Showing papers on "Hydrogen bond published in 1986"
TL;DR: In this article, the potential functions were developed for use in computer simulations of liquid alcohols and other molecules with hydroxyl groups, based on earlier work for liquid hydrocarbons and required introduction of few new parameters.
Abstract: Intermolecular potential functions have been developed for use in computer simulations of liquid alcohols and other molecules with hydroxyl groups. The functions are based on earlier work for liquid hydrocarbons and required introduction of few new parameters. Optimization of the parameters involved studids of hydrogen-bonded complexes and Monte Carlo simulations for liquid methanol. Further application then consisted of Monte Carlo simulations for liquid methanol, ethanol, 1-propanol, 2-propanol, and 2-methyl-2-propanol at 25 O C and 1 atm. Extensive thermodynamic and structural results are reported for the liquid alcohols and are compared with experimental data. The excellent accord between simulation and experiment is remarkable in view of the simple form and facile parametrization of the potential functions. The five liquid alcohols all feature winding hydrogen-bonded chains with averages of close to two hydrogen bonds per molecule. The hydrogen bonding is also found to have interesting effects on the torsional energy surfaces for molecules in the liquids. Most striking is a narrowing of the conformational energy wells for rotation about the C-0 bonds.
1,059 citations
TL;DR: Enrichment methods are described which greatly facilitate the isolation of mutant sequences and depend upon the introduction or elimination of a unique and silent restriction site near the site of mutagenesis.
Abstract: Structural studies on serine proteinases have shown that hydrogen bonds are involved in stabilizing the charged tetrahedral intermediate in the transition-state complex. However, little is known about the quantitative contribution of these interactions to transition-state stabilization. X-ray crystallographic studies of subtilisin (Robertus, J. D., Kraut, J., Alden, R. A. & Birktoft, J. J. Biochemistry, Wash. 11, 4293-4303 (1972)) have suggested that the amide side chain from asparagine-155 forms a hydrogen bond with the oxyanion produced on the substrate carbonyl oxygen in the tetrahedral intermediate. To study the importance of the Asn-155 hydrogen bond in stabilizing the tetrahedral intermediate, Asn-155 was substituted with Thr, His, Gin and Asp by using site-specific mutagenesis of the cloned subtilisin gene from B. amyloliquefaciens . These substitutions were intended to alter the position and charge of the potential hydrogen-bonding group at 155. Mutations of Asn-155 caused large decreases in substrate turnover, K cat (200- to 4000-fold), with marginal decreases in substrate binding, K M (up to 7-fold). The most dramatic effects were seen with Thr-155, where K cat was reduced 4000-fold with a slight increase in K M . Mutations of Asn-155 caused a loss in transition-state stabilization energy of 9.2-20 kJ mol -1 Simple enrichment methods are described which greatly facilitate the isolation of mutant sequences. These methods depend upon the introduction or elimination of a unique and silent restriction site near the site of mutagenesis.
379 citations
TL;DR: Les resultats d'etudes precedentes sur les polyamides amorphes sont applicables a ce polymere semi-cristallin this paper, i.e.
Abstract: Les resultats d'etudes precedentes sur les polyamides amorphes sont applicables a ce polymere semi-cristallin
358 citations
TL;DR: Examination of the hydrogen bonding patterns in the calcium-binding loops of ICaBP and the related protein, parvalbumin, reveals several conserved hydrogen bonds which are evidently important for loop stabilization.
325 citations
TL;DR: In this paper, the symbiotic relationship between X-ray crystallographic investigations and synthetic work has been recognized and researched in its most general context, and it has been shown that the coordinating influence of many transition metal complexes extends beyond their covalently-bonded first-sphere ligands to non-covalently bound chemical species in the so-called secondsphere.
