Showing papers on "Hydrogen bond published in 1995"

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

Abstract: We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use of a simple diagonal potential function and electrostatic potential fit atom centered charges. The need for a 10-12 function for representing hydrogen bonds is no longer necessary due to the improved performance of the new charge model and new van der Waals parameters. These new charges are determined using a 6-31G* basis set and restrained electrostatic potential (RESP) fitting and have been shown to reproduce interaction energies, free energies of solvation, and conformational energies of simple small molecules to a good degree of accuracy. Furthermore, the new RESP charges exhibit less variability as a function of the molecular conformation used in the charge determination. The new van der Waals parameters have been derived from liquid simulations and include hydrogen parameters which take into account the effects of any geminal electronegative atoms. The bonded parameters developed by Weiner et al. were modified as necessary to reproduce experimental vibrational frequencies and structures. Most of the simple dihedral parameters have been retained from Weiner et al., but a complex set of 4 and yj parameters which do a good job of reproducing the energies of the low-energy conformations of glycyl and alanyl dipeptides has been developed for the peptide backbone.

Characterization of c-h-o hydrogen-bonds on the basis of the charge-density

Abstract: It is shown that the total charge density is a valid source to confirm hydrogen bonding without invoking a reference charge density. A set of criteria are proposed based on the theory of “atoms in molecules” to establish hydrogen bonding, even for multiple interactions involving C-H-O hydrogen bonds. These criteria are applied to several van der Waals complexes. Finally a bifurcated intramolecular C-H-O hydrogen bond is predicted in the anti-AIDS drug AZT, which may highlight a crucial feature of the biological activity of a whole class of anti-AIDS drugs. Almost all the methods of physical chemistry, spectroscopy, and diffraction can be used to recognize and study hydrogen bonding.] Each technique focuses on specific properties in order to detect and characterize this phenomenon in its own way. This work is concerned with the manifestation of hydrogen bonding in the charge density obtained from ab initio calculations. Whereas crystallographers have concluded upon hydrogen bonding via purely geometrical criteria, recent deformation density2 studies allow one to observe hydrogen bonding beyond mere ge~metry.~ However, it is not necessary to subtract an arbitrary (promolecular) charge density from the total density to reveal hydrogen bonding, not even in the interpretation of X-ray experiment^.^ Boyd and Choi have shown in two important contribution^^^^ that the theory of “atoms in molecules’’ (AIM)7,8 can be used to characterize hydrogen bonding solely from the (total) charge density for a large set of acceptor molecules, involving HF and HC1 as donors. In a next stage Carroll and Bader performed a more extended analysis on a large set of BASE-HF comple~es.~ This theory has not only provided new insights in conventional intermolecular hydrogenI0.’ ] bonding but has also been successful in intramolecularI33l4 and x-type hydrogen bonds.I5 Drawing from earlier ob~ervations~~~~ ~.’~~~~ and the present work, we formulate eight concerted effects occurring in the charge density which are indicative of hydrogen bonding. All of these effects can be viewed as necessary criteria to conclude that hydrogen bonding is present. By observation one of these conditions has proven to be sufficient as well. This case study on C-H-O interactions shows that this less common type of hydrogen bonding obeys all of the proposed criteria. Moreover, the multiple interactions appearing in the present five examples do not impair the consistency of the global phenomenon of hydrogen bonding as it expresses itself in the charge density. In spite of an early affirmative infrared review,I6 the old controversy on whether C-H-O hydrogen bonds really exist continued for another decade,” but now the dust has settled’* (for an entertaining account of this controversy, see ref 19). The importance of these bonds has been recognized in crystal engineering’9,20 since C-H-O contacts have a determining influence on packing motifs.21

A hot spot of binding energy in a hormone-receptor interface

Abstract: The x-ray crystal structure of the complex between human growth hormone (hGH) and the extracellular domian of its first bound receptor (hGHbp) shows that about 30 side chains from each protein make contact. Individual replacement of contact residues in the hGHbp with alanine showed that a central hydrophobic region, dominated by two tryptophan residues, accounts for more than three-quarters of the binding free energy. This "functional epitope" is surrounded by less important contact residues that are generally hydrophilic and partially hydrated, so that the interface resembles a cross section through a globular protein. The functionally important residues on the hGHbp directly contact those on hGH. Thus, only a small and complementary set of contact residues maintains binding affinity, a property that may be general to protein-protein interfaces.

