Showing papers on "Hydrogen bond published in 1978"

Polarization model for water and its ionic dissociation products

Abstract: In order to achieve a simple description of aggregates of deformable water molecules, a new model has been constructed which treats H+ and O2− particles as the basic dynamical and structural elements. The H+ units are bare protons, while the O2− units possess a form of nonlocal polarizability consistent with their electronic structure. The model yields water molecules which have the correct geometry and dipole moment, and which engage in hydrogen bonding to one another. Minimum‐energy structures have been determined for the water dimer and trimer and for small hydrate clusters of H+ and OH−; comparison with relevant experiments and quantum–mechanical calculations is satisfactory.

Cryptates: inclusion complexes of macropolycyclic receptor molecules

Abstract: Molecular receptors use intermolecular interactions for the selective binding of substrates. Macropolycyclic molecules containing appropriate binding sites and cavities of suitable size and shape, may be designed so as to display molecular recognition in the formation of selective inclusion complexes, cryptates, with metal cations, anions and molecules. Macrocyclic receptors which form stable and selective complexes with primary ammonium and guanidinium groups are discussed; they display central and lateral discrimination. Enhanced rates of intramolecular thiolysis and hydrogen transfer have been observed when suitable reactive groups are attached to the receptor. Macrobicyclic ligands form very stable and selective cryptates with alkali and alkaline-earth cations; they may be modified so as to selectively complex toxic heavy metal cations. Binuclear cryptates of two types have been synthesized: macrobicyclic complexes of an ellipsoidal Bis-Tren ligand and cylindrical macrotricyclic complexes. They display interesting properties (like cation-cation interactions, copper protein type spectral parameters etc.) and are suitable for formation of “cascade complexes” by interaction of substrates with the bound cations. Spherical macrotricyclic receptors form cryptates with cations, anions and small inorganic species. They display tetrahedral recognition and may be considered as topologically optimal receptors for the ammonium ion, the water molecule, the halide ions, with which they form cryptates where the substrate is held in the intramolecular cavity by a tetrahedral array of hydrogen bonds. Finally, the macrobicyclic Bis-Tren system in its protonated form, complexes triatomic species like the azide anion. It represents a further step in the design of abiotic molecular receptors for polyatomic molecules or ions. The main lines of further developments in the chemistry of macropolycycles comprise the design of receptors for other important groups (carboxylate, phosphate), of polynuclear complexes and cascade complexes of potential use in polynuclear catalysis, of molecular catalysts as enzyme models and new chemical reagents.

Interaction of the peptide bond with solvent water: a vapor phase analysis.

Abstract: A dynamic technique, using radioactivity as a means of detection, makes it possible to measure the partial pressures of highly polar compounds in dilute aqueous solution. The results can be expressed in terms of the dimensionless distribution coefficient for transfer of a compound from dilute aqueous solution to the vapor phase. For acetic acid this coefficient is 1.1 X 10(-5), for acetamide 7.6 X 10(-8), for N-methylacetamide 4.1 X 10(-8), and for N,N-dimethylacetamide 5.4 X 10(-7). Thus acetamide is much more strongly solvated than the uncharged acetic acid molecule. The results suggest: (1) that the peptide bond represents an extreme among uncharged functional groups in the degree to which it is stabilized by solvent water; (2) that the very great hydrophilic character of the peptide bond may be associated mainly with hydrogen bonding of the solvent to the carbonyl oxygen atom (rather than the N-H group); and (3) that the observed equilibria of biosynthesis and hydrolysis of peptide bonds in aqueous solution are largely determined by differences between reactants and products in their free energies of solvation. It is anticipated that where "bound" water is found in proteins, it will often be found to be associated with peptide bonds, and will tend to be associated with the C-O group rather than with the N-H group.

