Showing papers on "Hydrogen bond published in 1968"

Solution Properties of Poly(N-isopropylacrylamide)

Abstract: Aqueous solutions of poly(N-isopropyl acrylamide) show a lower critical solution temperature. The thermodynamic properties of the system have been evaluated from the phase diagram and the heat absorbed during phase separation and the phenomenon is ascribed to be primarily due to an entropy effect. From viscosity, sedimentation, and light-scattering studies of solutions close to conditions of phase separation, it appears that aggregation due to formation of nonpolar and intermolecular hydrogen bonds is important. In addition, a weakening of the ordering effect of the water-amide hydrogen bonds as the temperature is raised contributes to the stability of the two-phase system.

Molecular conformation of poly(S‐lactic acid)

Abstract: The predominant role of van der Waal interactions in determining the helical conformations of a simple synthetic linear polymer, as well as helical polypeptides, was pointed out in systematic studies by Liquori et al.1,2. In the case of homopolypeptides the conformational analysis carried out on the basis of a simple semiempirical function describing the van der Waal pairwise interactions between the non directly bonded atoms lead to the conclusion that only five helices are allowed (Rα, β, γ, δ, Lα).2,3 In view of the close similarities with poly-L-alanine, we have investigated by x-ray and conformational analysis the molecular conformation of poly(S-lactic acid) which has recently been described by Kleine and Kleine4 and Schuls and Schwaab5 and studied in solution by Goodman and D'Alagni.6 In fact, this polymer may be related to the polypeptide by the interchange of a peptide bond with ester bond along the main chain. This operation is expected to involve only a relatively small change in the steric interaction within the possible helical conformation, but obviously rules out any possibility of hydrogen bonding.

Interchain hydrogen bonds via bound water molecules in the collagen triple helix

Abstract: If the collagen triple helix is so built as to have one set of NH O hydrogen bonds of the type N3H3(A) O2(B), then it is possible to have a linkage between N1H1(B) and O1(A) through the intermediary of a water molecule with an oxygen O leading to the formation of the hydrogen bonds N1(B) O and O (A). In the same configuration, another water molecule with an oxygen O can link two earbonyl oxygens of chains A and B forming the hydrogen bonds O O1(A) and O O0 (B). The two water oxygens also become receptors at the same time for CH O hydrogen bonds. Thus, the neighboring chains in the triple helix are held together by secondary valence bond linkages occurring regularly sit intervals of about 3 A along the length of the protofibril. The additional water molecules occur on the periphery of the proto-fibril and will contribute their full share towards stabilizing the structure in the solid state. In solution, they will be disturbed by the medium unless they are protected by long side groups. It appears that this type of two-bonded structure, in which one NH O bond is to a water molecule, can explain several observations on the stability and hydrogen exchange properties of collagen itself and related synthetic polypeptides. The nature of the water bonds and their strength are found to be better in the one-bonded structure proposed from Madras than in the one having the coordinates of Rich and Crick.

Molecular‐Orbital Studies of Hydrogen Bonds. An Ab Initio Calculation for Dimeric H2O

Abstract: The hydrogen‐bond energy and the most stable structure of the dimeric H2O system are calculated by the LCAO MO SCF method using a medium‐sized Gaussian orbital basis set. The most stable structure, found by a limited variation of the interatomic coordinates, is a linear hydrogen bond (stabilization energy 12.6 kcal mole−1) with an H···O distance of 1.72 A, and with the hydrogen‐acceptor molecule almost freely rotating around its molecular axis. The stretching of the proton donor O–H bond is calculated to be 0.12 A. A population anaysis near the energy minimum shows that the change in the population is distributed not only in the O···H–O fragment, but also delocalized into the neighboring O–H bonds. Hydrogen bonds of dimeric H2O other than the linear structure (cyclic and bifurcated) are also examined.

Some aspects of stereochemistry and hydrogen bonding of carbohydrates related to polysaccharide conformations

