Showing papers on "Hydrogen bond published in 1973"
TL;DR: In this article, it has been shown that potential energy nonadditivity should create an orientational bias for molecules in the liquid-vapor interface that is peculiar to water, and that the non-polar rigid-sphere solute in liquid water has a radial distribution function.
Abstract: Underlying assumptions have been examined in scaled-particle theory for the case of a rigid-sphere solute in liquid water. As a result, it has been possible to improve upon Pierotti’s corresponding analysis in a way that explicitly incorporates measured surface tensions and radial-distribution functions for pure water. It is pointed out along the way that potential energy nonadditivity should create an orientational bias for molecules in the liquid-vapor interface that is peculiar to water. Some specific conclusions have been drawn about the solvation mode for the nonpolar rigid-sphere solute.
592 citations
TL;DR: The kinetic data of inhibitor-enzyme interaction are reconciled with the structural model, and relations between enzyme-inhibitor interaction and productive enzyme-substrate interaction are proposed.
442 citations
TL;DR: The structural requirements for binding to the glucose/sorbose-transport system in the human erythrocyte were explored by measuring the inhibition constants, K(i), for specifically substituted analogues of d-glucose when l-sorbOSE was the penetrating sugar.
Abstract: The structural requirements for binding to the glucose/sorbose-transport system in the human erythrocyte were explored by measuring the inhibition constants, K(i), for specifically substituted analogues of d-glucose when l-sorbose was the penetrating sugar. Derivatives in which a hydroxyl group in the d-gluco configuration was inverted, or replaced by a hydrogen atom, at C-1, C-2, C-3, C-4 or C-6 of the d-glucose molecule, all bound to the carrier, confirming that no single hydroxyl group is essential for binding to the carrier. The binding and transport of 1-deoxy-d-glucose confirmed that the sugars bind in the pyranose form. The relative inhibition constants of d-glucose and its deoxy, epimeric and fluorinated analogues are consistent with the combination of beta-d-glucopyranose with the carrier by hydrogen bonds at C-1, C-3, probably C-4, and possibly C-6 of the sugar. Both polar and non-polar substituents at C-6 enhance the affinity of d-glucose derivatives relative to d-xylose, and d-galactose derivatives relative to l-arabinose, and it is suggested that the carrier region around C-6 of the sugar may contain both hydrophobic and polar binding groups. The spatial requirements at C-1, C-2, C-3, C-4 and C-6 were explored by comparing the relative binding of d-glucose and its halogeno and O-alkyl substituents. The carrier protein closely approaches the sugar except at C-3 in the d-gluco configuration, C-4 and C-6. d-Glucal was a good inhibitor, showing that a strict chair form is not essential for binding. 3-O-(2',3'-Epoxypropyl)-d-glucose, a potential substrate-directed alkylating agent, bound to the carrier, but did not inactivate it.
210 citations
TL;DR: The X‐ray fiber diffraction photograph obtained from bundles of fibers prepared from Fucus vesiculosus has been indexed to an orthorhombic unit cell in which the unit cell containing two disaccharide chain segments with space group P212121 is indexed.
Abstract: A structural investigation of the marine algal polysaccharide poly-α-L-guluronic acid is described. The molecular chains consist of 1 4 diaxially linked L-guluronic acid residues in the 1C chair conformation and are stabilized in a twofold helix conformation by an intra-molecular O(2)H … O(6)D hydrogen-bond. The X-ray fiber diffraction photograph has been indexed to an orthorhombic unit cell in which a = 8.6 A, b (fiber axis) = 8.7 A, c = 10.7 A.
A structure corresponding to the space group P212121 is proposed, in which all intermolecular hydrogen bonds interact with water molecules and in which all oxygen atoms except for the inaccessible bridge oxygens are involed. The relationship between the shape and structure of the polyguluronic acid molecule and its biological function is discussed.
208 citations
205 citations
TL;DR: The structure of ferricytochrome c2 from the non-sulfur purple photosynthetic bacterium Rhodospirillum rubrum has been determined at 2 A resolution by x-ray crystallographic methods and a hypothetical scheme for folding of the molecule is presented, which suggests that the site of interaction with physiological oxido-reductants is at the front of the cyto chrome c2 molecule.
199 citations
TL;DR: It is proposed that, in addition to stabilizing the collagen triple-helical structure due to the stereochemical properties of the pyrrolidine ring, hydroxyproline gives added stability by the formation of an extra hydrogen bond.
