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Commensal bacterium Clostridium paraputrificum J4 produces several extracellular chitinolytic enzymes including a 62 kDa chitinase Chit62J4 active toward 4-nitrophenyl N,N′-diacetyl-β-d-chitobioside (pNGG). We characterized the crude enzyme from bacterial culture fluid, recombinant enzyme rChit62J4, and its catalytic domain rChit62J4cat. This major chitinase, securing nutrition of the bacterium in the human intestinal tract when supplied with chitin, has a pH optimum of 5.5 and processes pNGG with Km = 0.24 mM and kcat = 30.0 s−1. Sequence comparison of the amino acid sequence of Chit62J4, determined during bacterial genome sequencing, characterizes the enzyme as a family 18 glycosyl hydrolase with a four-domain structure. The catalytic domain has the typical TIM barrel structure and the accessory domains—2x Fn3/Big3 and a carbohydrate binding module—that likely supports enzyme activity on chitin fibers. The catalytic domain is highly homologous to a single-domain chitinase of Bacillus cereus NCTU2. However, the catalytic profiles significantly differ between the two enzymes despite almost identical catalytic sites. The shift of pI and pH optimum of the commensal enzyme toward acidic values compared to the soil bacterium is the likely environmental adaptation that provides C. paraputrificum J4 a competitive advantage over other commensal bacteria.

The single-strand-specific S1 nuclease from Aspergillus oryzae is an archetypal enzyme of the S1-P1 family of nucleases with a widespread use for biochemical analyses of nucleic acids. We present the first X-ray structure of this nuclease along with a thorough analysis of the reaction and inhibition mechanisms and of its properties responsible for identification and binding of ligands. Seven structures of S1 nuclease, six of which are complexes with products and inhibitors, and characterization of catalytic properties of a wild type and mutants reveal unknown attributes of the S1-P1 family. The active site can bind phosphate, nucleosides, and nucleotides in several distinguished ways. The nucleoside binding site accepts bases in two binding modes-shallow and deep. It can also undergo remodeling and so adapt to different ligands. The amino acid residue Asp65 is critical for activity while Asn154 secures interaction with the sugar moiety, and Lys68 is involved in interactions with the phosphate and sugar moieties of ligands. An additional nucleobase binding site was identified on the surface, which explains the absence of the Tyr site known from P1 nuclease. For the first time ternary complexes with ligands enable modeling of ssDNA binding in the active site cleft. Interpretation of the results in the context of the whole S1-P1 nuclease family significantly broadens our knowledge regarding ligand interaction modes and the strategies of adjustment of the enzyme surface and binding sites to achieve particular specificity.

In the title compound, C15H15NO2, the dihedral angle between the benzene rings is 52.04 (5)° and the molecule has an E conformation about the central C=N bond. In the crystal, molecules are connected by O—H...N hydrogen bonds, forming zigzag chains along the b axis. The crystal packing also features weak C—H...O interactions.

In the title compound, [HgBr2(C22H28N2O6)], the HgII ion is bonded to two Br− ions and two N atoms of the chelating Schiff base ligand in a distorted tetrahedral geometry. The Schiff base ligand adopts an E,E conformation. The dihedral angle between the planes of the two halves of the central N,N′-dimethylethylenediamine part of the ligand is 2.3 (11)°. The crystal studied was twinned by pseudomerohedry [twin law (0-10/-100/00-1)]; the contribution of the minor twin component refined to 0.208 (3).

In the crystal structure of the title compound, C14H12BrNO2, the dihedral angle between the rings is 37.87 (10)° and the molecule has an E conformation about the central C=N bond. In the crystal, molecules are connected by intermolecular O—H...N hydrogen bonds into zigzag chains running parallel to the b axis. The packing also features C—H...O interactions.

The crystal structure of the title compound, C14H12N2O4, contains four crystallographically independent molecules in the asymmetric unit. All the molecules have similar conformations; the dihedral angles between the aromatic rings are 33.1 (1), 33.76 (9), 31.41 (9) and 32.56 (10)°. Intramolecular O—H...N hydrogen bonds form S(6) ring motifs in each molecule. In the crystal, there are two pairs of pseudo-inversion-related molecules. Along the c axis, molecules are stacked with π–π interactions between the 2-hydroxyphenyl and 4-methoxy-2-nitrophenyl rings [centroid–centroid distances = 3.5441 (12)–3.7698 (12) Å].

