Showing papers on "Hydrogen bond published in 1985"
TL;DR: The crystal structure of Pseudomonas putida cytochrome P-450cam in the ferric, camphor bound form has been determined and partially refined to R = 0.23 at 2.6 A.
783 citations
513 citations
TL;DR: The results are remarkable in that the charged oxygen atoms of the sulphate molecule, which is buried and completely inaccessible to the solvent, are not stabilized by the formation of salt-bridges but by hydrogen bonds donated by specific residues of the protein.
Abstract: An important question in understanding substrate binding by proteins is how charged groups are stabilized in the absence of their solvation shell. We have addressed this question here by solving the structure of the sulphate-binding protein of Salmonella typhimurium with bound substrate at 2.0 A resolution. The results are remarkable in that the charged oxygen atoms of the sulphate molecule, which is buried and completely inaccessible to the solvent, are not stabilized by the formation of salt-bridges but by hydrogen bonds donated by specific residues of the protein. These hydrogen bonds are in turn coupled via peptide units to several resonating hydrogen bonding systems. These findings may be of general significance for the role of electrostatic interactions in protein structure and function.
414 citations
TL;DR: Comparison of the backbone and deoxyribose ring torsion angles with those found by previous (nuclear magnetic resonance spectroscopy) studies of this adduct in solution demonstrates that the solid state geometry is substantially the same as that in solution.
Abstract: Crystals of the adduct of the anticancer drug cis-diamminedichloroplatinum(II), cis-DDP, with d(pGpG), its putative target on DNA in the cancer cell, have been obtained and used in an x-ray crystallographic study to elucidate the molecular structure to atomic resolution. Each of the four crystallographically independent cis-[Pt(NH3)2(d(pGpG))] molecules is comprised of a square-planar platinum atom bonded to two ammonia ligands and two N(7) atoms of guanosine nucleosides from the same chain. Base stacking of the two adjacent guanine rings is completely disrupted by coordination to the cis-(Pt(NH3)2)2+ unit. Comparison of the backbone and deoxyribose ring torsion angles with those found by previous (nuclear magnetic resonance spectroscopy) studies of this adduct in solution demonstrates that the solid state geometry is substantially the same as that in solution. The relevance of these results to the molecular mechanism of action of cis-DDP is discussed.
373 citations
TL;DR: Higher charge, specific fitting of more hydrogen bonds, and a more stable complex all contribute to the great effectiveness of [Co(NH3)6]3+ in stabilizing Z-DNA.
Abstract: In the equilibrium between B-DNA and Z-DNA in poly(dC-dG), the [Co(NH3)6]3+ ion stabilizes the Z form 4 orders of magnitude more effectively than the Mg2+ ion. The structural basis of this difference is revealed in Z-DNA crystal structures of d(CpGpCpGpCpG) stabilized by either Na+/Mg2+ or Na+/Mg2+ plus [Co(NH3)6]3+. The crystals diffract X-rays to high resolution, and the structures were refined at 1.25 A. The [Co(NH3)6]3+ ion forms five hydrogen bonds onto the surface of Z-DNA, bonding to a guanine O6 and N7 as well as to a phosphate group in the ZII conformation. The Mg2+ ion binds through its hydration shell with up to three hydrogen bonds to guanine N7 and O6. Higher charge, specific fitting of more hydrogen bonds, and a more stable complex all contribute to the great effectiveness of [Co(NH3)6]3+ in stabilizing Z-DNA.
221 citations
TL;DR: In this article, potential functions for water-water and water-ion interactions were developed to model nonadditive or many body effects, which were used to estimate solvation enthalpies and coordination numbers for several ionic species Na+, K+, Mg++, and Cl−.
