Weak interactions involving organic fluorine: analysis of structural motifs in Flunazirine and Haloperidol

The crystal structure of Flunazirine, an anticonvulsant drug, is analyzed in terms of intermolecular interactions involving fluorine. The structure displays motifs formed by only weak interactions C–H⋯F and C–H⋯π. The motifs thus generated show cavities, which could serve as hosts for complexation. The structure of Flunazirine displays cavities formed by C–H⋯F and C–H⋯π interactions. Haloperidol, an antipsychotic drug, shows F⋯F interactions in the crystalline lattice in lieu of Cl⋯Cl interactions. However, strong O–H⋯N interactions dominate packing. The salient features of the two structures in terms of intermolecular interactions reveal, even though organic fluorine has lower tendency to engage in hydrogen bonding and F⋯F interactions, these interactions could play a significant role in the design of molecular assemblies via crystal engineering.

Dicopper(II) complexes showing DNA hydrolase activity and monomeric adduct formation with bis(4-nitrophenyl)phosphate

Ferromagnetic dicopper(II) complexes [Cu(2)(mu-O(2)CCH(3))(mu-OH)(L)(2)(mu-L(1))](PF(6))(2), where L = 1,10-phenanthroline (phen), L(1) = H(2)O in 1 and L = dipyrido[3,2-d:2',3'-f]quinoxaline (dpq), L(1) = CH(3)CN in 2, are prepared and structurally characterized. Crystals of 1 and 2 belong to the monoclinic space group of P2(1)/n and P2(1)/m, respectively. The copper(II) centers display distorted square-pyramidal geometry having a phenanthroline base and two oxygen atoms of the bridging hydroxo and acetate group in the basal plane. The fifth coordination site has weak axially bound bridging solvent molecule H(2)O in 1 and CH(3)CN in 2. The Cu center dot center dot center dot Cu distances are 3.034 and 3.046 angstrom in 1 and 2, respectively. The complexes show efficient hydrolytic cleavage of supercoiled pUC19 DNA as evidenced from the mechanistic studies that include T4 DNA ligase experiments. The binuclear complexes form monomeric copper(II) adducts [Cu(L)(2)(BNPP)](PF(6)) (L = phen, 3; dpq, 4) with bis(4-nitrophenyl)phosphate (BNPP) as a model phosphodiester. The crystal structures of 3 and 4 reveal distorted trigonal bipyramidal geometry in which BNPP binds through the oxygen atom of the phosphate. The kinetic data of the DNA cleavage reactions of the binuclear complexes under pseudo- and true-Michaelis-Menten conditions indicate remarkable enhancement in the DNA hydrolysis rate in comparison to the control data. (C) 2011 Elsevier B.V. All rights reserved.

Volume Change Behaviour of Soil Influenced with Sulfuric Acid

The paper brings out the role of calcium carbonate (CaCO3) on the volume change behaviour of natural black cotton soil with 1N sulfuric acid (H2SO4) as pore fluid. Natural black cotton soil contained predominantly montmorillonite [Ca0.2(Al,Mg)2Si4 O10 (OH)2 .4H2O] along with other minerals such as amesite [(Mg Fe)2 Al (Si Al)2 O5 (OH)4], kalsilite [KAlSiO4] and quartz [SiO2]. The calcitic soil, reacted with H2SO4 during consolidation testing, showed the presence of the new mineral yavapaiite [K Fe(SO4)2]. Consequently, the carbonate soil treated with 1N H2SO4 led to higher swell at seating load and more compression upon loading than the soil with no carbonate. The swelling increased with increase in the amount of carbonate present in the soil.

Hexa-arm star shaped hydrazone derivatives from hexakis(4-formylphenoxy)-cyclotriphosphazene core

