Ray Crystal Structure Research Articles

A novel anionic di-oxido vanadium(V) Schiff base complex: Synthesis, spectral characterization, X ray crystal structure, catalytic activity for the preparation of tetrahydro-4H-chromene derivatives and antibacterial properties

In this work, a tridentate ONO Schiff base ligand,1-[(((2-hydroxyphenyl)imino)methyl)]naphthalen-2-ol [H2L] and its di-oxido vanadium(V) complex [(VO2(L)](NHET3) have been synthesized and fully characterized using elemental analysis, molar conductivity and FT-IR, UV–Vis, and 1HNMR spectroscopies. Single crystal X-ray diffraction was also used to accomplish the crystal structure of di-oxido vanadium(V) complex. The catalytic activity of the complex was also evaluated for the synthesis of tetrahydro-4H-chromene derivatives. The synthesized [VO2(L)](NHET3) complex showed superior catalytic characteristics in comparison to the previously reported catalysts. Furthermore,the antimicrobial properties of the complex against both gram-positive and gram-negative pathogens were evaluated, that an enhanced antibacterial activity was obtained with MIC values in the range of 100–200 µg/ml.

Crystal structure of Leishmania mexicana cysteine protease B in complex with a high-affinity azadipeptide nitrile inhibitor

Leishmania mexicana is an obligate intracellular protozoan parasite that causes the cutaneous form of leishmaniasis affecting South America and Mexico. The cysteine protease LmCPB is essential for the virulence of the parasite and therefore, it is an appealing target for antiparasitic therapy. A library of nitrile-based cysteine protease inhibitors was screened against LmCPB to develop a treatment of cutaneous leishmaniasis. Several compounds are sufficiently high-affinity LmCPB inhibitors to serve both as starting points for drug discovery projects and as probes for target validation. A 1.4 Å X ray crystal structure, the first to be reported for LmCPB, was determined for the complex of this enzyme covalently bound to an azadipeptide nitrile ligand. Mapping the structure-activity relationships for LmCPB inhibition revealed superadditive effects for two pairs of structural transformations. Therefore, this work advances our understanding of azadipeptidyl and dipeptidyl nitrile structure-activity relationships for LmCPB structure-based inhibitor design. We also tested the same series of inhibitors on related cysteine proteases cathepsin L and Trypanosoma cruzi cruzain. The modulation of these mammalian and protozoan proteases represents a new framework for targeting papain-like cysteine proteases.

Aggregation−induced emissions in columnar wedge−shaped pyridinium−based ionic liquid crystals

Two series of ILCs derived from wedge−shaped N-phenylpyridiniums 1–2 were prepared and their mesomorphic properties were investigated. The X−ray crystal structure analyses of two single crystals 2-PF6 (n = 12) and 2-NTf2 (n = 12) revealed that bilayer structures induced by H−bonds in the solid state were observed. A complementary dimeric structure induced by H−bonds in such type of wedge−shaped cation (or anion) moiety was attributed to the formation of columnar phases. The type of counter anions has a significant influence on the formation of the mesophase; five counter anions (i.e. X = PF6‾, BF4‾, OTf‾, SCN‾, RSO3‾) induced columnar mesophase. In contrast, anion X = Tf2N‾ as a bulky moiety and less H−bond active sites formed crystal phase. The powder XRD data appeared that the diameter of the hard columnar part increased with the effective ionic radius for different counter ion. A linear correlation plot (R2 = 0.9203) was obtained. All ethanol solutions of compounds 1–2 were detected without any observable signals on photoluminescence. But compounds 2-X will aggregate in the aqueous mixture with high water fractions (ƒw) needed to turn on their light emission process. Weak PL signals are recorded at ƒw < 50% because the luminogens 2-OTf are fully dissolved and quenched in these solvent compositions. The PL intensity started to enhance at ƒw > 50% till it reached to the maximum intensity at ƒw ~70%.

X–ray crystal structure, Hirshfeld surface analysis, DFT and electronic properties of (E)–4–chloro–N′–(2,4–dihydroxy–benzylidene) benzohydrazide

Abstract A new compound of the title Schiff base (C14H11ClN2O3) was synthesized and characterized by using spectroscopic tools such as IR, NMR (1H and 13C), UV visible spectral and finally the structure was confirmed by the single crystal X–ray diffraction studies. The compound was crystallized in the monoclinic crystal system, with the space group P21/c. The unit cell parameters were confirmed by single crystal X–ray diffraction. The molecular packing is controlled by intermolecular hydrogen bonds and π− π stacking interactions. The crystal and molecular structure of the title Schiff base are linked via few intermolecular O–H···O, N–H···O hydrogen bond and an intramolecular O–H···N hydrogen bond. Geometrical parameters have been carried out by the computational density functional theory (DFT) B3LYP/6–311 G (d,p) and compared with the XRD values. Further, Hirshfeld surface and electrostatic potential surface analysis were carried out to understand the intermolecular interactions along with their graphical visualization.

