Complexation of trivalent lanthanide cations by erythritol in the solid state. The crystal structure and FT-IR study of 2EuCl3.2C4H10O4.7H2O

Erythritol was chosen to study the interactions between metal ions and carbohydrates. FTIR spectroscopy results indicate that a EuCl3-erythritol complex different from a previously reported one was obtained. The crystal structure of EuCl3-erythritol complex, 2EuCl3.2C4H10O4.7H2O, Mr=443.49, a=13.846(3) A , b=7.4983(15) A, c=14.140(3) A, beta=116.39(3) degrees, V=1315.1(5) A(3), Z=4, mu=5.394 mm(-1) and R=0.0395 for 2965 observed reflections and 143 parameters, was determined. Characteristic of this complex is the presence of binuclear europium ions with different coordination structures. One Eu3+ ion is nine-coordinated, with five Eu-O bonds from water molecules, and four from hydroxyl groups of two erythritol molecules and another Eu3+ is eight-coordinated with two water molecules, two chloride ions, and four hydroxyl groups from two erythritol molecules. Erythritol provides two hydroxyl groups to one lanthanide ion and the other two to another rare earth ion. The OH, CO stretching and other vibrations are shifted in the IR spectra of the complexes and the results are consistent with the crystal structure.     

Calcium-binding to non-ionic lipids: crystal structure of a calcium chloride complex of geraniol.

X-ray diffraction data were used to determine the crystal structure of a calcium chloride complex of geraniol. The geraniol molecules assume a bilayer arrangement, with channels of calcium and chloride ions separating the bilayers. Each calcium ion is coordinated to the hydroxyl groups of two symmetry-related geraniol molecules and to four chloride ions. Our results demonstrate that hydrophobic interactions within a lipid bilayer can lead to an arrangement of hydroxyl groups suitable for binding calcium ions. Similar interactions may be involved in the calcium-binding sites on membrane surfaces.     

Complexation of trivalent lanthanide cations by D-ribose in the solid state. The crystal structure and FT-IR study of PrCl3-alpha-D-ribopyranose-5H2O

The crystal structure of praseodymium chloride.alpha-D-ribopyranose pentahydrate, PrCl3-C5H10O5-5 H2O, M(r)=487.47, a=9.1989(8), b=8.8214(7), c=9.8233(9) A, beta=94.060(3) degrees, V=795.2(1) A(3), Z=2, mu=0.71073 A and R=0.0418 for 1923 observed reflections and 172 parameters has been determined. The sugar provides three hydroxyl groups, ax-eq-ax for coordination. The Pr(3+) ion is nine-coordinated with five Pr-O bonds from water molecules, three from hydroxyl groups and one from chloride. The OH, CO stretching vibrations and COH bending vibrations are shifted in the complex IR spectrum and the hydroxyl groups, water molecules, chloride ions form an extensive hydrogen-bond network.     

Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation

We report here the 1.62 Å crystal structure of an intramolecular quadruplex DNA formed from a sequence in the promoter region of the c-kit gene. This is the first reported crystal structure of a promoter quadruplex and the first observation of localized magnesium ions in a quadruplex structure. The structure reveals that potassium and magnesium ions have an unexpected yet significant structural role in stabilizing particular quadruplex loops and grooves that is distinct from but in addition to the role of potassium ions in the ion channel at the centre of all quadruplex structures. The analysis also shows how ions cluster together with structured water molecules to stabilize the quadruplex arrangement. This particular quadruplex has been previously studied by NMR methods, and the present X-ray structure is in accord with the earlier topology assignment. However, as well as the observations of potassium and magnesium ions, the crystal structure has revealed a highly significant difference in the dimensions of the large cleft in the structure, which is a plausible target for small molecules. This difference can be understood by the stabilizing role of structured water networks.     

