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Sample records for bond forming hydrogenation

  1. 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 ...

  2. 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.

  3. 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.

  4. 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...

  5. Theoretical investigation on hydrogen bond interaction of diketo/keto-enol form uracil and thymine tautomers with intercalators.

    Science.gov (United States)

    Anithaa, V S; Vijayakumar, S; Sudha, M; Shankar, R

    2017-11-06

    The interaction of diketo and keto-enol form of thymine and uracil tautomers with acridine (Acr), phenazine (Phen), benzo[c]cinnoline (Ben), 1,10-phenanthroline (1,10-Phe), and 4,7-phenenthroline (4,7-Phe) intercalating drug molecules was studied using density functional theory at B3LYP/6-311++G** and M05-2×/6-311++G** levels of theory. From the interaction energy, it is found that keto-enol form tautomers have stronger interaction with intercalators than diketone form tautomers. On complex formation of thymine and uracil tautomers with benzo[c]cinnoline the drug molecules have high interaction energy values of -20.14 (BenT3) and -20.55 (BenU3) kcal mol -1 , while phenazine has the least interaction energy values of -6.52 (PhenT2) and -6.67 (PhenU2) kcal mol -1 . The closed shell intermolecular type interaction between the molecules with minimum elliptical value of 0.018 and 0.019 a.u at both levels of theory has been found from topological analysis. The benzo[c]cinnoline drug molecule with thymine and uracil tautomers has short range intermolecular N-H…N, C-H…O, and O-H...N hydrogen bonds (H-bonds) resulting in higher stability than other drug molecules. The proper hydrogen bonds N-H..N and O-H..N have the frequency shifted toward the lower side (red shifted) with the elongation in their bond length while the improper hydrogen bond C-H...O has the frequency shifted toward the higher side (blue shifted) of the spectral region with the contraction in their bond length. Further, the charge transfer between proton acceptor and donor along with stability of the bond is studied using natural bond orbital (NBO) analysis. Graphical abstract Hydrogen bond interaction of diketo/keto-enol form uracil and thymine tautomers with intercalators.

  6. 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)

  7. 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.

  8. 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

  9. Polarization and bonding of the intrinsic characteristic contours of hydrogen and fluorine atoms of forming a hydrogen fluoride molecule based on an ab initio study

    Science.gov (United States)

    Yang, Zhong-Zhi; Zhao, Dong-Xia; Wu, Yang

    2004-08-01

    The spatial changing feature of the shapes and sizes of the system consisted of one hydrogen atom and one fluorine atom of forming a hydrogen fluoride molecule is investigated. We give formalism of the potential acting on an electron in a molecule and derive its concrete expression in Hartree-Fock self-consistent molecular orbital theory including configuration interaction. The program of calculating the potential acting on an electron in a molecule is programmed and compiled in the framework of the MELD program package. We formulate briefly the approach of the molecular intrinsic characteristic contour (MICC) which is defined in terms of the classical turning points of electronic motion. The MICC for a molecular system is intrinsic and can be calculated by means of an ab initio CI method. Then, the polarization and bonding features of the intrinsic characteristic contours of hydrogen and fluorine atoms forming a hydrogen fluoride molecule are presented and discussed from ab initio calculations. Furthermore, electron density distribution as an added dimension has been demonstrated on the changing MICC and thus the vivid polarization and bonding features for a chemical process have been shown. It seems that at the early stage (internuclear distance Ind=5.0-20.0 a.u.) the fluorine atom gives more enthusiastic with the sensitive and expanded polarization to welcome coupling with the hydrogen atom while the latter has little response even "shy" with shrinking a bit its size at the beginning of putting the two atoms into a system and it is only around the critical point, the contact point (Ind=4.73 a.u.), that both of them stretch their hands and arms to meet and then fuse together.

  10. 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.

  11. 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 ...

  12. 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.

  13. 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 ...

  14. 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.

  15. 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, ...

  16. Organic salts formed by 2,4,6-triaminopyrimidine and selected carboxylic acids via a variety of hydrogen bonds: Synthons cooperation, and crystal structures

    Science.gov (United States)

    Xing, Peiqi; Li, Qingyun; Li, Yingying; Wang, Kunpeng; Zhang, Qi; Wang, Lei

    2017-05-01

    By using solvent evaporation method, 2,4,6-triaminopyrimidine (TAPI) is employed to crystallize with a variety of acids, including 3,5-dihydroxybenzoic acid (HDHBA), 3-nitrophthalic acid (H2NPA), 5-amino-2,4,6-triiodoisophthalic acid (H2ATIPIA), 2,5-dibromoterephthalic acid (H2DBTPA), 1,5-naphthalenedisulfonic acid (H2NDSA), sebacic acid (H2SA), 1,2,4-benzenetricarboxylic acid (H3BTA), and biphenyl-2,2‧,5,5'-tetracarboxylic acid (H4BPTA). In all eight complexes, protons are completely exchanged from O atom of acid to nitrogen of TAPI in 1, 3, 4, and, 5, partly transferred in 2, 6, 7, and 8. The crystal structure of all eight complexes exhibit that classical robust hydrogen bonds X-H⋯X (X = O/N) direct the molecular crystals to bind together in a stacking modes. Classical hydrogen bond Nsbnd H⋯O is participated in forming all eight organic salts, while hydrogen bonding Osbnd H⋯O are found in constructing the diversity structures in salts 1, 2, 3, 4, 6, and 7. The analysis shows that some classical supramolecular synthons, such as I R22(8), V R24(12), and VI S(6), are observed again in the construction of hydrogen-bonding networks. In the formation of layered and reticular structure, strong hydrogen bonds between water molecules and ligands having well-refined hydrogen atoms have been considered. Water molecules play an important role in building supramolecular structures of 1, 2, 3, 4, 7, and 8. Moreover, salts 1-8 are further characterized and analyzed by element analysis, infrared radiation, thermogravimetric analysis, proton nuclear magnetic resonance spectra, and mass spectra.

  17. 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...

  18. 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.

  19. 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.

  20. Hydrogen-bonded clusters of 1, 1'-ferrocenedicarboxylic acid on Au(111) are initially formed in solution

    Science.gov (United States)

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

    2015-03-01

    Low-temperature scanning tunneling microscopy is used to observe self-assembled structures of ferrocenedicarboxylic acid (Fc(COOH)2) on the Au(111) surface. The surface is prepared by pulse-deposition of Fc(COOH)2 dissolved in methanol, and the solvent is evaporated before imaging. While the rows of hydrogen-bonded dimers that are common for carboxylic acid species are observed, the majority of adsorbed Fc(COOH)2 is instead found in six-molecule clusters with a well-defined and chiral geometry. The coverage and distribution of these clusters are consistent with a random sequential adsorption model, showing that solution-phase species are determinative of adsorbate distribution for this system under these reaction conditions.

  1. 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.

  2. Water-bridged hydrogen bond formation between 5-hydroxylmethylcytosine (5-hmC) and its 3'-neighbouring bases in A- and B-form DNA duplexes.

    Science.gov (United States)

    Wang, Rui; Ranganathan, Srivathsan V; Valsangkar, Vibhav A; Magliocco, Stephanie M; Shen, Fusheng; Chen, Alan; Sheng, Jia

    2015-11-25

    5-Hydroxylmethylcytosine (5hmC) has been recognized as the sixth base with important biological functions in many tissues and cell types. We present here the high-resolution crystal structures and molecular simulation studies of both A-form and B-form DNA duplexes containing 5hmC. We observed that 5hmC interacts with its 3'-neighboring bases through water-bridged hydrogen bonds and these interactions may affect the further oxidation of 5hmC.

  3. 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.

  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. 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) ...

  6. Phase transition in triglycine family of hydrogen bonded ferroelectrics

    Indian Academy of Sciences (India)

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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Buthalital and methitural – 5,5-substituted derivatives of 2-thiobarbituric acid forming the same type of hydrogen-bonded chain

    Directory of Open Access Journals (Sweden)

    Thomas Gelbrich

    2017-12-01

    Full Text Available The molecule of buthalital, (I [systematic name: 5-(2-methylpropyl-5-(prop-2-en-1-yl-2-sulfanylidene-1,3-diazinane-4,6-dione], C11H16N2O2S, exhibits a planar pyrimidine ring, whereas the pyrimidine ring of methitural, (II [systematic name: 5-(1-methylbutyl-5-[2-(methylsulfanylethyl]-2-sulfanylidene-1,3-diazinane-4,6-dione], C12H20N2O2S2, is slightly puckered. (I and (II contain the same hydrogen-bonded chain structure in which each molecule is connected, via four N—H...O=C hydrogen bonds, to two other molecules, resulting in a hydrogen-bonded chain displaying a sequence of R22(8 rings. The same type of N—H...O=C hydrogen-bonded chain has previously been found in several 5,5-disubstituted derivatives of barbituric acid which are chemically closely related to (I and (II.

  12. 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.

  13. 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

  14. 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.

  15. 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...

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

    Science.gov (United States)

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

    2016-12-01

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

  17. 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.

  18. 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.

  19. 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.

  20. pH sensitive micelles formed by interchain hydrogen bonding of poly(methacrylic acid)- block–poly(ethylene oxide) copolymers

    Czech Academy of Sciences Publication Activity Database

    Koňák, Čestmír; Sedlák, M.

    2007-01-01

    Roč. 208, č. 17 (2007), s. 1893-1899 ISSN 1022-1352 R&D Projects: GA AV ČR IAA100500501; GA AV ČR IAA4050403; GA ČR GESON/06/E005 Institutional research plan: CEZ:AV0Z40500505 Keywords : association * dynamic light scattering * hydrogen bonding Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.046, year: 2007

  1. Induced Smectic X Phase Through Intermolecular Hydrogen-Bonded Liquid Crystals Formed Between Citric Acid and p- n-(Octyloxy)Benzoic Acid

    Science.gov (United States)

    Sundaram, S.; Subhasri, P.; Rajasekaran, T. R.; Jayaprakasam, R.; Senthil, T. S.; Vijayakumar, V. N.

    2017-08-01

    Hydrogen-bonded liquid crystal (HBLC) is synthesized from citric acid (CA) and 4-(octyloxy)benzoic acid (8OBA) with different mole ratios. Fourier transform infrared spectroscopy (FT-IR) confirms the presence of hydrogen bond between CA and 8OBA. Nuclear magnetic resonance (NMR) spectroscopic studies validate the intermolecular complementary, cyclic type of hydrogen bond, and molecular environment in the designed HBLC complex. Powder X-ray diffraction analysis reveals the monoclinic nature of liquid crystal complex in solid phase. Liquid crystal parameters such as phase transition temperature and enthalpy values for the corresponding mesogenic phases are investigated using a polarizing optical microscope (POM) and differential scanning calorimetry (DSC). It is observed that the change in chain length and steric hindrance while increasing the mole ratio in HBLC complex induces a new smectic X (Sm X) along with higher-order smectic G (Sm G) phases by quenching of smectic C (Sm C). From the experimental observations, induced Sm X phase has been identified as a finger print texture. Also, Sm G is a multi-colored mosaic texture in 1:1, 1:2, and 1:3 mol ratios. The optical tilt angle, thermal stability factor, and enhanced thermal span width of CA + 8OBA complex are discussed.

  2. 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 ...

  3. 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.

  4. 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 ...

  5. Probing hydrogen bonding interactions and proton transfer in proteins

    Science.gov (United States)

    Nie, Beining

    intermediate states of proteins. Our MD simulations on the structures of photoactive yellow protein (PYP) and its photoproducts provide deep insight into the much-debated structural nature of chromophore photo-isomerization. Our simulation data of three plausible photoproducts provide a specific guide on how to use time-resolved infrared spectroscopy to identify which photoproduct is formed after photo-isomerization. Our data also indicate that hydrogen bond with Tyr42 may be crucial to increase the proton affinity of the chromophore and trigger the intra-protein proton transfer during PYP photoreceptor activation.

  6. 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.

  7. 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

  8. 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...

  9. 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.

  10. 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...

  11. Supra-molecular hydrogen-bonding patterns in the N(9)-H protonated and N(7)-H tautomeric form of an N(6) -benzoyl-adenine salt: N (6)-benzoyl-adeninium nitrate.

    Science.gov (United States)

    Karthikeyan, Ammasai; Jeeva Jasmine, Nithianantham; Thomas Muthiah, Packianathan; Perdih, Franc

    2016-02-01

    In the title molecular salt, C12H10N5O(+)·NO3 (-), the adenine unit has an N (9)-protonated N(7)-H tautomeric form with non-protonated N(1) and N(3) atoms. The dihedral angle between the adenine ring system and the phenyl ring is 51.10 (10)°. The typical intra-molecular N(7)-H⋯O hydrogen bond with an S(7) graph-set motif is also present. The benzoyl-adeninium cations also form base pairs through N-H⋯O and C-H⋯N hydrogen bonds involving the Watson-Crick face of the adenine ring and the C and O atoms of the benzoyl ring of an adjacent cation, forming a supra-molecular ribbon with R 2 (2)(9) rings. Benzoyl-adeninum cations are also bridged by one of the oxygen atoms of the nitrate anion, which acts as a double acceptor, forming a pair of N-H⋯O hydrogen bonds to generate a second ribbon motif. These ribbons together with π-π stacking inter-actions between the phenyl ring and the five- and six-membered adenine rings of adjacent mol-ecules generate a three-dimensional supra-molecular architecture.

  12. Supra­molecular hydrogen-bonding patterns in the N(9)—H protonated and N(7)—H tautomeric form of an N6-benzoyl­adenine salt: N 6-benzoyl­adeninium nitrate

    Science.gov (United States)

    Karthikeyan, Ammasai; Jeeva Jasmine, Nithianantham; Thomas Muthiah, Packianathan; Perdih, Franc

    2016-01-01

    In the title molecular salt, C12H10N5O+·NO3 −, the adenine unit has an N 9-protonated N(7)—H tautomeric form with non-protonated N1 and N3 atoms. The dihedral angle between the adenine ring system and the phenyl ring is 51.10 (10)°. The typical intra­molecular N7—H⋯O hydrogen bond with an S(7) graph-set motif is also present. The benzoyl­adeninium cations also form base pairs through N—H⋯O and C—H⋯N hydrogen bonds involving the Watson–Crick face of the adenine ring and the C and O atoms of the benzoyl ring of an adjacent cation, forming a supra­molecular ribbon with R 2 2(9) rings. Benzoyl­adeninum cations are also bridged by one of the oxygen atoms of the nitrate anion, which acts as a double acceptor, forming a pair of N—H⋯O hydrogen bonds to generate a second ribbon motif. These ribbons together with π–π stacking inter­actions between the phenyl ring and the five- and six-membered adenine rings of adjacent mol­ecules generate a three-dimensional supra­molecular architecture. PMID:26958373

  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. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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 ...

  20. 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 ...

  1. 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

  2. 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 ...

  3. 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

  4. A natural grouping of motifs with an aspartate or asparagine residue forming two hydrogen bonds to residues ahead in sequence: their occurrence at alpha-helical N termini and in other situations.