The title compound, C3H6N4O2, exhibits partial disorder with the refined occupancy ratios of the two components being 0.582 (5):0.418 (5). In the major component, the nitroso groups have a relative syn spatial arrangement [O=N...N=O pseudo-torsion angle = 1.1 (4)°], whereas the other component has an anti disposition [177.6 (1)°]. The N—N=O moieties are almost coplanar with a dihedral angle of 5.3 (3)°, while in the minor occupied set of atoms, this angle is 8 (1)°. In both components, the imidazolidine ring adopts a twisted conformation on the C—C bond and the crystal structure shows the strain of this ring according to the N—CH2—CH2—N torsion angles [25.9 (5) and −23.8 (7)°]. In the crystal, molecules are linked by weak C—H...O hydrogen bonds.

In the title compound, [CuI(C12H9BrN2)(C18H15P)], the CuI ion is bonded to one I atom, one triphenylphosphane P atom and two N atoms of the diimine ligand in a distorted tetrahedral geometry. The Schiff base acts as a chelating ligand and coordinates to the CuI atom via two N atoms. In the diimine ligand, the dihedral angle between the pyridine and bromophenyl rings is 19.2 (2)°. In the crystal, molecules are connected by π–π stacking interactions between inversion-related pyridine rings [centroid–centroid distance = 3.404 (3) Å].

In the title compound, [ZnBr2(C17H14Cl4N2)], the ZnII ion is bonded to two bromide ions and two N atoms of the diimine ligand and displays a moderately distorted tetrahedral coordination geometry. The Schiff base ligand acts as a chelating ligand and coordinates to the ZnII atom via two N atoms.

In the title compound, C2H7N4O+·BF4−, intermolecular N—H...O hydrogen bonds connect the cations into chains parallel to the c axis, with graph-set motif C(4). These chains are in turn connected into a three-dimensional network by intermolecular N—H...F hydrogen bonds. The B—F distances distances in the anion are not equal.

In the title compound, C24H20N4, obtained through the condensation of naphthalene-2,3-diamine with formaldehyde in methanol, the molecule is located on a special position of site symmetry -4. Due to symmetry considerations, the aromatic rings are strictly perpendicular to each other. In the crystal, molecules are linked by pairs of C—H...π interactions into columns along [110].

In the title compound, C8H8N2O, the N—CH2 and CH2—O bond lengths can be correlated to the manifestation of an anomeric effect in the N—CH2—O moiety. In the crystal, intermolecular O—H...N hydrogen bonds link the molecules into zigzag chains, with graph-set motif C(6), parallel to [001]. These chains are further linked into sheets by weak nonclassical C—H...O hydrogen bonds.

In the molecule of the title compound, C20H26N2O2, the 1,3-diazinane ring adopts a slightly distorted chair conformation and the hydroxybenzyl substituents occupy equatorial positions on the N atoms of the heterocyclic ring. There are two intramolecular O—H...N hydrogen bonds between the N atoms of the 1,3-diazinane ring and the hydroxy groups of the aromatic rings, with an S(6) set-graph motif. However, the two observed intramolecular hydrogen-bond distances were different. Considering that both N atoms experience the same chemical environment, it is surprising to see the difference in O...N distances [2.6771 (14) and 2.8123 (12) Å]. The crystal structure is further stabilized by a C—H...π interaction.

The imidazole ring in the title compound, C27H22N8, adopts a slight envelope conformation with the C atom carrying the phenyl ring being the flap atom. The phenyl ring is almost perpendicular to the mean plane of the imidazole ring [dihedral angle = 88.90 (7)°]. The (1H-benzotriazol-1-yl)methyl groups bound to the imidazole ring are positioned on the same side of the imidazole ring. The dihedral angle between these benzotriazolyl rings is 17.71 (5)°. The crystal packing is stabilized by a C—H...π interaction, which connects the molecules into zigzag chains running along the b axis.

