WorldWideScience

Sample records for catalysis hydrogen bonding

  1. Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole.

    Directory of Open Access Journals (Sweden)

    Daniel A Kraut

    2006-04-01

    Full Text Available A longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis. Experimental evaluation of this contribution, however, has been difficult. We have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. Phenolates, analogs of the transition state and reaction intermediate, bind and accept two hydrogen bonds in an active site oxyanion hole. The binding of substituted phenolates of constant molecular shape but increasing pK(a models the charge accumulation in the oxyanion hole during the enzymatic reaction. As charge localization increases, the NMR chemical shifts of protons involved in oxyanion hole hydrogen bonds increase by 0.50-0.76 ppm/pK(a unit, suggesting a bond shortening of 0.02 A/pK(a unit. Nevertheless, there is little change in binding affinity across a series of substituted phenolates (DeltaDeltaG = -0.2 kcal/mol/pK(a unit. The small effect of increased charge localization on affinity occurs despite the shortening of the hydrogen bonds and a large favorable change in binding enthalpy (DeltaDeltaH = -2.0 kcal/mol/pK(a unit. This shallow dependence of binding affinity suggests that electrostatic complementarity in the oxyanion hole makes at most a modest contribution to catalysis of 300-fold. We propose that geometrical complementarity between the oxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution.

  2. On the role of interfacial hydrogen bonds in "on-water" catalysis

    CERN Document Server

    Karhan, Kristof; Kühne, Thomas D

    2014-01-01

    Numerous experiments have demonstrated that many classes of organic reactions exhibit increased reaction rates when performed in heterogeneous water emulsions. Despite enormous practical importance of the observed "on-water" catalytic effect and several mechanistic studies, its microscopic origins remains unclear. In this work, the second generation Car-Parrinello molecular dynamics method is extended to self-consistent charge density-functional based tight-binding in order to study "on-water" catalysis of the Diels-Alder reaction between dimethyl azodicarboxylate and quadricyclane. We find that the stabilization of the transition state by dangling hydrogen bonds exposed at the aqueous interfaces plays a significantly smaller role in "on-water" catalysis than has been suggested previously.

  3. Catalysis of Heterocyclic Azadiene Cycloaddition Reactions by Solvent Hydrogen Bonding: Concise Total Synthesis of Methoxatin.

    Science.gov (United States)

    Glinkerman, Christopher M; Boger, Dale L

    2016-09-28

    Although it has been examined for decades, no general approach to catalysis of the inverse electron demand Diels-Alder reactions of heterocyclic azadienes has been introduced. Typically, additives such as Lewis acids lead to nonproductive consumption of the electron-rich dienophiles without productive activation of the electron-deficient heterocyclic azadienes. Herein, we report the first general method for catalysis of such cycloaddition reactions by using solvent hydrogen bonding of non-nucleophilic perfluoroalcohols, including hexafluoroisopropanol (HFIP) and trifluoroethanol (TFE), to activate the electron-deficient heterocyclic azadienes. Its use in promoting the cycloaddition of 1,2,3-triazine 4 with enamine 3 as the key step of a concise total synthesis of methoxatin is described.

  4. Innovative Catalysis in Organic Synthesis Oxidation, Hydrogenation, and C-X Bond Forming Reactions

    CERN Document Server

    Andersson, Pher G

    2012-01-01

    Authored by a European team of leaders in the field, this book compiles innovative approaches for C-X bond forming processes frequently applied in organic synthesis. It covers all key types of catalysis, including homogeneous, heterogeneous, and organocatalysis, as well as mechanistic and computational studies. Special attention is focused on the improvement of efficiency and sustainability of important catalytic processes, such as selective oxidations, hydrogenation and cross-coupling reactions.The result is a valuable resource for both advanced researchers in academia and industry, as well a

  5. A conserved hydrogen-bond network in the catalytic centre of animal glutaminyl cyclases is critical for catalysis.

    Science.gov (United States)

    Huang, Kai-Fa; Wang, Yu-Ruei; Chang, En-Cheng; Chou, Tsung-Lin; Wang, Andrew H-J

    2008-04-01

    QCs (glutaminyl cyclases; glutaminyl-peptide cyclotransferases, EC 2.3.2.5) catalyse N-terminal pyroglutamate formation in numerous bioactive peptides and proteins. The enzymes were reported to be involved in several pathological conditions such as amyloidotic disease, osteoporosis, rheumatoid arthritis and melanoma. The crystal structure of human QC revealed an unusual H-bond (hydrogen-bond) network in the active site, formed by several highly conserved residues (Ser(160), Glu(201), Asp(248), Asp(305) and His(319)), within which Glu(201) and Asp(248) were found to bind to substrate. In the present study we combined steady-state enzyme kinetic and X-ray structural analyses of 11 single-mutation human QCs to investigate the roles of the H-bond network in catalysis. Our results showed that disrupting one or both of the central H-bonds, i.e., Glu(201)...Asp(305) and Asp(248)...Asp(305), reduced the steady-state catalysis dramatically. The roles of these two COOH...COOH bonds on catalysis could be partly replaced by COOH...water bonds, but not by COOH...CONH(2) bonds, reminiscent of the low-barrier Asp...Asp H-bond in the active site of pepsin-like aspartic peptidases. Mutations on Asp(305), a residue located at the centre of the H-bond network, raised the K(m) value of the enzyme by 4.4-19-fold, but decreased the k(cat) value by 79-2842-fold, indicating that Asp(305) primarily plays a catalytic role. In addition, results from mutational studies on Ser(160) and His(319) suggest that these two residues might help to stabilize the conformations of Asp(248) and Asp(305) respectively. These data allow us to propose an essential proton transfer between Glu(201), Asp(305) and Asp(248) during the catalysis by animal QCs.

  6. Hydrogen bonding controlled catalysis of a porous organic framework containing benzimidazole moieties

    KAUST Repository

    Liu, Bing

    2014-01-01

    A microporous organic framework (JUC-Z12) was synthesized quantitatively from tetra(4-formylphenyl)methane and 3,3′-diaminobenzidine. JUC-Z12 shows high thermal stability (>400 °C), a large surface area (SBET = 750 m2 g-1), a well-defined uniform micropore distribution (1.09 nm) and high Qst for H2 (-8.1 kJ mol-1), CO2 (-29.5 kJ mol-1), and CH 4 (-22.2 kJ mol-1). It also exhibits selective catalytic activities in the Knoevenagel reaction, which is supposed to be controlled by hydrogen bonding between substrates and JUC-Z12. The JUC-Z12 catalyst can be easily isolated from the reaction mixture by simple filtration and reused with high activity. This journal is © the Partner Organisations 2014.

  7. Cooperative catalysis of metal and O-H···O/sp3-C-H···O two-point hydrogen bonds in alcoholic solvents: Cu-catalyzed enantioselective direct alkynylation of aldehydes with terminal alkynes.

    Science.gov (United States)

    Ishii, Takaoki; Watanabe, Ryo; Moriya, Toshimitsu; Ohmiya, Hirohisa; Mori, Seiji; Sawamura, Masaya

    2013-09-27

    Catalyst-substrate hydrogen bonds in artificial catalysts usually occur in aprotic solvents, but not in protic solvents, in contrast to enzymatic catalysis. We report a case in which ligand-substrate hydrogen-bonding interactions cooperate with a transition-metal center in alcoholic solvents for enantioselective catalysis. Copper(I) complexes with prolinol-based hydroxy amino phosphane chiral ligands catalytically promoted the direct alkynylation of aldehydes with terminal alkynes in alcoholic solvents to afford nonracemic secondary propargylic alcohols with high enantioselectivities. Quantum-mechanical calculations of enantiodiscriminating transition states show the occurrence of a nonclassical sp(3)-C-H···O hydrogen bond as a secondary interaction between the ligand and substrate, which results in highly directional catalyst-substrate two-point hydrogen bonding.

  8. Relation between Hydrogen Evolution and Hydrodesulfurization Catalysis

    DEFF Research Database (Denmark)

    Šaric, Manuel; Moses, Poul Georg; Rossmeisl, Jan

    2016-01-01

    A relation between hydrogen evolution and hydrodesulfurization catalysis was found by density functional theory calculations. The hydrogen evolution reaction and the hydrogenation reaction in hydrodesulfurization share hydrogen as a surface intermediate and, thus, have a common elementary step...

  9. Hydroxide catalysis bonding of silicon carbide

    NARCIS (Netherlands)

    Veggel, A.A. van; Ende, D.A. van den; Bogenstahl, J.; Rowan, S.; Cunningham, W.; Gubbels, G.H.M.; Nijmeijer, H.

    2008-01-01

    For bonding silicon carbide optics, which require extreme stability, hydroxide catalysis bonding is considered [Rowan, S., Hough, J. and Elliffe, E., Silicon carbide bonding. UK Patent 040 7953.9, 2004. Please contact Mr. D. Whiteford for further information: D.Whiteford@admin.gla.ac.uk]. This techn

  10. Hydrogen Production by Homogeneous Catalysis: Alcohol Acceptorless Dehydrogenation

    DEFF Research Database (Denmark)

    Nielsen, Martin

    2015-01-01

    in hydrogen production from biomass using homogeneous catalysis. Homogeneous catalysis has the advance of generally performing transformations at much milder conditions than traditional heterogeneous catalysis, and hence it constitutes a promising tool for future applications for a sustainable energy sector...

  11. Mechanistic aspects of dinitrogen cleavage and hydrogenation to produce ammonia in catalysis and organometallic chemistry: relevance of metal hydride bonds and dihydrogen.

    Science.gov (United States)

    Jia, Hong-Peng; Quadrelli, Elsje Alessandra

    2014-01-21

    Dinitrogen cleavage and hydrogenation by transition-metal centers to produce ammonia is central in industry and in Nature. After an introductory section on the thermodynamic and kinetic challenges linked to N2 splitting, this tutorial review discusses three major classes of transition-metal systems (homogeneous, heterogeneous and biological) capable of achieving dissociation and hydrogenation of dinitrogen. Molecular complexes, solid-state Haber-Bosch catalytic systems, silica-supported tantalum hydrides and nitrogenase will be discussed. Emphasis is focused on the reaction mechanisms operating in the process of dissociation and hydrogenation of dinitrogen, and in particular on the key role played by metal hydride bonds and by dihydrogen in such reactions.

  12. Inorganic Chemistry in Hydrogen Storage and Biomass Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Thorn, David [Los Alamos National Laboratory

    2012-06-13

    Making or breaking C-H, B-H, C-C bonds has been at the core of catalysis for many years. Making or breaking these bonds to store or recover energy presents us with fresh challenges, including how to catalyze these transformations in molecular systems that are 'tuned' to minimize energy loss and in molecular and material systems present in biomass. This talk will discuss some challenging transformations in chemical hydrogen storage, and some aspects of the inorganic chemistry we are studying in the development of catalysts for biomass utilization.

  13. Photoinduced hydrogen-bonding dynamics.

    Science.gov (United States)

    Chu, Tian-Shu; Xu, Jinmei

    2016-09-01

    Hydrogen bonding dynamics has received extensive research attention in recent years due to the significant advances in femtolaser spectroscopy experiments and quantum chemistry calculations. Usually, photoexcitation would cause changes in the hydrogen bonding formed through the interaction between hydrogen donor and acceptor molecules on their ground electronic states, and such transient strengthening or weakening of hydrogen bonding could be crucial for the photophysical transformations and the subsequent photochemical reactions that occurred on a time scale from tens of femtosecond to a few nanoseconds. In this article, we review the combined experimental and theoretical studies focusing on the ultrafast electronic and vibrational hydrogen bonding dynamics. Through these studies, new mechanisms and proposals and common rules have been put forward to advance our understanding of the hydrogen bondings dynamics in a variety of important photoinduced phenomena like photosynthesis, dual fluorescence emission, rotational reorientation, excited-state proton transfer and charge transfer processes, chemosensor fluorescence sensing, rearrangements of the hydrogen-bond network including forming and breaking hydrogen bond in water. Graphical Abstract We review the recent advances on exploring the photoinduced hydrogen bonding dynamics in solutions through a joint approach of laser spectroscopy and theoretical calculation. The reviewed studies have put forward a new mechanism, new proposal, and new rule for a variety of photoinduced phenomena such as photosynthesis, dual fluorescence emission, rotational reorientation, excited-state proton transfer and charge transfer, chemosensor fluorescence sensing, and rearrangements of the hydrogen-bond network in water.

  14. Cationic reverse micelles create water with super hydrogen-bond-donor capacity for enzymatic catalysis: hydrolysis of 2-naphthyl acetate by alpha-chymotrypsin.

    Science.gov (United States)

    Moyano, Fernando; Falcone, R Dario; Mejuto, J C; Silber, Juana J; Correa, N Mariano

    2010-08-02

    Reverse micelles (RMs) are very good nanoreactors because they can create a unique microenvironment for carrying out a variety of chemical and biochemical reactions. The aim of the present work is to determine the influence of different RM interfaces on the hydrolysis of 2-naphthyl acetate (2-NA) by alpha-chymotrypsin (alpha-CT). The reaction was studied in water/benzyl-n-hexadecyldimethylammonium chloride (BHDC)/benzene RMs and, its efficiency compared with that observed in pure water and in sodium 1,4-bis-2-ethylhexylsulfosuccinate (AOT) RMs. Thus, the hydrolysis rates of 2-NA catalyzed by alpha-CT were determined by spectroscopic measurements. In addition, the method used allows the joint evaluation of the substrate partition constant K(p) between the organic and the micellar pseudophase and the kinetic parameters: catalytic rate constant k(cat), and the Michaelis constant K(M) of the enzymatic reaction. The effect of the surfactant concentration on the kinetics parameters was determined at constant W(0)=[H(2)O]/[surfactant], and the variation of W(0) with surfactant constant concentration was investigated. The results show that the classical Michaelis-Menten mechanism is valid for alpha-CT in all of the RMs systems studied and that the reaction takes place at both RM interfaces. Moreover, the catalytic efficiency values k(cat)/K(M) obtained in the RMs systems are higher than that reported in water. Furthermore, there is a remarkable increase in alpha-CT efficiency in the cationic RMs in comparison with the anionic system, presumably due to the unique water properties found in these confined media. The results show that in cationic RMs the hydrogen-bond donor capacity of water is enhanced due to its interaction with the cationic interface. Hence, entrapped water can be converted into "super-water" for the enzymatic reaction studied in this work.

  15. Hydrogen bonding in tight environments

    DEFF Research Database (Denmark)

    Pirrotta, Alessandro; Solomon, Gemma C.; Franco, Ignacio

    2016-01-01

    The single-molecule force spectroscopy of a prototypical class of hydrogen-bonded complexes is computationally investigated. The complexes consist of derivatives of a barbituric acid and a Hamilton receptor that can form up to six simultaneous hydrogen bonds. The force-extension (F-L) isotherms...... of the host-guest complexes are simulated using classical molecular dynamics and the MM3 force field, for which a refined set of hydrogen bond parameters was developed from MP2 ab initio computations. The F-L curves exhibit peaks that signal conformational changes during elongation, the most prominent...... of which is in the 60-180 pN range and corresponds to the force required to break the hydrogen bonds. These peaks in the F-L curves are shown to be sensitive to relatively small changes in the chemical structure of the host molecule. Thermodynamic insights into the supramolecular assembly were obtained...

  16. Why are Hydrogen Bonds Directional?

    Indian Academy of Sciences (India)

    ABHISHEK SHAHI; ELANGANNAN ARUNAN

    2016-10-01

    The recent IUPAC recommendation on the definition of hydrogen bonding points out that directionality is a defining characteristic of a hydrogen bond and the angle ∠X-H-Y is generally linear or 180◦. It also suggests that the X-H· · ·Y angle be greater than 110◦ for an interaction to be characterized as a hydrogenbond but does not provide any rationale for the same. This article reports a rationale for limiting the angle, based on the electron density topology using the quantum theory of atoms in molecules. Electron density topology for common hydrogen bond donors HF, HCl, HBr, HNC, HCN and HCCH are reported in this work. These calculations lead to an interesting observation that the atomic basins of H atom in all these donor molecules are limited justifying the restriction of hydrogen bond angle. Moreover, similar analysis on some hydrogen bonded complexes confirms that beyond this angle the acceptor atom Y starts interacting with the atomic basin on X. However, conclusions based on bond lengths and angles have to be treated with care and as the IUPAC recommendation points out that independent ‘evidence for bond formation’ in every case is important.

  17. Catalysis of Protein Disulfide Bond Isomerization in a Homogeneous Substrate†

    Science.gov (United States)

    Kersteen, Elizabeth A.; Barrows, Seth R.; Raines, Ronald T.

    2008-01-01

    Protein disulfide isomerase (PDI) catalyzes the rearrangement of nonnative disulfide bonds in the endoplasmic reticulum of eukaryotic cells, a process that often limits the rate at which polypeptide chains fold into a native protein conformation. The mechanism of the reaction catalyzed by PDI is unclear. In assays involving protein substrates, the reaction appears to involve the complete reduction of some or all of its nonnative disulfide bonds followed by oxidation of the resulting dithiols. The substrates in these assays are, however, heterogeneous, which complicates mechanistic analyses. Here, we report the first analysis of disulfide bond isomerization in a homogeneous substrate. Our substrate is based on tachyplesin I, a 17-mer peptide that folds into a _-hairpin stabilized by two disulfide bonds. We describe the chemical synthesis of a variant of tachyplesin I in which its two disulfide bonds are in a nonnative state and side chains near its N-and C-terminus contain a fluorescence donor (tryptophan) and acceptor (N_-dansyllysine). Fluorescence resonance energy transfer from 280 to 465 nm increases by 28-fold upon isomerization of the disulfide bonds into their native state (which has a lower E°_ = -0.313 V than does PDI). We use this continuous assay to analyze catalysis by wild-type human PDI and a variant in which the C-terminal cysteine residue within each Cys—Gly—His—Cys active site is replaced with alanine. We find that wild-type PDI catalyzes the isomerization of the substrate with kcat/KM = 1.7 _ 105 M–1M s–1, which is the largest value yet reported for catalysis of disulfide bond isomerization. The variant, which is a poor catalyst of disulfide bond reduction and dithiol oxidation, retains virtually all of the activity of wild-type PDI in catalysis of disulfide bond isomerization. Thus, the C-terminal cysteine residues play an insignificant role in the isomerization of the disulfide bonds in nonnative tachyplesin I. We conclude that

  18. Catalysis of protein disulfide bond isomerization in a homogeneous substrate.

    Science.gov (United States)

    Kersteen, Elizabeth A; Barrows, Seth R; Raines, Ronald T

    2005-09-13

    Protein disulfide isomerase (PDI) catalyzes the rearrangement of nonnative disulfide bonds in the endoplasmic reticulum of eukaryotic cells, a process that often limits the rate at which polypeptide chains fold into a native protein conformation. The mechanism of the reaction catalyzed by PDI is unclear. In assays involving protein substrates, the reaction appears to involve the complete reduction of some or all of its nonnative disulfide bonds followed by oxidation of the resulting dithiols. The substrates in these assays are, however, heterogeneous, which complicates mechanistic analyses. Here, we report the first analysis of disulfide bond isomerization in a homogeneous substrate. Our substrate is based on tachyplesin I, a 17-mer peptide that folds into a beta hairpin stabilized by two disulfide bonds. We describe the chemical synthesis of a variant of tachyplesin I in which its two disulfide bonds are in a nonnative state and side chains near its N and C terminus contain a fluorescence donor (tryptophan) and acceptor (N(epsilon)-dansyllysine). Fluorescence resonance energy transfer from 280 to 465 nm increases by 28-fold upon isomerization of the disulfide bonds into their native state (which has a lower E(o') = -0.313 V than does PDI). We use this continuous assay to analyze catalysis by wild-type human PDI and a variant in which the C-terminal cysteine residue within each Cys-Gly-His-Cys active site is replaced with alanine. We find that wild-type PDI catalyzes the isomerization of the substrate with kcat/K(M) = 1.7 x 10(5) M(-1) s(-1), which is the largest value yet reported for catalysis of disulfide bond isomerization. The variant, which is a poor catalyst of disulfide bond reduction and dithiol oxidation, retains virtually all of the activity of wild-type PDI in catalysis of disulfide bond isomerization. Thus, the C-terminal cysteine residues play an insignificant role in the isomerization of the disulfide bonds in nonnative tachyplesin I. We conclude

  19. Hydrogen Bonding in Hydrogenated Amorphous Germanium

    Institute of Scientific and Technical Information of China (English)

    M.S.Abo-Ghazala; S. Al Hazmy

    2004-01-01

    Thin films of hydrogenated amorphous germanium (a-Ge:H) were prepared by radio frequency glow discharge deposition at various substrate temperatures. The hydrogen distribution and bonding structure in a-Ge:H were discussed based on infrared absorption data. The correlation between infrared absorption spectra and hydrogen effusion measurements was used to determine the proportionality constant for each vibration mode of the Ge-H bonds. The results reveal that the bending mode appearing at 835 cm?1 is associated with the Ge-H2 (dihydride) groups on the internal surfaces of voids. While 1880 cm?1 is assigned to vibrations of Ge-H (monohydride) groups in the bulk, the 2000 cm?1 stretching mode is attributed to Ge-H and Ge-H2 bonds located on the surfaces of voids. For films associated with bending modes in the infrared spectra, the proportionality constant values of the stretching modes near 1880 and 2000 cm?1 are found to be lower than those of films which had no corresponding bending modes.

  20. Physical Nature of Hydrogen Bond

    CERN Document Server

    Zhyganiuk, I V

    2015-01-01

    The physical nature and the correct definition of hydrogen bond (H-bond) are considered.\\,\\,The influence of H-bonds on the thermodynamic, kinetic, and spectroscopic properties of water is analyzed.\\,\\,The conventional model of H-bonds as sharply directed and saturated bridges between water molecules is incompatible with the behavior of the specific volume, evaporation heat, and self-diffusion and kinematic shear viscosity coefficients of water. On the other hand, it is shown that the variation of the dipole moment of a water molecule and the frequency shift of valence vibrations of a hydroxyl group can be totally explained in the framework of the electrostatic model of H-bond.\\,\\,At the same time, the temperature dependences of the heat capacity of water in the liquid and vapor states clearly testify to the existence of weak H-bonds.\\,\\,The analysis of a water dimer shows that the contribution of weak H-bonds to its ground state energy is approximately 4--5 times lower in comparison with the energy of electr...

  1. Hydrogen bond and halogen bond inside the carbon nanotube

    Science.gov (United States)

    Wang, Weizhou; Wang, Donglai; Zhang, Yu; Ji, Baoming; Tian, Anmin

    2011-02-01

    The hydrogen bond and halogen bond inside the open-ended single-walled carbon nanotubes have been investigated theoretically employing the newly developed density functional M06 with the suitable basis set and the natural bond orbital analysis. Comparing with the hydrogen or halogen bond in the gas phase, we find that the strength of the hydrogen or halogen bond inside the carbon nanotube will become weaker if there is a larger intramolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom donor to the antibonding orbital of the X-H or X-Hal bond involved in the formation of the hydrogen or halogen bond and will become stronger if there is a larger intermolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom acceptor to the antibonding orbital of the X-H or X-Hal bond. According to the analysis of the molecular electrostatic potential of the carbon nanotube, the driving force for the electron-density transfer is found to be the negative electric field formed in the carbon nanotube inner phase. Our results also show that the X-H bond involved in the formation of the hydrogen bond and the X-Hal bond involved in the formation of the halogen bond are all elongated when encapsulating the hydrogen bond and halogen bond within the carbon nanotube, so the carbon nanotube confinement may change the blue-shifting hydrogen bond and the blue-shifting halogen bond into the red-shifting hydrogen bond and the red-shifting halogen bond. The possibility to replace the all electron nanotube-confined calculation by the simple polarizable continuum model is also evaluated.

  2. Imaging Hydrogen Bond in Real Space

    CERN Document Server

    Chen, Xiu; Liu, Lacheng; Liu, Xiaoqing; Cai, Yingxing; Liu, Nianhua; Wang, Li

    2013-01-01

    Hydrogen bond is often assumed to be a purely electrostatic interaction between a electron-deficient hydrogen atom and a region of high electron density. Here, for the first time, we directly image hydrogen bond in real space by room-temperature scanning tunneling microscopy (STM) with the assistance of resonant tunneling effect in double barrier mode. STM observations demonstrate that the C=O:HO hydrogen bonds lifted several angstrom meters above metal surfaces appear shuttle-like features with a significant contrast along the direction connected the oxygen and hydrogen atoms of a single hydrogen bond. The off-center location of the summit and the variance of the appearance height for the hydrogen bond with scanning bias reveal that there are certain hybridizations between the electron orbitals of the involved oxygen and hydrogen atoms in the C=O:HO hydrogen bond.

  3. Redox-controlled hydrogen bonding: turning a superbase into a strong hydrogen-bond donor.

    Science.gov (United States)

    Wild, Ute; Neuhäuser, Christiane; Wiesner, Sven; Kaifer, Elisabeth; Wadepohl, Hubert; Himmel, Hans-Jörg

    2014-05-12

    Herein the synthesis, structures and properties of hydrogen-bonded aggregates involving redox-active guanidine superbases are reported. Reversible hydrogen bonding is switched on by oxidation of the hydrogen-donor unit, and leads to formation of aggregates in which the hydrogen-bond donor unit is sandwiched by two hydrogen-bond acceptor units. Further oxidation (of the acceptor units) leads again to deaggregation. Aggregate formation is associated with a distinct color change, and the electronic situation could be described as a frozen stage on the way to hydrogen transfer. A further increase in the basicity of the hydrogen-bond acceptor leads to deprotonation reactions.

  4. Influence of temperature and hydroxide concentration on the settling time of hydroxy-catalysis bonds

    Energy Technology Data Exchange (ETDEWEB)

    Reid, S. [Institute for Gravitational Research, Department of Physics and Astronomy, University of Glasgow, SUPA, Scottish Universities Physics Alliance, Glasgow G12 8QQ (United Kingdom)]. E-mail: s.reid@physics.gla.ac.uk; Cagnoli, G. [Institute for Gravitational Research, Department of Physics and Astronomy, University of Glasgow, SUPA, Scottish Universities Physics Alliance, Glasgow G12 8QQ (United Kingdom); Elliffe, E. [Institute for Gravitational Research, Department of Physics and Astronomy, University of Glasgow, SUPA, Scottish Universities Physics Alliance, Glasgow G12 8QQ (United Kingdom); Faller, J. [JILA, NIST and University of Colorado Boulder, CO 80309 (United States); Hough, J. [Institute for Gravitational Research, Department of Physics and Astronomy, University of Glasgow, SUPA, Scottish Universities Physics Alliance, Glasgow, G12 8QQ (United Kingdom); Martin, I. [Institute for Gravitational Research, Department of Physics and Astronomy, University of Glasgow, SUPA, Scottish Universities Physics Alliance, Glasgow G12 8QQ (United Kingdom); Rowan, S. [Institute for Gravitational Research, Department of Physics and Astronomy, University of Glasgow, SUPA, Scottish Universities Physics Alliance, Glasgow G12 8QQ (United Kingdom)

    2007-04-09

    Many applications using bonded optical components have stringent requirements on the strength, rigidity, stability and alignment of the bonds. Hydroxy-catalysis bonding fulfills these requirements. Here we investigate methods by which the bonding time may be extended to better aid the precise prealignment of optical components through controlling the temperature and concentration of the bonding solution.

  5. Hydrogen bond dynamics in bulk alcohols

    NARCIS (Netherlands)

    Shinokita, Keisuke; Cunha, Ana V.; Jansen, Thomas L. C.; Pshenichnikov, Maxim S.

    2015-01-01

    Hydrogen-bonded liquids play a significant role in numerous chemical and biological phenomena. In the past decade, impressive developments in multidimensional vibrational spectroscopy and combined molecular dynamics-quantum mechanical simulation have established many intriguing features of hydrogen

  6. Strong, low-barrier hydrogen bonds may be available to enzymes.

    Science.gov (United States)

    Graham, Jacob D; Buytendyk, Allyson M; Wang, Di; Bowen, Kit H; Collins, Kim D

    2014-01-21

    The debate over the possible role of strong, low-barrier hydrogen bonds in stabilizing reaction intermediates at enzyme active sites has taken place in the absence of an awareness of the upper limits to the strengths of low-barrier hydrogen bonds involving amino acid side chains. Hydrogen bonds exhibit their maximal strengths in isolation, i.e., in the gas phase. In this work, we measured the ionic hydrogen bond strengths of three enzymatically relevant model systems in the gas phase using anion photoelectron spectroscopy; we calibrated these against the hydrogen bond strength of HF2(-), measured using the same technique, and we compared our results with other gas-phase experimental data. The model systems studied here, the formate-formic acid, acetate-acetic acid, and imidazolide-imidazole anionic complexes, all exhibit very strong hydrogen bonds, whose strengths compare favorably with that of the hydrogen bifluoride anion, the strongest known hydrogen bond. The hydrogen bond strengths of these gas-phase complexes are stronger than those typically estimated as being required to stabilize enzymatic intermediates. If there were to be enzyme active site environments that can facilitate the retention of a significant fraction of the strengths of these isolated (gas-phase), hydrogen bonded couples, then low-barrier hydrogen bonding interactions might well play important roles in enzymatic catalysis.

  7. Hydrogen Bonding to Alkanes: Computational Evidence

    DEFF Research Database (Denmark)

    Hammerum, Steen; Olesen, Solveig Gaarn

    2009-01-01

    The structural, vibrational, and energetic properties of adducts of alkanes and strong cationic proton donors were studied with composite ab initio calculations. Hydrogen bonding in [D-H+ H-alkyl] adducts contributes to a significant degree to the interactions between the two components, which...... is substantiated by NBO and AIM results. The hydrogen bonds manifest themselves in the same manner as conventional hydrogen bonds, D-H bond elongation, D-H vibrational stretching frequency red shift and intensity increase, and adduct stabilization. The alkane adducts also exhibit elongation of the C-H bonds...

  8. Hydrogen-bonded sheets in benzylmethylammonium hydrogen maleate.

    Science.gov (United States)

    Santacruz, Lynay; Abonia, Rodrigo; Cobo, Justo; Low, John N; Glidewell, Christopher

    2007-10-01

    In the title compound, C(8)H(12)N(+).C(4)H(3)O(4)(-), there is a short and almost linear but asymmetric O-H...O hydrogen bond in the anion. The ions are linked into C(2)(2)(6) chains by two short and nearly linear N-H...O hydrogen bonds and the chains are further weakly linked into sheets by a single C-H...O hydrogen bond.

  9. Hydrogen Bonds in Excited State Proton Transfer

    Science.gov (United States)

    Horke, D. A.; Watts, H. M.; Smith, A. D.; Jager, E.; Springate, E.; Alexander, O.; Cacho, C.; Chapman, R. T.; Minns, R. S.

    2016-10-01

    Hydrogen bonding interactions between biological chromophores and their surrounding protein and solvent environment significantly affect the photochemical pathways of the chromophore and its biological function. A common first step in the dynamics of these systems is excited state proton transfer between the noncovalently bound molecules, which stabilizes the system against dissociation and principally alters relaxation pathways. Despite such fundamental importance, studying excited state proton transfer across a hydrogen bond has proven difficult, leaving uncertainties about the mechanism. Through time-resolved photoelectron imaging measurements, we demonstrate how the addition of a single hydrogen bond and the opening of an excited state proton transfer channel dramatically changes the outcome of a photochemical reaction, from rapid dissociation in the isolated chromophore to efficient stabilization and ground state recovery in the hydrogen bonded case, and uncover the mechanism of excited state proton transfer at a hydrogen bond, which follows sequential hydrogen and charge transfer processes.

  10. Optimising hydrogen bonding in solid wood

    DEFF Research Database (Denmark)

    Engelund, Emil Tang

    2009-01-01

    The chemical bonds of wood are both covalent bonds within the wood polymers and hydrogen bonds within and between the polymers. Both types of bonds are responsible for the coherence, strength and stiffness of the material. The hydrogen bonds are more easily modified by changes in load, moisture...... and temperature. The distribution of bond lengths was examined using infrared spectroscopy (ATR-FTIR) both prior to treatments and after. The results show that the absorbance bands of the spectra related to the hydroxyl and carboxyl stretching vibrations were changed by the treatments. Apparently, the first...

  11. Hydrogen bond dynamics in bulk alcohols

    Energy Technology Data Exchange (ETDEWEB)

    Shinokita, Keisuke; Cunha, Ana V.; Jansen, Thomas L. C.; Pshenichnikov, Maxim S., E-mail: Maxim.Pchenitchnikov@RuG.nl [Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen (Netherlands)

    2015-06-07

    Hydrogen-bonded liquids play a significant role in numerous chemical and biological phenomena. In the past decade, impressive developments in multidimensional vibrational spectroscopy and combined molecular dynamics–quantum mechanical simulation have established many intriguing features of hydrogen bond dynamics in one of the fundamental solvents in nature, water. The next class of a hydrogen-bonded liquid—alcohols—has attracted much less attention. This is surprising given such important differences between water and alcohols as the imbalance between the number of hydrogen bonds, each molecule can accept (two) and donate (one) and the very presence of the hydrophobic group in alcohols. Here, we use polarization-resolved pump-probe and 2D infrared spectroscopy supported by extensive theoretical modeling to investigate hydrogen bond dynamics in methanol, ethanol, and isopropanol employing the OH stretching mode as a reporter. The sub-ps dynamics in alcohols are similar to those in water as they are determined by similar librational and hydrogen-bond stretch motions. However, lower density of hydrogen bond acceptors and donors in alcohols leads to the appearance of slow diffusion-controlled hydrogen bond exchange dynamics, which are essentially absent in water. We anticipate that the findings herein would have a potential impact on fundamental chemistry and biology as many processes in nature involve the interplay of hydrophobic and hydrophilic groups.

  12. Entropic origin of cobalt-carbon bond cleavage catalysis in adenosylcobalamin-dependent ethanolamine ammonia-lyase.

    Science.gov (United States)

    Wang, Miao; Warncke, Kurt

    2013-10-09

    Adenosylcobalamin-dependent enzymes accelerate the cleavage of the cobalt-carbon (Co-C) bond of the bound coenzyme by >10(10)-fold. The cleavage-generated 5'-deoxyadenosyl radical initiates the catalytic cycle by abstracting a hydrogen atom from substrate. Kinetic coupling of the Co-C bond cleavage and hydrogen-atom-transfer steps at ambient temperatures has interfered with past experimental attempts to directly address the factors that govern Co-C bond cleavage catalysis. Here, we use time-resolved, full-spectrum electron paramagnetic resonance spectroscopy, with temperature-step reaction initiation, starting from the enzyme-coenzyme-substrate ternary complex and (2)H-labeled substrate, to study radical pair generation in ethanolamine ammonia-lyase from Salmonella typhimurium at 234-248 K in a dimethylsulfoxide/water cryosolvent system. The monoexponential kinetics of formation of the (2)H- and (1)H-substituted substrate radicals are the same, indicating that Co-C bond cleavage rate-limits radical pair formation. Analysis of the kinetics by using a linear, three-state model allows extraction of the microscopic rate constant for Co-C bond cleavage. Eyring analysis reveals that the activation enthalpy for Co-C bond cleavage is 32 ± 1 kcal/mol, which is the same as for the cleavage reaction in solution. The origin of Co-C bond cleavage catalysis in the enzyme is, therefore, the large, favorable activation entropy of 61 ± 6 cal/(mol·K) (relative to 7 ± 1 cal/(mol·K) in solution). This represents a paradigm shift from traditional, enthalpy-based mechanisms that have been proposed for Co-C bond-breaking in B12 enzymes. The catalysis is proposed to arise from an increase in protein configurational entropy along the reaction coordinate.

  13. HYDROGEN BONDING IN POLYMERIC ADSORBENTS BASED ADSORPTION AND SEPARATION

    Institute of Scientific and Technical Information of China (English)

    XUMancai; SHIZuoqing; 等

    2000-01-01

    After a concise introduction of hydrogen bonding effects in solute-solute and solute-solvent bonding,the design of polymeric adsorbents based on hydrogen bonding ,selectivity in adsorption through hydrogen bonding,and characterization of hydrogen bonding in adsorption and separation were reviewed with 28 references.

  14. Water, Hydrogen Bonding and the Microwave Background

    Directory of Open Access Journals (Sweden)

    Robitaille P.-M.

    2009-04-01

    Full Text Available n this work, the properties of the water are briefly revisited. Though liquid water has a fleeting structure, it displays an astonishingly stable network of hydrogen bonds. Thus, even as a liquid, water possesses a local lattice with short range order. The presence of hydroxyl (O-H and hydrogen (H....OH2 bonds within water, indicate that it can simultaneously maintain two separate energy systems. These can be viewed as two very different temperatures. The analysis presented uses results from vibrational spec- troscopy, extracting the force constant for the hydrogen bonded dimer. By idealizing this species as a simple diatomic structure, it is shown that hydrogen bonds within wa- ter should be able to produce thermal spectra in the far infrared and microwave regions of the electromagnetic spectrum. This simple analysis reveals that the oceans have a physical mechanism at their disposal, which is capable of generating the microwave background.

  15. Methandiide as a non-innocent ligand in carbene complexes: from the electronic structure to bond activation reactions and cooperative catalysis.

    Science.gov (United States)

    Becker, Julia; Modl, Tanja; Gessner, Viktoria H

    2014-09-01

    The synthesis of a ruthenium carbene complex based on a sulfonyl-substituted methandiide and its application in bond activation reactions and cooperative catalysis is reported. In the complex, the metal-carbon interaction can be tuned between a Ru-C single bond with additional electrostatic interactions and a Ru=C double bond, thus allowing the control of the stability and reactivity of the complex. Hence, activation of polar and non-polar bonds (O-H, H-H) as well as dehydrogenation reactions become possible. In these reactions the carbene acts as a non-innocent ligand supporting the bond activation as nucleophilic center in the 1,2-addition across the metal-carbon double bond. This metal-ligand cooperativity can be applied in the catalytic transfer hydrogenation for the reduction of ketones. This concept opens new ways for the application of carbene complexes in catalysis.

  16. Thermodynamic Strategies for C-O Bond Formation and Cleavage via Tandem Catalysis.

    Science.gov (United States)

    Lohr, Tracy L; Li, Zhi; Marks, Tobin J

    2016-05-17

    To reduce global reliance on fossil fuels, new renewable sources of energy that can be used with the current infrastructure are required. Biomass represents a major source of renewable carbon based fuel; however, the high oxygen content (∼40%) limits its use as a conventional fuel. To utilize biomass as an energy source, not only with current infrastructure, but for maximum energy return, the oxygen content must be reduced. One method to achieve this is to develop selective catalytic methods to cleave C-O bonds commonly found in biomass (aliphatic and aromatic ethers and esters) for the eventual removal of oxygen in the form of volatile H2O or carboxylic acids. Once selective methods of C-O cleavage are understood and perfected, application to processing real biomass feedstocks such as lignin can be undertaken. This Laboratory previously reported that recyclable "green" lanthanide triflates are excellent catalysts for C-O bond-forming hydroalkoxylation reactions. Based on the virtues of microscopic reversibility, the same lanthanide triflate catalyst should catalyze the reverse C-O cleavage process, retrohydroalkoxylation, to yield an alcohol and an alkene. However, ether C-O bond-forming (retrohydroalkoxylation) to form an alcohol and alkene is endothermic. Guided by quantum chemical analysis, our strategy is to couple endothermic, in tandem, ether C-O bond cleavage with exothermic alkene hydrogenation, thereby leveraging the combined catalytic cycles thermodynamically to form an overall energetically favorable C-O cleavage reaction. This Account reviews recent developments on thermodynamically leveraged tandem catalysis for ether and more recently, ester C-O bond cleavage undertaken at Northwestern University. First, the fundamentals of lanthanide-catalyzed hydroelementation are reviewed, with particular focus on ether C-O bond formation (hydroalkoxylation). Next, the reverse C-O cleavage/retrohydroalkoxylation processes enabled by tandem catalysis are

  17. The effect of crystal orientation on the cryogenic strength of hydroxide catalysis bonded sapphire

    Science.gov (United States)

    Haughian, K.; Douglas, R.; van Veggel, A. A.; Hough, J.; Khalaidovski, A.; Rowan, S.; Suzuki, T.; Yamamoto, K.

    2015-04-01

    Hydroxide catalysis bonding has been used in gravitational wave detectors to precisely and securely join components of quasi-monolithic silica suspensions. Plans to operate future detectors at cryogenic temperatures has created the need for a change in the test mass and suspension material. Mono-crystalline sapphire is one candidate material for use at cryogenic temperatures and is being investigated for use in the KAGRA detector. The crystalline structure of sapphire may influence the properties of the hydroxide catalysis bond formed. Here, results are presented of studies of the potential influence of the crystal orientation of sapphire on the shear strength of the hydroxide catalysis bonds formed between sapphire samples. The strength was tested at approximately 8 K; this is the first measurement of the strength of such bonds between sapphire at such reduced temperatures. Our results suggest that all orientation combinations investigated produce bonds of sufficient strength for use in typical mirror suspension designs, with average strengths >23 MPa.

  18. Hydrogen bonds in PC61BM solids

    Science.gov (United States)

    Sheng, Chun-Qi; Li, Wen-Jie; Du, Ying-Ying; Chen, Guang-Hua; Chen, Zheng; Li, Hai-Yang; Li, Hong-Nian

    2015-09-01

    We have studied the hydrogen bonds in PC61BM solids. Inter-molecular interaction is analyzed theoretically for the well-defined monoclinic (P21/n) structure. The results indicate that PC61BM combines into C-H⋯Od bonded molecular chains, where Od denotes the doubly-bonded O atom of PC61BM. The molecular chains are linked together by C-H⋯Os bonds, where Os denotes the singly-bonded O atom of PC61BM. To reveal the consequences of hydrogen bond formation on the structural properties of PC61BM solids (not limited to the monoclinic structure), we design and perform some experiments for annealed samples with the monoclinic (P21/n) PC61BM as starting material. The experiments include differential scanning calorimetry, X-ray diffraction and infrared absorption measurements. Structural phase transitions are observed below the melting point. The C-H⋯Od bonds seem persisting in the altered structures. The inter-molecular hydrogen bonds can help to understand the phase separation in polymer/PC61BM blends and may be responsible for the existence of liquid PC61BM.

  19. On the nature of blueshifting hydrogen bonds.

    Science.gov (United States)

    Mo, Yirong; Wang, Changwei; Guan, Liangyu; Braïda, Benoît; Hiberty, Philippe C; Wu, Wei

    2014-07-01

    The block-localized wave function (BLW) method can derive the energetic, geometrical, and spectral changes with the deactivation of electron delocalization, and thus provide a unique way to elucidate the origin of improper, blueshifting hydrogen bonds versus proper, redshifting hydrogen bonds. A detailed analysis of the interactions of F(3)CH with NH(3) and OH(2) shows that blueshifting is a long-range phenomenon. Since among the various energy components contributing to hydrogen bonds, only the electrostatic interaction has long-range characteristics, we conclude that the contraction and blueshifting of a hydrogen bond is largely caused by electrostatic interactions. On the other hand, lengthening and redshifting is primarily due to the short-range n(Y)→σ*(X-H) hyperconjugation. The competition between these two opposing factors determines the final frequency change direction, for example, redshifting in F(3)CH⋅⋅⋅NH(3) and blueshifting in F(3)CH⋅⋅⋅OH(2). This mechanism works well in the series F(n)Cl(3)-n CH⋅⋅⋅Y (n=0-3, Y=NH(3), OH(2), SH(2)) and other systems. One exception is the complex of water and benzene. We observe the lengthening and redshifting of the O-H bond of water even with the electron transfer between benzene and water completely quenched. A distance-dependent analysis for this system reveals that the long-range electrostatic interaction is again responsible for the initial lengthening and redshifting.

  20. A HYDROGEN BONDING ASSISTED CATALYST SCREENED OUT VIA COMBINATORIAL CHEMISTRY STRATEGY

    Institute of Scientific and Technical Information of China (English)

    XUMancai; OUZhize; 等

    2000-01-01

    Possibilities for enhancement of catalytic reaction rate by combining phase transfer catalysis and hydrogen bonding of the catalyst with the substrate and reagent were studied.A phase transfer catalyst library with sixty polystyrene-supported quaternary ammonium salt catalysts was synthesized.The reduction of acetophenone by NaBH4 was used as the probing reaction to select out the ost active catalyst in the library by using iterative method.which was the gel-type triethanolamine aminsating strongly asic anion exchange resin with the crosslinking degeree of 2% A hydrogen bonding assisted catalytic mechanism was proposed to explain the high catalytic activity of the catalyst.

  1. Hydrogen Sulfide Induced Carbon Dioxide Activation by Metal-Free Dual Catalysis.

    Science.gov (United States)

    Kumar, Manoj; Francisco, Joseph S

    2016-03-18

    The role of metal free dual catalysis in the hydrogen sulfide (H2S)-induced activation of carbon dioxide (CO2) and subsequent decomposition of resulting monothiolcarbonic acid in the gas phase has been explored. The results suggest that substituted amines and monocarboxylic type organic or inorganic acids via dual activation mechanisms promote both activation and decomposition reactions, implying that the judicious selection of a dual catalyst is crucial to the efficient C-S bond formation via CO2 activation. Considering that our results also suggest a new mechanism for the formation of carbonyl sulfide from CO2 and H2S, these new insights may help in better understanding the coupling between the carbon and sulfur cycles in the atmospheres of Earth and Venus.

  2. The Nature of the Hydrogen Bond Outline of a Comprehensive Hydrogen Bond Theory

    CERN Document Server

    Gilli, Gastone

    2009-01-01

    Hydrogen bond (H-bond) effects are known: it makes sea water liquid, joins cellulose microfibrils in trees, shapes DNA into genes and polypeptide chains into wool, hair, muscles or enzymes. Its true nature is less known and we may still wonder why O-H...O bond energies range from less than 1 to more than 30 kcal/mol without apparent reason. This H-bond puzzle is re-examined here from its very beginning and presented as an inclusive compilation of experimental H-bond energies andgeometries.New concepts emerge from this analysis: new classes of systematically strong H-bonds (CAHBs and RAHBs: cha

  3. Modeling the Hydrogen Bond within Molecular Dynamics

    Science.gov (United States)

    Lykos, Peter

    2004-01-01

    The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.

  4. Intramolecular hydrogen bonding in medicinal chemistry.

    Science.gov (United States)

    Kuhn, Bernd; Mohr, Peter; Stahl, Martin

    2010-03-25

    The formation of intramolecular hydrogen bonds has a very pronounced effect on molecular structure and properties. We study both aspects in detail with the aim of enabling a more rational use of this class of interactions in medicinal chemistry. On the basis of exhaustive searches in crystal structure databases, we derive propensities for intramolecular hydrogen bond formation of five- to eight-membered ring systems of relevance in drug discovery. A number of motifs, several of which are clearly underutilized in drug discovery, are analyzed in more detail by comparing small molecule and protein-ligand X-ray structures. To investigate effects on physicochemical properties, sets of closely related structures with and without the ability to form intramolecular hydrogen bonds were designed, synthesized, and characterized with respect to membrane permeability, water solubility, and lipophilicity. We find that changes in these properties depend on a subtle balance between the strength of the hydrogen bond interaction, geometry of the newly formed ring system, and the relative energies of the open and closed conformations in polar and unpolar environments. A number of general guidelines for medicinal chemists emerge from this study.

  5. At the frontier between heterogeneous and homogeneous catalysis: hydrogenation of olefins and alkynes with soluble iron nanoparticles.

    Science.gov (United States)

    Rangheard, Claudine; de Julián Fernández, César; Phua, Pim-Huat; Hoorn, Johan; Lefort, Laurent; de Vries, Johannes G

    2010-09-28

    The use of non-supported Fe nanoparticles in the hydrogenation of unsaturated C-C bonds is a green catalytic concept at the frontier between homogeneous and heterogeneous catalysis. Iron nanoparticles can be obtained by reducing Fe salts with strong reductants in various solvents. FeCl(3) reduced by 3 equivalents of EtMgCl forms an active catalyst for the hydrogenation of a range of olefins and alkynes. Olefin hydrogenation is relatively fast at 5 bar using 5 mol% of catalyst. The catalyst is also active for terminal olefins and 1,1' and 1,2-cis disubstituted olefins while trans-olefins react much slower. 1-Octyne is hydrogenated to mixtures of 1-octene and octane. Kinetic studies led us to propose a mechanism for this latter transformation where octane is obtained by two different pathways. Characterization of the nanoparticles via TEM, magnetic measurements and poisoning experiments were undertaken to understand the true nature of our catalyst.

  6. Statistical theory for hydrogen bonding fluid system of AaDd type (Ⅱ): Properties of hydrogen bonding networks

    Institute of Scientific and Technical Information of China (English)

    WANG HaiJun; HONG XiaoZhong; GU Fang; BA XinWu

    2007-01-01

    Making use of the invariant property of the equilibrium size distribution of the hydrogen bonding clusters formed in hydrogen bonding system of AaDd type, the analytical expressions of the free energy in pregel and postgel regimes are obtained. Then the gel free energy and the scaling behavior of the number of hydrogen bonds in gel phase near the critical point are investigated to give the corresponding scaling exponents and scaling law. Meanwhile, some properties of intermolecular and intramolecular hydrogen bonds in the system, sol and gel phases are discussed. As a result, the explicit relationship between the number of intramolecular hydrogen bonds and hydrogen bonding degree is obtained.

  7. Halogen bonds in crystal engineering: like hydrogen bonds yet different.

    Science.gov (United States)

    Mukherjee, Arijit; Tothadi, Srinu; Desiraju, Gautam R

    2014-08-19

    The halogen bond is an attractive interaction in which an electrophilic halogen atom approaches a negatively polarized species. Short halogen atom contacts in crystals have been known for around 50 years. Such contacts are found in two varieties: type I, which is symmetrical, and type II, which is bent. Both are influenced by geometric and chemical considerations. Our research group has been using halogen atom interactions as design elements in crystal engineering, for nearly 30 years. These interactions include halogen···halogen interactions (X···X) and halogen···heteroatom interactions (X···B). Many X···X and almost all X···B contacts can be classified as halogen bonds. In this Account, we illustrate examples of crystal engineering where one can build up from previous knowledge with a focus that is provided by the modern definition of the halogen bond. We also comment on the similarities and differences between halogen bonds and hydrogen bonds. These interactions are similar because the protagonist atoms-halogen and hydrogen-are both electrophilic in nature. The interactions are distinctive because the size of a halogen atom is of consequence when compared with the atomic sizes of, for example, C, N, and O, unlike that of a hydrogen atom. Conclusions may be drawn pertaining to the nature of X···X interactions from the Cambridge Structural Database (CSD). There is a clear geometric and chemical distinction between type I and type II, with only type II being halogen bonds. Cl/Br isostructurality is explained based on a geometric model. In parallel, experimental studies on 3,4-dichlorophenol and its congeners shed light on the nature of halogen···halogen interactions and reveal the chemical difference between Cl and Br. Variable temperature studies also show differences between type I and type II contacts. In terms of crystal design, halogen bonds offer a unique opportunity in the strength, atom size and interaction gradation; this may be

  8. Advances in interactive supported electro-catalysis for hydrogen and oxygen electrode reactions

    Energy Technology Data Exchange (ETDEWEB)

    Nedeljko V Krstajic; Ljiljana M Vracar; Jelena M Jaksic; Milan M Jaksic [Faculty of Technology and Metallurgy, University of Belgrade, Belgrade, Serbia and Montenegro (Yugoslavia); Stelios G Neophytides; Miranda Labou; Jelena M Jaksic; Milan M Jaksic [Institute of Chemical Engineering and High Temperature Chemical Processes FORTH, and Department of Chemistry, University of Patras, 26500 Patras, (Greece); Reidar Tunold [University of Trondheim, NTNU, Institute of Industrial Electrochemistry, Trondheim, (Norway); Polycarpos Falaras [Institute of Physical Chemistry, NCSR Demokritos, Attikis, Athens, (Greece)

    2006-07-01

    Magneli phases have been introduced as an unique electron conductive and interactive support for electro-catalysis both in hydrogen (HELR) and oxygen (OELR) electrode reactions in water electrolysis and Low Temperature PEM Fuel Cells (LT PEM FC). The Strong Metal-Support Interaction (SMSI) that imposes the former implies: (i) the hypo-hyper-d inter-bonding effect and its catalytic consequences, and (ii) the interactive primary oxide (M-OH) spillover from the hypo-d-oxide support as a dynamic electrocatalytic contribution. The stronger the bonding, the more strained appear d-orbitals, thereby the less strong the intermediate adsorptive strength in the rate determining step (RDS), and consequently, the faster the facilitated catalytic electrode reaction arises. At the same time the primary oxide spillover transferred from the hypo-d-oxide support directly interferes and reacts either individually and directly to contribute to finish the oxygen reduction, or with other interactive species, like CO to contribute to the CO tolerance. In such a respect, the conditions to provide Au to act as the reversible hydrogen electrode have been proved either by its potentiodynamic surface reconstruction in a heavy water solution, or by the nano-structured SMSI Au on anatase titania with characteristic strained d-orbitals in such a hypo-hyper-d-interactive bonding (Au/TiO{sub 2}). In the same context, the monoatomic network dispersion of Pt upon Magneli phases makes it possible to produce an advanced interactive supported electro-catalyst for cathodic oxygen reduction (ORR). The strained hypo-hyper-d-inter-electronic and inter-d-orbital metal/hypo-d-oxide support bonding relative to the strength of the latter, has been inferred to be the basis of the synergistic electrocatalytic effect both in the HELR and ORR. (authors)

  9. Formaldoxime hydrogen bonded complexes with ammonia and hydrogen chloride

    Science.gov (United States)

    Golec, Barbara; Mucha, Małgorzata; Sałdyka, Magdalena; Barnes, Austin; Mielke, Zofia

    2015-02-01

    An infrared spectroscopic and MP2/6-311++G(2d,2p) study of hydrogen bonded complexes of formaldoxime with ammonia and hydrogen chloride trapped in solid argon matrices is reported. Both 1:1 and 1:2 complexes between formaldoxime and ammonia, hydrogen chloride have been identified in the CH2NOH/NH3/Ar, CH2NOH/HCl/Ar matrices, respectively, their structures were determined by comparison of the spectra with the results of calculations. In the 1:1 complexes present in the argon matrices the OH group of formaldoxime acts as a proton donor for ammonia and the nitrogen atom acts as a proton acceptor for hydrogen chloride. In the 1:2 complexes ammonia or hydrogen chloride dimers interact both with the OH group and the nitrogen atom of CH2NOH to form seven membered cyclic structures stabilized by three hydrogen bonds. The theoretical spectra generally agree well with the experimental ones, but they seriously underestimate the shift of the OH stretch for the 1:1 CH2NOH⋯NH3 complex.

  10. Cooperativity in Surface Bonding and Hydrogen Bonding of Water and Hydroxyl at Metal Surfaces

    DEFF Research Database (Denmark)

    Schiros, T.; Ogasawara, H.; Naslund, L. A.;

    2010-01-01

    of the mixed phase at metal surfaces. The surface bonding can be considered to be similar to accepting a hydrogen bond, and we can thereby apply general cooperativity rules developed for hydrogen-bonded systems. This provides a simple understanding of why water molecules become more strongly bonded...... to the surface upon hydrogen bonding to OH and why the OH surface bonding is instead weakened through hydrogen bonding to water. We extend the application of this simple model to other observed cooperativity effects for pure water adsorption systems and H3O+ on metal surfaces.......We examine the balance of surface bonding and hydrogen bonding in the mixed OH + H2O overlayer on Pt(111), Cu(111), and Cu(110) via density functional theory calculations. We find that there is a cooperativity effect between surface bonding and hydrogen bonding that underlies the stability...

  11. Water lubricates hydrogen-bonded molecular machines

    Science.gov (United States)

    Panman, Matthijs R.; Bakker, Bert H.; den Uyl, David; Kay, Euan R.; Leigh, David A.; Buma, Wybren Jan; Brouwer, Albert M.; Geenevasen, Jan A. J.; Woutersen, Sander

    2013-11-01

    The mechanical behaviour of molecular machines differs greatly from that of their macroscopic counterparts. This applies particularly when considering concepts such as friction and lubrication, which are key to optimizing the operation of macroscopic machinery. Here, using time-resolved vibrational spectroscopy and NMR-lineshape analysis, we show that for molecular machinery consisting of hydrogen-bonded components the relative motion of the components is accelerated strongly by adding small amounts of water. The translation of a macrocycle along a thread and the rotation of a molecular wheel around an axle both accelerate significantly on the addition of water, whereas other protic liquids have much weaker or opposite effects. We tentatively assign the superior accelerating effect of water to its ability to form a three-dimensional hydrogen-bond network between the moving parts of the molecular machine. These results may indicate a more general phenomenon that helps explain the function of water as the ‘lubricant of life’.

  12. Chiral benzimidazoles as hydrogen bonding organocatalysts

    OpenAIRE

    Nájera Domingo, Carmen; Yus Astiz, Miguel

    2015-01-01

    Several bifunctional organocatalysts bearing the benzimidazole unit have been designed in order to act as bifunctional systems by hydrogen bonding. Chiral 2-aminobenzimidazoles are conformational rigid guanidines able to catalyze enantioselectively Michael reaction, direct SN1 of alcohols, and aldol reactions. Some of these organocatalysts can be easily recovered by simple isolation methods and reused without loss of catalytic activity. Related (2-aminoalkyl)benzimidazoles have been used as c...

  13. Rhodium mediated bond activation: from synthesis to catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Ho, Hung-An [Iowa State Univ., Ames, IA (United States)

    2012-01-01

    Recently, our lab has developed monoanionic tridentate ligand, ToR, showing the corresponding coordination chemistry and catalyst reactivity of magnesium, zirconium, zinc and iridium complexes. This thesis details synthetic chemistry, structural study and catalytic reactivity of the ToR-supported rhodium compounds. Tl[ToR] has been proved to be a superior ligand transfer agent for synthesizing rhodium complexes. The salt metathesis route of Tl[ToM] with [Rh(μ-Cl)(CO)]2 and [Rh(μ- Cl)(COE)]2 gives ToMRh(CO)2 (2.2) and ToMRhH(β3-C8H13) (3.1) respectively while Tl[ToM] with [Rh(μ-Cl)(CO)]2 affords ToPRh(CO)2 (2.3). 2.2 reacts with both strong and weak electrophiles, resulting in the oxazoline N-attacked and the metal center-attacked compounds correspondingly. Using one of the metal center-attacked electrophiles, 2.3 was demonstrated to give high diastereoselectivity. Parallel to COE allylic C-H activation complex 3.1, the propene and allylbenzene allylic C-H activation products have also been synthesized. The subsequent functionalization attempts have been examined by treating with Brønsted acids, Lewis acids, electrophiles, nucleophiles, 1,3-dipolar reagents and reagents containing multiple bonds able to be inserted. Various related complexes have been obtained under these conditions, in which one of the azide insertion compounds reductively eliminates to give an allylic functionalization product stoichiometrically. 3.1 reacts with various primary alcohols to give the decarbonylation dihydride complex ToMRh(H)2CO (4.1). 4.1 shows catalytic reactivity for primary alcohol decarbonylation under a photolytic condition. Meanwhile, 2.2 has been found to be more reactive than 4.1 for catalytic alcohol decarbonylation under the same condition. Various complexes and primary

  14. Studies on Hydrogen Bonding Network Structures of Konjac Glucomannan

    Institute of Scientific and Technical Information of China (English)

    PANG Jie; SUN Yu-Jing; YANG You-Hui; CHEN Yuan-Yuan; CHEN Yi-Qing; SUN Yuan-Ming

    2008-01-01

    In this paper, the hydrogen bonding network models of konjac glucomannan (KGM) are predicted in the approach of molecular dynamics (MD). These models have been proved by experiments whose results are consistent with those from simulation.The results show that the hydrogen bonding network structures of KGM are stable and the key linking points of hydrogen bonding network are at the O(6) and O(2) positions on KGM ring. Moreover, acety1 has significant influence on hydrogen bonding network and hydrogen bonding network structures are more stable after deacetylation.

  15. Theoretical studies of the proton transfer behaviors in molecular complexes analogous to catalytic triad of serine protease:Toward understanding the existence and significance of the low-barrier hydrogen-bond in enzymatic catalysis

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    A representative acetate-(5-methylimidazole)-methanol system has been employed as a model of catalytic triad in serine protease to validate the formation processes of lowbarrier H-bonds(LBHB) at the B3LYP/6-311++G level of theory,and variable H-bonding characters from conventional ones to LBHBs have been represented along with the proceedings of proton transfer.Solvent effect is an important factor in modulation of the existence of an LBHB,where an LBHB(or a conventional H-bond) in the gas phase can be changed into a non-LBHB(an LBHB) upon solvation.The origin of the additional stabili-zation energy arising from the LBHB may be attributed to the H-bonding energy difference before and after proton transfer because the shared proton can freely move between the proton donor and proton acceptor.Most importantly,the order of magnitude of the stabilization energy depends on the studied systems.Furthermore,the nonexistence of LBHBs in the catalytic triad of serine proteases has been verified in a more sophisticated model treated using the ONIOM method.As a result,only the single proton transfer mechanism in the catalytic triad has been confirmed and the origin of the powerful catalytic efficiency of serine proteases should be attributed to other factors rather than the LBHB.

  16. AAA-DDD triple hydrogen bond complexes.

    Science.gov (United States)

    Blight, Barry A; Camara-Campos, Amaya; Djurdjevic, Smilja; Kaller, Martin; Leigh, David A; McMillan, Fiona M; McNab, Hamish; Slawin, Alexandra M Z

    2009-10-01

    Experiment and theory both suggest that the AAA-DDD pattern of hydrogen bond acceptors (A) and donors (D) is the arrangement of three contiguous hydrogen bonding centers that results in the strongest association between two species. Murray and Zimmerman prepared the first example of such a system (complex 3*2) and determined the lower limit of its association constant (K(a)) in CDCl(3) to be 10(5) M(-1) by (1)H NMR spectroscopy (Murray, T. J. and Zimmerman, S. C. J. Am. Chem. Soc. 1992, 114, 4010-4011). The first cationic AAA-DDD pair (3*4(+)) was described by Bell and Anslyn (Bell, D. A. and Anslyn, E. A. Tetrahedron 1995, 51, 7161-7172), with a K(a) > 5 x 10(5) M(-1) in CH(2)Cl(2) as determined by UV-vis spectroscopy. We were recently able to quantify the strength of a neutral AAA-DDD arrangement using a more chemically stable AAA-DDD system, 6*2, which has an association constant of 2 x 10(7) M(-1) in CH(2)Cl(2) (Djurdjevic, S., Leigh, D. A., McNab, H., Parsons, S., Teobaldi, G. and Zerbetto, F. J. Am. Chem. Soc. 2007, 129, 476-477). Here we report on further AA(A) and DDD partners, together with the first precise measurement of the association constant of a cationic AAA-DDD species. Complex 6*10(+)[B(3,5-(CF(3))(2)C(6)H(3))(4)(-)] has a K(a) = 3 x 10(10) M(-1) at RT in CH(2)Cl(2), by far the most strongly bound triple hydrogen bonded system measured to date. The X-ray crystal structure of 6*10(+) with a BPh(4)(-) counteranion shows a planar array of three short (NH...N distances 1.95-2.15 A), parallel (but staggered rather than strictly linear; N-H...N angles 165.4-168.8 degrees), primary hydrogen bonds. These are apparently reinforced, as theory predicts, by close electrostatic interactions (NH-*-N distances 2.78-3.29 A) between each proton and the acceptor atoms of the adjacent primary hydrogen bonds.

  17. Intramolecular hydrogen bonding in myricetin and myricitrin

    DEFF Research Database (Denmark)

    Vojta, Danijela; Dominkovic, Katarina; Miljanic, Snezana;

    2016-01-01

    The molecular structures of myricetin (3,3’,4’,5,5’,7-hexahydroxyflavone; MCE) and myricitrin (myricetin 3-O-rhamnoside; MCI) are investigated by quantum chemical calculations (B3LYP/6-311G**). Two preferred molecular rotamers of MCI are predicted, corresponding to different conformations of the O......-rhamnoside subunit. The rotamers are characterized by different hydrogen bonded cross-links between the hydroxy groups of the rhamnoside substituent and the parent MCE moiety. The predicted OH stretching frequencies are compared with vibrational spectra of MCE and MCI recorded for the sake of this investigation (IR...