Synthesis, Structure and Catalytic Oxidation of Ruthenium(III) Complexes Containing 1‐(Arylazo)naphthol Ligands Derived from β−Naphthol and Sterically Bulky Amines

AbstractA new class of ruthenium(III) complexes containing O, N donor functionalized azo derivatives were designed and synthesized. The synthesized compounds were characterized by fourier‐transform infrared (FTIR), ultraviolet–visible (UV‐vis) and electron paramagnetic resonance (EPR) spectral studies. The X−ray crystal structure of one of the complexes [Ru(L1)3] 1 has been determined. The catalytic activity of the complex [Ru(L1)3] 1 has been studied for the oxidation of primary and secondary alcohols to corresponding carbonyl compounds in the presence of N‐ Methylmorpholine‐N‐Oxide as co‐oxidant.

Immunoinformatics Based Vaccine Design for Zea M 1 Pollen Allergen

Objective: Zea m1 is one of the most common aeroallergens, causing allergy. This pollen allergen, present in maize, is responsible for type I hypersensitivity reaction. Despite having available X ray crystal structure of this pollen allergen, no definite vaccine has been developed for allergic disorder in humans. Method: In our present study, an epitope-based peptide vaccine against Zea m 1 pollen allergen, using a combination of B cell and T cell epitope predictions, followed by molecular docking and molecular dynamics simulation methods are carried out. Here, protein sequences of homologous pollen allergens of Zea m1 are collected and conserved regions present in them are investigated. Result: From the identified region of the allergenic protein, the peptide sequence KVPPGPNITTNY and the sequence AEWKPMKLSM are considered as the most potential B cell and T cell epitopes respectively. Furthermore, this predicted T cell epitope AEWKPMKLSM interacted with MHC allelic protein HLAB* 44:02 with the lowest IC 50 value (7.94 nM). This epitope perfectly fitted into the epitope binding groove of alpha helix of MHC I molecule with lowest energy weighted score -620.0, showing stability in MHC binding. This epitope also showed a good conservancy of 69.75% in world population coverage. Conclusion: The epitopes KVPPGPNITTNY and AEWKPMKLSM may be considered as potential peptide for peptide vaccine for pollen allergen after further experimental study. Key words: Immunoinformatics, Vaccine design, Zea m1 pollen allergen, B cell epitope, T cell epitope, Molecular docking, Molecular dynamics.

Syntheses, X‐ray crystal structures, and emission properties of protonated tripyridyltriazines and their ruthenium(II) complexes

AbstractA series of metal‐free compounds, ie, planar triprotonated triazine, triazineH3Cl(PF6)2 (1), planar triprotonated triazineH3Br(PF6)2 (2), and nonplanar monoprotonated triazineHPF6 (3), were prepared. Abbreviations used are triazine = tri‐2‐pyridyltriazine. Ruthenium complexes [RuCl(bpy)(L)](PF6), [RuCl(bpy)(L)](PF6)2, and [Ru(L)2](PF6)2 were also prepared, where bpy is 2,2′‐bipyridine and L's are triazine (4) and monoprotonated triazine (5), respectively. Ruthenium complexes [Ru(triazine)2](PF6)2 (6) were also prepared and crystallized. The X‐ray crystal structures of the 3 compounds 1, 2, and 3 and the complex 6 were determined. They were also characterized by electrospray ionization mass spectrometry, UV‐vis spectroscopy, and density functional theory calculations.

