier molecular orbital analysis is used to determine the charge transfer within the molecule. From molecular electrostatic potential map, it is evident that the negative electrostatic potential regions are mainly localized over the carbonyl group and mono substituted phenyl ring and are possible sites for electrophilic attack and, positive regions are localized around all para substituted phenyl and pyrazole ring, indicating possible sites for nucleophilic attack. First hyperpolarizability is calculated in order to find its role in nonlinear optics. The geometrical parameters are in agreement with experimental data. From the molecular docking studies, it is evident that the fluorine atom attached to phenyl ring and the carbonyl group attached to pyrazole ring are crucial for binding and the results draw us to the conclusion that the compound might exhibit phosphodiesterase inhibitory activity.

Molecular structure, FT-IR, vibrational assignments, HOMO-LUMO analysis and molecular docking study of 1-[5-(4-Bromophenyl)-3-(4-fluorophenyl)-4,5-dihydro-1H-pyrazol-1-yl]ethanone.

The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of 1-[5-(4-bromophenyl)-3-(4-fluorophenyl)-4,5-dihydro-1H-pyrazol-1-yl]ethanone have been investigated experimentally and theoretically using Gaussian09 software package. The title compound was optimized using the HF/6-31G(d) (6D, 7F), B3LYP/6-31G (6D, 7F) and B3LYP/6-311++G(d,p) (5D, 7F) calculations. The B3LYP/6-311++G(d,p) (5D, 7F) results and in agreement with experimental infrared bands. The geometrical parameters are in agreement with XRD data. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. Molecular electrostatic potential was also performed. From the MEP it is evident that the negative charge covers the C=O group and the positive region is over the rings. First hyperpolarizability is calculated in order to find its role in nonlinear optics. Molecular docking studies suggest that the compound might exhibit inhibitory activity against TPII and may act as anti-neoplastic agent.

Infrared spectrum, NBO, HOMO-LUMO, MEP and molecular docking studies (2E)-3-(3-nitrophenyl)-1-[4-piperidin-1-yl]prop-2-en-1-one.

FT-IR spectrum of (2E)-3-(3-nitrophenyl)-1-[4-piperidin-1-yl]prop-2-en-1-one was recorded and analyzed. The vibrational wavenumbers were computed using HF and DFT quantum chemical calculations. The data obtained from wavenumber calculations are used to assign IR bands. Potential energy distribution was done using GAR2PED software. The geometrical parameters of the title compound are in agreement with the XRD results. NBO analysis, HOMO-LUMO, first and second hyperpolarizability and molecular electrostatic potential results are also reported. The possible electrophile attacking sites of the title molecule is identified using MEP surface plot study. Molecular docking results predicted the anti-leishmanic activity for the compound.

FT-IR, NBO, HOMO-LUMO, MEP analysis and molecular docking study of Methyl N-({[2-(2-methoxyacetamido)-4-(phenylsulfanyl)phenyl]amino}[(methoxycarbonyl) imino]methyl)carbamate.

The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of Methyl N-({[2-(2-methoxyacetamido)-4-(phenylsulfanyl) phenyl]amino} [(methoxycarbonyl)imino]methyl)carbamate have been investigated using HF and DFT levels of calculations. The geometrical parameters are in agreement with XRD data. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. Molecular electrostatic potential study was also performed. The first and second hyperpolarizability was calculated in order to find its role in nonlinear optics. Molecular docking studies are also reported. Prediction of Activity Spectra analysis of the title compound predicts anthelmintic and antiparasitic activity as the most probable activity with Pa (probability to be active) value of 0.808 and 0.797, respectively. Molecular docking studies show that both the phenyl groups and the carbonyl oxygens of the molecule are crucial for bonding and these results draw us to the conclusion that the compound might exhibit pteridine reductase inhibitory activity.

Photoinduced reactions of 1-acetylisatin with phenylacetylenes.

[reaction: see text]Photoinduced reactions of 1-acetylisatin 1 with diphenylacetylenes 2a-2c afforded the corresponding 3-methylene-2-indolones 4a-4e and 5a-5e in 80-90% yields via a spirooxetene intermediate. Similar irradiation of 1 with phenylacetylene, on the other hand, resulted in efficient formation of two diastereoisomeric dispiro[3H-indole-3,2'-furan-3',3"-(3H)-indole]-2,5',2"(2H,5'H,2"H )triones 6 and 7 via a reaction sequence with initial formation of the spirooxetene intermediate. The regioselectivity in the photocycloaddition of 1 with phenylacetylene and the reaction mechanism for the formation of 6 and 7 are discussed.

