Showing papers on "Hydrogen bond published in 1998"
TL;DR: In this paper, a donor-donor-acceptor−acceptor −acceptor (DDAA) array of hydrogen bonding sites in the 4[1H]-pyrimidinone tautomer was used to preorganize the molecules for dimerization.
Abstract: 6-Methyl-2-butylureidopyrimidone dimerizes via four hydrogen bonds in the solid state as well as in CHCl3 solution via a donor−donor−acceptor−acceptor (DDAA) array of hydrogen bonding sites in the 4[1H]-pyrimidinone tautomer. An intramolecular hydrogen bond from the pyrimidine NH group to the urea oxygen atom preorganizes the molecules for dimerization. The dimerization constant of the dimer in CHCl3 exceeds 106 M-1. In CHCl3 containing DMSO, the dimer is in equilibrium with the monomeric 6[1H]-pyrimidinone tautomer. In 6-phenyl-2-butylureidopyrimidone, the 4[1H]-pyrimidinone tautomer coexists with the pyrimidin-4-ol form, which dimerizes with similar high dimerization constants via four hydrogen bonds in a DADA array. The latter tautomer predominates in derivatives with electronegative 6-substituents, like 6-nitrophenyl- and 6-trifluoromethyl-2-butylureidopyrimidone. Due to its simple preparation and high dimerization constant, the ureidopyrimidone functionality is a useful building block for supramolecu...
673 citations
TL;DR: In this article, the authors show that scalar couplings across the hydrogen bond are observable for 15N-labeled RNA for Watson−Crick base pairs in 15N labeled RNA.
Abstract: Hydrogen bonds play a key role in the stabilization of protein and nucleic acid secondary structure. Currently, most of the experimental evidence for the interaction of hydrogen bond donor and acceptor atoms is indirect. Here we show that scalar couplings across the hydrogen bond are observable for Watson−Crick base pairs in 15N-labeled RNA. These scalar couplings correlate the imino donor 15N nucleus and the corresponding acceptor 15N nucleus on the complementary base. The two-bond JNN couplings between the N3 of uridine and the N1 of adenosine, and between the N1 of guanosine and the N3 of cytidine, have values of approximately 7 Hz as determined by a novel quantitative J-correlation experiment for the 69-nucleotide T1 domain of the potato spindle tuber viroid. In contrast, for non-Watson−Crick base pairs the hydrogen bond acceptor is usually not a nitrogen, but an oxygen atom, and thus, the two-bond JNN couplings are not observed.
587 citations
TL;DR: X-ray diffraction of bacteriorhodopsin crystals grown in cubic lipid phase revealed unexpected two-fold symmetries that indicate merohedral twinning along the crystallographic c axis.
Abstract: Photoisomerization of the retinal of bacteriorhodopsin initiates a cyclic reaction in which a proton is translocated across the membrane. Studies of this protein promise a better understanding of how ion pumps function. Together with a large amount of spectroscopic and mutational data, the atomic structure of bacteriorhodopsin, determined in the last decade at increasing resolutions, has suggested plausible but often contradictory mechanisms. X-ray diffraction of bacteriorhodopsin crystals grown in cubic lipid phase revealed unexpected two-fold symmetries that indicate merohedral twinning along the crystallographic c axis. The structure, refined to 2.3 angstroms taking this twinning into account, is different from earlier models, including that most recently reported. One of the carboxyl oxygen atoms of the proton acceptor Asp85 is connected to the proton donor, the retinal Schiff base, through a hydrogen-bonded water and forms a second hydrogen bond with another water. The other carboxyl oxygen atom of Asp85 accepts a hydrogen bond from Thr89. This structure forms the active site. The nearby Arg82 is the center of a network of numerous hydrogen-bonded residues and an ordered water molecule. This network defines the pathway of the proton from the buried Schiff base to the extracellular surface.
558 citations
TL;DR: It is suggested that a set of well-defined structural elements is required for an interaction with P-glycoprotein, and a high percentage of amino acids with hydrogen bonding donor side chains is found in the transmembrane sequences of P- glycoprotein relevant for substrate interaction.
