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Sample records for stable hydrogen bonds

  1. 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.

  2. 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.

  3. High-energy, stable and recycled molecular solar thermal storage materials using AZO/graphene hybrids by optimizing hydrogen bonds.

    Science.gov (United States)

    Luo, Wen; Feng, Yiyu; Qin, Chengqun; Li, Man; Li, Shipei; Cao, Chen; Long, Peng; Liu, Enzuo; Hu, Wenping; Yoshino, Katsumi; Feng, Wei

    2015-10-21

    An important method for establishing a high-energy, stable and recycled molecular solar heat system is by designing and preparing novel photo-isomerizable molecules with a high enthalpy and a long thermal life by controlling molecular interactions. A meta- and ortho-bis-substituted azobenzene chromophore (AZO) is covalently grafted onto reduced graphene oxide (RGO) for solar thermal storage materials. High grafting degree and close-packed molecules enable intermolecular hydrogen bonds (H-bonds) for both trans-(E) and cis-(Z) isomers of AZO on the surface of nanosheets, resulting in a dramatic increase in enthalpy and lifetime. The metastable Z-form of AZO on RGO is thermally stabilized with a half-life of 52 days by steric hindrance and intermolecular H-bonds calculated using density functional theory (DFT). The AZO-RGO fuel shows a high storage capacity of 138 Wh kg(-1) by optimizing intermolecular H-bonds with a good cycling stability for 50 cycles induced by visible light at 520 nm. Our work opens up a new method for making advanced molecular solar thermal storage materials by tuning molecular interactions on a nano-template.

  4. Hydrogen spillover in Pt-single-walled carbon nanotube composites: formation of stable C-H bonds.

    Science.gov (United States)

    Bhowmick, Ranadeep; Rajasekaran, Srivats; Friebel, Daniel; Beasley, Cara; Jiao, Liying; Ogasawara, Hirohito; Dai, Hongjie; Clemens, Bruce; Nilsson, Anders

    2011-04-13

    Using in situ electrical conductivity and ex situ X-ray photoelectron spectroscopy (XPS) measurements, we have examined how the hydrogen uptake of single-walled carbon nanotubes (SWNTs) is influenced by the addition of Pt nanoparticles. The conductivity of platinum-sputtered single-walled carbon nanotubes (Pt-SWNTs) during molecular hydrogen exposure decreased more rapidly than that of the corresponding pure SWNTs, which supports a hydrogenation mechanism facilitated by "spillover" of dissociated hydrogen from the Pt nanoparticles. C 1s XPS spectra indicate that the Pt-SWNTs store hydrogen by means of chemisorption, that is, covalent C-H bond formation: molecular hydrogen charging at elevated pressure (8.27 bar) and room temperature yielded Pt-SWNTs with up to 16 ± 1.5 at. % sp(3)-hybridized carbon atoms, which corresponds to a hydrogen-storage capacity of 1.2 wt % (excluding the weight of Pt nanoparticles). Pt-SWNTs prepared by the Langmuir-Blodgett (LB) technique exhibited the highest Pt/SWNT ratio and also the best hydrogen uptake. © 2011 American Chemical Society

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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 ...

  10. 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.

  11. 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 ...

  12. 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...

  13. 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, ...

  14. 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.

  15. 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...

  16. 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.

  17. 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) ...

  18. Water-Stable Metal-Organic Framework with Three Hydrogen-Bond Acceptors: Versatile Theoretical and Experimental Insights into Adsorption Ability and Thermo-Hydrolytic Stability.

    Science.gov (United States)

    Roztocki, Kornel; Lupa, Magdalena; Sławek, Andrzej; Makowski, Wacław; Senkovska, Irena; Kaskel, Stefan; Matoga, Dariusz

    2018-03-02

    A new microporous cadmium metal-organic framework was synthesized both mechanochemically and in solution by using a sulfonyl-functionalized dicarboxylate linker and an acylhydrazone colinker. The three-dimensional framework is highly stable upon heating to 300 °C as well as in aqueous solutions at elevated temperatures or acidic conditions. The thermally activated material exhibits steep water vapor uptake at low relative pressures at 298 K and excellent recyclability up to 260 °C as confirmed by both quasi-equilibrated temperature-programmed desorption and adsorption (QE-TPDA) method as well as adsorption isotherm measurements. Reversible isotherms and hysteretic isobars recorded for the desorption-adsorption cycles indicate the maximum uptake of 0.19 g/g (at 298 K, up to p/p 0 = 1) or 0.18 g/g (at 1 bar, within 295-375 K range), respectively. The experimental isosteric heat of adsorption (48.9 kJ/mol) indicates noncoordinative interactions of water molecules with the framework. Exchange of the solvent molecules in the as-made material with water, performed in the single-crystal to single-crystal manner, allows direct comparison of both X-ray crystal structures. The single-crystal X-ray diffraction for the water-loaded framework demonstrates the orientation of water clusters in the framework cavities and reveals their strong hydrogen bonding with sulfonyl, acyl, and carboxylate groups of the two linkers. The grand canonical Monte Carlo (GCMC) simulations of H 2 O adsorption corroborate the experimental findings and reveal preferable locations of guest molecules in the framework voids at various pressures. Additionally, both experimental and GCMC simulation insights into the adsorption of CO 2 (at 195 K) on the activated framework are presented.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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...

  4. Stable atomic hydrogen: Polarized atomic beam source

    International Nuclear Information System (INIS)

    Niinikoski, T.O.; Penttilae, S.; Rieubland, J.M.; Rijllart, A.

    1984-01-01

    We have carried out experiments with stable atomic hydrogen with a view to possible applications in polarized targets or polarized atomic beam sources. Recent results from the stabilization apparatus are described. The first stable atomic hydrogen beam source based on the microwave extraction method (which is being tested ) is presented. The effect of the stabilized hydrogen gas density on the properties of the source is discussed. (orig.)

  5. 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.

  6. 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

  7. Hydrogen Bonding to Alkanes: Computational Evidence

    DEFF Research Database (Denmark)

    Hammerum, Steen; Olesen, Solveig Gaarn

    2009-01-01

    The structural, vibrational, and energetic properties of adducts of alkanes and strong cationic proton donors were studied with composite ab initio calculations. Hydrogen bonding in [D-H+ H-alkyl] adducts contributes to a significant degree to the interactions between the two components, which...... 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...

  8. 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.

  9. 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.

  10. 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.

  11. 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 ...

  12. 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.

  13. 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 ...

  14. 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.

  15. 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...

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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 ...

  1. 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 ...

  2. 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

  3. 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 ...

  4. 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

  5. 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

  6. 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...

  7. 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.

  8. 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, ...

  9. 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, ...

  10. 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).

  11. 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...

  12. 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.

  13. 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

  14. 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)

  15. 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

  16. 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

  17. Biogeochemistry of the stable hydrogen isotopes

    International Nuclear Information System (INIS)

    Estep, M.F.; Hoering, T.C.

    1980-01-01

    The fractionation of H isotopes between the water in the growth medium and the organically bonded H from microalgae cultured under conditions, where light intensity and wavelength, temperature, nutrient availability, and the H isotope ratio of the water were controlled, is reproducible and light dependent. All studies were based either on the H isotope ratios of the total organic H or on the lipids, where most of the H is firmly bonded to C. H bonded into other macromolecules, proteins, carbohydrates and nucleic acids, does not exchange with water, when algae are incubated in water enriched with deuterium. Only after the destruction of quaternary H bonds are labile hydrogens in macromolecules free to exchange with water. By growing algae (18 strains), including blue-green algae, green algae and diatoms, in continuous light, the isotope fractionations in photosynthesis were reproducibly -93 to -178 per thousand, depending on the organism tested. This fractionation was not temperature dependent. Microalgae grown in total darkness with an organic substrate did not show the isotope fractionation seen in cells grown in light. In both light- and dark-grown algae, however, additional depletion of deuterium (-30 to -60 per thousand) in cellular organic matter occurs during the metabolism of carbohydrates to form lipids. Plants from several natural populations also fractionated isotopes during photosynthesis by an average of -90 to -110 per thousand. In addition, the organically bonded H in nonsaponifiable lipids was further fractionated by -80 per thousand from that in saponifiable lipids, isolated from two geographically distinct populations of marsh plants. This difference between H isotope ratios of these two groups of lipids provides an endogenous isotopic marker. (author)

  18. 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 ...

  19. 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...

  20. 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...

  1. 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

  2. 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.

  3. 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.

  4. 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...

  5. 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 ...

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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, ...

  13. 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 ...

  14. 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 ...

  15. 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).

  16. 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 ...

  17. 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 ...

  18. 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).

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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...

  9. 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.

  10. 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)

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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:.

  18. Alkyl Radicals as Hydrogen Bond Acceptors: Computational Evidence

    DEFF Research Database (Denmark)

    Hammerum, Steen

    2009-01-01

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

  19. 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.

  20. 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

  1. 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 ...

  2. 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 ...

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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…

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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 ...

  7. 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 ...

  8. 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 ...

  9. 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 ...

  10. 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 ...

  11. 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)

  12. 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.

  13. 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 ...

  14. 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 ...

  15. 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 ...

  16. 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.

  17. 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.

  18. 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 ...

  19. 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 ...

  20. 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,.

  1. 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].

  2. 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.

  3. 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.

  4. [Fractionation of hydrogen stable isotopes in the human body].

    Science.gov (United States)

    Siniak, Iu E; Grigor'ev, A I; Skuratov, V M; Ivanova, S M; Pokrovskiĭ, B G

    2006-01-01

    Fractionation of hydrogen stable isotopes was studied in 9 human subjects in a chamber with normal air pressure imitating a space cabin. Mass-spectrometry of isotopes in blood, urine, saliva, and potable water evidenced increases in the contents of heavy H isotope (deuterium) in the body liquids as compared with water. These results support one of the theories according to which the human organism eliminates heavy stable isotopes of biogenous chemical elements.

  5. 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

  6. 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

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

    Science.gov (United States)

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

    2011-10-28

    Chiral recognition has been studied in neutral or ionic weakly bound complexes isolated in the gas phase by combining laser spectroscopy and quantum chemical calculations. Neutral complexes of the two enantiomers of lactic ester derivatives with chiral chromophores have been formed in a supersonic expansion. Their structure has been elucidated by means of IR-UV double resonance spectroscopy in the 3 μm region. In both systems described here, the main interaction ensuring the cohesion of the complex is a strong hydrogen bond between the chromophore and methyl-lactate. However, an additional hydrogen bond of much weaker strength plays a discriminative role between the two enantiomers. For example, the 1:1 heterochiral complex between R-(+)-2-naphthyl-ethanol and S-(+) methyl-lactate is observed, in contrast with the 1:1 homochiral complex which lacks this additional hydrogen bond. On the other hand, the same kind of insertion structures is formed for the complex between S-(±)-cis-1-amino-indan-2-ol and the two enantiomers of methyl-lactate, but an additional addition complex is formed for R-methyl-lactate only. This selectivity rests on the formation of a weak CHπ interaction which is not possible for the other enantiomer. The protonated dimers of Cinchona alkaloids, namely quinine, quinidine, cinchonine and cinchonidine, have been isolated in an ion trap and studied by IRMPD spectroscopy in the region of the ν(OH) and ν(NH) stretch modes. The protonation site is located on the alkaloid nitrogen which acts as a strong hydrogen bond donor in all the dimers studied. While the nature of the intermolecular hydrogen bond is similar in the homochiral and heterochiral complexes, the heterochiral complex displays an additional weak CHO hydrogen bond located on its neutral part, which results in slightly different spectroscopic fingerprints in the ν(OH) stretch region. This first spectroscopic evidence of chiral recognition in protonated dimers opens the way to the

  8. 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.

  9. 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.

  10. 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.

  11. 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...

  12. 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)

  13. 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...

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. The influence of large-amplitude librational motion on the hydrogen bond energy for alcohol–water complexes

    DEFF Research Database (Denmark)

    Andersen, Jonas; Heimdal, J.; Larsen, René Wugt

    2015-01-01

    unambiguous assignments of the intermolecular high-frequency out-of-plane and low-frequency in-plane donor OH librational modes for mixed alcohol–water complexes. The vibrational assignments confirm directly that water acts as the hydrogen bond donor in the most stable mixed complexes and the tertiary alcohol...

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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 ...

  4. 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.

  5. 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.

  6. 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 ...

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. Insights into the Electronic Structure of Ozone and Sulfur Dioxide from Generalized Valence Bond Theory: Addition of Hydrogen Atoms.

    Science.gov (United States)

    Lindquist, Beth A; Takeshita, Tyler Y; Dunning, Thom H

    2016-05-05

    Ozone (O3) and sulfur dioxide (SO2) are valence isoelectronic species, yet their properties and reactivities differ dramatically. In particular, O3 is highly reactive, whereas SO2 is chemically relatively stable. In this paper, we investigate serial addition of hydrogen atoms to both the terminal atoms of O3 and SO2 and to the central atom of these species. It is well-known that the terminal atoms of O3 are much more amenable to bond formation than those of SO2. We show that the differences in the electronic structure of the π systems in the parent triatomic species account for the differences in the addition of hydrogen atoms to the terminal atoms of O3 and SO2. Further, we find that the π system in SO2, which is a recoupled pair bond dyad, facilitates the addition of hydrogen atoms to the sulfur atom, resulting in stable HSO2 and H2SO2 species.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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)

  18. Two-dimensional gold nanostructures with high activity for selective oxidation of carbon–hydrogen bonds

    KAUST Repository

    Wang, Liang

    2015-04-22

    Efficient synthesis of stable two-dimensional (2D) noble metal catalysts is a challenging topic. Here we report the facile synthesis of 2D gold nanosheets via a wet chemistry method, by using layered double hydroxide as the template. Detailed characterization with electron microscopy and X-ray photoelectron spectroscopy demonstrates that the nanosheets are negatively charged and [001] oriented with thicknesses varying from single to a few atomic layers. X-ray absorption spectroscopy reveals unusually low gold–gold coordination numbers. These gold nanosheets exhibit high catalytic activity and stability in the solvent-free selective oxidation of carbon–hydrogen bonds with molecular oxygen.

  19. 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

  20. 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 ...

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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}.

  6. 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 .

  7. 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.

  8. Phase transitions and hydrogen bonding in deuterated calcium hydroxide: High-pressure and high-temperature neutron diffraction measurements

    International Nuclear Information System (INIS)

    Iizuka, Riko; Komatsu, Kazuki; Kagi, Hiroyuki; Nagai, Takaya; Sano-Furukawa, Asami; Hattori, Takanori; Gotou, Hirotada; Yagi, Takehiko

    2014-01-01

    In situ neutron diffraction measurements combined with the pulsed neutron source at the Japan Proton Accelerator Research Complex (J-PARC) were conducted on high-pressure polymorphs of deuterated portlandite (Ca(OD) 2 ) using a Paris–Edinburgh cell and a multi-anvil press. The atomic positions including hydrogen for the unquenchable high-pressure phase at room temperature (phase II′) were first clarified. The bent hydrogen bonds under high pressure were consistent with results from Raman spectroscopy. The structure of the high-pressure and high-temperature phase (Phase II) was concordant with that observed previously by another group for a recovered sample. The observations elucidate the phase transition mechanism among the polymorphs, which involves the sliding of CaO polyhedral layers, position modulations of Ca atoms, and recombination of Ca–O bonds accompanied by the reorientation of hydrogen to form more stable hydrogen bonds. - Graphical abstract: Crystal structures of high-pressure polymorphs of Ca(OD) 2 , (a) at room temperature (phase II′) and (b) at high temperature (phase II), were obtained from in situ neutron diffraction measurements. - Highlights: • We measured in situ neutron diffraction of high-pressure polymorphs of Ca(OD) 2 . • Hydrogen positions of the high-pressure phase are first determined. • The obtained hydrogen bonds reasonably explain Raman peaks of OH stretching modes. • A phase transition mechanism among the polymorphs is proposed

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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...

  17. 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.

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

    Science.gov (United States)

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

    2017-04-01

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

  19. 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.

  20. 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.

  1. Hydrogen bond strength in membrane proteins probed by time-resolved1H-detected solid-state NMR and MD simulations.

    Science.gov (United States)

    Medeiros-Silva, João; Jekhmane, Shehrazade; Baldus, Marc; Weingarth, Markus

    2017-10-01

    1 H-detected solid-state NMR in combination with 1 H/ 2 D exchange steps allows for the direct identification of very strong hydrogen bonds in membrane proteins. On the example of the membrane-embedded potassium channel KcsA, we quantify the longevity of such very strong hydrogen bonds by combining time-resolved 1 H-detected solid-state NMR experiments and molecular dynamics simulations. In particular, we show that the carboxyl-side chain of the highly conserved residue Glu51 is involved in ultra-strong hydrogen bonds, which are fully-water-exposed and yet stable for weeks. The astonishing stability of these hydrogen bonds is important for the structural integrity of potassium channels, which we further corroborate by computational studies. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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...

  7. 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.

  8. 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…

  9. 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.

  10. 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 ...

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. Hydrogen bond symmetrization and superconducting phase of HBr and HCl under high pressure: An ab initio study.

