Channel‐like crystal structure of cinchoninium L‐O‐phosphoserine salt dihydrate

Studies on the interactions between L ‐O‐ phosphoserine, as one of the simplest fragments of membrane components, and the Cinchona alkaloid cinchonine, in the crystalline state were performed. Cinchoninium L ‐O‐phosposerine salt dihydrate (PhSerCin) crystallizes in a monoclinic crystal system, space group P2₁, with unit cell parameters: a = 8.45400(10) Å, b = 7.17100(10) Å, c = 20.7760(4) Å, α = 90°, β = 98.7830(10)°, γ = 90°, Z = 2. The asymmetric unit consists of the cinchoninium cation linked by hydrogen bonds to a phosphoserine anion and two water molecules. Intermolecular hydrogen bonds connecting phosphoserine anions via water molecules form chains extended along the b axis. Two such chains symmetrically related by twofold screw axis create a “channel.” On both sides of this channel cinchonine cations are attached by hydrogen bonds in which the atoms N1, O12, and water molecules participate. This arrangement mimics the system of bilayer biological membrane. Chirality 2010. © 2009 Wiley‐Liss, Inc.     

Structural components of alginic acid. II. The crystalline structure of poly-alpha-L-guluronic acid. Results of x-ray diffraction and polarized infrared studies

A structural investigation of the marine algal polysaccharide poly-α-L -guluronic acid is described. The molecular chains consist of 1 → 4 diaxially linked L -guluronic acid residues in the 1C chair conformation and are stabilized in a twofold helix conformation by an intra-molecular O(2)H … O(6)D hydrogen-bond. The X-ray fiber diffraction photograph has been indexed to an orthorhombic unit cell in which a = 8.6 Å, b (fiber axis) = 8.7 Å, c = 10.7 Å. A structure corresponding to the space group P2₁2₁2₁ is proposed, in which all intermolecular hydrogen bonds interact with water molecules and in which all oxygen atoms except for the inaccessible bridge oxygens are involed. The relationship between the shape and structure of the polyguluronic acid molecule and its biological function is discussed.     

f-Element/crown ether complexes. 26. Crystallization of two hydrated forms of hydrogen bonded complexes of NdCl3·nH2O and 15-crown-5. Crystal structures of [Nd(OH2)9]Cl3·15-crown-5·H2O and [NdCl2(OH2)6]Cl·15-crown-5

When slowly evaporated, the reaction of NdCl₃· nH₂O with 15-crown-5 in a 3:1 mixture of acetonitrile:methanol produces two crystalline hydrates. The decahydrate, [Nd(OH₂)₉]Cl₃·15-crown-5·H₂O, is orthorhombic, P2₁2₁2₁, with (at −150 °C) a = 10.571(4), b = 15.220(7), c = 15.686(7) Å, and D_calc = 1.71 g cm⁻³ for Z = 4. These crystals are stable to the moisture in air. Each Nd is nine-coordinate with tricapped trigonal prismatic geometry. The nine coordinated water molecules are hydrogen bonded to two symmetry related crown ethers, all three chloride ions, and the tenth water molecule. The crown has a total of six hydrogen bonds, four on one side (two to a single oxygen atom) and two on the other. This ether exhibits conformational disorder. The hexahydrate, [NdCl₂(OH₂)₆]Cl·15-crown-5 is deliquescent, dissolving in air and recrystallizing as [NdCl₂(OH₂)₆]Cl. Crystals of this complex are monoclinic, P2₁/n, with (at 20 °C) a = 9.821(3), b = 16.978(9), c = 12.849(8) Å, β = 94.06(5)°, and D_calc = 1.80 g cm⁻³ for Z = 4. The Nd atom exists in a distorted dodecahedral geometry with one chlorine in an A site and one in a B site. The coordinated chlorine atoms accept hydrogen bonds producing polymeric zigzag hydrogen bonded chains along c. The third noncoordinated chloride ion accepts four hydrogen bonds, three from one formula unit and one from a second formula unit related by a unit translation along a. The crown ethers accept five hydrogen bonds, two on one side, and three on the other, thus separating the zigzag chains along b.     

f-Element/crown ether complexes. 16. Synthesis,crystallization and crystal structure of [Dy(OH2)8]Cl3·18-crown-6·4H2O