Abstract: P-glycoprotein actively transports a wide variety of chemically diverse compounds out of the cell. Based on a comparison of a hundred compounds previously tested as P-glycoprotein substrates, we suggest that a set of well-defined structural elements is required for an interaction with P-glycoprotein. The recognition elements are formed by two (type I unit) or three electron donor groups (type II unit) with a fixed spatial separation. Type I units consist of two electron donor groups with a spatial separation of 2.5 +/- 0.3 A. Type II units contain either two electron donor groups with a spatial separation of 4.6 +/- 0.6 A or three electron donor groups with a spatial separation of the outer two groups of 4.6 +/- 0.6 A. All molecules that contain at least one type I or one type II unit are predicted to be P-glycoprotein substrates. The binding to P-glycoprotein increases with the strength and the number of electron donor or hydrogen bonding acceptor groups forming the type I and type II units. Correspondingly, a high percentage of amino acids with hydrogen bonding donor side chains is found in the transmembrane sequences of P-glycoprotein relevant for substrate interaction. Molecules that minimally contain one type II unit are predicted to be inducers of P-glycoprotein over-expression.
526 citations
TL;DR: In this paper, the van't Hoff relationship was used to determine the hydrogen bond enthalpy of the Raman spectra from water in a range of conditions from ambient to above the critical point.
Abstract: The Raman spectrum from water was obtained for a range of conditions from ambient to above the critical point, 256 bar and 400 °C. A fluorescence-free sapphire high-pressure Raman cell was employed with which the Raman spectra from water were examined between 30 and 4000 cm−1. Computer deconvolution of the Raman OH-stretching contours allowed the hydrogen bond strength to be determined from the integrated component intensity ratios by use of the van’t Hoff relationship. This procedure yielded a hydrogen bond enthalpy of 2.53±0.10 kcal/mol which is in excellent agreement with previously reported values.
524 citations
TL;DR: This minireview will explain the original proposal, summarize the experimental data from the past few years, and argue that LBHBs do play important roles in enzymatic reactions.
509 citations
TL;DR: In this paper, the authors define the hydrogen bond as an attractive interaction between two molecular moieties in which at least one of them contains a hydrogen atom that plays a fundamental role.
Abstract: Hydrogen bonds (HBs) are the most important ‘weak’ interactions encountered in solid, liquid and gas phases. The HB can be defined as an attractive interaction between two molecular moieties in which at least one of them contains a hydrogen atom that plays a fundamental role. Classical HBs correspond to those formed by two heteroatoms, A and B, with a hydrogen atom bonded to one of them and located approximately in between (A–H···B). Recently, knowledge of the number of functional groups which act as hydrogen bond donors or acceptors has increased considerably and most of these new groups are discussed.
478 citations
TL;DR: A new empirical scoring function is presented that estimates the free energy of binding for a protein–ligand complex of known 3D structure and is suitable for the application in a 3D database search or de novo ligand design program such as LUDI.
Abstract: A dataset of 82 protein–ligand complexes of known 3D structure and binding constant Ki was analysed to elucidate the important factors that determine the strength of protein–ligand interactions. The following parameters were investigated: the number and geometry of hydrogen bonds and ionic interactions between the protein and the ligand, the size of the lipophilic contact surface, the flexibility of the ligand, the electrostatic potential in the binding site, water molecules in the binding site, cavities along the protein–ligand interface and specific interactions between aromatic rings. Based on these parameters, a new empirical scoring function is presented that estimates the free energy of binding for a protein–ligand complex of known 3D structure. The function distinguishes between buried and solvent accessible hydrogen bonds. It tolerates deviations in the hydrogen bond geometry of up to 0.25 A in the length and up to 30 °Cs in the hydrogen bond angle without penalizing the score. The new energy function reproduces the binding constants (ranging from 3.7 × 10-2 M to 1 × 10-14 M, corresponding to binding energies between -8 and -80 kJ/mol) of the dataset with a standard deviation of 7.3 kJ/mol corresponding to 1.3 orders of magnitude in binding affinity. The function can be evaluated very fast and is therefore also suitable for the application in a 3D database search or de novo ligand design program such as LUDI. The physical significance of the individual contributions is discussed.
452 citations
TL;DR: The use of different basic probe molecules whose IR spectra are sensitive to protonation and/or to the strength of Lewis acid-base interaction is described in this paper, where the results obtained for the characterization of the Lewis acid strength of more than 30 binary and ternary mixed oxides are interpreted on the basis of the different polarizing powers of the involved cations.
435 citations
TL;DR: A new electrostatic model that takes into consideration all electrostatic interactions up to 12 residues in distance in the helix and random-coil conformations, as well as the effect of ionic strength, has been implemented and found that for those peptides correctly predicted from the point of view of circular dichroism, the prediction of the NMR parameters is very good.
