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Sample records for additional hydrogen bond

  1. New hydrogen-bonding organocatalysts: Chiral cyclophosphazanes and phosphorus amides as catalysts for asymmetric Michael additions

    PubMed Central

    Klare, Helge; Neudörfl, Jörg M

    2014-01-01

    Summary Ten novel hydrogen-bonding catalysts based on open-chain PV-amides of BINOL and chinchona alkaloids as well as three catalysts based on rigid cis-PV-cyclodiphosphazane amides of N 1,N 1-dimethylcyclohexane-1,2-diamine have been developed. Employed in the asymmetric Michael addition of 2-hydroxynaphthoquinone to β-nitrostyrene, the open-chain 9-epi-aminochinchona-based phosphorus amides show a high catalytic activity with almost quantitative yields of up to 98% and enantiomeric excesses of up to 51%. The cyclodiphosphazane catalysts show the same high activity and give improved enantiomeric excesses of up to 75%, thus representing the first successful application of a cyclodiphosphazane in enantioselective organocatalysis. DFT computations reveal high hydrogen-bonding strengths of cyclodiphosphazane PV-amides compared to urea-based catalysts. Experimental results and computations on the enantiodetermining step with cis-cyclodiphosphazane 14a suggest a strong bidentate H-bond activation of the nitrostyrene substrate by the catalyst. PMID:24605142

  2. Hydrogen Bond Acceptors and Additional Cationic Charges in Methylene Blue Derivatives: Photophysics and Antimicrobial Efficiency

    PubMed Central

    Felgenträger, Ariane; Maisch, Tim; Dobler, Daniel; Späth, Andreas

    2013-01-01

    Photodynamic inactivation of bacteria (PIB) by efficient singlet oxygen photosensitizers might be a beneficial alternative to antibiotics in the struggle against multiresistant bacteria. Phenothiazinium dyes belong to the most prominent classes of such sensitizers due to their intense absorption in the red-light region (λabs, max ca. 600–680 nm, ε > 50000 L mol−1 cm−1), their low toxicity, and their attachment/penetration abilities. Except simple substituents like alkyl or hydroxyalkyl residues, nearly no modifications of the phenothiaziniums have been pursued at the auxochromic sites. By this, the properties of methylene blue derivatives and their fields of application are limited; it remains unclear if their potential antimicrobial efficacy may be enhanced, also to compete with porphyrins. We prepared a set of six mainly novel methylene blue derivatives with the ability of additional hydrogen bonding and/or additional cationic charges to study the substituents' effect on their activity/toxicity profiles and photophysical properties. Direct detection of singlet oxygen was performed at 1270 nm and the singlet oxygen quantum yields were determined. In suspensions with both, Gram-positive and Gram-negative bacteria, some derivatives were highly active upon illumination to inactivate S. aureus and E. coli up to 7 log10 steps (99.99999%) without inherent toxicities in the nonirradiated state. PMID:23509728

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

    PubMed

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

    2016-05-01

    Ozone (O3) and sulfur dioxide (SO2) are valence isoelectronic species, yet their properties and reactivities differ dramatically. In particular, O3 is highly reactive, whereas SO2 is chemically relatively stable. In this paper, we investigate serial addition of hydrogen atoms to both the terminal atoms of O3 and SO2 and to the central atom of these species. It is well-known that the terminal atoms of O3 are much more amenable to bond formation than those of SO2. We show that the differences in the electronic structure of the π systems in the parent triatomic species account for the differences in the addition of hydrogen atoms to the terminal atoms of O3 and SO2. Further, we find that the π system in SO2, which is a recoupled pair bond dyad, facilitates the addition of hydrogen atoms to the sulfur atom, resulting in stable HSO2 and H2SO2 species. PMID:27070292

  4. Influence of sulfur addition and S-induced wall catalytic effect on C-C bond cleavage and aromatics hydrogenation

    SciTech Connect

    Schmidt, E.; Song, C.; Schobert, H.H.

    1995-12-31

    Catalytic hydrocracking of 4-(-1-naphthylmethyl)bibenzyl NMBB predominately yielded naphthalene and 4-methylbibenzyl. Sulfur addition to most catalyst precursors lead to substantially higher catalyst activity and subsequently higher conversion. In order to clarify the effect of sulfur alone on model compound conversion, NMBB was treated with sulfur in concentrations of 1.2 to 3.4 wt%, corresponding to conditions present in catalytic runs with sulfur. It was found that increasing sulfur concentrations leads to higher NMBB conversion. Furthermore, sulfur had a permanent influence on the reactor walls. It reacted with the transition metals in the steel to form a microscopic black iron sulfide layer on the surface, which could not be removed mechanically. The {open_quotes}non catalytic{close_quotes} runs after experiments with added sulfur yielded higher conversion than normal runs with new reactors. This {open_quotes}wall catalytic effect{close_quotes} can be reduced by treating sulfided reactors with hydrochloric acid for a short period of time and subsequent immersing into a base bath over night. These results demonstrate the significant influence of sulfur addition and S-induced residual wall-effect on C-C bond cleavage and hydrogenation of aromatics in batch reactors.

  5. Influence of sulfur addition and S-induced wall catalytic effects on C-C bond cleavage and aromatics hydrogenation

    SciTech Connect

    Schmidt, E.; Song, Chunshan; Schobert, H.H.

    1995-12-31

    Catalytic hydrocracking of 4-(1-naphthylmethyl)bibenzyl, designated as NMBB, predominately yielded naphthalene and 4-methylbibenzyl. Sulfur addition to most catalyst precursors lead to substantially higher catalyst activity and subsequently higher conversion. NMBB was also treated with sulfur alone in the absence of catalysts in concentrations of 1.2 to 3.4 wt, corresponding to conditions present in catalytic runs with added sulfur to precursors. It was found that increasing sulfur concentrations lead to higher NMBB conversion. Furthermore, sulfur had a permanent influence on the reactor walls. It reacted with the transition metals in the stainless steel to form a microscopic black iron sulfide layer on the surface, which could not be removed mechanically. The {open_quotes}non-catalytic{close_quotes} runs which were done after experiments with added sulfur yielded higher conversions than normal runs done in new reactors. This {open_quotes}wall catalytic effect{close_quotes} can be reduced by treating sulfided reactors with hydrochloric acid for a short period of time and subsequent immersing into a base bath overnight. These results demonstrate the significant influence of sulfur addition and S-induced residual wall-effect on C-C bond cleavage and hydrogenation of aromatics in batch reactors.

  6. CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature

    PubMed Central

    Venable, Richard M.; Sodt, Alexander J.; Rogaski, Brent; Rui, Huan; Hatcher, Elizabeth; MacKerell, Alexander D.; Pastor, Richard W.; Klauda, Jeffery B.

    2014-01-01

    The C36 CHARMM lipid force field has been extended to include sphingolipids, via a combination of high-level quantum mechanical calculations on small molecule fragments, and validation by extensive molecular dynamics simulations on N-palmitoyl and N-stearoyl sphingomyelin. NMR data on these two molecules from several studies in bilayers and micelles played a strong role in the development and testing of the force field parameters. Most previous force fields for sphingomyelins were developed before the availability of the detailed NMR data and relied on x-ray diffraction of bilayers alone for the validation; these are shown to be too dense in the bilayer plane based on published chain order parameter data from simulations and experiments. The present simulations reveal O-H:::O-P intralipid hydrogen bonding occurs 99% of the time, and interlipid N-H:::O=C (26-29%, depending on the lipid) and N-H:::O-H (17–19%). The interlipid hydrogen bonds are long lived, showing decay times of 50 ns, and forming strings of lipids, and leading to reorientational correlation time of nearly 100 ns. The spontaneous radius of curvature for pure N-palmitoyl sphingomyelin bilayers is estimated to be 43–100 Å, depending on the assumptions made in assigning a bending constant; this unusual positive curvature for a two-tailed neutral lipid is likely associated with hydrogen bond networks involving the NH of the sphingosine group. PMID:24988348

  7. Mapping Buried Hydrogen-Bonding Networks.

    PubMed

    Thomas, John C; Goronzy, Dominic P; Dragomiretskiy, Konstantin; Zosso, Dominique; Gilles, Jérôme; Osher, Stanley J; Bertozzi, Andrea L; Weiss, Paul S

    2016-05-24

    We map buried hydrogen-bonding networks within self-assembled monolayers of 3-mercapto-N-nonylpropionamide on Au{111}. The contributing interactions include the buried S-Au bonds at the substrate surface and the buried plane of linear networks of hydrogen bonds. Both are simultaneously mapped with submolecular resolution, in addition to the exposed interface, to determine the orientations of molecular segments and directional bonding. Two-dimensional mode-decomposition techniques are used to elucidate the directionality of these networks. We find that amide-based hydrogen bonds cross molecular domain boundaries and areas of local disorder. PMID:27096290

  8. Photoinduced hydrogen-bonding dynamics.

    PubMed

    Chu, Tian-Shu; Xu, Jinmei

    2016-09-01

    Hydrogen bonding dynamics has received extensive research attention in recent years due to the significant advances in femtolaser spectroscopy experiments and quantum chemistry calculations. Usually, photoexcitation would cause changes in the hydrogen bonding formed through the interaction between hydrogen donor and acceptor molecules on their ground electronic states, and such transient strengthening or weakening of hydrogen bonding could be crucial for the photophysical transformations and the subsequent photochemical reactions that occurred on a time scale from tens of femtosecond to a few nanoseconds. In this article, we review the combined experimental and theoretical studies focusing on the ultrafast electronic and vibrational hydrogen bonding dynamics. Through these studies, new mechanisms and proposals and common rules have been put forward to advance our understanding of the hydrogen bondings dynamics in a variety of important photoinduced phenomena like photosynthesis, dual fluorescence emission, rotational reorientation, excited-state proton transfer and charge transfer processes, chemosensor fluorescence sensing, rearrangements of the hydrogen-bond network including forming and breaking hydrogen bond in water. Graphical Abstract We review the recent advances on exploring the photoinduced hydrogen bonding dynamics in solutions through a joint approach of laser spectroscopy and theoretical calculation. The reviewed studies have put forward a new mechanism, new proposal, and new rule for a variety of photoinduced phenomena such as photosynthesis, dual fluorescence emission, rotational reorientation, excited-state proton transfer and charge transfer, chemosensor fluorescence sensing, and rearrangements of the hydrogen-bond network in water. PMID:27491849

