Synthesis, density functional theory (DFT) studies and urease inhibition activity of chiral benzimidazoles.

A variety of benzimidazole by the heterocyclization of orthophenylenediamine were synthesized in 69-86% yields. The synthesized compounds 3a-f and 6a-f were characterized and further investigated as jack bean urease inhibitors. Density functional theory (DFT) studies were performed utilizing the basis set B3LYP/6-31G (d, p) to acquire perception into their structural properties. Frontier molecular orbital (FMO) analysis of all compounds 3a-f and 6a-f was computed at the same level of theory to get a notion about their chemical reactivity and stability. The mapping of the molecular electrostatic potential (MEP) over the entire stabilized molecular geometry indicated the reactive centers. They exhibited urease inhibition activity with IC50 between 22 and 99 µM. Compounds containing withdrawing groups on the benzene ring (3d, 6d) were not showing significant urease inhibition. The value obtained for 3a, 3b, 3f had shown their significant urease inhibition for both theoretical and experimental. Notably, the compound having S-configuration (3a) (22.26 ± 6.2 µM) was good as compared to its R enantiomer 3f (31.42 ± 23.3 µM). Despite this, we elaborated the computational studies of the corresponding compounds, to highlight electronic effect which include HOMO, LUMO, Molecular electrostatic potential (MEP) and molecular docking.

Phytochemical and antioxidant studies of Berberis lycium.

Six compounds have been isolated from methanolic and petroleum ether extracts of Berberis lycium (Barberry). Four out of six isolated compounds are reported for the first time from this plant. Purification of different compounds has been accomplished by conventional extraction and chromatographic techniques. The compounds have been structurally characterized by IR, Low Resolution MS, (1)H-NMR and (13)C-NMR spectroscopic techniques. All plant extracts and isolated compounds were assayed for the first time for their antioxidant activity.

Synthesis, crystal structure, DNA binding and in vitro biological studies of Ni(II), Cu(II) and Zn(II) complexes of N-phthaloylglycine.

Ni(II), Cu(II) and Zn(II) metal complexes of N-phthaloylglycine were synthesized, characterized, reported for single crystal X-ray diffraction analysis for Ni(II) complex, and investigated for their binding with DNA under physiological conditions, using spectroscopic (UV-visible and fluorescence) and hydrodynamic techniques. Experimental results from both spectroscopic methods were comparable and further supported by viscosity measurements. Binding constant "K(b)" obtained from both spectroscopic methods revealed significant binding of compounds with DNA via intercalation. Among all compounds comparatively good DNA binding was found for Zn(II) complex. Free energies of compounds-DNA interactions indicated spontaneity of their binding. Dynamic and bimolecular enhancement values disclose static process involved in compounds-DNA complex formation. All compounds exhibited broad range antibacterial, while Zn(II) complex exhibited best antitumor activity.

N,N-Dicyclo-hexyl-3,5-dinitro-benzamide.

In the title compound, C(19)H(25)N(3)O(5), the benzene ring is not coplanar with the amide group [dihedral angle = 61.90 (5)°]. The cyclo-hexyl rings are in chair conformations. There is a strong inter-molecular inter-action between the C=O group of the amide group and the nitro group of an adjoining mol-ecule, with a short O⋯N distance of 2.7862 (17) Å. In the crystal, C-H⋯O inter-actions occur along the [100] direction.

4-(Naphthalene-2-carboxamido)-pyridin-1-ium thio-cyanate-N-(pyridin-4-yl)naphthalene-2-carboxamide (1/1).

The asymmetric unit of the title compound, C(16)H(13)N(2)O(+)·NCS(-)·C(16)H(12)N(2)O, contains two N-(pyridin-4-yl)naphthalene-2-carboxamide mol-ecules, both are partially protonated in the pyridine moiety, i.e. the H atom attached to the pyridine N atom is partially occupied with an occupancy factor of 0.61 (3) and 0.39 (3), respectively. In the crystal, protonated and neutral N-(pyridin-4-yl)naphthalene-2-carboxamide mol-ecules are linked by N-H⋯N hydrogen bonding; the thio-cyanate counter-ion links with both protonated and neutral N-(pyridin-4-yl)naphthalene-2-carboxamide mol-ecules via N-H⋯S and N-H⋯N hydrogen bonding. The dihedral angles between the pyridine ring and naphthalene ring systems are 11.33 (6) and 9.51 (6)°, respectively. π-π stacking is observed in the crystal structure, the shortest centroid-centroid distance being 3.5929 (8) Å. The crystal structure was determined from a nonmerohedral twin {ratio of the twin components = 0.357 (1):0.643 (1) and twin law [-100 0-10 -101]}.

N,N-Dicyclo-hexyl-4-nitro-benzamide.