  18. Intramolecular hydrogen bonding in myricetin and myricitrin

    DEFF Research Database (Denmark)

    Vojta, Danijela; Dominkovic, Katarina; Miljanic, Snezana;

    2017-01-01

    The molecular structures of myricetin (3,3’,4’,5,5’,7-hexahydroxyflavone; MCE) and myricitrin (myricetin 3-O-rhamnoside; MCI) are investigated by quantum chemical calculations (B3LYP/6-311G**). Two preferred molecular rotamers of MCI are predicted, corresponding to different conformations of the O......-rhamnoside subunit. The rotamers are characterized by different hydrogen bonded cross-links between the hydroxy groups of the rhamnoside substituent and the parent MCE moiety. The predicted OH stretching frequencies are compared with vibrational spectra of MCE and MCI recorded for the sake of this investigation (IR...

  19. Constructing supramolecular nanostructure by hydrogen-bonding

    Institute of Scientific and Technical Information of China (English)

    LI YiBao; ZENG QingDao; WANG ZhiHui; QI GuiCun; GUAN Li; FAN XiaoLin; WANG Chen

    2008-01-01

    The diquinoxalino (2.3-2'.3'-a.c) phenazine (DQP), containing 6 nitrogen atoms, was synthesized, and its adsorption and self-assembling behavior on highly oriented pyrolytic graphite (HOPG) was studied by scanning tunneling microscopy (STM) under ambient conditions. With 1,14-tetradecanedioic acid as a bridge, uniform two-dimensional arrays of 1,14-tetradecanedioic acid/DQP nanostrueture were suc-cessfully fabricated. The result illustrates that it is possible to construct and control supramolecular nanostructure by intermolecular hydrogen-bonding.

  20. Molecular dynamics simulations of the hydration of poly(vinyl methyl ether): Hydrogen bonds and quasi-hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    WU RongLiang; JI Qing; KONG Bin; YANG XiaoZhen

    2008-01-01

    Atomistic detailed hydration structures of poly(vinyl methyl ether) (PVME) have been investigated by molecular dynamics simulations under 300 K at various concentrations. Both radial distribution func-tions and the distance distributions between donors and acceptors in hydrogen bonds show that the hydrogen bonds between the polymer and water are shorter by 0.005 nm than those between water molecules. The Quasi-hydrogen bonds take only 7.2% of the van der Waals interaction pairs. It was found the hydrogen bonds are not evenly distributed along the polymer chain, and there still exists a significant amount (10%) of ether oxygen atoms that are not hydrogen bonded to water at a concentra-tion as low as 3.3%. This shows that in polymer solutions close contacts occur not only between polymer chains but also between chain segments within the polymer, which leads to inefficient con-tacts between ether oxygen atoms and water molecules. Variation of the quasi-hydrogen bonds with the concentration is similar to that of hydrogen bonds, but the ratio of the repeat units forming quasi-hydrogen bonds to those forming hydrogen bonds approaches 0.2. A transition was found in the demixing enthalpy at around 30% measured by dynamic testing differential scanning calorimetry (DTDSC) for aqueous solutions of a mono-dispersed low molecular weight PVME, which can be related to the transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ~27%. The transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ~27% can be used to explain the demixing enthalpy transition at 30% at a molecular scale. In addition, at the concentration of 86%, each ether oxygen atom bonded with water is assigned 1.56 water molecules on average, and 'free' water molecules emerge at the concentration of around 54%.

  1. Molecular dynamics simulations of the hydration of poly(vinyl methyl ether):Hydrogen bonds and quasi-hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Atomistic detailed hydration structures of poly(vinyl methyl ether)(PVME) have been investigated by molecular dynamics simulations under 300 K at various concentrations. Both radial distribution functions and the distance distributions between donors and acceptors in hydrogen bonds show that the hydrogen bonds between the polymer and water are shorter by 0.005 nm than those between water molecules. The Quasi-hydrogen bonds take only 7.2% of the van der Waals interaction pairs. It was found the hydrogen bonds are not evenly distributed along the polymer chain,and there still exists a significant amount(10%) of ether oxygen atoms that are not hydrogen bonded to water at a concentration as low as 3.3%. This shows that in polymer solutions close contacts occur not only between polymer chains but also between chain segments within the polymer,which leads to inefficient contacts between ether oxygen atoms and water molecules. Variation of the quasi-hydrogen bonds with the concentration is similar to that of hydrogen bonds,but the ratio of the repeat units forming quasi-hydrogen bonds to those forming hydrogen bonds approaches 0.2. A transition was found in the demixing enthalpy at around 30% measured by dynamic testing differential scanning calorimetry(DTDSC) for aqueous solutions of a mono-dispersed low molecular weight PVME,which can be related to the transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ~27%. The transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ~27% can be used to explain the demixing enthalpy transition at 30% at a molecular scale. In addition,at the concentration of 86%,each ether oxygen atom bonded with water is assigned 1.56 water molecules on average,and ’free’ water molecules emerge at the concentration of around 54%.

  2. Effect of density of hydrogen-bonding donor on hydrogen-bonded multilayer buildup

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hongyu; MA Ning; WANG Zhiqiang

    2005-01-01

    The effect of density of hydrogen-bonding donor (HBD) on the formation of layer-by-layer assemblies of poly(4-vinylpyridine) and poly(4-vinylphenol) was investigated. For this purpose, a series of ethyl-substituted poly(4-vinylphenol) (EsPVPhf) with variable ethyl substitute percentage was synthesized by grafting the phenol moiety along the poly(4-vinylphenol) backbone with 1-bromoethane. UV-vis spectroscopy revealed a uniform deposition process of the hydrogen-bonded multilayer consisting of poly(4- vinylpyridine) (PVPy) and EsPVPhf with variable density of HBD. Notably, it was found that increasing the HBD density of EsPVPhf resulted in a marked decrease of both amount of polymers adsorbed and film thickness, which should be related to the EsPVPhf conformation change from coiled state to extended conformation in ethanol solution. Compared with the effect of charge density in polyelectrolyte multilayer, however, there does not exist a critical density of HBD in our case of hydrogen-bonded multilayer assembly. In addition, surface structures of PVPy/EsPVPhf multilayer films also can be tailored controllably by adjusting HBD density of EsPVPhf. As a result, a new method for tuning the structure of hydrogen-bonding-directed multilayer films was developed.

  3. Hydrogen bonding in asphaltenes and coal

    Energy Technology Data Exchange (ETDEWEB)

    Li, N.C.; Tewari, K.C.

    1978-04-01

    The objective of this program is to investigate and to determine the nature of hydrogen bonding and other molecular interactions that occur in asphaltene and coal liquids, and to seek possible correlations between the interactions and the viscosity. The asphaltene components of samples of centrifuged liquid product, CLP, and solvent-refined coal, SRC, supplied by the Pittsburgh Energy Research Center, are isolated by solvent fractionation. The compositions of the asphaltenes are obtained by elemental analysis and the molecular weights by vapor pressure osmometry. The acid/neutral and base components of the asphaltenes are separated and again elemental analysis and molecular weights are obtained. The magnetic resonance, infrared and calorimetric methods are used to determine the strength of hydrogen-bond and other molecular interactions in the fractions isolated. Investigations on the toluene-insoluble and heavy-oil fractions are also carried out. In addition, extensive proton magnetic resonance, near infrared and calorimetric studies are carried out for o-phenylphenol and quinoline, which serve as model compounds for the aromatic phenols and the heteronuclear aromatic base nitrogens, respectively, found in coal liquefaction products. This is the final report, giving a summary of activities under the Contract for the entire period.

  4. Tetrahedrality and hydrogen bonds in water

    Science.gov (United States)

    Székely, Eszter; Varga, Imre K.; Baranyai, András

    2016-06-01

    We carried out extensive calculations of liquid water at different temperatures and pressures using the BK3 model suggested recently [P. T. Kiss and A. Baranyai, J. Chem. Phys. 138, 204507 (2013)]. In particular, we were interested in undercooled regions to observe the propensity of water to form tetrahedral coordination of closest neighbors around a central molecule. We compared the found tetrahedral order with the number of hydrogen bonds and with the partial pair correlation functions unfolded as distributions of the closest, the second closest, etc. neighbors. We found that contrary to the number of hydrogen bonds, tetrahedrality changes substantially with state variables. Not only the number of tetrahedral arrangements increases with lowering the pressure, the density, and the temperature but the domain size of connecting tetrahedral structures as well. The difference in tetrahedrality is very pronounced between the two sides of the Widom line and even more so between the low density amorphous (LDA) and high density amorphous (HDA) phases. We observed that in liquid water and in HDA, the 5th water molecule, contrary to ice and LDA, is positioned between the first and the second coordination shell. We found no convincing evidence of structural heterogeneity or regions referring to structural transition.

  5. Metal — metal multiple bonded intermediates in catalysis

    Indian Academy of Sciences (India)

    John F Berry

    2015-02-01

    Metal–metal bonded Rh2 and Ru2 complexes having a paddlewheel-type structure are exceptional catalysts for a broad range of organic transformations. I review here the recent efforts towards the observation and characterization of intermediates in these reactions that have previously eluded detection. Specifically, mechanistic investigations of carbenoid and nitrenoid reactions of Rh2(II,II)-tetracarboxylate compounds have led to the observation of a metastable Rh2(II,II) carbene complex as well as a mixed-valent Rh2(II,III)-amido intermediate. Related Ru2 nitrido compounds have been studied and found to undergo intramolecular C–H amination reactions as well as intermolecular reaction with triphenylphosphine

  6. A Statistical Theory for Hydrogen Bonding Networks: One Component Case

    Institute of Scientific and Technical Information of China (English)

    WANG Hai-Jun; BA Xin-Wu; ZHAO Min; LI Ze-Sheng

    2000-01-01

    The theory of reversible gelation is shown to be applicable to the hydrogen bonding system by analyzing their similarities in statistical viewpoint. The size distribution of hydrogen bonding clusters, the gelation condition and the generalized scaling law can be obtained directly. These results show that such a system can undergo phase transition process. Furthermore, a relationship between Gibbs free energy of forming hydrogen bond and conversions of groups is given. As an example, the chemical shift of OH groups is considered.

  7. The role of hydrogen bonding in tethered polymer layers

    OpenAIRE

    Ren, C; Nap, R. J.; Szleifer, I.

    2008-01-01

    A molecular theory to study the properties of end tethered polymer layers, in which the polymers have the ability to form hydrogen bonds with water is presented. The approach combines the ideas of the single-chain mean-field theory to treat tethered layers with the approach of Dormidontova (Macromolecules, 2002 35,987) to include hydrogen bonds. The generalization includes the consideration of position dependent polymer-water and water-water hydrogen bonds. The theory is applied to model poly...

  8. Routes to Hydrogen Bonding Chain-End Functionalized Polymers.

    Science.gov (United States)

    Bertrand, Arthur; Lortie, Frédéric; Bernard, Julien

    2012-12-21

    The contribution of supramolecular chemistry to polymer science opens new perspectives for the design of polymer materials exhibiting valuable properties and easier processability due to the dynamic nature of non-covalent interactions. Hydrogen bonding polymers can be used as supramolecular units for yielding larger assemblies that possess attractive features, arising from the combination of polymer properties and the responsiveness of hydrogen bonds. The post-polymerization modification of reactive end-groups is the most common procedure for generating such polymers. Examples of polymerizations mediated by hydrogen bonding-functionalized precursors have also recently been reported. This contribution reviews the current synthetic routes toward hydrogen bonding sticker chain-end functionalized polymers.

  9. Cascade catalysis for the homogeneous hydrogenation of CO2 to methanol.

    Science.gov (United States)

    Huff, Chelsea A; Sanford, Melanie S

    2011-11-16

    This communication demonstrates the homogeneous hydrogenation of CO(2) to CH(3)OH via cascade catalysis. Three different homogeneous catalysts, (PMe(3))(4)Ru(Cl)(OAc), Sc(OTf)(3), and (PNN)Ru(CO)(H), operate in sequence to promote this transformation.

  10. Heterogeneous Catalysis: The Horiuti-Polanyi Mechanism and Alkene Hydrogenation

    Science.gov (United States)

    Mattson, Bruce; Foster, Wendy; Greimann, Jaclyn; Hoette, Trisha; Le, Nhu; Mirich, Anne; Wankum, Shanna; Cabri, Ann; Reichenbacher, Claire; Schwanke, Erika

    2013-01-01

    The hydrogenation of alkenes by heterogeneous catalysts has been studied for 80 years. The foundational mechanism was proposed by Horiuti and Polanyi in 1934 and consists of three steps: (i) alkene adsorption on the surface of the hydrogenated metal catalyst, (ii) hydrogen migration to the beta-carbon of the alkene with formation of a delta-bond…

  11. Hydrogen bonds in concreto and in computro

    Science.gov (United States)

    Stouten, Pieter F. W.; Kroon, Jan

    1988-07-01

    Molecular dynamics simulations of liquid water and liquid methanol have been carried out. For both liquids an effective pair potential was used. The models were fitted to the heat of vaporization, pressure and various radial distribution functions resulting from diffraction experiments on liquids. In both simulations 216 molecules were put in a cubic periodical ☐. The system was loosely coupled to a temperature bath and to a pressure bath. Following an initial equilibration period relevant data were sampled during 15 ps. The distributions of oxygen—oxygen distances in hydrogen bonds obtained from the two simulations are essentially the same. The distribution obtained from crystal data is somewhat different: the maximum has about the same position, but the curve is much narrower, which can be expected merely from the fact that diffraction experiments only supply average atomic positions and hence average interatomic distances. When thermal motion is taken into account a closer likeness is observed.

  12. Proton tunnelling in intermolecular hydrogen bonds

    Energy Technology Data Exchange (ETDEWEB)

    Horsewill, A.J. [Nottingham Univ. (United Kingdom); Johnson, M.R. [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France); Trommsdorff, H.P. [Grenoble-1 Univ., 38 (France)

    1997-04-01

    The wavefunctions of particles extend beyond the classically accessible regions of potential energy-surfaces (PES). A manifestation of this partial delocalization is the quantum-mechanical tunneling effect which enables a particle to escape from a metastable potential-well. Tunnelling is most important for the lightest atoms, so that the determination of its contribution to proton transfer, one of the most fundamental chemical reactions, is an important issue. QENS and NMR techniques have been employed to study the motion of protons in the hydrogen bond of benzoic-acid crystals, a system which has emerged as a particularly suitable model since proton transfer occurs in a near symmetric double-well potential. The influence of quantum tunnelling was revealed and investigated in these experiments. This work provides an experimental benchmark for theoretical descriptions of translational proton-tunnelling. (author). 7 refs.

  13. Porous Hydrogen-Bonded Organic Frameworks

    Directory of Open Access Journals (Sweden)

    Yi-Fei Han

    2017-02-01

    Full Text Available Ordered porous solid-state architectures constructed via non-covalent supramolecular self-assembly have attracted increasing interest due to their unique advantages and potential applications. Porous metal-coordination organic frameworks (MOFs are generated by the assembly of metal coordination centers and organic linkers. Compared to MOFs, porous hydrogen-bonded organic frameworks (HOFs are readily purified and recovered via simple recrystallization. However, due to lacking of sufficiently ability to orientate self-aggregation of building motifs in predictable manners, rational design and preparation of porous HOFs are still challenging. Herein, we summarize recent developments about porous HOFs and attempt to gain deeper insights into the design strategies of basic building motifs.

  14. Direct Acylation of C(sp(3))-H Bonds Enabled by Nickel and Photoredox Catalysis.

    Science.gov (United States)

    Joe, Candice L; Doyle, Abigail G

    2016-03-14

    Using nickel and photoredox catalysis, the direct functionalization of C(sp(3))-H bonds of N-aryl amines by acyl electrophiles is described. The method affords a diverse range of α-amino ketones at room temperature and is amenable to late-stage coupling of complex and biologically relevant groups. C(sp(3))-H activation occurs by photoredox-mediated oxidation to generate α-amino radicals which are intercepted by nickel in catalytic C(sp(3))-C coupling. The merger of these two modes of catalysis leverages nickel's unique properties in alkyl cross-coupling while avoiding limitations commonly associated with transition-metal-mediated C(sp(3))-H activation, including requirements for chelating directing groups and high reaction temperatures.

  15. Hydrogen-Bonded Liquid Crystal Nanocomposites.

    Science.gov (United States)

    Roohnikan, Mahdi; Toader, Violeta; Rey, Alejandro; Reven, Linda

    2016-08-23

    Nanoparticle-liquid crystal (NP-LC) composites based on hydrogen bonding were explored using a model system. The ligand shells of 3 nm diameter zirconium dioxide nanoparticles (ZrO2 NPs) were varied to control their interaction with 4-n-hexylbenzoic acid (6BA). The miscibility and effect of the NPs on the nematic order as a function of particle concentration was characterized by polarized optical microscopy (POM), fluorescence microscopy and (2)H NMR spectroscopy. Nonfunctionalized ZrO2 NPs have the lowest miscibility and strongest effect on the LC matrix due to irreversible binding of 6BA to the NPs via a strong zirconium carboxylate bond. The ZrO2 NPs were functionalized with 6-phosphonohexanoic acid (6PHA) or 4-(6-phosphonohexyloxy)benzoic acid (6BPHA) which selectively bind to the ZrO2 NP surface via the phosphonic acid groups. The miscibility was increased by controlling the concentration of the pendant CO2H groups by adding hexylphosphonic acid (HPA) to act as a spacer group. Fluorescence microscopy of lanthanide doped ZrO2 NPs showed no aggregates in the nematic phase below the NP concentration where aggregates are observed in the isotropic phase. The functionalized NPs preferably concentrate into LC defects and any remaining isotropic liquid but are still present throughout the nematic liquid at a lower concentration.

  16. Hydrogen Bonding in Thermoplastic Polyurethane Elastomers: IR Thermal Analysis

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The hydrogen bond percentage and its temperature dependence of the three TPU samples synthesized from polytetrahydrofuran, 4,4-diphenylmethane diisocyanate, N-methyl diethanol amine or 1,4-butane diol were studied by means of IR thermal analysis. The enthalpy and the entropy of the hydrogen bond dissociation were determined by the Vant Hoff plot.

  17. Predictions of Glass Transition Temperature for Hydrogen Bonding Biomaterials

    NARCIS (Netherlands)

    Sman, van der R.G.M.

    2013-01-01

    We show that the glass transition of a multitude of mixtures containing hydrogen bonding materials correlates strongly with the effective number of hydroxyl groups per molecule, which are available for intermolecular hydrogen bonding. This correlation is in compliance with the topological constraint

  18. Binding of reactive organophosphate by oximes via hydrogen bond

    Indian Academy of Sciences (India)

    Andrea Pappalardo; Maria E Amato; Francesco P Ballistreri; Valentina La Paglia Fragola; Gaetano A Tomaselli; Rosa Maria Toscano; Giuseppe Trusso Sfrazzetto

    2013-07-01

    In this contribution, the ability of simple oximes to bind a well-known nerve agent simulant (dimethylmethylphosphonate, DMMP) via hydrogen bond is reported. UV/Vis measurements indicate the formation of 1:1 complexes. 1H-, 31P-NMR titrations and T-ROESY experiments confirm that oximes bind the organophosphate via hydrogen bond.

  19. Gold Nanoparticle Assemblies through Hydrogen-Bonded Supramolecular Mediators

    NARCIS (Netherlands)

    Kinge, Sachin S.; Crego-Calama, Mercedes; Reinhoudt, David N.

    2007-01-01

    The synthesis of spherical gold nanoparticle assemblies with multicomponent double rosette molecular boxes as mediators is presented. These nine-component hydrogen-bonded supramolecular structures held together by 36 hydrogen bonds induce gold nanoparticle assembly. The morphologies of the nanoparti

  20. Temperature breaking of hydrogen bonds in ammonia studied by π --meson capture in hydrogen

    Science.gov (United States)

    Horváth, D.; Bannikov, A. V.; Kachalkin, A. K.; Lévay, B.; Petrukhin, V. I.; Vasilyev, V. A.; Yutlandov, I. A.; Strakovsky, I. I.

    1982-04-01

    The capture probability of stopped π - mesons by hydrogen atoms of ammonia increases with temperature in the liquid phase but in the supercritical phase it is temperature-independent. This can be attributed to the temperature breaking of hydrogen bonds. Rough estimates are given for the fraction of broken hydrogen bonds at various temperatures.

  1. Hydrogen-Bonding Surfaces for Ice Mitigation

    Science.gov (United States)

    Smith, Joseph G., Jr.; Wohl, Christopher J.; Kreeger, Richard E.; Hadley, Kevin R.; McDougall, Nicholas

    2014-01-01

    Ice formation on aircraft, either on the ground or in-flight, is a major safety issue. While ground icing events occur predominantly during the winter months, in-flight icing can happen anytime during the year. The latter is more problematic since it could result in increased drag and loss of lift. Under a Phase I ARMD NARI Seedling Activity, coated aluminum surfaces possessing hydrogen-bonding groups were under investigation for mitigating ice formation. Hydroxyl and methyl terminated dimethylethoxysilanes were prepared via known chemistries and characterized by spectroscopic methods. These materials were subsequently used to coat aluminum surfaces. Surface compositions were based on pure hydroxyl and methyl terminated species as well as mixtures of the two. Coated surfaces were characterized by contact angle goniometry. Receding water contact angle data suggested several potential surfaces that may exhibit reduced ice adhesion. Qualitative icing experiments performed under representative environmental temperatures using supercooled distilled water delivered via spray coating were inconclusive. Molecular modeling studies suggested that chain mobility affected the interface between ice and the surface more than terminal group chemical composition. Chain mobility resulted from the creation of "pockets" of increased free volume for longer chains to occupy.

  2. The influence of hydrogen bonding on partition coefficients

    Science.gov (United States)

    Borges, Nádia Melo; Kenny, Peter W.; Montanari, Carlos A.; Prokopczyk, Igor M.; Ribeiro, Jean F. R.; Rocha, Josmar R.; Sartori, Geraldo Rodrigues

    2017-02-01

    This Perspective explores how consideration of hydrogen bonding can be used to both predict and better understand partition coefficients. It is shown how polarity of both compounds and substructures can be estimated from measured alkane/water partition coefficients. When polarity is defined in this manner, hydrogen bond donors are typically less polar than hydrogen bond acceptors. Analysis of alkane/water partition coefficients in conjunction with molecular electrostatic potential calculations suggests that aromatic chloro substituents may be less lipophilic than is generally believed and that some of the effect of chloro-substitution stems from making the aromatic π-cloud less available to hydrogen bond donors. Relationships between polarity and calculated hydrogen bond basicity are derived for aromatic nitrogen and carbonyl oxygen. Aligned hydrogen bond acceptors appear to present special challenges for prediction of alkane/water partition coefficients and this may reflect `frustration' of solvation resulting from overlapping hydration spheres. It is also shown how calculated hydrogen bond basicity can be used to model the effect of aromatic aza-substitution on octanol/water partition coefficients.

  3. The influence of hydrogen bonding on partition coefficients

    Science.gov (United States)

    Borges, Nádia Melo; Kenny, Peter W.; Montanari, Carlos A.; Prokopczyk, Igor M.; Ribeiro, Jean F. R.; Rocha, Josmar R.; Sartori, Geraldo Rodrigues

    2017-01-01

    This Perspective explores how consideration of hydrogen bonding can be used to both predict and better understand partition coefficients. It is shown how polarity of both compounds and substructures can be estimated from measured alkane/water partition coefficients. When polarity is defined in this manner, hydrogen bond donors are typically less polar than hydrogen bond acceptors. Analysis of alkane/water partition coefficients in conjunction with molecular electrostatic potential calculations suggests that aromatic chloro substituents may be less lipophilic than is generally believed and that some of the effect of chloro-substitution stems from making the aromatic π-cloud less available to hydrogen bond donors. Relationships between polarity and calculated hydrogen bond basicity are derived for aromatic nitrogen and carbonyl oxygen. Aligned hydrogen bond acceptors appear to present special challenges for prediction of alkane/water partition coefficients and this may reflect `frustration' of solvation resulting from overlapping hydration spheres. It is also shown how calculated hydrogen bond basicity can be used to model the effect of aromatic aza-substitution on octanol/water partition coefficients.

  4. Hydrogen and Dihydrogen Bonds in the Reactions of Metal Hydrides.

    Science.gov (United States)

    Belkova, Natalia V; Epstein, Lina M; Filippov, Oleg A; Shubina, Elena S

    2016-08-10

    The dihydrogen bond-an interaction between a transition-metal or main-group hydride (M-H) and a protic hydrogen moiety (H-X)-is arguably the most intriguing type of hydrogen bond. It was discovered in the mid-1990s and has been intensively explored since then. Herein, we collate up-to-date experimental and computational studies of the structural, energetic, and spectroscopic parameters and natures of dihydrogen-bonded complexes of the form M-H···H-X, as such species are now known for a wide variety of hydrido compounds. Being a weak interaction, dihydrogen bonding entails the lengthening of the participating bonds as well as their polarization (repolarization) as a result of electron density redistribution. Thus, the formation of a dihydrogen bond allows for the activation of both the MH and XH bonds in one step, facilitating proton transfer and preparing these bonds for further transformations. The implications of dihydrogen bonding in different stoichiometric and catalytic reactions, such as hydrogen exchange, alcoholysis and aminolysis, hydrogen evolution, hydrogenation, and dehydrogenation, are discussed.

  5. Intermolecular hydrogen bonds: From temperature-driven proton transfer in molecular crystals to denaturation of DNA

    Indian Academy of Sciences (India)

    Mark Johnson

    2008-11-01

    We have combined neutron scattering and a range of numerical simulations to study hydrogen bonds in condensed matter. Two examples from a recent thesis will be presented. The first concerns proton transfer with increasing temperature in short inter-molecular hydrogen bonds [1,2]. These bonds have unique physical and chemical properties and are thought to play a fundamental role in processes like enzymatic catalysis. By combining elastic and inelastic neutron scattering results with ab initio, lattice dynamics and molecular dynamics simulations, low frequency lattice modes are identified which modulate the potential energy surface of the hydrogen bond proton and drive proton transfer. The second example concerns base-pair opening in DNA which is the fundamental physical process underlying biological processes like denaturation and transcription. We have used an emprical force field and a large scale, all-atom phonon calculation to gain insight into the base-pair opening modes and the apparent `energy gap' between the accepted frequencies for these modes (∼ 100 cm-1 or ∼ 140 K) and the temperature of the biological processes (room temperature to 100° C) [3]. Inelastic neutron scattering spectra on aligned, highly crystalline DNA samples, produced at the ILL, provide the reference data for evaluating the precision of these simulation results.

  6. The design of organic catalysis for epoxidation by hydrogen peroxide

    OpenAIRE

    Alder, Roger W.; Davis, Anthony P

    2005-01-01

    The potential of various organic species to catalyze epoxidation of ethene by hydrogen peroxide is explored with B3LYP/6-31G* DFT calculations. Electronic Supplementary Materials Supplementary material is available for this article at http://dx.doi.org/10.1007/s00894-005-0044-4.

  7. Heterogeneous Catalysis: Deuterium Exchange Reactions of Hydrogen and Methane

    Science.gov (United States)

    Mirich, Anne; Miller, Trisha Hoette; Klotz, Elsbeth; Mattson, Bruce

    2015-01-01

    Two gas phase deuterium/hydrogen exchange reactions are described utilizing a simple inexpensive glass catalyst tube containing 0.5% Pd on alumina through which gas mixtures can be passed and products collected for analysis. The first of these exchange reactions involves H[subscript 2] + D[subscript 2], which proceeds at temperatures as low as 77…

  8. Hirshfeld atom refinement for modelling strong hydrogen bonds.

    Science.gov (United States)

    Woińska, Magdalena; Jayatilaka, Dylan; Spackman, Mark A; Edwards, Alison J; Dominiak, Paulina M; Woźniak, Krzysztof; Nishibori, Eiji; Sugimoto, Kunihisa; Grabowsky, Simon

    2014-09-01

    High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of Z' > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O-H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.

  9. Short hydrogen bonds in the catalytic mechanism of serine proteases

    Directory of Open Access Journals (Sweden)

    VLADIMIR LESKOVAC

    2008-04-01

    Full Text Available The survey of crystallographic data from the Protein Data Bank for 37 structures of trypsin and other serine proteases at a resolution of 0.78–1.28 Å revealed the presence of hydrogen bonds in the active site of the enzymes, which are formed between the catalytic histidine and aspartate residues and are on average 2.7 Å long. This is the typical bond length for normal hydrogen bonds. The geometric properties of the hydrogen bonds in the active site indicate that the H atom is not centered between the heteroatoms of the catalytic histidine and aspartate residues in the active site. Taken together, these findings exclude the possibility that short “low-barrier” hydrogen bonds are formed in the ground state structure of the active sites examined in this work. Some time ago, it was suggested by Cleland that the “low-barrier hydrogen bond” hypothesis is operative in the catalytic mechanism of serine proteases, and requires the presence of short hydrogen bonds around 2.4 Å long in the active site, with the H atom centered between the catalytic heteroatoms. The conclusions drawn from this work do not exclude the validity of the “low-barrier hydrogen bond” hypothesis at all, but they merely do not support it in this particular case, with this particular class of enzymes.

  10. Modelling of spreading process: effect from hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    Li Xin; Hu Yuan-Zhong; Jiang Lan

    2008-01-01

    Lubricant spreading on solid substrates has drawn considerable attention not only for the microscopic wetting theory but also for the dramatic application in head-disk interface of magnetic storage drive systems. Molecular dynamic simulation based on a coarse-grained bead-spring model has been used to study such a spreading process.The spreading profiles indicate that the hydrogen bonds among lubricant molecules and the hydrogen bonds between lubricant molecules and polar atoms of solid substrates will complicate the spreading process in a tremendous degree.The hydrogen bonds among lubricant molecules will strengthen the lubricant combination intensity, which may hinder most molecules from flowing down to the substrates and diffusing along the substrates. And the hydrogen bonds between lubricant molecules and polar atoms of solid substrates will confine the lubricant molecules around polar atoms, which may hinder the molecules from diffusing along the substrates and cause precursor film to vanish.

  11. Specific Heat Properties of Proton Transfer in Hydrogen Bonded Systems

    Institute of Scientific and Technical Information of China (English)

    庞小峰; 封原平

    2003-01-01

    The thermodynamic properties of proton transport along hydrogen-bonded systems at finite temperatures have been studied by our model. We first derive the dynamic equations of the proton transport and find the solutions and the free energy of the systems. Finally, we obtain the specific heats of the hydrogen bonded systems, resulting from the motion of the soliton, by using transfer integral way. The theoretical value is basically consistent with the experimental data.

  12. Statistical Parameters for Hydrogen Bonding Networks: One Component Case

    Institute of Scientific and Technical Information of China (English)

    王海军; 洪晓钟; 赵敏; 巴信武

    2001-01-01

    Based on the analysis of network structures formed by hydrogen bonds as the sol-gel phase transition takesplace in a single component hydrogen bonding system, the theory of reversible gelation is applied to calculatesome statistical parameters that determine many physical and chemical properties of the networks. Then, thentunerical simulation of the number of active chains and dangling chains, the number of effective cross-linkages,the number of active and dangling mers and the modulus as a function of conversion are undertaken.

  13. Energetics of hydrogen bonding in proteins: a model compound study.

    OpenAIRE

    1996-01-01

    Differences in the energetics of amide-amide and amide-hydroxyl hydrogen bonds in proteins have been explored from the effect of hydroxyl groups on the structure and dissolution energetics of a series of crystalline cyclic dipeptides. The calorimetrically determined energetics are interpreted in light of the crystal structures of the studied compounds. Our results indicate that the amide-amide and amide-hydroxyl hydrogen bonds both provide considerable enthalpic stability, but that the amide-...

  14. How many hydrogen-bonded α-turns are possible?

    Science.gov (United States)

    Schreiber, Anette; Schramm, Peter; Hofmann, Hans-Jörg

    2011-06-01

    The formation of α-turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated α-turns with a hydrogen bond between the first and fifth amino acid employing the methods of ab initio MO theory in vacuum (HF/6-31G*, B3LYP/6-311 + G*) and in solution (CPCM/HF/6-31G*). Only few α-turn structures with glycine and alanine backbones fulfill the geometry criteria for the i←(i + 4) hydrogen bond satisfactorily. The most stable representatives agree with structures found in the Protein Data Bank. There is a general tendency to form additional hydrogen bonds for smaller pseudocycles corresponding to β- and γ-turns with better hydrogen bond geometries. Sometimes, this competition weakens or even destroys the i←(i + 4) hydrogen bond leading to very stable double β-turn structures. This is also the reason why an "ideal" α-turn with three central amino acids having the perfect backbone angle values of an α-helix could not be localized. There are numerous hints for stable α-turns with a distance between the C(α)-atoms of the first and fifth amino acid smaller than 6-7 Å, but without an i←(i + 4) hydrogen bond.

  15. Efficiency in chemistry: from hydrogen autotransfer to multicomponent catalysis.

    Science.gov (United States)

    Alonso, Francisco; Foubelo, Francisco; González-Gómez, José C; Martínez, Ricardo; Ramón, Diego J; Riente, Paola; Yus, Miguel

    2010-08-01

    A hydrogen autotransfer reaction has been applied to the α-alkylation of ketones, with primary alcohols as the electrophilic component, either under homogeneous (using a Ru complex as catalyst) or under heterogeneous (using Ni nanoparticles) conditions. This process is both very efficient (concerning atom economy) and ecologically friendly (water as the only by-product generated). On the other hand, three multicomponent reactions, namely, the Strecker reaction (without any catalyst), the aza-Sakurai process (catalyzed by ferrite), and the addition of in situ generated Zn enolates to chiral sulfinylimines (catalyzed by Cu), have proven to be very efficient in the generation of a diversity of polyfunctionalized molecules.

  16. The intrinsic mechanical loss factor of hydroxy-catalysis bonds for use in the mirror suspensions of gravitational wave detectors

    Energy Technology Data Exchange (ETDEWEB)

    Sneddon, P H [Institute for Gravitational Research, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ (United Kingdom); Bull, S [School of Chemical Engineering and Advanced Materials, University of Newcastle, Newcastle NE1 7RU (United Kingdom); Cagnoli, G [Institute for Gravitational Research, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ (United Kingdom); Crooks, D R M [Institute for Gravitational Research, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ (United Kingdom); Elliffe, E J [Institute for Gravitational Research, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ (United Kingdom); Faller, J E [JILA, NIST and University of Colorado, Boulder, CO 80309 (United States); Fejer, M M [Edward L Ginzton Laboratory, Stanford University, Stanford, CA 94305-4088 (United States); Hough, J [Institute for Gravitational Research, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ (United Kingdom); Rowan, S [Institute for Gravitational Research, Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ (United Kingdom)

    2003-12-07

    This paper describes investigations into the mechanical losses of bonds created by hydroxy-catalysis bonding. Evaluation of the magnitude of such losses is important for determining thermal noise levels in bonded suspensions for gravitational wave detectors. Three samples were investigated with bonds of varying geometries and surface areas. In two cases, the bonds were between two pieces of fused silica, whilst in the third a fused silica piece was attached to a sapphire substrate. In each case sodium silicate solution was used as the bonding agent. The thickness and Young's modulus of the bond material were evaluated enabling values for the intrinsic mechanical loss factor of the bonding material to be obtained.

  17. Nature of the N-H...S hydrogen bond.

    Science.gov (United States)

    Biswal, Himansu S; Wategaonkar, Sanjay

    2009-11-19

    The N-H...S hydrogen-bonded complexes of the model compounds of tryptophan (indole and 3-methylindole) and methionine (dimethyl sulfide, Me(2)S) have been characterized by a combination of experimental techniques like resonant two-photon ionization (R2PI), resonant ion dip infrared spectroscopy (RIDIRS), and fluorescence dip infrared spectroscopy (FDIRS) and computational methods like ab initio electronic structure calculations, atoms-in-molecules (AIM), natural bond orbital (NBO), and energy decomposition analyses. The results are compared with the N-H...O (M.H(2)O; M = indole, 3-methyl indole) sigma-type and N-H...Phi (M.benzene) pi-type hydrogen-bonded complexes. It was shown that the S(1)-S(0) band origin red shifts in the N-H...S hydrogen-bonded complexes correlated well with the polarizability of the acceptor rather than their proton affinity, contrary to the trend observed in most X-H...Y (X, Y = O, N, halogens, etc.) hydrogen-bonded systems. The red shift in the N-H stretching frequency in the N-H...S HB clusters (Me(2)S as HB acceptor) was found to be 1.8 times greater than that for the N-H...O hydrogen-bonded complexes (H(2)O as HB acceptor), although the binding energies for the two complexes were comparable. The energy decomposition analyses for all of the N-H...S hydrogen-bonded complexes showed that the correlation (or dispersion) energy has significant contribution to the total binding energy. It is pointed out that the binding energy of the N-H...S complex was also comparable to that of the indole.benzene complex, which is completely dominated by the dispersion interaction. Atoms-in-molcules (AIM) and natural bond orbital (NBO) analyses indicated a nontrivial electrostatic component in the hydrogen-bonding interaction. Greater dispersion contribution to the stabilization energy as well as greater red shifts in the N-H stretch relative to those of N-H...O hydrogen-bonded complexes makes the indole.dimethylsulfide complex unique in regard to the

  18. Alkyl Radicals as Hydrogen Bond Acceptors: Computational Evidence

    DEFF Research Database (Denmark)

    Hammerum, Steen

    2009-01-01

    , and gives rise to pronounced shifts of IR stretching frequencies and to increased absorption intensities. The hydrogen bond acceptor properties of alkyl radicals equal those of many conventional acceptors, e.g., the bond length changes and IR red-shifts suggest that tert-butyl radicals are slightly better...

  19. How universal are hydrogen bond correlations? A density functional study of intramolecular hydrogen bonding in low-energy conformers of α-amino acids

    Science.gov (United States)

    Ramaniah, Lavanya M.; Kamal, C.; Kshirsagar, Rohidas J.; Chakrabarti, Aparna; Banerjee, Arup

    2013-10-01

    Hydrogen bonding is one of the most important and ubiquitous interactions present in Nature. Several studies have attempted to characterise and understand the nature of this very basic interaction. These include both experimental and theoretical investigations of different types of chemical compounds, as well as systems subjected to high pressure. The O-H..O bond is of course the best studied hydrogen bond, and most studies have concentrated on intermolecular hydrogen bonding in solids and liquids. In this paper, we analyse and characterise normal hydrogen bonding of the general type, D-H...A, in intramolecular hydrogen bonding interactions. Using a first-principles density functional theory approach, we investigate low energy conformers of the twenty α-amino acids. Within these conformers, several different types of intramolecular hydrogen bonds are identified. The hydrogen bond within a given conformer occurs between two molecular groups, either both within the backbone itself, or one in the backbone and one in the side chain. In a few conformers, more than one (type of) hydrogen bond is seen to occur. Interestingly, the strength of the hydrogen bonds in the amino acids spans quite a large range, from weak to strong. The signature of hydrogen bonding in these molecules, as reflected in their theoretical vibrational spectra, is analysed. With the new first-principles data from 51 hydrogen bonds, various parameters relating to the hydrogen bond, such as hydrogen bond length, hydrogen bond angle, bond length and vibrational frequencies are studied. Interestingly, the correlation between these parameters in these bonds is found to be in consonance with those obtained in earlier experimental studies of normal hydrogen bonds on vastly different systems. Our study provides some of the most detailed first-principles support, and the first involving vibrational frequencies, for the universality of hydrogen bond correlations in materials.

  20. A rechargeable hydrogen battery based on Ru catalysis.

    Science.gov (United States)

    Hsu, Shih-Fan; Rommel, Susanne; Eversfield, Philipp; Muller, Keven; Klemm, Elias; Thiel, Werner R; Plietker, Bernd

    2014-07-01

    Apart from energy generation, the storage and liberation of energy are among the major problems in establishing a sustainable energy supply chain. Herein we report the development of a rechargeable H2 battery which is based on the principle of the Ru-catalyzed hydrogenation of CO2 to formic acid (charging process) and the Ru-catalyzed decomposition of formic acid to CO2 and H2 (discharging process). Both processes are driven by the same catalyst at elevated temperature either under pressure (charging process) or pressure-free conditions (discharging process). Up to five charging-discharging cycles were performed without decrease of storage capacity. The resulting CO2/H2 mixture is free of CO and can be employed directly in fuel-cell technology.

  1. Catalysis of peptide bond formation by histidyl-histidine in a fluctuating clay environment

    Science.gov (United States)

    White, D. H.; Erickson, J. C.

    1980-01-01

    The condensation of glycine to form oligoglycines during wet-dry fluctuations on clay surfaces was enhanced up to threefold or greater by small amounts of histidyl-histidine. In addition, higher relative yields of the longer oligomers were produced. Other specific dipeptides tested gave no enhancement, and imidazole, histidine, and N-acetylhistidine gave only slight enhancements. Histidyl-histidine apparently acts as a true catalyst (in the sense of repeatedly catalyzing the reaction), since up to 52 nmol of additional glycine were incorporated into oligoglycine for each nmol of catalyst added. This is the first known instance of a peptide or similar molecule demonstrating a catalytic turnover number greater than unity in a prebiotic oligomer synthesis reaction, and suggests that histidyl-histidine is a model for a primitive prebiotic proto-enzyme. Catalysis of peptide bond synthesis by a molecule which is itself a peptide implies that related systems may be capable of exhibiting autocatalytic growth.

  2. Quasi-Monolithic Structures for Spaceflight Using Hydroxide-Catalysis Bonding

    Science.gov (United States)

    Preston, Alix; Thorpe, J. Ira; Miner, Linda

    2012-01-01

    Future space-based missions will take measurements of the universe with unprecedented results. To do this, these missions will require materials and bonding techniques with ever-increasing stability in order to make their measurements. As an example, the Laser Interferometer Space Antenna (LISA) will detect and observe gravitational waves in the 0.1 mHz to 1 Hz frequency range with strain sensitivities on the order of 10(exp -21) at its most sensitive frequency. To make these measurements, critical components such as the optical bench or telescope support structure, will need to have path-length stabilities of better than 1 pm/(square root)Hz. The baseline construction method for the LISA optical bench is to affix fused silica optical components to a Zerodur baseplate using hydroxide-catalysis bonding (HCB). HCB is a recently developed technique that allows the bonding of glasses, some metals, and silicon carbide with significant strength and stability with a bond thickness of less than a few micrometers. In addition, a wide range of surface profiles can be bonded using only a small amount of hydroxide solution. These characteristics make HCB ideal for adhering optical components in complex optical systems. In addition to being used to construct the LISA optical bench, the HCB technique shows great promise for constructing other structures such as hollow retroreflectors to be used for lunar laser ranging, or a visible nulling coronograph to be used for exo-planet detection. Here we present construction techniques that could be used to make an optical bench, hollow retroreflector, nulling coronograph, or other quasi-monolithic structures using HCB. In addition, we present dimensional stability results of an optical bench that was made using HCB, as well as HCB strength measurements.

  3. Time-dependent density functional theory study on the electronic excited-state geometric structure, infrared spectra, and hydrogen bonding of a doubly hydrogen-bonded complex.

    Science.gov (United States)

    Liu, Yufang; Ding, Junxia; Liu, Ruiqiong; Shi, Deheng; Sun, Jinfeng

    2009-12-01

    The geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen-bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time-dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S(1) state of this doubly hydrogen-bonded FN-2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen-bonded FN-2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm(-1) observed in the IR spectra should be assigned as the doubly hydrogen-bonded FN-2MeOH complex from our calculated results. The electronic excited-state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S(1) state of the doubly hydrogen-bonded FN-2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen-bonded FN-MeOH complex and play important role on the photophysics of fluorenone in solutions.

  4. Mapping the force-field of a hydrogen bonded assembly

    Science.gov (United States)

    Moriarty, Philip

    2014-03-01

    Hydrogen-bonding underpins the structure, properties, and dynamics of a vast array of systems spanning a wide variety of scientific fields. From the striking complexity of the phase diagram of H2O and the elegance of base pair interactions in DNA, to the directionality inherent in supramolecular self-assembly at surfaces, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the H-bond, including the magnitude of the force and binding energy, force constant, and decay length associated with the interaction, have been vigorously debated for many decades. I will discuss how dynamic force microscopy (DFM) using a qPlus sensor can quantitatively map the tip-sample force-field for naphthalene tetracarboxylic diimide (NTCDI) molecules hydrogen-bonded in 2D assemblies. A comparison of experimental images and force spectra with their simulated counterparts from density functional theory calculations shows that image contrast due to intermolecular hydrogen bonds arises fundamentally from charge density depletion due to strong tip-sample interactions. Interpretation of DFM images of hydrogen bonds therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

  5. Hybrid Catalysis Enabling Room-Temperature Hydrogen Gas Release from N-Heterocycles and Tetrahydronaphthalenes.

    Science.gov (United States)

    Kato, Shota; Saga, Yutaka; Kojima, Masahiro; Fuse, Hiromu; Matsunaga, Shigeki; Fukatsu, Arisa; Kondo, Mio; Masaoka, Shigeyuki; Kanai, Motomu

    2017-02-15

    Hybrid catalyst systems to achieve acceptorless dehydrogenation of N-heterocycles and tetrahydronaphthalenes-model substrates for liquid organic hydrogen carriers-were developed. A binary hybrid catalysis comprising an acridinium photoredox catalyst and a Pd metal catalyst was effective for the dehydrogenation of N-heterocycles, whereas a ternary hybrid catalysis comprising an acridinium photoredox catalyst, a Pd metal catalyst, and a thiophosphoric imide organocatalyst achieved dehydrogenation of tetrahydronaphthalenes. These hybrid catalyst systems allowed for 2 molar equiv of H2 gas release from six-membered N-heterocycles and tetrahydronaphthalenes under mild conditions, i.e., visible light irradiation at rt. The combined use of two or three different catalyst types was essential for the catalytic activity.

  6. Hydrogen bonds in PC{sub 61}BM solids

    Energy Technology Data Exchange (ETDEWEB)

    Sheng, Chun-Qi [Department of Physics, Zhejiang University, Hangzhou 310027 (China); Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou 311121 (China); Li, Wen-Jie; Du, Ying-Ying; Chen, Guang-Hua; Chen, Zheng; Li, Hai-Yang; Li, Hong-Nian, E-mail: phylihn@mail.zju.edu.cn [Department of Physics, Zhejiang University, Hangzhou 310027 (China)

    2015-09-15

    We have studied the hydrogen bonds in PC{sub 61}BM solids. Inter-molecular interaction is analyzed theoretically for the well-defined monoclinic (P2{sub 1}/n) structure. The results indicate that PC{sub 61}BM combines into C–H⋯O{sub d} bonded molecular chains, where O{sub d} denotes the doubly-bonded O atom of PC{sub 61}BM. The molecular chains are linked together by C–H⋯O{sub s} bonds, where O{sub s} denotes the singly-bonded O atom of PC{sub 61}BM. To reveal the consequences of hydrogen bond formation on the structural properties of PC{sub 61}BM solids (not limited to the monoclinic structure), we design and perform some experiments for annealed samples with the monoclinic (P2{sub 1}/n) PC{sub 61}BM as starting material. The experiments include differential scanning calorimetry, X-ray diffraction and infrared absorption measurements. Structural phase transitions are observed below the melting point. The C–H⋯O{sub d} bonds seem persisting in the altered structures. The inter-molecular hydrogen bonds can help to understand the phase separation in polymer/PC{sub 61}BM blends and may be responsible for the existence of liquid PC{sub 61}BM.

  7. 15N and 1H Solid-State NMR Investigation of a Canonical Low-Barrier Hydrogen-Bond Compound: 1,8-bis(dimethylamino) naphthalene

    OpenAIRE

    White, Paul B.; Hong, Mei

    2015-01-01

    Strong or low-barrier hydrogen bonds have been often proposed in proteins to explain enzyme catalysis and proton transfer reactions. So far 1H chemical shifts and scalar couplings have been used as the main NMR spectroscopic signatures for strong H-bonds. In this work, we report simultaneous measurements of 15N and 1H chemical shifts and N-H bond lengths by solid-state NMR in 15N-labeled 1,8-bis(dimethylamino) naphthalene (DMAN), which contains a well known strong NHN H-bond. We complexed DMA...

  8. Redshift or adduct stabilization -- a computational study of hydrogen bonding in adducts of protonated carboxylic acids

    DEFF Research Database (Denmark)

    Olesen, Solveig Gaarn; Hammerum, Steen

    2009-01-01

    not always yield consistent predictions, as illustrated by the hydrogen bonds formed by the E and Z OH groups of protonated carboxylic acids. The delta-PA and the stabilization of a series of hydrogen bonded adducts indicate that the E OH group forms the stronger hydrogen bonds, whereas the bond length...... carboxylic acids are different. The OH bond length and IR redshift afford the better measure of hydrogen bond strength....

  9. Mapping the force field of a hydrogen-bonded assembly

    Science.gov (United States)

    Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N. R.; Kantorovich, L.; Moriarty, P.

    2014-05-01

    Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

  10. Terahertz Vibrations and Hydrogen-Bonded Networks in Crystals

    Directory of Open Access Journals (Sweden)

    Masae Takahashi

    2014-03-01

    Full Text Available The development of terahertz technology in the last few decades has made it possible to obtain a clear terahertz (THz spectrum. THz vibrations clearly show the formation of weak bonds in crystals. The simultaneous progress in the code of first-principles calculations treating noncovalent interactions has established the position of THz spectroscopy as a powerful tool for detecting the weak bonding in crystals. In this review, we are going to introduce, briefly, the contribution of weak bonds in the construction of molecular crystals first, and then, we will review THz spectroscopy as a powerful tool for detecting the formation of weak bonds and will show the significant contribution of advanced computational codes in treating noncovalent interactions. From the second section, following the Introduction, to the seventh section, before the conclusions, we describe: (1 the crystal packing forces, the hydrogen-bonded networks and their contribution to the construction of organic crystals; (2 the THz vibrations observed in hydrogen-bonded molecules; (3 the computational methods for analyzing the THz vibrations of hydrogen-bonded molecules; (4 the dispersion correction and anharmonicity incorporated into the first-principles calculations and their effect on the peak assignment of the THz spectrum (5 the temperature dependence; and (6 the polarization dependence of the THz spectrum.

  11. Hydrophobic interactions and hydrogen bonds in \\beta-sheet formation

    CERN Document Server

    Narayanan, Chitra

    2013-01-01

    In this study, we investigate interactions of extended conformations of homodimeric peptides made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains using all-atom molecular dynamics simulations to decipher driving forces for \\beta-sheet formation. We make use of a periodic boundary condition setup in which individual peptides are infinitely long and stretched. Dimers adopt \\beta-sheet conformations at short interpeptide distances (\\xi ~ 0.5 nm) and at intermediate distances (~ 0.8 nm), valine and leucine homodimers assume cross-\\beta-like conformations with side chains interpenetrating each other. These two states are identified as minima in the Potential of Mean Force (PMF). While the number of interpeptide hydrogen bonds increases with decreasing interpeptide distance, the total hydrogen bond number in the system does not change significantly, suggesting that formation of \\beta-sheet structures from extended conformations is not driven by hydrogen bonds. This is supported by...

  12. Infrared Spectra and Hydrogen Bonds of Biologically Active Benzaldehydes

    Science.gov (United States)

    Tolstorozhev, G. B.; Skornyakov, I. V.; Belkov, M. V.; Shimko, A. N.; Shadyro, O. I.; Brinkevich, S. D.; Samovich, S. N.

    2013-09-01

    IR-Fourier spectra of solutions and crystals of biologically active benzaldehyde derivatives were studied. Specific features of the formation of intra- and intermolecular hydrogen bonds were analyzed. Spectral signatures that characterized participation of the hydroxyl OH group and also the OCH3 and C=O groups in the formation of intramolecular hydrogen bonds of the three different types O-H···O-H, O-H···O-CH3, and O-H···O=C were revealed. Intramolecular hydrogen bonds of the types O-H···O-H and O-H···O-CH3 were absent for benzaldehyde derivatives in the crystal phase. Only hydroxyl and carbonyl groups participated in intermolecular interactions. This resulted in the formation of linear intermolecular dimers. Seven various configurations of the linear dimers were identified in solutions and crystals.

  13. Estimating the energy of intramolecular hydrogen bonds in chitosan oligomers

    Science.gov (United States)

    Mikhailov, G. P.; Lazarev, V. V.

    2016-07-01

    The effect the number of chitosan monomer units CTS n ( n = 1-5), the protonation of chitosan dimers, and the interaction between CTS n ( n = 1-3) and acetate ions have on the energy of intramolecular hydrogen bonds is investigated by means of QTAIM analysis and solving the vibrational problem within the cluster-continuum model. It is established that the number of H-bonds in CTS n is 2 n - 1 and the total energy of H-bonds grows by ~20 kJ/mol. It is concluded that the hydrogen bonds between CTS and acetate ions play a major role in the stabilization of polyelectrolyte complexes in dilute acetic acid solutions of CTS.

  14. Hydrogen Bonds and Vibrations of Water on (110) Rutile

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Nitin [ORNL; Neogi, Sanghamitra [Pennsylvania State University; Kent, Paul R [ORNL; Bandura, Andrei V. [St. Petersburg State University, St. Petersburg, Russia; Wesolowski, David J [ORNL; Cole, David R [ORNL; Sofo, Jorge O. [Pennsylvania State University

    2009-01-01

    We study the relation between hydrogen bonding and the vibrational frequency spectra of water on the (110) surface of rutile (α-TiO2) with three structural layers of adsorbed water. Using ab-initio molecular dynamics simulations at 280, 300 and 320K, we find strong, crystallographically-controlled adsorption sites, in general agreement with synchrotron X-ray and classical MD simulations. We demonstrate that these sites are produced by strong hydrogen bonds formed between the surface oxygen atoms and sorbed water molecules. The strength of these bonds is manifested by substantial broadening of the stretching mode vibrational band. The overall vibrational spectrum obtained from our simulations is in good agreement with inelastic neutron scattering experiments. We correlate the vibrational spectrum with different bonds at the surface in order to transform these vibrational measurements into a spectroscopy of surface interactions.

  15. Solvent effects on hydrogen bonding between primary alcohols and esters

    Institute of Scientific and Technical Information of China (English)

    DHARMALINGAM K.; RAMACHANDRAN K.; SIVAGURUNATHAN P.

    2006-01-01

    The interaction by hydrogen bond formation of some primary alcohols (1-heptanol, 1-octanol and 1-decanol) with esters (methyl methacrylate, ethyl methacrylate and butyl methacrylate) was investigated in non-polar solvents viz., n-heptane,CCh and benzene by means of FTIR spectroscopy. Formation constants and free energy changes of complex formation were determined. The dependence of the equilibrium constants and free energy changes of complex formation on the alkyl chain length of both the alcohols and esters are discussed. The solvent effect on the hydrogen bond formation is discussed in terms of specific interaction between the solute and solvent.

  16. On some hydrogen bond correlations at high pressures

    Science.gov (United States)

    Sikka, S. K.

    2007-09-01

    In situ high pressure neutron diffraction measured lengths of O H and H O pairs in hydrogen bonds in substances are shown to follow the correlation between them established from 0.1 MPa data on different chemical compounds. In particular, the conclusion by Nelmes et al that their high pressure data on ice VIII differ from it is not supported. For compounds in which the O H stretching frequencies red shift under pressure, it is shown that wherever structural data is available, they follow the stretching frequency versus H O (or O O) distance correlation. For compounds displaying blue shifts with pressure an analogy appears to exist with improper hydrogen bonds.

  17. Nature of hydrogen bonding in coal-derived asphaltenes

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, S.R.; Li, N.C.

    1978-02-01

    Reports are presented on near-infrared and proton magneti resonance studies of hydrogen bonding between the hydroxyl group of o-phenylphenol (OPP) and two coal derived asphaltenes, and their acid and base components. The asphaltenes were prepared from bituminous coal under the same conditions except that one was prepared using a CoMo catalyst. The results of the studies show that the use of the CoMo catalyst leads to a base asphaltene component of lower molecular weight and higher hydrogen-bond acceptor strength.

  18. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    OpenAIRE

    Nagy, Peter I.

    2014-01-01

    A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with in...

  19. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    OpenAIRE

    Nagy, Peter I.

    2014-01-01

    A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with int...

  20. Effects of ionic catalysis on hydrogen production by the steam gasification of cellulose

    Energy Technology Data Exchange (ETDEWEB)

    Su, Shen [State Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan 030001 (China); Graduate University of Chinese Academy of Sciences, Beijing 100039 (China); Li, Wen; Bai, Zongqing; Bai, Jin [State Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan 030001 (China); Xiang, Hongwei [Graduate University of Chinese Academy of Sciences, Beijing 100039 (China)

    2010-05-15

    In this study, significant effects of ionic catalysis on the formation of H{sub 2} and CO during the steam gasification process of cellulose are revealed. The energy of the C-H bonds of cellulose can be remarkably reduced by Na{sup +} and OH{sup -} ions produced by the dissociation of NaOH, enabling dehydrogenation of cellulose at low temperature. Dehydrogenation of cellulose is evidently affected by the concentration of Na{sup +} and OH{sup -} ions that cellulose can come into contact with. Higher concentrations of Na{sup +} and OH{sup -} ions can reduce the initial dehydrogenation temperature of cellulose to lower than 403 K. The production of CO increases after this remarkable dehydrogenation of cellulose, which indicates that the C-O bonds of cellulose are prone to forming CO by pyrolysis. (author)

  1. Quantum Confinement in Hydrogen Bond of DNA and RNA

    CERN Document Server

    Santos, da Silva dos; Ricotta, Regina Maria

    2015-01-01

    The hydrogen bond is a fundamental ingredient to stabilize the DNA and RNA macromolecules. The main contribution of this work is to describe quantitatively this interaction as a consequence of the quantum confinement of the hydrogen. The results for the free and confined system are compared with experimental data. The formalism to compute the energy gap of the vibration motion used to identify the spectrum lines is the Variational Method allied to Supersymmetric Quantum Mechanics.

  2. On the mechanism of hydrogen evolution catalysis by proteins: A case study with bovine serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Doneux, Th., E-mail: tdoneux@ulb.ac.b [Chimie Analytique et Chimie des Interfaces, Faculte des Sciences, Universite Libre de Bruxelles, Boulevard du Triomphe 2, CP 255, B-1050 Bruxelles (Belgium); Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno (Czech Republic); Ostatna, Veronika [Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno (Czech Republic); Palecek, Emil, E-mail: palecek@ibp.cz [Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno (Czech Republic)

    2011-10-30

    Highlights: > Proteins catalyse hydrogen evolution at mercury electrodes. > The adsorbed protein is the mediator and the buffer proton donor is the substrate. > The characteristics of the catalytic peak are connected to the protein properties. - Abstract: The catalysis of the hydrogen evolution reaction (HER) by proteins has been known for decades but was only recently found to be useful for electroanalytical purposes. The mechanism of the catalytic process is investigated at hanging mercury drop electrodes by cyclic voltammetry, with bovine serum albumin as a model system. It is shown that the catalyst is the protein in the adsorbed state. The influence of various parameters such as the accumulation time, scan rate or buffer concentration is studied, and interpreted in the framework of a surface catalytic mechanism. Under the experimental conditions used in the work, a 'total catalysis' phenomenon takes place, the rate of HER being limited by the diffusion of the proton donor. The adequacy of the existing models is discussed, leading to a call for the development of more refined models.

  3. The role of hydrogen bonds in the melting points of sulfonate-based protic organic salts

    DEFF Research Database (Denmark)

    Luo, Jiangshui

    2016-01-01

    there is evidence of bond formation [6]. Hydrogen bonds in the solid state fall into the classification of strong, moderate, and weak hydrogen bonds [7]. In molecular systems like H2O (vs. H2S) or NH3 (vs. PH3), strong hydrogen bonds lead to higher melting points. However, in organic salts, the situation may...

  4. Hydrogen bond templated 1:1 macrocyclization through an olefin metathesis/hydrogenation sequence.

    Science.gov (United States)

    Trita, Andrada Stefania; Roisnel, Thierry; Mongin, Florence; Chevallier, Floris

    2013-07-19

    The construction of pyridine-containing macrocyclic architectures using a nonmetallic template is described. 4,6-Dichlororesorcinol was used as an exotemplate to self-organize two aza-heterocyclic units by OH···N hydrogen bonds. Subsequent sequential double olefin metathesis/hydrogenation reactions employing a single ruthenium-alkylidene precatalyst open access to macrocyclic molecules.

  5. Alternation and tunable composition in hydrogen bonded supramolecular copolymers.

    Science.gov (United States)

    Felder, Thorsten; de Greef, Tom F A; Nieuwenhuizen, Marko M L; Sijbesma, Rint P

    2014-03-07

    Sequence control in supramolecular copolymers is limited by the selectivity of the associating monomer end groups. Here we introduce the use of monomers with aminopyrimidinone and aminohydroxynaphthyridine quadruple hydrogen bonding end groups, which both homodimerize, but form even stronger heterodimers. These features allow the formation of supramolecular copolymers with a tunable composition and a preference for alternating sequences.

  6. OH stretching frequencies in systems with intramolecular hydrogen bonds

    DEFF Research Database (Denmark)

    Spanget-Larsen, Jens; Hansen, Bjarke Knud Vilster; Hansen, Poul Erik

    2011-01-01

    OH stretching wavenumbers were investigated for 30 species with intramolecularly hydrogen bonded hydroxyl groups, covering the range from 3600 to ca. 1900 cm-1. Theoretical wavenumbers were predicted with B3LYP/6-31G(d) density functional theory using the standard harmonic approximation, as well...

  7. Templation in Noncovalent Synthesis of Hydrogen-Bonded Rosettes

    NARCIS (Netherlands)

    Crego-Calama, Mercedes; Reinhoudt, David N.; Cate, ten Matthijs G.J.; Schalley, Christoph A.; Vögtle, Fritz; Dötz, Karl Heinz

    2005-01-01

    In this chapter, hydrogen-bonded assemblies based on the rosette motif are used to describe some examples of templation in noncovalent synthesis. After a brief description of the synthesis and characterization of these assemblies, the guest-templated selection and amplification of the strongest bind

  8. Adhesion between silica surfaces due to hydrogen bonding

    Science.gov (United States)

    Bowen, James; Rossetto, Hebert L.; Kendall, Kevin

    2016-09-01

    The adhesion between surfaces can be enhanced significantly by the presence of hydrogen bonding. Confined water at the nanoscale can display behaviour remarkably different to bulk water due to the formation of hydrogen bonds between two surfaces. In this work we investigate the role of confined water on the interaction between hydrophilic surfaces, specifically the effect of organic contaminants in the aqueous phase, by measuring the peak adhesive force and the work of adhesion. Atomic force microscope cantilevers presenting hemispherical silica tips were interacted with planar single crystals of silica in the presence of dimethylformamide, ethanol, and formamide; solution compositions in the range 0-100 mol% water were investigated for each molecule. Each molecule was chosen for its ability to hydrogen bond with water molecules, with increasing concentrations likely to disrupt the structure of surface-bound water layers. With the exception of aqueous solutions containing low concentrations of ethanol, all molecules decreased the ability of confined water to enhance the adhesion between the silica surfaces in excess of the predicted theoretical adhesion due to van der Waals forces. The conclusion was that adhesion depends strongly on the formation of a hydrogen-bonding network within the water layers confined between the silica surfaces.

  9. Piezoelectric hydrogen bonding: computational screening for a design rationale.

    Science.gov (United States)

    Werling, Keith A; Griffin, Maryanne; Hutchison, Geoffrey R; Lambrecht, Daniel S

    2014-09-01

    Organic piezoelectric materials are promising targets in applications such as energy harvesting or mechanical sensors and actuators. In a recent paper (Werling, K. A.; et al. J. Phys. Chem. Lett. 2013, 4, 1365-1370), we have shown that hydrogen bonding gives rise to a significant piezoelectric response. In this article, we aim to find organic hydrogen bonded systems with increased piezo-response by investigating different hydrogen bonding motifs and by tailoring the hydrogen bond strength via functionalization. The largest piezo-coefficient of 23 pm/V is found for the nitrobenzene-aniline dimer. We develop a simple, yet surprisingly accurate rationale to predict piezo-coefficients based on the zero-field compliance matrix and dipole derivatives. This rationale increases the speed of first-principles piezo-coefficient calculations by an order of magnitude. At the same time, it suggests how to understand and further increase the piezo-response. Our rationale also explains the remarkably large piezo-response of 150 pm/V and more for another class of systems, the "molecular springs" (Marvin, C.; et al. J. Phys. Chem. C 2013, 117, 16783-16790.).

  10. Watson-Crick hydrogen bonding of unlocked nucleic acids

    DEFF Research Database (Denmark)

    Langkjær, Niels; Wengel, Jesper; Pasternak, Anna

    2015-01-01

    We herein describe the synthesis of two new unlocked nucleic acid building blocks containing hypoxanthine and 2,6-diaminopurine as nucleobase moieties and their incorporation into oligonucleotides. The modified oligonucleotides were used to examine the thermodynamic properties of UNA against unmo...... unmodified oligonucleotides and the resulting thermodynamic data support that the hydrogen bonding face of UNA is Watson-Crick like....