A series of novel hexasubstituted cyclophosphazene hydrazones [N(3)P(3)(-OC(6)H(4)-p-CH=N-NH-C(O)-C(6)H(4)-p-X)(6)] (X = H, Br, Cl, F, OH, OCH(3), CH(3), NO(2), NH(2)) were prepared by a sixfold condensation reaction of [N(3)P(3)(-OC(6)H(4)-p-CHO)(6)] with para-substituted benzoic hydrazides [NH(2)-NH-C(O)-C(6)H(4)-p-X] with excellent yields (91-98%). The structures of the compounds were confirmed by elemental analysis, FT-IR, (1)H, (13)C, (31)P, 2D-HSQC NMR and mass spectrometry (MALDI-TOF). All the synthesized cyclophosphazene hydrazones exhibit high thermal stability. The crystal structure of a homogeneously substituted hexakis(4-formylphenoxy)-cyclotriphosphazene was determined by X-ray diffraction analysis. The compound crystallizes in the monoclinic system, space group P2(1)/n with a = 16.558(3) angstrom, b = 10.250(2) angstrom, c = 23.429(5) angstrom, alpha = gamma = 90.00 degrees, beta = 90.461(4)degrees, V = 3976.5(14) angstrom(3) and Z = 4. The R value is 0.0823 for 4290 observed reflections. The conformations of the 4-formylphenoxy-groups are different at the three phosphorus atoms. (C) 2011 Elsevier B.V. All rights reserved.

2-{[{2-Hydroxy-3-[2-methyl-5-(propan-2-yl)phenoxy]propyl}(pyridin -2-ylmethyl)amino]methyl}phenol

In the title racemic compound, C(26)H(32)N(2)O(3), an intramolecular O-H center dot center dot center dot N hydrogen bond is formed between the phenolic OH group and the tertiary amine N atom. Another O-H center dot center dot center dot N hydrogen bond that is formed between the OH group and the pyridine N atom links the molecules into a polymeric chain extending along the a axis. The structure is further stabilized by intramolecular and intermolecular C-H center dot center dot center dot O interactions.

Performance Modeling based on Multidimensional Surface Learning for Performance Predictions of Parallel Applications in Non-Dedicated Environments

Modeling the performance behavior of parallel applications to predict the execution times of the applications for larger problem sizes and number of processors has been an active area of research for several years. The existing curve fitting strategies for performance modeling utilize data from experiments that are conducted under uniform loading conditions. Hence the accuracy of these models degrade when the load conditions on the machines and network change. In this paper, we analyze a curve fitting model that attempts to predict execution times for any load conditions that may exist on the systems during application execution. Based on the experiments conducted with the model for a parallel eigenvalue problem, we propose a multi-dimensional curve-fitting model based on rational polynomials for performance predictions of parallel applications in non-dedicated environments. We used the rational polynomial based model to predict execution times for 2 other parallel applications on systems with large load dynamics. In all the cases, the model gave good predictions of execution times with average percentage prediction errors of less than 20%

Charge Density Analysis of a Pentaborate Ion in an Ammonium Borate: Toward the Understanding of Topological Features in Borate Minerals

Structural and charge density distribution studies have been carried out on a single crystal data of an ammonium borate, [C(10)H(26)N(4)][B(5)O(6)(OH)(4)](2), synthesized by solvothermal method. Further, the experimentally observed geometry is used for the theoretical charge density calculations using the B3LYP/6-31G** level of theory, and the results are compared with the experimental values. Topological analysis of charge density based on the Atoms in Molecules approach for B-O bonds exhibit mixed covalent/ionic character. Detailed analysis of the hydrogen bonds in the crystal structure in the ammonium borate provides insights into the understanding of the reaction pathways that net atomic charges and electrostatic potential isosurfaces also give additional such systems. could result in the formation of borate minerals. The input to evaluate chemical and physical properties in such systems.

An eight-connected metal organic framework based on Cu(5) clusters: Synthesis, structure, magnetic and catalytic properties

A reaction of copper acetate, 5-nitroisophthalic acid in a water-methanol mixture under solvothermal condition results in a new metal-organic framework compound, [Cu(5)(mu(3)-OH)(2)(H(2)O)(6){(NO(2))-C(6)H(3)-(COO)(2)}(4)]center dot 5H(2)O, (1). The compound contains Cu5 pentameric cluster units connected by 5-nitro isophthalate (NIPA) moieties forming a CdCl(2)-like layer, which are further connected by another NIPA moiety forming the three-dimensional structure. The water molecules in (1) can be reversibly adsorbed. The removal of water accompanies a change in the colour as well as a structural re-organization. Magnetic studies suggest strong antiferromagnetie correlations between the Cu5 cluster units. The compound (1) exhibits heterogeneous Lewis acid catalysis for the cyanosilylation of imines with more than 95 % selectivity. Compound (1) has been characterized by IR, UV-vis, TGA, powder XRD studies.

