Showing papers on "Hydrogen bond published in 1997"

An Introduction to Hydrogen Bonding

Abstract: 1. Brief History 2. Nature and Properties 3. Strong Hydrogen Bonds 4. Moderate Hydrogen Bonds 5. Weak Hydrogen Bonds 6. Cooperativity, Patterns, Graph Set Theory, Liquid Crystals 7. Disorder, Proton Transfer, Isotope Effect, Ferroelectrics, Transitions 8. Water, Water Dimers, Ices, Hydrates 9. Inclusion Compounds 10. Hydrogen Bonding in Biological Molecules 11. Methods

Reversible Polymers Formed from Self-Complementary Monomers Using Quadruple Hydrogen Bonding

Abstract: Units of 2-ureido-4-pyrimidone that dimerize strongly in a self-complementary array of four cooperative hydrogen bonds were used as the associating end group in reversible self-assembling polymer systems. The unidirectional design of the binding sites prevents uncontrolled multidirectional association or gelation. Linear polymers and reversible networks were formed from monomers with two and three binding sites, respectively. The thermal and environmental control over lifetime and bond strength makes many properties, such as viscosity, chain length, and composition, tunable in a way not accessible to traditional polymers. Hence, polymer networks with thermodynamically controlled architectures can be formed, for use in, for example, coatings and hot melts, where a reversible, strongly temperature-dependent rheology is highly advantageous.

Spectroscopic characterization of interactions between PVP and indomethacin in amorphous molecular dispersions.

Abstract: Purpose. To study the molecular structure of indomethacin-PVP amorphous solid dispersions and identify any specific interactions between the components using vibrational spectroscopy.

Molecular-Level Processing of Conjugated Polymers. 4. Layer-by-Layer Manipulation of Polyaniline via Hydrogen-Bonding Interactions

Abstract: The molecular-level layer-by-layer processing of polyaniline with a variety of different nonionic water soluble polymers has been demonstrated. This new type of layer-by-layer adsorption process is driven by hydrogen-bonding interactions and has been accomplished with poly(vinylpyrrolidone), poly(vinyl alcohol), poly(acrylamide), and poly(ethylene oxide). FTIR spectroscopy measurements confirm a high level of hydrogen bonding between polyaniline and the nonionic polymer in the multilayer films. The effects of solution pH and polymer molecular weight on the deposition process were investigated. Comparisons with polyaniline films assembled via an electrostatic mechanism with sulfonated polystyrene indicate that the nonionic polymers adsorb onto polyaniline with a greater density of loops and tails and form highly interpenetrated bilayers with a high polyaniline content. The conductivities of these self-assembled multilayer films were found to be on the order of 1−4 S/cm for films doped with methane sulfonic...

Organic Fluorine Hardly Ever Accepts Hydrogen Bonds

Abstract: Statistical analysis of structural data and detailed inspection of individual crystal structures culled from the Cambridge Structural Database and the Brookhaven Protein Data Bank show that covalently bound fluorine (in contrast to anionic fluoride) hardly ever acts as a hydrogen-bond acceptor. The weakness of covalently bound fluorine as hydrogen-bond acceptor is backed by results of new molecular orbital calculations on model systems using ab initio intermolecular perturbation theory (IMPT), and is in accord with results of other physicochemical studies and with the physical properties of fluorinated organic compounds. Factors influencing the strength of hydrogen bonding in extended systems are discussed.

Strong hydrogen bonds in chemistry and biology

Abstract: Hydrogen bonds are a key feature of chemical structure and reactivity. Recently there has been much interest in a special class of hydrogen bonds called "strong" or "low-barrier" and characterized by great strength, short distances, a low or vanishing barrier to hydrogen transfer, and distinctive features in the NMR spectrum. Although the energy of an ordinary hydrogen bond is ca 5 kcal mol-1, the strength of these hydrogen bonds may be > or = 10 kcal mol-1. The properties of these hydrogen bonds have been investigated by many experimental techniques, as well as by calculation and by correlations among those properties. Although it has been proposed that strong, short, low-barrier hydrogen bonds are important in enzymatic reactions, it is concluded that the evidence for them in small molecules and in biomolecules is inconclusive.

Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein

Abstract: The 2.1-A resolution crystal structure of wild-type green fluorescent protein and comparison of it with the recently determined structure of the Ser-65 → Thr (S65T) mutant explains the dual wavelength absorption and photoisomerization properties of the wild-type protein. The two absorption maxima are caused by a change in the ionization state of the chromophore. The equilibrium between these states appears to be governed by a hydrogen bond network that permits proton transfer between the chromophore and neighboring side chains. The predominant neutral form of the fluorophore maximally absorbs at 395 nm. It is maintained by the carboxylate of Glu-222 through electrostatic repulsion and hydrogen bonding via a bound water molecule and Ser-205. The ionized form of the fluorophore, absorbing at 475 nm, is present in a minor fraction of the native protein. Glu-222 donates its charge to the fluorophore by proton abstraction through a hydrogen bond network, involving Ser-205 and bound water. Further stabilization of the ionized state of the fluorophore occurs through a rearrangement of the side chains of Thr-203 and His-148. UV irradiation shifts the ratio of the two absorption maxima by pumping a proton relay from the neutral chromophore’s excited state to Glu-222. Loss of the Ser-205–Glu-222 hydrogen bond and isomerization of neutral Glu-222 explains the slow return to the equilibrium dark-adapted state of the chromophore. In the S65T structure, steric hindrance by the extra methyl group stabilizes a hydrogen bonding network, which prevents ionization of Glu-222. Therefore the fluorophore is permanently ionized, causing only a 489-nm excitation peak. This new understanding of proton redistribution in green fluorescent protein should enable engineering of environmentally sensitive fluorescent indicators and UV-triggered fluorescent markers of protein diffusion and trafficking in living cells.

On the quantum nature of the shared proton in hydrogen bonds

Abstract: The relative influence of thermal and quantum fluctuations on the proton transfer properties of the charged water complexes H5O2+ and H3O2− was investigated with the use of ab initio techniques. These small systems can be considered as prototypical representatives of strong and intermediate-strength hydrogen bonds. The shared proton in the strongly hydrogen bonded H5O2+ behaved in an essentially classical manner, whereas in the H3O2− low-barrier hydrogen bond, quantum zero-point motion played a crucial role even at room temperature. This behavior can be traced back to a small difference in the oxygen-oxygen separation and hence to the strength of the hydrogen bond.

Hydrogen bonds and salt bridges across protein-protein interfaces.

Abstract: To understand further, and to utilize, the interactions across protein-protein interfaces, we carried out an analysis of the hydrogen bonds and of the salt bridges in a collection of 319 non-redundant protein-protein interfaces derived from high-quality X-ray structures. We found that the geometry of the hydrogen bonds across protein interfaces is generally less optimal and has a wider distribution than typically observed within the chains. This difference originates from the more hydrophilic side chains buried in the binding interface than in the folded monomer interior. Protein folding differs from protein binding. Whereas in folding practically all degrees of freedom are available to the chain to attain its optimal configuration, this is not the case for rigid binding, where the protein molecules are already folded, with only six degrees of translational and rotational freedom available to the chains to achieve their most favorable bound configuration. These constraints enforce many polar/charged residues buried in the interface to form weak hydrogen bonds with protein atoms, rather than strongly hydrogen bonding to the solvent. Since interfacial hydrogen bonds are weaker than the intra-chain ones to compete with the binding of water, more water molecules are involved in bridging hydrogen bond networks across the protein interface than in the protein interior. Interfacial water molecules both mediate non-complementary donor-donor or acceptor-acceptor pairs, and connect non-optimally oriented donor-acceptor pairs. These differences between the interfacial hydrogen bonding patterns and the intra-chain ones further substantiate the notion that protein complexes formed by rigid binding may be far away from the global minimum conformations. Moreover, we summarize the pattern of charge complementarity and of the conservation of hydrogen bond network across binding interfaces. We further illustrate the utility of this study in understanding the specificity of protein-protein associations, and hence in docking prediction and molecular (inhibitor) design.