  11. Controlling the amplification of chirality in hydrogen-bonded assemblies

    NARCIS (Netherlands)

    Mateos-Timoneda, Miguel A.; Crego-Calama, Mercedes; Reinhoudt, David N.

    2005-01-01

    The amplification of chirality (a high enantiomeric or diastereomeric excess induced by a small initial amount of chiral bias) on hydrogen-bonded assemblies has been studied using “sergeants-and-soldiers” experiments under thermodynamically controlled conditions. Here it is shown that different subs

  12. Hydrogen Bonding in Phosphine Oxide/Phosphate-Phenol Complexes

    NARCIS (Netherlands)

    Cuypers, R.; Sudhölter, E.J.R.; Zuilhof, H.

    2010-01-01

    To develop a new solvent-impregnated resin (SIR) system for the removal of phenols and thiophenols from water, complex formation by hydrogen bonding of phosphine oxides and phosphates is studied using isothermal titration calorimetry (ITC) and quantum chemical modeling. Six different computational m

  13. Hydrogen-bond acidity of ionic liquids: an extended scale†

    Science.gov (United States)

    Kurnia, Kiki A.; Lima, Filipa; Cláudio, Ana Filipa M.; Coutinho, João A. P.; Freire, Mara G.

    2015-01-01

    One of the main drawbacks comprising an appropriate selection of ionic liquids (ILs) for a target application is related to the lack of an extended and well-established polarity scale for these neoteric fluids. Albeit considerable progress has been made on identifying chemical structures and factors that influence the polarity of ILs, there still exists a high inconsistency in the experimental values reported by different authors. Furthermore, due to the extremely large number of possible ILs that can be synthesized, the experimental characterization of their polarity is a major limitation when envisaging the choice of an IL with a desired polarity. Therefore, it is of crucial relevance to develop correlation schemes and a priori predictive methods able to forecast the polarity of new (or not yet synthesized) fluids. In this context, and aiming at broadening the experimental polarity scale available for ILs, the solvatochromic Kamlet–Taft parameters of a broad range of bis(trifluoromethylsulfonyl)imide-([NTf2]−)-based fluids were determined. The impact of the IL cation structure on the hydrogen-bond donating ability of the fluid was comprehensively addressed. Based on the large amount of novel experimental values obtained, we then evaluated COSMO-RS, COnductor-like Screening MOdel for Real Solvents, as an alternative tool to estimate the hydrogen-bond acidity of ILs. A three-parameter model based on the cation–anion interaction energies was found to adequately describe the experimental hydrogen-bond acidity or hydrogen-bond donating ability of ILs. The proposed three-parameter model is also shown to present a predictive capacity and to provide novel molecular-level insights into the chemical structure characteristics that influence the acidity of a given IL. It is shown that although the equimolar cation–anion hydrogen-bonding energies (EHB) play the major role, the electrostatic-misfit interactions (EMF) and van der Waals forces (EvdW) also contribute

  14. Hydrogen bonds in concreto and in computro: the sequel

    Science.gov (United States)

    Stouten, Pieter F. W.; Van Eijck, Bouke P.; Kroon, Jan

    1991-02-01

    In the framework of our comparative research concerning hydrogen bonding in the crystalline and liquid phases we have carried out molecular dynamics (MD) simulations of liquid methanol. Six different rigid three site models are compared. Five of them had been reported in the literature and one (OM2) we developed by a fit to the experimental molar volume, heat of vaporization and neutron weighted radial distribution function. In general the agreement with experiment is satisfactory for the different models. None of the models has an explicit hydrogen bond potential, but five of the six models show a degree of hydrogen bonding comparable to experiments on liquid methanol. The analysis of the simulation hydrogen bonds indicates that there is a distinct preference of the O⋯O axis to lie in the acceptor lone pairs plane, but hardly any for the lone pair directions. Ab initio calculations and crystal structure statistics of OH⋯O hydrogen bonds agree with this observation. The O⋯O hydrogen bond length distributions are similar for most models. The crystal structures show a sharper O⋯O distribution. Explicit introduction of harmonic motion with a quite realistic root mean square amplitude of 0.08 Å to the thermally averaged crystal distribution results in a distribution comparable to OM2 although the maximum of the former is found at shorter distance. On the basis of the analysis of the static properties of all models we conclude that our OM2, Jorgenson's OPLS and Haughney, Ferrario and McDonald's HFM1 models are good candidates for simulations of liquid methanol under isothermal, isochoric conditions. Partly flexible and completely rigid OM2 are simulated at constant pressure and with fixed volume. The flexible simulations give essentially the same (correct) results under both conditions, which is not surprising because the flexible form was fitted under both conditions. Rigid OM2 has a similar potential energy but larger pressure in the

  15. Liquid state of hydrogen bond network in ice

    CERN Document Server

    Ryzhkin, M I; Sinitsyn, V V; Ryzhkin, I A

    2016-01-01

    Here we show that the Coulomb interaction between violations of the Bernal-Fowler rules leads to a temperature induced step-wise increase in their concentration by 6-7 orders of magnitude. This first-order phase transition is accompanied by commensurable decrease in the relaxation time and can be interpreted as melting of the hydrogen bond network. The new phase with the melted hydrogen lattice and survived oxygen one is unstable in the bulk of ice, and further drastic increase in the concentrations of oxygen interstitials and vacancies accomplishes the ice melting. The fraction of broken hydrogen bonds immediately after the melting is about 0.07 of their total number that implies an essential conservation of oxygen lattice in water.

  16. Liquid state of hydrogen bond network in ice

    Science.gov (United States)

    Ryzhkin, M. I.; Klyuev, A. V.; Sinitsyn, V. V.; Ryzhkin, I. A.

    2016-08-01

    Here we theoretically show that the Coulomb interaction between violations of the Bernal-Fowler rules leads to a temperature induced step-wise increase in their concentration by 6-7 orders of magnitude. This first-order phase transition is accompanied by commensurable decrease in the relaxation time and can be interpreted as melting of the hydrogen bond network. The new phase with the melted hydrogen lattice and survived oxygen one is unstable in the bulk of ice, and further drastic increase in the concentrations of oxygen interstitials and vacancies accomplishes the ice melting. The fraction of broken hydrogen bonds immediately after the melting is about 0.07 of their total number that implies an essential conservation of oxygen lattice in water.

  17. a Theoretical Investigation on 10-12 Potential of Hydrogen-Hydrogen Covalent Bond

    Science.gov (United States)

    Taneri, Sencer

    2013-05-01

    This is an analytical investigation of well-known 10-12 potential of hydrogen-hydrogen covalent bond. In this research, we will make an elaboration of the well-known 6-12 Lennard-Jones potential in case of this type of bond. Though the results are illustrated in many text books and literature, an analytical analysis for these potentials is missing almost everywhere. The power laws are valid for small radial distances, which are calculated to some extent. The internuclear separation as well as the binding energy of the hydrogen molecule are evaluated with success.

  18. Enantio- and periselective nitroalkene Diels-Alder reactions catalyzed by helical-chiral hydrogen bond donor catalysts.

    Science.gov (United States)

    Peng, Zhili; Narcis, Maurice J; Takenaka, Norito

    2013-08-19

    Helical-chiral double hydrogen bond donor catalysts promote the nitroalkene Diels-Alder reaction in an enantio- and periselective manner. This represents the first asymmetric catalytic nitroalkene Diels-Alder reaction via LUMO-lowering catalysis. To gain an insight into this new process, the substrate scope of our catalyst was investigated by exploiting readily available 5-substituted pentamethylcyclopentadienes. The catalyst was found to tolerate dienes with different steric demands as well as dienes substituted with heteroatoms. The synthetic utility of 5-substituted pentamethylcyclopentadienes is rather limited, and thus we have developed a three-step route to 1,4,5,5-tetrasubstituted cyclopentadienes from commercially available ketones.

  19. Enantio- and Periselective Nitroalkene Diels-Alder Reactions Catalyzed by Helical-Chiral Hydrogen Bond Donor Catalysts

    Directory of Open Access Journals (Sweden)

    Zhili Peng

    2013-08-01

    Full Text Available Helical-chiral double hydrogen bond donor catalysts promote the nitroalkene Diels-Alder reaction in an enantio- and periselective manner. This represents the first asymmetric catalytic nitroalkene Diels-Alder reaction via LUMO-lowering catalysis. To gain an insight into this new process, the substrate scope of our catalyst was investigated by exploiting readily available 5-substituted pentamethylcyclopentadienes. The catalyst was found to tolerate dienes with different steric demands as well as dienes substituted with heteroatoms. The synthetic utility of 5-substituted pentamethylcyclopentadienes is rather limited, and thus we have developed a three-step route to 1,4,5,5-tetrasubstituted cyclopentadienes from commercially available ketones.

  20. Stabilization of quinapril by incorporating hydrogen bonding interactions

    Directory of Open Access Journals (Sweden)

    Roy B

    2009-01-01

    Full Text Available In the present study stability of various known solvates of quinapril hydrochloride has been compared with nitromethane solvate. Nitromethane solvate was found to be more stable compared to other known solvates. Single crystal X-ray diffraction analysis of quinapril nitromethane solvate shows intermolecular hydrogen bonding between quinapril molecule and nitromethane. Stabilization of quinapril by forming strong hydrogen bonding network as in case of co-crystals was further studied by forming co-crystal with tris(hydroxymethylamino methane. Quinapril free base forms a stable salt with tris(hydroxymethylamino methane not reported earlier. Quinapril tris(hydroxymethylamino methane salt found to be stable even at 80° for 72 h i.e. hardly any formation of diketopiperazine and diacid impurity. As expected single crystal X-ray diffraction analysis reveals tris(hydroxymethylamino methane salt of quinapril shows complex hydrogen bonding network between the two entities along with ionic bond. The properties of this stable salt - stable in solid as well as solution phase, might lead to an alternate highly stable formulation.

  1. Autoinduced catalysis and inverse equilibrium isotope effect in the frustrated Lewis pair catalyzed hydrogenation of imines.

    Science.gov (United States)

    Tussing, Sebastian; Greb, Lutz; Tamke, Sergej; Schirmer, Birgitta; Muhle-Goll, Claudia; Luy, Burkhard; Paradies, Jan

    2015-05-26

    The frustrated Lewis pair (FLP)-catalyzed hydrogenation and deuteration of N-benzylidene-tert-butylamine (2) was kinetically investigated by using the three boranes B(C6F5)3 (1), B(2,4,6-F3-C6H2)3 (4), and B(2,6-F2-C6H3)3 (5) and the free activation energies for the H2 activation by FLP were determined. Reactions catalyzed by the weaker Lewis acids 4 and 5 displayed autoinductive catalysis arising from a higher free activation energy (2 kcal mol(-1)) for the H2 activation by the imine compared to the amine. Surprisingly, the imine reduction using D2 proceeded with higher rates. This phenomenon is unprecedented for FLP and resulted from a primary inverse equilibrium isotope effect.

  2. Effect of quantum nuclear motion on hydrogen bonding

    Energy Technology Data Exchange (ETDEWEB)

    McKenzie, Ross H., E-mail: r.mckenzie@uq.edu.au; Bekker, Christiaan [School of Mathematics and Physics, University of Queensland, Brisbane 4072 (Australia); Athokpam, Bijyalaxmi; Ramesh, Sai G. [Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012 (India)

    2014-05-07

    This work considers how the properties of hydrogen bonded complexes, X–H⋯Y, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor (X) and acceptor (Y) have the same proton affinity, is carried out. For quantitative comparisons, a parametrization specific to the O–H⋯O complexes is used. The vibrational energy levels of the one-dimensional ground state adiabatic potential of the model are used to make quantitative comparisons with a vast body of condensed phase data, spanning a donor-acceptor separation (R) range of about 2.4 − 3.0 Å, i.e., from strong to weak hydrogen bonds. The position of the proton (which determines the X–H bond length) and its longitudinal vibrational frequency, along with the isotope effects in both are described quantitatively. An analysis of the secondary geometric isotope effect, using a simple extension of the two-state model, yields an improved agreement of the predicted variation with R of frequency isotope effects. The role of bending modes is also considered: their quantum effects compete with those of the stretching mode for weak to moderate H-bond strengths. In spite of the economy in the parametrization of the model used, it offers key insights into the defining features of H-bonds, and semi-quantitatively captures several trends.

  3. Effect of quantum nuclear motion on hydrogen bonding

    Science.gov (United States)

    McKenzie, Ross H.; Bekker, Christiaan; Athokpam, Bijyalaxmi; Ramesh, Sai G.

    2014-05-01

    This work considers how the properties of hydrogen bonded complexes, X-H⋯Y, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor (X) and acceptor (Y) have the same proton affinity, is carried out. For quantitative comparisons, a parametrization specific to the O-H⋯O complexes is used. The vibrational energy levels of the one-dimensional ground state adiabatic potential of the model are used to make quantitative comparisons with a vast body of condensed phase data, spanning a donor-acceptor separation (R) range of about 2.4 - 3.0 Å, i.e., from strong to weak hydrogen bonds. The position of the proton (which determines the X-H bond length) and its longitudinal vibrational frequency, along with the isotope effects in both are described quantitatively. An analysis of the secondary geometric isotope effect, using a simple extension of the two-state model, yields an improved agreement of the predicted variation with R of frequency isotope effects. The role of bending modes is also considered: their quantum effects compete with those of the stretching mode for weak to moderate H-bond strengths. In spite of the economy in the parametrization of the model used, it offers key insights into the defining features of H-bonds, and semi-quantitatively captures several trends.

  4. Indirect Interactions Between Proton Donors Separated by Several Hydrogen Bonds

    CERN Document Server

    Ogawa, Takaya; Tamaki, Takanori; Yamaguchi, Takeo

    2016-01-01

    We expand the definition of our recently proposed proton conduction mechanism, the packed-acid mechanism, which occurs under conditions of concentrated proton donors. The original definition stated that acid-acid interactions, which help overcome the barrier of the rate-determining step, occur only when a hydrogen bond is formed directly between proton donors. Here, it is shown that proton donors can interact with each other even when the donors are separated via several H-bonds. The effect of these interactions on proton diffusivity is confirmed by ab initio calculations.

  5. Statistical theory for hydrogen bonding fluid system of A_aD_d type(II):Properties of hydrogen bonding networks

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Making use of the invariant property of the equilibrium size distribution of the hydrogen bonding clus- ters formed in hydrogen bonding system of AaDd type,the analytical expressions of the free energy in pregel and postgel regimes are obtained.Then the gel free energy and the scaling behavior of the number of hydrogen bonds in gel phase near the critical point are investigated to give the corre- sponding scaling exponents and scaling law.Meanwhile,some properties of intermolecular and in- tramolecular hydrogen bonds in the system,sol and gel phases are discussed.As a result,the explicit relationship between the number of intramolecular hydrogen bonds and hydrogen bonding degree is obtained.

  6. Hydrogen-hydrogen bonds in highly branched alkanes and in alkane complexes: A DFT, ab initio, QTAIM, and ELF study.

    Science.gov (United States)

    Monteiro, Norberto K V; Firme, Caio L

    2014-03-06

    The hydrogen-hydrogen (H-H) bond or hydrogen-hydrogen bonding is formed by the interaction between a pair of identical or similar hydrogen atoms that are close to electrical neutrality and it yields a stabilizing contribution to the overall molecular energy. This work provides new, important information regarding hydrogen-hydrogen bonds. We report that stability of alkane complexes and boiling point of alkanes are directly related to H-H bond, which means that intermolecular interactions between alkane chains are directional H-H bond, not nondirectional induced dipole-induced dipole. Moreover, we show the existence of intramolecular H-H bonds in highly branched alkanes playing a secondary role in their increased stabilities in comparison with linear or less branched isomers. These results were accomplished by different approaches: density functional theory (DFT), ab initio, quantum theory of atoms in molecules (QTAIM), and electron localization function (ELF).

  7. Shear Bond Strength of Resin Bonded to Bleached Enamel Using Different Modified 35% Hydrogen Peroxides

    Directory of Open Access Journals (Sweden)

    Moosavi H

    2015-12-01

    Full Text Available Statement of Problem: Bleaching systems with different concentrations and applications are widely used to improve the visual appearance of the teeth, but one of the complications of these materials is reduction of bond strength for immediately bonding to the bleached enamel. Objectives: The aim of this study was to evaluate the influence of using different modified hydrogen peroxide bleaching agents on the shear bond strength of composite resin bonded to the bleached enamel. Materials and Methods: Forty-eight sound extracted premolar teeth were collected, sectioned 1 mm below the CEJ to detach the root. The proximal surfaces of the teeth were flattened using diamond disks and silicon carbide papers to achieve flat homogeneous enamel surfaces without exposure to the dentin. The teeth were randomly divided into four groups as follows (n = 12: group 1: bleaching with 35% hydrogen peroxide gel; group 2: bleaching with 35% hydrogen peroxide gel contained (casein phosphopeptide-amorphous calcium phosphate (CPP-ACP; group 3: bleaching with 35% hydrogen peroxide gel combined with fluoride; and group 4: bleaching with 35% hydrogen peroxide applying one week before resin restoration placement. Composite resin, Clearfil AP-X (Kuraray, Tokyo, Japan, was bonded on each tooth in the mould (4 mm diameter × 3 mm height using Clearfil SE Bond (Kuraray, Tokyo, Japan. After 24 hours of storage and 1000 cycles of thermocycling, the shear bond strength of the specimens at a cross-head speed of 0.5 mm/min was measured in MPa. Data were analyzed using ANOVA and Tukey’s post-hoc test. Results: The minimum and maximum mean shear bond strength values were observed in groups 2 (15.82 ± 4.41 and 4 (21.00 ± 3.90, respectively. Multiple comparisons of groups revealed no significant differences among the groups except between group 4 and all the other groups. The most common type of failure was adhesive. Conclusions: Using modified bleaching agents decreased the bond

  8. The pnicogen bond: its relation to hydrogen, halogen, and other noncovalent bonds.

    Science.gov (United States)

    Scheiner, Steve

    2013-02-19

    Among a wide range of noncovalent interactions, hydrogen (H) bonds are well known for their specific roles in various chemical and biological phenomena. When describing conventional hydrogen bonding, researchers use the notation AH···D (where A refers to the electron acceptor and D to the donor). However, the AH molecule engaged in a AH···D H-bond can also be pivoted around by roughly 180°, resulting in a HA···D arrangement. Even without the H atom in a bridging position, this arrangement can be attractive, as explained in this Account. The electron density donated by D transfers into a AH σ* antibonding orbital in either case: the lobe of the σ* orbital near the H atom in the H-bonding AH···D geometry, or the lobe proximate to the A atom in the HA···D case. A favorable electrostatic interaction energy between the two molecules supplements this charge transfer. When A belongs to the pnictide family of elements, which include phosphorus, arsenic, antimony, and bismuth, this type of interaction is called a pnicogen bond. This bonding interaction is somewhat analogous to the chalcogen and halogen bonds that arise when A is an element in group 16 or 17, respectively, of the periodic table. Electronegative substitutions, such as a F for a H atom opposite the electron donor atom, strengthen the pnicogen bond. For example, the binding energy in FH(2)P···NH(3) greatly exceeds that of the paradigmatic H-bonding water dimer. Surprisingly, di- or tri-halogenation does not produce any additional stabilization, in marked contrast to H-bonds. Chalcogen and halogen bonds show similar strength to the pnicogen bond for a given electron-withdrawing substituent. This insensitivity to the electron-acceptor atom distinguishes these interactions from H-bonds, in which energy depends strongly upon the identity of the proton-donor atom. As with H-bonds, pnicogen bonds can extract electron density from the lone pairs of atoms on the partner molecule, such as N, O, and

  9. Contribution of Hydrogen Bonds to Paper Strength Properties.

    Directory of Open Access Journals (Sweden)

    Piotr Przybysz

    Full Text Available The objective of this work was to investigate the influence of hydrogen bonds between fibres on static and dynamic strength properties of paper. A commercial bleached pinewood kraft pulp was soaked in water, refined in a PFI, and used to form paper webs in different solvents, such as water, methanol, ethanol, n-propanol and n-butanol, to determine the effect of their dipole moment on static and dynamic strength properties of resulting paper sheets. Paper which was formed in water, being the solvent of the highest dipole moment among the tested ones, showed the highest breaking length and tear resistance. When paper webs were formed in n-butanol, which was the least polar among the solvents, these parameters were reduced by around 75%. These results provide evidence of the importance of water in paper web formation and strong impact of hydrogen bonds between fibres on strength properties of paper.

  10. Experimental and Theoretical Studies in Hydrogen-Bonding Organocatalysis

    Directory of Open Access Journals (Sweden)

    Matej Žabka

    2015-08-01

    Full Text Available Chiral thioureas and squaramides are among the most prominent hydrogen-bond bifunctional organocatalysts now extensively used for various transformations, including aldol, Michael, Mannich and Diels-Alder reactions. More importantly, the experimental and computational study of the mode of activation has begun to attract considerable attention. Various experimental, spectroscopic and calculation methods are now frequently used, often as an integrated approach, to establish the reaction mechanism, the mode of activation or explain the stereochemical outcome of the reaction. This article comprises several case studies, sorted according to the method used in their study. The aim of this review is to give the investigators an overview of the methods currently utilized for mechanistic investigations in hydrogen-bonding organocatalysis.

  11. Hydrogen bonding in oxalic acid and its complexes: A database study of neutron structures

    Indian Academy of Sciences (India)

    R Chitra; Amit Das; R R Choudhury; M Ramanadham; R Chidambaram

    2004-08-01

    The basic result of carboxylic group that the oxygen atom of the –OH never seems to be a hydrogen bond acceptor is violated in the cases, namely urea oxalic acid and bis urea oxalic acid complexes, where the hydroxyl oxygen atom is an acceptor of a weak N–H... O hydrogen bond. The parameters of this hydrogen bond, respectively in these structures are: hydrogen acceptor distance 2.110 Å and 2.127 Å and the bending angle at hydrogen, 165.6° and 165.8°. The bond strength around the hydroxyl oxygen is close to 1.91 valence units, indicating that it has hardly any strength left to form hydrogen bonds. These two structures being highly planar, force the formation of this hydrogen bond. As oxalic acid is the common moiety, the structures of the two polymorphs, -oxalic acid and -oxalic acid, also were looked into in terms of hydrogen bonding and packing.

  12. Ion Pairs or Neutral Molecule Adducts? Cooperativity in Hydrogen Bonding

    Science.gov (United States)

    DeKock, Roger L.; Schipper, Laura A.; Dykhouse, Stephanie C.; Heeringa, Lee P.; Brandsen, Benjamin M.

    2009-01-01

    We performed theoretical studies on the systems NH[subscript 3] times HF times mH[subscript 2]O, NH[subscript 3] times HCl times mH[subscript 2]O, with m = 0, 1, 2, and 6. The molecules with m = 0 form hydrogen-bonded adducts with little tendency to form an ion-pair structure. The molecule NH[subscript 3] times HCl times H[subscript 2]O cannot be…

  13. H/D Isotope Effects in Hydrogen Bonded Systems

    Directory of Open Access Journals (Sweden)

    Aleksander Filarowski

    2013-04-01

    Full Text Available An extremely strong H/D isotope effect observed in hydrogen bonded A-H…B systems is connected with a reach diversity of the potential shape for the proton/deuteron motion. It is connected with the anharmonicity of the proton/deuteron vibrations and of the tunneling effect, particularly in cases of short bridges with low barrier for protonic and deuteronic jumping. Six extreme shapes of the proton motion are presented starting from the state without possibility of the proton transfer up to the state with a full ionization. The manifestations of the H/D isotope effect are best reflected in the infra-red absorption spectra. A most characteristic is the run of the relationship between the isotopic ratio nH/nD and position of the absorption band shown by using the example of NHN hydrogen bonds. One can distinguish a critical range of correlation when the isotopic ratio reaches the value of ca. 1 and then increases up to unusual values higher than . The critical range of the isotope effect is also visible in NQR and NMR spectra. In the critical region one observes a stepwise change of the NQR frequency reaching 1.1 MHz. In the case of NMR, the maximal isotope effect is reflected on the curve presenting the dependence of Δd (1H,2H on d (1H. This effect corresponds to the range of maximum on the correlation curve between dH and ΔpKa that is observed in various systems. There is a lack in the literature of quantitative information about the influence of isotopic substitution on the dielectric properties of hydrogen bond except the isotope effect on the ferroelectric phase transition in some hydrogen bonded crystals.

  14. Electrostatics determine vibrational frequency shifts in hydrogen bonded complexes.

    Science.gov (United States)

    Dey, Arghya; Mondal, Sohidul Islam; Sen, Saumik; Ghosh, Debashree; Patwari, G Naresh

    2014-12-14

    The red-shifts in the acetylenic C-H stretching vibration of C-H∙∙∙X (X = O, N) hydrogen-bonded complexes increase with an increase in the basicity of the Lewis base. Analysis of various components of stabilization energy suggests that the observed red-shifts are correlated with the electrostatic component of the stabilization energy, while the dispersion modulates the stabilization energy.

  15. Hydrated alizarin complexes: hydrogen bonding and proton transfer.

    Science.gov (United States)

    Huh, Hyun; Cho, Sung Haeng; Heo, Jiyoung; Kim, Nam Joon; Kim, Seong Keun

    2012-07-07

    We investigated the hydrogen bonding structures and proton transfer for the hydration complexes of alizarin (Az) produced in a supersonic jet using fluorescence excitation (FE), dispersed laser induced fluorescence (LIF), visible-visible hole burning (HB), and fluorescence detected infrared (FDIR) spectroscopy. The FDIR spectrum of bare Az with two O-H groups exhibits two vibrational bands at 3092 and 3579 cm(-1), which, respectively, correspond to the stretching vibration of O1-H1 that forms a strong intramolecular hydrogen bond with the C9=O9 carbonyl group and the stretching vibration of O2-H2 that is weakly hydrogen-bonded to O1-H1. For the 1:1 hydration complex Az(H(2)O)(1), we identified three conformers. In the most stable conformer, the water molecule forms hydrogen bonds with the O1-H1 and O2-H2 groups of Az as a proton donor and proton acceptor, respectively. In the other conformers, the water binds to the C10=O10 group in two nearly isoenergetic configurations. In contrast to the sharp vibronic peaks in the FE spectra of Az and Az(H(2)O)(1), only broad, structureless absorption was observed for Az(H(2)O)(n) (n≥ 2), indicating a facile decay process, possibly due to proton transfer in the electronic excited state. The FDIR spectrum with the wavelength of the probe laser fixed at the broad band exhibited a broad vibrational band near the O2-H2 stretching vibration frequency of the most stable conformer of Az(H(2)O)(1). With the help of theoretical calculations, we suggest that the broad vibrational band may represent the occurrence of proton transfer by tunnelling in the electronic ground state of Az(H(2)O)(n) (n≥ 2) upon excitation of the O2-H2 vibration.

  16. Protonic transport through solitons in hydrogen-bonded systems

    Science.gov (United States)

    Kavitha, L.; Jayanthi, S.; Muniyappan, A.; Gopi, D.

    2011-09-01

    We offer an alternative route for investigating soliton solutions in hydrogen-bonded (HB) chains. We invoke the modified extended tangent hyperbolic function method coupled with symbolic computation to solve the governing equation of motion for proton dynamics. We investigate the dynamics of proton transfer in HB chains through bell-shaped soliton excitations, which trigger the bio-energy transport in most biological systems. This solitonic mechanism of proton transfer could play functional roles in muscular contraction, enzymatic activity and oxidative phosphorylation.

  17. ADSORPTION OF CAFFEINE BY HYDROGEN DONATING ADSORBENTS BASED ON HYDROGEN BONDING

    Institute of Scientific and Technical Information of China (English)

    XUMancai; SHIZuoqing; 等

    2000-01-01

    The adsorption isotherms of caffeine from aqueous solution onto three hydrogen donating adsorbents-hydroxypolystyrene,polystryene-azo-pyrogallol,and D72 resin-were measured.The adsorption enthalpies calculated from the isotherms according to the Clausisu-Clapeyron equation were -24-36kJ/mol,-32-37kJ/mol,and -19-24kJ/mol respectively.These values implied that the adsorption processes were based on hydrogen bonding.Furthermore.the mechanism of the adsorption of caffeine onto D72 resin was studied by IR spectra and the small molecular model experiments,and the results showed that the adsorption of caffeine onto hydrogen donating adsorbents was based on hydrogen bonding.

  18. The hydrogen-bond collective dynamics in liquid methanol

    Science.gov (United States)

    Bellissima, Stefano; de Panfilis, Simone; Bafile, Ubaldo; Cunsolo, Alessandro; González, Miguel Angel; Guarini, Eleonora; Formisano, Ferdinando

    2016-12-01

    The relatively simple molecular structure of hydrogen-bonded (HB) systems is often belied by their exceptionally complex thermodynamic and microscopic behaviour. For this reason, after a thorough experimental, computational and theoretical scrutiny, the dynamics of molecules in HB systems still eludes a comprehensive understanding. Aiming at shedding some insight into this topic, we jointly used neutron Brillouin scattering and molecular dynamics simulations to probe the dynamics of a prototypical hydrogen-bonded alcohol, liquid methanol. The comparison with the most thoroughly investigated HB system, liquid water, pinpoints common behaviours of their THz microscopic dynamics, thereby providing additional information on the role of HB dynamics in these two systems. This study demonstrates that the dynamic behaviour of methanol is much richer than what so far known, and prompts us to establish striking analogies with the features of liquid and supercooled water. In particular, based on the strong differences between the structural properties of the two systems, our results suggest that the assignment of some dynamical properties to the tetrahedral character of water structure should be questioned. We finally highlight the similarities between the characteristic decay times of the time correlation function, as obtained from our data and the mean lifetime of hydrogen bond known in literature.

  19. Substituent effects on hydrogen bonding of aromatic amide-carboxylate

    Science.gov (United States)

    Sen, Ibrahim; Kara, Hulya; Azizoglu, Akın

    2016-10-01

    N-(p-benzoyl)-anthranilic acid (BAA) derivatives have been synthesized with different substituents (X: Br, Cl, OCH3, CH3), and their crystal structures have been analyzed in order to understand the variations in their molecular geometries with respect to the substituents by using 1H NMR, 13C NMR, IR and X-ray single-crystal diffraction. The carboxylic acid group forms classic Osbnd H ⋯ O hydrogen bonded dimers in a centrosymmetric R22(8) ring motifs for BAA-Br and BAA-Cl. However, no carboxylic acid group forms classic Osbnd H ⋯ O hydrogen bonded dimers in BAA-OCH3 and BAA-CH3. The asymmetric unit consists of two crystallographically independent molecules in BAA-OCH3. DFT computations show that the interaction energies between monomer and dimer are in the range of 0.5-3.8 kcal/mol with the B3LYP/6-31 + G*, B3LYP/6-31 ++G*, B3LYP/6-31 ++G**, and B3LYP/AUG-cc-pVDZ levels of theory. The presence of different hydrogen bond patterns is also governed by the substrate. For monomeric compounds studied herein, theoretical calculations lead to two low-energy conformers; trans (a) and cis (b). Former one is more stable than latter by about 4 kcal/mol.

  20. Thioamides: versatile bonds to induce directional and cooperative hydrogen bonding in supramolecular polymers.

    Science.gov (United States)

    Mes, Tristan; Cantekin, Seda; Balkenende, Dirk W R; Frissen, Martijn M M; Gillissen, Martijn A J; De Waal, Bas F M; Voets, Ilja K; Meijer, E W; Palmans, Anja R A

    2013-06-24

    The amide bond is a versatile functional group and its directional hydrogen-bonding capabilities are widely applied in, for example, supramolecular chemistry. The potential of the thioamide bond, in contrast, is virtually unexplored as a structuring moiety in hydrogen-bonding-based self-assembling systems. We report herein the synthesis and characterisation of a new self-assembling motif comprising thioamides to induce directional hydrogen bonding. N,N',N''-Trialkylbenzene-1,3,5-tris(carbothioamide)s (thioBTAs) with either achiral or chiral side-chains have been readily obtained by treating their amide-based precursors with P2S5. The thioBTAs showed thermotropic liquid crystalline behaviour and a columnar mesophase was assigned. IR spectroscopy revealed that strong, three-fold, intermolecular hydrogen-bonding interactions stabilise the columnar structures. In apolar alkane solutions, thioBTAs self-assemble into one-dimensional, helical supramolecular polymers stabilised by three-fold hydrogen bonding. Concentration- and temperature-dependent self-assembly studies performed by using a combination of UV and CD spectroscopy demonstrated a cooperative supramolecular polymerisation mechanism and a strong amplification of supramolecular chirality. The high dipole moment of the thioamide bond in combination with the anisotropic shape of the resulting cylindrical aggregate gives rise to sufficiently strong depolarised light scattering to enable depolarised dynamic light scattering (DDLS) experiments in dilute alkane solution. The rotational and translational diffusion coefficients, D(trans) and D(rot), were obtained from the DDLS measurements, and the average length, L, and diameter, d, of the thioBTA aggregates were derived (L = 490 nm and d = 3.6 nm). These measured values are in good agreement with the value L(w) = 755 nm obtained from fitting the temperature-dependent CD data by using a recently developed equilibrium model. This experimental verification

  1. Hydrogen bond breaking in aqueous solutions near the critical point

    Science.gov (United States)

    Mayanovic, Robert A.; Anderson, Alan J.; Bassett, William A.; Chou, I.-Ming

    2001-01-01

    The nature of water-anion bonding is examined using X-ray absorption fine structure spectroscopy on a 1mZnBr2/6m NaBr aqueous solution, to near critical conditions. Analyses show that upon heating the solution from 25??C to 500??C, a 63% reduction of waters occurs in the solvation shell of ZnBr42-, which is the predominant complex at all pressure-temperature conditions investigated. A similar reduction in the hydration shell of waters in the Br- aqua ion was found. Our results indicate that the water-anion and water-water bond breaking mechanisms occurring at high temperatures are essentially the same. This is consistent with the hydration waters being weakly hydrogen bonded to halide anions in electrolyte solutions. ?? 2001 Elsevier Science B.V.

  2. Are non-linear C-H⋯O contacts hydrogen bonds or Van der Waals interactions?. Establishing the limits between hydrogen bonds and Van der Waals interactions

    Science.gov (United States)

    Novoa, Juan J.; Lafuente, Pilar; Mota, Fernando

    1998-07-01

    The hydrogen bond nature of angular C-H⋯O contacts is examined to determine when these contacts are better classified as hydrogen bonds or as Van der Waals bonds. To classify the bond we propose to look at the nature of the intermolecular bond critical point present in the electron density of the complex containing the bond. The physics behind this approach is explained using a qualitative orbital overlap model aimed at describing the main changes in the electronic density of the complex produced by the C-H⋯O bending.

  3. Effect of hydrogen bonding on infrared absorption intensity

    CERN Document Server

    Athokpam, Bijyalaxmi; McKenzie, Ross H

    2016-01-01

    We consider how the infrared intensity of an O-H stretch in a hydrogen bonded complex varies as the strength of the H-bond varies from weak to strong. We obtain trends for the fundamental and overtone transitions as a function of donor-acceptor distance R, which is a common measure of H-bond strength. Our calculations use a simple two-diabatic state model that permits symmetric and asymmetric bonds, i.e. where the proton affinity of the donor and acceptor are equal and unequal, respectively. The dipole moment function uses a Mecke form for the free OH dipole moment, associated with the diabatic states. The transition dipole moment is calculated using one-dimensional vibrational eigenstates associated with the H-atom transfer coordinate on the ground state adiabatic surface of our model. Over 20-fold intensity enhancements for the fundamental are found for strong H-bonds, where there are significant non-Condon effects. The isotope effect on the intensity yields a non-monotonic H/D intensity ratio as a function...

  4. Marvels of enzyme catalysis at true atomic resolution: distortions, bond elongations, hidden flips, protonation states and atom identities.

    Science.gov (United States)

    Neumann, Piotr; Tittmann, Kai

    2014-12-01

    Although general principles of enzyme catalysis are fairly well understood nowadays, many important details of how exactly the substrate is bound and processed in an enzyme remain often invisible and as such elusive. In fortunate cases, structural analysis of enzymes can be accomplished at true atomic resolution thus making possible to shed light on otherwise concealed fine-structural traits of bound substrates, intermediates, cofactors and protein groups. We highlight recent structural studies of enzymes using ultrahigh-resolution X-ray protein crystallography showcasing its enormous potential as a tool in the elucidation of enzymatic mechanisms and in unveiling fundamental principles of enzyme catalysis. We discuss the observation of seemingly hyper-reactive, physically distorted cofactors and intermediates with elongated scissile substrate bonds, the detection of 'hidden' conformational and chemical equilibria and the analysis of protonation states with surprising findings. In delicate cases, atomic resolution is required to unambiguously disclose the identity of atoms as demonstrated for the metal cluster in nitrogenase. In addition to the pivotal structural findings and the implications for our understanding of enzyme catalysis, we further provide a practical framework for resolution enhancement through optimized data acquisition and processing.

  5. Theoretical study of the interplay between lithium bond and hydrogen bond in complexes involved with HLi and HCN.

    Science.gov (United States)

    Li, Qingzhong; Hu, Ting; An, Xiulin; Li, Wenzuo; Cheng, Jianbo; Gong, Baoan; Sun, Jiazhong

    2009-12-21

    The lithium- and hydrogen-bonded complex of HLi-NCH-NCH is studied with ab initio calculations. The optimized structure, vibrational frequencies, and binding energy are calculated at the MP2 level with 6-311++G(2d,2p) basis set. The interplay between lithium bonding and hydrogen bonding in the complex is investigated with these properties. The effect of lithium bonding on the properties of hydrogen bonding is larger than that of hydrogen bonding on the properties of lithium bonding. In the trimer, the binding energies are increased by about 19% and 61% for the lithium and hydrogen bonds, respectively. A big cooperative energy (-5.50 kcal mol(-1)) is observed in the complex. Both the charge transfer and induction effect due to the electrostatic interaction are responsible for the cooperativity in the trimer. The effect of HCN chain length on the lithium bonding has been considered. The natural bond orbital and atoms in molecules analyses indicate that the electrostatic force plays a main role in the lithium bonding. A many-body interaction analysis has also been performed for HLi-(NCH)(N) (N=2-5) systems.

  6. A study of hydrogen-bond dynamics in carboxylic acids by NMR T1 measurements: isotope effects and hydrogen-bond length dependence

    Science.gov (United States)

    Agaki, T.; Imashiro, F.; Terao, T.; Hirota, N.; Hayashi, S.

    1987-08-01

    Proton (deuteron) transfer of hydrogen bonds in benzoic, glutaric and p-formylbenzoic acids was studied by proton (deuteron) T1 measurements. Deuteration of carboxylic protons was found to increase the barriers to classical proton jumping as well as quantum-mechanical tunneling. The former barriers increase as the hydrogen-bond distance increases.

  7. Electrostatically enhanced FF interactions through hydrogen bonding, halogen bonding and metal coordination: an ab initio study.

    Science.gov (United States)

    Bauzá, Antonio; Frontera, Antonio

    2016-07-27

    In this manuscript the ability of hydrogen and halogen bonding interactions, as well as metal coordination to enhance FF interactions involving fluorine substituted aromatic rings has been studied at the RI-MP2/def2-TZVPD level of theory. We have used 4-fluoropyridine, 4-fluorobenzonitrile, 3-(4-fluorophenyl)propiolonitrile and their respective meta derivatives as aromatic compounds. In addition, we have used HF and IF as hydrogen and halogen bond donors, respectively, and Ag(i) as the coordination metal. Furthermore, we have also used HF as an electron rich fluorine donor entity, thus establishing FF interactions with the above mentioned aromatic systems. Moreover, a CSD (Cambridge Structural Database) search has been carried out and some interesting examples have been found, highlighting the impact of FF interactions involving aromatic fluorine atoms in solid state chemistry. Finally, cooperativity effects between FF interactions and both hydrogen and halogen bonding interactions have been analyzed and compared. We have also used Bader's theory of "atoms in molecules" to further describe the cooperative effects.

  8. Hydrogen-bonding study of photoexcited 4-nitro-1,8-naphthalimide in hydrogen-donating solvents

    Directory of Open Access Journals (Sweden)

    Cao Jianfang

    2016-01-01

    Full Text Available The solute–solvent interactions of 4-nitro-1,8-naphthalimide (4NNI as a hydrogen bond acceptor in hydrogen donating methanol (MeOH solvent in electronic excited states were investigated by means of the time-dependent density functional theory(TDDFT. We calculated the S0 state geometry optimizations, electronic transition energies and corresponding oscillation strengths of the low-lying electronically excited states for the isolated 4NNi and hydrogen-bonded 4NNi-(MeOH1,4 complexes using the density functional theory (DFT and TDDFT methods. The electronic excitation energies of the hydrogen-bonded complexes are correspondingly decreased compared to that of the isolated 4NNi, which revealed that the intermolecular hydrogen bond C=O···H–O and N=O···H–O in the hydrogen-bonded 4NNi-(MeOH1,4 are strengthened in the electronically excited state. The calculated results are consistent with the mechanism that hydrogen bond strengthening will induce a redshift of the corresponding electronic spectra, while hydrogen bond weakening will cause a blueshift. Furthermore, we believe that the deduction we used to depict the trend of the hydrogen bond changes in excited states exists in many other fuorescent dyes in solution.

  9. A new method for quick predicting the strength of intermolecular hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    SUN ChangLiang; ZHANG Yan; JIANG XiaoNan; WANG ChangSheng; YANG ZhongZhi

    2009-01-01

    A new method is proposed to quick predict the strength of intermolecular hydrogen bonds. The method is employed to produce the hydrogen-bonding potential energy curves of twenty-nine hydro-gen-bonded dimers. The calculation results show that the hydrogen-bonding potential energy curves obtained from this method are in good agreement with those obtained from MP2/6-31+G** calculations by including the BSSE correction, which demonstrate that the method proposed in this work can be used to calculate the hydrogen-bonding interactions in peptides.

  10. A new method for quick predicting the strength of intermolecular hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    A new method is proposed to quick predict the strength of intermolecular hydrogen bonds.The method is employed to produce the hydrogen-bonding potential energy curves of twenty-nine hydro-gen-bonded dimers.The calculation results show that the hydrogen-bonding potential energy curves obtained from this method are in good agreement with those obtained from MP2/6-31+G calculations by including the BSSE correction,which demonstrate that the method proposed in this work can be used to calculate the hydrogen-bonding interactions in peptides.

  11. A QTAIM exploration of the competition between hydrogen and halogen bonding in halogenated 1-methyluracil: Water systems

    Science.gov (United States)

    Huan, Guo; Xu, Tianlv; Momen, Roya; Wang, Lingling; Ping, Yang; Kirk, Steven R.; Jenkins, Samantha; van Mourik, Tanja

    2016-10-01

    Using QTAIM we show that the hydrogen bonding complexes of 5-halogenated-1-methyluracil (XmU; X = F, Cl, Br, I or At) with a water molecule were always stronger than the corresponding halogen bonds. The strength of the hydrogen bond decreased with increasing halogen size. The hydrogen bonds displayed an admixture of covalent character but all the halogen bonds were purely electrostatic in nature. An F---O halogen bond was found and was facilitated by an intermediate F---H bonding interaction. The metallicity ξ(rb) of the C = O bonds neighboring the hydrogen bonds and of the C-X bonds contiguous with the halogen bonds was explored.

  12. Hydrogen-bonded clusters of ferrocenecarboxylic acid on Au(111).

    Science.gov (United States)

    Quardokus, Rebecca C; Wasio, Natalie A; Christie, John A; Henderson, Kenneth W; Forrest, Ryan P; Lent, Craig S; Corcelli, Steven A; Kandel, S Alex

    2014-09-14

    Self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH) contain two fundamental units, both stabilized by intermolecular hydrogen bonding: dimers and cyclic five-membered catemers. At surface coverages below a full monolayer, however, there is a significantly more varied structure that includes double-row clusters containing two to twelve FcCOOH molecules. Statistical analysis shows a distribution of cluster sizes that is sharply peaked compared to a binomial distribution. This rules out simple nucleation-and-growth mechanisms of cluster formation, and strongly suggests that clusters are formed in solution and collapse into rows when deposited on the Au(111) surface.

  13. Anharmonicity and hydrogen bonding in electrooptic sucrose crystal

    Science.gov (United States)

    Szostak, M. M.; Giermańska, J.

    1990-03-01

    The polarized absorption spectra of the sucrose crystal in the 5300 - 7300 cm -1 region have been measured. The assignments of all the eight OH stretching overtones are proposed and their mechanical anharmonicities are estimated. The discrepancies from the oriented gas model (OGM) in the observed relative band intensities, especially of the -CH vibrations, are assumed to be connected with vibronic couplings enhanced by the helical arrangement of molecules joined by hydrogen bondings. It seems that this kind of interactions might be important for the second harmonic generation (SHG) by the sucrose crystal.

  14. Positively charged phosphorus as a hydrogen bond acceptor

    DEFF Research Database (Denmark)

    Hansen, Anne Schou; Du, Lin; Kjærgaard, Henrik Grum

    2014-01-01

    alcohol-trimethylphosphine complexes have been detected. Initially, the complexes were detected using matrix isolation spectroscopy, which favors complex formation. Subsequently, the fundamental OH-stretching vibration was observed in room-temperature gas-phase spectra. On the basis of our measured OH......Phosphorus (P) is an element that is essential to the life of all organisms, and the atmospheric detection of phosphine suggests the existence of a volatile biogeochemical P cycle. Here, we investigate the ability of P to participate in the formation of OH···P hydrogen bonds. Three bimolecular...

  15. Fragility and cooperativity concepts in hydrogen-bonded organic glasses

    Energy Technology Data Exchange (ETDEWEB)

    Delpouve, N., E-mail: delpouve.nicolas@gmail.com [AMME-LECAP EA 4528 International Laboratory, University of Rouen, Avenue de l' Universite BP 12, 76801 Saint Etienne du Rouvray (France); Vuillequez, A.; Saiter, A.; Youssef, B.; Saiter, J.M. [AMME-LECAP EA 4528 International Laboratory, University of Rouen, Avenue de l' Universite BP 12, 76801 Saint Etienne du Rouvray (France)

    2012-09-01

    Molecular dynamics at the glass transition of three lactose/oil glassy systems have been investigated according to the cooperativity and fragility approaches. From Donth's approach, the cooperativity length is estimated by modulated temperature calorimetric measurements. Results reveal that modification of the disaccharide by oil leads to increase the disorder degree in the lactose, the size of the cooperative domains and the fragility index. These particular hydrogen-bonded organic glasses follow the general tendency observed on organic and inorganic polymers: the higher the cooperativity length, the higher the value of the fragility index at T{sub g}.

  16. Change in hydrogen bonding structures of a hydrogel with dehydration

    Science.gov (United States)

    Naohara, Ryo; Narita, Kentaro; Ikeda-Fukazawa, Tomoko

    2017-02-01

    To investigate the mechanisms of structural changes in polymer network and water during dehydration, X-ray diffraction of poly-N,N-dimethylacrylamide (PDMAA) hydrogels was measured. The variation process in the individual structures of water and PDMAA were analyzed by decomposition of the diffraction patterns to separate the respective contributions. The results show that the short-range structures of PDMAA expand during dehydration, whereas the network structure as a whole shrinks. The average length of the hydrogen bonds between water molecules increases with the process. The present results provide a direct evidence of the structural changes of water and polymer in the hydrogel during dehydration.

  17. Enthalpies of hydrogen bonding of quinoline with o-phenylphenol and of hydrogen-bonding reactions involving the acid and base components of a coal-derived asphaltene

    Energy Technology Data Exchange (ETDEWEB)

    Dietz, A.G.; Blaha, C.; Li, N.C.

    1977-01-01

    Calorimetric studies are reported of hydrogen bonding between quinoline (Qu) and o-phenylphenol (OPP). The enthalpies of hydrogen-bonding of the acid and base components of a coal-derived asphaltene with OPP and Qu are also reported. The results provide strong evidence that the acid and base components of asphaltene function substantially as hydrogen donor and acceptor, respectively. 1 figure, 1 table.

  18. Hydrogen bond dynamics in alcohols studied by 2D IR spectroscopy

    NARCIS (Netherlands)

    Shinokita, Keisuke; Cunha, Ana V.; Jansen, Thomas L C; Pshenichnikov, Maxim S.

    2015-01-01

    Ultrafast hydrogen-bond dynamics in alcohols are studied by 2D IR spectroscopy and combined molecular dynamics—quantum mechanical simulations on the OH stretching mode. Fast memory loss in *100 fs are attributed to intact hydrogen-bond fluctuations. Stable (at the experimental timescale) hydrogen bo

  19. Enhanced hydrogen evolution catalysis from chemically exfoliated metallic MoS2 nanosheets.

    Science.gov (United States)

    Lukowski, Mark A; Daniel, Andrew S; Meng, Fei; Forticaux, Audrey; Li, Linsen; Jin, Song

    2013-07-17

    Promising catalytic activity from molybdenum disulfide (MoS2) in the hydrogen evolution reaction (HER) is attributed to active sites located along the edges of its two-dimensional layered crystal structure, but its performance is currently limited by the density and reactivity of active sites, poor electrical transport, and inefficient electrical contact to the catalyst. Here we report dramatically enhanced HER catalysis (an electrocatalytic current density of 10 mA/cm(2) at a low overpotential of -187 mV vs RHE and a Tafel slope of 43 mV/decade) from metallic nanosheets of 1T-MoS2 chemically exfoliated via lithium intercalation from semiconducting 2H-MoS2 nanostructures grown directly on graphite. Structural characterization and electrochemical studies confirmed that the nanosheets of the metallic MoS2 polymorph exhibit facile electrode kinetics and low-loss electrical transport and possess a proliferated density of catalytic active sites. These distinct and previously unexploited features of 1T-MoS2 make these metallic nanosheets a highly competitive earth-abundant HER catalyst.

  20. Hydrogen bonding versus hyperconjugation in condensed-phase carbocations.

    Science.gov (United States)

    Reed, Christopher A; Stoyanov, Evgenii S; Tham, Fook S

    2013-06-21

    Hyperconjugative stabilization of positive charge in tertiary carbocations is the textbook explanation for their stability and low frequency νCH bands in their IR spectra have long been taken as confirming evidence. While this is substantiated in the gas phase by the very close match of the IR spectrum of argon-tagged t-butyl cation with that calculated under C(s) symmetry, the situation in condensed phases is much less clear. The congruence of νCH(max) of t-Bu(+) in superacid media (2830 cm(-1)) with that in the gas phase (2834 cm(-1)) has recently been shown to be accidental. Rather, νCH(max) varies considerably as a function of counterion in a manner that reveals the presence of significant C-H···anion hydrogen bonding. This paper addresses the question of the relative importance of hyperconjugation versus H-bonding. We show by assigning IR spectra in the νCH region to specific C-H bonds in t-butyl cation that the low frequency νCH(max) band in the IR spectrum of t-butyl cation, long taken as direct evidence for hyperconjugation, appears to be due mostly to H-bonding. The appearance of similar low frequency νCH bands in the IR spectra of secondary alkyl carboranes such as i-Pr(CHB11Cl11), which have predominant sp(3) centres rather than sp(2) centres (and are therefore less supportive of hyperconjugation), also suggests the dominance of H-bonding over hyperconjugation.

  1. Molecularly Tuning the Radicaloid N-H···O═C Hydrogen Bond.

    Science.gov (United States)

    Lu, Norman; Chung, Wei-Cheng; Ley, Rebecca M; Lin, Kwan-Yu; Francisco, Joseph S; Negishi, Ei-Ichi

    2016-03-01

    Substituent effects on the open shell N-H···O═C hydrogen-bond has never been reported. This study examines how 12 functional groups composed of electron donating groups (EDG), halogen atoms and electron withdrawing groups (EWG) affect the N-H···O═C hydrogen-bond properties in a six-membered cyclic model system of O═C(Y)-CH═C(X)N-H. It is found that group effects on this open shell H-bonding system are significant and have predictive trends when X = H and Y is varied. When Y is an EDG, the N-H···O═C hydrogen-bond is strengthened; and when Y is an EWG, the bond is weakened; whereas the variation in electronic properties of X group do not exhibit a significant impact upon the hydrogen bond strength. The structural impact of the stronger N-H···O═C hydrogen-bond are (1) shorter H and O distance, r(H···O) and (2) a longer N-H bond length, r(NH). The stronger N-H···O═C hydrogen-bond also acts to pull the H and O in toward one another which has an effect on the bond angles. Our findings show that there is a linear relationship between hydrogen-bond angle and N-H···O═C hydrogen-bond energy in this unusual H-bonding system. In addition, there is a linear correlation of the r(H···O) and the hydrogen bond energy. A short r(H···O) distance corresponds to a large hydrogen bond energy when Y is varied. The observed trends and findings have been validated using three different methods (UB3LYP, M06-2X, and UMP2) with two different basis sets.

  2. Infrared Spectroscopy of Hydrogen Bonds in Benzoic Acid Derivatives

    Science.gov (United States)

    Tolstorozhev, G. B.; Bel‧kov, M. V.; Skornyakov, I. V.; Bazyl, O. K.; Artyukhov, V. Ya.; Mayer, G. V.; Shadyro, O. I.; Kuzovkov, P. V.; Brinkevich, S. D.; Samovich, S. N.

    2014-03-01

    We have measured the Fourier transform IR spectra of CCl4 solutions of benzoic acid and its biologically active derivatives. We investigated the proton-acceptor properties of the studied molecules theoretically by the molecular electrostatic potential method. The calculations are compared with experimental results. Based on an estimate of the proton-acceptor properties, we give an interpretation of the specific features of the IR spectra of benzoic acid and its derivatives in the region of the O-H and C = O vibrations. The mechanisms for interactions of the molecules are determined by the nature of substituents which are added to the benzene ring in positions para and meta to the carboxyl group. We identify the conditions for appearance of intermolecular hydrogen bonds of O-H · · · O = C, O-H · · · O-H types with formation of cyclic and linear dimers. We show that intramolecular hydrogen bonds of the type O-H · · · O-CH3 prevent the hydroxyl groups from participating in intermolecular interactions.

  3. Insights into hydrogen bonding via ice interfaces and isolated water

    Science.gov (United States)

    Shultz, Mary Jane; Bisson, Patrick; Vu, Tuan Hoang

    2014-11-01

    Water in a confined environment has a combination of fewer available configurations and restricted mobility. Both affect the spectroscopic signature. In this work, the spectroscopic signature of water in confined environments is discussed in the context of competing models for condensed water: (1) as a system of intramolecular coupled molecules or (2) as a network with intermolecular dipole-dipole coupled O-H stretches. Two distinct environments are used: the confined asymmetric environment at the ice surface and the near-isolated environment of water in an infrared transparent matrix. Both the spectroscopy and the environment are described followed by a perspective discussion of implications for the two competing models. Despite being a small molecule, water is relatively complex; perhaps not surprisingly the results support a model that blends inter- and intramolecular coupling. The frequency, and therefore the hydrogen-bond strength, appears to be a function of donor-acceptor interaction and of longer-range dipole-dipole alignment in the hydrogen-bonded network. The O-H dipole direction depends on the local environment and reflects intramolecular O-H stretch coupling.

  4. Intramolecular hydrogen-bonding studies by NMR spectroscopy

    CERN Document Server

    Cantalapiedra, N A

    2000-01-01

    o-methoxybenzamide and N-methyl-o-methylbenzamide, using the pseudo-contact shifts calculated from the sup 1 H and sup 1 sup 3 C NMR spectra. The main conformation present in solution for o-fluorobenzamide was the one held by an intramolecular N-H...F hydrogen bond. Ab-initio calculations (at the RHF/6-31G* level) have provided additional data for the geometry of the individual molecules. A conformational equilibrium study of some nipecotic acid derivatives (3-substituted piperidines: CO sub 2 H, CO sub 2 Et, CONH sub 2 , CONHMe, CONEt sub 2) and cis-1,3-disubstituted cyclohexane derivatives (NHCOMe/CO sub 2 Me, NHCOMe/CONHMe, NH sub 2 /CO sub 2 H) has been undertaken in a variety of solvents, in order to predict the intramolecular hydrogen-bonding energies involved in the systems. The conformer populations were obtained by direct integration of proton peaks corresponding to the equatorial and axial conformations at low temperature (-80 deg), and by geometrically dependent coupling constants ( sup 3 J sub H s...

  5. Hydrogen bonding and multiphonon structure in copper pyrazine coordination polymers.

    Science.gov (United States)

    Brown, S; Cao, J; Musfeldt, J L; Conner, M M; McConnell, A C; Southerland, H I; Manson, J L; Schlueter, J A; Phillips, M D; Turnbull, M M; Landee, C P

    2007-10-15

    We report a systematic investigation of the temperature-dependent infrared vibrational spectra of a family of chemically related coordination polymer magnets based upon bridging bifluoride (HF(2)-) and terminal fluoride (F-) ligands in copper pyrazine complexes including Cu(HF(2))(pyz)(2)BF(4), Cu(HF(2))(pyz)(2)ClO(4), and CuF(2)(H(2)O)(2)(pyz). We compare our results with several one- and two-dimensional prototype materials including Cu(pyz)(NO(3))(2) and Cu(pyz)(2)(ClO(4))(2). Unusual low-temperature hydrogen bonding, local structural transitions associated with stronger low-temperature hydrogen bonding, and striking multiphonon effects that derive from coupling of an infrared-active fundamental with strong Raman-active modes of the pyrazine building-block molecule are observed. On the basis of the spectroscopic evidence, these interactions are ubiquitous to this family of coordination polymers and may work to stabilize long-range magnetic ordering at low temperature. Similar interactions are likely to be present in other molecule-based magnets.

  6. Dissociation Energies of Sulfur-Centered Hydrogen-Bonded Complexes.

    Science.gov (United States)

    Ghosh, Sanat; Bhattacharyya, Surjendu; Wategaonkar, Sanjay

    2015-11-01

    In this work we have determined dissociation energies of O-H···S hydrogen bond in the H2S complexes of various phenol derivatives using 2-color-2-photon photofragmentation spectroscopy in combination with zero kinetic energy photoelectron (ZEKE-PE) spectroscopy. This is the first report of direct determination of dissociation energy of O-H···S hydrogen bond. The ZEKE-PE spectra of the complexes revealed a long progression in the intermolecular stretching mode with significant anharmonicity. Using the anharmonicity information and experimentally determined dissociation energy, we also validated Birge-Sponer (B-S) extrapolation method, which is an approximate method to estimate dissociation energy. Experimentally determined dissociation energies were compared with a variety of ab initio calculations. One of the important findings is that ωB97X-D functional, which is a dispersion corrected DFT functional, was able to predict the dissociation energies in both the cationic as well as the ground electronic state very well for almost every case.

  7. Infrared intensities and charge mobility in hydrogen bonded complexes

    Energy Technology Data Exchange (ETDEWEB)

    Galimberti, Daria; Milani, Alberto; Castiglioni, Chiara [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta,” Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy)

    2013-08-21

    The analytical model for the study of charge mobility in the molecules presented by Galimberti et al.[J. Chem. Phys. 138, 164115 (2013)] is applied to hydrogen bonded planar dimers. Atomic charges and charge fluxes are obtained from density functional theory computed atomic polar tensors and related first derivatives, thus providing an interpretation of the IR intensity enhancement of the X–H stretching band observed upon aggregation. Our results show that both principal and non-principal charge fluxes have an important role for the rationalization of the spectral behavior; moreover, they demonstrate that the modulation of the charge distribution during vibrational motions of the –XH⋯Y– fragment is not localized exclusively on the atoms directly involved in hydrogen bonding. With these premises we made some correlations between IR intensities, interaction energies, and charge fluxes. The model was tested on small dimers and subsequently to the bigger one cytosine-guanine. Thus, the model can be applied to complex systems.

  8. Hydrogen bonded complexes of cyanuric acid with pyridine and guanidinium carbonate

    Indian Academy of Sciences (India)

    K Sivashankar

    2000-12-01

    Hydrogen bonded complexes of cyanuric acid (CA) with pyridine, [C3N3H3O3:C5H5N], 1, and guanidinium carbonate [C3H2N3][C(NH2)3], 2, have been prepared at room temperature and characterized by single-crystal X-ray diffraction. Structure of 1 shows pyridine molecules substituting the inter-tape hydrogen bond in CA by N-H…N and C-H…O hydrogen bonds. The structure reveals CA-pyridine hydrogen-bonded single helices held together by dimeric N-H…O hydrogen bonding between CA molecules. In 2, the CA tapes, resembling a sine wave interact with the guanidinium cations through N-H…O and N-H…N hydrogen bonds forming guanidinium cyanurate sheets.

  9. Reactions of the cumyloxyl and benzyloxyl radicals with strong hydrogen bond acceptors. Large enhancements in hydrogen abstraction reactivity determined by substrate/radical hydrogen bonding.

    Science.gov (United States)

    Salamone, Michela; DiLabio, Gino A; Bietti, Massimo

    2012-12-07

    A kinetic study on hydrogen abstraction from strong hydrogen bond acceptors such as DMSO, HMPA, and tributylphosphine oxide (TBPO) by the cumyloxyl (CumO(•)) and benzyloxyl (BnO(•)) radicals was carried out in acetonitrile. The reactions with CumO(•) were described in terms of a direct hydrogen abstraction mechanism, in line with the kinetic deuterium isotope effects, k(H)/k(D), of 2.0 and 3.1 measured for reaction of this radical with DMSO/DMSO-d(6) and HMPA/HMPA-d(18). Very large increases in reactivity were observed on going from CumO(•) to BnO(•), as evidenced by k(H)(BnO(•))/k(H)(CumO(•)) ratios of 86, 4.8 × 10(3), and 1.6 × 10(4) for the reactions with HMPA, TBPO, and DMSO, respectively. The k(H)/k(D) of 0.91 and 1.0 measured for the reactions of BnO(•) with DMSO/DMSO-d(6) and HMPA/HMPA-d(18), together with the k(H)(BnO(•))/k(H)(CumO(•)) ratios, were explained on the basis of the formation of a hydrogen-bonded prereaction complex between the benzyloxyl α-C-H and the oxygen atom of the substrates followed by hydrogen abstraction. This is supported by theoretical calculations that show the formation of relatively strong prereaction complexes. These observations confirm that in alkoxyl radical reactions specific hydrogen bond interactions can dramatically influence the hydrogen abstraction reactivity, pointing toward the important role played by structural and electronic effects.

  10. Hydrogen-Bonding Liquids at Mineral Surfaces: From Fundamentals to Applications

    OpenAIRE

    Phan, A. T. V.

    2016-01-01

    Molecular-level understanding of properties of hydrogen-bonding liquids and their mixtures at solid-liquid interfaces plays a significant role in several applications including membrane-based separations, shale gas production, etc. Liquid water and ethanol are common hydrogen-bonding fluids. All-atom equilibrium molecular dynamics simulations were employed to gain insights regarding the structure and dynamics of these hydrogen-bonding liquids on various free-standing solid surfaces. Models fo...

  11. Evidence of Hydrogen Bonding in Chloroform and Polyacrylates from NMR Measurements

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The presence of hydrogen bonding in chloroform and polyacrylate mixtures was demonstrated by observation of 1H- and 13C-NMR chemical shifts. Comparison of the nuclear magnetic resonance (NMR) chemical shift in polymer solutions with their low molecular mass analogues showed the effect of steric hindrance on hydrogen bonding. This initial investigation is helpful for understanding the intermolecular interaction in relatively weak hydrogen bonding polymer solutions.

  12. Estimation of Intramolecular Hydrogen-bonding Energy via the Substitution Method

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The intramolecular hydrogen-bonding energies for eighteen molecules were calculated based on the substitution method, and compared with those predicted by the cis-trans method.The energy values obtained from two methods are close to each other with a correlation coefficient of 0.96.Furthermore, the hydrogen-bonding energies based on the substitution method are consistent with the geometrical features of intramolecular hydrogen bonds.Both of them demonstrate that the substitution method is capable of providing a good estimation of intramolecular hydrogen-bonding energy.

  13. Weak C–H…O hydrogen bonds in alkaloids: An overview

    Indian Academy of Sciences (India)

    Rajnikant; Dinesh; Kamni

    2005-06-01

    An overview of general classification scheme, medicinal importance and crystal structure analysis with emphasis on the role of hydrogen bonding in some alkaloids is presented in this paper. The article is based on a general kind of survey while crystallographic analysis and role of hydrogen bonding are limited to only those alkaloids whose three-dimensional structure has been reported by us. The C–H…O hydrogen bonding in the solid state in alkaloids has been found to be predominant and this observation makes the role of hydrogen bonding in organic molecular assemblies very important.

  14. Glycine hydrogen fluoride: Remarkable hydrogen bonding in the dimeric glycine glycinium cation

    Science.gov (United States)

    Fleck, M.; Ghazaryan, V. V.; Petrosyan, A. M.