  9. A cooperative hydrogen bonding system with a Csbnd H⋯O hydrogen bond in ofloxacin

    NASA Astrophysics Data System (ADS)

    Gao, Xiuxiang; Liu, Yufeng; Li, Huizhen; Bian, Jiang; Zhao, Ying; Cao, Ye; Mao, Yuezhi; Li, Xin; Xu, Yizhuang; Ozaki, Yukihiro; Wu, Jinguang

    2013-05-01

    We have investigated a cooperative hydrogen bonding system with a Csbnd H⋯O hydrogen bond in ofloxacin by using NMR, UV-Vis spectra together with quantum chemistry calculation. Both pH-dependent NMR experiments and DFT calculation indicate that the intra-molecular Csbnd H⋯O hydrogen bond between an aromatic proton and an oxygen atom from the carboxyl group is formed. Notably, the Csbnd H⋯O hydrogen bond forms a cooperative hydrogen bonding system with a neighboring Osbnd H⋯O hydrogen bond between the carboxyl group and the keto oxygen. The cooperative hydrogen bonding system makes the formation and disruption of the Osbnd H⋯O and Csbnd H⋯O hydrogen bonds in a synergistic manner. Comparison on the pKa value of the carboxylic group in different fluoroquinolones compounds indicates that the Csbnd H⋯O hydrogen bond plays a significant role in stabilizing the Osbnd H⋯O hydrogen bond. In addition, the formation and disruption of the cooperative hydrogen bonding system could regulate the conformation of the carboxyl group, which affects the size of the conjugated system and spectral behavior of π-π transition of ofloxacin.

  10. Hydrogen Bonds in Polymer Folding

    NASA Astrophysics Data System (ADS)

    Borg, Jesper; Jensen, Mogens H.; Sneppen, Kim; Tiana, Guido

    2001-02-01

    We studied the thermodynamics of a homopolymeric chain with both van der Waals and directed hydrogen bond interaction. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give rise to long-range order and to conformations displaying secondary structures. For compact polymers a transition is found between helix-rich states and low-entropy sheet-dominated states. The consequences of this transition for protein folding and, in particular, for the problem of prions are discussed.

  11. 29 CFR 2580.412-20 - Use of existing bonds, separate bonds and additional bonding.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 9 2010-07-01 2010-07-01 false Use of existing bonds, separate bonds and additional..., separate bonds and additional bonding. (a) Additional bonding. Section 13 neither prevents additional... or separate bond. (b) Use of existing bonds. Insofar as a bond currently in use is adequate to...

  12. Werner Complexes with ω-Dimethylaminoalkyl Substituted Ethylenediamine Ligands: Bifunctional Hydrogen-Bond-Donor Catalysts for Highly Enantioselective Michael Additions.

    PubMed

    Ghosh, Subrata K; Ganzmann, Carola; Bhuvanesh, Nattamai; Gladysz, John A

    2016-03-18

    The racemic carbonate complex [Co(en)2 O2 CO](+) Cl(-) (en=1,2-ethylenediamine) and (S)-[H3 NCH((CH2 )n NHMe2 )CH2 NH3 ](3+) 3 Cl(-) (n=1-4) react (water, charcoal, 100 °C) to give [Co(en)2 ((S)-H2 NCH((CH2 )n NHMe2 )CH2 NH2 )](4+) 4 Cl(-) (3 a-d H(4+) 4 Cl(-) ) as a mixture of Λ/Δ diastereomers that separate on chiral-phase Sephadex columns. These are treated with NaOH/Na(+) BArf (-) (BArf =B(3,5-C6 H3 (CF3 )2 )4 ) to give lipophilic Λ- and Δ-3 a-d(3+) 3 BArf (-) , which are screened as catalysts (10 mol %) for additions of dialkyl malonates to nitroalkenes. Optimal results are obtained with Λ-3 c(3+) 3 BArf (-) (CH2 Cl2 , -35 °C; 98-82 % yields and 99-93 % ee for six β-arylnitroethenes). The monofunctional catalysts Λ- and Δ-[Co(en)3 ](3+) 3 BArf (-) give enantioselectivities of <10 % ee with equal loadings of Et3 N. The crystal structure of Δ-3 a H(4+) 4 Cl(-) provides a starting point for speculation regarding transition-state assemblies. PMID:26918320

  13. Contribution of hydrogen bonds to protein stability.

    PubMed

    Pace, C Nick; Fu, Hailong; Lee Fryar, Katrina; Landua, John; Trevino, Saul R; Schell, David; Thurlkill, Richard L; Imura, Satoshi; Scholtz, J Martin; Gajiwala, Ketan; Sevcik, Jozef; Urbanikova, Lubica; Myers, Jeffery K; Takano, Kazufumi; Hebert, Eric J; Shirley, Bret A; Grimsley, Gerald R

    2014-05-01

    Our goal was to gain a better understanding of the contribution of the burial of polar groups and their hydrogen bonds to the conformational stability of proteins. We measured the change in stability, Δ(ΔG), for a series of hydrogen bonding mutants in four proteins: villin headpiece subdomain (VHP) containing 36 residues, a surface protein from Borrelia burgdorferi (VlsE) containing 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa (RNase Sa) and T1 (RNase T1). Crystal structures were determined for three of the hydrogen bonding mutants of RNase Sa: S24A, Y51F, and T95A. The structures are very similar to wild type RNase Sa and the hydrogen bonding partners form intermolecular hydrogen bonds to water in all three mutants. We compare our results with previous studies of similar mutants in other proteins and reach the following conclusions. (1) Hydrogen bonds contribute favorably to protein stability. (2) The contribution of hydrogen bonds to protein stability is strongly context dependent. (3) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (4) Polar group burial can make a favorable contribution to protein stability even if the polar groups are not hydrogen bonded. (5) The contribution of hydrogen bonds to protein stability is similar for VHP, a small protein, and VlsE, a large protein. PMID:24591301

  14. Contribution of hydrogen bonds to protein stability

    PubMed Central

    Pace, C Nick; Fu, Hailong; Fryar, Katrina Lee; Landua, John; Trevino, Saul R; Schell, David; Thurlkill, Richard L; Imura, Satoshi; Scholtz, J Martin; Gajiwala, Ketan; Sevcik, Jozef; Urbanikova, Lubica; Myers, Jeffery K; Takano, Kazufumi; Hebert, Eric J; Shirley, Bret A; Grimsley, Gerald R

    2014-01-01

    Our goal was to gain a better understanding of the contribution of the burial of polar groups and their hydrogen bonds to the conformational stability of proteins. We measured the change in stability, Δ(ΔG), for a series of hydrogen bonding mutants in four proteins: villin headpiece subdomain (VHP) containing 36 residues, a surface protein from Borrelia burgdorferi (VlsE) containing 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa (RNase Sa) and T1 (RNase T1). Crystal structures were determined for three of the hydrogen bonding mutants of RNase Sa: S24A, Y51F, and T95A. The structures are very similar to wild type RNase Sa and the hydrogen bonding partners form intermolecular hydrogen bonds to water in all three mutants. We compare our results with previous studies of similar mutants in other proteins and reach the following conclusions. (1) Hydrogen bonds contribute favorably to protein stability. (2) The contribution of hydrogen bonds to protein stability is strongly context dependent. (3) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (4) Polar group burial can make a favorable contribution to protein stability even if the polar groups are not hydrogen bonded. (5) The contribution of hydrogen bonds to protein stability is similar for VHP, a small protein, and VlsE, a large protein. PMID:24591301

  15. Contribution of Hydrogen Bonds to Protein Stability

    NASA Astrophysics Data System (ADS)

    Pace, Nick

    2014-03-01

    I will discuss the contribution of the burial of polar groups and their hydrogen bonds to the conformational stability of proteins. We measured the change in stability, Δ(Δ G), for a series of hydrogen bonding mutants in four proteins: villin head piece subdomain (VHP) containing 36 residues, a surface protein from Borrelia burgdorferi (VlsE) containing 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa (RNase Sa) and T1 (RNase T1). Crystal structures were determined for three of the hydrogen bonding mutants of RNase Sa: S24A (1.1Å), Y51F(1.5Å), and T95A(1.3Å). The structures are very similar to wild type RNase Sa and the hydrogen bonding partners always form intermolecular hydrogen bonds to water in the mutants. We compare our results with previous studies of similar mutants in other proteins and reach the following conclusions: 1) Hydrogen bonds contribute favorably to protein stability. 2) The contribution of hydrogen bonds to protein stability is strongly context dependent. 3) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. 4) Polar group burial can make a favorable contribution to protein stability even if the polar groups are not hydrogen bonded. 5) The contribution of hydrogen bonds to protein stability is similar for VHP, a small protein, and VlsE, a large protein.

  16. 43 CFR 3154.2 - Additional bonding.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Additional bonding. 3154.2 Section 3154.2 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT... Requirements § 3154.2 Additional bonding. The authorized officer may increase the amount of any bond that...

  17. Hydrogen bonded structures in organic amine oxalates

    NASA Astrophysics Data System (ADS)

    Vaidhyanathan, R.; Natarajan, S.; Rao, C. N. R.

    2002-05-01

    Oxalates of n-propylamine, n-butylamine, ethylenediamine, 1,4-butanediamine, piperazine, guanidine and 1,4-diazabicyclo[2,2,2]octane (DABCO) have been synthesized and characterized by single crystal X-ray diffraction and other techniques. The amine oxalates show different types of hydrogen bonded networks, linear hydrogen bonded chains characterizing the oxalates of the first five amines. Guanidinium oxalate has a sheet like structure while DABCO oxalate has dimeric hydrogen bonded rings. Hydrogen bonded structures of these oxalates are discussed in detail, besides relating their thermal stability to the strengths of the networks.

