cis-Bis[1,1-dibenzyl-3-(furan-2-ylcarbonyl)thioureato-kappa(2)O,S]copper(II)

In the title compound, [Cu(C(20)H(17)N(2)O(2)S)(2)], the Cu(II) atom is coordinated by the S and O atoms of two 1,1-dibenzyl-3-(furan-2-ylcarbonyl)thioureate ligands in a distorted square-planar geometry. The two O and two S atoms are mutually cis to each other. The Cu-S and Cu-O bond lengths lie within the ranges of those found in related structures. The dihedral angle between the planes of the two chelating rings is 26.15 (6)degrees.

N-(2-furylcarbonyl)piperidine-1-carbothioamide

The title compound, C11H14N2O2S, was synthesized from furoyl isothiocyanate and piperidine in dry acetone. The thiourea group is in the thioamide form. The thiourea group makes a dihedral angle of 53.9 (1)degrees with the furan carbonyl group. In the crystal structure, molecules are linked by intermolecular N-H center dot center dot center dot O hydrogen bonds, forming one-dimensional chains along the c axis. An intramolecular N-H center dot center dot center dot O hydrogen bond is also present.

Density functional theory investigation of 3d, 4d, and 5d 13-atom metal clusters

The knowledge of the atomic structure of clusters composed by few atoms is a basic prerequisite to obtain insights into the mechanisms that determine their chemical and physical properties as a function of diameter, shape, surface termination, as well as to understand the mechanism of bulk formation. Due to the wide use of metal systems in our modern life, the accurate determination of the properties of 3d, 4d, and 5d metal clusters poses a huge problem for nanoscience. In this work, we report a density functional theory study of the atomic structure, binding energies, effective coordination numbers, average bond lengths, and magnetic properties of the 3d, 4d, and 5d metal (30 elements) clusters containing 13 atoms, M(13). First, a set of lowest-energy local minimum structures (as supported by vibrational analysis) were obtained by combining high-temperature first- principles molecular-dynamics simulation, structure crossover, and the selection of five well-known M(13) structures. Several new lower energy configurations were identified, e. g., Pd(13), W(13), Pt(13), etc., and previous known structures were confirmed by our calculations. Furthermore, the following trends were identified: (i) compact icosahedral-like forms at the beginning of each metal series, more opened structures such as hexagonal bilayerlike and double simple-cubic layers at the middle of each metal series, and structures with an increasing effective coordination number occur for large d states occupation. (ii) For Au(13), we found that spin-orbit coupling favors the three-dimensional (3D) structures, i.e., a 3D structure is about 0.10 eV lower in energy than the lowest energy known two-dimensional configuration. (iii) The magnetic exchange interactions play an important role for particular systems such as Fe, Cr, and Mn. (iv) The analysis of the binding energy and average bond lengths show a paraboliclike shape as a function of the occupation of the d states and hence, most of the properties can be explained by the chemistry picture of occupation of the bonding and antibonding states.

1-(2-furoyl)-3-(1-naphthyl)thiourea

In the title compound, C(16)H(12)N(2)O(2)S, the carbonylthiourea group forms dihedral angles of 75.4 (1) and 13.1 (2)degrees, respectively, with the naphthalene ring system and furan ring. The molecule adopts a trans-cis configuration with respect to the positions of the furoyl and naphthyl groups relative to the S atom across the thiourea C-N bonds. This geometry is stabilized by an N-H center dot center dot center dot center dot O intramolecular hydrogen bond. In the crystal structure, molecules are linked by N-H center dot center dot center dot S hydrogen bonds, forming centrosymmetric dimers which are interlinked through C-H center dot center dot center dot pi interactions.

Transition-metal 13-atom clusters assessed with solid and surface-biased functionals

First-principles density-functional theory studies have reported open structures based on the formation of double simple-cubic (DSC) arrangements for Ru(13), Rh(13), Os(13), and Ir(13), which can be considered an unexpected result as those elements crystallize in compact bulk structures such as the face-centered cubic and hexagonal close-packed lattices. In this work, we investigated with the projected augmented wave method the dependence of the lowest-energy structure on the local and semilocal exchange-correlation (xc) energy functionals employed in density-functional theory. We found that the local-density approximation (LDA) and generalized-gradient formulations with different treatment of the electronic inhomogeneities (PBE, PBEsol, and AM05) confirm the DSC configuration as the lowest-energy structure for the studied TM(13) clusters. A good agreement in the relative total energies are obtained even for structures with small energy differences, e. g., 0.10 eV. The employed xc functionals yield the same total magnetic moment for a given structure, i.e., the differences in the bond lengths do not affect the moments, which can be attributed to the atomic character of those clusters. Thus, at least for those systems, the differences among the LDA, PBE, PBEsol, and AM05 functionals are not large enough to yield qualitatively different results. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3577999]