    Science.gov (United States)

    Wan, W Y; Milner-White, E J

    1999-03-12

    Examination of the ways side-chain carboxylate and amide groups in high-resolution protein crystal structures form hydrogen bonds with main-chain atoms reveals that the most common category is a two-hydrogen-bond four to five residue motif with an aspartate or asparagine (Asx) at the first residue, for which we propose the name Asx-motif. Similar motifs with glutamate or glutamine residues at that position are rare. Asx-motifs occur typically as (1) a common feature of the N termini of alpha-helices called the Asx N-cap motif; (2) an independent motif, usually a beta-turn with an appropriately hydrogen-bonded Asx as the first residue; and (3) a motif incorporated in a beta-bulge loop. Asx-motifs are common, there being just under two-and-a-half in an average-sized protein subunit; of these, about 55 % are Asx N-cap motifs. Because they occur often in many situations, it seems that these motifs have an inherent propensity to form on their own rather than just being a feature stabilised at the end of a helix. Asx-motifs also occur in functionally interesting situations in aspartyl proteases, citrate synthase, EF hands, haemoglobins, lipocalins, glutathione reductase and the alpha/beta hydrolases. Copyright 1999 Academic Press.

  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. 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.

  8. 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.

  9. 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...

  10. A hydrogen-bonding network formed by the B10-E7-E11 residues of a truncated hemoglobin from Tetrahymena pyriformis is critical for stability of bound oxygen and nitric oxide detoxification.

    Science.gov (United States)

    Igarashi, Jotaro; Kobayashi, Kazuo; Matsuoka, Ariki

    2011-04-01

    Truncated hemoglobins (trHbs) are distributed from bacteria to unicellular eukaryotes and have roles in oxygen transport and nitric oxide detoxification. It is known that trHbs exist in ciliates of the Tetrahymena group, but trHb structure and function remain poorly understood. To investigate trHb function with respect to stability of bound oxygen and protein structure, we measured the oxygen binding kinetics of Tetrahymena pyriformis trHb, and determined the crystal structure of the protein. The O(2) association and dissociation rate constants of T. pyriformis trHb were 5.5 μM(-1 )s(-1) and 0.18 s(-1), respectively. The autooxidation rate constant was 3.8 × 10(-3) h(-1). These values are similar to those of HbN from Mycobacterium tuberculosis. The three-dimensional structure of an Fe(II)-O(2) complex of T. pyriformis trHb was determined at 1.73-Å resolution. Tyr25 (B10) and Gln46 (E7) were hydrogen-bonded to a heme-bound O(2) molecule. Tyr25 donated a hydrogen bond to the terminal oxygen atom, whereas Gln46 hydrogen-bonded to the proximal oxygen atom. Furthermore, Tyr25 was hydrogen-bonded to the Gln46 and Gln50 (E11) residues. Mutations at Tyr25, Gln46, and Gln50 increased the O(2) dissociation and autooxidation rate constants. An Fe(III)-H(2)O complex of T. pyriformis trHb was formed following reaction of the Fe(II)-O(2) complex of T. pyriformis trHb, in a crystal state, with nitric oxide. This suggests that T. pyriformis trHb functions in nitric oxide detoxification.

  11. 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, ...

  12. 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, ...

  13. 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.

  14. 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...

  15. 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 ...

  16. 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

  17. 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.

  18. 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.

  19. 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

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

    Science.gov (United States)

    Fedor, Anna M.; Toda, Megan J.

    2014-01-01

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

  1. 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)

  2. 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

  3. 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.

  4. 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.

  5. 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 ...

  6. 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...

  7. 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.

  8. 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 ...

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. Porous Hydrogen-Bonded Organic Frameworks

    Directory of Open Access Journals (Sweden)

    Yi-Fei Han

    2017-02-01

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

  14. 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.

  15. 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, ...

  16. 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 ...

  17. 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 ...

  18. 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).

  19. 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 ...

  20. 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).

  1. 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

  2. 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.

  3. Texaco, carbide form hydrogen plant venture

    International Nuclear Information System (INIS)

    Anon.

    1992-01-01

    This paper reports that Texaco Inc. and Union Carbide Industrial Gases Inc. (UCIG) have formed a joint venture to develop and operate hydrogen plants. The venture, named HydroGEN Supply Co., is owned by Texaco Hydrogen Inc., a wholly owned subsidiary of Texaco, and UCIG Hydrogen Services Inc., a wholly owned subsidiary of UCIG. Plants built by HydroGEN will combine Texaco's HyTEX technology for hydrogen production with UCIG's position in cryogenic and advanced air separation technology. Texaco the U.S. demand for hydrogen is expected to increase sharply during the next decade, while refinery hydrogen supply is expected to drop. The Clean Air Act amendments of 1990 require U.S. refiners to lower aromatics in gasoline, resulting in less hydrogen recovered by refiners from catalytic reforming units. Meanwhile, requirements to reduce sulfur in diesel fuel will require more hydrogen capacity

  4. 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.

  5. 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.

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

    Science.gov (United States)

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

    2017-10-06

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

  7. Hydrogen-bonding interactions between water and the one- and two-electron-reduced forms of vitamin K1: applying quinone electrochemistry to determine the moisture content of non-aqueous solvents.

    Science.gov (United States)

    Hui, Yanlan; Chng, Elaine Lay Khim; Chng, Cheryl Yi Lin; Poh, Hwee Ling; Webster, Richard D

    2009-02-04

    Vitamin K(1) (VK(1)) was shown by voltammetry and coulometry to undergo two chemically reversible one-electron reduction processes in acetonitrile (CH(3)CN) containing 0.2 M Bu(4)NPF(6) as the supporting electrolyte. The potential separation between the first and second electron-transfer steps diminished sequentially with the addition of water, so that at a H(2)O concentration of approximately 7 M (approximately 13% v/v) only one process was detected, corresponding to the reversible transfer of two electrons per molecule. The voltammetric behavior was interpreted on the basis of the degree of hydrogen bonding between the reduced forms of VK(1) with water in the solvent. It was found that the potential separation between the first and second processes was especially sensitive to water in the low molar levels (0.001-0.1 M); therefore, by measuring the peak separation as a function of controlled water concentrations (accurately determined by Karl Fischer coulometric titrations) it was possible to prepare calibration curves of peak separation versus water concentration. The calibration procedure is independent of the type of reference electrode and can be used to determine the water content of CH(3)CN between 0.01 and 5 M, by performing a single voltammetric scan in the presence of 1.0 mM VK(1). The voltammetry was also investigated in dichloromethane, dimethylformamide, and dimethyl sulfoxide. The reduction processes were monitored by in situ electrochemical UV-vis spectroscopy in CH(3)CN over a range of water concentrations (0.05-10 M) to spectroscopically identify the hydrogen-bonded species.

  8. 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

  9. 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.

  10. 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.

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

    Science.gov (United States)

    Wójcik, Marek J.

    1981-11-01

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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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:.

  2. 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...

  3. 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.

  4. 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

  5. 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 ...

  6. 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 ...

  7. 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

  8. 27 CFR 26.68 - Bond, Form 2898-Beer.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Bond, Form 2898-Beer. 26... Liquors and Articles in Puerto Rico Bonds § 26.68 Bond, Form 2898—Beer. Where a brewer intends to withdraw, for purpose of shipment to the United States, beer of Puerto Rican manufacture from bonded storage in...

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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

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

    Science.gov (United States)

    Xue, Feng

    2000-10-01

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

  8. 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....

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

    Science.gov (United States)

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

    2013-07-19

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

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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…

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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 ...

  3. 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 ...

  4. 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 ...

  5. 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 ...

  6. 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.

  7. 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 ...

  8. 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)

  9. 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 ...

  10. 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 ...

  11. 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.

  12. 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.

  13. 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 ...

  14. 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 ...

  15. 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,.

  16. 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].

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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).

  4. 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.

  5. Hydrogen-bonding patterns in 5-fluorocytosine–melamine co-crystal (4/1

    Directory of Open Access Journals (Sweden)

    Marimuthu Mohana

    2016-04-01

    Full Text Available The asymmetric unit of the title compound, 4C4H4FN3O·C3H6N6, comprises of two independent 5-fluorocytosine (5FC molecules (A and B and one half-molecule of melamine (M. The other half of the melamine molecule is generated by a twofold axis. 5FC molecules A and B are linked through two different homosynthons [R22(8 ring motif]; one is formed via a pair of N—H...O hydrogen bonds and the second via a pair of N—H...N hydrogen bonds. In addition to this pairing, the O atoms of 5FC molecules A and B interact with the N2 amino group on both sides of the melamine molecule, forming a DDAA array of quadruple hydrogen bonds and generating a supramolecular pattern. The 5FC (molecules A and B and two melamine molecules interact via N—H...O, N—H...N and N—H...O, N—H...N, C—H...F hydrogen bonds forming R66(24 and R44(15 ring motifs. The crystal structure is further strengthened by C—H...F, C—F...π and π–π stacking interactions.

  6. 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)

  7. 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...

  8. 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.

  9. 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

  10. Hydrogen-bonded encapsulation complexes in protic solvents.

    Science.gov (United States)

    Amaya, Toru; Rebek, Julius

    2004-11-03

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

  11. Nuclear quantum effects and hydrogen bond fluctuations in water

    Science.gov (United States)

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

    2013-01-01

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

  12. Experimental and Theoretical Studies in Hydrogen-Bonding Organocatalysis

    Directory of Open Access Journals (Sweden)

    Matej Žabka

    2015-08-01

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

  13. 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.

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

    African Journals Online (AJOL)

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

  15. H/D Isotope Effects in Hydrogen Bonded Systems

    Directory of Open Access Journals (Sweden)

    Aleksander Filarowski

    2013-04-01

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

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

    Science.gov (United States)

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

    2014-12-14

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

  17. 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.

  18. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-09-14

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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 27 CFR 26.67 - Bond, Form 2897-Wine.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Bond, Form 2897-Wine. 26.67 Section 26.67 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS LIQUORS AND ARTICLES FROM PUERTO RICO AND THE VIRGIN ISLANDS Taxpayment of Liquors and Articles in Puerto Rico Bonds ...

  15. Raman and DFT Study on N-H+…Cl- Hydrogen Bonding in 1,1,3,3-Tetra-Methylguanidinium Chloride forming an Ion-pair Molecule in the Vapor Phase

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Riisager, Anders; Fehrmann, Rasmus

    The chemistry of 1,1,3,3-tetramethylguanidinium ([TMGH]+) chloride, a low temperature (molten) ionic liquid, is discussed, based on its Raman spectra associated with ab initio molecular orbital DFT-type quantum mechanical calculations (with 6-311+G(d,p) basis sets) on “molecules” in isolated...... gaseous free states without any assumed symmetry. The calculations on the monomeric [TMGH]+ ion and the dimeric ion pair converged to give geometries near the established crystal structure of the [TMGH]Cl salt. This salt is known to contain dimeric ion pairs of the kind [TMGH]ClCl[TMGH](Fig.1...... that dimeric molecular ion pairs with four N-H+…Cl- hydrogen bonds seem to exist also in the solutions, and probably are responsible for the relatively high solubility of the “salt” in ethanol. The “salt” can be easily sublimed at about 200-230 oC. The Raman spectrum of the vapor at 225 ºC has a characteristic...

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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)

  1. 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

  2. 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

  3. 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 ...

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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}.

  9. 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 .

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. NH+-F hydrogen bonding in a fluorinated "proton sponge" derivative: integration of solution, solid-state, gas-phase, and computational studies.

    Science.gov (United States)

    Scerba, Michael T; Leavitt, Christopher M; Diener, Matthew E; DeBlase, Andrew F; Guasco, Timothy L; Siegler, Maxime A; Bair, Nathaniel; Johnson, Mark A; Lectka, Thomas

    2011-10-07

    We report detailed studies on the characterization of an intramolecular NH-F hydrogen bond formed within a fluorinated "proton sponge" derivative. An ammonium ion, generated from 8-fluoro-N,N-dimethylnaphthalen-1-amine, serves as a charged hydrogen bond donor to a covalently bound fluorine appropriately positioned on the naphthalene skeleton. Potentiometric titrations of various N,N-dimethylnaphthalen-1-amines demonstrate a significant increase in basicity when hydrogen bonding is possible. X-ray crystallography reveals that NH-F hydrogen bonding in protonated 8-fluoro-N,N-dimethylnaphthalen-1-amine is heavily influenced by ion pairing in the solid state; bifurcated and trifurcated hydrogen bonds are formed depending on the counterion utilized. Compelling evidence of hydrogen bonding in the 8-fluoro-N,N-dimethylnaphthyl-1-ammonium cation is provided by gas-phase cryogenic vibrational photodissociation spectroscopy. Solution-phase infrared spectroscopy provides complementary results, and the frequencies of the N-H stretching mode in both phases are in excellent agreement with the computed vibrational spectra. NMR analysis of protonated 8-fluoro-N,N-dimethylnaphthalen-1-amine demonstrates significant H-F coupling between the N-H hydrogen and fluorine that cannot be attributed to long-range, through-bond interactions; the couplings correlate favorably with calculated values. The results obtained from these experiments are congruent with the formation of an NH-F hydrogen bond upon protonation of 8-fluoro-N,N-dimethylnaphthalen-1-amine.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. A time-dependent density functional theory study on the effect of electronic excited-state hydrogen bonding on luminescent MOFs.

    Science.gov (United States)

    Ji, Min; Hao, Ce; Wang, Dandan; Li, Hongjiang; Qiu, Jieshan

    2013-03-14

    We have investigated a new silver-based luminescent metal-organic framework (MOF) using density functional theory and time-dependent density functional theory methods. We theoretically demonstrated that the H...O hydrogen bond is strengthened and the Ag-O coordination bond is shortened significantly due to strengthening of the hydrogen bond in the S(1) state. When the hydrogen bond is formed, the mechanism of luminescence changes from a ligand-to-metal charge transfer (LMCT) coupled with intraligand charge transfer (LLCT) to LMCT, and the luminescence is found to be enhanced.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. "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.

  8. 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.

  9. Forming and bonding techniques for high-strength aluminum alloys

    Science.gov (United States)

    Friedrich, Horst E.

    1995-02-01

    This article highlights the continued preference for aluminum as a structural material for aircraft, where demands for high performance coupled with the need for weight reduction have led to the use of high-strength aluminum alloys. The ever-increasing demand for a high level of integration of complex structural components calls for the development of appropriate manufacturing processes. As an example, superplastic forming is discussed, combined with innovative bonding techniques such as diffusion bonding and adhesive spot welding.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Phosphate bonded ceramics as candidate final-waste-form materials

    International Nuclear Information System (INIS)

    Singh, D.; Wagh, A.S.; Cunnane, J.; Sutaria, M.; Kurokawa, S.; Mayberry, J.

    1994-04-01

    Room-temperature setting phosphate-bonded ceramics were studied as candidate materials for stabilization of DOE low-level problem mixed wastes which cannot be treated by other established stabilization techniques. Phosphates of Mg, Mg-Na, Al and Zr were studied to stabilize ash surrogate waste containing RCRA metals as nitrates and RCRA organics. We show that for a typical loading of 35 wt.% of the ash waste, the phosphate ceramics pass the TCLP test. The waste forms have high compression strength exceeding ASTM recommendations for final waste forms. Detailed X-ray diffraction studies and differential thermal analyses of the waste forms show evidence of chemical reaction of the waste with phosphoric acid and the host matrix. The SEM studies show evidence of physical bonding. The excellent performance in the leaching tests is attributed to a chemical solidification and physical as well as chemical bonding of ash wastes in these phosphate ceramics

  16. Crystal structure of an unknown solvate of {2,2'-[ethane-1,2-diylbis(nitrilo-methanylyl-idene)]diphenolato-κ(4) O,N,N',O'}(N-ferrocenylisonicotinamide-κN (1))cobalt(II): a Co(II)-salen complex that forms hydrogen-bonded dimers.