Abstract: Although it has been appreciated for most of this century that the coordinating influence of many transition metal complexes extends beyond their covalently-bonded first-sphere ligands to non-covalently bound chemical species in the so-called second-sphere, it is only recently that the fundamental importance of the phenomenon has been recognized and researched in its most general context. Rapid progress has been possible in this relatively new area of supramolecular chemistry by appealing to the symbiotic relationship that exists between X-ray crystallographic investigations and synthetic work. The gamut of non-covalent bonds, including electrostatic forces, hydrogen bonding, charge transfer, and van der Waals interactions are available for exploitation in choosing or designing suitable molecular receptors for particular transition metal complexes. Crown ethers are the synthetic macrocycles par excellence for forming adducts with neutral and cationic complexes carrying protic ligands (NH3, H2O, CH3CN, etc.) in their first coordination spheres. Anionic complexes with electron-rich first-sphere ligands (e.g. CN⊖) form adducts with polyammonium macrocyclic receptors. In both situations, hydrogen bonds and electrostatic interactions provide the dominant sources of supramolecular stabilization. Spectroscopic studies (UV, IR, and NMR) reveal that the structural integrity of the adducts is usually maintained in solution. The transition metal complexes can be organometallic as well as inorganic. In complexes supporting organic ligands, such as 1,5-cyclooctadiene, norbornadiene, cyclopentadiene, 2,2′-bipyridine, and trimethylphosphane, the opportunity exists to match their steric and electronic characteristics with appropriate binding sites in the molecular receptor. With these ligands, the weaker categories of non-covalent bonding, e.g. charge transfer and van der Waals interactions, assume considerable importance. The phenomenon is also observable with naturally-occurring receptors such as the cyclodextrins and polyether antibiotics. Moreover, it extends beyond the territory of transition metal complexes to main group complexes such as ammonia-borane. As far as applications are concerned, it finds expression in areas as diverse as separation science and drug delivery systems.
203 citations
TL;DR: In this article, a simple model for the computation of intermolecular interactions is described, consisting of atom-atom potentials for the representation of repulsion and dispersion energies, and an evaluation of the electrostatic energy in terms of partitioned multipole moments of the monomer electron distributions.
Abstract: A simple model for the computation of intermolecular interactions is described. It consists of atom–atom potentials for the representation of repulsion and dispersion energies, and an evaluation of the electrostatic energy in terms of partitioned multipole moments of the monomer electron distributions. Applications are given in detail for hydrogen‐bonded dimers of the molecules HF, HCl, CO, N2, Cl2, HCN, CO2, N2O, OCS, HCCH, NCCN, and HCCCN, and the results compared with ab initio and experimental results. Hydrogen bond energies are obtained to better than 4 kJ mol−1, intermolecular separations to typically better than 0.15 A, and intermolecular angles within 5°, all compared with experiment. Force constants and vibrational frequencies are also well reproduced.
195 citations
TL;DR: The nitrogen-15 shifts demonstrate that protonation of the histidine imidazole ring at low pH in the transition-state or tetrahedral intermediate analogue complexes formed with phenylmethanesulfonyl fluoride and diisopropyl fluorophosphate triggers the disruption of the aspartate-histidine hydrogen bond.
Abstract: Nitrogen-15 NMR spectroscopy has been used to study the hydrogen-bonding interactions involving the histidyl residue in the catalytic triad of alpha-lytic protease in the resting enzyme and in the transition-state or tetrahedral intermediate analogue complexes formed with phenylmethanesulfonyl fluoride and diisopropyl fluorophosphate. The 15N shifts indicate that a strong hydrogen bond links the active site histidine and serine residues in the resting enzyme in solution. This result is at odds with interpretations of the X-ray diffraction data of alpha-lytic protease and of other serine proteases, which indicate that the serine and histidine residues are too far apart and not properly aligned for the formation of a hydrogen bond. In addition, the nitrogen-15 shifts demonstrate that protonation of the histidine imidazole ring at low pH in the transition-state or tetrahedral intermediate analogue complexes formed with phenylmethanesulfonyl fluoride and diisopropyl fluorophosphate triggers the disruption of the aspartate-histidine hydrogen bond. These results suggest a catalytic mechanism involving directed movement of the imidazole ring of the active site histidyl residue.
175 citations
TL;DR: In this article, the low-frequency shoulder of the Raman spectrum of liquid water was developed as a probe of in-phase collective motions in liquid water, and its relative intensity approached that of ice I as the supercooled liquid temperature tends toward the conjectured thermodynamic singularity in the vicinity of -46/sup 0/C.