    Science.gov (United States)

    Duan, Defang; Tian, Fubo; He, Zhi; Meng, Xing; Wang, Liancheng; Chen, Changbo; Zhao, Xiusong; Liu, Bingbing; Cui, Tian

    2010-08-21

    Ab initio calculations are performed to probe the hydrogen bonding, structural, and superconducting behaviors of HBr and HCl under high pressure. The calculated results show that the hydrogen bond symmetrization (Cmc2(1)-->Cmcm transition) of HBr and HCl occurs at 25 and 40 GPa, respectively, which can be attributed to the symmetry stretching A(1) mode softening. After hydrogen bond symmetrization, a pressure-induced soft transverse acoustic phonon mode of Cmcm phase is identified and a unique metallic phase with monoclinic structure of P2(1)/m (4 molecules/cell) for both compounds is revealed by ab initio phonon calculations. This phase preserves the symmetric hydrogen bond and is stable in the pressure range from 134 to 196 GPa for HBr and above 233 GPa for HCl, while HBr is predicted to decompose into Br(2)+H(2) above 196 GPa. Perturbative linear-response calculations predict that the phase P2(1)/m is a superconductor with T(c) of 27-34 K for HBr at 160 GPa and 9-14 K for HCl at 280 GPa.

  16. 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

  17. 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...

  18. 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

  19. 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

  20. Hydrogen-incorporated ZnO nanowire films: stable and high electrical conductivity

    Science.gov (United States)

    Kushwaha, Ajay; Aslam, M.

    2013-12-01

    Post-growth hydrogen annealing treatment of highly oriented ZnO nanowire (NW) films (ZnO : H) results in high electrical conductivity (3.7 × 103 S m-1) and fully suppressed defect emission at room temperature. The formation of hydrogen-related vacancy complexes is responsible for the suppression of vacancies ( V_{o}^{+} and V_{o}^{2+} ), leading to a reduction in defect-based emission. ZnO : H NW films show five orders larger stable electrical conductance with a four-fold increment in carrier mobility (7-28 cm2 V-1 s-1). As compared with pristine NWs, the carrier concentration in ZnO : H NW films increases from 1015 to 1019 cm-3, which is in the range of commercial transparent conducting oxides. X-ray photoelectron spectroscopy and secondary ion mass spectrometry analyses reveal stable OH bond formation, which strongly supports the prediction of H doping. These films offer a promising conducting oxide platform for photovoltaic applications.

  1. 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

    interaction potentials with the electron lone pairs of the oxygen atom of the water molecules and thus IXBs provide the most stable hydrated structures of the bromobenzene and iodobenzene radical cations. The results clearly distinguish the hydration behaviors resulting from the ionic hydrogen and halogen bonding interactions of fluorobenzene and iodobenzene cations, respectively, and establish the different bonding and structural features of the two interactions.

  2. 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)

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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...

  10. 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.

  11. 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.

  12. 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.

  13. Insights into Wilson's Warbler migration from analyses of hydrogen stable-isotope ratios

    Science.gov (United States)

    Jeffrey F. Kelly; Viorel Atudorei; Zachary D. Sharp; Deborah M. Finch

    2002-01-01

    Our ability to link the breeding locations of individual passerines to migration stopover sites and wintering locations is limited. Stable isotopes of hydrogen contained in bird feathers have recently shown potential in this regard. We measured hydrogen stable-isotope ratios (deltaD) of feathers from breeding, migrating, and wintering Wilson's Warblers. Analyses...

  14. Olefin metathesis and quadruple hydrogen bonding: A powerful combination in multistep supramolecular synthesis

    Science.gov (United States)

    Scherman, Oren A.; Ligthart, G. B. W. L.; Ohkawa, Haruki; Sijbesma, Rint P.; Meijer, E. W.

    2006-08-01

    We show that combining concepts generally used in covalent organic synthesis such as retrosynthetic analysis and the use of protecting groups, and applying them to the self-assembly of polymeric building blocks in multiple steps, results in a powerful strategy for the self-assembly of dynamic materials with a high level of architectural control. We present a highly efficient synthesis of bifunctional telechelic polymers by ring-opening metathesis polymerization (ROMP) with complementary quadruple hydrogen-bonding motifs. Because the degree of functionality for the polymers is 2.0, the formation of alternating, blocky copolymers was demonstrated in both solution and the bulk leading to stable, microphase-separated copolymer morphologies. ring-opening metathesis polymerization | self-assembly | block copolymer | retrosynthesis

  15. Relative stabilities and the spectral signatures of stacked and hydrogen-bonded dimers of serotonin

    Science.gov (United States)

    Dev, S.; Giri, K.; Majumder, M.; Sathyamurthy, N.

    2015-10-01

    The O-HṡṡṡN hydrogen-bonded dimer of serotonin is shown to be more stable than the stacked dimer in its ground electronic state, by using the Møller-Plesset second-order perturbation theory (MP2) and the 6-31g** basis set. The vertical excitation energy for the lowest π → π* transition for the monomer as well as the dimer is predicted by time-dependent density functional theory. The experimentally observed red shift of excitation wavelength on oligomerisation is explained in terms of the change in the HOMO-LUMO energy gap due to complex formation. The impact of dimer formation on the proton magnetic resonance spectrum of serotonin monomer is also examined.

  16. 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)

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. Stable catalyst layers for hydrogen permeable composite membranes

    Science.gov (United States)

    Way, J. Douglas; Wolden, Colin A

    2014-01-07

    The present invention provides a hydrogen separation membrane based on nanoporous, composite metal carbide or metal sulfide coated membranes capable of high flux and permselectivity for hydrogen without platinum group metals. The present invention is capable of being operated over a broad temperature range, including at elevated temperatures, while maintaining hydrogen selectivity.

  2. 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)

  3. 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.

  4. 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.

  5. Highly hydrothermally stable microporous silica membranes for hydrogen separation.

    Science.gov (United States)

    Wei, Qi; Wang, Fei; Nie, Zuo-Ren; Song, Chun-Lin; Wang, Yan-Li; Li, Qun-Yan

    2008-08-07

    Fluorocarbon-modified silica membranes were deposited on gamma-Al2O3/alpha-Al2O3 supports by the sol-gel technique for hydrogen separation. The hydrophobic property, pore structure, gas transport and separation performance, and hydrothermal stability of the modified membranes were investigated. It is observed that the water contact angle increases from 27.2+/-1.5 degrees for the pure silica membranes to 115.0+/-1.2 degrees for the modified ones with a (trifluoropropyl)triethoxysilane (TFPTES)/tetraethyl orthosilicate (TEOS) molar ratio of 0.6. The modified membranes preserve a microporous structure with a micropore volume of 0.14 cm3/g and a pore size of approximately 0.5 nm. A single gas permeation of H2 and CO2 through the modified membranes presents small positive apparent thermal activation energies, indicating a dominant microporous membrane transport. At 200 degrees C, a single H2 permeance of 3.1x10(-6) mol m(-2) s(-1) Pa(-1) and a H2/CO2 permselectivity of 15.2 were obtained after proper correction for the support resistance and the contribution from the defects. In the gas mixture measurement, the H2 permeance and the H2/CO2 separation factor almost remain constant at 200 degrees C with a water vapor pressure of 1.2x10(4) Pa for at least 220 h, indicating that the modified membranes are hydrothermally stable, benefiting from the integrity of the microporous structure due to the fluorocarbon modification.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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 ).

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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...

  3. 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

  4. Covalent functionalization of graphene by azobenzene with molecular hydrogen bonds for long-term solar thermal storage.

    Science.gov (United States)

    Feng, Yiyu; Liu, Hongpo; Luo, Wen; Liu, Enzuo; Zhao, Naiqin; Yoshino, Katsumi; Feng, Wei

    2013-11-19

    Reduced graphene oxide-azobenzene (RGO-AZO) hybrids were prepared via covalent functionalization for long-term solar thermal storage. Thermal barrier (ΔEa) of cis to tran reversion and thermal storage (ΔH) were improved by molecular hydrogen bonds (H-bonds) through ortho- or para-substitution of AZO. Intramolecular H-bonds thermally stabilized cis-ortho-AZO on RGO with a long-term half-life of 5400 h (ΔEa = 1.2 eV), which was much longer than that of RGO-para-AZO (116 h). RGO-para-AZO with one intermolecular H-bond showed a high density of thermal storage up to 269.8 kJ kg(-1) compared with RGO-ortho-AZO (149.6 kJ kg(-1)) with multiple intra- and intermolecular H-bonds of AZO according to relaxed stable structures. Thermal storage in experiment was the same order magnitude to theoretical data based on ΔH calculated by density functional theory and packing density. Photoactive RGO-AZO hybrid can be developed for high-performance solar thermal storage by optimizing molecular H-bonds.

  5. 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

  6. 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.

  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.

    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.

  8. 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.

  9. Effect of Substituents on the Bond Strength of Air-Stable Dicyanomethyl Radical Thermochromes.

    Science.gov (United States)

    Peterson, Joshua P; Geraskina, Margarita R; Zhang, Rui; Winter, Arthur H

    2017-06-16

    A series of substituted aryl dicyanomethyl radicals were synthesized, and the bonding thermodynamic parameters for self-dimerization were determined from van't Hoff plots obtained from variable-temperature electron paramagnetic resonance and ultraviolet-visible spectroscopy. At low temperatures, the radicals dimerize, but the colored, air-stable free radicals return upon heating. Heating and cooling cycles (5-95 °C) can be repeated without radical degradation and with striking thermochromic behavior. We find a linear free energy relationship between the Hammett para substituent parameter and the dimerization equilibrium constant, with para electron-donating substituents leading to a weaker bond and electron-withdrawing substituents leading to stronger bonds, following a captodative effect. Density functional theory investigations [B98D/6-31+G(d,p)] reveal that the dimers prefer a slip-stacked geometry and feature elongated bonds.

  10. Weak hydrogen bond topology in 1,1-difluoroethane dimer: A rotational study.

    Science.gov (United States)

    Chen, Junhua; Zheng, Yang; Wang, Juan; Feng, Gang; Xia, Zhining; Gou, Qian

    2017-09-07

    The rotational spectrum of the 1,1-difluoroethane dimer has been investigated by pulsed-jet Fourier transform microwave spectroscopy. Two most stable isomers have been detected, which are both stabilized by a network of three C-H⋯F-C weak hydrogen bonds: in the most stable isomer, two difluoromethyl C-H groups and one methyl C-H group act as the weak proton donors whilst in the second isomer, two methyl C-H groups and one difluoromethyl C-H group act as the weak proton donors. For the global minimum, the measurements have also been extended to its four 13 C isotopologues in natural abundance, allowing a precise, although partial, structural determination. Relative intensity measurements on a set of μ a -type transitions allowed estimating the relative population ratio of the two isomers as N I /N II ∼ 6/1 in the pulsed jet, indicating a much larger energy gap between these two isomers than that expected from ab initio calculation, consistent with the result from pseudo-diatomic dissociation energies estimation.

  11. Non-equilibrium hydrogen exchange for determination of H-bond strength and water accessibility in solid proteins.

    Science.gov (United States)

    Grohe, Kristof; Movellan, Kumar Tekwani; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus

    2017-05-01

    We demonstrate measurement of non-equilibrium backbone amide hydrogen-deuterium exchange rates (HDX) for solid proteins. The target of this study are the slowly exchanging residues in solid samples, which are associated with stable secondary-structural elements of proteins. These hydrogen exchange processes escape methods measuring equilibrium exchange rates of faster processes. The method was applied to a micro-crystalline preparation of the SH3 domain of chicken α-spectrin. Therefore, from a 100% back-exchanged micro-crystalline protein preparation, the supernatant buffer was exchanged by a partially deuterated buffer to reach a final protonation level of approximately 20% before packing the sample in a 1.3 mm rotor. Tracking of the HN peak intensities for 2 weeks reports on site-specific hydrogen bond strength and also likely reflects water accessibility in a qualitative manner. H/D exchange can be directly determined for hydrogen-bonded amides using 1 H detection under fast magic angle spinning. This approach complements existing methods and provides the means to elucidate interesting site-specific characteristics for protein functionality in the solid state.

  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. 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.

  1. 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

  2. Stable classical orbits for atomic hydrogen in magnetic and rotating electric fields

    International Nuclear Information System (INIS)

    Kazanskij, A.K.

    1989-01-01

    A hydrogen atom, being in a magnetic field and in a field of circulation-polarized electromagnetic wave propagating along the magnetic field is considered. Classical orbits in the hydrogen atom, being in various external fields, were investigated to find stable orbits. Determination of a stationary region for considering conditions is the result of invesigation

  3. Three-dimensional hydrogen-bonded structures in the hydrated proton-transfer salts of isonipecotamide with the dicarboxylic oxalic and adipic acid homologues.

    Science.gov (United States)

    Smith, Graham; Wermuth, Urs D

    2013-10-01

    The structures of the 1:1 hydrated proton-transfer compounds of isonipecotamide (piperidine-4-carboxamide) with oxalic acid, 4-carbamoylpiperidinium hydrogen oxalate dihydrate, C6H13N2O(+)·C2HO4(-)·2H2O, (I), and with adipic acid, bis(4-carbamoylpiperidinium) adipate dihydrate, 2C6H13N2O(+)·C6H8O4(2-)·2H2O, (II), are three-dimensional hydrogen-bonded constructs involving several different types of enlarged water-bridged cyclic associations. In the structure of (I), the oxalate monoanions give head-to-tail carboxylic acid O-H···O(carboxyl) hydrogen-bonding interactions, forming C(5) chain substructures which extend along a. The isonipecotamide cations also give parallel chain substructures through amide N-H···O hydrogen bonds, the chains being linked across b and down c by alternating water bridges involving both carboxyl and amide O-atom acceptors and amide and piperidinium N-H···O(carboxyl) hydrogen bonds, generating cyclic R4(3)(10) and R3(2)(11) motifs. In the structure of (II), the asymmetric unit comprises a piperidinium cation, half an adipate dianion, which lies across a crystallographic inversion centre, and a solvent water molecule. In the crystal structure, the two inversion-related cations are interlinked through the two water molecules, which act as acceptors in dual amide N-H···O(water) hydrogen bonds, to give a cyclic R4(2)(8) association which is conjoined with an R4(4)(12) motif. Further N-H···O(water), water O-H···O(amide) and piperidinium N-H···O(carboxyl) hydrogen bonds give the overall three-dimensional structure. The structures reported here further demonstrate the utility of the isonipecotamide cation as a synthon for the generation of stable hydrogen-bonded structures. The presence of solvent water molecules in these structures is largely responsible for the non-occurrence of the common hydrogen-bonded amide-amide dimer, promoting instead various expanded cyclic hydrogen-bonding motifs.

  4. Immobilized Bis-Indenyl Ligands for Stable and Cost-Effective Metallocene Catalysts of Hydrogenation and Polymerization Reactions

    Science.gov (United States)

    Simerly, Thomas Max

    Reactions of catalytic hydrogenations and polymerizations are widely used in industry for manufacture of fine chemicals, pharmaceuticals, and plastics. Homogeneous catalysts for the processes that have low stability and their separation is difficult. Therefore, the development of new highly active and stable catalysts for hydrogenations and polymerizations is a necessity. The objective of this research was the development of a strategy for immobilization of heterogeneous metallocene catalysts. First, a methodology of immobilization of bis-indenyl ligands on the surface of mesoporous silica gel was designed. Four bis-indenyl ligands containing functionalized tethers of various lengths with terminal alkene groups were synthesized. All bis-indenyl ligands were immobilized on the surface of mesoporous functionalized silica gel by two methods: hydrosilylation and thiol-ene coupling of the double bond. After comparing the results, the second strategy was chosen as more efficient. The materials can be used further as intermediates for synthesis of supported metallocene catalysts.

  5. 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.

  6. 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.

  7. Hydrogen bond assisted interaction of glutamine with chromium (III) complex of 8-hydroxyquinoline: Experimental and theoretical studies

    Science.gov (United States)

    Narayanan, Jayanthi; Carlos-Alberto, Aguilar H.; Arturo, Lazarini M.; Höpfl, Herbert; Enrique-Fernando, Velazquez C.; Fernando, Rocha A.; Fernando-Toyohiko, Wakida K.; Velazquez-Lopez, José E.; Lesli, Arroyo O.

    2018-03-01

    Chromium (III) complex [Cr (hq)3;C2H5OH] of 8-hydroxyquinoline (hq) was prepared and its structure was resolved by X-ray diffraction analysis at low-temperature, showing that Cr3+ ion presents in distorted octahedral geometry, and it is consistent with the DFT optimized structure. It was observed that solvent ethanol is involved a hydrogen bond with 8-hydroxyquinoline anion. Furthermore, the molecular orbital contributions to spectral bands observed for the complex were determined by TD-DFT. The interaction of [Cr (hq)3;C2H5OH] with glutamine (Gln) or asparagine (Asn) shows that the complex binds effectively with glutamine through hydrogen bonding (H2N+-HṡṡṡOethanol) to form a possible stable adduct [Cr (hq)3;C2H5OH)Gln], yielding its binding constant 10,000 times greater (1.4315 M-1) than that for Asn (5.0 × 10-4 M-1). This is apparently due to the formation of stable secondary coordination sphere through the hydrogen bond between the metal complex with Gln. This observation is good agreement with the total molecular energy as well as with the molecular orbital study, i.e. in the DFT calculation, a lower total molecular energy (-8299,549.441 kcal/mmol) for [Cr (hq)3;C2H5OH) Gln] was obtained than that resulted for [Cr (hq)3;C2H5OH)Asn] (-8194,799.867 kcal/mmol), establishing ethanol effectively stabilizes the interaction between glutamine and the complex. Finally, antibacterial properties of [Cr (hq)3;C2H5OH] against Gram positive Bacillus cereus and Gram negative Escherichia coli was also studied, and compared its bacterial growths for its adducts of glutamine or of asparagine.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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 ...