Spontaneous assembly of a hinged coordination network

Abstract: THE field of supramolecular chemistry has advanced to a stage at which it is possible to select building blocks that will self-assemble into structures with specific network topologies1–3. This makes possible the rational design and synthesis of molecular solids with potentially interesting properties. Here we report the construction of open, hinged networks from molecular building blocks. This class of materials has been predicted to exhibit unusual mechanical properties, including auxetic behaviour (negative Poisson's ratio) and negative coefficients of thermal expansion4–6. Our approach relies on the notion that rigid organic molecules of high symmetry will adopt one of only a few possible structures when linked via hydrogen bonds or coordination to metals7–9. We use trigonal lig-ands to make networks joined at the vertices by metal ions; the resulting networks are homeotypic10 with the honeycomb-like A1B2 and the hinge-like ThSi2 phases. The hinge-like network has channels of inner diameter 15 A, within which included molecules can be exchanged while the framework remains intact. We have not yet determined whether this material is auxetic.

Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water

Abstract: Charge defects in water created by excess or missing protons appear in the form of solvated hydronium H3O+ and hydroxyl OH− ions. Using the method of ab initio molecular dynamics, we have investigated the structure and proton transfer dynamics of the solvation complexes, which embed the ions in the network of hydrogen bonds in the liquid. In our ab initio molecular dynamics approach, the interatomic forces are calculated each time step from the instantaneous electronic structure using density functional methods. All hydrogen atoms, including the excess proton, are treated as classical particles with the mass of a deuterium atom. For the H3O+ ion we find a dynamic solvation complex, which continuously fluctuates between a (H5O2)+ and a (H9O4)+ structure as a result of proton transfer. The OH− has a predominantly planar fourfold coordination forming a (H9O5)− complex. Occasionally this complex is transformed in a more open tetrahedral (H7O4)− structure. Proton transfer is observed only for the more waterlike (H7O4)− complex. Transport of the charge defects is a concerted dynamical process coupling proton transfer along hydrogen bonds and reorganization of the local environment. The simulation results strongly support the structural diffusion mechanism for charge transport. In this model, the entire structure—and not the constituent particles—of the charged complex migrates through the hydrogen bond network. For H3O+, we propose that transport of the excess proton is driven by coordination fluctuations in the first solvation shell (i.e., second solvation shell dynamics). The rate‐limiting step for OH− diffusion is the formation of the (H7O4)− structure, which is the solvation state showing proton transfer activity.

Elastic modulus of the crystalline regions of cellulose polymorphs

Abstract: The elastic modulus El of the crystalline regions of cellulose polymorphs in the direction parallel to the chain axis was measured by x-ray diffraction. The El values of cellulose I, II, IIII, IIIII, and IVI were 138, 88, 87, 58, 75 GPa, respectively. This indicates that the skeletons of these polymorphs are completely different from each other in the mechanical point of view. The crystal transition induces a skeletal contraction accompanied by a change in intramolecular hydrogen bonds, which is considered to result in a drastic change in the El value of the cellulose polymorphs. © 1995 John Wiley & Sons, Inc.

