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Sample records for catalysis hydrogen bonding

  1. Hydrogen-bonding catalysis of sulfonium salts

    OpenAIRE

    Kaneko, Shiho; Kumatabara, Yusuke; Shimizu, Shoichi; Maruoka, Keiji; Shirakawa, Seiji

    2017-01-01

    Although quaternary ammonium and phosphonium salts are known as important catalysts in phase-transfer catalysis, the catalytic ability of tertiary sulfonium salts has not yet been well demonstrated. Herein, we demonstrate the catalytic ability of trialkylsulfonium salts as hydrogen-bonding catalysts on the basis of the characteristic properties of the acidic α hydrogen atoms on alkylsulfonium salts.

  2. New Architectures in Hydrogen Bond Catalysis

    Science.gov (United States)

    Rodriguez, Andrew A.; Yoo, Hoseong; Ziller, Joseph W.; Shea, Kenneth J.

    2009-01-01

    New achiral sulfamide, phosphoric triamide, and thiophosphoric triamide compounds have been synthesized. Their activity as hydrogen bond catalysts for the Friedel-Crafts and Baylis-Hillman reactions compares favorably with that of a known and active thiourea catalyst. The new compounds were also studied by X-ray crystallography and their solid state structures are described. PMID:20160884

  3. Enormous Hydrogen Bond Strength Enhancement through π-Conjugation Gain: Implications for Enzyme Catalysis.

    Science.gov (United States)

    Wu, Chia-Hua; Ito, Keigo; Buytendyk, Allyson M; Bowen, K H; Wu, Judy I

    2017-08-22

    Surprisingly large resonance-assistance effects may explain how some enzymes form extremely short, strong hydrogen bonds to stabilize reactive oxyanion intermediates and facilitate catalysis. Computational models for several enzymic residue-substrate interactions reveal that when a π-conjugated, hydrogen bond donor (XH) forms a hydrogen bond to a charged substrate (Y - ), XH can become significantly more π-electron delocalized, and this "extra" stabilization may boost the [XH···Y - ] hydrogen bond strength by ≥15 kcal/mol. This reciprocal relationship departs from the widespread pK a concept (i.e., the idea that short, strong hydrogen bonds form when the interacting moieties have matching pK a values), which has been the rationale for enzymic acid-base reactions. The findings presented here provide new insight into how short, strong hydrogen bonds could form in enzymes.

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

    Science.gov (United States)

    Karhan, Kristof; Khaliullin, Rustam Z.; Kühne, Thomas D.

    2014-12-01

    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.

  5. Contribution of a low-barrier hydrogen bond to catalysis is not significant in ketosteroid isomerase.

    Science.gov (United States)

    Jang, Do Soo; Choi, Gildon; Cha, Hyung Jin; Shin, Sejeong; Hong, Bee Hak; Lee, Hyeong Ju; Lee, Hee Cheon; Choi, Kwan Yong

    2015-05-01

    Low-barrier hydrogen bonds (LBHBs) have been proposed to have important influences on the enormous reaction rate increases achieved by many enzymes. Δ(5)-3-ketosteroid isomerase (KSI) catalyzes the allylic isomerization of Δ(5)-3-ketosteroid to its conjugated Δ(4)-isomers at a rate that approaches the diffusion limit. Tyr14, a catalytic residue of KSI, has been hypothesized to form an LBHB with the oxyanion of a dienolate steroid intermediate generated during the catalysis. The unusual chemical shift of a proton at 16.8 ppm in the nuclear magnetic resonance spectrum has been attributed to an LBHB between Tyr14 Oη and C3-O of equilenin, an intermediate analogue, in the active site of D38N KSI. This shift in the spectrum was not observed in Y30F/Y55F/D38N and Y30F/Y55F/Y115F/D38N mutant KSIs when each mutant was complexed with equilenin, suggesting that Tyr14 could not form LBHB with the intermediate analogue in these mutant KSIs. The crystal structure of Y30F/Y55F/Y115F/D38N-equilenin complex revealed that the distance between Tyr14 Oη and C3-O of the bound steroid was within a direct hydrogen bond. The conversion of LBHB to an ordinary hydrogen bond in the mutant KSI reduced the binding affinity for the steroid inhibitors by a factor of 8.1-11. In addition, the absence of LBHB reduced the catalytic activity by only a factor of 1.7-2. These results suggest that the amount of stabilization energy of the reaction intermediate provided by LBHB is small compared with that provided by an ordinary hydrogen bond in KSI.

  6. Selective Hydrogen Atom Abstraction via Induced Bond Polarization: The Direct -Arylation of Alcohols via Photoredox, HAT and Nickel Catalysis.

    Science.gov (United States)

    Twilton, Jack; Christensen, Melodie; DiRocco, Daniel A; Ruck, Rebecca T; Davies, Ian W; MacMillan, David William

    2018-02-28

    The combination of nickel metallaphotoredox catalysis, hydrogen atom transfer catalysis, and a Lewis acid activation mode, has led to the development of an arylation protocol for the selective functionalization of alcohol -hydroxy C-H bonds. This approach employs zinc-mediated alcohol deprotonation to activate -hydroxy C-H bonds while simultaneously suppressing C-O bond formation by inhibiting formation of nickel alkoxide species. The use of Zn based Lewis acids also deactivates other hydridic bonds such as -amino and -oxy C-H bonds. This technology facilitates rapid access to benzylic alcohols, an important motif in drug discovery. A 3-step synthesis of the Prozac exemplifies the utility of this new method. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. The hydrolysis of epoxides catalyzed by inorganic ammonium salts in water: kinetic evidence for hydrogen bond catalysis.

    Science.gov (United States)

    Nozière, B; Fache, F; Maxut, A; Fenet, B; Baudouin, A; Fine, L; Ferronato, C

    2018-01-17

    Naturally-occurring inorganic ammonium ions have been recently reported as efficient catalysts for some organic reactions in water, which contributes to the understanding of the chemistry in some natural environments (soils, seawater, atmospheric aerosols, …) and biological systems, and is also potentially interesting for green chemistry as many of their salts are cheap and non-toxic. In this work, the effect of NH 4 + ions on the hydrolysis of small epoxides in water was studied kinetically. The presence of NH 4 + increased the hydrolysis rate by a factor of 6 to 25 compared to pure water and these catalytic effects were shown not to result from other ions, counter-ions or from acid or base catalysis, general or specific. The small amounts of amino alcohols produced in the reactions were identified as the actual catalysts by obtaining a strong acceleration of the reactions when adding these compounds directly to the epoxides in water. Replacing the amino alcohols by other strong hydrogen-bond donors, such as trifluoroethanol (TFE) or hexafluoroisopropanol (HFIP) gave the same results, demonstrating that the kinetics of these reactions was driven by hydrogen-bond catalysis. Because of the presence of many hydrogen-bond donors in natural environments (for instance amines and hydroxy-containing compounds), hydrogen-bond catalysis is likely to contribute to many reaction rates in these environments.

  8. 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.

  9. Tetraalkylammonium Salts as Hydrogen-Bonding Catalysts

    OpenAIRE

    Shirakawa, Seiji; Liu, Shiyao; Kaneko, Shiho; Kumatabara, Yusuke; Fukuda, Airi; Omagari, Yumi; Maruoka, Keiji

    2015-01-01

    Although the hydrogen-bonding ability of the α hydrogen atoms on tetraalkylammonium salts is often discussed with respect to phase-transfer catalysts, catalysis that utilizes the hydrogen-bond-donor properties of tetraalkylammonium salts remains unknown. Herein, we demonstrate hydrogen-bonding catalysis with newly designed tetraalkylammonium salt catalysts in Mannich-type reactions. The structure and the hydrogen-bonding ability of the new ammonium salts were investigated by X-ray diffraction...

  10. 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.

  11. Chemisorption bonding and catalysis

    International Nuclear Information System (INIS)

    Danese, J.B.; Schrieffer, J.R.

    1976-01-01

    The general features of the LCAO--MO, Green's function, and multiple-scattering chi α methods and their applications to surfaces and surface-related problems are discussed. Emphasis is placed on the localization of bonding in surface complexes

  12. 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......, which indicates that the same catalyst should perform well for both hydrogen evolution and hydrogenation. If that catalyst also fulfills additional criteria for breaking carbon–sulfur bonds and releasing hydrogen sulfide, it will be a good hydrodesulfurization catalyst. The hydrogen evolution reaction...... is normally performed at room temperature and standard pressure, whereas the hydrodesulfurization reaction is driven by high temperature and pressure. Owing to the very different operating conditions, the adsorption free energy of hydrogen differs between hydrodesulfurization and the hydrogen evolution...

  13. The unique functional role of the C-HS hydrogen bond in the substrate specificity and enzyme catalysis of type 1 methionine aminopeptidase.

    Science.gov (United States)

    Reddi, Ravikumar; Singarapu, Kiran Kumar; Pal, Debnath; Addlagatta, Anthony

    2016-07-19

    It is intriguing how nature attains recognition specificity between molecular interfaces where there is no apparent scope for classical hydrogen bonding or polar interactions. Methionine aminopeptidase (MetAP) is one such enzyme where this fascinating conundrum is at play. In this study, we demonstrate that a unique C-HS hydrogen bond exists between the enzyme methionine aminopeptidase (MetAP) and its N-terminal-methionine polypeptide substrate, which allows specific interaction between apparent apolar interfaces, imposing a strict substrate recognition specificity and efficient catalysis, a feature replicated in Type I MetAPs across all kingdoms of life. We evidence this evolutionarily conserved C-HS hydrogen bond through enzyme assays on wild-type and mutant MetAP proteins from Mycobacterium tuberculosis that show a drastic difference in catalytic efficiency. The X-ray crystallographic structure of the methionine bound protein revealed a conserved water bridge and short contacts involving the Met side-chain, a feature also observed in MetAPs from other organisms. Thermal shift assays showed a remarkable 3.3 °C increase in melting temperature for methionine bound protein compared to its norleucine homolog, where C-HS interaction is absent. The presence of C-HS hydrogen bonding was also corroborated by nuclear magnetic resonance spectroscopy through a change in chemical shift. Computational chemistry studies revealed the unique role of the electrostatic environment in facilitating the C-HS interaction. The significance of this atypical hydrogen bond is underscored by the fact that the function of MetAP is essential for any living cell.

  14. 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. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Hydrogen bonding effect between active site and protein environment on catalysis performance in H2-producing [NiFe] hydrogenases.

    Science.gov (United States)

    Qiu, Siyao; Azofra, Luis Miguel; MacFarlane, Douglas R; Sun, Chenghua

    2018-02-28

    The interaction between the active site and the surrounding protein environment plays a fundamental role in the hydrogen evolution reaction (HER) in [NiFe] hydrogenases. Our density functional theory (DFT) findings demonstrate that the reaction Gibbs free energy required for the rate determining step decreases by 7.1 kcal mol -1 when the surrounding protein environment is taken into account, which is chiefly due to free energy decreases for the two H + /e - addition steps (the so-called Ni-SIa to I1, and Ni-C to Ni-R), being the largest thermodynamic impediments of the whole reaction. The variety of hydrogen bonds (H-bonds) between the amino acids and the active site is hypothesised to be the main reason for such stability: H-bonds not only work as electrostatic attractive forces that influence the charge redistribution, but more importantly, they act as an electron 'pull' taking electrons from the active site towards the amino acids. Moreover, the electron 'pull' effect through H-bonds via the S - in cysteine residues shows a larger influence on the energy profile than that via the CN - ligands on Fe.

  16. Structural and Kinetic Evidence for an Extended Hydrogen-Bonding Network in Catalysis of Methyl Group Transfer

    Energy Technology Data Exchange (ETDEWEB)

    Doukov,T.; Hemmi, H.; Drennan, C.; Ragsdale, S.

    2007-01-01

    The methyltetrahydrofolate (CH{sub 3}-H{sub 4}folate) corrinoid-ironsulfur protein (CFeSP) methyltransferase (MeTr) catalyzes transfer of the methyl group of CH3-H4folate to cob(I)amide. This key step in anaerobic CO and CO{sub 2} fixation is similar to the first half-reaction in the mechanisms of other cobalamin-dependent methyltransferases. Methyl transfer requires electrophilic activation of the methyl group of CH{sub 3}-H{sub 4}folate, which includes proton transfer to the N5 group of the pterin ring and poises the methyl group for reaction with the Co(I) nucleophile. The structure of the binary CH{sub 3}-H{sub 4}folate/MeTr complex (revealed here) lacks any obvious proton donor near the N5 group. Instead, an Asn residue and water molecules are found within H-bonding distance of N5. Structural and kinetic experiments described here are consistent with the involvement of an extended H-bonding network in proton transfer to N5 of the folate that includes an Asn (Asn-199 in MeTr), a conserved Asp (Asp-160), and a water molecule. This situation is reminiscent of purine nucleoside phosphorylase, which involves protonation of the purine N7 in the transition state and is accomplished by an extended H-bond network that includes water molecules, a Glu residue, and an Asn residue (Kicska, G. A., Tyler, P. C., Evans, G. B., Furneaux, R. H., Shi, W., Fedorov, A., Lewandowicz, A., Cahill, S. M., Almo, S. C., and Schramm, V. L. (2002) Biochemistry 41, 14489-14498). In MeTr, the Asn residue swings from a distant position to within H-bonding distance of the N5 atom upon CH{sub 3}-H{sub 4}folate binding. An N199A variant exhibits only {approx}20-fold weakened affinity for CH{sub 3}-H{sub 4}folate but a much more marked 20,000-40,000-fold effect on catalysis, suggesting that Asn-199 plays an important role in stabilizing a transition state or high energy intermediate for methyl transfer.

  17. X hydrogen bonds

    Indian Academy of Sciences (India)

    sigma electrons, can be hydrogen bond acceptors.11–14. The recent IUPAC report and recommendation on hydro gen bond have recognised the diverse nature of hydro- gen bond donors and acceptors.13,14. Unlike methane, hydrogen bonding by higher alkanes has not received much attention. One of the earlier works.

  18. Catalysis and Downsizing in Mg-Based Hydrogen Storage Materials

    Directory of Open Access Journals (Sweden)

    Jianding Li

    2018-02-01

    Full Text Available Magnesium (Mg-based materials are promising candidates for hydrogen storage due to the low cost, high hydrogen storage capacity and abundant resources of magnesium for the realization of a hydrogen society. However, the sluggish kinetics and strong stability of the metal-hydrogen bonding of Mg-based materials hinder their application, especially for onboard storage. Many researchers are devoted to overcoming these challenges by numerous methods. Here, this review summarizes some advances in the development of Mg-based hydrogen storage materials related to downsizing and catalysis. In particular, the focus is on how downsizing and catalysts affect the hydrogen storage capacity, kinetics and thermodynamics of Mg-based hydrogen storage materials. Finally, the future development and applications of Mg-based hydrogen storage materials is discussed.

  19. 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.

  20. Hydrogen bonded supramolecular materials

    CERN Document Server

    Li, Zhan-Ting

    2015-01-01

    This book is an up-to-date text covering topics in utilizing hydrogen bonding for constructing functional architectures and supramolecular materials. The first chapter addresses the control of photo-induced electron and energy transfer. The second chapter summarizes the formation of nano-porous materials. The following two chapters introduce self-assembled gels, many of which exhibit unique functions. Other chapters cover the advances in supramolecular liquid crystals and the versatility of hydrogen bonding in tuning/improving the properties and performance of materials. This book is designed

  1. Hydrogen tunneling links protein dynamics to enzyme catalysis.

    Science.gov (United States)

    Klinman, Judith P; Kohen, Amnon

    2013-01-01

    The relationship between protein dynamics and function is a subject of considerable contemporary interest. Although protein motions are frequently observed during ligand binding and release steps, the contribution of protein motions to the catalysis of bond making/breaking processes is more difficult to probe and verify. Here, we show how the quantum mechanical hydrogen tunneling associated with enzymatic C-H bond cleavage provides a unique window into the necessity of protein dynamics for achieving optimal catalysis. Experimental findings support a hierarchy of thermodynamically equilibrated motions that control the H-donor and -acceptor distance and active-site electrostatics, creating an ensemble of conformations suitable for H-tunneling. A possible extension of this view to methyl transfer and other catalyzed reactions is also presented. The impact of understanding these dynamics on the conceptual framework for enzyme activity, inhibitor/drug design, and biomimetic catalyst design is likely to be substantial.

  2. Catalysis of Ground State cis[Formula: see text] trans Isomerization of Bacteriorhodopsin's Retinal Chromophore by a Hydrogen-Bond Network.

    Science.gov (United States)

    Elghobashi-Meinhardt, Nadia; Phatak, Prasad; Bondar, Ana-Nicoleta; Elstner, Marcus; Smith, Jeremy C

    2018-03-08

    For the photocycle of the membrane protein bacteriorhodopsin to proceed efficiently, the thermal 13-cis to all-trans back-isomerization of the retinal chromophore must return the protein to its resting state on a time-scale of milliseconds. Here, we report on quantum mechanical/molecular mechanical energy calculations examining the structural and energetic determinants of the retinal cis-trans isomerization in the protein environment. The results suggest that a hydrogen-bonded network consisting of the retinal Schiff base, active site amino acid residues, and water molecules can stabilize the twisted retinal, thus reducing the intrinsic energy cost of the cis-trans thermal isomerization barrier.

  3. Intermolecular hydrogen bonds: From temperature-driven proton ...

    Indian Academy of Sciences (India)

    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 ...

  4. Monoiron hydrogenase catalysis: hydrogen activation with the formation of a dihydrogen, Fe-H(delta-)...H(delta+)-O, bond and methenyl-H4MPT+ triggered hydride transfer.

    Science.gov (United States)

    Yang, Xinzheng; Hall, Michael B

    2009-08-12

    A fully optimized resting state model with a strong Fe-H(delta-)...H(delta+)-O dihydrogen bond for the active site of the third type of hydrogenase, [Fe]-hydrogenase, is proposed from density functional theory (DFT) calculations on the reformulated active site from the recent X-ray crystal structure study of C176A (Cys176 was mutated to an alanine) mutated [Fe]-hydrogenase in the presence of dithiothreitol. The computed vibrational frequencies for this new active site model possess an average error of only +/-4.5 cm(-1) with respect to the wild-type [Fe]-hydrogenase. Based on this resting state model, a new mechanism with the following unusual aspects for hydrogen activation catalyzed by [Fe]-hydrogenase is also proposed from DFT calculations. (1) Unexpected dual pathways for H(2) cleavage with proton transfer to Cys176-sulfur or 2-pyridinol's oxygen for the formation and regeneration of the resting state with an Fe-H(delta-)...H(delta+)-O dihydrogen bond before the appearance of methenyl-H(4)MPT(+) (MPT(+)). (2) The strong dihydrogen bond in this resting state structure prevents D(2)/H(2)O exchange. (3) Only upon the arrival of MPT(+) with its strong hydride affinity can D(2)/H(2)O exchange take place as the arrival of MPT(+) triggers the breaking of the strong Fe-H(delta-)...H(delta+)-O dihydrogen bond by taking a hydride from the iron center and initiating the next H(2) (D(2)) cleavage. This new mechanism is completely different than that previously proposed (J. Am. Chem. Soc. 2008, 130, 14036) which was based on an active site model related to an earlier crystal structure. Here, Fe's role is H(2) capture and hydride formation without MPT(+) while the pyridone's special role involves the protection of the hydride by the dihydrogen bond.

  5. O hydrogen bonds in alkaloids

    Indian Academy of Sciences (India)

    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 ...

  6. Distance criterion for hydrogen bond

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Distance criterion for hydrogen bond. In a D-H ...A contact, the D...A distance must be less than the sum of van der Waals Radii of the D and A atoms, for it to be a hydrogen bond.

  7. What is a hydrogen bond?

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. What is a hydrogen bond? Precise definition of a hydrogen bond is still elusive!1. Several criteria are listed usually for X-H•••Y, X and Y initially thought to be F, O and N only1. Structural: The X-Y bond length is less than the sum of their van der Waals radii. X-H•••Y is ...

  8. Rectangular grids formed by hydrogen-bonding interactions ...

    Indian Academy of Sciences (India)

    Administrator

    Rectangular grids formed by hydrogen-bonding interactions between successive chains of linear polymers. [Co(II)-4,4¢-bpy-Co(II)]n and their inclusion properties: Synthesis and single crystal investigations. E SURESH 1 and MOHAN M BHADBHADE 2. 1Silicates and Catalysis Division, Central Salt & Marine Chemicals ...

  9. 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...

  10. Why are Hydrogen Bonds Directional?

    Indian Academy of Sciences (India)

    for an interaction to be characterized as a hydro- gen bond 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 topol- ogy for common hydrogen bond donors HF, HCl, ...

  11. Extremely efficient catalysis of carbon-carbon bond formation using "click" dendrimer-stabilized palladium nanoparticles.

    Science.gov (United States)

    Astruc, Didier; Ornelas, Cátia; Diallo, Abdou K; Ruiz, Jaime

    2010-07-20

    This article is an account of the work carried out in the authors' laboratory illustrating the usefulness of dendrimer design for nanoparticle palladium catalysis. The "click" synthesis of dendrimers constructed generation by generation by 1-->3 C connectivity, introduces 1,2,3-triazolyl ligands insides the dendrimers at each generation. Complexation of the ligands by Pd(II) followed by reduction to Pd(0) forms dendrimer-stabilized Pd nanoparticles (PdNPs) that are extremely reactive in the catalysis of olefin hydrogenation and C-C bond coupling reactions. The stabilization can be outer-dendritic for the small zeroth-generation dendrimer or intra-dendritic for the larger first- and second-generation dendrimers. The example of the Miyaura-Suzuki reaction that can be catalyzed by down to 1 ppm of PdNPs with a "homeopathic" mechanism (the less, the better) is illustrated here, including catalysis in aqueous solvents.

  12. 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

  13. 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

  14. Carbon-Oxygen Hydrogen Bonding in Biological Structure and Function

    Science.gov (United States)

    Horowitz, Scott; Trievel, Raymond C.

    2012-01-01

    Carbon-oxygen (CH···O) hydrogen bonding represents an unusual category of molecular interactions first documented in biological structures over 4 decades ago. Although CH···O hydrogen bonding has remained generally underappreciated in the biochemical literature, studies over the last 15 years have begun to yield direct evidence of these interactions in biological systems. In this minireview, we provide a historical context of biological CH···O hydrogen bonding and summarize some major advancements from experimental studies over the past several years that have elucidated the importance, prevalence, and functions of these interactions. In particular, we examine the impact of CH···O bonds on protein and nucleic acid structure, molecular recognition, and enzyme catalysis and conclude by exploring overarching themes and unresolved questions regarding unconventional interactions in biomolecular structure. PMID:23048026

  15. dimensional architectures via hydrogen bonds

    Indian Academy of Sciences (India)

    Administrator

    However, the utilization of hydrogen bond supramolecular syn- thons in assembling metal–organic frameworks is relatively less explored area of research. The combi- nation of these two aspects is expected to result in more control over the network geometries and there- fore the properties. The aim of the present work is to.

  16. Simple inorganic complexes but intricate hydrogen bonding ...

    Indian Academy of Sciences (India)

    Administrator

    We are interested in obtaining single crystals of metal-opda complexes because their crystal structures would show complex hydrogen bonding network due to the presence of. –NH2 groups in the opda ligand (hydrogen bonding donor sites) and inorganic anions having mostly oxo groups (hydrogen bonding acceptor sites) ...

  17. Reinforcing thermoplastics with hydrogen bonding bridged inorganics

    Energy Technology Data Exchange (ETDEWEB)

    Du Mingliang, E-mail: du@zstu.edu.c [Key Laboratory of Advanced Textile Materials and Manufacturing Technology, Ministry of Education, Zhejiang Sci-Tech University, Hangzhou 310018 (China); Guo Baochun, E-mail: psbcguo@scut.edu.c [Department of Polymer Materials and Engineering, South China University of Technology, Guangzhou 510640 (China); Liu Mingxian; Cai Xiaojia; Jia Demin [Department of Polymer Materials and Engineering, South China University of Technology, Guangzhou 510640 (China)

    2010-01-15

    A new reinforcing strategy for thermoplastics via hydrogen bonding bridged inorganics in the matrix was proposed. The hydrogen bonds could be formed in thermoplastics matrices with the incorporation of a little organics containing hydrogen bonding functionalities. Isotactic polypropylene (PP), polyamide 6 (PA 6), and high density polyethylene (HDPE), together with specific inorganics and organics were utilized to verify the effectiveness of the strategy. The investigations suggest that the hydrogen bonding bridged inorganics led to substantially increased flexural properties. The results of attenuated total refraction Fourier transform infrared spectroscopy (ATR-FTIR) and X-ray photoelectron spectra (XPS) indicate the formation of hydrogen bonding among the inorganics and organics in the composites.

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

    NARCIS (Netherlands)

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

    2010-01-01

    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. FeCl3 reduced by 3

  19. Hydrogen Bonding in the Electronic Excited State

    Science.gov (United States)

    Zhao, Guang-Jiu; Han, Ke-Li; DICP1101 Group Team

    2013-03-01

    Here, I will give a talk on our recent advances in electronic excited-state hydrogen-bonding dynamics and the significant role of excited-state hydrogen bonding on internal conversion (IC), electronic spectral shifts (ESS), photoinduced electron transfer (PET), fluorescence quenching (FQ), intramolecular charge transfer (ICT), and metal-to-ligand charge transfer (MLCT). The combination of various spectroscopic experiments with theoretical calculations has led to tremendous progress in excited-state hydrogen-bonding research. We first demonstrated that intermolecular hydrogen bond in excited state can be greatly strengthened or weakened for many chromophores. We have also clarified that intermolecular hydrogen-bond strengthening and weakening correspond to red-shifts and blue-shifts, respectively, in the electronic spectra. Moreover, radiationless deactivations (via IC, PET, ICT, MLCT, and so on) can be dramatically influenced by excited-state hydrogen bonding. GJZ and KLH thank the NSFC (Nos: 20903094 and 20833008) for financial support.

  20. Structural, intramolecular hydrogen bonding and vibrational studies ...

    Indian Academy of Sciences (India)

    The harmonic oscillator model of aromaticity (HOMA) index elucidated the impact of hydrogen bond- ing in the ring. Intramolecular hydrogen bonding energy has been calculated from topological study. The low wavenumber vibrational modes obtained from experimental FT-Raman spectrum also supported the presence.

  1. Simple inorganic complexes but intricate hydrogen bonding ...

    Indian Academy of Sciences (India)

    Administrator

    groups (hydrogen bonding acceptor sites) that stabi- lize the metal-opda cationic complex. The present contribution describes the synthesis and structural analysis of compounds [Zn(opda)2. (NO3)2] (1) and [Cd(opda)2(NO3)2] (2) emphasizing intricate supramolecular hydrogen bonding networks in their crystal structures.

  2. 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.

  3. Hydrogen bonds and twist in cellulose microfibrils.

    Science.gov (United States)

    Kannam, Sridhar Kumar; Oehme, Daniel P; Doblin, Monika S; Gidley, Michael J; Bacic, Antony; Downton, Matthew T

    2017-11-01

    There is increasing experimental and computational evidence that cellulose microfibrils can exist in a stable twisted form. In this study, atomistic molecular dynamics (MD) simulations are performed to investigate the importance of intrachain hydrogen bonds on the twist in cellulose microfibrils. We systematically enforce or block the formation of these intrachain hydrogen bonds by either constraining dihedral angles or manipulating charges. For the majority of simulations a consistent right handed twist is observed. The exceptions are two sets of simulations that block the O2-O6' intrachain hydrogen bond, where no consistent twist is observed in multiple independent simulations suggesting that the O2-O6' hydrogen bond can drive twist. However, in a further simulation where exocyclic group rotation is also blocked, right-handed twist still develops suggesting that intrachain hydrogen bonds are not necessary to drive twist in cellulose microfibrils. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Catalysis and co-catalysis of bond cleavages in coal and coal analogs

    Energy Technology Data Exchange (ETDEWEB)

    Miller, B.

    1990-01-01

    Progress is reported on the cleavage of bonds in coal and coal analogs. This quarter, 9-Phenylthioanthracene (9-PTA) was chosen as an appropriate substrate to test the hypothesis that reductive cleavage of bonds to aromatic rings caused by heating in hydrogen donor solvents, such as tetralin, may be catalyzed by electron donating agents in the absence of hydrogen bonding or acidic reagents. Ca. 0.02 M solutions of 9-PTA in tetralin (purified by chromatography on neutral alumina) were heated in glass ampoules. It was observed that decomposition of 9-PTA occurs on heating at temperatures as low as 250{degree}C, even in the absence of additives or catalysts. Reductive cleavage (measured by yields of anthracene), however, was invariably a minor process. Two major products, obtained at retention times of ca. 6.5 and 9.0 min., respectively, were observed in all runs. However, these products were obtained in rather variable yields, with an increase in the yield of one product often being accompanied by a decrease in the yield of the other. The nature of the products is unknown. GC-MS analysis is awaited. Addition of 2,6-xylenol, 1,3,5-trimethoxybenzene, or 1,4-dimethoxynaphthalene to the thermolysis mixtures appeared to offer, at best, only slight increases in reaction rates, and little change in product compositions.

  5. Lewis-acid catalysis of carbon carbon bond forming reactions in water

    NARCIS (Netherlands)

    Engberts, JBFN; Feringa, BL; Keller, E; Otto, S

    1996-01-01

    In this article, we review the recent progress that has been made in the field of Lewis-acid catalysis of carbon carbon-bond-forming reactions in aqueous solution. Since water hampers the hard hard interactions between the catalyst and the reactant, it often complicates catalysis. However, once

  6. Hydrogen Bonds and Life in the Universe.

    Science.gov (United States)

    Vladilo, Giovanni; Hassanali, Ali

    2018-01-03

    The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of life. With this aim in mind, we have explored which chemical and physical properties should be expected for life possibly different from the terrestrial one, but similarly sustained by genetic and catalytic molecules. We show that functional molecules performing genetic and catalytic tasks must feature a hierarchy of chemical interactions operating in distinct energy bands. Of all known chemical bonds and forces, only hydrogen bonds are able to mediate the directional interactions of lower energy that are needed for the operation of genetic and catalytic tasks. For this reason and because of the unique quantum properties of hydrogen bonding, the functional molecules involved in life processes are predicted to have extensive hydrogen-bonding capabilities. A molecular medium generating a hydrogen-bond network is probably essential to support the activity of the functional molecules. These hydrogen-bond requirements constrain the viability of hypothetical biochemistries alternative to the terrestrial one, provide thermal limits to life molecular processes, and offer a conceptual framework to define a transition from a "covalent-bond stage" to a "hydrogen-bond stage" in prebiotic chemistry.

  7. Hydrogen Bonds and Life in the Universe

    Science.gov (United States)

    2018-01-01

    The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of life. With this aim in mind, we have explored which chemical and physical properties should be expected for life possibly different from the terrestrial one, but similarly sustained by genetic and catalytic molecules. We show that functional molecules performing genetic and catalytic tasks must feature a hierarchy of chemical interactions operating in distinct energy bands. Of all known chemical bonds and forces, only hydrogen bonds are able to mediate the directional interactions of lower energy that are needed for the operation of genetic and catalytic tasks. For this reason and because of the unique quantum properties of hydrogen bonding, the functional molecules involved in life processes are predicted to have extensive hydrogen-bonding capabilities. A molecular medium generating a hydrogen-bond network is probably essential to support the activity of the functional molecules. These hydrogen-bond requirements constrain the viability of hypothetical biochemistries alternative to the terrestrial one, provide thermal limits to life molecular processes, and offer a conceptual framework to define a transition from a “covalent-bond stage” to a “hydrogen-bond stage” in prebiotic chemistry. PMID:29301382

  8. Versatile and Resilient Hydrogen-Bonded Host Frameworks.

    Science.gov (United States)

    Adachi, Takuji; Ward, Michael D

    2016-12-20

    Low-density molecular host frameworks, whether equipped with persistent molecular-scale pores or virtual pores that are sustainable only when occupied by guest molecules, have emerged as a promising class of materials owing to the ability to tailor the size, geometry, and chemical character of their free space through the versatility of organic synthesis. As such, molecular frameworks are promising candidates for storage, separations of commodity and fine chemicals, heterogeneous catalysis, and optical and electronic materials. Frameworks assembled through hydrogen bonds, though generally not stable toward collapse in the absence of guests, promise significant chemical and structural diversity, with pores that can be tailored for a wide range of guest molecules. The utility of these frameworks, however, depends on the resilience of n-dimensional hydrogen-bonded motifs that serve as reliable building blocks so that the molecular constituents can be manipulated without disruption of the anticipated global solid-state architecture. Though many hydrogen-bonded frameworks have been reported, few exist that are amenable to systematic modification, thus limiting the design of functional materials. This Account reviews discoveries in our laboratory during the past decade related to a series of host frameworks based on guanidinium cations and interchangeable organosulfonate anions, in which the 3-fold symmetry and hydrogen-bonding complementarity of these ions prompt the formation of a two-dimensional (2-D) quasi-hexagonal hydrogen-bonding network that has proven to be remarkably resilient toward the introduction of a wide range of organic pendant groups attached to the sulfonate. Since an earlier report in this journal that focused primarily on organodisulfonate host frameworks with lamellar architectures, this unusually persistent network has afforded an unparalleled range of framework architectures and hundreds of new crystalline materials with predictable solid

  9. 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...... are stronger in adducts of isobutane and in adducts of stronger acids. Intramolecular hydrogen bonding in protonated long-chain alcohols manifests itself in the same manner as intermolecular hydrogen bonding and can be equally strong. Udgivelsesdato: 12 juni 2009...

  10. Looking at hydrogen bonds in cellulose.

    Science.gov (United States)

    Nishiyama, Yoshiharu; Langan, Paul; Wada, Masahisa; Forsyth, V Trevor

    2010-11-01

    A series of cellulose crystal allomorphs has been studied using high-resolution X-ray and neutron fibre diffraction to locate the positions of H atoms involved in hydrogen bonding. One type of position was always clearly observed in the Fourier difference map (F(d)-F(h)), while the positions of other H atoms appeared to be less well established. Despite the high crystallinity of the chosen samples, neutron diffraction data favoured some hydrogen-bonding disorder in native cellulose. The presence of disorder and a comparison of hydrogen-bond geometries in different allomorphs suggests that although hydrogen bonding may not be the most important factor in the stabilization of cellulose I, it is essential for stabilizing cellulose III, which is the activated form, and preventing it from collapsing back to the more stable cellulose I.

  11. Intramolecular Energy Transfer, Charge Transfer & Hydrogen Bond

    Indian Academy of Sciences (India)

    Ultrafast Dynamics of Chemical Reactions in Condensed Phase: Intramolecular Energy Transfer, Charge Transfer & Hydrogen Bond. Dipak K. Palit Radaition & Photochemistry Division Bhabha Atomic Research Centre Mumbai 400 085, India.

  12. 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.

  13. PyBidine-Cu(OTf)2 -catalyzed asymmetric [3+2] cycloaddition with imino esters: harmony of Cu-Lewis acid and imidazolidine-NH hydrogen bonding in concerto catalysis.

    Science.gov (United States)

    Arai, Takayoshi; Ogawa, Hiroki; Awata, Atsuko; Sato, Makoto; Watabe, Megumi; Yamanaka, Masahiro

    2015-01-26

    A bis(imidazolidine)pyridine (PyBidine)-Cu(OTf)2 complex catalyzing the endo-selective [3+2] cycloaddition of nitroalkenes with imino esters was applied to the reaction of methyleneindolinones with imino esters to afford spiro[pyrrolidin-3,3'-oxindole]s in up to 98 % ee. X-ray crystallographic analysis of the PyBidine-Cu(OTf)2 complex and DFT calculations suggested that an intermediate Cu enolate of the imino ester reacts with nitroalkenes or methyleneindolinones, which are activated by NH-hydrogen bonding with the PyBidine-Cu(OTf)2 catalyst. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. The role of weak hydrogen bonds in chiral recognition.

    Science.gov (United States)

    Scuderi, Debora; Le Barbu-Debus, Katia; Zehnacker, A

    2011-10-28

    study of the complexes of Cinchona alkaloids involved in enantioselective catalysis. These examples show how secondary hydrogen bonds controlled by stereochemical factors govern molecular recognition processes. This journal is © the Owner Societies 2011

  15. Structural, intramolecular hydrogen bonding and vibrational studies ...

    Indian Academy of Sciences (India)

    The harmonic oscillator model of aromaticity (HOMA) index elucidated the impact of hydrogen bond- ing in the ring. Intramolecular hydrogen ... (Figure 3). The total ener- gies obtained for these possible conformers are listed in Table 1. ..... Structure, Reactivity and Intermolecular Forces: An. Euristic Interpretation by Means of ...

  16. Why are Hydrogen Bonds Directional?

    Indian Academy of Sciences (India)

    Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore,. Karnataka 560 012, India e-mail: ... Lewis succeeded in explaining the 'chemical bonds' that held the neutral molecules together. The covalent bonding has dominated chemistry so much over the last century and most chemists appear ...

  17. Versatile Hydrogen-Hydrogen Bond with a Difference

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 1; Issue 6. Versatile Hydrogen-Hydrogen Bond with a Difference. A G Samuelson. Research News Volume 1 ... Author Affiliations. A G Samuelson1. Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India.

  18. Intramolecularly Hydrogen-Bonded Polypyrroles as Electro-Optical Sensors

    National Research Council Canada - National Science Library

    Nicholson, Jesse

    2001-01-01

    We have developed a new class of polypyrroles bearing both hydrogen-bond acceptor and hydrogen-donor groups such that the intramolecular hydrogen bonding holds the system planar enhancing conjugation...

  19. Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

    Indian Academy of Sciences (India)

    Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

  20. 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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules.

    Science.gov (United States)

    Oksanen, Esko; Chen, Julian C-H; Fisher, Suzanne Zoë

    2017-04-07

    Abstract : The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. This article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.

  2. Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules

    Directory of Open Access Journals (Sweden)

    Esko Oksanen

    2017-04-01

    Full Text Available Abstract: The hydrogen bond (H bond is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. This article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.

  3. 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

  4. Simple inorganic complexes but intricate hydrogen bonding ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 121; Issue 2. Simple inorganic complexes but intricate hydrogen bonding networks: Synthesis and crystal structures of [MII(opda)2(NO3)2] (M = Zn and Cd; opda = orthophenylenediamine). Sabbani Supriya. Full Papers Volume 121 Issue 2 March 2009 pp 137-143 ...

  5. Structural, intramolecular hydrogen bonding and vibrational studies ...

    Indian Academy of Sciences (India)

    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 ...

  6. Characterization of Hydrogen Bonds by IR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Vojta, D.

    2012-05-01

    Full Text Available In the identification and quantification of hydrogen bond, as one of the most abundant non-covalent interactions in phenomena like self-assembly and molecular recognition, IR spectrosopy has been employed as the most sensitive method. The performance of the high dilution method enables determination of the stability constant of hydrogen-bonded complex as one of the most important thermodynamic quantities used in their characterization. However, the alleged experimental simplicity of the mentioned method is loaded with errors originating not only from researcher intervention but also independent from it. The second source of error is particularly emphasized and elaborated in this paper, which is designed as the recipe for the successful characterization of hydrogen bonds. Besides the enumeration of all steps in the determination of hydrogen-bonded stability constants, the reader can be acquainted with the most important ex perimental conditions that should be fulfilled in order to minimize the naturally occurring errors in this type of investigation. In the spectral analysis, the application of both uni- and multivariate approach has been discussed. Some computer packages, considering the latter, are mentioned, described, and recommended. KUI -10/2012Received August 1, 2011Accepted October 24, 2011

  7. Structural, intramolecular hydrogen bonding and vibrational studies

    Indian Academy of Sciences (India)

    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 ...

  8. 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.

  9. NMR studies of strong hydrogen bonds in enzymes and in a model compound

    Science.gov (United States)

    Harris, T. K.; Zhao, Q.; Mildvan, A. S.

    2000-09-01

    Hydrogen bond lengths on enzymes have been derived with high precision (≤±0.05 Å) from both the proton chemical shifts (δ) and the fractionation factors (φ) of the proton involved and were compared with those obtained from protein X-ray crystallography. Hydrogen bond lengths derived from proton chemical shifts were obtained from a correlation of 59 O-H⋯O hydrogen bond lengths, measured by small molecule high resolution X-ray crystallography, with chemical shifts determined by solid-state NMR in the same crystals [A. McDermott, C.F. Ridenour, Encyclopedia of NMR, Wiley, Sussex, England, 1996, 3820pp]. Hydrogen bond lengths were independently obtained from fractionation factors which yield distances between the two proton wells in quartic double minimum potential functions [M.M. Kreevoy, T.M. Liang, J. Am. Chem. Soc. 102 (1980) 3315]. The high precision hydrogen bond lengths derived from their corresponding NMR-measured proton chemical shifts and fractionation factors agree well with each other and with those reported in protein X-ray structures within the larger errors (±0.2-0.8 Å) in lengths obtained by protein X-ray crystallography. The increased precision in measurements of hydrogen bond lengths by NMR has provided insight into the contributions of short, strong hydrogen bonds to catalysis for several enzymes including ketosteroid isomerase, triosephosphate isomerase, and serine proteases. The O-H⋯O hydrogen bond length derived from the proton chemical shift in a model dihydroxy-naphthalene compound in aqueous solution agreed well with lengths of such hydrogen bonds determined by high resolution, small molecule X-ray diffraction.

  10. 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)

  11. Reversible, All-Aqueous Assembly of Hydrogen-Bonded Polymersomes

    Science.gov (United States)

    Wang, Yuhao; Sukhishvili, Svetlana

    2015-03-01

    We report on sub-micron-sized polymersomes formed through single-step, all-aqueous assembly of hydrogen-bonded amphiphilic polymers. The hollow morphology of these assemblies was revealed by transmission electron microscopy (TEM), cryogenic scanning electron microscopy (cryo-SEM) and confocal laser scanning microscopy (CLSM). Stable in acidic media, these polymersomes could be dissolved by exposure to basic pH values. Importantly, the diameter of assembled hollow structures could be controlled in a wide range from 30 nm to 1 μm by the molecular weight of hydrogen-bonding polymers. We will discuss key quantitative aspects of these assemblies, including kinetics of hollow structure formation, time evolution of polymersome size, and the role of polymer molecular weight on membrane thickness and bending rigidity. We believe that our approach demonstrates an efficient and versatile way to rationally design nanocontainers for drug delivery, catalysis and personal care applications. This work was supported by the Innovation & Entrepreneurship doctoral fellowship from Stevens Institute of Technology.

  12. Gold nanoparticle assemblies through Hydrogen-bonded supramolecular mediators

    NARCIS (Netherlands)

    Kinge, S.S.; Crego Calama, Mercedes; Reinhoudt, David

    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

  13. Optimising hydrogen bonding in solid wood

    DEFF Research Database (Denmark)

    Engelund, Emil Tang

    2009-01-01

    and temperature distorting the internal bonding state. A problem arises when studying hydrogen bonding in wood since matched wood specimens of the same species will have very different internal bonding states. Thus, possible changes in the bonding state due to some applied treatment such as conditioning...... or mechanical stress might be difficult to detect due to a large variation between the specimens. In this study, the modifications by all past external impacts such as climate and mechanical history were sought erased. This was done by heating specimens of pine (Pinus sylvestris L.) to 80 °C about 24 h while......, and load histories were assumed to be erased by this treatment. Thus, all specimens would be given a common starting point for further experiments. After the first treatment, the specimens were subjected to different climate histories in order to examine the impact of variations in air humidity...

  14. 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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

    Science.gov (United States)

    Mondal, Abhisek; Datta, Saumen

    2017-06-01

    Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  16. Hydrogen bonding in oxalic acid and its complexes

    Indian Academy of Sciences (India)

    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, ...

  17. Hydrogen bonding in oxalic acid and its complexes: A database ...

    Indian Academy of Sciences (India)

    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, ...

  18. 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...

  19. Intramolecular Energy Transfer, Charge Transfer & Hydrogen Bond

    Indian Academy of Sciences (India)

    Ultrafast Dynamics of Chemical Reactions in Condensed Phase: Intramolecular Energy Transfer, Charge Transfer & Hydrogen Bond · PowerPoint Presentation · Slide 3 · Slide 4 · Slide 5 · Slide 6 · Slide 7 · Slide 8 · Slide 9 · Slide 10 · Slide 11 · Slide 12 · Slide 13 · Slide 14 · Slide 15 · Slide 16 · Slide 17 · Slide 18 · Slide 19.

  20. Hydrogen bond donor–acceptor–donor organocatalysis for conjugate addition of benzylidene barbiturates via complementary DAD– ADA hydrogen bonding

    NARCIS (Netherlands)

    Leung, King-Chi; Cui, Jian-Fang; Hui, Tsz-Wai; Zhou, Zhong-Yuan; Wong, Man-Kin

    2014-01-01

    A new class of hydrogen bond donor-acceptor-donor (HB-DAD) organocatalysts has been developed for conjugate addition of benzylidene barbiturates. HB-DAD organocatalyst 1a (featuring para-chloro-pyrimidine as the hydrogen bond acceptor (HBA), N-H as the hydrogen bond donor (HBD) and a trifluoroacetyl

  1. 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

  2. Hydrogen and methane syntheses through radiation catalysis. Progress report, June 1, 1977--August 31, 1978

    International Nuclear Information System (INIS)

    Morse, J.G.

    1978-09-01

    Preliminary testing was performed of the concept of an electronic theory of catalysis to relate electrical properties of the catalysts to increased rates in radiation-induced reactions. The first system selected for study was the radiolysis of water as stimulated by absorption of gamma radiation, a system that has been thoroughly tested by numerous workers all in excellent agreement. Early results indicate a significant correspondence between hydrogen gas yield and the forbidden band gap (Eg) of the catalyst substrate, when Eg approximates the energy of the hydrogen-oxygen bond in the water molecule. Catalysts tested were TiO 2 , SrTiO 3 , Sb 2 O 3 , MoO 3 , Nb 2 O 5 , SnO 2 , CaO, HfO 2 , In 2 O 3 , and V 2 O 5 . Equipment to measure dielectric properties of solids has been built and calibrated, and will now be applied to pre- and post-irradiation testing of the catalysts used. Separate abstracts were prepared for the appendices: one a review of existing analytical models of photoelectrochemical cells and the other a theoretical modeling of semiconductor-electrolyte interfaces

  3. Studies of Metal-Metal Bonded Compounds in Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Berry, John [University of Wisconsin-Madison

    2018-01-19

    The focus in this grant period has been on the preparation and study of compounds containing two metals (M) and a reactive main group fragment (E) aligned in a M–M=E linear array. These structures contain multiple bonds that interconnect the M and E groups, and are structures that had been proposed, but never observed, before our work.