Usefulness of in Situ Single Crystal to Single Crystal Transformation (SCSC) Studies in Understanding the Temperature-Dependent Dimensionality Cross-over and Structural Reorganization in Copper-Containing Metal-Organic Frameworks (MOFs)

Two copper-containing compounds [Cu(3)(mu(3)-OH)(2)-(H(2)O)(2){(SO(3))-C(6)H(3)-(COO)(2)}(CH(3)COO)] , I, and [Cu(5)(mu(3)-OH)(2)(H(2)O)(6){(NO(2))-C(6)H(3)-(COO)(2)}(4)]center dot 5H(2)O, II, were prepared using sulphoisophthalic and nitroisophthalic acids. The removal of the coordinated water molecules in the compounds was investigated using in situ single crystal to single crystal (SCSC) transformation studies, temperature-dependent powder X-ray diffraction (PXRD), and thermogravimetric analysis (TGA). The efficacy of SCSC transformation studies were established by the observation of dimensionality cross-over from a two-dimensional (I) to a three-dimensional structure, Cu(6)(mu(3)-OH)(4){(SO(3))-C(6)H(3)-(COO)(2)}(2)(CH(3)COO)(2), Ia, during the removal of the coordinated water molecules. Compound H exhibited a structural reorganization forming Cu(5)(mu(2)-OH)(2){(NO(2))C(6)H(3)-(COO)(2))(4)], Ha, possessing trimeric (Cu(3)O(12)) and dimeric (Cu(2)O(8)) copper clusters. The PXRD studies indicate that the three-dimensional structure (Ia) is transient and unstable, reverting back to the more stable two-dimensional structure (I) on cooling to room temperature. Compound Ha appears to be more stable at room temperature. The rehydration/dehydration studies using a modified TGA setup suggest complete rehydration of the water molecules, indicating that the water molecules in both compounds are labile. A possible model for the observed changes in the structures has been proposed. Magnetic studies indicate changes in the exchanges between the copper centers in Ha, whereas no such behavior was observed in Ia.

Reversible Formation of a Planar Chiral Ferrocenylboroxine and Its Supramolecular Structure

The boronic acid (pS)-1,2-NpFcB(OH)(2) (1) was obtained by treatment of the lithiated species (pS)-1,2-NpFcLi with B(O(i)Pr)(3), followed by acidic workup; subsequent dehydration gave the enantiomerically pure boroxine [(pS)-1,2-NpFcBO](3) (2) in 49% isolated yield. Multinuclear and 2D NMR spectroscopies, single-crystal X-ray diffraction, and elemental analysis served to confirm the structure of 2. In the solid-state structure, all three of the naphthyl groups point in one direction and all of the ferrocenyl moieties are placed on the opposite face of the boroxine ring, which is also the preferred conformation in solution according to a (1)H, (1)H-NOESY experiment. Cyclic voltammetry revealed three separate reversible oxidation events, which suggests significant communication between the ferrocenyl moieties. These redox processes experience a cathodic shift upon addition of 4-dimethylaminopyridine (DMAP) as a Lewis base. The six-membered ring is opened upon treatment with hot CHCl(3)/MeOH to form the methoxy species (pS)-1,2-NpFcB(OH)(OMe) (3), which can be converted back to the cycle 2 by dissolution in wet CHCl(3), followed by column chromatography on silica gel.

Phenylboronic acids in crystal engineering: Utility of the energetically unfavorable syn,syn-conformation in co-crystal design

