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Hydrogen-bonding Network (hydrogen-bonding + network)
Kinds of Hydrogen-bonding Network Selected AbstractsTwo New Iron(II) Spin-Crossover Complexes with N4O2 Coordination Sphere and Spin Transition around Room TemperatureEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 36 2009Birgit Weber Abstract The reaction of iron(II) acetate with the tetradentate Schiff base like ligand H2L1 {[3,3,]-[4,5-dihydroxy-1,2-phenylenebis(iminomethylidyne)bis(2,4-pentanedion)]} leads to the formation of the complex [FeL1(MeOH)]. Reaction of this complex with pyridine (py) or N,N,-dimethylaminopyridine (dmap) leads to the two N4O2 -coordinated complexes [FeL1(py)2]·py (1) and [FeL1(dmap)2]·MeOH·0.5dmap (2). Both complexes are spin-crossover compounds that were characterised by using magnetic measurements, X-ray crystallography and temperature-dependent 1H NMR spectroscopy. Special attention was given to the role of the two hydroxy groups on the phenyl ring in the formation of a hydrogen-bonding network and the influence of this network on the spin-transition properties. Although only a gradual spin crossover was observed for both complexes, the transition temperature was shifted to higher temperatures relative to that of the complexes with no additional hydroxy groups at the Schiff base like ligand. The hydrogen-bonding network was responsible for this effect.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Crystal Structures of Conformationally Locked Cyclitols: An Analysis of Hydrogen-Bonded Architectures and their Implications in Crystal EngineeringEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 3 2007Goverdhan Mehta Abstract A qualitative study has been carried out on selected polycyclitols to evaluate the potential of conformational locking of hydroxy groups in lending predictability to the O,H···O hydrogen-bonding network observed in the crystal structures of such compounds. The polycyclitols employed in this study are conformationally locked with all the hydroxy groups destined to be axial owing to the trans ring fusion(s) in the polycyclic carbon framework. The consequent formation of intramolecular O,H···O hydrogen bonds between the 1,3- syn diaxial hydroxy groups now permits any packing pattern in the polycyclitols to be described in terms of a small group of intramolecularly bonded molecular motifs linked to their respective neighbors by four O,H···O bonds. By using this model and the results of CSD analyses of polyols as a guide, the O,H···O hydrogen-bonded packing motifs most likely to be observed in the crystal structure of each polycyclitol were proposed and compared with those obtained experimentally. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Environmentally friendly flame retardants.MAGNETIC RESONANCE IN CHEMISTRY, Issue S1 2007A detailed solid-state NMR study of melamine orthophosphate Abstract We used solid-state NMR spectroscopy to gain detailed information about the proton positions, proximities and the hydrogen-bonding network in the environmentally friendly flame retardant melamine orthophosphate (MP). High-resolution proton one- and two-dimensional solid-state NMR spectra were obtained at high external magnetic field in combination with fast magic angle spinning of the sample. Furthermore, we recorded homo- and heteronuclear correlation spectra of types 15N15N, 1H13C, 1H15N and 1H31P. In addition, we determined the geometry of the NH and NH2 groups in MP by 15N1H heteronuclear recoupling experiments. We were able to completely assign the different isotropic chemical shifts in MP. Furthermore, we could identify the protonation of the melamine and orthophosphate moieties. The experimental results are discussed in connection with the structural model obtained by powder X-ray diffraction together with a combined molecular modeling-Rietveld refinement approach (De Ridder et al. Helv. Chim. Acta 2004; 87: 1894). We show that the geometry of the NH2 groups can only be successfully estimated by solid-state NMR. Copyright © 2007 John Wiley & Sons, Ltd. [source] Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a ,-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolasePROTEIN SCIENCE, Issue 8 2009Taku Ohki Abstract Promiscuous 6-aminohexanoate-linear dimer (Ald)-hydrolytic activity originally obtained in a carboxylesterase with a ,-lactamase fold was enhanced about 80-fold by directed evolution using error-prone PCR and DNA shuffling. Kinetic studies of the mutant enzyme (Hyb-S4M94) demonstrated that the enzyme had acquired an increased affinity (Km = 15 mM) and turnover (kcat = 3.1 s,1) for Ald, and that a catalytic center suitable for nylon-6 byproduct hydrolysis had been generated. Construction