3-Acetyl-4-benzoyl-2-methyl-5-phenyl-3,3a-dihydropyrazolo[2,3-c]pyrimidine-7(6H)-thione.

The molecule of the title compound, C(22)H(19)N(3)O(2)S, is not planar. The dihedral angle between the two phenyl rings is 27.46 (7) degrees and in the dihydropyrazolopyrimidine ring the total puckering amplitude Q(T) is 0.526 (3) A. The structure is stabilized by both intra- and intermolecular C-H.O interaction, and by an intermolecular N-H.S hydrogen bond.

Pyridine-4-carbaldehyde azine.

In the crystal structure of the title compound, C(12)H(10)N(4), the pyridine ring makes a dihedral angle of 1.12 (9) degrees with the mean plane of the complete almost planar and crystallographically centrosymmetric molecule. There are stacks of parallel molecules along the a-axis direction, with alternate stacks having a herring-bone arrangement relative to each other and an interplanar spacing of 3.551 A.

Tris(8-quinolinolato-N,O)cobalt(III) ethanol solvate.

In the crystal of the title complex, [Co(C(9)H(6)NO)(3)].C(2)H(5)OH, the central Co atom has a distorted octahedral coordination comprised of three N atoms and three O atoms from the three 8-quinolinolato ligands. The three Co-O bond distances are in the range 1.887 (2)-1.910 (2) A, while the three Co-N bond distances range from 1.919 (2) to 1.934 (2) A. The solvent ethanol molecule forms an intermolecular O-H.O hydrogen bonding with a quinolinolato ligand.

Bis[N,N-bis(2-hydroxyethyl)dithiocarbamato]dimethyltin(IV).

The title compound, [Sn(CH(3))(2)(C(5)H(10)NO(2)S(2))(2)], has crystallographic mirror symmetry (C-Sn-C on mirror plane) and the coordination polyhedron around the Sn atom is a tetrahedron [C-Sn-C 139.3 (2) degrees and S-Sn-S 82.3 (1) degrees ] distorted towards a skew-trapezoidal bipyramid owing to an intramolecular Sn.S contact [3.0427 (6) A]. The molecules are linked into a linear chain by intermolecular O-H.O hydrogen bonds [O.O 2.646 (3) A].

Bis(N,N-dimethylthiocarbamoylthio)acetic acid.

Bis(N,N-dimethylthiocarbamoylthio)acetic acid, [(CH(3))(2)NC(=S)S](2)CHC(=O)OH or C(8)H(14)N(2)O(2)S(4), exists as a centrosymmetric hydrogen-bonded dimer [O.O 2.661 (3) A].

The manganese(III) complex with chelating Schiff base ligand: X-ray structure, spectroscopic and computational studies.

A new Mn(III) complex, [MnCl(H(2)O)(L)].H(2)O.C(2)H(5)OH, where L=2,2'-[1,2-phenylenebis[nitrilomethylylidene]]bis(6-methoxyphenolate), has been synthesized and characterized by single-crystal X-ray diffraction. There is a good agreement between calculated and experimental structural data. The complex is crystallized in orthorhombic with space group Pbca. The Mn1 atom is coordinated with one Schiff base ligand, one water molecule and one chloride anion, forming a six-coordination number. The electronic and fluorescence spectra of the complex were also studied.

1,2,3-Trimethoxy-5,11-dihydroindolo[1,2-b]isoquinoline-5,11-dione.

The title compound, C15H19NO5, crystallizes in the monoclinic space group P2(1)/c with four molecules in the asymmetric unit, which differ from each other in the orientation of their methoxy groups. Of the three methoxy groups in each molecule, one lies close to the plane of the molecule and the other two have an out-of-plane conformation where they point in opposite directions. In the crystal structure, four different types of pi-stacks are observed and the molecules pack in two different types of stacking sheets, with alternating molecules A and B in one ribbon and alternating molecules C and D in the other. The supramolecular structure is supported by C-H...O and pi-pi interactions.

The 143 and 300 K polymorphs of hexamethylenetetraminium 2,4-dinitrophenolate monohydrate.