    Science.gov (United States)

    Brautigam, Bryan; Herholdt, Chelsea; Farnsworth, William; Brudi, Ellen; McDonald, Eric; Wu, Guang; Contakes, Stephen

    2015-09-01

    The title compound, [CoFe(C5H5)(C16H14N2O2)(C11H9N2O)], was prepared as an air-stable red-brown solid by mixing equimolar amounts of {2,2'-[ethane-1,2-diylbis(nitrilo-methanylyl-idene)]diphenolato}cobalt(II) and N-ferrocenylisonicotinamide in dry di-chloro-methane under nitro-gen and was characterized by ESI-MS, IR, and single-crystal X-ray diffraction. The structure at 100 K has triclinic (P-1) symmetry and indicates that the complex crystallizes as a mixture of λ and δ conformers. It exhibits the expected square pyramidal geometry about Co, and forms hydrogen-bonded dimers through amide N-H groups and phenolate O atoms on an adjacent mol-ecule. The involvement of only half of the salen ring structure in hydrogen-bonding inter-actions results in slight folding of the salen ring away from the pyridine coordination site in the δ conformer with an inter-salicyl-idene fold angle of 9.9 (7)°. In contrast, the λ conformer is nearly planar. The dimers pack into an open structure containing channels filled with highly disordered solvent mol-ecules. These solvent molecules' contributions to the intensity data were removed with the SQUEEZE procedure [Spek (2015). Acta Cryst. C71, 9-18] available in PLATON.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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...

  2. 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.

  3. 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.

  4. 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 ...

  5. 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

  6. 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.

  7. 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

  8. Hydrogen Bonding in Ion-pair Molecules in Vapors over ionic liquids, studied by Raman Spectroscopy and ab initio Calculations

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    The hydrogen bonding interactions in selected archetypal vapor molecules formed in the gas phase over protic ionic liquids are discussed, based on Raman spectroscopy assisted with ab initio molecular orbital DFT-type quantum mechanical calculations (B3LYP with 6-311+G(d,p) basis sets) on assumed...... Ionic Liquid, To be submitted for J. Phys. Chem. A (2009)....

  9. Hydrogen bonds induced supramolecular self-assembly of azobenzene derivatives on the highly oriented pyrolytic graphite surface

    Science.gov (United States)

    Miao, Xinrui; Cheng, Zhiyu; Ren, Biye; Deng, Wenli

    2012-08-01

    The self-assembly of azobenzene derivatives (CnAzCOOH) with various lengths of peripheral alkyl chains (with carbon number of n = 8, 10, 12, 14, 16) were observed by scanning tunneling microscopy on highly oriented pyrolytic graphite (HOPG) surface. The effect of van der Waals interactions and the intermolecular hydrogen bonding on the two-dimensional self-assembly was systematically studied. No alkyl-chain length effect was observed according to the STM images. All kinds of CnAzCOOH adopting the same pattern self-assembled on the HOPG surface, suggesting the formation of the two-dimensional structures was dominated by the hydrogen bonding of the functional groups. It could be found that two CnAzCOOH molecules formed a hydrogen-bonded dimer with “head-to-head” fashion as expected; however, the dimers organized themselves in the form of relative complex lamellae. Three dimers as a group arranged side by side and formed a well-defined stripe with periodic dislocations due to the registry mechanism of the alkyl chain with the underlying HOPG surface. The hydrogen bonds between the adjacent dimers in one lamella were formed and dominated the self-assembled pattern.

  10. Two independent hydrogen bonded complexes of bis(1-piperidiniumacetate) hydrochloride in crystal and in the PM3 optimized structure

    International Nuclear Information System (INIS)

    Dega-Szafran, Z.; Petryna, M.; Dutkiewicz, G.; Kosturkiewicz, Z.

    2003-01-01

    Bis(1-piperidiniumacetate) hydrochloride, (PAA) 2 H · Cl + , has been synthesized and its structure solved by X-ray diffraction. The crystals belong to the triclinic system with two symmetrically independent hydrogen bonded complexes, denoted A and B, at two different inversion centers. The compound crystallizes in the space group P1 with a = 8.559(1), b = 9.625(1), c = 11.441(1) A, α = 74.85(1) o , β = 68.22(1) o , γ 84.10(1) o , Z = 2, R = 0.036. Each complex consists of two 1-piperidiniumacetate moieties. Four 1-piperidiniumacetates, as zwitterions, are held together by a network of hydrogen bonds of the types O...H...O (2.462(3) and 2.463(3) A), N-H...O (2.755(2) A) and N-H...Cl (3.167(2) A). Both N-H atoms in a complex A interact with chlorine anions. A number of weak C-H...Cl contacts stabilize the three-dimensional crystal structure. In the isolated molecule of (PAA) 2 H · Cl + optimized by the PM3 method, there also are two independent hydrogen bonded complexes. In complex A the natural form of 1-piperidineacetic acid interacts with its anionic form, while in complex B the 1-piperidiniumacetic acid, as a cation, forms a hydrogen bond with its zwitterionic form. FTIR spectrum of bis(1-piperidiniumacetate) hydrochloride has been analysed and discussed. (author)

  11. 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.

  12. 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

  13. 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...

  14. 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

  15. Bond forms of methane in porous system of coal II

    Czech Academy of Sciences Publication Activity Database

    Weishauptová, Zuzana; Medek, Jiří; Kovář, Lukáš

    2004-01-01

    Roč. 83, č. 13 (2004), s. 1759-1764 ISSN 0016-2361 R&D Projects: GA AV ČR IAA2046101; GA AV ČR KSK2067107 Institutional research plan: CEZ:AV0Z3046908 Keywords : coal-bed methane * absorption * fifth bond form Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.368, year: 2004

  16. Mullite/Mo interfaces formed by Intrusion bonding

    Energy Technology Data Exchange (ETDEWEB)

    Bartolome, Jose F.; Diaz, Marcos; Moya, Jose S.; Saiz, Eduardo; Tomsia, Antoni P.

    2003-04-30

    The microstructure and strength of Mo/mullite interfaces formed by diffusion bonding at 1650 C has been analyzed. Interfacial metal-ceramic interlocking contributes to flexural strength of approx. 140 MPa as measured by 3 point bending. Saturation of mullite with MoO2 does not affect the interfacial strength.

  17. 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

  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. Superplastic forming and diffusion bonding: Progress and trends

    Directory of Open Access Journals (Sweden)

    Zhiqiang Li

    2015-01-01

    Full Text Available This paper summarized recent progress in metal superplasticity and the application of Superplastic Forming/Diffusion Bonding (SPF/DB or SPF/Welding in typical structures. Various aerospace components such as three dimensional lattice structures made by SPF/DB have been demonstrated. In addition, some newly developed technologies, such as melt droplet spreading/thermo-mechanical forming (MDS/TMF, were also included. Finally, the future potential of SPF/DB technology was predicted.

  20. 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)

  1. On hydrogen bonding in 1,6-anhydro-beta-D-glucopyranose (levoglucosan): X-ray and neutron diffraction and DFT study.

    Science.gov (United States)

    Smrcok, Lubomír; Sládkovicová, Mariana; Langer, Vratislav; Wilson, Chick C; Koós, Miroslav

    2006-10-01

    The geometry of hydrogen bonds in 1,6-anhydro-beta-D-glucopyranose (levoglucosan) is accurately determined by refinement of time-of-flight neutron single-crystal diffraction data. Molecules of levoglucosan are held together by a hydrogen-bond array formed by a combination of strong O-H...O and supporting weaker C-H...O bonds. These are fully and accurately detailed by the neutron diffraction study. The strong hydrogen bonds link molecules in finite chains, with hydroxyl O atoms acting as both donors and acceptors of hydroxyl H atoms. A comparison of molecular and solid-state DFT calculations predicts red shifts of O-H and associated blue shifts of C-H stretching frequencies due to the formation of hydrogen bonds in this system.

  2. 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.

  3. Thermal decomposition of silane to form hydrogenated amorphous Si film

    Science.gov (United States)

    Strongin, Myron; Ghosh, Arup K.; Wiesmann, Harold J.; Rock, Edward B.; Lutz, III, Harry A.

    1980-01-01

    This invention relates to hydrogenated amorphous silicon produced by thermally decomposing silano (SiH.sub.4) or other gases comprising H and Si, at elevated temperatures of about 1700.degree.-2300.degree. C., and preferably in a vacuum of about 10.sup.-8 to 10.sup.-4 torr, to form a gaseous mixture of atomic hydrogen and atomic silicon, and depositing said gaseous mixture onto a substrate outside said source of thermal decomposition to form hydrogenated amorphous silicon.

  4. Thermal decomposition of silane to form hydrogenated amorphous Si

    Science.gov (United States)

    Strongin, M.; Ghosh, A.K.; Wiesmann, H.J.; Rock, E.B.; Lutz, H.A. III

    Hydrogenated amorphous silicon is produced by thermally decomposing silane (SiH/sub 4/) or other gases comprising H and Si, at elevated temperatures of about 1700 to 2300/sup 0/C, in a vacuum of about 10/sup -8/ to 10/sup -4/ torr. A gaseous mixture is formed of atomic hydrogen and atomic silicon. The gaseous mixture is deposited onto a substrate to form hydrogenated amorphous silicon.

  5. 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...

  6. 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.

  7. 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.

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

    Science.gov (United States)

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

    2014-08-12

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

  9. 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.

  10. 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.

  11. 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.

  12. 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...

  13. 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.

  14. 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.

  15. 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.

  16. Probing hydrogen bonding in cocrystals and amorphous dispersions using (14)N-(1)H HMQC solid-state NMR.

    Science.gov (United States)

    Tatton, Andrew S; Pham, Tran N; Vogt, Frederick G; Iuga, Dinu; Edwards, Andrew J; Brown, Steven P

    2013-03-04

    Cocrystals and amorphous solid dispersions have generated interest in the pharmaceutical industry as an alternative to more established solid delivery forms. The identification of intermolecular hydrogen bonding interactions in a nicotinamide palmitic acid cocrystal and a 50% w/w acetaminophen-polyvinylpyrrolidone solid dispersion are reported using advanced solid-state magic-angle spinning (MAS) NMR methods. The application of a novel (14)N-(1)H HMQC experiment, where coherence transfer is achieved via through-space couplings, is shown to identify specific hydrogen bonding motifs. Additionally, (1)H isotropic chemical shifts and (14)N electric field gradient (EFG) parameters, both accessible from (14)N-(1)H HMQC experiments, are shown to be sensitive to changes in hydrogen bonding geometry. Numerous indicators of molecular association are accessible from this experiment, including NH cross-peaks occurring from intermolecular hydrogen bonds and changes in proton chemical shifts or electric field gradient parameters. First-principles calculations using the GIPAW approach that yield accurate estimates of isotropic chemical shifts, and EFG parameters were used to assist in assignment. It is envisaged that (14)N-(1)H HMQC solid state NMR experiments could become a valuable screening technique of solid delivery forms in the pharmaceutical industry.

  17. Gas phase hydration of halogenated benzene cations. Is it hydrogen or halogen bonding?

    Science.gov (United States)

    Mason, Kyle A; Pearcy, Adam C; Attah, Isaac K; Platt, Sean P; Aziz, Saadullah G; El-Shall, M Samy

    2017-07-19

    Halogen bonding (XB) non-covalent interactions can be observed in compounds containing chlorine, bromine, or iodine which can form directed close contacts of the type R1-XY-R2, where the halogen X acts as a Lewis acid and Y can be any electron donor moiety including electron lone pairs on hetero atoms such as O and N, or π electrons in olefin double bonds and aromatic conjugated systems. In this work, we present the first evidence for the formation of ionic halogen bonds (IXBs) in the hydration of bromobenzene and iodobenzene radical cations in the gas phase. We present a combined thermochemical investigation using the mass-selected ion mobility (MSIM) technique and density functional theory (DFT) calculations of the stepwise hydration of the fluoro, chloro, bromo, and iodobenzene radical cations. The binding energy associated with the formation of an IXB in the hydration of the iodobenzene cation (11.2 kcal mol -1 ) is about 20% higher than the typical unconventional ionic hydrogen bond (IHB) of the CH δ+ OH 2 interaction. The formation of an IXB in the hydration of the iodobenzene cation involves a significant entropy loss (29 cal mol -1 K -1 ) resulting from the formation of a more ordered structure and a highly directional interaction between the oxygen lone pair of electrons of water and the electropositive region around the iodine atom of the iodobenzene cation. In comparison, the hydration of the fluorobenzene and chlorobenzene cations where IHBs are formed, -ΔS° = 18-21 cal mol -1 K -1 consistent with the formation of less ordered structures and loose interactions. The electrostatic potentials on the lowest energy structures of the hydrated halogenated benzene radical cations show clearly that the formation of an IXB is driven by a positively charged σ-hole on the external side of the halogen atom X along the C-X bond axis. The size of the σ-hole increases significantly in bromobenzene and iodobenzene radical cations which results in strong

  18. 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)

  19. 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.

  20. 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.

  1. 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.

  2. Female chacma baboons form strong, equitable, and enduring social bonds.

    Science.gov (United States)

    Silk, Joan B; Beehner, Jacinta C; Bergman, Thore J; Crockford, Catherine; Engh, Anne L; Moscovice, Liza R; Wittig, Roman M; Seyfarth, Robert M; Cheney, Dorothy L

    2010-11-01

    Analyses of the pattern of associations, social interactions, coalitions, and aggression among chacma baboons (Papio hamadryas ursinus) in the Okavango Delta of Botswana over a 16-year period indicate that adult females form close, equitable, supportive, and enduring social relationships. They show strong and stable preferences for close kin, particularly their own mothers and daughters. Females also form strong attachments to unrelated females who are close to their own age and who are likely to be paternal half-sisters. Although absolute rates of aggression among kin are as high as rates of aggression among nonkin, females are more tolerant of close relatives than they are of others with whom they have comparable amounts of contact. These findings complement previous work which indicates that the strength of social bonds enhances the fitness of females in this population and support findings about the structure and function of social bonds in other primate groups.

  3. 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)

  4. Crystal structure of an unknown solvate of {2,2′-[ethane-1,2-diylbis(nitrilo­methanylyl­idene)]diphenolato-κ4 O,N,N′,O′}(N-ferrocenylisonicotinamide-κN 1)cobalt(II): a CoII–salen complex that forms hydrogen-bonded dimers

    Science.gov (United States)

    Brautigam, Bryan; Herholdt, Chelsea; Farnsworth, William; Brudi, Ellen; McDonald, Eric; Wu, Guang; Contakes, Stephen

    2015-01-01

    The title compound, [CoFe(C5H5)(C16H14N2O2)(C11H9N2O)], was prepared as an air-stable red–brown solid by mixing equimolar amounts of {2,2′-[ethane-1,2-diylbis(nitrilo­methanylyl­idene)]diphenolato}cobalt(II) and N-ferrocenylisonicotinamide in dry di­chloro­methane under nitro­gen and was characterized by ESI–MS, IR, and single-crystal X-ray diffraction. The structure at 100 K has triclinic (P-1) symmetry and indicates that the complex crystallizes as a mixture of λ and δ conformers. It exhibits the expected square pyramidal geometry about Co, and forms hydrogen-bonded dimers through amide N—H groups and phenolate O atoms on an adjacent mol­ecule. The involvement of only half of the salen ring structure in hydrogen-bonding inter­actions results in slight folding of the salen ring away from the pyridine coordination site in the δ conformer with an inter-salicyl­idene fold angle of 9.9 (7)°. In contrast, the λ conformer is nearly planar. The dimers pack into an open structure containing channels filled with highly disordered solvent mol­ecules. These solvent molecules’ contributions to the intensity data were removed with the SQUEEZE procedure [Spek (2015). Acta Cryst. C71, 9–18] available in PLATON. PMID:26396858

  5. 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.