  18. Challenging Dogmas: Hydrogen Bond Revisited.

    PubMed

    Tafipolsky, Maxim

    2016-07-01

    Hydrogen bond directionality in the water dimer is explained on the basis of symmetry-adapted intermolecular perturbation theory which directly separates the intermolecular interaction energy into four physically interpretable components: electrostatics, exchange-repulsion, dispersion, and induction. Analysis of these four main contributions to the binding energy allows a deeper understanding of the dominant factors ruling the mutual arrangement of the two monomers. A preference for the linear configuration is shown to be due to a subtle interplay of all four energy components. While the first-order terms, electrostatic and exchange-repulsion, almost perfectly cancel each other near the equilibrium geometry of the dimer, the importance of the second- and higher-order terms, induction and dispersion, becomes evident. PMID:27299177

  19. Hydrogen-bonded polymer blends

    NASA Astrophysics Data System (ADS)

    Guigley, Kevin Scott

    This thesis discusses three topics in the general area of hydrogen bonded polymer blends. The first pertains to the blending of flame retardant polyphosphazenes. Poly[bis(n-alkyoxy)phosphazenes] blends with poly(butyl methacrylate- co-4-vinyl phenol) (BMAVPh) were initially studied. These results were compared to BMAVPh blends of analogous poly (vinyl n-alkyl ethers) and the phase behavior was similar. Next, poly[bis(carboxylatophenoxy)phosphazene] blends with a structural polyurethane foam were prepared via reactive mixing. The combustion behavior of these foams was analyzed qualitatively, by a horizontal flame test, and quantitatively, by oxygen index (OI) measurements. Both of these tests indicated a modest increase in flame resistance at loadings of 20 wt% and above. In the second topic, equilibrium constants determined from low molecular weight mixtures were used to successfully predict the phase behavior of analogous polymer blends. Due consideration was given to intramolecular screening and functional group accessibility, factors that are a direct consequence of chain connectivity. In the third topic, polymer blends involving an alternating 1:1 copolymer of tetrafluoroethylene (TFE) and a hexafluoroisopropanol modified vinyl ether (HFIPVE) were studied. This copolymer is interesting for both experimental and theoretical studies of the phase behavior of polymer blends because (1) it is amorphous and has a relatively low glass transition temperature (12°C); (2) it has a relatively low solubility parameter (≈7 (cal.cm-3)-0.5); (3) it is soluble in moderately polar solvents, and (4) it contains the hexafluoroisopropanol group that is a strong hydrogen bond donor. Experimental infrared and thermal analysis studies of polymer blends with (co)polymers containing acetoxy, methacrylate and aliphatic ether groups were studied and compared to theoretical predictions of miscibility maps.

  20. Orthogonal halogen and hydrogen bonds involving a peptide bond model† †Electronic supplementary information (ESI) available: Experimental part, DSC, IR spectroscopic and crystallographic data. CCDC 899779–899785. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4ce01514b Click here for additional data file. Click here for additional data file.

    PubMed Central

    Vasylyeva, Vera; Nayak, Susanta K.; Cavallo, Gabriella; Resnati, Giuseppe

    2014-01-01

    The peptide bond model N-methylacetamide self-assembles with a range of dihalotetrafluorobenzenes forming co-crystals that all show the occurrence of orthogonal hydrogen and halogen bonds. PMID:25663816

  1. Hydrogen bond dynamics in bulk alcohols

    SciTech Connect

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

    2015-06-07

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

  2. HYDROGEN BONDING IN THE METHANOL DIMER

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this work, two methanol molecules are placed in different arrangements to study hydrogen bonding in carbohydrate materials such as cellulose. Energy was calculated as a function of both hydrogen bond length and angle over wide ranges, using quantum mechanics (QM). The QM wavefunctions are analyze...

  3. Persistent hydrogen bonding in polymorphic crystal structures.

    PubMed

    Galek, Peter T A; Fábián, László; Allen, Frank H

    2009-02-01

    The significance of hydrogen bonding and its variability in polymorphic crystal structures is explored using new automated structural analysis methods. The concept of a chemically equivalent hydrogen bond is defined, which may be identified in pairs of structures, revealing those types of bonds that may persist, or not, in moving from one polymorphic form to another. Their frequency and nature are investigated in 882 polymorphic structures from the Cambridge Structural Database. A new method to compare conformations of equivalent molecules is introduced and applied to derive distinct subsets of conformational and packing polymorphs. The roles of chemical functionality and hydrogen-bond geometry in persistent interactions are systematically explored. Detailed structural comparisons reveal a large majority of persistent hydrogen bonds that are energetically crucial to structural stability. PMID:19155561

  4. Hydrogen-bond kinetics in liquid water

    NASA Astrophysics Data System (ADS)

    Luzar, Alenka; Chandler, David

    1996-01-01

    HYDROGEN bonds play a crucial role in the behaviour of water1-4 their spatial patterns and fluctuations characterize the structure and dynamics of the liquid5-7. The processes of breaking and making hydrogen bonds in the condensed phase can be probed indirectly by a variety of experimental techniques8, and more quantitative information can be obtained from computer simulations9. In particular, simulations have revealed that on long timescales the relaxation behaviour of hydrogen bonds in liquid water exhibit non-exponential kinetics7,10-13, suggesting that bond making and breaking are not simple processes characterized by well defined rate constants. Here we show that these kinetics can be understood in terms of an interplay between diffusion and hydrogen-bond dynamics. In our model, which can be extended to other hydrogen-bonded liquids, diffusion governs whether a specific pair of water molecules are near neighbours, and hydrogen bonds between such pairs form and persist at random with average lifetimes determined by rate constants for bond making and breaking.

  5. Charge-Assisted Hydrogen-Bonded Networks

    NASA Astrophysics Data System (ADS)

    Ward, Michael D.

    The importance of hydrogen bonds is widely recognized because of their role in defining the structure and properties of many compounds, including water, proteins, DNA, and polymers. Hydrogen bonding also has emerged as a critical tool in solid-state chemistry, in which the versatility of organic synthesis has been combined with the structure-directing properties of hydrogen-bond donor-acceptor pairs to steer molecular assembly into networks that reflect the symmetries of their molecular constituents. Although these efforts have been largely empirical, the dominance of hydrogen bonding among the multitude of intermolecular forces often leads to predictable control of crystal structure. Although charge-assisted hydrogen bonds (donors and acceptors with ionic character that reinforce the electrostatic character of the hydrogen bond) have been recognized for decades, their use in network design, particularly for “crystal engineering,” has grown substantially in the past decade. The evidence suggests that charge-assisted hydrogen bonds introduce extraordinary robustness to molecular networks that reflects a combination of strong intermolecular forces and structural compliance, thus facilitating design of organic solid-state materials.

  6. Alkyl Chlorides as Hydrogen Bond Acceptors

    SciTech Connect

    Nadas, Janos I; Vukovic, Sinisa; Hay, Benjamin

    2012-01-01

    To gain an understanding of the role of an alkyl chloride as a hydrogen bond acceptor, geometries and interaction energies were calculated at the MP2/aug-cc-pVDZ level of theory for complexes between ethyl chloride and representative hydrogen donor groups. The results establish that these donors, which include hydrogen cyanide, methanol, nitrobenzene, pyrrole, acetamide, and N-methylurea, form X-H {hor_ellipsis} Cl hydrogen bonds (X = C, N, O) of weak to moderate strength, with {Delta}E values ranging from -2.8 to -5.3 kcal/mol.

  7. Competing intramolecular vs. intermolecular hydrogen bonds in solution.

    PubMed

    Nagy, Peter I

    2014-01-01

    A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. PMID:25353178

  8. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    PubMed Central

    Nagy, Peter I.

    2014-01-01

    A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. PMID:25353178

  9. Intramolecular Hydrogen Bonding in Substituted Aminoalcohols.

    PubMed

    Lane, Joseph R; Schrøder, Sidsel D; Saunders, Graham C; Kjaergaard, Henrik G

    2016-08-18

    The qualifying features of a hydrogen bond can be contentious, particularly where the hydrogen bond is due to a constrained intramolecular interaction. Indeed there is disagreement within the literature whether it is even possible for an intramolecular hydrogen bond to form between functional groups on adjacent carbon atoms. This work considers the nature of the intramolecular interaction between the OH (donor) and NH2 (acceptor) groups of 2-aminoethanol, with varying substitution at the OH carbon. Gas-phase vibrational spectra of 1-amino-2-methyl-2-propanol (BMAE) and 1-amino-2,2-bis(trifluoromethyl)-2-ethanol (BFMAE) were recorded using Fourier transform infrared spectroscopy and compared to literature spectra of 2-aminoethanol (AE). Based on the experimental OH-stretching frequencies, the strength of the intramolecular hydrogen bond appears to increase from AE < BMAE ≪ BFMAE. Non-covalent interaction analysis shows evidence of an intramolecular hydrogen bond in all three molecules, with the order of the strength of interaction matching that of experiment. The experimental OH-stretching vibrational frequencies were found to correlate well with the calculated kinetic energy density, suggesting that this approach can be used to estimate the strength of an intramolecular hydrogen bond. PMID:27447952

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

    PubMed

    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. PMID:17143867

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

    PubMed

    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

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

    NASA Astrophysics Data System (ADS)

    Bower, John F.; Krische, Michael J.

    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.

  13. Hydrogen bonding nature during ADP crystallization

    NASA Astrophysics Data System (ADS)

    Sun, Congting; Xue, Dongfeng

    2014-02-01

    The hydrogen bonding nature during ADP crystallization is studied on the basis of anisotropic chemical bonding conditions in ADP crystal combined with in situ IR observation. The variations of hydrogen bonding nature of NH4+ and HPO4- groups dominate the transformation from the free hydrated ionic state to crystalline state during ADP crystallization. Anisotropic ADP crystal morphology depends on the anisotropic chemical bonding conditions along [1 0 0] and [1 0 1] directions. ADP crystal morphologies with different HPO4-n (n = 1-8) clusters can be calculated on the basis of hydrogen bonding conditions and HPO4-n cluster structures at the growth interface. Experimentally, in situ IR spectrum can record the breaking of P-O⋯H-O-H and H-N⋯H-O-H, and the formation of P-O⋯H-O-P and H-N⋯H-O-P hydrogen bonding during ADP crystallization. The present work provides a promising strategy to identify the chemical bonding nature during crystallization processes of molecular crystals from aqueous solution.

  14. Sharing in covalent and hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Perhacs, Pablo

    1998-11-01

    The sharing of a single electron between two spatial and spin coordinates ζ and ζsp/prime in a many electron system is discussed in terms of the single particle sharing amplitude, bonding is distinguished from non-bonding and anti- bonding. Molecules studied are the diatomics of seven of the first nine elements and the hydrides of the first row of eight elements. Analysis is extended to the complex of methane and hydrogen fluoride and to pairs of hydrogen fluoride, water, and ammonia. The behavior of hydrogen bonded complexes, is shown to have all the characteristics of covalent bonding. The ammonia dimer is shown not to be hydrogen bonded.