Abstract: Some general rules governing hydrogen bonding at the ring oxygens of furanosides, pyranosides, and bridge oxygens of glycosides have been formulated from existing data on crystal structures of carbohydrates. Ring oxygens of the majority of the glycopyranosides in the hemiacetal or acetal form are involved in hydrogen bonding such that the hydrogen bond direction is usually equatorial to the ring plane and not axial. In contrast, there are no known examples of ring oxygens of glycofuranosides and methyl-glycopyranosides displaying hydrogen bonding in the crystal. Also, the bridge oxygens of glycosides are not involved in hydrogen bonding. The observed shortening in the exocyclic and endocyclic anomeric C(1)O bonds and the geminal CO bonds indicate that compounds with two oxygen atoms attached to the same saturated carbon atom may participate in double-bond-no-bond resonance interaction in the same manner as difluoromethane. It is also possible that under these circumstances the carbon atom exhibits greater than tetracovalency. The “anomeric effect” may also be related to (a) the differences in the “double bonding” or bond shortening in the anomeric CO bonds of the anomeric glycopyranosides, (b) the shorter intramolecular O(1)…O(5) non-bonded interaction, and (c) the smaller O(1)C(1)O(5) valence angle in the equatorial anomer compared to the axial anomer. An analysis has been made of the energetically preferred conformations about the glycosyl and glycosidic bonds of 1,4- and 1,3-polysuc-charides. In the 1a, 4e-glycopyranosides the projected angle ϕ1 [O(5)C(1)OR, where R = C or H] is positive, while it is negative in the 1e, 4e-glycopyranosides. Angle ϕ2 [C(1)OC(4′)C(3′)] is positive in both the 1,4-anomeric polyglycosides. 1e, 4e- and 1a, 4e -polysaccharides are stabilized by intramolecular O(5)…HO(3′) and O(2′)…O(3′) hydrogen bonding, respectively, and generate linear and helical (cyclic) structures, respectively. 1e, 3e- and 1a, 3e-polysaccharides may be stablized by one of two possible intramolecular hydrogen-bonding schemes such that the 1a, 3e -polysaccharides generate helical structures while the 1a, 3e-polysaccharides generate nonhelical structures. The conformation about the C(5)C(6) bond in the pyranosides falls into two groups where the angle ϕ00 [O(5)C(5)C(6)O(6)] is either positive, ∼+60 ± 30°, or negative, ∼–60 ± 30°, the former conformation being found more frequently. In the furanosides the latter conformation is preferred.

Conformational studies of poly‐L‐alanine in water

Abstract: The conformational properties of poly-L-alanine have been examined in aqueous solutions in order to investigate the influence of hydrophobic interactions on the helix–random coil transition. Since water is a poor solvent for poly-L-alanine, water-soluble copolymers of the type (D, L-lysine)m–(Lalanine)n-(D, L-lysine)m, having 10, 160, 450, and 1000 alanyl residues, respectively, in the central block, were synthezised. The optical rotatory dispersion of the samples was investigated in the range 190–500 mμ, and the rotation at 231 mμ was related to the α-helix content, θH, of the alanine section. In salt-free solutions, at neutral pH, the three large polymers show high θH values, which are greatly reduced when the temperature is increased from 5 to 80°C. No helicity was observed for the small (n = 10) polymer. By applying the Lifson-Roig theory, the following parameters were obtained for the transition of a residue from a coil to a helical state: ν = 0.012; ΔH = −190 ± 40 cal./mole; ΔS = −0.55 ± 0.12 e.u. Since ΔH and ΔS differ from the values expected for a process involving only the formation of a hydrogen bond, and in a manner predicted by theories for the influence of hydrophobic bonding on helix stability, it is concluded that a hydrophobic interaction is also involved. In the presence of salt (0.2M NaCl), or when the e-amino groups of the lysyl residues are not protonated (pH = 12), the helical form of the two large polymers (n = 450 and n = 1000) is more stable than in water. Since the electrostatic repulsion between the lysine end blocks is greatly reduced under these conditions, the alanine helical sections fold back on themselves, and this conformation is stabilized by interchain hydrophobia bonds. This structure was predicted by the theory for the equilibrium between such interacting helices, non-interacting helices, and the random coil.

A neutron diffraction determination of the crystal structures of thiourea and deuterated thiourea above and below the ferroelectric transition

Abstract: The structures of thiourea, SC(NH2)2, and deuterated thiourea, SC(ND2)2, have been determined at room and liquid nitrogen temperatures from three-dimensional neutron diffraction data. No significant structural change on deuteration has been found. N—H⋯S hydrogen bonds occur in both materials at both temperatures with N—S distances of 3.35–3.43 A and N—H—S angles of 169–171° and, apart from these hydrogen atoms, the molecules are planar to within 0.010 A. An analysis of the thermal parameters of the atoms in each molecule in terms of rigid vibration parameters shows that at liquid nitrogen temperature the molecules are fairly rigid whereas at room temperature there are serious deviations from rigidity. Excellent agreement has been found between the thermal vibrations of the molecules at room temperature and the observed structure change to the lower ferroelectric state. A qualitative theory of the ferroelectric nature of thiourea is proposed which explains the observed temperature variation of the spontaneous polarization and coercive field in the lower ferroelectric region, in terms of a variable molecular orientation and a single hydrogen bond which is switched from one sublattice to the other during ferroelectric reversal.