Abstract: We have developed potential functions for water–water and water–ion interactions that include terms to model nonadditive or many body effects. Using these potential functions, we have obtained good agreement with experimental results for gas phase and condensed phase water calculations and excellent results for gas phase ion hydration enthalpies. Some gas phase ion–water cluster display unusual geometries such as the sodium complex with six waters, where four water molecules bind directly to sodium and the two remaining water molecules form hydrogen bonds with the first four water molecules. The chloride complex with four waters is also interesting in that all four waters cluster on the same side of the anion and form weak hydrogen bonds with each other in addition to the linear hydrogen bond each forms with the anion. We have also used the potentials to estimate solvation enthalpies and coordination numbers for several ionic species Na+, K+, Mg++, and Cl−, again obtaining good overall agreement with expe...
218 citations
185 citations
TL;DR: The structure of alpha-lytic protease, a serine protease produced by the bacterium Lysobacter enzymogenes, has been refined at 1.7 A resolution and showed that basic folding pathways are maintained despite chemical changes in the hydrophobic cores.
173 citations
171 citations
TL;DR: The crystal structure of both complexes was solved by X-ray diffraction to near-atomic resolution and a functional description of the various amino acids in quinoxaline antibiotics is given, together with possible modifications that might affect biological activity.
Abstract: Two members of the quinoxaline antibiotic family, echinomycin and triostin A, form crystals complexed to a DNA fragment with the sequence d(CpGpTpApCpG). The crystal structure of both complexes was solved by X-ray diffraction to near-atomic resolution. The two structures are similar to each other with differences in some details due to the shorter cross bridge of echinomycin. Both molecules act as bis intercalators surrounding the d(CpG) sequence at either end of the double helix. Alanine forms sequence-specific hydrogen bonds to guanines in the minor groove. The two central AT base pairs are held together by Hoogsteen base pairing with adenine in the syn conformation in both complexes. An octahedrally hydrated magnesium ion is found in the crystal lattice that plays an important role in organizing the lattice as well as stabilizing the complex by hydrogen bonding both to base pairs of DNA and to the quinoxaline ring nitrogen atoms in the major groove side of the DNA double helix. A functional description of the various amino acids in quinoxaline antibiotics is given, together with possible modifications that might affect biological activity.
169 citations
TL;DR: In this paper, the secondary structures of α-, β-, y- and ω-gliadins were studied by circular dichroism spectroscopy, and it was shown that α-helix and β-sheet are not stabilised by strong hydrophobic interactions.
TL;DR: The ordering of intra‐ and intermolecular hydrogen bonds involving peptide CO groups in collagen and related compounds was discussed and the interpretation of the amide I multicomponent structure in collagenand isomorphous oligo‐ and polypeptides was attempted.
Abstract: The infrared amide I band of collagens (rat and cod skin) and related compounds (polyproline, polyglycine, and polytripeptides) was studied. Assignment of amide I-band components for polyproline II and polytripeptides (Gly-Pro-Pro)n and (Gly-Pro-Gly)n in the solid state and water solution was made. Three amide I components observed in the polypeptide spectra were attributed to three different peptide CO groups in each triplet. On the basis of this assignment, the interpretation of the amide I multicomponent structure in collagen and isomorphous oligo- and polypeptides was attempted. The ordering of intra- and intermolecular hydrogen bonds involving peptide CO groups in collagen and related compounds was discussed.
TL;DR: The unusual mode of domain-domain association in the VL-VL dimer RHE correlates with its overall repulsive electrostatic energy, as opposed to negative energy values found in the domains of the other structures.
Abstract: Antigen-combining site arises by noncovalent association of the variable domain of the immunoglobulin heavy chain (VH) with that of the light chain (VL). To analyze the invariant features of the binding region (VL-VH domain interface), we compared the known immunoglobulin three-dimensional structures by a variety of methods. The interface forms a close-packed, twisted, prism-shaped "beta-barrel" characterized by cross-sectional dimensions 1.04 X 0.66 nm and a top-to-bottom twist angle of 212 degrees. The geometry of the interface is preserved via invariance of some 15 side chains, both inside the domains and on their surface. Buried polar residues form a conserved hydrogen-bonding network that has a similar topological connectivity in the two domain types; two hydrogen bonds contributed by invariant side chains extend across the interface and anchor the beta-sheets in their relative orientation. Invariant aromatic residues close-pack at the bottom of the binding-site beta-barrel with their ring planes oriented perpendicularly in the characteristic "herringbone" packing mode. Electrostatic computations that implicitly include solvent effects show the domains to be stabilized by large electrostatic forces. However, structures that were crystallized at lower pH have their electrostatic energies appropriately lowered, implying that full ionization of carboxyl side chains is essential for efficient electrostatic stabilization. The unusual mode of domain-domain association in the VL-VL dimer RHE correlates with its overall repulsive electrostatic energy (+54 kJ/mol), as opposed to negative (i.e., stabilizing) energy values (-263 to -543 kJ/mol) found in the domains of the other structures. The VL-VL dimer REI mimics closely the interface geometry of VL-VH dimers although its domain-domain contact area is lower by 18%.