  15. Hydrogen-bond symmetrization and molecular dissociation in hydrogen halids

    NASA Astrophysics Data System (ADS)

    Aoki, K.; Katoh, E.; Yamawaki, H.; Sakashita, M.; Fujihisa, H.

    1999-04-01

    Hydrogen chloride is a simple diatomic molecule forming a planar zig-zag chain of molecules connected by hydrogen bonds in the solid phase. Raman spectra were measured for solid HCl to 60 GPa at room temperature. The molecular stretching frequency falls toward zero at about 51 GPa, where the molecular vibrational peaks disappear and the lattice peaks remain. The spectral changes are very similar to those observed for HBr at about 42 GPa and interpreted as hydrogen bond symmetrization. Molecular dissociation into diatomic halogen molecules, which has been observed for HBr, does not occur in HCl.

  16. Bifunctional hydrogen bonds in monohydrated cycloether complexes.

    PubMed

    Vallejos, Margarita M; Angelina, Emilio L; Peruchena, Nélida M

    2010-03-01

    In this work, the cooperative effects implicated in bifunctional hydrogen bonds (H-bonds) were studied (in monohydrated six-membered cycloether) within the framework of the atoms in molecules (AIM) theory and of the natural bond orbitals (NBO) analysis. The study was carried out in complexes formed by six-membered cycloether compounds (tetrahydropyrane, 1,4-dioxane, and 1,3-dioxane) and a water molecule. These compounds were used as model systems instead of more complicated molecules of biological importance. All the results were obtained at the second-order Møller-Plesset (MP2) level theory using a 6-311++G(d,p) basis set. Attention was focused on the indicators of the cooperative effects that arise when a water molecule interacts simultaneously with a polar and a nonpolar portion of a six-membered cycloether (via bifunctional hydrogen bonds) and compared with conventional H-bonds where the water molecule only interacts with the polar portion of the cycloether. Different indicators of H-bonds strength, such as structural and spectroscopic data, electron charge density, population analysis, hyperconjugation energy and charge transference, consistently showed significant cooperative effects in bifunctional H-bonds. From the AIM, as well as from the NBO analysis, the obtained results allowed us to state that in the monohydrated six-membered cycloether, where the water molecule plays a dual role, as proton acceptor and proton donor, a mutual reinforcement of the two interactions occurs. Because of this feature, the complexes engaged by bifunctional hydrogen bonds are more stabilized than the complexes linked by conventional hydrogen bonds. PMID:20136161

  17. Bond additivity corrections for quantum chemistry methods

    SciTech Connect

    C. F. Melius; M. D. Allendorf

    1999-04-01

    In the 1980's, the authors developed a bond-additivity correction procedure for quantum chemical calculations called BAC-MP4, which has proven reliable in calculating the thermochemical properties of molecular species, including radicals as well as stable closed-shell species. New Bond Additivity Correction (BAC) methods have been developed for the G2 method, BAC-G2, as well as for a hybrid DFT/MP2 method, BAC-Hybrid. These BAC methods use a new form of BAC corrections, involving atomic, molecular, and bond-wise additive terms. These terms enable one to treat positive and negative ions as well as neutrals. The BAC-G2 method reduces errors in the G2 method due to nearest-neighbor bonds. The parameters within the BAC-G2 method only depend on atom types. Thus the BAC-G2 method can be used to determine the parameters needed by BAC methods involving lower levels of theory, such as BAC-Hybrid and BAC-MP4. The BAC-Hybrid method should scale well for large molecules. The BAC-Hybrid method uses the differences between the DFT and MP2 as an indicator of the method's accuracy, while the BAC-G2 method uses its internal methods (G1 and G2MP2) to provide an indicator of its accuracy. Indications of the average error as well as worst cases are provided for each of the BAC methods.

  18. Probing the Hydrogen Bond Strength at Single Bond Limit

    NASA Astrophysics Data System (ADS)

    Guo, Jing; Lü, Jing-Tao; Chen, Ji; Peng, Jinbo; Meng, Xiangzhi; Wang, Zhichang; Li, Xin-Zheng; Wang, Enge; Jiang, Ying

    2015-03-01

    Many extraordinary physical, chemical and biological properties of water are determined by hydrogen-bonding interaction between the water molecules. So far, the routine way to determine the hydrogen-bonding strength of water is probing the frequency shift of O-H stretching mode using various spectroscopic techniques, which all suffer from the difficulty of spectral assignment and the broadening of vibrational signals due to the lack of spatial resolution. In this talk, we show the ability to probe the hydrogen-bonding strength of interfacial water at single bond limit using resonantly enhanced inelastic electron tunneling spectroscopy (IETS) with a scanning tunneling microscope (STM). The conventional IET signals of water molecules are extremely weak and far beyond the experimental detection limit due to the negligible molecular density of states (DOS) around the Fermi level. This difficulty can be surmounted by turning on the tip-water coupling, which shifts and broadens the frontier molecular orbitals of water to the proximity of Fermi level, resulting in a resonantly enhanced IET process. International Center for Quantum Materials, School of Physics, Peking University.

  19. AMHB: (Anti)aromaticity-Modulated Hydrogen Bonding.

    PubMed

    Kakeshpour, Tayeb; Wu, Judy I; Jackson, James E

    2016-03-16

    This in silico survey shows that changes in the (anti)aromatic character of π-conjugated heterocycles can be used to fine-tune their hydrogen (H-)bond strengths. Upon H-bonding dimerization, the π-electrons of these rings can be polarized to reinforce or disrupt their (anti)aromatic π-conjugated circuits (πCCs) and stabilize or destabilize the resulting H-bonded complexes. H-bonding interactions that enhance aromaticity or relieve antiaromaticity are fortified, whereas those that intensify antiaromaticity or disrupt aromaticity are weakened, relative to analogues lacking full π-circuits. Computed dissected nucleus-independent chemical shifts, NICS(1)(zz), reveal a uniform pattern and document changes in the magnetic (anti)aromatic character of the heterocycles considered. Recognition of this (anti)aromaticity-modulated H-bonding (AMHB) phenomenon offers insights into a range of fields from organocatalysis and self-assembly to pharmaceutical chemistry and molecular biology. PMID:26860619

  20. Do Hydrogen Bonds Influence Excitonic Splittings?

    PubMed

    Balmer, Franziska A; Ottiger, Philipp; Leutwyler, Samuel

    2016-01-01

    The excitonic splitting and vibronic quenching of the inversion-symmetric homodimers of benzonitrile, (BN)2, and meta-cyanophenol, (mCP)2, are investigated by two-color resonant two-photon ionization spectroscopy. These systems have very different hydrogen bond strengths: the OH···N≡C bonds in (mCP)2 are ∼10 times stronger than the CH···N≡C hydrogen bonds in (BN)2. In (BN)2 the S0((1)Ag) → S1((1)Ag) transition is electric-dipole forbidden, while the S0((1)Ag) → S2((1)Bu) transition is allowed. The opposite holds for (mCP)2 due to the different transition dipole moment vector alignment. The S0 → S1S2 spectra of the dimers are compared and their excitonic splittings and vibronic quenchings are investigated by measuring the (13)C-substituted heterodimer isotopomers, for which the centrosymmetry is broken and both transitions are allowed. The excitonic splittings are determined as Δexc = 2.1 cm(-1) for (BN)2 and Δexc = 7.3 cm(-1) for (mCP)2. The latter exhibits a much stronger vibronic quenching, as the purely electronic splitting resulting from ab initio calculations is determined to be Δcalc = 179 cm-1, while in (BN)2 the calculated splitting is Δcalc = 10 cm(-1). The monomer site-shifts upon dimerization and comparing certain vibrations that deform the hydrogen bonds confirm that the OH···N≡C hydrogen bond is much stronger than the CH···N≡C bond. We show that the H-bonds have large effects on the spectral shifts, but little or no influence on the excitonic splitting. PMID:27131115

  1. Modeling the Hydrogen Bond within Molecular Dynamics

    ERIC Educational Resources Information Center

    Lykos, Peter

    2004-01-01

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

  2. New supramolecular architectures using hydrogen bonding

    SciTech Connect

    Zimmerman, S.C.; Baloga, M.H.; Fenlon, E.E.; Murray, T.J.

    1993-12-31

    Heterocyclic compounds containing two and three adjacent hydrogen bond donor and acceptor sites in all possible arrangements have been synthesized. The strength and selectivity with which each compounds binds its complement has been determined. The incorporation of these heterocyclic subunits into large structures that form supramolecular assemblies will be described.

  3. Hydrogen bonds in methane-water clusters.

    PubMed

    Salazar-Cano, Juan-Ramón; Guevara-García, Alfredo; Vargas, Rubicelia; Restrepo, Albeiro; Garza, Jorge

    2016-08-24

    Characterization of hydrogen bonds in CH4-(H2O)12 clusters was carried out by using several quantum chemistry tools. An initial stochastic search provided around 2 500 000 candidate structures, then, using a convex-hull polygon criterion followed by gradient based optimization under the Kohn-Sham scheme, a total of 54 well defined local minima were located in the Potential Energy Surface. These structures were further analyzed through second-order many-body perturbation theory with an extended basis set at the MP2/6-311++G(d,p) level. Our analysis of Gibbs energies at several temperatures clearly suggests a structural preference toward compact water clusters interacting with the external methane molecule, instead of the more commonly known clathrate-like structures. This study shows that CH4-(H2O)12 clusters may be detected at temperatures up to 179 K, this finding provides strong support to a recently postulated hypothesis that suggests that methane-water clusters could be present in Mars at these conditions. Interestingly, we found that water to water hydrogen bonding is strengthened in the mixed clusters when compared to the isolated water dimer, which in turn leads to a weakening of the methane to water hydrogen bonding when compared to the CH4-(H2O) dimer. Finally, our evidence places a stern warning about the abilities of popular geometrical criteria to determine the existence of hydrogen bonds. PMID:27492605

  4. Recodable surfaces based on switchable hydrogen bonds.

    PubMed

    Wedler-Jasinski, Nils; Delbosc, Nicolas; Virolleaud, Marie-Alice; Montarnal, Damien; Welle, Alexander; Barner, Leonie; Walther, Andreas; Bernard, Julien; Barner-Kowollik, Christopher