  4. Metal—metal multiple bonded intermediates in catalysis

    Indian Academy of Sciences (India)

    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 ...

  5. Case study of hydrogen bonding in a hydrophobic cavity.

    Science.gov (United States)

    Chen, Yi-Chen; Cheng, Chao-Sheng; Tjong, Siu-Cin; Yin, Hsien-Sheng; Sue, Shih-Che

    2014-12-18

    Protein internal hydrogen bonds and hydrophobicity determine protein folding and structure stabilization, and the introduction of a hydrogen bond has been believed to represent a better interaction for consolidating protein structure. We observed an alternative example for chicken IL-1β. The native IL-1β contains a hydrogen bond between the Y157 side-chain OηH and I133 backbone CO, whereby the substitution from Tyr to Phe abolishes the connection and the mutant without the hydrogen bond is more stable. An attempt to explain the energetic view of the presence of the hydrogen bond fails when only considering the nearly identical X-ray structures. Here, we resolve the mechanism by monitoring the protein backbone dynamics and interior hydrogen bond network. IL-1β contains a hydrophobic cavity in the protein interior, and Y157 is one of the surrounding residues. The Y157 OηH group introduces an unfavorable energy in the hydrophobic cavity, therefore sequestering itself by forming a hydrogen bond with the proximate residue I133. The hydrogen bonding confines Y157 orientation but exerts a force to disrupt the hydrogen bond network surrounding the cavity. The effect propagates over the entire protein and reduces the stability, as reflected in the protein backbone dynamics observed by an NMR hydrogen-deuterium (H/D) exchange experiment. We describe the particular case in which a hydrogen bond does not necessarily confer enhanced protein stability while the disruption of hydrophobicity must be integrally considered.

  6. Proposal of guideline for bonding to prevention of hydrogen embrittlement at Ta/Zr bond interface. Hydrogen embrittlement in SUS304ULC/Ta/Zr explosive bonded joint

    International Nuclear Information System (INIS)

    Saida, Kazuyoshi; Fujimoto, Tetsuya; Nishimoto, Kazutoshi

    2010-01-01

    The occurrence condition of hydrogen embrittlement cracking at Ta/Zr bond interface was investigated with respect to the hydrogen content and applied stress in order to propose a guideline for the explosive bonding procedure to prevention of hydrogen embrittlement. Hydrogen charging test was conducted for SUS304ULC/Ta/Zr explosive bonded joints applied the different flexural strains. A hydrogen embrittlement crack occurred in the Zr substrate at Ta/Zr bond interface after hydrogen charging, and it was initiated at shorter charging times when the augmented strain was increased. The occurrence condition of hydrogen embrittlement cracking at Ta/Zr bond interface was shifted to lower stress and hydrogen content with an increase in the amount of explosive during bonding. It was suggested that hydrogen embrittlement in Ta/Zr explosive bonded joint could be inhibited by reducing the initial hydrogen content in Ta substrate less than approx. 5 ppm. (author)

  7. Intermolecular hydrogen bonds: From temperature-driven proton ...

    Indian Academy of Sciences (India)

    Abstract. 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 ...

  8. 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...

  9. Hydrogen Bond Basicity Prediction for Medicinal Chemistry Design.

    Science.gov (United States)

    Kenny, Peter W; Montanari, Carlos A; Prokopczyk, Igor M; Ribeiro, Jean F R; Sartori, Geraldo Rodrigues

    2016-05-12

    Hydrogen bonding is discussed in the context of medicinal chemistry design. Minimized molecular electrostatic potential (Vmin) is shown to be an effective predictor of hydrogen bond basicity (pKBHX), and predictive models are presented for a number of hydrogen bond acceptor types relevant to medicinal chemistry. The problems posed by the presence of nonequivalent hydrogen bond acceptor sites in molecular structures are addressed by using nonlinear regression to fit measured pKBHX to calculated Vmin. Predictions are made for hydrogen bond basicity of fluorine in situations where relevant experimental measurements are not available. It is shown how predicted pKBHX can be used to provide insight into the nature of bioisosterism and to profile heterocycles. Examples of pKBHX prediction for molecular structures with multiple, nonequivalent hydrogen bond acceptors are presented.

  10. 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...

  11. Strong and weak hydrogen bonds in drug–DNA complexes

    Indian Academy of Sciences (India)

    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 ...

  12. 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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Concerted hydrogen atom and electron transfer mechanism for catalysis by lysine-specific demethylase.

    Science.gov (United States)

    Yu, Tao; Higashi, Masahiro; Cembran, Alessandro; Gao, Jiali; Truhlar, Donald G

    2013-07-18

    We calculate the free energy profile for the postulated hydride transfer reaction mechanism for the catalysis of lysine demethylation by lysine-specific demethylase LSD1. The potential energy surface is obtained by using combined electrostatically embedded multiconfiguration molecular mechanics (EE-MCMM) and single-configuration molecular mechanics (MM). We employ a constant valence bond coupling term to obtain analytical energies and gradients of the EE-MCMM subsystem, which contains 45 quantum mechanics (QM) atoms and which is parametrized with density functional calculations employing specific reaction parameters obtained by matching high-level wave function calculations. In the MM region, we employ the Amber ff03 and TIP3P force fields. The free energy of activation at 300 K is calculated by molecular dynamics (MD) umbrella sampling on a system with 102,090 atoms as the maximum of the free energy profile along the reaction coordinate as obtained by the weighted histogram analysis method with 17 umbrella sampling windows. This yields a free energy of activation of only 10 kcal/mol, showing that the previously postulated direct hydride transfer reaction mechanism is plausible, although we find that it is better interpreted as a concerted transfer of a hydrogen atom and an electron.

  14. 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…

  15. 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.

  16. Predictive Models for the Free Energy of Hydrogen Bonded Complexes with Single and Cooperative Hydrogen Bonds.

    Science.gov (United States)

    Glavatskikh, Marta; Madzhidov, Timur; Solov'ev, Vitaly; Marcou, Gilles; Horvath, Dragos; Varnek, Alexandre

    2016-12-01

    In this work, we report QSPR modeling of the free energy ΔG of 1 : 1 hydrogen bond complexes of different H-bond acceptors and donors. The modeling was performed on a large and structurally diverse set of 3373 complexes featuring a single hydrogen bond, for which ΔG was measured at 298 K in CCl 4 . The models were prepared using Support Vector Machine and Multiple Linear Regression, with ISIDA fragment descriptors. The marked atoms strategy was applied at fragmentation stage, in order to capture the location of H-bond donor and acceptor centers. Different strategies of model validation have been suggested, including the targeted omission of individual H-bond acceptors and donors from the training set, in order to check whether the predictive ability of the model is not limited to the interpolation of H-bond strength between two already encountered partners. Successfully cross-validating individual models were combined into a consensus model, and challenged to predict external test sets of 629 and 12 complexes, in which donor and acceptor formed single and cooperative H-bonds, respectively. In all cases, SVM models outperform MLR. The SVM consensus model performs well both in 3-fold cross-validation (RMSE=1.50 kJ/mol), and on the external test sets containing complexes with single (RMSE=3.20 kJ/mol) and cooperative H-bonds (RMSE=1.63 kJ/mol). © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Designing Homogeneous Bromine Redox Catalysis for Selective Aliphatic C-H Bond Functionalization.

    Science.gov (United States)

    Muniz, Kilian; Becker, Peter; Duhamel, Thomas; Martinez, Claudio

    2018-02-27

    The potential of homogeneous oxidation catalysis employing bromine has remained largely unexplored. The combination of tetraalkylammonium bromide and 3-chloroperbenzoic acid offers a unique catalyst system for the convenient and selective oxidation of saturated Csp3-H bonds upon photochemical initiation with visible light. It enables remote intramolecular, position-selective C-H amination as demonstrated for 20 different examples. For the first time, a N-halogenated intermediate could be isolated as the active catalyst state in a catalytic Hofmann-Löffler reaction. In addition, a novel expeditious one-pot synthesis of N-sulfonyloxaziridines from N-sulfonamides was developed and exemplified for 15 transformations. These pioneering examples provide a change in paradigm for molecular catalysis with bromine. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Hydrogen-bond interactions in morpholinium bromide

    Directory of Open Access Journals (Sweden)

    Alvaro S. de Sousa

    2011-10-01

    Full Text Available In the title compound, C4H10NO+·Br−, which was synthesized by dehydration of diethanolamine with HBr, morpholinium and bromide ions are linked into chains by N—H...Br hydrogen bonds describing a C21(4 graph-set motif. Weaker bifurcated N—H...Br interactions join centrosymmetrically related chains through alternating binary graph-set R42(8 and R22(4 motifs, to form ladders along [100]. In addition, C—H...O interactions between centrosymmetric morpholinium cations link ladders, via R^2_2(8 motifs, to yield sheets parallel to (101, which in turn are crosslinked by weak C—H...O interactions, related across a glide plane, to form a three-dimensional network.

  19. 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.

  20. 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.

  1. 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.

  2. Influence of hydrogen bonding on the generation and stabilization of ...

    Indian Academy of Sciences (India)

    Keywords. Hydrogen bonding; polymer liquid crystals; smectic; thermal properties; polymer. ... The occurrence of the smectic phases in some of the polymers indicated possibly self-assembly through the formation of hetero intermolecular hydrogen bonded networks. A smectic polymorphism and in addition, ...

  3. Hydrogen-bonding patterns involving a cyclic phosphate

    Indian Academy of Sciences (India)

    Administrator

    Hydrogen bonding as a structure-determinant is well-known in biology and chemistry. Phosphates, which always have electronegative oxygen atoms, bear no exception in their involvement in hydrogen bonding interactions. In biosystems the ubiquitous presence of water makes the study of structural patterns due to ...

  4. Hydrogen bonding in oxalic acid and its complexes: A database ...

    Indian Academy of Sciences (India)

    Abstract. 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 ...

  5. Noncovalent synthesis of nanostructures: combining coordination chemistry and hydrogen bonding

    NARCIS (Netherlands)

    Huck, W.T.S.; Huck, Wilhelm T.S.; Hulst, A.J.R.L.; Timmerman, P.; van Veggel, F.C.J.M.; Reinhoudt, David

    1997-01-01

    Rosettes that are held together by hydrogen bonds (see sketch on the right) were synthesized from metallodendrimers constructed by coordination chemistry. Two orthogonal, noncovalent interactions (metal-ligand and hydrogen bonding) were employed to build these nanosized dendrimers (M 7-28 kDa).

  6. Phase transition in triglycine family of hydrogen bonded ferroelectrics

    Indian Academy of Sciences (India)

    Hydrogen bonded ferroelectric crystals form a subclass of ferroelectrics in which hydrogen bonds play an important role in determining the properties. Triglycine family is one such class which includes triglycine sulphate (TGS), triglycine selenate. (TGSe), triglycine fluoroberyllate (TGFBe), mixed crystals like ...

  7. Effects of ion concentration on the hydrogen bonded structure of ...

    Indian Academy of Sciences (India)

    Molecular dynamics simulations of dilute and concentrated aqueous NaCl solutions are carried out to investigate the changes of the hydrogen bonded structures in the vicinity of ions for different ion concentrations. An analysis of the hydrogen bond population in the first and second solvation shells of the ions and in the bulk ...

  8. A novel hydrogen-bonded cyclic dibromide in an organic ...

    Indian Academy of Sciences (India)

    Unknown

    A novel hydrogen-bonded cyclic dibromide in an organic diammonium salt. #. BIKSHANDARKOIL R SRINIVASAN,1,* ... rangement of anions and cations may be viewed as a typical lamellar structure. The crystal water mole- cules can be ..... layers of organic (dbtmen)2+ cations (dashed lines indi- cate hydrogen bonding).

  9. Hydrogen bond and lifetime dynamics in diluted alcohols

    NARCIS (Netherlands)

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

    2017-01-01

    Hydrogen-bonding plays a crucial role in many chemical and biochemical reactions. Alcohols, with their hydrophilic and hydrophobic groups, constitute an important class of hydrogen-bonding molecules with functional tuning possibilities through changes in the hydrophobic tails. Recent studies

  10. Hydrogen bonds and antiviral activity of benzaldehyde derivatives

    Science.gov (United States)

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

    2012-09-01

    We have obtained the Fourier transform IR spectra of solutions of benzaldehyde derivatives having different antiviral activities against a herpes virus. We observe a correlation between the presence of hydrogen bonds in the benzaldehyde molecules and the appearance of antiviral properties in the compounds. For compounds having antiviral activity, we have obtained spectral data suggesting the existence of hydrogen bonds of the type C=OṡṡṡH-O and O-HṡṡṡO in the molecules. When the hydrogen atom in the hydroxyl groups are replaced by a methyl group, no intramolecular hydrogen bonds are formed and the compounds lose their antiviral activity.

  11. Predictions of glass transition temperature for hydrogen bonding biomaterials.

    Science.gov (United States)

    van der Sman, R G M

    2013-12-19

    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 theory, wherein the intermolecular hydrogen bonds constrain the mobility of the hydrogen bonded network. The finding that the glass transition relates to hydrogen bonding rather than free volume agrees with our recent finding that there is little difference in free volume among carbohydrates and polysaccharides. For binary and ternary mixtures of sugars, polyols, or biopolymers with water, our correlation states that the glass transition temperature is linear with the inverse of the number of effective hydroxyl groups per molecule. Only for dry biopolymer/sugar or sugar/polyol mixtures do we find deviations due to nonideal mixing, imposed by microheterogeneity.

  12. Hydrogen Bonding With a Hydrogen Bond: The CH4•••H2O Dimer ...

    Indian Academy of Sciences (India)

    X-H•••C hydrogen bonds in n-alkane-HX (X = F, OH) complexes are stronger than C-H•••X hydrogen bonds. R Parajuli* and E Arunan**. *Department of Physics, Amrit Campus, Tribhuvan University, Kathmandu, Nepal. **Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru 560012, India.

  13. Molecular structure and intramolecular hydrogen bonding in 2 ...

    Indian Academy of Sciences (India)

    (RCP) in the RAHB ring are valuable parameters for describing the bond. Positive values of Laplacian at .... RCP, and (d) Laplacian of total electronic density at RCP. shared interactions such as covalent bonds. In the lat- ..... ing vibrations with hydrogen bond strength have been known for a long time.53,54. The calculated.

  14. 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.

  15. 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.

  16. Short, strong hydrogen bonds on enzymes: NMR and mechanistic studies

    Science.gov (United States)

    Mildvan, A. S.; Massiah, M. A.; Harris, T. K.; Marks, G. T.; Harrison, D. H. T.; Viragh, C.; Reddy, P. M.; Kovach, I. M.

    2002-09-01

    The lengths of short, strong hydrogen bonds (SSHBs) on enzymes have been determined with high precision (±0.05 Å) from the chemical shifts ( δ), and independently from the D/ H fractionation factors ( φ) of the highly deshielded protons involved. These H-bond lengths agree well with each other and with those found by protein X-ray crystallography, within the larger errors of the latter method (±0.2 to±0.8 Å) [Proteins 35 (1999) 275]. A model dihydroxynaphthalene compound shows a SSHB of 2.54±0.04 Å based on δ=17.7 ppm and φ=0.56±0.04, in agreement with the high resolution X-ray distance of 2.55±0.06 Å. On ketosteroid isomerase, a SSHB is found (2.50±0.02 Å), based on δ=18.2 ppm and φ=0.34, from Tyr-14 to the 3-O - of estradiol, an analog of the enolate intermediate. Its strength is ˜7 kcal/mol. On triosephosphate isomerase, SSHBs are found from Glu-165 to the 1-NOH of phosphoglycolohydroxamic acid (PGH), an analog of the enolic intermediate (2.55±0.05 Å), and from His-95 to the enolic-O - of PGH (2.62±0.02 Å). In the methylglyoxal synthase-PGH complex, a SSHB (2.51±0.02 Å) forms between Asp-71 and the NOH of PGH with a strength of ≥4.7 kcal/mol. When serine proteases bind mechanism-based inhibitors which form tetrahedral Ser-adducts analogous to the tetrahedral intermediates in catalysis, the Asp⋯His H-bond of the catalytic triad becomes a SSHB [Proc. Natl Acad. Sci. USA 95 (1998) 14664], 2.49-2.63 Å in length. Similarly, on the serine-esterase, butyrylcholinesterase complexed with the mechanism-based inhibitor m-( N, N, N-trimethylammonio)-2,2,2-trifluoroacetophenone, a SSHB forms between Glu-327 and His-438 of the catalytic triad, 2.61±0.04 Å in length, based on δ=18.1 ppm and φ=0.65±0.10. Very similar results are obtained with (human) acetylcholinesterase. The strength of this SSHB is at least 4.9 kcal/mol.

  17. Enhancing the Hydrogen Activation Reactivity of Nonprecious Metal Substrates via Confined Catalysis Underneath Graphene.

    Science.gov (United States)

    Zhou, Yinong; Chen, Wei; Cui, Ping; Zeng, Jiang; Lin, Zhuonan; Kaxiras, Efthimios; Zhang, Zhenyu

    2016-10-12

    In the hydrogen evolution reaction (HER), the reactivity as a function of the hydrogen adsorption energy on different metal substrates follows a well-known volcano curve, peaked at the precious metal Pt. The goal of turning nonprecious metals into efficient catalysts for HER and other important chemical reactions is a fundamental challenge; it is also of technological significance. Here, we present results toward achieving this goal by exploiting the synergistic power of marginal catalysis and confined catalysis. Using density functional theory calculations, we first show that the volcano curve stays qualitatively intact when van der Waals attractions between a hydrogen adatom and different metal (111) surfaces are included. We further show that the hydrogen adsorption energy on the metal surfaces is weakened by 0.12-0.23 eV when hydrogen is confined between graphene and the metal surfaces, with Ni exhibiting the largest change. In particular, we find that the graphene-modified volcano curve peaks around Ni, whose bare surface already possesses moderate (or marginal) reactivity, and the corresponding HER rate of graphene-covered Ni is comparable to that of bare Pt. A hydrogen adatom has high mobility within the confined geometry. These findings demonstrate that graphene-covered Ni is an appealing effective, stable, and economical catalytic platform for HER.

  18. 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…

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

    Czech Academy of Sciences Publication Activity Database

    Doneux, T.; Ostatná, Veronika; Paleček, Emil

    2011-01-01

    Roč. 56, č. 25 (2011), s. 9337-9343 ISSN 0013-4686 R&D Projects: GA MŠk(CZ) ME09038; GA MŠk(CZ) LC06035 Grant - others:GA ČR(CZ) GAP301/11/2055 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : hydrogen evolution reaction * mediated catalysis * proton transfer Subject RIV: BO - Biophysics Impact factor: 3.832, year: 2011

  20. Hydrogen-deuterium exchange of weak carbon acids under phase-transfer catalysis conditions

    International Nuclear Information System (INIS)

    Feldman, D.; Halpern, M.; Rabinovitz, M.

    1985-01-01

    A practical method for hydrogen-deuterium exchange is obtained via extractive hydroxide ion initiated phase-transfer catalysis. The reaction of NaOD/D 2 O system allows the easy production of compounds that otherwise would require very strong bases and aprotic solvents. The strong basicity of OD - anion is attributable to its relative freedom from water molecules when OD - is extracted into the depth of the organic layer. 22 references, 1 table

  1. How resonance assists hydrogen bonding interactions: an energy decomposition analysis.

    Science.gov (United States)

    Beck, John Frederick; Mo, Yirong

    2007-01-15

    Block-localized wave function (BLW) method, which is a variant of the ab initio valence bond (VB) theory, was employed to explore the nature of resonance-assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between pi delocalization and hydrogen-bonding interactions. We examined the dimers of formic acid, formamide, 4-pyrimidinone, 2-pyridinone, 2-hydroxpyridine, and 2-hydroxycyclopenta-2,4-dien-1-one. In addition, we studied the interactions in beta-diketone enols with a simplified model, namely the hydrogen bonds of 3-hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of pi resonance, were decomposed into the Hitler-London energy (DeltaEHL), polarization energy (DeltaEpol), charge transfer energy (DeltaECT), and electron correlation energy (DeltaEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of pi conjugation on hydrogen bonding interactions. Although it has been proposed that resonance-assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole-dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term "resonance-assisted binding (RAB)" instead of "resonance-assisted hydrogen bonding (RHAB)" to highlight the electrostatic, which is a long-range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs. Copyright (c) 2006 Wiley Periodicals, Inc.

  2. 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.

  3. 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.

  4. Hydrogen bonding characterization in water and small molecules

    Science.gov (United States)

    Silvestrelli, Pier Luigi

    2017-06-01

    The prototypical hydrogen bond in water dimer and hydrogen bonds in the protonated water dimer, in other small molecules, in water cyclic clusters, and in ice, covering a wide range of bond strengths, are theoretically investigated by first-principles calculations based on density functional theory, considering not only a standard generalized gradient approximation functional but also, for the water dimer, hybrid and van der Waals corrected functionals. We compute structural, energetic, and electrostatic (induced molecular dipole moments) properties. In particular, hydrogen bonds are characterized in terms of differential electron density distributions and profiles, and of the shifts of the centres of maximally localized Wannier functions. The information from the latter quantities can be conveyed to a single geometric bonding parameter that appears to be correlated with the Mayer bond order parameter and can be taken as an estimate of the covalent contribution to the hydrogen bond. By considering the water trimer, the cyclic water hexamer, and the hexagonal phase of ice, we also elucidate the importance of cooperative/anticooperative effects in hydrogen-bonding formation.

  5. Probing hydrogen bonding interactions and proton transfer in proteins

    Science.gov (United States)

    Nie, Beining

    Scope and method of study. Hydrogen bonding is a fundamental element in protein structure and function. Breaking a single hydrogen bond may impair the stability of a protein. It is therefore important to probe dynamic changes in hydrogen bonding interactions during protein folding and function. Time-resolved Fourier transform infrared spectroscopy is highly sensitive to hydrogen bonding interactions. However, it lacks quantitative correlation between the vibrational frequencies and the number, type, and strength of hydrogen bonding interactions of ionizable and polar residues. We employ quantum physics theory based ab initio calculations to study the effects of hydrogen bonding interactions on vibrational frequencies of Asp, Glu, and Tyr residues and to develop vibrational spectral markers for probing hydrogen bonding interactions using infrared spectroscopy. In addition, proton transfer process plays a crucial role in a wide range of energy transduction, signal transduction, and enzymatic reactions. We study the structural basis for proton transfer using photoactive yellow protein as an excellent model system. Molecular dynamics simulation is employed to investigate the structures of early intermediate states. Quantum theory based ab initio calculations are used to study the impact of hydrogen bond interactions on proton affinity and proton transfer. Findings and conclusions. Our extensive density function theory based calculations provide rich structural, spectral, and energetic information on hydrogen bonding properties of protonated side chain groups of Asp/Glu and Tyr. We developed vibrational spectral markers and 2D FTIR spectroscopy for structural characterization on the number and the type of hydrogen bonding interactions of the COOH group of Asp/Glu and neutral phenolic group of Tyr. These developments greatly enhance the power of time-resolved FTIR spectroscopy as a major experimental tool for structural characterization of functionally important

  6. 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.

  7. Triplet-Triplet Energy Transfer Study in Hydrogen Bonding Systems.

    Science.gov (United States)

    Wang, Zhijia; Zhao, Jianzhang; Guo, Song

    2015-01-01

    The 2,6-diiodoBodipy-styrylBodipy hydrogen bonding system was prepared to study the effect of hydrogen bonding on the triplet-triplet-energy-transfer (TTET) process. 2,6-DiiodoBodipy linked with N-acetyl-2,6-diaminopyridine (D-2) was used as the triplet energy donor, and the styrylBodipy connected with thymine (A-1) was used as triplet energy acceptor, thus the TTET process was established upon photoexcitation. The photophysical processes of the hydrogen bonding system were studied with steady-state UV-vis absorption spectroscopy, fluorescence spectroscopy, fluorescence lifetime measurement and nanosecond time-resolved transient absorption spectroscopies. The TTET of the intramolecular/hydrogen bonding/intermolecular systems were compared through nanosecond transient absorption spectroscopy. The TTET process of the hydrogen bonding system is faster and more efficient (kTTET = 6.9 × 10(4) s(-1), ΦTTET = 94.0%) than intermolecular triplet energy transfer (kTTET = 6.0 × 10(4) s(-1), ΦTTET = 90.9%), but slower and less efficient than intramolecular triplet energy transfer (kTTET > 10(8) s(-1)). These results are valuable for designing self-assembly triplet photosensitizers and for the study of the TTET process of hydrogen bonding systems.

  8. Sphalerite is a geochemical catalyst for carbon-hydrogen bond activation.

    Science.gov (United States)

    Shipp, Jessie A; Gould, Ian R; Shock, Everett L; Williams, Lynda B; Hartnett, Hilairy E

    2014-08-12

    Reactions among minerals and organic compounds in hydrothermal systems are critical components of the Earth's deep carbon cycle, provide energy for the deep biosphere, and may have implications for the origins of life. However, there is limited information as to how specific minerals influence the reactivity of organic compounds. Here we demonstrate mineral catalysis of the most fundamental component of an organic reaction: the breaking and making of a covalent bond. In the absence of mineral, hydrothermal reaction of cis- and trans-1,2-dimethylcyclohexane is extremely slow and generates many products. In the presence of sphalerite (ZnS), however, the reaction rate increases dramatically and one major product is formed: the corresponding stereoisomer. Isotope studies show that the sphalerite acts as a highly specific heterogeneous catalyst for activation of a single carbon-hydrogen bond in the dimethylcyclohexanes.

  9. Dynamics of hydrogen bonds in water and consequences for the ...

    Indian Academy of Sciences (India)

    Figure. 1 summarizes the situation in a schematic and simplified way. As pointed out above, to know the behaviour of liquid water we must take into account the properties of the intermolecular hydrogen bonds (HB). The peculiar behaviour of liquid water is due to such bonds, more precisely, due to three of their properties:.

  10. 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...

  11. Cycloaddition Reaction of Hydrogen-Bonded Zn(II)

    Indian Academy of Sciences (India)

    J. Chem. Sci. Vol. 129, No. 2, February 2017, pp. 239–247. c Indian Academy of Sciences. DOI 10.1007/s12039-016-1218-6. REGULAR ARTICLE. Solid-state Photochemical [2+2] Cycloaddition Reaction of. Hydrogen-Bonded Zn(II) Metal Complex Containing Several Parallel. C=C Bonds. ABDUL MALIK P PEEDIKAKKAL.

  12. Defining the hydrogen bond: An account (IUPAC Technical Report)

    Czech Academy of Sciences Publication Activity Database

    Arunan, E.; Desiraju, G. R.; Klein, R. A.; Sadlej, J.; Scheiner, S.; Alkorta, I.; Clary, D. C.; Crabtree, R. H.; Dannenberg, J. J.; Hobza, Pavel; Kjaergaard, H. G.; Legon, A. C.; Mennucci, B.; Nesbitt, D. J.

    2011-01-01

    Roč. 83, č. 8 (2011), s. 1619-1636 ISSN 0033-4545 Institutional research plan: CEZ:AV0Z40550506 Keywords : bonding * electrostatic interactions * hydrogen bonding * molecular interactions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.789, year: 2011

  13. Hydrogen bond dynamics and vibrational spectral diffusion in ...

    Indian Academy of Sciences (India)

    Abstract. 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 ...

  14. Exchange of bonded hydrogen in amorphous silicon by deuterium

    International Nuclear Information System (INIS)

    Abeles, B.; Yang, L.; Leta, D.P.; Majkrazak, C.

    1987-01-01

    The authors show that bonded hydrogen in a-Si:H is readily exchanged by atomic deuterium when exposed to a deuterium plasma discharge. The effective diffusion coefficient for the D, H exchange, 10 -14 cm 2 /sec at 160 0 C, is comparable to that of interstitial hydrogen in c-Si

  15. 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.

  16. Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design.

    Science.gov (United States)

    Maguire, Jack B; Boyken, Scott E; Baker, David; Kuhlman, Brian

    2018-04-20

    Hydrogen bond networks play a critical role in determining the stability and specificity of biomolecular complexes, and the ability to design such networks is important for engineering novel structures, interactions, and enzymes. One key feature of hydrogen bond networks that makes them difficult to rationally engineer is that they are highly cooperative and are not energetically favorable until the hydrogen bonding potential has been satisfied for all buried polar groups in the network. Existing computational methods for protein design are ill-equipped for creating these highly cooperative networks because they rely on energy functions and sampling strategies that are focused on pairwise interactions. To enable the design of complex hydrogen bond networks, we have developed a new sampling protocol in the molecular modeling program Rosetta that explicitly searches for sets of amino acid mutations that can form self-contained hydrogen bond networks. For a given set of designable residues, the protocol often identifies many alternative sets of mutations/networks, and we show that it can readily be applied to large sets of residues at protein-protein interfaces or in the interior of proteins. The protocol builds on a recently developed method in Rosetta for designing hydrogen bond networks that has been experimentally validated for small symmetric systems but was not extensible to many larger protein structures and complexes. The sampling protocol we describe here not only recapitulates previously validated designs with performance improvements but also yields viable hydrogen bond networks for cases where the previous method fails, such as the design of large, asymmetric interfaces relevant to engineering protein-based therapeutics.

  17. Hydrogen-Bonded Homoleptic Fluoride-Diarylurea Complexes: Structure, Reactivity, and Coordinating Power.

    Science.gov (United States)

    Pfeifer, Lukas; Engle, Keary M; Pidgeon, George W; Sparkes, Hazel A; Thompson, Amber L; Brown, John M; Gouverneur, Véronique

    2016-10-04

    Hydrogen bonding with fluoride is a key interaction encountered when analyzing the mode of action of 5'-fluoro-5'-deoxyadenosine synthase, the only known enzyme capable of catalyzing the formation of a C-F bond from F - . Further understanding of the effect of hydrogen bonding on the structure and reactivity of complexed fluoride is therefore important for catalysis and numerous other applications, such as anion supramolecular chemistry. Herein we disclose a detailed study examining the structure of 18 novel urea-fluoride complexes in the solid state, by X-ray and neutron diffraction, and in solution phase and explore the reactivity of these complexes as a fluoride source in S N 2 chemistry. Experimental data show that the structure, coordination strength, and reactivity of the urea-fluoride complexes are tunable by modifying substituents on the urea receptor. Hammett analysis of aryl groups on the urea indicates that fluoride binding is dependent on σ p and σ m parameters with stronger binding being observed for electron-deficient urea ligands. For the first time, defined urea-fluoride complexes are used as fluoride-binding reagents for the nucleophilic substitution of a model alkyl bromide. The reaction is slower in comparison with known alcohol-fluoride complexes, but S N 2 is largely favored over E2, at a ratio surpassing all hydrogen-bonded complexes documented in the literature for the model alkyl bromide employed. Increased second-order rate constants at higher dilution support the hypothesis that the reactive species is a 1:1 urea-fluoride complex of type [UF] - (U = urea) resulting from partial dissociation of the parent compound [U 2 F] - . The dissociation processes can be quantified through a combination of UV and NMR assays, including DOSY and HOESY analyses that illuminate the complexation state and H-bonding in solution.

  18. Probing the nature of hydrogen bonds in DNA base pairs.

    Science.gov (United States)

    Mo, Yirong

    2006-07-01

    Energy decomposition analyses based on the block-localized wave-function (BLW-ED) method are conducted to explore the nature of the hydrogen bonds in DNA base pairs in terms of deformation, Heitler-London, polarization, electron-transfer and dispersion-energy terms, where the Heitler-London energy term is composed of electrostatic and Pauli-exchange interactions. A modest electron-transfer effect is found in the Watson-Crick adenine-thymine (AT), guanine-cytosine (GC) and Hoogsteen adenine-thymine (H-AT) pairs, confirming the weak covalence in the hydrogen bonds. The electrostatic attraction and polarization effects account for most of the binding energies, particularly in the GC pair. Both theoretical and experimental data show that the GC pair has a binding energy (-25.4 kcal mol(-1) at the MP2/6-31G** level) twice that of the AT (-12.4 kcal mol(-1)) and H-AT (-12.8 kcal mol(-1)) pairs, compared with three conventional N-H...O(N) hydrogen bonds in the GC pair and two in the AT or H-AT pair. Although the remarkably strong binding between the guanine and cytosine bases benefits from the opposite orientations of the dipole moments in these two bases assisted by the pi-electron delocalization from the amine groups to the carbonyl groups, model calculations demonstrate that pi-resonance has very limited influence on the covalence of the hydrogen bonds. Thus, the often adopted terminology "resonance-assisted hydrogen bonding (RHAB)" may be replaced with "resonance-assisted binding" which highlights the electrostatic rather than electron-transfer nature of the enhanced stabilization, as hydrogen bonds are usually regarded as weak covalent bonds.

  19. Formation of C–C Bonds via Iridium-Catalyzed Hydrogenation and Transfer Hydrogenation

    Science.gov (United States)

    Bower, John F.; Krische, Michael J.

    2011-01-01

    The formation of C–C bonds via catalytic hydrogenation and transfer hydrogenation enables carbonyl and imine addition in the absence of stoichiometric organometallic reagents. In this review, iridium-catalyzed C–C bond-forming hydrogenations and transfer hydrogenations are surveyed. These processes encompass selective, atom-economic methods for the vinylation and allylation of carbonyl compounds and imines. Notably, under transfer hydrogenation conditions, alcohol dehydrogenation drives reductive generation of organoiridium nucleophiles, enabling carbonyl addition from the aldehyde or alcohol oxidation level. In the latter case, hydrogen exchange between alcohols and π-unsaturated reactants generates electrophile–nucleophile pairs en route to products of hydro-hydroxyalkylation, representing a direct method for the functionalization of carbinol C–H bonds. PMID:21822399

  20. Examining student heuristic usage in a hydrogen bonding assessment.

    Science.gov (United States)

    Miller, Kathryn; Kim, Thomas

    2017-09-01

    This study investigates the role of representational competence in student responses to an assessment of hydrogen bonding. The assessment couples the use of a multiple-select item ("Choose all that apply") with an open-ended item to allow for an examination of students' cognitive processes as they relate to the assignment of hydrogen bonding within a structural representation. Response patterns from the multiple-select item implicate heuristic usage as a contributing factor to students' incorrect responses. The use of heuristics is further supported by the students' corresponding responses to the open-ended assessment item. Taken together, these data suggest that poor representational competence may contribute to students' previously observed inability to correctly navigate the concept of hydrogen bonding. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):411-416, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  1. Reassigning hydrogen-bond centering in dense ice

    International Nuclear Information System (INIS)

    Benoit, Magali; Romero, Aldo H.; Marx, Dominik

    2002-01-01

    Hydrogen bonds in H 2 O ice change dramatically upon compression. Thereby a hydrogen-bonded molecular crystal, ice VII, is transformed to an atomic crystal, ice X. Car-Parrinello simulations reproduce the features of the x-ray diffraction spectra up to about 170 GPa but allow for analysis in real space. Starting from molecular ice VII with static orientational disorder, dynamical translational disordering occurs first via creation of ionic defects, which results in a systematic violation of the ice rules. As a second step, the transformation to an atomic solid and thus hydrogen-bond centering occurs around 110 GPa at 300 K and no novel phase is found up to at least 170 GPa

  2. Dendritic biomimicry: microenvironmental hydrogen-bonding effects on tryptophan fluorescence.

    Science.gov (United States)

    Koenig, S; Müller, L; Smith, D K

    2001-03-02

    Two series of dendritically modified tryptophan derivatives have been synthesised and their emission spectra measured in a range of different solvents. This paper presents the syntheses of these novel dendritic structures and discusses their emission spectra in terms of both solvent and dendritic effects. In the first series of dendrimers, the NH group of the indole ring is available for hydrogen bonding, whilst in the second series, the indole NH group has been converted to NMe. Direct comparison of the emission wavelengths of analogous NH and NMe derivatives indicates the importance of the Kamlet-Taft solvent beta3 parameter, which reflects the ability of the solvent to accept a hydrogen bond from the NH group, an effect not possible for the NMe series of dendrimers. For the NH dendrimers, the attachment of a dendritic shell to the tryptophan subunit leads to a red shift in emission wavelength. This dendritic effect only operates in non-hydrogen-bonding solvents. For the NMe dendrimers, however, the attachment of a dendritic shell has no effect on the emission spectra of the indole ring. This proves the importance of hydrogen bonding between the branched shell and the indole NH group in causing the dendritic effect. This is the first time a dendritic effect has been unambiguously assigned to individual hydrogen-bonding interactions and indicates that such intramolecular interactions are important in dendrimers, just as they are in proteins. Furthermore, this paper sheds light on the use of tryptophan residues as a probe of the microenvironment within proteins--in particular, it stresses the importance of hydrogen bonds formed by the indole NH group.

  3. Excluded volume versus hydrogen bonding: complementary or incompatible concepts?

    Science.gov (United States)

    Nezbeda, Ivo; Škvor, Jiří

    2012-12-01

    An attempt has been made to assess individual effects of the repulsive and attractive interactions on the structure of associating fluids using short-range models descending from parent realistic models. It is shown that neither the excluded volume (repulsive interactions) nor the hydrogen bonding (attractive interactions) considered separately are able to produce the correct structure. However, when both these types of interactions are considered together, they faithfully reproduce the structure of water and other associating fluids. Consequently, although some properties of aqueous systems can be explained qualitatively/intuitively by hydrogen bonding only, disregarding simultaneously the excluded volume effects may be misleading.

  4. Hydrogen peroxide coordination to cobalt(II) facilitated by second-sphere hydrogen bonding

    Czech Academy of Sciences Publication Activity Database

    Wallen, C.M.; Palatinus, Lukáš; Bacsa, J.; Scarborough, C.C.

    2016-01-01

    Roč. 55, č. 39 (2016), s. 11902-11906 ISSN 0044-8249 Institutional support: RVO:68378271 Keywords : cobalt * hydrogen bonds * peroxides * peroxido ligands * second-sphere interactions Subject RIV: CC - Organic Chemistry

  5. Homogeneous Catalysis for Sustainable Hydrogen Storage in Formic Acid and Alcohols.

    Science.gov (United States)

    Sordakis, Katerina; Tang, Conghui; Vogt, Lydia K; Junge, Henrik; Dyson, Paul J; Beller, Matthias; Laurenczy, Gábor

    2018-01-24

    Hydrogen gas is a storable form of chemical energy that could complement intermittent renewable energy conversion. One of the main disadvantages of hydrogen gas arises from its low density, and therefore, efficient handling and storage methods are key factors that need to be addressed to realize a hydrogen-based economy. Storage systems based on liquids, in particular, formic acid and alcohols, are highly attractive hydrogen carriers as they can be made from CO 2 or other renewable materials, they can be used in stationary power storage units such as hydrogen filling stations, and they can be used directly as transportation fuels. However, to bring about a paradigm change in our energy infrastructure, efficient catalytic processes that release the hydrogen from these molecules, as well as catalysts that regenerate these molecules from CO 2 and hydrogen, are required. In this review, we describe the considerable progress that has been made in homogeneous catalysis for these critical reactions, namely, the hydrogenation of CO 2 to formic acid and methanol and the reverse dehydrogenation reactions. The dehydrogenation of higher alcohols available from renewable feedstocks is also described. Key structural features of the catalysts are analyzed, as is the role of additives, which are required in many systems. Particular attention is paid to advances in sustainable catalytic processes, especially to additive-free processes and catalysts based on Earth-abundant metal ions. Mechanistic information is also presented, and it is hoped that this review not only provides an account of the state of the art in the field but also offers insights into how superior catalytic systems can be obtained in the future.

  6. Inert C-H Bond Transformations Enabled by Organometallic Manganese Catalysis.

    Science.gov (United States)

    Hu, Yuanyuan; Zhou, Bingwei; Wang, Congyang

    2018-03-20

    (with or w/o bases) and acids, we disclosed a "dual activation" mode for performing manganese-catalyzed C-H bond transformations, that is, merging C-H activation by manganese catalysts and C-X multiple bond activation by Lewis acids. Consequently, the scope of C-H substrates could be expanded to include challenging ketones and olefinic C-H compounds. Additionally, the range of reaction partners could be significantly broadened to include those bearing more polarized C═O, C═N, and C≡N bonds such as aldehydes, imines, and nitriles. Remarkably, the innate reactivity of different C-H bonds in ketones could be reversed by manganese catalysis, and the reactions could even be carried out at room temperature. Our findings provide guiding information for the future development of manganese-catalyzed C-H activation reactions and beyond. Related important contributions from other groups are mentioned, and the remaining challenges and future perspective in this emerging area are also presented.

  7. Hydrogen-bonding directed crystal engineering of some molecular solids

    Science.gov (United States)

    Xue, Feng

    2000-10-01

    The design of crystalline clathrates and microporous solids is a contemporary goal in crystal engineering, in which hydrogen bonds play a central role because of their strength, directionality and flexibility. We have constructed various layer- and channel-type host structures by using hydrogen-bonding interactions. A novel hydrogen-bonded supramolecular rosette structure is generated from guanidinium and hydrogen carbonate ions in (1) and ( 2). The rosettes are fused into linear ribbons, which are cross-linked by terephthalate or 4-nitrobenzoate ions functioning as hydrogen-bond acceptors, resulting in anionic host layers with tetra-n-butylammonium guest species sandwiched between them. In (3) ˜ (6), new crystalline adducts of tetraalkylammonium terephthalate/trimesate with urea and water molecules result from hydrogen-bond directed assembly of complementary acceptors and donors that generate anionic channel- and layer-type host lattices for the accommodation of bulky hydrophobic cations. Some 4,4'-disubstituted biphenyls manifest their robustness and flexibility as supramolecular building blocks to construct host structures. 4,4'-biphenyl dicarboxylate ion has a strong tendency in generating ladder-type structure in (7) ˜ (10) due to its rigidity and effectiveness as a bifunctional hydrogen-bond acceptor. In (11) ˜ (15), 4,4 '-dicyanobiphenyl, 4,4'-bipyridine-N,N '-dioxide and 4,4'-dinitrobiphenyl exhibit a constructive interplay of strong and weak hydrogen bond functionalities that generate robust synthons. 4-Tritylbenzoic acid crystallizes via the carboxyl dimer supramolecular synthon to produce a wheel-and-axle host lattice that includes different aromatic solvents in its microporous framework in (16) ˜ (25 ), in which the host architecture is robust and yet adaptive. Based on the trigonal symmetry of 2,4,6-tris-4-(halo-phenoxy)-1,3,5-triazines (halo = chloro, bromo) and the Br3 or Cl3 supramolecular synthon, a new hexagonal host lattice has been designed

  8. Substituent Effects in CH Hydrogen Bond Interactions: Linear Free Energy Relationships and Influence of Anions.

    Science.gov (United States)

    Tresca, Blakely W; Hansen, Ryan J; Chau, Calvin V; Hay, Benjamin P; Zakharov, Lev N; Haley, Michael M; Johnson, Darren W

    2015-12-02

    Aryl CH hydrogen bonds (HBs) are now commonly recognized as important factors in a number of fields, including molecular biology, stereoselective catalysis, and anion supramolecular chemistry. As the utility of CH HBs has grown, so to has the need to understand the structure-activity relationship for tuning both their strength and selectivity. Although there has been significant computational effort in this area, an experimental study of the substituent effects on CH HBs has not been previously undertaken. Herein we disclose a systematic study of a single CH HB by using traditional urea donors as directing groups in a supramolecular binding cavity. Experimentally determined association constants are examined by a combination of computational (electrostatic potential) and empirical (σm and σp) values for substituent effects. The dominance of electrostatic parameters, as observed in a computational DFT study, is consistent with current CH HB theory; however, a novel anion dependence of the substituent effects is revealed in solution.

  9. 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.

  10. 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

  11. Dynamics of hydrogen bonds in water and consequences for the ...

    Indian Academy of Sciences (India)

    E-mail: jose.teixeira@cea.fr. Abstract. The dynamics of liquid water is evaluated by the coherent quasi-elastic scat- tering 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.

  12. Examining Student Heuristic Usage in a Hydrogen Bonding Assessment

    Science.gov (United States)

    Miller, Kathryn; Kim, Thomas

    2017-01-01

    This study investigates the role of representational competence in student responses to an assessment of hydrogen bonding. The assessment couples the use of a multiple-select item ("Choose all that apply") with an open-ended item to allow for an examination of students' cognitive processes as they relate to the assignment of hydrogen…

  13. Supramolecular materials based on hydrogen-bonded polymers

    NARCIS (Netherlands)

    ten Brinke, Gerrit; Ruokolainen, Janne; Ikkala, Olli; Binder, W

    2007-01-01

    Combining supramolecular principles with block copolymer self-assembly offers unique possibilities to create materials with responsive and/or tunable properties. The present chapter focuses on supramolecular materials based on hydrogen bonding and (block co-) polymers. Several cases will be

  14. Dynamics of hydrogen bonds in water and consequences for the ...

    Indian Academy of Sciences (India)

    Invited Papers Volume 71 Issue 4 October 2008 pp 761-768 ... 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 ... The results indicate a possible issue for the puzzle of the behaviour of supercooled water.

  15. Effects of dimethyl sulfoxide on the hydrogen bonding structure and ...

    Indian Academy of Sciences (India)

    Keywords. Aqueous NMA-DMSO solution; hydrogen-bond lifetime; structural relaxation times; self- diffusion coefficients; orientational relaxation times. 1. Introduction. Dimethyl sulfoxide (DMSO) is an important organic solvent, with immense significance in chemical and biological systems.1 In addition to being an effective.

  16. Polarization-induced sigma-holes and hydrogen bonding

    Czech Academy of Sciences Publication Activity Database

    Hennemann, M.; Murray, J. S.; Politzer, P.; Riley, Kevin Eugene; Clark, T.