  6. 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.

  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. High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

    Science.gov (United States)

    Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

    2015-01-01

    Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from

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

    OpenAIRE

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

    2017-01-01

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

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

    Indian Academy of Sciences (India)

    It has been shown earlier1 that the relaxed force constants (RFCs) could be used as a measure of bond strength only when the bonds form a part of the complete valence internal coordinates (VIC) basis. However, if the bond is not a part of the complete VIC basis, its RFC is not necessarily a measure of bond strength.

  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. 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.

  16. 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.

  17. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-28

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

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

    Directory of Open Access Journals (Sweden)

    Hardeep Saluja

    2016-06-01

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

  20. Z-H Bond Activation in (Di)hydrogen Bonding as a Way to Proton/Hydride Transfer and H2Evolution.

    Science.gov (United States)

    Belkova, Natalia V; Filippov, Oleg A; Shubina, Elena S

    2018-02-01

    The ability of neutral transition-metal hydrides to serve as a source of hydride ion H - or proton H + is well appreciated. The hydride ligands possessing a partly negative charge are proton accepting sites, forming a dihydrogen bond, M-H δ- ⋅⋅⋅ δ+ HX (M=transition metal or metalloid). On the other hand, some metal hydrides are able to serve as a proton source and give hydrogen bond of M-H δ+ ⋅⋅⋅X type (X=organic base). In this paper we analyse recent works on transition-metal and boron hydrides showing i) how formation of an intermolecular complex between the reactants changes the Z-H (M-H and X-H) bond polarity and ii) what is the implication of such activation in the mechanisms of hydrides reactions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. 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.

  2. 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

  3. Hydrogen- and Halogen-Bonds between Ions of like Charges: Are They Anti-Electrostatic in Nature?

    Science.gov (United States)

    Wang, Changwei; Fu, Yuzhuang; Zhang, Lina; Danovich, David; Shaik, Sason; Mo, Yirong

    2018-04-05

    Recent theoretical studies suggested that hydrogen bonds between ions of like charges are of a covalent nature due to the dominating n D →σ* H-A charge-transfer (CT) interaction. In this work, energy profiles of typical hydrogen (H) and halogen (X) bonding systems formed from ions of like charges are explored using the block-localized wavefunction (BLW) method, which can derive optimal geometries and wave functions with the CT interaction "turned off." The results demonstrate that the kinetic stability, albeit reduced, is maintained for most investigated systems even after the intermolecular CT interaction is quenched. Further energy decomposition analyses based on the BLW method reveal that, despite a net repulsive Coulomb repulsion, a stabilizing component exists due to the polarization effect that plays significant role in the kinetic stability of all systems. Moreover, the fingerprints of the augmented electrostatic interaction due to polarization are apparent in the variation patterns of the electron density. All in all, much like in standard H- and X-bonds, the stability of such bonds between ions of like charges is governed by the competition between the stabilizing electrostatic and charge transfer interactions and the destabilizing deformation energy and Pauli exchange repulsion. While in most cases of "anti-electrostatic" bonds the CT interaction is of a secondary importance, we also find cases where CT is decisive. As such, this work validates the existence of anti-electrostatic H- and X-bonds. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  4. Facilitation of Nanoscale Thermal Transport by Hydrogen Bonds

    OpenAIRE

    Zhang, Lin

    2017-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2013-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

    Heyrovská, Raji

    2006-01-01

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

  7. 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

    step in designing Mn III -peroxo complexes that convert cleanly to high-valent Mn-oxo species. Although some synthetic Mn IV -oxo complexes show great potential for oxidizing substrates with strong C-H bonds, most Mn IV -oxo species are sluggish oxidants. Both two-state reactivity and thermodynamic arguments have been put forth to explain these observations. To address these issues, we generated a series of Mn IV -oxo complexes supported by neutral, pentadentate ligands with systematically perturbed equatorial donation. Kinetic investigations of these complexes revealed a correlation between equatorial ligand-field strength and hydrogen-atom and oxygen-atom transfer reactivity. While this trend can be understood on the basis of the two-state reactivity model, the reactivity trend also correlates with variations in Mn III/IV reduction potential caused by changes in the ligand field. This work demonstrates the dramatic influence simple ligand perturbations can have on reactivity but also illustrates the difficulties in understanding the precise basis for a change in reactivity. In the enzyme manganese lipoxygenase, an active-site Mn III -hydroxo adduct initiates substrate oxidation by abstracting a hydrogen atom from a C-H bond. Precedent for this chemistry from synthetic Mn III -hydroxo centers is rare. To better understand hydrogen-atom transfer by Mn III centers, we developed a pair of Mn III -hydroxo complexes, formed in high yield from dioxygen oxidation of Mn II precursors, capable of attacking weak O-H and C-H bonds. Kinetic and computational studies show a delicate interplay between thermodynamic and steric influences in hydrogen-atom transfer reactivity, underscoring the potential of Mn III -hydroxo units as mild oxidants.

  8. Crystal structure and hydrogen bonding in N-(1-deoxy-β-d-fructopyranos-1-yl-2-aminoisobutyric acid

    Directory of Open Access Journals (Sweden)

    Valeri V. Mossine

    2018-01-01

    Full Text Available The title compound, alternatively called d-fructose-2-aminoisobutyric acid (FruAib, C10H19NO7, (I, crystallizes exclusively in the β-pyranose form, with two conformationally non-equivalent molecules [(IA and (IB] in the asymmetric unit. In solution, FruAib establishes an equilibrium, with 75.6% of the population consisting of β-pyranose, 10.4% β-furanose, 10.1% α-furanose, 3.0% α-pyranose and <0.7% the acyclic forms. The carbohydrate ring in (I has the normal 2C5 chair conformation and the amino acid portion is in the zwitterion form. Bond lengths and valence angles compare well with the average values from related pyranose structures. All carboxyl, hydroxy and ammonium groups are involved in hydrogen bonding and form a three-dimensional network of infinite chains that are connected through homodromic rings and short chains. Intramolecular hydrogen bonds bridge the amino acid and sugar portions in both molecules. A comparative Hirshfeld surfaces analysis of FruAib and four other sugar–amino acids suggests an increasing role of intramolecular heteroatom interactions in crystal structures with an increasing proportion of C—H bonds.

  9. Microscopic mechanism of electron transfer through the hydrogen bonds between carboxylated alkanethiol molecules connected to gold electrodes

    KAUST Repository

    Li, Yang

    2014-11-07

    © 2014 AIP Publishing LLC. The atomic structure and the electron transfer properties of hydrogen bonds formed between two carboxylated alkanethiol molecules connected to gold electrodes are investigated by employing the non-equilibrium Green\\'s function formalism combined with density functional theory. Three types of molecular junctions are constructed, in which one carboxyl alkanethiol molecule contains two methylene, -CH2, groups and the other one is composed of one, two, or three -CH2 groups. Our calculations show that, similarly to the cases of isolated carboxylic acid dimers, in these molecular junctions the two carboxyl, -COOH, groups form two H-bonds resulting in a cyclic structure. When self-interaction corrections are explicitly considered, the calculated transmission coefficients of these three H-bonded molecular junctions at the Fermi level are in good agreement with the experimental values. The analysis of the projected density of states confirms that the covalent Au-S bonds localized at the molecule-electrode interfaces and the electronic coupling between -COOH and S dominate the low-bias junction conductance. Following the increase of the number of the -CH2 groups, the coupling between -COOH and S decreases deeply. As a result, the junction conductance decays rapidly as the length of the H-bonded molecules increases. These findings not only provide an explanation to the observed distance dependence of the electron transfer properties of H-bonds, but also help the design of molecular devices constructed through H-bonds.

  10. 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.

  11. 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.

  12. 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.

  13. Leaching behavior of phosphate-bonded ceramic waste forms

    International Nuclear Information System (INIS)

    Singh, D.; Wagh, A.S.; Jeong, S.Y.; Dorf, M.

    1996-04-01

    Over the last few years, Argonne National Laboratory has been developing room-temperature-setting chemically bonded phosphate ceramics for solidifying and stabilizing low-level mixed wastes. This technology is crucial for stabilizing waste streams that contain volatile species and off-gas secondary waste streams generated by high-temperature treatment of such wastes. We have developed a magnesium phosphate ceramic to treat mixed wastes such as ash, salts, and cement sludges. Waste forms of surrogate waste streams were fabricated by acid-base reactions between the mixtures of magnesium oxide powders and the wastes, and phosphoric acid or acid phosphate solutions. Dense and hard ceramic waste forms are produced in this process. The principal advantage of this technology is that the contaminants are immobilized by both chemical stabilization and subsequent microencapsulation of the reaction products. This paper reports the results of durability studies conducted on waste forms made with ash waste streams spiked with hazardous and radioactive surrogates. Standard leaching tests such as ANS 16.1 and TCLP were conducted on the final waste forms. Fates of the contaminants in the final waste forms were established by electron microscopy. In addition, stability of the waste forms in aqueous environments was evaluated with long-term water-immersion tests

  14. Hydrogen bonding of tyrosine B10 to heme-bound oxygen in Ascaris hemoglobin. Direct evidence from UV resonance Raman spectroscopy.

    Science.gov (United States)

    Huang, S; Huang, J; Kloek, A P; Goldberg, D E; Friedman, J M

    1996-01-12

    The hemoglobin from Ascaris suum, a parasitic nematode, has a spontaneous dissociation rate for the dioxygen ligand that is 3 orders of magnitude less than for mammalian myoglobins or hemoglobins. In this hemoglobin, the distal histidine is replaced with a glutamine which is capable of forming a stabilizing hydrogen bond to the bound dioxygen. A single hydrogen bond from a glutamine is, under typical circumstances, not sufficient to account for the low off rate for oxygen. Several studies point to a second hydrogen bond to the heme-bound dioxygen originating from tyrosine B10 as the source of this unusual reactivity. In this study ultraviolet (UV) resonance Raman spectroscopy is used to directly observe the formation of this hydrogen bond upon oxygen binding. The study reveals that both oxygen and carbon monoxide induce similar conformational changes in the globin upon binding to the heme; however, in the case of oxygen, a strong hydrogen bond involving a tyrosine is also observed. Similar studies on the QE7L mutant of this Hb suggest that the glutamine plays a role in stabilizing a rigid tertiary structure associated with the distal heme pocket. This conformation maintains the tyrosine in an orientation conducive to hydrogen bond formation with a heme-bound dioxygen ligand.

  15. Quantum mechanics models of the methanol dimer: OH⋯O hydrogen bonds of β-d-glucose moieties from crystallographic data.

    Science.gov (United States)

    Cintrón, Michael Santiago; Johnson, Glenn P; French, Alfred D

    2017-04-18

    The interaction of two methanol molecules, simplified models of carbohydrates and cellulose, was examined using a variety of quantum mechanics (QM) levels of theory. Energy plots for hydrogen bonding distance (H⋯O) and angle (OH⋯O) were constructed. All but two experimental structures were located in stabilized areas on the vacuum phase energy plots. Each of the 399 models was analyzed with Bader's atoms-in-molecules (AIM) theory, which showed a widespread ability by the dimer models to form OH⋯O hydrogen bonds that have bond paths and Bond Critical Points. Continuum solvation calculations suggest that a portion of the energy-stabilized structures could occur in the presence of water. A survey of the Cambridge Structural Database (CSD) for all donor-acceptor interactions in β-D-glucose moieties examined the similarities and differences among the hydroxyl groups and acetal oxygen atoms that participate in hydrogen bonds. Comparable behavior was observed for the O2H, O3H, O4H, and O6H hydroxyls, acting either as acceptors or donors. Ring O atoms showed distinct hydrogen bonding behavior that favored mid-length hydrogen bonds. Published by Elsevier Ltd.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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)

  1. A quantum-chemical validation about the formation of hydrogen bonds and secondary interactions in intermolecular heterocyclic systems

    Directory of Open Access Journals (Sweden)

    Boaz Galdino Oliveira

    2009-08-01

    Full Text Available We have performed a detailed theoretical study in order to understand the charge density topology of the C2H4O···C2H2 and C2H4S···C2H2 heterocyclic hydrogen-bonded complexes. Through the calculations derived from Quantum Theory of Atoms in Molecules (QTAIM, it was observed the formation of hydrogen bonds and secondary interactions. Such analysis was performed through the determination of optimized geometries at B3LYP/6-31G(d,p level of theory, by which is that QTAIM topological operators were computed, such as the electronic density ρ(r, Laplacian Ñ2ρ(r, and ellipticity ε. The examination of the hydrogen bonds has been performed through the measurement of ρ(r, Ñ2ρ(r and ε between (O···H—C and (S···H—C, whereas the secondary interaction between axial hydrogen atoms Hα and carbon of acetylene. In this insight, it was verified the existence of secondary interaction only in C2H4S···C2H2 complex because its structure is propitious to form multiple interactions.

  2. 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...

  3. Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

    Science.gov (United States)

    Chaudhari, Sachin Rama; Suryaprakash, N.

    2012-05-01

    Benzene carboxylic acids and benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by 1H, 13C and 15N NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations.

  4. Effects of water contamination on the supercooled dynamics of a hydrogen-bonded model glass former.

    Science.gov (United States)

    Sjöström, Johan; Bergman, Rikard; Wadell, Carl; Moberg, Tobias; Swenson, Jan; Mattsson, Johan

    2011-03-03

    Broad-band dielectric spectroscopy is a commonly used tool in the study of glass-forming liquids. The high sensitivity of the technique together with the wide range of probed time scales makes it a powerful method for investigating the relaxation spectra of liquids. One particularly important class of glass-forming liquids that is often studied using this technique consists of liquids dominated by hydrogen (H) bond interactions. When investigating such liquids, particular caution has to be taken during sample preparation due to their often highly hygroscopic nature. Water can easily be absorbed from the atmosphere, and dielectric spectroscopy is a very sensitive probe of such contamination due to the large dipole moment of water. Our knowledge concerning the effects of small quantities of water on the dielectric properties of these commonly investigated liquids is limited. We here demonstrate the effects due to the presence of small amounts of water on the dielectric response of a typical H-bonded model glass former, tripropylene glycol. We show how the relaxation processes present in the pure liquid are affected by addition of water, and we find that a characteristic water induced relaxation response is observed for water contents as low as 0.15 wt%. We stress the importance of careful purification of hygroscopic liquids before experiments and quantify what the effects are if such procedures are not undertaken. © 2011 American Chemical Society

  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. The thermodynamic stability of hydrogen bonded and cation bridged complexes of humic acid models-A theoretical study

    International Nuclear Information System (INIS)

    Aquino, Adelia J.A.; Tunega, Daniel; Pasalic, Hasan; Haberhauer, Georg; Gerzabek, Martin H.; Lischka, Hans

    2008-01-01

    Hydrogen bonded and cation bridged complexation of poly(acrylic acid) oligomers, representing a model compound for humic acids, with acetic acid and the herbicide (4-chloro-2-methylphenoxy) acetic acid (MCPA) have been studied by means of density functional theory. Solvation effects were computed by means of a combination of microsolvation (explicit insertion of water molecules) and global solvation (polarizable continuum approach). The stability of hydrogen bonded complexes in solution is characterized by a strong competition between solute and solvent molecules. The cation bridged complexes of the negatively charged (deprotonated) ligands were found to be strongly favored explaining the capability of humic acids to fixate anionic species from soil solutions and the ability to form cross-linking structures within the humic acid macromolecules

  7. 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.