  16. 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 ...

  17. 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 ...

  18. 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.

  19. 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.

  20. 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 ...

  1. 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.

  2. 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.

  3. 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)....

  4. 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....

  5. 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.

  6. 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....

  7. 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.

  8. 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.)

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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...

  18. 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

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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...

  5. 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

  6. 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...

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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…

  12. 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…

  13. 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.

  14. 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” ...

  15. 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

  16. 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 ...

  17. 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...

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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 ...

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Expanding the isotopic toolbox: Applications of hydrogen and oxygen stable isotope ratios to food web studies

    OpenAIRE

    Hannah B Vander Zanden; David X Soto; Gabriel J Bowen; Keith A Hobson; Keith A Hobson

    2016-01-01

    The measurement of stable carbon (δ13C) and nitrogen (δ15N) isotopes in tissues of organisms has formed the foundation of isotopic food web reconstructions, as these values directly reflect assimilated diet. In contrast, stable hydrogen (δ2H) and oxygen (δ18O) isotope measurements have typically been reserved for studies of migratory origin and paleoclimate reconstruction based on systematic relationships between organismal tissue and local environmental water. Recently, innovative applicat...

  14. Expanding the Isotopic Toolbox: Applications of Hydrogen and Oxygen Stable Isotope Ratios to Food Web Studies

    OpenAIRE

    Vander Zanden, Hannah B.; Soto, David X.; Bowen, Gabriel J.; Hobson, Keith A.

    2016-01-01

    The measurement of stable carbon (δ13C) and nitrogen (δ15N) isotopes in tissues of organisms has formed the foundation of isotopic food web reconstructions, as these values directly reflect assimilated diet. In contrast, stable hydrogen (δ2H) and oxygen (δ18O) isotope measurements have typically been reserved for studies of migratory origin and paleoclimate reconstruction based on systematic relationships between organismal tissue and local environmental water. Recently, innovative applicatio...

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Vibrational Spectroscopy of Intramolecular Hydrogen Bonds in the Infrared and Near-Infrared Regions

    DEFF Research Database (Denmark)

    Schrøder, Sidsel Dahl

    and 1,4-diaminobutane). Experimentally, the hydrogen bonds have been studied with vibrational spectroscopy in the infrared and near-infrared regions. The focus is primarily on spectra recorded in the near-infrared regions, which in these studies are dominated by O-H and N-H stretching overtones....... 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...

  9. Conformational properties of oxazole-amino acids: effect of the intramolecular N-H···N hydrogen bond.

    Science.gov (United States)

    Siodłak, Dawid; Staś, Monika; Broda, Małgorzata A; Bujak, Maciej; Lis, Tadeusz

    2014-03-06

    Oxazole ring occurs in numerous natural peptides, but conformational properties of the amino acid residue containing the oxazole ring in place of the C-terminal amide bond are poorly recognized. A series of model compounds constituted by the oxazole-amino acids occurring in nature, that is, oxazole-alanine (L-Ala-Ozl), oxazole-dehydroalanine (ΔAla-Ozl), and oxazole-dehydrobutyrine ((Z)-ΔAbu-Ozl), was investigated using theoretical calculations supported by FTIR and NMR spectra and single-crystal X-ray diffraction. It was found that the main feature of the studied oxazole-amino acids is the stable conformation β2 with the torsion angles φ and ψ of -150°, -10° for L-Ala-Ozl, -180°, 0° for ΔAla-Ozl, and -120°, 0° for (Z)-ΔAbu-Ozl, respectively. The conformation β2 is stabilized by the intramolecular N-H···N hydrogen bond and predominates in the low polar environment. In the case of the oxazole-dehydroamino acids, the π-electron conjugation that is spread on the oxazole ring and C(α)═C(β) double bond is an additional stabilizing interaction. The tendency to adopt the conformation β2 clearly decreases with increasing the polarity of environment, but still the oxazole-dehydroamino acids are considered to be more rigid and resistant to conformational changes.

  10. Stable Failure-Inducing Micro-Silica Aqua Epoxy Bonding Material for Floating Concrete Module Connection

    Directory of Open Access Journals (Sweden)

    Jang-Ho Jay Kim

    2015-11-01

    Full Text Available Many recent studies in the development of floating concrete structures focused on a connection system made of modules. In the connection system, the modules are designed to be attached by pre-stressing (PS while floating on the water, which exposes them to loads on the surface of the water. Therefore, the development of a pre-connection material becomes critical to ensure successful bonding of floating concrete modules. Micro-silica mixed aqua-epoxy (MSAE was developed for this task. To find the proper MSAE mix proportion, 0% to 4% micro-silica was mixed in a standard mixture of aqua-epoxy for material testing. Also, the effect of micro-silica on the viscosity of the aqua epoxy was evaluated by controlling the epoxy silane at proportions of 0%, ±5%, and ±10%. After completion of the performance tests of the MSAE, we evaluated the effect of MSAE in a connected structure. The plain unreinforced concrete module joint specimens applied with MSAE at thicknesses of 5, 10, and 20 mm were prepared to be tested. Finally, we evaluated the performance of MSAE-applied reinforced concrete (RC module specimens connected by PS tendons, and these were compared with those of continuous RC and non-MSAE-applied beams. The results showed that the mix of micro-silica in the aqua-epoxy changed the performance of the aqua-epoxy and the mix ratio of 2% micro-silica gave a stable failure behavior. The flexural capacity of concrete blocks bonded with MSAE changed according to the bond thickness and was better than that of concrete blocks bonded with aqua-epoxy without micro-silica. Even though MSAE insignificantly increases the load-carrying capacity of the attached concrete module structure, the stress concentration reduction effect stabilized the failure of the structure.

  11. 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.

  12. 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.

  13. Energy transport mechanism in the form of proton soliton in a one-dimensional hydrogen-bonded polypeptide chain.

    Science.gov (United States)

    Kavitha, L; Priya, R; Ayyappan, N; Gopi, D; Jayanthi, S

    2016-01-01

    The dynamics of protons in a one-dimensional hydrogen-bonded (HB) polypeptide chain (PC) is investigated theoretically. A new Hamiltonian is formulated with the inclusion of higher-order molecular interactions between peptide groups (PGs). The wave function of the excitation state of a single particle is replaced by a new wave function of a two-quanta quasi-coherent state. The dynamics is governed by a higher-order nonlinear Schrödinger equation and the energy transport is performed by the proton soliton. A nonlinear multiple-scale perturbation analysis has been performed and the evolution of soliton parameters such as velocity and amplitude is explored numerically. The proton soliton is thermally stable and very robust against these perturbations. The energy transport by the proton soliton is more appropriate to understand the mechanism of energy transfer in biological processes such as muscle contraction, DNA replication, and neuro-electric pulse transfer on biomembranes.

  14. 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.

  15. 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.

  16. 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

  17. 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...

  18. 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...

  19. 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)

  20. 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.

  1. 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...

  2. 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.

  3. 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...

  4. 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.

  5. 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.

  6. 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.

  7. Stable hydrogen and carbon isotope ratios of extractable hydrocarbons in the Murchison meteorite

    Science.gov (United States)

    Krishnamurthy, R. V.; Epstein, S.; Pizzarello, S.; Cronin, J. R.; Yuen, G. U.

    1991-01-01

    A fairly fool-proof method to ensure that the compounds isolated from meteorites are truly part of the meteorites and not an artifact introduced by exposure to the terrestrial environment, storage, or handling is presented. The stable carbon and hydrogen isotope ratios in several of the chemical compounds extracted from the Murchison meteorite were measured. The results obtained by studying the amino acids in this meteorite gave very unusual hydrogen and carbon isotope ratios. The technique was extended to the different classes of hydrocarbons and the hydrocarbons were isolated using a variety of separation techniques. The results and methods used in this investigation are described in this two page paper.

  8. 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

  9. 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.

  10. 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)

  11. 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).

  12. 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).

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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.

  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. 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.

  6. 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.

  7. 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.

  8. 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.

  9. On the correlation between hydrogen bonding and melting points in the inositols

    Directory of Open Access Journals (Sweden)

    Sándor L. Bekö

    2014-01-01

    Full Text Available Inositol, 1,2,3,4,5,6-hexahydroxycyclohexane, exists in nine stereoisomers with different crystal structures and melting points. In a previous paper on the relationship between the melting points of the inositols and the hydrogen-bonding patterns in their crystal structures [Simperler et al. (2006. CrystEngComm 8, 589], it was noted that although all inositol crystal structures known at that time contained 12 hydrogen bonds per molecule, their melting points span a large range of about 170 °C. Our preliminary investigations suggested that the highest melting point must be corrected for the effect of molecular symmetry, and that the three lowest melting points may need to be revised. This prompted a full investigation, with additional experiments on six of the nine inositols. Thirteen new phases were discovered; for all of these their crystal structures were examined. The crystal structures of eight ordered phases could be determined, of which seven were obtained from laboratory X-ray powder diffraction data. Five additional phases turned out to be rotator phases and only their unit cells could be determined. Two previously unknown melting points were measured, as well as most enthalpies of melting. Several previously reported melting points were shown to be solid-to-solid phase transitions or decomposition points. Our experiments have revealed a complex picture of phases, rotator phases and phase transitions, in which a simple correlation between melting points and hydrogen-bonding patterns is not feasible.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. Caution on the use of liquid nitrogen traps in stable hydrogen isotope-ratio mass spectrometry

    Science.gov (United States)

    Coplen, T.B.; Qi, H.

    2010-01-01

    An anomalous stable hydrogen isotopic fractionation of 4 ??? in gaseous hydrogen has been correlated with the process of adding liquid nitrogen (LN2) to top off the dewar of a stainless-steel water trap on a gaseous hydrogen-water platinum equilibration system. Although the cause of this isotopic fractionation is unknown, its effect can be mitigated by (1) increasing the capacity of any dewars so that they do not need to be filled during a daily analytic run, (2) interspersing isotopic reference waters among unknowns, and (3) applying a linear drift correction and linear normalization to isotopic results with a program such as Laboratory Information Management System (LIMS) for Light Stable Isotopes. With adoption of the above guidelines, measurement uncertainty can be substantially improved. For example, the long-term (months to years) ??2H reproducibility (1?? standard deviation) of nine local isotopic reference waters analyzed daily improved substantially from about 1 ??? to 0.58 ???. This isotopically fractionating mechanism might affect other isotope-ratio mass spectrometers in which LN2 is used as a moisture trap for gaseous hydrogen. ?? This article not subject to U.S. Copyright. Published 2010 by the American Chemical Society.

  17. Caution on the use of liquid nitrogen traps in stable hydrogen isotope-ratio mass spectrometry

    Science.gov (United States)

    Coplen, Tyler B.; Qi, Haiping

    2010-01-01

    An anomalous stable hydrogen isotopic fractionation of 4 ‰ in gaseous hydrogen has been correlated with the process of adding liquid nitrogen (LN2) to top off the dewar of a stainless-steel water trap on a gaseous hydrogen-water platinum equilibration system. Although the cause of this isotopic fractionation is unknown, its effect can be mitigated by (1) increasing the capacity of any dewars so that they do not need to be filled during a daily analytic run, (2) interspersing isotopic reference waters among unknowns, and (3) applying a linear drift correction and linear normalization to isotopic results with a program such as Laboratory Information Management System (LIMS) for Light Stable Isotopes. With adoption of the above guidelines, measurement uncertainty can be substantially improved. For example, the long-term (months to years) δ2H reproducibility (1& sigma; standard deviation) of nine local isotopic reference waters analyzed daily improved substantially from about 1‰ to 0.58 ‰. This isotopically fractionating mechanism might affect other isotope-ratio mass spectrometers in which LN2 is used as a moisture trap for gaseous hydrogen

  18. Stable kilohertz spark discharges for high-efficiency conversion of methane to hydrogen and acetylene

    International Nuclear Information System (INIS)

    Li Xiaosong; Xu Yong; Wang Younian; Zhu Aimin; Lin Cankun; Shi Chuan

    2008-01-01

    Stable kilohertz spark discharges with a unique waveform of discharge current were studied for high-efficiency conversion of methane to hydrogen and acetylene at atmospheric pressure for the first time. Discharge stability was confirmed by the concentration variation in the product streams with 220 min discharge time using pure methane as the feed gas. Utilizing the stable kilohertz spark discharges, the hydrogen concentration in the product stream could be as high as 72.1 vol% at an energy cost of 6.7 eV per H 2 molecule produced and 81.5% of methane conversion. The acetylene concentration could reach 18.4 vol% at an energy cost of 21.2 eV per C 2 H 2 molecule produced and 70.3% of methane conversion. For methane conversion ranging from 51.9% to 81.5%, the energy costs were 6.6-10.7 eV per CH 4 molecule converted, 4.4-6.7 eV per H 2 molecule produced and 16.9-27.6 eV per C 2 H 2 molecule produced. This study showed the high-concentration production of CO x -free hydrogen and acetylene from methane at a low energy cost by stable kilohertz spark discharges

  19. Stable hydrogen, oxygen and sulfur isotopes composition in different tissues of cattle

    International Nuclear Information System (INIS)

    Sun Fengmei; Shi Guangyu; Wang Huiwen; Yang Shuming

    2012-01-01

    In order to research on stable hydrogen, oxygen, sulfur isotopes composition in different tissues of cattle, as well as the breed, δ 2 H and δ 34 S values of different defatted muscle, cattle tail hair, blood, liver, also δ 2h and δ 18 O values of water from muscle were determined by isotope ratio mass spectrometry. The stable sulfur isotope composition was not affected by cattle variety, meanwhile the hydrogen was uncertain; the δ 2 H and δ 34 S values between different defatted muscle, blood, liver, cattle hair were significantly different, at the same time the δ 34 S and δ 2 H values between each tissue were not significantly correlated; the δ 2 H values were strongly correlated with the δ 18 O values of muscle water. The above results indicated that stable sulfur and hydrogen isotopes fractionation in the various tissues were discrepant, thus the proper tissue should be selected according to the purpose and object in the beef traceability. (authors)

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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 ...

  6. 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

  7. 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

  8. Experimental and computational evidence for hydrogen bonding interaction between 2′-deoxyadenosine conjugate adduct and amino-terminated organic film on Si(001)

    Energy Technology Data Exchange (ETDEWEB)

    Szwajca, A., E-mail: Anna.Szwajca@amu.edu.pl [Faculty of Chemistry, A" . Mickiewicz University, Umultowska 89 b, 61-614 Poznań (Poland); Krzywiecki, M. [Institute of Physics-CSE, Silesian University of Technology, Konarskiego 22B, 44-100 Gliwice (Poland); Pluskota-Karwatka, D. [Faculty of Chemistry, A" . Mickiewicz University, Umultowska 89 b, 61-614 Poznań (Poland)

    2015-08-03

    A simple method for immobilization of malonaldehyde-acetaldehyde conjugate adduct with DNA base onto an amino-terminated surface of silicon from water solution is proposed. The Si(001) surface which contains OH groups was modified with 3-aminopropyltrimethoxysilane (APTMS) to serve as a linker between the silica surface and the organic adduct. The 2′-deoxyadenosine adduct was adsorbed on the APTMS/Si surface from acetonitrile/water solution. This nucleoside derivative is stable under laboratory conditions and emits a natural fluorescence, allowing for its adsorption on the APTMS/Si surface to be easily verified by fluorescence microscopy, non-contact atomic force microscopy and attenuated total reflectance Fourier transform infrared spectroscopy. The degree of surface coverage by the adduct was evaluated by X-ray photoelectron spectroscopy (XPS). Analysis of the XPS spectra revealed bands at 400.2 eV and 533.1 eV which are characteristic of a hydrogen bonded –NH{sub 2} and –OH group. This observation implies that the free electron donating –NH{sub 2} groups from the APTMS layer makes hydrogen bonds with the fluorescent adduct and immobilize it on the surface. The wetting angle of the APTMS/Si surface before and after adsorption of the nucleoside derivative does not differ significantly, which points to the involvement of an – OH group from 2′-deoxyadenosine to be involved in hydrogen bonding. These experimental results were further supported using quantum chemical calculations to demonstrate that the 2′deoxyadenosine adduct makes hydrogen bonds with the APTMS molecule. Furthermore, this hydrogen bond involves the –NH{sub 2} group from APTMS and –OH group at carbon atoms C3 and C6 from the deoxyribose ring of 2′deoxyadenosine. - Highlights: • DNA base adduct was immobilized onto amino-terminated silicon surface. • Hydrogen bonds were observed between aminosilane molecules and deoxyribose ring. • Fluorescent film was characterized by

  9. Temperature and Size Dependence of Characteristic Hydrogen-Bonded Network Structures with Ion Core Switching in Protonated (Methanol)6-10-(Water)1Mixed Clusters: A Revisit.