of various mutant enzymes revealed that the enhanced activity in the newly evolved enzyme is due to the substitutions R187S/F264C/D370Y. Crystal structures of Hyb-S4M94 with bound substrate suggested that catalytic function for Ald was improved by hydrogen-bonding/hydrophobic interactions between the AldCOOH and Tyr370, a hydrogen-bonding network from Ser187 to AldNH, and interaction between AldNH and Gln27-O, derived from another subunit in the homo-dimeric structure. In wild-type Ald-hydrolase (NylB), Ald-hydrolytic activity is thought to be optimized by the substitutions G181D/H266N, which improve an electrostatic interaction with AldNH (Kawashima et al., FEBS J 2009; 276:2547,2556). We propose here that there exist at least two alternative modes for optimizing the Ald-hydrolytic activity of a carboxylesterase with a ,-lactamase fold. [source] Crystal structure of 3-hydroxyanthranilic acid 3,4-dioxygenase from Saccharomyces cerevisiae: A special subgroup of the type III extradiol dioxygenasesPROTEIN SCIENCE, Issue 4 2006Xiaowu Li Abstract 3-Hydroxyanthranilic acid 3,4-dioxygenase (3HAO) is a non-heme ferrous extradiol dioxygenase in the kynurenine pathway from tryptophan. It catalyzes the conversion of 3-hydroxyanthranilate (HAA) to quinolinic acid (QUIN), an endogenous neurotoxin, via the activation of N-methyl-D-aspartate (NMDA) receptors and the precursor of NAD+ biosynthesis. The crystal structure of 3HAO from S. cerevisiae at 2.4 Å resolution shows it to be a member of the functionally diverse cupin superfamily. The structure represents the first eukaryotic 3HAO to be resolved. The enzyme forms homodimers, with two nickel binding sites per molecule. One of the bound nickel atoms occupies the proposed ferrous-coordinated active site, which is located in a conserved double-strand ,-helix domain. Examination of the structure reveals the participation of a series of residues in catalysis different from other extradiol dioxygenases. Together with two iron-binding residues (His49 and Glu55), Asp120, Asn51, Glu111, and Arg114 form a hydrogen-bonding network; this hydrogen-bond network is key to the catalysis of 3HAO. Residues Arg101, Gln59, and the substrate-binding hydrophobic pocket are crucial for substrate specificity. Structure comparison with 3HAO from Ralstonia metallidurans reveals similarities at the active site and suggests the same catalytic mechanism in prokaryotic and eukaryotic 3HAO. Based on sequence comparison, we suggest that bicupin of human 3HAO is the first example of evolution from a monocupin dimer to bicupin monomer in the diverse cupin superfamilies. Based on the model of the substrate HAA at the active site of Y3HAO, we propose a mechanism of catalysis for 3HAO. [source] New insights into intracellular lipid binding proteins: The role of buried waterPROTEIN SCIENCE, Issue 10 2002Christian Lücke Abstract The crystal structures of most intracellular lipid binding proteins (LBPs) show between 5 and 20 internally bound water molecules, depending on the presence or the absence of ligand inside the protein cavity. The structural and functional significance of these waters has been discussed for several LBPs based on studies that used various biophysical techniques. The present work focuses on two very different LBPs, heart-type fatty acid binding protein (H-FABP) and ileal lipid binding protein (ILBP). Using high-resolution nuclear magnetic resonance spectroscopy, certain resonances belonging to side-chain protons that are located inside the water-filled lipid binding cavity were observed. In the case of H-FABP, the pH- and temperature-dependent behavior of selected side-chain resonances (Ser82 OgH and the imidazole ring protons of His93) indicated an unusually slow exchange with the solvent, implying that the intricate hydrogen-bonding network of amino-acid side-chains and water molecules in the protein interior is very rigid. In addition, holo H-FABP appeared to display a reversible self-aggregation at physiological pH. For ILBP, on the other hand, a more solvent-accessible protein cavity was deduced based on the pH titration behavior of its histidine residues. Comparison with data from other LBPs implies that the evolutionary specialization of LBPs for certain ligand types was not only because of mutations of residues directly involved in ligand binding but also to a refinement of the internal water scaffold. [source] On the sequence of three related phases of [Ni(H2O)2(15-crown-5)](HSO4)2 in the temperature range 110,295,KACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2010Maxime A. Siegler Attempts to prepare the compound [Ni(H2O)2(15-crown-5)](X)2 were eventually successful with X = NO provided that a synthetic route aimed at restricting