Phenylboronic acids can exist, in principle, in three different conformers (syn,syn; syn,anti and anti,anti) with distinct energy profiles. In their native state, these compounds prefer the energetically favored syn, anti-conformation. In molecular complexes, however, the functionality exhibits conformational diversity. In this paper we report a series of co-crystals, with N-donor compounds, prepared by a design strategy involving the synthons based on the syn, syn-conformation of the boronic acid functionality. For this purpose, we employed compounds with the 1,2-diazo fragment (alprazolam, 1H-tetrazole, acetazolamide and benzotriazole), 1,10-phenanthroline and 2,2'-bipyridine for the co-crystallization experiments. However, our study shows that the mere presence of the 1,2-diazo fragment in the coformer does not guarantee the successful formation of co-crystals with a syn, syn-conformation of the boronic acid. [GRAPHICS] The -B(OH)(2) fragment makes unsymmetrical O-H center dot center dot center dot N heterosynthons with alprazolam (ALP) and 1,10-phenanthroline (PHEN). In the co-crystals of phenylboronic acids with 1H-tetrazole (TETR) and 2,2'-bipyridine (BPY), the symmetrical boronic acid dimer is the major synthon. In the BPY complex, boronic acid forms linear chains and the pyridine compound interacts with the lateral OH of boronic acid dimers that acts as a connector, thus forming a ladder structure. In the TETR complex, each heterocycle interacts with three boronic acids. While two boronic acids interact using the phenolic group, the third molecule generates O-H center dot center dot center dot N hydrogen bonds using the extra OH group, of -B(OH)(2) fragment, left after the dimer formation. Thus, although molecules were selected retrosynthetically with the 1,2-diazo fragment or with nearby hetero-atoms to induce co-crystal formation using the syn,syn-orientation of the -B(OH)(2) functionality, co-crystal formation is in fact selective and is probably driven by energy factors. Acetazolamide (ACET) contains self-complementary functional groups and hence creates stable homosynthons. Phenylboronic acids being weak competitors fail to perturb the homosynthons and hence the components crystallize separately. Therefore, besides the availability of possible hydrogen bond acceptors in the required position and orientation, the ability of the phenyl-boronic acid to perturb the existing interactions is also a prerequisite to form co-crystals. This is illustrated in the table below. In the case of ALP, PHEN and BPY, the native structures are stabilized by weak interactions and may be influenced by the boronic acid fragment. Thus phenylboronic acids can attain co-crystals with those compounds, wherein the cyclic O-H center dot center dot center dot N hydrogen bonds are stronger than the individual homo-interactions. This can lower the lattice energy of the molecular complex as compared with the individual crystals. [GRAPHICS] Phenylboronic acids show some selectivity in the formation of co-crystals with N-heterocycles. The differences in solubility of the components fall short to provide a possible reason for the selective formation of co-crystals only with certain compounds. These compounds, being weak acids, do not follow the Delta pK(a) analysis and hence fail to provide any conclusive observation. Theoretical results show that of the three conformers possible, the syn,anti conformer is the most stable. The relative stabilities of the three conformers syn,anti,syn,syn and anti,anti are 0.0, 2.18 and 3.14 kcal/mol, respectively. The theoretical calculations corroborate the fact that only energetically favorable synthons can induce the formation of heterosynthons, as in ALP and PHEN complexes. From a theoretical and structural analysis it is seen that phenylboronic acids will form interactions with those molecules wherein the heterocyclic and acidic fragments can interrupt the homosynthons. However, the energy profile is shallow and can be perturbed easily by the presence of competing functional groups (such as OH and COOH) in the vicinity. [GRAPHICS] .

Validation of a Modified Eddy Dissipation Concept Model for Stationary and Nonstationary Turbulent Diffusion Flames

A transient flame simulation tool based on unsteady Reynolds average Navier Stokes (RANS) is characterized for stationary and nonstationary flame applications with a motivation of performing computationally affordable flame stability studies. Specifically, the KIVA-3V code is utilized with incorporation of a recently proposed modified eddy dissipation concept for simulating turbulence-chemistry interaction along with a model for radiation loss. Detailed comparison of velocities, turbulent kinetic energies, temperature, and species are made with the experimental data of the turbulent, non-premixed DLR_A CH4/H-2/N-2 jet flame. The comparison shows that the model is able to predict flame structure very well. The effect of some of the modeling assumptions is assessed, and strategies to model a stationary diffusion flame are recommended. Unsteady flame simulation capabilities of the numerical model are assessed by simulating an acoustically excited, experimental, oscillatory H-2-air diffusion flame. Comparisons are made with oscillatory velocity field and OH plots, and the numerical code is observed to predict transient flame structure well.

