Independent Hydrogen Bonds Research Articles

Crystal structure and hydrogen-bonding system of cholic acid hemihydrate, C24H40O5�1/2H2O

Crystals of the hemihydrate of this bile acid are hexagonal, space groupP6522, a=b=13.736(8)A,c=85.06(6)A,V=13,899A3. The asymmetric unit contains two independent steroid molecules and one water molecule, the latter disordered over two nonequivalent positions.Z=12[2(C24H40O5)·1(H2O)],F(000)=5496. Structure solution by direct methods; refinement by least-squares, toR=0.072. The complex hydrogen-bond system comprises: (a) three standard ordered O-H⋯O hydrogen-bonds; (b) what is probably a symmetrically hydrogen-bonded carboxylic acid dimer, with a twofold rotation axisin the plane of the two carboxyl groups; (c) helical hydrogen-bonding chains about each 65 axis, disordered over four possible arrangements. In these helical chains, the six independent hydrogen-bonds can as a group be in either of two systems of nearly equivalent “flip-flop” arrangements: O-H⋯O ↔ O⋯H-O. Each helical system includes water, which can occupy either of two sites; thus, there is further disorder involving two sets of nonequivalent hydrogen-bonds with water as donor and acceptor. Many aggregation features here differ markedly from those in the crystal structures of either anhydrous cholic acid or cholic acid monohydrate.

Hydrogen bonds to carboxylate groups. The question of three-centre interactions

Hydrogen bond geometries as well as their stereochemical preferences have been compared for 255 small molecule carboxylate structures retrieved from the Cambridge Structural Database. A total of 974 independent hydrogen bonds were analysed. Hydrogen atoms cluster in the carboxylate lone-pair directions with no tendency to adopt a central, symmetric position between the two oxygens. The long, secondary H ⋯ O contacts of asymmetric syn hydrogen bonds do not affect either the overall geometries of the interactions or the total syn/anti distribution of accepted H-atoms, presumably due to very unfavourable CO ⋯ H angles. On this basis it is suggested that syn hydrogen bonds to carboxylates should be regarded most frequently as two-centre rather than three-centre (bifurcated) interactions. The statistical data also show that criteria traditionally used to infer three-centre hydrogen bonds are inadequate for carboxylate acceptors.

Volume transition in a gel driven by hydrogen bonding

INTERACTIONS between macromolecules fall into four categories: ionic, hydrophobic, van der Waals and hydrogen bonding. Phase transitions in polymer gels provide a means of studying these interactions. Many gels will undergo reversible, discontinuous volume changes in response to changes in, for example, temperature, gel composition or light irradiation1–5. These transitions result from the competition between repulsive intermolecular forces, usually electrostatic in nature, that act to expand the polymer network, and an attractive force that acts to shrink it. Volume transitions in gels have been observed that are driven by all of the above-mentioned forces except hydrogen bonding (ref 6–10; T.T. et al, unpublished data; H. Inomata et al., personal communication). Here we report on a phase transition in an interpenetrating polymer network of poly(acrylamide) and poly(acrylic acid) that completes this picture—it is controlled by cooperative 'zipping' interactions between the molecules which result from hydrogen bonding. Cooperativity is an essential feature of the interactions, in that independent hydrogen bonds would not provide a sufficient driving force for the transition. A further novel characteristic of this phase transition is that the swelling (in water) is induced by an increase rather than a decrease in temperature.

An experimental electron density study of NaHC2O4.H2O at 120 K

Sodium hydrogen oxalate monohydrate, Mr = 130.03, triclinic, P1, a = 6.4235 (7), b = 6.6580 (8), c = 5.6941 (10) A, a : 85-048 (9), /3= 110.100 (13), y = 104.963 (14) °, V = 220.94/~3, Z = 2, Dx = 1.954 Mg m -3, A(Mo Ka) = 0.71069/~, /1, = 0.293 mm-l, F(000) = 132, T = 120 K, R = 0.0279 for conventional refinement based on 3971 reflections with Fo 2 > 3tr(F2). The deformation electron density of NaHC2Oa.H20 has been measured at 120 K using X-ray and neutron diffraction techniques. X-X (high order) and X-N difference density maps are compared with deformation maps derived from a multipole model. Deformation densites in the covalent bonds of the HC204 ion are correlated with bond order. Deformation densities in the three independent hydrogen bonds are consistent with an electrostatic model for bonds of weak to intermediate strength in which polarization and other contributions become more important as the protonacceptor distance decreases. The hydrogen bonding affects both the covalent bonds and the lone-pair electron density of the acceptor oxygen atoms.