182 citations
174 citations
155 citations
TL;DR: Spectrophotometric, electron paramagnetic resonance, and magnetic susceptibility measurements indicate that the association of horseradish peroxidase with hydroxamic acids entails a transition from a mixed spin state of the enzyme to a high spin derivative.
149 citations
TL;DR: Mostad et al. as mentioned in this paper showed that there is no significant difference between the bond lengths and valence angles in the two compounds except for those atoms involved in hydrogen bonds, and that the standard deviations are quite well estimated in both the neutron and one of the x-ray studies.
Abstract: The amino acid L‐tyrosine (C9H11NO3) and its salt L‐tyrosine hydrochloride (C9H11NO3·HCl) crystallize respectively in the space groups P212121, a=6.913(3) A, b=21.118(10) A, c=5.832(3) A, and P21, a=11.083(5) A, b=9.041(4) A, c=5.099(3) A, β=91.82(3) A. Both structures have been refined by neutron diffraction techniques, and all the hydrogen atoms have been located precisely. The tyrosine molecule occurs in the zwitterion form in pure L‐tyrosine while both the amino group and the carboxyl group are protonated in the hydrochloride. In both crystalline compounds there is a three‐dimensional network of hydrogen bonds. Statistical tests show no significant differences between the bond lengths and valence angles in the compounds except for those atoms involved in hydrogen bonds. The conformational angles of the main chain (C, Cα, N, O1, O2) and those of the side chain differ only slightly in the two compounds while the mutual orientations of the main chain and of the side chain differ completely; in L‐tyrosine N is gauche with respect to Cγ of the phenyl group while in the hydrochloride N is nearly trans to Cγ. The barriers to rotation of the ammonium groups are estimated to be 8.3 kcal/mole in L‐tyrosine and 5.0 kcal/mole in the more weakly hydrogen bonded hydrochloride. Detailed statistical tests for L‐tyrosine show very good agreement between the heavy atom structural parameters obtained from our work and those found in previous x‐ray diffraction studies [A. Mostad, H. M. Nissen, and C. Ro/mming, Tetrahedron Lett. 1971, 2131, and Acta Chem. Scand. (to be published); J. Donohue and R. Bogg (private communication)]. Such tests also show that the standard deviations are quite well estimated in both the neutron and one of the x‐ray studies (Mostad et al.).
TL;DR: In this article, a general theoretical model for the IR spectra of the hydrogen bond was presented, which put on equal footing the Fermi resonance and the coupling between the high and low frequency modes.
TL;DR: In this paper, the Hartree-Fock approximation of the interaction between F− or the Cl− anion and water has been computed with a large basis set of Gaussian functions.
Abstract: The interaction between F− or the Cl− anion and water has been computed in the Hartree‐Fock approximation with a large basis set of Gaussian functions: The obtained energies and wavefunctions are therefore close to the Hartree‐Fock limit. We find that the geometrical configuration of maximal stability corresponds to a hydrogen‐bonded configuration between the water and the anion; however, the hydrogen bond is somewhat bent with a deviation from linearity of about 4.5° for F−–H2O and about 14.6° for Cl−–H2O. At the most stable configuration the oxygen‐anion distance is 4.75 a.u. for F− and 6.26 a.u. for Cl−. At the equilibrium configuration the Hartree‐Fock binding energy is 23.54 and 11.86 kcal/mole for the F−–H2O and the Cl−–H2O complex, respectively. The energy surfaces are analyzed in terms of an energy partitioning consisting of the energy of the water molecule in the field of the anion, the anion in the field of the molecule of water, and of the interaction energy between the water molecule and the a...
TL;DR: The precise molecular configurations of the amino acid serine (C3H~NO3) in crystals of Lserine monohydrate and DL-serine have been refined by neutron diffraction techniques as mentioned in this paper.