    2010-12-01

    Crystals of glycine hydrogen fluoride (Gly·HF) were prepared from an aqueous solution containing stoichiometric quantities of the components. The crystal structure of Gly·HF was determined, IR and Raman spectra were registered and are discussed. Gly·HF crystallizes in the orthorhombic space group Pbca with Z = 32. The most remarkable feature of the structure is the existence of symmetric dimeric glycine-glycinium cations with short hydrogen bonds (O⋯O distance of 2.446 Å), charge-counterbalanced by hydrogen bifluoride (F sbnd H⋯F) - anions - in addition to the expected glycinium cations and fluoride anions. These results were compared with previously published data on crystals grown in the system glycine-HF-H 2O.

  15. Bidentates versus monodentates in asymmetric hydrogenation catalysis: synergic effects on rate and allosteric effects on enantioselectivity.

    Science.gov (United States)

    Norman, David W; Carraz, Charles A; Hyett, David J; Pringle, Paul G; Sweeney, Joseph B; Orpen, A Guy; Phetmung, Hirrahataya; Wingad, Richard L

    2008-05-28

    acrylate substrates studied, the catalysts derived from the phosphino/phosphonite bidentates L A,B generally give superior enantioselectivities to the analogous diphosphonites L 2a and L 2b ; these results are rationalized in terms of delta/lambda-chelate conformations and allosteric effects of the substrates. The rate of hydrogenation of acrylate substrate A with heterochelate 3a is significantly faster than with the homochelate analogues [Rh( L 2a )(cod)]BF 4 and [Rh(dppe)(cod)]BF 4. A synergic effect on the rate is also observed with the monodentate analogues: the rate of hydrogenation with the mixture containing predominantly heteroligand complex 5 is faster than with the monophosphine complex 6 or monophosphonite complex 7. Thus the hydrogenation catalysis carried out with M and [Rh(cod) 2]BF 4 is controlled by the dominant and most efficient heteroligand complex 5. In this study, the heterodiphos chelate 3a is shown to be more efficient and gives the opposite sense of optical induction to the heteromonophos analogue 5.

  16. Energy-efficient green catalysis: supported gold nanoparticle-catalyzed aminolysis of esters with inert tertiary amines by C-O and C-N bond activations.

    Science.gov (United States)

    Bao, Yong-Sheng; Baiyin, Menghe; Agula, Bao; Jia, Meilin; Zhaorigetu, Bao

    2014-07-18

    Catalyzed by supported gold nanoparticles, an aminolysis reaction between various aryl esters and inert tertiary amines by C-O and C-N bond activations has been developed for the selective synthesis of tertiary amides. Comparison studies indicated that the gold nanoparticles could perform energy-efficient green catalysis at room temperature, whereas Pd(OAc)2 could not.

  17. Revealing the multi-bonding state between hydrogen and graphene-supported Ti clusters

    CERN Document Server

    Takahashi, Keisuke; Omori, Kengo; Mashoff, Torge; Convertino, Domenica; Miseikis, Vaidotas; Coletti, Camilla; Tozzini, Valentina; Heun, Stefan

    2016-01-01

    Hydrogen adsorption on graphene-supported metal clusters has brought much controversy due to the complex nature of the bonding between hydrogen and metal clusters. The bond types of hydrogen and graphene-supported Ti clusters are experimentally and theoretically investigated. Transmission electron microscopy shows that Ti clusters of nanometer-size are formed on graphene. Thermal desorption spectroscopy captures three hydrogen desorption peaks from hydrogenated graphene-supported Ti clusters. First principle calculations also found three types of interaction: Two types of bonds with different partial ionic character and physisorption. The physical origin for this rests on the charge state of the Ti clusters: when Ti clusters are neutral, H2 is dissociated, and H forms bonds with the Ti cluster. On the other hand, H2 is adsorbed in molecular form on positively charged Ti clusters, resulting in physisorption. Thus, this work clarifies the bonding mechanisms of hydrogen on graphene-supported Ti clusters.

  18. Altering intra- to inter-molecular hydrogen bonding by dimethylsulfoxide: A TDDFT study of charge transfer for coumarin 343

    Science.gov (United States)

    Liu, Xiaochun; Yin, Hang; Li, Hui; Shi, Ying

    2017-04-01

    DFT and TDDFT methods were carried out to investigate the influences of intramolecular and intermolecular hydrogen bonding on excited state charge transfer for coumarin 343 (C343). Intramolecular hydrogen bonding is formed between carboxylic acid group and carbonyl group in C343 monomer. However, in dimethylsulfoxide (DMSO) solution, DMSO 'opens up' the intramolecular hydrogen bonding and forms solute-solvent intermolecular hydrogen bonded C343-DMSO complex. Analysis of frontier molecular orbitals reveals that intramolecular charge transfer (ICT) occurs in the first excited state both for C343 monomer and complex. The results of optimized geometric structures indicate that the intramolecular hydrogen bonding interaction is strengthened while the intermolecular hydrogen bonding is weakened in excited state, which is confirmed again by monitoring the shifts of characteristic peaks of infrared spectra. We demonstrated that DMSO solvent can not only break the intramolecular hydrogen bonding to form intermolecular hydrogen bonding with C343 but also alter the mechanism of excited state hydrogen bonding strengthening.

  19. Catalysis of hydrolysis and nucleophilic substitution at the P-N bond of phosphoimidazolide-activated nucleotides in phosphate buffers

    Science.gov (United States)

    Kanavarioti, A.; Rosenbach, M. T.

    1991-01-01

    Phosphoimidazolide-activated derivatives of guanosine and cytidine 5'-monophosphates, henceforth called ImpN's, exhibit enhanced rates of degradation in the presence of aqueous inorganic phosphate in the range 4.0 catalysis of the P-N bond hydrolysis by phosphate. The first reaction results in the formation of nucleoside 5'-diphosphate and the second in nucleoside 5'-monophosphate. Analysis of the observed rates as well as the product ratios as a function of pH and phosphate concentration allow distinction between various mechanistic possibilities. The results show that both H2PO4- and HPO4(2-) participate in both hydrolysis and nucleophilic substitution. Statistically corrected biomolecular rate constants indicate that the dianion is 4 times more effective as a general base than the monoanion, and 8 times more effective as nucleophile. The low Bronsted value beta = 0.15 calculated for these phosphate species, presumed to act as general bases in facilitating water attack, is consistent with the fact that catalysis of the hydrolysis of the P-N bond in ImpN's has not been detected before. The beta nuc = 0.35 calculated for water, H2PO4-, HPO4(2-), and hydroxide acting as nucleophiles indicates a more associative transition state for nucleotidyl (O2POR- with R = nucleoside) transfers than that observed for phosphoryl (PO3(2-)) transfers (beta nuc = 0.25). With respect to the stability/reactivity of ImpN's under prebiotic conditions, our study shows that these materials would not suffer additional degradation due to inorganic phosphate, assuming the concentrations of phosphate, Pi, on prebiotic Earth were similar to those in the present oceans ([Pi] approximately 2.25 micromoles).

  20. NMR properties of hydrogen-bonded glycine cluster in gas phase

    Science.gov (United States)

    Carvalho, Jorge R.; da Silva, Arnaldo Machado; Ghosh, Angsula; Chaudhuri, Puspitapallab

    2016-11-01

    Density Functional Theory (DFT) calculations have been performed to study the effect of the hydrogen bond formation on the Nuclear Magnetic Resonance (NMR) parameters of hydrogen-bonded clusters of glycine molecules in gas-phase. DFT predicted isotropic chemical shifts of H, C, N and O of the isolated glycine with respect to standard reference materials are in reasonable agreement with available experimental data. The variations of isotropic and anisotropic chemical shifts for all atoms constituting these clusters containing up to four glycine molecules have been investigated systematically employing gradient corrected hybrid B3LYP functional with three different types of extended basis sets. The clusters are mainly stabilized by a network of strong hydrogen bonds among the carboxylic (COOH) groups of glycine monomers. The formation of hydrogen bond influences the molecular structure of the clusters significantly which, on the other hand, gets reflected in the variations of NMR properties. The carbon (C) atom of the sbnd COOH group, the bridging hydrogen (H) and the proton-donor oxygen (O) atom of the Osbnd H bond suffer downfield shift due to the formation of hydrogen bond. The hydrogen bond lengths and the structural complexity of the clusters are found to vary with the number of participating monomers. A direct correlation between the hydrogen bond length and isotropic chemical shift of the bridging hydrogen is observed in all cases. The individual variations of the principal axis elements in chemical shift tensor provide additional insight about the different nature of the monomers within the cluster.

  1. Water hydrogen bonding in proton exchange and neutral polymer membranes

    Science.gov (United States)

    Smedley, Sarah Black

    Understanding the dynamics of water sorbed into polymer films is critical to reveal structure-property relationships in membranes for energy and water treatment applications, where membranes must interact with water to facilitate or inhibit the transport of ions. The chemical structure of the polymer has drastic effects on the transport properties of the membrane due to the morphological structure of the polymer and how water is interacting with the functional groups on the polymer backbone. Therefore studying the dynamics of water adsorbed into a membrane will give insight into how water-polymer interactions influence transport properties of the film. With a better understanding of how to design materials to have specific properties, we can accelerate development of smarter materials for both energy and water treatment applications to increase efficiency and create high-flux materials and processes. The goal of this dissertation is to investigate the water-polymer interactions in proton exchange and uncharged membranes and make correlations to their charge densities and transport properties. A linear Fourier Transform Infrared (FTIR) spectroscopic method for measuring the hydrogen bonding distribution of water sorbed in proton exchange membranes is described in this thesis. The information on the distribution of the microenvironments of water in an ionic polymer is critical to understanding the effects of different acidic groups on the proton conductivity of proton exchange membranes at low relative humidity. The OD stretch of dilute HOD in H2O is a single, well-defined vibrational band. When HOD in dilute H2O is sorbed into a proton exchange membrane, the OD stretch peak shifts based on the microenvironment that water encounters within the nanophase separated structure of the material. This peak shift is a signature of different hydrogen bonding populations within the membrane, which can be deconvoluted rigorously for dilute HOD in H 2O compared to only

  2. A DFT Study on Intramolecular Hydrogen Bond in Substituted Catechols and Their Radicals

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Density functional theory (DFT) at B3LYP/6-31G(d,p) level was employed to calculate intramolecular hydrogen bond enthalpies (HIHB), O-H charge differences, O-H bond lengths and bond orders for various substituted catechols and their radicals generated after H-abstraction. It was found that although the charge difference between hydrogen-bonded H and O played a role in determining HIHB, HIHB was mainly governed by the hydrogen bond length. As the oxygen-centered radical has great tendency to form a chemical bond with the H atom, hydrogen bond lengths in catecholic radicals are systematically shorter than those in catechols. Hence, the HIHB for the former are higher than those for the latter.

  3. Evaluation of the individual hydrogen bonding energies in N-methylacetamide chains

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The individual hydrogen bonding energies in N-methylacetamide chains were evaluated at the MP2/6-31+G** level including BSSE correction and at the B3LYP/6-311++G(3df,2pd) level including BSSE and van der Waals correction.The calculation results indicate that compared with MP2 results,B3LYP calculations without van der Waals correction underestimate the individual hydrogen bonding energies about 5.4 kJ m ol-1 for both the terminal and central hydrogen bonds,whereas B3LYP calculations with van der Waals correction produce almost the same individual hydrogen bonding energies as MP2 does for those terminal hydrogen bonds,but still underestimate the individual hydrogen bonding energies about 2.5 kJ mol-1 for the hydrogen bonds near the center.Our calculation results show that the individual hydrogen bonding energy becomes more negative (more attractive) as the chain becomes longer and that the hydrogen bonds close to the interior of the chain are stronger than those near the ends.The weakest individual hydrogen bonding energy is about-29.0 kJ m ol-1 found in the dimer,whereas with the growth of the N-methylacetamide chain the individual hydrogen bonding energy was estimated to be as large as-62.5 kJ mol-1 found in the N-methylacetamide decamer,showing that there is a significant hydrogen bond cooperative effect in N-methylacetamide chains.The natural bond orbital analysis indicates that a stronger hydrogen bond corresponds to a larger positive charge for the H atom and a larger negative charge for the O atom in the N-H···O=C bond,corresponds to a stronger second-order stabilization energy between the oxygen lone pair and the N-H antibonding orbital,and corresponds to more charge transfer between the hydrogen bonded donor and acceptor molecules.

  4. Hydrogen-bond Specific Materials Modification in Group IV Semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Tolk, Norman H. [Vanderbilt Univ., Nashville, TN (United States); Feldman, L. C. [Vanderbilt Univ., Nashville, TN (United States); Luepke, G. [College of William and Mary, Williamsburg, VA (United States)

    2015-09-14

    Executive summary Semiconductor dielectric crystals consist of two fundamental components: lattice atoms and electrons. The former component provides a crystalline structure that can be disrupted by various defects or the presence of an interface, or by transient oscillations known as phonons. The latter component produces an energetic structure that is responsible for the optical and electronic properties of the material, and can be perturbed by lattice defects or by photo-excitation. Over the period of this project, August 15, 1999 to March 31, 2015, a persistent theme has been the elucidation of the fundamental role of defects arising from the presence of radiation damage, impurities (in particular, hydrogen), localized strain or some combination of all three. As our research effort developed and evolved, we have experienced a few title changes, which reflected this evolution. Throughout the project, ultrafast lasers usually in a pump-probe configuration provided the ideal means to perturb and study semiconductor crystals by both forms of excitation, vibrational (phonon) and electronic (photon). Moreover, we have found in the course of this research that there are many interesting and relevant scientific questions that may be explored when phonon and photon excitations are controlled separately. Our early goals were to explore the dynamics of bond-selective vibrational excitation of hydrogen from point defects and impurities in crystalline and amorphous solids, initiating an investigation into the behavior of hydrogen isotopes utilizing a variety of ultrafast characterization techniques, principally transient bleaching spectroscopy to experimentally obtain vibrational lifetimes. The initiative could be divided into three related areas: (a) investigation of the change in electronic structure of solids due to the presence of hydrogen defect centers, (b) dynamical studies of hydrogen in materials and (c) characterization and stability of metastable hydrogen

  5. Changes in active site histidine hydrogen bonding trigger cryptochrome activation.

    Science.gov (United States)

    Ganguly, Abir; Manahan, Craig C; Top, Deniz; Yee, Estella F; Lin, Changfan; Young, Michael W; Thiel, Walter; Crane, Brian R

    2016-09-06

    Cryptochrome (CRY) is the principal light sensor of the insect circadian clock. Photoreduction of the Drosophila CRY (dCRY) flavin cofactor to the anionic semiquinone (ASQ) restructures a C-terminal tail helix (CTT) that otherwise inhibits interactions with targets that include the clock protein Timeless (TIM). All-atom molecular dynamics (MD) simulations indicate that flavin reduction destabilizes the CTT, which undergoes large-scale conformational changes (the CTT release) on short (25 ns) timescales. The CTT release correlates with the conformation and protonation state of conserved His378, which resides between the CTT and the flavin cofactor. Poisson-Boltzmann calculations indicate that flavin reduction substantially increases the His378 pKa Consistent with coupling between ASQ formation and His378 protonation, dCRY displays reduced photoreduction rates with increasing pH; however, His378Asn/Arg variants show no such pH dependence. Replica-exchange MD simulations also support CTT release mediated by changes in His378 hydrogen bonding and verify other responsive regions of the protein previously identified by proteolytic sensitivity assays. His378 dCRY variants show varying abilities to light-activate TIM and undergo self-degradation in cellular assays. Surprisingly, His378Arg/Lys variants do not degrade in light despite maintaining reactivity toward TIM, thereby implicating different conformational responses in these two functions. Thus, the dCRY photosensory mechanism involves flavin photoreduction coupled to protonation of His378, whose perturbed hydrogen-bonding pattern alters the CTT and surrounding regions.

  6. Do cooperative cycles of hydrogen bonding exist in proteins?

    CERN Document Server

    Sharley, John N

    2016-01-01

    The closure of cooperative chains of Hydrogen Bonding, HB, to form cycles can enhance cooperativity. Cycles of charge transfer can balance charge into and out of every site, eliminating the charge build-up that limits the cooperativity of open unidirectional chains of cooperativity. If cycles of cooperative HB exist in proteins, these could be expected to be significant in protein structure and function in ways described below. We investigate whether cooperative HB cycles not traversing solvent, ligand or modified residues occur in protein by means including search of Nuclear Magnetic Resonance spectroscopy entries of the Protein Data Bank. We find no mention of an example of this kind of cycle in the literature. For amide-amide HB, for direct inter-amide interactions, when the energy associated with Natural Bond Orbital, NBO, steric exchange is deducted from that of NBO donor-acceptor interactions, the result is close to zero, so that HB is not primarily due to the sum of direct inter-amide NBO interactions....

  7. Effect of quantum nuclear motion on hydrogen bonding

    CERN Document Server

    McKenzie, Ross H; Athokpam, Bijyalaxmi; Ramesh, Sai G

    2014-01-01

    This work considers how the properties of hydrogen bonded complexes, D-H....A, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor (D) and acceptor (A) have the same proton affinity, is carried out. For quantitative comparisons, a parametrization specific to the O-H....O complexes is used. The vibrational energy levels of the one-dimensional ground state adiabatic potential of the model are used to make quantitative comparisons with a vast body of condensed phase data, spanning a donor-acceptor separation (R) range of about 2.4-3.0 A, i.e., from strong to weak bonds. The position of the proton and its longitudinal vibrational frequency, along with the isotope effects in both are discussed. An analysis of the secondary geometric isotope effects, using a simple extension of the two-state model, yields an improved agreement of the predicted variation with R of frequency isotope effects. The role of the b...

  8. Hydrogen-bonding Interactions between Apigenin and Ethanol/Water: A Theoretical Study

    Science.gov (United States)

    Zheng, Yan-Zhen; Zhou, Yu; Liang, Qin; Chen, Da-Fu; Guo, Rui; Lai, Rong-Cai

    2016-10-01

    In this work, hydrogen-bonding interactions between apigenin and water/ethanol were investigated from a theoretical perspective using quantum chemical calculations. Two conformations of apigenin molecule were considered in this work. The following results were found. (1) For apigenin monomer, the molecular structure is non-planar, and all of the hydrogen and oxygen atoms can be hydrogen-bonding sites. (2) Eight and seven optimized geometries are obtained for apigenin (I)–H2O/CH3CH2OH and apigenin (II)–H2O/CH3CH2OH complexes, respectively. In apigenin, excluding the aromatic hydrogen atoms in the phenyl substituent, all other hydrogen atoms and the oxygen atoms form hydrogen-bonds with H2O and CH3CH2OH. (3) In apigenin–H2O/CH3CH2OH complexes, the electron density and the E(2) in the related localized anti-bonding orbital are increased upon hydrogen-bond formation. These are the cause of the elongation and red-shift of the X‑H bond. The sum of the charge change transfers from the hydrogen-bond acceptor to donor. The stronger interaction makes the charge change more intense than in the less stable structures. (4) Most of the hydrogen-bonds in the complexes are electrostatic in nature. However, the C4‑O5···H, C9‑O4···H and C13‑O2···H hydrogen-bonds have some degree of covalent character. Furthermore, the hydroxyl groups of the apigenin molecule are the preferred hydrogen-bonding sites.

  9. Hydrogen-bonding Interactions between Apigenin and Ethanol/Water: A Theoretical Study

    Science.gov (United States)

    Zheng, Yan-Zhen; Zhou, Yu; Liang, Qin; Chen, Da-Fu; Guo, Rui; Lai, Rong-Cai

    2016-01-01

    In this work, hydrogen-bonding interactions between apigenin and water/ethanol were investigated from a theoretical perspective using quantum chemical calculations. Two conformations of apigenin molecule were considered in this work. The following results were found. (1) For apigenin monomer, the molecular structure is non-planar, and all of the hydrogen and oxygen atoms can be hydrogen-bonding sites. (2) Eight and seven optimized geometries are obtained for apigenin (I)–H2O/CH3CH2OH and apigenin (II)–H2O/CH3CH2OH complexes, respectively. In apigenin, excluding the aromatic hydrogen atoms in the phenyl substituent, all other hydrogen atoms and the oxygen atoms form hydrogen-bonds with H2O and CH3CH2OH. (3) In apigenin–H2O/CH3CH2OH complexes, the electron density and the E(2) in the related localized anti-bonding orbital are increased upon hydrogen-bond formation. These are the cause of the elongation and red-shift of the X−H bond. The sum of the charge change transfers from the hydrogen-bond acceptor to donor. The stronger interaction makes the charge change more intense than in the less stable structures. (4) Most of the hydrogen-bonds in the complexes are electrostatic in nature. However, the C4−O5···H, C9−O4···H and C13−O2···H hydrogen-bonds have some degree of covalent character. Furthermore, the hydroxyl groups of the apigenin molecule are the preferred hydrogen-bonding sites. PMID:27698481

  10. Investigating Hydrogen Bonding in Phenol Using Infrared Spectroscopy and Computational Chemistry

    Science.gov (United States)

    Fedor, Anna M.; Toda, Megan J.

    2014-01-01

    The hydrogen bonding of phenol can be used as an introductory model for biological systems because of its structural similarities to tyrosine, a para-substituted phenol that is an amino acid essential to the synthesis of proteins. Phenol is able to form hydrogen bonds readily in solution, which makes it a suitable model for biological…

  11. Reordering hydrogen bonds using Hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems

    NARCIS (Netherlands)

    Vreede, J.; Wolf, M.G.; de Leeuw, S.W.; Bolhuis, P.G.

    2009-01-01

    Hydrogen bonds play an important role in stabilizing (meta-)stable states in protein folding. Hence, they can potentially be used as a way to bias these states in molecular simulation methods. Previously, Wolf et al. showed that applying repulsive and attractive hydrogen bond biasing potentials in a

  12. Calorimetric Investigation of Hydrogen Bonding of Formamide and Its Methyl Derivatives in Organic Solvents and Water

    Science.gov (United States)

    Varfolomeev, Mikhail A.; Rakipov, Ilnaz T.; Solomonov, Boris N.

    2013-04-01

    Formamide and its derivatives have a large number of practical applications; also they are structural fragments of many biomolecules. Hydrogen bonds strongly affect their physicochemical properties. In the present work a calorimetric study of formamide and its methyl derivatives was carried out. Enthalpies of solution at infinite dilution of formamide, N-methylformamide, and N, N-dimethylformamide in organic solvents at 298.15 K were measured. The relationships between the obtained enthalpies of solvation and the structure of the studied compounds were observed. Hydrogen-bond enthalpies of amides with chlorinated alkanes, ethers, ketones, esters, nitriles, amines, alcohols, and water were determined. The strength of hydrogen bonds of formamide, N-methylformamide, and N, N-dimethylformamide with proton donor solvents is practically equal. Enthalpies of hydrogen bonds of formamide with the proton acceptor solvents are two times larger in magnitude than the enthalpies of N-methylformamide. The process of hydrogen bonding of amides in aliphatic alcohols and water is complicated. The obtained enthalpies of hydrogen bonding in aliphatic alcohols vary considerably from the amide structure due to the competition between solute-solvent and solvent-solvent hydrogen bonds. Fourier transform infrared spectroscopic measurements were carried out to explain the calorimetric data. Hydration enthalpies of methyl derivatives of formamides contain a contribution of the hydrophobic effect. New thermochemical data on the hydrogen bonding of formamides may be useful for predicting the properties of biomacromolecules.

  13. Covalent features in the hydrogen bond of a water dimer: molecular orbital analysis

    CERN Document Server

    Wang, Bo; Dai, Xing; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin

    2015-01-01

    The covalent-like characteristics of hydrogen bonds offer a new perspective on intermolecular interactions. Here, using density functional theory and post-Hartree-Fock methods, we reveal that there are two bonding molecular orbitals (MOs) crossing the O and H atoms of the hydrogen-bond in water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. These results illustrate the covalent-like character of the hydrogen bond between water molecules, which contributes to the essential understanding of ice, liquid water, related materials, and life sciences.

  14. General and Efficient C-C Bond Forming Photoredox Catalysis with Semiconductor Quantum Dots.

    Science.gov (United States)

    Caputo, Jill A; Frenette, Leah C; Zhao, Norman; Sowers, Kelly L; Krauss, Todd D; Weix, Daniel J

    2017-03-29

    Photoredox catalysis has become an essential tool in organic synthesis because it enables new routes to important molecules. However, the best available molecular catalysts suffer from high catalyst loadings and rely on precious metals. Here we show that colloidal nanocrystal quantum dots (QDs) can serve as efficient and robust, precious-metal free, photoassisted redox catalysts. A single-sized CdSe quantum dot (3.0 ± 0.2 nm) can replace several different dye catalysts needed for five different photoredox reactions (β-alkylation, β-aminoalkylation, dehalogenation, amine arylation, and decarboxylative radical formation). Even without optimization of the QDs or the reaction conditions, efficiencies rivaling those of the best available metal dyes were obtained.

  15. The strength of side chain hydrogen bonds in the plasma membrane

    Science.gov (United States)

    Hristova, Kalina; Sarabipour, Sarvenaz

    2013-03-01

    There are no direct quantitative measurements of hydrogen bond strengths in membrane proteins residing in their native cellular environment. To address this knowledge gap, here we use fluorescence resonance energy transfer (FRET) to measure the impact of hydrogen bonds on the stability of a membrane protein dimer in vesicles derived from eukaryotic plasma membranes, and we compare these results to previous measurements of hydrogen bond strengths in model lipid bilayers. We demonstrate that FRET measurements of membrane protein interactions in plasma membrane vesicles have the requisite sensitivity to quantify the strength of hydrogen bonds. We find that the hydrogen bond-mediated stabilization in the plasma membrane is small, only -0.7 kcal/mole. It is the same as in model lipid bilayers, despite the different nature and dielectric properties of the two environments.

  16. Pyrrolic Amide: A New Hydrogen Bond Building Block for Self-assembly

    Institute of Scientific and Technical Information of China (English)

    YIN Zhen-Ming; LI Jian-Feng; HE Jia-Qi; ZHU Xiao-Qing; CHENG Jin-Pei

    2003-01-01

    @@ Molecular self-assembly has emerged as a powerful technology for the synthesis of nanostructured materials. In design of various molecular assemblies, hydrogen bonding is a preferably selected intra- or inter-molecular weak interaction in recent research by virtue of the directionality and specificity. The research for novel hydrogen bond building blocks that self-assembly into well defined structures is great important not only for gaining an understanding of the concepts of self-assembly but also for the design of new molecular materials. Pyrrolic amide moiety has one hydrogen bond acceptor (C =O) and two hydrogen bond donors (pyrrole NH and amide NH). By deliberately design, pyrrolic amide compounds would be new kinds hydrogen bond building blocks. So, pyrrolic amide compounds 1 ~ 6, which bear one, two or three pyrrolic amide moieties respectively, were designed and synthesized.

  17. Metal-activated histidine carbon donor hydrogen bonds contribute to metalloprotein folding and function.

    Science.gov (United States)

    Schmiedekamp, Ann; Nanda, Vikas

    2009-07-01

    Carbon donor hydrogen bonds are typically weak interactions that contribute less than 2 kcal/mol, and provide only modest stabilization in proteins. One exception is the class of hydrogen bonds donated by heterocyclic side chain carbons. Histidine is capable of particularly strong interactions through the Cepsilon(1) and Cdelta(2) carbons when the imidazole is protonated or bound to metal. Given the frequent occurrence of metal-bound histidines in metalloproteins, we characterized the energies of these interactions through DFT calculations on model compounds. Imidazole-water hydrogen bonding could vary from -11.0 to -17.0 kcal/mol, depending on the metal identity and oxidation state. A geometric search of metalloprotein structures in the PDB identified a number of candidate His C-H...O hydrogen bonds which may be important for folding or function. DFT calculations on model complexes of superoxide reductase show a carbon donor hydrogen bond positioning a water molecule above the active site.

  18. Effect of Hydrogen Bonding on Linear and Nonlinear Rheology of Entangled Polymer Melts

    DEFF Research Database (Denmark)

    Shabbir, Aamir; Goldansaz, Hadi; Hassager, Ole

    2015-01-01

    to AA along the backbone. Assuming superposition holds and subtracting out the linear chain rheology from LVE, the hydrogen bonding contribution to LVE is exposed. Hydrogen bonding affects linear viscoelasticity at frequencies below the inverse reptation time. More specifically, the presence of hydrogen...... bonds causes G′ and G″ as a function of frequency to shift to a power law scaling of 0.5. Furthermore, the magnitude of G′ and G″ scales linearly with the number of hydrogen-bonding groups. The nonlinear extensional rheology shows extreme strain hardening. The magnitude of extensional stress has...... a strongly nonlinear dependence on the number of hydrogenbonding groups. These results are aimed at uncovering the molecular influence of hydrogen bonding on linear and nonlinear rheology to aid future molecular synthesis and model development....

  19. Reaction dynamics and statistical theory for the growth of hydrogen bonding clusters

    Institute of Scientific and Technical Information of China (English)

    WANG; Haijun; BA; Xinwu(巴信武); ZHAO; Min(赵敏)

    2002-01-01

    The similarities between the formation of hydrogen bonds and polycondensation reactions are stated from the statistical viewpoint, and then taking the hydrogen bonding system of AaDd type as an example, the growing process of hydrogen bonding clusters is investigated in terms of the theory of reaction dynamics and statistical theory for polymeric reactions. The two methods lead to the same conclusions, stating that the statistical theory for polymerization is applicable to the hydrogen bonding systems. Based on this consideration, the explicit relationship between the conversions of proton-donors and proton-acceptors and the Gibbs free energy of the system under study is given. Furthermore, the sol-gel phase transition is predicted to take place in some hydrogen bonding systems, and the corresponding generalized scaling laws describing this kind of phase transition are obtained.

  20. Effects of hydrogen-bond environment on single particle and pair dynamics in liquid water

    Indian Academy of Sciences (India)

    Amalendu Chandra; Snehasis Chowdhuri

    2001-10-01

    We have performed molecular dynamics simulations of liquid water at 298 and 258 K to investigate the effects of hydrogen-bond environment on various single-particle and pair dynamical properties of water molecules at ambient and supercooled conditions. The water molecules are modelled by the extended simple point charge (SPC/E) model. We first calculate the distribution of hydrogen-bond environment in liquid water at both temperatures and then investigate how the selfdiffusion and orientational relaxation of a single water molecule and also the relative diffusion and relaxation of the hydrogen-bond of a water pair depend on the nature of the hydrogen-bond environment of the tagged molecules. We find that the various dynamical quantities depend significantly on the hydrogen-bond environment, especially at the supercooled temperature. The present study provides a molecular-level insight into the dynamics of liquid water under ambient and supercooled conditions.

  1. Hydrogen bonding in transient bifunctional hypervalent radicals by neutralization-reionization mass spectrometry.

    Science.gov (United States)

    Shaffer, S A; Tureček, F

    1995-11-01

    Neutralization-reionization mass spectrometry is used to generate hypervalent 9-N-4 (ammonium) and 9-O-3 (oxonium) radicals derived from protonated α,ω-bis-(dimethylamino)alkanes and α,ω-dimethoxyalkanes, which exist as cyclic hydrogen-bonded structures in the gas phase. Collisional neutralization with dimethyl disulfide, trimethylamine, and xenon of the hydrogen-bonded onium cations followed by reionization with oxygen results in complete dissociation. Bond cleavages at the hypervalent nitrogen atoms are found to follow the order CH2-N>CH3-N>N-H, which differs from that in the monofunctional hydrogen-n-heptyldimethylammonium radical, which gives CH2-N>N-H>CH3-N. No overall stabilization through hydrogen bonding of the bifunctional hypervalent ammonium and oxonium radicals is observed. Subtle effects of ring size are found that tend to stabilize large ring structures and are attributed to intramolecular hydrogen bonding.

  2. Hydrogen bonding in the protic ionic liquid triethylammonium nitrate explored by density functional tight binding simulations

    CERN Document Server

    Zentel, Tobias

    2016-01-01

    The applicability of the density functional based tight binding (DFTB) method to the description of hydrogen bond dynamics and infrared spectroscopy is addressed for the exemplary protic ionic liquid triethylammonium nitrate. Potential energy curves for proton transfer in gas and liquid phase are shown to be comparable to high level coupled cluster theory in the thermally accessible range of bond lengths. Geometric correlations in the hydrogen bond dynamics are analyzed for a cluster of six ion pairs. Comparing DFTB and regular DFT data lends further support for the reliability of the DFTB method. Therefore, DFTB bulk simulations are performed to quantify the extent of geometric correlations in terms of Pauling's bond order model. Further, infrared (IR) absorption spectra are obtained and analyzed putting emphasis on the signatures of hydrogen bonding in the NH-stretching and far IR hydrogen bond range.

  3. Hydrogen bonding in the protic ionic liquid triethylammonium nitrate explored by density functional tight binding simulations

    Science.gov (United States)

    Zentel, Tobias; Kühn, Oliver

    2016-12-01

    The applicability of the density functional based tight binding (DFTB) method to the description of hydrogen bond dynamics and infrared (IR) spectroscopy is addressed for the exemplary protic ionic liquid triethylammonium nitrate. Potential energy curves for proton transfer in gas and liquid phases are shown to be comparable to the high level coupled cluster theory in the thermally accessible range of bond lengths. Geometric correlations in the hydrogen bond dynamics are analyzed for a cluster of six ion pairs. Comparing DFTB and DFT data lends further support for the reliability of the DFTB method. Therefore, DFTB bulk simulations are performed to quantify the extent of geometric correlations in terms of Pauling's bond order model. Further, IR absorption spectra are obtained using DFTB and analyzed putting emphasis on the signatures of hydrogen bonding in the NH-stretching and far IR hydrogen bond range.

  4. Replacing the hydrogen in the intermolecular hydrogen bond of the cyanuric acid-bipyridyl adduct by Ag(I)

    Indian Academy of Sciences (India)

    K Sivashankar; Anupama Ranganathan; V R Pedireddi

    2000-04-01

    A complex between cyanuric acid (CA), 4,4′-bipyridyl (BP) and Ag(I), with the composition, [Ag2(C3H2N3O3-N)2 (C10H8N2-N)] has been prepared. Crystal structure analysis shows that it has a chain structure in which the CA molecules are linked to the BP units through silver atoms by the formation of N-Ag-N bonds, wherein one of the hydrogens of CA is replaced by Ag(I), showing thereby the chains connected to one another by N-H${\\ldots}$O hydrogen bonds formed between the CA molecules. This intermolecular chain structure resembles the chain structure of the CA.BP adduct where CA-BP-CA chains formed by N-H${\\ldots}$N hydrogen bonds are linked to one another by N-H${\\ldots}$O hydrogen bonds between the CA molecules.

  5. Strong and weak hydrogen bonds in drug–DNA complexes: A statistical analysis

    Indian Academy of Sciences (India)

    Sunil K Panigrahi; Gautam R Desiraju

    2007-06-01

    A statistical analysis of strong and weak hydrogen bonds in the minor groove of DNA was carried out for a set of 70 drug–DNA complexes. The terms `strong’ and `weak’ pertain to the inherent strengths and weakness of the donor and acceptor fragments rather than to any energy considerations. The dataset was extracted from the protein data bank (PDB). The analysis was performed with an in-house software, hydrogen bond analysis tool (HBAT). In addition to strong hydrogen bonds such as O−H···O and N−H···O, the ubiquitous presence of weak hydrogen bonds such as C−H···O is implicated in molecular recognition. On an average, there are 1.4 weak hydrogen bonds for every strong hydrogen bond. For both categories of interaction, the N(3) of purine and the O(2) of pyrimidine are favoured acceptors. Donor multifurcation is common with the donors generally present in the drug molecules, and shared by hydrogen bond acceptors in the minor groove. Bifurcation and trifurcation are most commonly observed. The metrics for strong hydrogen bonds are consistent with established trends. The geometries are variable for weak hydrogen bonds. A database of recognition geometries for 26 literature amidinium-based inhibitors of Human African Trypanosomes (HAT) was generated with a docking study using seven inhibitors which occur in published crystal structures included in the list of 70 complexes mentioned above, and 19 inhibitors for which the drug–DNA complex crystal structures are unknown. The virtual geometries so generated correlate well with published activities for these 26 inhibitors, justifying our assumption that strong and weak hydrogen bonds are optimized in the active site.

  6. Kinetics and Catalysis Demonstrations.

    Science.gov (United States)

    Falconer, John L.; Britten, Jerald A.

    1984-01-01

    Eleven videotaped kinetics and catalysis demonstrations are described. Demonstrations include the clock reaction, oscillating reaction, hydrogen oxidation in air, hydrogen-oxygen explosion, acid-base properties of solids, high- and low-temperature zeolite reactivity, copper catalysis of ammonia oxidation and sodium peroxide decomposition, ammonia…

  7. Evidences for Cooperative Resonance-Assisted Hydrogen Bonds in Protein Secondary Structure Analogs

    Science.gov (United States)

    Zhou, Yu; Deng, Geng; Zheng, Yan-Zhen; Xu, Jing; Ashraf, Hamad; Yu, Zhi-Wu

    2016-11-01

    Cooperative behaviors of the hydrogen bonding networks in proteins have been discovered for a long time. The structural origin of this cooperativity, however, is still under debate. Here we report a new investigation combining excess infrared spectroscopy and density functional theory calculation on peptide analogs, represented by N-methylformamide (NMF) and N-methylacetamide (NMA). Interestingly, addition of the strong hydrogen bond acceptor, dimethyl sulfoxide, to the pure analogs caused opposite effects, namely red- and blue-shift of the N-H stretching infrared absorption in NMF and NMA, respectively. The contradiction can be reconciled by the marked lowering of the energy levels of the self-associates between NMA molecules due to a cooperative effect of the hydrogen bonds. On the contrary, NMF molecules cannot form long-chain cooperative hydrogen bonds because they tend to form dimers. Even more interestingly, we found excellent linear relationships between changes on bond orders of N-H/N-C/C = O and the hydrogen bond energy gains upon the formation of hydrogen bonding multimers in NMA, suggesting strongly that the cooperativity originates from resonance-assisted hydrogen bonds. Our findings provide insights on the structures of proteins and may also shed lights on the rational design of novel molecular recognition systems.

  8. NMR study of the FH⋯F hydrogen bond. Relation between hydrogen atom position and FH⋯F bond length

    Science.gov (United States)

    Panich, A. M.

    1995-07-01

    1H and 19F NMR study of (NH 4) 3BiBr 6NH 4Br·2NH 4HF 2 shows the bifluoride ion in this compound to be asymmetric with distances r( HF) = 1.042 ± 0.002 and R( FF) = 2.373 ± 0.008 Å. Existing NMR and neutron diffraction data for the FH⋯F hydrogen bond in solids have been studied to find a relation between the position of the hydrogen atom and FH⋯F bond length. Such a relation has been established and explained in the framework of the two-dimensional dynamic model of the hydrogen bond. The dependencies of r(AH) on R(AB) for the OH⋯O and FH⋯F bonds are shown to be similar.

  9. Hydrogen bonds of sodium alginate/Antarctic krill protein composite material.

    Science.gov (United States)

    Yang, Lijun; Guo, Jing; Yu, Yue; An, Qingda; Wang, Liyan; Li, Shenglin; Huang, Xuelin; Mu, Siyang; Qi, Shanwei

    2016-05-20

    Sodium alginate/Antarctic krill protein composite material (SA/AKP) was successfully obtained by blending method. The hydrogen bonds of SA/AKP composite material were analyzed by Fourier transform infrared spectroscopy (FT-IR) and Nuclear magnetic resonance hydrogen spectrum (HNMR). Experiment manifested the existence of intermolecular and intramolecular hydrogen bonds in SA/AKP system; strength of intermolecular hydrogen bond enhanced with the increase of AKP in the composite material and the interaction strength of hydrogen bonding followed the order: OH…Ether O>OH…π>OH…N. The percentage of intermolecular hydrogen bond decreased with increase of pH. At the same time, the effect of hydrogen bonds on properties of the composite material was discussed. The increase of intermolecular hydrogen bonding led to the decrease of crystallinity, increase of apparent viscosity and surface tension, as well as obvious decrease of heat resistance of SA/AKP composite material. SA/AKP fiber SEM images and energy spectrum showed that crystallized salt was separated from the fiber, which possibly led to the fibrillation of the composite fibers.

  10. A BRIEF HISTORY OF INDUSTRIAL CATALYSIS

    Energy Technology Data Exchange (ETDEWEB)

    Heinemann, Heinz

    1979-06-01

    This history covers: catalytic cracking and other acid catalysed reactions; zeolite catalysis; dual functional catalysis; hydrogenation catalysis and hydrogen production; catalytic hydrocarbon dehydrogenation; catalytic alkylation and dealkylation; catalytic coal liquefaction and gasification; heterogeneous oxidation, arnmoxidation, chlorination, and oxychlorination catalysis; olefin disproportionation catalysis; industrial homogeneous catalysis; catalytic polymerization; catalysis for motor vehicle emission control; fuel cell catalysis; and the profession of the catalytic chemist or engineer. The discussion is mostly limited to the rapid growth of industrial catalysis between the second World War and 1978.

  11. Intramolecular Hydrogen Bond in Biologically Active o-Carbonyl Hydroquinones

    Directory of Open Access Journals (Sweden)

    Maximiliano Martínez-Cifuentes

    2014-07-01

    Full Text Available Intramolecular hydrogen bonds (IHBs play a central role in the molecular structure, chemical reactivity and interactions of biologically active molecules. Here, we study the IHBs of seven related o-carbonyl hydroquinones and one structurally-related aromatic lactone, some of which have shown anticancer and antioxidant activity. Experimental NMR data were correlated with theoretical calculations at the DFT and ab initio levels. Natural bond orbital (NBO and molecular electrostatic potential (MEP calculations were used to study the electronic characteristics of these IHB. As expected, our results show that NBO calculations are better than MEP to describe the strength of the IHBs. NBO energies (∆Eij(2 show that the main contributions to energy stabilization correspond to LPàσ* interactions for IHBs, O1…O2-H2 and the delocalization LPàπ* for O2-C2 = Cα(β. For the O1…O2-H2 interaction, the values of ∆Eij(2 can be attributed to the difference in the overlap ability between orbitals i and j (Fij, instead of the energy difference between them. The large energy for the LP O2àπ* C2 = Cα(β interaction in the compounds 9-Hydroxy-5-oxo-4,8, 8-trimethyl-l,9(8H-anthracenecarbolactone (VIII and 9,10-dihydroxy-4,4-dimethylanthracen-1(4H-one (VII (55.49 and 60.70 kcal/mol, respectively when compared with the remaining molecules (all less than 50 kcal/mol, suggests that the IHBs in VIII and VII are strongly resonance assisted.

  12. Room Temperature Reactivity Of Silicon Nanocrystals With Solvents: The Case Of Ketone And Hydrogen Production From Secondary Alcohols: Catalysis?

    KAUST Repository

    El Demellawi, Jehad K.

    2015-05-29

    Although silicon nanoparticles dispersed in liquids are used in various applications ranging from bio-labeling to hydrogen production, their reactivities with their solvents and their catalytic properties re-main still unexplored. Here, we discovered that, because of their surface structures and mechanical strain, silicon nanoparticles react strongly with their solvents and may act as catalysts for the dehydrogenation, at room temperature, of secondary alcohols (e.g. isopropanol) to ketones and hydrogen. This catalytic reaction was followed by gas chromatography, pH measurements, mass spectroscopy and solidstate NMR. This discovery provides new understanding of the role played by silicon nanoparticles, and nanosilicon in general, in their stability in solvents in general as well as being candidates in catalysis.

  13. Statistical theory for hydrogen bonding fluid system of AaDd type (Ⅲ): Equation of state and fluctuations

    Institute of Scientific and Technical Information of China (English)

    WANG HaiJun; GU Fang; HONG XiaoZhong; BA XinWu

    2007-01-01

    The equation of the state of the hydrogen bonding fluid system of AaDd type is studied by the principle of statistical mechanics. The influences of hydrogen bonds on the equation of state of the system are obtained based on the change in volume due to hydrogen bonds. Moreover, the number density fluctuations of both molecules and hydrogen bonds as well as their spatial correlation property are investigated. Furthermore, an equation describing relation between the number density correlation function of "molecules-hydrogen bonds" and that of molecules and hydrogen bonds is derived. As application,taking the van der Waals hydrogen bonding fluid as an example, we considered the effect of hydrogen bonds on its relevant statistical properties.

  14. Red- and blue-shifted hydrogen bonds in the cis-trans noncyclic formic acid dimer.

    Science.gov (United States)

    Zhou, Pan-Pan; Qiu, Wen-Yuan

    2009-08-01

    The cis-trans noncyclic formic acid dimer was studied by means of MP2 method with 6-31G(d,p), 6-31+G(d,p) and 6-311+G(d,p) basis sets. It exhibits simultaneously red-shifted O-H...O and blue-shifted C-H...O hydrogen bonds. AIM and NBO analyses are performed at the MP2/6-31+G(d,p) level to explore their properties and origins. AIM analysis provides the evidence that the O-H bond becomes weaker and the C-H bond becomes stronger upon the hydrogen bond formations. Intermolecular and intramolecular hyperconjugations have important influence on the electron densities in the X-H (X = O, C) sigma bonding orbital and its sigma* antibonding orbital. The electron densities in the two orbitals are closely connected with the X-H (X = O, C) bond length, and they are used to quantitatively estimate the bond length variation. The larger amount of charge transfer in the red-shifted O-H...O hydrogen bond is due to its favorable H...O electron channel, whereas the H...O electron channel in the blue-shifted C-H...O hydrogen bond is weaker. Structural reorganization effects shorten the C-H bond by approximately 30% when compared to the C-H bond contraction upon the dimerization. Strikingly, it leads to a small elongation and a slight red shift of the O-H bond. Both rehybridization and repolarization result in the X-H (X = O, C) bond contraction, but their effects on the O-H bond do not hold a dominant position. The hydrogen-bonding processes go through the electrostatic attractions, van der Waals interactions, charge-transfer interactions, hydrogen-bonding interactions and electrostatic repulsions. Electrostatic attractions are of great importance on the origin of the red-shifted O-H...O hydrogen bond, especially the strong H(delta+)...O(delta-) attraction. For the blue-shifted C-H...O hydrogen bond, the considerable nucleus-nucleus repulsion between H and O atoms caused by the strong electrostatic attraction between C and O atoms is a possible reason for the C-H bond contraction and

  15. Thermotropic organization of hydrogen-bond-bridged bolaform amphiphiles.

    Science.gov (United States)

    Zhang, Jing; Zhou, Mingjun; Wang, Shan; Carr, Jessica; Li, Wen; Wu, Lixin

    2011-04-05

    A series of quaternary ammonium amphiphiles (A-n) bearing carboxylic acid groups were designed and synthesized. The branched bolaform structures can be constructed by dimerizations of carboxylic acid groups through intermolecular hydrogen bonding, as demonstrated by the Fourier transform infrared (FT-IR) spectra and the temperature-dependent FT-IR spectra. The thermotropic organizations of branched bolaform ammonium dimer complexes were characterized by differential scanning calorimetry, polarized optical microscopy, and X-ray diffraction. We investigated the influence of the spacer between the cationic group and the benzene ring on the thermotropic organization. A-6 with short lateral alkyl chains formed a simple layered structure at room temperature and exhibited smectic A mesophase above 145 °C, whereas A-8 with intermediate lateral chain length organized into smectic A phase over a wide temperature range. A further increase of the length (n = 10, 12) of the lateral chains resulted in the formation of lamellar structure with in-plane layered periodicity, which is rare in the organization of ionic compounds. A packing model of the quasi-2D lamellar was proposed on the basis of the experimental data of X-ray diffraction results. Notably, the quasi-2D lamellar structure could evolve into a simple layer with the increase of temperature. The present results showed a direct relationship in which the branched architecture can be applied to tune the self-assembly behavior of ionic amphiphiles and is allowed to construct new layered superstructure.

  16. Hydrogen-bond Specific Materials Modification in Group IV Semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Tolk, Norman H. [Vanderbilt Univ., Nashville, TN (United States); Feldman, L. C. [Vanderbilt Univ., Nashville, TN (United States); Luepke, G. [College of William and Mary, Williamsburg, VA (United States)

    2015-09-14

    Executive summary Semiconductor dielectric crystals consist of two fundamental components: lattice atoms and electrons. The former component provides a crystalline structure that can be disrupted by various defects or the presence of an interface, or by transient oscillations known as phonons. The latter component produces an energetic structure that is responsible for the optical and electronic properties of the material, and can be perturbed by lattice defects or by photo-excitation. Over the period of this project, August 15, 1999 to March 31, 2015, a persistent theme has been the elucidation of the fundamental role of defects arising from the presence of radiation damage, impurities (in particular, hydrogen), localized strain or some combination of all three. As our research effort developed and evolved, we have experienced a few title changes, which reflected this evolution. Throughout the project, ultrafast lasers usually in a pump-probe configuration provided the ideal means to perturb and study semiconductor crystals by both forms of excitation, vibrational (phonon) and electronic (photon). Moreover, we have found in the course of this research that there are many interesting and relevant scientific questions that may be explored when phonon and photon excitations are controlled separately. Our early goals were to explore the dynamics of bond-selective vibrational excitation of hydrogen from point defects and impurities in crystalline and amorphous solids, initiating an investigation into the behavior of hydrogen isotopes utilizing a variety of ultrafast characterization techniques, principally transient bleaching spectroscopy to experimentally obtain vibrational lifetimes. The initiative could be divided into three related areas: (a) investigation of the change in electronic structure of solids due to the presence of hydrogen defect centers, (b) dynamical studies of hydrogen in materials and (c) characterization and stability of metastable hydrogen

  17. Effects of hydrogen bond on 2-aminopyridine and its derivatives complexes in methanol solvent.

    Science.gov (United States)

    Zhao, Jinfeng; Song, Peng; Cui, Yanling; Liu, Xuemei; Sun, Shaowu; Hou, Siyao; Ma, Fengcai

    2014-10-15

    In the present work, the time-dependent density functional theory (TD-DFT) method was adopted to investigate the excited state hydrogen-bond dynamics of 2-aminopyridine monomer (2AP) and its derivatives in hydrogen donating methanol solvent. The calculated steady-state absorption and fluorescence spectra agree well with the experimental results. Theoretical results state that the bond lengths of both O-H and N-H bands are lengthened, while the intermolecular hydrogen bond lengths are shortened in the excited state. Further, the intermolecular hydrogen bonds are proved to be strengthened according to the calculated binding energy. As a reasonable explanation, the hydrogen bonds binding energy increases with multiple hydrogen-bonding interactions in the electronically excited state. In addition, the hydrogen bonding dynamics in the excited state were visualized by the spectral shifts of vibrational modes. The calculated infrared spectra of both O-H and N-H stretching vibrational regions revealed that the O-H and N-H stretching bands red-shift.

  18. An AAA-DDD triply hydrogen-bonded complex easily accessible for supramolecular polymers.

    Science.gov (United States)

    Han, Yi-Fei; Chen, Wen-Qiang; Wang, Hong-Bo; Yuan, Ying-Xue; Wu, Na-Na; Song, Xiang-Zhi; Yang, Lan

    2014-12-15

    For a complementary hydrogen-bonded complex, when every hydrogen-bond acceptor is on one side and every hydrogen-bond donor is on the other, all secondary interactions are attractive and the complex is highly stable. AAA-DDD (A=acceptor, D=donor) is considered to be the most stable among triply hydrogen-bonded sequences. The easily synthesized and further derivatized AAA-DDD system is very desirable for hydrogen-bonded functional materials. In this case, AAA and DDD, starting from 4-methoxybenzaldehyde, were synthesized with the Hantzsch pyridine synthesis and Friedländer annulation reaction. The association constant determined by fluorescence titration in chloroform at room temperature is 2.09×10(7)  M(-1) . The AAA and DDD components are not coplanar, but form a V shape in the solid state. Supramolecular polymers based on AAA-DDD triply hydrogen bonded have also been developed. This work may make AAA-DDD triply hydrogen-bonded sequences easily accessible for stimuli-responsive materials.

  19. The role of hydrogen bonding in excited state intramolecular charge transfer.

    Science.gov (United States)

    Chipem, Francis A S; Mishra, Anasuya; Krishnamoorthy, G

    2012-07-07

    Intramolecular charge transfer (ICT) that occurs upon photoexcitation of molecules is a vital process in nature and it has ample applications in chemistry and biology. The ICT process of the excited molecules is affected by several environmental factors including polarity, viscosity and hydrogen bonding. The effect of polarity and viscosity on the ICT processes is well understood. But, despite the fact that hydrogen bonding significantly influences the ICT process, the specific role of hydrogen bonding in the formation and stabilization of the ICT state is not unambiguously established. Some literature reports predicted that the hydrogen bonding of the solvent with a donor promotes the formation of a twisted intramolecular charge transfer (TICT) state. Some other reports stated that it inhibits the formation of the TICT state. Alternatively, it was proposed that the hydrogen bonding of the solvent with an acceptor favors the TICT state. It is also observed that a dynamic equilibrium is established between the free and the hydrogen bonded ICT states. This perspective focuses on the specific role played by hydrogen bonding of the solvent with the donor and the acceptor, and by proton transfer in the ICT process. The utility of such influence in molecular recognition and anion sensing is discussed with a few recent literature examples in the end.

  20. Multiscale Structure-Performance Relationships in Supported Palladium Catalysis for Multiphase Hydrogenations

    NARCIS (Netherlands)

    Bakker, J.J.W.

    2012-01-01

    The performance of heterogeneous catalysts in multiphase reactions in general is governed by different types of extrinsic and intrinsic structural effects on all length scales, i.e., on the macro- (m to cm), meso- (mm to µm), and microlevel (nm). This PhD research, with a catalysis-engineering appro

  1. Nuclear quantum effect on intramolecular hydrogen bond of hydrogen maleate anion: An ab initio path integral molecular dynamics study

    Science.gov (United States)

    Kawashima, Yukio; Tachikawa, Masanori

    2013-05-01

    Ab initio path integral molecular dynamics simulation was performed to understand the nuclear quantum effect on the hydrogen bond of hydrogen malonate anion. Static calculation predicted the proton transfer barrier as 0.12 kcal/mol. Conventional ab initio molecular dynamics simulation at 300 K found proton distribution with a double peak on the proton transfer coordinate. Inclusion of thermal effect alone elongates the hydrogen bond length, which increases the barrier height. Inclusion of nuclear quantum effect washes out this barrier, and distributes a single broad peak in the center. H/D isotope effect on the proton transfer is also discussed.

  2. Determining the Energetics of the Hydrogen Bond through FTIR: A Hands-On Physical Chemistry Lab Experiment

    Science.gov (United States)

    Guerin, Abby C.; Riley, Kristi; Rupnik, Kresimir; Kuroda, Daniel G.

    2016-01-01

    Hydrogen bonds are very important chemical structures that are responsible for many unique and important properties of solvents, such as the solvation power of water. These distinctive features are directly related to the stabilization energy conferred by hydrogen bonds to the solvent. Thus, the characterization of hydrogen bond energetics has…

  3. Correlation of structural order, anomalous density, and hydrogen bonding network of liquid water.

    Science.gov (United States)

    Bandyopadhyay, Dibyendu; Mohan, S; Ghosh, S K; Choudhury, Niharendu

    2013-07-25

    We use extensive molecular dynamics simulations employing different state-of-the-art force fields to find a common framework for comparing structural orders and density anomalies as obtained from different water models. It is found that the average number of hydrogen bonds correlates well with various order parameters as well as the temperature of maximum densities across the different models, unifying apparently disparate results from different models and emphasizing the importance of hydrogen bonding in determining anomalous properties and the structure of water. A deeper insight into the hydrogen bond network of water reveals that the solvation shell of a water molecule can be defined by considering only those neighbors that are hydrogen-bonded to it. On the basis of this view, the origin of the appearance of a non-tetrahedral peak at a higher temperature in the distribution of tetrahedral order parameters has been explained. It is found that a neighbor that is hydrogen-bonded to the central molecule is tetrahedrally coordinated even at higher temperatures. The non-tetrahedral peak at a higher temperature arises due to the strained orientation of the neighbors that are non-hydrogen-bonded to the central molecule. With the new definition of the solvation shell, liquid water can be viewed as an instantaneously changing random hydrogen-bonded network consisting of differently coordinated hydrogen-bonded molecules with their distinct solvation shells. The variation of the composition of these hydrogen-bonded molecules against temperature accounts for the density anomaly without introducing the concept of large-scale structural polyamorphism in water.

  4. Halogen Bonding or Hydrogen Bonding between 2,2,6,6-Tetramethyl-piperidine-noxyl Radical and Trihalomethanes CHX3 (X=Cl, Br, I)

    Institute of Scientific and Technical Information of China (English)

    Xiao-ran Zhao; Xue Pang; Xiao-qing Yan; Wei-jun Jin

    2013-01-01

    The halogen and hydrogen bonding complexes between 2,2,6,6-tetramethylpiperidine-noxyl and trihalomethanes (CHX3,X=Cl,Br,I) are simulated by computational quantum chemistry.The molecular electrostatic potentials,geometrical parameters and interaction energy of halogen and hydrogen bonding complexes combined with natural bond orbital analysis are obtained.The results indicate that both halogen and hydrogen bonding interactions obey the order Cl<Br<I,and hydrogen bonding is stronger than the corresponding halogen bond ing.So,hydrogen bonding complexes should be dominant in trihalomethanes.However,it is possible that halogen bonding complex is competitive,even preponderant,in triiodomethane due to the similar interaction energy.This work might provide useful information on specific solvent effects as well as for understanding the mechanism of nitroxide radicals as a bioprobe to interact with the halogenated compounds in biological and biochemical fields.

  5. The influence of boron doped nanodiamonds on hydrogen bonds in suspensions of protic solvents

    Science.gov (United States)

    Vervald, Alexey M.; Ekimov, Evgeny A.; Kudryavtsev, Oleg S.; Vlasov, Igor I.; Dolenko, Tatiana A.

    2016-04-01

    This work presents the results of study of the influence of BDND on hydrogen bonds of protonic solvents. In addition, the comparative analysis of the interactions of BDND and DND-COOH with solvents molecules was carried out. The analysis of temperature dependences of the quantitative characteristics of the stretching bands of OH groups of the solvents and the suspensions of NDs has shown that the BDND and DND differently weaken the hydrogen bonds in water and in water-ethanol solution with 70 vol. % ethanol content. In water-ethanol solution with 20 vol. % of ethanol the both NDs practically does not change the network of hydrogen bonds.

  6. Translational vibrations between chains of hydrogen-bonded molecules in solid-state aspirin form I

    Science.gov (United States)

    Takahashi, Masae; Ishikawa, Yoichi

    2013-06-01

    We perform dispersion-corrected first-principles calculations, and far-infrared (terahertz) spectroscopic experiments at 4 K, to examine translational vibrations between chains of hydrogen-bonded molecules in solid-state aspirin form I. The calculated frequencies and relative intensities reproduce the observed spectrum to accuracy of 11 cm-1 or less. The stronger one of the two peaks assigned to the translational mode includes the stretching vibration of the weak hydrogen bond between the acetyl groups of a neighboring one-dimensional chain. The calculation of aspirin form II performed for comparison gives the stretching vibration of the weak hydrogen bond in one-dimensional chain.

  7. H2XP:OH2 Complexes: Hydrogen vs. Pnicogen Bonds

    Directory of Open Access Journals (Sweden)

    Ibon Alkorta

    2016-02-01

    Full Text Available A search of the Cambridge Structural Database (CSD was carried out for phosphine-water and arsine-water complexes in which water is either the proton donor in hydrogen-bonded complexes, or the electron-pair donor in pnicogen-bonded complexes. The range of experimental P-O distances in the phosphine complexes is consistent with the results of ab initio MP2/aug’-cc-pVTZ calculations carried out on complexes H2XP:OH2, for X = NC, F, Cl, CN, OH, CCH, H, and CH3. Only hydrogen-bonded complexes are found on the H2(CH3P:HOH and H3P:HOH potential surfaces, while only pnicogen-bonded complexes exist on H2(NCP:OH2, H2FP:OH2, H2(CNP:OH2, and H2(OHP:OH2 surfaces. Both hydrogen-bonded and pnicogen-bonded complexes are found on the H2ClP:OH2 and H2(CCHP:OH2 surfaces, with the pnicogen-bonded complexes more stable than the corresponding hydrogen-bonded complexes. The more electronegative substituents prefer to form pnicogen-bonded complexes, while the more electropositive substituents form hydrogen-bonded complexes. The H2XP:OH2 complexes are characterized in terms of their structures, binding energies, charge-transfer energies, and spin-spin coupling constants 2hJ(O-P, 1hJ(H-P, and 1J(O-H across hydrogen bonds, and 1pJ(P-O across pnicogen bonds.

  8. Selective molecular recognition, C-H bond activation, and catalysis in nanoscale reaction vessels

    Energy Technology Data Exchange (ETDEWEB)

    Fiedler, Dorothea; Leung, Dennis H.; Raymond, Kenneth N.; Bergman, Robert G.

    2004-11-27

    Supramolecular chemistry represents a way to mimic enzyme reactivity by using specially designed container molecules. We have shown that a chiral self-assembled M{sub 4}L{sub 6} supramolecular tetrahedron can encapsulate a variety of cationic guests, with varying degrees of stereoselectivity. Reactive iridium guests can be encapsulated and the C-H bond activation of aldehydes occurs, with the host cavity controlling the ability of substrates to interact with the metal center based upon size and shape. In addition, the host container can act as a catalyst by itself. By restricting reaction space and preorganizing the substrates into reactive conformations, it accelerates the sigmatropic rearrangement of enammonium cations.

  9. Seeking for ultrashort "non-bonded" hydrogen-hydrogen contacts in some rigid hydrocarbons and their derivatives

    CERN Document Server

    Firouzi, Rohoullah

    2013-01-01

    In this communication a systematic computational survey is done on some rigid hydrocarbon skeletons and their chlorinated derivatives in order to seek for the so-called ultrashort "non-bonded" hydrogen-hydrogen contacts. It is demonstrated that upon a proper choice of the main hydrocarbons backbone and adding some bulky chlorine atoms instead of the original hydrogen atoms in parts of the employed hydrocarbons, the resulting strain triggers structural changes that yields ultrashort hydrogen-hydrogen contacts with distances as small as 1.38 Angstrom. Such ultrashort contacts is clearly less than the world record of a ultrashort non-bonded hydrogen-hydrogen contact, 1.56 Angstrom, very recently realized experimentally by Pascal and coworkers in in,in-bis(hydrosilane) [J. Am. Chem. Soc. 135, 13235 (2013)]. Accordingly, it is demonstrated that various backbones, e.g. half-cage pentacyclododecanes and tetracyclododecanes, after proper structural modifications, are capable to reveal ultrashort non-bonded hydrogen-h...

  10. Molecular recognition in homogeneous transition metal catalysis: a biomimetic strategy for high selectivity.

    Science.gov (United States)

    Das, Siddartha; Brudvig, Gary W; Crabtree, Robert H

    2008-01-28

    Traditional methods for selectivity control in homogeneous transition metal catalysis either employ steric effects in a binding pocket or chelate control. In a supramolecular strategy, encapsulation of the substrate can provide useful shape and size selectivity. A fully developed molecular recognition strategy involving hydrogen bonding or solvophobic forces has given almost completely regioselective functionalization of remote, unactivated C-H bonds.

  11. Deprotonated Dicarboxylic Acid Homodimers: Hydrogen Bonds and Atmospheric Implications

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Gao-Lei; Valiev, Marat; Wang, Xue-Bin

    2016-03-31

    Dicarboxylic acids represent an important class of water-soluble organic compounds found in the atmosphere. In this work we are studying properties of dicarboxylic acid homodimer complexes (HO2(CH2)nCO2-[HO2(CH2)nCO2H], n = 0-12), as potentially important intermediates in aerosol formation processes. Our approach is based on experimental data from negative ion photoelectron spectra of the dimer complexes combined with updated measurements of the corresponding monomer species. These results are analyzed with quantum-mechanical calculations, which provide further information about equilibrium structures, thermochemical parameters associated with the complex formation, and evaporation rates. We find that upon formation of the dimer complexes the electron binding energies increase by 1.3–1.7 eV (30.0–39.2 kcal/mol), indicating increased stability of the dimerized complexes. Calculations indicate that these dimer complexes are characterized by the presence of strong intermolecular hydrogen bonds with high binding energies and are thermodynamically favorable to form with low evaporation rates. Comparison with previously studied HSO4-[HO2(CH2)2CO2H] complex (J. Phys. Chem. Lett. 2013, 4, 779-785) shows that HO2(CH2)2CO2-[HO2(CH2)2CO2H] has very similar thermochemical properties. These results imply that dicarboxylic acids not only can contribute to the heterogeneous complexes formation involving sulfuric acid and dicarboxylic acids, but also can promote the formation of homogenous complexes by involving dicarboxylic acids themselves.

