Showing papers on "Hydrogen bond published in 1983"
898 citations
TL;DR: In this article, the properties of the hydrogen bonds in liquid water were analyzed using the results of molecular dynamics simulations of the MCY-CI model and the connectivity of the clusters was analyzed in terms of the bridgeless polygons which are formed by the bonds.
Abstract: Equilibrium and dynamical properties of the hydrogen bonds in liquid water are analysed using the results of molecular dynamics simulations of the MCY-CI model. Properties of the hydrogen bond clusters as functions of temperature are described. The connectivity of the clusters is analysed in terms of the bridgeless polygons which are formed by the bonds. The problem of obtaining a meaningful definition of bond lifetime is discussed, and the results of lifetime measurements based on alternative definitions are shown.
529 citations
TL;DR: Penicillopepsin has had its molecular structure refined by a restrained-parameter least-squares procedure at 1.8 A resolution to a conventional R -factor of 0.136, confirming the proposal that conformational mobility of the active site residues has no role in the enzymatic mechanism.
384 citations
TL;DR: In this paper, the motion of the atoms in the small protein bovine pancreatic trypsin inhibitor has been simulated for about 60 picoseconds using two different potential energy functions.
367 citations
365 citations
TL;DR: The crystal structure of bovine carboxypeptidase A (Cox) has been refined at 1.54 A resolution using the restrained least-squares algorithm of Hendrickson & Konnert (1981) and four examples of a reverse turn like structure requiring an aspartic acid or asparagine residue are observed in this structure.
359 citations
223 citations
TL;DR: The α-helix defined in 1951 by Pauling et al. as mentioned in this paper has 3.65 residues per turn (n) achieved with planar peptides, torsion angles of φ = −48° and ψ = −57° and hydrogen bonds which are close to linear.
Abstract: The α-helix defined in 1951 by Pauling et al.1 on the basis of model building and X-ray fibre diffraction data has 3.65 residues per turn (n) achieved with planar peptides, torsion angles of φ = −48° and ψ = −57° and hydrogen bonds which are close to linear. Although X-ray analyses of proteins have confirmed the general correctness of the model for the helix, recent high resolution (1.7–1.0 A) diffraction studies have shown that the parameters described by Pauling et al.1 and later by Perutz2 and Arnott and Wonacott3 are not a good description of the α-helices in globular proteins4–7, where the mean values of φ, ψ, are usually close to −63°, −42°. Here we show that these values arise as a mean of two significantly different classes in amphipathic helices depending on whether the peptide carbonyl oxygen is hydrogen bonded to a solvent or polar side-chain atom. The hydrogen bonds made by the hydrophilic carbonyls to the NH groups within helices are longer and less linear than those involving hydrophobic carbonyls. We also show that these effects are associated with a significant curvature of helices in globular proteins. For example, the α-helix in avian pancreatic peptide (aPP) has a radius of curvature of approximately 70 A. These results are of significance in the packing of helices in fibrous and globular proteins, in the calculation of their dipole moments, solvent accessibilities and internal energies, and in the theoretical estimation of spectroscopic properties such as circular dichroism and Raman scattering.
216 citations
TL;DR: Overall, PTI binding to kallikrein is similar to that of the trypsin complex, and the conformation of the groups at the active site is identical within experimental error (in spite of the different pH values of the two structures).
204 citations
TL;DR: For the first time, six‐parameter anisotropic thermal ellipsoids have been refined for each atom; these define the directions of the molecular motions in the polypeptide, indicating concerted vibrations.
Abstract: The 36-amino acid avian pancreatic polypeptide has been studied by x-ray analysis at 0.98-A resolution and refined using a restrained least-squares technique to an agreement factor of 15.6%. The polypeptide, which has a compact globular structure with a hydrophobic core, comprises a polyproline–like helix (residues 2–8) and an α-helix (residues 14–32). The molecule forms symmetrical dimers linked through zinc atoms in the crystal lattice. The high-resolution analysis defines sequence-dependent distortions in the α-helical parameters due to hydrogen bonding of water molecules and side chains. The thermal parameters indicate an increased flexibility of the main chain at the turn between the helices and in the C-terminal residues. For the first time, six-parameter anisotropic thermal ellipsoids have been refined for each atom; these define the directions of the molecular motions in the polypeptide, indicating concerted vibrations. The physiological roles of conformation, flexibility, and dynamics of this polypeptide hormone are discussed.