Specific Interactions and the Miscibility of Polymer Blends

Abstract: Preface, Glossary of Common Symbols 1. THE THERMODYNAMICS OF MIXING * Introduction to Theories of Mixing * Intermolecular Interactions * Regular Solutions * Polymer Solutions and Blends * Phase Separation in Polymer Solution and Blends * Simple Models for the Description of Phase Behavior of Polymer Blends * References 2. A PRACTICAL GUIDE TO POLYMER MISCIBILITY * Introduction * Estimation of x from Solubility Parameters * Simple Rules Governing Miscibility in Polymer Blends * Very Weak or Nonexistent Favorable Intermolecular Interactions * Relatively Weak Favorable Intermolecular Interactions * Relatively Strong Favorable Intermolecular Interactions * References 3. THE NATURE OF THE HYDROGEN BOND * Introduction * What Is a Hydrogen Bond? * Experimental Characterization of Hydrogen Bonds * Hydrogen Bonding in Polymers * References 4. EQUILIBRIUM CONSTANTS AND STOICHIOMETRY OF HYDROGEN BONDING * Introduction * Association Models and Equilibrium Constant Definitions * Stoichiometry of Hydrogen Bonding and Relationship to Infrared Spectroscopic Measurements * Hydrogen Bonding in Polymers * Flory Lattice Model for Mixing Heterogeneous Polymers * "Transferable" Equilibrium Constants * References 5. VIBRATIONAL SPECTROSCOPY AND THE HYDROGEN BOND * Introduction * Origin of Vibrational Spectrum * Practice of Infrared Spectroscopy * Vibrational Spectrum of Hydrogen Bonded Systems * Quantitative Infrared Spectroscopic Measurement of the Fraction of Hydrogen Bonded Groups * Mapping Phase Diagrams Using Infrared Spectroscopy * References 6. ASSOCIATION MODELS AND THERMODYNAMICS OF MIXING MOLECULES WITH STRONG SPECIFIC INTERACTIONS * Introduction-Why Use Association Models? * Hydrogen Bonding in Small Molecules-Open Chain Association in Mixtures Where One Component Self-Associates * Thermodynamics: Properties of Associated Solutions * A Simplified Expression for the Free Energy * Hydrogen Bonding in Polymer Mixtures_Linear Association * Chemical Potentials * Dependence of Equilibrium Constants on Molecular Weight and Chain Sti=ness * Phase Behavior * Self-Association and the Enthalpy and Entropy of Mixing * Free Volume Effects in Mixing of Polymers That Hydrogen Bond * References * Appendices: 1. Self-Association Through Formation of Cyclic Dimers 2. Linear Self-Association Described by Two Equilibrium Constants 7. CALCULATION OF PHASE DIAGRAMS OF STRONGLY INTERACTING POLYMERS * Introduction * Homopolymer (Self-Associated)-Homopolymer (non Self-Associated) Systems * Homopolymer (Self-Associated)-Copolymer (Non Self-Associated) Systems * Homopolymer (Non Self-Associated)-Copolymer (Self-Associated) Systems * Copolymer (Non Self-Associated)-Copolymer (Self-Associated) Systems * References Index 15 Tables, 242 Figures, 288 References

Femtosecond molecular-dynamics of tautomerization in model base-pairs

Abstract: Hydrogen bonds commonly lend robustness and directionality to molecular recognition processes and supramolecular structures. In particular, the two or three hydrogen bonds in Watson–Crick base pairs bind the double-stranded DNA helix and determine the complementarity of the pairing. Watson and Crick pointed out, however, that the possible tautomers of base pairs, in which hydrogen atoms become attached to the donor atom of the hydrogen bond, might disturb the genetic code, as the tautomer is capable of pairing with different partners. But the dynamics of hydrogen bonds in general, and of this tautomerization process in particular, are not well understood. Here we report observations of the femtosecond dynamics of tautomerization in model base pairs (7-azaindole dimers) containing two hydrogen bonds. Because of the femtosecond resolution of proton motions, we are able to examine the cooperativity of formation of the tautomer (in which the protons on each base are shifted sequentially to the other base), and to determine the characteristic timescales of the motions in a solvent-free environment. We find that the first step occurs on a timescale of a few hundred femtoseconds, whereas the second step, to form the full tautomer, is much slower, taking place within several picoseconds; the timescales are changed significantly by replacing hydrogen with deuterium. These results establish the molecular basis of the dynamics and the role of quantum tunnelling.