TL;DR: In this article, the mechanistic, kinetic and thermodynamic aspects of C H bond activation at metal centers were analyzed and it was concluded that thermodynamic constraints, notably those associated with the characteristic weakness of metal carbon bonds, are of dominant importance in limiting the reactivities of metal complexes toward C H bonds.
TL;DR: In this article, the chemistry and pharmacology and physicochemical properties of barbiturates, along with the tautomerism and solvation of the Barbituric acid ring are discussed.
Abstract: Publisher Summary This chapter provides information on the chemistry and pharmacology and physicochemical properties of barbiturates, along with the tautomerism and solvation of the barbituric acid ring. Barbituric acid exists in the solid state in the trioxo structure. NMR investigation of the oxo-hydroxy equilibrium indicates that only the oxo form is present in a solution in anhydrous DMSO. Several spectral properties of the barbituric acid are discussed using UV spectra, infrared and Raman spectroscopy, 1 H-NMR spectroscopy, 13 C-NMR spectroscopy, and mass spectrometry. In the crystalline state, barbiturates show several modes of intermolecular hydrogen bonding, which differ by the number of hydrogen bonds formed between the NH and CO groups. These hydrogen bonds are responsible for layer packing in the crystal lattice. Weak intermolecular van der Waals interactions of carbonyl groups are also responsible for the three-dimensional packing of the molecules in the crystal structure.
TL;DR: In this article, an analysis of the hydrogen bonding in 76 nucleoside and 11 nucleotide crystal structures was performed, and it was shown that the hydrogen bond lengths fall into well-defined categories according to the nature of the donor or acceptor groups.
TL;DR: Gel formation and the typical morphology of the gels are discussed as arising mainly from strong intermolecular hydrogen bonds between amide linkages holding the molecules together and the influence of chiral centers of the carbohydrate chain which might be responsible for helical aggregates to be formed.
TL;DR: In this paper, Bader et al. showed that the generalization of the bond-length-bond-order relationship of CC bonds may be extended to intermolecular hydrogen bonding.
TL;DR: In this article, the Gibbs free energies of transfer of gaseous solutes, nonelectrolytes, and ions from light to heavy water are interpreted in terms of the average number of hydrogen bonds broken or made in the water per particle of solute.
Abstract: The solvation of a particle in water, whether a ‘‘foreign’’ particle or a molecule of water, is expressed in terms of a non‐hydrogen‐bonding contribution to the pair potential and a contribution from hydrogen bonding. Only the latter depends on whether the water is H2O or D2O, since the hydrogen bond energy differs in these kinds of water. The effect of the isotopic constitution of the water on the solvation is examined for the cases of an inert solute, a water molecule, and a hydrogen‐bond‐forming solute. The average number of hydrogen bonds in which any water molecule in pure water participates is deduced from the Gibbs free energy and the enthalpy of condensation of H2O, D2O, and T2O molecules into the respective liquids. This number decreases from about 0.95 at 0 °C to about 0.35 at 100 °C, being a few percent higher in D2O than in H2O. The Gibbs free energies of transfer of gaseous solutes, nonelectrolytes, and ions from light to heavy water are interpreted in terms of the average number of hydrogen bonds broken or made in the water per particle of solute.