432 citations
TL;DR: In this paper, crystallographically characterised hydrogen bonds containing M-Cl, C-Cl or Cl-Cl and either HO or HN groups were analyzed and it was shown that M−Cl moieties are good, anisotropic hydrogen-bond acceptors forming hydrogen bonds similar in length to those of the chloride anion.
TL;DR: The first-order phase transition of water fractions closely associated with the polymer matrix is usually impossible to observe as mentioned in this paper, and these fractions are referred to as non-freezing water, whose melting/crystallization temperature and enthalpy are not significantly different from those of normal (bulk) water.
TL;DR: In this paper, the authors examined the hydrogen bonding between water and a series of small organic molecules via electronic structure calculations and found that acceptor sites corresponded closely to the positions of lone pairs as predicted by simple hybridization arguments.
Abstract: Hydrogen bonding between water and a series of small organic molecules was examined via electronic structure calculations. Several computational methods were examined, including both a hybrid density functional procedure (Becke3LYP) and second-order Moller−Plesset theory (MP2) coupled with a double-ζ basis set augmented by diffuse polarization functions on heteroatoms. The agreement between Becke3LYP and MP2 energies was generally good, as was the agreement with energies obtained using more sophisticated and costly methods. The energies and structures of 53 hydrogen-bonded complexes of water with various small organic molecules, including alcohols, thiols, ethers, thioethers, carboxylic acids, esters, amines, amides, nitriles, and nitro compounds, were then examined systematically using the Becke3LYP and MP2 procedures. The hydrogen bond geometries were generally linear, and acceptor sites corresponded closely to the positions of lone pairs as predicted by simple hybridization arguments. Structures with s...
TL;DR: In this paper, a new type of bonding, termed anti-hydrogen bond, was identified in the benzene dimer and other carbon proton donor complexes from correlated ab initio computations.
Abstract: A new type of bonding, termed anti-hydrogen bond, is identified in the benzene dimer and other carbon proton donor complexes from correlated ab initio computations. Gradient optimization of the benzene dimer at the MP2/6-31G* and MP2/6-31G** levels shows a shortening of the C−H bond of the proton donor and a blue-shift of the corresponding C−H stretching frequency. The harmonic C−H stretching vibrational frequency shift agrees well with that evaluated for various anharmonic approaches. The blue-shift of the C−H stretching frequency was also found in the case of benzene complexes with other carbon proton donors, CH4 and CHCl3. The anti-H-bonds are expected to be very significant for the structure and dynamics of biomolecules.
TL;DR: NMR observation of 15N---15N and 1H--- 15N scalar couplings across the hydrogen bonds in Watson-Crick base pairs in a DNA duplex, hJNN and hJHN represents new parameters of interest for both structural studies of DNA and theoretical investigations into the nature of the hydrogen Bonds.
Abstract: This paper describes the NMR observation of 15N—15N and 1H—15N scalar couplings across the hydrogen bonds in Watson–Crick base pairs in a DNA duplex, hJNN and hJHN. These couplings represent new parameters of interest for both structural studies of DNA and theoretical investigations into the nature of the hydrogen bonds. Two dimensional [15N,1H]-transverse relaxation-optimized spectroscopy (TROSY) with a 15N-labeled 14-mer DNA duplex was used to measure hJNN, which is in the range 6–7 Hz, and the two-dimensional hJNN-correlation-[15N,1H]-TROSY experiment was used to correlate the chemical shifts of pairs of hydrogen bond-related 15N spins and to observe, for the first time, hJHN scalar couplings, with values in the range 2–3.6 Hz. TROSY-based studies of scalar couplings across hydrogen bonds should be applicable for large molecular sizes, including protein-bound nucleic acids.
TL;DR: In this paper, a donor-acceptor-donoracceptor array of four hydrogen-bonding sites is used to pre-organize the molecule for dimerization. But the structure of the compound is unknown.
Abstract: Highly stable dimers are formed in solution and in the solid state by a class of readily synthesized, self-complementary building blocks for supramolecular chemistry, which associate through a donor-acceptor-donor-acceptor array of four hydrogen-bonding sites. An additional intramolecular hydrogen bond in the compound whose crystal structure is shown on the right preorganizes the molecule for dimerization.
TL;DR: Geometrical data on hydrogen bonds to halide ions from the currently available crystal structures are compiled in this paper, where hydrogen bonds from 25 donor types to fluoride, chloride, bromide and iodide ions are considered.