The title compound, C(19)H(26)N(2)O(3), crystallizes with two independent mol-ecules in the asymmetric unit which differ in the twist of the phenyl rings with respect to the plane of the amide group [the C-C-C-O torsion angles are 121.5 (3) and -119.6 (3)° in the two mol-ecules. Both cyclo-hexane rings adopt chair conformations. In the crystal, weak C-H⋯O inter-actions occur. The crystal studied was a non-merohedral twin with a minor component of 4.8 (1)%.

Cis-diastereoselectivity in pictet-spengler reactions of L-tryptophan and electronic circular dichroism studies.

The diastereoselective synthesis of optically active 1,3-disubstituted tetrahydro-ß-carbolines using polar protic Pictet-Spengler cyclization of (S)-tryptophan methyl ester with five aldehydes RCHO (R═CH(3), C(2)H(5), C(3)H(7), C(4)H(9), and C(6)H(5)) was studied. As an alternate route, the cyclization of (S)-tryptophan with the same aldehydes and subsequent methylation of the resulting tetrahydro-ß-carboline carboxylic acids were also performed for comparison. (13)C NMR and electronic circular dichroism (ECD) studies and time-dependent density functional theory ECD calculations data established the relative 1,3 cis/trans and the absolute configuration (1S,3S/ 1R,3S) of the synthesized compounds. The solid-state and solution ECD study of the prepared compounds, supported by ECD calculation and X-ray data, afforded a reliable ECD method for the configurational assignment of 1,3-disubstituted tetrahydro-ß-carbolines and revealed the stereochemical factors that determine the characteristic ECD data.

Dicyclo-hexyl-ammonium 3,5-dinitro-benzoate.

The asymmetric unit of the title salt, C(12)H(24)N(+)·C(7)H(3)N(2)O(6) (-), contains two cations and two anions. In the crystal, the cations and anions are connected by N-H⋯O hydrogen bonds, forming a 12-membered ring with an R(4) (4)(12) graph-set motif. The center of this 12-membered ring coincides with an inversion centre. π-π stacking is observed between parallel benzene rings [centroid-centriod distance = 3.771 (2) Å].

N,N-Dicyclo-hexyl-cyclo-hexa-ne-carboxamide.

In the title compound, C(19)H(33)NO, all three cyclo-hexane rings adopt chair conformations. The crystal packing features weak C-H⋯O inter-actions, forming a supra-molecular chain along the c axis.

Ethyl 2-(3,5-dinitro-benzamido)-benzoate.

The title mol-ecule, C(16)H(13)N(3)O(7), is slightly twisted, with the dihedral angle between the two benzene ring planes being 17.4 (1)°. An intra-molecular N-H⋯O hydrogen bond is observed. In the crystal, weak C-H⋯O hydrogen bonds link the mol-ecules into chains along the b axis.

N-(4-Bromo-phen-yl)-3,5-dinitro-benzamide.

The title mol-ecule, C(13)H(8)BrN(3)O(5), is slightly twisted, with the dihedral angle between the two benzene rings being 5.9 (1)°. In the crystal, N-H⋯O hydrogen bonds link the mol-ecules into one-dimensional chains running along [101]. Further stabilization of the crystal structure is provided by π-π inter-actions [shortest centroid-centroid distance = 3.6467 (17) Å].

A co-crystal of 3-(3,5-dinitro-benzo-yl)-1,1-dimethyl-thio-urea and N,N-dimethyl-3,5-dinitro-benzamide.

In the title compound, C(10)H(10)N(4)O(5)S·C(9)H(9)N(3)O(5), the amide groups of 3-(3,5-dinitro-benzo-yl)-1,1-dimethyl-thio-urea and N,N-dimethyl-3,5-dinitro-benzamide mol-ecules are oriented at dihedral angles of 39.13 (8) and 55.97 (11)°, respectively, to the attached benzene rings. In the crystal, the two mol-ecules are linked by an N-H⋯O hydrogen bond. Weak C-H⋯O link the mol-ecules into a sheet parallel to the bc plane. C-H⋯S inter-actions also occur.

Electrochemical and spectroscopic investigations of isoniazide and its analogs with ds.DNA at physiological pH: evaluation of biological activities.