When crystals of [Dy(OH₂)₇(OHMe)] [DyCl(OH₂)₂(18- crown-6)]₂Cl₇·2H₂O [1] are allowed to warm from 5 °C to ambient temperature (22 °C) under the original solvent mixture (1:3 CH₃OH: CH₃CN), they redissolve and the title complex can be isolated by slow evaporation of the resulting solution. The crystal structure of this complex, [Dy(OH₂)₈]Cl₃·18-crown-₆·4H₂O, has been determined. It crystallizes in the monoclinic space group, P2₁/c, with a = 10.395(1), b = 18.684(1), c = 16.259- (3) Å, β= 102.56(1)°, and D_calc = 1.61 g cm⁻³ for Z = 4. A final conventional R value of 0.041 was obtained by least-squares refinement using 3453 independent observed [F_o⩾5σ(F_o)] reflections. The [Dy(OH₂)₈]³⁺ cations and crown ether molecules are hydrogen bonded in a polymeric chain with the crown molecules separating the cations and a total of seven DyOH₂···O(crown ether) hydrogen bonds. The chains are connected by a hydrogen bonding network consisting of the cations, chloride ions, and uncoordinated water molecules. The geometry of the cation is best described as a bicapped trigonal prism with distortions on the reaction pathway toward dodecahedral symmetry. The two capping atoms average 2.41(1) Å from Dy, the remaining DyO distances average 2.38(2) Å. The 18-crown-6 molecule has the D_3d conformation normally observed except for a distortion of one OCCO unit containing the oxygen atom accepting two hydrogen bonds.     

Structural study of anhydrous tendon chitosan obtained via chitosan/acetic acid complex

The molecular structure and packing arrangement of anhydrous tendon chitosan was determined by the X-ray fibre diffraction method together with the linked-atom least-squares refinement technique. The specimen was prepared from chitosan/acetic acid complex which was obtained by exposing tendon chitosan to acetic acid vapour at room temperature for several days. There is high degree of orientation and crystallinity compared with the specimen obtained by the annealing method. Two chitosan chains are present in an orthorhombic unit cell of dimensions a = 8.26(2), b = 8.50(1), c (fibre axis) = 10.43(2) A and space group P2(1)2(1)2(1). The 2-fold helical chain is stabilised by O3 triple bond O5 hydrogen bond with the gt orientation of O6. There are direct hydrogen bonds (N2 triple bond O6) between adjacent chains along the a-axis, which makes a sheet structure parallel to the ac-plane. On the other hand, no hydrogen bond is found between the sheets.     

Crystal and Molecular Structure of a Cytosine Analog; 5-Bromo-6-Benzylamino Isocytosine

Abstract

Isocytosines are formal analogue of isoguanines for pairing with hydrogen bonds and are substrates for target enzymes for chemotherapy of infections diseases. The compound 5-bromo-6-benzylamino isocytosine crysta-Nized in space group P2₁/c with a =11.393(1)Å. b = 7.341(2)Å, c = 14.425(1) Å, β = 92.06(2)°. The structure was determined by heavy atom methods and refined by full matrix least squares to R = 6.8% based on 1935 X-ray structure amplitudes. The isocytosine ring in the molecule is protonated at N(3) with internal bond angle of 122° compared to 117° at N(1). The structure is stabilized by intermolecular hydrogen bonding pattern based on N-H.N and N-H…O hydrogen bonds.     

Crystal structure of (theophyllinato)methylmercury(II) monohydrate

The title compound belongs to space group P2₁/c, a = 10.884 Å, b = 9.187 Å, c = 14.458 Å, β = 131.02°, Z = 4. The structure was refined on 1355 nonzero reflections to an R factor of 0.059. The crystal contains discrete [CH₃Hg(theophyllinate)] molecules in which the proton initially bound to N7 is replaced by the CH₃Hg⁺ ion. The water molecule forms hydrogen bonds with both carbonyl oxygens, whereas an intermolecular contact of 2.98 Å is established between mercury and N9. The intramolecular Hg?O6 distance of 3.18 Å is consistent with the absence of significant Hg?carbonyl bonding interactions in the present structure.     