  12. Theoretical Studies in Heterogenous Catalysis: Towards a Rational Design of Novel Catalysts for Hydrodesulfurization and Hydrogen Production

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez,J.A.; Liu, P.

    2008-10-01

    Traditionally, knowledge in heterogeneous catalysis has come through empirical research. Nowadays, there is a clear interest to change this since millions of dollars in products are generated every year in the chemical and petrochemical industries through catalytic processes. To obtain a fundamental knowledge of the factors that determine the activity of heterogeneous catalysts is a challenge for modern science since many of these systems are very complex in nature. In principle, when a molecule adsorbs on the surface of a heterogeneous catalyst, it can interact with a large number of bonding sites. It is known that the chemical properties of these bonding sites depend strongly on the chemical environment around them. Thus, there can be big variations in chemical reactivity when going from one region to another in the surface of a heterogeneous catalyst. A main objective is to understand how the structural and electronic properties of a surface affect the energetics for adsorption processes and the paths for dissociation and chemical reactions. In recent years, advances in instrumentation and experimental procedures have allowed a large series of detailed works on the surface chemistry of heterogeneous catalysts. In many cases, these experimental studies have shown interesting and unique phenomena. Theory is needed to unravel the basic interactions behind these phenomena and to provide a general framework for the interpretation of experimental results. Ideally, theoretical calculations based on density-functional theory have evolved to the point that one should be able to predict patterns in the activity of catalytic surfaces. As in the case of experimental techniques, no single theoretical approach is able to address the large diversity of phenomena occurring on a catalyst. Catalytic surfaces are usually modeled using either a finite cluster or a two-dimensionally periodic slab. Many articles have been published comparing the results of these two approaches. An

  13. Quantification of hyperconjugative effect on the proton donor X-H bond length changes in the red- and blueshifted hydrogen-bonded complexes

    Science.gov (United States)

    Zhou, Pan-Pan; Qiu, Wen-Yuan; Jin, Neng-Zhi

    2012-08-01

    A whole dataset containing 55 hydrogen bonds were studied at the MP2/aug-cc-pVTZ level of theory. The changes of geometries and stretching vibrational frequencies show that there are 31 redshifted and 24 blueshifted hydrogen-bonded complexes. Natural bond orbital analysis was carried out at the B3LYP/aug-cc-pVTZ level of theory to obtain the electron densities in the bonding and antibonding orbitals of the proton donor X-H bond, which are closely associated with its bond length. Based on their relationship, a generally applicable method considering both the electron densities in the bonding and antibonding orbitals of the proton donor X-H bond has been developed to quantitatively describe the hyperconjugative effect on the X-H bond length changes in these hydrogen-bonded complexes.

  14. Role of hydrogen bonding in solubility of poly(N-isopropylacrylamide) brushes in sodium halide solutions

    Institute of Scientific and Technical Information of China (English)

    赵新军; 高志福

    2016-01-01

    By employing molecular theory, we systematically investigate the shift of solubility of poly(N-isopropylacrylamide) (PNIPAM) brushes in sodium halide solutions. After considering PNIPAM–water hydrogen bonds, water–anion hydro-gen bonds, and PNIPAM–anion bonds and their explicit coupling to the PNIPAM conformations, we find that increasing temperature lowers the solubility of PNIPAM, and results in a collapse of the layer at high enough temperatures. The combination of the three types of bonds would yield a decrease in the solubility of PNIPAM following the Hofmeister se-ries:NaCl>NaBr>NaI. PNIPAM–water hydrogen bonds are affected by water–anion hydrogen bonds and PNIPAM–anion bonds. The coupling of polymer conformations and the competition among the three types of bonds are essential for de-scribing correctly a decrease in the solubility of PNIPAM brushes, which is determined by the free energy associated with the formation of the three types of bonds. Our results agree well with the experimental observations, and would be very im-portant for understanding the shift of the lower critical solution temperature of PNIPAM brushes following the Hofmeister series.

  15. Quantum delocalization of protons in the hydrogen bond network of an enzyme active site

    CERN Document Server

    Wang, Lu; Boxer, Steven G; Markland, Thomas E

    2015-01-01

    Enzymes utilize protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.

  16. Microwave Measurements of Maleimide and its Doubly Hydrogen Bonded Dimer with Formic ACID*

    Science.gov (United States)

    Pejlovas, Aaron M.; Kang, Lu; Kukolich, Stephen G.

    2016-06-01

    The microwave spectra were measured for the maleimide monomer and the maleimide-formic acid doubly hydrogen bonded dimer using a pulsed-beam Fourier transform microwave spectrometer. Many previously studied doubly hydrogen bonded dimers are formed between oxygen containing species, so it is important to also characterize and study other dimers containing nitrogen, as hydrogen bonding interactions with nitrogen are found in biological systems such as in DNA. The transition state of the dimer does not exhibit C_2_V symmetry, so the tunneling motion was not expected to be observed based on the symmetry, but it would be very important to also observe the tunneling process for an asymmetric dimer. Single-line b-type transitions were observed, so the tunneling motion was not observed in our microwave spectra. The hydrogen bond lengths were determined using a nonlinear least squares fitting program. *Supported by the NSF CHE-1057796

  17. Perturbation calculations on the variation of hydrogen---bond energies with intermolecular distance

    NARCIS (Netherlands)

    Duijneveldt-van de Rijdt, J.G.C.M. van; Duijneveldt, F.B. van

    1968-01-01

    In previous perturbation calculations on the hydrogen bond [6] the short-range repulsion was seriously underestimated. It is shown that this can be remedied by choosing a more realistic model system and using exact 3-centre integrals.

  18. Double hydrogen bond mediating self-assembly structure of cyanides on metal surface

    Science.gov (United States)

    Wang, Zhongping; Xiang, Feifei; Lu, Yan; Wei, Sheng; Li, Chao; Liu, Xiaoqing; Liu, Lacheng; Wang, Li

    2016-10-01

    Cyanides with different numbers of -C≡N, 1,2,4,5-Tetracyanobenzene (TCNB) and 2,3-Dicyanonaphthalene (2,3-DCN) deposited on Ag(111) and Ag(110) surfaces, have been investigated by room temperature scanning tunneling microscopy (RTSTM), respectively. High resolution STM images show double hydrogen bond is the main driving force to form variety of self-assembly structures, indicating the double hydrogen bond affects the electron distribution of cyanides and leads to a more stable structure with lower energy. In addition, the difference between Ag(111) and Ag(110) surfaces in their lattice structure induces a bigger assembly structural change of 2,3-DCN than that of 1,2,4,5-TCNB, which confirms the fact that the opposite double hydrogen bond formation formed by 1,2,4,5-TCNB is more stable than the neighboring double hydrogen bond formation formed by molecule 2,3-DCN.

  19. Theoretical Chemistry Study of the Hydrogen-bonded Interaction between Acylamine and Chloromethane Compounds

    Institute of Scientific and Technical Information of China (English)

    GE Qing-Yu; WANG Hai-Jun; CHEN Jian-Hua

    2005-01-01

    The hydrogen-bonded interaction between acylamine and chloromethane was studied using theoretical calculation methods. Looking the interaction system as a hydrogen-bonded complex, the geometric optimization of the interaction system was performed with HF and B3LYP methods at 6-311++G** level. Stable structures of these complexes were obtained. Binding energies and some other physical chemistry parameters of them were computed and compared. According to the calculation results, it can be identified that DMA (DMF or DEF) can form stable complex with chloromethane by the hydrogen-bonded interaction between them. The stable orders of these hydrogen-bonded complexes were obtained and described as: DMF-CHCl3>DMF-CH2Cl2>DMF-CH3Cl, DEF-CHCl3>DEF-CH2Cl2>DEF-CH3Cl, DMA-CHCl3>DMA-CH2Cl2>DMA-CH3Cl, respectively.

  20. Hydrogen bonding in the crystal structure of the molecular salt of pyrazole-pyrazolium picrate.

    Science.gov (United States)

    Su, Ping; Song, Xue-Gang; Sun, Ren-Qiang; Xu, Xing-Man

    2016-06-01

    The asymmetric unit of the title organic salt [systematic name: 1H-pyrazol-2-ium 2,4,6-tri-nitro-phenolate-1H-pyrazole (1/1)], H(C3H4N2)2 (+)·C6H2N3O7 (-), consists of one picrate anion and one hydrogen-bonded dimer of a pyrazolium monocation. The H atom involved in the dimer N-H⋯N hydrogen bond is disordered over both symmetry-unique pyrazole mol-ecules with occupancies of 0.52 (5) and 0.48 (5). In the crystal, the component ions are linked into chains along [100] by two different bifurcated N-H⋯(O,O) hydrogen bonds. In addition, weak C-H⋯O hydrogen bonds link inversion-related chains, forming columns along [100].

  1. Water dynamics: relation between hydrogen bond bifurcations, molecular jumps, local density & hydrophobicity.

    Science.gov (United States)

    Titantah, John Tatini; Karttunen, Mikko

    2013-10-21

    Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. We employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total simulation time was ≈ 2 ns. Both bulk water and water in the presence of a small hydrophobic molecule were simulated. We show that large-angle jumps and bond bifurcations are fundamental properties of water dynamics and that they are intimately coupled to both local density and hydrogen bond strength oscillations in scales from about 60 to a few hundred femtoseconds: Local density differences are the driving force for bond bifurcations and the consequent large-angle jumps. The jumps are intimately connected to the recently predicted hydrogen bond energy asymmetry. Our analysis also appears to confirm the existence of the so-called negativity track provided by the lone pairs of electrons on the oxygen atom to enable water rotation.

  2. Theoretical Study on Measure of Hydrogen Bonding Strength: R-C≡N…pyrrole Complexes

    Institute of Scientific and Technical Information of China (English)

    史福强; 安静仪; 俞稼镛

    2005-01-01

    The R-C≡N…pyrrole (R=H, CH3, CH2F, CHF2, CF3, NH2, BH2, OH, F, CH2Cl, CHCl2, CCl3, Li, Na) complexes were considered as the simple sample for measure of hydrogen bonding strength. Density functional theory B3LYP/6-311 + + G** level was applied to the optimization of geometries of complexes and monomers. Measure of hydrogen bonding strength based on geometrical and topological parameters, which were derived from the AIM theory, was analyzed. Additionally, natural bond orbital (NBO) analysis and frequency calculations were performed.From the computation results it was found that the electronic density at N-H bond critical points was also strictly correlated with the hydrogen bonding strength.

  3. SN2-like reaction in hydrogen-bonded complexes: a theoretical study.

    Science.gov (United States)

    Wang, Weizhou; Zhang, Yu; Huang, Kaixun

    2005-10-20

    S(N)2-like reactions in hydrogen-bonded complexes have been investigated in this paper at a correlated MP2(full)/6-311++G(3df,3pd) level, employing FH...NH(3)...HF and ClH...NH(3)...HCl as model systems. The unconventional F(Cl)-H...N noncovalent bond and the conventional F(Cl)-H...N hydrogen bond can coexist in one complex which is taken as the reactant of the S(N)2-like reaction. The S(N)2-like reaction occurs along with the inversion of NH(3) and the interconversion of the unconventional F(Cl)-H...N noncovalent bond and the conventional F(Cl)-H...N hydrogen bond. In comparison with that of the isolated NH(3), the inversion barriers of the two complexes both are significantly reduced. The effect of carbon nanotube confinement on the inversion barrier is also discussed.

  4. Statistical theory for hydrogen bonding fluid system of AaDd type (I): The geometrical phase transition

    Institute of Scientific and Technical Information of China (English)

    WANG Haijun; HONG Xiaozhong; GU Fang; BA Xinwu

    2006-01-01

    The influence of hydrogen bonds on the physical and chemical properties of hydrogen bonding fluid system of AaDd type is investigated from two viewpoints by the principle of statistical mechanics. In detail, we proposed two new ways that can be used to obtain the equilibrium size distribution of the hydrogen bonding clusters, and derived the analytical expression of a relationship between the hydrogen bonding free energy and hydrogen bonding degree. For the nonlinear hydrogen bonding systems, it is shown that the sol-gel phase transition can take place under proper conditions, which is further proven to be a kind of geometrical phase transition rather than a thermodynamic one. Moreover, several problems associated with the geometrical phase transition and liquid-solid phase transition in nonlinear hydrogen bonding systems are discussed.

  5. Fine Structure of Hydrogen Bond in Cholic Acid Revealed by 2DIR Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Based on cryogenic FT-IR spectroscopic studies of hydrogen bonds in cholic acid, two-dimensional FT-IR spectroscopy was applied to enhance our understanding of the hydrogen bonds of cholic acid. Fine spectral structures were revealed by asynchronous 2D FT-IR spectra. The co-relationship among various bands was discussed according to the synchronous 2D FT-IR spectrum.

  6. Infrared spectra of hydrogen-bonded salicylic acid and its derivatives : Salicylic acid and acetylsalicylic acid

    Science.gov (United States)

    Wójcik, Marek J.

    1981-11-01

    Infrared spectra of hydrogen-bonded salicylic acid, O-deutero-salicylic acid and acetylsalicylic acid crystals have been studied experimentally and theoretically. Interpretation of these spectra was based on the Witkowski-Maréchal model. Semi-quantitative agreement between experimental and theoretical spectra can be achieved with the simplest form of this model, with values of interaction parameters transferable for equivalent intermolecular hydrogen bonds.

  7. Pressure-induced localisation of the hydrogen-bond network in KOH-VI

    Energy Technology Data Exchange (ETDEWEB)

    Hermann, Andreas, E-mail: a.hermann@ed.ac.uk; Nelmes, Richard J.; Loveday, John S. [Centre for Science at Extreme Conditions and SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom); Guthrie, Malcolm [Centre for Science at Extreme Conditions and SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom); European Spallation Source AB, P.O. Box 176, SE-22100 Lund (Sweden)

    2015-12-28

    Using a combination of ab initio crystal structure prediction and neutron diffraction techniques, we have solved the full structure of KOH-VI at 7 GPa. Rather than being orthorhombic and proton-ordered as had previously be proposed, we find that this high-pressure phase of potassium hydroxide is tetragonal (space group I4/mmm) and proton disordered. It has an unusual hydrogen bond topology, where the hydroxyl groups form isolated hydrogen-bonded square planar (OH){sub 4} units. This structure is stable above 6.5 GPa and, despite being macroscopically proton-disordered, local ice rules enforce microscopic order of the hydrogen bonds. We suggest the use of this novel type of structure to study concerted proton tunneling in the solid state, while the topology of the hydrogen bond network could conceivably be exploited in data storage applications based solely on the manipulations of hydrogen bonds. The unusual localisation of the hydrogen bond network under applied pressure is found to be favored by a more compact packing of the constituents in a distorted cesium chloride structure.

  8. Role of bonding mechanisms during transfer hydrogenation reaction on heterogeneous catalysts of platinum nanoparticles supported on zinc oxide nanorods

    Science.gov (United States)

    Al-Alawi, Reem A.; Laxman, Karthik; Dastgir, Sarim; Dutta, Joydeep

    2016-07-01

    For supported heterogeneous catalysis, the interface between a metal nanoparticle and the support plays an important role. In this work the dependency of the catalytic efficiency on the bonding chemistry of platinum nanoparticles supported on zinc oxide (ZnO) nanorods is studied. Platinum nanoparticles were deposited on ZnO nanorods (ZnO NR) using thermal and photochemical processes and the effects on the size, distribution, density and chemical state of the metal nanoparticles upon the catalytic activities are presented. The obtained results indicate that the bonding at Pt-ZnO interface depends on the deposition scheme which can be utilized to modulate the surface chemistry and thus the activity of the supported catalysts. Additionally, uniform distribution of metal on the catalyst support was observed to be more important than the loading density. It is also found that oxidized platinum Pt(IV) (platinum hydroxide) provided a more suitable surface for enhancing the transfer hydrogenation reaction of cyclohexanone with isopropanol compared to zero valent platinum. Photochemically synthesized ZnO supported nanocatalysts were efficient and potentially viable for upscaling to industrial applications.

  9. Infrared spectral evidence and DFT calculations of hydrogen-bonding and molecular structures of acetogenins

    Science.gov (United States)

    Afonso, Sabrina; Silva, Fabiano B.; Silva, Arnaldo F.; Scarminio, Ieda S.; Bruns, Roy E.

    2017-02-01

    FTIR spectra have been measured for 31 different five component - simplex centroid design solvent mixture extracts of shaded and sun-exposed Annonaceous leaves harvested in all four seasons. The spectral frequencies are characteristic of anonnaceous acetogenins known to be a major component of these leaves. Osbnd H stretching spectral bands in the 3100-3600 cm-1 region provide evidence of notable intensity changes for the shaded and sun-exposed leaves. Chemometric principal component analysis involving 264 spectra show that shaded samples tend to have more intense Osbnd H stretching bands than those grown in the sun. B3LYP density functional calculations indicate significant Osbnd H stretching band changes in this region owing to hydrogen bond formation. Weak Osbnd H intensity enhancements, around 40 km mol-1, occur when an Osbnd H group forms a hydrogen bond with the oxygen atom of an adjacent tetrahydrofuran ring oxygen atom. Much more intense enhancements, 400-500 km mol-1, are predicted to occur for acetogenins with two tetrahydrofuran rings for which the Osbnd H group hydrogen bonds with its fartherest removed tetrahydrofuran ring oxygen. Whereas weak or moderate H-bond stretching intensities are obtained for acetogenins with slightly bent carbon chain structures the strongest hydrogen bond intensities are calculated for molecules with a 45° V-type backbone structure. These important structural modifications as well as significant changes in bond lengths and angles owing to hydrogen bonding are detailed.

  10. Isotopic fractionation in proteins as a measure of hydrogen bond length

    Energy Technology Data Exchange (ETDEWEB)

    McKenzie, Ross H., E-mail: r.mckenzie@uq.edu.au [School of Mathematics and Physics, University of Queensland, Brisbane 4072 (Australia); Athokpam, Bijyalaxmi; Ramesh, Sai G. [Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012 (India)

    2015-07-28

    If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent, it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor Φ is correlated with the strength of the intramolecular hydrogen bonds. This correlation has been used to determine the length of the H-bonds (donor-acceptor separation) in a diverse range of enzymes and has been argued to support the existence of short low-barrier H-bonds. Starting with a potential energy surface based on a simple diabatic state model for H-bonds, we calculate Φ as a function of the proton donor-acceptor distance R. For numerical results, we use a parameterization of the model for symmetric O–H⋯O bonds [R. H. McKenzie, Chem. Phys. Lett. 535, 196 (2012)]. We consider the relative contributions of the O–H stretch vibration, O–H bend vibrations (both in plane and out of plane), tunneling splitting effects at finite temperature, and the secondary geometric isotope effect. We compare our total Φ as a function of R with NMR experimental results for enzymes, and in particular with an earlier model parametrization Φ(R), used previously to determine bond lengths.

  11. Unified description of hydrogen bonding by a two-state effective Hamiltonian

    CERN Document Server

    McKenzie, Ross H

    2011-01-01

    An effective Hamiltonian is considered for hydrogen bonding between two molecules due to the quantum mechanical interaction between the orbitals of the H-atom and the donor and acceptor atoms in the molecules. The Hamiltonian acts on two diabatic states and has a simple chemically motivated form for its matrix elements. The model gives insight into the "H-bond puzzle", describes different classes of bonds, and empirical correlations between the donor-acceptor distance $R$ and binding energies, bond lengths, and the softening of vibrational frequencies. A key prediction is the UV photo-dissociation of H-bonded complexes via an excited electronic state with an exalted vibrational frequency.

  12. Hydrogen Bonding: Between Strengthening the Crystal Packing and Improving Solubility of Three Haloperidol Derivatives

    Directory of Open Access Journals (Sweden)

    Hardeep Saluja

    2016-06-01

    Full Text Available The purpose of this study is to confirm the impact of polar functional groups on inter and intra-molecular hydrogen bonding in haloperidol (HP and droperidol (DP and, hence, their effects on dissolution using a new approach. To confirm our theory, a new molecule: deshydroxy-haloperidol (DHP was designed and its synthesis was requested from a contract laboratory. The molecule was then studied and compared to DP and HP. Unlike DHP, both the HP and DP molecules have hydrogen donor groups, therefore, DHP was used to confirm the relative effects of the hydrogen donor group on solubility and crystal packing. The solid dispersions of the three structurally related molecules: HP, DP, and DHP were prepared using PVPK30, and characterized using XRPD and IR. A comparative dissolution study was carried out in aqueous medium. The absence of a hydrogen bonding donor group in DHP resulted in an unexpected increase in its aqueous solubility and dissolution rate from solid dispersion, which is attributed to weaker crystal pack. The increased dissolution rate of HP and DP from solid dispersions is attributed to drug-polymer hydrogen bonding that interferes with the drug-drug intermolecular hydrogen bonding and provides thermodynamic stability of the dispersed drug molecules. The drug-drug intermolecular hydrogen bond is the driving force for precipitation and crystal packing.

  13. Co-existing Intermolecular Halogen Bonding and Hydrogen Bonding in the Compound Trans-5,10-bis(1-bromodifluoroacetyl-1-ethoxycarbonyl-methylidene)thianthrene

    Institute of Scientific and Technical Information of China (English)

    ZHU Shi-Fa祝诗发; ZHU Shi-Zheng朱士正; LIAO Yuan-Xi廖远熹; HUANG Chao-Feng黄超峰; LI Zhan-Ting黎占亭

    2004-01-01

    Trans-5,10-bis(1-bromodifluoroacetyl-1-ethoxycarbonyl-methylidene)thianthrene (1b) was prepared from the reaction of BrCF2COC(N2)CO2Et with thianthrene. X-ray single crystal diffraction analysis showed that the intermolecular halogen bonding and hydrogen bonding coexisted in this compound. The bromine atom acted as an electron acceptor in the halogen bond and an electron donor in the hydrogen bond. It is the first example that the bromine atom acted as such a dual role in the hydrogen and halogen bond.

  14. Hydrogen-bond dynamics in water explored by heterodyne-detected photon echo

    NARCIS (Netherlands)

    Yeremenko, S; Pshenichnikov, MS; Wiersma, DA; Pshenichnikov, Maxim S.

    2003-01-01

    Results of heterodyne-detected photon echo experiments on the OH stretching mode of water are reported and discussed. Two vibrational dynamical processes with time constants of 130 and 900 fs were identified. The former is attributed to bond breaking dynamics of a single hydrogen bond, the latter to

  15. Gas phase detection of the NH-P hydrogen bond and importance of secondary interactions

    DEFF Research Database (Denmark)

    Møller, Kristian Holten; Hansen, Anne Schou; Kjærgaard, Henrik Grum

    2015-01-01

    We have observed the NH···P hydrogen bond in a gas phase complex. The bond is identified in the dimethylamine-trimethylphosphine complex by a red shift of the fundamental NH-stretching frequency observed using Fourier transform infrared spectroscopy (FT-IR). On the basis of the measured NH...

  16. Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis.

    Science.gov (United States)

    Roca, Maite; De Maria, Leonardo; Wodak, Shoshana J; Moliner, Vicente; Tuñón, Iñaki; Giraldo, Jesús

    2008-02-01

    To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the guanosine glycosidic (Gchi) angle was used as the reaction coordinate, and computations were performed on two GpA ionic species: protonated (neutral) or deprotonated (negatively charged) guanosine ribose O2 '. Similar energetic profiles featuring two minima corresponding to the anti and syn Gchi regions were obtained for both ionic forms. For both forms the anti conformation was more stable than the syn, and barriers of approximately 4 kcal/mol were obtained for the anti --> syn transition. Structural analysis showed a remarkable sensitivity of the phosphate moiety to the conformation of the Gchi angle, suggesting a possible connection between this conformation and the mechanism of ribonucleotide cleavage. This hypothesis was confirmed by the second PMF calculations, for which the O2 '--P distance for the deprotonated GpA was used as reaction coordinate. The computations were performed from two selected starting points: the anti and syn minima determined in the first PMF study of the deprotonated guanosine ribose O2'. The simulations revealed that the O2 ' attack along the syn Gchi was more favorable than that along the anti Gchi: energetically, significantly lower barriers were obtained in the syn than in the anti conformation for the O--P bond formation; structurally, a lesser O2 '--P initial distance, and a better suited orientation for an in-line attack was observed in the syn relative to the anti conformation. These results are consistent with the catalytically competent conformation of barnase-ribonucleotide complex, which requires a guanine syn conformation of the substrate to enable abstraction of the ribose H2 ' proton by the general base Glu73, thereby suggesting a coupling between the reactive substrate conformation and enzyme structure

  17. Mechanical properties of a metal-organic framework containing hydrogen-bonded bifluoride linkers.

    Science.gov (United States)

    Li, Wei; Kiran, M S R N; Manson, Jamie L; Schlueter, John A; Thirumurugan, A; Ramamurty, U; Cheetham, Anthony K

    2013-05-18

    We report the mechanical properties of a framework structure, [Cu2F(HF)(HF2)(pyz)4][(SbF6)2]n (pyz = pyrazine), in which [Cu(pyz)2](2+) layers are pillared by HF2(-) anions containing the exceptionally strong F-H···F hydrogen bonds. Nanoindentation studies on single-crystals clearly demonstrate that such bonds are extremely robust and mechanically comparable with coordination bonds in this system.

  18. The quantum nature of the hydrogen bond: insight from path-integral molecular dynamics

    Science.gov (United States)

    Walker, Brent; Li, Xin-Zheng; Michaelides, Angelos

    2011-03-01

    Hydrogen (H) bonds are weak, generally intermolecular bonds, that hold together much of soft matter, the condensed phases of water, network liquids, and many ferroelectric crystals. The small mass of H means H-bonds are inherently quantum mechanical; effects such as zero point motion and tunneling should be considered, although often are not. In particular, a consistent picture of quantum nuclear effects on the strength of H-bonds and consequently the structure of H-bonded systems is still absent. Here, we report ab initio path-integral molecular dynamics studies on the quantum nature of the H-bond. Systematic examination of a range of H-bonded systems shows that quantum nuclei weaken weak H-bonds but strengthen relatively strong ones. This correlation arises from a competition between anharmonic intermolecular bond bending and intramolecular bond stretching. A simple rule of thumb enables predictions to be made for H-bonded bonded materials in general with merely classical knowledge (e.g. H-bond strength or H-bond length). Our work rationalizes the contrasting influence of quantum nuclear dynamics on a wide variety of materials, including liquid water and HF, and highlights the need for flexible molecules in force-field based studies of quantum nuclear dynamics.

  19. Catalysis of hydrolysis and nucleophilic substitution at the P-N bond of phosphoimidazolide-activated nucleotides in phosphate buffers

    Science.gov (United States)

    Kanavarioti, A.; Rosenbach, M. T.

    1991-01-01

    Phosphoimidazolide-activated derivatives of guanosine and cytidine 5'-monophosphates, henceforth called ImpN's, exhibit enhanced rates of degradation in the presence of aqueous inorganic phosphate in the range 4.0 phosphate. The first reaction results in the formation of nucleoside 5'-diphosphate and the second in nucleoside 5'-monophosphate. Analysis of the observed rates as well as the product ratios as a function of pH and phosphate concentration allow distinction between various mechanistic possibilities. The results show that both H2PO4- and HPO4(2-) participate in both hydrolysis and nucleophilic substitution. Statistically corrected biomolecular rate constants indicate that the dianion is 4 times more effective as a general base than the monoanion, and 8 times more effective as nucleophile. The low Bronsted value beta = 0.15 calculated for these phosphate species, presumed to act as general bases in facilitating water attack, is consistent with the fact that catalysis of the hydrolysis of the P-N bond in ImpN's has not been detected before. The beta nuc = 0.35 calculated for water, H2PO4-, HPO4(2-), and hydroxide acting as nucleophiles indicates a more associative transition state for nucleotidyl (O2POR- with R = nucleoside) transfers than that observed for phosphoryl (PO3(2-)) transfers (beta nuc = 0.25). With respect to the stability/reactivity of ImpN's under prebiotic conditions, our study shows that these materials would not suffer additional degradation due to inorganic phosphate, assuming the concentrations of phosphate, Pi, on prebiotic Earth were similar to those in the present oceans ([Pi] approximately 2.25 micromoles).

  20. Structural and medium effects on the reactions of the cumyloxyl radical with intramolecular hydrogen bonded phenols. The interplay between hydrogen-bonding and acid-base interactions on the hydrogen atom transfer reactivity and selectivity.

    Science.gov (United States)

    Salamone, Michela; Amorati, Riccardo; Menichetti, Stefano; Viglianisi, Caterina; Bietti, Massimo

    2014-07-03

    A time-resolved kinetic study on the reactions of the cumyloxyl radical (CumO(•)) with intramolecularly hydrogen bonded 2-(1-piperidinylmethyl)phenol (1) and 4-methoxy-2-(1-piperidinylmethyl)phenol (2) and with 4-methoxy-3-(1-piperidinylmethyl)phenol (3) has been carried out. In acetonitrile, intramolecular hydrogen bonding protects the phenolic O-H of 1 and 2 from attack by CumO(•) and hydrogen atom transfer (HAT) exclusively occurs from the C-H bonds that are α to the piperidine nitrogen (α-C-H bonds). With 3 HAT from both the phenolic O-H and the α-C-H bonds is observed. In the presence of TFA or Mg(ClO4)2, protonation or Mg(2+) complexation of the piperidine nitrogen removes the intramolecular hydrogen bond in 1 and 2 and strongly deactivates the α-C-H bonds of the three substrates. Under these conditions, HAT to CumO(•) exclusively occurs from the phenolic O-H group of 1-3. These results clearly show that in these systems the interplay between intramolecular hydrogen bonding and Brønsted and Lewis acid-base interactions can drastically influence both the HAT reactivity and selectivity. The possible implications of these findings are discussed in the framework of the important role played by tyrosyl radicals in biological systems.

  1. Assisted Tandem Catalysis : Metathesis Followed by Asymmetric Hydrogenation from a Single Ruthenium Source

    NARCIS (Netherlands)

    Renom-Carrasco, Marc; Gajewski, Piotr; Pignataro, Luca; de Vries, Johannes G.; Piarulli, Umberto; Gennari, Cesare; Lefort, Laurent

    2015-01-01

    Here we report the first example of a tandem metathesis-asymmetric hydrogenation protocol where the prochiral olefin generated by metathesis is hydrogenated with high enantioselectivity by an in situ formed chiral ruthenium catalyst. We show that either the ruthenium metathesis catalysts or the ruth

  2. An S-N2-model for proton transfer in hydrogen-bonded systems

    DEFF Research Database (Denmark)

    Kuznetsov, A.M.; Ulstrup, Jens

    2004-01-01

    A new mechanism of proton transfer in donor-acceptor complexes with long hydrogen bonds is suggested. The transition is regarded as totally adiabatic. Two closest water molecules that move synchronously by hindered translation to and from the reaction complex are crucial. The water molecules induce...... a shift of the proton from the donor to the acceptor with simultaneous breaking/formation of hydrogen bonds between these molecules and the proton donor and acceptor. Expressions for the activation barrier and kinetic hydrogen isotope effect are derived. The general scheme is illustrated with the use...... of model molecular potentials, and with reference to the excess proton conductivity in aqueous solution....

  3. Structural and theoretical investigations of short hydrogen bonds: neutron diffraction and plane-wave DFT calculations of urea phosphoric acid

    Science.gov (United States)

    Wilson, Chick C.; Morrison, Carole A.

    2002-08-01

    Low temperature neutron diffraction and high level computational methods have been applied to investigate the short hydrogen bond in urea-phosphoric acid. It is found that isolated molecule calculations predict a `normal' O-H⋯O hydrogen bond, in strong disagreement with the very short, 3 c-4 e hydrogen bond found from the neutron diffraction. Extending these calculations into a periodic environment using plane-wave DFT methods give much improved agreement with experiment, with a much shorter, stronger hydrogen bond, and significant elongation of the O-H `covalent' bond.

  4. A theoretical study of solvent effects on the characteristics of the intramolecular hydrogen bond in Droxidopa

    Indian Academy of Sciences (India)

    Mehdi Yoosefian; Hassan Karimi-Maleh; Afsaneh L Sanati

    2015-06-01

    The molecular structures and intramolecular hydrogen bond of Droxidopa have been investigated with density functional theory. It is found that strong hydrogen bonds (O–H…N and O…H–O) exist in the title compound. These hydrogen bonds play essential roles in determining conformational preferences and energy, which would have important effects in biological activity mechanisms that will strongly influence its characteristics in solution. A computational study of a representative number of actual and model structures was carried out in five solvents with different polarities and different types of interactions with solute molecules: water, ethanol, carbon tetrachloride, dimethyl sulfoxide, and tetrahydrofuran, utilizing the polarizable continuum model (PCM) model. The calculations were performed at the B3LYP/6-311++G(d,p) level of theory. In addition, the topological properties of the electron density distributions for O–H…N(O) intramolecular hydrogen bond were analyzed in terms of the Bader’s theory of atoms in molecules. Furthermore, the analyses of different hydrogen bonds in this molecule by quantum theory of natural bond orbital (NBO) methods support the density functional theory (DFT) results.

  5. Isotopic fractionation in proteins as a measure of hydrogen bond length

    CERN Document Server

    McKenzie, Ross H; Ramesh, Sai

    2015-01-01

    If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor $\\Phi$ is correlated with the strength of the intramolecular hydrogen bonds. This correlation has been used to determine the length of the H-bonds (donor-acceptor separation) in a diverse range of enzymes and has been argued to support the existence of short low-barrier H-bonds. Starting with a potential energy surface based on a simple diabatic state model for H-bonds we calculate $\\Phi$ as a function of the proton donor-acceptor distance $R$. For numerical results, we use a parameterization of the model for symmetric O-H.... O bonds. We consider the relative contributions of the O-H stretch vibration, O-H bend vibrations (both in plane and out of plane), tunnelling splitting effects at...

  6. The effect of intermolecular hydrogen bonding on the fluorescence of a bimetallic platinum complex.

    Science.gov (United States)

    Zhao, Guang-Jiu; Northrop, Brian H; Han, Ke-Li; Stang, Peter J

    2010-09-02

    The bimetallic platinum complexes are known as unique building blocks and arewidely utilized in the coordination-driven self-assembly of functionalized supramolecular metallacycles. Hence, photophysical study of the bimetallic platinum complexes will be very helpful for the understanding on the optical properties and further applications of coordination-driven self-assembled supramolecular metallacycles. Herein, we report steady-state and time-resolved spectroscopic experiments as well as quantum chemistry calculations to investigate the significant intermolecular hydrogen bonding effects on the intramolecular charge transfer (ICT) fluorescence of a bimetallic platinum compound 4,4'-bis(trans-Pt(PEt(3))(2)OTf)benzophenone 3 in solution. We demonstrated that the fluorescent state of compound 3 can be assigned as a metal-to-ligand charge transfer (MLCT) state. Moreover, it was observed that the formation of intermolecular hydrogen bonds can effectively lengthen the fluorescence lifetime of 3 in alcoholic solvents compared with that in hexane solvent. At the same time, the electronically excited states of 3 in solution are definitely changed by intermolecular hydrogen bonding interactions. As a consequence, we propose a new fluorescence modulation mechanism by hydrogen bonding to explain different fluorescence emissions of 3 in hydrogen-bonding solvents and nonhydrogen-bonding solvents.

  7. Is it homogeneous or heterogeneous catalysis derived from [RhCp*Cl2]2? In operando XAFS, kinetic, and crucial kinetic poisoning evidence for subnanometer Rh4 cluster-based benzene hydrogenation catalysis.

    Science.gov (United States)

    Bayram, Ercan; Linehan, John C; Fulton, John L; Roberts, John A S; Szymczak, Nathaniel K; Smurthwaite, Tricia D; Özkar, Saim; Balasubramanian, Mahalingam; Finke, Richard G

    2011-11-23

    Determining the true, kinetically dominant catalytically active species, in the classic benzene hydrogenation system pioneered by Maitlis and co-workers 34 years ago starting with [RhCp*Cl(2)](2) (Cp* = [η(5)-C(5)(CH(3))(5)]), has proven to be one of the most challenging case studies in the quest to distinguish single-metal-based "homogeneous" from polymetallic, "heterogeneous" catalysis. The reason, this study will show, is the previous failure to use the proper combination of: (i) in operando spectroscopy to determine the dominant form(s) of the precatalyst's mass under catalysis (i.e., operating) conditions, and then crucially also (ii) the previous lack of the necessary kinetic studies, catalysis being a "wholly kinetic phenomenon" as J. Halpern long ago noted. An important contribution from this study will be to reveal the power of quantitiative kinetic poisoning experiments for distinguishing single-metal, or in the present case subnanometer Rh(4) cluster-based catalysis, from larger, polymetallic Rh(0)(n) nanoparticle catalysis, at least under favorable conditions. The combined in operando X-ray absorption fine structure (XAFS) spectroscopy and kinetic evidence provide a compelling case for Rh(4)-based, with average stoichiometry "Rh(4)Cp*(2.4)Cl(4)H(c)", benzene hydrogenation catalysis in 2-propanol with added Et(3)N and at 100 °C and 50 atm initial H(2) pressure. The results also reveal, however, that if even ca. 1.4% of the total soluble Rh(0)(n) had formed nanoparticles, then those Rh(0)(n) nanoparticles would have been able to account for all the observed benzene hydrogenation catalytic rate (using commercial, ca. 2 nm, polyethyleneglycol-dodecylether hydrosol stabilized Rh(0)(n) nanoparticles as a model system). The results--especially the poisoning methodology developed and employed--are of significant, broader interest since determining the nature of the true catalyst continues to be a central, often vexing issue in any and all catalytic reactions

  8. Hydrogen bonding of formamide, urea, urea monoxide and their thio-analogs with water and homodimers

    Indian Academy of Sciences (India)

    Damanjit Kaur; Shweta Khanna

    2014-11-01

    Ab initio and DFT methods have been employed to study the hydrogen bonding ability of formamide, urea, urea monoxide, thioformamide, thiourea and thiourea monoxide with one water molecule and the homodimers of the selected molecules. The stabilization energies associated with themonohydrated adducts and homodimers’ formation were evaluated at B3LYP/6-311++G** and MP2/6-311++G∗∗ levels. The energies were corrected for zero-point vibrational energies and basis set superposition error using counterpoise method. Atoms in molecules study has been carried out in order to characterize the hydrogen bonds through the changes in electron density and laplacian of electron density. A natural energy decomposition and natural bond orbital analysis was performed to understand the nature of hydrogen bonding.

  9. Short Carboxylic Acid–Carboxylate Hydrogen Bonds Can Have Fully Localized Protons

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Jiusheng; Pozharski, Edwin; Wilson, Mark A.

    2017-01-17

    Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15–0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor–acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [O–O> = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O–O distance with increasing H-bond donor pKa. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid–carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.

  10. Delicate balance of hydrogen bonding forces in D-threoninol.

    Science.gov (United States)

    Vaquero-Vara, Vanesa; Zhang, Di; Dian, Brian C; Pratt, David W; Zwier, Timothy S

    2014-09-01

    The seven most stable conformers of D-threoninol (2(S)-amino-1,3(S)-butanediol), a template used for the synthesis of artificial nucleic acids, have been identified and characterized from their pure rotational transitions in the gas phase using chirped-pulse Fourier transform microwave spectroscopy. D-Threoninol is a close analogue of glycerol, differing by substitution of an NH2 group for OH on the C(β) carbon and by the presence of a terminal CH3 group that breaks the symmetry of the carbon framework. Of the seven observed structures, two are H-bonded cycles containing three H-bonds that differ in the direction of the H-bonds in the cycle. The other five are H-bonded chains containing OH···NH···OH H-bonds with different directions along the carbon framework and different dihedral angles along the chain. The two structural types (cycles and chains of H-bonds) are in surprisingly close energetic proximity. Comparison of the rotational constants with the calculated structures at the MP2/6-311++G(d,p) level of theory reveals systematic changes in the H-bond distances that reflect NH2 as a better H-bond acceptor and poorer donor, shrinking the H-bond distances by ∼0.2 Å in the former case and lengthening them by a corresponding amount in the latter. Thus revealed is the subtle effect of asymmetric substitution on the energy landscape of a simple molecule, likely to be important in living systems.

  11. Spectroscopic, DFT, and XRD Studies of Hydrogen Bonds in N-Unsubstituted 2-Aminobenzamides

    Directory of Open Access Journals (Sweden)

    Malose Jack Mphahlele

    2017-01-01

    Full Text Available The structures of the mono- and the dihalogenated N-unsubstituted 2-aminobenzamides were characterized by means of the spectroscopic (1H-NMR, UV-Vis, FT-IR, and FT-Raman and X-ray crystallographic techniques complemented with a density functional theory (DFT method. The hindered rotation of the C(O–NH2 single bond resulted in non-equivalence of the amide protons and therefore two distinct resonances of different chemical shift values in the 1H-NMR spectra of these compounds were observed. 2-Amino-5-bromobenzamide (ABB as a model confirmed the presence of strong intramolecular hydrogen bonds between oxygen and the amine hydrogen. However, intramolecular hydrogen bonding between the carbonyl oxygen and the amine protons was not observed in the solution phase due to a rapid exchange of these two protons with the solvent and fast rotation of the Ar–NH2 single bond. XRD also revealed the ability of the amide unit of these compounds to function as a hydrogen bond donor and acceptor simultaneously to form strong intermolecular hydrogen bonding between oxygen of one molecule and the NH moiety of the amine or amide group of the other molecule and between the amine nitrogen and the amide hydrogen of different molecules. DFT calculations using the B3LYP/6-311++G(d,p basis set revealed that the conformer (A with oxygen and 2-amine on the same side predominates possibly due to the formation of a six-membered intramolecular ring, which is assisted by hydrogen bonding as observed in the single crystal XRD structure.

  12. The two faces of hydrogen-bond strength on triple AAA-DDD arrays.

    Science.gov (United States)

    Lopez, Alfredo Henrique Duarte; Caramori, Giovanni Finoto; Coimbra, Daniel Fernando; Parreira, Renato Luis Tame; da Silva, Éder Henrique

    2013-12-01

    Systems that are connected through multiple hydrogen bonds are the cornerstone of molecular recognition processes in biology, and they are increasingly being employed in supramolecular chemistry, specifically in molecular self-assembly processes. For this reason, the effects of different substituents (NO2, CN, F, Cl, Br, OCH3 and NH2) on the electronic structure, and consequently on the magnitude of hydrogen bonds in triple AAA-DDD arrays (A=acceptor, D=donor) were evaluated in the light of topological [electron localization function (ELF) and quantum theory of atoms in molecules (QTAIM)], energetic [Su-Li energy-decomposition analysis (EDA) and natural bond orbital analysis (NBO)], and geometrical analysis. The results based on local H-bond descriptors (geometries, QTAIM, ELF, and NBO) indicate that substitutions with electron-withdrawing groups on the AAA module tend to strengthen, whereas electron-donating substituents tend to weaken the covalent character of the AAA-DDD intermolecular H-bonds, and also indicate that the magnitude of the effect is dependent on the position of substitution. In contrast, Su-Li EDA results show an opposite behavior when compared to local H-bond descriptors, indicating that electron-donating substituents tend to increase the magnitude of H-bonds in AAA-DDD arrays, and thus suggesting that the use of local H-bond descriptors describes the nature of H bonds only partially, not providing enough insight about the strength of such H bonds.

  13. Intramolecular Hydrogen Bonding in (2-Hydroxybenzoyl)benzoylmethane Enol

    DEFF Research Database (Denmark)

    Hansen, Bjarke Knud Vilster; Winther, Morten; Spanget-Larsen, Jens

    2014-01-01

    In the stable enol tautomer of the title compound (OHDBM), one carbonyl group is flanked by two β-hydroxy groups, giving rise to bifold intramolecular H-bonding. A similar situation is found in other β,β'-dihydroxy carbonyl compounds like chrysazin, anthralin, 2,2'-dihydroxybenzophenone, and the ......In the stable enol tautomer of the title compound (OHDBM), one carbonyl group is flanked by two β-hydroxy groups, giving rise to bifold intramolecular H-bonding. A similar situation is found in other β,β'-dihydroxy carbonyl compounds like chrysazin, anthralin, 2,2'-dihydroxybenzophenone......, and the dienol form of 1,3-dibenzoylacetone. But in these examples the two H-bonds are equivalent, while in the case of OHDBM they are chemically different, involving one enolic and one phenolic hydroxy group. OHDBM is thus an interesting model compound with two competing H-bonds to the same carbonyl group...

  14. A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase

    Energy Technology Data Exchange (ETDEWEB)

    Lyubimov, Artem Y. [Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Sinsheimer Laboratories, 1156 High Street, Santa Cruz, CA 95064 (United States); Chen, Lin; Sampson, Nicole S. [Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400 (United States); Vrielink, Alice, E-mail: alice.vrielink@uwa.edu.au [School of Biomedical, Biomolecular and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 (Australia); Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Sinsheimer Laboratories, 1156 High Street, Santa Cruz, CA 95064 (United States)

    2009-11-01

    The importance of active-site electrostatics for oxidative and reductive half-reactions in a redox flavoenzyme (cholesterol oxidase) have been investigated by a combination of biochemistry and atomic resolution crystallography. A detailed examination of active-site dynamics demonstrates that the oxidation of substrate and the re-oxidation of the flavin cofactor by molecular oxygen are linked by a single active-site asparagine. Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3β-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH⋯π interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall k{sub cat}. Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0 Å resolution) reveals significant perturbations in the active site. As predicted, Asp485 is oriented away from the flavin moiety, such that any stabilizing interaction with the reduced flavin is abolished. Met122 and Glu361 form unusual hydrogen bonds to the functional group of Asp485 and are displaced from the positions they occupy in the wild-type active site. The overall effect is to disrupt the stabilization of the reduced FAD cofactor during catalysis. Furthermore, a narrow transient channel that is shown to form when the wild-type Asn485 forms the NH⋯π interaction with FAD and that has been proposed to function as an access route of molecular oxygen, is not observed in either of the mutant structures, suggesting that the dynamics of the active site are altered.

  15. Theoretical study of bifurcated bent blue-shifted hydrogen bonds CH2…Y

    Institute of Scientific and Technical Information of China (English)

    LI AnYong

    2008-01-01

    Ab initio quantum chemistry methods were applied to study the bifurcated bent hydrogen bonds Y… MP2/6-311++G(2df,2p) levels. The results show that in each complex there are two equivalent natural bond orbital analysis shows that these blue-shifted H-bonds are caused by three factors: large rehybridization; small direct intermolecular hyperconjugation and larger indirect intermolecular hy-perconjugation; large decrease of intramolecular hyperconjugation. The topological analysis of elec-tron density shows that in each complex there are three intermolecular critical points: there is one bond critical point between the acceptor atom Y and each hydrogen, and there is a ring critical point inside the tetragon YHCH, so these interactions are exactly H-bonding.

  16. Heterogeneous and homogeneous catalysis for the hydrogenation of carboxylic acid derivatives: history, advances and future directions.

    Science.gov (United States)

    Pritchard, James; Filonenko, Georgy A; van Putten, Robbert; Hensen, Emiel J M; Pidko, Evgeny A

    2015-06-01

    The catalytic reduction of carboxylic acid derivatives has witnessed a rapid development in recent years. These reactions, involving molecular hydrogen as the reducing agent, can be promoted by heterogeneous and homogeneous catalysts. The milestone achievements and recent results by both approaches are discussed in this Review. In particular, we focus on the mechanistic aspects of the catalytic hydrogenation and highlight the bifunctional nature of the mechanism that is preferred for supported metal catalysts as well as homogeneous transition metal complexes.

  17. Production of hydrogen by electron transfer catalysis using conventional and photochemical means

    Science.gov (United States)

    Rillema, D. P.

    1981-03-01

    Alternate methods of generating hydrogen from the sulfuric acid thermal or electrochemical cycles are presented. A number of processes requiring chemical, electrochemical or photochemical methods are also presented. These include the design of potential photoelectrodes and photocatalytic membranes using Ru impregnated nafion tubing, and the design of experiments to study the catalyzed electrolytic formation of hydrogen and sulfuric acid from sulfur dioxide and water using quinones as catalysts. Experiments are carried out to determine the value of these approaches to energy conversion.

  18. Density functional theory, natural bond orbital and quantum theory of atoms in molecule analyses on the hydrogen bonding interactions in tryptophan-water complexes

    Indian Academy of Sciences (India)

    Xiqian Niu; Zhengguo Huang; Lingling Ma; Tingting Shen; Lingfei Guo

    2013-07-01

    The tryptophan-water (Trp-H2O) complexes formed by hydrogen bonding interactions were investigated at the B97XD/6-311++G(d,p) level. Five Trp-H2O complexes possessing various types of hydrogen bonds (H-bonds) were characterized by geometries, energies, vibrational frequencies. The nature of the H-bonds were characterized by the natural bond orbital (NBO) and the quantum theory of atoms in molecule (QTAIM) analyses as well. The intramolecular H-bond formed between the amino and carboxyl oxygen atom of tryptophan was retained in most of the complexes, and the cooperativity between the intra and intermolecular H-bonds exist in some complexes. The intramolecular H-bond and some intermolecular H-bonds are strong and have partial covalent character. The H-bonds formed between carboxyl and oxygen/nitrogen atoms are stronger than other H-bonds. The H-bonds involving methylene of tryptophan as H-donor are weak H-bonds. For all complexes,ele and ex makes major contributions to the total interaction energy (MP2), while disp is the smallest component of the interaction energy. Both hydrogen bonding interaction and structural deformation play important roles in the relative stabilities of the complexes. Regardless of strong H-bonds, the stabilities of some complexes are weakened by the serious structural deformations.

  19. Efficient hydrogen evolution catalysis using ternary pyrite-type cobalt phosphosulphide

    KAUST Repository

    Cabán-Acevedo, Miguel

    2015-09-14

    The scalable and sustainable production of hydrogen fuel through water splitting demands efficient and robust Earth-abundant catalysts for the hydrogen evolution reaction (HER). Building on promising metal compounds with high HER catalytic activity, such as pyrite structure cobalt disulphide (CoS 2), and substituting non-metal elements to tune the hydrogen adsorption free energy could lead to further improvements in catalytic activity. Here we present a combined theoretical and experimental study to establish ternary pyrite-type cobalt phosphosulphide (CoPS) as a high-performance Earth-abundant catalyst for electrochemical and photoelectrochemical hydrogen production. Nanostructured CoPS electrodes achieved a geometrical catalytic current density of 10 mA cm at overpotentials as low as 48mV, with outstanding long-term operational stability. Integrated photocathodes of CoPS on n -p-p silicon micropyramids achieved photocurrents up to 35 mA cm at 0 V versus the reversible hydrogen electrode (RHE), onset photovoltages as high as 450 mV versus RHE, and the most efficient solar-driven hydrogen generation from Earth-abundant systems.

  20. Atomic-Scale Mechanism for Hydrogenation of o-Cresol on Pt Catalysis

    Science.gov (United States)

    Li, Yaping; Liu, Zhimin; Xue, Wenhua; Crossley, Steven; Jentoft, Friederike; Wang, Sanwu

    Biofuels derived from lignocellulosic biomass have received significant attention lately due to increasing environmental concerns. With first-principles density-functional theory and ab initio molecular dynamic simulations, we investigated the atomic-scale mechanism of o-cresol hydrogenation on the Pt(111) surface. The formation of 2-methyl-cyclohexanone (the intermediate product) was found to involve two steps. The first step is the dehydrogenation, that is, the H atom in the hydroxyl group moves to the Pt surface. The second step is the hydrogenation, that is, the H atoms on Pt react with the carbon atoms in the aromatic ring. The first step involves a smaller barrier, suggesting that dehydrogenation occurs first, followed by hydrogenation of the ring. In particular, tautomerization is found to occur via a two-step process over the catalyst. On the other hand, 2-methyl-cyclohexanol (the final product) is produced through two paths. One is direct hydrogenation of the aromatic ring. Another pathway includes partial hydrogenation of the ring, dehydrogenation of -OH group, finally hydrogenation of remaining C atoms and the O atom. Our theoretical results agree well with the experimental observations. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of NERSC, XSEDE, TACC.

  1. Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution.

    Science.gov (United States)

    Desai, Bijoy J; Goto, Yuki; Cembran, Alessandro; Fedorov, Alexander A; Almo, Steven C; Gao, Jiali; Suga, Hiroaki; Gerlt, John A

    2014-10-21

    Hydrogen bonds between backbone amide groups of enzymes and their substrates are often observed, but their importance in substrate binding and/or catalysis is not easy to investigate experimentally. We describe the generation and kinetic characterization of a backbone amide to ester substitution in the orotidine 5'-monophosphate (OMP) decarboxylase from Methanobacter thermoautotrophicum (MtOMPDC) to determine the importance of a backbone amide-substrate hydrogen bond. The MtOMPDC-catalyzed reaction is characterized by a rate enhancement (∼10(17)) that is among the largest for enzyme-catalyzed reactions. The reaction proceeds through a vinyl anion intermediate that may be stabilized by hydrogen bonding interaction between the backbone amide of a conserved active site serine residue (Ser-127) and oxygen (O4) of the pyrimidine moiety and/or electrostatic interactions with the conserved general acidic lysine (Lys-72). In vitro translation in conjunction with amber suppression using an orthogonal amber tRNA charged with L-glycerate ((HO)S) was used to generate the ester backbone substitution (S127(HO)S). With 5-fluoro OMP (FOMP) as substrate, the amide to ester substitution increased the value of Km by ∼1.5-fold and decreased the value of kcat by ∼50-fold. We conclude that (i) the hydrogen bond between the backbone amide of Ser-127 and O4 of the pyrimidine moiety contributes a modest factor (∼10(2)) to the 10(17) rate enhancement and (ii) the stabilization of the anionic intermediate is accomplished by electrostatic interactions, including its proximity of Lys-72. These conclusions are in good agreement with predictions obtained from hybrid quantum mechanical/molecular mechanical calculations.

  2. Hydrogen-bond-dynamics-based switching of conductivity and magnetism: a phase transition caused by deuterium and electron transfer in a hydrogen-bonded purely organic conductor crystal.

    Science.gov (United States)

    Ueda, Akira; Yamada, Shota; Isono, Takayuki; Kamo, Hiromichi; Nakao, Akiko; Kumai, Reiji; Nakao, Hironori; Murakami, Youichi; Yamamoto, Kaoru; Nishio, Yutaka; Mori, Hatsumi

    2014-08-27

    A hydrogen bond (H-bond) is one of the most fundamental and important noncovalent interactions in chemistry, biology, physics, and all other molecular sciences. Especially, the dynamics of a proton or a hydrogen atom in the H-bond has attracted increasing attention, because it plays a crucial role in (bio)chemical reactions and some physical properties, such as dielectricity and proton conductivity. Here we report unprecedented H-bond-dynamics-based switching of electrical conductivity and magnetism in a H-bonded purely organic conductor crystal, κ-D3(Cat-EDT-TTF)2 (abbreviated as κ-D). This novel crystal κ-D, a deuterated analogue of κ-H3(Cat-EDT-TTF)2 (abbreviated as κ-H), is composed only of a H-bonded molecular unit, in which two crystallographically equivalent catechol-fused ethylenedithiotetrathiafulvalene (Cat-EDT-TTF) skeletons with a +0.5 charge are linked by a symmetric anionic [O···D···O](-1)-type strong H-bond. Although the deuterated and parent hydrogen systems, κ-D and κ-H, are isostructural paramagnetic semiconductors with a dimer-Mott-type electronic structure at room temperature (space group: C2/c), only κ-D undergoes a phase transition at 185 K, to change to a nonmagnetic insulator with a charge-ordered electronic structure (space group: P1). The X-ray crystal structure analysis demonstrates that this dramatic switching of the electronic structure and physical properties originates from deuterium transfer or displacement within the H-bond accompanied by electron transfer between the Cat-EDT-TTF π-systems, proving that the H-bonded deuterium dynamics and the conducting TTF π-electron are cooperatively coupled. Furthermore, the reason why this unique phase transition occurs only in κ-D is qualitatively discussed in terms of the H/D isotope effect on the H-bond geometry and potential energy curve.

  3. Isolation of Cellulose Nanofibers: Effect of Biotreatment on Hydrogen Bonding Network in Wood Fibers

    Directory of Open Access Journals (Sweden)

    Sreekumar Janardhnan

    2011-01-01

    Full Text Available The use of cellulose nanofibres as high-strength reinforcement in nano-biocomposites is very enthusiastically being explored due to their biodegradability, renewability, and high specific strength properties. Cellulose, through a regular network of inter- and intramolecular hydrogen bonds, is organized into perfect stereoregular configuration called microfibrils which further aggregate to different levels to form the fibre. Intermolecular hydrogen bonding at various levels, especially at the elementary level, is the major binding force that one need to overcome to reverse engineer these fibres into their microfibrillar level. This paper briefly describes a novel enzymatic fibre pretreatment developed to facilitate the isolation of cellulose microfibrils and explores effectiveness of biotreatment on the intermolecular and intramolecular hydrogen bonding in the fiber. Bleached Kraft Softwood Pulp was treated with a fungus (OS1 isolated from elm tree infected with Dutch elm disease. Cellulose microfibrils were isolated from these treated fibers by high-shear refining. The % yield of nanofibres and their diameter distribution (<50 nm isolated from the bio-treated fibers indicated a substantial increase compared to those isolated from untreated fibers. FT-IR spectral analysis indicated a reduction in the density of intermolecular and intramolecular hydrogen bonding within the fiber. X-ray spectrometry indicated a reduction in the crystallinity. Hydrogen bond-specific enzyme and its application in the isolation of new generation cellulose nano-fibers can be a huge leap forward in the field of nano-biocomposites.

  4. Self-assembly of hydrogen-bonded two-dimensional quasicrystals

    Science.gov (United States)

    Wasio, Natalie A.; Quardokus, Rebecca C.; Forrest, Ryan P.; Lent, Craig S.; Corcelli, Steven A.; Christie, John A.; Henderson, Kenneth W.; Kandel, S. Alex

    2014-03-01

    The process of molecular self-assembly on solid surfaces is essentially one of crystallization in two dimensions, and the structures that result depend on the interplay between intermolecular forces and the interaction between adsorbates and the underlying substrate. Because a single hydrogen bond typically has an energy between 15 and 35 kilojoules per mole, hydrogen bonding can be a strong driver of molecular assembly; this is apparent from the dominant role of hydrogen bonding in nucleic-acid base pairing, as well as in the secondary structure of proteins. Carboxylic acid functional groups, which provide two hydrogen bonds, are particularly promising and reliable in creating and maintaining surface order, and self-assembled monolayers of benzoic acids produce structure that depends on the number and relative placement of carboxylic acid groups. Here we use scanning tunnelling microscopy to study self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH), and find that, rather than producing dimeric or linear structures typical of carboxylic acids, FcCOOH forms highly unusual cyclic hydrogen-bonded pentamers, which combine with simultaneously formed FcCOOH dimers to form two-dimensional quasicrystallites that exhibit local five-fold symmetry and maintain translational and rotational order (without periodicity) for distances of more than 400 ångströms.

  5. Calculation of Bond-length, Bond-energy and Force Constant of Hydrogen Molecule by Classical Mechanics

    Institute of Scientific and Technical Information of China (English)

    ChenJing

    2004-01-01

    Until recently the hydrogen molecule structural parameters are calculated with the methods of quantum mechanics. To achieve results close to experimental values, the wave function used is complicated and has no clear physical meaning. Because the distribution of the electron probability density is a statistical rule, the macro-time has actually been used in the concept on a electron cloud graph. Here are obtained three formulas with a classical mechanics method on the bond-length re , bond-energy De and force constant k of the ground state hydrogen molecule, which have a clear physical meaning but no artificial parameters, and compared with experimental values, the relative errors are respectively less than 1% , 2% and 4% .

  6. The discovery of the hydrogen bond from p-Nitrothiophenol by Raman spectroscopy: Guideline for the thioalcohol molecule recognition tool

    Science.gov (United States)

    Ling, Yun; Xie, Wen Chang; Liu, Guo Kun; Yan, Run Wen; Wu, De Yin; Tang, Jing

    2016-01-01

    Inter- and intra- molecular hydrogen bonding plays important role in determining molecular structure, physical and chemical properties, which may be easily ignored for molecules with a non-typical hydrogen bonding structure. We demonstrated in this paper that the hydrogen bonding is responsible for the different Raman spectra in solid and solution states of p-Nitrothiophenol (PNTP). The consistence of the theoretical calculation and experiment reveals that the intermolecular hydrogen bonding yields an octatomic ring structure (8) of PNTP in the solid state, confirmed by the characteristic S-H---O stretching vibration mode at 2550 cm−1; when it comes to the solution state, the breakage of hydrogen bond of S-H---O induced the S-H stretching vibration at 2590 cm−1. Our findings may provide a simple and fast method for identifying the intermolecular hydrogen bonding. PMID:27659311

  7. Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability

    Energy Technology Data Exchange (ETDEWEB)

    Sigala, Paul A.; Ruben, Eliza A.; Liu, Corey W.; Piccoli, Paula M. B.; Hohenstein, Edward G.; Martinez, Todd J.; Schultz, Arthur J.; Herschiag, Daniel

    2015-05-06

    Hydrogen bonds profoundly influence the architecture and activity of biological macromolecules. Deep appreciation of hydrogen bond contributions to biomolecular function thus requires a detailed understanding of hydrogen bond structure and energetics and the relationship between these properties. Hydrogen bond formation energies (Delta G(f)) are enormously more favorable in aprotic solvents than in water, and two classes of contributing factors have been proposed to explain this energetic difference, focusing respectively on the isolated and hydrogen-bonded species: (I) water stabilizes the dissociated donor and acceptor groups much better than aprotic solvents, thereby reducing the driving force for hydrogen bond formation; and (II) water lengthens hydrogen bonds compared to aprotic environments, thereby decreasing the potential energy within the hydrogen bond. Each model has been proposed to provide a dominant contribution to Delta G(f), but incisive tests that distinguish the importance of these contributions are lacking. Here we directly test the structural basis of model II. Neutron crystallography, NMR spectroscopy, and quantum mechanical calculations demonstrate that O-H center dot center dot center dot O hydrogen bonds in crystals, chloroform, acetone, and water have nearly identical lengths and very similar potential energy surfaces despite Delta G(f) differences >8 kcal/mol across these solvents. These results rule out a substantial contribution from solvent-dependent differences in hydrogen bond structure and potential energy after association (model II) and thus support the conclusion that differences in hydrogen bond Delta G(f) are predominantly determined by solvent interactions with the dissociated groups (model I). These findings advance our understanding of universal hydrogen-bonding interactions and have important implications for biology and engineering.

  8. Complexation of two non-fully hydrogen bonded aromatic hydrazide heptamers toward n-octyl-α-L-glucopyranoside in chloroform

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Two aromatic hydrazide haptamers have been prepared,with both consisting of two hydrogen bonded folded segments. Compared to their fully hydrogen bonded analogues,the flexibility of their backbones increases due to lack of one or two intramolecular hydrogen bonds at the middle aromatic unit. (2D) 1H NMR,circular dichroism and fluorescent studies revealed that both oligomers moderately complex n-octyl-α-L-glucopyranoside in chloroform.

  9. Fracture toughness of hydroxide catalysis bonds between silicon carbide and Zerodur low thermal expansion glass-ceramic

    NARCIS (Netherlands)

    Ende, D.A. van den; Gubbels, G.H.M.

    2014-01-01

    In many optical and precision engineering applications, low thermal distortion materials need to be bonded together reliably. Since high temperature bonding process ultimately introduce stresses in the bond, rendering it dimensionally instable, room temperature or near room temperature processes are

  10. Energy decomposition analysis of cation-π, metal ion-lone pair, hydrogen bonded, charge-assisted hydrogen bonded, and π-π interactions.

    Science.gov (United States)

    Sharma, Bhaskar; Srivastava, Hemant Kumar; Gayatri, Gaddamanugu; Sastry, Garikapati Narahari

    2015-03-30

    This study probes the nature of noncovalent interactions, such as cation-π, metal ion-lone pair (M-LP), hydrogen bonding (HB), charge-assisted hydrogen bonding (CAHB), and π-π interactions, using energy decomposition schemes-density functional theory (DFT)-symmetry-adapted perturbation theory and reduced variational space. Among cation-π complexes, the polarization and electrostatic components are the major contributors to the interaction energy (IE) for metal ion-π complexes, while for onium ion-π complexes (NH4+, PH4+, OH3+, and SH3+) the dispersion component is prominent. For M-LP complexes, the electrostatic component contributes more to the IE except the dicationic metal ion complexes with H2 S and PH3 where the polarization component dominates. Although electrostatic component dominates for the HB and CAHB complexes, dispersion is predominant in π-π complexes.