Infrared, Raman, and Near-Infrared Spectroscopic Evidence for the Coexistence of Various Hydrogen-Bond Forms in Poly(acrylic acid)

Abstract: Fourier-transform infrared (FT-IR), near-infrared (NIR)-excited FT-Raman, and FT-NIR spectra have been measured for poly(acrylic acid) (PAA) in a cast film over a temperature range of 40−140 °C, to investigate structures of hydrogen bonds and their dissociation. The CO stretching bands in the FT-IR spectra are unraveled by a prevalent multiple species model for small aliphatic acids with various kinds of associated forms of carboxylic acid groups, namely cyclic dimer, linearly associated oligomers of COOH, and free COOH groups. These different structures of hydrogen bond persist even when the temperature rises well above the glass transition temperature. The FT-Raman spectra confirm the existence of such COOH groups. Temperature-dependent intensity changes in the first overtone of an OH stretching mode of PAA reveal that the COOH groups dissociate significantly at high temperatures. We propose that the coexistence of various possible hydrogen-bond forms analogous to those in small aliphatic acids best int...

Photo-induced electron and energy transfer in non-covalently bonded supramolecular assemblies

Abstract: Covalently linked chromophore–quencher complexes are widespread in the area of transition-metal photochemistry and as models for photosynthesis. This review surveys recent examples of supramolecular complexes in which interacting chromophore and quencher fragments are instead held together by non-covalent interactions such as hydrogen bonding, aromatic π-stacking, hydrophobic interactions and labile metal–ligand coordinate bonds. The use of these methods to assemble multi-component photo-active complexes has led to the preparation of many highly sophisticated systems for energy transfer or charge separation which would not be accessible by ‘conventional’ synthetic methodology.

A new approach for the fabrication of an alternating multilayer film of poly(4-vinylpyridine) and poly(acrylic acid) based on hydrogen bonding

Abstract: A new approach for the fabrication of a multilayer film assembly is explored, which is based on the alternating assembling of poly(4-vinylpyridine) and poly(acrylic acid) via hydrogen bonding. The homogeneous multilayer films were characterized by UV-Vis, X-ray diffraction and atomic force microscopy (AFM) measurements. The nature of interaction between the two polymers is identified as hydrogen bonding by IR spectroscopy.

The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding

Abstract: We have previously studied the ability of various structural descriptors to distinguish between biologically active and inactive compounds (ref 1). This paper examines the degree to which these descriptors encode information relevant to the forces of ligand-receptor binding, namely hydrophobic, dispersion, electrostatic, steric, and hydrogen bonding interactions. This is assessed by the ability to accurately predict values for physical properties of a structure related to each of the interactions, from the known values for other structures which are shown to be structurally similar to the first by the descriptor in question. Our results suggest that the differences we observed in the ability of descriptors to separate active from inactive molecules may be explained by the degree to which they encode information relevant to ligand-receptor binding. In particular we found that the MACCS structural key descriptor implicitly contains a great deal of information relevant to each type of interaction.

Cosmetic composition containing thickening agent of siloxane polymer with hydrogen-bonding groups

Abstract: An invention is disclosed which comprises gelling agents which (1) contain both siloxane groups and hydrogen-bonding groups to thicken compositions containing silicone fluids (volatile and/or non-volatile silicone fluids); (2) are non-flowable solids at room temperature; and (3) dissolve in a fluid which contains silicone at a temperature of 25-250 degrees C to form a translucent or clear solution at a temperature in this range. Cosmetic compositions may be made by adding at least one active ingredient such as an antiperspirant.