Complexation of trivalent lanthanide cations by inositols in the solid state: crystal structure and an FT-IR study of PrCl3.myo-inositol.9 H2O

The title compound, PrCl3.C6H12O6.9 H2O crystallized in the monoclinic space group P2(1)/n with cell dimensions a = 15.8293(3), b = 8.67750(10), c = 16.2292(3) A, beta = 107.0788(8) degrees, V = 2130.92(6) A3 and Z = 4. Each Pr ion is coordinated to nine oxygen atoms, two from the inositol and seven from water molecules, with Pr-O distances from 2.4729 to 2.6899 A; the other two water molecules are hydrogen-bonded. No direct contacts exist between Pr and Cl. There is an extensive network of hydrogen bonds formed by hydroxyl groups, water molecules, and chloride ions. The IR spectra of Pr-, Nd-, and Sm-inositol complexes are similar, which shows that the three metal ions have the same coordination mode. The IR results are consistent with the crystal structure.     

Interactions between metal ions and carbohydrates. The coordination behavior of neutral erythritol to neodymium ion

A single crystal of a coordinated complex of neutral erythritol (C4H10O4,E) with a neodymium ion, NdE(II), was synthesized and studied using FT-IR and X-ray diffraction analysis. In NdE(II) (NdCl3.2.5C4H10O4.C2H5OH) the Nd3+ coordinates with one chloride ion and eight OH groups from three erythritol molecules. There are two neodymium centers linked by one erythritol molecule with same coordination structure in the molecule. Two erythritol molecules provide 1,3,4-hydroxyl groups to coordinate with a neodymium ion; another erythritol molecule coordinates to two Nd ions via its 1,2-hydroxyl groups and 3,4-hydroxyl groups, respectively. The OH groups of erythritol act as ligand to coordinate to neodymium ions, and OH groups of erythritol form hydrogen bond networks that link chain and layer together to build three-dimensional structures. The ratio of metal to ligand is 1:2.5. The structure of NdE(II) is more complicated than the previously reported NdE(I), which is NdCl3.C4H10O4.6H2O; in NdE(I), Nd3+ is coordinated to four hydroxyl groups from two erythritol molecules, four water molecules and one chloride ion. The results indicate the complexity of metal-sugar interaction.     

Molecular and crystal structures of N-arylglycopyranosylamines formed by reaction between sulfanilamide and D-ribose, D-arabinose and D-mannose

The X-ray crystal structures of three monosaccharide derivatives prepared by the reaction of sulfanilamide with D-ribose, D-arabinose, and D-mannose have been determined. The derivatives are N-(p-sulfamoylphenyl)-alpha-D-ribopyranosylamine (1), N-(p-sulfamoylphenyl)-alpha-D-arabinopyranosylamine (2), and N-(p-sulfamoylphenyl)-beta-D-mannopyranosylamine monohydrate (3). The monosaccharide ring of 1 and 2 has the 1C4 conformation, stabilized in 1 by an intramolecular hydrogen bond from 0-2 to 0-4. Compound 3 has the 4C1 conformation at the monosaccharide ring and the gt conformation at the C-6-O-6 side chain. Occupancy of the water molecule in the crystal of 3 actually examined was 22%. The degree of interaction between sulfamoyl groups and monosaccharide moieties varies from structure to structure. The packing arrangement of 2 involves hydrogen bonding between sulfamoyl groups and monosaccharide hydroxyl groups, but interactions of this type are fewer in 1, and in 3 the hydrogen bonds are either strictly between monosaccharide hydroxyl groups or strictly between sulfamoyl groups. Pairs of hydrogen bonds (two-point contacts) link neighboring molecules in all three structures, between screw-axially related molecules in 1 and 2 and between translationally related molecules in 3. The contact in 3 defined by the O-3-H...O-5 and O-6-H...O-4 hydrogen bonds is found in several other N-aryl-beta-D-mannopyranosylamine crystal structures and is apparently an especially favorable mode of intermolecular interaction in these compounds.     