Chain Length Effects on Helix-Hairpin Distribution in Short Peptides with Aib-(D)Ala and Aib-Aib Segments

The Aib-(D)Ala dipeptide segment has a tendency to form both type-I'/III' and type-I/III beta-turns. The occurrence of prime turns facilitates the formation of beta-hairpin conformations, while type-I/III turns can nucleate helix formation. The octapeptide Boc-Leu-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-OMe (1) has been previously shown to form a beta-hairpin in the crystalline state and in solution. The effects of sequence truncation have been examined using the model peptides Boc-Phe-Val-Aib-Xxx-Leu-Phe-NHMe (2, 6), Boc-Val-Aib-Xxx-Leu-NHMe (3, 7), and Boc-Aib-Xxx-NHMe (4, 8), where Xxx = (D)Ala, Aib. For peptides with central Aib-Aib segments, Boc-Phe-Val-Aib-Aib-Leu-Phe-NHMe (6), Boc-Val-Aib-Aib-Leu-NHMe (7), and Boc-Aib-Aib-NHMe (8) helical conformations have been established by NMR studies in both hydrogen bonding (CD(3)OH) and non-hydrogen bonding (CDCl(3)) solvents. In contrast, the corresponding hexapeptide Boc-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-NHMe (2) favors helical conformations in CDCl(3) and beta-hairpin conformations in CD(3)OH. The beta-turn conformations (type-I'/III) stabilized by intramolecular 4 -> 1 hydrogen bonds are observed for the peptide Boc-Aib-(D)Ala-NHMe (4) and Boc-Aib-Aib-NIiMe (8) in crystals. The tetrapeptide Boc-Val-Aib-Aib-Leu-NHMe (7) adopts an incipient 3(10)-helical conformation stabilized by three 4 -> 1 hydrogen bonds. The peptide Boc-Val-Aib-(D)Ala-Leu-NHMe (3) adopts a novel et-turn conformation, stabilized by three intramolecular hydrogen bonds (two 4 -> 1 and one 5 -> 1). The Aib-L(D)Ala segment adopts a type-I' beta-turn conformation. The observation of an NOE between Val (1) NH <-> HNCH(3) (5) in CD(3)OH suggests, that the solid state conformation is maintained in methanol solutions. (C) 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 744-756, 2011.

Ferrocene-Conjugated Copper(II) Complexes of L-Methionine and Phenanthroline Bases: Synthesis, Structure, and Photocytotoxic Activity

Ferrocene-conjugated reduced Schiff base (Fc-metH) copper(II) complexes of L-methionine and phenanthroline bases, namely, Cu(Fc-met)(B)](NO3), where B is 1,10-phenanthroline (phen in 1), dipyrido3,2-d:2',3'-f]quinoxaline (dpq in 2), dipyrido3,2-a:2',3'-c]phenazine (dppz in 3), and 2-(naphthalen-1-yl)-1H-imidazo4,5-f]1,10]phenanthroline (nip in 4), were prepared and characterized and their photocytotoxicity studied (Fc = ferrocenyl moiety). Complexes Cu(Ph-met)(B)](NO3) of the reduced Schiff base from benzaldehyde and L-methionine (Ph-metH) and B (phen in 5, dppz in 6) were prepared and used as control species. Complexes 1 and 5 were structurally characterized by X-ray crystallography. Complex 1 as a discrete monomer has a CuN3OS core with the thiomethyl group as the axial ligand. Complex 5 has a polymeric structure with a CuN3O2 core in the solid state. Complexes 5 and 6 are formulated as Cu(Ph-met)(B)(H2O)] (NO3) in an aqueous phase based on the mass spectral data. Complexes 1-4 showed the Cu(II)-Cu(I) and Fc(+)-Fc redox couples at similar to 0.0 and similar to 0.5 V vs SCE, respectively, in DMF-0.1 M (Bu4N)-N-n](ClO4). A Cu(II)-based weak d-d band near 600 nm and a relatively strong ferrocenyl band at similar to 450 nm were observed in DMF-Tris-HCl buffer (1:4 v/v). The complexes bind to calf thymus DNA, exhibit moderate chemical nuclease activity forming (OH)-O-center dot radical species, and are efficient photocleavers of pUC19 DNA in visible light of 454, 568, and 647 rim, forming (OH)-O-center dot radical as the reactive oxygen species. They are cytotoxic in HeLa (human cervical cancer) and MCF-7 (human breast cancer) cells, showing an enhancement of cytotoxicity upon visible light irradiation. Significant change in the nuclear morphology of the HeLa cells was observed with 3 in visible light compared to the nonirradiated sample. Confocal imaging using 4 showed its nuclear localization within the HeLa cells.