In the title compound, C17H18N8, the imidazolidine ring adopts an envelope conformation with the substituents at the N atoms in trans positions with respect to the central ring. The dihedral angle between the two benzotriazole rings is 71.65 (10)°. In the crystal, non-classical C—H...N interactions link the molecules into helical chains along the b axis. The crystal packing is further stabilized by weak C—H...π interactions.

The title compound, C18H20Br2N2O2, the heterocyclic ring adopts a chair conformation. The benzene rings make dihedral angles of 86.84 (10) and 60.73 (10)° with the mean plane of the heterocyclic ring. The dihedral angle between the two benzene rings is 79.77 (10)°. The molecular structure is stabilized by two intramolecular hydrogen bonds between the phenolic hydroxy groups and N atoms with graph-set motif S(6). The crystal structure is stabilized by weak C—H...π interactions.

In the title compound, C13H27N4+·I−, the ethylene bridge is distorted from the ideal D2d symmetry wherein an N—C—C—N planar bridge, around whose C—C bond the C—N and C—H bonds are exactly eclipsed, is disordered over two sites with equal occupancies. In both disorder components, the hexyl chain adopts an ideal all-trans conformation. In the crystal, adjacent ions are connected by C—H...I hydrogen bonds, forming ionic pairs that are further linked into chains along [101] via a second C—H...I interaction.

In the title hexahydropyrimidine derivative, C28H42N2O4·0.19H2O, the 1,3-diazinane ring has a chair conformation with a diequatorial substitution. The asymmetric unit contains one half-organic molecule and a solvent water molecule with occupany 0.095. The molecule lies on a mirror plane perpendicular to [010] which passes through the C atoms at the 2- and 5-positions of the heterocyclic system. The partially occupied water molecule is also located on this mirror plane. The dihedral angle between the planes of the aromatic rings is 17.71 (3)°. Two intramolecular O—H...N hydrogen bonds with graph-set motif S(6) are present. No remarkable intermolecular contacts exist in the crystal structure.

The title compound, C18H20N2O2, was prepared by Mannich-type reaction of phenol, ethane-1,2-diamine and formaldehyde. The heterocyclic rings adopt half-chair conformations. The acyclic methylene groups attached to the N atoms are in an axial position. In the crystal, weak C—H...O hydrogen bonds link the molecules into dimers. These dimers are further connected via C—H...π contacts.

The title structure, 3C2H7N4O+·HFPO3−·FPO32−·H2O, contains three independent 2-carbamoylguanidinium cations, one fluorophosphonate, one hydrogen fluorophosphonate and one water molecule. There are three different layers in the structure that are nearly perpendicular to the c axis. Each layer contains a cation and the layers differ by the respective presence of the water molecule, the hydrogen fluorophosphonate and fluorophosphonate anions. N—H...O hydrogen bonds between the guanylurea molecules that interconnect the molecules within each layer are strong. The layers are interconnected by strong and weak O—H...O hydrogen bonds between the anions and water molecules, respectively. Interestingly, the configuration of the layers is quite similar to that observed in 2-carbamoylguanidinium hydrogen fluorophosphonate [Fábry et al. (2012). Acta Cryst. C68, o76–o83]. There is also present a N—H...F hydrogen bond in the structure which occurs quite rarely.

In the title molecule, C17H20N2O2, the imidazolidine ring adopts a twist conformation. The mean plane through the five atoms of the imidazolidine ring makes dihedral angles of 70.18 (4) and 74.14 (4)° with the planes of the two aromatic rings. The dihedral angle between the benzene rings is 53.11 (5)°. Both phenol –OH groups form intramolecular hydrogen bonds to the N atoms, with graph-set motif S(6). In the crystal, pairs of O—H...O hydrogen bonds link the molecules into dimers with R44(18) ring motifs. The crystal packing is further stabilized by C—H...O and weak C—H...π interactions.