Metal ion interactions with sugars. The crystal structure and FT-IR study of the NdCl3-ribose complex

The single-crystal structure of neodymium chloride-ribopyranose pentahydrate, NdCl3.C5H10O5.5H2O was determined to have Mr=490.80, a=9.138(11), b=8.830(10), c=9.811(11) A, beta=94.087(18) degrees, V=789.7(16) A3, P2(1), Z=2, mu=0.71073 A and R=0.0198 for 2075 observed reflections. The ligand of the title complex was observed in a disordered state and two molecular configurations of NdCl3.C5H10O5.5H2O were found in the single crystal as a pair of isomers. Both ligand moieties of the two molecules are ribopyranose forms, providing three hydroxyl groups in ax-eq-ax orientation for coordination. One ligand of the pair of isomers is beta-D-ribopyranose in the 1C4 conformation, and the other is alpha-D-ribopyranose in the 4C1 conformation. The Nd3+ ion is nine-coordinated with five Nd-O bonds from water molecules, three Nd-O bonds from hydroxyl groups of the ribopyranose and one Nd-Cl bond from chloride ion. The hydroxyl groups, water molecules, chloride ions form an extensive hydrogen-bond network. The IR spectral C-C,O-H,C-O and C-O-H vibrations were observed to be shifted in the complex and the IR results are in accordance with those of X-ray spectroscopy.     

Structure of the ion channel peptide antibiotic gramicidin A

The crystal structure of the uncomplexed orthorhombic form of gramicidin A has been determined at 0.86 A resolution. The polypeptide crystallizes from ethanol as a left-handed, double-stranded, antiparallel beta 5.6-helical dimer that is 31 A long and an average of 4.8 A in diameter. The uncomplexed channel does not contain ions or solvent molecules, and its diameter is not uniform but varies from a minimum of 3.85 A to a maximum of 5.47 A. There are three empty cavities in the channel that have a diameter exceeding 5.25 A and appear to be large enough to accommodate water molecules or potassium ions in a chemically reasonable coordination environment. The observed crystal structure does not offer any obvious clues as to why an antiparallel beta 5.6-helix cannot function as an ion channel in lipid bilayers.     

Interactions between metal ions and carbohydrates. Syntheses and spectroscopic studies of several lanthanide nitrate-D-galactitol complexes

Two complexes of neutral D-galactitol (C(6)H(14)O(6), G) with terbium nitrate, TbGN(I) and TbGN(II), and one complex with samarium nitrate SmGN were synthesized and characterized. From IR, FIR, THz and luminescence spectra the possible coordinations were suggested, and the single-crystal X-ray diffraction results confirm the spectroscopic conclusions. In TbGN(I) (Tb(NO(3))(3)·C(6)H(14)O(6)·3H(2)O), the Tb(3+) is 9-coordinated with three water molecules and six OH groups from two D-galactitol molecules. Nitrate ions do not coordinate to metal ions, which is different from other reported lanthanide nitrate-D-galactitol complexes. In TbGN(II) and SmGN (Ln(NO(3))(3)·C(6)H(14)O(6)), Ln(3+) is 10-coordinated with six OH groups from two D-galactitol molecules and four oxygen from two bidentate nitrate ions, and one nitrate ion is hydrogen bonded. No water exists in the structures. D-Galactitol molecules provide their 1-, 2- and 3-hydroxyl groups to coordinate with one metal ion and their 4-, 5- and 6-hydroxyl groups to coordinate with another metal ion in the three structures. There is still a new topological structure that can be observed for lanthanide-d-galactitol complexes, which indicates that the coordinations between hydroxyl groups and metal ions are complicated.     