202 citations
TL;DR: The 132 picosecond simulation of atomic motion in bovine pancreatic trypsin inhibitor protein generated in the accompanying paper is analysed here using a variety of different methods to give a conceptual model for protein dynamics in which the molecule vibrates about a particular conformation but then suddenly changes conformation, jumping over an energy barrier into a new region of conformational space.
TL;DR: In this paper, two exothermic peaks of crystallization of water sorbed on polyhydroxystyrene were observed, one was a sharp peak (Peak I) observed at about 255 K in a d.s.c. curve; the other was a small broad peak (peak II) observed by using differential scanning calorimetry.
TL;DR: In this article, the authors studied the proton spin-lattice relaxation times (T1) of a series of benzoic acid derivatives and decanoic acid over a wide range of temperature and analyzed the results in terms of double proton switching along the hydrogen bonds.
Abstract: We have studied the proton spin‐lattice relaxation times (T1) of a series of benzoic acid (BAC) derivatives and decanoic acid (DAC) over a wide range of temperature and analyzed the results in terms of the double proton switching along the hydrogen bonds. The proton T1 in the high temperature region are analyzed using the classical jump model and the barrier heights for the proton transfer are determined. The thermodynamic parameters for the equilibria between the two configurations in the solid state are also determined by the FT–IR measurements. It is shown that the energetics and dynamics of the proton transfer in DAC and the para‐ and meta‐substituted BAC are all similar, but they are very different in the ortho‐substituted ones. It is suggested that the low temperature behavior of the proton T1 of the dimers of carboxylic acid is due to the tunneling and the asymmetry of the potential brings in a small activation energy.
TL;DR: Spectroscopic studies of base-hydrogen halide complexes are reviewed in this paper, including previously unpublished data for complexes of hydrogen chloride and hydrogen bromide with a variety of bases in argon matrices.
TL;DR: The structure of the water in crystals of human and tortoise egg-white lysozyme, which contain about 350 and about 650 water molecules per protein molecule, has been studied by X-ray refinement at high resolution and suggests that there is a local ordering controlled by the nature of the protein surface.
TL;DR: A complex of RNase A with a transition-state analog, uridine vanadate, has been studied by a combination of neutron and x-ray diffraction, and nitrogen NE2 of histidine-12 was found to form a hydrogen bond to the equatorial oxygen O8, while nitrogen NZ of lysine-41 makes a clear hydrogen Bond to the apical oxygen O2'.
Abstract: A complex of RNase A with a transition-state analog, uridine vanadate, has been studied by a combination of neutron and x-ray diffraction. The vanadium atom occupies the center of a distorted trigonal bipyramid, with the ribose oxygen O2' at the apical position. Contrary to expectations based on the straightforward interpretation of the known in-line mechanism of action of RNase, nitrogen NE2 of histidine-12 was found to form a hydrogen bond to the equatorial oxygen O8, while nitrogen NZ of lysine-41 makes a clear hydrogen bond to the apical oxygen O2'. Nitrogen ND1 of histidine-119 appears to be within a hydrogen-bond distance of the other apical oxygen, O7. Two other hydrogen bonds between the vanadate and the protein are made by nitrogen NE2 of glutamine-11 and by the amide nitrogen of phenylalanine-120. The observed geometry of the complex may necessitate reinterpretation of the mechanism of action of RNase.
TL;DR: In this paper, high-resolution neutron diffraction studies of ice Ih (hexagonal ice) have been done at 60, 123, and 223 K. The molecular geometry found in previous studies is confirmed with an O-H length of 1.01 A and an H-O-H angle of 109.5/sup 0/.
Abstract: High-resolution neutron diffraction studies of ice Ih (hexagonal ice) have been done at 60, 123, and 223 K. The molecular geometry found in previous studies is confirmed with an O-H length of 1.01 A and an H-O-H angle of 109.5/sup 0/. The thermal motion follows a harmonic oscillator behavior. The scattering density in the middle of the hydrogen bond indicates that the hydrogen atom motion extends beyond the midpoint of the oxygen-oxygen bond. 1 figure, 2 tables.