  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. 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

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Mechanistic Insights on C-O and C-C Bond Activation and Hydrogen Insertion during Acetic Acid Hydrogenation Catalyzed by Ruthenium Clusters in Aqueous Medium

    Energy Technology Data Exchange (ETDEWEB)

    Shangguan, Junnan; Olarte, Mariefel V.; Chin, Ya-Huei [Cathy

    2016-06-07

    Catalytic pathways for acetic acid (CH3COOH) and hydrogen (H2) reactions on dispersed Ru clusters in the aqueous medium and the associated kinetic requirements for C-O and C-C bond cleavages and hydrogen insertion are established from rate and isotopic assessments. CH3COOH reacts with H2 in steps that either retain its carbon backbone and lead to ethanol, ethyl acetate, and ethane (47-95 %, 1-23 %, and 2-17 % carbon selectivities, respectively) or break its C-C bond and form methane (1-43 % carbon selectivities) at moderate temperatures (413-523 K) and H2 pressures (10-60 bar, 298 K). Initial CH3COOH activation is the kinetically relevant step, during which CH3C(O)-OH bond cleaves on a metal site pair at Ru cluster surfaces nearly saturated with adsorbed hydroxyl (OH*) and acetate (CH3COO*) intermediates, forming an adsorbed acetyl (CH3CO*) and hydroxyl (OH*) species. Acetic acid turnover rates increase proportionally with both H2 (10-60 bar) and CH3COOH concentrations at low CH3COOH concentrations (<0.83 M), but decrease from first to zero order as the CH3COOH concentration and the CH3COO* coverages increase and the vacant Ru sites concomitantly decrease. Beyond the initial CH3C(O)-OH bond activation, sequential H-insertions on the surface acetyl species (CH3CO*) lead to C2 products and their derivative (ethanol, ethane, and ethyl acetate) and the competitive C-C bond cleavage of CH3CO* causes the eventual methane formation. The instantaneous carbon selectivities towards C2 species (ethanol, ethane, and ethyl acetate) increase linearly with the concentration of proton-type Hδ+ (derived from carboxylic acid dissociation) and chemisorbed H*. The selectivities towards C2 products decrease with increasing temperature, because of higher observed barriers for C-C bond cleavage than H-insertion. This study offers an interpretation of mechanism and energetics and provides kinetic evidence of carboxylic acid assisted proton-type hydrogen (Hδ+) shuffling during H

  16. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

    Energy Technology Data Exchange (ETDEWEB)

    Mori, Yukie, E-mail: mori.yukie@ocha.ac.jp; Masuda, Yuichi

    2015-09-08

    Highlights: • MD simulations were performed to study dynamics of strong hydrogen bonds. • Nuclear magnetic relaxation times of proton were measured in solution. • The hydrogen bond of dibenzoylmethane enol is asymmetric in methanol solution. • Formation or breakage of intermolecular hydrogen bonds can trigger proton transfer. • Dimethylsulfoxide may form a bifurcated hydrogen bond with a hydrogen-bonded system. - Abstract: Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl{sub 4}, acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the {sup 17

  17. 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 ...

  18. 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 ...

  19. 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 ...

  20. Hydrogen gas driven permeation through tungsten deposition layer formed by hydrogen plasma sputtering

    International Nuclear Information System (INIS)

    Uehara, Keiichiro; Katayama, Kazunari; Date, Hiroyuki; Fukada, Satoshi

    2015-01-01

    Highlights: • H permeation tests for W layer formed by H plasma sputtering are performed. • H permeation flux through W layer is larger than that through W bulk. • H diffusivity in W layer is smaller than that in W bulk. • The equilibrium H concentration in W layer is larger than that in W bulk. - Abstract: It is important to evaluate the influence of deposition layers formed on plasma facing wall on tritium permeation and tritium retention in the vessel of a fusion reactor from a viewpoint of safety. In this work, tungsten deposition layers having different thickness and porosity were formed on circular nickel plates by hydrogen RF plasma sputtering. Hydrogen permeation experiment was carried out at the temperature range from 250 °C to 500 °C and at hydrogen pressure range from 1013 Pa to 101,300 Pa. The hydrogen permeation flux through the nickel plate with tungsten deposition layer was significantly smaller than that through a bare nickel plate. This indicates that a rate-controlling step in hydrogen permeation was not permeation through the nickel plate but permeation though the deposition layer. The pressure dependence on the permeation flux differed by temperature. Hydrogen permeation flux through tungsten deposition layer is larger than that through tungsten bulk. From analysis of the permeation curves, it was indicated that hydrogen diffusivity in tungsten deposition layer is smaller than that in tungsten bulk and the equilibrium hydrogen concentration in tungsten deposition layer is enormously larger than that in tungsten bulk at same hydrogen pressure.

  1. 75 FR 55849 - Proposed Collection; Comment Request for Form 1097-BTC, Bond Tax Credit

    Science.gov (United States)

    2010-09-14

    ... 1097-BTC, Bond Tax Credit AGENCY: Internal Revenue Service (IRS), Treasury. ACTION: Notice and request... comments concerning Form 1097-BTC, Bond Tax Credit. DATES: Written comments should be received on or before... INFORMATION: Title: Form 1097-BTC, Bond Tax Credit. Abstract: This is an information return for reporting tax...

  2. 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.

  3. 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 ...

  4. 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.

  5. 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.

  6. 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)....

  7. 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.

  8. A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method

    DEFF Research Database (Denmark)

    Kromann, Jimmy Charnley; Christensen, Anders Steen; Svendsen, Casper Steinmann

    2014-01-01

    We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction en...... vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent, compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible....

  9. 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.

  10. 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.)

  11. CMPO-calix[4]arenes with spacer containing intramolecular hydrogen bonding: effect of local rigidification on solvent extraction toward f-block elements.

    Science.gov (United States)

    Chu, Hongzhu; He, Lutao; Jiang, Qian; Fang, Yuyu; Jia, Yiming; Yuan, Xiangyang; Zou, Shuliang; Li, Xianghui; Feng, Wen; Yang, Yuanyou; Liu, Ning; Luo, Shunzhong; Yang, Yanqiu; Yang, Liang; Yuan, Lihua

    2014-01-15

    To understand intramolecular hydrogen bonding in effecting liquid-liquid extraction behavior of CMPO-calixarenes, three CMPO-modified calix[4]arenes (CMPO-CA) 5a-5c with hydrogen-bonded spacer were designed and synthesized. The impact of spacer rotation that is hindered by introduction of intramolecular hydrogen bonding upon extraction of La(3+), Eu(3+), Yb(3+), Th(4+), and UO2(2+) has been examined. The results show that 5b and 5c containing only one hydrogen bond with a less hindered rotation spacer extract La(3+) more efficiently than 5a containing two hydrogen bonds with a more hindered rotation spacer, demonstrating the importance of local rigidification of spacer in the design of extractants in influencing the coordination environment. The large difference in extractability between La(3+) and Yb(3+) (or Eu(3+)) by 5b (or 5c), and the small difference by 5a, suggests intramolecular hydrogen bonding do exert pronounced influence upon selective extraction of light and heavy lanthanides. Log-log plot analysis indicates a 1:1, 2:1 and 1:1 stoichiometry (ligand/metal) for the extracted complex formed between 5b and La(3+), Th(4+), UO2(2+), respectively. Additionally, their corresponding acyclic analogs 7a-7c exhibit negligible extraction toward these metal ions. These results reveal the possibility of selective extraction via tuning local chelating surroundings of CMPO-CA by aid of intramolecular hydrogen bonding. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. 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.

  13. 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.

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

    Science.gov (United States)

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

    2008-04-01

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

  15. Chiral and achiral crystals, charge-assisted hydrogen-bond patterns and self-organization of selected solid diaminium thiosulfates.

    Science.gov (United States)

    Brozdowska, Agnieszka; Chojnacki, Jarosław

    2017-06-01

    A series of diaminium thiosulfates, derivatives of diamines: NH 2 CH 2 CH(CH 3 )NH 2 (1) and NH 2 (CH 2 ) n NH 2 , n = 3-6 [(2)-(5)] and thiosulfuric acid were prepared and their structures determined by single-crystal X-ray diffraction analysis. Compounds (1), (2) and (4) turned out to be hydrates. The crystal structure of 1,2-propylenediaminium thiosulfate is chiral and exhibits spontaneous resolution. Crystals for both enantiomers [(1a) and (1b)] were obtained with high enantiometric excess and examined. An extended network of strong, charge-assisted hydrogen bonding of the + N-H...O - type (also O-H...O and O-H...S for hydrates) is most likely the main factor defining crystal packing and the variable conformation of the cations. The formation of chiral hydrogen-bond motifs - distorted cubans - seems to induce the formation of chiral solid-state structure from achiral components in the case of (4). Diaminium thiosulfates with an odd number of C atoms in the alkyl chain [compounds (1), (2) and (4)] form three-dimensional supramolecular networks, while in the case of diaminium salts with an even number of C atoms [(3) and (5)], two-dimensional layers of hydrogen-bond domains are observed. The aminium thiosulfates were also characterized by elemental analysis, NMR and Fourier transform (FT)-IR spectroscopy. The conformations of α,ω-alkyldiaminium cations in the solid state are discussed and rationalized by DFT calculations.

  16. Syntheses, Crystal Structures, Magnetic Behaviours, and Thermal Properties of Three Hydrogen-Bonding Networks Containing Dicyanamide and 4-Hydroxypyridine

    Directory of Open Access Journals (Sweden)

    Lingling Zheng

    2013-01-01

    Full Text Available Three new dicyanamide-bridged polymeric complexes of {[Mn(dca2(L2]·2H2O}n (1, {[Cd(dca2(L2]·2H2O}n (2, and {[Co(dca2(L2]2(L}n (3 (dca = dicyanamide, L = pyridinium-4-olate have been synthesized and structurally characterized. In the three compounds, the protons of hydroxyl groups of 4-hydroxypyridine transfer to pyridyl nitrogen atoms. Compounds 1 and 2 are isomorphous forming one-dimensional [M(dca2(L2]n chains where metals are connected by double dca anions. These one-dimensional chains are extended into two-dimensional layers through weak C–H⋯N hydrogen bonds. Further, these layers are assembled into a three-dimensional supramolecular network through N–H⋯O, O–H⋯O hydrogen bonds. Complex 3 is a coordination layer of (4, 4 topology with octahedral metal centers linked by four single μ1,5-bridges. These layers are interlocked by N–H⋯O, O–H⋯O hydrogen bonds from coordinated water molecules and free L molecules, which leads to a three-dimensional supramolecular architecture. The variable temperature magnetic susceptibilities measurement of compounds 1 and 3 shows the existence of weak antiferromagnetic interactions between the metal centers. The thermogravimetric analyses of the compounds 1–3 are also discussed.

  17. A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

    Science.gov (United States)

    Hamdani, Hazrina Yusof; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2015-09-01

    A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods.

  18. A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

    International Nuclear Information System (INIS)

    Hamdani, Hazrina Yusof; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2015-01-01

    A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods

  19. A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

    Energy Technology Data Exchange (ETDEWEB)

    Hamdani, Hazrina Yusof, E-mail: hazrina@mfrlab.org [School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi (Malaysia); Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas (Malaysia); Artymiuk, Peter J., E-mail: p.artymiuk@sheffield.ac.uk [Dept. of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 T2N Sheffield (United Kingdom); Firdaus-Raih, Mohd, E-mail: firdaus@mfrlab.org [School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi (Malaysia)

    2015-09-25

    A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods.

  20. Shape memory effect of thermoplastic segmented polyurethanes with self-complementary quadruple hydrogen bonding in soft segments

    Science.gov (United States)

    Zhu, Yong; Hu, Jinlian; Liu, Yijun

    2009-01-01

    This paper describes the fact that a kind of thermoplastic shape memory polyurethane with self-complementary quadruple hydrogen bonding units in soft segments can present a significant shape memory effect under the usually used thermodynamic programming condition. Compared with the control sample, it was observed that the introduction of self-complementary quadruple hydrogen bonding into soft segments increases the glass transition temperature from 28.3 ° C to 73.3 ° C. Therefore, the temporary deformation can be fixed well after cooling at room temperature; subsequently thermal responsive shape memory recovery can be triggered by heating up to 86 ° C. The immediate shape recovery ratio and shape fixity ratio can be 95.8% and 95.9%. Even after 24 hours relaxation for the stretched films, the corresponding Rr and Rf can be 94% and 60%. In contrast, the sample without quadruple hydrogen bonding shows that the elasticity and the deformation cannot be fixed after 24 hours relaxation. Supplementary material in the form of a doc file available from the journal web page at 10.1140/epje/i2008-10395-2 and are accessible for authorised users.

  1. 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.

  2. Hydrogen bonds, interfacial stiffness moduli, and the interlaminar shear strength of carbon fiber-epoxy matrix composites

    Directory of Open Access Journals (Sweden)

    John H. Cantrell

    2015-03-01

    Full Text Available The chemical treatment of carbon fibers used in carbon fiber-epoxy matrix composites greatly affects the fraction of hydrogen bonds (H-bonds formed at the fiber-matrix interface. The H-bonds are major contributors to the fiber-matrix interfacial shear strength and play a direct role in the interlaminar shear strength (ILSS of the composite. The H-bond contributions τ to the ILSS and magnitudes KN of the fiber-matrix interfacial stiffness moduli of seven carbon fiber-epoxy matrix composites, subjected to different fiber surface treatments, are calculated from the Morse potential for the interactions of hydroxyl and carboxyl acid groups formed on the carbon fiber surfaces with epoxy receptors. The τ calculations range from 7.7 MPa to 18.4 MPa in magnitude, depending on fiber treatment. The KN calculations fall in the range (2.01 – 4.67 ×1017 N m−3. The average ratio KN/|τ| is calculated to be (2.59 ± 0.043 × 1010 m−1 for the seven composites, suggesting a nearly linear connection between ILSS and H-bonding at the fiber-matrix interfaces. The linear connection indicates that τ may be assessable nondestructively from measurements of KN via a technique such as angle beam ultrasonic spectroscopy.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Mechanisms of hydrogen induced delayed cracking in hydride forming materials

    International Nuclear Information System (INIS)

    Dutton, R.; Nuttall, K.; Puls, M.P.; Simpson, L.A.