Abstract: The low-frequency shoulder of the OH stretching Raman spectrum is developed as a probe of in-phase collective motions in liquid water. Its relative intensity approaches that of ice I as the supercooled liquid temperature tends toward the conjectured thermodynamic singularity in the vicinity of -46/sup 0/C. The collective band appears despite the large disorder of the OH stretching frequencies in the liquid compared to the strength of the resonance coupling. The resonance condition required for collective OH motions leads us to conjecture that patches of water molecules with similar hydrogen bond energies, which are capable of sustaining the resonance, appear as water is supercooled toward T/sub s/.
165 citations
TL;DR: Estimates of the net contributions of hydrogen bonds of different types (neutral-neutral and neutral-charged) are essentially identical with those obtained by a complementary approach on the tyrosyl tRNA synthetase-substrate complex.
Abstract: The affinities of a large number of deoxy and fluorodeoxy sugars for the glucose binding site in glycogen phosphorylase have been measured, and polarities and relative strengths of the hydrogen bonds at each position have been predicted on the basis of these data. Comparison with the recently refined X-ray crystal structure of the phosphorylase-glucose complex shows a generally good correlation between predicted and observed bond strengths, vindicating this approach to the evaluation of hydrogen bonding. Estimates of the net contributions of hydrogen bonds of different types (neutral-neutral and neutral-charged) are essentially identical with those obtained by a complementary approach on the tyrosyl tRNA synthetase-substrate complex [Fersht, A. R., Shi, J. P., Knill-Jones, J., Lowe, D. M., Wilkinson, A. J., Blow, D. M., Brick, P., Cortes, P., Waye, M. M. Y., & Winter, G. (1985) Nature (London) 314, 235-238]. The carbohydrate binding site structure determined is compared with that recently determined for the arabinose binding protein.
163 citations
131 citations
TL;DR: The X-ray structure of a monoclinic crystal of 1-methyl-3-ethylimidazolium iodide, [MeEtim]l, reveals the presence of discrete hydrogen-bonded ion-pairs as mentioned in this paper.
Abstract: The X-ray structure of a monoclinic crystal of 1-methyl-3-ethylimidazolium iodide, [MeEtim]l, reveals the presence of discrete hydrogen-bonded ion-pairs [r{C(2)H ⋯ l–}= 0.293 nm]: the structural implications of the presence of hydrogen-bonding in ionic liquids based upon [MeEtim]X–AlX3(X = Cl or Br) mixtures are discussed.
TL;DR: The geometry of hydrogen donor molecules bound to horseradish peroxidase and a hypothetical model of the enzyme structure obtained by computer-aided simulation procedures suggest that the binding of these donor molecules and competitive inhibitors occur in the vicinity of the heme peripheral 8-methyl group.
TL;DR: The topological properties of the charge density of hydrogen-bonded complexes between nitrites and hydrogen chloride correlate linearly with theoretical estimates of the hydrogenbond energy.
TL;DR: A nearest-neighbor model is adequate for prediction of stabilization due to dangling ends and terminal base pairs on the core helix GCGC, and results suggest stacking and hydrogen bonding make roughly comparable favorable contributions to the stability of a terminal base pair.
Abstract: The stabilizing effects of dangling ends and terminal base pairs on the core helix GCGC are reported. Enthalpy and entropy changes of helix formation were measured spectrophotometrically for AGCGCU, UGCGCA, GGCGCCp, CGCGCGp, and the corresponding pentamers XGCGCp and GCGCYp containing the GCGC core plus a dangling end. Each 5' dangling end increases helix stability at 37 degrees C roughly 0.2 kcal/mol and each 3' end from 0.8 to 1.7 kcal/mol. The free energy increments for dangling ends on GCGC are similar to the corresponding increments reported for the GGCC core [Freier, S. M., Alkema, D., Sinclair, A., Neilson, T., & Turner, D. H. (1985) Biochemistry 24, 4533-4539], indicating a nearest-neighbor model is adequate for prediction of stabilization due to dangling ends. Nearest-neighbor parameters for prediction of the free energy effects of adding dangling ends and terminal base pairs next to G.C pairs are presented. Comparison of these free energy changes is used to partition the free energy of base pair formation into contributions of "stacking" and "pairing". If pairing contributions are due to hydrogen bonding, the results suggest stacking and hydrogen bonding make roughly comparable favorable contributions to the stability of a terminal base pair. The free energy increment associated with forming a hydrogen bond is estimated to be -1 kcal/mol of hydrogen bond.