    Science.gov (United States)

    Katada, Marusu; Hsu, Po-Jen; Fujii, Asuka; Kuo, Jer-Lai

    2017-07-27

    Hydrogen-bonded network structures and preferential ion core in the protonated methanol-water mixed clusters, H + (methanol) n -(water) 1 (n = 6-10), were explored by a combination of infrared spectroscopy and theoretical calculations. Infrared spectra of the OH stretch region of the clusters were measured at the two different temperature ranges by using Ar-tagging. Stable isomer structures of the clusters were searched by the multiscale modeling approach and temperature dependent infrared spectra were simulated based on the statistical populations of the isomers. The combined experimental and theoretical studies revealed that the characteristic multiring structures begin to form at n = 7 under the low temperature condition and they are preferential at the wide temperature range in n ≥ 8. It was also demonstrated that the preferential ion core type changes from methanol (MeOH 2 + ) to water (H 3 O + ) with increasing cluster size. In n ≤ 8, the observed infrared spectral features partly depend on the monitoring vibrational predissociation channel, and weak correlations between the hydrogen-bonded network structure and preferential dissociation channels were suggested. However, the ion core type does not necessarily correlate to the preferential dissociation channel. This implies that large rearrangement of the hydrogen-bonded network structure occurs prior to the dissociation.

  10. Spectral analysis and DFT computations of the hydrogen bonded complex between 2,6-diaminopyridine with 2,6-dichloro-4-nitrophenol in different solvents

    Science.gov (United States)

    Al-Ahmary, Khairia M.; Soliman, Saied M.; Habeeb, Moustafa M.; Al-Obidan, Areej H.

    2017-09-01

    New hydrogen bonded complex between 2,6-dichloro-4-nitrophenol (DCNP), proton donor with the proton acceptor 2,6-diaminopyridine (DAP) has been synthesized and characterized in solution and solid state by different spectroscopic techniques. Electronic spectra were used to identify the novel proton transfer complex through appearance of new absorption bands in acetonitrile (CH3CN), methanol (CH3OH) and mixture composed from 1:1 methanol and acetonitrile (AN-Me). The complex stoichiometry was determined to be 1:1 by job's method and photometric titrations. The formation constant was determined by applying minimum-maximum absorbances method where it reached high values confirming the complex high stability. A spectroscopic method for determining DAP was presented and validated statistically. The solid complex was characterized by elemental analysis, infrared and 1H NMR studies where the hydrogen bonded reaction occurs between the phenolic OH with the pyridine ring nitrogen as well as one amino group of DNP. The density functional theory DFT (B3LYP) method has been used to energy optimization of the reactants and complex in the ground state using two basis sets 6-31G(d) and 6-31 G+(d,p). The first one led to energy optimized structure through bifurcated hydrogen bond between OH of DCNP with the ring nitrogen and one amino group of DAP with optimization energy -1998.7 Hartree. The second one gave an optimized structure thought hydrogen bonding between OH and one amino group with lowered optimization energy -2018.1 Hartree. Hence, the experimental results will be simulated with the most stable one at DFT/B3LYB 6-31G+ (d,p). The most reactive electrophilic and nucleophilic sites of DCNP and DAP were predicted using the molecular electrostatic potential. The theoretical electronic spectra in the gas phase and the investigated solvents were calculated at TD-DFT/B3LYP 6-31G+ (d,p) and compared with measured electronic spectra where a satisfactory results have been obtained

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. Probing the Low-Barrier Hydrogen Bond in Hydrogen Maleate in the Gas Phase: A Photoelectron Spectroscopy and ab Initio Study

    Energy Technology Data Exchange (ETDEWEB)

    Woo, Hin-koon; Wang, Xue B.; Wang, Lai S.; Lau, Kai Chung

    2005-12-01

    The strength of the low-barrier hydrogen bond in hydrogen maleate in the gas phase was investigated by low-temperature photoelectron spectroscopy and ab initio calculations. Photoelectron spectra of maleic and fumaric acid monoanions (cis-/trans-HO2CCHdCHCO2 -) were obtained at low temperatures and at 193 nm photon energy. Vibrational structure was observed for trans-HO2CCHdCHCO2 - due to the OCO bending modes; however, cis-HO2CCHdCHCO2 - yielded a broad and featureless spectrum. The electron binding energy of cis-HO2CCHdCHCO2 - is about 1 eV blue-shifted relative to trans-HO2CCHdCHCO2 - due to the formation of intramolecular hydrogen bond in the cis-isomer. Theoretical calculations (CCSD(T)/ aug-cc-pVTZ and B3LYP/aug-cc-pVTZ) were carried out to estimate the strength of the intramolecular hydrogen bond in cis-HO2CCHdCHCO2 -. Combining experimental and theoretical calculations yields an estimate of 21.5 ( 2.0 kcal/mol for the intramolecular hydrogen bond strength in hydrogen maleate.

  16. Probing hydrogen bond interactions in a shear thickening polysaccharide using nonlinear shear and extensional rheology.

    Science.gov (United States)

    Jaishankar, Aditya; Wee, May; Matia-Merino, Lara; Goh, Kelvin K T; McKinley, Gareth H

    2015-06-05

    Mamaku gum is a polysaccharide extracted from the fronds of the black tree fern found in New Zealand. The cooked pith has traditionally been used for various medicinal purposes and as a food source by the Maori people of New Zealand. It has potential applications as a thickener in the food industry and as a palliative for patients with dysphagia. Studies on the shear rheology of Mamaku gum have revealed that the gum exhibits shear thickening at a critical shear rate due to a transition from intra- to inter-molecular chain interactions upon shear-induced chain elongation. In this paper, we demonstrate that these interactions are primarily due to hydrogen bonding. We perform extensional rheology on mixtures of Mamaku gum and urea (a known disruptor of hydrogen bonds) to quantify the nature of these interactions. Capillary Breakup Extensional Rheometry (CaBER) performed on the pure Mamaku gum solutions yield plateau values of the Trouton ratio as high as ∼10(4), showing that the viscoelasticity of the gum in uniaxial elongation is much higher than in shear. For all Mamaku concentrations tested, the extensional viscosity decreases upon increasing urea concentration. Furthermore, the relaxation time decreases exponentially with increasing urea concentration. This exponential relationship is independent of the Mamaku concentration, and is identical to the relationships between urea concentration and characteristic timescales measured in nonlinear shear rheology. We show using the sticky reptation model for polymers with multiple sticker groups along the backbone how such a relationship is consistent with a linear decrease in the free energy for hydrogen bond dissociation. We then demonstrate that a time-concentration superposition principle can be used to collapse the viscoelastic properties of the Mamaku-gum/urea mixtures. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Two new hydrogen bond-supported supramolecular compounds assembly from polyoxovanadate and organoamines

    International Nuclear Information System (INIS)

    Duan Weijie; Cui Xiaobing; Xu Yan; Xu Jiqing; Yu Haihui; Yi Zhihui; Cui Jiwen; Wang Tiegang

    2007-01-01

    Two novel organic-inorganic hybrid compounds based on organoamines and polyoxovanadates formulated as (H 2 dien) 4 [H 10 V 18 O 42 (PO 4 )](PO 4 ).2H 2 O (1) (dien=diethylenetriamine) and (Him) 8 [HV 18 O 42 (PO 4 )] (2) (im=imidazole) have been prepared under hydrothermal conditions by using different starting materials, and characterized by elemental analyses, IR, ESR, XPS, TGA and single-crystal X-ray diffraction analyses. Crystal data for compound 1: C 16 H 74 N 12 O 52 V 18 P 2 , Monoclinic, space group C2/c, a=23.9593(4) A, b=13.0098(2) A, c=20.1703(4) A, β=105.566(3) o , V=6056.6(19) A 3 , Z=4; for compound 2, C 24 H 41 N 16 O 46 V 18 P, Tetragonal, space group I4/mmm, a=13.5154(8) A, b=13.5154(8) A, c=19.1136 A, β=90 o , V=3491.4(3) A 3 , Z=2. Compound 1 consists of protonated diens together with polyoxovanadates [H 10 V 18 O 42 (PO 4 )] 5- . Compound 2 is composed of protonated ims and polyoxovanadates [HV 18 O 42 (PO 4 )] 8- . There are hydrogen-bonding interactions between polyoxovanadates and different organoamines in 1 and 2. Polyoxovanadates are linked through H 2 dien into a three-dimensional network via hydrogen bonds in 1, while polyoxovanadates are linked by Him into a two-dimensional layer network via hydrogen bonds in 2. The crystal packing patterns of the two compounds reveal various supramolecular frameworks. - Graphical abstract: Two new organic-inorganic hybrid compounds based on [V 18 O 42 (PO 4 )] building blocks have been hydrothermally synthesized. 1 is the first 3-D supramolecular network structure consisting of [V 18 O 42 (PO 4 )] unit, while 2 possesses 2-D layered supramolecular structure

  18. Thermal generation and mobility of charge carriers in collective proton transport in hydrogen-bonded chains

    Energy Technology Data Exchange (ETDEWEB)

    Peyrard, M.; Boesch, R.; Kourakis, I. (Dijon Univ., 21 (France). Faculte des Sciences)

    1991-01-01

    The transport of protons in hydrogen-bonded systems is a long standing problem which has not yet obtained a satisfactorily theoretical description. Although this problem was examined first for ice, it is relevant in many systems and in particular in biology for the transport along proteins or for proton conductance across membranes, an essential process in cell life. The broad relevance makes the study of proton conduction very appealing. Since the original work of Bernal and Fowler on ice, the idea that the transport occurs through chains of hydrogen bonds has been well accepted. Such proton wires'' were invoked by Nagle and Morowitz for proton transport across membranes proteins and more recently across lipid bilayers. In this report, we assume the existence of such an hydrogen-bonded chain and discuss its consequences on the dynamics of the charge carriers. We show that this assumption leads naturally to the idea of soliton transport and we put a special emphasis on the role of the coupling between the protons and heavy ions motions. The model is presented. We show how the coupling affects strongly the dynamics of the charge carriers and we discuss the role it plays in the thermal generation of carriers. The work presented has been performed in 1986 and 87 with St. Pnevmatikos and N. Flyzanis and was then completed in collaboration with D. Hochstrasser and H. Buettner. Therefore the results presented in this part are not new but we think that they are appropriate in the context of this multidisciplinary workshop because they provide a rather complete example of the soliton picture for proton conduction. This paper discusses the thermal generation of the charge carriers when the coupling between the protons and heavy ions dynamics is taken into account. The results presented in this part are very recent and will deserve further analysis but they already show that the coupling can assist for the formation of the charge carriers.

  19. Red/blue shifting hydrogen bonds in acetonitrile-dimethyl sulphoxide solutions: FTIR and theoretical studies

    Science.gov (United States)

    Kannan, P. P.; Karthick, N. K.; Mahendraprabu, A.; Shanmugam, R.; Elangovan, A.; Arivazhagan, G.

    2017-07-01

    FTIR spectra of neat acetonitrile (AN), dimethyl sulphoxide (DMSO) and their binary solutions at various mole fractions have been recorded at room temperature. Theoretical calculations have also been carried out on acetonitrile (monomer, dimer), dimethyl sulphoxide (monomer, dimer) and AN - DMSO complex molecules. 1:2 (AN:DMSO) and 2:1 complexation through the red shifting (AN) C - H ⋯ O = S(DMSO) and blue shifting (DMSO) C - H ⋯ N ≡ C(AN) hydrogen bonds has been identified. The experimental and theoretical studies favour the presence of both the monomer and dimer in liquid AN, but only closed dimers in DMSO. The dipole-dipole interactions existed in AN and DMSO dimers disappear in the complex molecules. Partial π bond between S and O atoms, and three lone pair of electrons on oxygen atom of DMSO have been noticed theoretically.

  20. Preparation and analysis of evaporatively bonded superalloys for use in hydrogen burning gas turbines

    Science.gov (United States)

    Tatsinkou Nguelo, Serges Eric

    Superalloys for use in hydrogen-burning gas turbines must demonstrate long-term durability in environments that may be more corrosive than typical turbines due to the presence of impurities in the combusted syngas. This long-term durability implies high oxidation and spallation resistance to different types of corrosion attacks as well as a high strength to be able to withstand the residual stresses induced by the temperature gradients. The performance of these superalloys in these environments can only be realistically assessed if their design involves a good understanding of the types of microcontaminants present in the syngas as well as resulting stresses induced during high temperature operation. This work has two main goals: 1) Characterize the composition of typical syngas combustion flue gases and 2) Successfully fabricate bi-layer structures of iron- and nickel-based superalloys using evaporative metal bonding (EMB) and perform a finite element analysis to predict the stresses at the bonding surface at all temperatures.

  1. 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.

  2. Hydrogen-bonding interactions in thiosemicarbazones of carboxylic acids: Structure of 2-ketobutyric acid thiosemicarbazone hemihydrate

    International Nuclear Information System (INIS)

    Sonawane, P.; Chikate, R.; Kumbhar, A.; Padhye, S.; Doedens, R.J.

    1991-01-01

    2-Thiosemicarbazonobutanoic acid hemihydrate, C 5 H 9 N 3 O 2 S.0.5H 2 O, M r =184.22, triclinic, Panti 1, a=8.163(2), b=8.868(2), c=12.438(2) A, α=72.99(2), β=79.47(2), γ=84.06(2)deg, V=845.3(3) A 3 , Z=4, D x =1.447 Mg m -3 , λ(Mo Kα)=0.71073 A, μ=0.332 mm -1 , F(000)=392, T=296 K, R=0.038 for 3830 independent reflections with I>3σ(I). Three hydrogen bonds link the two crystallographically independent molecules in a pairwise fashion. The two molecules both have E configurations about each C-N and N-N bond, but differ by nearly 180deg in the orientation of the -COOH group. (orig.)

  3. Halogen bonding versus hydrogen bonding induced 2D self-assembled nanostructures at the liquid-solid interface revealed by STM.

    Science.gov (United States)

    Wu, Yican; Li, Jinxing; Yuan, Yinlun; Dong, Meiqiu; Zha, Bao; Miao, Xinrui; Hu, Yi; Deng, Wenli

    2017-01-25

    We design a bifunctional molecule (5-bromo-2-hexadecyloxy-benzoic acid, 5-BHBA) with a bromine atom and a carboxyl group and its two-dimensional self-assembly is experimentally and theoretically investigated by using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The supramolecular self-organization of 5-BHBA in two different solvents (1-octanoic acid and n-hexadecane) at the liquid-solid interface at different solution concentrations is obviously different due to the cooperative and competitive intermolecular halogen and hydrogen bonds. Three kinds of nanoarchitectures composed of dimers, trimers and tetramers are formed at the 1-octanoic acid/graphite interface based on -COOHHOOC-, triangular C[double bond, length as m-dash]OBrH-C, -BrO(H), BrBr, and OH interactions. Furthermore, by using n-hexadecane as the solvent, two kinds of self-assembled linear patterns can be observed due to the coadsorption, in which the dimers are formed by intermolecular -COOHHOOC- hydrogen bonds. The molecule-solvent and solvent-solvent van der Waals force and intermolecular hydrogen bonds dominate the formation of coadsorbed patterns. We propose that the cooperative and competitive halogen and hydrogen bonds are related to the polarity of the solvent and the type of molecule-solvent interaction. The intermolecular binding energy of different dimers and their stability are supported by theoretical calculations. The result provides a new and innovative insight to induce the 2D self-assembled nanostructures by halogen and hydrogen bonds at the liquid-solid interface.

  4. Stable gold(III) catalysts by oxidative addition of a carbon-carbon bond.

    Science.gov (United States)

    Wu, Chung-Yeh; Horibe, Takahiro; Jacobsen, Christian Borch; Toste, F Dean

    2015-01-22

    Low-valent late transition-metal catalysis has become indispensable to chemical synthesis, but homogeneous high-valent transition-metal catalysis is underdeveloped, mainly owing to the reactivity of high-valent transition-metal complexes and the challenges associated with synthesizing them. Here we report a carbon-carbon bond cleavage at ambient conditions by a Au(i) complex that generates a stable Au(iii) cationic complex. In contrast to the well-established soft and carbophilic Au(i) catalyst, this Au(iii) complex exhibits hard, oxophilic Lewis acidity. For example, we observed catalytic activation of α,β-unsaturated aldehydes towards selective conjugate additions as well as activation of an unsaturated aldehyde-allene for a [2 + 2] cycloaddition reaction. The origin of the regioselectivity and catalytic activity was elucidated by X-ray crystallographic analysis of an isolated Au(iii)-activated cinnamaldehyde intermediate. The concepts revealed suggest a strategy for accessing high-valent transition-metal catalysis from readily available precursors.