    1977-01-01

    Mechanisms which have been formulated to describe delayed hydrogen cracking in hydride-forming metals are reviewed and discussed. Particular emphasis is placed on the commercial alloy Zr--2.5% Nb (Cb) which is extensively used in nuclear reactor core components. A quantitative model for hydrogen cracking in this material is presented and compared with available experimental data. The kinetics of crack propagation are controlled by the growth of hydrides at the stressed crack tip by the diffusive ingress of hydrogen into this region. The driving force for the diffusion flux is provided by the local stress gradient which interacts with both hydrogen atoms in solution and hydrogen atoms being dissolved and reprecipitated at the crack tip. The model is developed using concepts of elastoplastic fracture mechanics. Stage I crack growth is controlled by hydrides growing in the elastic stress gradient, while Stage II is controlled by hydride growth in the plastic zone at the crack tip. Recent experimental observations are presented which indicate that the process occurs in an intermittent fashion; hydride clusters accumulate at the crack tip followed by unstable crack advance and subsequent crack arrest in repeated cycles

  9. 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.

  10. 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...

  11. 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

  12. 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

  13. 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

  14. Discovery of molluscicidal and cercaricidal activities of 3-substituted quinazolinone derivatives by a scaffold hopping approach using a pseudo-ring based on the intramolecular hydrogen bond formation.

    Science.gov (United States)

    Guo, Wei; Zheng, Lv-Yin; Li, Yong-Dong; Wu, Ren-Miao; Chen, Qiang; Yang, Ding-Qiao; Fan, Xiao-Lin

    2016-06-10

    Discovery of novel topological agents against Oncomelania hupensis snails and cercariae remains a significant challenge in current Schistosomiasis control. A pseudo-ring formed from salicylanilide by an intramolecular hydrogen bond led to the discovery of 3-substituted quinazolinone derivatives which showed a potent molluscicidal and cercaricidal activities. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  15. Hydrogen bonding discotic liquid crystals: Synthesis, self-assembly, and molecular recognition

    Science.gov (United States)

    Bushey, Mark Lawrence

    The triamides shown below form discotic liquid crystalline phases with intermolecular hydrogen bonding stabilizing the columnar structure, A and B. The mesomorphic orientations of the columns are dependent on the amide side chain. Three mesophasic orientations are described: columns aligned perpendicular to the surface, columns aligned parallel to the surface in a radial pattern, and columns aligned parallel to the surface in a parallel or aligned pattern. The aggregation of the tridodecyloxy-triamides show N-H shifting in the IR at elevated temperatures, an indication that hydrogen bonding is important in the association of liquid crystalline mesophases. Powder X-ray diffraction studies indicate packing of the columns into a hexagonal lattice.* Studies on triamides with chiral side chains result in molecules stacking into columns displaying a helical pitch. In concentrated solutions of dodecane, molecules with chiral side chains display behavior consistent with chiral nematic liquid crystals; a super helical packing of the chiral columns. These superhelical packed systems show temperature dependent selective reflection of visible light and fingerprint textures. Atomic force microscopy (AFM) confirms in sub-monolayer films, that molecules preferring an edge-on orientation form long columns on highly ordered pyrolytic graphite (HOPG), those that prefer a face-on orientation form large amorphous domains. Electrostatic force microscopy (EFM) images of the domains of molecules in the edge-on orientation provides no discernible polarity, imaging of the domains of molecules in the face-on orientation indicates a negative polar orientation. Scanning probe measurements (SPM) of the tridodecynyl-triamide have shown similar edge-on orientations of other tridodecyloxy-triamides. Powder X-ray diffraction of these liquid crystalline phases shows a hexagonal packing of the columnar assembly. Electro-optic switching studies indicate a piezoelectric switching mechanism, possibly

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

    Indian Academy of Sciences (India)

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

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

    Science.gov (United States)

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

    2017-12-12

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

  18. 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...

  19. 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...

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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…

  5. 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…

  6. 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.

  7. 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” ...

  8. 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 ...

  9. 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...

  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. 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.

  12. 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

  13. 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 ...

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. Luminescent lanthanide complexes with 4-acetamidobenzoate: Synthesis, supramolecular assembly via hydrogen bonds, crystal structures and photoluminescence

    International Nuclear Information System (INIS)

    Yin Xia; Fan Jun; Wang Zhihong; Zheng Shengrun; Tan Jingbo; Zhang Weiguang

    2011-01-01

    Four new luminescent complexes, namely, [Eu(aba) 2 (NO 3 )(C 2 H 5 OH) 2 ] (1), [Eu(aba) 3 (H 2 O) 2 ].0.5 (4, 4'-bpy).2H 2 O (2), [Eu 2 (aba) 4 (2, 2'-bpy) 2 (NO 3 ) 2 ].4H 2 O (3) and [Tb 2 (aba) 4 (phen) 2 (NO 3 ) 2 ].2C 2 H 5 OH (4) were obtained by treating Ln(NO 3 ) 3 .6H 2 O and 4-acetamidobenzoic acid (Haba) with different coligands (4, 4'-bpy=4, 4'-bipyridine, 2, 2'-bpy=2, 2'-bipyridine, and phen=1, 10-phenanthroline). They exhibit 1D chains (1-2) and dimeric structures (3-4), respectively. This structural variation is mainly attributed to the change of coligands and various coordination modes of aba molecules. Moreover, the coordination units are further connected via hydrogen bonds to form 2D even 3D supramolecular networks. These complexes show characteristic emissions in the visible region at room temperature. In addition, thermal behaviors of four complexes have been investigated under air atmosphere. The relationship between the structures and physical properties has been discussed. - Graphical abstract: Structure variation of four complexes is attributed to the change of coligands and various coordination modes of aba molecules. Moreover, they show characteristic emissions in the visible region. Highlights: → Auxiliary ligands have played the crucial roles on the structures of the resulting complexes. → Isolated structure units are further assembled via H-bonds to form supramolecular networks. → These solid-state complexes exhibit strong, characteristic emissions in the visible region.

  19. 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.

  20. 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.

  1. 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.

  2. Fac and mer isomers of Ru(II) tris(pyrazolyl-pyridine) complexes as models for the vertices of coordination cages: structural characterisation and hydrogen-bonding characteristics.

    Science.gov (United States)

    Metherell, Alexander J; Cullen, William; Stephenson, Andrew; Hunter, Christopher A; Ward, Michael D

    2014-01-07

    We have prepared a series of mononuclear fac and mer isomers of Ru(II) complexes containing chelating pyrazolyl-pyridine ligands, to examine their differing ability to act as hydrogen-bond donors in MeCN. This was prompted by our earlier observation that octanuclear cube-like coordination cages that contain these types of metal vertex can bind guests such as isoquinoline-N-oxide (K = 2100 M(-1) in MeCN), with a significant contribution to binding being a hydrogen-bonding interaction between the electron-rich atom of the guest and a hydrogen-bond donor site on the internal surface of the cage formed by a convergent set of CH2 protons close to a 2+ metal centre. Starting with [Ru(L(H))3](2+) [L(H) = 3-(2-pyridyl)-1H-pyrazole] the geometric isomers were separated by virtue of the fact that the fac isomer forms a Cu(I) adduct which the mer isomer does not. Alkylation of the pyrazolyl NH group with methyl iodide or benzyl bromide afforded [Ru(L(Me))3](2+) and [Ru(L(bz))3](2+) respectively, each as their fac and mer isomers; all were structurally characterised. In the fac isomers the convergent group of pendant -CH2R or -CH3 protons defines a hydrogen-bond donor pocket; in the mer isomer these protons do not converge and any hydrogen-bonding involving these protons is expected to be weaker. For both [Ru(L(Me))3](2+) and [Ru(L(bz))3](2+), NMR titrations with isoquinoline-N-oxide in MeCN revealed weak 1 : 1 binding (K ≈ 1 M(-1)) between the guest and the fac isomer of the complex that was absent with the mer isomer, confirming a difference in the hydrogen-bond donor capabilities of these complexes associated with their differing geometries. The weak binding compared to the cage however occurs because of competition from the anions, which are free to form ion-pairs with the mononuclear complex cations in a way that does not happen in the cage complexes. We conclude that (i) the presence of fac tris-chelate sites in the cage to act as hydrogen-bond donors, and (ii

  3. Chemical modelling of complex organic molecules with peptide-like bonds in star-forming regions

    Science.gov (United States)

    Quénard, David; Jiménez-Serra, Izaskun; Viti, Serena; Holdship, Jonathan; Coutens, Audrey

    2018-02-01

    Peptide bonds (N-C = O) play a key role in metabolic processes since they link amino acids into peptide chains or proteins. Recently, several molecules containing peptide-like bonds have been detected across multiple environments in the interstellar medium, growing the need to fully understand their chemistry and their role in forming larger pre-biotic molecules. We present a comprehensive study of the chemistry of three molecules containing peptide-like bonds: HNCO, NH2CHO, and CH3NCO. We also included other CHNO isomers (HCNO, HOCN) and C2H3NO isomers (CH3OCN, CH3CNO) to the study. We have used the UCLCHEM gas-grain chemical code and included in our chemical network all possible formation/destruction pathways of these peptide-like molecules recently investigated either by theoretical calculations or in laboratory experiments. Our predictions are compared to observations obtained towards the proto-star IRAS 16293-2422 and the L1544 pre-stellar core. Our results show that some key reactions involving the CHNO and C2H3NO isomers need to be modified to match the observations. Consistently with recent laboratory findings, hydrogenation is unlikely to produce NH2CHO on grain surfaces, while a combination of radical-radical surface reactions and gas-phase reactions is a better alternative. In addition, better results are obtained for NH2CHO when a slightly higher activation energy of 25 K is considered for the gas-phase reaction NH2 + H2CO → NH2CHO + H. Finally, our modelling shows that the observed correlation between NH2CHO and HNCO in star-forming regions may come from the fact that HNCO and NH2CHO react to temperature in the same manner rather than from a direct chemical link between the two species.

  4. 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...

  5. 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.

  6. 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.

  7. Theoretical Study on Effects of Hydrogen-Bonding and Molecule-Cation Interactions on the Sensitivity of HMX.

    Science.gov (United States)

    Li, Yunlu; Wu, Junpeng; Cao, Duanlin; Wang, Jianlong

    2016-10-04

    To assess the effects of weak interactions on the sensitivity of HMX, eleven complexes of HMX (where six of them are hydrogen-bonding complexes, and the other five are molecular-cation complexes) have been studied via quantum chemical treatment. The geometric and electronic structures were determined using DFT-B3LYP and MP2(full) methods with the 6-311++G(2df, 2p) and aug-cc-pVTZ basis sets. The changes of the bond dissociation energy (BDE) of the trigger bond (N-NO2 in HMX) and nitro group charge have been computed on the detail consideration to access the sensitivity changes of HMX. The results indicate that upon complex forming, the BDE increases and the charge of nitro group turns more negative in complexes, suggesting that the strength of the N-NO2 trigger bond is enhanced then the sensitivity of HMX is reduced. Atom-in-molecules analysis have also been carried to understand the nature of intermolecular interactions and the strength of trigger bonds.

  8. Influence of hydrogen bond accepting ability of anions on the adsorption performance of ionic liquid surface molecularly imprinted polymers.

    Science.gov (United States)

    Zhu, Guifen; Gao, Xia; Wang, Xiaolong; Wang, Jianji; Fan, Jing

    2018-01-12

    To illuminate the influence mechanism of anionic structure of ionic liquids (ILs) on the adsorption performance of surface molecularly imprinted polymers (MIPs), in this work, six newly designed MIPs were prepared on the surface of amino-poly(styrene-divinylbenzene) particles by using imidazolium ILs with the same cation [C 4 mim] + but different anions (Cl, CH 3 SO 3 , PF 6 , BF 4 , C 4 F 7 O 2 , C 4 F 9 SO 3 ) as template molecules, methacrylic acid as functional monomer, and ethylene dimethacrylate as cross-linker. The resulting MIP materials were characterized by IR and SEM, and the influence of hydrogen bond accepting ability of anions on the adsorption performance of the MIPs for the ILs was investigated in acetonitrile. It was found that adsorption capacity of the MIPs towards the ILs decreased in the order MIP [C4mim][Cl]  > MIP [C4mim][C4F7O2]  ≥ MIP [C4mim][BF4] and MIP [C4mim][CH3SO3]  > MIP [C4mim][C4F9SO3]  > MIP [C4mim][PF6] , which is in good agreement with the ability of anions of the ILs to form hydrogen bonds. Ultraviolet, 1 H-NMR and 35 Cl-NMR spectroscopy was then used to study the interactions of anions of the ILs with the functional monomer. It was found that the hydrogen bond interaction between anions of the ILs and acidic proton of the functional monomer was the main driving force for the high adsorption selectivity of the imprinted polymers, and the stronger hydrogen bond interaction indicates higher binding capacity and higher selectivity of the polymers towards the ILs. It was also verified that the ILs with stronger hydrogen bond accepting ability of anions could be selectively extracted by the corresponding IL-MIPs. These results may provide new insight into the recognition mechanism of MIPs for ILs, and are also useful for the rational design of this new class of imprinting materials. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. 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.

  10. Transition-metal-catalyzed enantioselective heteroatom-hydrogen bond insertion reactions.

    Science.gov (United States)

    Zhu, Shou-Fei; Zhou, Qi-Lin

    2012-08-21

    Carbon-heteroatom bonds (C-X) are ubiquitous and are among the most reactive components of organic compounds. Therefore investigations of the construction of C-X bonds are fundamental and vibrant fields in organic chemistry. Transition-metal-catalyzed heteroatom-hydrogen bond (X-H) insertions via a metal carbene or carbenoid intermediate represent one of the most efficient approaches to form C-X bonds. Because of the availability of substrates, neutral and mild reaction conditions, and high reactivity of these transformations, researchers have widely applied transition-metal-catalyzed X-H insertions in organic synthesis. Researchers have developed a variety of rhodium-catalyzed asymmetric C-H insertion reactions with high to excellent enantioselectivities for a wide range of substrates. However, at the time that we launched our research, very few highly enantioselective X-H insertions had been documented primarily because of a lack of efficient chiral catalysts and indistinct insertion mechanisms. In this Account, we describe our recent studies of copper- and iron-catalyzed asymmetric X-H insertion reactions by using chiral spiro-bisoxazoline and diimine ligands. The copper complexes of chiral spiro-bisoxazoline ligands proved to be highly enantioselective catalysts for N-H insertions of α-diazoesters into anilines, O-H insertions of α-diazoesters into phenols and water, O-H insertions of α-diazophosphonates into alcohols, and S-H insertions of α-diazoesters into mercaptans. The iron complexes of chiral spiro-bisoxazoline ligands afforded the O-H insertion of α-diazoesters into alcohols and water with unprecedented enantioselectivities. The copper complexes of chiral spiro-diimine ligands exhibited excellent reactivity and enantioselectivity in the Si-H insertion of α-diazoacetates into a wide range of silanes. These transition-metal-catalyzed X-H insertions have many potential applications in organic synthesis because the insertion products, including chiral

  11. 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.