Abstract: Geometrical data on hydrogen bonds to halide ions are compiled from the currently available crystal structures. Hydrogen bonds from 25 donor types to fluoride, chloride, bromide and iodide ions are considered. Compared with earlier compilations, the increased data volume allows a finer subdivision of O—H and N—H donors, and the donors C—H, S—H and P—H can be included. For a given donor type, the hydrogen-bond distance typically increases by over 0.5 A from fluoride to chloride, 0.15 A from chloride to bromide and 0.25 A from bromide to iodide acceptors. The strongest of the C—H donors considered, chloroform, forms hydrogen bonds with chloride ions with an average H⋯Cl separation of only 2.39 A and an average C⋯Cl separation of 3.42 A. The lengthening of the N—H covalent bond in hydrogen bonds to chloride ions is quantified from neutron diffraction data.
TL;DR: In this article, changes in the hydrogen bond network of water in the first hydration shell of urea and guanidinium were analyzed in terms of the random network model using Monte Carlo simulations.
Abstract: The mechanism of the denaturing effects of urea and the guanidinium ion on proteins is still an unsolved and important problem in protein chemistry. Changes in the hydrogen bond network of water in the first hydration shell of urea and guanidinium were analyzed in terms of the random network model using Monte Carlo simulations. Bulk water consists of two populations of hydrogen bonds: a predominantly linear population and a small but significant population of slightly longer and more bent hydrogen bonds. In the first shell of urea, hydrogen bonds between waters solvating the amino groups were shorter and more linear on average than those in bulk water. These changes are caused by a depletion of the more distorted hydrogen bonds. These changes in hydration water structure have previously been seen only around nonpolar solutes of solute groups. Thus urea, being entirely polar, is anomalous in this regard. Hydrogen bonds around guanidinium were longer and more bent than those in bulk water. These distortion...
TL;DR: In this article, an X-ray diffraction investigation has been made of the crystal structure to determine the distribution of hydrogen bonds, to understand the crystalline thermal expansion and to determine influence of water on the polymer crystals and crystallisation process.
TL;DR: In this article, the electronic properties of three-centered hydrogen bonds (HBs) were investigated by means of the atoms in molecules (AIM) approach, and the existence of bifurcated bond paths in the AIM analysis with electron densities was shown.
Abstract: The nature of bifurcated or three-centered hydrogen bonds (HB) has been investigated. Different families of compounds were chosen: monomers with intramolecular three-centered HB, dimers with a HB donor (HBD) and a molecule with two HB acceptor (HBA) groups, and trimers with one HBD and two HBAs. All the systems were optimized at the B3LYP/6-31G* level, and, in the case of the complexes, the interaction energies were evaluated and corrected with the basis set superposition error (BSSE). The electronic nature of these three-centered HBs was analyzed by means of the atoms in molecules (AIM) approach. The present study indicates the existence of bifurcated bond paths in the AIM analysis with electron densities that can be classified as follows: (i) compounds with symmetric three-centered HBs presenting two symmetric bond critical points with equal values of electron density; (ii) compounds with asymmetric three-centered HBs presenting two bond critical points with different values of electron density; (iii)...
TL;DR: In this paper, the authors used the ab initio total energy method based on the gradient-corrected local density approximation to model the experimentally observed water monolayer on the MgO (100) surface and showed that the lateral interactions between the adsorbed water molecules, the formation of hydrogen bonds, and the resulting strong dimerization of the adsorbate promote the dissociation of two out of six water molecules in the surface unit cell.
Abstract: Using the ab initio total energy method based on the gradient-corrected local density approximation we have modeled the experimentally observed ( $3\ifmmode\times\else\texttimes\fi{}2$) water monolayer on the MgO (100) surface. The lateral interactions between the adsorbed water molecules, the formation of hydrogen bonds, and the resulting strong dimerization of the adsorbate promote the dissociation of two out of six water molecules in the surface unit cell. Although, on the theoretical grounds, water dissociation on a defective MgO surface has been already reported, this is the first theoretical evidence of water dissociation on the perfect MgO (100) surface.
TL;DR: In this article, the authors summarize the recent advances in the analysis and interpretation of FT-IR spectra of lipids and lipid mixtures with regard to hydrogen bonding and ion bonding.
TL;DR: The hydrogen-bonded and free OH stretch modes of Cl-(H2O)n (n = 1−5) have been observed by vibrational predissociation spectroscopy in the 2.6−3.2 μm region as mentioned in this paper.