  11. Probing defects and correlations in the hydrogen-bond network of ab initio water

    CERN Document Server

    Gasparotto, Piero; Ceriotti, Michele

    2016-01-01

    The hydrogen-bond network of water is characterized by the presence of coordination defects relative to the ideal tetrahedral network of ice, whose fluctuations determine the static and time-dependent properties of the liquid. Because of topological constraints, such defects do not come alone, but are highly correlated coming in a plethora of different pairs. Here we discuss in detail such correlations in the case of ab initio water models and show that they have interesting similarities to regular and defective solid phases of water. Although defect correlations involve deviations from idealized tetrahedrality, they can still be regarded as weaker hydrogen bonds that retain a high degree of directionality. We also investigate how the structure and population of coordination defects is affected by approximations to the inter-atomic potential, finding that in most cases, the qualitative features of the hydrogen bond network are remarkably robust.

  12. Investigation of Highly Designable Dented Structures in HP Model with Hydrogen Bond Energy

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei; HUANG Shengyou; YU Tao; ZOU Xianwu

    2007-01-01

    Some highly designable protein structures have dented on the surface of their native structures, and are not full compactly folded. According to hydrophobic-polar (HP) model the most designable structures are full compactly folded. To investigate the designability of the dented structures, we introduce the hydrogen bond energy in the secondary structures by using the secondary-structure-favored HP model proposed by Ou-yang etc. The result shows that the average designability increases with the strength of the hydrogen bond. The designabilities of the structures with same dented shape increase exponentially with the number of secondary structure sites. The dented structures can have the highest designabilities for a certain value of hydrogen bond energy density.

  13. Effects of hydrogen bonding on current-voltage characteristics of molecular junctions

    Science.gov (United States)

    Kula, Mathias; Jiang, Jun; Lu, Wei; Luo, Yi

    2006-11-01

    We present a first-principles study of hydrogen bonding effect on current-voltage characteristics of molecular junctions. Three model charge-transfer molecules, 2'-amino-4,4'-di(ethynylphenyl)-1-benzenethiolate (DEPBT-D), 4,4'-di(ethynylphenyl)-2'-nitro-1-benzenethiolate (DEPBT-A), and 2'-amino-4,4'-di(ethynylphenyl)-5'-nitro-1-benzenethiolate (DEPBT-DA), have been examined and compared with the corresponding hydrogen bonded complexes formed with different water molecules. Large differences in current-voltage characteristics are observed for DEPBT-D and DEPBT-A molecules with or without hydrogen bonded waters, while relatively small differences are found for DEPBT-DA. It is predicted that the presence of water clusters can drastically reduce the conductivities of the charge-transfer molecules. The underlying microscopic mechanism has been discussed.

  14. Inversion of the balance between hydrophobic and hydrogen bonding interactions in protein folding and aggregation.

    Directory of Open Access Journals (Sweden)

    Anthony W Fitzpatrick

    2011-10-01

    Full Text Available Identifying the forces that drive proteins to misfold and aggregate, rather than to fold into their functional states, is fundamental to our understanding of living systems and to our ability to combat protein deposition disorders such as Alzheimer's disease and the spongiform encephalopathies. We report here the finding that the balance between hydrophobic and hydrogen bonding interactions is different for proteins in the processes of folding to their native states and misfolding to the alternative amyloid structures. We find that the minima of the protein free energy landscape for folding and misfolding tend to be respectively dominated by hydrophobic and by hydrogen bonding interactions. These results characterise the nature of the interactions that determine the competition between folding and misfolding of proteins by revealing that the stability of native proteins is primarily determined by hydrophobic interactions between side-chains, while the stability of amyloid fibrils depends more on backbone intermolecular hydrogen bonding interactions.

  15. The hydrogen bond stabilizing effect in enammonium salts of captodative aminoalkenes containing a carbonyl group

    Science.gov (United States)

    Fedorov, S. V.; Rulev, A. Yu; Chipanina, N. N.; Sherstyannikova, L. V.; Turchaninov, V. K.

    2004-03-01

    Enhanced stability of enammonium salts of captodative carbonyl-containing aminoalkenes as compared to the salts of simple enamines is discussed on the basis of 1H and 13C NMR, IR, UV spectroscopy and the results quantum chemical calculations. Stabilization of the N-protonated form of captodative aminoalkenes is due to either intramolecular (NH +⋯OC) or intermolecular (NH +⋯Solv or NH +⋯X -) hydrogen bonding, whereas the C-protonated form is destabilized due to umpolung of the carbon-carbon double bond. The formation of bifurcated (three-centered) hydrogen bond between the enammonium cation and the solvent is demonstrated. The three-centered solvate complex is characterized by nonclassical dependence of the chemical shift of the bridging hydrogen atom from the proton-acceptor power of the solvent.

  16. EPR spin Hamiltonian parameters of encapsulated spin-labels: impact of the hydrogen bonding topology.

    Science.gov (United States)

    Frecus, Bogdan; Rinkevicius, Zilvinas; Murugan, N Arul; Vahtras, Olav; Kongsted, Jacob; Ågren, Hans

    2013-02-21

    Encapsulation of spin-labels into "host" compounds, like cucurbit[n]urils or cyclodextrins, in solutions has profound effects on the EPR spin Hamiltonian parameters of the spin-labels. In this work we study the microscopic origin of the EPR spin Hamiltonian parameters of spin-labels enclosed in hydrophobic cavities. We focus on the dependence of the EPR properties of encapsulated spin-labels on the hydrogen bonding topologies that occur upon encapsulation, and quantize various contributions to these parameters according to specific hydrogen bonding patterns. The obtained results provide refined insight into the role of the hydrogen bonding induced encapsulation shifts of EPR spin Hamiltonian parameters in solvated "spin-label@host compound" complexes.

  17. Concerted hydrogen-bond breaking by quantum tunneling in the water hexamer prism.

    Science.gov (United States)

    Richardson, Jeremy O; Pérez, Cristóbal; Lobsiger, Simon; Reid, Adam A; Temelso, Berhane; Shields, George C; Kisiel, Zbigniew; Wales, David J; Pate, Brooks H; Althorpe, Stuart C

    2016-03-18

    The nature of the intermolecular forces between water molecules is the same in small hydrogen-bonded clusters as in the bulk. The rotational spectra of the clusters therefore give insight into the intermolecular forces present in liquid water and ice. The water hexamer is the smallest water cluster to support low-energy structures with branched three-dimensional hydrogen-bond networks, rather than cyclic two-dimensional topologies. Here we report measurements of splitting patterns in rotational transitions of the water hexamer prism, and we used quantum simulations to show that they result from geared and antigeared rotations of a pair of water molecules. Unlike previously reported tunneling motions in water clusters, the geared motion involves the concerted breaking of two hydrogen bonds. Similar types of motion may be feasible in interfacial and confined water.

  18. Bifunctional Asymmetric Catalysis with Hydrogen Chloride: Enantioselective Ring-Opening of Aziridines Catalyzed by a Phosphinothiourea.

    Science.gov (United States)

    Mita, Tsuyoshi; Jacobsen, Eric N

    2009-06-01

    Ring-opening of aziridines with hydrogen chloride to form β-chloroamine derivatives is catalyzed by a chiral phosphinothiourea derivative in high yields and with high enantioselectivities. On the basis of (31)P NMR studies, activation of HCl appears to proceed via quantitative protonation of the catalyst to afford a phosphonium chloride complex.

  19. Intramolecular competition between n-pair and π-pair hydrogen bonding: Microwave spectrum and internal dynamics of the pyridine–acetylene hydrogen-bonded complex

    Energy Technology Data Exchange (ETDEWEB)

    Mackenzie, Rebecca B.; Dewberry, Christopher T.; Leopold, Kenneth R., E-mail: A.C.Legon@bristol.ac.uk, E-mail: david.tew@bristol.ac.uk, E-mail: kleopold@umn.edu [Department of Chemistry, University of Minnesota, 207 Pleasant St., SE, Minneapolis, Minnesota 55455 (United States); Coulston, Emma; Cole, George C. [Department of Chemistry, University of Exeter, Stocker Road, Exeter EX4 4QD (United Kingdom); Legon, Anthony C., E-mail: A.C.Legon@bristol.ac.uk, E-mail: david.tew@bristol.ac.uk, E-mail: kleopold@umn.edu; Tew, David P., E-mail: A.C.Legon@bristol.ac.uk, E-mail: david.tew@bristol.ac.uk, E-mail: kleopold@umn.edu [Department of Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS (United Kingdom)

    2015-09-14

    a-type rotational spectra of the hydrogen-bonded complex formed from pyridine and acetylene are reported. Rotational and {sup 14}N hyperfine constants indicate that the complex is planar with an acetylenic hydrogen directed toward the nitrogen. However, unlike the complexes of pyridine with HCl and HBr, the acetylene moiety in HCCH—NC{sub 5}H{sub 5} does not lie along the symmetry axis of the nitrogen lone pair, but rather, forms an average angle of 46° with the C{sub 2} axis of the pyridine. The a-type spectra of HCCH—NC{sub 5}H{sub 5} and DCCD—NC{sub 5}H{sub 5} are doubled, suggesting the existence of a low lying pair of tunneling states. This doubling persists in the spectra of HCCD—NC{sub 5}H{sub 5}, DCCH—NC{sub 5}H{sub 5}, indicating that the underlying motion does not involve interchange of the two hydrogens of the acetylene. Single {sup 13}C substitution in either the ortho- or meta-position of the pyridine eliminates the doubling and gives rise to separate sets of spectra that are well predicted by a bent geometry with the {sup 13}C on either the same side (“inner”) or the opposite side (“outer”) as the acetylene. High level ab initio calculations are presented which indicate a binding energy of 1.2 kcal/mol and a potential energy barrier of 44 cm{sup −1} in the C{sub 2v} configuration. Taken together, these results reveal a complex with a bent hydrogen bond and large amplitude rocking of the acetylene moiety. It is likely that the bent equilibrium structure arises from a competition between a weak hydrogen bond to the nitrogen (an n-pair hydrogen bond) and a secondary interaction between the ortho-hydrogens of the pyridine and the π electron density of the acetylene.

  20. Experimental and theoretical studies on a novel helical architecture driven by hydrogen and halogen bonding interactions

    Indian Academy of Sciences (India)

    QING ZHU LIU; SHAN SHAN WANG; TENG FEI WANG; JIAN GUO LIN; XUE HAI JU; LING QIU

    2016-12-01

    A novel two-dimensional (2D), layered, helical supramolecular architecture constructed via cooperative hydrogen bond and halogen bonds was synthesized and characterized: [(BMBA)₂(TPB)]n (1) [BMBA= 3-bromo-2-methylbenzoic acid, TPB = 1,2,3,4-tetra-(4-pyridyl)-butane]. Density functional theory (DFT) calculations were carried out to investigate the nature of intermolecular interactions between BMBA and TPB. The cooperation between hydrogen bond and halogen bond in building up the open organic architecture was demonstrated elaborately. Complex 1 exhibits strong photoluminescence and high thermal stability. The nature of electronic transitions in the photoluminescent process was investigated by means of time-dependent DFT (TDDFT) calculations and molecular orbital analyses, revealing that the luminescent property of the helical supramolecular architecture of 1 was ligand-based. Periodic DFT calculations show that 1 is an electrical insulator with a band gap of 3.29 eV.

  1. Indications of chemical bond contrast in AFM images of a hydrogen-terminated silicon surface

    Science.gov (United States)

    Labidi, Hatem; Koleini, Mohammad; Huff, Taleana; Salomons, Mark; Cloutier, Martin; Pitters, Jason; Wolkow, Robert A.

    2017-01-01

    The origin of bond-resolved atomic force microscope images remains controversial. Moreover, most work to date has involved planar, conjugated hydrocarbon molecules on a metal substrate thereby limiting knowledge of the generality of findings made about the imaging mechanism. Here we report the study of a very different sample; a hydrogen-terminated silicon surface. A procedure to obtain a passivated hydrogen-functionalized tip is defined and evolution of atomic force microscopy images at different tip elevations are shown. At relatively large tip-sample distances, the topmost atoms appear as distinct protrusions. However, on decreasing the tip-sample distance, features consistent with the silicon covalent bonds of the surface emerge. Using a density functional tight-binding-based method to simulate atomic force microscopy images, we reproduce the experimental results. The role of the tip flexibility and the nature of bonds and false bond-like features are discussed. PMID:28194036

  2. Recognizing molecular patterns by machine learning: an agnostic structural definition of the hydrogen bond

    CERN Document Server

    Gasparotto, Piero

    2014-01-01

    The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding -- a central concept to our understanding of the physical chemistry of water, biological systems and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a ...

  3. Performance of a Nonempirical Density Functional on Molecules and Hydrogen-Bonded Complexes

    CERN Document Server

    Mo, Yuxiang; Car, Roberto; Staroverov, Viktor N; Scuseria, Gustavo E; Tao, Jianmin

    2016-01-01

    Recently, Tao and Mo (TM) derived a new meta-generalized gradient approximation based on a model exchange hole. In this work, the performance of this functional is assessed on standard test sets, using the 6-311++G(3df,3pd) basis set. These test sets include 223 G3/99 enthalpies of formation, 58 electron affinities, 8 proton affinities, 96 bond lengths, 82 harmonic vibrational frequencies, and 10 hydrogen-bonded molecular complexes. Our calculations show that the TM functional can achieve remarkable accuracy for most molecular properties, improving upon non-empirical density functionals considered here. In particular, it delivers the best accuracy for proton affinities, harmonic vibrational frequencies, and hydrogen-bonded dissociation energies and bond lengths, compared to other semilocal density-functional approximations considered in this work.

  4. Indications of chemical bond contrast in AFM images of a hydrogen-terminated silicon surface

    Science.gov (United States)

    Labidi, Hatem; Koleini, Mohammad; Huff, Taleana; Salomons, Mark; Cloutier, Martin; Pitters, Jason; Wolkow, Robert A.

    2017-02-01

    The origin of bond-resolved atomic force microscope images remains controversial. Moreover, most work to date has involved planar, conjugated hydrocarbon molecules on a metal substrate thereby limiting knowledge of the generality of findings made about the imaging mechanism. Here we report the study of a very different sample; a hydrogen-terminated silicon surface. A procedure to obtain a passivated hydrogen-functionalized tip is defined and evolution of atomic force microscopy images at different tip elevations are shown. At relatively large tip-sample distances, the topmost atoms appear as distinct protrusions. However, on decreasing the tip-sample distance, features consistent with the silicon covalent bonds of the surface emerge. Using a density functional tight-binding-based method to simulate atomic force microscopy images, we reproduce the experimental results. The role of the tip flexibility and the nature of bonds and false bond-like features are discussed.

  5. Proton tunnelling and deuteration-induced phase transitions in hydrogen-bonded crystals

    Energy Technology Data Exchange (ETDEWEB)

    Matsuo, Takasuke [Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka (Japan). E-mail: matsuo@chem.sci.osaka-u.ac.jp; Inaba, Akira; Yamamuro, Osamu; Onoda-Yamamuro, Noriko [Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka (Japan)

    2000-10-09

    Experimental facts about appearance of new crystalline phases at low temperature related to deuterium substitution are collected and mechanisms of the isotope effect discussed. Compounds considered are (i) tri-alkali hydrogen selenates and sulphates, (ii) ammonium hexachlorometallates, (iii) bromo- and iodo-hydroxyphenalenone and (iv) chromium hydrogen dioxide. In (i), (iii) and (iv), linear O-H-O hydrogen bonds are involved. Proton tunnelling is the likely mechanism of the peculiar phase behaviour of (i). Definitely the tunnelling plays an essential role in (iii) but not in the extreme situation in (iv). In (ii), rotational tunnelling of an ammonium ion is the likely ingredient of the deuteration-induced phase transitions. The term proton cloud is introduced to describe the quantum mechanical distribution of the nucleus in the hydrogen bond and in the multi-valley rotational potential for an ammonium ion. (author)

  6. On the relation between hydrogen bonds, tetrahedral order and molecular mobility in model water

    CERN Document Server

    Pereyra, R G; Malaspina, D C; Carignano, M A

    2013-01-01

    We studied by molecular dynamics simulations the relation existing between the lifetime of hydrogen bonds, the tetrahedral order and the diffusion coefficient of model water. We tested four different models: SPC/E, TIP4P-Ew, TIP5P-Ew and Six-site, these last two having sites explicitly resembling the water lone pairs. While all the models perform reasonably well at ambient conditions, their behavior is significantly different for temperatures below 270 K. The models with explicit lone-pairs have a longer hydrogen bond lifetime, a better tetrahedral order and a smaller diffusion coefficient than the models without them.

  7. DNA-inspired hierarchical polymer design: electrostatics and hydrogen bonding in concert.

    Science.gov (United States)

    Hemp, Sean T; Long, Timothy E

    2012-01-01

    Nucleic acids and proteins, two of nature's biopolymers, assemble into complex structures to achieve desired biological functions and inspire the design of synthetic macromolecules containing a wide variety of noncovalent interactions including electrostatics and hydrogen bonding. Researchers have incorporated DNA nucleobases into a wide variety of synthetic monomers/polymers achieving stimuli-responsive materials, supramolecular assemblies, and well-controlled macromolecules. Recently, scientists utilized both electrostatics and complementary hydrogen bonding to orthogonally functionalize a polymer backbone through supramolecular assembly. Diverse macromolecules with noncovalent interactions will create materials with properties necessary for biomedical applications.

  8. Chirality Synchronization of Hydrogen-Bonded Complexes of Achiral N-Heterocycles.

    Science.gov (United States)

    Buchs, Jens; Vogel, Laura; Janietz, Dietmar; Prehm, Marko; Tschierske, Carsten

    2017-01-02

    2,4-Diamino-6-phenyl-1,3,5-triazines carrying a single oligo(ethylene oxide) (EO) chain form an optically isotropic mesophase composed of a conglomerate of macroscopic chiral domains with opposite sense of chirality even though the constituent molecules are achiral. This mesophase was proposed to result from the helical packing of hydrogen-bonded triazine aggregates, providing long-range chirality synchronization. The results provide first evidence for macroscopic achiral symmetry breaking upon conglomerate formation in an amorphous isotropic phase formed by hydrogen-bonded associates of simple N-heterocycles that are related to prebiotic molecules.

  9. QUANTUM-MECHANICAL PROPERTIES OF PROTON TRANSPORT IN THE HYDROGEN-BONDED MOLECULAR SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    PANG XIAO-FENG; LI PING

    2000-01-01

    The dynamic equations of the proton transport along the hydrogen bonded molecular systems have been obtainedby using completely quantum-mechanical method to be based on new Hamiltonian and model we proposed. Somequantum-mechanical features of the proton-solitons have also been given in such a case. The alternate motion of twodefects resulting from proton transfer occurred in the systems can be explained by the results. The results obtainedshow that the proton-soliton has corpuscle feature and obey classical equations of motion, while the free soliton movesin uniform velocity along the hydrogen bonded chains.

  10. Measurement and modelling of hydrogen bonding in 1-alkanol plus n-alkane binary mixtures

    DEFF Research Database (Denmark)

    von Solms, Nicolas; Jensen, Lars; Kofod, Jonas L.;

    2007-01-01

    Two equations of state (simplified PC-SAFT and CPA) are used to predict the monomer fraction of 1-alkanols in binary mixtures with n-alkanes. It is found that the choice of parameters and association schemes significantly affects the ability of a model to predict hydrogen bonding in mixtures, even...... studies, which is clarified in the present work. New hydrogen bonding data based on infrared spectroscopy are reported for seven binary mixtures of alcohols and alkanes. (C) 2007 Elsevier B.V. All rights reserved....

  11. Hydrogen bonding in asphaltenes and coal. Comprehensive progress report, December 1975--Februray 1977. [13 references

    Energy Technology Data Exchange (ETDEWEB)

    Li, N.C.

    1977-01-01

    Proton magnetic resonance (PMR) studies are reported of hydrogen bonding between the OH proton of o-phenylphenol (OPP) and the nitrogen electron donor of quinoline (Qu). Data are also reported on the hydrogen bonding of a coal-derived asphaltene and its acid and base components with OPP. Determination was made of the equilibrium constants of the 1:1 complex between OPP and Qu at 39, 32, 1, and -18/sup 0/C from the PMR studies. Qualitative results are reported for the interaction between the base fraction of asphaltene and OPP at 32, 1, and -26/sup 0/C.

  12. Discrete kink dynamics in hydrogen-bonded chains: The one-component model

    DEFF Research Database (Denmark)

    Karpan, V. M.; Zolotaryuk, Yaroslav; Christiansen, Peter Leth

    2002-01-01

    We study topological solitary waves (kinks and antikinks) in a nonlinear one-dimensional Klein-Gordon chain with the on-site potential of a double-Morse type. This chain is used to describe the collective proton dynamics in quasi-one-dimensional networks of hydrogen bonds, where the on-site poten......We study topological solitary waves (kinks and antikinks) in a nonlinear one-dimensional Klein-Gordon chain with the on-site potential of a double-Morse type. This chain is used to describe the collective proton dynamics in quasi-one-dimensional networks of hydrogen bonds, where the on...

  13. Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations

    Directory of Open Access Journals (Sweden)

    Sandeep Kumar Mishra

    2017-03-01

    Full Text Available The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.

  14. Experimental quantification of electrostatics in X-H···π hydrogen bonds.

    Science.gov (United States)

    Saggu, Miguel; Levinson, Nicholas M; Boxer, Steven G

    2012-11-21

    Hydrogen bonds are ubiquitous in chemistry and biology. The physical forces that govern hydrogen-bonding interactions have been heavily debated, with much of the discussion focused on the relative contributions of electrostatic vs quantum mechanical effects. In principle, the vibrational Stark effect, the response of a vibrational mode to electric field, can provide an experimental method for parsing such interactions into their electrostatic and nonelectrostatic components. In a previous study we showed that, in the case of relatively weak O-H···π hydrogen bonds, the O-H bond displays a linear response to an electric field, and we exploited this response to demonstrate that the interactions are dominated by electrostatics (Saggu, M.; Levinson, N. M.; Boxer, S. G. J. Am. Chem. Soc.2011, 133, 17414-17419). Here we extend this work to other X-H···π interactions. We find that the response of the X-H vibrational probe to electric field appears to become increasingly nonlinear in the order O-H electrostatic binding energies of the interactions, which are found to agree closely with the results of energy calculations. Taken together, these results highlight that with careful calibration vibrational probes can provide direct measurements of the electrostatic components of hydrogen bonds.

  15. Theoretical Study of Intramolecular Interactions in Peri-Substituted Naphthalenes: Chalcogen and Hydrogen Bonds

    Directory of Open Access Journals (Sweden)

    Goar Sánchez–Sanz

    2017-02-01

    Full Text Available A theoretical study of the peri interactions, both intramolecular hydrogen (HB and chalcogen bonds (YB, in 1-hydroxy-8YH-naphthalene, 1,4-dihydroxy-5,8-di-YH-naphthalene, and 1,5-dihydroxy-4,8-di-YH-naphthalene, with Y = O, S, and Se was carried out. The systems with a OH:Y hydrogen bond are the most stable ones followed by those with a chalcogen O:Y interaction, those with a YH:O hydrogen bond (Y = S and Se being the least stable ones. The electron density values at the hydrogen bond critical points indicate that they have partial covalent character. Natural Bond Orbital (NBO analysis shows stabilization due to the charge transfer between lone pair orbitals towards empty Y-H that correlate with the interatomic distances. The electron density shift maps and non-covalent indexes in the different systems are consistent with the relative strength of the interactions. The structures found on the CSD were used to compare the experimental and calculated results.

  16. Molecular deformation mechanisms in cellulose allomorphs and the role of hydrogen bonds.

    Science.gov (United States)

    Djahedi, Cyrus; Berglund, Lars A; Wohlert, Jakob

    2015-10-05

    Differences in tensile properties between cellulose crystal allomorphs cannot be rationalized by simply counting hydrogen bonds. From molecular dynamics computer simulations the cooperative nature of energy contributions to axial cellulose crystal modulus becomes apparent. Using a decomposition of inter and intramolecular forces as a function of tensile strain, the three allomorphs show dramatic differences in terms of how the contributions to elastic energy are distributed between covalent bonds, angles, dihedrals, electrostatic forces, dispersion and steric forces.

  17. Intermolecular Hydrogen Bonding in Peptide and Modified Jeffamine Organogels

    Science.gov (United States)

    Savin, Daniel; Richardson, Adam

    2011-03-01

    In these studies, we present two systems whereby supramolecular assembly results in rigid organogels. First, a series of AB diblock copolymers consisting of poly(Lysine(Z)) (P(Lys(Z)) blocks were synthesized and found to form stable, rigid organogels in THF (ca. 1 - 1.5 wt.% solutions) and chloroform at room temperature. In these systems, the protecting group on the P(Lys) side-chains remains intact and gel formation results from the assembly of the solventphobic P(Lys(Z)) chains through intermolecular beta-sheet formation. The non-peptide block was found to have an effect on organogel properties due to interfacial frustration, which disrupts H-bonding. Second, Jeffamine polymers were modified in a facile way to incorporate intermolecular H-bonding groups to yield networks able to gel various solvents as well as mineral and canola oil. We present the physical and rheological properties of the organogels produced.

  18. FTIR study of H-bonds cooperativity in complexes of 1,2-dihydroxybenzene with proton acceptors in aprotic solvents: influence of the intramolecular hydrogen bond.

    Science.gov (United States)

    Varfolomeev, Mikhail A; Abaidullina, Dilyara I; Gainutdinova, Aliya Z; Solomonov, Boris N

    2010-12-01

    FTIR spectroscopic study of hydrogen bonding of 1,2-dihydroxybenzene (catechol) with proton acceptors has been carried out. The influence of intramolecular and intermolecular hydrogen bonds on the strengths of each other in complexes of 1,2-dihydroxybenzene with various proton acceptors has been analyzed. It was shown that intramolecular hydrogen bond is strengthened when 1,2-dihydroxybenzene interacts with bases (ethers, amines, nitriles, etc.) in inert solvents. The contribution of the cooperativity of intramolecular hydrogen bonds in the frequency of stretching vibrations of O-H groups linearly depends on the proton acceptor ability of the bases. The solvent effect on hydrogen bond cooperativity in 1,2-dihydroxybenzene-base complexes has been studied. The approach to determine the influence of cooperative effects on the formation of intermolecular complexes with 1,2-dihydroxybenzene is proposed. It was shown that the strength of intramolecular hydrogen bonds in the complexes of 1,2-dihydroxybenzene with bases due to cooperativity of interactions increases by 30-70%, and the strength of intermolecular hydrogen bond by 7-22%.

  19. Low temperature FTIR spectroscopy and hydrogen bonding in cytosine polycrystals

    Science.gov (United States)

    Rozenberg, M.; Shoham, G.; Reva, I.; Fausto, R.

    2004-01-01

    The FTIR spectra of both the pure NH and isotopically substituted ND (90% D) polycrystalline cytosine were recorded in the range 400-4000 cm -1 as a function of temperature (10-300 K). For the first time, uncoupled NH(D) stretching mode bands of amine and imine groups were observed in the spectra of isotopically diluted cytosine at low temperatures. These bands correspond to the three distinct H-bonds that are present in the crystal, in agreement with the available data obtained by structural methods. At least nine bands were observed below 1000 cm -1 and, in consonance with their temperature and isotopic exchange behavior, were assigned to the NH proton out-of-the-plane bending modes. Six of these bands were found to correspond to additional "disordered" H-bonds, which could not be observed by structural methods. Empirical correlations of spectral and thermodynamic parameters enabled to estimate the contribution of the H-bonds to the sublimation enthalpy of the crystal, in agreement with independent experimental data.

  20. Light induced production of hydrogen from water by catalysis with ruthenium melanoidins

    Energy Technology Data Exchange (ETDEWEB)

    Serban, Andrei; Nissenbaum, Arie [Weizmann Inst. of Science, Rehovot (Israel)

    2000-08-01

    A ruthenium containing melanoidin (a condensation product of amino acids and carbohydrates) was found to photocatalyze hydrogen production from water under light irradiation with {lambda} < 320 nm, in the presence of EDTA as an electron donor and methyl viologen as an electron relay. Tracer experiments indicate that the hydrogen evolved originates from water. The bimolecular quenching constant for the quenching of melanoidin fluorescence by methyl viologen is large (k{sub {theta}} {approx} 10{sup 9}) suggesting a diffusion controlled reaction rate. The small Stern-Volmer constant(K{sub SV} {approx} 10) indicates an inefficient electron transfer between the excited melanoidin and the methyl viologen, perhaps due to the difficulties in removing O{sub 2} from the polymer. The Ru-melanoidin photocatalyst is stable under prolonged irradiation times and, due to its insolubility in water, is suitable for recycling. (Author)

  1. Precise tuning in platinum-nickel/nickel sulfide interface nanowires for synergistic hydrogen evolution catalysis

    Science.gov (United States)

    Wang, Pengtang; Zhang, Xu; Zhang, Jin; Wan, Sheng; Guo, Shaojun; Lu, Gang; Yao, Jianlin; Huang, Xiaoqing

    2017-01-01

    Comprising abundant interfaces, multicomponent heterostructures can integrate distinct building blocks into single entities and yield exceptional functionalities enabled by the synergistic components. Here we report an efficient approach to construct one-dimensional metal/sulfide heterostructures by directly sulfuring highly composition-segregated platinum-nickel nanowires. The heterostructures possess a high density of interfaces between platinum-nickel and nickel sulfide components, which cooperate synergistically towards alkaline hydrogen evolution reaction. The platinum-nickel/nickel sulfide heterostructures can deliver a current density of 37.2 mA cm−2 at an overpotential of 70 mV, which is 9.7 times higher than that of commercial Pt/C. The heterostructures also offer enhanced stability revealed by long-term chronopotentiometry measurements. The present work highlights a potentially powerful interface-engineering strategy for designing multicomponent heterostructures with advanced performance in hydrogen evolution reaction and beyond. PMID:28239145

  2. Kinetic solvent effects on hydrogen abstraction reactions from carbon by the cumyloxyl radical. The role of hydrogen bonding.

    Science.gov (United States)

    Bietti, Massimo; Salamone, Michela

    2010-08-20

    A kinetic study of the H-atom abstraction reactions from 1,4-cyclohexadiene and triethylamine by the cumyloxyl radical has been carried out in different solvents. Negligible effects are observed with 1,4-cyclohexadiene, whereas with triethylamine a significant decrease in rate constant (k(H)) is observed on going from benzene to MeOH. A good correlation between log k(H) and the solvent hydrogen bond donor parameter alpha is observed, indicative of an H-bonding interaction between the amine lone pair and the solvent.

  3. Learning Probabilistic Models of Hydrogen Bond Stability from Molecular Dynamics Simulation Trajectories

    KAUST Repository

    Chikalov, Igor

    2011-04-02

    Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. H-bonds involving atoms from residues that are close to each other in the main-chain sequence stabilize secondary structure elements. H-bonds between atoms from distant residues stabilize a protein’s tertiary structure. However, H-bonds greatly vary in stability. They form and break while a protein deforms. For instance, the transition of a protein from a nonfunctional to a functional state may require some H-bonds to break and others to form. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor. Other local interactions may reinforce (or weaken) an H-bond. This paper describes inductive learning methods to train a protein-independent probabilistic model of H-bond stability from molecular dynamics (MD) simulation trajectories. The training data describes H-bond occurrences at successive times along these trajectories by the values of attributes called predictors. A trained model is constructed in the form of a regression tree in which each non-leaf node is a Boolean test (split) on a predictor. Each occurrence of an H-bond maps to a path in this tree from the root to a leaf node. Its predicted stability is associated with the leaf node. Experimental results demonstrate that such models can predict H-bond stability quite well. In particular, their performance is roughly 20% better than that of models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a given conformation. The paper discusses several extensions that may yield further improvements.

  4. Intramolecular hydrogen bonding and cooperative interactions in carbohydrates via the molecular tailoring approach.

    Science.gov (United States)

    Deshmukh, Milind M; Bartolotti, Libero J; Gadre, Shridhar R

    2008-01-17

    In spite of many theoretical and experimental attempts for understanding intramolecular hydrogen bonding (H-bonding) in carbohydrates, a direct quantification of individual intramolecular H-bond energies and the cooperativity among the H-bonded networks has not been reported in the literature. The present work attempts, for the first time, a direct estimation of individual intramolecular O-H...O interaction energies in sugar molecules using the recently developed molecular tailoring approach (MTA). The estimated H-bond energies are in the range of 1.2-4.1 kcal mol(-1). It is seen that the OH...O equatorial-equatorial interaction energies lie between 1.8 and 2.5 kcal mol(-1), with axial-equatorial ones being stronger (2.0-3.5 kcal mol(-1)). The strongest bonds are nonvicinal axial-axial H-bonds (3.0-4.1 kcal mol(-1)). This trend in H-bond energies is in agreement with the earlier reports based on the water-water H-bond angle, solvent-accessible surface area (SASA), and (1)H NMR analysis. The contribution to the H-bond energy from the cooperativity is also estimated using MTA. This contribution is seen to be typically between 0.1 and 0.6 kcal mol(-1) when H-bonds are a part of a relatively weak equatorial-equatorial H-bond network and is much higher (0.5-1.1 kcal mol(-1)) when H-bonds participate in an axial-axial H-bond network.

  5. Neutron diffraction study of hydrogen-bond symmetrization in δ-AlOOD

    Science.gov (United States)

    Sano-Furukawa, A.; Hattori, T.; Kuribayashi, T.

    2013-12-01

    δ-AlOOH, a high-pressure polymorph of diaspore, is an important hydrous mineral in the deep earth that has the ability to transport hydrogen into the lower mantle. Theoretical studies have pointed out that hydrogen would locate at the center between two oxygen atoms at high pressure, which is so called hydrogen-bond symmetrization [1]. It was also suggested that the symmetrization would trigger the increase of bulk modulus, which is one of the important parameters of minerals at high pressure. The transition of δ-AlOOH(D) at high pressure has been suggested by X-ray and neutron diffraction [2, 3]. X-ray diffraction study found that the axes a and b where the hydrogen bond is oriented become less compressible above 12 GPa in δ-AlOOD. Neutron diffraction study on δ-AlOOD up to 9.2 GPa showed the increase of O-D bond distance, that is considered as a precousor phenomena of the symmetrization. However, the pressure was insufficient to observe the symmetrization. To investigate the symmetrization of hydrogen bond directly, we conducted neutron diffraction experiments to 16.7 GPa at PLANET, MLF in J-PARC. Powder sample of δ-AlOOD was loaded in Paris-Edinburgh press with double-toroid sintered diamond anvils with methanol-ethanol mixture of pressure medium. In the experiments, the disappearance of 120 refrection was observed at 12.1 GPa, indicating the transition from P21nm to Pnnm, which can be attributed to the disorder of hydrogen bond or the symmtrization. Results of Rietveld refienment will be shown in the presentation. [1] Tsuchiya et al., Geophys. Res. Lett., 29, 1909, 2002. [2] Sano-Furukawa et al., Am. Mineral., 93, 1558-1567, 2008. [3] Sano-Furukawa et al., Am. Mineral., 94, 1255-1261, 2009.

  6. The effect of furcated hydrogen bond and coordination bond on luminescent behavior of metal-organic framework [CuCN·EIN]: a TDDFT study.

    Science.gov (United States)

    Wu, Danyang; Mi, Weihong; Ji, Min; Hao, Ce; Qiu, Jieshan

    2012-11-01

    The hydrogen bonding in electronically excited-state of the metal-organic framework [CuCN·EIN] was studied using time-dependent density functional theory (TDDFT). The representative fragment of [CuCN·EIN] was employed for the computation. The geometric structures, binding energies and IR spectra in both ground state and electronically excited state S(1) of the complex were computed using DFT and TDDFT methods to investigate excited-state hydrogen-bonding and coordination bonding, respectively. Based on the analysis of the frontier molecular orbitals and the electronic configuration of the complex, the ligand-to-metal charge transfer (LMCT) luminescence was confirmed. Furthermore, furcated hydrogen bonds are both strengthened in the S(1) state slightly. And then, the strengthening of the hydrogen bonds in the S(1) state goes against the charge transfer from ligand to metal and then should be in favor of the luminescence. In particular, we also discuss strengthening or weakening behavior of the coordination bonds in the S(1) state for the first time. Based on the results of the bond lengths and vibration frequency of the coordination bond, we can conclude that the coordination bond Cu(7)-N(8) is strengthened in the S(1) state. And the strengthening of the coordination bond Cu(7)-N(8) should also be in favor of the luminescence.

  7. Electron-electron interactions in the chemical bond: ``1/3” Effect in the bond length of hydrogen molecule

    Indian Academy of Sciences (India)

    P Ganguly

    2001-10-01

    The prominent ``1/3” effect observed in the Hall effect plateaus of twodimensional electron gas (2DEG) systems has been postulated to indicating 1/3 fractional charge quasiparticle excitations arising from electron-electron interactions. Tunneling shot-noise experiments on 2DEF exhibiting fractional quantum Hall effect (FQHE) shows evidence for tunnelling of particles with and /3 charges for a constant band mass. A ``1/3” effect in the hydrogen molecule is seen in as much as its internuclear distance, - = - + +, with |+/-| = 1/3. This is examined in terms of electron-electron interactions involving electron- and hole quasiparticles, (-) and (ℎ+), equivalent to those observed in FQHE shot-noise experiments. The (/) ratio of the (-) and (ℎ+) quasiparticles is kept at 1: -3. Instead of a 2DEG, these particles are treated as being in flat Bohr orbits. A treatment in the language of charge-flux tube composites for the hydrogen atom as well as the hydrogen molecule is attempted. Such treatment gives important insights into changes in chemical potential and bond energy on crossing a phase boundary during the atom-bond transition as well as on models for FQHE itself.

  8. Theoretical study of bifurcated bent blue-shifted hydrogen bonds CH2…Y

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Ab initio quantum chemistry methods were applied to study the bifurcated bent hydrogen bonds Y… H2CZ (Z = O, S, Se) and Y…H2CZ2 (Z = F, Cl, Br) (Y = Cl-, Br-) at the MP2/6-311++G(d,p) and MP2/6-311++G(2df,2p) levels. The results show that in each complex there are two equivalent blue-shifted H-bonds Y…H—C, and that the interaction energies and blue shifts are large, the energy of each Y…H—C H-bond is 15-27 kJ/mol, and Δr(CH) = -0.1 - -0.5 pm and Δv(CH) = 30 - 80 cm-1. The natural bond orbital analysis shows that these blue-shifted H-bonds are caused by three factors: large rehybridization; small direct intermolecular hyperconjugation and larger indirect intermolecular hy- perconjugation; large decrease of intramolecular hyperconjugation. The topological analysis of elec- tron density shows that in each complex there are three intermolecular critical points: there is one bond critical point between the acceptor atom Y and each hydrogen, and there is a ring critical point inside the tetragon YHCH, so these interactions are exactly H-bonding.

  9. Hydrogen bond network topology in liquid water and methanol: a graph theory approach.

    Science.gov (United States)

    Bakó, Imre; Bencsura, Akos; Hermannson, Kersti; Bálint, Szabolcs; Grósz, Tamás; Chihaia, Viorel; Oláh, Julianna

    2013-09-28

    Networks are increasingly recognized as important building blocks of various systems in nature and society. Water is known to possess an extended hydrogen bond network, in which the individual bonds are broken in the sub-picosecond range and still the network structure remains intact. We investigated and compared the topological properties of liquid water and methanol at various temperatures using concepts derived within the framework of graph and network theory (neighbour number and cycle size distribution, the distribution of local cyclic and local bonding coefficients, Laplacian spectra of the network, inverse participation ratio distribution of the eigenvalues and average localization distribution of a node) and compared them to small world and Erdős-Rényi random networks. Various characteristic properties (e.g. the local cyclic and bonding coefficients) of the network in liquid water could be reproduced by small world and/or Erdős-Rényi networks, but the ring size distribution of water is unique and none of the studied graph models could describe it. Using the inverse participation ratio of the Laplacian eigenvectors we characterized the network inhomogeneities found in water and showed that similar phenomena can be observed in Erdős-Rényi and small world graphs. We demonstrated that the topological properties of the hydrogen bond network found in liquid water systematically change with the temperature and that increasing temperature leads to a broader ring size distribution. We applied the studied topological indices to the network of water molecules with four hydrogen bonds, and showed that at low temperature (250 K) these molecules form a percolated or nearly-percolated network, while at ambient or high temperatures only small clusters of four-hydrogen bonded water molecules exist.

  10. Thermoresponsive synergistic hydrogen bonding switched by several guest units in a water-soluble polymer.

    Science.gov (United States)

    Hao, Zhenhua; Li, Guangxiang; Yang, Ke; Cai, Yuanli

    2013-03-12

    Thermoresponsive synergistic hydrogen bonding (H-bonding) switched by several guest units in a water-soluble polymer is reported. Adjusting the distribution of guest units can effectively change the synergistic H-bonding inside polymer chains, thus widely switch the preorganization and thermoresponsive behavior of a water-soluble polymer. The synergistic H-bonding is also evidenced by converting less polar aldehyde groups into water-soluble oxime groups, which bring about the lowering-down of cloud point and an amplified hysteresis effect. This is a general approach toward the wide tunability of thermosensitivity of a water-soluble polymer simply by adjusting the distribution of several guest H-bonding units.

  11. Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories

    KAUST Repository

    Chikalov, Igor

    2011-02-15

    Background: Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. They form and break while a protein deforms, for instance during the transition from a non-functional to a functional state. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor.Methods: This paper describes inductive learning methods to train protein-independent probabilistic models of H-bond stability from molecular dynamics (MD) simulation trajectories of various proteins. The training data contains 32 input attributes (predictors) that describe an H-bond and its local environment in a conformation c and the output attribute is the probability that the H-bond will be present in an arbitrary conformation of this protein achievable from c within a time duration ?. We model dependence of the output variable on the predictors by a regression tree.Results: Several models are built using 6 MD simulation trajectories containing over 4000 distinct H-bonds (millions of occurrences). Experimental results demonstrate that such models can predict H-bond stability quite well. They perform roughly 20% better than models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a conformation. In most tests, about 80% of the 10% H-bonds predicted as the least stable are actually among the 10% truly least stable. The important attributes identified during the tree construction are consistent with previous findings.Conclusions: We use inductive learning methods to build protein-independent probabilistic models to study H-bond stability, and demonstrate that the models perform better than H-bond energy alone. 2011 Chikalov et al; licensee BioMed Central Ltd.

  12. Controllable synthesis of VSB-5 microspheres and microrods: growth mechanism and selective hydrogenation catalysis.

    Science.gov (United States)

    Liu, Shu-Juan; Cheng, Hai-Yang; Zhao, Feng-Yu; Gong, Jun-Yan; Yu, Shu-Hong

    2008-01-01

    Nanoporous VSB-5 nickel phosphate molecular sieves with relatively well controllable sizes and morphology of microspheres assembled from nanorods were synthesized at 140 degrees C over a short time in the presence of hexamethylenetetramine (HMT) by a facile hydrothermal method. The pH value, reaction time, and ratio of HMT to NaHPO2.H2O crucially influence the morphology and quality of the final products. By adjusting the pH value of the initial reaction solution, the morphology changes from disperse rods to microspheres assembled from rods and finally to a large quantity of fibers, and the diameters of the VSB-5 rods can be varied. The catalytic activity of VSB-5 in selective hydrogenation of several unsaturated organic compounds was tested. Nickel(II) in VSB-5 can selectively catalyze hydrogenation of C=C in trans-cinnamaldehyde and 3-methylcrotonaldehyde. In addition, since nitrobenzene (NB) and 2-chloronitrobenzene could be reduced to aniline (AN) and 2-chloroaniline with high selectivity, VSB-5 could have potential applications in synthesizing dyes, agrochemicals, and pharmaceuticals.

  13. Dynamics of hydrogen bonds in water and consequences for the unusual behaviour of supercooled water

    Indian Academy of Sciences (India)

    José Teixeira

    2008-10-01

    The dynamics of liquid water is evaluated by the coherent quasi-elastic scattering at two different momentum transfers, in order to discriminate hydrogen bond life-time from molecular dynamics. The results indicate a possible issue for the puzzle of the behaviour of supercooled water.

  14. Hydrogen bonding properties and intermediate structure of N-(2-carboxyphenyl)salicylidenimine

    NARCIS (Netherlands)

    Ligtenbarg, Alette G.J.; Hage, Ronald; Meetsma, Auke; Feringa, Ben L.

    1999-01-01

    The hydrogen bonding properties, the nature of the tautomeric structure and dimerization of N-(2-carboxyphenyl)salicylidenimine 1 has been studied. The crystal and molecular structure of 1 has been determined by single-crystal X-ray diffraction analysis. This compound forms a dimer in the solid stat

  15. NMR Determination of Hydrogen Bond Thermodynamics in a Simple Diamide: A Physical Chemistry Experiment

    Science.gov (United States)

    Morton, Janine G.; Joe, Candice L.; Stolla, Massiel C.; Koshland, Sophia R.; Londergan, Casey H.; Schofield, Mark H.

    2015-01-01

    Variable temperature NMR spectroscopy is used to determine the ?H° and ?S° of hydrogen bond formation in a simple diamide. In this two- or three-day experiment, students synthesize N,N'-dimethylmalonamide, dimethylsuccinamide, dimethylglutaramide, or dimethyladipamide from methylamine and the corresponding diester (typically in 50% recrystallized…

  16. Phonon driven proton transfer in crystals with short strong hydrogen bonds

    NARCIS (Netherlands)

    Fontaine-Vive, F.; Johnson, M.R.; Kearley, G.J.; Cowan, J.A.; Howard, J.A.K.; Parker, S.F.

    2006-01-01

    Recent work on understanding why protons migrate with increasing temperature in short, strong hydrogen bonds is extended here to three more organic, crystalline systems. Inelastic neutron scattering and density functional theory based simulations are used to investigate structure, vibrations, and dy

  17. Observed and predicted hydrogen bond motifs in crystal structures of hydantoins, dihydrouracils and uracils

    NARCIS (Netherlands)

    Cruz-Cabeza, A.J.; Schwalbe, C.H.

    2012-01-01

    A survey of crystal structures containing hydantoin, dihydrouracil and uracil derivatives in the Cambridge Structural Database revealed four main types of hydrogen bond motifs when derivatives with extra substituents able to interfere with the main motif are excluded. All these molecules contain two

  18. Hydrogen bond fluctuations of the hydration shell of the bromide anion

    NARCIS (Netherlands)

    Timmer, R.L.A.; Bakker, H.J.

    2009-01-01

    We study the hydrogen bond dynamics of solutions of LiBr and NaBr in isotopically diluted water (2% HDO:D2O) with femtosecond spectral hole-burning spectroscopy. We study the frequency fluctuations of the O-H stretch vibrations of the HDO molecules and observe spectral dynamics with time constants o

  19. Conductivity properties of proton transfer and influence of temperature on it in hydrogen-bonded systems

    Institute of Scientific and Technical Information of China (English)

    PANGXiao-feng; YUJia-feng

    2004-01-01

    We study and calculate the mobility and oonductivity of proton transfer and influence of temperature on it by pang's dynamic model in hydrogen bonded systems, which ooincide with experiments. We further study the mechanism of magnetization of ciguid water in the basis of this model.

  20. Hydrogen bonding interactions between ethylene glycol and water: density, excess molar volume, and spectral study

    Institute of Scientific and Technical Information of China (English)

    ZHANG JianBin; ZHANG PengYan; MA Kai; HAN Fang; CHEN GuoHua; WEI XiongHui

    2008-01-01

    Studies of the density and the excess molar volume of ethylene glycol (EG)-water mixtures were carried out to illustrate the hydrogen bonding interactions of EG with water at different temperatures, The re-sults suggest that a likely complex of 3 ethylene glycol molecules bonding with 4 water molecules in an ethylene glycol-water mixture (EGW) is formed at the maximal excess molar volume, which displays stronger absorption capabilities for SO2 when the concentration of SO2 reaches 400×106 (volume ratio) in the gas phase. Meanwhile, FTIR and UV spectra of EGWs were recorded at various EG concentra-tions to display the hydrogen bonding interactions of EG with water. The FTIR spectra show that the stretching vibrational band of hydroxyl in the EGWs shifts to a lower frequency and the bending vibra-tional band of water shifts to a higher frequency with increasing the EG concentration, respectively. Furthermore, the UV spectra show that the electron transferring band of the hydroxyl oxygen in EG shows red shift with increasing the EG concentration. The frequency shifts in FTIR spectra and the shifts of absorption bands in UV absorption spectra of EGWs are interpreted as the strong hydrogen bonding interactions of the hydrogen atoms in water with the hydroxyl oxygen atoms of EG.

  1. Strong Screening Effect of Polyhedral Oligomeric Silsesquioxanes (POSS Nanoparticles on Hydrogen Bonded Polymer Blends

    Directory of Open Access Journals (Sweden)

    Chin-Wei Chiou

    2014-03-01

    Full Text Available In this study we used anionic living polymerization to prepare two different homopolymers: a poly(methyl methacrylate (PMMA and a PMMA derivative presenting polyhedral oligomeric silsesquioxane (PMA-POSS units as its side chains. We then employed differential scanning calorimetry (DSC, Fourier transform infrared (FTIR spectroscopy, and wide-angle X-ray diffraction (WAXD to investigate the miscibility and specific interactions of PMMA and PMA-POSS with three hydrogen bonding donor compounds: poly(vinyl phenol (PVPh, phenolic resin, and bisphenol A (BPA. DSC revealed that all of the PVPh/PMMA, phenolic/PMMA, and BPA/PMMA blends exhibited a single glass transition temperature, characteristic of miscible systems; FTIR spectroscopic analyses revealed that such miscibility resulted from hydrogen bonding interactions between the C=O groups of PMMA and the OH groups of these three hydrogen bonding donor compounds. In contrast, all of the PVPh/PMA-POSS, phenolic/PMA-POSS, and BPA/PMA-POSS blends were immiscible: DSC revealed two glass transition temperatures arising from strong screening effects (FTIR spectroscopy and high degrees of aggregation (WAXD of the POSS nanoparticles. We propose that the value of the intramolecular screening effect (γ should be very close to 1 for all PMA-POSS blend systems when POSS nanoparticles appear as the side chains of PMMA, such that the OH groups of the hydrogen bonding donor compounds cannot interact with the C=O groups of PMA-POSS.

  2. Conductivity properties of proton transfer and influence of temperature on it in hydrogen-bonded systems

    Institute of Scientific and Technical Information of China (English)

    PANG Xiao-feng; YU Jia-feng

    2004-01-01

    We study and calculate the mobility and conductivity of proton transfer and influence of temperature on it by pang's dynamic model in hydrogen bonded systems, which coincide with experiments. We further study the mechanism of magnetization of ciguid water in the basis of this model.

  3. Isotope effects on chemical shifts in the study of intramolecular hydrogen bonds

    DEFF Research Database (Denmark)

    Hansen, Poul Erik

    2015-01-01

    The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between “static” ...

  4. New Hydrogen Bonded Supramolecular Hydrogels Formed through Gelating Two Isomeric Building Units Simultaneously

    Institute of Scientific and Technical Information of China (English)

    Ji Wei WU; Li Ming TANG; Kai CHEN; Liang YAN; Yu Jiang WANG

    2006-01-01

    New hydrogen bonded supramolecular hydrogels were formed through simultaneously gelating two isomeric building units, 4-oxo-4-(2-pyridinylamino)butanoic acid (G1) and 4-oxo-4-(3-pyridinylamino)butanoic acid (G2) at various molar ratios in water.

  5. Hydrogen-bonding patterns in 5-fluorocytosine–melamine co-crystal (4/1

    Directory of Open Access Journals (Sweden)

    Marimuthu Mohana

    2016-04-01

    Full Text Available The asymmetric unit of the title compound, 4C4H4FN3O·C3H6N6, comprises of two independent 5-fluorocytosine (5FC molecules (A and B and one half-molecule of melamine (M. The other half of the melamine molecule is generated by a twofold axis. 5FC molecules A and B are linked through two different homosynthons [R22(8 ring motif]; one is formed via a pair of N—H...O hydrogen bonds and the second via a pair of N—H...N hydrogen bonds. In addition to this pairing, the O atoms of 5FC molecules A and B interact with the N2 amino group on both sides of the melamine molecule, forming a DDAA array of quadruple hydrogen bonds and generating a supramolecular pattern. The 5FC (molecules A and B and two melamine molecules interact via N—H...O, N—H...N and N—H...O, N—H...N, C—H...F hydrogen bonds forming R66(24 and R44(15 ring motifs. The crystal structure is further strengthened by C—H...F, C—F...π and π–π stacking interactions.

  6. Communication: Hydrogen bonding interactions in water-alcohol mixtures from X-ray absorption spectroscopy

    Science.gov (United States)

    Lam, Royce K.; Smith, Jacob W.; Saykally, Richard J.

    2016-05-01

    While methanol and ethanol are macroscopically miscible with water, their mixtures exhibit negative excess entropies of mixing. Despite considerable effort in both experiment and theory, there remains significant disagreement regarding the origin of this effect. Different models for the liquid mixture structure have been proposed to address this behavior, including the enhancement of the water hydrogen bonding network around the alcohol hydrophobic groups and microscopic immiscibility or clustering. We have investigated mixtures of methanol, ethanol, and isopropanol with water by liquid microjet X-ray absorption spectroscopy on the oxygen K-edge, an atom-specific probe providing details of both inter- and intra-molecular structure. The measured spectra evidence a significant enhancement of hydrogen bonding originating from the methanol and ethanol hydroxyl groups upon the addition of water. These additional hydrogen bonding interactions would strengthen the liquid-liquid interactions, resulting in additional ordering in the liquid structures and leading to a reduction in entropy and a negative enthalpy of mixing, consistent with existing thermodynamic data. In contrast, the spectra of the isopropanol-water mixtures exhibit an increase in the number of broken alcohol hydrogen bonds for mixtures containing up to 0.5 water mole fraction, an observation consistent with existing enthalpy of mixing data, suggesting that the measured negative excess entropy is a result of clustering or micro-immiscibility.

  7. Spectroscopic identification of ethanol-water conformers by large-amplitude hydrogen bond librational modes

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, J.; Wugt Larsen, R., E-mail: rewl@kemi.dtu.dk [Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kongens Lyngby (Denmark); Heimdal, J. [MAX-IV Laboratory, Lund University, P.O. Box 118, 22100 Lund (Sweden)

    2015-12-14

    The far-infrared absorption spectra have been recorded for hydrogen-bonded complexes of water with ethanol embedded in cryogenic neon matrices at 2.8 K. The partial isotopic H/D-substitution of the ethanol subunit enabled by a dual inlet deposition procedure enables the observation and unambiguous assignment of the intermolecular high-frequency out-of-plane and the low-frequency in-plane donor OH librational modes for two different conformations of the mixed binary ethanol/water complex. The resolved donor OH librational bands confirm directly previous experimental evidence that ethanol acts as the O⋯HO hydrogen bond acceptor in the two most stable conformations. In the most stable conformation, the water subunit forces the ethanol molecule into its less stable gauche configuration upon dimerization owing to a cooperative secondary weak O⋯HC hydrogen bond interaction evidenced by a significantly blue-shift of the low-frequency in-plane donor OH librational band origin. The strong correlation between the low-frequency in-plane donor OH librational motion and the secondary intermolecular O⋯HC hydrogen bond is demonstrated by electronic structure calculations. The experimental findings are further supported by CCSD(T)-F12/aug-cc-pVQZ calculations of the conformational energy differences together with second-order vibrational perturbation theory calculations of the large-amplitude donor OH librational band origins.

  8. Vibrational Spectroscopy of Intramolecular Hydrogen Bonds in the Infrared and Near-Infrared Regions

    DEFF Research Database (Denmark)

    Schrøder, Sidsel Dahl

    and 1,4-diaminobutane). Experimentally, the hydrogen bonds have been studied with vibrational spectroscopy in the infrared and near-infrared regions. The focus is primarily on spectra recorded in the near-infrared regions, which in these studies are dominated by O-H and N-H stretching overtones...

  9. Spectroscopic identification of ethanol-water conformers by large-amplitude hydrogen bond librational modes

    DEFF Research Database (Denmark)

    Andersen, Jonas; Heimdal, J.; Larsen, René Wugt

    2015-01-01

    The far-infrared absorption spectra have been recorded for hydrogen-bonded complexes of water with ethanol embedded in cryogenic neon matrices at 2.8 K. The partial isotopic H/D-substitution of the ethanol subunit enabled by a dual inlet deposition procedure enables the observation and unambiguous...

  10. Imidazole tailored deep eutectic solvents for CO2 capture enhanced by hydrogen bonds.

    Science.gov (United States)

    Cao, Lingdi; Huang, Junhua; Zhang, Xiangping; Zhang, Suojiang; Gao, Jubao; Zeng, Shaojuan

    2015-11-07

    Deep eutectic solvents (DESs) have emerged as promising alternative candidates for CO2 capture in recent years. In this work, several novel DESs were firstly prepared to enhance CO2 absorption. Structural and physical properties of DESs were investigated, as well as their absorption performance of CO2. A distinct depression in the melting point up to 80 K of DESs was observed compared with that of BMIMCl. The observed red shifts of the C2H group in an imidazolium ring and its chemical shifts downfield in NMR spectra are indicative of a hydrogen bond interaction between BMIMCl and MEA. In particular, CO2 uptake in MEA : ILs (4 : 1) at room temperature and atmospheric pressure is up to 21.4 wt%, which is higher than that of 30 wt% MEA (13%). A hydrogen bond related mechanism was proposed in which ILs act as a medium to improve CO2 uptake through hydrogen bonds. Finally, the firstly reported overall heat of CO2 absorption is slightly higher than that of 30 wt% MEA, implying that the hydrogen bonds of DESs contribute to the overall heat of CO2 absorption. This study reveals that the heat of CO2 absorption can be tailored by the proper molar ratio of MEA and ILs.

  11. Hydrogen bonding versus stacking stabilization by modified nucleobases incorporated in PNA. DNA duplexes

    DEFF Research Database (Denmark)

    Sen, Anjana; Nielsen, Peter E

    2009-01-01

    The effects of incorporation of the modified nucleobases, 2,6-diaminopurine (D) (substituting for adenine) and 7-chloro-1,8-naphthyridin-2-(1H)-one (bicyclic thymine, bT) (substituting for thymine), that stabilize PNA.DNA duplex formation by increasing hydrogen bonding and/or base pair stacking...

  12. Ladderlike oligomers; intramolecular hydrogen bonding, push-pull character, and electron affinity.

    Science.gov (United States)

    Pieterse, K; Vekemans, J A; Kooijman, H; Spek, A L; Meijer, E W

    2000-12-15

    Symmetrical 2,5-bis(2-aminophenyl)pyrazines have been synthesized by application of the Stille coupling strategy. These cotrimers feature three important properties, namely strong intramolecular hydrogen bonding, push-pull character, and high electron affinity. The presence of intramolecular hydrogen bonds has been confirmed by 1H NMR, IR spectroscopy, and single-crystal X-ray diffraction. The hydrogen bond strength can be increased by substituting the amino groups with stronger electron-withdrawing functionalities. Despite the anticipated enhanced pi-conjugation through planarization, a hypsochromic shift was observed in the UV/Vis spectra, explained by a decrease in push-pull character. The electron affinity of the cotrimers was deduced from the first reduction potentials measured by cyclic voltammetry and is related to the electron-withdrawing character of the amino substituents. The results obtained have been compared with those of the corresponding 4-aminophenyl analogues and show that intramolecular hydrogen bonds can be used to design polymers with enhanced pi conjugation as well as a high electron affinity.

  13. Neural Plasticity and Memory: Is Memory Encoded in Hydrogen Bonding Patterns?

    Science.gov (United States)

    Amtul, Zareen; Rahman, Atta-Ur

    2016-02-01

    Current models of memory storage recognize posttranslational modification vital for short-term and mRNA translation for long-lasting information storage. However, at the molecular level things are quite vague. A comprehensive review of the molecular basis of short and long-lasting synaptic plasticity literature leads us to propose that the hydrogen bonding pattern at the molecular level may be a permissive, vital step of memory storage. Therefore, we propose that the pattern of hydrogen bonding network of biomolecules (glycoproteins and/or DNA template, for instance) at the synapse is the critical edifying mechanism essential for short- and long-term memories. A novel aspect of this model is that nonrandom impulsive (or unplanned) synaptic activity functions as a synchronized positive-feedback rehearsal mechanism by revising the configurations of the hydrogen bonding network by tweaking the earlier tailored hydrogen bonds. This process may also maintain the elasticity of the related synapses involved in memory storage, a characteristic needed for such networks to alter intricacy and revise endlessly. The primary purpose of this review is to stimulate the efforts to elaborate the mechanism of neuronal connectivity both at molecular and chemical levels.

  14. Phase transition in triglycine family of hydrogen bonded ferroelectrics: An interpretation based on structural studies

    Indian Academy of Sciences (India)

    R R Choudhury; R Chitra; P U Sastry; Amit Das; M Ramanadham

    2004-07-01

    Using the crystal structure, a comprehensive interpretation of the origin of ferroelectricity in the hydrogen bonded triglycine family of crystals is given. Our detailed analysis showed that the instability of nitrogen double well potential plays a driving role in the mechanism of the ferroelectric transitions in these crystals.

  15. Crystal structures and hydrogen bonding in the morpholinium salts of four phenoxyacetic acid analogues

    Directory of Open Access Journals (Sweden)

    Graham Smith

    2015-11-01

    Full Text Available The anhydrous salts morpholinium (tetrahydro-2-H-1,4-oxazin-4-ium phenoxyacetate, C4H10NO+·C8H7O3−, (I, morpholinium (4-fluorophenoxyacetate, C4H10NO+·C8H6 FO3−, (II, and isomeric morpholinium (3,5-dichlorophenoxyacetate (3,5-D, (III, and morpholinium (2,4-dichlorophenoxyacetic acid (2,4-D, C4H10NO+·C8H5Cl2O3−, (IV, have been determined and their hydrogen-bonded structures are described. In the crystals of (I, (III and (IV, one of the the aminium H atoms is involved in a three-centre asymmetric cation–anion N—H...O,O′ R12(4 hydrogen-bonding interaction with the two carboxyl O-atom acceptors of the anion. With the structure of (II, the primary N—H...O interaction is linear. In the structures of (I, (II and (III, the second N—H...Ocarboxyl hydrogen bond generates one-dimensional chain structures extending in all cases along [100]. With (IV, the ion pairs are linked though inversion-related N—H...O hydrogen bonds [graph set R42(8], giving a cyclic heterotetrameric structure.

  16. Hydrogen-bonded Lamellar Network of Pyromellitic Acid Pillared by 8-Hydroxyquinoline

    Institute of Scientific and Technical Information of China (English)

    WANG, Lei; ZHANG, Hong; ZHANG, Jing-Ping; GAO, Fei-Xue; HUA, Rui-Mao; ZHOU, Guang-Yuan

    2006-01-01

    8-Hydroxyquinoline (8-q) salt of pyromellitic acid (benzene-1,2,4,5-tetracarboxylic acid, H4bta) forms robust lamellar structure where [H2bta]2- anions build up sheets through strong hydrogen bonds in two dimensions and[H-8-q]+ cations act as pillars to afford an extended three dimensional network.

  17. Efficient Energy Transfer in Supramolecular, Hydrogen-Bonded Polypyridylruthenium-Osmium Complexes

    NARCIS (Netherlands)

    Rau, Sven; Schäfer, Bernhard; Schebesta, Sebastian; Grüßing, André; Poppitz, Wolfgang; Walther, Dirk; Duati, Marco; Browne, Wesley R.; Vos, Johannes G.

    2003-01-01

    Hydrogen bond association between ruthenium bibenzimidazole and carboxylated polypyridylosmium complexes results in stable supramolecular aggregates. The determined stability constant of logK approximate to 6 +/- 0.3 allows efficient energy transfer from the ruthenium to the osmium moiety. (C) Wiley

  18. The electron density distribution in the hydrogen bond. A quantum chemical and crystallographic study

    NARCIS (Netherlands)

    Feil, Dirk

    1990-01-01

    With the help of Hartree—Fock—Slater calculations in which very large basis sets are employed, the polarisation of the water molecule by an electric field is explored. The various features in the electron density distribution are encountered again in the long hydrogen bond in the water dimer, showin

  19. Hydrogen-bond basicity of push-pull α,β-unsaturated enaminoketones

    Science.gov (United States)

    Vdovenko, Sergey I.; Gerus, Igor I.; Fedorenko, Elena A.; Kukhar, Valery P.