Myoglobin discriminates between O2, NO, and CO by electrostatic interactions with the bound ligand

Abstract: Most biological substrates have distinctive sizes, shapes, and charge distributions which can be recognized specifically by proteins. In contrast, myoglobin must discriminate between the diatomic gases O2, CO, and NO which are apolar and virtually the same size. Selectivity occurs at the level of the covalent Fe-ligand complexes, which exhibit markedly different bond strengths and electrostatic properties. By pulling a water molecule into the distal pocket, His64(E7)1 inhibits the binding of all three ligands by a factor of ∼10 compared to that observed for protoheme-imidazole complexes in organic solvents. In the case of O2 binding, this unfavorable effect is overcome by the formation of a strong hydrogen bond between His64(E7) and the highly polar FeO2 complex. This favorable electrostatic interaction stabilizes the bound O2 by a factor of ∼1000, and the net result is a 100-fold increase in overall affinity compared to model hemes or mutants with an apolar residue at position 64. Electrostatic interaction between FeCO and His64 is very weak, resulting in only a two- to three-fold stabilization of the bound state. In this case, the inhibitory effect of distal pocket water dominates, and a net fivefold reduction in K CO is observed for the wild-type protein compared to mutants with an apolar residue at position 64. Bound NO is stabilized ∼tenfold by hydrogen bonding to His64. This favorable interaction with FeNO exactly compensates for the tenfold inhibition due to the presence of distal pocket water, and the net result is little change in K NO when the distal histidine is replaced with apolar residues. Thus, it is the polarity of His64 which allows discrimination between the diatomic gases. Direct steric hindrance by this residue plays a minor role as judged by: (1) the independence of K O2, K CO, and K NO on the size of apolar residues inserted at position 64, and (2) the observation of small decreases, not increases, in CO affinity when the mobility of the His64 side chain is increased. Val68(E11) does appear to hinder selectively the binding of CO. However, the extent is no more than a factor of 2–5, and much smaller than electrostatic stabilization of bound O2 by the distal histidine.

Molecular and Crystal Structure of Hydrated Chitosan

Abstract: The molecular and crystal structure of the hydrated form of chitosan, which was obtained by deacetylation of chitin from crab tendon, was determined by the X-ray fiber diffraction method and the linked-atom least-squares method. The chitosan chains crystallize in an orthorhombic unit cell with dimensions a = 8.95(4), b = 16.97(6), c (fiber axis) = 10.34(4) A and a space group P212121. The chain conformation is a 2-fold helix stabilized by O3---O5 hydrogen bond with the gt orientation of O6. The unit cell contains four chains and eight water molecules. There are direct hydrogen bonds (N2---O6) between adjacent chains along the b-axis, which makes a sheet structure parallel to the bc-plane. These sheets stack along the a-axis. Each sheet is related to its neighboring sheet by 21-symmetry along the b-axis. Water molecules form columns between these sheets and contribute to stabilize the structure by making water-bridges between polymer chains.

Two Dimensional Ice Adsorbed on Mica Surface

Abstract: First principles molecular dynamics simulations have been performed on water adsorption at the surface of muscovite mica. At monolayer coverage we found water to condense into a fully connected two dimensional hydrogen bond network, which we denote as 2D ice. The structure is stable up to 300 K and it is proposed as a candidate for the solidlike structure recently detected in scanning polarization force microscopy on the hydrated muscovite surface at room temperature [Hu et al., Science 268, 267 (1995)].

Theoretical treatments of hydrogen bonding

Abstract: The Hydrogen Bond: An Electrostatic Interaction? (A. Buckingham). Ab Initio Methods Applied to Hydrogen-Bonded Systems (J. de Rejdt & F. van Duijneveldt). Density Functional Theory and its Application to Hydrogen-Bonded Systems (H. Guo, et al.). Ab Initio GIAO Magnetic Shielding Tensor for Hydrogen-Bonded Systems (J. Hinton & K. Wolinski). Hydrogen Bonding by Semiempirical Molecular Orbital Methods (D. Hadzi & J. Koller). Simulating Proton Transfer Processes: Quantum Dynamics Embedded in a Classical Environment (H. Berendsen & J. Mavri). Theory of Solvent Effects and the Description of Chemical Reactions: Proton and Hydride Transfer Processes (O. Tapia, et al.). Infrared Spectra of Hydrogen Bonds: Basic Theories, Indirect and Direct Relaxation Mechanisms in Weak Hydrogen-Bonded Systems (O. Henri-Rousseau & P. Blaise). Infrared Pump-Probe Spectroscopy of Water on Pico- and Subpicosecond Time Scales (S. Bratos & A. Laubereau). Hydrogen Bonding and Nuclear Magnetic Relaxation in Liquids (H. Hertz). Collective Behavior of Hydrogen Bonds in Ferroelectrics and Proton Glasses (R. Blinc & R. Pirc). Computational Experiments on Hydrogen-Bonded Systems: From Gas Phase to Solutions (E. Clementi & G. Corongiu). Epilogue: On Hydrogen-Bond Computations in Very Large Chemical Systems (E. Clementi). Indexes. List of Compounds and Hydrogen-Bonded Systems.