In Silico Inhibitory Activity against Caspase 3 by Zinc (II) Coordinated Complexes

Aims: The presented research paper is aimed to prevalence of apoptosis for the first time by using in silico molecular docking and simulation using caspase-3 zymogen and zinc-coordinated compounds. Antioxidant activities of the coordinated complexes were compared to the positive controls (BHT and ascorbic acid). Study design: Molecular docking analysis was performed by using Autodock 4.2, setting at 150x140x110 Gridbox, center at -57.616, 31.092, 88.666 with 0.375 A spacing. Their antioxidant activity was tested by FRAP and DPPH assay. Place and Duration of Study: Department of Chemistry and department of molecular medicine, Faculty of Medicine, University of Malaya laboratories between January 2014 – July 2014 Methodology: Compounds derived from zinc(II) ion give rise to coordination complexes exhibited CHN, NMR (H & C) and FT-IR spectra consistent with the proposed structures. Based on the xShort Research Article Gwaram and Hassandarvish; IJBcRR, 5(1): 27-38, 2015; Article no. IJBcRR.2015.004 28 ray crystal structure, one of the derivatives is a mononuclear square-pyramidal metal complex, with τ value of 0.35. The molecular docking simulation formed between compounds and caspase 3 showed the ligands bind to the active-site gorge well positioned in the active-site gorge. Results: The residues that have been involved in this protein-ligand interaction docked well by using Autodock 4.2, setting at 150x140x110 Gridbox, center at -57.616, 31.092, 88.666 with 0.375 A spacing in the hydrophobic pocket. Their antioxidant activity tested revealed their FRAP assay values of 531.11±0.021 and 1886.11±0.008 higher than value of 187.3±2.6 shown by BHT used as standard. The compounds showed IC50 values 21.50±0.009 and 14.80±0.002 lower than ascorbic acid with an IC50 value of 2.26±0.001 μg/mL. Conclusion: Synthesized zinc(II) complexes have been confirmed to inhibit the activity of caspase 3 both in silico and in vitro and were tested for antioxidant activity by both FRAP and DPPH methods.

Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1 (100.57)

Abstract ERAP1 trims antigen precursors to fit into MHC class I proteins. To perform this function, ERAP1 has unique substrate preferences, trimming long peptides while sparing shorter ones. To identify the structural basis for ERAP1’s unusual properties, we determined the X ray crystal structure of human ERAP1 bound to bestatin. The structure reveals an open conformation with a large interior compartment. An extended groove originating from the enzyme’s catalytic center can accommodate long peptides and has features that explain ERAP1’s broad specificity for antigenic peptide precursors. Structural and biochemical analysis suggest a mechanism for ERAP1’s length-dependent trimming activity, whereby binding of long but not short substrates induces a conformational change with reorientation of a key catalytic residue towards the active site. ERAP1’s unique structural elements suggest how a generic aminopeptidase structure has been adapted for the specialized function of trimming antigenic precursors.

ChemInform Abstract: Design, Synthesis, and Kinetic Evaluation of a Unique Class of Elastase Inhibitors, the Peptidyl α-Ketobenzoxazoles, and the X- Ray Crystal Structure of the Covalent Complex Between Porcine Pancreatic Elastase and Ac-Ala-Pro-Val-2-Ben

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Divergence in proteins‐ Study of Cytochrome b5 isoforms using core‐swap mutants

Two isoforms of mammalian Cytochrome b5 exhibit remarkably different biophysical properties in spite of similar sequence and structure. The Outer mitochondrial membrane cytochrome b5 (OMb5) is presently the most stable isoform when compared to its evolutionary counterpart, the micrososmal cytochrome b5 (Mcb5). In order to understand the biophysical properties of the individual proteins, we have constructed a core swap mutant (hybb5) incorporating features from these two isoforms. The X‐ ray crystal structure, at 1.7 Å, of hybb5 has been solved and shows structural features similar to its parent proteins. The thermal stability, stability towards chaotropic agents, redox potential and heme transfer properties of hybb5 seems to have shifted in the direction of OMb5. In parallel we have performed a 10 ns Molecular dynamics simulation of OMb5, Mcb5 and hybb5. The results concur with the experimental data in that hybb5 behaves with characteristics of the OMb5 sub family. Circular Dichroism experiments of the heme free proteins (apo‐form) indicated the presence of tertiary structure. We are at present trying to further understand the apo form of hybb5 and linking it to functional divergence of OMb5 and Mcb5. The subtle structural changes that contribute to different properties in the two isoforms are being investigated via MD simulations.