Preparation and hydrogen bonding studies of phenylhydrazone derivatives of alloxan: crystal and molecular structure of pyrimidine-2(1H),4(3H),5,6-tetraone 5-(2-nitrophenyl)hydrazone

Eight phenylhydrazone derivatives of pyrimidine-2(1H),4(3H),5,6-tetraone, or 5-oxobarbituric acid (alloxan), are described. Spectroscopic pyrimidine (1H n.m.r., i.r.) data indicate the presence of extensive hydrogen bonding which, as shown by X-ray crystallographic data for the title hydrazone, includes both intra- and inter-molecular interactions. The title hydrazone, C10H7N5O5, is monoclinic, space group P21/a, a= 9.104(8), b= 17.975(13), c= 10.333(8)A, β= 113.5(1)°, Z= 4.2145 Independent reflections have been measureed on a diffractometer and the structure has been determined by direct methods and refined to R 0.074. There are four independent hydrogen bonds in the asymmetric unit: two intramolecular bonds which link N(7)–H(7) to an o-NO2 group of the benzene ring and to a carbonyl group of the barbiturate ring and two intermolecular bonds which link NH sites of the barbiturate ring to a solvent NN-dimethylformamide oxygen atom and to a carbonyl oxygen atom of another barbiturate ring across a centre of symmetry.

Crystal and molecular structure of 1-amino-1-methylethylphosphonic acid monohydrate

The crystal and molecular structure of 1-amino-1-methylethylphosphonic acid monohydrate (C3H10NO3P·H2O) has been determined by single-crystal X-ray diffraction methods. The crystals are orthorhombic:Pna21,a=11.665(2),b=9.415(1),c=6.386(1) A,Z=4. The structure was solved by the heavy-atom method and refined to a finalR=0.028. The molecule exists as a zwitterion, H 3 + N-C-(CH3)2-PO34H−. There are six independent hydrogen bonds in the structure, three of the type N-H⋯O with lengths 2.904(5), 2.745(6), and 2.765(5) A and three of the type O-H⋯O with lengths 2.754(4), 2.833 (7), and 2.548(5) A.

Crystal and molecular structure of glycinium diphenylphosphate

The crystal and molecular structure of glycinium diphenylphosphate, C14H16NO6P, has been determined by X-ray methods. The crystals are orthorhombic:Pbca (No. 61),a=11.412(3),b=24.624(7),c=10.775(3) A,Z=8. The structure was solved by direct methods and refined to anR value of 0.043 for 1289 nonzero independent amplitudes. The molecule exists in the structure as+NH3CH2CO2H,(C6H5O)2PO 2 − and is planar except for the N atom, which deviates by 0.49 A from the plane defined by C(1), C(2), O(5), and O(6) atoms, respectively. The conformation of the diphenylphosphate anion isgauche with respect to both P-O ester bonds. There are four crystallographically independent hydrogen bonds, three of the N-H⋯O type and one of the O-H⋯O type.

The crystal and molecular structure of bromhexine·HCl

The crystals of bromhexine-HCl, C14H21 N2Br2Cl, are orthorhombic, space group Pca21 with a=14.598(2)A, b=12.461(3)A, c=9.186(1)A and Z=4. Intensity data for 967 reflections (Fobs>6σ(F)) were collected on a Rigaku-Denki automatic fourcircle diffractometer. The structure was solved by the Patterson and Fourier methods. Refinements were carried out to the final R value of 0.082. The cyclo-hexane ring has a normal chair form and the benzene ring is planar. There are three independent hydrogen bonds in the structure. One is an intermolecular hydrogen bond (N-H…Cl−) and the others are intramolecular hydrogen bonds (N-H…Br, N+-H…Cl−). Apart from the hydrogen bonding system the molecules are held together in the crystal by van der Waals force.

The structure of Dimethylaminomethanediphosphonic Acid, C3H11NO6P2

AbstractMr = 218.9, monoclinic, P 21/c, a = 6.870(1), b = 10.824(2), c = 11.337(2) Å, β = = 94.59(2)0, Z = 4, V = 840.5(3) Å3, Dx = 1.73 Mgm−3. Final R = 0.033 for 2648 independent reflections, excluding those with |F0| < 3σ(F0). Intensities were measured with an automatic diffractometer. This organophosphorous compound is characterized by two PC bonds. Four symmetrically independent intermolecular hydrogen bonds determine the threedimensional packing of the molecules and the unique chemical properties of the campound.