In title compound, C15H14N2O2, the dihedral angle between the 3,4-dimethoxyphenyl group and the benzimidazole system is 26.47 (6)°. In the crystal, neighbouring molecules are linked by N—H...N hydrogen bonds into C(4) chains propagating along the c-axis direction. The crystal structure also features weak C—H...O interactions.

The asymmetric unit of the title compound, C12H11NO4, contains two molecules. In the crystal, neighbouring molecules are linked together by O—H...O hydrogen bonds into dimers. The dimers are arranged into columns parallel to the a axis, meditated by π–π interactions [centroid–centroid distances = 3.856 (3) and 3.857 (3) Å]. The crystal structure is further stabilized by weak intermolecular C—H...O interactions. The crystal studied was a non-merohedral twin with a ratio of the twin components of 0.657 (11):0.343 (11).

At 120 K, the title compound, C24H42NO2P, crystallizes in a unit cell with a doubled a parameter compared with the room-temperature structure. There are four molecules in the asymmetric unit, one of which shows extensive disorder in a 0.588 (3):0.412 (3) ratio. In the crystal, numerous C—H...O interactions link the molecules.

The title compound, C25H30N2O6, has the imidazolidine ring in an envelope conformation. There are two intramolecular O—H...N hydrogen-bond interactions with graph-set motif S(6). The cyclohexane ring adopts a slightly distorted chair conformation. One methyl carboxylate substituent forms a dihedral angle of 12.00 (5)° with the plane of the benzene ring, while the other methyl carboxylate group is almost coplanar, making a dihedral angle of 2.26 (9)°. In the crystal, pairs of intermolecular C—H...O hydrogen bonds form racemic dimers, corresponding to an R22(18) graph-set motif. Further weak C—H...O interactions generate a chain running along the c axis.

The title compound, C29H38N2O6, was prepared as model for studying intramolecular hydrogen-bonding interactions. Molecules of the title compound are located on a crystallographic twofold rotation axis, which passes through the C atom linked to the two N atoms on the imidazolidine ring. The molecular structure shows the existence of two intramolecular O—H...N hydrogen-bonding interactions between the two N atoms of the imidazolidine moiety and the hydroxy groups in the aromatic rings. The crystal structure shows the strain of ring fusion in the perhydrobenzimidazole moiety according to the endocyclic bond angles and the torsion angles, which evidence a puckering of the cyclohexane ring with respect to normal tetrahedral bond angles in an ideal chair conformation.

The title compound C14H29N4+·I− salt, was obtained by the reaction of cage adamanzane-type aminal 1,3,6,8-tetraazatricyclo[4.3.1.13,8]undecane with heptyl iodide. In the cation, the bond lengths and angles are within normal ranges, except for one N—C(ring) bond distance of 1.542 (3) Å, which is unexpectedly long compared with related compounds. In the crystal, ions are linked through C—H...I hydrogen bonds. The crystal studied was a non-merohedral twin with a minor twin domain of 6.56 (5)%.

A new monoclinic polymorph of the title compound, C8H12N4, in the space group P21/n (Z = 4) is reported. The previously known form was also monoclinic, P21/c (Z = 4), but the unit-cell parameters and crystal packing were different [Shoja & Saba (1993). Acta Cryst. C49, 354–355]. The hexahydropyrimidine ring of the title compound adopts a chair conformation with a diequatorial substitution and with the CH2-C[triple-bond]N groups oriented nearly parallel and in the same direction [NC—CH2...CH2—CN pseudo torsion angle = −6.27 (18)°]. In the crystal, intermolecular C—H... N hydrogen bonds connects the molecules into a chain along the b axis.

In the crystal structure of the title compound, C21H24I2N2O2, the two N atoms of the imidazolidine moiety are linked to the hydroxy groups by intramolecular O—H...N hydrogen-bonding interactions. The cyclohexane ring adopts a chair conformation and the heterocyclic ring to which it is fused has a twisted envelope conformation.

The complete molecule of the title compound, C31H42N2O6, is generated by crystallographic twofold symmetry, with one C atom lying on the axis. The dihedral angle between the aromatic rings is 57.03 (6)°. The central heterocyclic ring adopts a half-chair conformation. The molecular conformation is stabilized by two intramolecular O—H...N hydrogen bonds with the N atoms of the heterocyclic ring as the acceptors. In the crystal, molecules are linked into chains along the c axis by non-classical C—H...O hydrogen bonds.