    2010-08-01

    A method is proposed for evaluating the hydrogen-bond basicity of certain conformers of two push-pull enaminoketones with the general formula R sbnd C(O) sbnd CH dbnd CH sbnd N(CH 3) 2, where R=CH 3 (DMBN); R=CF 3 (DMTBN). It has been shown, for both enaminoketones, that the ( EE) conformer has a higher basicity than the ( EZ) conformer. Moreover, the (DMBN) has one of the highest general p KHB values in the hydrogen-bond basicity scale of ketones. Substitution of the CH 3-group in (DMBN) with the CF 3-group in (DMTBN) reduces general p KHB sharply as a consequence of electron withdrawal of CF 3-group. Hydrogen bond sites are also discussed; it is shown that, in both enaminoketones, carbonyl oxygen possesses the maximal basicity, whereas nitrogen of the dimethylamino group has less basicity, and the vinyl moiety is the least basic site. Enthalpies of hydrogen bond formation (-Δ H) in absolute values, as well as the respective p KHB values, are greater for the ( EE) conformer than for the ( EZ) as a consequence of greater contribution of resonance structure in the ( EE) form. ?

  20. Scales of Hydrogen-Bonding Workshop Held in London, England on 1-3 July 1987

    Science.gov (United States)

    1987-07-03

    UNDERSTANDING OF THE HYDROGEN-BOND INTERACTION Pierre-Charles Maria and Jean-Francois Gal Laboratoire de Chimie Physique Organique , Universite de Nice - Parc...Faculte des Sciences 2 Rue de Ia Houssiniere 44072 Nantes cedex 03 FRANCE Dr Pierre-Charles Maria Laboratorie de Chimie Physique Organic Dr Jean

  1. The effect of large amplitude motions on the transition frequency redshift in hydrogen bonded complexes

    DEFF Research Database (Denmark)

    Mackeprang, Kasper; Kjærgaard, Henrik Grum; Salmi, Teemu

    2014-01-01

    -stretching transition. The model accurately predicts the transition wavenumbers of the vibrations in water dimer compared to experimental values and provides a physical picture that explains the redshift of the hydrogen bonded OH-oscillator. We find that it is unnecessary to include all six intermolecular modes...

  2. Ultrafast OH-stretching frequency shifts of hydrogen- bonded 2-naphthol photoacid-base complexes in solution

    Directory of Open Access Journals (Sweden)

    Batista VictorS.

    2013-03-01

    Full Text Available We characterize the transient solvent-dependent OH-stretching frequency shifts of photoacid 2-naphthol hydrogen-bonded with CH3CN in the S0- and S1-states using a combined experimental and theoretical approach, and disentangle specific hydrogen-bonding contributions from nonspecific dielectric response.

  3. On Hydrogen Bonding in the Intramolecularly Chelated Taitomers of Enolic Malondialdehyde and its Mono- and Dithio-Analogues

    DEFF Research Database (Denmark)

    Carlsen, Lars; Duus, Fritz

    1980-01-01

    The intramolecular hydrogen bondings in enolic malondialdehyde and it mono- and dithio-analogues have been evaluated by a semiempricial SCF–MO–CNDO method. The calculations predict that the hydrogen bonds play an important part in the stabilities of malondialdehyde and monothiomalondialdehyde, wh...

  4. Hydrophobic, Polar and Hydrogen Bonding Based Drug-Receptor Interaction of Tetrahydroimidazobenzodiazepinones

    Directory of Open Access Journals (Sweden)

    V. K. Sahu

    2008-01-01

    Full Text Available Anti-HIV drug discovery has been increasingly focusing on HIV-1-RT (reverse transcriptase as a potential therapeutic target. Tetrahydroimidazobenzodiazepinone (TIBO belongs to non-nucleoside group of reverse transcriptase inhibitors (NNRTIs. A computational chemistry study has been performed on a series of tetrahydroimidazo-benzodiazepinones as HIV-1-NNRT inhibitors. Problem statement: In order to search out new drug of desired activity from the lead compounds, there was need to know the interaction of drugs with their receptor i.e., type of force(s that have predominant role. Approach: Log P and SASA have been used for measurement of hydrophobic interaction, energy of protonation for measurement of most favorable hydrogen bond acceptor site, bond length and bond strain for measurement of strength of hydrogen bond formed between drug and receptor, atomic charges, ionization potential, electronegativity, E‡n and E‡m and their difference ΔE‡nm for measurement of polar interaction. The 3D modeling and geometry optimization of the compounds and receptor amino acids have been done by semiempirical method with MOPAC2002 associated with CAChe software. Results: The study has shown that hydrophobic interaction is predominant and made major contribution, while hydrogen bonding and polar interactions help in proper orientation of the compound (or its functional groups to make maximam interaction. Conclusion: In this study theoretical technique has been discussed by which new hypothetical HIV-1-NNRT inhibitors can be developed prior to their synthesis only by introducing effective hydrophobic substituents at specific sites.

  5. Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

    Energy Technology Data Exchange (ETDEWEB)

    Gasparotto, Piero; Ceriotti, Michele, E-mail: michele.ceriotti@epfl.ch [Laboratory of Computational Science and Modeling, and National Center for Computational Design and Discovery of Novel Materials MARVEL, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland)

    2014-11-07

    The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding – a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

  6. Tunneling and delocalization effects in hydrogen bonded systems: a study in position and momentum space.

    Science.gov (United States)

    Morrone, Joseph A; Lin, Lin; Car, Roberto

    2009-05-28

    Novel experimental and computational studies have uncovered the proton momentum distribution in hydrogen bonded systems. In this work, we utilize recently developed open path integral Car-Parrinello molecular dynamics methodology in order to study the momentum distribution in phases of high pressure ice. Some of these phases exhibit symmetric hydrogen bonds and quantum tunneling. We find that the symmetric hydrogen bonded phase possesses a narrowed momentum distribution as compared with a covalently bonded phase, in agreement with recent experimental findings. The signatures of tunneling that we observe are a narrowed distribution in the low-to-intermediate momentum region, with a tail that extends to match the result of the covalently bonded state. The transition to tunneling behavior shows similarity to features observed in recent experiments performed on confined water. We corroborate our ice simulations with a study of a particle in a model one-dimensional double well potential that mimics some of the effects observed in bulk simulations. The temperature dependence of the momentum distribution in the one-dimensional model allows for the differentiation between ground state and mixed state tunneling effects.

  7. Hydrogen Bonds in Coal——The Influence of Coal Rank and the Recognition of a New Hydrogen Bond in Coal

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    By means of in-situ diffuse reflectance FTIR, the IR spectra of 6 coals with different ranks were obtained from room temperature to 230 ℃. A new curve fitting method was used to recognize the different hydrogen bonds in the coals, and the influence of coal ranks on the distribution of hydrogen bonds(HBs) in the coals and their thermal stability were discussed. The results show that there is another new HB(around 2514 cm-1) between the -SH in mercaptans or thiophenols and the nitrogen in the pyridine-like compounds in the coals, and the evidence for that was provided. The controversial band of the HB between hydroxyl and the nitrogen of the pyridine-like compounds was determined in the range of 3028-2984 cm-1, and the result is consistent with but more specific than that of Painter et al.. It was found that the stability of different HBs in the coals is influenced by both coal rank and temperature. For some HBs, the higher the coal rank, the higher the stability of them. Within the temperature range of our research, the stability of the HB between the hydroxyl and the π bond increases to some extent for some coals at temperatures higher than 110 or 140 ℃.

  8. Si-H bond dynamics in hydrogenated amorphous silicon

    Science.gov (United States)

    Scharff, R. Jason; McGrane, Shawn D.

    2007-08-01

    The ultrafast structural dynamics of the Si-H bond in the rigid solvent environment of an amorphous silicon thin film is investigated using two-dimensional infrared four-wave mixing techniques. The two-dimensional infrared (2DIR) vibrational correlation spectrum resolves the homogeneous line shapes ( 4ps waiting times. The Si-H stretching mode anharmonic shift is determined to be 84cm-1 and decreases slightly with vibrational frequency. The 1→2 linewidth increases with vibrational frequency. Frequency dependent vibrational population times measured by transient grating spectroscopy are also reported. The narrow homogeneous line shape, large inhomogeneous broadening, and lack of spectral diffusion reported here present the ideal backdrop for using a 2DIR probe following electronic pumping to measure the transient structural dynamics implicated in the Staebler-Wronski degradation [Appl. Phys. Lett. 31, 292 (1977)] in a-Si:H based solar cells.

  9. Transfer hydrogenation catalysis in cells as a new approach to anticancer drug design.

    Science.gov (United States)

    Soldevila-Barreda, Joan J; Romero-Canelón, Isolda; Habtemariam, Abraha; Sadler, Peter J

    2015-03-20

    Organometallic complexes are effective hydrogenation catalysts for organic reactions. For example, Noyori-type ruthenium complexes catalyse reduction of ketones by transfer of hydride from formate. Here we show that such catalytic reactions can be achieved in cancer cells, offering a new strategy for the design of safe metal-based anticancer drugs. The activity of ruthenium(II) sulfonamido ethyleneamine complexes towards human ovarian cancer cells is enhanced by up to 50 × in the presence of low non-toxic doses of formate. The extent of conversion of coenzyme NAD(+) to NADH in cells is dependent on formate concentration. This novel reductive stress mechanism of cell death does not involve apoptosis or perturbation of mitochondrial membrane potentials. In contrast, iridium cyclopentadienyl catalysts cause cancer cell death by oxidative stress. Organometallic complexes therefore have an extraordinary ability to modulate the redox status of cancer cells.

  10. Study on UV, IR and NMR Spectra of Double Hydrogen-bonded Complexes

    Institute of Scientific and Technical Information of China (English)

    ZHU Liang-Liang; TENG Qi-Wen; WU Shi

    2006-01-01

    AM1, PM3 and DFT methods were used to study on the hydrogen-bonded dimer of melamine and [1,3] dioxane-2,4,6-trione. The electronic spectra, IR and NMR spectra of some complexes were calculated with INDO/SCI, AM1 and B3LYP/6-31G(d) methods, respectively. It is demonstrated that the negative stability energy is responsible for the formation of the complexes. Stabilization energies of these complexes were altered among the variations of electric property and steric effects of the monomers. HOMO-LUMO energy gaps were shrunk and the blue-shift of absorptions in the electronic spectra occurred. The vibrations of N-H bonds and chemical shifts of the protons changed with the formation of hydrogen bonds.

  11. Structure and property of the hydrogen bonding complex between triazines and water

    Institute of Scientific and Technical Information of China (English)

    LI; Quan

    2006-01-01

    Density functional theory B3LYP is employed to obtain the optimized geometries of the ground state and interaction energy for triazines and water complexes. The results show that the 1,2,3-triazine-water, 1,2,4-triazine-water and 1,3,5-triazine-water complex on the ground state have Cs, Cs and C1 symmetry, and strong hydrogen bonding interaction with -17.83, -17.38 and -13.55 kJ/mol after basis set superposition error and zero-point vibration energy correction, respectively, and bond in the triazines complex. The first singlet (n, π*) vertical excitation energy of the monomer and the hydrogen bonding complexes between triazines and water is investigated by time-dependent density functional theory.

  12. Density Functional Theory Study of Hydrogen Bonds of Bipyridine with 1,3,5-Benzenetricarboxylic Acid

    Institute of Scientific and Technical Information of China (English)

    LI Quan; ZHAO Keqing

    2009-01-01

    The hydrogen-bonded dimer and trimer formed between 1,3,5-benzenetricarboxylic acid and bipyridine have been investigated using a density functional theory(DFT)method and 6-31++G** basis set.The interaction enerstretching modes in the dimer and trimer red-shifted relative to those of the 1,3,5-benzenetricarhoxylic acid monomer.The natural bond orbit analysis shows that the inter-molecular charge transfers are 0.60475e and 1.20225e for the dimer and trimer,respectively.Thermodynamic analysis indicates that the formation of trimer is an exothermic H-O intermolecular hydrogen bonds between bipyridine and 1,3,5-benzenetricarboxylic acid,which is in good agreement with the experimental results.

  13. Solid-phase synthesis of short α-helices stabilized by the hydrogen bond surrogate approach.

    Science.gov (United States)

    Patgiri, Anupam; Menzenski, Monica Z; Mahon, Andrew B; Arora, Paramjit S

    2010-11-01

    Stabilized α-helices and nonpeptidic helix mimetics have emerged as powerful molecular scaffolds for the discovery of protein-protein interaction inhibitors. Protein-protein interactions often involve large contact areas, which are often difficult for small molecules to target with high specificity. The hypothesis behind the design of stabilized helices and helix mimetics is that these medium-sized molecules may pursue their targets with higher specificity because of a larger number of contacts. This protocol describes an optimized synthetic strategy for the preparation of stabilized α-helices that feature a carbon-carbon linkage in place of the characteristic N-terminal main-chain hydrogen bond of canonical helices. Formation of the carbon-carbon bond is enabled by a microwave-assisted ring-closing metathesis reaction between two terminal olefins on the peptide chain. The outlined strategy allows the synthesis and purification of a hydrogen bond surrogate (HBS) α-helix in ∼ 1 week.

  14. Variation of persistence length with concentration in a hydrogen bonding polymer solution

    Science.gov (United States)

    Sukumaran, S.; Beaucage, G.

    2000-03-01

    Miscibility of some polymers in water is usually attributed to the ability of the polymer to hydrogen bond with water. Hydrogen bonding contributes a strong interaction component to the free energy that enhances mixing between the polymer and water. It is widely known that certain conformations of the polymer have significantly higher dipole moment and consequently higher affinity for water. If the solvent alters the bond rotation energetics of the polymer it is natural to expect the average local structure of the chain to be affected leading to a change in the persistence length. Small angle neutron scattering experiments were performed on aqueous (D2O) solutions of a polymer (PEO or PVME) at different concentrations to investigate the microscopic structure of these solutions. The persistence length was strongly dependent on concentration. A simple physical explanation for this phenomenon will be provided. Possible ramifications of such a phenomenon in understanding phase behavior will be indicated.

  15. Multiple hydrogen bonding in excited states of aminopyrazine in methanol solution: time-dependent density functional theory study.

    Science.gov (United States)

    Chai, Shuo; Yu, Jie; Han, Yong-Chang; Cong, Shu-Lin

    2013-11-01

    Aminopyrazine (AP) and AP-methanol complexes have been theoretically studied by using density functional theory (DFT) and time-dependent density functional theory (TDDFT). The excited-state hydrogen bonds are discussed in detail. In the ground state the intermolecular multiple hydrogen bonds can be formed between AP molecule and protic solvents. The AP monomer and hydrogen-bonded complex of AP with one methanol are photoexcited initially to the S2 state, and then transferred to the S1 state via internal conversion. However the complex of AP with two methanol molecules is directly excited to the S1 state. From the calculated electronic excited energies and simulated absorption spectra, we find that the intermolecular hydrogen bonds are strengthened in the electronic excited states. The strengthening is confirmed by the optimized excited-state geometries. The photochemical processes in the electronic excited states are significantly influenced by the excited-state hydrogen bond strengthening.

  16. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.

    Science.gov (United States)

    Yesselman, Joseph D; Horowitz, Scott; Brooks, Charles L; Trievel, Raymond C

    2015-03-01

    The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding.

  17. Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations

    DEFF Research Database (Denmark)

    Eildal, Jonas N N; Hultqvist, Greta; Balle, Thomas;

    2013-01-01

    -protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as β-strands to form an extended antiparallel β-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains...... of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding...... to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ΔΔG = 1.3 to >3.8 kcal mol(-1...

  18. Chemical bonding in hydrogen and lithium under pressure

    Energy Technology Data Exchange (ETDEWEB)

    Naumov, Ivan I.; Hemley, Russell J. [Geophysical Laboratory, Carnegie Institution of Washington, 5251 Broad Branch Rd. NW, Washington, DC 20015 (United States); Hoffmann, Roald [Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 (United States); Ashcroft, N. W. [Laboratory of Atomic and Solid State Physics and Cornell Center for Materials Research, Cornell University, Clark Hall, Ithaca, New York 14853 (United States)

    2015-08-14

    Though hydrogen and lithium have been assigned a common column of the periodic table, their crystalline states under common conditions are drastically different: the former at temperatures where it is crystalline is a molecular insulator, whereas the latter is a metal that takes on simple structures. On compression, however, the two come to share some structural and other similarities associated with the insulator-to-metal and metal-to-insulator transitions, respectively. To gain a deeper understanding of differences and parallels in the behaviors of compressed hydrogen and lithium, we performed an ab initio comparative study of these systems in selected identical structures. Both elements undergo a continuous pressure-induced s-p electronic transition, though this is at a much earlier stage of development for H. The valence charge density accumulates in interstitial regions in Li but not in H in structures examined over the same range of compression. Moreover, the valence charge density distributions or electron localization functions for the same arrangement of atoms mirror each other as one proceeds from one element to the other. Application of the virial theorem shows that the kinetic and potential energies jump across the first-order phase transitions in H and Li are opposite in sign because of non-local effects in the Li pseudopotential. Finally, the common tendency of compressed H and Li to adopt three-fold coordinated structures as found is explained by the fact that such structures are capable of yielding a profound pseudogap in the electronic densities of states at the Fermi level, thereby reducing the kinetic energy. These results have implications for the phase diagrams of these elements and also for the search for new structures with novel properties.

  19. Chemical bonding in hydrogen and lithium under pressure.

    Science.gov (United States)

    Naumov, Ivan I; Hemley, Russell J; Hoffmann, Roald; Ashcroft, N W

    2015-08-14

    Though hydrogen and lithium have been assigned a common column of the periodic table, their crystalline states under common conditions are drastically different: the former at temperatures where it is crystalline is a molecular insulator, whereas the latter is a metal that takes on simple structures. On compression, however, the two come to share some structural and other similarities associated with the insulator-to-metal and metal-to-insulator transitions, respectively. To gain a deeper understanding of differences and parallels in the behaviors of compressed hydrogen and lithium, we performed an ab initio comparative study of these systems in selected identical structures. Both elements undergo a continuous pressure-induced s-p electronic transition, though this is at a much earlier stage of development for H. The valence charge density accumulates in interstitial regions in Li but not in H in structures examined over the same range of compression. Moreover, the valence charge density distributions or electron localization functions for the same arrangement of atoms mirror each other as one proceeds from one element to the other. Application of the virial theorem shows that the kinetic and potential energies jump across the first-order phase transitions in H and Li are opposite in sign because of non-local effects in the Li pseudopotential. Finally, the common tendency of compressed H and Li to adopt three-fold coordinated structures as found is explained by the fact that such structures are capable of yielding a profound pseudogap in the electronic densities of states at the Fermi level, thereby reducing the kinetic energy. These results have implications for the phase diagrams of these elements and also for the search for new structures with novel properties.

  20. Spectroscopic identification of ethanol-water conformers by large-amplitude hydrogen bond librational modes

    DEFF Research Database (Denmark)

    Andersen, Jonas; Heimdal, J.; Larsen, René Wugt

    2015-01-01

    assignment of the intermolecular high-frequency out-of-plane and the low-frequency in-plane donor OH librational modes for two different conformations of the mixed binary ethanol/water complex. The resolved donor OH librational bands confirm directly previous experimental evidence that ethanol acts as the O......⋯HO hydrogen bond acceptor in the two most stable conformations. In the most stable conformation, the water subunit forces the ethanol molecule into its less stable gauche configuration upon dimerization owing to a cooperative secondary weak O⋯HC hydrogen bondinteraction evidenced by a significantly blue......-shift of the low-frequency in-plane donor OH librational band origin. The strong correlation between the low-frequency in-plane donor OH librational motion and the secondary intermolecular O⋯HC hydrogen bond is demonstrated by electronic structure calculations. The experimental findings are further supported...

  1. Unconventional N-H…N Hydrogen Bonds Involving Proline Backbone Nitrogen in Protein Structures.

    Science.gov (United States)

    Deepak, R N V Krishna; Sankararamakrishnan, Ramasubbu

    2016-05-10

    Contrary to DNA double-helical structures, hydrogen bonds (H-bonds) involving nitrogen as the acceptor are not common in protein structures. We systematically searched N-H…N H-bonds in two different sets of protein structures. Data set I consists of neutron diffraction and ultrahigh-resolution x-ray structures (0.9 Å resolution or better) and the hydrogen atom positions in these structures were determined experimentally. Data set II contains structures determined using x-ray diffraction (resolution ≤ 1.8 Å) and the positions of hydrogen atoms were generated using a computational method. We identified 114 and 14,347 potential N-H…N H-bonds from these two data sets, respectively, and 56-66% of these were of the Ni+1-Hi+1…Ni type, with Ni being the proline backbone nitrogen. To further understand the nature of such unusual contacts, we performed quantum chemical calculations on the model compound N-acetyl-L-proline-N-methylamide (Ace-Pro-NMe) with coordinates taken from the experimentally determined structures. A potential energy profile generated by varying the ψ dihedral angle in Ace-Pro-NMe indicates that the conformation with the N-H…N H-bond is the most stable. An analysis of H-bond-forming proline residues reveals that more than 30% of the proline carbonyl groups are also involved in n → π(∗) interactions with the carbonyl carbon of the preceding residue. Natural bond orbital analyses demonstrate that the strength of N-H…N H-bonds is less than half of that observed for a conventional H-bond. This study clearly establishes the H-bonding capability of proline nitrogen and its prevalence in protein structures. We found many proteins with multiple instances of H-bond-forming prolines. With more than 15% of all proline residues participating in N-H…N H-bonds, we suggest a new, to our knowledge, structural role for proline in providing stability to loops and capping regions of secondary structures in proteins.

  2. Reordering hydrogen bonds using hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems.

    Science.gov (United States)

    Vreede, Jocelyne; Wolf, Maarten G; de Leeuw, Simon W; Bolhuis, Peter G

    2009-05-07

    Hydrogen bonds play an important role in stabilizing (meta-)stable states in protein folding. Hence, they can potentially be used as a way to bias these states in molecular simulation methods. Previously, Wolf et al. showed that applying repulsive and attractive hydrogen bond biasing potentials in an alternating way significantly accelerates the folding process (Wolf, M. G.; de Leeuw, S. W. Biophys. J. 2008, 94, 3742). As the biasing potentials are only active during a fixed time interval, this alternating scheme does not represent a thermodynamic equilibrium. In this work, we present a Hamiltonian replica exchange molecular dynamics (REMD) scheme that aims to shuffle and reorder hydrogen bonds in the protein backbone. We therefore apply adapted hydrogen bond potentials in a Hamiltonian REMD scheme, which we call hydrogen bond switching (HS). To compare the performance of the HS to a standard REMD method, we performed HS and temperature REMD simulations of a beta-heptapeptide in methanol. Both methods sample the conformational space to a similar extent. As the HS simulation required only five replicas, while the REMD simulation required 20 replicas, the HS method is significantly more efficient. We tested the HS method also on a larger system, 16-residue polyalanine in water. Both of the simulations starting from a completely unfolded and a folded conformation resulted in an ensemble with, apart from the starting structure, similar conformational minima. We can conclude that the HS method provides an efficient way to sample the conformational space of a protein, without requiring knowledge of the folded states beforehand. In addition, these simulations revealed that convergence was hampered by replicas having a preference for specific biasing potentials. As this sorting effect is inherent to any Hamiltonian REMD method, finding a solution will result in an additional increase in the efficiency of Hamiltonian REMD methods in general.

  3. Electronic structure contribution to hydrogen bonding interaction of a water dimer

    CERN Document Server

    Zhang, Zhiyuan; Wang, Bo; Wang, Zhigang

    2016-01-01

    Hydrogen bond (H-bond) covalency has recently been observed in ice and liquid water, while the penetrating molecular orbitals (MOs) in the H-bond region of most typical water dimer system, (H2O)2, have also been discovered. However, obtaining the quantitative contribution of these MOs to the H-bond interaction is still problematic. In this work, we introduced the orbital-resolved electron density projected integral (EDPI) along the H-bond to approach this problem. The calculations show that, surprisingly, the electronic occupied orbital (HOMO-4) of (H2O)2 accounts for about 40% of the electron density at the bond critical point. Moreover, the charge transfer analysis visualizes the electron accumulating effect of the orbital interaction within the H-bond between water molecules, supporting its covalent-like character. Our work expands the classical understanding of H-bond with specific contributions from certain MOs, and will also advance further research into such covalency and offer quantitative electronic ...

  4. Strength and nature of hydrogen bonding interactions in mono- and di-hydrated formamide complexes.

    Science.gov (United States)

    Angelina, Emilio L; Peruchena, Nélida M

    2011-05-12

    In this work, mono- and di-hydrated complexes of the formamide were studied. The calculations were performed at the MP2/6-311++G(d,p) level of approximation. The atoms in molecules theory (AIM), based on the topological properties of the electronic density distribution, was used to characterize the different types of bonds. The analysis of the hydrogen bonds (H-bonds) in the most stable mono- and di-hydrated formamide complexes shows a mutual reinforcement of the interactions, and some of these complexes can be considered as "bifunctional hydrogen bonding hydration complexes". In addition, we analyzed how the strength and the nature of the interactions, in mono-hydrated complexes, are modified by the presence of a second water molecule in di-hydrated formamide complexes. Structural changes, cooperativity, and electron density redistributions demonstrate that the H-bonds are stronger in the di-hydrated complexes than in the corresponding mono-hydrated complexes, wherein the σ- and π-electron delocalization were found. To explain the nature of such interactions, we carried out the atoms in molecules theory in conjunction with reduced variational space self-consistent field (RVS) decomposition analysis. On the basis of the local Virial theorem, the characteristics of the local electron energy density components at the bond critical points (BCPs) (the 1/4∇ (2)ρ(b) component of electron energy density and the kinetic energy density) were analyzed. These parameters were used in conjunction with the electron density and the Laplacian of the electron density to analyze the characteristics of the interactions. The analysis of the interaction energy components for the systems considered indicates that the strengthening of the hydrogen bonds is manifested by an increased contribution of the electrostatic energy component represented by the kinetic energy density at the BCP.

  5. The use of ultrasmall iron(0) nanoparticles as catalysts for the selective hydrogenation of unsaturated C-C bonds.

    Science.gov (United States)

    Kelsen, Vinciane; Wendt, Bianca; Werkmeister, Svenja; Junge, Kathrin; Beller, Matthias; Chaudret, Bruno

    2013-04-28

    The performance of well-defined ultrasmall iron(0) nanoparticles (NPs) as catalysts for the selective hydrogenation of unsaturated C-C and C=X bonds is reported. Monodisperse iron nanoparticles of about 2 nm size are synthesized by the decomposition of {Fe(N[Si(CH3)3]2)2}2 under dihydrogen. They are found to be active for the hydrogenation of various alkenes and alkynes under mild conditions and weakly active for C=O bond hydrogenation.

  6. Industrial Ziegler-type hydrogenation catalysts made from Co(neodecanoate)2 or Ni(2-ethylhexanoate)2 and AlEt3: evidence for nanoclusters and sub-nanocluster or larger Ziegler-nanocluster based catalysis.

    Science.gov (United States)

    Alley, William M; Hamdemir, Isil K; Wang, Qi; Frenkel, Anatoly I; Li, Long; Yang, Judith C; Menard, Laurent D; Nuzzo, Ralph G; Özkar, Saim; Yih, Kuang-Hway; Johnson, Kimberly A; Finke, Richard G

    2011-05-17

    XAFS results also imply that the catalyst solutions are a mixture of the metal clusters described above, plus unreduced metal ions. The kinetics-based Hg(0) poisoning evidence suggests that Co and Ni Ziegler nanoclusters (i.e., M(≥4)) are the most active Ziegler-type hydrogenation catalysts in these industrial systems. Overall, the novelty and primary conclusions of this study are as follows: (i) this study examines Co- and Ni-based catalysts made from the actual industrial precursor materials, catalysts that are notoriously problematic regarding their characterization; (ii) the Z-contrast STEM results reported herein represent, to our knowledge, the best microscopic analysis of the industrial Co and Ni Ziegler-type hydrogenation catalysts; (iii) this study is the first explicit application of an established method, using multiple analytical methods and kinetics-based studies, for distinguishing homogeneous from heterogeneous catalysis in these Ziegler-type systems; and (iv) this study parallels the successful study of an Ir model Ziegler catalyst system, thereby benefiting from a comparison to those previously unavailable findings, although the greater M-M bond energy, and tendency to agglomerate, of Ir versus Ni or Co are important differences to be noted. Overall, the main result of this work is that it provides the leading hypothesis going forward to try to refute in future work, namely, that sub, M(≥4) to larger, M(n) Ziegler nanoclusters are the dominant, industrial, Co- and Ni- plus AlR(3) catalysts in Ziegler-type hydrogenation systems.

  7. Bio-inspired transition metal-organic hydride conjugates for catalysis of transfer hydrogenation: experiment and theory.

    Science.gov (United States)

    McSkimming, Alex; Chan, Bun; Bhadbhade, Mohan M; Ball, Graham E; Colbran, Stephen B

    2015-02-09

    Taking inspiration from yeast alcohol dehydrogenase (yADH), a benzimidazolium (BI(+) ) organic hydride-acceptor domain has been coupled with a 1,10-phenanthroline (phen) metal-binding domain to afford a novel multifunctional ligand (L(BI+) ) with hydride-carrier capacity (L(BI+) +H(-) ⇌L(BI) H). Complexes of the type [Cp*M(L(BI) )Cl][PF6 ]2 (M=Rh, Ir) have been made and fully characterised by cyclic voltammetry, UV/Vis spectroelectrochemistry, and, for the Ir(III) congener, X-ray crystallography. [Cp*Rh(L(BI) )Cl][PF6 ]2 catalyses the transfer hydrogenation of imines by formate ion in very goods yield under conditions where the corresponding [Cp*Ir(L(BI) )Cl][PF6 ] and [Cp*M(phen)Cl][PF6 ] (M=Rh, Ir) complexes are almost inert as catalysts. Possible alternatives for the catalysis pathway are canvassed, and the free energies of intermediates and transition states determined by DFT calculations. The DFT study supports a mechanism involving formate-driven RhH formation (90 kJ mol(-1) free-energy barrier), transfer of hydride between the Rh and BI(+) centres to generate a tethered benzimidazoline (BIH) hydride donor, binding of imine substrate at Rh, back-transfer of hydride from the BIH organic hydride donor to the Rh-activated imine substrate (89 kJ mol(-1) barrier), and exergonic protonation of the metal-bound amide by formic acid with release of amine product to close the catalytic cycle. Parallels with the mechanism of biological hydride transfer in yADH are discussed.

  8. Final Report: Cathode Catalysis in Hydrogen/Oxygen Fuel Cells: New Catalysts, Mechanism, and Characterization

    Energy Technology Data Exchange (ETDEWEB)

    Gewirth, Andrew A. [Univ. of Illinois, Urbana, IL (United States). Dept. of Chemistry; Kenis, Paul J. [Univ. of Illinois, Urbana, IL (United States). Dept. of Chemical and Biomolecular Engineering; Nuzzo, Ralph G. [Univ. of Illinois, Urbana, IL (United States). Dept. of Chemistry; Rauchfuss, Thomas B. [Univ. of Illinois, Urbana, IL (United States). Dept. of Chemistry

    2016-01-18

    In this research, we prosecuted a comprehensive plan of research directed at developing new catalysts and new understandings relevant to the operation of low temperature hydrogen-oxygen fuel cells. The focal point of this work was one centered on the Oxygen Reduction Reaction (ORR), the electrochemical process that most fundamentally limits the technological utility of these environmentally benign energy conversion devices. Over the period of grant support, we developed new ORR catalysts, based on Cu dimers and multimers. In this area, we developed substantial new insight into design rules required to establish better ORR materials, inspired by the three-Cu active site in laccase which has the highest ORR onset potential of any material known. We also developed new methods of characterization for the ORR on conventional (metal-based) catalysts. Finally, we developed a new platform to study the rate of proton transfer relevant to proton coupled electron transfer (PCET) reactions, of which the ORR is an exemplar. Other aspects of work involved theory and prototype catalyst testing.

  9. Catalysis with Cu(II) (bpy) improves alkaline hydrogen peroxide pretreatment.

    Science.gov (United States)

    Li, Zhenglun; Chen, Charles H; Liu, Tongjun; Mathrubootham, Vaidyanathan; Hegg, Eric L; Hodge, David B

    2013-04-01

    Copper(II) 2,2'-bipyridine (Cu(II) (bpy))-catalyzed alkaline hydrogen peroxide (AHP) pretreatment was performed on three biomass feedstocks including alkali pre-extracted switchgrass, silver birch, and a hybrid poplar cultivar. This catalytic approach was found to improve the subsequent enzymatic hydrolysis of plant cell wall polysaccharides to monosaccharides for all biomass types at alkaline pH relative to uncatalyzed pretreatment. The hybrid poplar exhibited the most significant improvement in enzymatic hydrolysis with monomeric sugar release and conversions more than doubling from 30% to 61% glucan conversion, while lignin solubilization was increased from 36.6% to 50.2% and hemicellulose solubilization was increased from 14.9% to 32.7%. It was found that Cu(II) (bpy)-catalyzed AHP pretreatment of cellulose resulted in significantly more depolymerization than uncatalyzed AHP pretreatment (78.4% vs. 49.4% decrease in estimated degree of polymerization) and that carboxyl content the cellulose was significantly increased as well (fivefold increase vs. twofold increase). Together, these results indicate that Cu(II) (bpy)-catalyzed AHP pretreatment represents a promising route to biomass deconstruction for bioenergy applications.

  10. Influence of the interfacial peptide organization on the catalysis of hydrogen evolution.

    Science.gov (United States)

    Doneux, Th; Dorcák, V; Palecek, E

    2010-01-19

    The hydrogen evolution reaction is catalyzed by peptides and proteins adsorbed on electrode materials with high overpotentials for this reaction, such as mercury. The catalytic response characteristics are known to be very sensitive to the composition and structure of the investigated biomolecule, opening the way to the implementation of a label-free, reagentless electroanalytical method in protein analysis. Herein, it is shown using the model peptide Cys-Ala-Ala-Ala-Ala-Ala that the interfacial organization significantly influences the catalytic behavior. This peptide forms at the electrode two distinct films, depending on the concentration and accumulation time. The low-coverage film, composed of flat-lying molecules (area per molecule of approximately 250-290 A(2)), yields a well-defined catalytic peak at potentials around -1.75 V. The high-coverage film, made of upright-oriented peptides (area per molecule of approximately 43 A(2)), is catalytically more active and the peak is observed at potentials less negative by approximately 0.4 V. The higher activity, evidenced by constant-current chronopotentiometry and cyclic voltammetry, is attributed to an increase in the acid dissociation constant of the amino acid residues as a result of the low permittivity of the interfacial region, as inferred from impedance measurements. An analogy is made to the known differences in acidic-basic behaviors of solvent-exposed and hydrophobic domains of proteins.

  11. RAFT Polymerization of Styrene and Maleimide in the Presence of Fluoroalcohol: Hydrogen Bonding Effects with Classical Alternating Copolymerization as Reference

    Directory of Open Access Journals (Sweden)

    Fangjun Yao

    2017-03-01

    Full Text Available The impacts of hydrogen bonding on polymerization behavior has been of interest for a long time; however, universality and in-depth understanding are still lacking. For the first time, the effect of hydrogen bonding on the classical alternating-type copolymerization of styrene and maleimide was explored. N-phenylmaleimide (N-PMI/styrene was chosen as a model monomer pair in the presence of hydrogen bonding donor solvent 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP, which interacted with N-PMI via hydrogen bonding. Reversible addition-fragmentation chain transfer polymerization (RAFT technique was used to guarantee the “living” polymerization and thus the homogeneity of chain compositions. In comparison with the polymerization in nonhydrogen bonding donor solvent (toluene, the copolymerization in HFIP exhibited a high rate and a slight deviation from alternating copolymerization tendency. The reactivity ratios of N-PMI and St were revealed to be 0.078 and 0.068, respectively, while the reactivity ratios in toluene were 0.026 and 0.050. These interesting results were reasonably explained by using computer simulations, wherein the steric repulsion and electron induction by the hydrogen bonding between HFIP and NPMI were revealed. This work first elucidated the hydrogen bonding interaction in the classical alternating-type copolymerization, which will enrich the research on hydrogen bonding-induced polymerizations.

  12. Theoretical Studies on the Hydrogen Bond Transfer and Proton Transfer between Anamorphoses of the Dihydrated Glycine Complex

    Institute of Scientific and Technical Information of China (English)

    WANG Ke-Cheng; MENG Xiang-Jun; SHI Jin; LI Bing-Huan

    2007-01-01

    The conversion between anamorphoses of the dihydrated glycine complex was studied by means of B3LYP/6-31++G**. It was found that proton transfer was accompanied by hydrogen bond transfer in the process of conversion between different kinds of anamorphoses. With proton transfer, the electrostatic action was notably increased and the hydrogen-bonding action was evidently strengthened when the dihydrated neutral glycine complex converts into dihydrated zwitterionic glycine complex. The activation energy required for hydrogen bond transfer between dihydrated neutral glycine complexes is very low (6.32 kJ·mol-1); however, the hydrogen bond transfer between dihydrated zwitterionic glycine complexes is rather difficult with the required activation energy of 13.52 kJ·mol-1 due to the relatively strong electrostatic action. The activation energy required by proton transfer is at least 27.33 kJ·mol-1, higher than that needed for hydrogen bond transfer. The activation energy for either hydrogen bond transfer or proton transfer is in the bond-energy scope of medium-strong hydrogen bond, so the four kinds of anamorphoses of the dihydrated glycine complex could convert mutually.

  13. O-H···S hydrogen bonds conform to the acid-base formalism.

    Science.gov (United States)

    Bhattacharyya, Surjendu; Bhattacherjee, Aditi; Shirhatti, Pranav R; Wategaonkar, Sanjay

    2013-08-29

    Hydrogen bonding interaction between the ROH hydrogen bond donor and sulfur atom as an acceptor has not been as well characterized as the O-H···O interaction. The strength of O-H···O interactions for a given donor has been well documented to scale linearly with the proton affinity (PA) of the H-bond acceptor. In this regard, O-H···O interactions conform to the acid-base formalism. The importance of such correlation is to be able to estimate molecular property of the complex from the known thermodynamic data of its constituents. In this work, we investigate the properties of O-H···S interaction in the complexes of the H-bond donor and sulfur containing acceptors of varying proton affinity. The hydrogen bonded complexes of p-Fluorophenol (FP) with four different sulfur containing acceptors and their oxygen analogues, namely H2O/H2S, MeOH/MeSH, Me2O/Me2S and tetrahydrofuran (THF)/tetrahydrothiophene (THT) were characterized in regard to its S1-S0 excitation spectra and the IR spectra. Two-color resonantly enhanced multiphoton ionization (2c-R2PI), resonant ion-dip infrared (RIDIR) spectroscopy, and IR-UV hole burning spectroscopic techniques were used to probe the hydrogen bonds in the aforementioned complexes. The spectroscopic data along with the ab initio calculations were used to deduce the strength of the O-H···S hydrogen bonding interactions in these system relative to that in the O-H···O interactions. It was found that, despite being dominated by the dispersion interaction, the O-H···S interactions conform to the acid-base formalism as in the case of more conventional O-H···O interactions. The dissociation energies and the red shifts in the O-H stretching frequencies correlated very well with the proton affinity of the acceptors. However, the O-H···S interaction did not follow the same correlation as that in the O-H···O H-bond. The energy decomposition analysis showed that the dissociation energies and the red shifts in the O

  14. Large Angular Jump Mechanism Observed for Hydrogen Bond Exchange in Aqueous Perchlorate Solution

    Energy Technology Data Exchange (ETDEWEB)

    Ji, Minbiao; /SLAC, PULSE /Stanford U., Phys. Dept.; Odelius3, Michael; /Stockholm U.; Gaffney1, K.J.; /aff SLAC, PULSE

    2010-06-11

    The mechanism for hydrogen bond (H-bond) switching in solution has remained subject to debate despite extensive experimental and theoretical studies. We have applied polarization-selective multidimensional vibrational spectroscopy to investigate the H-bond exchange mechanism in aqueous NaClO{sub 4} solution. The results show that a water molecule shifts its donated H-bonds between water and perchlorate acceptors by means of large, prompt angular rotation. Using a jump-exchange kinetic model, we extract an average jump angle of 49 {+-} 4{sup o}, in qualitative agreement with the jump angle observed in molecular dynamics simulations of the same aqueous NaClO{sub 4} solution.

  15. Molecular structure and intramolecular hydrogen bonding in 2-hydroxybenzophenones: A theoretical study

    Indian Academy of Sciences (India)

    Mansoureh Zahedi-Tabrizi; Sayyed Faramarz Tayyari; Farideh Badalkhani-Khamseh; Reihaneh Ghomi; Fatemeh Afshar-Qahremani

    2014-07-01

    The intramolecular hydrogen bonding (IHB) in a series of 3-, 4- and 5-substituted 2-hydroxybenzophenone (HBP) is studied using density functional theory calculations. All calculations are performed at the B3LYP level, using 6-311++G∗∗ basis set. To understand the substitution effects on the nature of IHB and the electronic structure of the chelated ring system, the vibrational frequencies, 1H chemical shift, topological parameters, natural bond orders and natural charges over atoms involved in the chelated ring of HBP and its derivatives were calculated. TheWiberg bond indices and the natural charges over atoms involved in the chelated ring have been computed using the natural bond orbital (NBO) analysis. The computations were further complemented with an atoms-in-molecules (AIM) topological analysis to characterize the nature of the IHB in the considered molecules. Several correlations between geometrical parameters, 1H NMR chemical shift and topological parameters with the IHB strength are obtained.

  16. Hydrogen bond dynamics in liquid water: Ab initio molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Cheolhee; Kim, Eunae [College of Pharmacy, Chosun University, Gwangju (Korea, Republic of); Yeom, Min Sun [Korea Institute of Science and Technology Information, Daejeon (Korea, Republic of)

    2016-01-15

    The effect of intermolecular interaction on the distribution of the harmonic vibrational frequencies of water molecules was investigated through ab initio molecular dynamics simulations based on the Born-Oppenheimer approach. For single water, the effect of the dynamics of the oxygen atom in single water and the simulation time step on the frequency distribution were examined. The distributions of the OH stretching and HOH bending vibrational frequencies of liquid water were compared to those of single water. The probability distributions of the change in OH bond length and the lifetime of the dangling OH bond were also obtained. The distribution of the frequencies was strongly affected by the long lifetime of the dangling OH bond, resulting in the formation of hydrogen bonds between water molecules.

  17. Halogen- and hydrogen-bonding catenanes for halide-anion recognition.

    Science.gov (United States)

    Gilday, Lydia C; Beer, Paul D

    2014-07-01

    Halogen-bonding (XB) interactions were exploited in the solution-phase assembly of anion-templated pseudorotaxanes between an isophthalamide-containing macrocycle and bromo- or iodo-functionalised pyridinium threading components. (1)H NMR spectroscopic titration investigations demonstrated that such XB interpenetrated assemblies are more stable than analogous hydrogen bonding (HB) pseudorotaxanes. The stability of the anion-templated halogen-bonded pseudorotaxane architectures was exploited in the preparation of new halogen-bonding interlocked catenane species through a Grubbs' ring-closing metathesis (RCM) clipping methodology. The catenanes' anion recognition properties in the competitive CDCl(3)/CD(3) OD 1:1 solvent mixture revealed selectivity for the heavier halides iodide and bromide over chloride and acetate.

  18. Molecular modeling of heterogeneous catalysis

    Science.gov (United States)

    Gislason, Jason Joseph

    A novel method for modeling heterogeneous catalysis was developed to further facilitate the understanding of catalytic reactor mechanisms. The method employs molecular dynamics simulations, statistical mechanical, and Unity Bond Index - Quadratic Exponential Potential (UBI-QEP) calculations to calculate the rate constants for reactions on metal surfaces. The primary difficulty of molecular dynamics simulations on metal surfaces has been the lack of reliable reactive potential energy surfaces. We have overcome this through the development of the Normalized Bond Index - Reactive Potential Function (NBI-RPF), which can accurately describe the reaction of adsorbates on metal surfaces. The first calculations of rate constants for a reaction on a metal surface using molecular dynamics simulations are presented. This method is applied to the determination of the mechanism for selective hydrogenation of acetylene in an ethylene rich flow. It was determined that the selectivity for acetylene hydrogenation is attributable to the higher reactivity of acetylene versus ethylene with respect to hydrogenation by molecular hydrogen. It was shown that hydrogen transfer from the carbonaceous layer to acetylene or ethylene is insignificant in the hydrogenation process. Molecular dynamics simulations and molecular mechanics calculations were used to determine the diffusion rate constants for dimethylnaphthalene isomers is mordenite. 2,6-dimethylnaphthalene and 2,7-dimethylnaphthalene were found to have similar diffusion rate constants. Grand canonical Monte Carlo calculations were performed on the competitive adsorption of 2,6-dimethylnaphthalene and 2,7-dimethylnaphthalene in type X zeolites exchanged individually with barium, calcium, potassium, and rubidium ions, calcium exchanged MCM-22, and hydrogen form mordenite (MOR), X zeolite, Y zeolite, hypBEB, ZSM- 12, and MCM-22. These calculations showed that barium exchanged X zeolite was the most selective toward 2

  19. NQR application to the study of hydrogen dynamics in hydrogen-bonded molecular dimers

    Science.gov (United States)

    Asaji, Tetsuo

    2016-12-01

    The temperature dependences of 1H NMR as well as 35Cl NQR spin-lattice relaxation times T 1 were investigated in order to study the hydrogen transfer dynamics in carboxylic acid dimers in 3,5-dichloro- and 2,6-dichlorobenzoic acids. The asymmetry energy A/ k B and the activation energy V/ k B for the hydrogen transfer were estimated to be 240 K and 900 K, and 840 K and 2500 K, respectively, for these compounds. In spite of a large asymmetric potential the quantum nature of hydrogen transfer is recognized in the slope of the temperature dependence of T 1 on the low-temperature side of the T 1 minimum. The NQR T 1 measurements was revealed to be a good probe for the hydrogen transfer dynamics.

  20. Molecular water oxidation catalysis

    CERN Document Server

    Llobet, Antoni

    2014-01-01

    Photocatalytic water splitting is a promising strategy for capturing energy from the sun by coupling light harvesting and the oxidation of water, in order to create clean hydrogen fuel. Thus a deep knowledge of the water oxidation catalysis field is essential to be able to come up with useful energy conversion devices based on sunlight and water splitting. Molecular Water Oxidation Catalysis: A Key Topic for New Sustainable Energy Conversion Schemes presents a comprehensive and state-of-the-art overview of water oxidation catalysis in homogeneous phase, describing in detail the most importan

  1. Statistical theory for hydrogen bonding fluid system of A_aD_d type(Ⅲ):Equation of state and fluctuations

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The equation of the state of the hydrogen bonding fluid system of AaDd type is studied by the principle of statistical mechanics. The influences of hydrogen bonds on the equation of state of the system are obtained based on the change in volume due to hydrogen bonds. Moreover,the number density fluc-tuations of both molecules and hydrogen bonds as well as their spatial correlation property are inves-tigated. Furthermore,an equation describing relation between the number density correlation function of "molecules-hydrogen bonds" and that of molecules and hydrogen bonds is derived. As application,taking the van der Waals hydrogen bonding fluid as an example,we considered the effect of hydrogen bonds on its relevant statistical properties.

  2. Density Functional Theory Study of Red-shifted Hydrogen Bonds of 4-Pyridinemethanol with Water

    Institute of Scientific and Technical Information of China (English)

    LI Quan; CAI Jing; CHEN Jun-Rong; ZHAO Ke-Qing

    2008-01-01

    The hydrogen bonds of 1∶1 and 1∶2 complexes formed between 4-pyridinemethanol and water have been investigated using a density functional theory (DFT) method and 6-311++G** basis set, and three and eight stable geometries have been obtained for 1∶1 and 1∶2 complexes, respectively.The interaction energy is -20.536 and -44.256 kJ/mol for the most stable 1∶1 and 1∶2 complexes, respectively, after the basis set superposition error and zero-point corrections.The formation of O-H…N(O) hydrogen bonds makes O-H symmetric stretching modes in the complexes red-shifted relative to those of the monomer.The natural bond orbit analysis indicates that the intermolecular charge transfer between 4-pyridinemethanol and water is 0.02642 e and 0.03813 e for the most stable 1∶1 and 1∶2 complexes, respectively.In addition, TD-B3LYP/6-311++G** calculations show that formation of water-OH…N and water-OH…OH hydrogen bonds makes maximum absorbance wavelength λmax blue-shifted 8-16 nm and red-shifted 4-11 nm compared to that of 4-pyridinemethanol monomer molecule, respectively.

  3. Investigation on Thermal and Optical Properties of Hydrogen-Bonded Binary Liquid Crystals

    Science.gov (United States)

    Ranjeeth kumar, T.; Sundaram, S.; Vasanthi, T.; Subhasri, P.; Chitravel, T.; Senthil, T. S.; Jayaprakasam, R.; Vijayakumar, V. N.

    2016-12-01

    A homologous series of hydrogen-bonded liquid crystals (HBLCs) are synthesized and characterized. Intermolecular hydrogen bonding occurs between 4-methoxycinnamic acid (4MCA) and p-n-alkyloxy benzoic acids (nOBA, where n = 3, 7 to 12). These binary complexes have been obtained by following well-designed synthesis route. The subsequent binary complexes have been characterized by polarizing optical thermal microscopy (POM), differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR). The present work explains the details of the association between the mesogenic phase behavior and H-bonding in the homologous series of 4MCA + nOBA. Nematic phase is interrelated with the closed dimers between acid molecules through the formation of strong hydrogen bonds. But, high concentrations are linked to the manifestation of smectic phases that disturb the local order of the nematic phase. As a result, the higher-order mesophases are observed in the present binary complex series. The inclusion of nematic LC (4MCA) in the nOBA alters the melting temperature and the clearing temperature as lower than those of the individual. Also, the wide mesophase regions of the present series are identified compared to those of the constituent mesogens. The optical tilt angle of binary mixtures for smectic C phase and thermal stability factors of the mesogenic phases have been discussed.

  4. Stabilities and Spectroscopy of Hydrogen Bonding Complexes Formed by 2,4-Bis(acrylamido)pyrimidines

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ye; LI Ting; TENG Qi-Wen

    2008-01-01

    Hydrogen bonds play important roles to living organisms containing pyrimidine-based derivatives.The electronic structures of the hydrogen bonding complexes formed by 2,4-bis(acrylamido)pyrimidine (2,4-BAAP) derivatives with 1-substituted uracil were studied using Austin Model 1 (AMl) and density function theory (DFT) methods.The UV and NMR spectra of the complexes were calculated with the INDO/CIS (configuration interaction for singlet in intermediate neglect of differential overlap) and B3LYP/6-31G(d)methods.It was shown that the complexes could be formed via the triple hydrogen bonding between two monomers owing to the negative binding energies.The binding energies of the complexes were weakened in the presence of substituents,but this weakening effect depended on the simultaneous influence of the electronic and steric effects.The binding energies of the complexes were also decreased owing to the formation of the isomeric complexes in the presence of piperidyl on 2,4-BAAP.The energy gaps of the complexes were lessened in the presence of electron-donating groups.Holes and electrons were easily injected to the complexes due to the extension of the conjugation chain.The first UV absorptions of the complexes relative to those of the parent compound were red-shifted because of the narrow energy gaps.The chemical shifts of the carbon atoms on the C=O bonds in the complexes were changed downfield.

  5. The Role of Molecule Clustering by Hydrogen Bond in Hydrous Ethanol on Laminar Burning Velocity

    Directory of Open Access Journals (Sweden)

    I Made Suarta

    2016-01-01

    Full Text Available The role of hydrogen bond molecule clustering in laminar burning velocities was observed. The water in hydrous ethanol can change the interaction between water-ethanol molecules. A certain amount of water can become oxygenated which increases the burning velocity. The hydrogen bond interaction pattern of ethanol and water molecules was modeled. Based on the molecular model, azeotropic behavior emerges from ethanol-water hydrogen bond, which is at a 95.1%v composition. The interaction with water molecule causes the ethanol molecule to be clustered with centered oxygenated compound. So, it supplies extra oxygen and provides intermolecular empty spaces that are easily infiltrated by the air. In the azeotropic composition, the molecular bond chain is the shortest, so hypothetically the burning velocity is anticipated to increase. The laminar burning velocity of ethanol fuel was tested in a cylindrical explosion bomb in lean, stoichiometric, and rich mixtures. The experimental result showed that the maximum burning velocity occurred at hydrous ethanol of 95.5%v composition. This discrepancy is the result of the addition of energy from 7.7% free ethanol molecules that are not clustered. At the rich mixture, the burning velocity of this composition is higher than that of anhydrous ethanol.

  6. Photochemistry of hydrogen bonded heterocycles probed by photodissociation experiments and ab initio methods.

    Science.gov (United States)

    Slavíček, Petr; Fárník, Michal

    2011-07-14

    In this perspective article, we focus on the photochemistry of five-membered nitrogen containing heterocycles (pyrrole, imidazole and pyrazole) in clusters. These heterocycles represent paradigmatic structures for larger biologically active heterocyclic molecules and complexes. The dimers of the three molecules are also archetypes of different bonding patterns: N-H···π interaction, N-H···N hydrogen bond and double hydrogen bond. We briefly review available data on photochemistry of the title molecules in the gas phase, but primarily we focus on the new reaction channels opened upon the complexation with other heterocycles or solvent molecules. Based on ab initio calculations we discuss various possible reactions in the excited states of the clusters: (1) hydrogen dissociation, (2) hydrogen transfer between the heterocyclic units, (3) molecular ring distortion, and (4) coupled electron-proton transfer. The increasing photostability with complexity of the system can be inferred from experiments with photodissociation in these clusters. A unified view on photoinduced processes in five-membered N-heterocycles is provided. We show that even though different deactivation channels are energetically possible for the complexed heterocycles, in most cases the major result is a fast reconstruction of the ground state. The complexed or solvated heterocycles are thus inherently photostable although the stability can in principle be achieved via different reaction routes.

  7. A molecular dynamics study of guest-host hydrogen bonding in alcohol clathrate hydrates.

    Science.gov (United States)

    Hiratsuka, Masaki; Ohmura, Ryo; Sum, Amadeu K; Alavi, Saman; Yasuoka, Kenji

    2015-05-21

    Clathrate hydrates are typically stabilized by suitably sized hydrophobic guest molecules. However, it has been experimentally reported that isomers of amyl-alcohol C5H11OH can be enclosed into the 5(12)6(4) cages in structure II (sII) clathrate hydrates, even though the effective radii of the molecules are larger than the van der Waals radii of the cages. To reveal the mechanism of the anomalous enclathration of hydrophilic molecules, we performed ab initio and classical molecular dynamics simulations (MD) and analyzed the structure and dynamics of a guest-host hydrogen bond for sII 3-methyl-1-butanol and structure H (sH) 2-methyl-2-butanol clathrate hydrates. The simulations clearly showed the formation of guest-host hydrogen bonds and the incorporation of the O-H group of 3-methyl-1-butanol guest molecules into the framework of the sII 5(12)6(4) cages, with the remaining hydrophobic part of the amyl-alcohol molecule well accommodated into the cages. The calculated vibrational spectra of alcohol O-H bonds showed large frequency shifts due to the strong guest-host hydrogen bonding. The 2-methyl-2-butanol guests form strong hydrogen bonds with the cage water molecules in the sH clathrate, but are not incorporated into the water framework. By comparing the structures of the alcohols in the hydrate phases, the effect of the location of O-H groups in the butyl chain of the guest molecules on the crystalline structure of the clathrate hydrates is indicated.

  8. New insights about the hydrogen bonds formed between acetylene and hydrogen fluoride: π ⋯ H, C ⋯ H and F ⋯ H

    Science.gov (United States)

    Silva, Denize S.; Oliveira, Boaz G.

    2017-02-01

    A theoretical study of hydrogen bond strength and bond properties in the C2H2 ⋯(HF)-T, C2H2 ⋯ 2(HF)-T, C2H2 ⋯ 2(HF), C2H2 ⋯ 3(HF) and C2H2 ⋯ 4(HF) complexes was carried out at the B3LYP/6-311 ++G(d,p) theory level. In these systems, a strength competition between the π ⋯ H and C ⋯ H interactions was examined. Specifically the F ⋯ H hydrogen bond, its properties were studied through a comparison between the hydrogen fluoride and the higher-order complexes (trimer, tetramer and pentamer). Regarding the electronic properties, the hydrogen bond strength could not be determined by the supermolecule approach. Thus, the hydrogen bond energies were computed via NBO calculations. Additionally to NBO, the ChelpG charge calculations were used to interpret the intermolecular charge transfer. The QTAIM integrations were useful to predict the covalent character of the π ⋯ H, C ⋯ H and F ⋯ H hydrogen bonds. Moreover, values of hybrid orbitals (s and p) and atomic radii were also determined in order to justify the red shifts in the stretch frequencies of the Hsbnd F bonds.

  9. Solvent-induced differentiation of protein backbone hydrogen bonds in calmodulin.

    Science.gov (United States)

    Juranić, Nenad; Atanasova, Elena; Streiff, John H; Macura, Slobodan; Prendergast, Franklyn G

    2007-07-01

    In apo and holoCaM, almost half of the hydrogen bonds (H-bonds) at the protein backbone expected from the corresponding NMR or X-ray structures were not detected by h3JNC' couplings. The paucity of the h3JNC' couplings was considered in terms of dynamic features of these structures. We examined a set of seven proteins and found that protein-backbone H-bonds form two groups according to the h3JNC' couplings measured in solution. H-bonds that have h3JNC' couplings above the threshold of 0.2 Hz show distance/angle correlation among the H-bond geometrical parameters, and appear to be supported by the backbone dynamics in solution. The other H-bonds have no such correlation; they populate the water-exposed and flexible regions of proteins, including many of the CaM helices. The observed differentiation in a dynamical behavior of backbone H-bonds in apo and holoCaM appears to be related to protein functions.

  10. Structural, intramolecular hydrogen bonding and vibrational studies on 3-amino-4-methoxy benzamide using density functional theory

    Indian Academy of Sciences (India)

    G SUBHAPRIYA; S KALYANARAMAN; S GANDHIMATHI; N SURUMBARKUZHALI; V KRISHNAKUMAR

    2017-02-01

    An extensive theoretical study on the molecular structure and vibrational analysis of 3-amino-4- methoxy benzamide (3A4MBA) was undertaken using density functional theoretical (DFT) method. The possibility of formation of intramolecular hydrogen bonding was identified from structural parameter analysis and confirmed with the natural bond orbital (NBO), molecular electrostatic potential (MEP) and natural charge analysis. The harmonic oscillator model of aromaticity (HOMA) index elucidated the impact of hydrogen bonding in the ring. Intramolecular hydrogen bonding energy has been calculated from topological study. The lowwavenumber vibrational modes obtained from experimental FT-Raman spectrum also supported the presence of hydrogen bonding. Bands are assigned for vibrational frequencies using DFT/B3LYP/6-311++G** level of theory.

  11. Hydrogen bond dynamics and vibrational spectral diffusion in aqueous solution of acetone: A first principles molecular dynamics study

    Indian Academy of Sciences (India)

    Bhabani S Mallik; Amalendu Chandra

    2012-01-01

    We present an ab initio molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous solution of acetone at room temperature. It is found that the frequencies of OD bonds in the acetone hydration shell have a higher stretch frequency than those in the bulk water. Also, on average, the frequencies of hydration shell OD modes are found to increase with increase in the acetone-water hydrogen bond distance. The vibrational spectral diffusion of the hydration shell water molecules reveals three time scales: A short-time relaxation (∼80 fs) corresponding to the dynamics of intact acetone-water hydrogen bonds, a slower relaxation (∼1.3 ps) corresponding to the lifetime of acetone-water hydrogen bonds and another longer time constant (∼12 ps) corresponding to the escape dynamics of water from the solute hydration shell. The present first principles results are compared with those of available experiments and classical simulations.

  12. Carbon-tuned bonding method significantly enhanced the hydrogen storage of BN-Li complexes.

    Science.gov (United States)

    Deng, Qing-ming; Zhao, Lina; Luo, You-hua; Zhang, Meng; Zhao, Li-xia; Zhao, Yuliang

    2011-11-01

    Through first-principles calculations, we found doping carbon atoms onto BN monolayers (BNC) could significantly strengthen the Li bond on this material. Unlike the weak bond strength between Li atoms and the pristine BN layer, it is observed that Li atoms are strongly hybridized and donate their electrons to the doped substrate, which is responsible for the enhanced binding energy. Li adsorbed on the BNC layer can serve as a high-capacity hydrogen storage medium, without forming clusters, which can be recycled at room temperature. Eight polarized H(2) molecules are attached to two Li atoms with an optimal binding energy of 0.16-0.28 eV/H(2), which results from the electrostatic interaction of the polarized charge of hydrogen molecules with the electric field induced by positive Li atoms. This practical carbon-tuned BN-Li complex can work as a very high-capacity hydrogen storage medium with a gravimetric density of hydrogen of 12.2 wt%, which is much higher than the gravimetric goal of 5.5 wt % hydrogen set by the U.S. Department of Energy for 2015.

  13. The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain.

    Directory of Open Access Journals (Sweden)

    Søren W. Pedersen

    Full Text Available Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds and destabilizes hydrogen bonds formed by the carbonyl oxygen. The overall stability of the PDZ domain generally decreased for all amide-to-ester mutants due to an increase in the unfolding rate constant. For this particular region of the PDZ domain, it is therefore clear that native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding. Moreover, three of the five amide-to-ester mutants displayed an increase in the folding rate constant suggesting that the hydrogen bonds are involved in non-native interactions in the transition state for folding.

  14. Small-molecule recognition for controlling molecular motion in hydrogen-bond-assembled rotaxanes.

    Science.gov (United States)

    Martinez-Cuezva, Alberto; Berna, Jose; Orenes, Raul-Angel; Pastor, Aurelia; Alajarin, Mateo

    2014-06-23

    Di(acylamino)pyridines successfully template the formation of hydrogen-bonded rotaxanes through five-component clipping reactions. A solid-state study showed the participation of the pyridine nitrogen atom in the stabilization of the mechanical bond between the thread and the benzylic amide macrocycle. The addition of external complementary binders to a series of interlocked bis(2,6-di(acylamino)pyridines) promoted restraint of the back and forward ring motion. The original translation can be restored through a competitive recognition event by the addition of a preorganized bis(di(acylamino)pyridine) that forms stronger ADA-DAD complexes with the external binders.

  15. Chemical Bonding States of TiC Films before and after Hydrogen Ion Irradiation

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    TiC films deposited by rf magnetron sputtering followed by Ar+ ion bombardment were irradiated with a hydrogen ion beam. X-ray photoelectron spectroscopy (XPS) was used for characterization of the chemical bonding states of C and Ti elements of the TiC films before and after hydrogen ion irradiation, in order to understand the effect of hydrogen ion irradiation on the films and to study the mechanism of hydrogen resistance of TiC films. Conclusions can be drawn that ion bombardment at moderate energy can cause preferential physical sputtering of carbon atoms from the surface of low atomic number (Z) material. This means that ion beam bombardment leads to the formation of a non-stoichiometric composition of TiC on the surface.TiC films prepared by ion beam mixing have the more excellent characteristic of hydrogen resistance. One important cause, in addition to TiC itself, is that there are many vacant sites in TiC created by ion beam mixing.These defects can easily trap hydrogen and effectively enhance the effect of hydrogen resistance.

  16. On the Correlation between the Blue Shift of Hydrogen Bonding and the Proton Donor-Proton Acceptor Distance

    Institute of Scientific and Technical Information of China (English)

    WANG,Jin-Ti(王金姼); FENG,Yong(封勇); LIU,Lei(刘磊); LI,Xiao-Song(李晓松); GUO,Qing-Xiang(郭庆祥)

    2004-01-01

    It is demonstrated that in all types of hydrogen bonds (X-H…Y) there is a balance between the long-range attractive orbital interactions and short-range Pauli/nucleus repulsions. When the proton acceptor approaches the proton donor from distance, the hydrogen bonding energy becomes more negative at relatively large distance, goes through a minimum, and then starts to become less negative when the short-range repulsive forces come into effect.Meanwhile, the X-H bond length increases at relatively large distances, goes through a maximum and starts to shorten when the short-range repulsive forces come into effect. Whether the hydrogen bond is red or blue shifted is dictated by the energy minimum position. If at the energy minimum position the X-H bond length is shorter than that for the free monomer, the hydrogen bond is blue shifted and vice versa. Further studies demonstrate that the recent report about the correlation of C-H bond lengths with proton donor-acceptor distance in F3C-H…OH2 and F3C-H…Cl- is not fully correct because the authors conducted an inappropriate comparison. Furthermore, it is shown for the first time that the Pauli/nucleus repulsion theory is applicable to the blue-shifted hydrogen bonds in the X-H…π complexes and the blue-shifted lithium bonds in the X-Li…Y complexes.

  17. Investigations into the nature of halogen- and hydrogen-bonding interactions of some heteroaromatic rings with dichlorine monoxide.