  12. Using multiple hydrogen bonding cross-linkers to access reversibly responsive three dimensional graphene oxide architecture

    Science.gov (United States)

    Han, Junkai; Shen, Yongtao; Feng, Wei

    2016-07-01

    Three-dimensional (3D) graphene materials have attracted a lot of attention for efficiently utilizing inherent properties of graphene sheets. However, 3D graphene materials reported in the previous literature are constructed through covalent or weak non-covalent interactions, causing permanent structure/property changes. In this paper, a novel 3D graphene material of dynamic interactions between lamellas with 2-ureido-4[1H]-pyrimidinone as a supra-molecular motif has been synthesized. This 3D graphene material shows enhanced sheet interactions while the cross-linking takes place. With proper solvent stimulation, the integrated 3D graphene material can disassemble as isolated sheets. The driving force for the 3D structure assembly or disassembly is considered to be the forming or breaking of the multiple hydrogen bonding pairs. Furthermore, the 3D material is used as an intelligent dye adsorber to adsorb methylene blue and release it. The controllable and reversible characteristic of this 3D graphene material may open an avenue to the synthesis and application of novel intelligent materials.Three-dimensional (3D) graphene materials have attracted a lot of attention for efficiently utilizing inherent properties of graphene sheets. However, 3D graphene materials reported in the previous literature are constructed through covalent or weak non-covalent interactions, causing permanent structure/property changes. In this paper, a novel 3D graphene material of dynamic interactions between lamellas with 2-ureido-4[1H]-pyrimidinone as a supra-molecular motif has been synthesized. This 3D graphene material shows enhanced sheet interactions while the cross-linking takes place. With proper solvent stimulation, the integrated 3D graphene material can disassemble as isolated sheets. The driving force for the 3D structure assembly or disassembly is considered to be the forming or breaking of the multiple hydrogen bonding pairs. Furthermore, the 3D material is used as an

  13. 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.

  14. Double Hydrogen Bonding between Side Chain Carboxyl Groups in Aqueous Solutions of Poly (β-L-Malic Acid): Implication for the Evolutionary Origin of Nucleic Acids

    Science.gov (United States)

    Francis, Brian R.; Watkins, Kevin; Kubelka, Jan

    2017-01-01

    The RNA world hypothesis holds that in the evolutionary events that led to the emergence of life RNA preceded proteins and DNA and is supported by the ability of RNA to act as both a genetic polymer and a catalyst. On the other hand, biosynthesis of nucleic acids requires a large number of enzymes and chemical synthesis of RNA under presumed prebiotic conditions is complicated and requires many sequential steps. These observations suggest that biosynthesis of RNA is the end product of a long evolutionary process. If so, what was the original polymer from which RNA and DNA evolved? In most syntheses of simpler RNA or DNA analogs, the D-ribose phosphate polymer backbone is altered and the purine and pyrimidine bases are retained for hydrogen bonding between complementary base pairs. However, the bases are themselves products of complex biosynthetic pathways and hence they too may have evolved from simpler polymer side chains that had the ability to form hydrogen bonds. We hypothesize that the earliest evolutionary predecessor of nucleic acids was the simple linear polyester, poly (β-D-malic acid), for which the carboxyl side chains could form double hydrogen bonds. In this study, we show that in accord with this hypothesis a closely related polyester, poly (β-L-malic acid), uses carboxyl side chains to form robust intramolecular double hydrogen bonds in moderately acidic solution. PMID:29061955

  15. 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.

  16. Analysis of the radical hydrogen transfer pathway for cleaving strong bonds in coal

    Energy Technology Data Exchange (ETDEWEB)

    Autrey, S.T.; Camaioni, D.M.; Ferris, K.F.; Franz, J.A.

    1993-09-01

    Hydrogen transfer processes involving radical intermediates are of key importance in the liquefaction of coal. While the primary function of donor solvents is to transfer H{lg_bullet} to coal-derived radicals that form when weak bonds are cleaved thermolytically, growing evidence suggests that the donor solvent can play a role in promoting cleavage of strong {alpha}-bonds. McMillen and Malhotra have explained the results in terms of a single-step mechanism referred to as radical H-transfer (RHT). Mechanistic kinetic models have been used to suggest the importance of RHT pathways in anthracene- and pyrene-based solvent systems. However, we question the reliability of these approaches because little experimental data exists to support the 16.5 kcal/mol intrinsic barriers they assume for RHT reactions. Unambiguous evidence for RHT is very difficult to obtain experimentally because at the temperatures required to activate the RHT reaction, a suite of multistep reactions can occur, which yield the same products, i.e. H-elimination from hydroaryl radicals followed by ipso addition. For this reason, we have sought to gain insight to barrier heights for RHT from theory. This paper reports our use of Marcus theory in combination with ab initio and semiempirical molecular orbital methods to show how the intrinsic barriers for RHT reactions depend on structural and thermodynamic properties of the reacting partners. In addition, reactions thought to be mediated by RHT are reexamined using mechanistic kinetic modeling (MKM) to determine the extent to which these reactions can be explained by conventional pathways.

  17. 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.

  18. 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.

  19. 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.

  20. 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...

  1. Bridging of anions by hydrogen bonds in nest motifs and its significance for Schellman loops and other larger motifs within proteins.

    Science.gov (United States)

    Afzal, Avid M; Al-Shubailly, Fawzia; Leader, David P; Milner-White, E James

    2014-11-01

    The nest is a protein motif of three consecutive amino acid residues with dihedral angles 1,2-αR αL (RL nests) or 1,2-αL αR (LR nests). Many nests form a depression in which an anion or δ-negative acceptor atom is bound by hydrogen bonds from the main chain NH groups. We have determined the extent and nature of this bridging in a database of protein structures using a computer program written for the purpose. Acceptor anions are bound by a pair of bridging hydrogen bonds in 40% of RL nests and 20% of LR nests. Two thirds of the bridges are between the NH groups at Positions 1 and 3 of the motif (N1N3-bridging)-which confers a concavity to the nest; one third are of the N2N3 type-which does not. In bridged LR nests N2N3-bridging predominates (14% N1N3: 75% N2N3), whereas in bridged RL nests the reverse is true (69% N1N3: 25% N2N3). Most bridged nests occur within larger motifs: 45% in (hexapeptide) Schellman loops with an additional 4 → 0 hydrogen bond (N1N3), 11% in Schellman loops with an additional 5 → 1 hydrogen bond (N2N3), 12% in a composite structure including a type 1β-bulge loop and an asx- or ST- motif (N1N3)-remarkably homologous to the N1N3-bridged Schellman loop-and 3% in a composite structure including a type 2β-bulge loop and an asx-motif (N2N3). A third hydrogen bond is a previously unrecognized feature of Schellman loops as those lacking bridged nests have an additional 4 → 0 hydrogen bond. © 2014 Wiley Periodicals, Inc.

  2. Towards quantifying the role of exact exchange in the prediction hydrogen bond spin-spin coupling constants involving fluorine

    Energy Technology Data Exchange (ETDEWEB)

    San Fabián, J.; Omar, S.; García de la Vega, J. M., E-mail: garcia.delavega@uam.es [Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid (Spain)

    2016-08-28

    The effect of a fraction of Hartree-Fock exchange on the calculated spin-spin coupling constants involving fluorine through a hydrogen bond is analyzed in detail. Coupling constants calculated using wavefunction methods are revisited in order to get high-level calculations using the same basis set. Accurate MCSCF results are obtained using an additive approach. These constants and their contributions are used as a reference for density functional calculations. Within the density functional theory, the Hartree-Fock exchange functional is split in short- and long-range using a modified version of the Coulomb-attenuating method with the SLYP functional as well as with the original B3LYP. Results support the difficulties for calculating hydrogen bond coupling constants using density functional methods when fluorine nuclei are involved. Coupling constants are very sensitive to the Hartree-Fock exchange and it seems that, contrary to other properties, it is important to include this exchange for short-range interactions. Best functionals are tested in two different groups of complexes: those related with anionic clusters of type [F(HF){sub n}]{sup −} and those formed by difluoroacetylene and either one or two hydrogen fluoride molecules.

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

    Indian Academy of Sciences (India)

    Unknown

    multaneous thermal analyses apparatus. A heating rate of 4°C/min was chosen for the measurement. ... The technical details of data acquisition and some selected crystal refinement results are summarized in table 1. ... be attributed to the vibrations of the organic cation. 1 can be dehydrated to form the corresponding an-.

  4. Hydrogen retention in carbon-tungsten co-deposition layer formed by hydrogen RF plasma

    International Nuclear Information System (INIS)

    Katayama, K.; Kawasaki, T.; Manabe, Y.; Nagase, H.; Takeishi, T.; Nishikawa, M.

    2006-01-01

    Carbon-tungsten co-deposition layers (C-W layers) were formed by sputtering method using hydrogen or deuterium RF plasma. The deposition rate of the C-W layer by deuterium plasma was faster than that by hydrogen plasma, where the increase of deposition rate of tungsten was larger than that of carbon. This indicates that the isotope effect on sputtering-depositing process for tungsten is larger than that for carbon. The release curve of hydrogen from the C-W layer showed two peaks at 400 deg. C and 700 deg. C. Comparing the hydrogen release from the carbon deposition layer and the tungsten deposition layer, it is considered that the increase of the release rate at 400 deg. C is affected by tungsten and that at 700 deg. C is affected by carbon. The obtained hydrogen retention in the C-W layers which have over 60 at.% of carbon was in the range between 0.45 and 0.16 as H/(C + W)

  5. 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.

  6. 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.

  7. 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.

  8. Role of intrinsic hydrogen bonds in the assembly of perylene imide derivatives in solution and at the liquid-solid interface.

    Science.gov (United States)

    Guo, Zongxia; Wang, Kun; Yu, Ping; Zhang, Shengyue; Sun, Kai; Li, Zhibo

    2017-08-30

    The impact of hydrogen bond formation on the supramolecular assembly of two perylene imide derivatives (PMAMI and PDINH) was systematically investigated in solution and at the liquid-solid interface. PDINH has intrinsic hydrogen bond sites, but this is not the case for PMAMI. The solution assembly was explored by morphological methods (SEM, AFM, TEM and cryo-TEM) and spectral characterization (UV-vis, FL, XRD, and FTIR spectra). The surface assembly at the liquid-solid interface was detected by scanning tunneling microscopy (STM). It was found that in a mixed solution (THF/MeOH, 10 v%/90 v%), PMAMI formed nanofibers together with large sheet structures and PDINH assembled into uniform nanosheets, suggesting different molecular packing routes. The assembled structures could be adjusted by varying the solvent polarity for both molecules. At the liquid-solid interface, clearly distinguished surface nanostructures from PMAMI and PDINH were easily observed. Based on all spectral and morphological characterizations, it was suggested that in solution the assembly of PMAMI was mainly derived by π-π stacking interactions; on the other hand, the synergetic interaction of hydrogen bonds and π-π stacking was the reason for the hierarchical assembly of PDINH. Hydrogen bonds could be formed both for PMAMI and PDINH and stabilized nanostructures at the liquid-solid interface. This investigation could be useful in designing perylene imide-based building blocks for fabricating supramolecular assemblies with predetermined nanostructures and properties.

  9. Microwave measurements of the tropolone–formic acid doubly hydrogen bonded dimer

    Energy Technology Data Exchange (ETDEWEB)

    Pejlovas, Aaron M.; Kukolich, Stephen G. [Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 (United States); Serrato, Agapito; Lin, Wei [Department of Chemistry, University of Texas Rio Grande Valley, Brownsville, Texas 78520 (United States)

    2016-01-28

    The microwave spectrum was measured for the doubly hydrogen bonded dimer formed between tropolone and formic acid. The predicted symmetry of this dimer was C{sub 2v}(M), and it was expected that the concerted proton tunneling motion would be observed. After measuring 25 a- and b-type rotational transitions, no splittings which could be associated with a concerted double proton tunneling motion were observed. The calculated barrier to the proton tunneling motion is near 15 000 cm{sup −1}, which would likely make the tunneling frequencies too small to observe in the microwave spectra. The rotational and centrifugal distortion constants determined from the measured transitions were A = 2180.7186(98) MHz, B = 470.873 90(25) MHz, C = 387.689 84(22) MHz, D{sub J} = 0.0100(14) kHz, D{sub JK} = 0.102(28) kHz, and D{sub K} = 13.2(81) kHz. The B3LYP/aug-cc-pVTZ calculated rotational constants were within 1% of the experimentally determined values.

  10. Role of Hydrogen Bonding in the Formation of Adenine Chains on Cu(110 Surfaces

    Directory of Open Access Journals (Sweden)

    Lanxia Cheng

    2016-12-01

    Full Text Available Understanding the adsorption properties of DNA bases on metal surfaces is fundamental for the rational control of surface functionalization leading to the realisation of biocompatible devices for biosensing applications, such as monitoring of particular parameters within bio-organic environments and drug delivery. In this study, the effects of deposition rate and substrate temperature on the adsorption behavior of adenine on Cu(110 surfaces have been investigated using scanning tunneling microscopy (STM and density functional theory (DFT modeling, with a focus on the characterization of the morphology of the adsorbed layers. STM results revealed the formation of one-dimensional linear chains and ladder-like chains parallel to the [110] direction, when dosing at a low deposition rate at room temperature, followed by annealing to 490 K. Two mirror related, well-ordered chiral domains oriented at ±55° with respect to the [110] direction are formed upon deposition on a substrate kept at 490 K. The molecular structures observed via STM are rationalized and qualitatively described on the basis of the DFT modeling. The observation of a variety of ad-layer structures influenced by deposition rate and substrate temperature indicates that dynamic processes and hydrogen bonding play an important role in the self-assembly of adenine on the Cu(110 surface.

  11. Luminescent lanthanide complexes with 4-acetamidobenzoate: Synthesis, supramolecular assembly via hydrogen bonds, crystal structures and photoluminescence

    Science.gov (United States)

    Yin, Xia; Fan, Jun; Wang, Zhi Hong; Zheng, Sheng Run; Tan, Jing Bo; Zhang, Wei Guang

    2011-07-01

    Four new luminescent complexes, namely, [Eu(aba) 2(NO 3)(C 2H 5OH) 2] ( 1), [Eu(aba) 3(H 2O) 2]·0.5 (4, 4'-bpy)·2H 2O ( 2), [Eu 2(aba) 4(2, 2'-bpy) 2(NO 3) 2]·4H 2O ( 3) and [Tb 2(aba) 4(phen) 2(NO 3) 2]·2C 2H 5OH ( 4) were obtained by treating Ln(NO 3) 3·6H 2O and 4-acetamidobenzoic acid (Haba) with different coligands (4, 4'-bpy=4, 4'-bipyridine, 2, 2'-bpy=2, 2'-bipyridine, and phen=1, 10-phenanthroline). They exhibit 1D chains ( 1- 2) and dimeric structures ( 3- 4), respectively. This structural variation is mainly attributed to the change of coligands and various coordination modes of aba molecules. Moreover, the coordination units are further connected via hydrogen bonds to form 2D even 3D supramolecular networks. These complexes show characteristic emissions in the visible region at room temperature. In addition, thermal behaviors of four complexes have been investigated under air atmosphere. The relationship between the structures and physical properties has been discussed.

  12. Miscibility and Hydrogen Bonding in Blends of Poly(4-vinylphenol/Poly(vinyl methyl ketone

    Directory of Open Access Journals (Sweden)

    Hana Bourara

    2014-10-01

    Full Text Available The miscibility and phase behavior of poly(4-vinylphenol (PVPh with poly(vinyl methyl ketone (PVMK was investigated by differential scanning calorimetry (DSC, Fourier transform infrared spectroscopy (FTIR and scanning electron microscopy (SEM. It was shown that all blends of PVPh/PVMK are totally miscible. A DSC study showed the apparition of a single glass transition (Tg over their entire composition range. When the amount of PVPh exceeds 50% in blends, the obtained Tgs are found to be significantly higher than those observed for each individual component of the mixture, indicating that these blends are capable of forming interpolymer complexes. FTIR analysis revealed the existence of preferential specific interactions via hydrogen bonding between the hydroxyl and carbonyl groups, which intensified when the amount of PVPh was increased in blends. Furthermore, the quantitative FTIR study carried out for PVPh/PVMK blends was also performed for the vinylphenol (VPh and vinyl methyl ketone (VMK functional groups. These results were also established by scanning electron microscopy study (SEM.