Isolation of bacteriophage MX4, a generalized transducing phage for Myxococcus xanthus.

The structure of α-chitin has been determined by X-ray diffraction, based on the intensity data from deproteinized lobster tendon. Least-squares refinement shows that adjacent chains have alternating sense (i.e. are antiparallel). In addition, there is a statistical distribution of side-chain orientations, such that all the hydroxyl groups form hydrogen bonds. The unit cell is orthorhombic with dimensions a = 0.474 ± 0.001 nm, b = 1.886 ± 0.002 nm and c = 1.032 ± 0.002 nm (fiber axis); the space group is P2₁2₁2₁ and the cell contains disaccharide sections of the two chains passing through the center and corner of the ab projection. The chains form hydrogen-bonded sheets linked by CO…HN bonds approximately parallel to the a axis, and each chain has an O-3′H…O.5 intramolecular hydrogen bond, similar to that in cellulose. Adjacent chains along the ab diagonal have different conformations for the CH₂OH groups: on one chain these groups form O.6H…O.6′ intermolecular hydrogen bonds to the CH₂OH group on the adjacent chain along the ab diagonal. The latter group is oriented to form an intramolecular O.6′H…O.7 bond to the carboxyl oxygen on the next residue. The results indicate that a statistical mixture of CH₂OH orientations is present, equivalent to half oxygens on each residue, each forming inter- and intramolecular hydrogen bonds. As a result the structure contains two types of amide groups, which differ in their hydrogen bonding, and account for the splitting of the amide I band in the infrared spectrum. The Inability of this chitin polymorph to swell on soaking in water is explained by the extensive intermolecular hydrogen bonding.     

Conformation of the cyclic tetrapeptide dihydrochlamydocin. Iabu-L-Phe D-Pro-LX, and experimental values for 3 leads to 1 intramolecular hydrogen bonds by X-ray diffraction.

Chlamydocin, Iabu-L -Phe-D -Pro-L X, is a naturally occurring cyclic tetrapeptide that exhibits high cytostatic activity. The conformation of the peptide ring, as well as the stereo configuration in the vicinity of the epoxide ring, have been established by a single-crystal X-ray study of dihydrochlamydocin: C₂₈H₄₀N₄O₆·H₂O. It crystallizes in the monoclinic space group P2₁ with a = 12.616(6) Å, b = 12.355(6) Å, c = 9.442(5) Å, and β = 99.5(1)°. The structure was solved by the symbolic addition procedure for phase determination followed by the tangent formula method of phase refinement. This structure represents the first cyclic tetrapeptide in which all four peptide units have been found in the trans conformation; however, each peptide unit is significantly nonplanar with ω angles deviating by 14–24° from the ideal value of 180°. This molecule contains two intramolecular 3 → 1 hydrogen bonds and experimentally determined parameters for these seven-membered turns are presented.     

Structure of a cellulose II-hydrazine complex

The structure of a crystalline cellulose II-hydrazine complex has been determined by x-ray diffraction methods as part of an investigation of cellulose-solvent interaction. The complex studied was that formed when Fortisan fibers were swollen in hydrazine and then vacuumdried. The unit cell is monoclinic with dimensions a = 9.37 Å, b = 19.88 Å, c = 10.39 Å, and γ = 120.0° and contains disaccharide segments of four chains, with one hydrazine per glucose residue. In view of the limited x-ray intensity data, the structure has been determined based on an approximate unit cell containing two chain segments, with a = 4.69 Å, using the linked-atom least-squares refinement procedures. The refined model contains antiparallel cellulose chains that are linked by both intermolecular hydrogen bonds and hydrogen-bonded hydrazine molecules. The parallel chains in the 020 planes are packed in register, leading to stacks of chains analogous to those in chitin. All the hydroxyl groups are satisfactorily hydrogen-bonded, and each hydrazine forms four donor and two acceptor hydrogen bonds, including an N? H…N bond between hydrazines. From this work it can be seen that the interaction of cellulose II with hydrazine involves scission of the intermolecular hydrogen bonds followed by disruption of the stacks of quarter-staggered chains. The latter effect is probably necessary for hydrazine to act as a cellulose solvent.     