water was followed. Application of this method was extended to make the analogous compound with X = HSO, for which three symmetry-related phases were isolated between 295 and 110,K: a room-temperature phase with Z, = ½ [phase (I)], an intermediate-temperature phase with Z, = 1 [phase (II)] and a low-temperature phase with Z, = 2 [phase (III)]. The phases are related by two reversible solid,solid phase transitions, and both transitions take place without a significant loss of crystallinity. In the phase sequence (I) , (II) , (III) (Z,: ½, 1 , 2), the crystal packing remains remarkably similar but the degree of order in the crystal changes significantly; the structure is very disordered at room and intermediate temperatures but is ordered at 110,K. The compound [Ni(H2O)2(15-crown-5)](HSO4)2 has a complicated hydrogen-bonding network, which contains O,H...O bonds between the counterions. Structural changes are largest along some face-diagonal directions in the sequence (I) , (II) , (III). [source] Structures of relevant ammonium salts in fertilizersACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2010J. M. Montejo-Bernardo The crystal structures of two double salts of ammonium nitrate (AN) and ammonium sulfate (AS) are reported. The double salts 2NH4NO3·(NH4)2SO4 (2AN·AS) and 3NH4NO3·(NH4)2SO4 (3AN·AS) show a very similar crystal structure packing with alternating layers of anions and cations. The solid-state ionic distribution is controlled by an extensive hydrogen-bonding network with ammonium groups as the donors and O atoms acting as the acceptors. Crystallographic studies were conducted at both room temperature (293,K) and 100,K. Increasing the temperature involves shortening the b axis in the case of the 3AN·AS salt. Quantification of fertilizer mixtures using the Rietveld method was also carried out by means of the structural models reported in this paper for both salts. [source] Hydrogen bonding and ,,, interactions in 1-benzofuran-2,3-dicarboxylic acid and its 1:1 cocrystals with pyridine, phenazine and 1,4-phenylenediamineACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2009Hatem M. Titi The structure of 1-benzofuran-2,3-dicarboxylic acid (BFDC), C10H6O5, (I), exhibits an intramolecular hydrogen bond between one ,COOH group and the other, while the second carboxyl function is involved in intermolecular hydrogen bonding to neighbouring species. The latter results in the formation of flat one-dimensional hydrogen-bonded chains in the crystal structure, which are ,,, stacked along the normal to the plane of the molecular framework, forming a layered structure. 1:1 Cocrystallization of BFDC with pyridine, phenazine and 1,4-phenylenediamine is associated with H-atom transfer from BFDC to the base and charge-assisted hydrogen bonding between the BFDC, monoanion and the corresponding ammonium species, while preserving, in all cases, the intramolecular hydrogen bond between the carboxyl and carboxylate functions. The pyridinium 2-carboxylato-1-benzofuran-3-carboxylic acid, C5H6N+·C10H5O5,, (II), and phenazinium 3-carboxylato-1-benzofuran-2-carboxylic acid, C12H9N2+·C10H5O5,, (III), adducts form discrete hydrogen-bonded ion-pair entities. In the corresponding crystal structures, the two components are arranged in either segregated or mixed ,,, stacks, respectively. On the other hand, the structure of 4-aminoanilinium 2-carboxylato-1-benzofuran-3-carboxylic acid, C6H9N2+·C10H5O5,, (IV), exhibits an intermolecular hydrogen-bonding network with three-dimensional connectivity. Moreover, this fourth structure exhibits induction of supramolecular chirality by the extended hydrogen bonding, leading to a helical arrangement of the interacting moieties around 21 screw axes. The significance of this study is that it presents the first crystallographic characterization of pure BFDC, and manifestation of its cocrystallization with a variety of weakly basic amine molecules. It confirms the tendency of BFDC to preserve its intramolecular hydrogen bond and to prefer a monoanionic form in supramolecular association with other components. The aromaticity of the flat benzofuran residue plays an important role in directing either homo- or heteromolecular ,,, stacking in the first three structures, while the occurrence of a chiral architecture directed by multiple hydrogen bonding is the dominant feature in the fourth. [source] Octakis(dimethylammonium) hexa-,2 -chlorido-hexachloridotrinickelate(II) dichloride: a linear trinickel complex with asymmetric bridgingACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2009Allison Gerdes The title compound, (C2H8N)8[Ni3Cl12]Cl2, crystallizes as linear [Ni3Cl12]6, complex anions with inversion symmetry, separated from one another by dimethylammonium