TL;DR: In this paper, Fourier transform infra-red (FTi.r) studies of the polymer blend system poly(hydroxy ether of bisphenol A) (phenoxy)-poly(e-caprolactone) (PCL) are presented.
TL;DR: The linkage between cytochrome a redox state and chromophore/protein interaction energy provides a mechanism by which electron-transfer events and protein structure are coupled.
Abstract: The heme a formyl group of cytochrome a in cytochrome oxidase appears to be involved in a hydrogen-bond interaction with a proton donor associated with the polypeptide backbone [Callahan, P.M., & Babcock, G.T. (1983) Biochemistry 22, 452-461]. Resonance Raman and optical absorption spectroscopies have been applied to the beef heart and Thermus thermophilus proteins and to heme a and copper porphyrin a models in order to assess the spectroscopic manifestations and the energetics of the hydrogen-bond interaction. We find a linear relationship between optical absorption red shift and carbonyl vibrational frequency decrease for a series of hydrogen-bonded model complexes; the magnitude of both changes increases as the hydrogen-bond strength increases. Comparison of the model compound data with analogous data for the proteins indicates that the strength of the formyl hydrogen bond in situ increases by 2-2.5 kcal/mol upon reduction of ferric cytochrome a. The selective stabilization of reduced cytochrome a by the stronger hydrogen bond is expected to increase the redox potential of this center; the energy made available as the hydrogen bond strengthens during reduction may be used to drive redox-coupled events in the protein. Thus, the linkage between cytochrome a redox state and chromophore/protein interaction energy provides a mechanism by which electron-transfer events and protein structure are coupled. Two models, which incorporate this linkage into a redox-driven proton pump centered at cytochrome a in cytochrome oxidase, are presented.
TL;DR: Etude de polymere atactique isotactique et syndiotactique as discussed by the authors, a.k.a., polymer atactiques isotactiques, isometry.
Abstract: Etude de polymere atactique isotactique et syndiotactique. Comparaison avec le spectre en solution
TL;DR: In this paper, the rotational transitions of (H2O,H35Cl) and (H 2O, H37Cl) have been observed and assigned in the frequency range 7-18 GHz.
TL;DR: In this paper, the signal multiplets and magnitudes of isotope effects are used to assign the spectra of carbohydrates as shown for both..cap alpha..- and..beta..-forms of the 6-linked and 4-linked disaccharides.
Abstract: /sup 13/C NMR measurements have been made in dimethylsulfoxide-d/sub 6/ solutions of some carbohydrates (methyl ..cap alpha..-D-gluco- and galactopyranosides, melibiose, maltose, and ..beta..-cyclodextrin) in which exchangeable protons have been partially deuterated. Signals from single carbon atoms are observed as a series of multiplets (singlets to octets) with intensity ratios that vary quantitatively with OH:OD ratios. Partial deuteration of exchangeable protons in molecules permits direct observation of the different isotopomers measured under conditions of slow exchange and the resonance line separations can be analyzed in terms of the two-bond (..beta..) and three-bond (..gamma..) istope effects that contribute to the deuterium-induced secondary isotope shift. Magnitudes of ..beta.. and ..gamma.. effects are found to vary with configuration of carbon atoms, and substitution and hydrogen bonding of hydroxyl groups. Signal multiplets and magnitudes of isotope effects are used to assign the spectra of carbohydrates as shown for both ..cap alpha..- and ..beta..-forms of the ..cap alpha..1-..-->..6-linked (melibiose) and ..cap alpha..1..-->..4-linked (maltose) reducing disaccharides. The method also confirms the presence and direction of intramolecular hydrogen bonding in ..cap alpha..1..-->..4 glucosides (i.e., C2'-O2'...H-O-C3) by observation of an isotope effect on C2' transmitted through a hydrogen bond. Measurements by NMR spectroscopy of secondary isotope multiplets of partiallymore » labeled entities (SIMPLE NMR) have widespread application for signal assignment and for studying isotope effects in molecules. 5 figures, 4 tables.« less
TL;DR: In this article, angle resolved photoemission and thermal desorption studies of atomic hydrogen adsorbed onto the (111) surface of Cu show that the bonding of H to Cu is very similar to H bonding on transition metals.
