Showing papers on "Hydrogen bond published in 1972"

On the Symmetry of the Hydrogen Bonds in Ice VII

Abstract: The interaction of the hydrogen atoms with nearest neighbor oxygen atoms in the hydrogen bonds of ice VII are approximated by two equivalent Morse potentials. With the inclusion of a repulsive oxygen—oxygen interaction, the model predicts a transition to symmetric hydrogen bonding in ice VII at a pressure between 350 and 800 kbar.

The Crystal Structure of Adenosine

Abstract: The crystal structure of adenosine, C10Ht3NsO4, has been determined from the intensities of 1333 reflections, each measured at least four times on an automated diffractomcter. The crystals are monoclinic, space group P21, with a=4.825 (1), b= 10"282 (2), c= 11.823 (1)/~, fl=99.30 (1) °, and two molecules per cell. Least-squares refinement of coordinates and anisotropic temperature factors for all atoms, including hydrogen, led to an R index of 0-024 and standard deviations of about 0.003 A, for bond distances between pairs of heavy atoms. The anomalous scattering by nitrogen and oxygen was used to confirm the absolute configuration of the sugar ring. The conformation of the ribose ring is C(3') endo; the torsion angle about the glycosidic bond is 9.9 °. Intermolecular interactions include a full complement of hydrogen bonds, a relatively short C(2)-H.. .O(2') contact (3.09 A,), and parallel stacking of adenine rings with an interplanar spacing of 3"57/~.

Survey of the geometry and environment of water molecules in crystalline hydrates studied by neutron diffraction

Abstract: 1972) The bond lengths and angles in water molecules, derived from over 40 neutron-diffraction studies of crystalline hydrates, are analysed statistically. A 'quasi-normal' spread of the dimensions and con- sequent deviations from an average model, affecting both water molecules and their environment, is associated with strains due to local failures of Pauling's second rule. This interpretation is consistent with linear correlations between pairs of bond lengths and/or angles. A new, more general classification of water molecules in crystalline hydrates, based on cation coordination, is proposed. The water mol- ecules are arranged in five classes, according to the number of coordinated cations and to the position of the cations with respect to the lone-pair orbitals; each class may be further subdivided on the basis of the chemical nature of the cations. Introduction The water molecule plays an important role in the packing of crystalline hydrates, both because it partici- pates in hydrogen bonds linking anions and also be- cause, through its lone-pair orbitals, it is a satisfactory ligand for many cations. The approximately tetrahedral environment usually assumed by the water molecule has often been idealized and used for tentative estimates of the hydrogen-atom coordinates; constant molecular geometry and, some- times, linearity of hydrogen bonds and/or planarity of the water-acceptor group are assumed. In fact, both the conformation of the water molecule and the geom- etry of its environment do depend, to some extent, on the specific situations in different compounds. Neutron diffraction is the only technique that allows unambiguous location of hydrogen atoms of the water molecule in solid hydrates with estimated standard deviations (e.s.d.'s) comparable with those of the other atoms; while very accurate X-ray data may allow the location of hydrogen atoms, their e.s.d.'s are generally too high for quantitative discussion. Of the fifty or so crystal structures of hydrates (April 1972)studied in three dimensions by neutron diffraction, the results for 41 are reviewed here, with the 90 water molecules involved. Compounds with disorder in water molecules (cf. Ferraris, Jones & Yerkess, 1972b) or other atoms or atomic groups (cf. some alums) have been excluded. The appropriate planes (Fig. 1) and bond lengths and angles were recomputed and are summarized in Tables 1 and 2 according to a classification reported be- low. All distances and angles are uncorrected for thermal motion since, even when reported, such corrections are merely indicative. While Tables 1 and 2 deal with * Paper presented at the 6th Hungarian Conference on X-ray, Electron, and Neutron Diffraction; 28th May-lst June 1972, Si6fok, Hungary. Research supported by the C. N. R. all types of hydrogen bonds involving water molecules, the results to be discussed concern mainly O...O hydrogen bonds, since only for these does the number of cases studied by neutron diffraction allow statistical correlations. The following symbols are used (Fig. 1): W= oxygen atom of the water molecule; HI, H2 = hydrogen atoms of the water molecule; A 1,A2 = acceptors of hydrogen bonds; C1, C2, C3 = atoms contacting W; ~0 = H- W-H angle; tpl = A 1. • • W. • • A 2 angle; cq, ~2 = W-H- • • A angles; J~,Jz=angles between W...C1 and W-H; 7r = plane of the water molecule; zq = plane of 14, C2 and C3; ?1, Yz = angles between H- • • A and n; e~, ez, e3 = angles between W. • • C and n; e = C2. • • W. • • C3 angle; ~, = angle between ~z and nl; oA, o)2 =angles between the ~z-nl intersection straight line and W-H. ;~ ~C3