Abstract: The precise molecular configurations of the amino acid serine (C3H~NO3) in crystals of L-serine monohydrate and DL-serine have been refined by neutron diffraction techniques. The neutron diffraction data collected for DL-serine were used in conjunction with earlier X-ray results to refine the atomic structural parameters. The unknown structure of L-serine. H20 was solved by direct methods, thus confirming that the negative scattering length for hydrogen in neutron diffraction is not an obstacle to the use of such methods even with a comparatively high percentage of scattering by hydrogen atoms [~b2/all ~omsb~ = 0\"26]. Both compounds show the characteristics of most of ths crystalline amino acids previously studied: The serine molecules are zwitterionic. There are three-dimensional networks of hydrogen bonds. The calculated barriers to rotati3n of the ammonium groups are 7.3 kcal mole -1 in L-serine. H20 and 10.9 kcal mole -1 in DL-serine. The molecular packing in the two crystals is remarkably similar. There are structurally identical layers parallel to the main faces of the two crystals. In Lserine. H20 these layers are tied together by hydrogen bonds formed through interleaving sheets of water molecules. A previous X-ray study of anhydrous L-serine [Benedetti, Pedone & Sirigo (1972). Cryst. Struct. Commun. 1, 35-37] shows that the packing in this structure is quite different. Statistical tests indicat.z that the portion of the serine molecule not involved in hydrogen bonding has the same geometry in both crystals we have studied and in anhydrous L-serine, to the limits of experimental accuracy. In L-serine. H20, a(X-X) and a(X-H) are respectively 0.003, 0.006 A, and in DL-serine 0\"001, o.ool A.
TL;DR: In this article, the influence of the coupling of the proton movement and the H bond stretching vibration in a double minimum potential energy surface on the energy levels, transitions, induced dipole moments and polarisabilities is calcualted ab initio as a function of an electric field for the H5O+2 system.
Abstract: The influence of the coupling of the proton movement and the H bond stretching vibration in a double minimum potential energy surface on the energy levels, transitions, induced dipole moments and polarisabilities is calcualted ab initio as a function of an electric field for the H5O+2 system. The high polarisability of the hydrogen bonds remains to a large extent unchanged due to the coupling. New types of transitions occur, particularly when the tunnelling frequency and the frequency of the bond stretching vibration are comparable in size. Especially in this case numerous Fermi resonances occur due to the shift of the energy levels in the electric field, which leads to a considerable increase in the number of transitions. It is shown that the change of the frequencies of the transitions due to the induced dipole interaction of the bonds with fields from their environment is a decisive cause of the variety of energy level differences observed as a continuous absorption in the i.r. spectrum of such systems.
TL;DR: The sodium salt of guanylyl-3',5'-cytidine crystallizes in a monoclinic unit cell with one molecule in the asymmetric unit with geometry very similar to those which have been derived from studies of fiber x-ray diffraction patterns of double-stranded RNA, even though the latter do not yield data at atomic resolution.
Abstract: The sodium salt of guanylyl-3′,5′-cytidine crystallizes in a monoclinic unit cell with one molecule in the asymmetric unit. Each molecule is related to another molecule by a 2-fold rotation axis which results in the formation of an antiparallel, right-handed double helix with complementary hydrogen bonding between the guanine and cytosine residues. The crystal is heavily hydrated with 36 water molecules in the unit cell. The geometry of this crystalline double helix is very similar to those which have been derived from studies of fiber x-ray diffraction patterns of double-stranded RNA, even though the latter do not yield data at atomic resolution.
TL;DR: In this paper, the structure of the ferro electric phase of Triglycine sulfate has been refined from neutron diffraction data and the hydrogen bonding scheme proposed by Hoshino, Okaya and Pepinsky has been confirmed.
Abstract: The structure of the ferro electric phase of Triglycine Sulfate has been refined from neutron diffraction data. The hydrogen bonding scheme proposed by Hoshino, Okaya and Pepinsky2 has been confirmed. The short hydrogen bond between glycine II and glycinium III that has been postulated to cause the transition has been found to have an O-O distance of 2.50 A with the hydrogen atom 1.1 A from the glycinium III ion. The glycinium I ion contains an ammonium group which moves about 1 A in the transition. This group is 0.4 A out of the plane of the carboxyl group. A possible transition mechanism is discussed.
TL;DR: The results of these and similar calculations are used to calculate the lattice energy of ice I, which agrees well with the experimental value as discussed by the authors, and are shown to be less stable than the noncyclic one.
Abstract: Ab initio LCAO‐SCF molecular orbital calculations have been carried out with an extensive basis set to determine the stabilization energies of a cyclic trimer, a cyclic tetramer, and various noncyclic oligomers of water. The cyclic trimer is shown to be less stable than the noncyclic one. It is concluded that appreciable nonadditive effects are not present in cyclic polymers of water and that these structures show no special stability (compared to noncyclic ones) other than that to be expected from their extra hydrogen bond. Finally, the results of these and similar calculations are used to calculate the lattice energy of ice I, which agrees well with the experimental value.