The title compound, 3,5,7-triaza-1-azoniatricyclo[3.3.1.1(3,7)]decane 2,4-dinitrophenolate monohydrate, C6H13N4+*C6H3N2O5-*H2O, the 1:1 hydrate adduct of hexamethylenetetramine (HMT) and 2,4-dinitrophenol, undergoes a temperature phase transition. In the room-temperature phase, the adduct crystallizes in the monoclinic P2(1)/m space group, whereas in the low-temperature phase, the adduct crystallizes in the triclinic P1 space group. This phase transition is reversible, with the transition temperature at 273 K, and the phase transition is governed by hydrogen bonds and weak interactions. In both these temperature-dependent polymorphs, the crystal structure is alternately layered with sheets of hexamethylenetetramine and sheets of dinitrophenol stacked along the c axis. The hexamethylenetetramine and dinitrophenol moieties are linked by intermolecular hydrogen bonds. The water molecule in the adduct plays an important role, forming O-H...O hydrogen bonds which, together with C-H...O hydrogen bonds, bridge the adducts into molecular ribbons. Extra hydrogen bonds and weak interactions exist for the low-temperature polymorph and these interconnect the molecular ribbons into a three-dimensional packing structure. Also in these two temperature-dependent polymorphs, dinitrophenol acts as a hydrogen-bond acceptor and HMT acts as a hydrogen-bond donor.

Bis(dicyclohexylammonium 3-thienylacetate).

The triclinic cell of the title compound contains 2C(12)H(24)N(+) x 2C(6)H(5)O(2)S(-) ion pairs that are linked by four hydrogen bonds [N...O = 2.728 (3) and 2.758 (3) A] across a centre of inversion.

5-amino-4-(4-diethylaminophenyl)-2-(4-hydroxyphenyl)-7-(pyrrolidin-1-yl)-1,6-naphthyridine-8-carbonitrile.

In the title compound, C29H30N6O, the naphthyridine moiety is planar with a dihedral angle between the fused rings of 1.9 (1) degrees. The phenol ring is nearly coplanar, while the diethylaminophenyl substituent is orthogonal to the central naphthyridine ring and the pyrrolidine ring makes an angle of 11.2 (1) degrees with it. The O atom of the hydroxy substituent is coplanar with the phenyl ring to which it is attached. The molecular structure is stabilized by a C-H...N-type intramolecular hydrogen bond and the packing is stabilized by intermolecular C-H...pi, O-H...N and N-H...O hydrogen bonds.

Heterometallic polymeric clusters containing tetraselenotungstate anion: one-dimensional helical chain [[La(Me2SO)8.

[PPh4]2[WSe4] reacts with an equivalent of [Ag(MeCN)4][ClO4] in DMF to afford a linear polymeric cluster [[Ph4P][(mu-WSe4)Ag]]n (1). Treatment of cluster 1 with excess La(NO3)3.3H2O in Me2SO solution resulted in the formation of a helical chain polymeric cluster [[La(Me2SO)8][(mu-WSe4)3Ag3]]n (2). Cluster 2 crystallizes in the monoclinic space group P2(1/n) with four formula units in a cell of dimensions a = 12.7642(5) A, b = 24.1725(9) A, c = 19.4012(7) A, and beta = 103.546(11) degrees. Refinement by full-matrix least-squares techniques gave final residuals R = 0.0540 and Rw = 0.1116 for 494 variables and 7593 reflections (Fo(2) > 2.0sigma(Fo(2))). The anion [[(mu-WSe4)3Ag3]]n(3n-) in 2 can be described as a butterfly-type SeWSe3Ag2 basic repeating unit linked through interactions with a Ag atom of one fragment and a Ag atom of another to form an intriguing helical array. The CuCN, KCN, and [Et4N]2[WSe4] reaction system resulted in the formation of a novel three-dimensional cluster [[Et4N]2[(mu4-WSe4)Cu4(CN)4]]n (4) either in DMF/2-picoline or in solid at 80 degrees C. Cluster 4 crystallizes in the orthorhombic space group Fddd with cell constants a = 11.090(2) A, b = 23.206(5) A, c = 23.910(5) A, and Z = 8. Anisotropic refinement with 1510 reflections (Fo(2) > 2.0sigma(Fo(2))) and 82 parameters for all non-hydrogen atoms yielded the values of R = 0.0428 and Rw = 0.0887. The anion structure of 4 is built up from a WSe4Cu4 unit bridged by cyanide ligands to form a three-dimensional cross framework. The air- and moisture-stable polymeric clusters easily decompose into small molecular clusters when treated with ligands such as PPh3 and pyridine (Py). Cluster 2 exhibits both strong optical absorption and an optical self-focusing effect (effective alpha2 = 2.2 x 10(-9) m2.W(-1), n2 = 6.8 x 10(-15) m2.W(-1); examined in a 0.13 mM DMF solution). Cluster 4 shows good photostability in the process of measurement and a large optical limiting effect (the limiting threshold is ca. 0.2 J.cm(-2)).