    2012-01-01

    Roč. 18, č. 6 (2012), s. 2461-2469 ISSN 1610-2940 Institutional research plan: CEZ:AV0Z40550506 Keywords : hydrogen bond * sigma-hole * polarization * field effect * ab initio calculation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.984, year: 2012

  17. Hydrogen bonding in oxalic acid and its complexes: A database ...

    Indian Academy of Sciences (India)

    –COOH as an acceptor in the case of biomolecules was carried out by Ramanad- ham and coworkers [4]. A method was proposed to distinguish between ionized and neutral carboxyl group based on hydrogen bonding properties of OH of COOH. A more general survey of all the carboxylic acid structures determined using ...

  18. Hydrogen bonding of formamide, urea, urea monoxide and their thio ...

    Indian Academy of Sciences (India)

    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 ...

  19. Binding of reactive organophosphate by oximes via hydrogen bond

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 125; Issue 4. Binding of reactive organophosphate by oximes via hydrogen bond. Andrea Pappalardo Maria E Amato Francesco P Ballistreri Valentina La Paglia Fragola Gaetano A Tomaselli Rosa Maria Toscano Giuseppe Trusso Sfrazzetto. Volume 125 Issue 4 July ...

  20. Binding of reactive organophosphate by oximes via hydrogen bond

    Indian Academy of Sciences (India)

    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 ...

  1. Formation of a hydrogen-bonded barbiturate [2]-rotaxane.

    Science.gov (United States)

    Tron, Arnaud; Thornton, Peter J; Rocher, Mathias; Jacquot de Rouville, Henri-Pierre; Desvergne, Jean-Pierre; Kauffmann, Brice; Buffeteau, Thierry; Cavagnat, Dominique; Tucker, James H R; McClenaghan, Nathan D

    2014-03-07

    Interlocked structures containing the classic Hamilton barbiturate binding motif comprising two 2,6-diamidopyridine units are reported for the first time. Stable [2]-rotaxanes can be accessed either through hydrogen-bonded preorganization by a barbiturate thread followed by a Cu(+)-catalyzed "click" stoppering reaction or by a Cu(2+)-mediated Glaser homocoupling reaction.

  2. NMR and IR investigations of strong intramolecular hydrogen bonds

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Spanget-Larsen, Jens

    2017-01-01

    For the purpose of this review, strong hydrogen bonds have been defined on the basis of experimental data, such as OH stretching wavenumbers, vOH, and OH chemical shifts, dOH (in the latter case after correction for ring current effects). Limits for O–H···Y systems are taken as 2800 > vOH > 1800 ...

  3. Organic ferroelectrics based on hydrogen-bonded supermolecules

    International Nuclear Information System (INIS)

    Horiuchi, Sachio; Kumai, Reiji; Tokura, Yoshinori

    2007-01-01

    This article describes a new design strategy and prospective approaches to the fabrication of novel organic ferroelectrics. Ferroelectricity and a significant dielectric response as well as collective proton transfer are demonstrated in the hydrogen-bonded supramolecular chains composed of 2,5-dihydroxy-p-benzoquinone derivatives (acid) and nitrogen-containing aromatic bases. (author)

  4. 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.

  5. Effects of dimethyl sulfoxide on the hydrogen bonding structure

    Indian Academy of Sciences (India)

    Effects of dimethyl-sulfoxide (DMSO) on the hydrogen bonding structure and dynamics in aqueousN-methylacetamide (NMA) solution are investigated by classical molecular dynamics simulations. Themodifications of structure and interaction between water and NMA in presence of DMSO molecules are calculatedby ...

  6. Dielectric relaxation and hydrogen bonding studies of 1,3 ...

    Indian Academy of Sciences (India)

    tric spectrometry of associating liquids. To find hydrogen bond concentration, dielectric relaxation studies have been performed on alcohol–alcohol mixtures and on mixtures of alcohols with water [20–37]. Crossely [38] had studied the dielectric permittivity and loss for a series of diols and concluded that the relaxation times ...

  7. Hydrogen Bonding Patterns in a Series of 3-Spirocyclic Oxindoles

    African Journals Online (AJOL)

    NICO

    Hydrogen Bonding Patterns in a Series of. 3-Spirocyclic Oxindoles. Andreas Lemmerer* and Joseph P. Michael. Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, P.O. WITS 2050, South Africa. Received 24 May 2010, revised 5 October 2010, accepted 29 October 2010.

  8. π Hydrogen bonded complexes of Acetic acid and Trifluoroacetic ...

    Indian Academy of Sciences (India)

    Matrix isolation infrared spectra of O-H···π Hydrogen bonded complexes of Acetic acid and Trifluoroacetic acid with Benzene. PUJARINI BANERJEE, INDRANI BHATTACHARYA and TAPAS CHAKRABORTY. ∗. Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata 700 032, India.

  9. Hydrogen bonding of formamide, urea, urea monoxide and their thio ...

    Indian Academy of Sciences (India)

    Abstract. Ab initio and DFT methods have been employed to study the hydrogen bonding ability of for- mamide, urea, urea monoxide, thioformamide, thiourea and thiourea monoxide with one water molecule and the homodimers of the selected molecules. The stabilization energies associated with the monohydrated ...

  10. Understanding hydrogen bonding and determination of in-crystal dipol

    Indian Academy of Sciences (India)

    Wintec

    asparaginium ion and the picrate in the other complex. We have additionally performed theoretical calcu- lations at the density functional theory (DFT) level to understand the origin of enhancement of the dipole moments in the two systems. Keywords. X-ray diffraction; experimental charge density; hydrogen bonding; dipole ...

  11. Effects of ion concentration on the hydrogen bonded structure of ...

    Indian Academy of Sciences (India)

    WINTEC

    Effects of ion concentration on the hydrogen bonded structure of water in the vicinity of ions in aqueous NaCl solutions. A NAG. 1. , D CHAKRABORTY and A CHANDRA*. Department of Chemistry, Indian Institute of Technology, Kanpur 208 016. 1. Present address: Department of Chemistry and Chemical Engineering,.

  12. Influence of hydrogen bonding on the generation and stabilization of ...

    Indian Academy of Sciences (India)

    ety totally vanquished liquid crystalline phases while biphenylene and naphthalene units did only reduce the transition .... firms the fact that during heating some of the amide–ester hydrogen bonds change into amide–amide ... their potential applications in LC displays, NLO materials, information storage devices etc. [12].

  13. Phase transition in triglycine family of hydrogen bonded ...

    Indian Academy of Sciences (India)

    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.

  14. Hydrogen bonding in thiobenzamide synthon and its Cadmium ...

    Indian Academy of Sciences (India)

    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.

  15. Understanding the Relationship Between Kinetics and Thermodynamics in CO 2 Hydrogenation Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Jeletic, Matthew S. [Catalysis Science Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Hulley, Elliott B. [Catalysis Science Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Helm, Monte L. [Catalysis Science Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Mock, Michael T. [Catalysis Science Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Appel, Aaron M. [Catalysis Science Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Wiedner, Eric S. [Catalysis Science Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Linehan, John C. [Catalysis Science Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States

    2017-08-14

    Linear free-energy relationships have been identified that link the kinetic activity for catalytic hydrogenation of CO2 to formate with the thermodynamic driving force for the rate-limiting steps of catalysis. Cobalt and rhodium bis(diphosphine) complexes with different hydricities (G°H-), acidities (pKa), and free energies for H2 addition (G°H2) were examined. Catalytic CO2 hydrogenation was studied under 1.8 and 20 atm of pressure (1:1 CO2:H2) at room temperature in tetrahydrofuran with a spread of turnover frequencies (TOF) ranging from 0 to 74,000 h-1. The catalysis was followed by 1H and 31P NMR in real time under all conditions to yield information about the rate determining step. Catalysts exhibiting the highest activities were found to have hydride transfer and hydrogen addition steps that were each downhill by approximately 6 to 7 kcal/mol, and the deprotonation step was thermoneutral. The research by M.S.J., A.M.A., E.S.W., and J.C.L. was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The research by E.B.H., M.L.H., and M.T.M. (X-ray crystallography, synthesis) was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. The authors thank Dr. Samantha A. Burgess for assistance in collecting cyclic voltammetry data. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  16. 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

    2015-07-15

    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

  17. 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

  18. Structure and weak hydrogen bonds in liquid acetaldehyde

    Directory of Open Access Journals (Sweden)

    Cordeiro Maria A. M.

    2004-01-01

    Full Text Available Monte Carlo simulations have been performed to investigate the structure and hydrogen bonds formation in liquid acetaldehyde. An all atom model for the acetaldehyde have been optimized in the present work. Theoretical values obtained for heat of vaporisation and density of the liquid are in good agreement with experimental data. Graphics of radial distribution function indicate a well structured liquid compared to other similar dipolar organic liquids. Molecular mechanics minimization in gas phase leads to a trimer of very stable structure. The geometry of this complex is in very good agreement with the rdf. The shortest site-site correlation is between oxygen and the carbonyl hydrogen, suggesting that this correlation play a important role in the liquid structure and properties. The OxxxH average distance and the C-HxxxO angle obtained are characteristic of weak hydrogen bonds.

  19. Ascorbic acid as a bifunctional hydrogen bond donor for the synthesis of cyclic carbonates from CO2 under ambient conditions

    KAUST Repository

    Arayachukiat, Sunatda

    2017-07-14

    Readily available ascorbic acid was discovered as an environmentally benign hydrogen bond donor (HBD) for the synthe-sis of cyclic organic carbonates from CO2 and epoxides in the presence of nucleophilic co-catalysts. The ascorbic acid/TBAI (TBAI: tetrabutylammonium iodide) binary system could be applied for the cycloaddition of CO2 to various epoxides under ambient or mild conditions. DFT calculations and catalysis experiments revealed an intriguing bifunctional mechanism in the step of CO2 insertion involving different hydroxyl moieties (enediol, ethyldiol) of the ascorbic acid scaffold.

  20. Dangling-bond defects and hydrogen passivation in germanium

    Science.gov (United States)

    Weber, Justin R.

    2008-03-01

    The application of germanium in complementary metal-oxide semiconductor (CMOS) technology is hampered by high interface-state densities, the microscopic origin of which has remained elusive. Using first-principles calculations, we have investigated the atomic and electronic structure of prototype germanium dangling-bond defects [1]. The computational approach is based on density functional theory, and in order to overcome band-gap problems we have also performed quasiparticle calculations based on the GW approach. Surprisingly, the germanium dangling bonds give rise to electronic levels below the valence-band maximum. They therefore occur exclusively in the negative charge state, explaining why they have eluded observation with electron spin resonance. The associated fixed charge is likely responsible for threshold-voltage shifts and poor performance of n-channel transistors. At silicon/silicon dioxide interfaces, hydrogen is successfully used to passivate dangling-bond defects. We have therefore also investigated the interaction of hydrogen with germanium. In contrast to silicon and other semiconductors in which hydrogen behaves as an amphoteric impurity, interstitial hydrogen in germanium is stable only in the negative charge state, i.e., it behaves exclusively as an acceptor. Passivation of dangling bonds by hydrogen will therefore be ineffective, again explaining experimental observations. Other cases where unusual interfacial defects and problems with hydrogen passivation may occur will be discussed. Work performed in collaboration with A. Janotti, P. Rinke, and C. G. Van de Walle, and supported by the Semiconductor Research Corporation. 1. J. R. Weber, A. Janotti, P. Rinke, and C. G. Van de Walle, Appl. Phys. Lett. 91, 142101 (2007).

  1. A systematic structural study of halogen bonding versus hydrogen bonding within competitive supramolecular systems

    Directory of Open Access Journals (Sweden)

    Christer B. Aakeröy

    2015-09-01

    Full Text Available As halogen bonds gain prevalence in supramolecular synthesis and materials chemistry, it has become necessary to examine more closely how such interactions compete with or complement hydrogen bonds whenever both are present within the same system. As hydrogen and halogen bonds have several fundamental features in common, it is often difficult to predict which will be the primary interaction in a supramolecular system, especially as they have comparable strength and geometric requirements. To address this challenge, a series of molecules containing both hydrogen- and halogen-bond donors were co-crystallized with various monotopic, ditopic symmetric and ditopic asymmetric acceptor molecules. The outcome of each reaction was examined using IR spectroscopy and, whenever possible, single-crystal X-ray diffraction. 24 crystal structures were obtained and subsequently analyzed, and the synthon preferences of the competing hydrogen- and halogen-bond donors were rationalized against a background of calculated molecular electrostatic potential values. It has been shown that readily accessible electrostatic potentials can offer useful practical guidelines for predicting the most likely primary synthons in these co-crystals as long as the potential differences are weighted appropriately.

  2. Synthetic multivalent DNAzymes for enhanced hydrogen peroxide catalysis and sensitive colorimetric glucose detection.

    Science.gov (United States)

    Yang, Deng-Kai; Kuo, Chia-Jung; Chen, Lin-Chi

    2015-01-26

    A peroxidase-mimic DNAzyme is a G-quadruplex (G4) DNA-hemin complex, in which the G4-DNA resembles an apoenzyme, and hemin is the cofactor for hydrogen peroxide (H2O2) catalysis. Twenty-one-mer CatG4 is a well-proven G4-DNA as well as a hemin-binding aptamer for constituting a DNAzyme. This work studied if a multivalent DNAzyme with accelerated catalysis could be constructed using a multimeric CatG4 with hemin. We compared CatG4 monomer, dimer, trimer, and tetramer, which were prepared by custom oligo synthesis, for G4 structure formation. According to circular dichroism (CD) analysis, we found that a CatG4 multimer exhibited more active G4 conformation than the sum effect of equal-number CatG4 monomers. However, the DNAzyme kinetics was not improved monotonically along with the subunit number of a multimeric CatG4. It was the trivalent DNAzyme, trimeric CatG4:hemin, resulting in the rapidest H2O2 catalysis instead of a tetravalent one. We discovered that the trivalent DNAzyme's highest catalytic rate was correlated to its most stable hemin-binding G4 structure, evidenced by CD melting temperature analysis. Finally, a trivalent DNAzyme-based colorimetric glucose assay with a detection limit as low as 10 μM was demonstrated, and this assay did not need adenosine 5'-tri-phosphate disodium salt hydrate (ATP) as a DNAzyme boosting agent. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Computer simulation of hydrogen diffusion and hydride precipitation at Ta/Zr bond interface. Hydrogen embrittlement in SUS304ULC/Ta/Zr explosive bonded joint

    International Nuclear Information System (INIS)

    Saida, Kazuyoshi; Fujimoto, Tetsuya; Nishimoto, Kazutoshi

    2010-01-01

    The concentration of hydrogen and precipitation of zirconium hydrides in Ta/Zr explosive bonded joint were analysed by computer simulation. Numerical model of hydride precipitation under hydrogen diffusion was simplified by the alternate model coupled the macroscopic hydrogen diffusion with the microscopic hydride precipitation. Effects of the initial hydrogen content in Ta, working degree of Zr and post-bond heat treatment on the hydrogen diffusion and hydride precipitation were investigated. Hydrogen was rapidly diffused from Ta substrate into Zr after explosive bonding and temporarily concentrated at Ta/Zr bond interface. Zirconium hydrides were precipitated and grew at Ta/Zr bond interface, and the precipitation zone of hydrides was enlarged with the lapse of time. The precipitation of zirconium hydrides was promoted when the initial hydrogen content in Ta and working degree of Zr were increased. The concentration of hydrogen and precipitation of hydrides at the bond interface were reduced and diminished by post-bond heat treatment at 373 K. It was deduced that hydrogen embrittlement in Ta/Zr explosive bonded joint was caused by the precipitation of zirconium hydrides and concentration of hydrogen at Ta/Zr bond interface during the diffusion of hydrogen containing in Ta substrate. (author)

  4. 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......There are three main types of interactions inside organic salts - electrostatic interaction, hydrogen bonding and van der Waals force [1-4]. While van der Waals force is relatively weak, it is hydrogen bonding and particularly electrostatic interaction that determine the lattice energies of ionic...

  5. Competition of hydrogen bonds and halogen bonds in complexes of hypohalous acids with nitrogenated bases.

    Science.gov (United States)

    Alkorta, Ibon; Blanco, Fernando; Solimannejad, Mohammad; Elguero, Jose

    2008-10-30

    A theoretical study of the complexes formed by hypohalous acids (HOX, X = F, Cl, Br, I, and At) with three nitrogenated bases (NH 3, N 2, and NCH) has been carried out by means of ab initio methods, up to MP2/aug-cc-pVTZ computational method. In general, two minima complexes are found, one with an OH...N hydrogen bond and the other one with a X...N halogen bond. While the first one is more stable for the smallest halogen derivatives, the two complexes present similar stabilities for the iodine case and the halogen-bonded structure is the most stable one for the hypoastatous acid complexes.

  6. 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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Strong and weak hydrogen bonds in drug–DNA complexes: A ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    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.

  8. Molecular and ionic hydrogen bond formation in fluorous solvents.

    Science.gov (United States)

    O'Neal, Kristi L; Weber, Stephen G

    2009-01-08

    There are only a few studies of noncovalent association in fluorous solvents and even fewer that are quantitative. A full understanding, particularly of stoichiometry and binding strength of noncovalent interactions in fluorous solvents could be very useful in improved molecular-receptor-based extractions, advancements in sensor technologies, crystal engineering, and supramolecular chemistry. This work investigates hydrogen bonding between heterocyclic bases and a perfluoropolyether with a terminal carboxylic acid group (Krytox 157FSH (1)), chiefly in FC-72 (a mixture of perfluorohexanes). In particular, we were interested in whether or not proton transfer occurs, and if so, under what conditions in H-bonded complexes. Continuous variations experiments show that in FC-72 weaker bases (pyrazine, pyrimidine, and quinazoline) form 1:1 complexes with 1, whereas stronger bases (quinoline, pyridine, and isoquinoline) form 1:3 complexes. Ultraviolet and infrared spectral signatures reveal that the 1:1 complexes are molecular (B.HA) whereas the 1:3 complexes are ionic (BH+.A-HAHA). Infrared spectra of 1:3 ionic complexes are discussed in detail. Literature and experimental data on complexes between N-heterocyclic bases and carboxylic acids in a range of solvents are compiled to compare solvent effects on proton transfer. Polar solvents support ionic hydrogen bonds at a 1:1 mol ratio. In nonpolar organic solvents, ionic hydrogen bonds are only observed in complexes with 1:2 (base/acid) stoichiometries. In fluorous solvents, a larger excess of acid, 1:3, is necessary to facilitate proton transfer in hydrogen bonds between carboxylic acids and the bases studied.

  9. Coupling of protein motions and hydrogen transfer during catalysis by Escherichia coli dihydrofolate reductase.

    Science.gov (United States)

    Swanwick, Richard S; Maglia, Giovanni; Tey, Lai-hock; Allemann, Rudolf K

    2006-02-15

    The enzyme DHFR (dihydrofolate reductase) catalyses hydride transfer from NADPH to, and protonation of, dihydrofolate. The physical basis of the hydride transfer step catalysed by DHFR from Escherichia coli has been studied through the measurement of the temperature dependence of the reaction rates and the kinetic isotope effects. Single turnover experiments at pH 7.0 revealed a strong dependence of the reaction rates on temperature. The observed relatively large difference in the activation energies for hydrogen and deuterium transfer led to a temperature dependence of the primary kinetic isotope effects from 3.0+/-0.2 at 5 degrees C to 2.2+/-0.2 at 40 degrees C and an inverse ratio of the pre-exponential factors of 0.108+/-0.04. These results are consistent with theoretical models for hydrogen transfer that include contributions from quantum mechanical tunnelling coupled with protein motions that actively modulate the tunnelling distance. Previous work had suggested a coupling of a remote residue,Gly121, with the kinetic events at the active site. However, pre-steady-state experiments at pH 7.0 with the mutant G121V-DHFR, in which Gly121 was replaced with valine, revealed that the chemical mechanism of DHFR catalysis was robust to this replacement. The reduced catalytic efficiency of G121V-DHFR was mainly a consequence of the significantly reduced pre-exponential factors, indicating the requirement for significant molecular reorganization during G121V-DHFR catalysis. In contrast, steady-state measurements at pH 9.5, where hydride transfer is rate limiting, revealed temperature-independent kinetic isotope effects between 15 and 35 degrees C and a ratio of the pre-exponential factors above the semi-classical limit, suggesting a rigid active site configuration from which hydrogen tunnelling occurs. The mechanism by which hydrogen tunnelling in DHFR is coupled with the environment appears therefore to be sensitive to pH.

  10. Hydrogen-bonded encapsulation complexes in protic solvents.

    Science.gov (United States)

    Amaya, Toru; Rebek, Julius

    2004-11-03

    We describe here the behavior of the hydrogen-bonded capsule 1.1 and its complexes in protic solvents. The kinetics and thermodynamics of the encapsulation process were determined through conventional (1)H NMR methods. The enthalpies and entropies of encapsulation are both positive, indicating a process that liberates solvent molecules. The rates of dissociation-association of the capsule were comparable to the rates for the in-out exchange of large guests, which suggests that guest exchange occurs by complete dissociation of the capsule in protic solvents. The stability of the hydrogen-bonded capsule 1.1 toward protic solvents depends strongly on the guests, with the best guest being dimethylstilbene 8. The results establish guidelines for the properties of capsules that could be accessed in water.

  11. Nuclear quantum effects and hydrogen bond fluctuations in water

    Science.gov (United States)

    Ceriotti, Michele; Cuny, Jérôme; Parrinello, Michele; Manolopoulos, David E.

    2013-01-01

    The hydrogen bond (HB) is central to our understanding of the properties of water. However, despite intense theoretical and experimental study, it continues to hold some surprises. Here, we show from an analysis of ab initio simulations that take proper account of nuclear quantum effects that the hydrogen-bonded protons in liquid water experience significant excursions in the direction of the acceptor oxygen atoms. This generates a small but nonnegligible fraction of transient autoprotolysis events that are not seen in simulations with classical nuclei. These events are associated with major rearrangements of the electronic density, as revealed by an analysis of the computed Wannier centers and 1H chemical shifts. We also show that the quantum fluctuations exhibit significant correlations across neighboring HBs, consistent with an ephemeral shuttling of protons along water wires. We end by suggesting possible implications for our understanding of how perturbations (solvated ions, interfaces, and confinement) might affect the HB network in water. PMID:24014589

  12. 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.

  13. NMR studies of solid pentachlorophenol-4-methylpyridine complexes exhibiting strong OHN hydrogen bonds: geometric H/D isotope effects and hydrogen bond coupling cause isotopic polymorphism.

    Science.gov (United States)

    Ip, Brenda C K; Shenderovich, Ilya G; Tolstoy, Peter M; Frydel, Jaroslaw; Denisov, Gleb S; Buntkowsky, Gerd; Limbach, Hans-Heinrich

    2012-11-26

    We have studied the hydrogen bond interactions of (15)N labeled 4-methylpyridine (4-MP) with pentachlorophenol (PCP) in the solid state and in polar solution using various NMR techniques. Previous spectroscopic, X-ray, and neutron crystallographic studies showed that the triclinic 1:1 complex (4-MPPCP) exhibits the strongest known intermolecular OHN hydrogen bond in the solid state. By contrast, deuteration of the hydrogen bond gives rise to the formation of a monoclinic structure exhibiting a weaker hydrogen bond. By performing NMR experiments at different deuterium fractions and taking advantage of dipolar (1)H-(15)N recoupling under combined fast MAS and (1)H decoupling, we provide an explanation of the origin of the isotopic polymorphism of 4-MPPCP and improve previous chemical shift correlations for OHN hydrogen bonds. Because of anharmonic ground state vibrations, an ODN hydrogen bond in the triclinic form exhibits a shorter oxygen-hydron and a longer oxygen-nitrogen distance as compared to surrounding OHN hydrogen bonds, which also implies a reduction of the local dipole moment. The dipole-dipole interaction between adjacent coupled OHN hydrogen bonds which determines the structure of triclinic 4-MPPCP is then reduced by deuteration, and other interactions become dominant, leading to the monoclinic form. Finally, the observation of stronger OHN hydrogen bonds by (1)H NMR in polar solution as compared to the solid state is discussed.

  14. Synthesis, crystal structures, hydrogen bonding graph-sets and ...

    African Journals Online (AJOL)

    Synthesis, crystal structures, hydrogen bonding graph-sets and theoretical studies of nickel (+II) co-ordinations with pyridine-2,6-dicarboxamide oxime. ... which crystallized in the monoclinic space group C2/c with a = 14.915(2), b = 0.895(2), c = 8.205(1) Å, β = 114.69(1), and Z = 4. The complex consists of discrete cations ...

  15. 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.

  16. 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.

  17. Intramolecular hydrogen bonding and tautomerism in Schiff bases ...

    Indian Academy of Sciences (India)

    N and keto-amine, O…H-N forms) in this series. The molecular structure of 8 has been determined crystallographically, and observed that the compound is in the form of phenol-imine, defined by the strong intramolecular [O-H…N = 1.72(3), 1.81(2) Å] hydrogen bonds. Compound 8 crystallizes in the monoclinic space group ...

  18. Hydrogen bonding lowers intrinsic nucleophilicity of solvated nucleophiles.

    Science.gov (United States)

    Chen, Xin; Brauman, John I

    2008-11-12

    The relationship between nucleophilicity and the structure/environment of the nucleophile is of fundamental importance in organic chemistry. In this work, we have measured nucleophilicities of a series of substituted alkoxides in the gas phase. The functional group substitutions affect the nucleophiles through ion-dipole, ion-induced dipole interactions and through hydrogen bonding whenever structurally possible. This set of alkoxides serves as an ideal model system for studying nucleophiles under microsolvation settings. Marcus theory was applied to analyze the results. Using Marcus theory, we separate nucleophilicity into two independent components, an intrinsic nucleophilicity and a thermodynamic driving force determined solely by the overall reaction exothermicity. It is found that the apparent nucleophilicities of the substituted alkoxides are always much lower than those of the unsubstituted ones. However, ion-dipole, ion-induced dipole interactions, by themselves, do not significantly affect the intrinsic nucleophilicity; the decrease in the apparent nucleophilicity results from a weaker thermodynamic driving force. On the other hand, hydrogen bonding not only stabilizes the nucleophile but also increases the intrinsic barrier height by 3 to approximately 4 kcal mol (-1). In this regard, the hydrogen bond is not acting as a perturbation in the sense of an external dipole but more directly affects the electronic structure and reactivity of the nucleophilic alkoxide. This finding offers a deeper insight into the solvation effect on nucleophilicity, such as the remarkably lower reactivities in nucleophilic substitution reactions in protic solvents than in aprotic solvents.

  19. Subtle differences in the hydrogen bonding of alcohol to divalent oxygen and sulfur

    DEFF Research Database (Denmark)

    Du, Lin; Tang, Shanshan; Hansen, Anne Schou

    2017-01-01

    complexes are more stable and form stronger hydrogen bonds compared to complexes with MeOH and EtOH, which are comparable, and only for the stronger hydrogen bond donor (TFE) are the small differences in acceptor molecules highlighted. The equilibrium constant for complex formation was determined from......The Osingle bondH⋯O and Osingle bondH⋯S hydrogen bonds were investigated by gas phase FTIR spectroscopy of alcohol–dimethylether and alcohol–dimethylsulfide complexes, with alcohols of increasing hydrogen bond donor strength; methanol (MeOH), ethanol (EtOH) and 2,2,2-trifluoroethanol (TFE). The TFE...

  20. A novel tubular hydrogen-bond pattern in a new diazaphosphole oxide: a combination of X-ray crystallography and theoretical study of hydrogen bonds.

    Science.gov (United States)

    Sabbaghi, Fahimeh; Pourayoubi, Mehrdad; Farhadipour, Abolghasem; Ghorbanian, Nazila; Andreev, Pavel V

    2017-07-01

    In the structure of 2-(4-chloroanilino)-1,3,2λ 4 -diazaphosphol-2-one, C 12 H 11 ClN 3 OP, each molecule is connected with four neighbouring molecules through (N-H) 2 ...O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R 3 3 (12) and R 4 3 (14) hydrogen-bond ring motifs, combined with a C(4) chain motif. The hole constructed in the tubular architecture includes a 12-atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other. One of the N-H groups of the diazaphosphole ring, not co-operating in classical hydrogen bonding, takes part in an N-H...π interaction. This interaction occurs within the tubular array and does not change the dimension of the hydrogen-bond pattern. The energies of the N-H...O and N-H...π hydrogen bonds were studied by NBO (natural bond orbital) analysis, using the experimental hydrogen-bonded cluster of molecules as the input file for the chemical calculations. In the 1 H NMR experiment, the nitrogen-bound proton of the diazaphosphole ring has a high value of 17.2 Hz for the 2 J H-P coupling constant.

  1. Hydrogen bond stabilities in membrane-reconstituted alamethicin from amide-resolved hydrogen-exchange measurements.

    Science.gov (United States)

    Dempsey, C E; Handcock, L J

    1996-01-01

    Amide-resolved hydrogen-deuterium exchange-rate constants were measured for backbone amides of alamethicin reconstituted in dioleoylphosphatidylcholine vesicles by an exchange-trapping method combined with high-resolution nuclear magnetic resonance spectroscopy. In vesicles containing alamethicin at molar ratios between 1:20 and 1:100 relative to lipid, the exchange-rate constants increased with increasing volume of the D20 buffer in which the vesicles were suspended, indicating that exchange under these conditions is dominated by partitioning of the peptide into the aqueous phase. This was supported by observation of a linear relationship between the exchange-rate constants for amides in membrane-reconstituted alamethicin and those for amides in alamethicin dissolved directly into D2O buffer. Significant protection of amides from exchange with D2O buffer in membrane-reconstituted alamethicin is interpreted in terms of stabilization by helical hydrogen bonding. Under conditions in which amide exchange occurred by partitioning of the peptide into solution, only lower limits for hydrogen-bond stabilities in the membrane were determined; all the potentially hydrogen-bonded amides of alamethicin are at least 1000-fold exchange protected in the membrane-bound state. When partitioning of alamethicin into the aqueous phase was suppressed by hydration of reconstituted vesicles in a limiting volume of water [D2O:dioleoylphosphatidylcholine:alamethicin; 220:1:0.05; (M:M:M)], the exchange-protection factors exhibited helical periodicity with highly exchange-protected, and less well-protected, amides on the nonpolar and polar helix faces, respectively. The exchange data indicate that, under the conditions studied, alamethicin adopts a stable helical structure in DOPC bilayers in which all the potentially hydrogen-bonded amides are stabilized by helical hydrogen bonds. The protection factors define the orientation of the peptide helix with respect to an aqueous phase, which is

  2. Hydrogen bond stabilities in membrane-reconstituted alamethicin from amide-resolved hydrogen-exchange measurements.

    Science.gov (United States)

    Dempsey, C E; Handcock, L J

    1996-04-01

    Amide-resolved hydrogen-deuterium exchange-rate constants were measured for backbone amides of alamethicin reconstituted in dioleoylphosphatidylcholine vesicles by an exchange-trapping method combined with high-resolution nuclear magnetic resonance spectroscopy. In vesicles containing alamethicin at molar ratios between 1:20 and 1:100 relative to lipid, the exchange-rate constants increased with increasing volume of the D20 buffer in which the vesicles were suspended, indicating that exchange under these conditions is dominated by partitioning of the peptide into the aqueous phase. This was supported by observation of a linear relationship between the exchange-rate constants for amides in membrane-reconstituted alamethicin and those for amides in alamethicin dissolved directly into D2O buffer. Significant protection of amides from exchange with D2O buffer in membrane-reconstituted alamethicin is interpreted in terms of stabilization by helical hydrogen bonding. Under conditions in which amide exchange occurred by partitioning of the peptide into solution, only lower limits for hydrogen-bond stabilities in the membrane were determined; all the potentially hydrogen-bonded amides of alamethicin are at least 1000-fold exchange protected in the membrane-bound state. When partitioning of alamethicin into the aqueous phase was suppressed by hydration of reconstituted vesicles in a limiting volume of water [D2O:dioleoylphosphatidylcholine:alamethicin; 220:1:0.05; (M:M:M)], the exchange-protection factors exhibited helical periodicity with highly exchange-protected, and less well-protected, amides on the nonpolar and polar helix faces, respectively. The exchange data indicate that, under the conditions studied, alamethicin adopts a stable helical structure in DOPC bilayers in which all the potentially hydrogen-bonded amides are stabilized by helical hydrogen bonds. The protection factors define the orientation of the peptide helix with respect to an aqueous phase, which is

  3. Metal and hydrogen catalysis in isotopic hydrogen exchange in some biologically important heterocyclic compounds

    International Nuclear Information System (INIS)

    Buncel, E.; Joly, H.A.; Jones, J.R.; Onyido, I.

    1989-01-01

    This study reports on the catalytic roles of metal and hydrogen ions in tritium exchange in some heterocyclic substrates which occur as residues in many biologically important molecules. We have found that detritiation of 1-methyl[2- 3 H]imidazole is inhibited by a number of metal ions. As well, inhibition of exchange rates was noted with Ag(I) and Cu(II) for [2- 3 H]thiazole and 1-methyl[8- 3 H]inosine, with Ag(I) for [2- 3 H]benzothiazole, and with Cu(II) for 1-methyl[8- 3 H]guanosine. A complete mechanistic description, which includes the various metal ion-coordinated species generated under the experimental conditions, is presented. The results demonstrate the reactivity order: protonated >> metal-coordinated >> neutral substrates. The differential catalytic effects of metal and hydrogen ions in these processes are discussed in terms of the extent of charge developed on the ligating heteroatom in the reaction intermediate. (author). 13 refs.; 1 fig

  4. Hydrogen bonding. 47. Characterization of the ethylene glycol-heptane partition system: hydrogen bond acidity and basicity of peptides.

    Science.gov (United States)

    Abraham, M H; Martins, F; Mitchell, R C; Salter, C J

    1999-02-01

    Twelve measured ethylene glycol-heptane partition coefficients, Peh, have been combined with 20 measured literature values and 44 indirectly determined values to give a set of 76 values. Excluding one value for benzamide, the log Peh values are correlated through our general solvation equation, log Peh = 0.336 - 0.075R2 - 1. 201pi2H - 3.786 Sigmaalpha2H - 2.201 Sigmabeta2H + 2.085Vx with r2 = 0.966, sd = 0.28, and F = 386. The solute descriptor R2 is the excess molar refraction, pi2H is the dipolarity/polarizability, Sigmaalpha2H and Sigmabeta2H are the overall hydrogen bond acidity and basicity, and Vx is the McGowan volume. The log Peh equation has then been used to obtain descriptors for eleven peptides, all of which are end-protected. It is shown that for these end-protected peptides, hydrogen bond basicity makes a greater contribution to log Peh than does hydrogen bond acidity.

  5. CH···π interactions do not contribute to hydrogen transfer catalysis by glycerol dehydratase.

    Science.gov (United States)

    Liu, Yuemin; Gallo, August A; Xu, Wu; Bajpai, Rakesh; Florián, Jan

    2011-10-20

    The role of the nonbonded CH···π interaction in the hydrogen abstraction from glycerol by the coenzyme B(12)-independent glycerol dehydratase (GDH) was examined using the QM/MM (ONIOM), MP2, and CCSD(T) methods. The studied CH···π interaction included the hydrogen atom of the -C(2)H(OH)- group of the glycerol substrate and the tyrosine-339 residue of the dehydratase. A contribution of this interaction to the stabilization of the transition state for the transfer of a hydrogen atom from the adjacent terminal C(1)H(2)(OH) group to cysteine 433 was determined by ab initio HF, MP2, and CCSD(T) calculations with the aug-cc-pvDZ basis set for the corresponding methane/benzene, methanol/phenol, and glycerol radical/phenol subsystems. The calculated CH···π distance, defined as the distance between the H atom and the center of the phenol ring, shortened from 2.62 to 2.52 Å upon going from the ground- to the transition-state of the GDH-catalyzed reaction. However, this shortening was not accompanied by the expected lowering of the CH···π interaction free energy. Instead, this interaction remained weak (about -1 kcal/mol) along the entire reaction coordinate. Additionally, the mutual orientation of the CH group and the phenol ring did not change significantly during the reaction. These results suggest that the phenol group of the tyrosine-339 does not contribute to lowering the activation barrier in the enzyme, but do not exclude the possibility that tyrosine 339 facilitates proper orientation of glycerol for the electrostatic catalysis, or inhibits side-reactions of the reactive glycerol radical intermediate.

  6. The H-Index Unambiguously Discriminates between Hydrogen Bonding and Improper Blue-Shifting Hydrogen Bonding

    Czech Academy of Sciences Publication Activity Database

    Hobza, Pavel

    2001-01-01

    Roč. 3, č. 13 (2001), s. 2555-2556 ISSN 1463-9076 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : improper H-bonding * blue-shifting Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.787, year: 2001

  7. Experimental and theoretical investigation of Fe-catalysis phenomenon in hydrogen thermal desorption from hydrocarbon plasma-discharge films from T-10 tokama

    Science.gov (United States)

    Stankevich, Vladimir G.; Sukhanov, Leonid P.; Svechnikov, Nicolay Yu.; Lebedev, Alexey M.; Menshikov, Kostantin A.; Kolbasov, Boris N.

    2017-10-01

    Investigations of the effect of Fe impurities on D2 thermal desorption (TD) from homogeneous CDx films (x ˜ 0.5) formed in the D-plasma discharge of the T-10 tokamak were carried out. The experimental TD spectra of the films showed two groups of peaks at 650-850 K and 900-1000 K for two adsorption states. The main result of the iron catalysis effect consists in the shift of the high-temperature peak by -24 K and in the increase in the fraction of the weakly bonded adsorption states. To describe the effect of iron impurities on TD of hydrogen isotopes, a structural cluster model based on the interaction of the Fe+ ion with the 1,3-C6H8 molecule was proposed. The potential energy surfaces of chemical reactions with the H2 elimination were calculated using ab initio methods of quantum chemistry. It was established that the activation barrier of hydrogen TD is reduced by about 1 eV due to the interaction of the Fe+ ion with the π-subsystem of the 1,3-C6H8 molecule leading to a redistribution of the double bonds along the carbon system. Contribution to the topical issue "Plasma Sources and Plasma Processes (PSPP)"", edited by Luis Lemos Alves, Thierry Belmonte and Tiberiu Minea

  8. 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.

  9. Can QTAIM topological parameters be a measure of hydrogen bonding strength?

    Science.gov (United States)

    Mo, Yirong

    2012-05-31

    The block-localized wave function (BLW) method, which is the simplest variant of ab initio valence bond (VB) theory, together with the quantum theory of atoms in molecules (QTAIM) approach, have been used to probe the intramolecular hydrogen bonding interactions in a series of representative systems of resonance-assisted hydrogen bonds (RAHBs). RAHB is characteristic of the cooperativity between the π-electron delocalization and hydrogen bonding interactions and is identified in many biological systems. While the deactivation of the π resonance in these RAHB systems by the use of the BLW method is expected to considerably weaken the hydrogen bonding strength, little change on the topological properties of electron densities at hydrogen bond critical points (HBCPs) is observed. This raises a question of whether the QTAIM topological parameters can be an effective measure of hydrogen bond strength.

  10. Effects of hydrogen bonds on solid state TATB, RDX, and DATB under high pressures

    International Nuclear Information System (INIS)

    Guo Feng; Hu Hai-Quan; Zhang Hong; Cheng Xin-Lu

    2014-01-01

    To probe the behavior of hydrogen bonds in solid energetic materials, we conduct ReaxFF and SCC–DFTB molecular dynamics simulations of crystalline TATB, RDX, and DATB. By comparing the intra- and inter-molecular hydrogen bonding rates, we find that the crystal structures are stabilized by inter-molecular hydrogen bond networks. Under high-pressure, the inter- and intra-molecular hydrogen bonds in solid TATB and DATB are nearly equivalent. The hydrogen bonds in solid TATB and DATB are much shorter than in solid RDX, which suggests strong hydrogen bond interactions existing in these energetic materials. Stretching of the C–H bond is observed in solid RDX, which may lead to further decomposition and even detonation. (condensed matter: structural, mechanical, and thermal properties)

  11. Computational evaluations of charge coupling and hydrogen bonding in the active site of a family 7 cellobiohydrolase.

    Science.gov (United States)

    Granum, David M; Vyas, Shubham; Sambasivarao, Somisetti V; Maupin, C Mark

    2014-01-16

    Solution pH and the pKa values of ionizable residues are critical factors known to influence enzyme catalysis, structural stability, and dynamical fluctuations. Presented here is an exhaustive computational study utilizing long time constant pH molecular dynamics, pH replica exchange simulations, and kinetic modeling to evaluate pH-dependent conformations, charge dynamics, residue pKa values, and the catalytic activity-pH profile for cellobiohydrolase Cel7B from Melanocarpus albomyces . The predicted pKa values support the role of Glu212 as the catalytic nucleophile and Glu217 as the acid-base residue. The presence of a charge-correlated active site and an extensive hydrogen bonding network is found to be critical in enabling favorable residue orientations for catalysis and shuttling excess protons around the active site. Clusters of amino acids are identified that act in concert to effectively modulate the optimal pH for catalysis while elevating the overall catalytic rate with respect to a noncoupled system. The work presented here demonstrates the complex and critical role of coupled ionizable residues to the proper functioning of cellobiohydrolase Cel7B, functionally related glycosyl hydrolases, and enzymes in general. The simulations also support the use of the CpHMD for the accurate prediction of residue pKa values and to evaluate the impact of pH on protein structure and charge dynamics.

  12. Substituent Effects on Hydrogen Bonds in DNA : A Kohn-Sham DFT Approach

    NARCIS (Netherlands)

    Guerra, Célia Fonseca; Bickelhaupt, F. Matthias

    2006-01-01

    In this Chapter, we discuss how the hydrogen bonds in Watson-Crick base pairs can be tuned both structurally and in terms of bond strength by exposing the DNA bases to different kinds of substitutions: (1) substitution in the X-H Y hydrogen bonding moiety, (2) remote substitution, i.e., introducing

  13. Strong and weak hydrogen bonds in drug–DNA complexes: A ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    The metrics for strong hydrogen bonds are consistent with established trends. The geometries are variable for weak hydrogen bonds. .... 'moderate'. Jeffrey's terminology is in keeping with the biological literature where bonds such ... to minimization keeping the heavy atoms rigid. This was carried out in MOE with the MMFFx ...

  14. On differences between hydrogen bonding and improper blue-shifting hydrogen bonding

    Czech Academy of Sciences Publication Activity Database

    Zierkiewicz, W.; Jurečka, Petr; Hobza, Pavel

    2005-01-01

    Roč. 6, č. 4 (2005), s. 609-617 ISSN 1439-4235 R&D Projects: GA ČR(CZ) GA203/05/0009; GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : ab initio calculations * density functional calculations * H-bonding Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.607, year: 2005

  15. Hydrogen-Bonding Modification in Biuret Under Pressure.

    Science.gov (United States)

    Borstad, Gustav M; Ciezak-Jenkins, Jennifer A

    2017-02-02

    Biuret (C 2 H 5 N 3 O 2 ) has been studied to 30 GPa by Raman spectroscopy and 50 GPa by X-ray diffraction. Raman peaks exhibit shoulders and splitting that suggests that the molecules undergo reorientation in response to compression. These are observed in three pressure ranges: the first from 3-5 GPa, the second from 8-12 GPa, and finally from 16-20 GPa. The particular modes in the sample that are observed to change in the Raman are strongly linked to the molecular vibrations involving the N-H and the C═O bond, which are most strongly coupled to the hydrogen-bonded lattice structure. The X-ray diffraction suggests that the crystal maintains a monoclinic structure to the highest pressures studied. Although there was a considerable degree of hysteresis observed in some X-ray runs, all the changes observed under pressure are reversible.

  16. 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.

  17. Chemical bonding of hydrogen molecules to transition metal complexes

    International Nuclear Information System (INIS)

    Kubas, G.J.

    1990-01-01

    The complex W(CO) 3 (PR 3 ) 2 (H 2 ) (CO = carbonyl; PR 3 = organophosphine) was prepared and was found to be a stable crystalline solid under ambient conditions from which the hydrogen can be reversibly removed in vacuum or under an inert atmosphere. The weakly bonded H 2 exchanges easily with D 2 . This complex represents the first stable compound containing intermolecular interaction of a sigma-bond (H-H) with a metal. The primary interaction is reported to be donation of electron density from the H 2 bonding electron pair to a vacant metal d-orbital. A series of complexes of molybdenum of the type Mo(CO)(H 2 )(R 2 PCH 2 CH 2 PR 2 ) 2 were prepared by varying the organophosphine substitutent to demonstrate that it is possible to bond either dihydrogen or dihydride by adjusting the electron-donating properties of the co-ligands. Results of infrared and NMR spectroscopic studies are reported. 20 refs., 5 fig

  18. Chemical bonding of hydrogen molecules to transition metal complexes

    Energy Technology Data Exchange (ETDEWEB)

    Kubas, G.J.

    1990-01-01

    The complex W(CO){sub 3}(PR{sub 3}){sub 2}(H{sub 2}) (CO = carbonyl; PR{sub 3} = organophosphine) was prepared and was found to be a stable crystalline solid under ambient conditions from which the hydrogen can be reversibly removed in vacuum or under an inert atmosphere. The weakly bonded H{sub 2} exchanges easily with D{sub 2}. This complex represents the first stable compound containing intermolecular interaction of a sigma-bond (H-H) with a metal. The primary interaction is reported to be donation of electron density from the H{sub 2} bonding electron pair to a vacant metal d-orbital. A series of complexes of molybdenum of the type Mo(CO)(H{sub 2})(R{sub 2}PCH{sub 2}CH{sub 2}PR{sub 2}){sub 2} were prepared by varying the organophosphine substitutent to demonstrate that it is possible to bond either dihydrogen or dihydride by adjusting the electron-donating properties of the co-ligands. Results of infrared and NMR spectroscopic studies are reported. 20 refs., 5 fig.

  19. 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}.

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

    International Nuclear Information System (INIS)

    Delpouve, N.; Vuillequez, A.; Saiter, A.; Youssef, B.; Saiter, J.M.

    2012-01-01

    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 g .

  1. 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.

  2. Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry.

    Science.gov (United States)

    Morrison, Lindsay J; Chai, Wenrui; Rosenberg, Jake A; Henkelman, Graeme; Brodbelt, Jennifer S

    2017-08-02

    Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.