Hydrogen-bond structure in carbohydrate crystals

Abstract: So that possible relationships between hydrogen-bond lengths and hydrogen-bond types could be investigated, it was decided to study by neutron diffraction the crystal structures of several molecules having nearly the same size and shape. Feasibility of crystallization of a homogeneous species was a prime criterion. The three methyl pyranosides selected for the studies had been previously investigated by X-ray diffraction. These were the crystals of methyl ..cap alpha..-glucopyranoside, methyl ..cap alpha..-mannopyranoside, and methyl ..cap alpha..-altopyranoside. Hydrogen bonding in these three structures is especially significant because they contain examples of five of the ten possible types of O-H-O interactions shown in Table I. The results of these neutron diffraction studies provided a systematic relationship between hydrogen-bond length and hydrogen-bond type in the three structures. Not all crystalline carbohydrates fall into their classifications as ''neatly'' as did those from the first three pyranosides. Complicating factors include the competitive effects of hydrogen bonds, polar and dipolar interactions, and van der Waals forces. Most noticeable feature of Table I is the predominance of the bonds of the donor-acceptor type which correspond to the shorter, stronger bonds and are part of the infinite chains or are the inner bonds of finite chains, a consequence ofmore » the ''cooperative effect'' which is also discussed. The anomeric effect of hydrogen bonding is also evaluated and the results are tabulated. Table II illustrates comparative X-ray data and neutron diffraction data on H--O bond lengths. Authors believe that the systematics of the hydrogen-bond data presented will form a useful framework with which to compare future experimental measurements and theoretical calculations.« less

Role of hydrophobicity in the binding of coenzymes

Abstract: We calculate the loss of surface area accessible to solvent associated with coenzyme binding in Clostridium flavodoxin, in dogfish lactate dehydrogenase, and in lobster glyceraldehyde-3-phosphate dehydrogenase. The coenzymes are nearly buried in the complexes and lose on the order of 600 A*, while the proteins lose a similar amount of accessible surface area. Some of the loss can be attributed to conforma- tion changes in the protein, at least in the case of lactate de- hydrogenase, where we show that the apoenzyme has a larger Hydrophobic, electrostatic, and van der Waals forces are involved in all the various types of interactions made by the polypeptide chain of a protein: interactions with itself to fold into a globular structure; association with other chains to form multisubunit complexes; and the binding of small ligands. Thus when structural data are available from x-ray crystallography, the geometrical arrangement of polar atoms shows the presence of intra- and intermolecular hydrogen bonds and charge in- teractions and the volume of the Voronoi polyhedron around each atom describes the atomic packing (Richards, 1974; Chothia & Janin, 1975). The role of hydrophobicity can be assessed using the concept of accessible surface area (Lee & Richards, 1971). For a given protein atom this is the area of the surface over which the center of a water molecule can be placed while it is in van der Waals contact with the atom and not penetrating any other protein atom. Each square angstrom of protein accessible surface that is removed from contact with the solvent gives a hydrophobic free energy of 25 cal (Chothia, 1974). How do these different forces create the specific strong bonds that are essential for biological systems? From an analysis of the structure of the interfaces that occur between protein monomers, we concluded that hydrophobicity is the major force stabilizing protein-protein association; van der Waals forces and hydrogen bonds (i.e., complementarity) play

Effects of hydrogen bonding on the Raman intensities of methanol, ethanol and water

Abstract: The absolute Raman intensities of methanol, ethanol and water in the gas and liquid phases have been measured using 514.5 and 337.1 nm excitation. Large intensity changes were observed for the Raman lines of the OH stretching vibrations in changing from gas to liquid. The observed intensity changes are interpreted as due to the additional contribution of the charge transfer electronic excited state arising from hydrogen bond formation. The Raman intensities of methanol, ethanol and water in alkali halide solutions were also studied. The observed effects of halide ions on the intensities and their excitation wavelength dependences were found to be well correlated with the known charge transfer states resulting from electron transfer from the halide ion to the surrounding solvent molecules.

The 310 helical conformation of a pentapeptide containing a-aminoisobutyric acid (Aib): X-ray crystal structure of Tos-(Aib)5 OMe

Abstract: The pentapeptide Tos-(Aib)5-OMe adopts a 310 helical conformation in the solid state, with three consecutive Type III B-turns stabilized by intramolecular hydrogen bonds.