TL;DR: In this article, a simple electrostatic model was employed to explain the observed shift in binding energy and relate it to differences in structure and hydrogen bonding, and two conclusions can be drawn: structural differences must be considered when interpreting photoelectron spectra for inorganic crystalline substances; hydrogen bonding with anions may have a measurable effect on the binding energy of core electrons of the cations.
Abstract: The aluminum (2p) electron spectra of several anhydrous and “hydrous” aluminum oxides have been recorded, and the binding energies have been measured. A simple electrostatic model is employed to explain the observed shift in binding energy and relate it to differences in structure and hydrogen bonding. Two conclusions can be drawn: structural differences must be considered when interpreting photoelectron spectra for inorganic crystalline substances; and hydrogen bonding with anions may have a measurable effect on the binding energy of core electrons of the cations.
TL;DR: The results indicate that interactions occur with the two residues next to the scissible bond, Ly1 and Ly2, but not with residue Ly3, while refined concepts concerning the relative importance of different sets of enzyme-substrate interactions in determining reactivity are led to.
Abstract: Peptide substrates of the general structure Ac-Tyr-Ly1-Ly2-..-Lym-NH2 and Ac-Phe-Ly1-NH2 have been synthesized and subjected to alpha-chymotrypsin-catalyzed hydrolysis to collect information on the interactions between the enzyme active site and the amino-acid residues Ly1, Ly2, etc., C-terminal to the susceptible bond of the peptide. For this purpose changes in the dissociation constants of the enzyme-substrate complexes and in the rate constants of acylation have been related to the structural variations of the substrates. The results indicate that interactions occur with the two residues next to the scissible bond, Ly1 and Ly2, but not with residue Ly3. Structural description of individual interactions was carried out with the aid of skeletal models of the active site. From such combination of kinetic and structural data a plausible interaction scheme for the substrate side C-terminal to the scissible bond has been deduced. This interaction scheme, which defines conformation and orientation of this part of the substrate within the active site, is characterized by the presence of a single hydrogen bond occurring between NH(Ly2) and O(Phe-41). No donor interacting with the back-bone carbonyl groups of residues Ly1 and Ly2 could be detected in the model of alpha-chymotrypsin. The effect of modification of the side chains of residues Ly1 and Ly2 on the kinetic constants was shown to be consistent with the interactions assumed to occur between the side chains of these residues and the active site. The interpretation of the results obtained from these specificity studies have led to refined concepts concerning the relative importance of different sets of enzyme-substrate interactions in determining reactivity.
TL;DR: The intensities of the indolyl 1La and 1Lb absorption bands were investigated by using 5‐methoxyindole as a model compound and found hydrogen bonding to 1‐methyl‐2‐pyrrolidinone does not measurably affect the total near‐ultraviolet oscillator strength of indoles.
Abstract: The intensities of the indolyl 1La and 1Lb absorption bands were investigated by using 5-methoxyindole as a model compound. With 5-methoxyindole dissolved in weakly interacting solvents, almost the entire 1Lb electronic transition occurs at longer wavelengths than the 1La transition. The resolved spectrum of 5-methoxyindole permitted estimation of its oscillator strengths and also those of other indoles dissolved in cyclohexane: indole, 0.129 (1La), 0.019 (1Lb); 5-methylindole, 0.129 (1La), 0.027 (1Lb); 5-methoxyindole, 0.138 (1La), 0.045 (1Lb); 3-methylindole and N-stearyl-L-tryptophan n-hexyl ester, 0.127 (1La), 0.027 (1Lb). Hydrogen bonding to 1-methyl-2-pyrrolidinone does not measurably affect the total near-ultraviolet oscillator strength of indoles (less than 5% change). In water and ethanol, the oscillator strength of 3-methylindole and tryptophan is 15–20% less than that of 3-methylindole dissolved in cyclohexane. The spectra of the N-stearyl n-hexyl esters of tryptophan and 1-methyltryptophan dissolved in methylcyclohexane can be generated by using 1La and 1Lb bands having shapes similar to those observed for 5-methoxyindole, if the 1La and 1Lb bands are shifted so that their O-O bands overlap (289.5 nm for tryptophan and 299.5 nm for 1-methyltryptophan).