1.4 Å structure of photoactive yellow protein, a cytosolic photoreceptor: Unusual fold, active site, and chromophore

Abstract: A photosensing protein directs light energy captured by its chromophore into a photocycle. The protein's structure must accommodate the photocycle and promote the resulting chemical or conformational changes that lead to signal transduction. The 1.4 A crystallographic structure of photoactive yellow protein, determined by multiple isomorphous replacement methods, provides the first view at atomic resolution of a protein with a photocycle. The alpha/beta fold, which differs from the original chain tracing, shows striking similarity to distinct parts of the signal transduction proteins profilin and the SH2 domain. In the dark state structure of photoactive yellow protein, the novel 4-hydroxycinnamyl chromophore, covalently attached to Cys69, is buried within the major hydrophobic core of the protein and is tethered at both ends by hydrogen bonds. In the active site, the yellow anionic form of the chromophore is stabilized by hydrogen bonds from the side chains of Tyr42 and buried Glu46 to the phenolic oxygen atom and by electrostatic complementarity with the positively charged guanidinium group of Arg52. Thr50 further interlocks Tyr42, Glu46, and Arg52 through a network of active site hydrogen bonds. Arg52, located in a concavity of the protein surface adjacent to the dominant patch of negative electrostatic potential, shields the chromophore from solvent and is positioned to form a gateway for the phototactic signal. Overall, the high-resolution structure of photoactive yellow protein supports a mechanism whereby electrostatic interactions create an active site poised for photon-induced rearrangements and efficient protein-mediated signal transduction.

Thermotropic liquid crystals formed by intermolecular hydrogen bonding interactions

Abstract: The role of hydrogen bonding in the formation or stabilization of liquid crystalline phases has only recently been appreciated. Following the first, wellestablished examples of liquid crystal formation from the dimerization of aromatic carboxylic acids, through hydrogen bonding, several classes of compounds have recently been synthesized, the liquid crystalline behavior of which is also dependent on intermolecular hydrogen bonds between similar or dissimilar molecules. In this review the main classes of compounds exhibiting liquid crystallinity due to hydrogen bonding are presented to show the diversity of organic compounds that can be used as building elements in liquid crystals. The molecules are either of the rigid-rod anisotropic or amphiphilic types such as molecules appropriately functionalized with pyridyl and carboxyl groups, whose interaction leads to the formation of liquid crystals; amphiphilic carbohydrates and amphiphilic and bolaamphiphilic compounds with multiple hydroxyl groups whose dimerization or association is indispensable for the formation of liquid crystals; and certain amphiphilic carboxylic acids with monomeric or polymeric mesogens and amphiphilic-type compounds bearing different moieties, whose interaction may lead to the formation of mesomorphic compounds. Associated with the macroscopic display of liquid crystalline phases is the supramolecular structure, and therefore rather extended discussion of these structures are included in this review.

Conjugated Aromatic Polyimines. 2. Synthesis, Structure, and Properties of New Aromatic Polyazomethines.

Abstract: : A series of 20 conjugated aromatic Polyimines, containing p-phenylene, p-biphenylene, p-terphenylene, 4,4'- stilbene, and 1,5-naphthalene linkages in the backbone and various electron-donating and electron-withdrawing side-group substitutions, have been synthesized, characterized, and used to investigate the effects of molecular structure on the electronic structure and properties of conjugated polymers. Soluble gallium trichloride or diarylphosphate complexes of the aromatic polyimines in organic solvents facilitated their solution spectroscopic characterization and their processing into thin film and coatings. Electrochemical reduction of the aromatic polyimines was reversible with formal potential of -1.93 to -1.52 V (SCE) and 0.22 to 0.86 charge transferred whereas oxidation was irreversible. The electron affinity and ionization potentials of the series of polymers varied from 2.46 to 2.94 eV and from 4.80 to 5.38 eV, respectively. The associated LUMO and HOMO energy levels are thus tunable by up to 0.48 eV and 0.58 eV, respectively. The electrochemically and optically determined LUMO-HOMO energy gaps of thin films were very close and in the range of 2.08-2.77 eV. The results of this study show that aromatic polyimines are an interesting class of pi-conjugated polymers whose structure and properties can be regulated over a wide range by variation in backbone structure, side group substitution, and through intramolecular hydrogen bonding or complexation, backbone planarity. jg