  5. Isomorphous Crystals from Diynes and Bromodiynes Involved in Hydrogen and Halogen Bonds

    Directory of Open Access Journals (Sweden)

    Pierre Baillargeon

    2016-04-01

    Full Text Available Isomorphous crystals of two diacetylene derivatives with carbamate functionality (BocNH-CH2-diyne-X, where X = H or Br have been obtained. The main feature of these structures is the original 2D arrangement (as supramolecular sheets or walls in which the H bond and halogen bond have a prominent effect on the whole architecture. The two diacetylene compounds harbor neighboring carbamate (Boc protected amine and conjugated alkyne functionalities. They differ only by the nature of the atom located at the penultimate position of the diyne moiety, either a hydrogen atom or a bromine atom. Both of them adopt very similar 2D wall organizations with antiparallel carbamates (as in antiparallel beta pleated sheets. Additional weak interactions inside the same walls between molecular bricks are H bond interactions (diyne-H···O=C or halogen bond interactions (diyne-Br···O=C, respectively. Based on crystallographic atom coordinates, DFT (B3LYP/6-31++G(d,p and DFT (M06-2X/6-31++G(d,p calculations were performed on these isostructural crystals to gain insight into the intermolecular interactions.

  6. Non-orthogonal and orthogonal valence bond wavefunctions in the hydrogen molecule: the diabatic view

    Science.gov (United States)

    Angeli, Celestino; Cimiraglia, Renzo; Malrieu, Jean-Paul

    2013-07-01

    The ability of the valence bond (VB) approach to describe a molecular system in 'chemical terms' finds its theoretical justification in the fact that the VB wavefunctions are supposed to be diabatic, i.e. with a well-defined nature, not depending on the nuclear geometry. The intimate nature of the VB wavefunctions is here analysed by computing the non-adiabatic coupling for the simple, paradigmatic case of the hydrogen (H2) molecule. This analysis reveals that the neutral and ionic VB wavefunctions cannot be considered as diabatic states, given that they present a large non-adiabatic coupling. The diabatic states, obtained by a suitable transformation of the VB wavefunctions, are found to be the wavefunctions of the orthogonal VB (OVB) approach, which therefore gains a legitimacy in the analysis of the composition of the adiabatic wavefunctions. Such an analysis has some bearing on the description of the nature of the chemical bond in H2: the neutral structure gives a dissociative curve and the bond is due to the stabilisation brought by the ionic structure that mixes together with the neutral structure in the ground state wavefunction at short internuclear distances. The ability of the (at first glance) neutral VB wavefunction based on the 1s orbitals to describe in a compact way the ground state (and therefore the chemical bond) is ascribed to an almost optimal mixing in this wavefunction of the diabatic neutral and ionic states at all internuclear distances.

  7. Bonding titanium on multi-walled carbon nanotubes for hydrogen storage: An electrochemical approach

    Energy Technology Data Exchange (ETDEWEB)

    Brieno-Enriquez, K.M.; Ledesma-Garcia, J. [Centro de Investigacion y Desarrollo Tecnologico en Electroquimica, S.C., Parque Tecnologico Queretaro-Sanfandila, Pedro Escobedo, Qro, C.P. 76703 (Mexico); Perez-Bueno, J.J., E-mail: jperez@cideteq.mx [Centro de Investigacion y Desarrollo Tecnologico en Electroquimica, S.C., Parque Tecnologico Queretaro-Sanfandila, Pedro Escobedo, Qro, C.P. 76703 (Mexico); Godinez, Luis A. [Centro de Investigacion y Desarrollo Tecnologico en Electroquimica, S.C., Parque Tecnologico Queretaro-Sanfandila, Pedro Escobedo, Qro, C.P. 76703 (Mexico); Terrones, H. [Instituto Potosino de Investigacion Cientifica y Tecnologica, Division de Materiales Avanzados, Camino a la Presa San Jose 2055, Col. Lomas 4o Seccion C.P. 78216, San Luis Potosi (Mexico); Angeles-Chavez, C. [Instituto Mexicano del Petroleo, Programa de Ingenieria Molecular, Eje Central Lazaro Cardenas 152, A.P. 14-805, 07730 Mexico D.F. (Mexico)

    2009-06-15

    This work explores the use of some procedures, involving electrochemistry, in order to bond atomic Ti on the outer surface of multi-walled carbon nanotubes (MWNTs). It is assumed that each titanium atom has the potential of host up to four hydrogen molecules and relinquish them by heated. As a way to spread and stick nanotubes on an electrode, a tested route was drying a solution with nanotubes on a glassy carbon flat electrode. The MWNTs were treated by anodic polarization in organic media. Dichloromethane was selected as the medium and titanium tetrachloride as the precursor for attaching atomic Ti onto the nanotubes. The hydrogen adsorption, estimated from voltamperometry was five times higher on Ti-MWNTs that on bare nanotubes. The use of anodic polarization during the preparation of Ti-MWNTs may represent great significance in procedure, which was manifest during the voltamperometric evaluation of samples.

  8. Hydrogen-Bonded Polymer-Porphyrin Assemblies in Water: Supramolecular Structures for Light Energy Conversion.

    Science.gov (United States)

    Kutz, Anne; Alex, Wiebke; Krieger, Anja; Gröhn, Franziska

    2017-09-01

    In this study, a new type of functional, self-assembled nanostructure formed from porphyrins and polyamidoamine dendrimers based on hydrogen bonding in an aqueous solution is presented. As the aggregates formed are promising candidates for solar-energy conversion, their photocatalytic activity is tested using the model reaction of methyl viologen reduction. The self-assembled structures show significantly increased activity as compared to unassociated porphyrins. Details of interaction forces driving the supramolecular structure formation and regulating catalytic efficiency are fundamentally discussed. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Structures of two thermolysin-inhibitor complexes that differ by a single hydrogen bond.

    Science.gov (United States)

    Tronrud, D E; Holden, H M; Matthews, B W

    1987-01-30

    The mode of binding to thermolysin of the ester analog Cbz-GlyP-(O)-Leu-Leu has been determined by x-ray crystallography and shown to be virtually identical (maximum difference 0.2 angstrom) with the corresponding peptide analog Cbz-GlyP-(NH)-Leu-Leu. The two inhibitors provide a matched pair of enzyme-inhibitor complexes that differ by 4.1 kilocalories per mole in intrinsic binding energy but are essentially identical except for the presence or absence of a specific hydrogen bond.

  10. A Solute's Perspective on How TMAO, Urea and GdnHCl Affect Water's Hydrogen Bonding Ability

    OpenAIRE

    Pazos, Ileana M.; Gai, Feng

    2012-01-01

    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 pep...

  11. Interpreting Quasi-Thermal Effects in Ultrafast Spectroscopy of Hydrogen-Bonded Systems.

    Science.gov (United States)

    Stingel, Ashley M; Petersen, Poul B

    2018-03-15

    Vibrational excitation of molecules in the condensed phase relaxes through vibrational modes of decreasing energy to ultimately generate an equilibrium state in which the energy is distributed among low-frequency modes. In ultrafast vibrational spectroscopy, changes in the vibrational features of hydrogen-bonded NH and OH stretch modes are typically observed to persist long after these high-frequency vibrations have relaxed. Due to the resemblance to the spectral changes caused by heating the sample, these features are typically described as arising from a hot ground state. However, these spectral features appear on ultrafast time scales that are much too fast to result from a true thermal state, and significant differences between the thermal difference spectrum and the induced quasi-thermal changes in ultrafast spectroscopy are often observed. Here, we examine and directly compare the thermal and quasi-thermal responses of the hydrogen-bonded homodimer of 7-azaindole with temperature-dependent FTIR spectroscopy and ultrafast mid-IR continuum spectroscopy. We find that the thermal difference spectra contain contributions from both dissociation of the hydrogen bonds and from frequency shifts due to changes in the thermal population of low-frequency modes. The transient spectra in ultrafast vibrational spectroscopy are also found to contain two contributions: initial frequency shifts over 2.3 ± 0.11 ps associated with equilibration of the initial excitation, and frequency shifts associated with the excitation of several fingerprint modes, which decay over 21.8 ± 0.11 ps, giving rise to a quasi-thermal response caused by a distribution of fingerprint modes being excited within the sample ensemble. This resembles the thermal frequency shifts due to population changes of low-frequency modes, but not the overall thermal spectrum, which is dominated by features caused by dimer dissociation. These findings provide insight into the changes in the vibrational spectrum

  12. Intramolecular hydrogen bond in molecular and proton-transfer forms of Schiff bases

    Energy Technology Data Exchange (ETDEWEB)

    Filarowski, A.; Koll, A.; Karpfen, A.; Wolschann, P

    2004-02-16

    The force field and structural parameters modifications upon the formation of intramolecular hydrogen bond and proton transfer reaction in N-methyl-2-hydroxybenzylidene amine (HBZA) are determined on the basis of ab initio and DFT calculations. Reliability of the calculations is verified by comparing of the theoretical vibrational spectra with those experimentally determined in the gas phase. A model of resonance interactions is applied and the quantitative contribution of ortho-quinoid structure in the particular conformers is estimated. A comparison is also made to the systems without {pi}-electron coupling (Mannich bases)

  13. Changes in energy of three types of hydrogen bonds upon excitation of aminocoumarins determined from absorption solvatochromic experiments.

    Science.gov (United States)

    Krystkowiak, Ewa; Maciejewski, Andrzej

    2011-06-21

    Absorption spectra of 6-aminocoumarin (6AC) and 7-aminocoumarins (C120 and C151) were studied in polyfluorinated alcohols: (1,1,1,3,3,3-hexafluoroisopropanol (HFIP), 2,2,2-trifluoroethanol (TFE)), in water and in methanol, and compared to those taken in 1-chloro-n-alkanes. According to our results, the observed unusual blue-shift of a long-wavelength band in absorption spectra in strong protic solvents is direct evidence of significant weakening of a NH-O hydrogen bond. The results obtained for the aminocoumarins in HFIP, which in contrast to aliphatic alcohols does not form hydrogen bonds of the acceptor type, prove that the decrease in the energy of the NH-O hydrogen bond upon excitation to the lowest S(1)-LE state is significantly greater than the increase in the energy of hydrogen bonds made by the oxygen atom of carbonyl group OH-O. It is in contrast to theoretical calculations for C151 [Y. Liu, J. Ding, R. Liu, D. Shi and J. Sun, J. Photochem. Photobiol. A, 2009, 201, 203-207]. A comparison of the absorption spectra measured in DMSO and in 1-chloro-n-alkanes shows that the energy of two N-HO hydrogen bonds considerably increases as a result of excitation. These results are consistent with those of the theoretical calculations [Y. Liu, J. Ding, R. Liu, D. Shi and J. Sun, J. Photochem. Photobiol. A, 2009, 201, 203-207; P. Zhou, P. Song, J. Liu, K. Han and G. He, Phys. Chem. Chem. Phys., 2009, 11, 9440-9449]. In this study we applied the procedure proposed by us in J. Photochem. Photobiol. A, 2006, 184, 250-264 for the determination of changes in hydrogen bond energy as a result of electronic excitation based on analysis of the absorption spectra of the probe studied in the solvents interacting with it exclusively nonspecifically and in those forming hydrogen bonds with it.

  14. A 2D Substitutional Solid Solution through Hydrogen Bonding of Molecular Building Blocks.

    Science.gov (United States)

    MacLeod, Jennifer M; Lipton-Duffin, Josh; Fu, Chaoying; Taerum, Tyler; Perepichka, Dmitrii F; Rosei, Federico

    2017-09-26

    Two-dimensional (2D) molecular self-assembly allows for the formation of well-defined supramolecular layers with tailored geometrical, compositional, and chemical properties. To date, random intermixing and entropic effects in these systems have largely been associated with crystalline disorder and glassy phases. Here we describe a 2D crystalline self-assembled molecular system that exhibits random incorporation of substitutional molecules. The lattice is formed from a mixture of trimesic acid (TMA) and terthienobenzenetricarboxylic acid (TTBTA), C 3 -symmetric hydrogen-bonding units of very different sizes (0.79 and 1.16 nm, respectively), at the solution-highly oriented pyrolitic graphite (HOPG) interface. Remarkably, the TTBTA substitutes into the TMA lattice at a fixed stoichiometry near 12%. The resulting lattice constant is consistent with Vegard's law prediction for an alloy with a composition TMA 0.88 TTBTA 0.12 , and the substrate orientation of the lattice is defined by an epitaxial relation with the HOPG substrate. The Gibbs free energy for the TMA/TTBTA lattice was elucidated by considering the entropy of intermixing, via Monte Carlo simulations of multiplicity of the substitutional lattices, and the enthalpy of intermixing, via density functional theory calculations. The latter show that both the bond enthalpy of the H-bonded lattice and the adsorption enthalpy of the molecule/substrate interactions play important roles. This work provides insight into the manifestation of entropy in a molecular crystal constrained by both epitaxy and intermolecular interactions and demonstrates that a randomly intermixed yet crystalline 2D solid can be formed through hydrogen bonding of molecular building blocks of very different size.

  15. Measuring terrestrial subsidies to aquatic food webs using stable isotopes of hydrogen.

    Science.gov (United States)

    Doucett, Richard R; Marks, Jane C; Blinn, Dean W; Caron, Melanie; Hungate, Bruce A

    2007-06-01

    Understanding river food webs requires distinguishing energy derived from primary production in the river itself (autochthonous) from that produced externally (allochthonous), yet there are no universally applicable and reliable techniques for doing so. We compared the natural abundance stable isotope ratios of hydrogen (deltaD) of allochthonous and autochthonous energy sources in four different aquatic ecosystems. We found that autochthonous organic matter is uniformly far more depleted in deuterium (lower deltaD values) than allochthonous: an average difference of approximately 100% per hundred. We also found that organisms at higher trophic levels, including both aquatic invertebrates and fish, have deltaD values intermediate between aquatic algae and terrestrial plants. The consistent differences between leaves and algae in deltaD among these four watersheds, along with the intermediate values in higher trophic levels, indicate that natural abundance hydrogen isotope signatures are a powerful tool for partitioning energy flow in aquatic ecosystems.

  16. Multisample conversion of water to hydrogen by zinc for stable isotope determination

    Science.gov (United States)

    Kendall, C.; Coplen, T.B.

    1985-01-01

    Two techniques for the conversion of water to hydrogen for stable isotope ratio determination have been developed that are especially suited for automated multisample analysis. Both procedures involve reaction of zinc shot with a water sample at 450 ??C. in one method designed for water samples in bottles, the water is put in capillaries and is reduced by zinc in reaction vessels; overall savings in sample preparation labor of 75% have been realized over the standard uranium reduction technique. The second technique is for waters evolved under vacuum and is a sealed-tube method employing 9 mm o.d. quartz tubing. Problems inherent with zinc reduction include surface inhomogeneity of the zinc and exchange of hydrogen both with the zinc and with the glass walls of the vessels. For best results, water/zinc and water/glass surface area ratios of vessels should be kept as large as possible.

  17. Palladium - silicon nanocomposites as a stable electrocatalyst for hydrogen evolution reaction.

    Science.gov (United States)

    Yin, Kui; Cheng, Yafei; Jiang, Binbin; Liao, Fan; Shao, Mingwang

    2018-07-15

    Pd nanoparticles grown in-situ on the surface of silicon nanowires (Pd-SiNW nanocomposites) were employed as electrocatalysts in hydrogen evolution reaction and exhibited satisfactory catalytic performance. Here, SiNWs served as the carrier with vast surface area. It is interesting to note that Pd-SiNW nanocomposites were more stable for hydrogen evolution reaction than the commercial Pt/C catalysts, which might be attributed to the three-dimensional crisscrossing structure of the composites and the strong interaction between Pd and Si. The strong interaction is due to the low lattice mismatch in the epitaxial growth of Pd particles on the surface of Si. Such special structure and interaction help to tightly hold Pd nanoparticles, which could avoid the loss of catalysts and keep the catalyst from being agglomerated and growing large. Copyright © 2018 Elsevier Inc. All rights reserved.

  18. A new class of cuprous bromide cluster-based hybrid materials: direct observation of the stepwise replacement of hydrogen bonds by coordination bonds.