Adsorption of γ‐aminopropyltriethoxysilane onto bulk iron from aqueous solutions

Abstract: The adsorption of γ-aminopropyltriethoxysilane (γ-APS) onto mechanically polished iron coupons from 1% aqueous solutions has been investigated using reflection–absorption infrared spectroscopy. Thick films were formed on the coupons during 1-hr exposures to the γ-APS solutions. The outermost portion of these films consisted of highly hydrolyzed polysiloxanes that were weakly bound and easily desorbed by cold water. This fraction of the films was characterized by an infrared band near 1575 cm−1 that was tentatively assigned to the NH2 deformation of acceptor amine groups in strong hydrogen bonds or to coordination of the amino nitrogen atoms to silicon atoms. Removal of the weakly bound outermost portion of the films with water revealed an incompletely hydrolyzed, strongly bound film approximately 60 A in thickness characterized by a band near 1510 cm−1 that was assigned to NH groups. Formation of NH3+ groups indicated that γ-APS may have been adsorbed initially as cyclic, internal zwitterions.

On NO−3–H2O interactions in aqueous solutions

Abstract: The scattering of x rays from a concentrated NH4NO3 aqueous solution has been measured and analyzed at 25°C. It is shown that the sample may be considered as a solution of nitrate ions in water. In this way the existence of discrete NO−3–H2O interactions is demonstrated unequivocally. Good agreement with experimental data is achieved through a model in which each O atom in the nitrate ion gives rise to three weak hydrogen bonds with water molecules.

Theory of lower critical solution points in aqueous mixtures

Abstract: Two decorated lattice models of hydrogen bonded mixtures are presented that exhibit lower critical solution temperatures and closed‐loop coexistence curves and that account for the strongly asymmetric closed‐loop coexistence curves found in many aqueous mixtures. The models are extensions of an earlier decorated lattice model that produces only symmetric closed‐loop curves. They incorporate asymmetries in both directional and nondirectional energies as well as the possibility of multiple hydrogen bonding in water. The models are exactly soluble in terms of the spin‐1/2 Ising model, and exhibit nonclassical critical behavior at both upper and lower critical solution temperatures. The hydrogen bond energies in the models are in good agreement with those in real systems, and one of the models gives coexistence curves that are in reasonable quantitative agreement with most of the mixtures considered.

13C and proton nuclear magnetic resonance studies of bradykinin and selected peptide fragments

Abstract: Complete /sup 13/C chemical shift assignments of the nonapeptide bradykinin have been made on the basis of pH titration studies and the examination of peptide fragments. Hysteresis effects previously reported for the /sup 13/C shifts of the Arg/sup 9/ resonances as a function of pH and interpreted to reflect an intramolecular salt bridge involving the Arg/sup 1/ guanido and the Arg/sup 9/ carboxyl (Ivanov, V. T., et al. (1975) Bioorg. Khim. 1, 1241; Proc. 4th Am. Pept. Symp., 151) were not observed in the present study. Chemical shifts of the proline carbons indicate that the trans configuration about the three X-Pro peptide bonds is strongly favored in all cases, although the minor cis resonances accounting for approximately 10% of the proline intensity can also be observed. In addition, there appears to be no significant pH sensitivity of the cis reversible trans equilibria. Studies of the solvent dependence (water ..-->.. methanol) of the carbonyl shifts are consistent with the possibility of an intramolecular hydrogen bond involving the Ser/sup 6/ carbonyl oxygen. Preliminary /sup 1/H nuclear magnetic resonance studies of the amide proton region of bradykinin and the C-terminal tetrapeptide Ser-Pro-Phe-Arg are also reported. In the latter peptide, the Phe/sup 8/ andmore » Arg/sup 9/ amide proton resonances appear as two sets of resonances corresponding to the cis and trans configurations of the Ser-Pro bond. The temperature dependenceof the proton shifts of the amide resonances is independent of whether the Ser-Pro bond is cis or trans, indicating that any intramolecular hydrogen bonding existing only for the trans peptide is insufficient to significantly reduce this parameter. Measurements of the /sup 13/C spin-lattice relaxation times indicate rapid internal motion for all of the peptide side chains, supporting the interpretation that bradykinin exists in solution primarily in a disordered state.« less

Base pairing structure in the poly d(G-T) double helix: wobble base pairs

Abstract: High resolution nuclear magnetic resonance (NMR) and ethidium bromide binding studies are used to demonstrate that poly d(G-T) forms an ordered double helical structure at low temperatures (below 24 degrees C in 0.3 M NaCl) in which G and T are hydrogen bonded together in a wobble base pair hydrogen bonding scheme as proposed earlier by Lezius and Domin. Alternative hydrogen bonding schemes involving the tautomeric form of either T or G, such as have been proposed to account for mutation rates in DNA synthesis, are eliminated.