Donor-Acceptor Interactions at Interfaces

Abstract: Nearly all intermolecular interactions in solution and at interfaces can be reduced to two phenomena: London dispersion forces, and electron donor-acceptor (acid-base) interactions. Hydrogen bonds are included in acid-base interactions, and dipole phenomena are usually negligibly small. Earlier popular notions that all “polar” groups can interact with each other are shown untenable; donor-donor and acceptor-acceptor interactions are negligibly small compared to donor-acceptor interactions. Supporting data include surface and interfacial tensions, contact angles, and adsorption of polymers from organic solvents onto inorganic powders.

Valinomycin crystal structure determination by direct methods.

Abstract: The conformation of an uncomplexed form of the antibiotic valinomycin (C54N6O18H90) has been determined by direct methods including a novel technique for strong enantiomorph discrimination via the calculation and systematic analysis of cosine invariants of a special type. The intramolecular hydrogen bonding scheme and the isopropyl group stereochemistry of uncomplexed valinomycin are compatible with interpretations of spectral measurements for the complexed and uncomplexed molecule in solution but are different from any previously proposed structure. The simple conformational change of a hydrogen bond shift, which could be induced by the process of potassium ion complexing, transforms the uncomplexed into the complexed structure.

The crystal structure of the orthorhombic form of l-(+)-histidine

Abstract: L-(+)-Histidine (C6NaO2H9) crystallizes in the orthorhombic space group P212121, with a = 5-177, b = 7.322, c= 18.87 A, and Z=4. Data were collected with Mo Kct radiation, using balanced filters. The structure was solved by direct phasing methods and refined to a final agreement index of 0.034 for all reflections. The conformation of the molecule is that of the open, extended form, and is stabilized principally by an imramolecular hydrogen bond between the amino nitrogen atom and the adjacent imidazole nitrogen atom. Where this conformation is found in proteins, it is likely to reduce the chemical reactivity of tha+ ;midazole group, because one of the imidazole nitrogen atoms is sterically hindered by the peptide ba,.~, one.

The crystal and molecular structure of trehalose dihydrate

Abstract: The crystal structure of trehalose dihydrate has been solved by direct methods and refined to an R index of 0-057 using anisotropic refinement. The space group is P212121 and four formula units of C12HzzOz~.2HzO are contained in the unit cell of dimensions a= 17.90, b= 12.21 and c= 7.586 A. The two glucopyranose residues in the trehalose molecule have the chair 4C1 form, and are bonded by the a 1 --+ 1 glycosidic link in approximate twofold symmetry. Departures from symmetry are found in torsion angles about the e 1 -+ 1 link and in conformations of the primary alcohol groups O(6)H and O(6')H. The C-O bond lengths show systematic trends similar to those in other e-pyranose sugars and at the same time show some characteristic features related to the e 1 -~1 link of the two glucose residues. There are two indirect intramolecular hydrogen bonds incorporating water molecules. Neither the ring oxygens nor the glycosidic linkage oxygen accept hydrogen bonds. The molecular packing in the crystal is mainly determined by the hydrogen bonds.

Near‐Infrared Studies of the Structure of Water. III. Mixed Solvent Systems

Abstract: The near‐infrared absorption of water in the 7000‐cm−1 region has been studied for pure water and solutions of water‐acetone and water‐dioxane between 0 and 80°C. The absorption was resolved into Gaussian components and the component bands were used to calculate the mole fraction of water species with 0, 1, and 2 of the hydrogen atoms involved in hydrogen bonding. The data do not agree with the presence of significant effects due to Fermi resonance. A model of water with three spectroscopically distinct species agrees with the analysis of the bands.

Microwave Spectrum, Dipole Moment, and Intramolecular Hydrogen Bond of 2-Methoxyethanol

Abstract: The minimum energy conformation of 2-methoxyethanol (CH3OCH2CH2OH) has been determined from an analysis of its microwave spectrum. The rotational constants of the normal species are: A = 12982.35, B = 2742.48, and C = 2468.10 MHz; the dipole moment components are μa = 2.03, μb = 1.15, and μ = 2.36 ± 0.03 D. For the CH3OCH2CH2OD species: A = 12385.71, B = 2724.74, and C = 2431.42 MHz. The conformation consistent with this data is gauche about each of the C—C, C—O(H) and C—O(ether) bonds, having dihedral angles of 57 ± 3°, 45 ± 5°, and 8 ± 3°, respectively. This distorted conformation is one in which the hydroxyl hydrogen atom is approximately aligned with the nearest sp3 lone pair electrons of the ether oxygen atom. Transitions in three excited torsional states have also been observed but no other rotational isomer was detected.