cations and noncoordinated chloride ions. The gross structural arrangement of the trinickel complex is as a segment of face-sharing NiCl6 octahedra similar to the (NiCl3)n chains of CsNiCl3 -type compounds. On closer inspection, the regular coordination geometry of the complex consists of octahedral NiCl6 in the center linked by two symmetrically bridging chloride ions to square-pyramidal NiCl5 on each end. A long semicoordinate bond is formed by each of the terminal NiII cations, to give a 5+1 coordination geometry and form an asymmetric bridge to the central NiII cation. The dimethylammonium cations surround the complex with an extensive hydrogen-bonding network, linking the complex to the noncoordinated chloride ions. Asymmetric bridging in the complex arises from short hydrogen bonds from the same dimethylammonium cation to the apical and asymmetric bridging chloride ions, causing the complex to scissor outward. [source] Supramolecular motifs in the first structures of organic carboxylate salts of 1-(diaminomethylene)thiourea (HATU)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2009gorzata Ho The structures of the first two organic carboxylate salts of 1-(diaminomethylene)thiourea (HATU), namely 1-(diaminomethylene)thiouron-1-ium formate, C2H7N4S+·HCOO,, (I), and bis[1-(diaminomethylene)thiouron-1-ium] oxalate dihydrate, 2C2H7N4S+·C2O42,·2H2O, (II), in which the oxalate lies on a symmetry centre, possess different extended hydrogen-bonding networks with different graph-set motifs. The R22(8) motif present in (I) does not appear in (II), but an R21(6) motif is present in both (I) and (II). Compound (I) has a three-dimensional hydrogen-bonding network, whereas (II) has a layered structure with layers joined by hydrogen-bonding motifs that form R42(8) patterns. This work extends the known supramolecular structural data for HATU to include these organic carboxylates in addition to the previously characterized salts with inorganic acids. [source] Products of the interaction of (1-diaminomethylene)thiourea with hydrofluoric acidACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2009gorzata Ho The salts 1-(diaminomethylene)thiouron-1-ium hydrogen difluoride, C2H7N4S+·HF2,, (I), and bis[1-(diaminomethylene)thiouron-1-ium] hexafluoridosilicate, 2C2H7N4S+·SiF62,, (II), have both been obtained from the reaction of (1-diaminomethylene)thiourea (HATU) with hydrofluoric acid. Both compounds contain extensive networks of N,H...F hydrogen bonds. The hydrogen difluoride salt contains four independent asymmetric [HF2], anions. In the hexafluoridosilicate salt, the centrosymmetric [SiF6]2, anion is distorted, although this distortion is not clearly correlated with the N,H...F hydrogen-bonding network. [source] Bis[2-(2-hydroxyethyl)pyridinium] ,-decavanadato-bis[pentaaquamanganate(II)] tetrahydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2009Lenka Kli, tincová The structure of the title compound, (C7H10NO)2[Mn2V10O28(H2O)10]·4H2O or (C5H4NHCH2CH2OH)2[{Mn(H2O)5}2V10O28]·4H2O, at 293,(2),K has triclinic (P) symmetry. The asymmetric unit consists of one half of a decavanadate anion of Ci symmetry, one [Mn(H2O)5]2+ group, one 2-(2-hydroxyethyl)pyridinium cation and two solvent water molecules. The decavanadate ion bridges between two [Mn(H2O)5]2+ groups, thus forming a dodecanuclear complex unit. Complex units are connected via a hydrogen-bonding network, forming supramolecular layers lying in the (001) plane. Cations and solvent water molecules are located between these layers. [source] Salts of maleic and fumaric acids with oxine: the role of isomeric acids in hydrogen-bonding patternsACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2009S. Franklin Both maleic and fumaric acid readily form adducts or complexes with other organic molecules. The 1:1 adduct formed by quinolin-8-ol (oxine) with maleic and fumaric acid are salts, namely 8-hydroxyquinolinium hydrogen maleate, C9H8NO+·C4H3O4,, (I), and 8-hydroxyquinolinium hydrogen fumarate, C9H8NO+·C4H3O4,, (II). The cations and anions of both salts are linked by ionic N+,H...O, hydrogen bonds. The maleate salt crystallizes in the space group P212121, while the fumarate salt crystallizes in P. The maleic and fumaric acids in their complex forms exist as semimaleate and semifumarate ions (mono-ionized state), respectively. Classical N,H...O and O,H...O hydrogen bonds, together with short C,H...O contacts, generate an extensive hydrogen-bonding network. The crystal structures of the maleate and fumarate salts of oxine have been elucidated to study the importance of noncovalent interactions in the aggregation and interaction patterns of biological molecules. The structures of the salts of the Z and E isomers of butenedioic