Experimental conformational study of two peptides containing α-aminoisobutyric acid. Crystal structure of N-acetyl-α-aminoisobutyric acid methylamide†

Abstract: Some theoretical studies have predicted that the conformational freedom of the α-aminoisobutyric acid (H-Aib-OH) residue is restricted to the α-helical region of the Ramachandran map. In order to obtain conformational experimental data, two model peptide derivatives, MeCO-Aib-NHMe 1 and ButCO-LPro-Aib-NHMe 2, have been investigated. The Aib dipeptide 1 crystallizes in the monoclinic system (a = 12.71 A, b = 10.19 A, c = 7.29 A, β = 110.02°, Cc space group) and its crystal structure was elucidated by x-ray diffraction analysis. The azimuthal angles depicting the molecular conformation (ϕ = −55.5°, ψ = −39.3°) fall in the α-helical region of the Ramachandran map and molecules are hydrogen-bonded in a three-dimensional network. In CCl4 solution, ir spectroscopy provides evidence for the occurrence of the so-called 5 and C7 conformers stabilized by the intramolecular i i and i + 2 i hydrogen bonds, respectively. The tripeptide 2 was studied in various solvents [CCl4, CD2Cl2, CDCl3, (CD3)2SO, and D2O] by ir and pmr spectroscopies. It was shown to accommodate predominantly the βII folded state stabilized by the i + 3 i hydrogen bond. All these experimental findings indicate that the Aib residue displays the same conformational behavior as the other natural chiral amino acid residues.

Dielectric and Mechanical Relaxations in a Nafion Precursor

Abstract: The dielectric and mechanical properties of a Nafion precursor have been determined from -196 to +80 °C. The material is a partly crystalline perfluorinated polymer containing a SO2F group at the end of each per. fluorinated ether side chain. Four relaxations are observed. labeled 1, fr, IS", and a in order of increasing temperature. The two relaxations can be partially resolved only at very low frequencies (ca. 0.1 Hz). The 7 relaxation is assigned to motion of the SO2F group, fl' to backbone (-(CF 2)"-) motions, d" to side chain motions (-(CF(CF3)0CF 2)5-), and a to the glass transition. The effect of ionic forces on the properties of polymers has received considerable attention in recent years. 28 Despite this effort, however, a number of factors have still not been elucidated completely, either because of the inherent difficulty of the problem (such as clustering of the ionic groups in media of low dielectric constant) or because of the difficulty of ob- taining an ionic polymer of varying ion contents which has a structurally exact nonionic analogue. The latter is needed in order to be able to separate clearly the effects of ionic inter- actions alone from those due to other factors such as molecular weight, sequence distribution, etc. In the case of copolymers containing acidic groups, the ion content can be varied by utilizing different degrees of neutralization of the carboxylic acid groups 26-41 and by esterification. 7 However, the unique properties of the proton in general, and its participation in hydrogen bonding in particular, confer special properties onto the acidic analogues of these ionomers which may invalidate any direct comparison with the salts. This paper concerns itself with an investigation of a non- ionic material which is the chemical precursor of the family of ionic polymers known as Nafions, developed by Du Pont for use primarily as electrolyte separators. It consists of a tetrafluoroethylene backbone, with a perfluoronated ether side chain which is terminated by an SO2F group (I)

Conformation of erabutoxins a and b in aqueous solution as studied by nuclear magnetic resonance and circular dichroism.