X-ray structure of the dipotassium salt of D-mannose 1-phosphate 3.25 hydrate

The first crystal structure of mannose 1-phosphate is described. The dipotassium hydrate salt crystallizes in the P2(1)2(1)2 space group. There are two independent dianions (I and II) in the asymmetric unit, which are alpha anomers adopting the 4C(1) chair conformation. The main difference between the two mannose 1-phosphate dianions is the orientation of the phosphate group with relation to the pyranosyl ring. In I, one of the phosphate oxygen atoms is antiperiplanar positions with respect to carbon atom C-1, whereas the two others are situated synclinally. The corresponding orientations of the terminal phosphate oxygen atoms in II are synperiplanar and anticlinal. The potassium cations are six- and seven-coordinate, mainly with O atoms of hydroxyl groups and water molecules. There are potassium channels extending along the c-axis. In the packing arrangement, water molecules and mannose phosphate groups also define two different types of layers parallel to a-axis. Within water channels there are extensive hydrogen-bonding networks.     

Crystal structures of 26 kDa Clonorchis sinensis glutathione S-transferase reveal zinc binding and putative metal binding

The crystal structures of CsGST in two different space groups revealed that Asp26 and His79 coordinate a zinc ion. In one space group, His46 of an adjacent molecule participates in the coordination within 2.0 Å. In the other space group, Asp26, His79 and a water molecule coordinate a zinc ion. The CsGST–D26H structure showed that four histidine residues – His26 and His79 from one molecule and the same residues from a symmetry-related neighboring molecule – coordinate a zinc ion. The coordinated zinc ions are located between two molecules and mediate molecular contacts within the crystal.     

Metal-ion interactions with sugars. Crystal structure and FT-IR study of PrCl3-D-ribose complex

A single-crystal of PrCl3.D-ribose.5H2O was obtained from a methanol-water solution and its structure determined by X-ray crystallography. Two configurations of the complex, as a pair of isomers, were found in the single-crystal in a disordered state, which differs from that reported previously. The ligand of one of the complexes is alpha-D-ribopyranose in the 4C1 conformation, and the ligand of the other is beta-D-ribopyranose in the 1C4 conformation. The alpha:beta anomeric ratio is 54:46. Both ligands of the two isomers provide three hydroxyl groups in an axial-equatorial-axial orientation for coordination. The Pr3+ ion is nine-coordinated, with five Pr-O bonds from water molecules, three Pr-O bonds from the hydroxyl groups of the D-ribopyranose and one Pr-Cl bond from chloride ion. The hydroxyl groups, water molecules, and chloride ions form an extensive hydrogen-bond network. The IR spectral C-C, O-H, C-O, and C-O-H vibrations are shifted in the complex, compared to those in d-ribose, and the IR results are in accord with those obtained from the X-ray diffraction study.     

Metal-ion interactions with sugars. Crystal structures and FT-IR studies of the LaCl3-ribopyranose and CeCl3-ribopyranose complexes

Single crystals of LaCl3.C5H10O5.5H2O (1) and CeCl3.C5H10O5.5H2O (2) were obtained from ethanol-water solutions and their structures determined by X-ray. The two complexes are isomorphous. Two configurations of complex 1 or complex 2, as a pair of isomers, were found in each single crystal in a disordered state. The ligand of one of the isomer is alpha-D-ribopyranose in the 4C1 conformation, the ligand of the other is beta-D-ribopyranose in the 1C4 conformation. For complex 1, the alpha:beta anomeric ratio is 51:49, and for complex 2, the ratio is 52:48. Both ligands of the two isomers provide three hydroxyl groups in ax-eq-ax orientation for coordination. The Ln3+ (Ln = La or Ce) ion is nine-coordinated with five Ln-O bonds from water molecules, three Ln-O bonds from hydroxyl groups of the D-ribopyranose, and one Ln-Cl bond from chloride ion. The hydroxyl groups, water molecules, and chloride ions form an extensive hydrogen-bond network. The IR spectral C-C, O-H, C-O, and C-O-H vibrations were observed to be shifted in both the two complexes and the IR results are in accord with those of X-ray diffraction.     