The Structure of Vitamin B$_{12}$. VII. The X-ray Analysis of the Vitamin B$_{12}$ Coenzyme

Abstract: The three-dimensional molecular structure of coenzyme B 12 (59-deoxyadenosylcobalamin) has been determined by X-ray diffraction. The crystals, as grown from an acetone-water solution and photographed wet, are orthorhombic (space group P 2 1 2 1 2 1 ) with a = 27·93, b = 21·73 and c = 15·34 A. Four coenzyme molecules (C 72 H 100 O 17 N 18 PCo) and about 68 water molecules make up the unit cell. 3068 Bragg reflexions, extending to a spacing of 0·9 A, were measured with the crystals in contact with their mother liquor. The intensities were estimated visually from Weissenberg films taken with Cu Kα radiation. The cobalt atoms were easily located from the Patterson synthesis. The structure was solved in three steps, using first cobalt alone, then cobalt and 53 light atoms, and in the third approximation, 106 atoms, which included nearly the full asymmetric unit, except for water and hydrogen. Refinement of the atomic coordinates was accomplished initially by calculation of difference syntheses and finally by differential synthesis. The atomic positions have standard deviations of about 0·04 A. The conformation of the molecule is very similar to cyanocobalamin. The principal differences are in the orientation of the acetamide and propionamide side chains. Factors which influence the conformation of the corrin nucleus are analysed by comparing several corrinoids of known structure. Features of the molecule which have been examined in detail include the pucker in the pyrroline rings, the bend in the corrin macrocycle, the conformation of the nucleotide and nucleoside moieties and the orientation of the deoxyadenosine moiety with respect to the corrin nucleus. The packing of the molecules and the hydrogen bonding is discussed and compared with that found in the wet and dry vitamin B 12 crystals. Each coenzyme molecule participates in 18 direct intermolecular hydrogen bonds.

Matrix-isolation study of the hydrogen cyanide dimer.

Abstract: On the basis of the infrared spectra of HCN and DCN in Ar, N2, and CO matrices at temperatures from 4.5° to 20.5°K, it is concluded that there is no evidence for rotation of the monomeric species in these matrices and that the dimer has a linear or nearly linear HCN·HCN structure. The Lippincott‐type potential is used to calculate frequencies for the stretching of the hydrogen bond and for the torsion about the hydrogen bond. These calculated frequencies are compared with our observed far‐infrared spectra of dimers in the matrix and with available Raman data on crystalline HCN and DCN.

Specific hydrogen bonding of barbiturates to adenine derivatives.

Abstract: Barbiturates form strong, specific hydrogen bonds with derivatives of adenine. This highly specific interaction which is more extensive than the hydrogen bonding between thymine (or uracil) derivatives and adenine derivatives may help to explain the different biological effects of barbiturates.

Hydrogen bonding in pyridine

Abstract: The pyridine-water and pyridine-methanol hydrogen-bonded systems have been examined using the extended Hiickel theory (EHT). Of the various conformations studied, the one in which the hydrogen approaches the pyridine lone pair forming a linear arrangement of the 0-H. . .N grouping is of lowest energy. In this case, for both water and methanol, a reasonable potential energy curve is obtained for the hydrogen-bonded system. From this curve it is concluded that the heat of formation is -2.3 kcal/mol, the equilibrium distance between the oxygen and nitrogen atom 2.76 A, and the force constant 0.10-0.11 X 1Oj dyn/cm. The nitrogen lone-pair orbital shifts progressively to lower energy as water or methanol approachs the pyridine molecule. The calculated blue shift is about twice as large for water than methanol. At fixed positions of the heavy nuclei, the proton was transferred from oxygen to the nitrogen atom. A double energy minimum was obtained with an energy barrier of approximately 0.7 eV for the proton transfer at the equilibrium distance of 0-N separation. As the proton shifts over from oxygen to nitrogen, as expected, the 0-H overlap population decreases and the H-N increases. While the charge on oxygen increases and for nitrogen decreases, it stays essentially constant at about +0.4 electron for hydrogen during the transfer. For the (n,a*) excited state, the results parallel qualitatively those for the ground state. Finally, it is of interest to mention that the carbon-I3 chemical shifts, calculated from the EHT wave function, are in reasonable agreement with the experimental values. great number of facts about the hydrogen bond are A fairly well understood; what is not so clear is the interpretation that should be given to them. Pimentel and McClellan, Coulson, and Bratoz5 provided re(1) This work was supported by a research grant from the University of Puerto Rico. It was presented at the Euchem Symposium held on April 16-21, 1967, in Mittenwald, Germany. (2) Cornell University, Ithaca, N. Y. (3) G . C. Pimentel and A. L. McClellan, “The Hydrogen Bond,” W. H. Freeman and Co., San Francisco, Calif., 1960, Chapter 8. views of the concepts used in the theoretical interpretation of the hydrogen bond. These will be presented in brief form before discussing our calculations. The classical electrostatic model of the hydrogen bond has enjoyed substantial support and there are two main (4) C. A. Coulson in “Hydrogen Bonding,” D. Hadzi, Ed., Pergamon (5) S. Bratoz in “Advances in Quantum Chemistry,” Vol. 111, P. 0. Press, London, 1959. Lowdin, Ed., Academic Press Inc., New York, N. Y., 1967. Adam, Grimison, Hofmann, Zuazaga de Ortiz H Bonding in Pyridine