acid (maleic and fumaric acid, respectively) with quinolin-8-ol are compared. [source] The new three-dimensional supramolecule bis{,-2-[(4-hydroxybenzoyl)hydrazonomethyl]phenolato}bis[aquacopper(II)] dinitrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2008Hua Yin In the title centrosymmetric binuclear complex, [Cu2(C14H11N2O3)2(H2O)2](NO3)2, the two metal centres are bridged by the phenolate O atoms of the ligand, forming a Cu2O2 quadrangle. Each Cu atom has a distorted square-pyramidal geometry, with the basal donor atoms coming from the O,N,O,-tridentate ligand and a symmetry-related phenolate O atom. The more weakly bound apical donor O atom is supplied by a coordinated water molecule. When a further weak Cu...O interaction with the 4-hydroxy O atom of a neighbouring cation is considered, the extended coordination sphere of the Cu atom can be described as distorted octahedral. This interaction leads to two-dimensional layers, which extend parallel to the (100) direction. The two-dimensional polymeric structure contrasts with other reported structures involving salicylaldehyde benzoylhydrazone ligands, which are usually discrete mono- or dinuclear Cu complexes. The nitrate anions are involved in a three-dimensional hydrogen-bonding network, featuring intermolecular N,H...O and O,H...O hydrogen bonds. [source] An unusual two-dimensional hydrogen-bonding network in bis(2,9-dimethyl-1,10-phenanthrolin-1-ium) peroxodisulfate dihydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2008Miguel Angel Harvey The title compound, 2C14H13N2+·S2O82,·2H2O, is a protonated amine salt which is formed from two rather uncommon ionic species, namely a peroxodisulfate (pds2,) anion, which lies across a crystallographic inversion centre, and a 2,9-dimethyl-1,10-phenanthrolin-1-ium (Hdmph+) cation lying in a general position. Each pds2, anion binds to two water molecules through strong water,peroxo O,H...O interactions, giving rise to an unprecedented planar network of hydrogen-bonded macrocycles which run parallel to (100). The atoms of the large R88(30) rings are provided by four water molecules bridging in fully extended form (...H,O,H...) and four pds2, anions alternately acting as long (...O,S,O,O,S,O...) and short (...O,S,O...) bridges. The Hdmph+ cations, in turn, bind to these units through hydrogen bonds involving their protonated N atoms. In addition, the crystal structure also contains ,,, and aromatic,peroxo C,H...O interactions. [source] 4-Oxocyclohexanecarboxylic acid: hydrogen bonding in the monohydrate of a ,-keto acidACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2004Alan Barcon The title monohydrate, C7H10O3·H2O, aggregates as a complex hydrogen-bonding network, in which the water molecule accepts a hydrogen bond from the carboxyl group of one molecule and donates hydrogen bonds to ketone and carboxyl Czdbnd;O functions in two additional molecules, yielding a sheet-like structure of parallel ribbons. The keto acid adopts a chiral conformation through rotation of the carboxyl group by 62.50,(15)° relative to the plane defined by its point of attachment and the ketone C and O atoms. Two C,H,O close contacts exist in the structure. [source] 2-Amino-5-methyl-1,3,4-thiadiazole and 2-amino-5-ethyl-1,3,4-thiadiazoleACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2001Daniel E. Lynch The structures of 2-amino-5-methyl-1,3,4-thiadiazole, C3H5N3S, and 2-amino-5-ethyl-1,3,4-thiadiazole, C4H7N3S, have been determined for comparison with unsubstituted 2-amino-1,3,4-thiadiazole. Despite their different space groups (P21/n and Pbca, respectively), the packing modes of the methyl and ethyl derivatives are similar, with comparable three-dimensional hydrogen-bonding associations. This is in contrast to the hydrogen-bonding network in 2-amino-1,3,4-thiadiazole, which is one-dimensional and has denser packing. It is shown that both packing forms are different polymorphs of a specific subunit of each array. [source] Expansion of the aspartate ,-semialdehyde dehydrogenase family: the first structure of a fungal orthologACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2010Buenafe T. Arachea The enzyme aspartate semialdehyde dehydrogenase (ASADH) catalyzes a critical transformation that produces the first branch-point intermediate in an essential microbial amino-acid biosynthetic pathway. The first structure of an ASADH isolated from a fungal species (Candida albicans) has been determined as a complex with its pyridine nucleotide cofactor. This enzyme is a functional dimer, with a similar overall fold and domain organization to the structurally characterized bacterial ASADHs. However, there are differences in the secondary-structural elements and in cofactor binding