Interaction and binding of isonicotinic acid hydrazide (INH) and its two analogs; pyrazine carboxylic acid hydrazide (PCH) and 2,4-dihydroxy benzoic acid hydrazide (2,4-DHBAH) with DNA has been investigated by UV-spectroscopy and cyclic voltammetry (CV) at physiological conditions of pH and temperature. Experimental results from both techniques were in good agreement and indicated stronger binding and formation of hydrazides-DNA complexes via intercalation. Among three hydrazides, 2,4-DHBAH showed greater interaction toward DNA at stomach pH (4.7) as evident from its comparatively greater binding constant, {K(b); 2.02 × 10(4) M(-1) (UV), 3.13 × 10(4) M(-1) (CV)}. The greater binding site size (n = 3) for 2,4-DHBAH at stomach pH inferred 3:1 binding stoichiometry and possibility of electrostatic interactions or hydrogen bonding along with intercalative mode of interaction between 2,4-DHBAH and DNA. The free energies of hydrazides-DNA complexes indicated the spontaneity of their binding. 2,4-DHBAH has shown promising anti-bacterial activities while anti-oxidant and cytotoxic potentials were exhibited by all three hydrazides.

1-Benzoyl-3-(naphthalen-1-yl)thio-urea.

In the title compound, C(18)H(14)N(2)OS, the dihedral angle between the mean planes of the 3-naphthyl and 1-benzoyl rings is 20.7 (1)°. The crystal packing is stabilized by weak N-H⋯S inter-actions. Intra-molecular N-H⋯O and C-H⋯O hydrogen bonding is also observed.

1-(4,6-Dimethyl-pyrimidin-2-yl)thio-urea.

In the crystal structure of the title compound, C(7)H(10)N(4)S, weak inter-molecular N-H⋯S inter-actions form a two-dimensional network parallel to the ab plane. An intra-molecular N-H⋯N hydrogen bond occurs.

1-(4,6-Dimethyl-pyrimidin-2-yl)-3-(3,5-dinitro-benzo-yl)thio-urea monohydrate.

The organic molecule in the title mol-ecule, C(14)H(12)N(6)O(5)S·H(2)O, is roughly planar with a maximum deviation of 0.156 (2) Å. An intra-molecular N-H⋯N hydrogen bond occurs. In the crystal, inter-molecular N-H⋯O and O-H⋯O hydrogen-bonding inter-actions connect the mol-ecules into a two-dimensional network that lies parallel to (101).

Ethyl 2-[3-(3,5-Dinitrobenzo-yl)thio-ureido]benzoate.

In the title compound, C(17)H(14)N(4)O(7)S, the dihedral angle between the two benzene rings is 9.04 (15)°. The centroid-centroid distance of 3.9825 (19) Šbetween nearly parallel benzene rings of adjacent mol-ecules suggests the existence of π-π stacking. Inter-molecular and intra-mol-ecular N-H⋯O hydrogen bonding is present in the structure. The eth-oxy group is disordered over two sets of sites with an occupancy ratio of 0.580 (15):0.420 (15). The crystal studied was an inversion twin.

3-Cyclo-hexyl-1-(3,5-dinitro-benzo-yl)thio-urea.

The structure of the title thio-urea derivative, C(14)H(16)N(4)O(5)S, features an almost planar central C(2)N(2)OS fragment (r.m.s. deviation = 0.005 Å), an arrangement stabilized by an intra-molecular N-H⋯O hydrogen bond. The terminal rings are twisted out of this plane, the dihedral angle formed with the benzene ring being 33.22 (10)°. The cyclo-hexyl ring is disordered, with two orientations (50:50) being resolved. The mean plane passing through the atoms of each disordered component forms dihedral angles of 65.7 (2) and 82.4 (3)° with the central plane. Centrosymmetric dimers mediated by an eight-membered {⋯HNC=S}(2) synthon occur in the crystal.

1-(3,5-Dinitro-benzo-yl)-3,3-dipropyl-thio-urea.

The title thio-urea derivative, C(14)H(18)N(4)O(5)S, features two substantial twists between its component fragments: the dihedral angle between the SN(2)C (thio-urea) and ONC(2) (amide) residues is 48.89 (7)° and that between the benzene ring and the amide residue is 30.27 (7)°. In the crystal, mol-ecules are linked by bifurcated N-H⋯(O,S) hydrogen bonds, generating [001] supra-molecular chains.

4-Nitro-N-(4-nitro-benzo-yl)benzamide.

The central acetyl-acetamide moiety in the title compound, C(14)H(9)N(3)O(6), is buckled [e.g. the C-N-C-O torsion angle is 14.3 (6)°] but the r.m.s. deviation for the five atoms is 0.044 Å. The benzene rings lie on the same side of the central plane, forming dihedral angles of 37.17 (15) and 28.58 (19)° with it. The dihedral angle between the two rings is 17.8 (2)° indicating that the mol-ecule is curved. The carbonyl groups are syn to each other and anti to the amino H atom. This allows for the formation of N-H⋯O hydrogen bonds in the crystal, which leads to twisted chains along the b axis. Positional disorder (50:50) of the O atoms was modelled for both the nitro groups.