  3. Estimating the energy of intramolecular hydrogen bonds from1H NMR and QTAIM calculations.

    Science.gov (United States)

    Afonin, Andrei V; Vashchenko, Alexander V; Sigalov, Mark V

    2016-11-29

    The values of the downfield chemical shift of the bridge hydrogen atom were estimated for a series of compounds containing an intramolecular hydrogen bond O-HO, O-HN, O-HHal, N-HO, N-HN, C-HO, C-HN and C-HHal. Based on these values, the empirical estimation of the hydrogen bond energy was obtained by using known relationships. For the compounds containing an intramolecular hydrogen bond, the DFT B3LYP/6-311++G(d,p) method was used both for geometry optimization and for QTAIM calculations of the topological parameters (electron density ρ BCP and the density of potential energy V in the critical point of the hydrogen bond). The calculated geometric and topological parameters of hydrogen bonds were also used to evaluate the energy of the hydrogen bond based on the equations from the literature. Comparison of calibrating energies from the 1 H NMR data with the energies predicted by calculations showed that the most reliable are the linear dependence on the topological ρ BCP and V parameters. However, the correct prediction of the hydrogen bond energy is determined by proper fitting of the linear regression coefficients. To obtain them, new linear relationships were found between the calculated ρ BCP and V parameters and the hydrogen bond energies obtained from empirical 1 H NMR data. These relationships allow the comparison of the energies of different types of hydrogen bonds for various molecules and biological ensembles.

  4. Detection of a transient intramolecular hydrogen bond using 1JNH scalar couplings

    Science.gov (United States)

    Xiang, ShengQi; Zweckstetter, Markus

    2014-06-01

    Hydrogen bonds are essential for the structure, stability and folding of proteins. The identification of intramolecular hydrogen bonds, however, is challenging, in particular in transiently folded states. Here we studied the presence of intramolecular hydrogen bonds in the folding nucleus of the coiled-coil structure of the GCN4 leucine zipper. Using one-bond 1JNH spin-spin coupling constants and hydrogen/deuterium exchange, we demonstrate that a transient intramolecular hydrogen bond is present in the partially helical folding nucleus of GCN(16-31). The data demonstrate that 1JNH couplings are a sensitive tool for the detection of transient intramolecular hydrogen bonds in challenging systems where the effective/useable protein concentration is low. This includes peptides at natural abundance but also uniformly labeled biomolecules that are limited to low concentrations because of precipitation or aggregation.

  5. NMR and IR Investigations of Strong Intramolecular Hydrogen Bonds

    Directory of Open Access Journals (Sweden)

    Poul Erik Hansen

    2017-03-01

    Full Text Available For the purpose of this review, strong hydrogen bonds have been defined on the basis of experimental data, such as OH stretching wavenumbers, νOH, and OH chemical shifts, δOH (in the latter case, after correction for ring current effects. Limits for O–H···Y systems are taken as 2800 > νOH > 1800 cm−1, and 19 ppm > δOH > 15 ppm. Recent results as well as an account of theoretical advances are presented for a series of important classes of compounds such as β-diketone enols, β-thioxoketone enols, Mannich bases, proton sponges, quinoline N-oxides and diacid anions. The O···O distance has long been used as a parameter for hydrogen bond strength in O–H···O systems. On a broad scale, a correlation between OH stretching wavenumbers and O···O distances is observed, as demonstrated experimentally as well as theoretically, but for substituted β-diketone enols this correlation is relatively weak.

  6. 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.

  7. Measurement and Theory of Hydrogen Bonding Contribution to Isosteric DNA Base Pairs

    OpenAIRE

    Khakshoor, Omid; Wheeler, Steven E.; Houk, K. N.; Kool, Eric T.

    2012-01-01

    We address the recent debate surrounding the ability of 2,4-difluorotoluene (F), a low-polarity mimic of thymine (T), to form a hydrogen-bonded complex with adenine in DNA. The hydrogen bonding ability of F has been characterized as small to zero in various experimental studies, and moderate to small in computational studies. However, recent X-ray crystallographic studies of difluorotoluene in DNA/RNA have indicated, based on interatomic distances, possible hydrogen bonding interactions betwe...

  8. Bio- and air-tolerant carbon–carbon bond formations via organometallic ruthenium catalysis

    Czech Academy of Sciences Publication Activity Database

    Adriaenssens, Louis; Severa, Lukáš; Vávra, Jan; Šálová, Tereza; Hývl, Jakub; Čížková, Martina; Pohl, Radek; Šaman, David; Teplý, Filip

    2009-01-01

    Roč. 74, 7/8 (2009), s. 1023-1034 ISSN 0010-0765 R&D Projects: GA ČR GA203/09/0705; GA ČR GA203/09/1614 Institutional research plan: CEZ:AV0Z40550506 Keywords : ruthenium * organometallic catalysis * C-C coupling * [2+2+2]cycloadditions Subject RIV: CC - Organic Chemistry Impact factor: 0.856, year: 2009

  9. HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis.

    Science.gov (United States)

    Durrant, Jacob D; McCammon, J Andrew

    2011-11-01

    In the current work, we present a hydrogen-bond analysis of 2673 ligand-receptor complexes that suggests the total number of hydrogen bonds formed between a ligand and its receptor is a poor predictor of ligand potency; furthermore, even that poor prediction does not suggest a statistically significant correlation between hydrogen-bond formation and potency. While we are not the first to suggest that hydrogen bonds on average do not generally contribute to ligand binding affinities, this additional evidence is nevertheless interesting. The primary role of hydrogen bonds may instead be to ensure specificity, to correctly position the ligand within the active site, and to hold the protein active site in a ligand-friendly conformation. We also present a new computer program called HBonanza (hydrogen-bond analyzer) that aids the analysis and visualization of hydrogen-bond networks. HBonanza, which can be used to analyze single structures or the many structures of a molecular dynamics trajectory, is open source and python implemented, making it easily editable, customizable, and platform independent. Unlike many other freely available hydrogen-bond analysis tools, HBonanza provides not only a text-based table describing the hydrogen-bond network, but also a Tcl script to facilitate visualization in VMD, a popular molecular visualization program. Visualization in other programs is also possible. A copy of HBonanza can be obtained free of charge from http://www.nbcr.net/hbonanza. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Tracking Reactive Water and Hydrogen-Bonding Networks in Photosynthetic Oxygen Evolution.

    Science.gov (United States)

    Barry, Bridgette A; Brahmachari, Udita; Guo, Zhanjun

    2017-08-15

    In oxygenic photosynthesis, photosystem II (PSII) converts water to molecular oxygen through four photodriven oxidation events at a Mn 4 CaO 5 cluster. A tyrosine, YZ (Y161 in the D1 polypeptide), transfers oxidizing equivalents from an oxidized, primary chlorophyll donor to the metal center. Calcium or its analogue, strontium, is required for activity. The Mn 4 CaO 5 cluster and YZ are predicted to be hydrogen bonded in a water-containing network, which involves amide carbonyl groups, amino acid side chains, and water. This hydrogen-bonded network includes amino acid residues in intrinsic and extrinsic subunits. One of the extrinsic subunits, PsbO, is intrinsically disordered. This extensive (35 Å) network may be essential in facilitating proton release from substrate water. While it is known that some proteins employ internal water molecules to catalyze reactions, there are relatively few methods that can be used to study the role of water. In this Account, we review spectroscopic evidence from our group supporting the conclusion that the PSII hydrogen-bonding network is dynamic and that water in the network plays a direct role in catalysis. Two approaches, transient electron paramagnetic resonance (EPR) and reaction-induced FT-IR (RIFT-IR) spectroscopies, were used. The EPR experiments focused on the decay kinetics of YZ• via recombination at 190 K and the solvent isotope, pH, and calcium dependence of these kinetics. The RIFT-IR experiments focused on shifts in amide carbonyl frequencies, induced by photo-oxidation of the metal cluster, and on the isotope-based assignment of bands to internal, small protonated water clusters at 190, 263, and 283 K. To conduct these experiments, PSII was prepared in selected steps along the catalytic pathway, the S n state cycle (n = 0-4). This cycle ultimately generates oxygen. In the EPR studies, S-state dependent changes were observed in the YZ• lifetime and in its solvent isotope effect. The YZ• lifetime depended on

  11. 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.

  12. Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture

    Science.gov (United States)

    Penner, Robert C.; Andersen, Ebbe S.; Jensen, Jens L.; Kantcheva, Adriana K.; Bublitz, Maike; Nissen, Poul; Rasmussen, Anton M. H.; Svane, Katrine L.; Hammer, Bjørk; Rezazadegan, Reza; Nielsen, Niels Chr.; Nielsen, Jakob T.; Andersen, Jørgen E.

    2014-12-01

    Proteins fold into three-dimensional structures, which determine their diverse functions. The conformation of the backbone of each structure is locally at each Cα effectively described by conformational angles resulting in Ramachandran plots. These, however, do not describe the conformations around hydrogen bonds, which can be non-local along the backbone and are of major importance for protein structure. Here, we introduce the spatial rotation between hydrogen bonded peptide planes as a new descriptor for protein structure locally around a hydrogen bond. Strikingly, this rotational descriptor sampled over high-quality structures from the protein data base (PDB) concentrates into 30 localized clusters, some of which correlate to the common secondary structures and others to more special motifs, yet generally providing a unifying systematic classification of local structure around protein hydrogen bonds. It further provides a uniform vocabulary for comparison of protein structure near hydrogen bonds even between bonds in different proteins without alignment.

  13. The Origin of the Non-Additivity in Resonance-Assisted Hydrogen Bond Systems.

    Science.gov (United States)

    Lin, Xuhui; Zhang, Huaiyu; Jiang, Xiaoyu; Wu, Wei; Mo, Yirong

    2017-11-09

    The concept of resonance-assisted hydrogen bond (RAHB) has been widely accepted, and its impact on structures and energetics can be best studied computationally using the block-localized wave function (BLW) method, which is a variant of ab initio valence bond (VB) theory and able to derive strictly electron-localized structures self-consistently. In this work, we use the BLW method to examine a few molecules that result from the merging of two malonaldehyde molecules. As each of these molecules contains two hydrogen bonds, these intramolecular hydrogen bonds may be cooperative or anticooperative, depended on their relative orientations, and compared with the hydrogen bond in malonaldehyde. Apart from quantitatively confirming the concept of RAHB, the comparison of the computations with and without π resonance shows that both σ-framework and π-resonance contribute to the nonadditivity in these RAHB systems with multiple hydrogen bonds.

  14. Hydrogen Bonding and Stability of Hybrid Organic-Inorganic Perovskites

    KAUST Repository

    El-Mellouhi, Fedwa

    2016-09-08

    In the past few years, the efficiency of solar cells based on hybrid organic–inorganic perovskites has exceeded the level needed for commercialization. However, existing perovskites solar cells (PSCs) suffer from several intrinsic instabilities, which prevent them from reaching industrial maturity, and stabilizing PSCs has become a critically important problem. Here we propose to stabilize PSCs chemically by strengthening the interactions between the organic cation and inorganic anion of the perovskite framework. In particular, we show that replacing the methylammonium cation with alternative protonated cations allows an increase in the stability of the perovskite by forming strong hydrogen bonds with the halide anions. This interaction also provides opportunities for tuning the electronic states near the bandgap. These mechanisms should have a universal character in different hybrid organic–inorganic framework materials that are widely used.

  15. Structure, vibrations, and hydrogen bond parameters of dibenzotetraaza[14]annulene

    Science.gov (United States)

    Gawinkowski, S.; Eilmes, J.; Waluk, J.

    2010-07-01

    Geometry and vibrational structure of dibenzo[ b, i][1,4,8,11]tetraaza[14]annulene (TAA) have been studied using infrared and Raman spectroscopy combined with quantum-chemical calculations. The assignments were proposed for 106 out of the total of 108 TAA vibrations, based on comparison of the theoretical predictions with the experimental data obtained for the parent molecule and its isotopomer in which the NH protons were replaced by deuterons. Reassignments were suggesteded for the NH stretching and out-of-plane vibrations. The values of the parameters of the intramolecular NH⋯N hydrogen bonds were analysed in comparison with the corresponding data for porphyrin and porphycene, molecules with the same structural motif, a cavity composed of four nitrogen atoms and two inner protons. Both experiment and calculations suggest that the molecule of TAA is not planar and is present in a trans tautomeric form, with the protons located on the opposite nitrogen atoms.

  16. Evaluation of one-dimensional potential energy surfaces for prediction of spectroscopic properties of hydrogen bonds in linear bonded complexes.

    Science.gov (United States)

    Jouypazadeh, Hamidreza; Farrokhpour, Hossein; Solimannejad, Mohammad

    2017-05-01

    This work evaluated the reliability of the one-dimensional potential energy surface for calculating the spectroscopic properties (rovibrational constants and rotational line energies) of hydrogen bonds in linear bonded complexes by comparing theoretical results with the corresponding experimental results. For this purpose, two hydrogen bonded complexes were selected: the HCN···HCN homodimer and the HCN···HF heterodimer. The one-dimensional potential energy surfaces related to the hydrogen bonds in these complexes were calculated using different computational methods and basis sets. The calculated potential curve of each complex was fitted to an analytical one-dimensional potential function to obtain the potential parameters. The obtained analytical potential function of each complex was used in a two-particle Schrödinger equation to obtain the rovibrational energy levels of the hydrogen bond. Using the calculated rovibrational levels, the rovibrational spectra and constants of each complex were calculated and compared with experimental data available from the literature. Compared with experimental data, the calculated one-dimensional potential energy surface at the QCISD/aug-cc-pVDZ level of theory was found to predict the spectroscopic properties of hydrogen bonds better than the potential curves obtained using other computational methods, especially for the HCN···HCN homodimer complex. Generally, the results obtained for the HCN···HCN homodimer complex were closer to experimental data than those obtained for the HCN···HF heterodimer complex. The investigation performed in this work showed that the one-dimensional potential curve related to the hydrogen bond between two linear molecules can be used to predict the spectroscopic constants of hydrogen bonds. Graphical abstract Potential energy curves of HCN···HCN and HCN···HF complexes calculated at the different computational levels.

  17. A density functional theory study on the hydrogen bonding interactions between luteolin and ethanol.

    Science.gov (United States)

    Zheng, Yan-Zhen; Xu, Jing; Liang, Qin; Chen, Da-Fu; Guo, Rui; Fu, Zhong-Min

    2017-08-01

    Ethanol is one of the most commonly used solvents to extract flavonoids from propolis. Hydrogen bonding interactions play an important role in the properties of liquid system. The main objective of the work is to study the hydrogen bonding interactions between flavonoid and ethanol. Luteolin is a very common flavonoid that has been found in different geographical and botanical propolis. In this work, it was selected as the representative flavonoid to do detailed research. The study was performed from a theoretical perspective using density functional theory (DFT) method. After careful optimization, there exist nine optimized geometries for the luteolin - CH 3 CH 2 OH complex. The binding distance of X - H···O, and the bond length, vibrational frequency, and electron density changes of X - H all indicate the formation of the hydrogen bond in the optimized geometries. In the optimized geometries, it is found that: (1) except for the H2', H5', and H6', CH 3 CH 2 OH has formed hydrogen bonds with all the hydrogen and oxygen atoms in luteolin. The hydrogen atoms in the hydroxyl groups of luteolin form the strongest hydrogen bonds with CH 3 CH 2 OH; (2) all of the hydrogen bonds are closed-shell interactions; (3) the strongest hydrogen bond is the O3' - H3'···O in structure A, while the weakest one is the C3 - H3···O in structure E; (4) the hydrogen bonds of O3' - H3'···O, O - H···O4, O - H···O3' and O - H···O7 are medium strength and covalent dominant in nature. While the other hydrogen bonds are weak strength and possess a dominant character of the electrostatic interactions in nature.

  18. Discrete kink dynamics in hydrogen-bonded chains: The two-component model

    DEFF Research Database (Denmark)

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

    2004-01-01

    -proton interaction in the hydrogen bond. (ii) a harmonic coupling between the protons in adjacent hydrogen bonds, and (iii) a harmonic coupling between the nearest-neighbor heavy ions (an isolated diatomic chain with the lowest acoustic band) or instead a harmonic on-site potential for the heavy ions (a diatomic...

  19. Self-assembly of a [2 x 2] hydrogen bonded grid

    NARCIS (Netherlands)

    Lipkowski, P.R.; Bielejewska, A.G.; Kooijman, Huub; Spek, Anthony L.; Timmerman, P.; Reinhoudt, David

    1999-01-01

    Formation of 24 cooperative hydrogen bonds drives the spontaneous assembly of a rigid bifunctional trimelamine and bis(barbituric acid) to give selectively the [2 × 2] hydrogen-bonded grid, in preference to the corresponding [1 × 1] or polymeric assemblies.

  20. 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…

  1. Molecular insight into the hydrogen bonding and micro-segregation of a cryoprotectant molecule.

    Science.gov (United States)

    Towey, J J; Soper, A K; Dougan, L

    2012-11-29

    Glycerol-water liquid mixtures are intriguing hydrogen-bonded systems and essential in many fields of chemistry, ranging from basic molecular research to widespread use in industrial and biomedical applications as cryoprotective solutions. Despite much research on these mixtures, the details of their microscopic structure are still not understood. One common notion is that glycerol acts to diminish the hydrogen bonding ability of water, a recurring hypothesis that remains untested by direct experimental approaches. The present work characterizes the structure of glycerol-water mixtures, across the concentration range, using a combination of neutron diffraction experiments and computational modeling. Contrary to previous expectations, we show that the hydrogen bonding ability of water is not diminished in the presence of glycerol. We show that glycerol-water hydrogen bonds effectively take the place of water-water hydrogen bonds, allowing water to maintain its full hydrogen bonding capacity regardless of the quantity of glycerol in the environment. We provide a quantitative measurement of all hydrogen bonding in the system and reveal a concentration range where a microsegregated, bipercolating liquid mixture exists in coexistence with a considerable interface region. This work highlights the role of hydrogen bonding connectivity rather than water structuring/destructuring effects in these important cryoprotective systems.

  2. The elusive≡ CH··· O complex in the hydrogen bonded systems of ...

    Indian Academy of Sciences (India)

    Hydrogen-bonded complexes of phenylacetylene (PhAc) with methanol (MeOH) and diethylether (DEE) were studied using matrix isolation infrared spectroscopy. This study specifically searched for the ≡CH · · ·O hydrogen bonded complex in these systems, which manifest a n-σ* interaction and which is a local minimum ...

  3. Watson-Crick hydrogen bonds : Nature and role in DNA replication

    NARCIS (Netherlands)

    Guerra, Célia Fonseca; Bickelhaupt, F. Matthias

    2006-01-01

    The hydrogen bonds in DNA Watson–Crick base pairs have long been considered predominantly electrostatic phenomena. In this chapter, we show with state-of-the-art calculations that this is not true and that electrostatic interactions and covalent contributions in these hydrogen bonds are in fact of

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

    Indian Academy of Sciences (India)

    Unknown

    Abstract. 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.

  5. Kinetic stabilities of double, tetra- and hexarosette hydrogen-bonded assemblies

    NARCIS (Netherlands)

    Prins, L.J.; Neuteboom, Edda E.; Paraschiv, V.; Crego Calama, Mercedes; Timmerman, P.; Reinhoudt, David

    2002-01-01

    A study of the kinetic stabilities of hydrogen-bonded double, tetra-, and hexarosette assemblies, comprising 36, 72, and 108 hydrogen bonds, respectively, is described. The kinetic stabilities are measured using both chiral amplification and racemization experiments. The chiral amplification studies

  6. Quantification of Hydrogen Bond Strength Based on Interaction Coordinates: A New Approach.

    Science.gov (United States)

    Pandey, Sarvesh Kumar; Manogaran, Dhivya; Manogaran, Sadasivam; Schaefer, Henry F

    2017-08-17

    A new approach to quantify hydrogen bond strengths based on interaction coordinates (HBSBIC) is proposed and is very promising. In this research, it is assumed that the projected force field of the fictitious three atoms fragment (DHA) where D is the proton donor and A is the proton acceptor from the full molecular force field of the H-bonded complex characterizes the hydrogen bond. The "interaction coordinate (IC)" derived from the internal compliance matrix elements of this three-atom fragment measures how the DH covalent bond (its electron density) responds to constrained optimization when the HA hydrogen bond is stretched by a known amount (its electron density is perturbed by a specified amount). This response of the DH bond, based on how the IC depends on the electron density along the HA bond, is a measure of the hydrogen bond strength. The inter- and intramolecular hydrogen bond strengths for a variety of chemical and biological systems are reported. When defined and evaluated using the IC approach, the HBSBIC index leads to satisfactory results. Because this involves only a three-atom fragment for each hydrogen bond, the approach should open up new directions in the study of "appropriate small fragments" in large biomolecules.

  7. Neutron diffraction of α, β and γ cyclodextrins: hydrogen bonding patterns

    International Nuclear Information System (INIS)

    Hingerty, B.E.; Klar, B.; Hardgrove, G.; Betzel, C.; Saenger, W.

    1983-01-01

    Cyclodextrins (CD's) are torus-shaped molecules composed of six (α), seven (β) or eight (γ) (1 → 4) linked glucoses. α-CD has been shown to have two different structures with well-defined hydrogen bonds, one tense and the other relaxed. An induced-fit-like mechanism for α-CD complex formation has been proposed. Circular hydrogen bond networks have also been found for α-CD due to the energetically favored cooperative effect. β-CD with a disordered water structure possesses an unusual flip-flop hydrogen bonding system of the type O-H H-O representing an equilibrium between two states; O-H O reversible H-O. γ-CD with a disordered water structure similar to β-CD also possesses the flip-flop hydrogen bond. This study demonstrates that hydrogen bonds are operative in disordered systems and display dynamics even in the solid state

  8. 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

    . The number of AA side groups (hydrogen-bonding groups) after hydrolysis is determined from NMR measurements. We show that using the theoretical dependency of modulus and reptation time on the packing length, we can account for the changes in linear viscoelasticity due to transformation of nBA side groups...... 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...

  9. Towards a unified description of the hydrogen bond network of liquid water: A dynamics based approach

    International Nuclear Information System (INIS)

    Ozkanlar, Abdullah; Zhou, Tiecheng; Clark, Aurora E.

    2014-01-01

    The definition of a hydrogen bond (H-bond) is intimately related to the topological and dynamic properties of the hydrogen bond network within liquid water. The development of a universal H-bond definition for water is an active area of research as it would remove many ambiguities in the network properties that derive from the fixed definition employed to assign whether a water dimer is hydrogen bonded. This work investigates the impact that an electronic-structure based definition, an energetic, and a geometric definition of the H-bond has upon both topological and dynamic network behavior of simulated water. In each definition, the use of a cutoff (either geometric or energetic) to assign the presence of a H-bond leads to the formation of transiently bonded or broken dimers, which have been quantified within the simulation data. The relative concentration of transient species, and their duration, results in two of the three definitions sharing similarities in either topological or dynamic features (H-bond distribution, H-bond lifetime, etc.), however no two definitions exhibit similar behavior for both classes of network properties. In fact, two networks with similar local network topology (as indicated by similar average H-bonds) can have dramatically different global network topology (as indicated by the defect state distributions) and altered H-bond lifetimes. A dynamics based correction scheme is then used to remove artificially transient H-bonds and to repair artificially broken bonds within the network such that the corrected network exhibits the same structural and dynamic properties for two H-bond definitions (the properties of the third definition being significantly improved). The algorithm described represents a significant step forward in the development of a unified hydrogen bond network whose properties are independent of the original hydrogen bond definition that is employed

  10. 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…

  11. Iron-Catalyzed C-O Bond Activation: Opportunity for Sustainable Catalysis.

    Science.gov (United States)

    Bisz, Elwira; Szostak, Michal

    2017-10-23

    Oxygen-based electrophiles have emerged as some of the most valuable cross-coupling partners in organic synthesis due to several major strategic and environmental benefits, such as abundance and potential to avoid toxic halide waste. In this context, iron-catalyzed C-O activation/cross-coupling holds particular promise to achieve sustainable catalytic protocols due to its natural abundance, inherent low toxicity, and excellent economic and ecological profile. Recently, tremendous progress has been achieved in the development of new methods for functional-group-tolerant iron-catalyzed cross-coupling reactions by selective C-O cleavage. These methods establish highly attractive alternatives to traditional cross-coupling reactions by using halides as electrophilic partners. In particular, new easily accessible oxygen-based electrophiles have emerged as substrates in iron-catalyzed cross-coupling reactions, which significantly broaden the scope of this catalysis platform. New mechanistic manifolds involving iron catalysis have been established; thus opening up vistas for the development of a wide range of unprecedented reactions. The synthetic potential of this sustainable mode of reactivity has been highlighted by the development of new strategies in the construction of complex motifs, including in target synthesis. The most recent advances in sustainable iron-catalyzed cross-coupling of C-O-based electrophiles are reviewed, with a focus on both mechanistic aspects and synthetic utility. It should be noted that this catalytic manifold provides access to motifs that are often not easily available by other methods, such as the assembly of stereodefined dienes or C(sp 2 )-C(sp 3 ) cross-couplings, thus emphasizing the synthetic importance of this mode of reactivity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Comparison of the proton-transfer paths in hydrogen bonds from theoretical potential-energy surfaces and the concept of conservation of bond order III. O-H-O hydrogen bonds.

    Science.gov (United States)

    Majerz, Irena; Olovsson, Ivar

    2010-01-01

    The quantum-mechanically derived reaction coordinates (QMRC) for the proton transfer in O-H-O hydrogen bonds have been derived from ab initio calculations of potential-energy surfaces. A comparison is made between the QMRC and the corresponding bond-order reaction coordinates (BORC) derived by applying the Pauling bond order concept together with the principle of conservation of bond order. In agreement with earlier results for N-H-N(+) hydrogen bonds there is virtually perfect agreement between the QMRC and BORC curves for intermolecular O-H-O hydrogen bonds. For intramolecular O-H-O hydrogen bonds, the donor and acceptor parts of the molecule impose strong constraints on the O···O distance and the QMRC does not follow the BORC relation in the whole range. The neutron-determined proton positions are located close to the theoretically calculated potential-energy minima, and where the QMRC and the BORC curves coincide with each other. The results confirm the universal character of intermolecular hydrogen bonds: BORC is identical with QMRC and the proton can be moved from donor to acceptor keeping its valency equal to 1. The shape of PES for intramolecular hydrogen bonds is more complex as it is sensitive to the geometry of the molecule as well as of the hydrogen bridge. This journal is © the Owner Societies 2010

  13. Hydrogen-bond detection in peptides by 1H-nuclear magnetic resonance through a hydrogen-chlorine exchange reaction

    International Nuclear Information System (INIS)

    Kondo, Michio; Nishi, Ichiro; Yamamoto, Makoto; Jelokhani-Niaraki, M.; Kodama, Hiroaki; Okamoto, Kouji.

    1994-01-01

    NMR spectroscopy is a versatile method for the conformational analysis of peptides and proteins. The hydrogen-chlorine exchange of amide NH protons is detected by 1 H NMR and used as a method to distinguish between intramolecularly hydrogen-bonded and solvent-exposed NH moieties. The method has been applied to hydrogen bond detection in naturally occurring antibiotic peptides, such as gramicidin S, and CH 3 CONH-X (X=alkyl- or aryl-) derivatives. The deuterium exchange method was compared with this method in parallel experiments. In the case of chlorine exchange, in contrast to deuterium exchange, the hydrogen-bonded amide protons are replaced much faster than their solvent-exposed counterparts and the duration of the experiments is considerably less. It is highly possible that the hydrogen-chlorine exchange reaction under the present experimental conditions, in the dark and at room temperature, proceeds through an electrophilic polar mechanism. (author)

  14. Intramolecular hydrogen bond: Can it be part of the basis set of ...

    Indian Academy of Sciences (India)

    IMHB appears in one of the equivalent complete VIC basis sets, its RFC could be used as a measure of bond strength parameter. Keywords. Hydrogen bond; intramolecular; relaxed force constant; normal mode analysis; bond strength parameter. 1. Introduction. The advantages of the compliance constants (the inverse.

  15. 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.

  16. Hydrogen bonding-mediated dehydrogenation in the ammonia borane combined graphene oxide systems

    Science.gov (United States)

    Kuang, Anlong; Liu, Taijuan; Kuang, Minquan; Yang, Ruifeng; Huang, Rui; Wang, Guangzhao; Yuan, Hongkuan; Chen, Hong; Yang, Xiaolan

    2018-03-01

    The dehydrogenation of ammonia borane (AB) adsorbed on three different graphene oxide (GO) sheets is investigated within the ab initio density functional theory. The energy barriers to direct combination the hydrogens of hydroxyl groups and the hydridic hydrogens of AB to release H2 are relatively high, indicating that the process is energetically unfavorable. Our theoretical study demonstrates that the dehydrogenation mechanism of the AB-GO systems has undergone two critical steps, first, there is the formation of the hydrogen bond (O-H-O) between two hydroxyl groups, and then, the hydrogen bond further react with the hydridic hydrogens of AB to release H2 with low reaction barriers.

  17. Isolation of a mixed valence diiron hydride: evidence for a spectator hydride in hydrogen evolution catalysis.

    Science.gov (United States)

    Wang, Wenguang; Nilges, Mark J; Rauchfuss, Thomas B; Stein, Matthias

    2013-03-06

    The mixed-valence diiron hydrido complex (μ-H)Fe2(pdt)(CO)2(dppv)2 ([H1](0), where pdt =1,3-propanedithiolate and dppv = cis-1,2-C2H2(PPh2)2), was generated by reduction of the differous hydride [H1](+) using decamethylcobaltocene. Crystallographic analysis shows that [H1](0) retains the stereochemistry of its precursor, where one dppv ligand spans two basal sites and the other spans apical and basal positions. The Fe---Fe bond elongates to 2.80 from 2.66 Å, but the Fe-P bonds only change subtly. Although the Fe-H distances are indistinguishable in the precursor, they differ by 0.2 Å in [H1](0). The X-band electron paramagnetic resonance (EPR) spectrum reveals the presence of two stereoisomers, the one characterized crystallographically and a contribution of about 10% from a second symmetrical (sym) isomer wherein both dppv ligands occupy apical-basal sites. The unsymmetrical (unsym) arrangement of the dppv ligands is reflected in the values of A((31)P), which range from 31 MHz for the basal phosphines to 284 MHz for the apical phosphine. Density functional theory calculations were employed to rationalize the electronic structure of [H1](0) and to facilitate spectral simulation and assignment of EPR parameters including (1)H and (31)P hyperfine couplings. The EPR spectra of [H1](0) and [D1](0) demonstrate that the singly occupied molecular orbital is primarily localized on the Fe center with the longer bond to H, that is, Fe(II)-H···Fe(I). The coupling to the hydride is A((1)H) = 55 and 74 MHz for unsym- amd sym-[H1](0), respectively. Treatment of [H1](0) with H(+) gives 0.5 equiv of H2 and [H1](+). Reduction of D(+) affords D2, leaving the hydride ligand intact. These experiments demonstrate that the bridging hydride ligand in this complex is a spectator in the hydrogen evolution reaction.

  18. Hydration dynamics of a lipid membrane: Hydrogen bond networks and lipid-lipid associations

    Science.gov (United States)

    Srivastava, Abhinav; Debnath, Ananya

    2018-03-01

    Dynamics of hydration layers of a dimyristoylphosphatidylcholine (DMPC) bilayer are investigated using an all atom molecular dynamics simulation. Based upon the geometric criteria, continuously residing interface water molecules which form hydrogen bonds solely among themselves and then concertedly hydrogen bonded to carbonyl, phosphate, and glycerol head groups of DMPC are identified. The interface water hydrogen bonded to lipids shows slower relaxation rates for translational and rotational dynamics compared to that of the bulk water and is found to follow sub-diffusive and non-diffusive behaviors, respectively. The mean square displacements and the reorientational auto-correlation functions are slowest for the interfacial waters hydrogen bonded to the carbonyl oxygen since these are buried deep in the hydrophobic core among all interfacial water studied. The intermittent hydrogen bond auto-correlation functions are calculated, which allows breaking and reformations of the hydrogen bonds. The auto-correlation functions for interfacial hydrogen bonded networks develop humps during a transition from cage-like motion to eventual power law behavior of t-3/2. The asymptotic t-3/2 behavior indicates translational diffusion dictated dynamics during hydrogen bond breaking and formation irrespective of the nature of the chemical confinement. Employing reactive flux correlation analysis, the forward rate constant of hydrogen bond breaking and formation is calculated which is used to obtain Gibbs energy of activation of the hydrogen bond breaking. The relaxation rates of the networks buried in the hydrophobic core are slower than the networks near the lipid-water interface which is again slower than bulk due to the higher Gibbs energy of activation. Since hydrogen bond breakage follows a translational diffusion dictated mechanism, chemically confined hydrogen bond networks need an activation energy to diffuse through water depleted hydrophobic environments. Our calculations

  19. Melting of hydrogen bonds in uracil derivatives probed by infrared spectroscopy and ab initio molecular dynamics.

    Science.gov (United States)

    Szekrényes, Zsolt; Kamarás, Katalin; Tarczay, György; Llanes-Pallás, Anna; Marangoni, Tomas; Prato, Maurizio; Bonifazi, Davide; Björk, Jonas; Hanke, Felix; Persson, Mats

    2012-04-19

    The thermal response of hydrogen bonds is a crucial aspect in the self-assembly of molecular nanostructures. To gain a detailed understanding of their response, we investigated infrared spectra of monomers and hydrogen-bonded dimers of two uracil-derivative molecules, supported by density functional theory calculations. Matrix isolation spectra of monomers, temperature dependence in the solid state, and ab initio molecular dynamics calculations give a comprehensive picture about the dimer structure and dynamics of such systems as well as a proper assignment of hydrogen-bond affected bands. The evolution of the hydrogen bond melting is followed by calculating the C═O···H-N distance distributions at different temperatures. The result of this calculation yields excellent agreement with the H-bond melting temperature observed by experiment.

  20. Ultrafast conversions between hydrogen bonded structures in liquid water observed by femtosecond x-ray spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Wen, Haidan; Huse, Nils; Schoenlein, Robert W.; Lindenberg, Aaron M.

    2010-05-01

    We present the first femtosecond soft x-ray spectroscopy in liquids, enabling the observation of changes in hydrogen bond structures in water via core-hole excitation. The oxygen K-edge of vibrationally excited water is probed with femtosecond soft x-ray pulses, exploiting the relation between different water structures and distinct x-ray spectral features. After excitation of the intramolecular OH stretching vibration, characteristic x-ray absorption changes monitor the conversion of strongly hydrogen-bonded water structures to more disordered structures with weaker hydrogen-bonding described by a single subpicosecond time constant. The latter describes the thermalization time of vibrational excitations and defines the characteristic maximum rate with which nonequilibrium populations of more strongly hydrogen-bonded water structures convert to less-bonded ones. On short time scales, the relaxation of vibrational excitations leads to a transient high-pressure state and a transient absorption spectrum different from that of statically heated water.

  1. Ligand Self-Sorting and Nonlinear Effects in Dinuclear Asymmetric Hydrogenation: Complexity in Catalysis

    NARCIS (Netherlands)

    Terrade, F.G.; Lutz, M.; Reek, J.N.H.

    2013-01-01

    Nature has been a source of inspiration for scientists as billion years of evolution have resulted in magnificent examples of how processes can be controlled efficiently. In the field of supramolecular catalysis, enzymes have been the major source of inspiration. As such, many synthetic systems have

  2. 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

    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...

  3. Observation of Weak C-H...O Hydrogen Bonding by Unactivated Alkanes

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xue B.; Woo, Hin-koon; Boggavarapu, Kiran; Wang, Lai S.

    2005-08-12

    Weak C-H...O hydrogen bonding has been recognized to play a major role in biological molecular structures and functions. A newly developed low-temperature photoelectron spectroscopy apparatus is used here to study the C-H...O hydrogen bonding between unactivated alkanes and the carboxylate functional group. We observed that gaseous linear carboxylates, CH3(CH2)nCO2-, assume folded structures at low temperatures due to weak C-H...O hydrogen bonding between the terminal CH3 and CO2- groups for n-5. Temperature-dependent studies showed that the folding transition depends on both the temperature and the aliphatic chain length. Theoretical calculations revealed that for n = 3-8, the folded conformations are more stable than the linear structures, but C-H...O hydrogen bonding only forms for species with n-5 due to steric constraint in the smaller species. One C-H...O hydrogen-bond is formed in the n = 5 and 6 species, whereas two C-H...O hydrogen-bonds are formed for n = 7 and 8. Comparison of the photoelectron spectral shifts for the folded relative to the linear conformations yielded lower limits for the strength of the C-H...O hydrogen-bonds in CH3(CH2)nCO2-, ranging from 1.2 kcal/mol for n = 5 to 4.4 kcal/mol for n = 8.

  4. 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.

  5. Hydrogen bonding energy determined by molecular dynamics simulation and correlation to properties of thermoplastic starch films.

    Science.gov (United States)

    Yang, Jinhui; Tang, Kangkang; Qin, Guoqiang; Chen, Yanxue; Peng, Ling; Wan, Xia; Xiao, Huining; Xia, Qiuyang

    2017-06-15

    The molecular dynamics (MD) simulation method was used to investigate the hydrogen bonding energy of starch/glycerol system under different temperatures (range from 90°C to 120°C) and different glycerol contents (range from 20% to 40%, based on dry starch weight). These effects on the hydrogen bonding energy (including the total hydrogen bonding energy, hydrogen bonding energy of starch/starch, glycerol/glycerol, and starch/glycerol) were analyzed in detail. Meanwhile, glycerol plasticized starch films were prepared using casting method. The relationship between the hydrogen bonding energy and the performances of thermoplastic starch film (TPSF), such as crystallinity, mechanical properties and water uptake determined experimentally, were revealed and discussed. The results indicated that glycerol/starch film contained strong hydrogen bonding interaction which could be increased by decreasing the temperature or increasing the glycerol content. The hydrogen bonding interaction is the key factor for the preparation of the plasticized starch material, and the plasticized mechanism can be interpreted according to the analytical results of the simulation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Influence of Intramolecular Charge Transfer and Nuclear Quantum Effects on Intramolecular Hydrogen Bonds in Azopyrimidines.

    Science.gov (United States)

    Bártová, Kateřina; Čechová, Lucie; Procházková, Eliška; Socha, Ondřej; Janeba, Zlatko; Dračínský, Martin

    2017-10-06

    Intramolecular hydrogen bonds (IMHBs) in 5-azopyrimidines are investigated by NMR spectroscopy and DFT computations that involve nuclear quantum effects. A series of substituted 5-phenylazopyrimidines with one or two hydrogen bond donors able to form IMHBs with the azo group is prepared by azo coupling. The barrier of interconversion between two rotamers of the compounds with two possible IMHBs is determined by variable temperature NMR spectroscopy and it is demonstrated that the barrier is significantly affected by intramolecular charge transfer. Through-hydrogen-bond scalar coupling is investigated in 15 N labeled compounds and the stability of the IMHBs is correlated with experimental NMR parameters and rationalized by path integral molecular dynamics simulations that involve nuclear quantum effects. Detailed information on the hydrogen bond geometry upon hydrogen-to-deuterium isotope exchange is obtained from a comparison of experimental and calculated NMR data.

  7. Probing the Hydrogen Bonding of the Ferrous-NO Heme Center of nNOS by Pulsed Electron Paramagnetic Resonance.

    Science.gov (United States)

    Astashkin, Andrei V; Chen, Li; Elmore, Bradley O; Kunwar, Deepak; Miao, Yubin; Li, Huiying; Poulos, Thomas L; Roman, Linda J; Feng, Changjian

    2015-06-25

    Oxidation of L-arginine (L-Arg) to nitric oxide (NO) by NO synthase (NOS) takes place at the heme active site. It is of current interest to study structures of the heme species that activates O2 and transforms the substrate. The NOS ferrous-NO complex is a close mimic of the obligatory ferric (hydro)peroxo intermediate in NOS catalysis. In this work, pulsed electron-nuclear double resonance (ENDOR) spectroscopy was used to probe the hydrogen bonding of the NO ligand in the ferrous-NO heme center of neuronal NOS (nNOS) without a substrate and with L-Arg or N-hydroxy-L-arginine (NOHA) substrates. Unexpectedly, no H-bonding interaction connecting the NO ligand to the active site water molecule or the Arg substrate was detected, in contrast to the results obtained by X-ray crystallography for the Arg-bound nNOS heme domain [Li et al. J. Biol. Inorg. Chem. 2006, 11, 753-768]. The nearby exchangeable proton in both the no-substrate and Arg-containing nNOS samples is located outside the H-bonding range and, on the basis of the obtained structural constraints, can belong to the active site water (or OH). On the contrary, in the NOHA-bound sample, the nearby exchangeable hydrogen forms an H-bond with the NO ligand (on the basis of its distance from the NO ligand and a nonzero isotropic hfi constant), but it does not belong to the active site water molecule because the water oxygen atom (detected by (17)O ENDOR) is too far. This hydrogen should therefore come from the NOHA substrate, which is in agreement with the X-ray crystallography work [Li et al. Biochemistry 2009, 48, 10246-10254]. The nearby nonexchangeable hydrogen atom assigned as H(ε) of Phe584 was detected in all three samples. This hydrogen atom may have a stabilizing effect on the NO ligand and probably determines its position.

  8. Soliton patterns and breakup thresholds in hydrogen-bonded chains

    International Nuclear Information System (INIS)

    Tchakoutio Nguetcho, A.S.; Kofane, T.C.

    2006-12-01

    We study the dynamics of protons in hydrogen-bonded quasi one-dimensional networks in terms of a diatomic lattice model of protons and heavy ions, with a phi-four on-site substrate potential. We show that the model with linear and nonlinear coupling between lattice sites of the quartic type for the protons admits a richer dynamics that cannot be found with linear coupling. Depending on the two types of physical boundary conditions namely, the drop and condensate types of boundary conditions, and on conditions that require the presence of linear and nonlinear dispersion terms, soliton patterns that are represented by soliton with compact support, peak, drop, bell, cusp, shock, kink, bubble and loop solitons, are derived within a continuum approximation. The phase trajectories, as well as an analytical analysis, provide information on an disintegration of soliton patterns upon reaching some critical values of the lattice parameters. The total energies of soliton patterns are exactly calculated in the displacive limit. We also show that when the phonon anharmonism is taken into account, the width and the energy of soliton patterns are in qualitative agreement with experimental data. (author)

  9. Protonation Dynamics and Hydrogen Bonding in Aqueous Sulfuric Acid.

    Science.gov (United States)

    Niskanen, Johannes; Sahle, Christoph J; Juurinen, Iina; Koskelo, Jaakko; Lehtola, Susi; Verbeni, Roberto; Müller, Harald; Hakala, Mikko; Huotari, Simo

    2015-09-03

    Hydration of sulfuric acid plays a key role in new-particle formation in the atmosphere. It has been recently proposed that proton dynamics is crucial in the stabilization of these clusters. One key question is how water molecules mediate proton transfer from sulfuric acid, and hence how the deprotonation state of the acid molecule behaves as a function concentration. We address the proton transfer in aqueous sulfuric acid with O K edge and S L edge core-excitation spectra recorded using inelastic X-ray scattering and with ab initio molecular dynamics simulations in the concentration range of 0-18.0 M. Throughout this range, we quantify the acid-water interaction with atomic resolution. Our simulations show that the number of donated hydrogen bonds per Owater increases from 1.9 to 2.5 when concentration increases from 0 to 18.0 M, in agreement with a rapid disappearance of the pre-edge feature in the O K edge spectrum. The simulations also suggest that for 1.5 M sulfuric acid SO4(2-) is most abundant and that its concentration falls monotonously with increasing concentration. Moreover, the fraction of HSO4(-) peaks at ∼12 M.

  10. Can Csbnd H⋯Fsbnd C hydrogen bonds alter crystal packing features in the presence of Nsbnd H⋯Odbnd C hydrogen bond?

    Science.gov (United States)

    Yadav, Hare Ram; Choudhury, Angshuman Roy

    2017-12-01

    Intermolecular interactions involving organic fluorine have been the contemporary field of research in the area of organic solid state chemistry. While a group of researchers had refuted the importance of "organic fluorine" in guiding crystal structures, others have provided evidences for in favor of fluorine mediated interactions in the solid state. Many systematic studies have indicated that the "organic fluorine" is capable of offering weak hydrogen bonds through various supramolecular synthons, mostly in the absence of other stronger hydrogen bonds. Analysis of fluorine mediated interaction in the presence of strong hydrogen bonds has not been highlighted in detail. Hence a thorough structural investigation is needed to understand the role of "organic fluorine" in crystal engineering of small organic fluorinated molecules having the possibility of strong hydrogen bond formation in the solution and in the solid state. To fulfil this aim, we have synthesized a series of fluorinated amides using 3-methoxyphenylacetic acid and fluorinated anilines and studied their structural properties through single crystal and powder X-ray diffraction methods. Our results indicated that the "organic fluorine" plays a significant role in altering the packing characteristics of the molecule in building specific crystal lattices even in the presence of strong hydrogen bond.

  11. The role of uranium-arene bonding in H2O reduction catalysis

    Science.gov (United States)

    Halter, Dominik P.; Heinemann, Frank W.; Maron, Laurent; Meyer, Karsten

    2018-03-01

    The reactivity of uranium compounds towards small molecules typically occurs through stoichiometric rather than catalytic processes. Examples of uranium catalysts reacting with water are particularly scarce, because stable uranyl groups form that preclude the recovery of the uranium compound. Recently, however, an arene-anchored, electron-rich uranium complex has been shown to facilitate the electrocatalytic formation of H2 from H2O. Here, we present the precise role of uranium-arene δ bonding in intermediates of the catalytic cycle, as well as details of the atypical two-electron oxidative addition of H2O to the trivalent uranium catalyst. Both aspects were explored by synthesizing mid- and high-valent uranium-oxo intermediates and by performing comparative studies with a structurally related complex that cannot engage in δ bonding. The redox activity of the arene anchor and a covalent δ-bonding interaction with the uranium ion during H2 formation were supported by density functional theory analysis. Detailed insight into this catalytic system may inspire the design of ligands for new uranium catalysts.

  12. 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

  13. Influence of intramolecular and intermolecular hydrogen bonding on the fluorescence decay time of indigo derivatives

    International Nuclear Information System (INIS)

    Schneider, S.; Lill, E.; Hefferle, P.; Doerr, F.