    2016-07-01

    We introduce recodable surfaces solely based on reversible artificial hydrogen bonding interactions. We show that a symmetrical oligoamide (SOA) attached to poly(methyl methacrylate) (PMMA) can be repeatedly immobilized and cleaved off spatially defined surface domains photochemically functionalized with asymmetric oligoamides (AOAs). The spatially resolved recodability is imaged and quantified via ToF-SIMS. PMID:27339101

  5. Photochromic supramolecular azopolyimides based on hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Schab-Balcerzak, Ewa; Flakus, Henryk; Jarczyk-Jedryka, Anna; Konieczkowska, Jolanta; Siwy, Mariola; Bijak, Katarzyna; Sobolewska, Anna; Stumpe, Joachim

    2015-09-01

    The approach of deriving new photoresponsive active supramolecular azopolymers based on the hydrogen bonds is described. Polymers with imide rings, i.e., poly(esterimide)s and poly(etherimide)s, with phenolic hydroxyl or carboxylic groups were applied as matrixes for the polymer-dye supramolecular systems. Supramolecular films were built on the basis of the hydrogen bonds between the functional groups of the polymers and various azochromophores, that is, 4-phenylazophenol, 4-[4-(6-hydroxyhexyloxy)phenylazo]benzene, 4-[4-(6-hexadecaneoxy)phenylazo]pyridine and 4-(4-hydroxyphenylazo)pyridine. The hydrogen bonding interaction in azo-systems were studied by Fourier transform infrared spectroscopy and for selected assembles by 1H NMR technique. The obtained polyimide azo-assembles were characterized by X-ray diffraction and DSC measurements. H-bonds allow attaching a chromophore to each repeating unit of the polymer, thereby suppressing the macroscopic phase separation except for the systems based on 4-[4-(6-hydroxyhexyloxy)phenylazo]benzene. H-bonds systems were amorphous and revealed glass transition temperatures lower than for the polyimide matrixes (170-260 °C). The photoresponsive behavior of the azo-assemblies was tasted in holographic recording experiment.

  6. Supramolecular polymerisation in water; elucidating the role of hydrophobic and hydrogen-bond interactions† †Electronic supplementary information (ESI) available: Experimental details, characterization by IR and UV spectroscopy and dynamic light scattering, video files of optical microscopy imaging. See DOI: 10.1039/c5sm02843d Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file.

    PubMed Central

    Leenders, Christianus M. A.; Baker, Matthew B.; Pijpers, Imke A. B.; Lafleur, René P. M.; Albertazzi, Lorenzo

    2016-01-01

    Understanding the self-assembly of small molecules in water is crucial for the development of responsive, biocompatible soft materials. Here, a family of benzene-1,3,5-tricarboxamide (BTA) derivatives that comprise a BTA moiety connected to an amphiphilic chain is synthesised with the aim to elucidate the role of hydrophobic and hydrogen-bonding interactions in the self-assembly of these BTAs. The amphiphilic chain consists of an alkyl chain with a length of 10, 11, or 12 methylene units, connected to a tetraethylene glycol (at the periphery). The results show that an undecyl spacer is the minimum length required for these BTAs to self-assemble into supramolecular polymers. Interestingly, exchange studies reveal only minor differences in exchange rates between BTAs containing undecyl or dodecyl spacers. Additionally, IR spectroscopy provides the first experimental evidence that hydrogen-bonding is operative and contributes to the stabilisation of the supramolecular polymers in water. PMID:26892482

  7. Tunneling spectroscopy measurements on hydrogen-bonded supramolecular polymers

    NASA Astrophysics Data System (ADS)

    Vonau, François; Shokri, Roozbeh; Aubel, Dominique; Bouteiller, Laurent; Guskova, Olga; Sommer, Jens-Uwe; Reiter, Günter; Simon, Laurent

    2014-06-01

    We studied the formation of hydrogen-bonded supramolecular polymers of Ethyl Hexyl Urea Toluene (EHUT) on a gold (111) surface by low temperature scanning tunneling microscopy. Tunneling spectroscopy performed along an individual molecule embedded in a self-assembled layer revealed strong changes in the value of the HOMO-LUMO gap. A variation of the LUMO state is attributed to the effect of space charge accumulation resulting from anisotropic adhesion of the molecule. In addition, for specific tunneling conditions, changes induced through the formation of hydrogen bonds became visible in the differential conductance (dI/dV) maps; isolated molecules, hydrogen bonded dimers and supramolecular polymers of EHUT were distinguishable through their electronic properties.

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

    PubMed Central

    Habermann, S. M.; Murphy, K. P.

    1996-01-01

    Differences in the energetics of amide-amide and amide-hydroxyl hydrogen bonds in proteins have been explored from the effect of hydroxyl groups on the structure and dissolution energetics of a series of crystalline cyclic dipeptides. The calorimetrically determined energetics are interpreted in light of the crystal structures of the studied compounds. Our results indicate that the amide-amide and amide-hydroxyl hydrogen bonds both provide considerable enthalpic stability, but that the amide-amide hydrogen bond is about twice that of the amide-hydroxyl. Additionally, the interaction of the hydroxyl group with water is seen most readily in its contributions to entropy and heat capacity changes. Surprisingly, the hydroxyl group shows weakly hydrophobic behavior in terms of these contributions. These results can be used to understand the effects of mutations on the stability of globular proteins. PMID:8819156

  9. Far-Infrared Signatures of Hydrogen Bonding in Phenol Derivatives.

    PubMed

    Bakker, Daniël J; Peters, Atze; Yatsyna, Vasyl; Zhaunerchyk, Vitali; Rijs, Anouk M

    2016-04-01

    One of the most direct ways to study the intrinsic properties of the hydrogen-bond interaction is by gas-phase far-infrared (far-IR) spectroscopy because the modes involving hydrogen-bond deformation are excited in this spectral region; however, the far-IR regime is often ignored in molecular structure identification due to the absence of strong far-IR light sources and difficulty in assigning the observed modes by quantum chemical calculations. Far-IR/UV ion-dip spectroscopy using the free electron laser FELIX was applied to directly probe the intramolecular hydrogen-bond interaction in a family of phenol derivatives. Three vibrational modes have been identified, which are expected to be diagnostic for the hydrogen-bond strength: hydrogen-bond stretching and hydrogen-bond-donating and -accepting OH torsion vibrations. Their position is evaluated with respect to the hydrogen bond strength, that is, the length of the hydrogen-bonded OH length. This shows that the hydrogen bond stretching frequency is diagnostic for the size of the ring that is closed by the hydrogen bond, while the strength of the hydrogen bond can be determined from the hydrogen-bond-donating OH torsion frequency. The combination of these two normal modes allows the direct probing of intramolecular hydrogen-bond characteristics using conformation-selective far-IR vibrational spectroscopy. PMID:26982390

  10. Bond additivity corrections for quantum chemistry methods

    SciTech Connect

    Melius, C.F.; Allendorf, M.D.

    2000-03-23

    New bond additivity correction (BAC) methods have been developed for the G2 method, BAC-G2, as well as for a hybrid density functional theory (DFT) Moller-Plesset (MP)2 method, BAC-hybrid. These BAC methods use a new form of BAC corrections, involving atomic, molecular, and bond-wise additive terms. These terms enable one to treat positive and negative ions as well as neutrals. The BAC-G2 method reduces errors in the G2 method due to nearest-neighbor bonds. The parameters within the BAC-G2 method only depend on atom types. Thus the BAC-G2 method can be used to determine the parameters needed by BAC methods involving lower levels of theory, such as BAC-hybrid and BAC-MP4. The BAC-hybrid method is expected to scale well for large molecules. The BAC-hybrid method uses the differences between the DFT and MP2 predictions as an indication of the method's accuracy, whereas the BAC-G2 method uses its internal methods (G1 and G2MP2) to accomplish this. A statistical analysis of the error in each of the methods is presented on the basis of calculations performed for large sets (more than 120) of molecules.

  11. Effective Binding of Methane Using a Weak Hydrogen Bond.

    PubMed

    Henley, Alice; Bound, Michelle; Besley, Elena

    2016-05-26

    The weak hydrogen bond is an important type of noncovalent interaction, which has been shown to contribute to stability and conformation of proteins and large biochemical membranes, stereoselectivity, crystal packing, and effective gas storage in porous materials. In this work, we systematically explore the interaction of methane with a series of functionalized organic molecules specifically selected to exhibit a weak hydrogen bond with methane molecules. To enhance the strength of hydrogen bond interactions, the functional groups include electron-enriched sites to allow sufficient polarization of the C-H bond of methane. The binding between nine functionalized benzene molecules and methane has been studied using the second order Møller-Plesset perturbation theory to reveal that benzenesulfonic acid (C6H5-SO3H) and phenylphosphonic acid (C6H5-PO3H2) have the greatest potential for efficient methane capture through hydrogen bonding interactions. Both acids exhibit efficient binding potential with up to three methane molecules. For additional insight, the atomic charge distribution associated with each binding site is presented. PMID:27148999

  12. In situ modification of nanostructure configuration through the manipulation of hydrogen bonded amphiphile self-association.

    PubMed

    Hiscock, Jennifer R; Bustone, Gianluca P; Wilson, Ben; Belsey, Kate E; Blackholly, Laura R

    2016-05-14

    Herein, we report the synthesis of a novel amphiphilic salt containing a number of hydrogen bond donating (HBD) and accepting (HBA) functionalities. This amphiphile has been shown to self-associate via hydrogen bond formation in a DMSO solution, confirmed through a combination of NMR, UV-Vis and dynamic light scattering and supported by X-ray diffraction studies. The combination of different HBD and HBA functionalities within the amphiphile structure gives rise to a variety of competitive, self-associative hydrogen bonding modes that result in the formation of 'frustrated' hydrogen bonded nanostructures. These nanostructures can be altered through the addition of competitive HBD arrays and/or HBA anionic guests. The addition of these competitive species modifies the type of self-associative hydrogen bonding modes present between the amphiphilic molecules, triggering the in situ formation of novel hydrogen bonded nanostructures. PMID:27052095

  13. Formaldoxime hydrogen bonded complexes with ammonia and hydrogen chloride

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  14. Femtosecond dynamics in hydrogen-bonded solvents

    SciTech Connect

    Castner, E.W. Jr.; Chang, Y.J.

    1993-09-01

    We present results on the ultrafast dynamics of pure hydrogen-bonding solvents, obtained using femtosecond Fourier-transform optical-heterodyne-detected, Raman-induced Kerr effect spectroscopy. Solvent systems we have studied include the formamides, water, ethylene glycol, and acetic acid. Inertial and diffusive motions are clearly resolved. We comment on the effect that such ultrafast solvent motions have on chemical reactions in solution.