that are likely to cause the lower catalytic efficiency of this fungal enzyme. Alterations in the dimer interface, through deletion of a helical subdomain and replacement of amino acids that participate in a hydrogen-bonding network, interrupt the intersubunit-communication channels required to support an alternating-site catalytic mechanism. The detailed functional information derived from this new structure will allow an assessment of ASADH as a possible target for antifungal drug development. [source] A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2009Artem Y. Lyubimov Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3,-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH..., interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall kcat. Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0,Å resolution) reveals significant perturbations in the active site. As predicted, Asp485 is oriented away from the flavin moiety, such that any stabilizing interaction with the reduced flavin is abolished. Met122 and Glu361 form unusual hydrogen bonds to the functional group of Asp485 and are displaced from the positions they occupy in the wild-type active site. The overall effect is to disrupt the stabilization of the reduced FAD cofactor during catalysis. Furthermore, a narrow transient channel that is shown to form when the wild-type Asn485 forms the NH..., interaction with FAD and that has been proposed to function as an access route of molecular oxygen, is not observed in either of the mutant structures, suggesting that the dynamics of the active site are altered. [source] A neutron crystallographic analysis of phosphate-free ribonuclease A at 1.7,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2009Daichi Yagi A neutron crystallographic analysis of phosphate-free bovine pancreatic RNase A has been carried out at 1.7,Å resolution using the BIX-4 single-crystal diffractometer at the JRR-3 reactor of the Japan Atomic Energy Agency. The high-resolution structural model allowed us to determine that His12 acts mainly as a general base in the catalytic process of RNase A. Numerous other distinctive structural features such as the hydrogen positions of methyl groups, hydroxyl groups, prolines, asparagines and glutamines were also determined at 1.7,Å resolution. The protonation and deprotonation states of all of the charged amino-acid residues allowed us to provide a definitive description of the hydrogen-bonding network around the active site and the H atoms of the key His48 residue. Differences in hydrogen-bond strengths for the ,-helices and ,-sheets were inferred from determination of the hydrogen-bond lengths and the H/D-exchange ratios of the backbone amide H atoms. The correlation between the B factors and hydrogen-bond lengths of the hydration water molecules was also determined. [source] Structural and functional role of water molecules in bovine pancreatic phospholipase A2: a data-mining approachACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2009Shankar Prasad Kanaujia The water molecules in 25 (21 high-resolution and four atomic resolution) crystal structures of bovine pancreatic phospholipase A2 have been analyzed in order to identify the invariant water molecules and their possible roles. A total of 24 water molecules have been identified that are invariant in all 25 crystal structures examined. These include the catalytic water molecule, which is directly involved in the enzyme mechanism, and the conserved structural water molecule, which stabilizes the extended hydrogen-bonding network of the active site. Furthermore, many other water molecules stabilize the structure, whilst a few have been found to maintain the active-site geometry and provide coordination to the functionally important calcium ion. The invariant water molecules have been carefully examined and their possible roles in the structure and/or function are discussed. Molecular-dynamics studies of all 25 crystal structures have also been carried out and the results provide a good explanation of and support the findings obtained from the crystal structures. [source] Production and X-ray crystallographic analysis of fully deuterated human carbonic anhydrase IIACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2006Monika Budayova-Spano Human carbonic anhydrase II (HCA II) is a zinc metalloenzyme that catalyzes the reversible hydration and dehydration of carbon dioxide and bicarbonate, respectively. The rate-limiting step in catalysis is the intramolecular transfer of a proton between the zinc-bound solvent (H2O/OH,) and the proton-shuttling residue His64. This distance (,7.5,Å) is spanned by a well defined active-site solvent network stabilized by amino-acid side chains (Tyr7, Asn62, Asn67, Thr199 and Thr200). Despite the availability of high-resolution (,1.0,Å) X-ray crystal structures of HCA II, there is currently no definitive information available on the positions and orientations of the H atoms of the solvent network or active-site amino acids and their ionization states. In preparation for neutron diffraction studies to elucidate this hydrogen-bonding network, perdeuterated HCA II has been expressed, purified, crystallized and its X-ray structure determined to 1.5,Å resolution. The refined structure is highly isomorphous with hydrogenated HCA II, especially with regard to the active-site architecture and solvent network. This work demonstrates the suitability of these crystals for neutron macromolecular crystallography. [source] Self-Assembly of Amylin(20,29) Amide-Bond Derivatives into Helical Ribbons and Peptide Nanotubes rather than FibrilsCHEMISTRY - A EUROPEAN JOURNAL, Issue 14 2006Ronald C. Elgersma Abstract Uncontrolled aggregation of proteins or polypeptides can be detrimental for normal cellular processes in healthy organisms. Proteins or polypeptides that form these amyloid deposits differ in their primary sequence but share a common structural motif: the (anti)parallel , sheet. A well-accepted approach for interfering with ,-sheet formation is the design of soluble ,-sheet peptides to disrupt the hydrogen-bonding network; this ultimately leads to the disassembly of the aggregates or fibrils. Here, we describe the synthesis, spectroscopic analysis, and aggregation behavior, imaged by electron microscopy, of several backbone-modified amylin(20,29) derivatives. It was found that these amylin derivatives were not able to form fibrils and to some extent were able to inhibit fibril growth of native amylin(20,29). However, two of the amylin peptides were able to form large supramolecular assemblies, like helical ribbons and peptide nanotubes, in which ,-sheet formation was clearly absent. This was quite unexpected since these peptides have been designed as soluble ,-sheet breakers for disrupting the characteristic hydrogen-bonding network of (anti)parallel , sheets. The increased hydrophobicity and the presence of essential amino acid side chains in the newly designed amylin(20,29) derivatives were found to be the driving force for self-assembly into helical ribbons and peptide nanotubes. This example of controlled and desired peptide aggregation may be a strong impetus for research on bionanomaterials in which special shapes and assemblies are the focus of interest. [source] Orientational Control of Guest Molecules in an Organic Intercalation System by Host Polymer TacticityCHEMISTRY - A EUROPEAN JOURNAL, Issue 8 2006Shinya Oshita Abstract Four kinds of stereoregular poly(muconic acid)s, which are synthesized by topochemical polymerization and subsequent solid-state hydrolysis, are used as the organic host materials for intercalation. We describe the reaction behavior and layered structure of intercalation compounds using stereoregular poly(muconic acid)s and n -alkylamines as host and guest, respectively. The packing structure of the guest alkylamines was determined by X-ray diffractions as well as IR and Raman spectroscopies. We have found that the orientation of the guest molecules is controlled by the host polymer tacticity, depending on the structure of the two-dimensional hydrogen-bonding network formed in the polymer sheets of the crystals. [source] Hydrogen-Bonding Cooperativity: Using an Intramolecular Hydrogen Bond To Design a Carbohydrate Derivative with a Cooperative Hydrogen-Bond Donor CentreCHEMISTRY - A EUROPEAN JOURNAL, Issue 17 2004Virginie Vicente Dr. Abstract Neighbouring groups can be strategically located to polarise HO,,,OH intramolecular hydrogen bonds in an intended direction. A group with a unique hydrogen-bond donor or acceptor character, located at hydrogen-bonding distance to a particular OH group, has been used to initiate the hydrogen-bond network and to polarise a HO,,,OH hydrogen bond in a predicted direction. This enhanced the donor character of a particular OH group and made it a cooperative hydrogen-bond centre. We have proved that a five-membered-ring intramolecular hydrogen bond established between an amide NH group and a hydroxy group (1,2-e,a), which is additionally located in a 1,3 -cis- diaxial relationship to a second hydroxy group, can be used to select a unique direction on the six-membered-ring intramolecular hydrogen bond between the two axial OH groups, so that one of them behaves as an efficient cooperative donor. Talose derivative 3 was designed and synthesised to prove this hydrogen-bonding network by NMR spectroscopy, and the mannopyranoside derivatives 1 and 2 were used as models to demonstrate