Abstract: The hydrogen-bonded and free OH stretch modes of Cl-(H2O)n (n = 1−5) have been observed by vibrational predissociation spectroscopy in the 2.6−3.2 μm region. Besides demonstrating that all clusters form strong ionic hydrogen bonds, the spectra provide clear evidence of water−water hydrogen-bonding networks in n = 4 and n = 5, with the broad spectrum of n = 5 resembling that of large neutral water clusters. No water−water hydrogen bonding is seen in n = 2 and n = 3, but these clusters appear to be solvated asymmetrically. While the data suggest that Cl- ion is solvated on the surface of water clusters, there are discrepancies between the observed spectra and ab initio predictions. This disagreement may stem from either zero-point motion or high cluster temperature, which tend to disrupt hydrogen bonding among the waters.
TL;DR: It is shown that the rate and selectivity of transport in these membranes is dramatically altered by the chemical identity of the R group, which was accomplished by chemisorbing thiols to the Au tubule surfaces.
Abstract: : We recently described polymeric membranes that contain a collection of monodisperse Au nanotubules with inside diameters of molecular dimensions (<1 nm). W showed that these membranes can be used to cleanly separate small molecules on the basis of molecular size. These membranes can also show charge-based transport selectivity which can be reversible switched between cation and anion-selective states. In addition to molecular size- and charge-based selectivity, chemical interactions (e.g., hydrogen bonding or hydrophobic interactions) between the membrane material and the molecule to be transport can be used to control transport selectivity. The introduction of such chemically-based transport selectivity into the Au nanotubule membranes is described here. This was accomplished by chemisorbing thiols (R-SH) to the Au tubule surfaces. Membranes derivatized with two different R groups - the hydrophobic R = -C16H33 and the more hydrophilic R = -C2H4-OH - were prepared. We show here that the rate and selectivity of transport in these membranes is dramatically altered by the chemical identity of the R group.
TL;DR: In this paper, reflection absorption infrared spectroscopy (RAIRS) was used to investigate the chemisorption of glycine and its fully deuterated analogue d 5 -glycine, vacuum deposited on a clean Cu{110} surface.
TL;DR: The C2H4N4O4 is a high explosive with high performance and low sensitivity as mentioned in this paper, which is a variant of push-pull ethylene with two intramolecular hydrogen bonds between the nitro-O atoms and the amino-H atoms.
Abstract: The title compound (C2H4N4O4) is a novel and interesting high explosive with high performance and low sensitivity. Single-crystal X-ray diffraction studies of the compound show that the molecules in the crystal structure have bond lengths and bond angles as expected for this type of push–pull ethylene. There are two intramolecular hydrogen bonds present between the nitro-O atoms and the amino-H atoms. The geometry of the molecule indicates that there is extensive π conjugation present. The molecular packing is built up by infinite two-dimensional wave-shaped layers, with extensive intermolecular hydrogen bonding within the layers and ordinary van der Waals interactions between the layers. The crystal packing explains some of the physico–chemical properties of the compound such as the absence of a melting point, its low solubility and its low sensitivity to friction and impact compared with the common high explosive RDX (1,3,5-triaza-1,3,5-trinitrocyclohexane).
TL;DR: In this article, first-principles calculations based on density-functional theory and the pseudopotential method are used to investigate the energetics of adsorption of the series of molecules H 2 O, CH 3 OH, H 2O 2 and HCO 2 H on the TiO 2 (110) surface.
TL;DR: In this article, the authors provide an overview of a range of experimental studies from this laboratory in which the structure, orientation, and hydrogen bonding of interfacial water molecules at liquid interfaces are directly probed by resonant vibrational sum frequency spectroscopy.
Abstract: The structure and hydrogen bonding of water molecules provides this unique solvent with properties essential to many physical, chemical, and biological processes. The intermolecular hydrogen bonding between water molecules in the bulk medium is disrupted at the surface, imparting the surface with unique structural and thermodynamic properties. We provide an overview of a range of experimental studies from this laboratory in which the structure, orientation, and hydrogen bonding of interfacial water molecules at liquid interfaces are directly probed by resonant vibrational sum frequency spectroscopy. The studies provide insight into the difference in water structure and hydrogen bonding at an air/water interface relative to the interface between two bulk immiscible liquids, namely the CCl4/H2O interface. Also described are studies aimed at understanding how the presence of a charged alkyl surfactant alters the structure of water at these two interfaces. In both cases field-induced alignment of water molecu...