    Science.gov (United States)

    Wu, Junyong

    2014-09-01

    We have studied the structures, properties, and nature of halogen- and hydrogen-bonding interactions between some heteroaromatic rings (C(5)H(5)N, C(4)H(4)O, and C(4)H(4)S) with Cl(2)O at the MP2/aug-cc-pVTZ level. We also considered the solvent effect on the halogen bonds and hydrogen bonds in the C(5)H(5)N-Cl(2)O complexes and found that the solvent has a weakening effect on the π-type halogen bond and hydrogen bond but a prominent enhancing effect on σ-type halogen bond. The complexes have also been analyzed with symmetry adapted perturbation theory method (SAPT).

  18. Synthesis of Ni3S2 nanotube arrays on nickel foam by catalysis of thermal reduced graphene for hydrogen evolution reaction

    Science.gov (United States)

    Jinlong, Lv; Miura, Hideo; Meng, Yang; Tongxiang, Liang

    2017-03-01

    The thermal reduced graphene oxide deposition on nickel foam was successfully synthesized by ultrasonic and subsequent thermal reduction process. Ultrathin mesoporous Ni3S2 was formed on the bare nickel foam after hydrothermal process, while Ni3S2 nanotube arrays were formed on the surface of nickel foam with the thermal reduced graphene oxide due to catalysis action of thermal reduced graphene oxide. The resulting Ni3S2 nanotube arrays exhibited higher catalytic activity than ultrathin mesoporous Ni3S2 for hydrogen evolution reaction. In addition, and excellent stability was also obtained in Ni3S2 nanotube arrays.

  19. O-H···C hydrogen bond in the methane-water complex

    Science.gov (United States)

    Isaev, A. N.

    2016-10-01

    Quantum chemical calculations were performed at different levels of theory (SCF, DFT, MP2, and CCSD(T)) to determine the geometry and electronic structure of the HOH···CH4 complex formed by water and methane molecules, in which water is a proton donor and methane carbon ( sp 3) is an acceptor. The charge distribution on the atoms of the complex was analyzed by the CHelpG method and Hirshfeld population analysis; both methods revealed the transfer of electron charge from methane to water. According to the natural bond orbital (NBO) analysis data, the charge transfer upon complexation is caused by the interaction between the σ orbital of the axial C-H bond of methane directed along the line of the O-H···C hydrogen bridge and the antibonding σ* orbital of the O-H bond of the water molecule. Topological analysis of electron density in the HOH···CH4 complex by the AIM method showed that the parameters of the critical point of the bond between hydrogen and acceptor (carbon atom) for the O-H···C interaction are typical for H-bonded systems (the magnitude of electron density at the critical point of the bond, the sign and value of the Laplacian). It was concluded that the intermolecular interaction in the complex can be defined as an H bond of O-H···σ(C-H) type, whose energy was found to be 0.9 kcal/mol in MP2/aug-cc-pVQZ calculations including the basis set superposition error (BSSE).

  20. Transfer Hydrogenation of C= C Double Bonds Catalyzed by Ruthenium Amido-Complexes:Scopes, Limitation and Enantioselectivity

    Institute of Scientific and Technical Information of China (English)

    XUE,Dong; CHENG,Ying-Chun; CUI,Xin; WANG,Qi-Wei; ZHU,Jin; DENG,Jin-Gen

    2004-01-01

    @@ The reduction of C = C double bonds is one of the most fundamental synthetic transformations and plays a key role in the manufacturing of a wide variety of bulk and fine chemicals. Hydrogenation of olefinic substrates can be achieved readily with molecular hydrogen in many cases, but transfer hydrogenation methods using suitable donor molecules such as formic acid or alcohols are receiving increasing attention as possible synthetic alternatives because it requires no special equipment and avoids the handling of potentially hazardous gaseous hydrogen.

  1. Investigation of bonded hydrogen defects in nanocrystalline diamond films grown with nitrogen/methane/hydrogen plasma at high power conditions

    Science.gov (United States)

    Tang, C. J.; Hou, Haihong; Fernandes, A. J. S.; Jiang, X. F.; Pinto, J. L.; Ye, H.

    2017-02-01

    In this work, we investigate the influence of some growth parameters such as high microwave power ranging from 3.0 to 4.0 kW and N2 additive on the incorporation of bonded hydrogen defects in nanocrystalline diamond (NCD) films grown through a small amount of pure N2 addition into conventional 4% CH4/H2 plasma using a 5 kW microwave plasma CVD system. Incorporation form and content of hydrogen point defects in the NCD films produced with pure N2 addition was analyzed by employing Fourier-transform infrared (FTIR) spectroscopy for the first time. A large amount of hydrogen related defects was detected in all the produced NCD films with N2 additive ranging from 29 to 87 μm thick with grain size from 47 nm to 31 nm. Furthermore, a specific new H related sharp absorption peak appears in all the NCD films grown with pure N2/CH4/H2 plasma at high powers and becomes stronger at powers higher than 3.0 kW and is even stronger than the 2920 cm-1 peak, which is commonly found in CVD diamond films. Based on these experimental findings, the role of high power and pure nitrogen addition on the growth of NCD films including hydrogen defect formation is analyzed and discussed.

  2. Modeling the vapor-liquid equilibria of polymer-solvent mixtures: Systems with complex hydrogen bonding behavior

    DEFF Research Database (Denmark)

    Tsivintzelis, Ioannis; Kontogeorgis, Georgios

    2009-01-01

    The vapor–liquid equilibria of binary polymer–solvent systems was modeled using the Non-Random Hydrogen Bonding (NRHB) model. Mixtures of poly(ethylene glycol), poly(propylene glycol), poly(vinyl alcohol) and poly(vinyl acetate) with various solvents were investigated, while emphasis was put...... on hydrogen bonding systems, in which functional groups of the polymer chain can self-associate or cross-associate with the solvent molecules. Effort has been made to explicitly account for all hydrogen bonding interactions. The results reveal that the NRHB model offers a flexible approach to account...... the complexity of the examined systems....

  3. The influence of large-amplitude librational motion on the hydrogen bond energy for alcohol–water complexes

    DEFF Research Database (Denmark)

    Andersen, Jonas; Heimdal, J.; Larsen, René Wugt

    2015-01-01

    unambiguous assignments of the intermolecular high-frequency out-of-plane and low-frequency in-plane donor OH librational modes for mixed alcohol–water complexes. The vibrational assignments confirm directly that water acts as the hydrogen bond donor in the most stable mixed complexes and the tertiary alcohol...... is a superior hydrogen bond acceptor. The class of large-amplitude donor OH librational motion is shown to account for up to 5.1 kJ mol-1 of the destabilizing change of vibrational zero-point energy upon intermolecular OH...O hydrogen bond formation. The experimental findings are supported by complementary...

  4. A quasi-diamondoid hydrogen-bonded framework in anhydrous sulfanilic acid.

    Science.gov (United States)

    Low, John N; Glidewell, Christopher

    2002-04-01

    The title compound (C(6)H(7)NO(3)S) exists as a zwitterion (4-ammoniobenzenesulfonate), +H(3)NC(6)H(4)SO(3)-, and these units are linked into a three-dimensional framework by two distinct two-centre N-H* * *O hydrogen bonds [H* * *O 1.84 and 1.87 A; N* * *O 2.767 (2) and 2.746 (2) A; N-H* * *O 166 and 172 degrees ] and a planar three-centre N-H* * *(O)(2) hydrogen bond [H* * *O 2.03 and 2.37 A; N* * *O 2.816 (2) and 2.877 (2) A; N-H* * *O 162 and 111 degrees; O* * *H* * *O 86 degrees ].

  5. IR study on hydrogen bonding in epoxy resin-silica nanocomposites

    Institute of Scientific and Technical Information of China (English)

    Wei Zhang; Abbas A. Dehghani-Sanij; Richard S. Blackburn

    2008-01-01

    The chemical and physical interactions between ingredients in composites play an important role in the improvement of service prop-sity loss of isocyanate absorption band in conjunction with the intensity growth of carboxyl absorption band indicates the progress of reaction. FT-IR spectroscopy was also adopted to examine the intermolecular hydrogen bonding of epoxy resin with silica as well as intramolecular one within polymer matrix. The vibration frequency of carboxyl group (-C=O) and hydroxyl group (-OH) shifts from 1736 to 1728 cm-1and 3420 to 3414 cm-1, respectively, indicating the occurrence of hydrogen bonding between -C=O and -OH. The vibration frequency of Si-OH moves from 3435 to 3414 cm -1, suggesting the involvement of silica. Whereas the vibration frequency of pending -OH in polymer chain moves from 3435 to 3420 cm-1 or 3414 cm-1, proposing that this kind of interaction can also happen within polymer matrix.

  6. A first-principles investigation into the hydrogen bond interaction in β-HMX

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A theoretical study of structural and electronic properties of β-HMX crystal is performed using density-functional theory(DFT). The total density of states(TDOS) is presented. The atomic orbit projected density of state(PDOS) from the p-type orbit of C,N,O and the s-type orbit of H is discussed. The study by analyzing the PDOS shows that the structure of β-HMX crystal possesses C-H···O intra- and inter-molecular hydrogen-bonding. There exists a hydrogen bonding between H5 -1s and O12 -2p orbits,between H19 -1s and O28 -2p orbits of intra molecules,and between H19 -1s and O24 -2p orbits of inter molecules. The Mulliken population analysis is also made.

  7. A study on polymorphism of hydrogen-bonded thermotropic liquid crystals

    Science.gov (United States)

    Rajanandkumar, R.; Pongali Sathya Prabu, N.; Murugadass, K.; Madhu Mohan, M. L. N.

    2016-09-01

    A novel mesogenic homologous series comprising of eight hydrogen-bonded liquid crystalline complexes are isolated and analyzed by forming a hydrogen bond between p-n alkyloxy benzoic acids (where n represent alkyloxy carbon number which varies from 5 to 12) and mesaconic acid, respectively. Eight synthesized complexes are subjected to Fourier transform infra-red spectroscopy, polarizing optical microscopy and differential scanning calorimetry studies to meet the basic characterization. The variation of optical tilt angle with respect to temperature in various conventional and smectic X phases are investigated and analyzed. A phase diagram is constructed to elucidate the mesogenic behavior of novel liquid crystalline series. The Cox ratio that reveals the order of various mesophases and the stability factor, to invoke the thermal stability of mesophases, is studied under the results of DSC thermogram.

  8. A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method

    DEFF Research Database (Denmark)

    Kromann, Jimmy Charnley; Christensen, Anders Steen; Svendsen, Casper Steinmann;

    2014-01-01

    We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction en...... vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent, compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible....... energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and 3 or more imaginary frequencies using PM6-D3H+ implemented...

  9. On the correlation between hydrogen bonding and melting points in the inositols

    DEFF Research Database (Denmark)

    Bekö, Sándor L; Alig, Edith; Schmidt, Martin U;

    2014-01-01

    Inositol, 1,2,3,4,5,6-hexahydroxycyclohexane, exists in nine stereoisomers with different crystal structures and melting points. In a previous paper on the relationship between the melting points of the inositols and the hydrogen-bonding patterns in their crystal structures [Simperler et al. (2006...... ▶). CrystEngComm 8, 589], it was noted that although all inositol crystal structures known at that time contained 12 hydrogen bonds per molecule, their melting points span a large range of about 170 °C. Our preliminary investigations suggested that the highest melting point must be corrected for the effect...... of molecular symmetry, and that the three lowest melting points may need to be revised. This prompted a full investigation, with additional experiments on six of the nine inositols. Thirteen new phases were discovered; for all of these their crystal structures were examined. The crystal structures of eight...

  10. Influences of Temperature on Proton Conductivity in the Hydrogen-Bond Molecular Systems with Damping

    Institute of Scientific and Technical Information of China (English)

    PANG Xiao-Feng; YU Jia-Feng

    2007-01-01

    Influences of temperature of medium on proton conductivity in hydrogen-bonded systems exposed in an electric-field are numerically studied by the fourth-order Runge-Kutta method with our model. The results obtained show that the proton soliton is very robust against thermal perturbation and damping of medium, and is thermally stable in the temperature range T ≤273 K. From the simulation we find out that the mobility (or velocity) of proton conduction in ice crystal is a nonmonotonic function of temperature in the temperature range 170-273 K: i.e., it increases initially, reaches a maximum at about 191 K, subsequently decreases to a minimum at about 211 K, and then increases again. This changed rule of mobility is qualitatively consistent with its experimental data in ice in the same temperature range. This result provides an evidence for existence of solitons in the hydrogen-bonded systems.

  11. Competing hydrogen bonding in methoxyphenols: The rotational spectrum of o-vanillin

    Science.gov (United States)

    Cocinero, Emilio J.; Lesarri, Alberto; Écija, Patricia; Basterretxea, Francisco; Fernández, José A.; Castaño, Fernando

    2011-05-01

    The conformational preferences of o-vanillin have been investigated in a supersonic jet expansion using Fourier transform microwave (FT-MW) spectroscopy. Three molecular conformations were derived from the rotational spectrum. The two most stable structures are characterized by a moderate O sbnd H···O dbnd C hydrogen bond between the aldehyde and the hydroxyl groups, with the methoxy side chain either in plane (global minimum a- cis-trans) or out of plane (a- cis-gauche) with respect to the aromatic ring. In the third conformer the aldehyde group is rotated by ca. 180°, forming a O sbnd H···O hydrogen bond between the methoxy and hydroxyl groups (s- trans-trans). Rotational parameters and relative populations are provided for the three conformations, which are compared with the results of ab initio (MP2) and density-functional (B3LYP, M05-2X) theoretical predictions.

  12. Crystal structure and hydrogen-bonding patterns in 5-fluorocytosinium picrate

    Directory of Open Access Journals (Sweden)

    Marimuthu Mohana

    2017-03-01

    Full Text Available In the crystal structure of the title compound, 5-fluorocytosinium picrate, C4H5FN3O+·C6H2N3O7−, one N heteroatom of the 5-fluorocytosine (5FC ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11° with the ring of the picrate (PA− anion. In the crystal, the 5FC+ cation interacts with the PA− anion through three-centre N—H...O hydrogen bonds, forming two conjoined rings having R21(6 and R12(6 motifs, and is extended by N—H...O hydrogen bonds and C—H...O interactions into a two-dimensional sheet structure lying parallel to (001. Also present in the crystal structure are weak C—F...π interactions.

  13. Hydrogen-Bonded Organic Frameworks (HOFs): A New Class of Porous Crystalline Proton-Conducting Materials.

    Science.gov (United States)

    Karmakar, Avishek; Illathvalappil, Rajith; Anothumakkool, Bihag; Sen, Arunabha; Samanta, Partha; Desai, Aamod V; Kurungot, Sreekumar; Ghosh, Sujit K

    2016-08-26

    Two porous hydrogen-bonded organic frameworks (HOFs) based on arene sulfonates and guanidinium ions are reported. As a result of the presence of ionic backbones appended with protonic source, the compounds exhibit ultra-high proton conduction values (σ) 0.75× 10(-2)  S cm(-1) and 1.8×10(-2)  S cm(-1) under humidified conditions. Also, they have very low activation energy values and the highest proton conductivity at ambient conditions (low humidity and at moderate temperature) among porous crystalline materials, such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs). These values are not only comparable to the conventionally used proton exchange membranes, such as Nafion used in fuel cell technologies, but is also the highest value reported in organic-based porous architectures. Notably, this report inaugurates the usage of crystalline hydrogen-bonded porous organic frameworks as solid-state proton conducting materials.

  14. Improvement of silicon direct bonding using surfaces activated by hydrogen plasma treatment

    CERN Document Server

    Choi, W B; Lee Jae Sik; Sung, M Y

    2000-01-01

    The plasma surface treatment, using hydrogen gas, of silicon wafers was studied as a pretreatment for silicon direct bonding. Chemical reactions of the hydrogen plasma with the surfaces were used for both surface activation and removal of surface contaminants. Exposure of the silicon wafers to the plasma formed an active oxide layer on the surface. This layer was hydrophilic. The surface roughness and morphology were examined as functions of the plasma exposure time and power. The surface became smoother with shorter plasma exposure time and lower power. In addition, the plasma surface treatment was very efficient in removing the carbon contaminants on the silicon surface. The value of the initial surface energy, as estimated by using the crack propagation method, was 506 mJ/M sup 2 , which was up to about three times higher than the value for the conventional direct bonding method using wet chemical treatments.

  15. Slow dielectric response of Debye-type in water and other hydrogen bonded liquids

    Science.gov (United States)

    Jansson, Helén; Bergman, Rikard; Swenson, Jan

    2010-05-01

    The slow dynamics of some hydrogen bonded glass-forming liquids has been investigated by broadband dielectric spectroscopy. We show that the polyalcohols glycerol, xylitol, and sorbitol, and mixtures of glycerol and water, and in fact, even pure water exhibit a process of Debye character at longer time-scales than the glass transition and viscosity related α-relaxation. Even if it is less pronounced, this process displays many similarities to the well-studied Debye-like process in monoalcohols. It can be observed in both the negative derivative of the real part of the permittivity or in the imaginary part of the permittivity, if the conductivity contribution is reduced. In the present study the conductivity contribution has been suppressed by use of a thin Teflon film placed between the sample and one of the electrodes. The new findings might have important implications for the structure and dynamics of hydrogen bonded liquids in general, and for water in particular.

  16. Ammonia as a case study for the spontaneous ionization of a simple hydrogen-bonded compound.

    Science.gov (United States)

    Palasyuk, Taras; Troyan, Ivan; Eremets, Mikhail; Drozd, Vadym; Medvedev, Sergey; Zaleski-Ejgierd, Patryk; Magos-Palasyuk, Ewelina; Wang, Hongbo; Bonev, Stanimir A; Dudenko, Dmytro; Naumov, Pavel

    2014-03-24

    Modern ab initio calculations predict ionic and superionic states in highly compressed water and ammonia. The prediction apparently contradicts state-of-the-art experimentally established phase diagrams overwhelmingly dominated by molecular phases. Here we present experimental evidence that the threshold pressure of ~120 GPa induces in molecular ammonia the process of autoionization to yet experimentally unknown ionic compound--ammonium amide. Our supplementary theoretical simulations provide valuable insight into the mechanism of autoionization showing no hydrogen bond symmetrization along the transformation path, a remarkably small energy barrier between competing phases and the impact of structural rearrangement contribution on the overall conversion rate. This discovery is bridging theory and experiment thus opening new possibilities for studying molecular interactions in hydrogen-bonded systems. Experimental knowledge on this novel ionic phase of ammonia also provides strong motivation for reconsideration of the theory of molecular ice layers formation and dynamics in giant gas planets.

  17. Substituent effects in double-helical hydrogen-bonded AAA-DDD complexes.

    Science.gov (United States)

    Wang, Hong-Bo; Mudraboyina, Bhanu P; Wisner, James A

    2012-01-27

    Two series of DDD and AAA hydrogen-bond arrays were synthesized that form triply-hydrogen-bonded double-helical complexes when combined in CDCl(3) solution. Derivatization of the DDD arrays with electron-withdrawing groups increases the complex association constants by up to a factor of 30 in those arrays examined. Derivatization of the AAA arrays with electron donating substituents reveals a similar magnitude effect on the complex stabilities. The effect of substitution on both types of arrays are modeled quite satisfactorily (R(2) > 0.96 in all cases) as free energy relationships with respect to the sums of their Hammett substituent constants. In all, the complex stabilities can be manipulated over more than three orders of magnitude (>20 kJ mol(-1)) using this type of modification.

  18. Aliphatic C-H---Anion Hydrogen Bonds: Weak Contacts or Strong Interactions?

    Energy Technology Data Exchange (ETDEWEB)

    Hay, Benjamin [ORNL; Pedzisa, Lee [ORNL

    2009-01-01

    Electronic structure calculations, MP2/aug-cc-pVDZ, are used to determine C H---Cl hydrogen bond energies for a series of XCH3 donor groups in which the electron-withdrawing ability of X is varied over a wide range of values. When attached to polarizing substituents, aliphatic CH groups are moderate to strong hydrogen bond donors, exhibiting interaction energies comparable to those obtained with O H and N H groups. The results explain why aliphatic C H donors are observed to function as competitive binding sites in solution and suggest that such C H---anion contacts should be considered as possible contributors when evaluating the denticity of an anion receptor.

  19. Tandem Catalysis Utilizing Olefin Metathesis Reactions.

    Science.gov (United States)

    Zieliński, Grzegorz K; Grela, Karol

    2016-07-01

    Since olefin metathesis transformation has become a favored synthetic tool in organic synthesis, more and more distinct non-metathetical reactions of alkylidene ruthenium complexes have been developed. Depending on the conditions applied, the same olefin metathesis catalysts can efficiently promote isomerization reactions, hydrogenation of C=C double bonds, oxidation reactions, and many others. Importantly, these transformations can be carried out in tandem with olefin metathesis reactions. Through addition of one portion of a catalyst, a tandem process provides structurally advanced products from relatively simple substrates without the need for isolation of the intermediates. These aspects not only make tandem catalysis very attractive from a practical point of view, but also open new avenues in (retro)synthetic planning. However, in the literature, the term "tandem process" is sometimes used improperly to describe other types of multi-reaction sequences. In this Concept, a number of examples of tandem catalysis involving olefin metathesis are discussed with an emphasis on their synthetic value.

  20. Hydrogen bonding-assisted thermal conduction in β-sheet crystals of spider silk protein

    Science.gov (United States)

    Zhang, Lin; Chen, Teli; Ban, Heng; Liu, Ling

    2014-06-01

    Using atomistic simulations, we demonstrate that β-sheet, an essential component of spider silk protein, has a thermal conductivity 1-2 orders of magnitude higher than that of some other protein structures reported in the literature. In contrast to several other nanostructured materials of similar bundled/layered structures (e.g. few-layer graphene and bundled carbon nanotubes), the β-sheet is found to uniquely feature enhanced thermal conductivity with an increased number of constituting units, i.e. β-strands. Phonon analysis identifies inter-β-strand hydrogen bonding as the main contributor to the intriguing phenomenon, which prominently influences the state of phonons in both low- and high-frequency regimes. A thermal resistance model further verifies the critical role of hydrogen bonding in thermal conduction through β-sheet structures.Using atomistic simulations, we demonstrate that β-sheet, an essential component of spider silk protein, has a thermal conductivity 1-2 orders of magnitude higher than that of some other protein structures reported in the literature. In contrast to several other nanostructured materials of similar bundled/layered structures (e.g. few-layer graphene and bundled carbon nanotubes), the β-sheet is found to uniquely feature enhanced thermal conductivity with an increased number of constituting units, i.e. β-strands. Phonon analysis identifies inter-β-strand hydrogen bonding as the main contributor to the intriguing phenomenon, which prominently influences the state of phonons in both low- and high-frequency regimes. A thermal resistance model further verifies the critical role of hydrogen bonding in thermal conduction through β-sheet structures. Electronic supplementary information (ESI) available: Structure of the β-sheets, computational model, determination of area and temperature gradient, and additional phonon DOS results. See DOI: 10.1039/c4nr01195c

  1. Chiral Hydrogen Bond Environment Providing Unidirectional Rotation in Photoactive Molecular Motors.

    Science.gov (United States)

    García-Iriepa, Cristina; Marazzi, Marco; Zapata, Felipe; Valentini, Alessio; Sampedro, Diego; Frutos, Luis Manuel

    2013-05-02

    Generation of a chiral hydrogen bond environment in efficient molecular photoswitches is proposed as a novel strategy for the design of photoactive molecular motors. Here, the following strategy is used to design a retinal-based motor presenting singular properties: (i) a single excitation wavelength is needed to complete the unidirectional rotation process (360°); (ii) the absence of any thermal step permits the process to take place at low temperatures; and (iii) the ultrafast process permits high rotational frequencies.

  2. Hydrogen-bonded proton transfer in the protonated guanine-cytosine (GC+H)+ base pair.

    Science.gov (United States)

    Lin, Yuexia; Wang, Hongyan; Gao, Simin; Schaefer, Henry F

    2011-10-13

    The single proton transfer at the different sites of the Watson-Crick (WC) guanine-cytosine (GC) DNA base pair are studied here using density functional methods. The conventional protonated structures, transition state (TS) and proton-transferred product (PT) structures of every relevant species are optimized. Each transition state and proton-transferred product structure has been compared with the corresponding conventional protonated structure to demonstrate the process of proton transfer and the change of geometrical structures. The relative energies of the protonated tautomers and the proton-transfer energy profiles in gas and solvent are analyzed. The proton-transferred product structure G(+H(+))-H(+)C(N3)(-H(+))(PT) has the lowest relative energy for which only two hydrogen bonds exist. Almost all 14 isomers of the protonated GC base pair involve hydrogen-bonded proton transfer following the three pathways, with the exception of structure G-H(+)C(O2). When the positive charge is primarily "located" on the guanine moiety (H(+)G-C, G-H(+)C(C4), and G-H(+)C(C6)), the H(1) proton transfers from the N(1) site of guanine to the N(3) site of cytosine. The structures G-H(+)C(C5) and G-H(+)C(C4) involve H(4a) proton transfer from the N(4) of cytosine to the O(6) site of guanine. H(2a) proton transfer from the N(2) site of guanine to the O(2) site of cytosine is found only for the structure G-H(+)C(C4). The structures to which a proton is added on the six-centered sites adjoining the hydrogen bonds are more prone to proton transfer in the gas phase, whereas a proton added on the minor groove and the sites adjoining the hydrogen bonds is favorable to the proton transfer in energy in the aqueous phase.

  3. Synthesis of 2,6-diaminopyridine substituted -oxoketene ,-acetals: Crystal structure and hydrogen bonding interactions

    Indian Academy of Sciences (India)

    Okram Mukherjee Singh; Laishram Ronibala Devi; Neeladri Das

    2013-09-01

    Polyaza -oxoketene ,-acetals can exist as either enamino or imino tautomeric forms. Based on the spectroscopic data and structural analysis of one of the ,-acetals, the stereochemistry was unambiguously assigned as an all--configuration. The crystal structure confirms the enamino structure and shows extensive use of C-H…X (X = N, O, and S) weak hydrogen bonding interactions, thereby generating a 3-dimensional network in solid state.

  4. Molecularly Defined Nanostructures Based on a Novel AAA-DDD Triple Hydrogen-Bonding Motif.

    Science.gov (United States)

    Papmeyer, Marcus; Vuilleumier, Clément A; Pavan, Giovanni M; Zhurov, Konstantin O; Severin, Kay

    2016-01-26

    A facile and flexible method for the synthesis of a new AAA-DDD triple hydrogen-bonding motif is described. Polytopic supramolecular building blocks with precisely oriented AAA and DDD groups are thus accessible in few steps. These building blocks were used for the assembly of large macrocycles featuring four AAA-DDD interactions and a macrobicyclic complex with a total of six AAA-DDD interactions.

  5. From ab initio quantum chemistry to molecular dynamics: The delicate case of hydrogen bonding in ammonia

    CERN Document Server

    Boese, A D; Martin, J M L; Marx, D; Chandra, Amalendu; Martin, Jan M.L.; Marx, Dominik

    2003-01-01

    The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liq...

  6. Hydrogen bonding induced polymorphism in the scandium(III) complex with ε-caprolactam

    Energy Technology Data Exchange (ETDEWEB)

    Virovets, Alexander V.; Peresypkina, Eugenia V. [Institute of Inorganic Chemistry SB RAS, Novosibirsk (Russian Federation); Novosibirsk State Univ. (Russian Federation); Cherkasova, Elizaveta V.; Cherkasova, Tatjana G. [Kuzbass State Technical Univ., Kemerovo (Russian Federation)

    2015-11-01

    Two polymorphs of [Sc(cpl){sub 6}][Cr(NCS){sub 6}] (cpl=ε- C{sub 6}H{sub 11}NO), trigonal and monoclinic, form purple elongated narrow plates and brownish-purple prisms and are formed concomitantly irrespectively of the crystallization conditions. In the trigonal polymorph both cation and anion possess C{sub 3i} site symmetry while in the monoclinic form cation and anion lie on inversion centre and 2-fold axis respectively. The nature of the polymorphism traces back to a redistribution of inter- and intramolecular hydrogen bonds that causes different conformation of the complex cations, different hydrogen bonding and different molecular packings. The [Sc(cpl){sub 6}]{sup 3+} cations in the structure of the trigonal polymorph form intermolecular N(H)..S, and in the monoclinic form both N(H)..S inter- and N(H)..O intramolecular hydrogen bonds with NCS groups of [Cr(NCS){sub 6}]{sup 3-} and cpl ligands. This aggregation leads to chains, where the cations and the anions alternate, in the trigonal modification and to layers, in which each ion is surrounded by four counterions, in the monoclinic form. Both polymorphs possess thermochromic properties, and a reversible color change from light purple to dark green takes place at 470-475 K.

  7. Theoretical Studies on the Stabilities and Hydrogen Bond Actions of (H2O)n Clusters

    Institute of Scientific and Technical Information of China (English)

    MENG Xiang-Jun; WANG Ke-Cheng; WU Wen-Sheng; LI Bing-Huan; WANG De-Jin

    2006-01-01

    The stable configurations and hydrogen bond nature of (H2O)n clusters (n = 3~6) have been investigated by the B3LYP method at the 6-31++g** level. Upon calculation, four conclusions have been drawn: (1) In the (H2O)3~5 clusters, cyclic configurations were confirmed to be the most stable. But in the (H2O)3~4 ones, only cyclic configurations could be observed. From n= 5 ((H2O)5 clusters), three-dimensional configuration could be found; (2) In the (H2O)6 clusters, all configurations are inclined to be three-dimensional except the most stable configuration which is cyclic; (3) The stable order of (H2O)6 clusters indicates that it is the arrangement of hydrogen bond that plays a decisive role in the cluster stabilities, the zero-point energy is also important, and cluster stabilities are independent on the number of hydrogen bonds; (4) There exist strong cooperativity and superadditivity in the (H2O)n clusters.

  8. Discrete kink dynamics in hydrogen-bonded chains: the one-component model.

    Science.gov (United States)

    Karpan, V M; Zolotaryuk, Y; Christiansen, P L; Zolotaryuk, A V

    2002-12-01

    We study topological solitary waves (kinks and antikinks) in a nonlinear one-dimensional Klein-Gordon chain with the on-site potential of a double-Morse type. This chain is used to describe the collective proton dynamics in quasi-one-dimensional networks of hydrogen bonds, where the on-site potential plays the role of the proton potential in the hydrogen bond. The system supports a rich variety of stationary kink solutions with different symmetry properties. We study the stability and bifurcation structure of all these stationary kink states. An exactly solvable model with a piecewise "parabola-constant" approximation of the double-Morse potential is suggested and studied analytically. The dependence of the Peierls-Nabarro potential on the system parameters is studied. Discrete traveling-wave solutions of a narrow permanent profile are shown to exist, depending on the anharmonicity of the Morse potential and the cooperativity of the hydrogen bond (the coupling constant of the interaction between nearest-neighbor protons).

  9. On the correlation between hydrogen bonding and melting points in the inositols

    Directory of Open Access Journals (Sweden)

    Sándor L. Bekö

    2014-01-01

    Full Text Available Inositol, 1,2,3,4,5,6-hexahydroxycyclohexane, exists in nine stereoisomers with different crystal structures and melting points. In a previous paper on the relationship between the melting points of the inositols and the hydrogen-bonding patterns in their crystal structures [Simperler et al. (2006. CrystEngComm 8, 589], it was noted that although all inositol crystal structures known at that time contained 12 hydrogen bonds per molecule, their melting points span a large range of about 170 °C. Our preliminary investigations suggested that the highest melting point must be corrected for the effect of molecular symmetry, and that the three lowest melting points may need to be revised. This prompted a full investigation, with additional experiments on six of the nine inositols. Thirteen new phases were discovered; for all of these their crystal structures were examined. The crystal structures of eight ordered phases could be determined, of which seven were obtained from laboratory X-ray powder diffraction data. Five additional phases turned out to be rotator phases and only their unit cells could be determined. Two previously unknown melting points were measured, as well as most enthalpies of melting. Several previously reported melting points were shown to be solid-to-solid phase transitions or decomposition points. Our experiments have revealed a complex picture of phases, rotator phases and phase transitions, in which a simple correlation between melting points and hydrogen-bonding patterns is not feasible.

  10. Self-assembly of thiophene derivatives on highly oriented pyrolytic graphite: hydrogen bond effect.

    Science.gov (United States)

    Xu, Li-Ping; Liu, Yibiao; Zhao, Jing; Wang, Shuqi; Lin, Chen-Sheng; Zhang, Rui-Qin; Wen, Yongqiang; Du, Hongwu; Zhang, Xueji

    2013-02-01

    In this paper, to elucidate the hydrogen bond effect on the assembly behavior, we studied the assembly structures of two carboxylic substituted thiophene derivatives on highly oriented pyrolytic graphite (HOPG) by scanning tunneling microscopy. Here thiophene-2-carboxylic acid (TCA) and thiophene-2,5-dicarboxylic acid (TDA) were employed. TDA molecules spontaneously adsorb on the HOPG surface and self-organize into a two-dimensional (2D) assembly with well-defined structure. Two types of domain could be observed. Each TDA molecule appears as a round circle with two small faint dots and forms hydrogen bonds with neighbours. Besides monolayer structure, a bilayer structure of TDA adlayer on HOPG was also observed in this research. Remnant TDA molecules adsorb on the monolayer of TDA and bilayer structure is formed. In contrast to TDA, no ordered structure of TCA on HOPG can be observed. TCA molecules have high propensity to form dimers through H-bond between carboxylic groups. But TCA dimer is not stable enough for either adsorption or imaging. Our result provides a new example for understanding hydrogen effect on stabilizing and controlling two-dimensional assembly structure and is helpful for surface nanofabrication and development of electric nanodevices.

  11. Three closely related dibenzazepine carboxylic acids: hydrogen-bonded aggregation in one, two and three dimensions.

    Science.gov (United States)

    Sanabría, Carlos M; Palma, Alirio; Cobo, Justo; Glidewell, Christopher

    2014-03-01

    In the structure of (6R*,11R*)-5-acetyl-11-ethyl-6,11-dihydro-5H-dibenzo[b,e]azepine-6-carboxylic acid, C19H19NO3, (I), the molecules are linked into sheets by a combination of O-H...O and C-H...O hydrogen bonds; in the structure of the monomethyl analogue (6RS,11SR)-5-acetyl-11-ethyl-2-methyl-6,11-dihydro-5H-dibenzo[b,e]azepine-6-carboxylic acid, C20H21NO3, (II), the molecules are linked into simple C(7) chains by O-H...O hydrogen bonds; and in the structure of the dimethyl analogue (6RS,11SR)-5-acetyl-11-ethyl-1,3-dimethyl-6,11-dihydro-5H-dibenzo[b,e]azepine-6-carboxylic acid, C21H23NO3, (III), a combination of O-H...O, C-H...O and C-H...π(arene) hydrogen bonds links the molecules into a three-dimensional framework structure. None of these structures exhibits the R2(2)(8) dimer motif characteristic of simple carboxylic acids.

  12. Hydrogen bond-promoted metallic state in a purely organic single-component conductor under pressure.

    Science.gov (United States)

    Isono, Takayuki; Kamo, Hiromichi; Ueda, Akira; Takahashi, Kazuyuki; Nakao, Akiko; Kumai, Reiji; Nakao, Hironori; Kobayashi, Kensuke; Murakami, Youichi; Mori, Hatsumi

    2013-01-01

    Purely organic materials are generally insulating. Some charge-carrier generation, however, can provide them with electrical conductivity. In multi-component organic systems, carrier generation by intermolecular charge transfer has given many molecular metals. By contrast, in purely organic single-component systems, metallic states have rarely been realized although some neutral-radical semiconductors have been reported. Here we uncover a new type of purely organic single-component molecular conductor by utilizing strong hydrogen-bonding interactions between tetrathiafulvalene-based electron-donor molecules. These conductors are composed of highly symmetric molecular units constructed by the strong intra-unit hydrogen bond. Moreover, we demonstrate that, in this system, charge carriers are produced by the partial oxidation of the donor molecules and delocalized through the formation of the symmetric intra-unit hydrogen bonds. As a result, our conductors show the highest room-temperature electrical conductivity and the metallic state under the lowest physical pressure among the purely organic single-component systems, to our knowledge.

  13. Theoretical Study on the Structures and Properties of Hydrogen Bonding Complexes between Diazines and Water

    Institute of Scientific and Technical Information of China (English)

    LI, Quan; HUANG, Fang-Qian; HU, Jing-Dan; ZHAO, Ke-Qing

    2006-01-01

    Density functional theory B3LYP method and second-order Moller-Plesset perturbation theory MP2 method were employed to obtain the optimized geometries of the ground state and interaction energy for diazines and water complexes. The results show that the ground state complexes have strong hydrogen bonding interaction with -20.99,- 16.73 and - 15.31 kJ/mol after basis set superposition error and zero-point vibration energy correction for pyridazine-water, pyrimidine-water and pyrazine-water, respectively, and large red-shift for the symmetric H-O stretching vibration frequencies due to the formation of N…H-O hydrogen bond in the diazine-water complexes.The NBO analysis indicates that intermolecular charge transfer are 0.0316, 0.0255 and 0.0265 e respectively. In addition, the first singlet (n,π*) vertical excitation energy of the monomer and the hydrogen bonding complexes between diazines and water was investigated by time-dependent density functional theory.

  14. Molecular structure of hydrazoic acid with hydrogen-bonded tetramers in nearly planar layers.

    Science.gov (United States)

    Evers, Jürgen; Göbel, Michael; Krumm, Burkhard; Martin, Franz; Medvedyev, Sergey; Oehlinger, Gilbert; Steemann, Franz Xaver; Troyan, Ivan; Klapötke, Thomas M; Eremets, Mikhail I

    2011-08-10

    Hydrazoic acid (HN(3))--potentially explosive, highly toxic, and very hygroscopic--is the simplest covalent azide and contains 97.7 wt % nitrogen. Although its molecular structure was established decades ago, its crystal structure has now been solved by X-ray diffraction for the first time. Molecules of HN(3) are connected to each other by hydrogen bonds in nearly planar layers parallel to (001) with stacking sequence A, B, ... The layer distance, at 2.950(1) Å, is shorter than that in 2H-graphite [3.355(2) Å]. The hydrogen bonds N-H···N are of great interest, since the azido group consists of three homonuclear atoms with identical electronegativity, but different formal charges. These hydrogen bonds are bifurcated into moderate ones with ≈2.0 Å and into weak ones with ≈2.6 Å. The moderate ones build up tetramers (HN(3))(4) in a nearly planar net of eight-membered rings. To the best of our knowledge, such a network of tetramers of a simple molecule is unique.

  15. Desolvation penalty for burying hydrogen-bonded peptide groups in protein folding.

    Science.gov (United States)

    Baldwin, Robert L

    2010-12-16

    A novel analysis of the enthalpy of protein unfolding is proposed and used to test for a desolvation penalty when hydrogen-bonded peptide groups are desolvated via folding. The unfolding enthalpy has three components, (1) the change when peptide hydrogen bonds are broken and the exposed -CO and -NH groups are solvated, (2) the change when protein-protein van der Waals interactions are broken and replaced by protein-water van der Waals interactions, and (3) the change produced by the hydrophobic interaction when nonpolar groups in the protein interior (represented as a liquid hydrocarbon) are transferred to water. A key feature of the analysis is that the enthalpy change from the hydrophobic interaction goes through 0 at 22 °C according to the liquid hydrocarbon model. Protein unfolding enthalpies are smaller at 22 °C than the enthalpy change for unfolding an alanine peptide helix. Data in the literature indicate that the van der Waals contribution to the unfolding enthalpy is considerably larger than the unfolding enthalpy itself at 22 °C, and therefore, a sizable desolvation penalty is predicted. Such a desolvation penalty was predicted earlier from electrostatic calculations of a stabilizing interaction between water and the hydrogen-bonded peptide group.

  16. Structure and Hydrogen Bonding of Water in Polyacrylate Gels: Effects of Polymer Hydrophilicity and Water Concentration.

    Science.gov (United States)

    Mani, Sriramvignesh; Khabaz, Fardin; Godbole, Rutvik V; Hedden, Ronald C; Khare, Rajesh

    2015-12-10

    The ability to tune the hydrophilicity of polyacrylate copolymers by altering their composition makes these materials attractive candidates for membranes used to separate alcohol-water mixtures. The separation behavior of these polyacrylate membranes is governed by a complex interplay of factors such as water and alcohol concentrations, water structure in the membrane, polymer hydrophilicity, and temperature. We use molecular dynamics simulations to investigate the effect of polymer hydrophilicity and water concentration on the structure and dynamics of water molecules in the polymer matrix. Samples of poly(n-butyl acrylate) (PBA), poly(2-hydroxyethyl acrylate) (PHEA), and a 50/50 copolymer of BA and HEA were synthesized in laboratory, and their properties were measured. Model structures of these systems were validated by comparing the simulated values of their volumetric properties with the experimental values. Molecular simulations of polyacrylate gels swollen in water and ethanol mixtures showed that water exhibits very different affinities toward the different (carbonyl, alkoxy, and hydroxyl) functional groups of the polymers. Water molecules are well dispersed in the system at low concentrations and predominantly form hydrogen bonds with the polymer. However, water forms large clusters at high concentrations along with the predominant formation of water-water hydrogen bonds and the acceleration of hydrogen bond dynamics.

  17. Cross-coupling of C(sp)-H Bonds with Organometallic Reagents via Pd(II)/Pd(0) Catalysis**

    Science.gov (United States)

    Wasa, Masayuki; Engle, Keary M; Yu, Jin-Quan

    2010-12-01

    Palladium-catalyzed C-H activation/C-C bond-forming reactions have emerged as a promising class of synthetic tools in organic chemistry. Among the many different means of forging C-C bonds using Pd-mediated C-H activation, a new horizon in this field is Pd(II)-catalyzed cross-coupling of C-H bonds with organometallic reagents via a Pd(II)/Pd(0) catalytic cycle. While this type of reaction has proven to be effective for the selective functionalization of aryl C(sp(2))-H bonds, the focus of this review is on Pd(II)-catalyzed C(sp(3))-H activation/C-C cross-coupling, a topic of particular importance because reactions of this type enable fundamentally new methods for bond construction. Since our laboratory's initial report on cross-coupling of C-H bonds in 2006, this area has expanded rapidly, and the unique ability of Pd(II) catalysts to cleave and functionalize alkyl C(sp(3))-H bonds has been exploited to develop protocols for forming an array of C(sp(3))-C(sp(2)) and C(sp(3))-C(sp(3)) bonds. Furthermore, enantioselective C(sp(3))-H activation/C-C cross-coupling has been achieved through the use of chiral amino acid-derived ligands, offering a novel technique for producing enantioenriched molecules. Although this nascent field remains at an early stage of development, further investigations hold the potential to revolutionalize the way in which chiral molecules are synthesized in industrial and academic laboratories.

  18. Subsurface hydrogen bonds at the polar Zn-terminated ZnO(0001) surface

    DEFF Research Database (Denmark)

    Hellström, Matti; Beinik, Igor; Broqvist, Peter;

    2016-01-01

    The role of hydrogen and other defects in the stabilization of polar oxide interfaces is a matter of significant fundamental and practical interest. Using experimental (scanning tunneling microscopy, x-ray photoelectron spectroscopy) and theoretical (density functional theory) surface science...... (hcp) and zinc-blende (fcc) lattice positions, giving a characteristic “striped” c(√12×√12)R30° surface morphology with three types of rows: wurtzite Zn, zinc-blende Zn, and Zn vacancies. Interstitial H plays a central role in such a reconstruction, as it helps to compensate the excessive Zn deficiency....... We propose a model in which hydrogen occupies positions in half of the vacancy rows to form hydroxide ions that can participate in hydrogen bonds in the O subsurface layer as a result of the mixed wurtzite/zinc-blende stacking....

  19. Electronic structure of planar-quasicycled organic molecules with intramolecular hydrogen bond

    Directory of Open Access Journals (Sweden)

    ALEXEI N. PANKRATOV

    2007-03-01

    Full Text Available By means of the HF/6-311G(d,p method, the electronic structure of the series of organic molecules, among which are malonaldehyde, acetylacetone, thiomalonaldehyde,’the derivatives of aniline 2-XC6H4NH2, phenol 2-XC6H4OH, benzenethiol 2-XC6H4SH (X = CHO, COOH, COO-, NO, NO2, OH, OCH3, SH, SCH3, F, Cl, Br, 8-hydroxyquinoline, 8-mercaptoquinoline, tropolone, has been studied. The intramolecular hydrogen bond (IHB has been established to lead to a local electron redistribution in quasicycle, and primarily to the electron density transfer between the direct IHB participants – from the hydrogen atom toward the proton-aceptor atom. On forming the IHB of the S–H···O type, the electron density in general decreases on the sulphohydryl hydrogen atom and increases on the sulphur atom.

  20. Using Raman Spectroscopy and ab initio Calculations to Investigate lntermolecular Hydrogen Bonds in Binary Mixture (Tetrahydrofuran+Water)

    Institute of Scientific and Technical Information of China (English)

    WU Nan-nan; OUYANG Shun-li; LI Zuo-wei; LIU Jing-yao; GAO Shu-qin

    2011-01-01

    We analyzed the properties and structures of the hydrogen-bonded complexes of tetrahydrofuran(THF)and water by means of experimental Raman spectra and ab initio calculations.The optimized geometries and vibrational frequencies of the neat THF molecule and its hydrogen-bonded complexes with water(THF/H2O) were calculated at the MP2/6-31 l+G(d,p) level of theory.We found that the intermolecular hydrogen bonds which are formed from the binary mixtures of the neat THF and water with different molar ratios could explain the changes in wavenumber position and linewidth very well.The combination of ab initio calculations and experimental Raman spectral data provides an insight into the hydrogen bonds leading to the concentration dependent changes in the spectral features.

  1. Vibrational transitions in hydrogen bonded bimolecular complexes - A local mode perturbation theory approach to transition frequencies and intensities

    Science.gov (United States)

    Mackeprang, Kasper; Kjaergaard, Henrik G.

    2017-04-01

    The local mode perturbation theory (LMPT) model was developed to improve the description of hydrogen bonded XH-stretching transitions, where X is typically O or N. We present a modified version of the LMPT model to extend its application from hydrated bimolecular complexes to hydrogen bonded bimolecular complexes with donors such as alcohols, amines and acids. We have applied the modified model to a series of complexes of different hydrogen bond type and complex energy. We found that the differences between local mode (LM) and LMPT calculated fundamental XH-stretching transition wavenumbers and oscillator strengths were correlated with the strength of the hydrogen bond. Overall, we have found that the LMPT model in most cases predicts transition wavenumbers within 20 cm-1 of the experimental values.

  2. Novel hot-melting hyperbranched poly(ester-amine) bearing self-complementary quadruple hydrogen bonding units

    Institute of Scientific and Technical Information of China (English)

    Yi Peng Qiu; Li Ming Tang; Yu Wang; Shi You Guan

    2008-01-01

    Hyperbranched poly(amine-ester)s bearing serf-complementary quadruple hydrogen bonding units display excellent mechanical and temperature-dependent melt rheological properties,which make them suitable as novel hot-melting materials.

  3. Quantum molecular dynamics and molecular interactions studied by NMR and INS Nuclear magnetic resonance; Proton tunnelling; Hydrogen bond

    CERN Document Server

    Jones, N

    2002-01-01

    The wavefunction of a particle extends into the classically forbidden barrier region of the potential energy surface. The consequence of this partial delocalisation is the phenomenon of quantum tunnelling, an effect which enables a particle to penetrate a potential barrier of magnitude greater than the energy of the particle. The tunnelling probability is an exponential function of the particle mass. The effect is therefore an important contribution to the behaviour of light atoms, in particular the proton. The hydrogen bond has long been appreciated to be an essential component of many biological and chemical systems, and the proton transfer reaction in the hydrogen bond is fundamental to many of these processes. The proton behaviour in the hydrogen bonds of benzoic acid, acetylacetone and calix-4-arene has been studied. A variety of techniques, both experimental and computational, were adopted for the study of the three hydrogen bonded systems. The complementary spectroscopic techniques of inelastic neutron...

  4. Investigation of hydrogen bonded molecular solids by diffraction, spectroscopy, and computational chemistry

    Science.gov (United States)

    Hudson, Matthew R.

    The nature of hydrogen-bonding interactions in the solid state is examined through the investigation of molecular crystals by incoherent inelastic neutron scattering (INS) spectroscopy, Raman spectroscopy, X-ray and neutron diffraction, and computational chemistry. The molecular solids studied range from small organic molecules to larger inorganic acid salts. Hydrogen bonding is the primary mode of interaction in the solid state for each of the systems studied. INS spectra were collected at 25 K for each molecular solid and the motions of the hydrogen atoms assigned. Raman spectra were collected at 78 and 298 K to aid in the molecular mode assignments of the INS spectra and to examine possible phase changes as a function of temperature. Neutron diffraction was employed, when possible, to accurately locate the hydrogen atom positions, and X-ray diffraction was performed to obtain accurate unit cell dimensions and to obtain initial characterizations of the samples. The diffraction structures served as the basis for solid-state density functional theory (DFT) calculations. DFT simulations were used to aid in the vibrational normal mode assignments, to investigate possible solid-phase transitions, and as a test of the limits of basis sets and the available DFT theory. Of the six molecular solids studied, several important observations were made: (1) the determination of a structural phase transition in L-alanine alaninium nitrate by both spectroscopic and theoretical methods, (2) the structure of picolinic acid was elucidated at 25 K and room-temperature by the combination of INS and theory, (3) glycine lithium sulfate was found to be a useful test of DFT to accurately optimize the structure and calculate the normal modes of a complex 3D network of hydrogen-bonding interactions, (4) nicotinic acid was found to be a useful test of one dimensional hydrogen-bonding interactions with pi-stacking interactions dominating the orthogonal directions, and (5) parabanic acid

  5. C-H(ax)...Y(ax) contacts in cyclohexane derivatives revisited-identification of improper hydrogen-bonded contacts.

    Science.gov (United States)

    Kolocouris, Antonios

    2009-03-06

    The structure of 111 cyclohexane derivatives bearing the axial substitution Y(ax)-C was optimized at the B3LYP/6-31+G(d,p) level. The natural bond orbital analysis revealed the presence of overlap interactions between the axial substituent and the antibonding sigma*(C-Hax) orbitals; these calculated hyperconjugative interactions suggest the presence of improper H-bonded contacts. The addition of an appropriate bridging fragment between the axial substituent and cyclohexane carbon strengthens significantly the hydrogen-bonding component of the contact and several structures of axially substituted cyclohexane derivatives including such hydrogen-bonded C-H(ax)...Y(ax)-C contacts were retrieved from the Cambridge Crystallographic Database. Overall, the calculations predicted that the C-H(ax)...Y(ax)-C contacts in common cyclohexane derivatives that are generally thought to be steric in nature (Pauli repulsive forces) include an improper hydrogen-bonding component.

  6. Slow magnetic relaxation in a hydrogen-bonded 2D array of mononuclear dysprosium(III) oxamates.

    Science.gov (United States)

    Fortea-Pérez, Francisco R; Vallejo, Julia; Julve, Miguel; Lloret, Francesc; De Munno, Giovanni; Armentano, Donatella; Pardo, Emilio

    2013-05-01

    The reaction of N-(2,6-dimethylphenyl)oxamic acid with dysprosium(III) ions in a controlled basic media afforded the first example of a mononuclear lanthanide oxamate complex exhibiting a field-induced slow magnetic relaxation behavior typical of single-ion magnets (SIMs). The hydrogen-bond-mediated self-assembly of this new bifunctional dysprosium(III) SIM in the solid state provides a unique example of 2D hydrogen-bonded polymer with a herringbone net topology.

  7. Heterogeneous Catalysis.

    Science.gov (United States)

    Vannice, M. A.

    1979-01-01

    Described is a graduate course in catalysis offered at Penn State University. A detailed course outline with 30 lecture topics is presented. A list of 42 references on catalysis used in place of a textbook is provided. (BT)

  8. Hydrogen bonding in thiobenzamide synthon and its Cadmium complex: Crystal structure and Hirshfeld analysis

    Indian Academy of Sciences (India)

    INES RIGANE; SIWAR WALHA; ABDELHAMID BEN SALAH

    2016-09-01

    The thiobenzamid TBA and its Cd(II) complex, dichlorothiobenzamidecadmium(II) [Cd(TBA)Cl₂] complex has been synthesized and characterized by FT-IR, FT-Raman and UV–Vis spectroscopy. The crystal and molecular structure of TBA and [Cd(TBA)Cl₂] were determined by single crystal X-ray diffraction analysis. The molecular arrangement in the crystal structure of TBA can be described on the basis of supramolecular dimeric synthons built up by four independent TBA molecules stacked via N-H. . .S hydrogen bonds. The 3D Hirshfeld surfaces and the associated 2D fingerprint plots were investigated for intermolecular interactions. The N-H. . .S hydrogen bond percentages were estimated to be 23.1%, 22.9%, 30.6% and 27.3% of Hirshfeld surfaces area respectively for each TBA molecule. Synthons are associated through C–H. . . π interactions at percentage of 33.8%, 38.2%, 24.3% and 19.4% to result in 3D network. The dichlorothiobenzamide cadmium(II) complex bonded by sulfur atom of thiobenzamide shows a double chain of distorted octahedra around the cadmium atoms running along the a axis and the packing is stabilized by intra- and inter-chain hydrogen bonding interactions of the type N–H. . .Cl and aromatic π. . .π stacking interactions between ring centroids at 21.8% and 7.6% of the Hirshfeld surface area, respectively. The decomposition of the complex to cadmium sulfide has been investigated by thermogravimetric analysis (TGA).

  9. Comparative investigation of hydrogen bonding in silicon based PECVD grown dielectrics for optical waveguides

    Science.gov (United States)

    Ay, F.; Aydinli, A.

    2004-06-01

    Silicon oxide, silicon nitride and silicon oxynitride layers were grown by a PECVD technique. The resulting refractive indices of the layers varied between 1.47 and 1.93. The compositional properties of the layers were analyzed by FTIR and ATR infrared spectroscopy techniques. Comparative investigation of bonding structures for the three different layers was performed. Special attention was given to analyze N-H bond stretching absorption at 3300-3400 cm -1. Quantitative results for hydrogen related bonding concentrations are presented based on IR analysis. An annealing study was performed in order to reduce or eliminate this bonding types. For the annealed samples the N-H bond concentration was strongly reduced as verified by FTIR transmittance and ATR spectroscopic methods. A correlation between the N-H concentration and absorption loss was verified for silicon oxynitride slab waveguides. Moreover, a single mode waveguide with silicon oxynitride core layer was fabricated. Its absorption and insertion loss values were determined by butt-coupling method, resulting in low loss waveguides.

  10. Effect of pressure on methylated glycine derivatives: relative roles of hydrogen bonds and steric repulsion of methyl groups.

    Science.gov (United States)

    Kapustin, Eugene A; Minkov, Vasily S; Boldyreva, Elena V

    2014-06-01

    Infinite head-to-tail chains of zwitterions present in the crystals of all amino acids are known to be preserved even after structural phase transitions. In order to understand the role of the N-H...O hydrogen bonds linking zwitterions in these chains in structural rearrangements, the crystal structures of the N-methyl derivatives of glycine (N-methylglycine, or sarcosine, with two donors for hydrogen bonding; two polymorphs of N,N-dimethylglycine, DMG-I and DMG-II, with one donor for hydrogen bond; and N,N,N-trimethylglycine, or betaine, with no hydrogen bonds) were studied at different pressures. Methylation has not only excluded the formation of selected hydrogen bonds, but also introduced bulky mobile fragments into the structure. The effects of pressure on the systems of the series were compared with respect to distorting and switching over hydrogen bonds and inducing reorientation of the methylated fragments. Phase transitions with fragmentation of the single crystals into fine powder were observed for partially methylated N-methyl- and N,N-dimethylglycine, whereas the structural changes in betaine were continuous with some peculiar features in the 1.4-2.9 GPa pressure range and accompanied by splitting of the crystals into several large fragments. Structural rearrangements in sarcosine and betaine were strongly dependent on the rate of pressure variation: the higher the rate of increasing pressure, the lower the pressure at which the phase transition occurred.

  11. Theoretical study of the N-H…O red-shifted and blue-shifted hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    YANG Yong; ZHANG WeiJun; PEI ShiXin; SHAO Jie; HUANG Wei; GAO XiaoMing

    2007-01-01

    Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO…HNO, HCOOH…HNO, HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F. The geometric structures and vibrational frequencies of these six complexes at the MP2/6-31+G(d,p), MP2/6-311++G(d,p), B3LYP/6-31+G(d,p) and B3LYP/6-311++G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO…HNO and HCOOH…HNO the N-H bond is strongly contracted and N-H…O blue-shifted hydrogen bonds are observed. While in complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F, the N-H bond is elongated and N-H…O red-shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X-H bond length in the X-H…Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X-H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO…HNO and HCOOH…HNO, the shortening effects dominate which lead to the blue shift of the N-H stretching frequencies. In complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F where elongating effects are dominant, the N-H…O hydrogen bonds are red-shifted.

  12. Dependence of (35)Cl NQR on hydrogen bonding and temperature in dichlorophenol-aniline charge transfer complexes.

    Science.gov (United States)

    Ramananda, D; Ramesh, K P; Uchil, J

    2007-10-01

    The hydrogen-bonded charge transfer complexes of aniline with pi-acceptors (or proton donors) such as 2,5-, 2,6-, 3,4- and 3,5-dichlorophenol were prepared. The (35)Cl nuclear quadrupole resonance (NQR) frequencies of these charge transfer complexes in the temperature range 77-300 K were measured to ascertain the existence or otherwise of a phase transition upon complex formation. Further, the NQR frequency and asymmetry parameter of the electric field gradient at the site of quadrupole nucleus were used to estimate the chemical bond parameters, namely ionic bond, double bond character of the carbon-chlorine(C--Cl) bond and the percentage charge transfer between the donor-acceptor components in charge transfer complexes. The effect of hydrogen bonding and temperature on the charge transfer process is analysed.

  13. Mechanism of -O-O- bond activation and catalysis by RuIII-pac complexes (pac = polyaminocarboxylate)

    Indian Academy of Sciences (India)

    Debabrata Chatterjee

    2012-11-01

    This paper presents the mechanistic aspects of the -O-O- bond activation by the Ru-pac (pac = polyaminocarboxylate) complex leading to the formation of various catalytic active species, viz. [RuIII(pac)(OOH)]2−, [RuIV(pac)(OH)]− and [RuV(pac)(O)]−, and their reactivity towards oxidation of a few organic compounds.

  14. Neutron Crystallography, Molecular Dynamics, and Quantum Mechanics Studies of the Nature of Hydrogen Bonding in Cellulose I beta

    Science.gov (United States)

    In the crystal structure of cellulose Ibeta, disordered hydrogen (H) bonding can be represented by the average of two mutually exclusive H bonding schemes that have been designated A and B. An unanswered question is whether A and B interconvert dynamically, or whether they are static but present in ...

  15. Thermodynamically leveraged Tandem catalysis for ester RC(O)O-R' bond hydrogenolysis. scope and mechanism.

    Energy Technology Data Exchange (ETDEWEB)

    Lohr, Tracy L.; Li, Zhi; Assary, Rajeev S.; Curtiss, Larry A.; Marks, Tobin J.

    2015-06-01

    Rapid and selective formal hydrogenolysis of aliphatic ester RC(O)O-R' linkages is achieved by a tandem homogeneous metal triflate + supported palladium catalytic system. The triflate catalyzes the mildly exothermic, turnover-limiting O-R' cleavage process, whereas the exothermic hydrogenation of the intermediate alkene further drives the overall reaction to completion.

  16. Molecular dynamics simulation of the formation of sp3 hybridized bonds in hydrogenated diamondlike carbon deposition processes.

    Science.gov (United States)

    Murakami, Yasuo; Horiguchi, Seishi; Hamaguchi, Satoshi

    2010-04-01

    The formation process of sp3 hybridized carbon networks (i.e., diamondlike structures) in hydrogenated diamondlike carbon (DLC) films has been studied with the use of molecular-dynamics simulations. The processes simulated in this study are injections of hydrocarbon (CH3 and CH) beams into amorphous carbon (a-C) substrates. It has been shown that diamondlike sp3 structures are formed predominantly at a subsurface level when the beam energy is relatively high, as in the "subplantation" process for hydrogen-free DLC deposition. However, for hydrogenated DLC deposition, the presence of abundant hydrogen at subsurface levels, together with thermal spikes caused by energetic ion injections, substantially enhances the formation of carbon-to-carbon sp3 bonds. Therefore, the sp3 bond formation process for hydrogenated DLC films essentially differs from that for hydrogen-free DLC films.

  17. Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds

    Science.gov (United States)

    Yexin, Feng; Ji, Chen; Xin-Zheng, Li; Enge, Wang

    2016-01-01

    The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice. Project supported by the National Natural Science Foundation of China (Grant Nos. 11275008, 91021007, and 10974012) and the China Postdoctoral Science Foundation (Grant No. 2014M550005).

  18. On the Importance of CP-corrected Gradient Optimization in the Study of Hydrogen Bonded Systems

    Institute of Scientific and Technical Information of China (English)

    王伟周; 蒲雪梅; 郑文旭; 黄宁表; 田安民

    2003-01-01

    Geometries, harmonic vibrational frequencies and interaction energies of the water-hydrogen sulfide dimer, hydrogen fluoride dimer and glycine zwitterion-water dimer were determined by the counterpoise-corrected (CP-corrected) gradient optimization that explicitly corrects for the basis set superpusition error (BSSE) and CP-uncorrected (normal) gradient opfimization respectively at the B3LYP and MP2 levels of theory, employing the popular Pople's standard 6-31G(d), 6-31G(d,p) and 6-311+ +G(d,p) basis sets in order to assess the importance of CP-corrected gradient optimiTation in the study of hydrogen bonded systems. The normal optimization of these three H-bonded systems obtained using these popular basis sets all yielded erratic results, whereas use of CP-corrected gradient optimization led to consistent results with those from larger basis sets. So this CP receipt becomes useful and necessary to correctly describe large systems, where the use of small basis sets may be necessary.

  19. Selectivity of Chemisorbed Oxygen in C–H Bond Activation and CO Oxidation and Kinetic Consequences for CH₄–O₂ Catalysis on Pt and Rh Clusters

    Energy Technology Data Exchange (ETDEWEB)

    Chin, Ya-Huei; Buda, Corneliu; Neurock, Matthew; Iglesia, Enrique

    2011-10-06

    Rate measurements, density functional theory (DFT) within the framework of transition state theory, and ensemble-averaging methods are used to probe oxygen selectivities, defined as the reaction probability ratios for O* reactions with CO and CH₄, during CH₄–O₂ catalysis on Pt and Rh clusters. CO₂ and H₂O are the predominant products, but small amounts of CO form as chemisorbed oxygen atoms (O*) are depleted from cluster surfaces. Oxygen selectivities, measured using ¹²CO–¹³CH₄–O₂ reactants, increase with O₂/ CO ratio and O* coverage and are much larger than unity at all conditions on Pt clusters. These results suggest that O* reacts much faster with CO than with CH₄, causing any CO that forms and desorbs from metal cluster surfaces to react along the reactor bed with other O* to produce CO₂ at any residence time required for detectable extents of CH₄ conversion. O* selectivities were also calculated by averaging DFTderived activation barriers for CO and CH₄ oxidation reactions over all distinct surface sites on cubo-octahedral Pt clusters (1.8 nm diameter, 201 Pt atoms) at low O* coverages, which are prevalent at low O₂ pressures during catalysis. CO oxidation involves non-activated molecular CO adsorption as the kinetically relevant step on exposed Pt atoms vicinal of chemisorbed O* atoms (on *–O* site pairs). CH₄ oxidation occurs via kinetically relevant C–H bond activation on *–* site pairs involving oxidative insertion of a Pt atom into one of the C–H bonds in CH₄, forming a three-centered HC₃–Pt–H transition state. C–H bond activation barriers reflect the strength of Pt–CH₃ and Pt–H interactions at the transition state, which correlates, in turn, with the Pt coordination and with CH₃ * binding energies. Ensemble-averaged O* selectivities increase linearly with O₂/CO ratios, which define the O* coverages, via a proportionality constant. The proportionality constant is given by the ratio of rate

  20. Computational evidence for intramolecular hydrogen bonding and nonbonding X···O interactions in 2'-haloflavonols

    Directory of Open Access Journals (Sweden)

    Tânia A. O. Fonseca

    2012-01-01

    Full Text Available The conformational isomerism and stereoelectronic interactions present in 2'-haloflavonols were computationally analyzed. On the basis of the quantum theory of atoms in molecules (QTAIM and natural bond orbital (NBO analysis, the conformer stabilities of 2'-haloflavonols were found to be dictated mainly by a C=O···H–O intramolecular hydrogen bond, but an unusual C–F···H–O hydrogen-bond and intramolecular C–X···O nonbonding interactions are also present in such compounds.