TL;DR: In this article, the molecular structure of γ-aminopropyltriethoxysilane (γ-APS) coupling agent was studied on silicon powder by diffuse reflectance Fourier Transform Infrared (FT-IR) spectroscopy.
TL;DR: The crystal structure of aspirin has been redetermined by X-ray diffraction analysis at room temperature by taking account of the non-rigidity of the molecule and applying the condition of vanishing stress.
Abstract: The crystal structure of aspirin has been redetermined by X-ray diffraction analysis at room temperature. The lattice energy, the eleastic constants and the structure parameters corresponding to the equilibrium of a model potential of aspirin crystal have been calculated by taking account of the non-rigidity of the molecule and applying the condition of vanishing stress. The model potential consists of the exp-6 type dispersion and exchange repulsion terms, the Lippincott type hydrogen bond stretching terms and the electrostatic interaction terms between fixed atomic charges. The atomic coordinates of the calculated structure agree well with those determined crystallographically.
TL;DR: In this paper, the authors calculated water-water two-body interaction potentials with an ab initio MO method by varying not only the OO distance but also the OH distance, and obtained ROO=2.79 A, ROH=0.977 A with the binding energy of 15.8 kcal/mol per H2O molecule.
Abstract: The OO distance in ice (2.76 A) is much shorter than in water dimer (2.98 A). No first principle potential function has successfully described the observed OO shrinkage. We have calculated water–water two‐body interaction potentials with an ab initio MO method by varying not only the OO distance but also the OH distance. New analytical fits of two‐body potential functions have been obtained. The nearest‐neighbor three‐body potential has been evaluated for proton‐ordered ice–Ih structures. With ab initio one, two, and nearest‐neighbor three‐body potentials, ∠HOH fixed at the monomer value, we have been able to obtain ROO=2.79 A, ROH=0.977 A with the binding energy of 15.8 kcal/mol per H2O molecule for proton‐ordered antiferroelectric ice Ih and ROO=2.85 A, ROH=0.972 A with the binding energy of 14.3 kcal/mol per molecule for ferroelectric ice Ih. The three‐body interaction, aided by the two‐body interaction, contributes to the OO shrinkage. Factors that would favor larger ROH stretch and ROO shrinkage have...
TL;DR: The hydrogen bond is unquestionably an essential idea in explaining the structure of natural proteins and synthetic polyamides as well as small molecule association phenomena, intramolecular ring closure, and catalysis as discussed by the authors.
Abstract: Ever since its discovery [1] almost a century ago, the hydrogen bond, its character, and effect on molecular structure and properties have been the topic of numerous studies [2,3] The hydrogen bond is unquestionably an essential idea in explaining the structure of natural proteins and synthetic polyamides as well as small molecule association phenomena, intramolecular ring closure, and catalysis
TL;DR: In this article, the adsorption characteristics of various polyacetic amino acids onto aluminum oxide (γ-Al 2 O 3 ) were examined, and a quantitative model was formulated which considered the pH-dependent speciation of the oxide surface, speciation and electrostatic interactions based on the zeta potential measurements.
TL;DR: In this article, the proton transfer process of 2naphthol in its first excited singlet state was investigated in water/methanol mixtures at different temperatures.
Abstract: Using picosecond spectroscopic techniques, the proton transfer process of 2‐naphthol in its first excited singlet state is investigated in water/methanol mixtures at different temperatures. The proton transfer rate is found to increase as the temperature increases, and to decrease as the methanol concentration increases. A Markov random walk theory previously used to electron transfer kinetics is employed to analyze the data. By this method, a water cluster containing 4±1 members is shown to be the proton acceptor. Suggestively, a ‘‘four‐cluster’’ structure (H9O4)+ has been hypothesized as the most probable hydrating unit for the proton in acid–base equilibria, charge transfer, and other chemical systems. The observed activation energy of 3.45 kcal/mol in pure water is attributed to the energy required for rearrangement of the hydrogen bonding in the normal water structure to form the proton accepting cluster. Proton transfer kinetics thus exactly parallels electron transfer kinetics in aqueous media. The...