Quantitative study on hydrogen bonding between urethane compound and ethers by infrared spectroscopy

Abstract: A quantitative infrared spectroscopic study of a model urethane-type compound was carried out in order to obtain basic data on hydrogen bonding in polyurethanes. First, the absolute intensity of free NH groups of N-phenylurethane, which was adopted as the model urethane, was determined by Wilson-Wells' method to be 3.59 × 103l./mole-cm.2. The free NH of this urethane absorbed at 3447 cm.−1, and hydrogen-bonded NH absorbed near 3300 cm.−1. Then, the extents of hydrogen bonding of the urethane at various concentrations were determined, and the hydrogen bonding between the urethane and ethers was studied by using the above-mentioned absolute intensity. For comparison, diphenylamine was also used as proton donor. Di-n-butyl ether and poly-(oxyethylene glycol) were examined and proved to be able to act as proton acceptors. The frequency shifts of NH stretching vibration of diphenylamine and N-phenylurethane caused by hydrogen bonding with di-n-butyl ether were 96 cm.−1 and 150 cm.−1, respectively. The equilibrium constants were 4.8 × 10−1l./mole for the former system 4.6 × 10−1l./mole for the latter.

Hydrogen Dibromide Radical: Infrared Detection through the Matrix Isolation Technique

Abstract: When hydrogen chloride–chlorine–argon mixtures are passed through a glow discharge and the products are condensed at 14°K, two conspicuous infrared absorptions at 956 and 696 cm−1 result Concentration dependence of intensities, isotopic labeling, and force‐field calculations lead to assignment of these bands to hydrogen dichloride The force field calculated supports a linear, centrosymmetric (D∞h) structure with hydrogen bond strength apparently comparable to or exceeding those attributed to HCl2− in various crystals

Hydrogen‐Bond Studies. XXIX. Crystal Structure of Perchloric Acid Dihydrate, H5O2+ClO4−

Abstract: The crystal structure of HClO4·2H2O has been determined from single‐crystal x‐ray data obtained at −190°C. The crystals are orthorhombic, space group Pnma, with four formula units in a cell of dimensions: a = 5.819, b = 10.598, c = 7.369 A. The water molecules are bonded to each other into pairs by a very short hydrogen bond (2.424 A), forming H5O2+ ions. With the space group chosen there is a center of symmetry in the middle of this hydrogen bond; the H5O2+ ion is perfectly staggered. The H5O2+ ions are hydrogen bonded to the ClO4− ions into layers, which are held together by van der Waals forces. The average Cl–O distance in the perchlorate ion is 1.438 A.

Spectroscopic Studies of Mixed Amine Carbonyl Complexes of d6 Structure. II. Solvent Effect on the Ultraviolet and Visible Absorption Spectra of Diamine-tetracarbonyl Complexes of Chromium(0), Molybdenum(0) and Tungsten(0)

Abstract: Absorption bands, especially metal to amine charge transfer bands of bipyridyl- and phenanthroline-tetracarbonyl chromium (0), molybdenum (0) and tungsten (0) are shifted in various solvents by less than 4500 cm−1. The shift is discussed in accordance with McRae’s equation, which was derived with the point-dipole approximation. The solvents can be classified into two groups, the alcohol and the ester group. When three constants corresponding to (1) the interaction between induced dipoles of the solute and of the solvent, (2) the interaction between permanent dipole of the solute and induced dipole of the solvent, and (3) the interaction between permanent dipoles of the solute and of the solvent, are duely chosen for the two groups of solvent individually, the experimental values are satisfactorily accounted for. Short range interactions, such as hydrogen bonding can be ignored.