Reactivity ratios determination and NMR characterization of 2-hydroxy ethyl methacrylate and methyl methacrylate copolymers

Reaction of 2, 2'-dipyridylamine (DPA) with hexafluorophosphoric acid (HPF6) in methanol generates white rod-shaped crystals of HDPA.PF6,H 2O. The salt is characterised by C, H and N analyses, FT-IR, 1H NMR, mass spectroscopy and molar conductance measurement. The X- ray crystal structure of the salt has been determined. The structure shows that the salt is monomeric. The amine nitrogen is strongly hydrogen bonded with oxygen atom of water. Two pyridyl rings are almost planar which is a rarity in the coordination chemistry of DPA. Semi- empirical AM1 calculation was also Abstract : NMR has proven to be one of the most informative technique for the investigation of copolymer microstructure as chemical shifts are sensitive to compositional and configurational sequences of copolymers. The HEMA/MMA copolymers were prepared by free radical bulk polymerization at 70 oC. The copolymer composition was determined from 1H NMR spec trum which is then used to determine the reactivity ratios. The reactivity ratios obtained from KT, EVM and least square methods are r HEMA = 0.98, r MMA = 0.82; r HEMA = 0.88, r MMA = 0.81 and r HEMA = 0.92, r MMA = 0.81 respectively. 1 H and 13 C{ 1 H} NMR spectra were analyzed with the help of DEPT, 2D HSQC and 2D TOCSY spectrum. The long range interactions of carbonyl carbon with methoxy protons and oxy methylene carbon with hydroxyl proton were determined with the help of heteronuclear multiple bond coherence (H MBC) spectrum. With the help of 2D spectra it was found that carbonyl, α-methyl and quaternary carbon of HEMA and MMA unit were sensitive to various configurational sequences as in poly(2-hydroxy ethyl methacrylate) and poly(methyl methacrylate). The carbonyl and

PL-02-02: Beta-secretase as a therapeutic target

Finding inhibitors of Aβ42 generation is a major goal of Alzheimer's disease drug development. Two target protease activities, β–and γ–secretase, were operationally defined in the early 90s, but progress in this area was slow, because the actual enzymes were not understood at the molecular level. Some years ago we identified a novel membrane bound aspartic protease, BACE1, as β–secretase. This finding has been confirmed and BACE1 and its homolog BACE2 have been characterized in detail by many groups. Major progress has been made in two areas: First, the x–ray crystal structure, which is critical for rational inhibitor design, has been solved and shown to be similar to that of other pepsin family members. Second, knockout studies show that BACE1 is critical for Aβ generation, but the knockout mice show an otherwise normal phenotype, raising the possibility that therapeutic BACE1 inhibition could be accomplished without major mechanism based toxicity. However, target–mediated toxicity of β–secretase inhibition cannot be ruled out based on the currently available data alone. While various peptidic β–secretase inhibitors have been published, the key challenge now is the generation of more drug–like compounds that could be developed for therapeutic purposes. Other current areas of investigation, including identification of additional BACE1 substrates, the potential role of BACE1 overexpression in AD and the phenotype of BACE2 knockout mice will be discussed.

CB1 and CB2 Cannabinoid Receptor Binding Studies Based on Modeling and Mutagenesis Approaches

In absence of X ray crystal structures of G-protein coupled receptors (GPCRs)-ligand complexes, computer-aided molecular modeling together with site-directed mutagenesis studies become of great importance in order to provide in-silico predictions that facilitate the development of new ligands. In this context, the present review addresses the application of these strategies to the CB(1) and CB(2) cannabinoid receptors. The combination of these complementary approaches represents a tool of considerable value which has allowed to understand the specific ligand-receptor interactions.

The Synthesis by Decarboxylation Reactions and Crystal Structures of 1, n–Bis(diphenylphosphino)alkane(pentafluorophenyl)‐platinum(II) Complexes

AbstractDecarboxylation reactions between the complexes cis–[PtCl2L] (L = 1, n–bis(diphenylphosphino)–ethane (n = 2, dppe), –propane (n = 3, dppp) or –butane (n = 4, dppb)) and thallium(I) pentafluorobenzoate in pyridine give cis–[PtCl(C6F5)L] and cis–[Pt(C6F5)2L] complexes in high yields with short reaction times. X–ray crystal structures of cis–[PtCl(C6F5)(dppe)] · 0.5 C5H5N, cis–[PtCl(C6F5)(dppp)], cis–[PtCl(C6F5)(dppb)] · C3H6O, cis–[Pt(C6F5)2L] (L = dppe, dppp and dppb) and the reactants cis–[PtCl2(dppp)] (as a CH2Cl2 solvate) and cis–[PtCl2(dppb)] show monomeric structures with chelating diphosphine ligands in all cases rather than dimers with bridging diphosphines. 31P NMR data are consistent with these structures in solution.