Topography of cyclodextrin inclusion complexes : Part II. The iodine-cyclohexa-amylose tetrahydrate complex; its molecular geometry and cage-type crystal structure

Iodine-cyclohexa-amylose tetrahydrate [(C₆H₁₀O₅)₆ ·I₂·d4H₂O] crystallizes in the orthorhombic space-group P2₁2₁2₁, a  14.240 Å, b  36.014 Å, c  9.558 Å. The structure was solved by heavy-atom techniques and refined by least-squares methods to a conventional discrepancy index R  0.148 for the 2872 observed data. The six d-glucose residues are in the C1 chair conformation; the conformational angles vary in magnitude from 45 to 66°, the angles O(5)-C(5)-C(6)-O(6) are close to · 70°, and the six O(4) atoms are almost coplanar (r.m. s. displacement 0.13 Å). Only four of the six O(2) ?O(3) intramolecular hydrogen bonds have formed, which renders the molecule less symmetrical and more conical-shaped than in the previously determined α-cyclodextrin-potassium acetate complex. The iodine molecule is coaxial with the cyclohexa-amylose molecule. The I-I distance is a conventional 2.677 Å. Close interactions between the iodine atoms and the host molecule comprise carbon atoms C(5) and C(6) and oxygen atoms O(4), with interatomic distances all equal to or greater than van der Waals contacts. Intermolecular, almost-linear, short contacts O ? I-I?O with I?O distances of 3.22 and 3.07 Å indicate attractive interaction.The molecules are arranged in herring-bone “cage-type” fashion, with the four water molecules as space-filling mediators; the structure is held together by an intricate network of hydrogen bonds.     

Purification,crystallization, and preliminary X-ray studies on the rhizome lectin from stinging nettle and its complex with NN′N″-triacetylchitotriose

Single crystals were grown from affinity-purified stinging nettle lectin and from its complex with the specific trisaccharide NN′N″ -triacetylchitotriose by vapor diffusion at room temperature. The lectin crystallizes in space group P2₁2₁2₁ with unit cell dimensions a = 54.3 (1) Å, b = 62.2 (1) Å, and c = 92.4 (2) Å, and diffracts to 3.0 Å resolution. The asymmetric unit contains three lectin monomers. The crystals of the lectin-trisaccharide complex have space group P2₁2₁2₁ with cell constants a = 37.69 (4) Å, b = 48.97 (6) Å, and c = 57.32 (4) Å. These crystals diffract to at least 2.0 Å resolution and the asymmetric unit contains one lectin monomer. A three-dimensional X-ray structure determination is on its way. © 1993 Wiley-Liss, Inc.     

The crystal structure of 2-deoxy-β-d-arabino-hexopyranose at −150°

2-Deoxy-β-d-arabino-hexopyranose, C₆H₁₂O₅, is orthorhombic, P2₁2₁2₁, with cell dimensions at ?150° [20°], a = 6.484(2) [6.510(3)], b = 10.364(2) [10.427(4)], c = 11.134(3) [11.153(5)] Å, V = 748.2 [757.1] ų, Z = 4, D_x = 1.457 [1.440], and D_m = [1.455] g.cm^?3. The intensities of 1269 reflections were measured by using MoKα radiation. The structure was solved by direct methods, and refined by full-matrix least-squares, with anisotropic, thermal parameters for the carbon and oxygen atoms, and isotropic parameters for the hydrogen atoms. The pyranose has the ⁴C₁(d) conformation, with puckering parameters Q = 0.563 Å, θ = 3.9°, and ? = 350.3°. The departure from ideality is very small, and less than that in β-d-glucopyranose, Q = 0.584 Å and θ = 6.9°. The β-glycosidic, CO bond is short, 1.383(4) Å, and the OCOH torsion angle is ?87°, consistent with the anomeric effect. The hydrogen-bonding scheme consists of infinite chains, with side chains terminating at a ring-oxygen atom.     