  15. Electrostatic model for hydrogen bonds in alcohols

    SciTech Connect

    Giguere, P.A.; Pigeon-Gosselin, M.

    1988-11-01

    The authors have measured the Raman spectra of liquid methanol at temperatures between 50/sup 0/ and -77/sup 0/C. The weak O-H stretching bands appear, under amplification, more and more asymmetric as the temperature is lowered. They can be decomposed into three Gaussian components centered at about 3220, 3310, and 3400 cm/sup -1/. The former, predominant at low temperature, corresponds to single, linear hydrogen bonds (LHB) between two molecules. The other two are assigned to branched hydrogen bonds, respectively bifurcated (BHB), between three molecules, and trifurcated (THB), between four molecules. They conclude that the molecular structure of liquid alcohols is not chain-like, as presumed so far, but a three-dimensional network featuring a mixture of single (LBH), and multiple hydrogen bonds (BHB, and THB). They are mainly electrostatic in nature, their relative proportions and geometry governed by the packing conditions for minimum energy. They form distinct trimers and tetramers in dilute solutions of alcohols in inert solvents and frozen matrices, and the latter even in the vapor.

  16. Anesthesia cutoff phenomenon: Interfacial hydrogen bonding

    SciTech Connect

    Chiou, J.S.; Ma, S.M.; Kamaya, H.; Ueda, I. )

    1990-05-04

    Anesthesia cutoff refers to the phenomenon of loss of anesthetic potency in a homologous series of alkanes and their derivatives when their sizes become too large. In this study, hydrogen bonding of 1-alkanol series (ethanol to eicosanol) to dipalmitoyl-L-alpha-phosphatidylcholine (DPPC) was studied by Fourier transform infrared spectroscopy (FTIR) in DPPC-D2O-in-CCl4 reversed micelles. The alkanols formed hydrogen bonds with the phosphate moiety of DPPC and released the DPPC-bound deuterated water, evidenced by increases in the bound O-H stretching signal of the alkanol-DPPC complex and also in the free O-D stretching band of unbound D2O. These effects increased according to the elongation of the carbon chain of 1-alkanols from ethanol (C2) to 1-decanol (C10), but suddenly almost disappeared at 1-tetradecanol (C14). Anesthetic potencies of these alkanols, estimated by the activity of brine shrimps, were linearly related to hydrogen bond-breaking activities below C10 and agreed with the FTIR data in the cutoff at C10.

  17. The CH/π hydrogen bond: Implication in chemistry

    NASA Astrophysics Data System (ADS)

    Nishio, M.

    2012-06-01

    The CH/π hydrogen bond is the weakest extreme of hydrogen bonds that occurs between a soft acid CH and a soft base π-system. Implication in chemistry of the CH/π hydrogen bond includes issues of conformation, crystal packing, and specificity in host/guest complexes. The result obtained by analyzing the Cambridge Structural Database is reviewed. The peculiar axial preference of isopropyl group in α-phellandrene and folded conformation of levopimaric acid have been explained in terms of the CH/π hydrogen bond, by high-level ab initio MO calculations. Implication of the CH/π hydrogen bond in structural biology is also discussed, briefly.

  18. Electron collisions with hydrogen-bonded complexes

    SciTech Connect

    Freitas, T. C.; Sanchez, S. d'A.; Bettega, M. H. F.; Varella, M. T. do N.

    2011-12-15

    We investigated elastic collisions of low-energy electrons with the hydrogen-bonded formic-acid dimer, formamide dimer, and formic-acid-formamide complex. We focused on how the {pi}{sup *} shape resonances of the isolated monomers are affected when bonded to another molecule. The scattering cross sections were computed with the Schwinger multichannel method with pseudopotentials in the static-exchange and static-exchange-plus-polarization approximations, for energies ranging from 1 to 6 eV. The present results support the existence of two low-lying {pi}{sup *} shape resonances for the formic-acid dimer, as suggested in previous theoretical and experimental studies. We also found low-lying {pi}{sup *} shape resonances for the formamide dimer and for the formic-acid-formamide complex. For the dimers, the presence of a center of inversion is key to understanding how these resonances arise from linear combinations of the {pi}{sup *} anion states of the respective monomers. For the formic-acid-formamide complex, the resonances are more localized on each unit, lying at lower energies with respect to the isolated monomers. The present results suggest that if there is no delocalization of the {pi}{sup *} resonances over the pair for hydrogen-bonded molecules, then their positions would lie below those of the units.

  19. Femtosecond pump-probe measurements of solvation by hydrogen-bonding interactions.

    PubMed

    Pines, Ehud; Pines, Dina; Ma, Ying-Zhong; Fleming, Graham R

    2004-09-20

    An additional ultrafast blue shift in the transient absorption spectra of hydrogen-bonding complexes of a strong photoacid, 8-hydroxypyrene 1,3,6-trisdimethylsulfonamide (HPTA), over the solvation response of the uncomplexed HPTA and also over that of the methoxy derivative of the photoacid (MPTA) in the presence of the hydrogen-bonding base was observed on optical excitation of the photoacid. The additional 55 +/- 10 fs solvation response was found to be about 35 % and 19% of the total C(t) of HPTA in dichloromethane (DCM) when it was hydrogen-bonded to dimethylsulfoxide (DMSO) and dioxane, respectively, and about 29% of the total C(t) of HPTA in dichloroethane (DCE) when it was hydrogen-bonded to DMSO. We have assigned this additional dynamic spectral shift to a transient change in the hydrogen bond (O-H...O) that links HPTA to the complexing base, after the electronic excitation of the photoacid. PMID:15499848

  20. Hydrogen bonding at the aerosol interface

    SciTech Connect

    Zhang, J.X.; Aiello, D.; Aker, P.M. )

    1995-01-12

    Morphology-dependent stimulated Raman scattering (MDSRS) has been used to monitor the degree of hydrogen bonding in water aerosols generated by a vibrating orifice aerosol generator (VOAG). The results show that aerosols created by a VOAG suffer extensive structural disruption and that the disruption is most pronounced at the aerosol surface. Laboratory aerosols prepared in this way do not appropriately mimic those found in the atmosphere, and the mass accommodation coefficients measured using such aerosols should not be used in global climate modeling calculations. 25 refs., 10 figs.

  1. An optimal hydrogen-bond surrogate for α-helices.

    PubMed

    Joy, Stephen T; Arora, Paramjit S

    2016-04-14

    Substitution of a main chain i → i + 4 hydrogen bond with a covalent bond can nucleate and stabilize the α-helical conformation in peptides. Herein we describe the potential of different alkene isosteres to mimic intramolecular hydrogen bonds and stabilize α-helices in diverse peptide sequences. PMID:27046675

  2. 30 CFR 256.53 - Additional bonds.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Resources BUREAU OF OCEAN ENERGY MANAGEMENT, REGULATION, AND ENFORCEMENT, DEPARTMENT OF THE INTERIOR... commence. (1)(i) You must furnish the Regional Director a $200,000 bond that guarantees compliance with all... approved. (ii) The Regional Director may authorize you to submit the $200,000 lease exploration bond...

  3. Tetrahedrality and hydrogen bonds in water

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  4. Water's dual nature and its continuously changing hydrogen bonds.

    PubMed

    Henchman, Richard H

    2016-09-28

    A model is proposed for liquid water that is a continuum between the ordered state with predominantly tetrahedral coordination, linear hydrogen bonds and activated dynamics and a disordered state with a continuous distribution of multiple coordinations, multiple types of hydrogen bond, and diffusive dynamics, similar to that of normal liquids. Central to water's heterogeneous structure is the ability of hydrogen to donate to either one acceptor in a conventional linear hydrogen bond or to multiple acceptors as a furcated hydrogen. Linear hydrogen bonds are marked by slow, activated kinetics for hydrogen-bond switching to more crowded acceptors and sharp first peaks in the hydrogen-oxygen radial distribution function. Furcated hydrogens, equivalent to free, broken, dangling or distorted hydrogens, have barrierless, rapid kinetics and poorly defined first peaks in their hydrogen-oxygen radial distribution function. They involve the weakest donor in a local excess of donors, such that barrierless whole-molecule vibration rapidly swaps them between the linear and furcated forms. Despite the low number of furcated hydrogens and their transient existence, they are readily created in a single hydrogen-bond switch and free up the dynamics of numerous surrounding molecules, bringing about the disordered state. Hydrogens in the ordered state switch with activated dynamics to make the non-tetrahedral coordinations of the disordered state, which can also combine to make the ordered state. Consequently, the ordered and disordered states are both connected by diffusive dynamics and differentiated by activated dynamics, bringing about water's continuous heterogeneity. PMID:27447299

  5. Hydrogen Bond Basicity Prediction for Medicinal Chemistry Design.

    PubMed

    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. PMID:26872049

  6. Negligible Isotopic Effect on Dissociation of Hydrogen Bonds.

    PubMed

    Ge, Chuanqi; Shen, Yuneng; Deng, Gang-Hua; Tian, Yuhuan; Yu, Dongqi; Yang, Xueming; Yuan, Kaijun; Zheng, Junrong

    2016-03-31

    Isotopic effects on the formation and dissociation kinetics of hydrogen bonds are studied in real time with ultrafast chemical exchange spectroscopy. The dissociation time of hydrogen bond between phenol-OH and p-xylene (or mesitylene) is found to be identical to that between phenol-OD and p-xylene (or mesitylene) in the same solvents. The experimental results demonstrate that the isotope substitution (D for H) has negligible effects on the hydrogen bond kinetics. DFT calculations show that the isotope substitution does not significantly change the frequencies of vibrational modes that may be along the hydrogen bond formation and dissociation coordinate. The zero point energy differences of these modes between hydrogen bonds with OH and OD are too small to affect the activation energy of the hydrogen bond dissociation in a detectible way at room temperature. PMID:26967376

  7. Hydrogen Bond Nanoscale Networks Showing Switchable Transport Performance

    NASA Astrophysics Data System (ADS)

    Long, Yong; Hui, Jun-Feng; Wang, Peng-Peng; Xiang, Guo-Lei; Xu, Biao; Hu, Shi; Zhu, Wan-Cheng; Lü, Xing-Qiang; Zhuang, Jing; Wang, Xun

    2012-08-01

    Hydrogen bond is a typical noncovalent bond with its strength only one-tenth of a general covalent bond. Because of its easiness to fracture and re-formation, materials based on hydrogen bonds can enable a reversible behavior in their assembly and other properties, which supplies advantages in fabrication and recyclability. In this paper, hydrogen bond nanoscale networks have been utilized to separate water and oil in macroscale. This is realized upon using nanowire macro-membranes with pore sizes ~tens of nanometers, which can form hydrogen bonds with the water molecules on the surfaces. It is also found that the gradual replacement of the water by ethanol molecules can endow this film tunable transport properties. It is proposed that a hydrogen bond network in the membrane is responsible for this switching effect. Significant application potential is demonstrated by the successful separation of oil and water, especially in the emulsion forms.