Are there hydrogen bonds in supercritical water

Abstract: The proton NMR chemical shift has been measured for water from 25 to 600 °C and from 1 to 400 bar, conditions extending well beyond the critical point. Dilute solutes were employed as chemical shift references to avoid the effect of the varying magnetic susceptibility. The large changes in chemical shift (4.1 ppm) are interpreted as changes in the hydrogen bond network, because all other intermolecular interactions are known to result in much smaller effects. Using a linear relation between chemical shift and the mean number of hydrogen bonds, the NMR results show there are still 29% as many hydrogen bonds at 400 °C and 400 bar (ρ = 0.52 g/cm3 ) as for room temperature water. The present results are compared to other measurements and calculations.

Excited-State Processes in 8-Hydroxyquinoline: Photoinduced Tautomerization and Solvation Effects

Abstract: 8-Hydroxyquinoline (8-HQ), referred as to oxine in analytical chemistry, is a fluorogenic ligand. Its lack of fluorescence in water and alkanes, and its low quantum yield in many other organic solvents, are rationalized in the present study in terms of photoinduced formation of a nonfluorescent tautomeric form 8-HQ(T*). In water, intermolecular proton transfers with surrounding water molecules are expected, but intrinsic intramolecular proton transfer between the −OH and ⩾N functions cannot be ruled out because the presence of a weak internal H bond can be inferred from the ground-state properties of 8-HQ such as pKa values or solubility. In organic solvents, vapor pressure osmometry measurements in conjunction with infrared spectra allow us to show that (i) in alkane solvents, a very stable dimer is formed in the ground state (Kdim = 7 × 107 at 25 °C); biprotonic concerted proton transfers are then expected to occur within the dimer upon excitation, as was previously reported for 7-azaindole; (ii) in chl...

Novel Folding Patterns in a Family of Oligoanthranilamides: Non-Peptide Oligomers That Form Extended Helical Secondary Structures

Abstract: Anthranilamide derivatives are used as the basis for a series of novel oligomers that fold into helical secondary structures in the solid state. When combined with pyridine-2,6-dicarboxylic acid and 4,6-dimethoxy-1,3-diaminobenzene subunits, oligoanthranilamides can be induced to take up a coiled conformation corresponding to two turns of a helix. X-ray crystallography shows that intramolecular hydrogen bonding and π−π stacking interactions are important in stabilizing the extended helical structures. Furthermore, both experimental and calculated 1H NMR methods indicate that related conformations are taken up by the oligomers in chloroform solution.

Theoretical Calculation of Substituent Effects on the O−H Bond Strength of Phenolic Antioxidants Related to Vitamin E

Abstract: Calculations on phenol and a large number of phenols substituted with methyl, methoxyl, and amino groups have yielded reliable gas-phase O−H bond dissociation energies, BDE(ArO−H)gas. Geometries for the phenol, ArOH, and aryloxyl radical, ArO, were optimized at the (semiempirical) AM1 level followed by single point density functional theory (DFT) calculations using a 6-31G basis set supplemented with p-functions on the hydrogen atom and the B3LYP density functional. This gave BDE(PhO−H)gas = 86.46 kcal/mol, which is in good agreement with the experimental value of 87.3 ± 1.5 kcal/mol. All but one of the compounds and conformations examined had weaker O−H BDE's than phenol, the exception being o-methoxyphenol with the O−H group pointing toward this substituent (BDE = 87.8 kcal/mol). Where comparison was possible, calculated differences in O−H BDE's were in excellent agreement with experiment (better than 1 kcal/mol). A simple group additivity scheme also gave excellent agreement with calculated BDE (ArO−H)...