Bioactive peptides: Conformational studies of [TYR4] cyclolinopeptide A

The solid state conformational analysis of [Tyr⁴] cyclolinopeptide A has been carried out by x-ray diffraction studies. The crystal structure of the monoclinic form, grown from a dioxane-water mixture [a = 9.849 (5) Å, b = 20.752 (4) Å, c = 16.728 (5) Å, β = 98.83 (3)°, space group P2₁, Z = 2], shows the presence of five intramolecular N-H? O?C hydrogen bonds, with formation of one C₁₇ ring structure, one α-turn (C₁₃), one inverse γ-turn (C₇), and two β-turns (C₁₀, one of type III and one of type 1). The Pro¹-Pro² peptide unit is cis (ω = 5°) all others are trans. The structure is almost superimposable with that of cyclolinopeptide A. The rms deviation for the atoms of the backbones is on the average 0.33 Å. © 1995 John Wiley & Sons, Inc.     

Crystal Structure of 2′-Deoxycytidine Hemidihydrogenphosphate Reveals C+·C Base Pairs and Tight,Hydrogen-Bonded (H2PO4 −)∞ Columns (1)

Abstract

2′-Deoxycytidine hemidihydrogenphosphate has been crystallized in the hexagonal space group P6₂ with α=25.839(3), c = 12.529(1) Å. The structure has been solved using the Patterson search method. The asymmetric unit contains two protonated, base-paired 2′-deoxycytidine dimers and two H₂PO₄ ^? anions. The C⁺·C base pairs are composed of a protonated and a neutral species each and are triple H-bonded, the central N(3)…N(3) bonds being 2.850(7) and 2.884(5) Å. The conformations of the four nucleosides fall in the same category (sugar puckers 2·-endo, glycosidic links anti) but in one of them the glycosidic torsion angle is quite low with consequences in other geometrical parameters. The H₂PO₄ ^? anions are located on twofold axes and form two types of tight columns with P…P separations about 4.18 Å The neighboring units along a column are linked via two very short O…H…O hydrogen bonds (O…O about 2.49 Å) leading to effective equalization of the P-O bonds. The base pairs of the two dC⁺·dC cations are coplanar and form layers perpendicular to the phosphate columns repeating every c/3. Within the layers, the dimers form a network through 0(5′)…O(2) hydrogen bonds but their primary intermolecular interactions have the form of H-bond anchors [N(4)-H…O-P and 0(3′)-H…O-P] to the phosphate groups.     

Metal ions-nucleobases interactions: preparation and crystal structures of trichloroadeninium zinc(ii)(form ii) and a similar zinc complex of arprinocid [6-amino-9-(2-chloro-6-fluorobenzyl)purine]

Two zinc complexes—trichloroadeninium zinc(II)(Form 11), C₅H₆N₅Cl₃Zn [structure(I)] and a similar complex of Arprinocid, (6-amino-9-(2-chloro-6-fluorobenzyl)purine], C₁₂H₁₀N₅FCl₄Zn [structure(II)]—have been prepared Structure(I) crystallizes in the space group P2₁/c with a = 8.223(1)Å, b = 6.755(1) Å, c = 18.698(3) Å, β = 96.10(2)°,and Z = 4. Structure(II) crystallizes in the space group P2₁/c with a = 8.209(2) Å, b = 6.421(8) Å, c = 31.794(8) Å, β = 90.76(2)°, and Z = 4. Both of these structures were solved by the heavy atom method using diffractometric data and refined to R = 0.028 [structure(I)] and 0.038 [structure(II)]. Zinc with a distorted tetrahedral coordination having three chlorines and N(7) as ligators, protonation of the adenine moiety at N(1), dissymmetry of exocyclic angles at N(7), and an interligand hydrogen bond (“indirect chelation”) involving one of the three chlorines, coordinated to zinc and a proton of the exocylic amino group are the striking features common to both structures. Similar types of indirect chelation as observed in the different complexes of purines have been discussed. The zinc ion deviates from the imidazole plane by 0.412 Å in structure(I) and 0.524 Å in Structure(II). The imidazol and pyrimidine planes fold about the C(4)-C(5) bond by 2.4° in strctur(I) and 3.8° in structure(II). In structure(I), inversion related molecules are paired through N(9)-H…N(3) hydrogen bonds. N-H…Cl hydrogen bonds and C(8)-H…Cl interactions have been observed in both structures.     