TL;DR: In this paper, a polybutadiene of narrow molecular weight distribution was modified using 4-phenyl-1, 2,4-triazoline-3,5-dione.
Abstract: Polybutadiene of narrow molecular weight distribution was modified using 4-phenyl-1, 2,4-triazoline-3,5-dione. The degree of modification was 1% and 2% with respect to the repeating units. Hydrogen bonding between the highly polar urazole groups thus incorporated into the polymer gives rise to the formation of a thermoreversible elastomeric network. Dynamic mechanical measurements in the temperature range between 220 and 330 K support the picture of the thermoreversible hydrogen bond interaction. The rubber elastic plateau is shifted to higher temperatures and lower frequencies. The increase in the plateau modulus cannot be attributed solely to the contribution of the network structure but is mainly a consequence of the broadening of the relaxation time spectrum in the modified samples. From the temperature dependence of the shift factors log(aT) it is concluded that the general WLF approach fails. The strong temperature dependence of the apparent activation energy of flow is a consequence of the temperature dependence of the hydrogen bond interaction.
TL;DR: The crystal and molecular structure of quercetin, one of the bioflavonoids found in plants, is described in this article, and the structure is of interest because of the variety of biological systems affected by it.
Journal Article•
TL;DR: In this article, the respective values of the chain modulus of elasticity in cellulose I and II were used to determine the conformation of the cellulose chain in the native and regenerated fibers.
Abstract: The respective values of the chain modulus of elasticity in cellulose I and II were used to determine the conformation of the cellulose chain in the native and regenerated fibers, and the number of intramolecular hydrogen bonds in the monomeric unit. -- AATA
TL;DR: Calculated energy of interaction between nitrogen bases of nucleic acid has been calculated as a function of parameters determining the mutual position of two bases and refined atom-atom potential functions are suggested.
Abstract: Energy of interaction between nitrogen bases of nucleic acids has been calculated as a function of parameters determining the mutual position of two bases. Refined atom-atom potential functions are suggested. These functions contain terms proportional to the first (electrostatics), sixth (or tenth for the atoms forming a hydrogen bond) and twelfth (repulsion of all atoms) powers of interatomic distance. Calculations have shown that there are two groups of minima of the base interaction energy. The minima of the first group correspond to coplanar arrangement of the base pairs and hydrogen bond formation. The minima of the second group correspond to the position of bases one above the other in almost parallel planes. There are 28 energy minima corresponding to the formation of coplanar pairs with two (three for the G:C pair) almost linear N-H … O and (or) N-H … N hydrogen bonds. The position of nitrogen bases paired by two such H-bonds in any crystal of nucleic acid component, in polynucleotide com...
TL;DR: In this paper, the solvent in an aqueous solution of two nonpolar atomic solutes which are constrained to an interatomic distance corresponding to a solvent-separated free energy minimum is analyzed.
Abstract: We present a dynamical analysis of the solvent in an aqueous solution of two nonpolar atomic solutes which are constrained to an interatomic distance corresponding to a solvent‐separated free energy minimum. The results are obtained from a molecular dynamics simulation using ST2 model water. Molecular mobility for solvent near the solutes is seen to be retarded, as evidenced in translational diffusion and rotational reorientation. These slower net motions are analogous to pure solvent dynamics at a temperature reduced by 10–15 °C. An analysis of intermolecular hydrogen bonding reveals that solvation shell molecules have correspondingly longer bond half‐lives compared to bulk molecules, by a factor of 1.5–2.0. The spectral densities for intermolecular vibrations are computed from translational and rotational velocity autocorrelation functions for shell and bulk motions. These densities are seen to correlate well with the local binding energy distributions.
TL;DR: The hydrogen-bonded structure of the model agrees with the finding that dodecyl sulfate associates much more readily with proteins than does tetradecyltrimethylammonium chloride.
TL;DR: In this article, the authors investigated the effect of the basis set superposition error on the calculated hydrogen bond energies for a number of water-formamide and methanol−formamide complexes at both SCF and correlated levels.