The title compound, C16H14Cl2N4, is isomorphous with 2,9-dimethyl-6H,13H-5:12,7:14-dimethanodibenzo[d,i]-[1,3,6,8]tetraazecine [Rivera et al. (2009). Acta Cryst. E65, o2553] and has twofold symmetry, with two carbon atoms located on a twofold axis. Only van der Waals forces occur between molecules in the crystal. In the isomorphous compound the crystal structure is stabilized by weak C—H...π interactions.

In the title compound, C25H32Cl2N2O2, there are two intramolecular O—H... N hydrogen-bonding interactions between the hydroxy groups on the aromatic rings and the two N atoms of the heterocyclic group. The cyclohexane ring adopts a chair conformation and the imidazolidine unit to which it is fused has a twisted envelope conformation. The asymmetric unit comprises one half-molecule which is completed by a twofold rotation axis. A C—H...O interaction is observed in the crystal structure.

In the title hydrated molecular salt, (C5H8N3)2[Zn(C7H3NO4)2]·H2O, the ZnII atom is coordinated by two O,N,O′-tridentate pyridine-2,6-dicarboxylate dianions, generating a slightly distorted trans-ZnN2O4 octahedral coordination geometry for the metal ion. In the crystal, a network of O—H...O, N—H...O and C—H...O hydrogen bonds involving the cations, anions and water molecules results in a three-dimensional network.

In the title compound, K2Co(H2P2O7)2·2H2O, the octahedrally coordinated Co2+ ion lies on an inversion centre. Two bidentate dihydrogendiphosphate anions form the equatorial plane of the [CoO6] octahedron which is completed by two water molecules in axial positions. This results in isolated {Co(H2O)2[H2P2O7]2}4− entities linked into a three-dimensional network through K—O bonds and O—H...O hydrogen-bonding interactions involving the dihydrogendiphosphate anions and water molecules. The dihydrogendiphosphate anion, (H2P2O7)2−, is bent and shows an almost eclipsed conformation.

The asymmetric unit of the title compound, C18H22Br2N2O2, contains one half-molecule that is related to the other half by a center of inversion located at the mid-point of the central C—C bond. The hydroxy (phenolic) groups are linked to the N atoms by O—H...N hydrogen bonds, which generate S(6) rings.

In the title compound, C21H18N8, the two (benzotriazol-1-yl)methyl groups are located in an anti position with respect to the benzimidazoline moiety. The dihedral angles between the benzotriazole ring systems and the central benzimidazoline moiety are 57.03 (4) and 81.01 (3)°. The crystal packing is stabilized by two C—H...π interactions.

The asymmetric unit of the title compound, H3O+·ClO4−·C20H24O6, contains two molecules/ions of each species. Both dibenzo-18-crown-6 molecules have a complexed hydronium ion inside their cavity with O—H...O and O—H...(O,O) links between the two species. The associated perchlorate anions also accept O—H...O hydrogen bonds from the hydronium ion. Both crown ether molecules are present in a butterfly conformation with approximate C2v symmetry and their cavities are closed by the benzene ring of a neighbouring molecule. The packing is consolidated by C—H...O and C—H...π interactions.

In the title compound, C17H19NO3, the molecule has an E configuration with respect to the C=N bond and the dihedral angle between the aromatic rings is 56.07 (5)°. In the crystal, inversion dimers linked by pairs of C—H...O hydrogen bonds occur. The dimers are linked by weak C—H...π interactions, forming a three-dimensional network.

Molecules of the the title compound, C21H24Cl2N2O2, are located on a twofold rotation axis, which passes through the C atom linking the two N atoms. Two intramolecular O—H...N hydrogen bonds were observed. In the crystal, non-classical intermolecular C—H...O hydrogen bonds link the molecules into chains along the a axis. The crystal studied was a racemic twin.