The crystal structure of α-glycylglycine

Abstract: The cystal structure of the α crystal form of glycylglyeine, -CO 2 CH 2 NHCOCH 2 NH 3 + , has been investigted. The cell dimensions are a = 7·70, b = 9·57, c = 9·48 A β = 124°35'. The space group is P2 1 /a with four molecules per cell. Mo kα rays were used. The trial structure was derived by use of part-cell Patterson methods and modlfied Banerjee equations. Final refinement was by block-diagnol anisotropic least-squares adjustment to an R of 12·3 and yielded standard deviations of about 0·007A in bond lengths.The intramolecular chemical bond lengths and interbond angles agree well with those found for the same molecule in the previously reported β crystal form but the configuration of the molecule is somewhat different. There is an angle of about 22·4° between the plane of the amide group and that of the carboxyl group. In the β crystal these group were coplanar within experimental error. Since the α form is probably the stable form, this distortion presumbly permits better molecular packing with stronger hydrogen bonds and van Waals interactions.

Crystal Structure and Phase Transition of (Glycine)2HNO3 I. Crystal Structure Determination of Ferro- and Paraelectric Phases

Abstract: The crystal structures of ferroelectric and paraelectric (Glycine) 2 HNO 3 were determined by X-ray as well as by neutron diffraction methods at -150°C and at room temperature, respectively. One of the glycine molecules has the zwitter-ion configuration and another is mono-protonated. Thus the chemical formula should be written as NH 3 + CH 2 COO - ·NH 3 + CH 2 COOH·NO 3 - . Both glycine ions as well as the nitrate ion are nearly planar within the experimental error. A short O-H…O bond, about 2.45A, connects two glycine ions of the different configuration and a proton is attached to the oxygen of the glycinium ion. The paraelectric structure is a disordered one based upon the ferroelectric structure. Such a type of the order-disorder phase transition and the above-mentioned strong hydrogen bond may play an important role for the ferroelectric behaviour of the crystal, which is very similar to the case of (Glycine) 3 H 2 SO 4 .

Effect of side chains on the conformational energy and rotational strength of the n-pi transition for some alpha-helical poly-alpha-amino acids.

Abstract: Calculations of the dependence of the conformational energy and the rotational strength of the amide n–π* electronic transition (in a series of α-helical polyhel-α- amino acids with different side chains) on conformation have been carried out. The conformational energies were computed by procedures developed in this laboratory; the computation of rotational strengths was carried out by the method of Schellman and Oriel, with a slight modification. Polyamino acids with both nonpolar and polar side chains were considered; in the latter case, it was assumed that the only influence of the polar side chain was on the backbone conformation and on the electrostatic field which perturbs the amide chromophore of the backbone. Only conformations in the range of backbone dihedral angles of the right- and left-handed a-helices were considered, and the assumption of regularity (i.e., uniformity of dihedral angles in every residue) was made. The rotational strength per residue was found to vary markedly with chain length (in oligomers of up to 40 residues long); both the conformational energy per residue and the rotational strength per residue were found to vary significantly with the backbone conformation, which in turn depends on the nature of the side chain. The geometry of the hydrogen bond in the α-helical backbone is the most important factor which influences the dependence of the rotational strength on conformation. The implications of these results, for the interpretation of experimental circular dichroism and optical rotatory dispersion data, are discussed.

Structure of piperazine hexahydrate

Abstract: Piperazine hexahydrate, C4N2H10·6H2O, forms monoclinic pseudo‐tetragonal and usually strongly twinned crystals, melting at 44°C. The structure has been determined using x‐ray counter data obtained at room temperature. The space group is P21 / n, with Z = 2, and cell dimensions are a = 6.309, b = 6.323, and c = 14.912 A, β = 94.96°. The hydrogen‐bonded water molecules form puckered layers of almost tetragonal symmetry composed of edge‐sharing pentagons, which are joined into a three‐dimensional framework by hydrogen bonds to the nitrogen atoms of the piperazine molecules. The twin laws are explained as stacking faults of the water layers. The hydrogen atoms are disordered within the water layers and ordered between the oxygen and nitrogen atoms. The bond lengths and angles of the piperazine molecule are normal. The structure is related to the clathrate hydrate structures because of the pentagonal geometry of the water structure.