TL;DR: The structure of tris(2,2'-bipyridine)cobalt(II) dichloride-2-water-ethanol, (Co(C/sub 10/H/sub 8/N/sub 2/)/sub 3/)Cl/sub 6/2H/Sub 2/OC/sub 5/OH (1), and tris
Abstract: The structures of tris(2,2'-bipyridine)cobalt(II) dichloride-2-water-ethanol, (Co(C/sub 10/H/sub 8/N/sub 2/)/sub 3/)Cl/sub 2/2H/sub 2/OC/sub 2/H/sub 5/OH (1), and tris(2,2'-bipyridine)cobalt(I) chloride-water, Co(C/sub 10/H/sub 8/N/sub 2/)/sub 3/ClH/sub 2/O (2), have been determined in order to compare bonding of the high-spin d/sup 7/ and high-spin d/sup 8/ configurations and to better understand the electron-transfer reactivity of this couple. Compound 1 crystallizes in the hexagonal crystal system, space group P6/sub 5/22, with a = 13.403 (2) A, c = 62.566 (10) A, and Z = 12. The structure refined to a final R value of 0.056. The coordination spere consists of the six nitrogen atoms of the three bipyridine ligands in an octahedral arrangement about the cobalt with an average Co-N bond length of 2.128 (8) A. One of the chloride ions is surrounded by twelve C-H Cl hydrogen bonds involving the H3 and H3' protons on the bipyridine ligands. Compound 2 crystallizes in the orthorhombic crystal system, space group Pna2/sub 1/, with a = 9.713 (6) A, b = 21.666 (10) A, c = 13.062 (7) A, and Z = 4. The structure refined to a final R value of 0.084. The geometry of the coordination sphere of 2 is almost identical with that ofmore » 1, with an average Co-N bond length of 2.11 (2) A. Hydrogen bonding between the H3 and H3' protons on the bipyridine ligand and the chloride ion is also observed in 2. The C-H Cl hydrogen bonding observed in these complexes and the bond length changes in 1, 2, and tris(2,2'-bipyridine)cobalt(III) are discussed and related to electron-transfer barriers for the series. 48 references, 1 figure, 9 tables.« less
TL;DR: Circular dichroism spectroscopy strongly suggests that the alpha-helix content is sufficient for only five helices, if each helix is composed of 20 or more residues, and suggests that there is substantial beta-sheet conformation in bacteriorhodopsin.
TL;DR: In this paper, the infrared spectra of argon matrices containing water and acetylene showed that acetylene forms a hydrogen bond to water and C 2 HD can form either a hydrogen or a deuterium bond.
TL;DR: The crystallographic results suggest two major corrections in the published primary structure of the variant-3 protein neurotoxin from the scorpion Centruroides sculpturatus Ewing; one of these has been confirmed by new chemical sequence data.
TL;DR: In this article, the relationship between molecular structure and intramolecular hydrogen bonding in polyfunctional oxonium ions in terms of enthalpy (..delta..H/sub HB//sup 0/) and entropy of the internal bond; the thermal stability of the bond as reflected by the bond opening temperature T, the bond weakening factor, and the entropy of cyclization per single C-C, C-O, or C-N bond incorporated into the ring.
Abstract: Observations are reported of the relationship between molecular structure and intramolecular hydrogen bonding in polyfunctional oxonium ions in terms of enthalpy (..delta..H/sub HB//sup 0/) and entropy (..delta..S/sub HB/) of the internal bond; the thermal stability of the bond as reflected by the bond opening temperature T, the bond weakening factor ..delta..H/sub BWF/, and the entropy of cyclization per single C-C, C-O, or C-N bond incorporated into the ring ..delta..S/sub HB/n/. In the smallest compounds the cyclic structure may only amount to a stabilized cis conformation, while in the largest compounds the hydrogen bond approaches its full intermolecular strength. Combined with previous results, the present data show that intramolecular bonding is prevalent in complex organic ions. 1 figure, 2 tables.