  8. Interpretation of Spectroscopic Markers of Hydrogen Bonds.

    PubMed

    Scheiner, Steve

    2016-07-18

    Quantum calculations are used to examine whether an AH⋅⋅⋅D H-bond is unambiguously verified by a downfield shift of the bridging proton's NMR signal or a red (or blue) shift of the AH stretching frequency in the IR spectrum. It is found that such IR band shifts will occur even if the two groups experience weak or no attractive force, or if they are drawn in so close together that their interaction is heavily repulsive. The mere presence of a proton-acceptor molecule can affect the chemical shielding of a position occupied by a protondonor by virtue of its electron density, even if there is no H-bond present. This density-induced shielding is heavily dependent on position around the proton-acceptor atom, and varies from one group to another. Evidence of a hydrogen bond rests on the measurement of a proton deshielding in excess of what is caused purely by the presence of the proton acceptor species. PMID:27043717

  9. Pyranose sulfamates: conformation and hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Kubicki, Maciej; Codding, Penelope W.; Litster, Stephen A.; Szkaradziñska, Maria B.; Bassyouni, Hanan A. R.

    1999-01-01

    The crystal structure of a new anticonvulsant drug, topiramate — 2,3:4,5-bis- O-(1-methylethylidene)- β-D-fructopyranose sulfamate ( 1), together with those of three similar but biologically almost inactive sugar sulfamates: 4,5- O-cyclohexylidene-2,3- O-(1-methyl-ethylidene)- β-D-fructopyranose sulfamate ( 2), 2,3:- O-(1-methylethylidene)- β-D-fructo-pyranose sulfamate ( 3), and 1,2:3,4-bis- O-(1-methylethylidene)- α-D-galactopyranose sulfamate ( 4), have been determined by X-rays. The pyranose rings adopt distorted twist-boat 2S O conformations as a result of flattening of the chair conformation, observed in free pyranoses, by the fused five-membered ring(s). In 3 an unfavourable gauche-trans conformation about C1-C2 bond is observed. The active compound, topiramate ( 1), shows, in comparison with the other three compounds, a different disposition of nitrogen and oxygen atoms from the sulfamate group with respect to the O1-S1 bond. As a result, the nitrogen atom in 1 is ca. 1 Å farther from the O6 pyranose ring oxygen atom than in the other three compounds. This difference describes the mutual disposition of the hydrophilic and hydrophobic parts of the molecule, and can be related to the difference in biological activity. In all compounds, hydrogen bonds connect molecules into three-dimensional networks; simple chains and more complicated rings are found and described using the graph set notation.

  10. Hydrogen bonding on the surface of poly(2-methoxyethyl acrylate).

    PubMed

    Li, Guifeng; Ye, Shen; Morita, Shigeaki; Nishida, Takuma; Osawa, Masatoshi

    2004-10-01

    Hydrogen bonding on the interface and in the bulk of a poly(2-methoxyethyl acrylate) (PMEA) thin film has been investigated by sum frequency generation, infrared reflection absorption, and Raman scattering measurements in different kinds of solutions containing hydrogen-bonding donators. These results indicate that the majority of the carbonyl groups on the PMEA surface are hydrogen-bonded with water or ethanol molecules, while the PMEA bulk is still dominated by the free carbonyl group. PMID:15453716

  11. n→π* Interactions Are Competitive with Hydrogen Bonds.

    PubMed

    Newberry, Robert W; Orke, Samuel J; Raines, Ronald T

    2016-08-01

    Because carbonyl groups can participate in both hydrogen bonds and n→π* interactions, these two interactions likely affect one another. Herein, enhancement of an amidic n→π* interaction is shown to reduce the ability of β-keto amides to tautomerize to the enol, indicating decreased hydrogen-bonding capacity of the amide carbonyl group. Thus, an n→π* interaction can have a significant effect on the strength of a hydrogen bond to the same carbonyl group. PMID:27409515

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  13. Hydrogen bonds in concreto and in computro

    NASA Astrophysics Data System (ADS)

    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.

  14. Intramolecular Hydrogen Bonding in Benzoxazines: When Structural Design Becomes Functional.

    PubMed

    Froimowicz, Pablo; Zhang, Kan; Ishida, Hatsuo

    2016-02-18

    The future evolution of benzoxazines and polybenzoxazines as advanced molecular, structural, functional, engineering, and newly commercial materials depends to a great extent on a deeper and more fundamental understanding at the molecular level. In this contribution, the field of benzoxazines is briefly introduced along with a more detailed review of ortho-amide-functional benzoxazines, which are the main subjects of this article. Provided in this article are the detailed and solid scientific evidences of intramolecular five-membered-ring hydrogen bonding, which is supposed to be responsible for the unique and characteristic features exhibited by this ever-growing family of ortho-functionalized benzoxazines. One-dimensional (1D) (1)H NMR spectroscopy was used to study various concentrations of benzoxazines in various solvents with different hydrogen-bonding capability and at various temperatures to investigate in detail the nature of hydrogen bonding in both ortho-amide-functionalized benzoxazine and its para counterpart. These materials were further investigated by two-dimensional (2D) (1)H-(1)H nuclear Overhauser effect spectroscopy (NOESY) to verify and support the conclusions derived during the 1D (1)H NMR experiments. Only highly purified single-crystal benzoxazine samples have been used for this study to avoid additional interactions caused by any impurities. PMID:26797690

  15. Hydrogen-Bonded Liquid Crystal Nanocomposites.

    PubMed

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

    2016-08-23

    Nanoparticle-liquid crystal (NP-LC) composites based on hydrogen bonding were explored using a model system. The ligand shells of 3 nm diameter zirconium dioxide nanoparticles (ZrO2 NPs) were varied to control their interaction with 4-n-hexylbenzoic acid (6BA). The miscibility and effect of the NPs on the nematic order as a function of particle concentration was characterized by polarized optical microscopy (POM), fluorescence microscopy and (2)H NMR spectroscopy. Nonfunctionalized ZrO2 NPs have the lowest miscibility and strongest effect on the LC matrix due to irreversible binding of 6BA to the NPs via a strong zirconium carboxylate bond. The ZrO2 NPs were functionalized with 6-phosphonohexanoic acid (6PHA) or 4-(6-phosphonohexyloxy)benzoic acid (6BPHA) which selectively bind to the ZrO2 NP surface via the phosphonic acid groups. The miscibility was increased by controlling the concentration of the pendant CO2H groups by adding hexylphosphonic acid (HPA) to act as a spacer group. Fluorescence microscopy of lanthanide doped ZrO2 NPs showed no aggregates in the nematic phase below the NP concentration where aggregates are observed in the isotropic phase. The functionalized NPs preferably concentrate into LC defects and any remaining isotropic liquid but are still present throughout the nematic liquid at a lower concentration. PMID:27466705

  16. Measuring Electrostatic Fields in Both Hydrogen Bonding and non-Hydrogen Bonding Environments using Carbonyl Vibrational Probes

    PubMed Central

    Fried, Stephen D.; Bagchi, Sayan; Boxer, Steven G.

    2013-01-01

    Vibrational probes can provide a direct read-out of the local electrostatic field in complex molecular environments, such as protein binding sites and enzyme active sites. This information provides an experimental method to explore the underlying physical causes of important biomolecular processes such as binding and catalysis. However, specific chemical interactions such as hydrogen bonds can have complicated effects on vibrational probes and confound simple electrostatic interpretations of their frequency shifts. We employ vibrational Stark spectroscopy along with infrared spectroscopy of carbonyl probes in different solvent environments and in Ribonuclease S to understand the sensitivity of carbonyl frequencies to electrostatic fields, including those due to hydrogen bonds. Additionally, we carried out molecular dynamics simulations to calculate ensemble-averaged electric fields in solvents and in Ribonuclease S, and found excellent correlation between calculated fields and vibrational frequencies. These data enabled the construction of a robust field-frequency calibration curve for the C=O vibration. The present results suggest that carbonyl probes are capable of quantitatively assessing the electrostatics of hydrogen bonding, making them promising for future study of protein function. PMID:23808481

  17. Intramolecular Charge-Assisted Hydrogen Bond Strength in Pseudochair Carboxyphosphate

    PubMed Central

    2015-01-01

    Carboxyphosphate, a suspected intermediate in ATP-dependent carboxylases, has not been isolated nor observed directly by experiment. Consequently, little is known concerning its structure, stability, and ionization state. Recently, carboxyphosphate as either a monoanion or dianion has been shown computationally to adopt a novel pseudochair conformation featuring an intramolecular charge-assisted hydrogen bond (CAHB). In this work, additive and subtractive correction schemes to the commonly employed open–closed method are used to estimate the strength of the CAHB. Truhlar’s Minnesota M06-2X functional with Dunning’s aug-cc-pVTZ basis set has been used for geometry optimization, energy evaluation, and frequency analysis. The CHARMM force field has been used to approximate the Pauli repulsive terms in the closed and open forms of carboxyphosphate. From our additive correction scheme, differential Pauli repulsion contributions between the pseudochair (closed) and open conformations of carboxyphosphate are found to be significant in determining the CAHB strength. The additive correction modifies the CAHB prediction (ΔEclosed–open) of −14 kcal/mol for the monoanion and −12 kcal/mol for the dianion to −22.9 and −18.4 kcal/mol, respectively. Results from the subtractive technique reinforce those from our additive procedure, where the predicted CAHB strength ranges from −17.8 to −25.4 kcal/mol for the monoanion and from −15.7 to −20.9 kcal/mol for the dianion. Ultimately, we find that the CAHB in carboxyphosphate meets the criteria for short-strong hydrogen bonds. However, carboxyphosphate has a unique energy profile that does not result in the symmetric double-well behavior of low-barrier hydrogen bonds. These findings provide deeper insight into the pseudochair conformation of carboxyphosphate, and lead to an improved mechanistic understanding of this intermediate in ATP-dependent carboxylases. PMID:25405523

  18. Hydrogen bonding in phytohormone-auxin (IAA) and its derivatives

    NASA Astrophysics Data System (ADS)

    Kojić-Prodić, Biserka; Kroon, Jan; Puntarec, Vitomir

    1994-06-01

    The significant importance of hydrogen bonds in biological structures and enzymatic reactions has been demonstrated in many examples. As a part of the molecular recognition study of auxins (plant growth hormones) the influence of hydrogen bonding on molecular conformation, particularly of the carboxyl group, which is one of the biologically active ligand sites, has been studied by X-ray diffraction and computational chemistry methods. The survey includes about 40 crystal structures of free auxins such as indol-3-ylacetic acid and its n-alkylated and halogenated derivatives but also bound auxins such as N-(indol-3-ylacetyl)- L-amino acids, and carbohydrate conjugates. The study includes hydrogen bonds of the NH⋯O and OH⋯O types. The classification of hydrogen bond patterns based on the discrimination between the centrosymmetric and non-centrosymmetric space groups and several examples of hydrogen bond systematics on graph set analysis are also shown.