    Science.gov (United States)

    Zhang, Xian-Ming; Hou, Juan-Juan; Guo, Cai-Hong; Li, Chun-Fang

    2015-01-20

    Although a variety of functional metal-organic frameworks (MOFs) have been synthesized, post-modified, and applied in various areas, there is little knowledge about how molecular cluster building units are stepwise evolved into MOFs via intermediates. Coordination bonds are generally stronger than hydrogen bonds, and thus equivalent replacement of X-H···Y hydrogen bonds by X-M-Y coordination bonds can transform hydrogen bond networks into MOFs. In this work, solvothermal in situ reduction reactions of CuBr2 and 1,4-diazoniabicyclo[2,2,2]octane (DABCO) generated a myriad of tunable photoluminescent cuprous body-centered cubic bromide cluster-based networks with the general formula [Cu4+xH4-xBr6(DABCO)4](HCO2)2·S (x = 0, 0.56, 0.81, 1.27, 1.39, 2.56, 2.78, and 4 for compounds 1-8, respectively). All of these compounds crystallize in the cubic space group with the largest volume difference being only 5.2%, but they belong to three remarkably different kinds of crystals. Complex 1 is a molecular crystal and consists of tetrahedral [Cu4Br6(HDABCO)4](2+) clusters with monodentate HDABCO groups that are supported via N-H···Br synthons in the hydrogen bond network. Compound 8 is a [Cu8Br6](2+) cube cluster-based MOF with bridged DABCO ligands. Complexes 2-7 are seemingly impossible Cu/H-substituted solid solutions of 1 and 8. The CuBr framework components in 1-8 are Cu4Br6, Cu4.56Br6, Cu4.81Br6, Cu5.27Br6, Cu5.39Br6, Cu6.56Br6, Cu6.78Br6, and Cu8Br6, respectively. Crystallization kinetics studies revealed that the [Cu4Br6(HDABCO)4](2+) cluster-based hydrogen bond network (1) was initially formed such that N-H···Br hydrogen bonds could be stepwise replaced by N-Cu-Br coordination bonds to form the [Cu8Br6](2+) cube cluster-based MOF (8) via solid solutions. These observations directly reveal the equivalence and transformation between the N-H···Br hydrogen bond and the N-Cu-Br coordination bond and the evolutionary mechanism of a molecular crystal to a MOF via

  19. Vibrational analysis on the revised potential energy curve of the low-barrier hydrogen bond in photoactive yellow protein

    Directory of Open Access Journals (Sweden)

    Yusuke Kanematsu

    2016-01-01

    Full Text Available Photoactive yellow protein (PYP has a characteristic hydrogen bond (H bond between p-coumaric acid chromophore and Glu46, whose OH bond length has been observed to be 1.21 Å by the neutron diffraction technique [Proc. Natl. Acad. Sci. 106, 440–4]. Although it has been expected that such a drastic elongation of the OH bond could be caused by the quantum effect of the hydrogen nucleus, previous theoretical computations including the nuclear quantum effect have so far underestimated the bond length by more than 0.07 Å. To elucidate the origin of the difference, we performed a vibrational analysis of the H bond on potential energy curve with O…O distance of 2.47 Å on the equilibrium structure, and that with O…O distance of 2.56 Å on the experimental crystal structure. While the vibrationally averaged OH bond length for equilibrium structure was underestimated, the corresponding value for crystal structure was in reasonable agreement with the corresponding experimental values. The elongation of the O…O distance by the quantum mechanical or thermal fluctuation would be indispensable for the formation of a low-barrier hydrogen bond in PYP.

  20. Manganese-Oxygen Intermediates in O-O Bond Activation and Hydrogen-Atom Transfer Reactions.

    Science.gov (United States)

    Rice, Derek B; Massie, Allyssa A; Jackson, Timothy A

    2017-11-21

    Biological systems capitalize on the redox versatility of manganese to perform reactions involving dioxygen and its derivatives superoxide, hydrogen peroxide, and water. The reactions of manganese enzymes influence both human health and the global energy cycle. Important examples include the detoxification of reactive oxygen species by manganese superoxide dismutase, biosynthesis by manganese ribonucleotide reductase and manganese lipoxygenase, and water splitting by the oxygen-evolving complex of photosystem II. Although these enzymes perform very different reactions and employ structurally distinct active sites, manganese intermediates with peroxo, hydroxo, and oxo ligation are commonly proposed in catalytic mechanisms. These intermediates are also postulated in mechanisms of synthetic manganese oxidation catalysts, which are of interest due to the earth abundance of manganese. In this Account, we describe our recent efforts toward understanding O-O bond activation pathways of Mn III -peroxo adducts and hydrogen-atom transfer reactivity of Mn IV -oxo and Mn III -hydroxo complexes. In biological and synthetic catalysts, peroxomanganese intermediates are commonly proposed to decay by either Mn-O or O-O cleavage pathways, although it is often unclear how the local coordination environment influences the decay mechanism. To address this matter, we generated a variety of Mn III -peroxo adducts with varied ligand environments. Using parallel-mode EPR and Mn K-edge X-ray absorption techniques, the decay pathway of one Mn III -peroxo complex bearing a bulky macrocylic ligand was investigated. Unlike many Mn III -peroxo model complexes that decay to oxo-bridged-Mn III Mn IV dimers, decay of this Mn III -peroxo adduct yielded mononuclear Mn III -hydroxo and Mn IV -oxo products, potentially resulting from O-O bond activation of the Mn III -peroxo unit. These results highlight the role of ligand sterics in promoting the formation of mononuclear products and mark an important

  1. Intra- und intermolecular hydrogen bonds. Spectroscopic, quantum chemical and molecular dynamics studies

    International Nuclear Information System (INIS)

    Simperler, A.

    1999-03-01

    Intra- and intermolecular H-bonds have been investigated with spectroscopic, quantum chemical, and molecular dynamics methods. The work is divided into the following three parts: 1. Intramolecular interactions in ortho-substituted phenols. Theoretical and experimental data that characterizes the intramolecular hydrogen bonds in 48 different o-substituted phenols are discussed. The study covers various kinds of O-H ... Y -type interactions (Y= N, O, S, F, Cl, Br, I, C=C, C=-C, and C-=N). The bond strength sequences for several series of systematically related compounds as obtained from IR spectroscopy data (i.e., v(OH) stretching frequencies) are discussed and reproduced with several theoretical methods (B3LYP/6-31G(d,p), B3LYP/6-311G(d,p), B3LYP/6-31++G(d,p), B3LYP/DZVP, MP2/6-31G(d,p), and MP2/6-31++G(d,p) levels of theory). The experimentally determined sequences are interpreted in terms of the intrinsic properties of the molecules: hydrogen bond distances, Mulliken partial charges, van der Waals radii, and electron densities of the Y-proton acceptors. 2. Competitive hydrogen bonds and conformational equilibria in 2,6-disubstituted phenols containing two different carbonyl substituents. The rotational isomers of ten unsymmetrical 2,6-disubstituted phenols as obtained by combinations of five different carbonyl substituents (COOH, COOCH 3 , CHO, COCH 3 , and CONH 2 ) have been theoretically investigated at the B3LYP/6-31G(d,p) level of theory. The relative stability of four to five conformers of each compound were determined by full geometry optimization for free molecules as well as for molecules in reaction fields with dielectric constants up to ε=37.5. A comparison with IR spectroscopic data of available compounds revealed excellent agreement with the theoretically predicted stability sequences and conformational equilibria. The stability of a conformer could be interpreted to be governed by the following two contributions: (i) an attractive hydrogen bond

  2. Simultaneous determination of stable carbon, oxygen, and hydrogen isotopes in cellulose.

    Science.gov (United States)

    Loader, N J; Street-Perrott, F A; Daley, T J; Hughes, P D M; Kimak, A; Levanič, T; Mallon, G; Mauquoy, D; Robertson, I; Roland, T P; van Bellen, S; Ziehmer, M M; Leuenberger, M

    2015-01-06

    A technological development is described through which the stable carbon-, oxygen-, and nonexchangeable hydrogen-isotopic ratios (δ(13)C, δ(18)O, δ(2)H) are determined on a single carbohydrate (cellulose) sample with precision equivalent to conventional techniques (δ(13)C 0.15‰, δ(18)O 0.30‰, δ(2)H 3.0‰). This triple-isotope approach offers significant new research opportunities, most notably in physiology and medicine, isotope biogeochemistry, forensic science, and palaeoclimatology, when isotopic analysis of a common sample is desirable or when sample material is limited.

  3. Authenticity and Traceability of Vanilla Flavors by Analysis of Stable Isotopes of Carbon and Hydrogen

    DEFF Research Database (Denmark)

    Hansen, Anne-Mette Sølvbjerg; Fromberg, Arvid; Frandsen, Henrik Lauritz

    2014-01-01

    Authenticity and traceability of vanilla flavors were investigated using gas chromatographyisotope ratio mass spectrometry (GC-IRMS). Vanilla flavors produced by chemical synthesis (n = 2), fermentation (n = 1), and extracted from two different species of the vanilla orchid (n = 79) were analyzed....... The authenticity of the flavor compound vanillin was evaluated on the basis of measurements of ratios of carbon stable isotopes (delta C-13). It was found that results of delta C-13 for vanillin extracted from Vanilla planifolia and Vanilla tahitensis were significantly different (t test) and that it was possible...... to differentiate these two groups of natural vanillin from vanillin produced otherwise. Vanilla flavors were also analyzed for ratios of hydrogen stable isotopes (delta H-2). A graphic representation of delta C-13 versus delta H-2 revealed that vanillin extracted from pods grown in adjacent geographic origins...

  4. Hydrogen atoms in acetylsalicylic acid (Aspirin): the librating methyl group and probing the potential well in the hydrogen-bonded dimer

    Science.gov (United States)

    Wilson, Chick C.

    2001-02-01

    The structure of acetylsalicylic acid (2-(acetoyloxy)benzoic acid; Aspirin) has been studied by variable temperature single crystal neutron diffraction. The usual large torsional librational motion of the terminal methyl group is observed and its temperature dependence analysed using a simple model for the potential, yielding the force constant and barrier height for this motion. In addition, asymmetry of the scattering density of the proton involved in the hydrogen bond forming the carboxylic acid dimer motif is observed at temperatures above 200 K. This asymmetry is discussed in terms of its possible implications for the shape of the hydrogen bonding potential well.

  5. Theoretical modeling of infrared spectra of the hydrogen and deuterium bond in aspirin crystal

    Science.gov (United States)

    Ghalla, Houcine; Rekik, Najeh; Michta, Anna; Oujia, Brahim; Flakus, Henryk T.

    2010-01-01

    An extended quantum theoretical approach of the ν IR lineshape of cyclic dimers of weakly H-bonded species is proposed. We have extended a previous approach [M.E.-A. Benmalti, P. Blaise, H.T. Flakus, O. Henri-Rousseau, Chem. Phys. 320 (2006) 267] by accounting for the anharmonicity of the slow mode which is described by a "Morse" potential in order to reproduce the polarized infrared spectra of the hydrogen and deuterium bond in acetylsalicylic acid (aspirin) crystals. From comparison of polarized IR spectra of isotopically neat and isotopically diluted aspirin crystals it resulted that centrosymmetric aspirin dimer was the bearer of the crystal main spectral properties. In this approach, the adiabatic approximation is performed for each separate H-bond bridge of the dimer and a strong non-adiabatic correction is introduced into the model via the resonant exchange between the fast mode excited states of the two moieties. Within the strong anharmonic coupling theory, according to which the X-H→⋯Y high-frequency mode is anharmonically coupled to the H-bond bridge, this model incorporated the Davydov coupling between the excited states of the two moieties, the quantum direct and indirect dampings and the anharmonicity for the H-bond bridge. The spectral density is obtained within the linear response theory by Fourier transform of the damped autocorrelation functions. The evaluated spectra are in fairly good agreement with the experimental ones by using a minimum number of independent parameters. The effect of deuteration has been well reproduced by reducing simply the angular frequency of the fast mode and the anharmonic coupling parameter.

  6. Influence of 5f electrons on structure and bonding in the actinide-hydrogen intermetallics

    International Nuclear Information System (INIS)

    Ward, J.W.

    1984-01-01

    Complexa phases form for the Th + H and U + H systems that are found with no other metals. In the Pa + H system, simple bcc C15 Laves and A15 phases can form, dependent on temperature and composition. The phase transformations appear to b magnetically driven, as a resutl of the decoupling of the metallic 5f electron bonding that occurs during hydriding; the C15 phases contain two kinds of Pa atoms-the one sublattice being still fully f-bonded and the other magnetic. This is a unique situation in solid state physics which defies a valence description. A similar situation obtains for A15 β - UH 3 structure. The parent metals themselves exhibit electronegativities not unlike those of the mid-3d transition metals (e.g., Fe) because the valence electrons re tied up in metallic bonding. However, under the driving force for hydriding, the lattices can open up, decoupling the f-bonding and inducing magnetism. The systems then aggressively form very stable hydrides typical of highly-electropositive metals. Beyond uranium the trivalent metallic state is favored and rare-earth-like hydrides are found for Np + H and Pu + H. Nevertheless, the solid-state and transport properties are markedly different than for the rare-earth hydrides, showing that the latent influence of the 5f electrons is still strong

  7. The hydrogen bond strength of the phenol-phenolate anionic complex: a computational and photoelectron spectroscopic study.

    Science.gov (United States)

    Buytendyk, Allyson M; Graham, Jacob D; Collins, Kim D; Bowen, Kit H; Wu, Chia-Hua; Wu, Judy I

    2015-10-14

    The phenol-phenolate anionic complex was studied in vacuo by negative ion photoelectron spectroscopy using 193 nm photons and by density functional theory (DFT) computations at the ωB97XD/6-311+G(2d,p) level. We characterize the phenol-phenolate anionic complex as a proton-coupled phenolate pair, i.e., as a low-barrier hydrogen bond system. Since the phenol-phenolate anionic complex was studied in the gas phase, its measured hydrogen bond strength is its maximal ionic hydrogen bond strength. The D(PhO(-)···HOPh) interaction energy (26-30 kcal mol(-1)), i.e., the hydrogen bond strength in the PhO(-)···HOPh complex, is quite substantial. Block-localized wavefunction (BLW) computations reveal that hydrogen bonded phenol rings exhibit increased ring π-electron delocalization energies compared to the free phenol monomer. This additional stabilization may explain the stronger than expected proton donating ability of phenol.

  8. Vibrational signatures of cation-anion hydrogen bonding in ionic liquids: a periodic density functional theory and molecular dynamics study.

    Science.gov (United States)

    Mondal, Anirban; Balasubramanian, Sundaram

    2015-02-05

    Hydrogen bonding in alkylammonium based protic ionic liquids was studied using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. Normal-mode analysis within the harmonic approximation and power spectra of velocity autocorrelation functions were used as tools to obtain the vibrational spectra in both the gas phase and the crystalline phases of these protic ionic liquids. The hydrogen bond vibrational modes were identified in the 150-240 cm(-1) region of the far-infrared (far-IR) spectra. A blue shift in the far-IR mode was observed with an increasing number of hydrogen-bonding sites on the cation; the exact peak position is modulated by the cation-anion hydrogen bond strength. Sub-100 cm(-1) bands in the far-IR spectrum are assigned to the rattling motion of the anions. Calculated NMR chemical shifts of the acidic protons in the crystalline phase of these salts also exhibit the signature of cation-anion hydrogen bonding.

  9. COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures.

    Science.gov (United States)

    Firdaus-Raih, Mohd; Hamdani, Hazrina Yusof; Nadzirin, Nurul; Ramlan, Effirul Ikhwan; Willett, Peter; Artymiuk, Peter J

    2014-07-01

    Hydrogen bonds are crucial factors that stabilize a complex ribonucleic acid (RNA) molecule's three-dimensional (3D) structure. Minute conformational changes can result in variations in the hydrogen bond interactions in a particular structure. Furthermore, networks of hydrogen bonds, especially those found in tight clusters, may be important elements in structure stabilization or function and can therefore be regarded as potential tertiary motifs. In this paper, we describe a graph theoretical algorithm implemented as a web server that is able to search for unbroken networks of hydrogen-bonded base interactions and thus provide an accounting of such interactions in RNA 3D structures. This server, COGNAC (COnnection tables Graphs for Nucleic ACids), is also able to compare the hydrogen bond networks between two structures and from such annotations enable the mapping of atomic level differences that may have resulted from conformational changes due to mutations or binding events. The COGNAC server can be accessed at http://mfrlab.org/grafss/cognac. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Hydrogen-Bonded Polymer-Small Molecule Complexes with Tunable Mechanical Properties.

    Science.gov (United States)

    Liu, Tianqi; Peng, Xin; Chen, Ya-Nan; Bai, Qing-Wen; Shang, Cong; Zhang, Lin; Wang, Huiliang

    2018-03-13

    A novel type of polymeric material with tunable mechanical properties is fabricated from polymers and small molecules that can form hydrogen-bonded intermolecular complexes (IMCs). In this work, poly(vinyl alcohol) (PVA)-glycerol hydrogels are first prepared, and then they are dried to form IMCs. The tensile strengths and moduli of IMCs decrease dramatically with increasing glycerol content, while the elongations increase gradually. The mechanical properties are comparable with or even superior to those of common engineering plastics and rubbers. The IMCs with high glycerol content also show excellent flexibility and cold-resistance at subzero temperatures. Cyclic tensile and stress relaxation tests prove that there is an effective energy dissipation mechanism in IMCs and dynamic mechanical analysis confirms their physical crosslinking nature. FTIR and NMR characterizations prove the existence of hydrogen bonding between glycerol and PVA chains, which suppresses the crystallization of PVA from X-ray diffraction measurement. These PVA-glycerol IMCs may find potential applications in barrier films, biomedical packaging, etc., in the future. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Comparison of Degrees of Potential-Energy-Surface Anharmonicity for Complexes and Clusters with Hydrogen Bonds

    Science.gov (United States)

    Kozlovskaya, E. N.; Doroshenko, I. Yu.; Pogorelov, V. E.; Vaskivskyi, Ye. V.; Pitsevich, G. A.