The title compound, (C10H28N4)[MnCl4(H2O)2]Cl2·2H2O, consists of isolated octahedral [MnCl4(H2O)2]2− anions, tetraprotonated 1,4,8,11-tetraazoniacyclotetradecane cations, chloride anions and water molecules connected by a network of hydrogen bonds. The MnII atom is situated on an inversion centre, and the 1,4,8,11-tetraazoniacyclotetradecane cation is located on a mirror plane.

The title Schiff base compound, C15H14BrNO2, was prepared by the condensation of 2,3-dimethoxybenzaldehyde with 4-bromoaniline. It adopts an E configuration with respect to the C=N bond. The dihedral angle between the two aromatic rings is 56.79 (8)°. Weak C—H...O and C—-H...π bonds can be found in the crystal structure.

The title Schiff base compound, C16H16BrNO3, adopts an E configuration with respect to the C=N bond. The dihedral angle between the two aromatic rings is 64.02 (6)°.

The crystal structure of the title compound, C7H10N+·H2PO3−, has been reported previously by Sabounchei & Naghipour [Asian J. Chem. (2003), 15, 1677–1686]. A new look at this compound has revealed doubling of the unit cell. The asymmetric unit consists of two 4-methylanilinium cations and two dihydrogen phosphite anions. The crystal structure is built upon alternating layers of organic cations and dihydrogen phosphite anions stacked along c. The organic layer is stabilized by C—H...π interactions. Weak aromatic π–π stacking interactions with centroid–centroid distances of 4.6147 (12), 4.6917 (12), 4.6932 (13) and 4.8366 (13) Å are also observed in the structure. The dihydrogen phosphite anions are linked by O—H...O hydrogen bonds into chains running parallel to the a-axis direction. These chains are connected to the cation layer by N—H...O hydrogen bonds.

The asymmetric unit of the title compound, C18H18Cl2N2O2, contains one half of an independent molecule, the other half being generated via a centre of inversion at the molecular centroid. In the crystal structure, molecular chains are formed through non-classical C—H... O hydrogen bonds between an axial H atom of the oxazine ring and the O atom of a neighbouring molecule.

In the structure of the title compound, C13H18N2O2S, molecules are linked together by intermolecular C—H...S interactions into one-dimensional extended chains along the a axis. The crystal packing is further influenced by weak C—H...O interactions.

The molecular structure of the title compound, C21H26N2O2, shows two intramolecular O—H...N hydrogen-bonding interactions. In the crystal structure, molecular chains are formed along the c axis through weak C—H...O interactions. Neighbouring chains are weakly associated along the a axis via C—H...π interactions.

In the crystal structure of the title compound, C12H14N2O3, molecules are packed into layers parallel to (100). Each layer contains centrosymmetric dimers formed by a pair of strong O—H...N hydrogen bonds with an R22(10) motif, while strong O—H...O hydrogen bonds forming C(10) chains connect molecules into a two-dimensional network. Additional stabilization is supplied by weak C—H...O hydrogen bonds and weak π–π stacking interactions with centroid–centroid distances in the range 3.4220 (7)–3.9616 (7) Å.

The title compound, C21H26N2O4, adopts an E configuration with respect to the azomethine C=N bonds. The dihedral angle between the two rings is 8.16 (8)°. The crystal structure is stabilized by weak intermolecular C—H...O interactions.

Dinickel(II) silicon bis[diphosphate(4−)], Ni2Si(P2O7)2, is isotypic with other phosphates of the formula M2Si(P2O7)2 (M = Co, Cd). All atoms except Si (site symmetry 2) are found in general positions. Ni2O10 dimers formed from edge-sharing NiO6 octahedra are linked by corners and O—P—O bridges, forming slabs parallel to (100), which are in turn interconnected by O—Si—O contacts.

In the title compound, Pb2(HPO3)(NO3)2, the two distinct Pb2+ ions (both with site symmetry m) adopt irregular PbO10 coordination polyhedra. The structure is completed by two distinct nitrate groups (in which one O atom and the N atom have m site symmetry for both ions) and an HPO32− anion (in which one O atom and the P and H atoms have m site symmetry). The connectivity of the PbO10, NO3 and HPO3 units in the crystal structure results in a three-dimensional network.