TL;DR: Evidence is presented that the interaction of the uncomplexed antibiotic with polar solvent molecules leads to conformational rearrangements which can be characterized by a step-wise opening of a closed structure stabilized by intramolecular hydrogen bond formation.
Abstract: The 13C nuclear magnetic resonance spectra of the membrane-active antibiotic valinomycin and its alkali-ion complexes are interpreted. From the 13C chemical shifts and infrared absorptions of the highly stable K+, Rb+ and Cs+ complexes in methanol it is concluded that the ligand conformations of these complexes must be similar. The essential features are the coordination of all ester carbonyl groups with the cation in addition to the formation of intramolecular hydrogen bonds between the amide groups. In contrast to these results the weaker Na+ complex of the antibiotic exhibits different spectral properties which are more similar to those of the uncomplexed antibiotic in polar solvents thus indicating the existence of a considerably different ligand conformation in this complex. The structure of the Na+ complex can be characterized by a reduced number of coordinated ester carbonyl groups and intramolecular hydrogen bonds between the amide groups as compared to the complexes with larger cations.
The conformational rearrangements occurring during the complexation of cations are compared to those observed for the uncomplexed valinomycin in solvent systems of different polarities. Evidence is presented that the interaction of the uncomplexed antibiotic with polar solvent molecules leads to conformational rearrangements which can be characterized by a step-wise opening of a closed structure stabilized by intramolecular hydrogen bond formation.
TL;DR: The crystal structure of nylon 12 was determined by x-ray diffraction as mentioned in this paper using a doubly oriented specimen of the yarn and showed that the unit cell is monoclinic with a = 9.38 A, b = 32.2 A, c = 4.87 A and β = 121.5°.
Abstract: The crystal structure of nylon 12 prepared by polymerization of dodecalactam has been determined by x-ray diffraction. Nylon 12 fiber exhibits only the γ form as its stable crystal structure. The unit cell of nylon 12 was determined with the aid of the x-ray diffraction pattern of a doubly oriented specimen. The unit cell is monoclinic with a = 9.38 A, b = 32.2 A (fiber axis), c = 4.87 A and β = 121.5° and contains four repeating monomer units. The chain is planar zigzag for the most part but is twisted at the position of amide groups, forming hydrogen bonds between neighboring parallel chains. The chain conformation is similar to that of the γ form of nylon 6 proposed by Arimoto. It was deduced from the calculations that there are two chain conformations statistically coexistent according to the direction of twisting. In each conformation, hydrogen bonds are formed between parallel chains to make pleated sheetlike structures. The sheets are nearly parallel to (200) and in the sheet the directions of the neighboring chains are antiparallel, as is the case with nylon 6.
TL;DR: Iodine-cyclohexa-amylose tetrahydrate (C6H10O5)6 ·I2·d4H2O] was solved by heavy-atom techniques and refined by least-squares methods to a conventional discrepancy index R 0.148 for the 2872 observed data as mentioned in this paper.
TL;DR: In this article, the effect of an external field on the oxonium ion, H3O+, has been studied with the MO-LCAO method in order to determine its equilibrium geometry.
Abstract: The oxonium ion, H3O+, has been studied with the MO-LCAO method in order to determine its equilibrium geometry. The main purpose has been to study effects of the external electrostatic forces exerted on the ion situated in crystals whose structures are experimentally known. Calculations have also been performed on the free ion, where the energy minimum is found for a non-planar conformation with H-O-H angles of 116.6° and O-H distances of 0.96 A. The effect of an external field is essentially to lengthen the O-H distances and decrease the H-O-H angles in order to form approximately linear hydrogen bonds.
TL;DR: The rate of the reaction between hydrogen peroxide and cysteine or cysteamine is proportional to [H2O2] and [NH3+CHXCH2S]- consistent with nucleophilic attack by the thiolate ions on peroxide oxygen.
Abstract: The rate of the reaction between hydrogen peroxide and cysteine or cysteamine is proportional to [H2O2] and [NH3+CHXCH2S–](X = H or CO2–) consistent with nucleophilic attack by the thiolate ions on peroxide oxygen. The rate decreases at higher pH where loss of the NH3+ proton occurs, and it is suggested that hydrogen bonding between this group and hydrogen peroxide facilitates the reaction.