Precision neutron diffraction structure determination of protein and nucleic acid components. VIII: the crystal and molecular structure of the β-form of the amino acidl-glutamic acid

Abstract: A neutron diffraction study of the β-form of L-glutamic acid, C5H9NO4, has been carried out. The structure is orthorhombic: space groupP212121,a= 5·159(5),b= 17·30(2),c= 6·948(7) A andz = 4. Least-squares refinements based on 803 reflexions led to a final conventionalR value of 0·026, and bond lengths involving hydrogen atoms have been determined with an average precision of 0·004 A. The molecule is in the zwitterion form, and no intramolecular hydrogen bonds have been found. The hydrogen atom involved in a strong hydrogen bond between two carboxyl groups in adjacent molecules (0 ... 0 distance 2·519(2) A) is covalently bonded to the carboxyl group belonging to the side chain of the amino acid. This side chain is buckled with Cδ gauche to Cα with respect to the C β —C γ bond. The bond angles involving carbon atoms in the side chain are accordingly strained.

Coupling of Hydrogen Bonding to Orientational Fluctuation Modes in the Liquid Crystal PHBA

Abstract: In the liquid state, the molecules of the carboxylic acids are associated in pairs by hydrogen bonds connecting their acid groups. If these dimers are long and rigid, they can form a nematic phase. The dimer molecules of the liquid crystal p-hexyloxybenzoic acid have been deuterated on the hydrogen bonds, and the nuclear quadrupolar spin-lattice relaxation rate 1/T 1 of these deuterons has been studied. In the nematic phase, 1/T 1 is frequency dependent between 2.7 and 13.8 MHz; its temperature behavior is identical with that of the parameter S describing the orientational order of the nematic phase. In the isotropic phase, 1/T 1 behaves in the same way as in conventional nematics: at high nuclear frequencies, it is still frequency dependent, and rather unsensitive to temperature in the vicinity of the nematic-isotropic transition; at low frequencies, it has no frequency dependence, but diverges when the transition temperature T c is approached from above: The “critical frequency” which separates...

Association by Hydrogen Bonding of Mononucleotides in Aqueous Solution

Abstract: Evidence for hydrogen bonding between 5'-ribonucleotides in water has been obtained from a 220-MHz proton magnetic resonance study of nitrogenous protons. The amino groups of GMP, AMP, and CMP exhibit proton resonance lines which are somewhat broadened by proton exchange with the solvent at 0 degrees ; their downfield Shifts in mixtures of mononucleotides provide the basis for the following order of base-pairing tendencies: GMP.CMP > AMP.UMP. Hydrogen bonding is also observed in other pairs of mononucleotides, notably GMP.UMP, AMP.CMP, and CMP.UMP, to a lesser extent in GMP.IMP, CMP.XMP, and possibly in CMP.IMP. In agreement with previous reports, hydrophobic interactions of mononucleotides have also been observed; base pairing occurs in addition to vertical stacking of these bases, their hydrogen bonding to water, or self-association. Only CMP shows clear evidence of self-association via hydrogen bonding in water; the evidence for GMP is less direct, and that for AMP is negative. This lack of observable self-association may occur as a result of competition from strong stacking interactions. Only CMP shows restricted rotation of the amino group at 0 degrees and neutral pH. As expected, higher temperatures increase the rate of rotation of the amino group for CMP, as well as accelerate the rate of proton exchange between water and the amino protons of mononucleotides.High-resolution proton magnetic resonance spectroscopy could prove to be a valuable tool in mapping out the specificities conferred by hydrogen bonding between biomolecules in aqueous solution.

Crystal structures of complexes between alkali-metal salts and cyclic polyethers. Part III. Aquo-(2,3-benzo-1,4,7,10,13-pentaoxacyclopentadec-2-ene)sodium iodide

Abstract: The crystal structure of the title complex determined from three-dimensional diffractometer data. Z= 4 in an orthorhambic unit cell having a= 12·271, b= 9·550, c= 15·719 A, and space group P212121. Full-matrix least-squares refinement based on 887 observations has led to R 0·048 for the correct absolute configuration of the molecule.The sodium ion is surrounded by a pentagonal pyramid of oxygen atoms. The base is formed by those of the cyclic ether with Na–O 2·35(1)–2·43(1)A and the sodium ion is 0·75 A from this plane towards the apical water molecule, Na–O 2·29(1)A. The iodide ion does not interact with the sodium ion but may form hydrogen bonds to water molecules [O⋯I 3·47(1) and 3·51(1)A], linking the complexes in chains along the b-axis of the crystal.