  13. 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.

  14. 46 CFR 308.529 - Surety Bond B, Form MA-309.

    Science.gov (United States)

    2010-10-01

    ... Shipping MARITIME ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS WAR RISK INSURANCE War Risk Cargo Insurance Ii-Open Policy War Risk Cargo Insurance § 308.529 Surety Bond B, Form MA-309. An Assured who elects to substitute a surety bond for a collateral deposit fund shall submit Form MA-309...

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

    Science.gov (United States)

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

    2015-06-25

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

  18. Modeling the vapor-liquid equilibria of polymer-solvent mixtures: Systems with complex hydrogen bonding behavior

    DEFF Research Database (Denmark)

    Tsivintzelis, Ioannis; Kontogeorgis, Georgios

    2009-01-01

    The vapor–liquid equilibria of binary polymer–solvent systems was modeled using the Non-Random Hydrogen Bonding (NRHB) model. Mixtures of poly(ethylene glycol), poly(propylene glycol), poly(vinyl alcohol) and poly(vinyl acetate) with various solvents were investigated, while emphasis was put...... on hydrogen bonding systems, in which functional groups of the polymer chain can self-associate or cross-associate with the solvent molecules. Effort has been made to explicitly account for all hydrogen bonding interactions. The results reveal that the NRHB model offers a flexible approach to account...

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

    OpenAIRE

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

    2011-01-01

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

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

    International Nuclear Information System (INIS)

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

    2007-01-01

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

  1. 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. 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...

  3. 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.

  4. Kinetics of Exchange Between Zero-, One-, and Two-Hydrogen-Bonded States of Methyl and Ethyl Acetate in Methanol

    Science.gov (United States)

    Chuntonov, Lev; Pazos, Ileana M.; Ma, Jianqiang; Gai, Feng

    2015-01-01

    It has recently been shown that the ester carbonyl stretching vibration can be used as a sensitive probe of local electrostatic field in molecular systems. To further characterize this vibrational probe and extend its potential applications, we studied the kinetics of chemical exchange between differently hydrogen-bonded (H-bonded) ester carbonyl groups of methyl acetate (MA) and ethyl acetate (EA) in methanol. We found that while both MA and EA can form zero, one, or two H-bonds with the solvent, the population of the 2hb state in MA is significantly smaller than that in EA. Using a combination of linear and non-linear infrared measurements and numerical simulations, we further determined the rate constants for the exchange between these differently H-bonded states. We found that for MA the chemical exchange reaction between the two dominant states (i.e., 0hb and 1hb states) has a relaxation rate constant of 0.14 ps−1, whereas for EA the three-state chemical exchange reaction occurs in a predominantly sequential manner with the following relaxation rate constants: 0.11 ps−1 for exchange between 0hb and 1hb states, 0.12 ps−1 for exchange between 1hb and 2hb states. PMID:25738661

  5. 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.

  6. Synthesis, Structure and Spectroscopy of Two Structurally Related Hydrogen Bonded Compounds in the dpma/HClO4 System; dpma (dimethylphosphorylmethanamine

    Directory of Open Access Journals (Sweden)

    Guido J. Reiss

    2013-06-01

    Full Text Available The new phosphine oxide compound, (dimethylphosphorylmethanaminium perchlorate, dpmaHClO4 (1, was synthesized by the reaction of (dimethylphosphoryl methanamine (dpma with concentrated perchloric acid. (Dimethylphosphorylmethanaminium perchlorate (dimethylphosphorylmethanamine solvate, dpmaHClO4•dpma (2 was obtained by the slow evaporation of an equimolar methanolic solution of 1 and dpma at room temperature. For both compounds, single-crystal X-ray structures, IR and Raman spectra are reported. The assignment of the spectroscopic data were supported by quantum chemical calculations at the B3LYP/6-311G(2d,p level of theory. In 1, the dpmaH cations form polymeric, polar double-strands along [010] by head to tail connections via N–H∙∙∙O hydrogen bonds. The perchlorate anions are located between these strands attached by one medium strong and two weaker un-bifurcated hydrogen bonds (monoclinic, centrosymmetric space group C2/c, a = 17.8796(5 Å, b = 5.66867(14 Å, c = 17.0106(5 Å, β = 104.788(3°, V = 1666.9(1 Å3, Z = 8, T = 293 K, R(F [I > 2σ(I] = 0.0391, wR(F2 [all] = 0.1113. In 2, besides the N–H∙∙∙O hydrogen bonds, medium strong N–H∙∙∙N hydrogen bonds are present. One dpmaH cation and the neutral dpma molecule are connected head to tail by two N–H∙∙∙O hydrogen bonds forming a monocationic cyclic unit. These cyclic units are further connected by N–H∙∙∙O and N–H∙∙∙N hydrogen bonds forming polymeric, polar double-strands along [001]. The perchlorate anions fill the gaps between these strands, and each [ClO4]− anion is weakly connected to the NH2 group by one N–H∙∙∙O hydrogen bond (orthorhombic, non-centrosymmetric space group Pca21 (No. 29, a = 18.5821(5 Å, b = 11.4320(3 Å, c = 6.89400(17 Å, V = 1464.50(6 Å3, Z = 4, T = 100 K, R(F [I > 2σ(I] = 0.0234, wR(F2 [all] = 0.0575. Both structures are structurally related, and their commonalities are discussed in terms of a graph

  7. 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

  8. 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)

  9. 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).

  10. 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).

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. Potential mesogens based on pyridine derivatives: The geometric structure, conformational properties and characteristics of intermolecular hydrogen bonds

    Science.gov (United States)

    Fedorov, Mikhail S.; Giricheva, Nina I.; Shpilevaya, Kseniya E.; Lapykina, Elena A.; Syrbu, Svetlana A.

    2017-03-01

    Conformational properties of the main part (excluding sbnd OC3H7 radicals) of the p-n-propyloxybenzoic (A1) and p-n-propyloxycinnamic (A2) acids molecules (relating to mesomorphic compounds) as well as p-n-propyloxybenzoic acid pyridine ester (B1) and p-n-propyloxyphenylazopyridine (B2) molecules (relating to non-mesomorphic compounds) were studied by DFT(B3LYP)/cc-pVTZ method. It was shown that the main parts of A1 and A2 acids are rigid. The barrier to internal rotation of pyridine fragment in the B1 and B2 molecules depends on the nature of the bridging group. It was determined that all studied A1⋯B1, A2⋯B1 and A2⋯B2 complexes are characterized by a strong hydrogen bond. The binding energy of complexes (≈14 kcal/mol, with BSSE corrections, DFT(B97D)/6-311++G**) exceeds the energy per hydrogen bond in the corresponding acid dimers (≈10 kcal/mol). The structural non-rigidity of A⋯B complexes is mainly caused by possibility of sbnd OC3H7 radicals internal rotation and A and B molecules rotation about the (H)O⋯N line. The characteristics of intermolecular hydrogen bonds were determined by NBO-analysis. The obtained results indicate that examined complexes correspond to the basic requirements to mesogen molecular forms. The thermodynamic functions of the gas-phase complexation reactions (idealized model of the complexes formation in the condensed state) were calculated. Preliminary studies of mesogen-non-mesogen A1⋯B2 system by differential scanning calorimetry and polarizing optical microscopy, showed that it has mesomorphic properties.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. Effect of water storage on resin-dentin bond strengths formed by different bonding approaches

    Directory of Open Access Journals (Sweden)

    Martins G

    2009-01-01

    Full Text Available Objectives: The purpose of this study was to evaluate the influence of water storage on resin-dentin bond strengths [µTBS] using different adhesive bonding approaches. Materials and Methods: Flat superficial dentin surfaces of 24 extracted human third molars were exposed and polished to create a standardized smear layer. The teeth were randomly distributed into four different groups: Three-step etch-and-rinse (Adper Scotchbond Multi-Purpose, 3M ESPE - SBMP, two-step etch-and-rinse (Adper Single Bond 2, 3 M ESPE - SB; two-step self-etch (AdheSE, Ivoclar/Vivadent - AD; and self-etch 1 step (Adper Prompt L-Pop, 3M ESPE - LP. Following the adhesive application (n = 6, resin composite was incrementally applied (Filtek™ Supreme XT - 3 M ESPE in order to obtain bonded sticks, with a cross-sectioned area of 0.81 mm 2 . The bonded sticks were randomly divided and assigned to be tested after one day [OD] (n 30 or six months [6 M] of water storage [6 M] (n = 30. Results: Two-way ANOVA and Tukey′s test showed that none of the adhesives showed degradation after 6 M. SB achieved the highest µTBS both in the [OD] (49.13 MPa and [6M] (40.27 MPa. Despite the highest values in both time evaluations, the µTBS of SB significantly reduced after 6M. LP showed the lowest µTBS in both periods of evaluation (18.35 and 18.34 MPa. Conclusions: Although a significant degradation was only observed for SB, this was the adhesive that showed the highest µTBS after 6 M of water storage.

  10. 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.

  11. Ultrafast forward and backward electron transfer dynamics of coumarin 337 in hydrogen-bonded anilines as studied with femtosecond UV-pump/IR-probe spectroscopy.

    Science.gov (United States)

    Ghosh, Hirendra N; Verma, Sandeep; Nibbering, Erik T J

    2011-02-10

    Femtosecond infrared spectroscopy is used to study both forward and backward electron transfer (ET) dynamics between coumarin 337 (C337) and the aromatic amine solvents aniline (AN), N-methylaniline (MAN), and N,N-dimethylaniline (DMAN), where all the aniline solvents can donate an electron but only AN and MAN can form hydrogen bonds with C337. The formation of a hydrogen bond with AN and MAN is confirmed with steady state FT-IR spectroscopy, where the C═O stretching vibration is a direct marker mode for hydrogen bond formation. Transient IR absorption measurements in all solvents show an absorption band at 2166 cm(-1), which has been attributed to the C≡N stretching vibration of the C337 radical anion formed after ET. Forward electron transfer dynamics is found to be biexponential with time constants τ(ET)(1) = 500 fs, τ(ET)(2) = 7 ps in all solvents. Despite the presence of hydrogen bonds of C337 with the solvents AN and MAN, no effect has been found on the forward electron transfer step. Because of the absence of an H/D isotope effect on the forward electron transfer reaction of C337 in AN, hydrogen bonds are understood to play a minor role in mediating electron transfer. In contrast, direct π-orbital overlap between C337 and the aromatic amine solvents causes ultrafast forward electron transfer dynamics. Backward electron transfer dynamics, in contrast, is dependent on the solvent used. Standard Marcus theory explains the observed backward electron transfer rates.

  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.

    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.

  13. 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

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    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.

  14. 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.

  15. Hydrogen bonding of sulfur ligands in blue copper and iron-sulfur proteins: detection by resonance raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mino, Y.; Loehr, T.M.; Wada, K.; Matsubara, H.; Sanders-Loehr, J.

    1987-12-15

    The resonance Raman spectrum of the blue copper protein azurin from Alcaligenes denitrificans exhibits nine vibrational modes between 330 and 460 cm/sup -1/, seven of which shift 0.4-3.0 cm/sup -1/ to lower energy after incubation of the protein in D/sub 2/O. These deuterium-dependent shifts have been previously ascribed to exchangeable protons on imidazole ligands or to exchangeable protons on amide groups which are hydrogen bonded to the cysteine thiolate ligands (a feature common to all blue copper proteins of known structure). In order to distinguish between these two possibilities, a systematic investigation of Fe/sub 2/S/sub 2/(Cys)/sub 4/-containing proteins was undertaken. Extensive hydrogen bonding between sulfur ligands and the polypeptide backbone had been observed in the crystal structure of ferredoxin from Spirulina platensis. The resonance Raman spectrum of this protein is typical of a chloroplast-type ferredoxin and exhibits deuterium-dependent shifts of -0.3 to -0.5 cm/sup -1/ in the Fe-S modes at 283, 367, and 394 cm/sup -1/ and -0.6 to -0.8 cm/sup -1/ in the Fe-S modes at 328 and 341 cm/sup -1/. Considerably greater deuterium sensitivity is observed in the Raman spectra of spinach ferredoxin and bovine adrenodoxin, particularly for the symmetric stretching vibration of the Fe/sub 2/S/sub 2/ moiety at approx. 390 cm/sup -1/. This feature decreases of 9.8 and 1.1 cm/sup -1/, respectively, for the two oxidized proteins in D/sub 2/O and by 1.8 cm/sup -1/ for reduced adrenodoxin in D/sub 2/O. These results suggest that the bridging sulfido groups may be more extensively hydrogen bonded in spinach ferredoxin and adrenodoxin than in S. platensis ferredoxin, with a further increase in hydrogen-bond strength in the reduced form of adrenodoxin.

  16. 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.

  17. 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.

  18. 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.

  19. Thermodynamics of single polyethylene and polybutylene glycols with hydrogen-bonding ends: A transition from looped to open conformations

    Science.gov (United States)

    Lee, Eunsang; Paul, Wolfgang

    2018-02-01

    A variety of linear polymer precursors with hydrogen bonding motifs at both ends enable us to design supramolecular polymer systems with tailored macroscopic properties including self-healing. In this study, we investigate thermodynamic properties of single polyethylene and polybutylene glycols with hydrogen bonding motifs. In this context, we first build a coarse-grained model of building blocks of the supramolecular polymer system based on all-atom molecular structures. The density of states of the single precursor is obtained using the stochastic approximation Monte Carlo method. Constructing canonical partition functions from the density of states, we find the transition from looped to open conformations at transition temperatures which are non-monotonously changing with an increasing degree of polymerization due to the competition between chain stiffness and loop-forming entropy penalty. In the complete range of chain length under investigation, a coexistence of the looped and open morphologies at the transition temperature is shown regardless of whether the transition is first-order-like or continuous. Polyethylene and polybutylene glycols show similar behavior in all the thermodynamic properties but the transition temperature of the more flexible polybutylene glycol is shown to change more gradually.

  20. Solvation of apolar compounds in protic ionic liquids: the non-synergistic effect of electrostatic interactions and hydrogen bonds.

    Science.gov (United States)

    Sedov, I A; Magsumov, T I; Salikov, T M; Solomonov, B N

    2017-09-27

    The solvation properties of protic ionic liquids such as alkylammonium salts are still virtually uncharacterized. Both electrostatic interactions between charged particles and hydrogen bond networks in a solvent are known to hinder the solubility of apolar species. Protic ionic liquids can be a priori expected to dissolve hydrocarbons worse than aprotic ionic liquids which do not form hydrogen bonds between the ions. We measured the limiting activity coefficients of several alkanes and alkylbenzenes in propylammonium and butylammonium nitrates at 298 K. Surprisingly, we observed the tendency of higher solubility than for the same compounds in aprotic ionic liquids with a similar molar volume. The calculations of the excess Gibbs free energies using test particle insertions into the snapshots of molecular dynamics trajectories reproduced lower values in protic rather than in aprotic ionic liquids for both methane molecules and hard sphere solutes. This can be explained by the favorable solvation of apolar species in the apolar domain of nanostructured PILs. For the first time, we point out at the essential difference between the solvation properties of two types of ionic liquids and prove that it arises from the cavity formation term.