    1981-01-01

    It is well known that both intramolecular and intermolecular hydrogen bonding can lead to drastic changes in the lifetime of the first excited singlet state. By employing a synchronously pumped, mode-locked dye-laser for excitation in connection with a continuously operated streak camera for detection, the solvent-dependent fluorescence decay times of several indigo derivatives were determined with high temporal resolution (approx. 5 ps with deconvolution). It is found that in indigo dyes intramolecular hydrogen bonding gives rise to a strong fluorescence quenching; intermolecular hydrogen bonding can also provide a channel for fast radiationless deactivation in those derivatives in which the former are not present. (author)

  14. 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.

  15. 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.

  16. 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.

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

    Science.gov (United States)

    White, Paul B; Hong, Mei

    2015-09-03

    Strong or low-barrier hydrogen bonds have often been proposed in proteins to explain enzyme catalysis and proton-transfer reactions. So far (1)H 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 (15)N and (1)H chemical shifts and N-H bond lengths by solid-state NMR in (15)N-labeled 1,8-bis(dimethylamino)naphthalene (DMAN), which contains a well-known strong NHN H-bond. We complexed DMAN with three different counteranions to examine the effects of the chemical environment on the H-bond lengths and chemical shifts. All three DMAN compounds exhibit significantly elongated N-H distances compared to the covalent bond length, and the (1)H(N) chemical shifts are larger than ∼17 ppm, consistent with strong NHN H-bonds in the DMAN cation. However, the (15)N and (1)H chemical shifts and the precise N-H distances differ among the three compounds, and the (15)N chemical shifts show opposite dependences on the proton localization from the general trend in organic compounds, indicating the significant effects of the counteranions on the electronic structure of the H-bond. These data provide useful NMR benchmarks for strong H-bonds and caution against the sole reliance on chemical shifts for identifying strong H-bonds in proteins since neighboring side chains can exert influences on chemical shifts similar to those of the bulky organic anions in DMAN. Instead, N-H bond lengths should be measured, in conjunction with chemical shifts, as a more fundamental parameter of H-bond strength.

  18. Eukaryotic Catalase-Peroxidase: The Role of the Trp-Tyr-Met Adduct in Protein Stability, Substrate Accessibility, and Catalysis of Hydrogen Peroxide Dismutation.

    Science.gov (United States)

    Gasselhuber, Bernhard; Carpena, Xavi; Graf, Michael M H; Pirker, Katharina F; Nicolussi, Andrea; Sündermann, Axel; Hofbauer, Stefan; Zamocky, Marcel; Furtmüller, Paul G; Jakopitsch, Christa; Oostenbrink, Chris; Fita, Ignacio; Obinger, Christian

    2015-09-08

    Recently, it was demonstrated that bifunctional catalase-peroxidases (KatGs) are found not only in archaea and bacteria but also in lower eukaryotes. Structural studies and preliminary biochemical data of the secreted KatG from the rice pathogen Magnaporthe grisea (MagKatG2) suggested both similar and novel features when compared to those of the prokaryotic counterparts studied so far. In this work, we demonstrate the role of the autocatalytically formed redox-active Trp140-Tyr273-Met299 adduct of MagKatG2 in (i) the maintenance of the active site architecture, (ii) the catalysis of hydrogen peroxide dismutation, and (iii) the protein stability by comparing wild-type MagKatG2 with the single mutants Trp140Phe, Tyr273Phe, and Met299Ala. The impact of disruption of the covalent bonds between the adduct residues on the spectral signatures and heme cavity architecture was small. By contrast, loss of its integrity converts bifunctional MagKatG2 to a monofunctional peroxidase of significantly reduced thermal stability. It increases the accessibility of ligands due to the increased flexibility of the KatG-typical large loop 1 (LL1), which contributes to the substrate access channel and anchors at the adduct Tyr. We discuss these data with respect to those known from prokaryotic KatGs and in addition present a high-resolution structure of an oxoiron compound of MagKatG2.

  19. 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.

  20. An algorithm to locate optimal bond breaking points on a potential energy surface for applications in mechanochemistry and catalysis

    Science.gov (United States)

    Bofill, Josep Maria; Ribas-Ariño, Jordi; García, Sergio Pablo; Quapp, Wolfgang

    2017-10-01

    The reaction path of a mechanically induced chemical transformation changes under stress. It is well established that the force-induced structural changes of minima and saddle points, i.e., the movement of the stationary points on the original or stress-free potential energy surface, can be described by a Newton Trajectory (NT). Given a reactive molecular system, a well-fitted pulling direction, and a sufficiently large value of the force, the minimum configuration of the reactant and the saddle point configuration of a transition state collapse at a point on the corresponding NT trajectory. This point is called barrier breakdown point or bond breaking point (BBP). The Hessian matrix at the BBP has a zero eigenvector which coincides with the gradient. It indicates which force (both in magnitude and direction) should be applied to the system to induce the reaction in a barrierless process. Within the manifold of BBPs, there exist optimal BBPs which indicate what is the optimal pulling direction and what is the minimal magnitude of the force to be applied for a given mechanochemical transformation. Since these special points are very important in the context of mechanochemistry and catalysis, it is crucial to develop efficient algorithms for their location. Here, we propose a Gauss-Newton algorithm that is based on the minimization of a positively defined function (the so-called σ -function). The behavior and efficiency of the new algorithm are shown for 2D test functions and for a real chemical example.

  1. 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

  2. Direct 13C-detected NMR experiments for mapping and characterization of hydrogen bonds in RNA

    International Nuclear Information System (INIS)

    Fürtig, Boris; Schnieders, Robbin; Richter, Christian; Zetzsche, Heidi; Keyhani, Sara; Helmling, Christina; Kovacs, Helena; Schwalbe, Harald

    2016-01-01

    In RNA secondary structure determination, it is essential to determine whether a nucleotide is base-paired and not. Base-pairing of nucleotides is mediated by hydrogen bonds. The NMR characterization of hydrogen bonds relies on experiments correlating the NMR resonances of exchangeable protons and can be best performed for structured parts of the RNA, where labile hydrogen atoms are protected from solvent exchange. Functionally important regions in RNA, however, frequently reveal increased dynamic disorder which often leads to NMR signals of exchangeable protons that are broadened beyond 1 H detection. Here, we develop 13 C direct detected experiments to observe all nucleotides in RNA irrespective of whether they are involved in hydrogen bonds or not. Exploiting the self-decoupling of scalar couplings due to the exchange process, the hydrogen bonding behavior of the hydrogen bond donor of each individual nucleotide can be determined. Furthermore, the adaption of HNN-COSY experiments for 13 C direct detection allows correlations of donor–acceptor pairs and the localization of hydrogen-bond acceptor nucleotides. The proposed 13 C direct detected experiments therefore provide information about molecular sites not amenable by conventional proton-detected methods. Such information makes the RNA secondary structure determination by NMR more accurate and helps to validate secondary structure predictions based on bioinformatics.

  3. Interfacial electrochemistry of colloidal ruthenium dioxide and catalysis of the photochemical generation of hydrogen from water

    NARCIS (Netherlands)

    Kleijn, J.M.

    1987-01-01

    The formation of hydrogen from water using solar energy is a very attractive research topic, because of the potential use of hydrogen as an alternative, clean fuel. It has been shown by many workers in the field that photochemical hydrogen generation can be achieved in an aqueous system,

  4. 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.

  5. Radical SAM Catalysis via an Organometallic Intermediate with an Fe–[5′-C]-Deoxyadenosyl Bond

    Science.gov (United States)

    Horitani, Masaki; Shisler, Krista; Broderick, William E.; Hutcheson, Rachel U.; Duschene, Kaitlin S.; Marts, Amy R.; Hoffman, Brian M.; Broderick, Joan B.

    2016-01-01

    Radical SAM enzymes use a [4Fe-4S] cluster to cleave S-adenosylmethionine (SAM) to initiate diverse radical reactions. These are thought to involve the 5′-deoxyadenosyl radical intermediate, which has not yet been detected. Here we rapid freeze-quench trap a catalytically competent intermediate in the reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme. Characterization of the intermediate by electron paramagnetic resonance and 13C, 57Fe electron-nuclear double resonance spectroscopies reveals that it contains an organometallic center in which 5′-carbon of a SAM-derived deoxyadenosyl moiety forms a bond to the unique iron of the [4Fe-4S] cluster. Discovery of this intermediate extends the list of enzymatic bio-organometallic centers to the radical SAM enzymes, the largest enzyme superfamily known, and reveals intriguing parallels to B12 radical enzymes. PMID:27174986

  6. 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

  7. Hydrogen bond dynamical properties of adsorbed liquid water monolayers with various TiO2 interfaces

    Science.gov (United States)

    English, Niall J.; Kavathekar, Ritwik S.; MacElroy, J. M. D.

    2012-12-01

    Equilibrium classical molecular dynamics (MD) simulations have been performed to investigate the hydrogen-bonding kinetics of water in contact with rutile-(110), rutile-(101), rutile-(100), and anatase-(101) surfaces at room temperature (300 K). It was observed that anatase-(101) exhibits the longest-lived hydrogen bonds in terms of overall persistence, followed closely by rutile-(110). The relaxation times, defined as the integral of the autocorrelation of the hydrogen bond persistence function, were also longer for these two cases, while decay of the autocorrelation function was slower. The increased number and overall persistence of hydrogen bonds in the adsorbed water monolayers at these surfaces, particularly for anatase-(101), may serve to promote possible water photolysis activity thereon.

  8. Sorption of CO2 in a hydrogen-bonded diamondoid network of sulfonylcalix[4]arene

    Energy Technology Data Exchange (ETDEWEB)

    Sinnwell, Michael A.; Atwood, Jerry L.; Thallapally, Praveen K.

    2018-03-29

    An organic material, p-tert-butyltetrasulfonylcalix[4]arene, self-assembles via hydrogen bonding to form a diamondoid supramolecular network. Possessing discrete, zero-dimensional (0D) microcavities, the thiacalixarene derivative adsorbs CO2 at high pressures

  9. Alignment of paired molecules of C60 within a hexagonal platform networked through hydrogen-bonds.

    Science.gov (United States)

    Hisaki, Ichiro; Nakagawa, Shoichi; Sato, Hiroyasu; Tohnai, Norimitsu

    2016-07-28

    We demonstrate, for the first time, that a hydrogen-bonded low-density organic framework can be applied as a platform to achieve periodic alignment of paired molecules of C60, which is the smallest example of a finite-numbered cluster of C60. The framework is a layered assembly of a hydrogen-bonded 2D hexagonal network (LA-H-HexNet) composed of dodecadehydrotribenzo[18]annulene derivatives.

  10. Hydrogen bonds of DsrD protein revealed by neutron crystallography

    International Nuclear Information System (INIS)

    Chatake, Toshiyuki; Higuchi, Yoshiki; Mizuno, Nobuhiro; Tanaka, Ichiro; Niimura, Nobuo; Morimoto, Yukio

    2008-01-01

    Hydrogen bonds of DNA-binding protein DsrD have been determined by neutron diffraction. In terms of proton donors and acceptors, DsrD protein shows striking differences from other proteins. The features of hydrogen bonds in DsrD protein from sulfate-reducing bacteria have been investigated by neutron protein crystallography. The function of DsrD has not yet been elucidated clearly, but its X-ray crystal structure revealed that it comprises a winged-helix motif and shows the highest structural homology to the DNA-binding proteins. Since any neutron structure of a DNA recognition protein has not yet been obtained, here detailed information on the hydrogen bonds in the winged-helix-motif protein is given and the following features found. (i) The number of hydrogen bonds per amino acid of DsrD is relatively fewer than for other proteins for which neutron structures were determined previously. (ii) Hydrogen bonds are localized between main-chain and main-chain atoms; there are few hydrogen bonds between main-chain and side-chain atoms and between side-chain and side-chain atoms. (iii) Hydrogen bonds inducted by protonation of specific amino acid residues (Glu50) seem to play an essential role in the dimerization of DsrD. The former two points are related to the function of the DNA-binding protein; the three-dimensional structure was mainly constructed by hydrogen bonds in main chains, while the side chains appeared to be used for another role. The latter point would be expected to contribute to the crystal growth of DsrD

  11. 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.

  12. Strategies To Increase the Thermal Stability of Truly Biomimetic Hydrogels: Combining Hydrophobicity and Directed Hydrogen Bonding

    OpenAIRE

    Yuan, Hongbo; Xu, Jialiang; van Dam, Eliane P.; Giubertoni, Giulia; Rezus, Yves L. A.; Hammink, Roel; Bakker, Huib J.; Zhan, Yong; Rowan, Alan E.; Xing, Chengfen; Kouwer, Paul H. J.

    2017-01-01

    Enhancing the thermal stability of proteins is an important task for protein engineering. There are several ways to increase the thermal stability of proteins in biology, such as greater hydrophobic interactions, increased helical content, decreased occurrence of thermolabile residues, or stable hydrogen bonds. Here, we describe a well-defined polymer based on β-helical polyisocyanotripeptides (TriPIC) that uses biological approaches, including hydrogen bonding and hydrophobic interactions fo...

  13. Catalyst System for Hydrogenation Catalysis Based on Multiarm Hyperbranched Polymer Templated Metal (Au, Pt, Pd, Cu Nanoparticles

    Directory of Open Access Journals (Sweden)

    Yunfeng Shi

    2017-09-01

    Full Text Available With a hyperbranched poly(amidoamine core and many water-soluble poly(ethylene glycol monomethyl ether arms connected by pH-sensitive acylhydrazone bonds, multiarm hyperbranched polymer was used as nanoreactor and reductant to prepare metal nanoparticles endowed with intelligence and biocompatibility. The multiarm hyperbranched polymer encapsulated nanoparticles (NPs showed excellent catalytic activity for hydrogenation, thus an excellent catalyst system for hydrogenation was established. The rate constants could reach as high as 3.48 L·s−1·m−2, which can be attributed to the lack of surface passivation afforded by the multiarm hyperbranched polymer.

  14. Toward accurate prediction of potential energy surfaces and the spectral density of hydrogen bonded systems

    International Nuclear Information System (INIS)

    Rekik, Najeh

    2014-01-01

    Despite the considerable progress made in quantum theory and computational methods, detailed descriptions of the potential energy surfaces of hydrogen-bonded systems have not yet been achieved. In addition, the hydrogen bond (H-bond) itself is still so poorly understood at the fundamental level that it remains unclear exactly what geometry constitutes a “real” H-bond. Therefore, in order to investigate features essential for hydrogen bonded complexes, a simple, efficient, and general method for calculating matrix elements of vibrational operators capable of describing the stretching modes and the H-bond bridges of hydrogen-bonded systems is proposed. The derived matrix elements are simple and computationally easy to evaluate, which makes the method suitable for vibrational studies of multiple-well potentials. The method is illustrated by obtaining potential energy surfaces for a number of two-dimensional systems with repulsive potentials chosen to be in Gaussian form for the stretching mode and of the Morse-type for the H-bond bridge dynamics. The forms of potential energy surfaces of weak and strong hydrogen bonds are analyzed by varying the asymmetry of the Gaussian potential. Moreover, the choice and applicability of the selected potential for the stretching mode and comparison with other potentials used in the area of hydrogen bond research are discussed. The approach for the determination of spectral density has been constructed in the framework of the linear response theory for which spectral density is obtained by Fourier transform of the autocorrelation function of the dipole moment operator of the fast mode. The approach involves anharmonic coupling between the high frequency stretching vibration (double well potential) and low-frequency donor-acceptor stretching mode (Morse potential) as well as the electrical anharmonicity of the dipole moment operator of the fast mode. A direct relaxation mechanism is incorporated through a time decaying exponential

  15. Explicit consideration of spatial hydrogen bonding direction for activity coefficient prediction based on implicit solvation calculations.

    Science.gov (United States)

    Chen, Wei-Lin; Lin, Shiang-Tai

    2017-08-09

    The activity coefficient of a chemical in a mixture is important in understanding the thermodynamic properties and non-ideality of the mixture. The COSMO-SAC model based on the result of quantum mechanical implicit solvation calculations has been shown to provide reliable predictions of activity coefficients for mixed fluids. However, it is found that the prediction accuracy is in general inferior for associating fluids. Existing methods for describing the hydrogen-bonding interaction consider the strength of the interaction based only on the polarity of the screening charges, neglecting the fact that the formation of hydrogen bonds requires a specific orientation between the donor and acceptor pairs. In this work, we propose a new approach that takes into account the spatial orientational constraints in hydrogen bonds. Based on the Valence Shell Electron Pair Repulsion (VSEPR) theory, the molecular surfaces associated with the formation of hydrogen bonds are limited to those in the projection of the lone pair electrons of hydrogen bond acceptors, in addition to the polarity of the surface screening charges. Our results show that this new directional hydrogen bond approach, denoted as the COSMO-SAC(DHB) model, requires fewer universal parameters and is significantly more accurate and reliable compared to previous models for a variety of properties, including vapor-liquid equilibria (VLE), infinite dilution activity coefficient (IDAC) and water-octanol partition coefficient (K ow ).

  16. Effect of cooperative hydrogen bonding in azo-hydrazone tautomerism of azo dyes.

    Science.gov (United States)

    Ozen, Alimet Sema; Doruker, Pemra; Aviyente, Viktorya

    2007-12-27

    Azo-hydrazone tautomerism in azo dyes has been modeled by using density functional theory (DFT) at the B3LYP/6-31+G(d,p) level of theory. The most stable tautomer was determined both for model compounds and for azo dyes Acid Orange 7 and Solvent Yellow 14. The effects of the sulfonate group substitution and the replacement of the phenyl group with naphthyl on the tautomer stability and on the behavior in solvent have been discussed. Intramolecular hydrogen bond energies have been estimated for the azo and hydrazone tautomers to derive a relationship between the tautomer stability and the hydrogen bond strength. The transition structures for proton transfer displayed resonance assisted strong hydrogen bonding properties within the framework of the electrostatic-covalent hydrogen bond model (ECHBM). Evolution of the intramolecular hydrogen bond with changing structural and environmental factors during the tautomeric conversion process has been studied extensively by means of the atoms-in-molecules (AIM) analysis of the electron density. The bulk solvent effect was examined using the self-consistent reaction field model. Special solute-solvent interactions were further investigated by means of quantum mechanical calculations after defining the first-solvation shell by molecular dynamics simulations. The effect of cooperative hydrogen bonding with solvent molecules on the tautomer stability has been discussed.

  17. Solvatomagnetic Comparison Method: A Proper Quantification of Solvent Hydrogen-Bond Basicity.

    Science.gov (United States)

    Laurence, Christian; Legros, Julien; Nicolet, Pierre; Vuluga, Daniela; Chantzis, Agisilaos; Jacquemin, Denis

    2014-07-10

    The hydrogen-bond-acceptor basicity of an important class of solvents, the amphiprotic solvents (water, alcohols, primary and secondary amides, and carboxylic acids), has not yet been properly parametrized. In this work, the first scale of solvent hydrogen-bond basicity applicable to amphiprotic solvents is established by means of a new method that compares the 19 F NMR chemical shifts of 4-fluorophenol and 4-fluoroanisole in hydrogen-bond-acceptor solvents. This so-called solvatomagnetic comparison method is free of the shortcomings of the solvatochromic comparison method used so far and is easier to carry out than the pure base calorimetric method. The validity of the new scale is assessed by good linear correlations with spectroscopic, thermodynamic, and kinetic solute properties depending on the solvent hydrogen-bond basicity. In such correlation analysis of solvent effects on physicochemical properties, solvent and solute hydrogen-bond basicity scales must not be mixed, since it is shown here that solute and solvent scales are not equivalent. A comprehensive collection of parameters quantifying the hydrogen-bond basicity is presented for 168 solvents.

  18. 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.

  19. 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.

  20. New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

    Directory of Open Access Journals (Sweden)

    Pavel Nagorny

    2016-12-01

    Full Text Available Hydrogen bond donor catalysis represents a rapidly growing subfield of organocatalysis. While traditional hydrogen bond donors containing N–H and O–H moieties have been effectively used for electrophile activation, activation based on other types of non-covalent interactions is less common. This mini review highlights recent progress in developing and exploring new organic catalysts for electrophile activation through the formation of C–H hydrogen bonds and C–X halogen bonds.

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

    International Nuclear Information System (INIS)

    Mackenzie, Rebecca B.; Dewberry, Christopher T.; Leopold, Kenneth R.; Coulston, Emma; Cole, George C.; Legon, Anthony C.; Tew, David P.

    2015-01-01

    a-type rotational spectra of the hydrogen-bonded complex formed from pyridine and acetylene are reported. Rotational and 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 5 H 5 does not lie along the symmetry axis of the nitrogen lone pair, but rather, forms an average angle of 46° with the C 2 axis of the pyridine. The a-type spectra of HCCH—NC 5 H 5 and DCCD—NC 5 H 5 are doubled, suggesting the existence of a low lying pair of tunneling states. This doubling persists in the spectra of HCCD—NC 5 H 5 , DCCH—NC 5 H 5 , indicating that the underlying motion does not involve interchange of the two hydrogens of the acetylene. Single 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 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 −1 in the C 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

  2. Solution and solid-phase halogen and C-H hydrogen bonding to perrhenate.

    Science.gov (United States)

    Massena, Casey J; Riel, Asia Marie S; Neuhaus, George F; Decato, Daniel A; Berryman, Orion B

    2015-01-28

    (1)H NMR spectroscopic and X-ray crystallographic investigations of a 1,3-bis(4-ethynyl-3-iodopyridinium)benzene scaffold with perrhenate reveal strong halogen bonding in solution, and bidentate association in the solid state. A nearly isostructural host molecule demonstrates significant C-H hydrogen bonding to perrhenate in the same phases.

  3. Indirect measurement of the cooperative hydrogen bonding of polymers using NMR quadrupole relaxation and PFG methods

    Czech Academy of Sciences Publication Activity Database

    Kříž, Jaroslav; Dybal, Jiří

    2008-01-01

    Roč. 265, č. 1 (2008), s. 225-232 ISSN 1022-1360. [European Symposium on Polymer Spectroscopy /17./. Seggauberg Leibnitz, 09.9.2007-12.09.2007] R&D Projects: GA AV ČR IAA400500604 Institutional research plan: CEZ:AV0Z40500505 Keywords : cooperative bonding * hydrogen bond * NMR * poly(4-vinylphenol) Subject RIV: CD - Macromolecular Chemistry

  4. Facilitation of Nanoscale Thermal Transport by Hydrogen Bonds

    OpenAIRE

    Zhang, Lin

    2017-01-01

    Thermal transport performance at the nanoscale and/or of biomaterials is essential to the success of many new technologies including nanoelectronics, biomedical devices, and various nanocomposites. Due to complicated microstructures and chemical bonding, thermal transport process in these materials has not been well understood yet. In terms of chemical bonding, it is well known that the strength of atomic bonding can significantly affect thermal transport across materials or across interfaces...

  5. Competition between halogen, dihalogen and hydrogen bonds in bromo- and iodomethanol dimers

    Czech Academy of Sciences Publication Activity Database

    Riley, K. E.; Řezáč, Jan; Hobza, Pavel

    2013-01-01

    Roč. 19, č. 7 (2013), s. 2879-2883 ISSN 1610-2940 R&D Projects: GA ČR GBP208/12/G016 Grant - others:Operational Program Research and Development for Innovations(XE) CZ 1.05/2.1.00/03/0058 Institutional support: RVO:61388963 Keywords : dihalogen bond * halogen bond * hydrogen bond * noncovalent interactions Subject RIV: CE - Biochemistry Impact factor: 1.867, year: 2013

  6. Dependence of the length of the hydrogen bond on the covalent and cationic radii of hydrogen, and additivity of bonding distances

    Czech Academy of Sciences Publication Activity Database

    Heyrovská, Raji

    2006-01-01

    Roč. 432, č. 1-3 (2006), s. 348-351 ISSN 0009-2614 R&D Projects: GA MŠk(CZ) LC06035 Institutional research plan: CEZ:AV0Z50040507 Keywords : length of the hydrogen bond * ionic radius * Golden ratio Subject RIV: BO - Biophysics Impact factor: 2.462, year: 2006

  7. A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor.

    Directory of Open Access Journals (Sweden)

    Jarosław Poznański

    Full Text Available Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors.

  8. A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor.

    Science.gov (United States)

    Poznański, Jarosław; Poznańska, Anna; Shugar, David

    2014-01-01

    Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors.

  9. 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

  10. 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.

  11. 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

  12. An energetic scale for equilibrium H/D fractionation factors illuminates hydrogen bond free energies in proteins

    Science.gov (United States)

    Cao, Zheng; Bowie, James U

    2014-01-01

    Equilibrium H/D fractionation factors have been extensively employed to qualitatively assess hydrogen bond strengths in protein structure, enzyme active sites, and DNA. It remains unclear how fractionation factors correlate with hydrogen bond free energies, however. Here we develop an empirical relationship between fractionation factors and free energy, allowing for the simple and quantitative measurement of hydrogen bond free energies. Applying our empirical relationship to prior fractionation factor studies in proteins, we find: [1] Within the folded state, backbone hydrogen bonds are only marginally stronger on average in α-helices compared to β-sheets by ∼0.2 kcal/mol. [2] Charge-stabilized hydrogen bonds are stronger than neutral hydrogen bonds by ∼2 kcal/mol on average, and can be as strong as –7 kcal/mol. [3] Changes in a few hydrogen bonds during an enzyme catalytic cycle can stabilize an intermediate state by –4.2 kcal/mol. [4] Backbone hydrogen bonds can make a large overall contribution to the energetics of conformational changes, possibly playing an important role in directing conformational changes. [5] Backbone hydrogen bonding becomes more uniform overall upon ligand binding, which may facilitate participation of the entire protein structure in events at the active site. Our energetic scale provides a simple method for further exploration of hydrogen bond free energies. PMID:24501090

  13. Fluorine as a hydrogen-bond acceptor: experimental evidence and computational calculations.

    Science.gov (United States)

    Dalvit, Claudio; Invernizzi, Christian; Vulpetti, Anna

    2014-08-25

    Hydrogen-bonding interactions play an important role in many chemical and biological systems. Fluorine acting as a hydrogen-bond acceptor in intermolecular and intramolecular interactions has been the subject of many controversial discussions and there are different opinions about it. Recently, we have proposed a correlation between the propensity of fluorine to be involved in hydrogen bonds and its (19)F NMR chemical shift. We now provide additional experimental and computational evidence for this correlation. The strength of hydrogen-bond complexes involving the fluorine moieties CH2F, CHF2, and CF3 was measured and characterized in simple systems by using established and novel NMR methods and compared to the known hydrogen-bond complex formed between acetophenone and p-fluorophenol. Implications of these results for (19)F NMR screening are analyzed in detail. Computed values of the molecular electrostatic potential at the different fluorine atoms and the analysis of the electron density topology at bond critical points correlate well with the NMR results. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Supramolecular assembly of Yin(IV) porphyrin cations stabilized by ionic hydrogen bonding interactions

    Energy Technology Data Exchange (ETDEWEB)

    Jo, Hwa Jin; Kim, Sung Hyun; Kim, Hee Joon [Dept. of Applied Chemistry, Kumoh National Institute of Technology, Gumi (Korea, Republic of)

    2015-09-15

    Our concern for hydrogen-bonded supramolecular assembly with metalloporphyrins led us to exploiting ionic hydrogen bonds, a special class of hydrogen bonds formed between ions and molecules. Because these interactions have up to a third of the strength of covalent bonds, they are expected to be very useful in self-assembly in supramolecular chemistry and molecular crystals. Here we report the preparation and supramolecular assembly of highly charged tin(IV) porphyrin cations stabilized by ionic hydrogen-bonding interactions. We demonstrated that tin(IV) porphyrin cations such as [Sn(OH{sub 2}){sub 2}(T{sup H}PyP)]{sup 6+} can be a useful three-dimensional building block for the construction of porous porphyrin materials. Our X-ray structural analysis revealed that [Sn(OH{sub 2}){sub 2}(T{sup H}PyP)]{sup 6+} cations act as ionic hydrogen-bonding donors possessing electro-deficient six protons from the two axially coordinated aqua ligands and the four equatorial pyridinium peripheral groups.

  15. Hydrogen-bonding interactions in T-2 toxin studied using solution and solid-state NMR.

    Science.gov (United States)

    Chaudhary, Praveen; Shank, Roxanne A; Montina, Tony; Goettel, James T; Foroud, Nora A; Hazendonk, Paul; Eudes, François

    2011-10-01

    The structure of T-2 toxin in the solid-state is limited to X-ray crystallographic studies, which lack sufficient resolution to provide direct evidence for hydrogen-bonding interactions. Furthermore, its solution-structure, despite extensive Nuclear Magnetic Resonance (NMR) studies, has provided little insight into its hydrogen-bonding behavior, thus far. Hydrogen-bonding interactions are often an important part of biological activity. In order to study these interactions, the structure of T-2 toxin was compared in both the solution- and solid-state using NMR Spectroscopy. It was determined that the solution- and solid-state structure differ dramatically, as indicated by differences in their carbon chemical shifts, these observations are further supported by solution proton spectral parameters and exchange behavior. The slow chemical exchange process and cross-relaxation dynamics with water observed between the hydroxyl hydrogen on C-3 and water supports the existence of a preferential hydrogen bonding interaction on the opposite side of the molecule from the epoxide ring, which is known to be essential for trichothecene toxicity. This result implies that these hydrogen-bonding interactions could play an important role in the biological function of T-2 toxin and posits towards a possible interaction for the trichothecene class of toxins and the ribosome. These findings clearly illustrate the importance of utilizing solid-state NMR for the study of biological compounds, and suggest that a more detailed study of this whole class of toxins, namely trichothecenes, should be pursued using this methodology.

  16. The hydrogen bond in ice probed by soft x-ray spectroscopy and density functional theory

    International Nuclear Information System (INIS)

    Nilsson, A.; Ogasawara, H.; Cavalleri, M.; Nordlund, D.; Nyberg, M.; Wernet, Ph.; Pettersson, L.G.M.

    2005-01-01

    We combine photoelectron and x-ray absorption spectroscopy with density functional theory to derive a molecular orbital picture of the hydrogen bond in ice. We find that the hydrogen bond involves donation and back-donation of charge between the oxygen lone pair and the O-H antibonding orbitals on neighboring molecules. Together with internal s-p rehybridization this minimizes the repulsive charge overlap of the connecting oxygen and hydrogen atoms, which is essential for a strong attractive electrostatic interaction. Our joint experimental and theoretical results demonstrate that an electrostatic model based on only charge induction from the surrounding medium fails to properly describe the internal charge redistributions upon hydrogen bonding

  17. 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.

  18. Hydrogen bond nature of ferroelectric material studied by X-ray and neutron diffraction. Electric dipole moment and proton tunneling

    International Nuclear Information System (INIS)

    Noda, Yukio; Kiyanagi, Ryoji; Mochida, Tomoyuki; Sugawara, Tadashi

    2006-01-01

    Hydrogen bond nature of MeHPLN and BrHPLN is studied using x-ray and neutron diffraction technique. We found that electric dipole moment of hydrogen atom plays an important role for the phase transition, and proton tunneling model is confirmed on this isolated hydrogen bond system. (author)

  19. Understanding the Thermodynamics of Hydrogen Bonding in Alcohol-Containing Mixtures: Cross-Association.

    Science.gov (United States)

    Fouad, Wael A; Wang, Le; Haghmoradi, Amin; Asthagiri, D; Chapman, Walter G

    2016-04-07

    The thermodynamics of hydrogen bonding in 1-alcohol + water binary mixtures is studied using molecular dynamic (MD) simulation and the polar and perturbed chain form of the statistical associating fluid theory (polar PC-SAFT). The fraction of free monomers in pure saturated liquid water is computed using both TIP4P/2005 and iAMOEBA simulation water models. Results are compared to spectroscopic data available in the literature as well as to polar PC-SAFT. Polar PC-SAFT models hydrogen bonds using single bondable association sites representing electron donors and electron acceptors. The distribution of hydrogen bonds in pure alcohols is computed using the OPLS-AA force field. Results are compared to Monte Carlo (MC) simulations available in the literature as well as to polar PC-SAFT. The analysis shows that hydrogen bonding in pure alcohols is best predicted using a two-site model within the SAFT framework. On the other hand, molecular simulations show that increasing the concentration of water in the mixture increases the average number of hydrogen bonds formed by an alcohol molecule. As a result, a transition in association scheme occurs at high water concentrations where hydrogen bonding is better captured within the SAFT framework using a three-site alcohol model. The knowledge gained in understanding hydrogen bonding is applied to model vapor-liquid equilibrium (VLE) and liquid-liquid equilibrium (LLE) of mixtures using polar PC-SAFT. Predictions are in good agreement with experimental data, establishing the predictive power of the equation of state.

  20. A hydrogen-bonding network plays a catalytic role in photosynthetic oxygen evolution

    Science.gov (United States)

    Polander, Brandon C.; Barry, Bridgette A.

    2012-01-01

    In photosystem II, oxygen evolution occurs by the accumulation of photo-induced oxidizing equivalents at the oxygen-evolving complex (OEC). The sequentially oxidized states are called the S0-S4 states, and the dark stable state is S1. Hydrogen bonds to water form a network around the OEC; this network is predicted to involve multiple peptide carbonyl groups. In this work, we tested the idea that a network of hydrogen bonded water molecules plays a catalytic role in water oxidation. As probes, we used OEC peptide carbonyl frequencies, the substrate-based inhibitor, ammonia, and the sugar, trehalose. Reaction-induced FT-IR spectroscopy was used to describe the protein dynamics associated with the S1 to S2 transition. A shift in an amide CO vibrational frequency (1664 (S1) to 1653 (S2) cm-1) was observed, consistent with an increase in hydrogen bond strength when the OEC is oxidized. Treatment with ammonia/ammonium altered these CO vibrational frequencies. The ammonia-induced spectral changes are attributed to alterations in hydrogen bonding, when ammonia/ammonium is incorporated into the OEC hydrogen bond network. The ammonia-induced changes in CO frequency were reversed or blocked when trehalose was substituted for sucrose. This trehalose effect is attributed to a displacement of ammonia molecules from the hydrogen bond network. These results imply that ammonia, and by extension water, participate in a catalytically essential hydrogen bond network, which involves OEC peptide CO groups. Comparison to the ammonia transporter, AmtB, reveals structural similarities with the bound water network in the OEC. PMID:22474345

  1. 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.

  2. A Computational and Theoretical Study of Conductance in Hydrogen-bonded Molecular Junctions

    Science.gov (United States)

    Wimmer, Michael

    This thesis is devoted to the theoretical and computational study of electron transport in molecular junctions where one or more hydrogen bonds are involved in the process. While electron transport through covalent bonds has been extensively studied, in recent work the focus has been shifted towards hydrogen-bonded systems due to their ubiquitous presence in biological systems and their potential in forming nano-junctions between molecular electronic devices and biological systems. This analysis allows us to significantly expand our comprehension of the experimentally observed result that the inclusion of hydrogen bonding in a molecular junction significantly impacts its transport properties, a fact that has important implications for our understanding of transport through DNA, and nano-biological interfaces in general. In part of this work I have explored the implications of quasiresonant transport in short chains of weakly-bonded molecular junctions involving hydrogen bonds. I used theoretical and computational analysis to interpret recent experiments and explain the role of Fano resonances in the transmission properties of the junction. In a different direction, I have undertaken the study of the transversal conduction through nucleotide chains that involve a variable number of different hydrogen bonds, e.g. NH˙˙˙O, OH˙˙˙O, and NH˙˙˙N, which are the three most prevalent hydrogen bonds in biological systems and organic electronics. My effort here has focused on the analysis of electronic descriptors that allow a simplified conceptual and computational understanding of transport properties. Specifically, I have expanded our previous work where the molecular polarizability was used as a conductance descriptor to include the possibility of atomic and bond partitions of the molecular polarizability. This is important because it affords an alternative molecular description of conductance that is not based on the conventional view of molecular orbitals as

  3. Linking protein structure and dynamics to catalysis: the role of hydrogen tunnelling

    Science.gov (United States)

    Klinman, Judith P

    2006-01-01

    Early studies of enzyme-catalysed hydride transfer reactions indicated kinetic anomalies that were initially interpreted in the context of a ‘tunnelling correction’. An alternate model for tunnelling emerged following studies of the hydrogen atom transfer catalysed by the enzyme soybean lipoxygenase. This invokes full tunnelling of all isotopes of hydrogen, with reaction barriers reflecting the heavy atom, environmental reorganization terms. Using the latter approach, we offer an integration of the aggregate data implicating hydrogen tunnelling in enzymes (i.e. deviations from Swain–Schaad relationships and the semi-classical temperature dependence of the hydrogen isotope effect). The impact of site-specific mutations of enzymes plays a critical role in our understanding of the factors that control tunnelling in enzyme reactions. PMID:16873120

  4. 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

    2015-06-07

    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.

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

    Science.gov (United States)

    Rillema, D. P.

    1981-01-01

    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.

  6. 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.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    , 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......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...

  8. 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.

  9. Micro-reactor for heterogeneous catalysis. Application: hydrogen production from methyl-cyclohexane; Microreacteur pour la catalyse heterogene. Application: production d'hydrogene a partir du methylcyclohexane

    Energy Technology Data Exchange (ETDEWEB)

    Roumanie, M.; Pijolat, C. [Ecole des Mines de Saint Etienne, Centre SPIN (DMICC/LPMG/URA/CNRS-D2021), 42 - Saint Etienne (France); Meille, V.; Bellefon, C. de [Centre National de la Recherche Scientifique (CNRS/CPE), Lab. de Genie des Procedes Catalytiques, 69 - Villeurbanne (France); Pouteau, P.; Delattre, C. [CEA Grenoble, Lab. d' Electronique et de Technologie de l' Informatique (LETI), 38 (France)

    2004-07-01

    First developed by the pharmaceutical industry to find new drugs (combinatorial analysis), the lab on chip is also extremely interesting for the catalysis field. This major interest comes from the miniaturize size and the high surface on volume ratio which lead to improve mass and heat transfer but also the safety in regards of industrial application. The use of micro-technology and the miniaturization of various systems such as micro-fuel cell is also a current field of activity. So for the future research the production of hydrogen is a point to develop in order to supply a micro-fuel cell. The aim of this work is to study and to realize an autonomous catalytic micro-reactor for hydrogen production from methyl-cyclohexane. For this reaction of dehydrogenation, the common catalyst is platinum supported on alumina. Consequently, the general objectives of this work are: 1)to develop a micro-reactor with its heaters, sensors...2)to deposit catalysts in the micro-reactor 3)to study the catalytic conversion of this system.

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

    Science.gov (United States)

    Sigala, Paul A; Ruben, Eliza A; Liu, Corey W; Piccoli, Paula M B; Hohenstein, Edward G; Martínez, Todd J; Schultz, Arthur J; Herschlag, 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 (ΔGf) 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 ΔGf, 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···O hydrogen bonds in crystals, chloroform, acetone, and water have nearly identical lengths and very similar potential energy surfaces despite ΔGf 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 ΔGf 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.

  11. Isotope dependent, temperature regulated, energy repartitioning in a low-barrier, short-strong hydrogen bonded cluster

    NARCIS (Netherlands)

    Li, X. H.; Oomens, J.; Eyler, J. R.; Moore, D. T.; Iyengar, S. S.

    2010-01-01

    We investigate and analyze the vibrational properties, including hydrogen/deuterium isotope effects, in a fundamental organic hydrogen bonded system using multiple experimental (infrared multiple photon dissociation and argon-tagged action spectroscopy) and computational techniques. We note a

  12. Decolorization of Synthetic Dyes by Hydrogen Peroxide with Heterogeneous Catalysis by Mixed Iron Oxides

    Czech Academy of Sciences Publication Activity Database

    Baldrian, Petr; Merhautová, Věra; Gabriel, Jiří; Nerud, František; Stopka, Pavel; Hrubý, Martin; Beneš, Milan J.

    2006-01-01

    Roč. 66, - (2006), s. 258-264 ISSN 0926-3373 R&D Projects: GA AV ČR IBS5020306 Institutional research plan: CEZ:AV0Z50200510; CEZ:AV0Z40320502; CEZ:AV0Z40500505 Keywords : degradation * synthetic dyes * hydrogen peroxide Subject RIV: EE - Microbiology, Virology Impact factor: 3.942, year: 2006

  13. Enthalpy of cooperative hydrogen bonding in complexes of tertiary amines with aliphatic alcohols: Calorimetric study

    International Nuclear Information System (INIS)

    Zaitseva, Ksenia V.; Varfolomeev, Mikhail A.; Novikov, Vladimir B.; Solomonov, Boris N.

    2011-01-01

    Research highlights: → Solution enthalpies of aliphatic alcohols in tertiary amines and vice versa were measured. → The enthalpies of specific interaction of amines in aliphatic alcohols are lower than the enthalpies of hydrogen bonding in 1:1 complexes amine-alcohol determined in base media. → Hydrogen bond cooperativity factors in multi-particle complexes of alcohols with aromatic amines are approximately equal for all alcohols. → Hydrogen bond cooperativity factors in multi-particle complexes of alcohols with trialkylamines decrease with increasing of alkyl radical length in alcohol and amine molecules. - Abstract: The work is devoted to the investigation of thermodynamics of specific interaction of the tertiary aliphatic and aromatic amines with associated solvents as which aliphatic alcohols were taken. Solution enthalpies of aliphatic alcohols in amines (tri-n-propylamine, 2-methylpyridine, 3-methylpyridine, N-methylimidazole) as well as amines in alcohols were measured at infinite dilution. The enthalpies of specific interaction (H-bonding) in systems studied were determined based on experimental data. The enthalpies of specific interaction of amines in aliphatic alcohols significantly lower than the enthalpies of hydrogen bonding in complexes amine-alcohol of 1:1 composition determined in base media due to the reorganization of aliphatic alcohols as solvents. The determination of solvent reorganization contribution makes possible to define the hydrogen bonding enthalpies of amines with clusters of alcohols. Obtained enthalpies of hydrogen bonding in multi-particle complexes are sensitive to the influence of cooperative effect. It was shown, that hydrogen bond cooperativity factors in multi-particle complexes of alcohols with amines are approximately equal for all alcohols when pyridines and N-methylimidazole as solutes are used. At the same time, H-bonding cooperativity factors in complexes of trialkylamines with associative species of alcohols

  14. A Direct Proof of the Resonance-Impaired Hydrogen Bond (RIHB) Concept.

    Science.gov (United States)

    Lin, Xuhui; Wu, Wei; Mo, Yirong

    2018-01-24

    The concept of resonance-enhanced hydrogen bond (RAHB) has been widely accepted and applied as it highlights the positive impact of π-conjugation on intramolecular H-bonds. However, electron delocalization is directional and there is a possibility that π-resonance goes from the H-bond acceptor to the H-bond donor, leading to a negative impact on H-bonds. Here we used the block-localized wavefunction (BLW) method which is a variant of ab initio valence bond (VB) theory and able to derive strictly electron-localized structures self-consistently, to quantify the interplay between H-bond and π-resonance in the terms of geometry, energetics and spectral properties. The comparison of geometrical optimizations with and without π-resonance shows that conjugation can indeed either enhance or weaken intramolecular H-bonds. We further experimented with various substituents attached to either the H-bond acceptor and/or H-bond donor side(s) to tune the H-bonding strength in both directions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Hydrogen bond dynamics governs the effective photoprotection mechanism of plant phenolic sunscreens.

    Science.gov (United States)

    Liu, Fang; Du, Likai; Lan, Zhenggang; Gao, Jun

    2017-02-15

    Sinapic acid derivatives are important sunscreen species in natural plants, which could provide protection from solar UV radiation. Using a combination of ultrafast excited state dynamics, together with classical molecular dynamics studies, we demonstrate that there is direct coupling of hydrogen bond motion with excited state photoprotection dynamics as part of the basic mechanism in solution. Beyond the intra-molecular degree of freedom, the inter-molecular motions on all timescales are potentially important for the photochemical or photophysical events, ranging from the ultrafast hydrogen bond motion to solvent rearrangements. This provides not only an enhanced understanding of the anomalous experimental spectroscopic results, but also the key idea in the development of sunscreen agents with improved photo-chemical properties. We suggest that the hydrogen bond dynamics coupled excited state photoprotection mechanism may also be possible in a broad range of bio-related molecules in the condensed phase.

  16. Mechanical tunability via hydrogen bonding in metal-organic frameworks with the perovskite architecture.

    Science.gov (United States)

    Li, Wei; Thirumurugan, A; Barton, Phillip T; Lin, Zheshuai; Henke, Sebastian; Yeung, Hamish H-M; Wharmby, Michael T; Bithell, Erica G; Howard, Christopher J; Cheetham, Anthony K

    2014-06-04

    Two analogous metal-organic frameworks (MOFs) with the perovskite architecture, [C(NH2)3][Mn(HCOO)3] (1) and [(CH2)3NH2][Mn(HCOO)3] (2), exhibit significantly different mechanical properties. The marked difference is attributed to their distinct modes of hydrogen bonding between the A-site amine cation and the anionic framework. The stronger cross-linking hydrogen bonding in 1 gives rise to Young's moduli and hardnesses that are up to twice those in 2, while the thermal expansion is substantially smaller. This study presents clear evidence that the mechanical properties of MOF materials can be substantially tuned via hydrogen-bonding interactions.

  17. Structures and the Hydrogen Bonding Abilities of Estrogens Studied by Supersonic Jet/laser Spectroscopy

    Science.gov (United States)

    Morishima, Fumiya; Inokuchi, Yoshiya; Ebata, Takayuki

    2013-06-01

    Estrone, estradiol, estriol are known as endogenous estrogen which have the same steroidal frame with different substituent, leading to difference of physiological activity upon the formation of hydrogen bond with estrogen receptor. In the present study, structures of estrogens and their hydrated clusters in a supersonic jet have been studied by various laser spectroscopic techniques and density functional theory calculation to study how the difference of substituents affects their hydrogen bonding ability. Infrared spectra in the OH stretching region indicate a formation of intramolecular hydrogen-bond in estriol, which may lead to weaker physiological activity among the three estrogens. We also measured electronic and infrared spectra of 1:1 hydrated clusters of estrogen. The results show a switch of stable hydration site from the phenolic OH group to the five member ring by substituting one more OH group.

  18. 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.