Structure of 6,3':6,5'-dianhydro-5,5-dibromo-5,6-dihydro-6,6-dihydroxy-1-(.BETA.-D-xylofuranosyl)uracil.

The title compound, C9H8Br2N2O6, crystallizes as hemihydrate in space group P62 with a=12.612 (1), c=13.431 (1) A, and Z=6. The structure was solved by a combination of the direct and the heavy atom methods and refined to an R value of 0.051. The novel structure having two oxygen bridges between the base and the sugar was confirmed by the analysis. The base is oriented anti with respect to the sugar with torsional angles C (6)-N (1)-C (1')-O (1')=57.2°and C (6)-N (1)-C(1')-C(2')=-55.6°, and the sugar ring is in a half-chair form, C(1')-endo-C(2')-exo. The oxygen atom of the water molecule lies on the two-fold axis and three independent hydrogen bonds connect the molecules of nucleoside and water in the crystals.

Crystal structures of polymorphs of .ALPHA.-((tert-butylamino)methyl)-2-chloro-4-hydroxybenzyl alcohol hydrochloride (HOKU-81).

The crystal structures of the two crystalline forms (I and II) of α-[(tert-butylamino)-methyl]-2-chloro-4-hydroxybenzyl alcohol hydrochloride (HOKU-81), which is one of the metabolites of tulobuterol hydrochloride (C-78) and a potent β2-adrenergic stimulant, have been determined by X-ray structure analysis. The structures were solved by direct methods and refined by the block-diagonal least-squares method including anisotropic thermal parameters to final R values of 0.051 and 0.050 for Forms I and II, respectively. The molecular conformations in the two forms are similar, but nevertheless the crystal structures are very different. In Form I, independent hydrogen bonds of four types are formed, while three types of independent hydrogen bond are formed in Form Ii, producing characteristic molecular sheets in the crystals. Comparison of the crystal structures of the polymorphs between HOKU-81 and C-78 indicates that some of the differences of physico-chemical properties are attributable to the differences of crystal packings. Furthermore, comparison of the molecular conformations of HOKU-81 and C-78 with those of the other adrenergic agents having an ethanolamine side chain shows that these compounds have homologous conformations in the aliphatic side chain.

VISCOSITY MEASUREMENTS OF ALCOHOL-WATER MIXTURES AND THE STRUCTURE OF WATER

In a previous paper (Ageno, 1967), a model of the hydrogen bond was proposed that gave a unique structure for water and was used for viscosity measurements. In this paper, an attempt is made to confirm some results obtained by using this model and interpretation by performing new experiments not involving viscosity measurements but using the heat of vaporization of ice and water from which the main chain length (L) of a linear chain of water molecules can be determined independently. An equation is derived for determining L as a function of the difference between the heat of vaporization of water at a given temperature and the external work done in the transformation of the liquid into saturated steam at that temperature. The results demonstrated that a water molecule can be involved in no more than 2 independent hydrogen bonds, and a primary alcohol molecule in no more than one.

The Crystal Structure and the Absolute Configuration of (+)-2-Benzylglutamic Acid Hydrobromide Dihydrate

Abstract The crystal structure of (+)-2-benzylglutamic acid hydrobromide dihydrate has been determined using three-dimensional X-ray intensity data. The crystal is orthorhombic, with four formula units in a unit cell with the dimensions: a=8.38, b=10.54, and c=17.68 Å, the space group being P212121. The structure was solved by the heavy atom method, and its parameters were refined by the least-squares method using anisotropic thermal parameters, the final R being 0.073. The absolute configuration of the glutamic acid has also been determined to be d-(+)-2-benzylglutamic acid, [α]d20+1.65° (c 10, 4 n HCl). The conformation of the carbon skeleton of the glutamic acid is different from any of the glutamic acids so far analyzed, due to the internal rotations of the C–C bonds. A detailed comparison of the conformations of several glutamic acids and glutamines will be given. Nine independent hydrogen bonds make a rather unique and complicated three-dimensional network. Among these, two between the carboxyl groups (donor) and the water molecules (acceptor) are found to be fairly strong, their bond lengths being 2.55 and 2.51 Å.