COPPER CAUGHT BINDING NO, 02

X -RAY CRYSTAL STRUCTURES of two different copper-containing metalloenzymes have revealed novel metal adducts of nitric oxide (NO) and oxygen that may be key intermediates in these enzymes' catalytic mechanisms. The ways in which NO and 0 2 bind to copper in the active sites of these two enzymes have not previously been seen in nature. A team led by structural biologists Michael E. P. Murphy and Elitza I. Tocheva of the University of British Columbia, Vancouver, trapped the novel Cu-NO complex in NO-saturated crystals of nitrite reductase, a bacterial enzyme that produces NO from nitrite [ Science , 304 , 867 (2004)}. The NO molecule is bound side on to the enzyme's copper atom—that is, the nitrogen and oxygen atoms are nearly equidistant from the copper in the 1.3-Â X-ray structure. This unusual Cu-NO binding mode is unprecedented in both synthetic and biological systems, Murphy says. The unusual Cu-0 2 complex was observed in ...

X‐ray Crystallographic Study of Copper(II), Cobalt(II) and Silver(I) Complexes of Ligands Containing Two Oxine Subunits Linked by Xylylene Spacer Groups

AbstractX‐ray crystal structures are reported for six transition‐metal complexes of the ligands 1,2‐bis(8‐quinolyloxymethyl)benzene (3) and 1,3‐bis(8‐quinolyloxymethyl)benzene (4). In three mononuclear copper(II) and cobalt(II) complexes, 3 acts as a chelating ligand with either N,O,N′‐tridentate or N,O,O′,N′‐tetradentate coordination. A novel dinuclear silver(I) complex of 3 is shown to be stabilised by a number of weak metal−ligand contacts and multiple intramolecular π−π stacking interactions. In two dinuclear copper(II) nitrate complexes of 4, the ligand adopts very different bridging modes of coordination. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2004)

Coordination number 12 in praseodymium and 11 in neodymium complexes with organofluorotitanate ligands

The complexes of [Pr{(C 5Me 5) 2Ti 2F 7} 3] 2 and [Nd{(C 5Me 5) 2Ti 2F 7} 3] 3 were obtained by the reaction of [Hdmpy] +[(C 5Me 5) 2Ti 2F 7] − 1 (dmpy=2,6–dimethylpyridine, C 5H 3NMe 2), with praseodymium(III) and neodymium(III) trifluoromethanesulfonate. The X–ray crystal structures of 2 and 3 exhibit a fluorine environment of 12 at the praseodymium and of 11 at the neodymium with [(C 5Me 5) 2Ti 2F 7] − acting as well as a tetra- and as a three-fluorodentate ligand. Both complexes retained their structures in solution. Complex 2 is the first molecular compound containing PrF bonds.

SDR Structure, Mechanism of Action, and Substrate Recognition

Short chain dehydrogenases/reductases (SDR) constitute a large protein family. The SDR family now includes more than 1,000 enzymes from humans, mammals, insects and bacteria, and exhibits a wide variety of substrate specificity for steroids, retinoids, prostaglandins, sugars, alcohols and other small molecules. These enzymes have a residue identity level of 15-30 perent. Much has been done in the last decade to understand the structure function relationships in the SDR enzymes. This review summarizes recent progress of structural and functional studies of the enzymes belonging to the SDR family (X ray crystal structure analyses and site directed mutagenesis studies). Based on these studies, the three dimensional structure, catalytic mechanism, coenzyme specificity, and substrate specificity of the SDR enzymes are discussed. Keywords: SDR structure, Short chain dehydrogenase, Oxidoreductase, MDR enzymes, Monomeric enzymes, Single domain protein, Rossmann fold, C terminal residues, Coenzyme binding mode, pyrophosphate moiety, active site cleft, ser tyr lys triad, deprotonated phenolic group, coenzyme specificity, Substrate specificity, membrane spainnig domain

Electrochemical studies of copper(II) complexes derived from bulky Schiff bases. The crystal structure of bis[N-(1- adamantyl)-salicylaldiminato]copper(II)

Three Schiff base ligands and their corresponding copper(II) complexes have been prepared and characterized. Elemental analyses, mass spectra, i.r., electronic spectra, μeff and the X- ray crystal structure for one of the complexes, as well as elemental analyses, mass spectra, i.r., electronic and 1H n.m.r. spectra of the ligands, have been obtained. The X-ray study shows that the geometry around the metal atom is intermediate between square planar and tetrahedral. Electrochemical studies on the complexes reveal a dependence of the CuII/CuI potentials on the extent of distortion of the planar structure observed in solid state.