Structure of a cellulose I–ethylenediamine complex

The structure of a crystalline cellulose I–ethylenediamine complex has been determined by x-ray diffraction methods as part of an investigation of cellulose–solvent interaction. The complex studied is that formed when native ramie fibers are swollen in ethylenediamine and then vacuum-dried. The unit cell is monoclinic with dimensions a = 12.87 Å, b = 9.52 Å, c = 10.35 Å, and γ = 118.8°, and it contains disaccharide segments of two chains, with one ethylenediamine per glucose residue. The refined model contains parallel cellulose chains that are linked by hydrogen-bonded ethylenediamine molecules. The chains along the b-axis are packed in register, leading to stacks of chains analogous to those in chitin. All the hydroxyl groups are satisfactorily hydrogen-bonded and each ethylenediamine forms four donor and two acceptor hydrogen bonds. From this work it can be seen that the interaction of cellulose I with ethylenediamine involves scission of the intermolecular hydrogen bonds followed by disruption of the stacks of quarter-staggered chains.     

Structural components of alginic acid. I. The crystalline structure of poly-beta-D-mannuronic acid. Results of x-ray diffraction and polarized infrared studies

A Structure determination of the naturally occuring marine algal polysaccharide poly-β-D -mannuronic acid is described. The structure consists of 1e → 4e linked D -mannuronic acid chains with the monosaccharide units in the C1 chair conformation. The X-ray fiber diffraction photograph obtained from bundles of fibers prepared from Fucus vesiculosus has been indexed to an orthorhombic unit cell in which a =7.6 Å, b (fiber axis) = 10.4 Å, c = 8.6 Å, the unit cell containing two disaccharide chain segments with space group P2₁2₁2₁. A sheet-like structure involving one intra-chain, one intra-sheet, and one inter-sheet hydrogen bond per monosaccharide is proposed. Features of the chain-packing arrangement are compared with mannan.     

Metal complexes of virus inhibitors. Part III. Coordination properties of 1-n-propyl-2-α-hydroxybenzylbenzimidazole and the X-ray crystal structure of Ni(C17H18N2O)2(C17H17N2O)1(ClO4)1

Complexes are described of Cobalt(II) and Nickel- (II) salts with the title ligand L. The X-ray crystal structure is described of NiL₂L′₁(ClO₄)₁. One ligand molecule (L′) in this complex is deprotonated and the structure involves strongly hydrogen bonded dimers with OHO bonds = 2.56 Å and 2.62 Å and a NiNi bond = 4.77 Å. The corresponding Cobalt complex is thought to be similar but no other compounds containing L′ were obtained.     

Chain length dependent transition of 310- to α-helix of Boc-(Ala-Aib)n-OMe

An apolar synthetic octapeptide, Boc-(Ala-Aib)₄-OMe, was crystallized in the triclinic space group P1 with cell dimensions a = 11.558 Å, b = 11.643 Å, c = 9.650 Å, α = 120.220°, β = 107.000°, γ = 90.430°, V = 1055.889 ų, Z = 1, C₃₄H₆₀O₁₁N₈·H₂O. The calculated crystal density was 1.217 g/cm³ and the absorption coefficient ? was 6.1. All the intrahelical hydrogen bonds are of the 3₁₀ type, but the torsion angles, ? and ψ, of Ala(5) and Ala(7) deviate from the standard values. The distortion of the 3₁₀-helix at the C-terminal half is due to accommodation of the bulky Boc group of an adjacent peptide in the nacking. A water molecule is held between the N-terminal of one peptide and the C-terminal of the other. The oxygen atom of water forms hydrogen bonds with N (1) -H and N (2) -H, which are not involved in the intrahelical hydrogen bonds. The hydrogen atoms of water also formed hydrogen bonds with carbonyl oxygens of the adjacent peptide molecule. On the other hand, ¹H-nmr analysis revealed that the octapeptide took an α-helical structure in a CD₃CN solution. The longer peptides, Boc-(Ala-Aib)₆-OMe and Boc-(Ala-Aib)₈-OMe, were also shown to take an α-helical structure in a CD₃CN solution. An α-helical conformation of the hexadecapeptide in the solid state was suggested by x-ray analysis of the crystalline structure. Thus, the critical length for transition from the 3₁₀- to α-helix of Boc-(Ala-Aib)_n-OMe is 8. © 1993 John Wiley & Sons, Inc.