Sugar complexation with calcium ion. Crystal structure and FT-IR study of a hydrated calcium chloride complex of D-ribose

The single crystal structure of CaCl(2).C(5)H(10)O(5).3H(2)O was determined with M(r)=315.16, a=7.537(3), b=11.426(5), c=15.309(6) A, beta=90 degrees, V=1318.3(9) A(3), P2(1)2(1)2(1), Z=2, mu=0.71073 A and R=0.0398 for 2322 observed reflections. The ribose moiety of the complex exists as a furanose with alpha-D configuration. All five oxygen atoms of the ribose molecule are involved in calcium binding. Each calcium ion is shared by two such sugar molecules, coordinating through O(1), O(2), O(3) of one molecule and O(4) and O(5) of the other. The C-C, O-H, C-O and C-O-H vibrations are shifted and the relative intensities changed in the complex IR spectrum, corresponding to the changes in bond distances and angles of the sugar structure. All the hydroxyl groups, water molecules and chloride ions are involved in forming an extensive hydrogen-bond network of O-H...Cl...O-H structure, and the chloride ions play an important role in the crystal packing.     

Interactions between metal ions and carbohydrates. The coordination behavior of neutral erythritol to lanthanum and erbium ions

Lanthanide ions and erythritol form metal–alditol complexes with various structures. Lanthanum nitrate and erbium chloride coordinate to erythritol to give new coordination structures. The lanthanum nitrate–erythritol complex (LaEN), 2La(NO₃)₃·C₄H₁₀O₄·8H₂O, La³⁺ exhibits the coordination number of 11 (namely 11 polar atoms bound to one lanthanum) and is 11-coordinated to two hydroxyl groups from one erythritol molecule, six oxygen atoms from three nitrate ions and three water molecules. One erythritol molecule is coordinated to two La³⁺ ions and links the two metal ions together. The ratio of M:L is 2:1. The erbium chloride–erythritol complex (ErE), ErCl₂·C₄H₉O₄·2C₂H₅OH was obtained from ErCl₃ and erythritol in aqueous ethanol solution and the structure shows that deprotonation reaction occurs in the reaction process. The Er³⁺ cation is 8-coordinated with three hydroxyl groups of one erythritol molecule, two hydroxyl groups from another erythritol molecule, two ethanol molecules, and one chloride ion. Erythritol provides its three hydroxyl groups to one erbium cation and two hydroxyl groups to another erbium cation, that is, one hydroxyl group is coordinated to two metal ions and therefore loses its hydrogen atom and becomes a oxygen bridge. Another chloride ion is hydrogen bonded in the structure. The results indicate the complexity of metal–sugar coordination.     

Interactions between metal ions and carbohydrates: the coordination behavior of neutral erythritol to zinc and europium nitrate

The single crystals of coordinated complexes of neutral erythritol (C4H10O4) with zinc nitrate and europium nitrate were synthesized and studied using FT-IR and single crystal X-ray diffraction analysis. In the structure of Zn(NO3)2.C4H10O4, ZnEN (E denotes erythritol, N represents nitrate), Zn2+ is coordinated to four hydroxyl groups from two erythritol molecules and two oxygen atoms from two nitrates. Two Zn2+ are connected by one erythritol molecule to form Zn(C4H10O4)(NO3)2 chain, and layers formed by above chain pile to produce 3D structures. In the structure of Eu(NO3)3.C4H10O4.C2H5OH, EuEN, Eu3+ is 10-coordinated by six oxygen atoms from three nitrate ions, three hydroxyl groups from one erythritol molecule and one hydroxyl group from ethanol. In the above erythritol complexes, two hydroxyl groups of erythritol coordinate to one metal ion and the other two to another metal ion or erythritol acts as three-hydroxyl groups donor. The OH groups of erythritol act as ligand to coordinate to metal ions on one hand, one the other hand, OH groups form hydrogen bonds network to build three-dimensional structures.     