    2018-01-01

    Previously calculated multidimensional potential-energy surfaces of the MeOH monomer and dimer, water dimer, malonaldehyde, formic acid dimer, free pyridine-N-oxide/trichloroacetic acid complex, and protonated water dimer were analyzed. The corresponding harmonic potential-energy surfaces near the global minima were constructed for series of clusters and complexes with hydrogen bonds of different strengths based on the behavior of the calculated multidimensional potential-energy surfaces. This enabled the introduction of an obvious anharmonicity parameter for the calculated potential-energy surfaces. The anharmonicity parameter was analyzed as functions of the size of the analyzed area near the energy minimum, the number of points over which energies were compared, and the dimensionality of the solved vibrational problem. Anharmonicity parameters for potential-energy surfaces in complexes with strong, medium, and weak H-bonds were calculated under identical conditions. The obtained anharmonicity parameters were compared with the corresponding diagonal anharmonicity constants for stretching vibrations of the bridging protons and the lengths of the hydrogen bridges.

  12. Hydrogen Bond Induces Hierarchical Self-Assembly in Liquid-Crystalline Block Copolymers.

    Science.gov (United States)

    Huang, Shuai; Pang, Linlin; Chen, Yuxuan; Zhou, Liming; Fang, Shaoming; Yu, Haifeng

    2018-03-01

    Microphase-separated structures of block copolymers (BCs) with a size of sub-10 nm are usually obtained by hydrogen-bond-induced self-assembly of BCs through doping with small molecules as functional additives. Here, fabrication of hierarchically self-assembled sub-10 nm structures upon microphase separation of amphiphilic liquid-crystalline BCs (LCBCs) at the existence of hydrogen bonds but without any dopants is reported. The newly introduced urethane groups in the side chain of the hydrophobic block of LCBCs interact with the ether groups of the hydrophilic poly(ethylene oxide) (PEO) block, leading to imperfect crystallization of the PEO blocks. Both crystalline and amorphous domains coexist in the separated PEO phase, enabling a lamellar structure to appear inside the PEO nanocylinders. This provides an elegant method to fabricate controllable sub-10 nm microstructures in well-defined polymer systems without the introduction of any dopants. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Release properties of tannic acid from hydrogen bond driven antioxidative cellulose nanofibrous films.

    Science.gov (United States)

    Zhou, Bin; Hu, Xiaoqian; Zhu, Jinjin; Wang, Zhenzhen; Wang, Xichang; Wang, Mingfu

    2016-10-01

    Layer-by-layer (LBL) assembled films have been exploited for surface-mediated bioactive compound delivery. Here, an antioxidative hydrogen-bonded multilayer electrospun nanofibrous film was fabricated from tannic acid (TA), acting as a polyphenolic antioxidant, and poly(ethylene glycol) (PEG) via layer-by-layer assembly. It overcame the burst release behavior of nanofibrous carrier, due to the reversible/dynamic nature of hydrogen bond, which was responded to external stimuli. The PEG/TA nanofibrous films disassembled gradually and released TA to the media, when soaked in aqueous solutions. The release rate of TA increased with increasing bilayer number, pH and temperature, but decreased with enhancing ionic strength. The surface morphology of the nanofibrous mats was observed by scanning electron microscopy (SEM). The following antioxidant activity assay revealed that it could scavenge DPPH free radicals and ABTS(+) cation radicals, a major biological activity of polyphenols. This technology can be used to fabricate other phenolic-containing slowly releasing antioxidative nanofibrous films. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Fabrication of extremely thermal-stable GaN template on Mo substrate using double bonding and step annealing process

    Science.gov (United States)

    Qing, Wang; Yang, Liu; Yongjian, Sun; Yuzhen, Tong; Guoyi, Zhang

    2016-08-01

    A new layer transfer technique which comprised double bonding and a step annealing process was utilized to transfer the GaN epilayer from a sapphire substrate to a Mo substrate. Combined with the application of the thermal-stable bonding medium, the resulting two-inch-diameter GaN template showed extremely good stability under high temperature and low stress state. Moreover, no cracks and winkles were observed. The transferred GaN template was suitable for homogeneous epitaxial, thus could be used for the direct fabrication of vertical LED chips as well as power electron devices. It has been confirmed that the double bonding and step annealing technique together with the thermal-stable bonding layer could significantly improve the bonding strength and stress relief, finally enhancing the thermal stability of the transferred GaN template. Project supported by the Guangdong Innovative Research Team Program (No. 2009010044), the China Postdoctoral Science Foundation (No. 2014M562233), the National Natural Science Foundation of Guangdong, China (No. 2015A030312011), and the Opened Fund of the State Key Laboratory on Integrated Optoelectronics (No. IOSKL2014KF17).

  15. Accurate Bond Lengths to Hydrogen Atoms from Single?Crystal X?ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks

    OpenAIRE

    Dittrich, Birger; L?bben, Jens; Mebs, Stefan; Wagner, Armin; Luger, Peter; Flaig, Ralf

    2017-01-01

    Abstract Amino acid structures are an ideal test set for method?development studies in crystallography. High?resolution X?ray diffraction data for eight previously studied genetically encoding amino acids are provided, complemented by a non?standard amino acid. Structures were re?investigated to study a widely applicable treatment that permits accurate X?H bond lengths to hydrogen atoms to be obtained: this treatment combines refinement of positional hydrogen?atom parameters with aspherical s...

  16. Hydrogen-Bonding Interactions in Luminescent Quinoline-Triazoles with Dominant 1D Crystals

    Directory of Open Access Journals (Sweden)

    Shi-Qiang Bai

    2017-09-01

    Full Text Available Quinoline-triazoles 2-((4-(diethoxymethyl-1H-1,2,3-triazol-1-ylmethylquinoline (1, 2-((4-(m-tolyl-1H-1,2,3-triazol-1-ylmethylquinoline (2 and 2-((4-(p-tolyl-1H-1,2,3-triazol-1-ylmethylquinoline (3 have been prepared with CuAAC click reactions and used as a model series to probe the relationship between lattice H-bonding interaction and crystal direction of growth. Crystals of 1–3 are 1D tape and prism shapes that correlate with their intermolecular and solvent 1D lattice H-bonding interactions. All compounds were thermally stable up to about 200 C and blue-green emissive in solution.

  17. Benchmark, DFT assessments, cooperativity, and energy decomposition analysis of the hydrogen bonds in HCN/HNC oligomeric complexes.

    Science.gov (United States)

    de Oliveira, Paulo McMiller C; Silva, Juliana A B; Longo, Ricardo L

    2017-02-01

    Hydrogen cyanide (HCN) and its tautomer hydrogen isocyanide (HNC) are relevant for extraterrestrial chemistry and possible relation to the origin of biomolecules. Several processes and reactions involving these molecules depend on their intermolecular interactions that can lead to aggregates and liquids especially due to the hydrogen bonds. It is thus important to comprehend, to describe, and to quantify their hydrogen bonds, mainly their nature and the cooperativity effects. A systematic study of all linear complexes up to pentamers of HCN and HNC is presented. CCSD(T)/CBS energy calculations, with and without basis set superposition error (BSSE) corrections for energies and geometries, provided a suitable set of benchmarks. Approximated methods based on the density functional theory (DFT) such as BP86, PBE, TPSS, B3LYP, CAM-B3LYP with and without dispersion corrections and long-range corrections, were assessed to describe the interaction energies and cooperativity effects. These assessments are relevant to select DFT functionals for liquid simulations. Energy decomposition analysis was performed at the PBE/STO-TZ2P level and provided insights into the nature of the hydrogen bonds, which are dominated by the electrostatic component. In addition, several linear relationships between the various energy components and the interaction energy were obtained. The cooperativity energy was also found to be practically linear with respect to the interaction energy, which may be relevant for designing and/or correcting empirical force fields. Graphical Abstract Hydrogen bonds in HCN/HNC oligomeric complexesᅟ.

  18. 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

  19. Microwave Spectrum of Hydrogen Bonded HEXAFLUOROISOPROPANOL•••WATER Complex

    Science.gov (United States)

    Shahi, Abhishek; Arunan, Elangannan

    2014-06-01

    Stabilizing α-helical structure of protein and dissolving a hard to dissolve polymer, polythene terphthalete, are some of the unique properties of the organic solvent Hexafluoroisopropanol (HFIP). After determining the complete microwave spectrum of HFIP monomer, we have recorded the spectrum of HFIP***H_2O complex. Ab initio calculations were used to optimize three different possible structures. The global minimum, structure 1, had HFIP as proton donor. Another promising structure, Structure 2, has been obtained from a molecular dynamic study. A total of 46 observed lines have been fitted well for obtaining the rotational and distortion constants within experimental uncertainty. The observed rotational constants are A = 1134.53898(77) MHz, B = 989.67594(44) MHz and C = 705.26602(20) MHz. Interestingly, the rotational constants of structure 1, structure 2 and experiments were very close. Experimentally observed distortion constants were close to structure 1. b-type transitions were stronger than c-type which is also consistent with the calculated dipole moment components of structure 1. Calculations predict a non-zero a-dipole moment but experimentally a-type transitions were absent. Microwave spectra of two of the deuterium isotopologues of this complex i.e. HFIP***D_2O (30 transitions) and HFIP***HOD (33 transitions) have been also observed. Search for other isotopologues are in progress. To characterize the nature of hydrogen bonding, Atoms in Molecules and Natural Bond Orbital theoretical analysis have been done. Experimental structure and these theoretical analyses indicate that the hydrogen bonding in HFIP***H_2O complex is stronger than that in water dimer. A. Shahi and E. Arunan, Talk number RK16, 68th International Symposium on Molecular Spectroscopy 2013, Ohio, USA. Yamaguchi, T.; Imura, S.; Kai, T.; Yoshida, K. Zeitschrift für Naturforsch. A 2013, 68a, 145.

  20. Hydrogen-bond memory and water-skin supersolidity resolving the Mpemba paradox.

    Science.gov (United States)

    Zhang, Xi; Huang, Yongli; Ma, Zengsheng; Zhou, Yichun; Zhou, Ji; Zheng, Weitao; Jiang, Qing; Sun, Chang Q

    2014-11-14

    The Mpemba paradox, that is, hotter water freezes faster than colder water, has baffled thinkers like Francis Bacon, René Descartes, and Aristotle since B.C. 350. However, a commonly accepted understanding or theoretical reproduction of this effect remains challenging. Numerical reproduction of observations, shown herewith, confirms that water skin supersolidity [Zhang et al., Phys. Chem. Chem. Phys., DOI: ] enhances the local thermal diffusivity favoring heat flowing outwardly in the liquid path. Analysis of experimental database reveals that the hydrogen bond (O:H-O) possesses memory to emit energy at a rate depending on its initial storage. Unlike other usual materials that lengthen and soften all bonds when they absorb thermal energy, water performs abnormally under heating to lengthen the O:H nonbond and shorten the H-O covalent bond through inter-oxygen Coulomb coupling [Sun et al., J. Phys. Chem. Lett., 2013, 4, 3238]. Cooling does the opposite to release energy, like releasing a coupled pair of bungees, at a rate of history dependence. Being sensitive to the source volume, skin radiation, and the drain temperature, the Mpemba effect proceeds only in the strictly non-adiabatic 'source-path-drain' cycling system for the heat "emission-conduction-dissipation" dynamics with a relaxation time that drops exponentially with the rise of the initial temperature of the liquid source.

  1. How far can a single hydrogen bond tune the spectral properties of the GFP chromophore?

    DEFF Research Database (Denmark)

    Kiefer, Hjalte; Lattouf, Elie; Persen, Natascha Wardinghus

    2015-01-01

    Photoabsorption of the hydrogen-bonded complex of a neutral and an anionic Green Fluorescent Protein chromophore has been studied using a new dual-detection approach to action-absorption spectroscopy. Following absorption of one photon, dissociation through a single channel ensures that the full...... time, the apparent effect of the H-bond for the neutral chromophore is as large as 0.5 eV, red-shifting the absorption maximum of the isolated neutral (340 nm) to that measured in the dimer (393 nm) and various proteins ([similar]395 nm). This shift results from changes in the topography of potential...... absorption spectrum is measured. Our theoretical account of the spectral shape reveals that the anionic 0–0 transition (464 nm) is blue-shifted compared to that of the wild-type protein (478 nm) due to the stronger H-bond in the dimer, and represents an upper bound for that of the isolated anion. At the same...

  2. Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions, Chemical Properties, and Ligand/Protein Fluorine NMR Screening.

    Science.gov (United States)

    Dalvit, Claudio; Vulpetti, Anna

    2016-05-23

    It is known that strong hydrogen-bonding interactions play an important role in many chemical and biological systems. However, weak or very weak hydrogen bonds, which are often difficult to detect and characterize, may also be relevant in many recognition and reaction processes. Fluorine serving as a hydrogen-bond acceptor has been the subject of many controversial discussions and there are different opinions about it. It now appears that there is compelling experimental evidence for the involvement of fluorine in weak intramolecular or intermolecular hydrogen bonds. Using established NMR methods, we have previously characterized and measured the strengths of intermolecular hydrogen-bond complexes involving the fluorine moieties CH2 F, CHF2 , and CF3 , and have compared them with the well-known hydrogen-bond complex formed between acetophenone and the strong hydrogen-bond donor p-fluorophenol. We now report evidence for the formation of hydrogen bonds involving fluorine with significantly weaker donors, namely 5-fluoroindole and water. A simple NMR method is proposed for the simultaneous measurement of the strengths of hydrogen bonds between an acceptor and a donor or water. Important implications of these results for enzymatic/chemical reactions involving fluorine, for chemical and physical properties, and for ligand/protein (19) F NMR screening are analyzed through experiments and theoretical simulations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. On the occurrence of three-center hydrogen bonds in cyclodextrins in crystalline form and in aqueous solution: comparison of neutron diffraction and molecular dynamics results.

    Science.gov (United States)

    Koehler, J E; Saenger, W; van Gunsteren, W F

    1988-08-01

    Three-center (bifurcated) hydrogen bonds may play a role by serving as an intermediate state between different dynamically changing hydrogen bonding patterns. Hydrogen bonding configurations can be studied experimentally by neutron diffraction and theoretically by computer simulation techniques. Here, both methods are used to analyse the occurrence of three-center hydrogen bonds in crystals of cyclodextrins. Almost all experimentally observed three-center hydrogen bonds in the crystal are reproduced in the molecular dynamics (MD) simulations, even as far as the detailed asymmetric geometry is concerned. On the basis of this result a MD simulation of cyclodextrin in aqueous solution is searched for the occurrence of three-center hydrogen bonds. Significant differences are found. In solution more different three-center hydrogen bonds per alpha-cyclodextrin molecule are observed than in the crystal but the population (existence as percent of the simulation period) of each three-center hydrogen bond is lower in solution than in crystal. These may indeed serve as intermediate states in the process of changing one hydrogen bonding pattern into another.

  4. Neutral iodotriazoles as scaffolds for stable halogen-bonded assemblies in solution.

    Science.gov (United States)

    Maugeri, Leonardo; Asencio-Hernández, Julia; Lébl, Tomáš; Cordes, David B; Slawin, Alexandra M Z; Delsuc, Marc-André; Philp, Douglas

    2016-10-01

    The halogen bond (XB) donor properties of neutral 1,4-diaryl-5-iodo-1,2,3-triazoles are explored using a combination of computational and experimental results and are shown to be competitive in halogen bonding efficiency with the classic pentafluoroiodobenzene XB donor. The S N Ar reactivity of these donors permits the facile assembly of an iodotriazole functionalised with a 3-oxypyridine XB acceptor, thus generating a molecular scaffold capable of undergoing dimerisation through the formation of two halogen bonds. The formation of this halogen-bonded dimer is demonstrated by 1 H and DOSY NMR experiments and a plausible structure generated using DFT calculations.

  5. "Predicting" Polymorphs of Pharmaceuticals Using Hydrogen Bond Propensities: Probenecid and Its Two Single-Crystal-to-Single-Crystal Phase Transitions.

    Science.gov (United States)

    Nauha, Elisa; Bernstein, Joel

    2015-06-01

    The recently developed hydrogen-bonding propensity tool in the Cambridge Structural Database software package (Mercury) was tested to predict polymorphs. The compounds for the study were chosen from a list of approximately 300 pharmaceutically important compounds, for which multiple crystal forms had not been previously reported. The hydrogen-bonding propensity analysis was carried out on approximately 60 randomly selected compounds from this list. Several compounds with a high probability for exhibiting polymorphism in the analysis were chosen for a limited experimental crystal form screening. One of the compounds, probenecid, did not yield polymorphs by traditional solution crystallization screening, but differential scanning calorimetry revealed three polymorphs. All of them exhibit the same hydrogen bonding and transform via two reversible single-crystal-to single-crystal transformations, which have been characterized in detail through three single-crystal structure determinations at appropriate temperatures. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

  6. Conserved water-mediated hydrogen bond network between TM-I, -II, -VI, and -VII in 7TM receptor activation

    DEFF Research Database (Denmark)

    Nygaard, Rie; Hansen, Louise Valentin; Mokrosinski, Jacek

    2010-01-01

    Five highly conserved polar residues connected by a number of structural water molecules together with two rotamer micro-switches, TrpVI:13 and TyrVII:20, constitute an extended hydrogen bond network between the intracellular segments of TM-I, -II, -VI, and -VII of 7TM receptors. Molecular dynamics...... simulations showed that, although the fewer water molecules in rhodopsin were relatively movable, the hydrogen bond network of the beta2-adrenergic receptor was fully loaded with water molecules that were surprisingly immobilized between the two rotamer switches, both apparently being in their closed...... (AsnI:18, AspII:10, and AsnVII:13), whereas others (AsnVII:12 and AsnVII:16) located one helical turn apart and sharing a water molecule were shown to be essential for agonist-induced signaling. It is concluded that the conserved water hydrogen bond network of 7TM receptors constitutes an extended...