Abstract: Ab initio calculations of hydrogen bond energies for a number of water–formamide and methanol–formamide complexes are reported at both the SCF and correlated levels. Full gradient optimizations of these structures have been performed for basis sets of double zeta and double zeta plus polarization quality. For both water and methanol, the most stable 1:1 complex is found to be a cyclic double hydrogen bonded structure. Basis set effects on the calculated hydrogen bond energies were investigated as was the magnitude of the basis set superposition error. In all cases investigated, the addition of polarization functions to the basis set is found to decrease the calculated binding energy by approximately 2–4 kcal/mol, while correlation is found to increase the binding energy by ≂1 kcal/mol. Calculations on dihydrated formamide indicate a small three‐body contribution to the total binding energy.
TL;DR: In this paper, X-ray crystallography was used to analyze the properties of the H3PO4 and L-His salt, showing that the strong hydrogen bonding significantly affects the P-O bond strength.
Abstract: Salts of composition Im.H3PO4 and L-His.2H3PO4 were prepared and analyzed by X-ray crystallography. The Im salt forms a rather complicated crystal structure with two chemical formula units in the crystal chemical unit and the crystals of the His salt contain unionized molecular H3PO4. There are networks of short strong hydrogen bonds in both crystals, and the hydrogen bonding noticeably affects the O-atom thermal vibrations. The hydrogenbonding geometries indicate that N-H...O-P and P-O-H...O-P bonds are generally the strongest N-H...O and O-H...O bonds that can form in biochemical systems, and the strong hydrogen bonding significantly affects the P-O bond strengths. Crystal data: L-histidinium dihydrogen orthophosphate 10N302 .H2PO4 .Ha PO4,
TL;DR: In this paper, the influence of variations in each of these parameters on types I, III and IV bonds (and thus also on H phi interactions) was delineated, and the optimal conditions for elution were determined.
TL;DR: In this paper, the room temperature crystal structures of three hydroxy-flavone derivatives have been solved, and the relationships between molecular conformation and solid-state aggregate patterns of 3-hydroxyflavones and related molecules are discussed in terms of possible ground state solute solute-solvent and solvent-solute solution structures.
TL;DR: The experimental and ab initio dissociation energies of the (H2O)n(CH3CN)mH+ ions are reported in this article, and the experimental energies range from 10−35 kcal/mol.
Abstract: Experimental and ab initio dissociation energies of the (H2O)n(CH3CN)mH+ ions are reported. The experimental energies range from 10–35 kcal/mol. The proton is best stabilized by placing the maximum number of acetonitrile molecules close to the protonated center in such a way that the formation of a network of strong hydrogen bonds is still possible. Other results from this work are: (1) Distinct solvent shells can be distinguished in these complex ions. (2) Mixtures of several isomeric structures are unlikely for n≤4. (3) When a water or an acetonitrile molecule clusters with (H2O)(CH3CN)H+, the proton is transferred from the acetonitrile to the water. (4) Although electrostatic interactions make the dominant contribution to the bonding in these systems, polarization and charge‐transfer effects contribute also. (5) There is a cooperativity effect among the hydrogen bonds that leads to extensive changes in geometry and charge distribution as successive hydrogen bonds are formed. (6) The relative complexati...
TL;DR: The ammonium group is completely ordered and linked by one single and several polyfurcated N...O hydrogen bonds varying from 2.800 to 3"498 (5) ~.
Abstract: MgNH4PO4.6H20 (struvite), Mr=245'4, Pmn2, a=6.955(1), b=6.142(1), c=11.218(2)A, V= 479.2 (2) ]k 3, Z = 2, Dx = 1.70 Mg m -3, neutrons, A 1.179/~, /z = 0.03 mm -t, room temperature. The structure was refined from 685 unique neutron diffraction data to R -- 0.032. The ammonium group is completely ordered and linked by one single and several polyfurcated N...O hydrogen bonds varying from 2.800 (5) to 3"498 (5) ~. Six out of eight W...O hydrogen bonds donated by the water molecules are in the range 2.630 (4)-2.649 (5) A. A survey of hydrogen bonds studied by neutron diffraction reveals, on
TL;DR: The crystal structure of N-(n-octyl)-D-gluconamide (space group P21, a = 5.252(1), b = 32.426(9), c = 4.805(1) A, β = 94.96(5)° ) was determined by X-ray diffraction methods and refined to R = 0.046 as mentioned in this paper.