  19. Effect of small cage guests on hydrogen bonding of tetrahydrofuran in binary structure II clathrate hydrates.

    Science.gov (United States)

    Alavi, Saman; Ripmeester, John A

    2012-08-07

    Molecular dynamics simulations of the pure structure II tetrahydrofuran clathrate hydrate and binary structure II tetrahydrofuran clathrate hydrate with CO(2), CH(4), H(2)S, and Xe small cage guests are performed to study the effect of the shape, size, and intermolecular forces of the small cages guests on the structure and dynamics of the hydrate. The simulations show that the number and nature of the guest in the small cage affects the probability of hydrogen bonding of the tetrahydrofuran guest with the large cage water molecules. The effect on hydrogen bonding of tetrahydrofuran occurs despite the fact that the guests in the small cage do not themselves form hydrogen bonds with water. These results indicate that nearest neighbour guest-guest interactions (mediated through the water lattice framework) can affect the clathrate structure and stability. The implications of these subtle small guest effects on clathrate hydrate stability are discussed.

  20. Hydrogenation of benzaldehyde via electrocatalysis and thermal catalysis on carbon-supported metals

    Energy Technology Data Exchange (ETDEWEB)

    Song, Yang; Sanyal, Udishnu; Pangotra, Dhananjai; Holladay, Jamie D.; Camaioni, Donald M.; Gutiérrez, Oliver Y.; Lercher, Johannes A.

    2018-03-01

    Abstract Selective reduction of benzaldehyde to benzyl alcohol on C-supported Pt, Rh, Pd, and Ni in aqueous phase was conducted using either directly H2 (thermal catalytic hydrogenation, TCH) or in situ electrocatalytically generated hydrogen (electrocatalytic hydrogenation, ECH). In TCH, the intrinsic activity of the metals at room temperature and 1 bar H2 increased in the sequence Rh/C < Pt/C < Pd/C, while Ni/C is inactive at these conditions due to surface oxidation in the absence of cathodic potential. The reaction follows a Langmuir-Hinshelwood mechanism with the second hydrogen addition to the adsorbed hydrocarbon being the rate-determining step. All tested metals were active in ECH of benzaldehyde, although hydrogenation competes with the hydrogen evolution reaction (HER). The minimum cathodic potentials to obtain appreciable ECH rates were identical to the onset potentials of HER. Above this onset, the relative rates of H reacting to H2 and H addition to the hydrocarbon determines the selectivity to ECH and TCH. Accordingly, the selectivity of the metals towards ECH increases in the order Ni/C < Pt/C < Rh/C < Pd/C. Pd/C shows exceptionally high ECH selectivity due to its surprisingly low HER reactivity under the reaction conditions. Acknowledgements The authors would like to thank the groups of Hubert A. Gasteiger at the Technische Universität München of Jorge Gascon at the Delft University of Technology for advice and valuable discussions. The authors are grateful to Nirala Singh, Erika Ember, Gary Haller, and Philipp Rheinländer for fruitful discussions. We are also grateful to Marianne Hanzlik for TEM measurements and to Xaver Hecht and Martin Neukamm for technical support. Y.S. would like to thank the Chinese Scholarship Council for the financial support. The research described in this paper is part of the Chemical Transformation Initiative at Pacific Northwest National Laboratory (PNNL), conducted under the Laboratory Directed Research and

  1. Molecular structure and intramolecular hydrogen bonding in 2 ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 126; Issue 4 ... 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 ...

  2. Structural and vibrational spectral studies on hydrogen bonded salts ...

    Indian Academy of Sciences (India)

    analysis was carried out to interpret hyperconjucative interaction and intramolecular charge transfer (ICT). This analysis gives the precise insight into the nature of H-bond interactions. ..... ing vibrations from the primary amines occur in the region 3600–3300 cm−1.19,20 In the present case, 4- choloanilinium cation has more ...

  3. Structural and vibrational spectral studies on hydrogen bonded salts ...

    Indian Academy of Sciences (India)

    The optimized molecular geometry and computed vibrational spectra are compared with experimental results, which show significant agreement. The natural bond orbital (NBO) analysis was carried out to interpret hyperconjucative interaction and intramolecular charge transfer (ICT). This analysis gives the precise insight ...

  4. 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.

  5. A Critical Check for the Role of Resonance in Intramolecular Hydrogen Bonding.

    Science.gov (United States)

    Jiang, Xiaoyu; Zhang, Huaiyu; Wu, Wei; Mo, Yirong

    2017-11-27

    Although resonance-assisted H-bonds (RAHBs) are well recognized, the role of π resonance in RAHBs is controversial, as the seemingly enhanced H-bonds in unsaturated compounds may result from the constraints imposed by the σ skeleton. Herein the block-localized wave function (BLW) method, which can derive optimal yet resonance-quenched structures with related physiochemical properties, was employed to examine the correlation between π resonance and the strength of intramolecular RAHBs. Examination of a series of paradigmatic molecules with RAHBs and their saturated analogues showed that it is inappropriate to compare a conjugated system with its saturated counterpart, as they may have quite different σ frameworks. Nevertheless, comparison between a conjugated system and its resonance-quenched (i.e., electron-localized) state, which have identical σ skeletons, shows that in all studied cases, π resonance unanimously reduces the bonding distance by 0.111-0.477 Å, strengthens the bonding by 40-56 %, and redshifts the D-H vibrational frequency by 104-628 cm -1 . Furthermore, there is an excellent correlation between hydrogen-bonding strength and the classical Coulomb attraction between the hydrogen-bond donor and the acceptor, which suggests that the dominant role of the electrostatic interaction in H-bonds and RAHBs originates from the charge flow from H-bond donors to acceptors through π conjugation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Hydrogen bonded complexes of cyanuric acid with pyridine and ...

    Indian Academy of Sciences (India)

    Unknown

    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 ...

  7. Uniform graphitic carbon nitride nanorod for efficient photocatalytic hydrogen evolution and sustained photoenzymatic catalysis.

    Science.gov (United States)

    Liu, Jian; Huang, Jianhui; Zhou, Han; Antonietti, Markus

    2014-06-11

    Uniform graphitic carbon nitride nanorods (CNR) were facilely obtained by a morphology-preserving strategy by templating a chiral mesostructured silica nanorod. The hexagonal mesostructured pore structures of one-dimensional silica nanorods can provide nanoconfinement space for carbon nitride condensation to perfect layered structures. CNR demonstrated excellent photocatalytic capability in generating hydrogen from water even with a small specific surface area, compared with its mesoporous counterpart. For further application demonstration, the CNR was used for photocatalytic regeneration of NAD(+) to NADH, the biological form of hydrogen. The in situ NADH regeneration system was further coupled with l-glutamate dehydrogenase for sustainable generation of l-glutamate from α-ketoglutarate. The high yield and high efficiency obtained here point a high-throughput and sustainable way for practical enzymatic applications.

  8. Some Brief Notes on Theoretical and Experimental Investigations of Intramolecular Hydrogen Bonding

    Directory of Open Access Journals (Sweden)

    Lucjan Sobczyk

    2016-12-01

    Full Text Available A review of selected literature data related to intramolecular hydrogen bonding in ortho-hydroxyaryl Schiff bases, ortho-hydroxyaryl ketones, ortho-hydroxyaryl amides, proton sponges and ortho-hydroxyaryl Mannich bases is presented. The paper reports on the application of experimental spectroscopic measurements (IR and NMR and quantum-mechanical calculations for investigations of the proton transfer processes, the potential energy curves, tautomeric equilibrium, aromaticity etc. Finally, the equilibrium between the intra- and inter-molecular hydrogen bonds in amides is discussed.

  9. 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. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Similar strength of the NH⋯O and NH⋯S hydrogen bonds in binary complexes

    DEFF Research Database (Denmark)

    Andersen, Cecilie Lindholm; Jensen, Christine S.; Mackeprang, Kasper

    2014-01-01

    to be extremely small with only 5 and 19 cm-1 for DMA-DME and DMA-DMS, respectively. The experimentally determined integrated absorbance has been combined with a calculated oscillator strength to determine an equilibrium constant of 2 × 10-3 and 4 × 10-3 for the DMA-DME and DMA-DMS complexes, respectively....... The topological analyses reveal that several hydrogen bond interactions are present in the complexes. The calculated binding energies, geometric parameters, observed redshifts, and topological analyses suggest that oxygen and sulfur are hydrogen bond acceptors of similar strength. (Graph Presented)....

  11. Side-by-Side Comparison of Hydroperoxide and Corresponding Alcohol as Hydrogen-Bond Donors

    DEFF Research Database (Denmark)

    Møller, Kristian Holten; Tram, Camilla Mia; Kjærgaard, Henrik Grum

    2017-01-01

    Hydroperoxides are formed in significant amounts in the atmosphere by oxidation of volatile organic compounds and are key in aerosol formation. In a room-temperature experiment, we detected the formation of bimolecular complexes of tert-butyl hydroperoxide (t-BuOOH) and the corresponding alcohol...... results, we find that the hydroperoxide complex is stabilized by ∼4 kJ/mol (Gibbs free energy) more than the alcohol complex. Measured red shifts show the same trend in hydrogen-bond strength with trimethylamine (N acceptor atom) and dimethyl sulfide (S acceptor atom) as the hydrogen-bond acceptors....

  12. Newly detected specific hydrogenation of the conjugated double bond of unsaturated alkaloid lactones by Aspergillus sp.

    Science.gov (United States)

    Guan, Hong; You, Song; Yang, Li; Wang, Xu; Ni, Rui

    2005-08-01

    A new isolate of Aspergillus sp. hydrogenated the gamma,delta-double bond of securinine (143 mg l(-1)) to give 14,15-dihydrosecurinine at over 98% (w/w) yield after 8 h. It also hydrogenated the C11(13) double bond of 3-hydroxy-1(10),3,11(13)-guaiatriene-12,6-olide-2-one (HGT) (200 mg l(-1)) to give 3-hydroxy-1(10),3-guaiadiene-12,6-olide-2-one with over 98% (w/w) conversion after 24 h.

  13. 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....

  14. Effect of pressure on hydrogen bonding in glycerol: A molecular dynamics investigation

    Science.gov (United States)

    Root, Leslie J.; Berne, B. J.

    1997-09-01

    We report results of a molecular dynamics study of liquid glycerol at the experimental density and at a series of elevated densities corresponding in our model to pressures of up to 0.7 GPa. We find that the degree of hydrogen bonding increases with increasing pressure over the range studied, and that the width of the hydrogen bond angle distribution increases with increasing pressure. The relevance to the experimental finding by Cook et al. [R. L. Cook, H. E. King, C. A. Herbst, and D. R. Herschbach, J. Chem. Phys. 100, 5178 (1994)] that the fragility of glycerol increases with increasing pressure is discussed.

  15. Long range order and hydrogen bonding in liquid methanol: A Monte Carlo simulation

    Energy Technology Data Exchange (ETDEWEB)

    Shilov, I.Y.; Rode, B.M. [Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck (Austria); Durov, V.A. [Department of Physical Chemistry, Faculty of Chemistry, Lomonosov Moscow State University, Moscow (Russian Federation)

    1999-02-01

    A Monte Carlo simulation of liquid methanol was performed in NVT ensemble at 298 K using a cubic simulation box containing 500 molecules. Long-range correlations in the liquid are discussed on the basis of site-site radial distribution functions. Hydrogen bonding and topological structure of the methanol aggregates were evaluated in detail, namely the number of linked molecules, formation of branches and cyclic structures. The necessity of larger simulation boxes for a full structural description and thermodynamic characterization of hydrogen-bonded liquids is clearly established by the results. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)

  16. Distinguishing between homogeneous and heterogeneous hydrogen-evolution catalysis with molecular cobalt complexes.

    Science.gov (United States)

    Sconyers, David J; Blakemore, James D

    2017-06-29

    Molecular proton-reduction catalysts can decompose under the acidic conditions required for hydrogen evolution, resulting in formation of secondary metal-containing materials. Using an electrochemical quartz crystal microbalance (EQCM), we report a new method for probing electrodeposition of catalytically active heterogeneous material from molecular precursors. The data collected suggest that EQCM can provide a direct measure of the homogeneity of molecular proton-reduction catalysts over short timescales.

  17. Influence of the interfacial peptide organization on the catalysis of hydrogen evolution

    Czech Academy of Sciences Publication Activity Database

    Doneux, T.; Dorčák, Vlastimil; Paleček, Emil

    2010-01-01

    Roč. 26, č. 2 (2010), s. 1347-1353 ISSN 0743-7463 R&D Projects: GA MŠk(CZ) LC06035 Grant - others:GA AV ČR(CZ) KAN400310651 Program:KA Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : catalytic hydrogen evolution * peptide * constant-current chronopotentiometry Subject RIV: BO - Biophysics Impact factor: 4.269, year: 2010

  18. 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.

  19. Chemical Warfare Agent Surface Adsorption: Hydrogen Bonding of Sarin and Soman to Amorphous Silica.

    Science.gov (United States)

    Davis, Erin Durke; Gordon, Wesley O; Wilmsmeyer, Amanda R; Troya, Diego; Morris, John R

    2014-04-17

    Sarin and soman are warfare nerve agents that represent some of the most toxic compounds ever synthesized. The extreme risk in handling such molecules has, until now, precluded detailed research into the surface chemistry of agents. We have developed a surface science approach to explore the fundamental nature of hydrogen bonding forces between these agents and a hydroxylated surface. Infrared spectroscopy revealed that both agents adsorb to amorphous silica through the formation of surprisingly strong hydrogen-bonding interactions with primarily isolated silanol groups (SiOH). Comparisons with previous theoretical results reveal that this bonding occurs almost exclusively through the phosphoryl oxygen (P═O) of the agent. Temperature-programmed desorption experiments determined that the activation energy for hydrogen bond rupture and desorption of sarin and soman was 50 ± 2 and 52 ± 2 kJ/mol, respectively. Together with results from previous studies involving other phosphoryl-containing molecules, we have constructed a detailed understanding of the structure-function relationship for nerve agent hydrogen bonding at the gas-surface interface.

  20. Hydrogen reactivity of palladium nanoparticles coated with mixed monolayers of alkyl thiols and alkyl amines for sensing and catalysis applications.

    Science.gov (United States)

    Moreno, Monica; Ibañez, Francisco J; Jasinski, Jacek B; Zamborini, Francis P

    2011-03-30

    Palladium monolayer-protected clusters (MPCs) coated with octylamines (C8NH(2)), hexanethiolates (C6S), and mixed monolayers of C8NH(2) and C6S exhibit significantly different reactivities with hydrogen gas, depending on the relative amounts of the two ligands coating the Pd nanoparticle surface, as determined by UV-vis spectroscopy of Pd MPCs in solution and electronic measurements of films of Pd MPCs as a function of exposure time to hydrogen. The average estimated composition of the ~3.0 nm diameter Pd MPCs was Pd(919)(C6S)(192) or Pd(919)(C8NH(2))(177-x)(C6S)(x), where x was varied to be 0, 3, 10, 16, 32, or 81 by the synthesis of pure C8NH(2) Pd MPCs and subsequent liquid-phase place exchange with a varied amount of C6SH. When x = 0-10, the Pd MPCs react strongly with H(2), leading to aggregated particles in solution and large irreversible changes in the morphology of films accompanied by an increase in film conductivity by 2-5 orders of magnitude. Pd(919)(C6S)(192) MPCs are stable against significant aggregation in solution and do not exhibit large film morphology changes, but they are also not highly reactive to H(2), as determined by minimal changes in the optical properties of solutions and the small, irreversible changes in the conductivity of films in the presence of H(2). Finally, when x is 32 and 81, the Pd MPCs are fairly stable, exhibit minimal aggregation or morphology changes, and readily react with H(2) based on the significant, reversible changes in film conductivity in the presence of H(2). Pd MPCs with mixed monolayers have the benefit of high H(2) reactivity while maintaining the structural stability necessary for sensing and catalysis applications.

  1. 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.

  2. HR-EELS study of hydrogen bonding configuration, chemical and thermal stability of detonation nanodiamond films

    Energy Technology Data Exchange (ETDEWEB)

    Michaelson, Sh.; Akhvlediani, R. [Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000 (Israel); Petit, T.; Girard, H.A.; Arnault, J.C. [CEA, LIST, Diamond Sensors Laboratory, F-91191 Gif sur Yvette (France); Hoffman, A., E-mail: choffman@tx.technion.ac.il [Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000 (Israel)

    2014-06-01

    Nano-diamond films composed of 3–10 nm grains prepared by the detonation method and deposited onto silicon substrates by drop-casting were examined by high resolution electron energy loss spectroscopy (HR-EELS), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and secondary ion mass spectroscopy (SIMS). The impact of (i) ex-situ ambient annealing at 400 °C and (ii) ex-situ hydrogenation on hydrogen bonding and its thermal stability were examined. In order to clarify the changes in hydrogen bonding configuration detected on the different surfaces as a function of thermal annealing, in-situ hydrogenation by thermally activated atomic hydrogen was performed and examined. This study provides direct evidence that the exposure to ambient conditions and medium temperature ambient annealing have a pronounced effect on the hydrogen-carbon bonding configuration onto the nano-diamond surfaces. In-situ 1000 °C annealing results in irreversible changes of the film surface and partial nano-diamond silicidation.

  3. The π-Tetrel Bond and its Influence on Hydrogen Bonding and Proton Transfer.

    Science.gov (United States)

    Wei, Yuanxin; Li, Qingzhong; Scheiner, Steve

    2017-12-01

    The positive region that lies above the plane of F 2 TO (T=C and Si) interacts with malondialdehyde (MDA), which contains an intramolecular H-bond. The T atom of F 2 TO can lie either in the MDA molecular plane, forming a T⋅⋅⋅O tetrel bond, or F 2 TO can stack directly above MDA in a parallel arrangement. The former structure is more stable than the latter, and in either case, F 2 SiO engages in a much stronger interaction than does F 2 CO, reaching nearly 200 kJ mol -1 . The π-tetrel bond strengthens/weakens the MDA H-bond when the bond is formed to the hydroxyl/carbonyl group of MDA, and causes an accompanying inhibition/promotion of proton transfer within this H-bond; this effect is stronger for F 2 SiO. These same aspects can be tuned by substituents placed on any of the C atoms of MDA, although their effects are not fully correlated with the electron-withdrawing or electron-releasing properties of the substituent. A new type of π-π tetrel bond occurs when the π-hole on the T atom of F 2 TO approaches the middle carbon atom of MDA from above, and a similar configuration is also found between F 2 TO and benzene. Evidence for extensive C⋅⋅⋅C π-π tetrel bonding in crystal materials is presented. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Competition between Halogen, Hydrogen and Dihydrogen Bonding in Brominated Carboranes

    Czech Academy of Sciences Publication Activity Database

    Fanfrlík, Jindřich; Holub, Josef; Růžičková, Z.; Řezáč, Jan; Lane, P. D.; Wann, D. A.; Hnyk, Drahomír; Růžička, A.; Hobza, Pavel

    2016-01-01

    Roč. 17, č. 21 (2016), s. 3373-3376 ISSN 1439-4235 R&D Projects: GA ČR(CZ) GBP208/12/G016; GA ČR(CZ) GA15-05677S Institutional support: RVO:61388963 ; RVO:61388980 Keywords : bromine * carboranes * halogen bonds * sigma holes * X-ray crystal structure Subject RIV: CF - Physical ; Theoretical Chemistry ; CA - Inorganic Chemistry (UACH-T) Impact factor: 3.075, year: 2016

  5. Reaction mechanism of oxidation, hydroxylation, and epoxidation by hypofluorous acid: A theoretical study of unusual H-bond-assisted catalysis

    Czech Academy of Sciences Publication Activity Database

    Srnec, Martin; Ončák, Milan; Zahradník, Rudolf

    2008-01-01

    Roč. 112, č. 6 (2008), s. 3631-3637 ISSN 1089-5639 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z40400503 Keywords : hypofluorous acid * self-catalysis * Rozen oxidation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.871, year: 2008

  6. 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 < N-H < S-H. The observed effects are consistent with differences in atomic polarizabilities of the X-H groups. Nonetheless, we find that the X-H stretching vibrations of the model compounds indole and thiophenol report quantitatively on the electric fields they experience when complexed with aromatic hydrogen-bond acceptors. These measurements can be used to estimate the 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.

  7. Hydrogen-Bonding Interactions in T-2 Toxin Studied Using Solution and Solid-State NMR

    Directory of Open Access Journals (Sweden)

    Paul Hazendonk

    2011-10-01

    Full Text Available The structure of T-2 toxin in the solid-state is limited to X-ray crystallographic studies, which lack sufficient resolution to provide direct evidence for hydrogen-bonding interactions. Furthermore, its solution-structure, despite extensive Nuclear Magnetic Resonance (NMR studies, has provided little insight into its hydrogen-bonding behavior, thus far. Hydrogen-bonding interactions are often an important part of biological activity. In order to study these interactions, the structure of T-2 toxin was compared in both the solution- and solid-state using NMR Spectroscopy. It was determined that the solution- and solid-state structure differ dramatically, as indicated by differences in their carbon chemical shifts, these observations are further supported by solution proton spectral parameters and exchange behavior. The slow chemical exchange process and cross-relaxation dynamics with water observed between the hydroxyl hydrogen on C-3 and water supports the existence of a preferential hydrogen bonding interaction on the opposite side of the molecule from the epoxide ring, which is known to be essential for trichothecene toxicity. This result implies that these hydrogen-bonding interactions could play an important role in the biological function of T-2 toxin and posits towards a possible interaction for the trichothecene class of toxins and the ribosome. These findings clearly illustrate the importance of utilizing solid-state NMR for the study of biological compounds, and suggest that a more detailed study of this whole class of toxins, namely trichothecenes, should be pursued using this methodology.

  8. 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.

  9. 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.

  10. Supramolecular catalysis: Refocusing catalysis

    NARCIS (Netherlands)

    van Leeuwen, P.W.N.M.; Freixa, Z.; van Leeuwen, P.W.N.M.

    2008-01-01

    This chapter contains sections titled: * Introduction: A Brief Personal History * Secondary Phosphines or Phosphites as Supramolecular Ligands * Host-Guest Catalysis * Ionic Interactions as a Means to Form Heterobidentate Assembly Ligands * Ditopic Ligands for the Construction of Bidentate Phosphine

  11. Cycloaddition Reaction of Hydrogen-Bonded Zn(II)

    Indian Academy of Sciences (India)

    2.2 Synthesis of Complexes. 2.2a [{Zn(H2O)3(bpe)2}2(bpe)](NO3)4·3bpe·14H2O. (1): Single crystals of 1 were synthesized based on the reported procedure with a slight modification.12. Zn(NO3)26H2O (14mg, .... ity of coumarin in solid state as shown in Figure 2. Here, θ1 represents rotational angle of one double bond.

  12. 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...

  13. Spectroscopic studies of hydrogen-bond structures and dynamics of partially methylated p-tert-butylcalix[6]arenes

    NARCIS (Netherlands)

    Janssen, R.G.; Janssen, Rob G.; Verboom, Willem; Lutz, Bert T.G.; van der Maas, John H.; Maczka, Myrek; van Duynhoven, John P.M.; van Duynhoven, J.P.M.; Reinhoudt, David

    1996-01-01

    Hydrogen-bond structures of partially methylated p-tert-butylcalix[6]arenes were investigated both in solution and the solid state by Fourier transform infrared spectroscopy (FTIR). The hydrogen bonds in these macrocycles are preferentially of the three-centred and cooperative types. The dynamic

  14. Single Molecule Force Spectroscopy of self complementary hydrogen-bonded supramolecular systems: dimers, polymers and solvent effects

    NARCIS (Netherlands)

    Embrechts, A.

    2011-01-01

    The work described in this Thesis aimed at a better understanding of the structure-property relationships of supramolecular assemblies with a specific focus on hydrogen-bond dimers and polymers. The hydrogen-bond strength of (supra)molecular complexes in different solvents is usually determined by

  15. A Unified Theory for the Blue- and Red-Shifting Phenomena in Hydrogen and Halogen Bonds.

    Science.gov (United States)

    Wang, Changwei; Danovich, David; Shaik, Sason; Mo, Yirong

    2017-04-11

    Typical hydrogen and halogen bonds exhibit red-shifts of their vibrational frequencies upon the formation of hydrogen and halogen bonding complexes (denoted as D···Y-A, Y = H and X). The finding of blue-shifts in certain complexes is of significant interest, which has led to numerous studies of the origins of the phenomenon. Because charge transfer mixing (i.e., hyperconjugation in bonding systems) has been regarded as one of the key forces, it would be illuminating to compare the structures and vibrational frequencies in bonding complexes with the charge transfer effect "turned on" and "turned off". Turning off the charge transfer mixing can be achieved by employing the block-localized wave function (BLW) method, which is an ab initio valence bond (VB) method. Further, with the BLW method, the overall stability gained in the formation of a complex can be analyzed in terms of a few physically meaningful terms. Thus, the BLW method provides a unified and physically lucid way to explore the nature of red- and blue-shifting phenomena in both hydrogen and halogen bonding complexes. In this study, a direct correlation between the total stability and the variation of the Y-A bond length is established based on our BLW computations, and the consistent roles of all energy components are clarified. The n(D) → σ*(Y-A) electron transfer stretches the Y-A bond, while the polarization due to the approach of interacting moieties reduces the HOMO-LUMO gap and results in a stronger orbital mixing within the YA monomer. As a consequence, both the charge transfer and polarization stabilize bonding systems with the Y-A bond stretched and red-shift the vibrational frequency of the Y-A bond. Notably, the energy of the frozen wave function is the only energy component which prefers the shrinking of the Y-A bond and thus is responsible for the associated blue-shifting. The total variations of the Y-A bond length and the corresponding stretching vibrational frequency are thus

  16. Matrix isolation infrared spectra of O-H···π Hydrogen bonded ...

    Indian Academy of Sciences (India)

    Matrix isolation infrared spectra of O-H···π Hydrogen bonded complexes of Acetic acid and Trifluoroacetic acid with Benzene. PUJARINI BANERJEE, INDRANI BHATTACHARYA and TAPAS CHAKRABORTY. ∗. Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata 700 032, India.

  17. Unusual intramolecular CHO hydrogen bonding interaction between a sterically bulky amide and uranyl oxygen.

    Science.gov (United States)

    Kannan, Shanmugaperumal; Kumar, Mukesh; Sadhu, Biswajit; Jaccob, Madhavan; Sundararajan, Mahesh

    2017-12-12

    The selective separation of toxic heavy metals such as uranyl can be accomplished using ligands with stereognostic hydrogen bonding interactions to the uranyl oxo group, as proposed by Raymond and co-workers (T. S. Franczyk, K. R. Czerwinski and K. N. Raymond, J. Am. Chem. Soc., 1992, 114, 8138-8146). Recently, several ligands possessing this weak interaction have been proposed involving the hydrogen bonding of NH and OH based moieties with uranyl oxygen. We herein report the structurally and spectroscopically characterized CHO hydrogen bonding using a sterically bulky amide based ligand. In conjunction with experiments, electronic structure calculations are carried out to understand the structure, binding and the strength of the CHO hydrogen bonding interactions. This weak interaction is mainly due to the steric effect caused by a bulky substituent around the donor group which has direct relevance in designing novel ligands in nuclear waste management processes. Although the kinetics are very slow, the ligand is also highly selective to uranyl in the presence of other interfering ions such as lanthanides.

  18. Engineering Hydrogen Bonding Interaction and Charge Separation in Bio-Polymers for Green Lubrication.

    Science.gov (United States)

    Mu, Liwen; Shi, Yijun; Hua, Jing; Zhuang, Wei; Zhu, Jiahua

    2017-06-08

    Synthetic additives are widely used in lubricants nowadays to upgrade lubrication properties. The potential of integrating sustainable components in modern lubricants has rarely been studied yet. In this work, two sustainable resources lignin and gelatin have been synergistically incorporated into ethylene glycol (EG), and their tribological properties were systematically investigated. The abundant hydrogen bonding sites in lignin and gelatin as well as their interchain interaction via hydrogen bonding play the dominating roles in tuning the physicochemical properties of the mixture and improving lubricating properties. Moreover, the synergistic combination of lignin and gelatin induces charge separation of gelatin that enables its preferable adsorption on the friction surface through electrostatic force and forms a robust lubrication layer. This layer will be strengthened by lignin through the interpolymer chain hydrogen bonding. At an optimized lignin:gelatin mass ratio of 1:1 and 19 wt % loading of each in EG, the friction coefficient can be greatly stabilized and the wear loss was reduced by 89% compared to pure EG. This work presents a unique synergistic phenomenon between gelatin and lignin, where hydrogen bonding and change separation are revealed as the key factor that bridges the individual components and improves overall lubricating properties.

  19. 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

    changes and the redshift favor the Z OH group, matching the results of NBO and AIM calculations. This reflects that the thermochemistry of adduct formation is not a good measure of the hydrogen bond strength in charged adducts, and that the ionic interactions in the E and Z adducts of protonated...

  20. Control of structural isomerism in noncovalent hydrogen-bonded assemblies using peripheral chiral information

    NARCIS (Netherlands)

    Prins, L.J.; Jolliffe, K.A.; Hulst, A.J.R.L.; Timmerman, P.; Reinhoudt, David

    2000-01-01

    The results of a systematic study of the structural isomerism in more than 30 noncovalent hydrogen-bonded assemblies are described. These dynamic assemblies, composed of three calix[4]arene dimelamines and six barbiturates/cyanurates, can be present in three isomeric forms with either D3, C3h, or Cs

  1. Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes

    DEFF Research Database (Denmark)

    Pirrotta, Alessandro; De Vico, Luca; Solomon, Gemma C.

    2017-01-01

    to inform about molecular recognition events at the single-molecule limit. For this, we consider the force-conductance characteristics of a prototypical class of hydrogen bonded bimolecular complexes sandwiched between gold electrodes. The complexes consist of derivatives of a barbituric acid and a Hamilton...

  2. Noncovalent assembly of a fifteen-component hydrogen-bonded nanostructure

    NARCIS (Netherlands)

    Jolliffe, K.A.; Timmerman, P.; Reinhoudt, David

    1999-01-01

    A total of 72 hydrogen bonds are formed in the spontaneous association of calix[4]arene tetramelamine and barbituric acid derivatives to give nanosized assemblies of the type represented in the picture. These consist of 15 components that assemble in a completely diastereoselective sense: of the

  3. Strong and weak hydrogen bonds in drug–DNA complexes: A ...

    Indian Academy of Sciences (India)

    ... 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.

  4. The nature of hydrogen bonding in R-2(2)(8) crystal motifs - a computational exploration

    Czech Academy of Sciences Publication Activity Database

    Deepa, Palanisamy; Solomon, R. V.; Vedha, S. A.; Kolandaivel, P.; Venuvanalingam, P.

    2014-01-01

    Roč. 112, č. 24 (2014), s. 3195-3205 ISSN 0026-8976 Institutional support: RVO:61388963 Keywords : NCI plot * hydrogen bonds * R-2(2)(8) motif * organic crystals * NBO * QTAIM analysis Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.720, year: 2014

  5. Hydrogen Bonding Interactions and Enthalpy Relaxation in Sugar/Protein Glasses.

    Science.gov (United States)

    Sydykov, Bulat; Oldenhof, Harriëtte; Sieme, Harald; Wolkers, Willem F

    2017-03-01

    In this study, hydrogen bonding interactions and enthalpy relaxation phenomena of sugar and sugar/protein glasses have been studied using Fourier transform infrared spectroscopy and differential scanning calorimetry. The sugar OH band in Fourier transform infrared spectra was used to derive the glass transition temperature, T g , and the wavenumber-temperature coefficient (WTC) of the OH band. A study on mixtures of sucrose and albumin revealed that the glass transition temperature and strength of hydrogen bonds increased with increasing percentages of albumin. WTC g and T g derived from sucrose/albumin glasses showed a negative linear correlation. The Lu-Weiss equation was used to fit T g data of sucrose/albumin mixtures. An inflection point was observed at a 1:1 mass ratio, which coincided with an inflection of the OH-stretching band denoting a change in hydrogen bonding interactions. Enthalpy relaxation, which is seen as an endothermic event superimposed on the glass transition in differential scanning calorimetry thermograms, increases with increasing storage temperature. Activation energies of enthalpy relaxation of sucrose and sucrose/albumin glasses were determined to be 332 and 236 kJ mol -1 , respectively. Addition of albumin to sucrose increases the T g , average strength of hydrogen bonding, heterogeneity, and the enthalpy relaxation time, making the glass more stable during storage at room temperature. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

  6. Flip-flop motion of circular hydrogen bond array in thiacalix[4]arene

    Czech Academy of Sciences Publication Activity Database

    Lang, J.; Vágnerová, K.; Czernek, Jiří; Lhoták, P.

    2006-01-01

    Roč. 18, č. 4 (2006), s. 371-381 ISSN 1061-0278 R&D Projects: GA AV ČR KJB4050311 Institutional research plan: CEZ:AV0Z40500505 Keywords : flip-flop motion * hydrogen bond * enthalpy Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.861, year: 2006

  7. 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…

  8. What Is a Hydrogen Bond? Resonance Covalency in the Supramolecular Domain

    Science.gov (United States)

    Weinhold, Frank; Klein, Roger A.

    2014-01-01

    We address the broader conceptual and pedagogical implications of recent recommendations of the International Union of Pure and Applied Chemistry (IUPAC) concerning the re-definition of hydrogen bonding, drawing upon the recommended IUPAC statistical methodology of mutually correlated experimental and theoretical descriptors to operationally…

  9. 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.

  10. 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” ...

  11. Watson-Crick hydrogen bonds. Nature and role in DNA replication

    NARCIS (Netherlands)

    Guerra, Célia Fonseca; Bickelhaupt, F. Matthias

    2006-01-01

    Genetic information is found in the DNA. This information is found to be on adenine (A), thymine (T), guanine (G), and cytosine (C) occurs in a DNA strand. The two strands of the DNA double helix are held together by the hydrogen bonds of the Watson-Crick base pairs that form selectively between A

  12. Influence of hydrogen bonding on the generation and stabilization

    Indian Academy of Sciences (India)

    Induction and stabilization of liquid crystallinity through hydrogen bonding (HB) are now well-established. Interesting observations made on the influence of HB on LC behaviour of amido diol-based poly(esteramide)s, poly(esteramide)s containing nitro groups and azobenzene mesogen-based polyacrylates will be ...

  13. Restructuring the crystalline cellulose hydrogen bond network enhances its depolymerization rate

    Science.gov (United States)

    Shishir P.S. Chundawat; Giovanni Bellesia; Nirmal Uppugundla; Leonardo da Costa Sousa; Dahai Gao; Albert M. Cheh; Umesh P. Agarwal; Christopher M. Bianchetti; George N. Phillips; Paul Langan; Venkatesh Balan; S. Gnanakaran; Bruce E. Dale

    2011-01-01

    Conversion of lignocellulose to biofuels is partly inefficient due to the deleterious impact of cellulose crystallinity on enzymatic saccharification. We demonstrate how the synergistic activity of cellulases was enhanced by altering the hydrogen bond network within crystalline cellulose fibrils. We provide a molecular-scale explanation of these phenomena through...

  14. 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.

    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)

  15. 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.

  16. Excited state hydrogen bonding fluorescent probe: Role of structure and environment

    International Nuclear Information System (INIS)

    Dey, Debarati; Sarangi, Manas Kumar; Ray, Angana; Bhattacharyya, Dhananjay; Maity, Dilip Kumar

    2016-01-01

    An environment sensitive fluorescent probe, 11-benzoyl-dibenzo[a,c]phenazine (BDBPZ), has been synthesized and characterized that acts via excited state hydrogen bonding (ESHB). On interaction with hydrogen bond donating solvents the fluorescence intensity of BDBPZ increases abruptly with a concomitant bathochromic shift. The extent of fluorescence increment and the red-shift of λ max depend on hydrogen bond donating ability of the solvent associated. ESHB restricts the free rotation of the benzoyl group and hence blocks the non-radiative deactivation pathway. BDBPZ forms an exciplex with organic amine in nonpolar medium that readily disappears on increasing the polarity of the solvent. In polar environment the fluorescence of both the free molecule and excited state hydrogen bonded species are quenched on addition of amine unlike its parent dibenzo[a,c]phenazine (DBPZ), that remains very much inaccessible towards the solvent as well as quencher molecules due to its structure. This newly synthesized derivative BDBPZ is much more interactive due to the benzoyl group that is flanked outside the skeletal aromatic rings of DBPZ, which helps to sense the environment properly and thus shows better ESHB capacity than DBPZ.

  17. Effect of intramolecular hydrogen bonding and electron donation on substituted anthrasemiquinone characteristics

    International Nuclear Information System (INIS)

    Pal, H.; Mukherjee, T.

    1994-01-01

    The acid-base and redox characteristics of the semiquinones of a number of hydroxy and amino-substituted anthraquinones have been investigated. Results are explained on the basis of electron-donating properties and intramolecular hydrogen bond forming capabilities of the substituents. (author). 4 refs., 1 tab., 1 fig

  18. Dynamics of Long-Distance Hydrogen-Bond Networks in Photosystem II.

    Science.gov (United States)

    Guerra, Federico; Siemers, Malte; Mielack, Christopher; Bondar, Ana-Nicoleta

    2018-03-28

    Photosystem II uses the energy of absorbed light to split water molecules, generating molecular oxygen, electrons and protons. The four protons generated during each reaction cycle are released to the lumen via mechanisms that are poorly understood. Given the complexity of photosystem II, which consists of multiple protein subunits and cofactor molecules and hosts numerous waters, a fundamental issue is finding transient networks of hydrogen bonds that bridge potential proton donor and acceptor groups. Here, we address this issue by performing all-atom molecular dynamics simulations of wild type and mutant photosystem II monomers, which we analyze using a new protocol designed to facilitate efficient analysis of hydrogen-bond networks. Our computations reveal that local protein/water hydrogen-bond networks can assemble transiently in photosystem II, such that the reaction center connects to the lumen. The dynamics of the hydrogen-bond networks couple to the protonation state of specific carboxylate groups, and are altered in a mutant with defective proton transfer. Simulations on photosystem II without its extrinsic PsbO subunit provide a molecular interpretation of the elusive functional role of this subunit.

  19. Energy Transfer to the Hydrogen Bond in the (H2O)2+ H2O Collision.

    Science.gov (United States)

    Shin, H K

    2017-12-08

    Trajectory procedures are used to study the collision between the vibrationally excited H 2 O and the ground-state (H 2 O) 2 with particular reference to energy transfer to the hydrogen bond through the inter- and intramolecular pathways. In nearly 98% of the trajectories, energy transfer processes occur on a subpicosecond scale (≤0.7 ps). The H 2 O transfers approximately three-quarters of its excitation energy to the OH stretches of the dimer. The first step of the intramolecular pathway in the dimer involves a near-resonant first overtone transition from the OH stretch to the bending mode. The energy transfer probability in the presence of the 1:2 resonance is 0.61 at 300 K. The bending mode then redistributes its energy to low-frequency intermolecular vibrations in a series of small excitation steps, with the pathway which results in the hydrogen-bonding modes gaining most of the available energy. The hydrogen bonding in ∼50% of the trajectories ruptures on vibrational excitation, leaving one quantum in the bend of the monomer fragment. In a small fraction of trajectories, the duration of collision is longer than 1 ps, during which the dimer and H 2 O form a short-lived complex through a secondary hydrogen bond, which undergoes large amplitude oscillations.

  20. Photoswitchable Intramolecular Hydrogen Bonds in 5-Phenylazopyrimidines Revealed By In Situ Irradiation NMR Spectroscopy

    Czech Academy of Sciences Publication Activity Database

    Procházková, Eliška; Čechová, Lucie; Kind, J.; Janeba, Zlatko; Thiele, C. M.; Dračínský, Martin

    2018-01-01

    Roč. 24, č. 2 (2018), s. 492-498 ISSN 0947-6539 R&D Projects: GA ČR GA15-11223S Institutional support: RVO:61388963 Keywords : azopyrimidines * heterocycles * hydrogen bonds * NMR spectroscopy * UV/Vis in situ irradiation Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 5.317, year: 2016

  1. On prediction of OH stretching frequencies in intramolecularly hydrogen bonded systems

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Spanget-Larsen, Jens

    2012-01-01

    OH stretching frequencies are investigated for a series of non-tautomerizing systems with intramolecular hydrogen bonds. Effective OH stretching wavenumbers are predicted by the application of empirical correlation procedures based on the results of B3LYP/6-31G(d) theoretical calculations in the ...

  2. A theoretical perspective of the nature of hydrogen-bond types - the atoms in molecules approach

    Czech Academy of Sciences Publication Activity Database

    Pandiyan, B. V.; Kolandaivel, P.; Deepa, Palanisamy

    2014-01-01

    Roč. 112, č. 12 (2014), s. 1609-1623 ISSN 0026-8976 Institutional support: RVO:61388963 Keywords : hydrogen bond * proton affinity * deprotanation enthalpy * atoms in molecules * chemical shift Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.720, year: 2014

  3. 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.

    2015-01-01

    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. PMID:25791197

  4. Quantum variational transition state theory for hydrogen tunneling in enzyme catalysis.

    Science.gov (United States)

    Pollak, Eli

    2012-11-01

    Experiments in recent years have shown that there is a large kinetic isotope effect in the rate of transfer of hydrogen or deuterium in enzymatic reactions of soybean lipoxygenase-1. The kinetic isotope effect (KIE) is only weakly temperature dependent but varies significantly in the presence of mutants whose functional groups are located rather far from the reaction center. In this paper we suggest that variational transition state theory as applied to dissipative systems, above the crossover temperature between deep tunneling and thermal activation, may be used as a paradigm for understanding the dynamics of these reactions. We find that the theory fits the experimental data rather well. The effects of different mutants are readily interpreted in terms of the friction they exert on the reaction center. Increasing the distal functional group increases the friction and thus lowers the kinetic isotope effect.

  5. Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

    International Nuclear Information System (INIS)

    Gasparotto, Piero; Ceriotti, Michele

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

    Science.gov (United States)

    Gasparotto, Piero; Ceriotti, Michele

    2014-11-01

    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 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.

  7. 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.

  8. Vibron hopping and bond anharmonicity in hot dense hydrogen

    Science.gov (United States)

    Feldman, J. L.; Johnson, J. Karl; Hemley, Russell J.

    2009-02-01

    The Raman-active vibron of dense hydrogen has been shown to exhibit unexpected changes as a function of pressure and temperature to above 100GPa. To understand these results we have performed supercell-based calculations using Van Kranendonk theory taking into account the renormalization of the hopping parameter by the lattice vibrations. We find that the major temperature dependence at this level of theory comes from the differences in populations of rotational states. The theory provides a fair description of the experimental results up to 70GPa. We examine in detail a number of assumptions made in the application of the Van Kranendonk model to hydrogen as a function of pressure and temperature. We also present results of hybrid path integral molecular dynamics calculations in the fluid state at a low pressure (7GPa) near the melting temperature. An amorphous-solid model of the fluid predicts that the Raman vibron frequencies change little upon melting, in agreement with experiment. The Van Kranendonk theory with fixed rotational identities of the molecules tends to predict more peaks in the Raman spectrum than are observed experimentally.

  9. Relation between volume expansion and hydrogen bond networks for CO2-alcohol mixtures at 40 °C.

    Science.gov (United States)

    Aida, Tsutomu; Aizawa, Takafumi; Kanakubo, Mitsuhiro; Nanjo, Hiroshi

    2010-11-04

    We experimentally determined the density and mole fraction of CO(2) (x(CO(2))) for CO(2)-alcohol (methanol, ethanol, propanol, butanol, isopropyl alcohol, and tert-butyl alcohol) mixtures and performed molecular dynamics (MD) simulations to study the mechanisms of volume expansion at 40 °C. The volume as calculated by vapor-liquid equilibrium (VLE) data increased with decreasing alkyl chain length, although there was no effect of branched alkyl groups. Analysis of the hydrogen bond network showed that the average number of hydrogen bonds per alcohol molecule decreased with increasing branched methyl groups. At pure alcohol condition, large size hydrogen bond networks were made. With further addition of CO(2) molecules, it became difficult to contain the large hydrogen bond networks. Furthermore, the hydrogen bond networks changed to a cyclic pentamer or tetramer, and volume expansion occurred.

  10. 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. © 2014 Wiley Periodicals, Inc.

  11. Neutron and high-pressure X-ray diffraction study of hydrogen-bonded ferroelectric rubidium hydrogen sulfate.

    Science.gov (United States)

    Binns, Jack; McIntyre, Garry J; Parsons, Simon

    2016-12-01

    The pressure- and temperature-dependent phase transitions in the ferroelectric material rubidium hydrogen sulfate (RbHSO 4 ) are investigated by a combination of neutron Laue diffraction and high-pressure X-ray diffraction. The observation of disordered O-atom positions in the hydrogen sulfate anions is in agreement with previous spectroscopic measurements in the literature. Contrary to the mechanism observed in other hydrogen-bonded ferroelectric materials, H-atom positions are well defined and ordered in the paraelectric phase. Under applied pressure RbHSO 4 undergoes a ferroelectric transition before transforming to a third, high-pressure phase. The symmetry of this phase is revised to the centrosymmetric space group P2 1 /c, resulting in the suppression of ferroelectricity at high pressure.

  12. 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...... 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...

  13. Layered vanadyl (IV) nitroprusside: Magnetic interaction through a network of hydrogen bonds

    Energy Technology Data Exchange (ETDEWEB)

    Gil, D.M. [Instituto de Química Física, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Lorenzo 456, T4000CAN San Miguel de Tucumán (Argentina); Osiry, H. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México (Mexico); Pomiro, F.; Varetti, E.L. [CEQUINOR (CONICET-UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 47 and 115, 1900, La Plata (Argentina); Carbonio, R.E. [INFIQC – CONICET, Departamento de Físico Química, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre esq, Medina Allende, Ciudad Universitaria, X5000HUA Córdoba (Argentina); Alejandro, R.R. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México (Mexico); Ben Altabef, A. [INQUINOA-UNT-CONICET, Instituto de Química Física, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Lorenzo 456, T4000CAN San Miguel de Tucumán (Argentina); and others

    2016-07-15

    The hydrogen bond and π-π stacking are two non-covalent interactions able to support cooperative magnetic ordering between paramagnetic centers. This contribution reports the crystal structure and related magnetic properties for VO[Fe(CN){sub 5}NO]·2H{sub 2}O, which has a layered structure. This solid crystallizes with an orthorhombic unit cell, in the Pna2{sub 1} space group, with cell parameters a=14.1804(2), b=10.4935(1), c=7.1722(8) Å and four molecules per unit cell (Z=4). Its crystal structure was solved and refined from powder X-ray diffraction data. Neighboring layers remain linked through a network of hydrogen bonds involving a water molecule coordinated to the axial position for the V atom and the unbridged axial NO and CN ligands. An uncoordinated water molecule is found forming a triple bridge between these last two ligands and the coordinated water molecule. The magnetic measurements, recorded down to 2 K, shows a ferromagnetic interaction between V atoms located at neighboring layers, with a Curie-Weiss constant of 3.14 K. Such ferromagnetic behavior was interpreted as resulting from a superexchange interaction through the network of strong OH····O{sub H2O}, OH····N{sub CN}, and OH····O{sub NO} hydrogen bonds that connects neighboring layers. The interaction within the layer must be of antiferromagnetic nature and it was detected close to 2 K. - Graphical abstract: Coordination environment for the metals in vanadyl (II) nitroprusside dihydrate. Display Omitted - Highlights: • Crystal structure of vanadyl nitroprusside dehydrate. • Network of hydrogen bonds. • Magnetic interactions through a network of hydrogen bonds. • Layered transition metal nitroprussides.