The quantum dynamics of an excess proton in water

Abstract: The quantum dynamics and energetics of an excess proton in water have been studied computationally. Comparison of a quantum mechanical treatment of the transferring proton and the water solvent is made with a classical treatment of the same system. The exchange of the proton between two water molecules is found to be an activationless quantum process. Analysis of the microscopic structure of the solvent around the proton transfer complex is also carried out, and the quantum infrared spectrum of the transferring proton is calculated and analyzed in terms of Zundel polarization. The Grotthus mechanism for proton migration in water is also examined within the context of the model. Grotthus behavior is suggested to depend critically on the dynamics of water molecules in the second solvation shell of the H5O+2 complex, as well as the inward fluctuations of the oxygen–oxygen distance of water molecules that hydrogen bond to the H5O+2 complex in the first solvation shell. The quantum effects on the nuclear dynam...

Hydrogen bonding in imidazolium salts and its implications for ambient-temperature halogenoaluminate(III) ionic liquids

Abstract: The salts [emim]X (X = Br or I, emim = 1-ethyl-3-methylimidazolium) and [emim][AlBr4] have been prepared as solid-state models of the [emim]X–AlX3(X = Cl or Br) ionic liquid systems. All three have been characterised crystallographically. The salts [emim]X (X = Br or I) are isomorphous and are composed of ions in an extended hydrogen-bonded network. The implications of these results for both the structure and solvent properties of the ionic liquids are discussed.

Catalytic Addition of Aromatic Carbon–Hydrogen Bonds to Olefins with the Aid of Ruthenium Complexes

Abstract: Ruthenium complexes, e.g., Ru(H)2(CO)(PPh3)3, have been found to catalyze the addition of ortho C–H bonds of aromatic ketones to olefins with a high degree of efficiency and selectivity. 2′-Methylacetophenone reacts with various types of terminal olefins to give 1 : 1 coupling products in good to excellent yields. The C–C bond formation takes place exclusively at the terminal carbon atom of olefins except for styrene which affords a mixture of two regioisomers. Acetylnaphthalenes, cyclic aromatic ketones, and heteroaromatic ketones also react with triethoxyvinylsilane to give 1 : 1 addition products in virtually quantitative yields. From 2′-acetonaphthone or 3-acetylthiophene, in which two different reaction sites are available, only one out of four possible regioisomers is obtained. The importance of the coordination of the oxygen atom of the ketone to ruthenium and the intervention of a cyclometallation intermediate are suggested. A deuterium labeling experiment using acetophenone-d5 and triethoxyvinyls...

Direct evaluation of electronic coupling mediated by hydrogen bonds: implications for biological electron transfer

Abstract: Three supramolecular bischromophoric systems featuring zinc(II) and iron(III) porphyrins have been synthesized to evaluate the relative magnitudes of electronic coupling provided by hydrogen, sigma, and pi bonds. Laser flash excitation generates the highly reducing singlet excited state of the (porphinato)zinc chromophore that can subsequently be electron transfer quenched by the (porphinato)iron(III) chloride moiety. Measurement of the photoinduced electron transfer rate constants enables a direct comparison of how well these three types of chemical interactions facilitate electron tunneling. In contrast to generally accepted theory, electronic coupling modulated by a hydrogen-bond interface is greater than that provided by an analogous interface composed entirely of carbon-carbon sigma bonds. These results bear considerably on the analysis of through-protein electron transfer rate data as well as on the power of theory to predict the path traversed by the tunneling electron in a biological matrix; moreover, they underscore the cardinal role played by hydrogen bonds in biological electron transfer processes.

Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR.

Abstract: The presence and location of water of hydration (that is, bound water) in the solution structure of human interleukin-1 beta (hIL-1 beta) was investigated with water-selective two-dimensional heteronuclear magnetic resonance spectroscopy. It is shown here that in addition to water at the surface of the protein and ordered internal water molecules involved in bridging hydrogen bonds, positionally disordered water is present within a large, naturally occurring hydrophobic cavity located at the center of the molecule. These water molecules of hydration have residency times in the range of 1 to 2 nanoseconds to 100 to 200 microseconds and can be readily detected by nuclear magnetic resonance (NMR). Thus, large hydrophobic cavities in proteins may not be truly empty, as analysis of crystal structures appears to show, but may contain mobile water molecules that are crystallographically invisible but detectable by NMR.

An analysis of side chain interactions and pair correlations within antiparallel β‐sheets: The differences between backbone hydrogen‐bonded and non‐hydrogen‐bonded residue pairs

Abstract: Cross-strand pair correlations are calculated for residue pairs in anti-parallel beta-sheet for two cases: pairs whose backbone atoms are hydrogen bonded together (H-bonded site) and pairs which are not (non-H-bonded site). The statistics show that this distinction is important. When glycine is located on the edge of a sheet, it shows a 3:1 preference for the H-bonded site. The strongest observed correlations are for pairs of disulfide-bonded cystines, many of which adopt a close-packed conformation with each cystine in a spiral conformation of opposite chirality to its partner. It is likely that these pairs are a signature for the family of small, cystine-rich proteins. Most other strong positive and negative correlations involve charged and polar residues. It appears that electrostatic compatibility is the strongest factor affecting pair correlation. Significant correlations are observed for beta- and gamma-branched residues in the non-H-bonded site. An examination of the structures shows a directionality in side chain packing. There is a correlation between (1) the directionality in the packing interactions of non-H-bonded beta- and gamma-branched residue pairs, (2) the handedness of the observed enantiomers of chiral beta-branched side chains, and (3) the handedness of the twist of beta-sheet. These findings have implications for the formation of beta-sheets during protein folding and the mechanism by which the sheet becomes twisted.

Characterization of Unimolecular Micelles of Random Copolymers of Sodium 2-(Acrylamido)-2-methylpropanesulfonate and Methacrylamides Bearing Bulky Hydrophobic Substituents

Abstract: The self-organization of random copolymers of sodium 2-(acrylamido)-2-methylpropanesulfonate and methacrylamides bearing bulky hydrophobic groups, such as lauryl (LA), cyclododecyl (CD), and 1-adamantyl (AD) groups, was investigated by fluorescence, NMR relaxation, FTIR, light scattering, and SAXS techniques. In aqueous solution, the hydrophobes in these polymers form clusters as a result of either intramolecular or intermolecular self-association. Studies of nonradiative energy transfer between polymers labeled with naphthalene and pyrene revealed that the polymers having the CD and AD groups formed unimolecular micelles (unimers) in a wide range of concentrations up to several weight percent, whereas the polymer having the LA groups could exist as a unimer only in a much lower concentration range (

Sio-...hosi hydrogen bonds in as-synthesized high-silica zeolites

Abstract: The positive charge of quaternary ammonium cations used in structure-directing agents in high-silica zeolites is balanced by a nonprotonated defect site (siloxy group). This siloxy group functions as hydrogen bond acceptor in SiO{sup -}...HOSi hydrogen bonds. This paper presents the {sup 1}H MAS NMR spectra of a variety of as-synthesized, high-silica zeolites prepared with different quaternary ammonium cations as structure-directing agents. The NMR results obtained are used to construct a model for the structure of the defect sites in as-synthesized, high-silica zeolites. 37 refs., 10 figs., 2 tabs.