Abstract: The 270-MHz nuclear magnetic resonance (NMR) spectra of erabutoxins a and b have been observed in 2H2O solution. By the use of convolution difference and double resonance techniques, proton signals in the aromatic and methyl regions have been assigned. From the pH dependence of NMR chemical shifts, the pKa value of His-26 of erabutoxin b is found to be 5.8, whereas His-7 of erabutoxins a and b is not protonated at pH above 3. The imidazole ring of His-7 is protonated upon the denaturation at pH 2.85. The acid denaturation process has been followed by the His-26 and methyl proton signals and is found to be reversible but is slow as compared with NMR chemical shift time scale. The circular dichroism (CD) of erabutoxin b has also been observed. The denaturation is found to involve a major change from the β-rich conformation to a disordered one. The NMR and CD changes upon acid denaturation are satisfactorily explained by the two-state process. The deuterium exchange rates of the C-2 protons of His-26 and His-7 of erabutoxin b indicate that His-26 is exposed to the solvent whereas His-7 is tightly buried in the interior of the protein globule. The pKa value of Tyr-25 is as high as about 12.0, possibly due to the hydrogen bond formation between the hydroxyl group of Tyr-25 and a carboxylate group. The hydroxyl group of Tyr-25 is reversibly titrated so that this group is not buried tightly in the interior of the protein globule. The line width of the aromatic proton signals of Tyr-25 is significantly broad at room temperature, suggesting a restricted rotation of the aromatic ring. The aromatic proton signals of Trp-29 are fairly sharp; this aromatic ring is exposed and mobile. Except for His-7, the micro-environments of Tyr-25, His-26, and Trp-29 residues and methyl proton signals of valine and isoleucine are consistent with the locations of α carbon atoms as elucidated by X-ray crystal analyses.

Conformation of poly(L‐arginine). I. Effects of anions

Abstract: The conformational transition of poly(L-agrignine) by binding with various mono-, di-, and polyvalent anions, especially with SO, was studied by CD measurements. The intramolecular random coil-to-α-helix conformational transition and the subsequent transition to the β-turn-like structure was caused by binding with SO. The binding data obtained from equilibrium dialysis experiments showed that the α-helical conformation of poly(L-arginine) is stabilized at a 1:3 stoichiometric ratio of bound SO to arginine residue; at higher free SO concentrations, the α-helix converts to the β-turn-like structure accompanied by a decrease in amount of bound SO. The same conformaitonal transition of poly(L-arginine) also occurred in the solutions of other divalent anions (SO, CO, and HPO) and polyvalent anions (P2O, P3O). Among the monovalent anions examined, CIO and dodecyl sulfate were effective in including α-helical conformation, while the other monovalent anions (OH−, Cl−, F−, H2PO, HCO and CIO) failed to induce poly(L-arginine) to assume the α-helical conformation. Thus, we noticed that, except for dodecyl sufate, the terahedral structure is common to the α-helix-forming anions. A well-defined model to the α-helical poly(L-arginine)/anion complex was proposed, in which both the binding stoichiometry of anions to the arginine residue and the tetrahedral structure of anions were taken into consideration. Based on these results, it was concluded that the tetrahedral-type anions stabilize the α-helical conformation of poly(L-arginine) by crosslinking between two guanidinium groups of nearby side chains on the same α-helix through the ringed structures stabilized by hydrogen bonds as well as by electrostatic interaction. Throughout the study it was noticed that the structural behavior of poly(L-arginine) toward anions is distinct from that of poly(L-lysine).

Crystallographic factors affecting the structure of polymeric spherulites. II. X-ray diffraction analysis of directionally solidified polyamides and general conclusions

Abstract: The morphological diversity in even‐even nylons described in Paper I was found to be the result of crystallographic factors related to the high extent of hydrogen bonding Among all spherulitic species in these polyamides, only positive spherulites crystallize in accordance with the phenomenological theory of Keith and Padden However, as a result of their unit cell orientation which renders the hydrogen‐bonded sheets radial and the molecular chains almost tangential, folding occurs predominantly into the melt rather than in the usual tangential manner The microstructure of negative spherulites departs from the norm in that long ribbonlike lamellae are absent; instead, negative fibrils are composed of short segments containing tangentially arranged stacks of hydrogen‐bonded sheets In spherulitic aggregates the molecular chains are crystallized at the unusually acute angle of 49° to the direction of solidification The preferred direction of fibrillar growth in these aggregates is oblique to the spheruli