  14. Contributions to reversed-phase column selectivity: III. Column hydrogen-bond basicity.

    Science.gov (United States)

    Carr, P W; Dolan, J W; Dorsey, J G; Snyder, L R; Kirkland, J J

    2015-05-22

    Column selectivity in reversed-phase chromatography (RPC) can be described in terms of the hydrophobic-subtraction model, which recognizes five solute-column interactions that together determine solute retention and column selectivity: hydrophobic, steric, hydrogen bonding of an acceptor solute (i.e., a hydrogen-bond base) by a stationary-phase donor group (i.e., a silanol), hydrogen bonding of a donor solute (e.g., a carboxylic acid) by a stationary-phase acceptor group, and ionic. Of these five interactions, hydrogen bonding between donor solutes (acids) and stationary-phase acceptor groups is the least well understood; the present study aims at resolving this uncertainty, so far as possible. Previous work suggests that there are three distinct stationary-phase sites for hydrogen-bond interaction with carboxylic acids, which we will refer to as column basicity I, II, and III. All RPC columns exhibit a selective retention of carboxylic acids (column basicity I) in varying degree. This now appears to involve an interaction of the solute with a pair of vicinal silanols in the stationary phase. For some type-A columns, an additional basic site (column basicity II) is similar to that for column basicity I in primarily affecting the retention of carboxylic acids. The latter site appears to be associated with metal contamination of the silica. Finally, for embedded-polar-group (EPG) columns, the polar group can serve as a proton acceptor (column basicity III) for acids, phenols, and other donor solutes. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Hydrogen bonds and local symmetry in the crystal structure of gibbsite.

    Science.gov (United States)

    Vyalikh, Anastasia; Zesewitz, Konrad; Scheler, Ulrich

    2010-11-01

    First-principles quantum mechanical calculations of NMR chemical shifts and quadrupolar parameters have been carried out to assign the (27)Al MAS NMR resonances in gibbsite. The (27)Al NMR spectrum shows two signals for octahedral aluminum revealing two aluminum sites coordinated by six hydroxyl groups each, although the crystallographic positions of the two Al sites show little difference. The presence of two distinguished (27)Al NMR resonances characterized by rather similar chemical shifts but quadrupolar coupling constants differing by roughly a factor of two is explained by different character of the hydrogen bonds, in which the hydroxyls forming the corresponding octahedron around each aluminum site, are involved. The Al-I site characterized by a C(Q) = 4.6 MHz is surrounded by OH-groups participating in four intralayer and two interlayer hydrogen bonds, while the Al-II site with the smaller quadrupolar constant (2.2 MHz) is coordinated by hydroxides, of which two point toward the intralayer cavities and four OH-bonds are aligned toward the interlayer gallery. In high-resolution solid-state (1)H CRAMPS (combination of rotation and multiple-pulse spectroscopy) four signals with an intensity ratio of 1:2:2:1 are resolved which allow to distinguish six nonequivalent hydrogen sites reported in the gibbsite crystal structure and to ascribe them to two types of structural OH groups associated with intralayer and interlayer hydrogen bonds. This study can be applied to characterize the gibbsite-like layer-intergallery interactions associated with hydrogen bonding in the more complex systems, such as synthetic aluminum layered double hydroxides. 2010 John Wiley & Sons, Ltd.

  16. 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.

  17. Simulations of chemical catalysis

    Science.gov (United States)

    Smith, Gregory K.

    This dissertation contains simulations of chemical catalysis in both biological and heterogeneous contexts. A mixture of classical, quantum, and hybrid techniques are applied to explore the energy profiles and compare possible chemical mechanisms both within the context of human and bacterial enzymes, as well as exploring surface reactions on a metal catalyst. A brief summary of each project follows. Project 1 - Bacterial Enzyme SpvC The newly discovered SpvC effector protein from Salmonella typhimurium interferes with the host immune response by dephosphorylating mitogen-activated protein kinases (MAPKs) with a beta-elimination mechanism. The dynamics of the enzyme substrate complex of the SpvC effector is investigated with a 3.2 ns molecular dynamics simulation, which reveals that the phosphorylated peptide substrate is tightly held in the active site by a hydrogen bond network and the lysine general base is positioned for the abstraction of the alpha hydrogen. The catalysis is further modeled with density functional theory (DFT) in a truncated active-site model at the B3LYP/6-31 G(d,p) level of theory. The truncated model suggested the reaction proceeds via a single transition state. After including the enzyme environment in ab initio QM/MM studies, it was found to proceed via an E1cB-like pathway, in which the carbanion intermediate is stabilized by an enzyme oxyanion hole provided by Lys104 and Tyr158 of SpvC. Project 2 - Human Enzyme CDK2 Phosphorylation reactions catalyzed by kinases and phosphatases play an indispensable role in cellular signaling, and their malfunctioning is implicated in many diseases. Ab initio quantum mechanical/molecular mechanical studies are reported for the phosphoryl transfer reaction catalyzed by a cyclin-dependent kinase, CDK2. Our results suggest that an active-site Asp residue, rather than ATP as previously proposed, serves as the general base to activate the Ser nucleophile. The corresponding transition state features a

  18. Intramolecular hydrogen bonding in 5-nitrosalicylaldehyde: IR spectrum and quantum chemical calculations

    Science.gov (United States)

    Moosavi-Tekyeh, Zainab; Taherian, Fatemeh; Tayyari, Sayyed Faramarz

    2016-05-01

    The structural parameters, and vibrational frequencies of 5-nitrosalicylaldehyde (5NSA) were studied by the FT-IR and Raman spectra and the quantum chemical calculations carried out at the B3LYP/6-311++G(d,p) level of theory in order to investigate the intramolecular hydrogen bonding (IHB) present in its structure. The strength and nature of IHB in the optimized structure of 5NSA were studied in detail by means of the atoms in molecules (AIM) and the natural bond orbital (NBO) approaches. The results obtained were then compared with the corresponding data for its parent molecule, salicylaldehyde (SA). Comparisons made between the geometrical structures for 5NSA and SA, their OH/OD stretching and out-of-plane bending modes, their enthalpies for the hydrogen bond, and their AIM parameters demonstrated a stronger H-bonding in 5NSA compared with that in SA. The calculated binding enthalpy (ΔHbind) for 5NSA was -10.92 kcal mol-1. The observed νOH and γOH appeared at about 3120 cm-1 and 786 cm-1 respectively. The stretching frequency shift of H-bond formation was 426 cm-1 which is consistent with ΔHbind and the strength of H-bond in 5NSA. The delocalization energies and electron delocalization indices derived by the NBO and AIM approaches indicate that the resonance effects were responsible for the stronger IHB in 5NSA than in SA.

  19. 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.

  20. Hydrogen-deuterium exchange in spiro cyclic ketones: a search for intramolecular catalysis

    International Nuclear Information System (INIS)

    Hsu, R.C.L.

    1979-01-01

    The synthesis and characterization of 1'-hydroxy-3',3'-dimethylspiro[cyclohexane-1,2'-indan]-4-one (17b), 1'-amino-3',3'-dimethylspiro[cyclohexane-1,2'-indan]4-one (6a), 1'-N,N-dimethylamino-3',3'-dimethylspiro[cyclohexane-1,2'-indan]-4-one (6c) and 1'-[N-ethyl-α(d 2 )-amino]-3'-3'-dimethylspiro[cyclohexane-1,2'-indan]-4-one (6b) are described. The hydrogen-deuterium exchange reactions of aminoketones 6b and 6c with CH 3 OD are too fast to be followed by the mass spectrometric methodology. However, the H/D exchange between hydroxyketone 17b and CH 3 OD is shown to be intramolecularly catalyzed under both basic and neutral conditions. The rate constant for the exchange of C(3)-axial-H in 17b is 35 times greater than the rate constant for the exchange of an axial α-H in 4-t-butylcyclohexanone

  1. 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.

  2. 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.

  3. Effect of hydrogen bonding on the infrared absorption intensity of OH stretch vibrations

    Science.gov (United States)

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

    2017-05-01

    We consider how the infrared intensity of a hydrogen-bonded OH stretch varies from weak to strong H-bonds using a theoretical model. We obtain trends for the fundamental and overtone transition intensities as a function of the donor-acceptor distance, a common measure of H-bond strength. Building upon our earlier work using a two-diabatic state model, we introduce a Mecke function-based dipole moment for the H-bond and calculate transition moments using one-dimensional vibrational eigenstates along the H-atom transfer coordinate. The fundamental intensity is found to be over 20-fold enhanced for strong H-bonds, where non-Condon effects are significant. We analyse isotope effects, including the secondary geometric isotope effect. The first overtone intensity varies non-monotonically with H-bond strength; suppression occurs for weak bonds but strong enhancements are possible for strong H-bonds. We also study how these trends are affected by Mecke parameter variations. For a few specific dimers, we compare our results with earlier works.

  4. Comparison of hydrogen bonding in 1-octanol and 2-octanol as probed by spectroscopic techniques.

    Science.gov (United States)

    Palombo, Francesca; Sassi, Paola; Paolantoni, Marco; Morresi, Assunta; Cataliotti, Rosario Sergio

    2006-09-14

    Liquid 1-octanol and 2-octanol have been investigated by infrared (IR), Raman, and Brillouin experiments in the 10-90 degrees C temperature range. Self-association properties of the neat liquids are described in terms of a three-state model in which OH oscillators differently implicated in the formation of H-bonds are considered. The results are in quantitative agreement with recent computational studies for 1-octanol. The H-bond probability is obtained by Raman data, and a stochastic model of H-bonded chains gives a consistent picture of the self-association characteristics. Average values of hydrogen bond enthalpy and entropy are evaluated. The H-bond formation enthalpy is ca. -22 kJ/mol and is slightly dependent on the structural isomerism. The different degree of self-association for the two octanols is attributed to entropic factors. The more shielded 2-isomer forms larger fractions of smaller, less cooperative, and more ordered clusters, likely corresponding to cyclic structures. Signatures of a different cluster organization are also evidenced by comparing the H-bond energy dispersion (HBED) of OH stretching IR bands. A limiting cooperative H-bond enthalpy value of 27 kJ/mol is found. It is also proposed that the different H-bonding capabilities may modulate the extent of interaggregate hydrocarbon interactions, which is important in explaining the differences in molar volume, compressibility, and vaporization enthalpy for the two isomers.

  5. 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.

  6. 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

  7. 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.

  8. Microwave spectroscopy of 2-(trifluoromethyl)pyridine⋯water complex: Molecular structure and hydrogen bond

    Science.gov (United States)

    Li, Xiaolong; Zheng, Yang; Gou, Qian; Feng, Gang; Xia, Zhining

    2018-01-01

    In order to explore the -CF3 substitution effect on the complexation of pyridine, we investigated the 2-(trifluoromethyl)pyridine⋯water complex by using pulsed jet Fourier transform microwave spectroscopy complemented with quantum chemical calculations. Experimental assignment and ab initio calculations confirmed that the observed complex is stabilized through N⋯H-O and O⋯H-C hydrogen bonds forming a five-membered ring structure. The bonding distance in N⋯H-O is determined to be 2.027(2) Å, whilst that in O⋯H-C interaction is 2.728(2) Å. The quantum theory of atoms in molecules analysis indicates that the interaction energy of N⋯H-O hydrogen bond is ˜22 kJ mol-1 and that for O⋯H-C hydrogen bond is ˜5 kJ mol-1. The water molecule lies almost in the plane of the aromatic ring in the complex. The -CF3 substitution to pyridine quenches the tunneling splitting path of the internal motion of water molecule.

  9. Probing for and Quantifying Agonist Hydrogen Bonds in α6β2 Nicotinic Acetylcholine Receptors.

    Science.gov (United States)

    Post, Michael R; Lester, Henry A; Dougherty, Dennis A

    2017-04-04

    Designing subtype-selective agonists for neuronal nicotinic acetylcholine receptors is a challenging and significant goal aided by intricate knowledge of each subtype's binding patterns. We previously reported that in α6β2 receptors, acetylcholine makes a functional cation-π interaction with Trp149, but nicotine and TC299423 do not, suggesting a distinctive binding site. This work explores hydrogen binding at the backbone carbonyl associated with α6β2 Trp149. Substituting residue i + 1, Thr150, with its α-hydroxy analogue (Tah) attenuates the carbonyl's hydrogen bond accepting ability. At α6(T150Tah)β2, nicotine shows a 24-fold loss of function, TC299423 shows a modest loss, and acetylcholine shows no effect. Nicotine was further analyzed via a double-mutant cycle analysis utilizing N'-methylnicotinium, which indicated a hydrogen bond in α6β2 with a ΔΔG of 2.6 kcal/mol. Thus, even though nicotine does not make the conserved cation-π interaction with Trp149, it still makes a functional hydrogen bond to its associated backbone carbonyl.

  10. The hydrogen-bonding ability of the amino acid glutamine revealed by neutron diffraction experiments.

    Science.gov (United States)

    Rhys, N H; Soper, A K; Dougan, L

    2012-11-15

    Hydrogen bonding between glutamine residues has been identified as playing an important role in the intermolecular association and aggregation of proteins. To establish the molecular mechanisms of glutamine interactions, neutron diffraction coupled with hydrogen/deuterium isotopic substitution in combination with computational modeling has been used to investigate the structure and hydration of glutamine in aqueous solution. The final structures obtained are consistent with the experimental data and provide insight into the hydrogen-bonding ability of glutamine. We find that the backbone of glutamine is able to coordinate more water molecules than the side chain, suggesting that charged groups on the glutamine molecule are more successful in attracting water than the dipole in the side chain. In both the backbone and the side chain, we find that the carbonyl groups interact more readily with water molecules than the amine groups. We find that glutamine-glutamine interactions are present, despite their low concentration in this dilute solution. This is evidenced through the occurrence of dimers of glutamine molecules in the solution, demonstrating the effective propensity of this molecule to associate through backbone-backbone, backbone-side chain, and side chain-side chain hydrogen bond interactions. The formation of dimers of glutamine molecules in such a dilute solution (30 mg/mL glutamine) may have implications in the aggregation of glutamine-rich proteins in neurological diseases where aggregation is prevalent.

  11. 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....... Overtone spectra have been recorded with intracavity laser photoacoustic laser spectroscopy and conventional long path absorption spectroscopy. Theoretically, a combination of electronic structure calculations and local mode models have been employed to guide the assignment of bands in the vibrational......,4-diaminobutane, no sign of intramolecular N-H···N hydrogen bonds were identified in the overtone spectra. However, theoretical analyzes indicate that intramolecular N-H···N hydrogen bonds are present in all three diamines if two hydrogen atoms on one of the methylene groups are substituted with triuoromethyl...

  12. Crystal structure, vibrational spectra and DFT studies of hydrogen bonded 1,2,4-triazolium hydrogenselenate

    Science.gov (United States)

    Arjunan, V.; Thirunarayanan, S.; Marchewka, M. K.; Mohan, S.

    2017-10-01

    The new hydrogen bonded molecular complex 1,2,4-triazolium hydrogenselenate (THS) is prepared by the reaction of 1H-1,2,4-triazole and selenic acid. This complex is stabilised by N-H⋯O and C-H⋯O hydrogen bonding and electrostatic attractive forces between 1H and 1,2,4-triazolium cations and hydrogen selenate anions. The XRD studies revealed that intermolecular proton transfer occur from selenic acid to 1H-1,2,4-triazole molecule, results in the formation of 1,2,4-triazolium hydrogenselenate which contains 1,2,4-triazolium cations and hydrogenselenate anions. The molecular structure of THS crystal has also been optimised by using Density Functional Theory (DFT) using B3LYP/cc-pVTZ and B3LYP/6-311++G** methods in order to find the whole characteristics of the molecular complex. The theoretical structural parameters such as bond length, bond angle and dihedral angle determined by DFT methods are well agreed with the XRD parameters. The atomic charges and thermodynamic properties are also calculated and analysed. The energies of frontier molecular orbitals HOMO, LUMO, HOMO-1, LUMO+1 and LUMO-HUMO energy gap are calculated to understand the kinetic stability and chemical reactivity of the molecular complex. The natural bond orbital analysis (NBO) has been performed in order to study the intramolecular bonding interactions and delocalisation of electrons. These intra molecular charge transfer may induce biological activities such as antimicrobials, antiinflammatory, antifungal etc. The complete vibrational assignments of THS have been performed by using FT-IR and FT-Raman spectra.

  13. Communication: A hydrogen-bonded difluorocarbene complex: Ab initio and matrix isolation study

    Science.gov (United States)

    Sosulin, Ilya S.; Shiryaeva, Ekaterina S.; Tyurin, Daniil A.; Feldman, Vladimir I.

    2017-10-01

    Structure and spectroscopic features of the CF2⋯HF complexes were studied by ab initio calculations at the CCSD(T) level and matrix isolation FTIR spectroscopy. The calculations predict three stable structures. The most energetically favorable structure corresponds to hydrogen bonding of HF to the lone pair of the C atom (the interaction energy of 3.58 kcal/mol), whereas two less stable structures are the H⋯F bonded complexes (the interaction energies of 0.30 and 0.24 kcal/mol). The former species was unambiguously characterized by the absorptions in the FTIR spectra observed after X-ray irradiation of fluoroform in a xenon matrix at 5 K. The corresponding features appear at 3471 (H-F stretching), 1270 (C-F symmetric stretching, shoulder), 1175 (antisymmetric C-F stretching), and 630 (libration) cm-1, in agreement with the computational predictions. To our knowledge, it is the first hydrogen-bonded complex of dihalocarbene. Possible weaker manifestations of the H⋯F bonded complexes were also found in the C-F stretching region; however, their assignment is tentative. The H⋯C bonded complex is protected from reaction yielding a fluoroform molecule by a remarkably high energy barrier (23.85 kcal/mol), so it may be involved in various chemical reactions.

  14. The nature of hydrogen-bonding interactions in nonsteroidal anti-inflammatory drugs revealed by polarized IR spectroscopy

    Science.gov (United States)

    Hachuła, Barbara

    2018-01-01

    The influence of hydrogen-bonding interactions in the solid phase on the IR spectroscopic pattern of the νOsbnd H band of nonsteroidal anti-inflammatory drugs (NSAIDs) was studied experimentally by IR spectroscopy with the use of polarized light at two temperatures (293 K and 77 K) and in isotopic dilution. The neat and deuterated crystals of (S)-naproxen ((S)-NPX), (R)-flurbiprofen ((R)-FBP), (RS)-flurbiprofen ((RS)-FBP) and (RS)-ketoprofen ((RS)-KTP) were obtained by melt crystallization between the two squeezed CaF2 plates. The vibrational spectra of selected α-aryl propionic acid derivatives (2APAs) reflected the characteristics of their hydrogen-bond networks, i.e., 2APAs were characterized by the chain ((S)-NPX, (R)-FBP) and by dimeric ((RS)-FBP, (RS)-KTP) arrangement of hydrogen bonds in the crystal lattice. Spectroscopic results showed that the interchain (through-space) exciton coupling, between two laterally-spaced hydrogen bonds, dominates in the crystals of four NSAIDs. The same exciton coupled hydrogen bonds were also responsible for the H/D isotopic recognition mechanism in the crystalline spectra of deuterated 2APAs. The presented spectral results may help to predict the hydrogen bond motifs in the crystalline NSAIDs, which structures are not yet known, based on their IR spectra of hydrogen bond in the crystals.

  15. The Muon F-µ+-F Hydrogen Bond-like Complex.

    Science.gov (United States)

    Blinc, Robert; Lahajnar, Gojmir; Potočnik, Anton

    2011-09-01

    Muon spin rotation (µSR) and relaxation has been used to study the local magnetic structure of K3Fe5F15. A collinear F-µ+-F "hydrogen bond-like" symmetric double minimum type complex with a F...F distance of 2.8 Å and a separation between the two minima of 0.8 Å has been found in the paramagnetic phase. The apparent central position of the muon seems to be the result of fast muon tunneling between two equivalent minima in the F-µ+-F bond.

  16. Thermodynamic functions of hydrogen bonding of amines in methanol derived from solution calorimetry data and headspace analysis

    International Nuclear Information System (INIS)

    Zaitseva, Ksenia V.; Varfolomeev, Mikhail A.; Solomonov, Boris N.

    2012-01-01

    Highlights: ► Solution enthalpies and activity coefficients of amines in methanol were measured. ► Thermodynamic functions of H-bonding of amines with methanol were determined. ► Specific interaction entropy of amines in methanol can be about zero or positive. ► Cooperativity of H-bonds in methanol media is smaller than in water solutions. ► A new view on analysis of specific interaction of solute with methanol is presented. - Abstract: Reactivity and equilibrium properties of organic molecules in self-associated liquids greatly depend on the hydrogen bonding with solvent. This work contains comprehensive thermodynamic analysis of hydrogen bonding of aliphatic and aromatic amines in self-associated solvent methanol. Enthalpies of solution at infinite dilution and limiting activity coefficients for the studied systems were measured experimentally. Enthalpies and Gibbs energies of hydrogen bonding of amines with neat methanol were determined. These values were found to be decreased compared with hydrogen bond energy in equimolar complexes “methanol–amine” determined in inert solvent or base media. A linear dependence between enthalpies and Gibbs energies of hydrogen bonding of amines with neat methanol was observed. It was firstly revealed that the entropy of specific interactions of amines with neat methanol can be about zero or positive. Disruption of solvent–solvent hydrogen bonds can be regarded as the most important step during dissolution of amine in methanol. It was found that the cooperative effect influences on the Gibbs energies of hydrogen bonding of amines in methanol, but in a lesser extent than in aqueous solutions. The new results show that the hydrogen bonding process in the self-associated solvents differs significantly from equimolar complexation in aprotic media.

  17. μSR in two-dimensional hydrogen bonding system squaric acid

    International Nuclear Information System (INIS)

    Nishiyama, Kusuo; Nishiyama, Sumie W.; Shimomura, Koichiro; Kubo, Kenya; Maruta, Goro; Higemoto, Wataru

    2006-01-01

    Squaric acid, a famous two-dimensional hydrogen-bonded system was studied by μSR. From the temperature dependence of the muon spin relaxation rate as well as from the crystal axis dependences, different muon sites at low temperature (10K) and at high temperature (300K) were found. The nuclear dipole field was calculated for possible muon sites. At low temperature the muon attaches C?O...HO acceptor oxygen, while at 300K the muon occupies the regular hydrogen sites

  18. 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...

  19. Role of the Distal Hydrogen-Bonding Network in Regulating Oxygen Affinity in the Truncated Hemoglobin III from Campylobacter jejuni

    OpenAIRE

    Mañez, Pau Arroyo; Lu, Changyuan; Boechi, Leonardo; Martí, Marcelo A.; Shepherd, Mark; Wilson, Jayne Louise; Poole, Robert K.; Luque, F. Javier; Yeh, Syun-Ru; Estrin, Darío A.

    2011-01-01

    Oxygen affinity in heme-containing proteins is determined by a number of factors, such as the nature and conformation of the distal residues that stabilize the heme bound-oxygen via hydrogen-bonding interactions. The truncated hemoglobin III from Campylobacter jejuni (Ctb) contains three potential hydrogen-bond donors in the distal site: TyrB10, TrpG8, and HisE7. Previous studies suggested that Ctb exhibits an extremely slow oxygen dissociation rate due to an interlaced hydrogen-bonding netwo...

  20. Electronic dipole moment and tunneling state of hydrogen atom in hydrogen-bond materials revealed by neutron and X-ray structure analyses

    International Nuclear Information System (INIS)

    Kiyanagi, Ryoji; Noda, Yukio; Mochida, Tomoyuki; Sugawara, Tadashi

    2007-01-01

    The isolated hydrogen-bonded materials, 5-methyl-9-hydroxyphenalenone (MeHPLN) and 5-bromo-9-hydroxyphenalenone (Br-HPLN), were studied by means of X-ray and neutron diffraction methods. It was found that the position of the nucleus of the hydrogen atom in the hydrogen-bond region does not agree with the center of mass of the electron cloud of the hydrogen atom. This leads to a local electronic dipole moment in the hydrogen-bond region. Using the experimentally obtained dipole moment, phase transition temperatures for MeHPLN and BrHPLN were calculated based on a tunneling model. Result shows good agreement with the ones obtained by a dielectric measurement. (author)

  1. A hydrogen-bonded electron-tunneling circuit reads the base composition of unmodified DNA

    International Nuclear Information System (INIS)

    He Jin; Lin Lisha; Liu Hao; Zhang Peiming; Lindsay, S M; Lee, Myeong; Sankey, O F

    2009-01-01

    Using a tunnel junction in which one electrode is guanidinium-functionalized (to trap DNA via hydrogen bonding to the backbone phosphates) and a second electrode which is functionalized with a base (to capture its complementary target on the DNA), current versus distance curves are obtained which yield an accurate measure of the base composition of DNA oligomers. With this long tunneling path, resolution is limited to sequence blocks of about twenty bases or larger, because of the need to form a large-area tunnel junction. A shorter hydrogen-bonded path across bases will be required for DNA sequencing. Nonetheless, these measurements point the way to a new type of nanoscale sensor.

  2. 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.

  3. 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, eve...... 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....... though pure-component liquid densities and vapour pressures are predicted equally accurately for the associating compound. As was the case in the study of pure components, there exists some confusion in the literature about the correct interpretation and comparison of experimental data and theoretical...

  4. Studies of Hydrogen Bonding Between N, N-Dimethylacetamide and Primary Alcohols

    Directory of Open Access Journals (Sweden)

    M. S. Manjunath

    2009-01-01

    Full Text Available Hydrogen bonding between N, N-dimethylacetamide (DMA and alcohols has been studied in carbon tetrachloride solution by an X-band Microwave bench at 936GHz. The dielectric relaxation time (τ of the binary system are obtained by both Higasi's method and Gopalakrishna method. The most likely association complex between alcohol and DMA is 1:1 stoichiometric complex through the hydroxyl group of the alcohol and the carbonyl group of amide. The results show that the interaction between alcohols and amides is 1:1 complex through the free hydroxyl group of the alcohol and the carbonyl group of amide and the alkyl chain-length of both the alcohols and amide plays an important role in the determination of the strength of hydrogen bond (O-H: C=O formed and suggests that the proton donating ability of alcohols is in the order: 1-propanol < 1-butanol < 1-pentanol and the accepting ability of DMA.

  5. 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...... 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...

  6. Temperature Dependence in the Terahertz Spectrum of Nicotinamide: Anharmonicity and Hydrogen-Bonded Network.

    Science.gov (United States)

    Takahashi, Masae; Okamura, Nubuyuki; Fan, Xinyi; Shirakawa, Hitoshi; Minamide, Hiroaki

    2017-04-06

    We have investigated the terahertz-spectral property of nicotinamide focusing on the temperature dependence in the range of 14-300 K. We observed that almost all peaks in the terahertz spectrum of the nicotinamide crystal showed a remarkable shift with temperature, whereas the lowest-frequency peak at 34.8 cm -1 showed a negligible shift with temperature. By analyzing the terahertz spectrum with the dispersion-corrected density functional theory calculations, we found that the difference in the temperature dependence of the peak shift is well understood in terms of the presence/absence of stretching vibration of the intermolecular hydrogen bond in the mode and the change of cell parameters. The anharmonicity in the dissociation potential energy of very weak intermolecular hydrogen bonding causes the remarkable peak shift with temperature in the terahertz spectrum of nicotinamide. This finding suggests that the assignment and identification of peaks in the terahertz spectrum are systematically enabled by temperature-dependent measurements.

  7. 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.

  8. 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.

  9. Visible light catalysis-assisted assembly of Ni(h)-QD hollow nanospheres in situ via hydrogen bubbles.

    Science.gov (United States)

    Li, Zhi-Jun; Fan, Xiang-Bing; Li, Xu-Bing; Li, Jia-Xin; Ye, Chen; Wang, Jiu-Ju; Yu, Shan; Li, Cheng-Bo; Gao, Yu-Ji; Meng, Qing-Yuan; Tung, Chen-Ho; Wu, Li-Zhu

    2014-06-11

    Hollow spheres are one of the most promising micro-/nanostructures because of their unique performance in diverse applications. Templates, surfactants, and structure-directing agents are often used to control the sizes and morphologies of hollow spheres. In this Article, we describe a simple method based on visible light catalysis for preparing hollow nanospheres from CdE (E = Te, Se, and S) quantum dots (QDs) and nickel (Ni(2+)) salts in aqueous media. In contrast to the well-developed traditional approaches, the hollow nanospheres of QDs are formed in situ by the photogeneration of hydrogen (H2) gas bubbles at room temperature. Each component, that is, the QDs, metal ions, ascorbic acid (H2A), and visible light, is essential for the formation of hollow nanospheres. The quality of the hollow nanospheres depends on the pH, metal ions, and wavelength and intensity of visible light used. Of the various metal ions investigated, including Cu(+), Cu(2+), Fe(2+), Fe(3+), Ni(2+), Mn(2+), RuCl5(2-), Ag(+), and PtCl4(2-), Ni(2+) ions showed the best ability to generate H2 and hollow-structured nanospheres under visible light irradiation. The average diameter and shell thickness of the nanospheres ranged from 10 to 20 nm and from 3 to 6 nm, respectively, which are values rarely reported in the literature. Studies using high-resolution transmission electron microscopy (HRTEM), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), inductively coupled plasma-mass spectroscopy (ICP-AES), and steady-state and time-resolved spectroscopy revealed the chemical nature of the hollow nanospheres. Additionally, the hollow-structured nanospheres exhibit excellent photocatalytic activity and stability for the generation of H2 with a rate constant of 21 μmol h(-1) mg(-1) and a turnover number (TON) of 137,500 or 30,250 for CdTe QDs or nickel, respectively, under visible light irradiation for 42 h.

  10. Separation of planar rotamers through intramolecular hydrogen bonding in polysubstituted 5-nitrosopyrimidines

    Czech Academy of Sciences Publication Activity Database

    Čechová, Lucie; Procházková, Eliška; Císařová, I.; Dračínský, Martin; Janeba, Zlatko

    2014-01-01

    Roč. 50, č. 94 (2014), s. 14892-14895 ISSN 1359-7345 R&D Projects: GA MV VG20102015046; GA ČR GA13-24880S Institutional support: RVO:61388963 Keywords : hydrogen bonds * 5-nitrosopyrimidines * NMR spectroscopy Subject RIV: CC - Organic Chemistry Impact factor: 6.834, year: 2014 http://pubs.rsc.org/en/content/articlepdf/2014/cc/c4cc06978a

  11. Mirror symmetry breaking in cubic phases and isotropic liquids driven by hydrogen bonding.

    Science.gov (United States)

    Alaasar, Mohamed; Poppe, Silvio; Dong, Qingshu; Liu, Feng; Tschierske, Carsten

    2016-11-24

    Achiral supramolecular hydrogen bonded complexes between rod-like 4-(4-alkoxyphenylazo)pyridines and a taper shaped 4-substituted benzoic acid form achiral (Ia3[combining macron]d) and chiral "Im3[combining macron]m-type" bicontinuous cubic (I432) phases and a chiral isotropic liquid mesophase (Iso 1 [ * ] ). The chiral phases, resulting from spontaneous mirror symmetry breaking, represent conglomerates of macroscopic chiral domains eventually leading to uniform chirality.

  12. Single-crystal neutron diffraction studies of hydrogen-bonded systems: Two recent examples from IPNS

    Energy Technology Data Exchange (ETDEWEB)

    Koetzle, Thomas F. [IPNS Division, Argonne National Laboratory, Argonne, IL 60439 (United States)], E-mail: tkoetzle@anl.gov; Piccoli, Paula M.B.; Schultz, Arthur J. [IPNS Division, Argonne National Laboratory, Argonne, IL 60439 (United States)

    2009-02-21

    Beginning with work in the 1950s at the first generation of research reactors, studies of hydrogen-bonded systems have been a prime application for single-crystal neutron diffraction. The range of systems studied was extended in the 1960s and 1970s, with the advent of high flux reactor sources, and beginning around 1980 studies at pulsed neutron sources have made increasingly important contributions. Recently at the Argonne Intense Pulsed Neutron Source (IPNS), working with collaborators, we completed two studies of hydrogen-bonded systems that will serve to illustrate topics of current interest. In the first study, on andrographolide, an active diterpenoid natural product, our neutron diffraction results definitively characterize the hydrogen-bonding interactions. The second IPNS study is on tetraacetylethane (TAE), a {beta}-diketone enol system with a very short, strong intramolecular O-H...O hydrogen bond. At IPNS, we have determined the neutron crystal structure of TAE at five temperatures between 20 and 298 K to investigate changes in the structure with temperature and to probe for disorder. Despite the successes illustrated by the two examples presented here and by many other studies, at present applications of single-crystal neutron diffraction continue to be extremely flux limited and constrained by the requirement for mm-size crystals for many problems. These limitations are being addressed through the realization of powerful instruments at a new generation of pulsed neutron sources, including in the USA the TOPAZ and MaNDi single-crystal diffractometers that are under development at the Spallation Neutron Source (SNS)

  13. Single-crystal neutron diffraction studies of hydrogen-bonded systems: Two recent examples from IPNS

    Science.gov (United States)

    Koetzle, Thomas F.; Piccoli, Paula M. B.; Schultz, Arthur J.

    2009-02-01

    Beginning with work in the 1950s at the first generation of research reactors, studies of hydrogen-bonded systems have been a prime application for single-crystal neutron diffraction. The range of systems studied was extended in the 1960s and 1970s, with the advent of high flux reactor sources, and beginning around 1980 studies at pulsed neutron sources have made increasingly important contributions. Recently at the Argonne Intense Pulsed Neutron Source (IPNS), working with collaborators, we completed two studies of hydrogen-bonded systems that will serve to illustrate topics of current interest. In the first study, on andrographolide, an active diterpenoid natural product, our neutron diffraction results definitively characterize the hydrogen-bonding interactions. The second IPNS study is on tetraacetylethane (TAE), a β-diketone enol system with a very short, strong intramolecular O-H⋯O hydrogen bond. At IPNS, we have determined the neutron crystal structure of TAE at five temperatures between 20 and 298 K to investigate changes in the structure with temperature and to probe for disorder. Despite the successes illustrated by the two examples presented here and by many other studies, at present applications of single-crystal neutron diffraction continue to be extremely flux limited and constrained by the requirement for mm-size crystals for many problems. These limitations are being addressed through the realization of powerful instruments at a new generation of pulsed neutron sources, including in the USA the TOPAZ and MaNDi single-crystal diffractometers that are under development at the Spallation Neutron Source (SNS).

  14. Single-crystal neutron diffraction studies of hydrogen-bonded systems: Two recent examples from IPNS

    International Nuclear Information System (INIS)

    Koetzle, Thomas F.; Piccoli, Paula M.B.; Schultz, Arthur J.

    2009-01-01

    Beginning with work in the 1950s at the first generation of research reactors, studies of hydrogen-bonded systems have been a prime application for single-crystal neutron diffraction. The range of systems studied was extended in the 1960s and 1970s, with the advent of high flux reactor sources, and beginning around 1980 studies at pulsed neutron sources have made increasingly important contributions. Recently at the Argonne Intense Pulsed Neutron Source (IPNS), working with collaborators, we completed two studies of hydrogen-bonded systems that will serve to illustrate topics of current interest. In the first study, on andrographolide, an active diterpenoid natural product, our neutron diffraction results definitively characterize the hydrogen-bonding interactions. The second IPNS study is on tetraacetylethane (TAE), a β-diketone enol system with a very short, strong intramolecular O-H...O hydrogen bond. At IPNS, we have determined the neutron crystal structure of TAE at five temperatures between 20 and 298 K to investigate changes in the structure with temperature and to probe for disorder. Despite the successes illustrated by the two examples presented here and by many other studies, at present applications of single-crystal neutron diffraction continue to be extremely flux limited and constrained by the requirement for mm-size crystals for many problems. These limitations are being addressed through the realization of powerful instruments at a new generation of pulsed neutron sources, including in the USA the TOPAZ and MaNDi single-crystal diffractometers that are under development at the Spallation Neutron Source (SNS).

  15. 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

  16. Effects of ions on hydrogen-bonding water networks in large aqueous nanodrops.

    Science.gov (United States)

    O'Brien, Jeremy T; Williams, Evan R

    2012-06-20

    Ensemble infrared photodissociation (IRPD) spectra in the hydrogen stretch region (~2800-3800 cm(-1)) are reported for aqueous nanodrops containing ~250 water molecules and either SO(4)(2-), I(-), Na(+), Ca(2+), or La(3+) at 133 K. Each spectrum has a broad feature in the bonded-OH region (~2800-3500 cm(-1)) and a sharp feature near 3700 cm(-1), corresponding to the free-OH stretch of surface water molecules that accept two hydrogen bonds and donate one hydrogen bond (AAD water molecules). A much weaker band corresponding to AD surface water molecules is observed for all ions except SO(4)(2-). The frequencies of the AAD free-OH stretch red-shift with increasingly positive charge, consistent with a Stark effect as a result of the ion's electric field at the droplet surface, and from which the corresponding frequency for water molecules at the surface of neutral nanodrops of this size is estimated to be 3699.3-3700.1 cm(-1). The intensity of the AAD band increases with increasing positive charge, consistent with a greater population of AAD water molecules for the more positively charged nanodrops. The spectra of M(H(2)O)(~250), M = Na(+) and I(-), are very similar, whereas those for Ca(2+) and SO(4)(2-) have distinct differences. These results indicate that the monovalent ions do not affect the hydrogen-bonding network of the majority of water molecules whereas this network is significantly affected in nanodrops containing the multivalent ions. The ion-induced effect on water structure propagates all the way to the surface of the nanodrops, which is located more than 1 nm from the ion.

  17. Photochemistry of hydrogen bonded heterocycles probed by photodissociation experiments and ab initio methods

    Czech Academy of Sciences Publication Activity Database

    Slavíček, Petr; Fárník, Michal

    2011-01-01

    Roč. 13, č. 26 (2011), s. 12123-12137 ISSN 1463-9076 R&D Projects: GA ČR GA203/09/0422; GA ČR GAP208/11/0161 Institutional research plan: CEZ:AV0Z40400503 Keywords : photochemistry * hydrogen bonded heterocycles * ab initio methods Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.573, year: 2011

  18. Termodynamic Stability of Hydrogen-Bonded Systems in Polar and Nonpolar Environments

    Czech Academy of Sciences Publication Activity Database

    Pašalič, H.; Aquino, A. J. A.; Tunega, D.; Haberhauer, G.; Gerzabek, M. H.; Georg, H. C.; Moraes, T. F.; Coutinho, K.; Canuto, S.; Lischka, Hans

    2010-01-01

    Roč. 31, č. 10 (2010), s. 2046-2055 ISSN 0192-8651 R&D Projects: GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : hydrogen-bonded systems * complexation in solution * thermodynamic properties * explicit and implicit solvation models * molecular dynamics and Monte Carlo simulations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.050, year: 2010

  19. Hydrogen-bond network and pH sensitivity in human transthyretin

    Energy Technology Data Exchange (ETDEWEB)

    Yokoyama, Takeshi, E-mail: tyokoya3@pha.u-toyama.ac.jp; Mizuguchi, Mineyuki; Nabeshima, Yuko [University of Toyama, 2630 Sugitani, Toyama 930-0914 (Japan); Kusaka, Katsuhiro; Yamada, Taro [Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan); Hosoya, Takaaki [Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan); Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511 (Japan); Ohhara, Takashi [Comprehensive Research Organization for Science and Society, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan); Kurihara, Kazuo [Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195 (Japan); Tanaka, Ichiro [Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan); Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511 (Japan); Niimura, Nobuo [Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan)

    2013-11-01

    The neutron crystal structure of human transthyretin is presented. Transthyretin (TTR) is a tetrameric protein. TTR misfolding and aggregation are associated with human amyloid diseases. Dissociation of the TTR tetramer is believed to be the rate-limiting step in the amyloid fibril formation cascade. Low pH is known to promote dissociation into monomer and the formation of amyloid fibrils. In order to reveal the molecular mechanisms underlying pH sensitivity and structural stabilities of TTR, neutron diffraction studies were conducted using the IBARAKI Biological Crystal Diffractometer with the time-of-flight method. Crystals for the neutron diffraction experiments were grown up to 2.5 mm{sup 3} for four months. The neutron crystal structure solved at 2.0 Å revealed the protonation states of His88 and the detailed hydrogen-bond network depending on the protonation states of His88. This hydrogen-bond network is involved in monomer–monomer and dimer–dimer interactions, suggesting that the double protonation of His88 by acidification breaks the hydrogen-bond network and causes the destabilization of the TTR tetramer. Structural comparison with the X-ray crystal structure at acidic pH identified the three amino acid residues responsible for the pH sensitivity of TTR. Our neutron model provides insights into the molecular stability related to amyloidosis.

  20. Observation of Cysteine Thiolate and -S...H-O Intermolecular Hydrogen Bond

    Energy Technology Data Exchange (ETDEWEB)

    Woo, Hin-koon; Lau, Kai Chung; Wang, Xue B.; Wang, Lai S.

    2006-11-23

    The cysteine anion was produced in the gas phase by electrospray ionization and investigated by photoelectron spectroscopy at low-temperature (70K). The cysteine anion was found to exhibit the thiolate form [-SCH2CH(NH2)CO2H], rather than the expected carboxylate form [HSCH2CH(NH2)CO2 -]. This observation was confirmed by two control experiments i.e. methyl cysteine [CH3SCH2CH(NH2)CO2-] and cysteine methyl ester [-SCH2CH(NH2)CO2CH3]. The electron binding energy of [-CH2CH(NH2)CO2H] was measured to be about 0.7 eV blue-shifted relative to [-SCH2CH(NH2)CO2CH3] due to the formation of an intramolecular –S-…HO2C– hydrogen bond in the cysteine hiolate. Theoretical calculations at the CCSD(T)/6-311++G(2df,p) and B3LYP/6-311++G(2df,p) levels were carried out to estimate the strength of this intramolecular –S-…HO2C– hydrogen bond. Combining experimental measurements and theoretical calculations yielded an estimated value of 16.4 ± 2.0 kcal/mol for the –S-…HO2C– intramolecular hydrogen bond strength.

  1. Hydrogen-bond network and pH sensitivity in human transthyretin.

    Science.gov (United States)

    Yokoyama, Takeshi; Mizuguchi, Mineyuki; Nabeshima, Yuko; Kusaka, Katsuhiro; Yamada, Taro; Hosoya, Takaaki; Ohhara, Takashi; Kurihara, Kazuo; Tanaka, Ichiro; Niimura, Nobuo

    2013-11-01

    Transthyretin (TTR) is a tetrameric protein. TTR misfolding and aggregation are associated with human amyloid diseases. Dissociation of the TTR tetramer is believed to be the rate-limiting step in the amyloid fibril formation cascade. Low pH is known to promote dissociation into monomer and the formation of amyloid fibrils. In order to reveal the molecular mechanisms underlying pH sensitivity and structural stabilities of TTR, neutron diffraction studies were conducted using the IBARAKI Biological Crystal Diffractometer with the time-of-flight method. Crystals for the neutron diffraction experiments were grown up to 2.5 mm(3) for four months. The neutron crystal structure solved at 2.0 Å revealed the protonation states of His88 and the detailed hydrogen-bond network depending on the protonation states of His88. This hydrogen-bond network is involved in monomer-monomer and dimer-dimer interactions, suggesting that the double protonation of His88 by acidification breaks the hydrogen-bond network and causes the destabilization of the TTR tetramer. Structural comparison with the X-ray crystal structure at acidic pH identified the three amino acid residues responsible for the pH sensitivity of TTR. Our neutron model provides insights into the molecular stability related to amyloidosis.

  2. Visible absorbing croconium dyes with intramolecular hydrogen bonding: A combined experimental and computational study

    Science.gov (United States)

    Prabhakar, Ch.; Promila; Tripathi, Anuj; Bhanuprakash, K.; Jayathirtharao, V.

    2017-10-01

    Croconium molecules CR1-CR4 with break-in conjugation (Csbnd N Bonding) was synthesized by condensation of croconic acid and arylamines. By using combined experimental and theoretical methods like UV-visible spectra, DFT and TDDFT studies, we have characterized electronic absorption properties. The reported molecules are having absorption in visible region ranging from 450 to 550 nm with large extinction coefficient (2.5-5.0 × 104 M-1 cm-1). We find that CR2 and CR4 are showing 50 to 100 nm red shifted absorption than CR1 and CR3. This red shift is possibly due to presence of intramolecular hydrogen bonding in CR2 and CR4. Further this is supported by DFT studies, in case of CR2 and CR4 shows strong intramolecular hydrogen bonding between oxygen of carboxylate group (at ortho position of phenyl ring) and hydrogen of nitrogen attached to the central croconate ring. It is also observed that, there is small diradicaloid character in these molecules. This study is helpful in design and synthesis of new croconium dyes which are useful in materials applications.

  3. 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.

  4. Measuring the relative hydrogen-bonding strengths of alcohols in aprotic organic solvents.

    Science.gov (United States)

    Tessensohn, Malcolm E; Lee, Melvyn; Hirao, Hajime; Webster, Richard D

    2015-01-12

    Voltammetric experiments with 9,10-anthraquinone and 1,4-benzoquinone performed under controlled moisture conditions indicate that the hydrogen-bond strengths of alcohols in aprotic organic solvents can be differentiated by the electrochemical parameter ΔEp (red) =|Ep (red(1)) -Ep (red(2)) |, which is the potential separation between the two one-electron reduction processes. This electrochemical parameter is inversely related to the strength of the interactions and can be used to differentiate between primary, secondary, tertiary alcohols, and even diols, as it is sensitive to both their steric and electronic properties. The results are highly reproducible across two solvents with substantially different hydrogen-bonding properties (CH3 CN and CH2 Cl2 ) and are supported by density functional theory calculations. This indicates that the numerous solvent-alcohol interactions are less significant than the quinone-alcohol hydrogen-bonding interactions. The utility of ΔEp (red) was illustrated by comparisons between 1) 3,3,3-trifluoro-n-propanol and 1,3-difluoroisopropanol and 2) ethylene glycol and 2,2,2-trifluoroethanol. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Thermodynamic stability of hydrogen-bonded systems in polar and nonpolar environments.