Effect of cooking on non-starch polysaccharides of hard-to-cook beans

Experiments carried out to study changes induced by hard-to-cook (HTC) phenomenon in the non-starch polysaccharides of beans stored at 30 degrees C and 75% RH for 8 months showed that the development of HTC did not affect the amounts of soluble and insoluble fibre in cooked seeds but changed their carbohydrates physical properties. Aged beans non-starch polysaccharides presented lower water-solubility and underwent lower degradation of galacturonans and arabinose-rich polysaccharides when submitted to cooking. The decrease in non-starch polysaccharides water-solubility produced a shift in the polymers fractionation profile which resulted in an increase of weak and middle-alkali soluble polymers bulk as well as in their arabinose and uronic acid contents. Uronic acid contents were higher in polymers released by 1 M NaOH and in the cellulose-rich residues while the arabinose contents were higher in the mild-alkali soluble polymers of aged seeds. Methylation analysis showed no evident alterations in the xyloglucans and arabinans branching degree with beans ageing. However, both, the molecular mass of water-soluble pectins and CDTA-soluble pectins, increased. Even though changes in the non-starch polysaccharide solubility were not related to the decrease in the arabinan and xyloglucan degree of branching they may be related to the formation of new chemical interactions other than hydrogen bond. There was a correlation between acidic and neutral polysaccharides insolubilisation in beans ageing and probably in beans hardening. After processing, aged seeds present higher amounts of insoluble fibre when compared to normal beans. (C) 2008 Elsevier Ltd. All rights reserved.

Synthesis, antichagasic in vitro evaluation, cytotoxicity assays, molecular modeling and SAR/QSAR studies of a 2-phenyl-3-(1-phenyl-1H-pyrazol-4-yl)-acrylic acid benzylidene-carbohydrazide series

Chagas disease (American trypanosomiasis) is one of the most important parasitic diseases with serious social and economic impacts mainly on Latin America. This work reports the synthesis, in vitro trypanocidal evaluation, cytotoxicity assays, and molecular modeling and SAR/QSAR studies of a new series of N-phenylpyrazole benzylidene-carbohydrazides. The results pointed 6k (X = H, Y = p-NO(2), pIC(50) = 4.55 M) and 6l (X = F, Y = p-CN, pIC(50) = 4.27 M) as the most potent derivatives compared to crystal violet (pIC(50) = 3.77 M). The halogen-benzylidene-carbohydrazide presented the lowest potency whereas 6l showed the most promising pro. le with low toxicity (0% of cell death). The best equation from the 4D-QSAR analysis (Model 1) was able to explain 85% of the activity variability. The QSAR graphical representation revealed that bulky X-substituents decreased the potency whereas hydrophobic and hydrogen bond acceptor Y-substituents increased it. (C) 2008 Elsevier Ltd. All rights reserved.

Solvent Effects in Optical Spectra of ortho-Aminobenzoic Acid Derivatives

We investigated three amino derivatives of ortho-aminobenzoic or anthranilic acid (o-Abz): a) 2-Amino-benzamide (AbzNH(2)); b) 2-Amino-N-methyl-benzamide (AbzNHCH(3)) and c) 2-Amino-N-N`-dimethyl-bezamide (AbzNH(CH(3))(2)), see Scheme 1. We describe the results of ab-initio calculations on the structural characteristics of the compounds and experimental studies about solvent effects in their absorption and steady-state and time-resolved emission properties. Ab-initio calculations showed higher stability for the rotameric conformation in which the oxygen of carbonyl is near to the nitrogen of ortho-amino group. The derivatives present decrease in the delocalization of pi electron, and absorption bands are blue shifted compared to the parent compound absorption, the extent of the effect increasing from to Abz-NH(2) to Abz-NHCH(3) Abz-NH(CH(3))(2). Measurements performed in several solvents have shown that the the dependence of Stokes shift of the derivatives with the orientational polarizability follows the Onsager-Lippert model for general effects of solvent. However deviation occurred in solvents with properties of Bronsted acids, or electron acceptor characteristics, so that hydrogen bonds formed with protic solvents predominates over intramolecular hydrogen bond. In most solvents the fluorescence decay of AbzNH(2) and AbzNHCH(3) was fitted to a single exponential with lifetimes around 7.0 ns and no correlation with polarity of the solvent was observed. The fluorescence decay of AbzN(CH(3))(2) showed lifetimes around 2.0 ns, consistent with low quantum yield of the compound. The spectroscopic properties of the monoamino derivative AbzNHCH(3) are representative of the properties presented by Abz labelled peptides and fatty acids previously studied.