  7. Predicting anisotropic thermal displacements for hydrogens from solid-state NMR: a study on hydrogen bonding in polymorphs of palmitic acid.

    Science.gov (United States)

    Wang, Luther; Uribe-Romo, Fernando J; Mueller, Leonard J; Harper, James K

    2018-03-28

    The hydrogen-bonding environments at the COOH moiety in eight polycrystalline polymorphs of palmitic acid are explored using solid-state NMR. Although most phases have no previously reported crystal structure, measured 13C chemical shift tensors for COOH moieties, combined with DFT modeling establish that all phases crystallize with a cyclic dimer (R22(8)) hydrogen bonding arrangement. Phases A2, Bm and Em have localized OH hydrogens while phase C has a dynamically disordered OH hydrogen. The phase designated As is a mix of five forms, including 27.4% of Bm and four novel phases not fully characterized here due to insufficient sample mass. For phases A2, Bm, Em, and C the anisotropic uncertainties in the COOH hydrogen atom positions are established using a Monte Carlo sampling scheme. Sampled points are retained or rejected at the ±1σ level based upon agreement of DFT computed 13COOH tensors with experimental values. The collection of retained hydrogen positions bear a remarkable resemblance to the anisotropic displacement parameters (i.e. thermal ellipsoids) from diffraction studies. We posit that this similarity is no mere coincidence and that the two are fundamentally related. The volumes of NMR-derived anisotropic displacement ellipsoids for phases with localized OH hydrogens are 4.1 times smaller than those derived from single crystal X-ray diffraction and 1.8 times smaller than the volume of benchmark single crystal neutron diffraction values.

  8. Modeling the Solid-Liquid Equilibrium in Pharmaceutical-Solvent Mixtures: Systems with Complex Hydrogen Bonding Behvaior

    DEFF Research Database (Denmark)

    Tsivintzelis, Ioannis; Economou, Ioannis; Kontogeorgis, Georgios

    2009-01-01

    A methodology is suggested for modeling the phase equilibria of complex chemical mixtures with an equation of state (EoS) for the case where only limited experimental data exist. The complex hydrogen bonding behavior is explicitly accounted for and the corresponding parameters are adopted from...... simpler molecules of similar chemical structure and/or are fitted to Hansen's partial solubility parameters. The methodology is applied to modeling the solubility of three pharmaceuticals, namely acetanilide, phenacetin, and paracetamol, using the nonrandom hydrogen bonding (NRHB) EoS. In all cases...... and solid state, Delta Cp = Cp-l - Cps, in the determination of solid chemical potential and, also, of the polymorphism of drugs....

  9. The interplay between surface-water and hydrogen bonding in a water adlayer on Pt(111) and Ag(111)

    Energy Technology Data Exchange (ETDEWEB)

    Delle Site, Luigi [Max-Planck-Institut fuer Polymerforschung, Ackermannweg 10, D-55128 Mainz (Germany); Ghiringhelli, Luca M [Max-Planck-Institut fuer Polymerforschung, Ackermannweg 10, D-55128 Mainz (Germany); Andreussi, Oliviero [Scuola Normale Superiore, Piazza dei Cavalieri 7, 56100 Pisa (Italy); Donadio, Davide [Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI-Campus, via Giuseppe Buffi 13, CH-6900 Lugano (Switzerland); Parrinello, Michele [Scuola Normale Superiore, Piazza dei Cavalieri 7, 56100 Pisa (Italy)

    2007-06-20

    The structure of a water adlayer on a Pt(111) surface is investigated by means of extensive first-principles calculations. Allowing for proton disorder, the ground state energy for the {radical}3 x {radical}3R30{sup o} structure can be found. This results from an interplay between water/metal chemical bonding and the hydrogen bonding of the water network. This picture is supported by substituting Pt(111) with Ag(111): the almost inert surface allows for the reconstruction of the hydrogen network. (fast track communication)

  10. The interplay between surface-water and hydrogen bonding in a water adlayer on Pt(111) and Ag(111)

    International Nuclear Information System (INIS)

    Delle Site, Luigi; Ghiringhelli, Luca M; Andreussi, Oliviero; Donadio, Davide; Parrinello, Michele

    2007-01-01

    The structure of a water adlayer on a Pt(111) surface is investigated by means of extensive first-principles calculations. Allowing for proton disorder, the ground state energy for the √3 x √3R30 o structure can be found. This results from an interplay between water/metal chemical bonding and the hydrogen bonding of the water network. This picture is supported by substituting Pt(111) with Ag(111): the almost inert surface allows for the reconstruction of the hydrogen network. (fast track communication)

  11. Ab initio localized charge distributions. Theory and a detailed analysis of the water dimer-hydrogen bond

    Energy Technology Data Exchange (ETDEWEB)

    Jensen, J.H.; Gordon, M.S. [Ames Lab., IA (United States)

    1995-05-18

    The method of localized charge distributions, originally implemented for semiempirical molecular orbital (MO) theory, is reintroduced and implemented for ab initio self-consistent field MO theory. This theory is then used in conjunction with localized second-order Moller-Plesset (MP2) pair energies to analyze the hydrogen bond in the water dimer. It is found that this hydrogen bond can be explained as the competition between the intrawater electronic kinetic energy pressure and the interwater potential energy suction. 27 refs., 24 figs.

  12. Investigation of hydrogen bonding in 3-methylindole · H 2O cluster by mass analyzed threshold ionization

    Science.gov (United States)

    Georgiev, S.; Neusser, H. J.

    2004-05-01

    The adiabatic ionization energies and the threshold ion vibrational spectra of 3-methylindole and the 3-methylindole · H 2O cluster and the hydrogen bonding energy of the latter have been measured with mass analyzed threshold ionization (MATI) technique. Dissociation of the cluster has been detected as a breakdown of the threshold ion signal at the parent mass channel and the simultaneous increase of the signal at the fragment mass channel. Comparison with our previous work on indole · H 2O shows that there is only a small influence of the methyl group on the ionization energy and the hydrogen bonding strength.

  13. Measurement and theory of hydrogen bonding contribution to isosteric DNA base pairs.

    Science.gov (United States)

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

    2012-02-15

    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 between F and natural bases in nucleic acid duplexes and in a DNA polymerase active site. Since F is widely used to measure electrostatic contributions to pairing and replication, it is important to quantify the impact of this isostere on DNA stability. Here, we studied the pairing stability and selectivity of this compound and a closely related variant, dichlorotoluene deoxyriboside (L), in DNA, using both experimental and computational approaches. We measured the thermodynamics of duplex formation in three sequence contexts and with all possible pairing partners by thermal melting studies using the van't Hoff approach, and for selected cases by isothermal titration calorimetry (ITC). Experimental results showed that internal F-A pairing in DNA is destabilizing by 3.8 kcal/mol (van't Hoff, 37 °C) as compared with T-A pairing. At the end of a duplex, base-base interactions are considerably smaller; however, the net F-A interaction remains repulsive while T-A pairing is attractive. As for selectivity, F is found to be slightly selective for adenine over C, G, T by 0.5 kcal mol, as compared with thymine's selectivity of 2.4 kcal/mol. Interestingly, dichlorotoluene in DNA is slightly less destabilizing and slightly more selective than F, despite the lack of strongly electronegative fluorine atoms. Experimental data were complemented by computational results, evaluated at the M06-2X/6-31+G(d) and MP2/cc-pVTZ levels of theory. These computations suggest that the pairing energy of F to A

  14. Hydrogen bonded 1D-3D supramolecular structures from Benzylamine and organic acidic components

    Science.gov (United States)

    Gao, Xingjun; Li, XiaoLiang; Jin, Shouwen; Hu, Kaikai; Guo, Jianzhong; Guo, Ming; Xu, Weiqiang; Wang, Daqi

    2018-03-01

    Cocrystallization of the commonly available organic amine, benzylamine, with a series of organic acids afforded a total of seven organic salts with the compositions: (benzylamine)2: (p-nitrophenol)2: (H2O) (1) [(HL)2+⋯(npl-)2⋯(H2O), npl- = p-nitrophenolate], (benzylamine): (4-tert-butylbenzoic acid) (2) [(HL+)⋯(tba-), tba- = 4-tert-butylbenzoate], (benzylamine): (3,4-dichlorobenzoic acid) (3) [(HL+)⋯dcba-), dcba- = 3,4-dichlorobenzoate], (benzylamine): (2,5-dihydroxybenzoic acid) (4) [(HL+)⋯(dhba-), dhba- = 2,5-dihydroxybenzoate], (benzylamine): (2-bromo-but-2-enedioic acid) (5) [(HL+)⋯(Hbba-), Hbba- = 2-bromo-hydrogenbut-2-enedioate], (benzylamine): (2,6-pyridinedicarboxylic acid) (6) [(HL+)⋯(Hpdc-), Hpdc- = 2,6-pyridine hydrogendicarboxylate], and (benzylamine)2: (3-nitrophthalic acid): 2(H2O) (7) [(HL+)2⋯(npa2-)⋯(H2O)2, npa2- = 3-nitrophthalate]. The seven salts have been characterised by X-ray diffraction analysis, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The results reveal that among the seven investigated crystals the NH2 in the benzylamine are protonated when the organic acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted Nsbnd H⋯O hydrogen bond between the NH3+ and deprotonated acidic groups. Except the Nsbnd H⋯O hydrogen bond, the Osbnd H⋯O hydrogen bonds (charge assisted or neutral) were also found at the salts 1, 4, 5, 6, and 7. Further analysis of the crystal packing of the salts indicated that a different family of additional CHsbnd O/CH2sbnd O, CH-π/CH2-π, Cπ-Cπ, Osbnd O, O-Cπ, O-π, and Cl-π associations also contribute to the stabilization and expansion of the total high-dimensional framework structures. For the coexistence of the various weak nonbonding interactions, these structures adopted a variety of

  15. Influences of Structure Disorder and Temperature on Properties of Proton Conductivity in Hydrogen-Bond Molecular Systems

    International Nuclear Information System (INIS)

    Pang Xiaofeng; Yu Jiafeng

    2007-01-01

    The dynamic properties of proton conductivity along hydrogen-bonded molecular systems, for example, ice crystal, with structure disorder or damping and finite temperatures exposed in an externally applied electric-field have been numerically studied by Runge-Kutta way in our soliton model. The results obtained show that the proton-soliton is very robust against the structure disorder including the fluctuation of the force constant and disorder in the sequence of masses and thermal perturbation and damping of medium, the velocity of its conductivity increases with increasing of the externally applied electric-field and decreasing of the damping coefficient of medium, but the proton-soliton disperses for quite great fluctuation of the force constant and damping coefficient. In the numerical simulation we find that the proton-soliton in our model is thermally stable in a large region of temperature of T≤273 K under influences of damping and externally applied electric-field in ice crystal. This shows that our model is available and appropriate to ice.

  16. Hydroxyalkoxy radicals: importance of intramolecular hydrogen bonding on chain branching reactions in the combustion and atmospheric decomposition of hydrocarbons.

    Science.gov (United States)

    Davis, Alexander C; Francisco, Joseph S

    2014-11-20

    During both the atmospheric oxidation and combustion of volatile organic compounds, sequential addition of oxygen can lead to compounds that contain multiple hydrogen-bonding sites. The presence of two or more of these sites on a hydrocarbon introduces the possibility of intramolecular H-bonding, which can have a stabilizing effect on the reactants, products, and transition states of subsequent reactions. The present work compares the absolute energies of two sets of conformations, those that contain intramolecular H-bonds and those that lack intramolecular H-bonds, for each reactant, product, and transition state species in the 1,2 through 1,7 H-migrations and Cα-Cβ, Cα-H, and Cα-OH-bond scission reactions in the n-hydroxyeth-1-oxy through n-hydroxyhex-1-oxy radicals, for n ranging from 1 to 6. The difference in energy between the two conformations represents the balance between the stabilizing effects of H-bonds and the steric cost of bringing the two H-bonding sites together. The effect of intramolecular H-bonding and the OH group is assessed by comparing the net intramolecular H-bond stabilization energies, the reaction enthalpies, and barrier heights of the n-hydroxyalkoxy radical reactions with the corresponding alkoxy radicals values. The results suggest that there is a complex dependence on the location of the two H-bonding groups, the location of the abstraction or bond scission, and the shape of the transition state that dictates the extent to which intramolecular H-bonding effects the relative importance of H-migration and bond scission reactions for each n-hydroxyalkoxy radical. These findings have important implications for future studies on hydrocarbons with multiple H-bonding sites.

  17. [FHF]−—The Strongest Hydrogen Bond under the Influence of External Interactions

    Directory of Open Access Journals (Sweden)

    Sławomir J. Grabowski

    2015-12-01

    Full Text Available A search through the Cambridge Structural Database (CSD for crystal structures containing the [FHF]− anion was carried out. Forty five hydrogen bifluoride structures were found mainly with the H-atom moved from the mid-point of the F…F distance. However several [FHF]− systems characterized by D∞h symmetry were found, the same as this anion possesses in the gas phase. The analysis of CSD results as well as the analysis of results of ab initio calculations on the complexes of [FHF]− with Lewis acid moieties show that the movement of the H-atom from the central position depends on the strength of interaction of this anion with external species. The analysis of the electron charge density distribution in complexes of [FHF]− was performed with the use of the Quantum Theory of Atoms in Molecules (QTAIM approach and the Natural Bond Orbitals (NBO method.

  18. Hydrogen bonding-assisted interaction between amitriptyline hydrochloride and hemoglobin: spectroscopic and molecular dynamics studies.

    Science.gov (United States)

    Maurya, Neha; Maurya, Jitendra Kumar; Kumari, Meena; Khan, Abbul Bashar; Dohare, Ravins; Patel, Rajan

    2017-05-01

    Herein, we have explored the interaction between amitriptyline hydrochloride (AMT) and hemoglobin (Hb), using steady-state and time-resolved fluorescence spectroscopy, UV-visible spectroscopy, and circular dichroism spectroscopy, in combination with molecular docking and molecular dynamic (MD) simulation methods. The steady-state fluorescence reveals the static quenching mechanism in the interaction system, which was further confirmed by UV-visible and time-resolved fluorescence spectroscopy. The binding constant, number of binding sites, and thermodynamic parameters viz. ΔG, ΔH, ΔS are also considered; result confirms that the binding of the AMT with Hb is a spontaneous process, involving hydrogen bonding and van der Waals interactions with a single binding site, as also confirmed by molecular docking study. Synchronous fluorescence, CD data, and MD simulation results contribute toward understanding the effect of AMT on Hb to interpret the conformational change in Hb upon binding in aqueous solution.

  19. Coupling between Molecular Mobility and Kinetics of Crystal Growth in a Hydrogen-Bonded Liquid

    DEFF Research Database (Denmark)

    Sanz, Alejandro; Niss, Kristine

    2017-01-01

    Our aim here is to gain new insight into the nature of the crystalline phase formed in supercooled glycerol near the glass transition temperature and to establish the interrelationship between the kinetics of crystal growth and fundamental dynamic properties. The liquid’s dynamics...... rate. The coupling between dynamic properties, such as dielectric α relaxation time, viscosity, and self-diffusion coefficient, and the characteristic crystal growth time is analyzed. We find that the crystal growth time scales with the glycerol’s self-diffusion coefficient as taucryst ∝ D−0...... and the crystalline development in glycerol, a hydrogen-bonded liquid, is studied by means of dielectric spectroscopy. We monitored the kinetics of crystallization by isothermal treatment at temperatures between 220 and 240 K (Tg = 185 K). Given the thermal protocol employed, we stimulated the growth...

  20. Dimeric Self-assembling via Hydrogen Bonding and Emissive Behavior of a New Copper (I Complex

    Directory of Open Access Journals (Sweden)

    Juciely M. dos Reis

    2017-04-01

    Full Text Available This work describes the synthesis, structural characterization and emissive behavior of a new copper (I complex based on 1-thiocarbamoyl-5-(4-methoxiphenyl-3-phenyl-4,5-dihydro-1H-pyrazole ligand. A dimeric self-assembling via hydrogen bonding was determined by analyzing the short contacts present in the solid-state structure by means of X-ray crystallography. The spectroscopic properties were determined using UV-Vis and fluorescence experiments and an interesting behavior as bluish luminescence was assigned mainly to the mixed (MLCT + IL electronic transitions of the Cu(Id10 ® (S=C–Nligand type. The complete characterization of the new copper (I complex also included elemental analyses and IR spectroscopy. DOI: http://dx.doi.org/10.17807/orbital.v9i1.952