    Science.gov (United States)

    Pasalić, Hasan; Aquino, Adélia J A; Tunega, Daniel; Haberhauer, Georg; Gerzabek, Martin H; Georg, Herbert C; Moraes, Tatiane F; Coutinho, Kaline; Canuto, Sylvio; Lischka, Hans

    2010-07-30

    The thermodynamic properties of a selected set of benchmark hydrogen-bonded systems (acetic acid dimer and the complexes of acetic acid with acetamide and methanol) was studied with the goal of obtaining detailed information on solvent effects on the hydrogen-bonded interactions using water, chloroform, and n-heptane as representatives for a wide range in the dielectric constant. Solvent effects were investigated using both explicit and implicit solvation models. For the explicit description of the solvent, molecular dynamics and Monte Carlo simulations in the isothermal-isobaric (NpT) ensemble combined with the free energy perturbation technique were performed to determine solvation free energies. Within the implicit solvation approach, the polarizable continuum model and the conductor-like screening model were applied. Combination of gas phase results with the results obtained from the different solvation models through an appropriate thermodynamic cycle allows estimation of complexation free energies, enthalpies, and the respective entropic contributions in solution. Owing to the strong solvation effects of water the cyclic acetic acid dimer is not stable in aqueous solution. In less polar solvents the double hydrogen bond structure of the acetic acid dimer remains stable. This finding is in agreement with previous theoretical and experimental results. A similar trend as for the acetic acid dimer is also observed for the acetamide complex. The methanol complex was found to be thermodynamically unstable in gas phase as well as in any of the three solvents. 2010 Wiley Periodicals, Inc.

  6. Solute's perspective on how trimethylamine oxide, urea, and guanidine hydrochloride affect water's hydrogen bonding ability.

    Science.gov (United States)

    Pazos, Ileana M; Gai, Feng

    2012-10-18

    While the thermodynamic effects of trimethylamine oxide (TMAO), urea, and guanidine hydrochloride (GdnHCl) on protein stability are well understood, the underlying mechanisms of action are less well characterized and, in some cases, even under debate. Herein, we employ the stretching vibration of two infrared (IR) reporters, i.e., nitrile (C≡N) and carbonyl (C═O), to directly probe how these cosolvents mediate the ability of water to form hydrogen bonds with the solute of interest, e.g., a peptide. Our results show that these three agents, despite having different effects on protein stability, all act to decrease the strength of the hydrogen bonds formed between water and the infrared probe. While the behavior of TMAO appears to be consistent with its protein-protecting ability, those of urea and GdnHCl are inconsistent with their role as protein denaturants. The latter is of particular interest as it provides strong evidence indicating that although urea and GdnHCl can perturb the hydrogen-bonding property of water their protein-denaturing ability does not arise from a simple indirect mechanism.

  7. Ultrasonic and IR study of intermolecular association through hydrogen bonding in ternary liquid mixtures.

    Science.gov (United States)

    Awasthi, Aashees; Shukla, J P

    2003-08-01

    Complex formation in ternary liquid mixtures of dimethylsulfoxide (DMSO) with phenol and o-cresol in carbontetrachloride has been studied by measuring ultrasonic velocity at 2 MHz, in the concentration range of 0.019-0.162 (in mole fraction of DMSO) at varying temperatures of 20, 30 and 40 degrees C. Using measured values of ultrasonic velocity, other parameters such as adiabatic compressibility, intermolecular free length, molar sound velocity, molar compressibility, specific acoustic impedance and molar volume have been evaluated. These parameters have been utilized to study the solute-solute interactions in these systems. The ultrasonic velocity shows a maxima and adiabatic compressibility a corresponding minima as a function of concentration for these mixtures. The results indicate the occurrence of complex formation between unlike molecules through intermolecular hydrogen bonding between oxygen atom of DMSO molecule and hydrogen atom of phenol and o-cresol molecules. The excess values of adiabatic compressibility and intermolecular free length have also been evaluated. The variation of both these parameters with concentration also indicates the possibility of the complex formation in these systems. Further, to investigate the presence of O-HO bond complexes and the strength of molecular association with concentrations, the infrared spectra of both the systems, DMSO-phenol and DMSO-o-cresol, have been recorded for various concentrations at room temperature (20 degrees C). The results obtained using infrared spectroscopy for both the systems also support the occurrence of complex formation through intermolecular hydrogen bonding in these ternary liquid mixtures.

  8. Self-Healing Gelatin Hydrogels Cross-Linked by Combining Multiple Hydrogen Bonding and Ionic Coordination.

    Science.gov (United States)

    Zhang, Guangzhao; Lv, Lei; Deng, Yonghong; Wang, Chaoyang

    2017-06-01

    Self-healing hydrogels have been studied by many researchers via multiple cross-linking approaches including physical and chemical interactions. It is an interesting project in multifunctional hydrogel exploration that a water soluble polymer matrix is cross-linked by combining the ionic coordination and the multiple hydrogen bonds to fabricate self-healing hydrogels with injectable property. This study introduces a general procedure of preparing the hydrogels (termed gelatin-UPy-Fe) cross-linked by both ionic coordination of Fe 3+ and carboxyl group from the gelatin and the quadruple hydrogen bonding interaction from the ureido-pyrimidinone (UPy) dimers. The gelatin-UPy-Fe hydrogels possess an excellent self-healing property. The effects of the ionic coordination of Fe 3+ and quadruple hydrogen bonding of UPy on the formation and mechanical behavior of the prepared hydrogels are investigated. In vitro drug release of the gelatin-UPy-Fe hydrogels is also observed, giving an intriguing glimpse into possible biological applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Effect of hydrogen bonds on pKa values: importance of networking.

    Science.gov (United States)

    Shokri, Alireza; Abedin, Azardokht; Fattahi, Alireza; Kass, Steven R

    2012-06-27

    The pK(a) of an acyclic aliphatic heptaol ((HOCH(2)CH(2)CH(OH)CH(2))(3)COH) was measured in DMSO, and its gas-phase acidity is reported as well. This tertiary alcohol was found to be 10(21) times more acidic than tert-butyl alcohol in DMSO and an order of magnitude more acidic than acetic acid (i.e., pK(a) = 11.4 vs 12.3). This can be attributed to a 21.9 kcal mol(-1) stabilization of the charged oxygen center in the conjugate base by three hydrogen bonds and another 6.3 kcal mol(-1) stabilization resulting from an additional three hydrogen bonds between the uncharged primary and secondary hydroxyl groups. Charge delocalization by both the first and second solvation shells may be used to facilitate enzymatic reactions. Acidity constants of a series of polyols were also computed, and the combination of hydrogen-bonding and electron-withdrawing substituents was found to afford acids that are predicted to be extremely acidic in DMSO (i.e., pK(a) acids represent an attractive class of Brønsted acid catalysts.

  10. Strategies To Increase the Thermal Stability of Truly Biomimetic Hydrogels: Combining Hydrophobicity and Directed Hydrogen Bonding

    Science.gov (United States)

    2017-01-01

    Enhancing the thermal stability of proteins is an important task for protein engineering. There are several ways to increase the thermal stability of proteins in biology, such as greater hydrophobic interactions, increased helical content, decreased occurrence of thermolabile residues, or stable hydrogen bonds. Here, we describe a well-defined polymer based on β-helical polyisocyanotripeptides (TriPIC) that uses biological approaches, including hydrogen bonding and hydrophobic interactions for its exceptional thermal stability in aqueous solutions. The multiple hydrogen bonding arrays along the polymer backbone shield the hydrophobic core from water. Variable temperature CD and FTIR studies indicate that, on heating, a better packed polymer conformation further stiffens the backbone. Driven by hydrophobic interactions, TriPIC solutions give fully reversible hydrogels that can withstand high temperatures (80 °C) for extended times. Cryo-scanning electron microscopy (cryo-SEM), small-angle X-ray scattering (SAXS), and thorough rheological analysis show that the hydrogel has a bundled architecture, which gives rise to strain stiffening effects on deformation of the gel, analogous to many biological hydrogels. PMID:29213150

  11. Strategies To Increase the Thermal Stability of Truly Biomimetic Hydrogels: Combining Hydrophobicity and Directed Hydrogen Bonding.

    Science.gov (United States)

    Yuan, Hongbo; Xu, Jialiang; van Dam, Eliane P; Giubertoni, Giulia; Rezus, Yves L A; Hammink, Roel; Bakker, Huib J; Zhan, Yong; Rowan, Alan E; Xing, Chengfen; Kouwer, Paul H J

    2017-11-28

    Enhancing the thermal stability of proteins is an important task for protein engineering. There are several ways to increase the thermal stability of proteins in biology, such as greater hydrophobic interactions, increased helical content, decreased occurrence of thermolabile residues, or stable hydrogen bonds. Here, we describe a well-defined polymer based on β-helical polyisocyanotripeptides (TriPIC) that uses biological approaches, including hydrogen bonding and hydrophobic interactions for its exceptional thermal stability in aqueous solutions. The multiple hydrogen bonding arrays along the polymer backbone shield the hydrophobic core from water. Variable temperature CD and FTIR studies indicate that, on heating, a better packed polymer conformation further stiffens the backbone. Driven by hydrophobic interactions, TriPIC solutions give fully reversible hydrogels that can withstand high temperatures (80 °C) for extended times. Cryo-scanning electron microscopy (cryo-SEM), small-angle X-ray scattering (SAXS), and thorough rheological analysis show that the hydrogel has a bundled architecture, which gives rise to strain stiffening effects on deformation of the gel, analogous to many biological hydrogels.

  12. 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.

  13. Covalent binding of sulfamethazine to natural and synthetic humic acids: assessing laccase catalysis and covalent bond stability.

    Science.gov (United States)

    Gulkowska, Anna; Sander, Michael; Hollender, Juliane; Krauss, Martin

    2013-07-02

    Sulfonamide antibiotics form stable covalent bonds with quinone moieties in organic matter via nucleophilic addition reactions. In this work, we combined analytical electrochemistry with trace analytics to assess the catalytic role of the oxidoreductase laccase in the binding of sulfamethazine (SMZ) to Leonardite humic acid (LHA) and to four synthetic humic acids (SHAs) polymerized from low molecular weight precursors and to determine the stability of the formed bonds. In the absence of laccase, a significant portion of the added SMZ formed covalent bonds with LHA, but only a very small fraction (<0.4%) of the total quinone moieties in LHA reacted. Increasing absolute, but decreasing relative concentrations of SMZ-LHA covalent bonds with increasing initial SMZ concentration suggested that the quinone moieties in LHA covered a wide distribution in reactivity for the nucleophilic addition of SMZ. Laccase catalyzed the formation of covalent bonds by oxidizing unreactive hydroquinone moieties in LHA to reactive, electrophilic quinone moieties, of which a large fraction (5%) reacted with SMZ. Compared to LHA, the SHA showed enhanced covalent bond formation in the absence of laccase, suggesting a higher reactivity of their quinone moieties toward nucleophilic addition. This work supports that binding to soil organic matter (SOM) is an important process governing the fate, bioactivity, and extractability of sulfonamides in soils.

  14. From Coordination Cages to a Stable Crystalline Porous Hydrogen-Bonded Framework

    Energy Technology Data Exchange (ETDEWEB)

    Ju, Zhanfeng [State Key Lab of Structure Chemistry, Fujian Institute of Research on the Structure of Matter, CAS, Fuzhou 350002 P. R. China; Liu, Guoliang [State Key Lab of Structure Chemistry, Fujian Institute of Research on the Structure of Matter, CAS, Fuzhou 350002 P. R. China; Chen, Yu-Sheng [ChemMatCARS, Center for Advanced Radiation Sources, The University of Chicago, Argonne Illinois 60439 USA; Yuan, Daqiang [State Key Lab of Structure Chemistry, Fujian Institute of Research on the Structure of Matter, CAS, Fuzhou 350002 P. R. China; Chen, Banglin [Department of Chemistry, University of Texas at San Antonio, San Antonio Texas 78249-0698 USA

    2017-03-20

    A stable framework has been constructed through multiple charge-assisted H-bonds between cationic coordination cages and chloride ions. The framework maintained its original structure upon desolvation, which has been established by single-crystal structure analysis. This is the first fully characterized stable porous framework based on coordination cages after desolvation, with a moderately high Brunauer–Emmett–Teller (BET) surface area of 1201 m2 g-1. This work will not only give a light to construct stable porous frameworks based on coordination cages and thus broaden their applications, but will also provide a new avenue to the assembly of other porous materials such as porous organic cages and hydrogen-bonded organic frameworks (HOFs) through non covalent bonds.

  15. Bridging the Gap: From Model Surfaces to Nanoparticle Analogs for Selective Oxidation and Steam Reforming of Methanol and Selective Hydrogenation Catalysis

    Science.gov (United States)

    Boucher, Matthew B.

    Most industrial catalysts are very complex, comprising of non-uniform materials with varying structures, impurities, and interaction between the active metal and supporting substrate. A large portion of the ongoing research in heterogeneous catalysis focuses on understanding structure-function relationships in catalytic materials. In parallel, there is a large area of surface science research focused on studying model catalytic systems for which structural parameters can be tuned and measured with high precision. It is commonly argued, however, that these systems are oversimplified, and that observations made in model systems do not translate to robust catalysts operating in practical environments; this discontinuity is often referred to as a "gap." The focus of this thesis is to explore the mutual benefits of surface science and catalysis, or "bridge the gap," by studying two catalytic systems in both ultra-high vacuum (UHV) and near ambient-environments. The first reaction is the catalytic steam reforming of methanol (SRM) to hydrogen and carbon dioxide. The SRM reaction is a promising route for on-demand hydrogen production. For this catalytic system, the central hypothesis in this thesis is that a balance between redox capability and weak binding of reaction intermediates is necessary for high SRM activity and selectivity to carbon dioxide. As such, a new catalyst for the SRM reaction is developed which incorporates very small amounts of gold (liquid-phase, stirred-tank batch reactor under a hydrogen head pressure of approximately 7 bar. Palladium alloyed into the surface of otherwise inactive copper nanoparticles shows a marked improvement in selectivity when compared to monometallic palladium catalysts with the same metal loading. This effect is attributed hydrogen spillover onto the copper surface. In summary, the development of new, highly active and selective catalysts for the methanol steam reforming reaction and for the partial hydrogenation of alkynes

  16. Atomic configuration of hydrogenated and clean tantalum(111) surfaces: Bond relaxation, energy entrapment and electron polarization

    Science.gov (United States)

    Bo, Maolin; Li, Lei; Guo, Yongling; Yao, Chuang; Peng, Cheng; Sun, Chang Q.

    2018-01-01

    By studying the tantalum (Ta)(111) surface with X-ray photoemission spectroscopy and density functional theory, we determined binding energy values for the clean Ta(111) (+3.068 eV) and hydrogenated Ta(111) (+3.421 eV) surfaces with an isolated atom level of 18.977 eV. Using the bond-band barrier and zone-selective electron spectroscopy correlation, we investigated the mechanism of hydrogenation adsorption on the Ta(111) surface. We found the local densities of states of the first layer of Ta atoms in the reconstructed structure, which formed on the adsorbent hydrogen of the surface chemical bond contracts and dipole polarization. Moreover, we showed that on the Ta(111) surface, the hydrogen-induced surface core level shifts are dominated by quantum entrapment and are proportional to the calculated hybridized orbitals of the valence band. The latter is therefore correlated to the local surface chemical reactivity and is useful for other adsorbate systems on transition metals.

  17. Fabrication of a facile electrochemical biosensor for hydrogen peroxide using efficient catalysis of hemoglobin on the porous Pd@Fe3O4-MWCNT nanocomposite.

    Science.gov (United States)

    Baghayeri, Mehdi; Veisi, Hojat

    2015-12-15

    In this work, a sensitive amperometric biosensor for hydrogen peroxide based on synergetic catalysis of hemoglobin and porous Pd@Fe3O4-MWCNT nanocomposite has been constructed. With attention to the utilities of large surface area and outstanding catalytic performance, Pd@Fe3O4-MWCNT nanocomposite was employed as the nano-stabilizer for the immobilization of hemoglobin (Hb). The immobilized Hb on the surface of nanocomposite as an electrochemical biosensor efficiently catalyzed the reduction of hydrogen peroxide, amplified the electrochemical signal and enhanced the sensitivity. Results of voltammetry and electrochemical impedance examinations showed that the nanocomposite could enhance the electron conductivity and provide more sites for the immobilization of Hb. A linear response from 0.2-500 µM with detection limit of 0.063 µM for hydrogen peroxide was achieved. The apparent Michaelis-Menten constant Kapp(M) value was 21 µM. Thus, the nanocomposite could be applied for fabrication of a third generation biosensor for hydrogen peroxide with high sensitivity, selectivity and low detection limit. The excellent performance of the biosensor indicated its promising prospect as a valuable tool in simple and fast hydrogen peroxide detection in environmental and clinical applications. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Nucleophilicities of Lewis Bases B and Electrophilicities of Lewis Acids A Determined from the Dissociation Energies of Complexes B⋯A Involving Hydrogen Bonds, Tetrel Bonds, Pnictogen Bonds, Chalcogen Bonds and Halogen Bonds.

    Science.gov (United States)

    Alkorta, Ibon; Legon, Anthony C

    2017-10-23

    It is shown that the dissociation energy D e for the process B⋯A = B + A for 250 complexes B⋯A composed of 11 Lewis bases B (N₂, CO, HC≡CH, CH₂=CH₂, C₃H₆, PH₃, H₂S, HCN, H₂O, H₂CO and NH₃) and 23 Lewis acids (HF, HCl, HBr, HC≡CH, HCN, H₂O, F₂, Cl₂, Br₂, ClF, BrCl, H₃SiF, H₃GeF, F₂CO, CO₂, N₂O, NO₂F, PH₂F, AsH₂F, SO₂, SeO₂, SF₂, and SeF₂) can be represented to good approximation by means of the equation D e = c ' N B E A , in which N B is a numerical nucleophilicity assigned to B, E A is a numerical electrophilicity assigned to A, and c ' is a constant, conveniently chosen to have the value 1.00 kJ mol -1 here. The 250 complexes were chosen to cover a wide range of non-covalent interaction types, namely: (1) the hydrogen bond; (2) the halogen bond; (3) the tetrel bond; (4) the pnictogen bond; and (5) the chalcogen bond. Since there is no evidence that one group of non-covalent interaction was fitted any better than the others, it appears the equation is equally valid for all the interactions considered and that the values of N B and E A so determined define properties of the individual molecules. The values of N B and E A can be used to predict the dissociation energies of a wide range of binary complexes B⋯A with reasonable accuracy.

  19. Nucleophilicities of Lewis Bases B and Electrophilicities of Lewis Acids A Determined from the Dissociation Energies of Complexes B⋯A Involving Hydrogen Bonds, Tetrel Bonds, Pnictogen Bonds, Chalcogen Bonds and Halogen Bonds

    Directory of Open Access Journals (Sweden)

    Ibon Alkorta

    2017-10-01

    Full Text Available It is shown that the dissociation energy D e for the process B⋯A = B + A for 250 complexes B⋯A composed of 11 Lewis bases B (N2, CO, HC≡CH, CH2=CH2, C3H6, PH3, H2S, HCN, H2O, H2CO and NH3 and 23 Lewis acids (HF, HCl, HBr, HC≡CH, HCN, H2O, F2, Cl2, Br2, ClF, BrCl, H3SiF, H3GeF, F2CO, CO2, N2O, NO2F, PH2F, AsH2F, SO2, SeO2, SF2, and SeF2 can be represented to good approximation by means of the equation D e = c ′ N B E A , in which N B is a numerical nucleophilicity assigned to B, E A is a numerical electrophilicity assigned to A, and c ′ is a constant, conveniently chosen to have the value 1.00 kJ mol−1 here. The 250 complexes were chosen to cover a wide range of non-covalent interaction types, namely: (1 the hydrogen bond; (2 the halogen bond; (3 the tetrel bond; (4 the pnictogen bond; and (5 the chalcogen bond. Since there is no evidence that one group of non-covalent interaction was fitted any better than the others, it appears the equation is equally valid for all the interactions considered and that the values of N B and E A so determined define properties of the individual molecules. The values of N B and E A can be used to predict the dissociation energies of a wide range of binary complexes B⋯A with reasonable accuracy.

  20. Theoretical exploration of the mechanism of riboflavin formation from 6,7-dimethyl-8-ribityllumazine: nucleophilic catalysis, hydride transfer, hydrogen atom transfer, or nucleophilic addition?

    Science.gov (United States)

    Breugst, Martin; Eschenmoser, Albert; Houk, K N

    2013-05-01

    The cofactor riboflavin is biochemically synthesized by a constitutionally intricate process in which two molecules of 6,7-dimethyl-8-ribityllumazine react with each other to form one molecule of the cofactor and one molecule of 5-amino-6-(ribitylamino)uracil. Remarkably, this complex molecular transformation also proceeds non-enzymatically in boiling aqueous solution at pH 7.3. Four different mechanistic pathways for this transformation (nucleophilic catalysis, hydride transfer, hydrogen atom transfer, and a nucleophilic addition mechanism) have now been analyzed by density functional theory [M06-2X/def2-TZVPP/CPCM//M06-2X/6-31+G(d,p)/IEFPCM]. On the basis of these computational results, a so far unpublished nucleophilic addition mechanism is the lowest energy pathway yielding riboflavin. The previously proposed mechanism involving nucleophilic catalysis is higher in energy but is still a viable alternative for an enzyme-catalyzed process assisted by suitably positioned catalytic groups. Pathways involving the transfer of a hydride ion or of a hydrogen atom are predicted to proceed through higher energy transition states and intermediates.

  1. Unifying Exchange Sensitivity in Transition-Metal Spin-State Ordering and Catalysis through Bond Valence Metrics.

    Science.gov (United States)

    Gani, Terry Z H; Kulik, Heather J

    2017-11-14

    Accurate predictions of spin-state ordering, reaction energetics, and barrier heights are critical for the computational discovery of open-shell transition-metal (TM) catalysts. Semilocal approximations in density functional theory, such as the generalized gradient approximation (GGA), suffer from delocalization error that causes them to overstabilize strongly bonded states. Descriptions of energetics and bonding are often improved by introducing a fraction of exact exchange (e.g., erroneous low-spin GGA ground states are instead correctly predicted as high-spin with a hybrid functional). The degree of spin-splitting sensitivity to exchange can be understood based on the chemical composition of the complex, but the effect of exchange on reaction energetics within a single spin state is less well-established. Across a number of model iron complexes, we observe strong exchange sensitivities of reaction barriers and energies that are of the same magnitude as those for spin splitting energies. We rationalize trends in both reaction and spin energetics by introducing a measure of delocalization, the bond valence of the metal-ligand bonds in each complex. The bond valence thus represents a simple-to-compute property that unifies understanding of exchange sensitivity for catalytic properties and spin-state ordering in TM complexes. Close agreement of the resulting per-metal-organic-bond sensitivity estimates, together with failure of alternative descriptors demonstrates the utility of the bond valence as a robust descriptor of how differences in metal-ligand delocalization produce differing relative energetics with exchange tuning. Our unified description explains the overall effect of exact exchange tuning on the paradigmatic two-state FeO + /CH 4 reaction that combines challenges of spin-state and reactivity predictions. This new descriptor-sensitivity relationship provides a path to quantifying how predictions in transition-metal complex screening are sensitive to the

  2. Reversible swelling-shrinking behavior of hydrogen-bonded free-standing thin film stabilized by catechol reaction.

    Science.gov (United States)

    Sun, Jiaxing; Su, Chao; Zhang, Xuejian; Yin, Wenjing; Xu, Jian; Yang, Shuguang

    2015-05-12

    Dopamine-modified poly(acrylic acid) (PAA-dopa) and poly(vinylpyrrolidone) (PVPON) was layer-by-layer (LbL) assembled to prepare thin film based on hydrogen bonding. The carboxylic group of acrylic acid and the phenolic hydroxyl group of dopamine can both act as hydrogen bond donors. The critical assembly and the critical disintegration pH values of PVPON/PAA-dopa film are enhanced compared with PVPON/PAA film. The hydrogen-bonded PVPON/PAA-dopa thin film can be cross-linked via catechol chemistry of dopamine. After cross-linking, the film can be exfoliated from the substrate in alkaline solution to get a free-standing film. Moreover, by tuning the pH value, deprotonation and protonation of PAA will make the hydrogen bond in the film break and reconstruct, which induces that the free-standing film has a reversible swelling-shrinking behavior.

  3. Spectroscopic Investigation of the Formation and Disruption of Hydrogen Bonds in Pharmaceutical Semicrystalline Dispersions.

    Science.gov (United States)

    Van Duong, Tu; Reekmans, Gunter; Venkatesham, Akkaladevi; Van Aerschot, Arthur; Adriaensens, Peter; Van Humbeeck, Jan; Van den Mooter, Guy

    2017-05-01

    We recently found that indomethacin (IMC) can effectively act as a powerful crystallization inhibitor for polyethylene glycol 6000 (PEG) despite the fact that the absence of interactions between the drug and the carrier in the solid state was reported in the literature. However, in the present study, we investigate the possibility of drug-carrier interactions in the liquid state to explain the polymer crystallization inhibition effect of IMC. We also aim to discover other potential PEG crystallization inhibitors. Drug-carrier interactions in both liquid and solid state are characterized by variable temperature Fourier transform infrared spectroscopy (FTIR) and cross-polarization magic angle spinning 13 C nuclear magnetic resonance spectroscopy (CP/MAS NMR). In the liquid state, FTIR data show evidence of the breaking of hydrogen bonding between IMC molecules to form interactions of the IMC monomer with PEG. The drug-carrier interactions are disrupted upon storage and polymer crystallization, resulting in segregation of IMC from PEG crystals that can be observed under polarized light microscopy. This process is further confirmed by 13 C NMR since in the liquid state, when the IMC/PEG monomer units ratio is below 2:1, IMC signals are undetectable because of the loss of cross-polarization efficiency in the mobile IMC molecules upon attachment to PEG chains via hydrogen bonding. This suggests that each ether oxygen of the PEG unit can form hydrogen bonds with two IMC molecules. The NMR spectrum of IMC shows no change in solid dispersions with PEG upon storage, indicating the absence of interactions in the solid state, hence confirming previous studies. The drug-carrier interactions in the liquid state elucidate the crystallization inhibition effect of IMC on PEG as well as other semicrystalline polymers such as poloxamer and Gelucire. However, hydrogen bonding is a necessary but apparently not a sufficient condition for the polymer crystallization inhibition. Screening

  4. 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)

  5. Hydrogen bonding in protic ionic liquids: structural correlations, vibrational spectroscopy, and rotational dynamics of liquid ethylammonium nitrate

    Science.gov (United States)

    Zentel, Tobias; Overbeck, Viviane; Michalik, Dirk; Kühn, Oliver; Ludwig, Ralf

    2018-02-01

    The properties of the hydrogen bonds in ethylammonium nitrate (EAN) are analyzed by using molecular dynamics simulations and infrared as well as nuclear magnetic resonance experiments. EAN features a flexible three-dimensional network of hydrogen bonds with moderate strengths, which makes it distinct from related triethylammonium-based ionic liquids. First, the network’s flexibility is manifested in a not very pronounced correlation of the hydrogen bond geometries, which is caused by rapid interchanges of bonding partners. The large flexibility of the network also leads to a substantial broadening of the mid-IR absorption band, with the contributions due to N–H stretching motions ranging from 2800 to 3250 cm‑1. Finally, the different dynamics are also seen in the rotational correlation of the N–H bond vector, where a correlation time as short as 16.1 ps is observed.

  6. Solid-State17O NMR Reveals Hydrogen-Bonding Energetics: Not All Low-Barrier Hydrogen Bonds Are Strong.

    Science.gov (United States)

    Lu, Jiasheng; Hung, Ivan; Brinkmann, Andreas; Gan, Zhehong; Kong, Xianqi; Wu, Gang

    2017-05-22

    While NMR and IR spectroscopic signatures and structural characteristics of low-barrier hydrogen bond (LBHB) formation are well documented in the literature, direct measurement of the LBHB energy is difficult. Here, we show that solid-state 17 O NMR spectroscopy can provide unique information about the energy required to break a LBHB. Our solid-state 17 O NMR data show that the HB enthalpy of the O⋅⋅⋅H⋅⋅⋅N LBHB formed in crystalline nicotinic acid is only 7.7±0.5 kcal mol -1 , suggesting that not all LBHBs are particularly strong. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Halogen and Hydrogen Bonding between (N-Halogeno)-succinimides and Pyridine Derivatives in Solution, the Solid State and In Silico.

    Science.gov (United States)

    Stilinović, Vladimir; Horvat, Gordan; Hrenar, Tomica; Nemec, Vinko; Cinčić, Dominik

    2017-04-19

    A study of strong halogen bonding within three series of halogen-bonded complexes, derived from seven para-substituted pyridine derivatives and three N-halosuccinimides (iodo, bromo and chloro), has been undertaken with the aid of single-crystal diffraction, solution complexation and computational methods. The halogen bond was compared with the hydrogen bond in an equivalent series based on succinimide. The halogen-bond energies are in the range -60 to -20 kJ mol -1 and change regularly with pyridine basicity and the Lewis acidity of the halogen. The halogen-bond energies correlate linearly with the product of charges on the contact atoms, which indicates a predominantly electrostatic interaction. The binding enthalpies in solution are around 19 kJ mol -1 less negative due to solvation effects. The optimised geometries of the complexes in the gas phase are comparable to those of the solid-state structures, and the effects of the supramolecular surroundings in the latter are discussed. The bond energies for the hydrogen-bonded series are intermediate between the halogen-bond energies of iodine and bromine, although there are specific differences in the geometries of the halogen- and hydrogen-bonded complexes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Hydrogen-bond network and pH sensitivity in transthyretin: Neutron crystal structure of human transthyretin.

    Science.gov (United States)

    Yokoyama, Takeshi; Mizuguchi, Mineyuki; Nabeshima, Yuko; Kusaka, Katsuhiro; Yamada, Taro; Hosoya, Takaaki; Ohhara, Takashi; Kurihara, Kazuo; Tomoyori, Katsuaki; Tanaka, Ichiro; Niimura, Nobuo

    2012-02-01

    Transthyretin (TTR) is a tetrameric protein associated with human amyloidosis. In vitro, the formation of amyloid fibrils by TTR is known to be promoted by low pH. Here we show the neutron structure of TTR, focusing on the hydrogen bonds, protonation states and pH sensitivities. A large crystal was prepared at pD 7.4 for neutron protein crystallography. Neutron diffraction studies were conducted using the IBARAKI Biological Crystal Diffractometer with the time-of-flight method. The neutron structure solved at 2.0Å resolution revealed the protonation states of His88 and the detailed hydrogen-bond network depending on the protonation states of His88. This hydrogen-bond network is composed of Thr75, Trp79, His88, Ser112, Pro113, Thr118-B and four water molecules, and is involved in both monomer-monomer and dimer-dimer interactions, suggesting that the double protonation of His88 by acidification breaks the hydrogen-bond network and causes the destabilization of the TTR tetramer. In addition, the comparison with X-ray structure at pH 4.0 indicated that the protonation occurred to Asp74, His88 and Glu89 at pH 4.0. Our neutron model provides insights into the molecular stability of TTR related to the hydrogen-bond network, the pH sensitivity and the CH···O weak hydrogen bond. Copyright © 2012 Elsevier Inc. All rights reserved.

  9. Molecular Dynamics Investigation of the Effects of Concentration on Hydrogen Bonding in Aqueous Solutions of Methanol, Ethylene Glycol and Glycerol

    International Nuclear Information System (INIS)

    Zhang, Ning; Li, Weizhong; Chen, Cong; Zuo, Jianguo; Weng, Lindong

    2013-01-01

    Hydrogen bonding interaction between alcohols and water molecules is an important characteristic in the aqueous solutions of alcohols. In this paper, a series of molecular dynamics simulations have been performed to investigate the aqueous solutions of low molecular weight alcohols (methanol, ethylene glycol and glycerol) at the concentrations covering a broad range from 1 to 90 mol %. The work focuses on studying the effect of the alcohols molecules on the hydrogen bonding of water molecules in binary mixtures. By analyzing the hydrogen bonding ability of the hydroxyl (-OH) groups for the three alcohols, it is found that the hydroxyl group of methanol prefers to form more hydrogen bonds than that of ethylene glycol and glycerol due to the intra-and intermolecular effects. It is also shown that concentration has significant effect on the ability of alcohol molecule to hydrogen bond water molecules. Understanding the hydrogen bonding characteristics of the aqueous solutions is helpful to reveal the cryoprotective mechanisms of methanol, ethylene glycol and glycerol in aqueous solutions

  10. Local electronic and geometrical structures of hydrogen-bonded complexes studied by soft X-ray spectroscopy

    International Nuclear Information System (INIS)

    Luo, Y.

    2004-01-01

    Full text: The hydrogen bond is one of the most important forms of intermolecular interactions. It occurs in all-important components of life. However, the electronic structures of hydrogen-bonded complexes in liquid phases have long been difficult to determine due to the lack of proper experimental techniques. In this talk, a recent joint theoretical and experimental effort to understand hydrogen bonding in liquid water and alcohol/water mixtures using synchrotron radiation based soft-X-ray spectroscopy will be presented. The complexity of the liquid systems has made it impossible to interpret the spectra with physical intuition alone. Theoretical simulations have thus played an essential role in understanding the spectra and providing valuable insights on the local geometrical and electronic structures of these liquids. Our study sheds light on a 40-year controversy over what kinds of molecular structures are formed in pure liquid methanol. It also suggests an explanation for the well-known puzzle of why alcohol and water do not mix completely: the system must balance nature's tendency toward greater disorder (entropy) with the molecules' tendency to form hydrogen bonds. The observation of electron sharing and broken hydrogen bonding local structures in liquid water will be presented. The possible use of X-ray spectroscopy to determinate the local arrangements of hydrogen-bonded nanostructures will also been discussed

  11. 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 ...

  12. Hydrogen-Bond Accepting Properties of New Heteroaromatic Ring Chemical Motifs: A Theoretical Study.

    Science.gov (United States)

    Graton, Jérôme; Le Questel, Jean-Yves; Maxwell, Peter; Popelier, Paul

    2016-02-22

    The prediction of hydrogen-bond (H-bond) acceptor ability is crucial in drug design. This important property is quantified in a large pKBHX database of consistently measured values. We aim to expand the chemical diversity of the studied H-bond acceptors and to increase the range of H-bond strength considered. Two quantum chemical descriptors are contrasted, called ΔE(H) (the change in the energy of a topological hydrogen atom upon complexation) and Vmin (the local minimum in the electrostatic potential on the H-bond accepting site). We performed a systematic analysis of the correlations between pKBHX and Vmin for an initial set of 106 compounds (including O- and N-containing subsets, as well as compounds including sulfur, chlorine, and π-bases). Correlations improve for family dependent subsets, and after outlier treatment, a set of 90 compounds was used to set up a linear equation to predict pKBHX from Vmin. This equation and a previously published equation [Green and Popelier J. Chem. Inf. 2014, 54 (2), 553-561], to predict pKBHX from ΔE(H), were used to predict the pKBHX values for 22 potentially biologically active heteroaromatic ring compounds, [Pitt et al. J. Med. Chem. 2009, 52 (9), 2952-2963], among which several structures still remain experimentally unavailable. H-Bond basicity of sp(2) nitrogen sites were consistently predicted with both descriptors. A worse agreement was found with carbonyl acceptor sites, with the stronger deviations observed for the lactam groups. It was shown that secondary interactions involving the neighboring NH group were influencing the results. Substitution of the NH group with an NMe group resulted in an improved consistency from both Vmin and ΔE(H) predictions, the latter being more prominently affected by the methyl substitution. Both approaches appear as efficient procedures for the H-bond ability prediction of novel heteroaromatic rings. Nevertheless, the ΔE(H) parameter presents slight chemical structure limitations

  13. Hydrogen–Hydrogen Bonding in Planar Biphenyl, Predicted by Atoms-In-Molecules Theory, Does Not Exist

    NARCIS (Netherlands)

    Poater, J; Sola, M.; Bickelhaupt, F.M.

    2006-01-01

    Based on an Atoms-in-Molecules (AIM) analysis, Matta et al. (Chem. Eur. J.2003, 9, 1940) recently claimed evidence for the existence of hydrogen–hydrogen bonding between ortho-hydrogen atoms, pointing towards each other from adjacent phenyl groups in planar biphenyl. This AIM result is opposed to

  14. High strength films from oriented, hydrogen-bonded "graphamid" 2D polymer molecular ensembles.

    Science.gov (United States)

    Sandoz-Rosado, Emil; Beaudet, Todd D; Andzelm, Jan W; Wetzel, Eric D

    2018-02-27

    The linear polymer poly(p-phenylene terephthalamide), better known by its tradename Kevlar, is an icon of modern materials science due to its remarkable strength, stiffness, and environmental resistance. Here, we propose a new two-dimensional (2D) polymer, "graphamid", that closely resembles Kevlar in chemical structure, but is mechanically advantaged by virtue of its 2D structure. Using atomistic calculations, we show that graphamid comprises covalently-bonded sheets bridged by a high population of strong intermolecular hydrogen bonds. Molecular and micromechanical calculations predict that these strong intermolecular interactions allow stiff, high strength (6-8 GPa), and tough films from ensembles of finite graphamid molecules. In contrast, traditional 2D materials like graphene have weak intermolecular interactions, leading to ensembles of low strength (0.1-0.5 GPa) and brittle fracture behavior. These results suggest that hydrogen-bonded 2D polymers like graphamid would be transformative in enabling scalable, lightweight, high performance polymer films of unprecedented mechanical performance.

  15. Hydrogen thermal reductive Cu nanowires in low temperature Cu-Cu bonding

    Science.gov (United States)

    Du, Li; Shi, Tielin; Su, Lei; Tang, Zirong; Liao, Guanglan

    2017-07-01

    Nanostructures have attracted great interest in interconnect applications. Herein, we present a novel low temperature, template-less method for directly preparing Cu nanowires through a hydrogen thermal decomposition-reduction route of Cu(OH)2  →  CuO  →  Cu. The thermal treatments are performed at relatively low temperatures of 180 °C-200 °C to meet the low thermal budget in the semiconductor industry. Cu(OH)2 nanowires are completely transformed into Cu nanowires and the morphologies of the nanowires are successfully preserved without shrinkage of volume and size. Sintering of Cu nanowires occurs at a low temperature of 400 °C in Ar ambient and 350 °C in H2 ambient, respectively. Based on this phenomenon, we innovatively apply the as-synthesized Cu nanowires in Cu-Cu bonding at 150 °C-400 °C. The bonded samples exhibit high shear strengths where Cu nanowires have transformed into Cu nanoparticles, mainly attributed to the enhanced atom diffusion with the existence of nanowires. The present work demonstrates the feasibility of hydrogen thermal reductive Cu nanowires in low temperature Cu-Cu bonding.

  16. Versatile cooperative ligand effects in group 9 transition metal catalysis: Applications in transfer hydrogenation & hydrogen autotransfer reactions, ketene & ketene imine synthesis and hydroformylation

    NARCIS (Netherlands)

    Tang, Z.

    2015-01-01

    Cooperative ligand effects of transition metal complexes have a profound impact on the reaction outcome of catalytic reactions, and development of (new) cooperative metal-ligand systems is a hot topic in current catalysis research. Conventional ligands with hydride-accepting/delivering activities

  17. Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family

    Directory of Open Access Journals (Sweden)

    Dallakyan Sargis

    2008-08-01

    Full Text Available Abstract Background Gram-negative bacteria use periplasmic-binding proteins (bPBP to transport nutrients through the periplasm. Despite immense diversity within the recognized substrates, all members of the family share a common fold that includes two domains that are separated by a conserved hinge. The hinge allows the protein to cycle between open (apo and closed (ligated conformations. Conformational changes within the proteins depend on a complex interplay of mechanical and thermodynamic response, which is manifested as an increase in thermal stability and decrease of flexibility upon ligand binding. Results We use a distance constraint model (DCM to quantify the give and take between thermodynamic stability and mechanical flexibility across the bPBP family. Quantitative stability/flexibility relationships (QSFR are readily evaluated because the DCM links mechanical and thermodynamic properties. We have previously demonstrated that QSFR is moderately conserved across a mesophilic/thermophilic RNase H pair, whereas the observed variance indicated that different enthalpy-entropy mechanisms allow similar mechanical response at their respective melting temperatures. Our predictions of heat capacity and free energy show marked diversity across the bPBP family. While backbone flexibility metrics are mostly conserved, cooperativity correlation (long-range couplings also demonstrate considerable amount of variation. Upon ligand removal, heat capacity, melting point, and mechanical rigidity are, as expected, lowered. Nevertheless, significant differences are found in molecular cooperativity correlations that can be explained by the detailed nature of the hydrogen bond network. Conclusion Non-trivial mechanical and thermodynamic variation across the family is explained by differences within the underlying H-bond networks. The mechanism is simple; variation within the H-bond networks result in altered mechanical linkage properties that directly affect

  18. Gas phase hydration of halogenated benzene cations. Is it hydrogen or halogen bonding?

    Science.gov (United States)

    Mason, Kyle A; Pearcy, Adam C; Attah, Isaac K; Platt, Sean P; Aziz, Saadullah G; El-Shall, M Samy

    2017-07-19

    Halogen bonding (XB) non-covalent interactions can be observed in compounds containing chlorine, bromine, or iodine which can form directed close contacts of the type R1-XY-R2, where the halogen X acts as a Lewis acid and Y can be any electron donor moiety including electron lone pairs on hetero atoms such as O and N, or π electrons in olefin double bonds and aromatic conjugated systems. In this work, we present the first evidence for the formation of ionic halogen bonds (IXBs) in the hydration of bromobenzene and iodobenzene radical cations in the gas phase. We present a combined thermochemical investigation using the mass-selected ion mobility (MSIM) technique and density functional theory (DFT) calculations of the stepwise hydration of the fluoro, chloro, bromo, and iodobenzene radical cations. The binding energy associated with the formation of an IXB in the hydration of the iodobenzene cation (11.2 kcal mol -1 ) is about 20% higher than the typical unconventional ionic hydrogen bond (IHB) of the CH δ+ OH 2 interaction. The formation of an IXB in the hydration of the iodobenzene cation involves a significant entropy loss (29 cal mol -1 K -1 ) resulting from the formation of a more ordered structure and a highly directional interaction between the oxygen lone pair of electrons of water and the electropositive region around the iodine atom of the iodobenzene cation. In comparison, the hydration of the fluorobenzene and chlorobenzene cations where IHBs are formed, -ΔS° = 18-21 cal mol -1 K -1 consistent with the formation of less ordered structures and loose interactions. The electrostatic potentials on the lowest energy structures of the hydrated halogenated benzene radical cations show clearly that the formation of an IXB is driven by a positively charged σ-hole on the external side of the halogen atom X along the C-X bond axis. The size of the σ-hole increases significantly in bromobenzene and iodobenzene radical cations which results in strong

  19. Fine Tuning and Specific Binding Sites with a Porous Hydrogen-Bonded Metal-Complex Framework for Gas Selective Separations.

    Science.gov (United States)

    Bao, Zongbi; Xie, Danyan; Chang, Ganggang; Wu, Hui; Li, Liangying; Zhou, Wei; Wang, Hailong; Zhang, Zhiguo; Xing, Huabin; Yang, Qiwei; Zaworotko, Michael J; Ren, Qilong; Chen, Banglin

    2018-04-04

    Research on hydrogen-bonded organic frameworks (HOFs) has been developed for quite a long time; however, those with both established permanent porosities and functional properties are extremely rare due to weak hydrogen-bonding interactions among molecular organic linkers, which are much more fragile and difficult to stabilize. Herein, through judiciously combining the superiority of both the moderately stable coordination bonds in metal-organic frameworks and hydrogen bonds, we have realized a microporous hydrogen-bonded metal-complex or metallotecton framework HOF-21, which not only shows permanent porosity, but also exhibits highly selective separation performance of C 2 H 2 /C 2 H 4 at room temperature. The outstanding separation performance can be ascribed to sieving effect confined by the fine-tuning pores and the superimposed hydrogen-bonding interaction between C 2 H 2 and SiF 6 2- on both ends as validated by both modeling and neutron powder diffraction experiments. More importantly, the collapsed HOF-21 can be restored by simply immersing it into water or salt solution. To the best of our knowledge, such extraordinary water stability and restorability of HOF-21 were observed for the first time in HOFs, underlying the bright perspective of such new HOF materials for their industrial usage.

  20. Bane of Hydrogen-Bond Formation on the Photoinduced Charge-Transfer Process in Donor–Acceptor Systems

    KAUST Repository

    Alsam, Amani Abdu

    2017-03-14

    Controlling the ultrafast dynamical process of photoinduced charge transfer at donor acceptor interfaces remains a major challenge for physical chemistry and solar cell communities. The process is complicated by the involvement of other complex dynamical processes, including hydrogen bond formation, energy transfer, and solvation dynamics occurring on similar time scales. In this study, we explore the remarkable impact of hydrogen-bond formation on the interfacial charge transfer between a negatively charged electron donating anionic porphyrin and a positively charged electron accepting pi-conjugated polymer, as a model system in solvents with different polarities and capabilities for hydiogen bonding using femtosecond transient absorption spectroscopy. Unlike the conventional understanding of the key role of hydrogen bonding in promoting the charge-transfer process, our steadystate and time-resolved results reveal that the intervening hydrogen-bonding environment and, consequently, the probable longer spacing between the donor and acceptor molecules significantly hinders the charge-transfer process between them. These results show that site-specific hydrogen bonding and geometric considerations between donor and acceptor can be exploited to control both the charge-transfer dynamics and its efficiency not only at donor acceptor interfaces but also in complex biological systems.