Synthesis, X-ray analysis and DFT study of 2-amino-3-(N-oxipiridin-4-ilsulfanil)-propionic acid dihydrate

The title compound, C(8)H(14)N(2)O(5)S 2(H(2)O), 2-amino-3-(N-oxipiridin-4-ilsulfanil)-propionic acid dihydrate, is obtained by the reaction of cysteine and 4-nitropyridine N-oxide in dimethylformamide, removing the NO(2) group from the benzene ring and releasing nitrous acid into the solution. The molecule exists as a Zwitterion. Hydrogen bond interactions involving the title molecule and water molecules allow the formation of R(5)(5)(23) edge fused rings parallel to (010). Water molecules are connected independently, forming infinite chains (wires), in square wave form, along the b-axis. The chirality of the cysteine molecule used in the synthesis is retained in the title molecule. A density functional theory (DFT) optimized structure at the B3LYP/6-311G(3df,2p) level allows comparison of calculated and experimental IR spectra.

Electronic properties of a methane-water solution

Electronic properties of a methane-water solution were investigated by a sequential quantum mechanical/molecular dynamics approach. Upon hydration methane acquires an induced dipole moment of similar to 0.5 +/- 0.2 D. This is related to polarisation effects and to weak methane-water hydrogen bond interactions. From gas phase to solution, the first vertical excitation and ionisation energies of methane are red-shifted by 0.45 +/- 0.25 and 0.87 +/- 0.40 eV, respectively. We also report results for the dynamic polarisability of methane in water. In comparison with water, no difference was found for the average monomeric dipole moment of water molecules in close interaction with methane. (c) 2011 Elsevier B.V. All rights reserved.

Calculations of vibrational frequencies, Raman activities and degrees of depolarization for complexes involving water, methanol and ethanol

Raman activities and degrees of depolarization are reported for 14 complexes involving methanol, ethanol and water using the MP2/aug-cc-pVDZ model. For ethanol both trans and gauche isomers are considered. The red-shifts of the OH stretching and the blue shifts of the bending tau(CO-OH) mode were analyzed for the proton-donor molecules upon hydrogen bond. The shift of the nu(CO) stretching mode of the alcohol molecules are also analyzed and found to be specific giving characterization of the amphoteric relation, being positive for the proton-acceptor and negative for the proton-donor molecule. (c) 2008 Elsevier B.V. All rights reserved.

Ab initio study of the EFG at the N sites in imidazole

We study the nuclear quadrupole interaction at the nitrogen sites in the molecular and crystalline phases of the imidazole compound. We use PAW which is a state-of-the-art method to calculate the electronic structure and electric field gradient at the nucleus in the framework of the density functional theory. The quadrupole frequencies at both imino and amino N sites are in excellent agreement with measurements. This is the first time that the electric field gradient at crystalline imidazole is correctly treated by an ab initio theoretical approach.

Spin current in the Mobius cyclacene belts

We report on density functional theory studies of the electronic structure and magnetic properties of Mobius-[n]cyclacenes. The geometry of Mobius bands presents a modulation of bond lengths that is needed to accommodate the twist. This modulation takes the form of bond alternation defects analogous to those of solitons in polyacetylene. The ground state of all Mobius bands is a triplet, with a spin density distribution that follows the bond length modulation. A molecular dynamics simulation of the Mobius cyclacene at 300 K shows that the twist travels around the belt inducing a magnetic current. (C) 2009 Elsevier B. V. All rights reserved.

Identification of a novel ligand binding motif in the transthyretin channel

The design of therapeutic compounds targeting transthyretin (TTR) is challenging due to the low specificity of interaction in the hormone binding site. Such feature is highlighted by the interactions of TTR with diclofenac, a compound with high affinity for TTR, in two dissimilar modes, as evidenced by crystal structure of the complex. We report here structural analysis of the interactions of TTR with two small molecules, 1-amino-5-naphthalene sulfonate (1,5-AmNS) and 1-anilino-8-naphthalene sulfonate (1,8-ANS). Crystal structure of TTR: 1,8-ANS complex reveals a peculiar interaction, through the stacking of the naphthalene ring between the side-chain of Lys15 and Leu17. The sulfonate moiety provides additional interaction with Lys15` and a water-mediated hydrogen bond with Thr119`. The uniqueness of this mode of ligand recognition is corroborated by the crystal structure of TTR in complex with the weak analogue 1,5-AmNS, the binding of which is driven mainly by hydrophobic partition and one electrostatic interaction between the sulfonate group and the Lys15. The ligand binding motif unraveled by 1,8-ANS may open new possibilities to treat TTR amyloid diseases by the elucidation of novel candidates for a more specific pharmacophoric pattern. (C) 2009 Published by Elsevier Ltd.

Tightened Lieb-Oxford Bound for Systems of Fixed Particle Number

The Lieb-Oxford bound is a constraint upon approximate exchange-correlation functionals. We explore a nonempirical tightening of that bound in both universal and electron number-dependent form. The test functional is PBE. Regarding both atomization energies (slightly worsened) and bond lengths (slightly improved), we find the PBE functional to be remarkably insensitive to the value of the Lieb-Oxford bound. This both rationalizes the use of the original Lieb-Oxford constant in PBE and suggests that enhancement factors more sensitive to sharpened constraints await discovery.