the presence in solution of the 1,2-(e,a)/five-membered-ring intramolecular hydrogen bond. Once a well-defined hydrogen-bond is formed between the OH and the amido groups of a pyranose ring, these hydrogen-bonding groups no longer act as independent hydrogen-bonding centres, but as hydrogen-bonding arrays. This introduces a new perspective on the properties of carbohydrate OH groups and it is important for the de novo design of molecular recognition processes, at least in nonpolar media. Carbohydrates 1,3 have shown to be efficient phosphate binders in nonpolar solvents owing to the presence of cooperative hydroxy centres in the molecule. [source] Electrically Conductive Hydrogen-Bond-Based Supramolecular Polymer with a Tetrathiafulvalene Moiety: Modulation of Electrical Conductivity and Flexibility of Film by External StimulusCHEMISTRY - AN ASIAN JOURNAL, Issue 10 2010Seong Jib Choi Best supporting role in a film! The 2-deoxyguanosine derivatives having tetrathiafulvalene moieties for a construction of stimuli-responsive supramolecular polymer have been prepared. Owing to a hydrogen-bonding network, the self-supporting film can be fabricated by a simple procedure. The electrical conductivity and flexibility of the film can be modulated by oxidants. The film with TCNQ exhibits electrical conductivity of 3.7×10,2,S,cm,1. [source] Spin-Crossover Physical Gels: A Quick Thermoreversible Response Assisted by Dynamic Self-OrganizationCHEMISTRY - AN ASIAN JOURNAL, Issue 1 2007Tsuyohiko Fujigaya Abstract Iron(II) triazolate coordination polymers with lipophilic sulfonate counterions with alkyl chains of different lengths have been synthesized. In hydrocarbon solvents, these polymers formed a physical gel and showed a thermoreversible spin transition upon the sol,gel phase transition. The formation of a hydrogen-bonding network between the triazolate moieties and sulfonate ions, bridged by water molecules, was found to play an important role in the spin-crossover event. The spin-transition temperature was tuned over a wide range by adding a small amount of 1-octanol, a scavenger for hydrogen-bonding interactions. This additive was essential for the iron(II) species to adopt a low-spin state. Compared with nongelling references in aromatic solvents, the spin-crossover physical gels are characterized by their quick thermal response, which is due to a rapid restoration of the hydrogen-bonding network, possibly because of a dynamic structural ordering through an enhanced lipophilic interaction of the self-assembling components in hydrocarbon solvents. [source] Glycosylation Enhances Peptide Hydrophobic Collapse by Impairing SolvationCHEMPHYSCHEM, Issue 11 2010Shanmei Cheng Dr. Abstract Post-translational N-glycosylation of proteins is ubiquitous in eukaryotic cells, and has been shown to influence the thermodynamics of protein collapse and folding. However, the mechanism for this influence is not well understood. All-atom molecular dynamics simulations are carried out to study the collapse of a peptide linked to a single N-glycan. The glycan is shown to perturb the local water hydrogen-bonding network, rendering it less able to solvate the peptide and thus enhancing the hydrophobic contribution to the free energy of collapse. The enhancement of the hydrophobic collapse compensates for the weakened entropic coiling due to the bulky glycan chain and leads to a stronger burial of hydrophobic surface, presumably enhancing folding. This conclusion is reinforced by comparison with coarse-grained simulations, which contain no explicit solvent and correspondingly exhibit no significant thermodynamic changes on glycosylation. [source] Supramolecular motifs in the first structures of organic carboxylate salts of 1-(diaminomethylene)thiourea (HATU)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2009gorzata Ho The structures of the first two organic carboxylate salts of 1-(diaminomethylene)thiourea (HATU), namely 1-(diaminomethylene)thiouron-1-ium formate, C2H7N4S+·HCOO,, (I), and bis[1-(diaminomethylene)thiouron-1-ium] oxalate dihydrate, 2C2H7N4S+·C2O42,·2H2O, (II), in which the oxalate lies on a symmetry centre, possess different extended hydrogen-bonding networks with different graph-set motifs. The R22(8) motif present in (I) does not appear in (II), but an R21(6) motif is present in both (I) and (II). Compound (I) has a three-dimensional hydrogen-bonding network, whereas (II) has a layered structure with layers joined by hydrogen-bonding motifs that form R42(8) patterns. This work extends the known supramolecular structural data for HATU to include these organic carboxylates in addition to the previously characterized salts with inorganic acids. [source] | ||||||||||||||||||||||||||||