Atomic resolution analysis of a 2:1 complex of CpG and acridine orange.

Cytidylyl-3', 5'-guanosine and acridine orange crystallize in a highly-ordered triclinic lattice which diffracts X-rays to 0.85 angstrom resolution. The crystal structure has been solved and refined to a residual factor of 9.5%. The two dinucleoside phosphate molecules form an antiparallel double helix with the acridine orange intercalated between them. The two base pairs of the double helical fragment have a twist angle of 10 degrees and it is found to have a C3' endo-(3', 5')-C2' endo mixed sugar puckering along the nucleotide backbone as has been observed for other simple intercalator complexes. Twenty-five water molecules have been located in the lattice together with a sodium ion. The intercalator double helical fragments form sheets which are held together by van der Waals interactions in one direction and hydrogen bonding interactions in the other. The crystal lattice contains aqueous channels in which sixteen water molecules are hydrogen bonded to the nucleotide, none to the intercalator, five water molecules are coordinated about the sodium ion and four water molecules bind solely to other water molecules. The bases in the base pairs have a dihedral angle of 7 to 8 degrees between them.     

Crystal structure and conformational analysis of angiotensinogen fragments

The tripeptide acetyl-L-prolyl-L-phenylalanyl-L-histidine crystallizes in the orthorhombic space group P2(1)2(1)2(1) with eight molecules in a unit cell of dimensions a = 9.028(2), b = 140.54(6) and c = 42.41(1)A. The structure has been solved by direct methods and refined to an R value of 0.056 for 2904 observed reflections. The molecule exists as a zwitterion with terminal (His)CO2- and (imidazole)H+ as charged groups. The two peptide molecules in the structure adopt a type I beta-turn with Pro and Phe as the corner residues. The main conformational difference between the two crystallographically independent molecules is seen to be in the histidine side-chain orientations. The molecules arrange themselves in sheets perpendicular to the c axis. All hydrophobic side chains lie on one side of the sheets thus generated, whereas the hydrophilic groups are located on the other side. An interesting feature of the crystal structure is the existence of a water layer between adjacent peptide sheets. The conformational study of the isolated Ac-His-Pro-Phe-His-MA using energy calculations gives a rather limited number of stable conformers. The most stable corresponds to a type I beta-turn stabilized through two hydrogen bonds, followed by a less stable type II beta-turn (delta E = 2.0 kcal) and a partly helical structure (delta E = 2.6 kcal).     

Staggered molecular packing in crystals of a collagen-like peptide with a single charged pair

The crystal structure of the triple-helical peptide, (Pro-Hyp-Gly)(4)-Glu-Lys-Gly-(Pro-Hyp-Gly)(5) has been determined to 1.75 A resolution. This peptide was designed to examine the effect of a pair of adjacent, oppositely charged residues on collagen triple-helical conformation and intermolecular interactions. The molecular conformation (a 7(5) triple helix) and hydrogen bonding schemes are similar to those previously reported for collagen triple helices and provides a second instance of water mediated N--H . . . O==C interchain hydrogen bonds for the amide group of the residue following Gly. Although stereochemically capable of forming intramolecular or intermolecular ion pairs, the lysine and glutamic acid side-chains instead display direct interactions with carbonyl groups and hydroxyproline hydroxyl groups or interactions mediated by water molecules. Solution studies on the EKG peptide indicate stabilization at neutral pH values, where both Glu and Lys are ionized, but suggest that this occurs because of the effects of ionization on the individual residues, rather than ion pair formation. The EKG structure suggests a molecular mechanism for such stabilization through indirect hydrogen bonding. The molecular packing in the crystal includes an axial stagger between molecules, reminiscent of that observed in D-periodic collagen fibrils. The presence of a Glu-Lys-Gly triplet in the middle of the sequence appears to mediate this staggered molecular packing through its indirect water-mediated interactions with backbone C==O groups and side chains.