  19. Universal prediction of intramolecular hydrogen bonds in organic crystals.

    PubMed

    Galek, Peter T A; Fábián, László; Allen, Frank H

    2010-04-01

    A complete exploration of intramolecular hydrogen bonds (IHBs) has been undertaken using a combination of statistical analyses of the Cambridge Structural Database and computation of ab initio interaction energies for prototypical hydrogen-bonded fragments. Notable correlations have been revealed between computed energies, hydrogen-bond geometries, donor and acceptor chemistry, and frequencies of occurrence. Significantly, we find that 95% of all observed IHBs correspond to the five-, six- or seven-membered rings. Our method to predict a propensity for hydrogen-bond occurrence in a crystal has been adapted for such IHBs, applying topological and chemical descriptors derived from our findings. In contrast to intermolecular hydrogen bonding, it is found that IHBs can be predicted across the complete chemical landscape from a single optimized probability model, which is presented. Predictivity of 85% has been obtained for generic organic structures, which can exceed 90% for discrete classes of IHB. PMID:20305358

  20. Hydrogen bonding of water-ethanol in alcoholic beverages.

    PubMed

    Nose, Akira; Hojo, Masashi

    2006-10-01

    An alcoholic beverage is a type of water-ethanol solution with flavor and taste. The properties of the hydrogen bonding of water-ethanol in alcoholic beverages have not been clarified sufficiently. We investigated factors that could affect the hydrogen-bonding structure of water-ethanol on the basis of proton nuclear magnetic resonance (1H NMR) chemical shifts of the OH of water-ethanol and Raman OH stretching spectra. Not only acids (H+ and HA: undissociated acids) but also bases (OH- and A-: conjugate-base anions from weak acids) strengthened the hydrogen-bonding structure of water-ethanol. It was also demonstrated that the hydrogen bonding is strengthened by chemical components in alcoholic beverages (whiskey, Japanese sake, shochu). It can be suggested that hydrogen-bonding donors as well as acceptors in alcohol beverages, which exist as the initial components or are gained later on, should cause the tight association between water and ethanol molecules. PMID:17116572

  1. New Phases of Hydrogen-Bonded Systems at Extreme Conditions

    SciTech Connect

    Manaa, M R; Goldman, N; Fried, L E

    2006-10-23

    We study the behavior of hydrogen-bonded systems under high-pressure and temperature. First principle calculations of formic acid under isotropic pressure up to 70 GPa reveal the existence of a polymerization phase at around 20 GPa, in support of recent IR, Raman, and XRD experiments. In this phase, covalent bonding develops between molecules of the same chain through symmetrization of hydrogen bonds. We also performed molecular dynamics simulations of water at pressures up to 115 GPa and 2000 K. Along this isotherm, we are able to define three different phases. We observe a molecular fluid phase with superionic diffusion of the hydrogens for pressure 34 GPa to 58 GPa. We report a transformation to a phase dominated by transient networks of symmetric O-H hydrogen bonds at 95-115 GPa. As in formic acid, the network can be attributed to the symmetrization of the hydrogen bond, similar to the ice VII to ice X transition.

  2. Molecular orbital analysis of the hydrogen bonded water dimer

    NASA Astrophysics Data System (ADS)

    Wang, Bo; Jiang, Wanrun; Dai, Xin; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin

    2016-02-01

    As an essential interaction in nature, hydrogen bonding plays a crucial role in many material formations and biological processes, requiring deeper understanding. Here, using density functional theory and post-Hartree-Fock methods, we reveal two hydrogen bonding molecular orbitals crossing the hydrogen-bond’s O and H atoms in the water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. Our finding sheds light on the essential understanding of hydrogen bonding in ice, liquid water, functional materials and biological systems.

  3. Molecular orbital analysis of the hydrogen bonded water dimer

    PubMed Central

    Wang, Bo; Jiang, Wanrun; Dai, Xin; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin

    2016-01-01

    As an essential interaction in nature, hydrogen bonding plays a crucial role in many material formations and biological processes, requiring deeper understanding. Here, using density functional theory and post-Hartree-Fock methods, we reveal two hydrogen bonding molecular orbitals crossing the hydrogen-bond’s O and H atoms in the water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. Our finding sheds light on the essential understanding of hydrogen bonding in ice, liquid water, functional materials and biological systems. PMID:26905305

  4. Hydrogen bonds and antiviral activity of benzaldehyde derivatives

    NASA Astrophysics Data System (ADS)

    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.

  5. New Insights into Hydrogen Bonding and Stacking Interactions in Cellulose

    SciTech Connect

    Langan, Paul

    2011-01-01

    In this quantum chemical study, we explore hydrogen bonding (H-bonding) and stacking interactions in different crystalline cellulose allomorphs, namely cellulose I and cellulose IIII. We consider a model system representing a cellulose crystalline core, made from six cellobiose units arranged in three layers with two chains per layer. We calculate the contributions of intrasheet and intersheet interactions to the structure and stability in both cellulose I and cellulose IIII crystalline cores. Reference structures for this study were generated from molecular dynamics simulations of water-solvated cellulose I and IIII fibrils. A systematic analysis of various conformations describing different mutual orientations of cellobiose units is performed using the hybrid density functional theory (DFT) with the M06-2X with 6-31+G (d, p) basis sets. We dissect the nature of the forces that stabilize the cellulose I and cellulose IIII crystalline cores and quantify the relative strength of H-bonding and stacking interactions. Our calculations demonstrate that individual H-bonding interactions are stronger in cellulose I than in cellulose IIII. We also observe a significant contribution from cooperative stacking interactions to the stabilization of cellulose I . In addition, the theory of atoms-in-molecules (AIM) has been employed to characterize and quantify these intermolecular interactions. AIM analyses highlight the role of nonconventional CH O H-bonding in the cellulose assemblies. Finally, we calculate molecular electrostatic potential maps for the cellulose allomorphs that capture the differences in chemical reactivity of the systems considered in our study.

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

    PubMed

    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. PMID:27401347

  7. Red-Shifting versus Blue-Shifting Hydrogen Bonds: Perspective from Ab Initio Valence Bond Theory.

    PubMed

    Chang, Xin; Zhang, Yang; Weng, Xinzhen; Su, Peifeng; Wu, Wei; Mo, Yirong

    2016-05-01

    Both proper, red-shifting and improper, blue-shifting hydrogen bonds have been well-recognized with enormous experimental and computational studies. The current consensus is that there is no difference in nature between these two kinds of hydrogen bonds, where the electrostatic interaction dominates. Since most if not all the computational studies are based on molecular orbital theory, it would be interesting to gain insight into the hydrogen bonds with modern valence bond (VB) theory. In this work, we performed ab initio VBSCF computations on a series of hydrogen-bonding systems, where the sole hydrogen bond donor CF3H interacts with ten hydrogen bond acceptors Y (═NH2CH3, NH3, NH2Cl, OH(-), H2O, CH3OH, (CH3)2O, F(-), HF, or CH3F). This series includes four red-shifting and six blue-shifting hydrogen bonds. Consistent with existing findings in literature, VB-based energy decomposition analyses show that electrostatic interaction plays the dominating role and polarization plays the secondary role in all these hydrogen-bonding systems, and the charge transfer interaction, which denotes the hyperconjugation effect, contributes only slightly to the total interaction energy. As VB theory describes any real chemical bond in terms of pure covalent and ionic structures, our fragment interaction analysis reveals that with the approaching of a hydrogen bond acceptor Y, the covalent state of the F3C-H bond tends to blue-shift, due to the strong repulsion between the hydrogen atom and Y. In contrast, the ionic state F3C(-) H(+) leads to the red-shifting of the C-H vibrational frequency, owing to the attraction between the proton and Y. Thus, the relative weights of the covalent and ionic structures essentially determine the direction of frequency change. Indeed, we find the correlation between the structural weights and vibrational frequency changes. PMID:27074500

  8. Intramolecular Hydrogen Bonds in Low-Molecular-Weight Polyethylene Glycol.

    PubMed

    Kozlowska, Mariana; Goclon, Jakub; Rodziewicz, Pawel

    2016-04-18

    We used static DFT calculations to analyze, in detail, the intramolecular hydrogen bonds formed in low-molecular-weight polyethylene glycol (PEG) with two to five repeat subunits. Both red-shifted O-H⋅⋅⋅O and blue-shifting C-H⋅⋅⋅O hydrogen bonds, which control the structural flexibility of PEG, were detected. To estimate the strength of these hydrogen bonds, the quantum theory of atoms in molecules was used. Car-Parrinello molecular dynamics simulations were used to mimic the structural rearrangements and hydrogen-bond breaking/formation in the PEG molecule at 300 K. The time evolution of the H⋅⋅⋅O bond length and valence angles of the formed hydrogen bonds were fully analyzed. The characteristic hydrogen-bonding patterns of low-molecular-weight PEG were described with an estimation of their lifetime. The theoretical results obtained, in particular the presence of weak C-H⋅⋅⋅O hydrogen bonds, could serve as an explanation of the PEG structural stability in the experimental investigation. PMID:26864943

  9. Are aromatic carbon donor hydrogen bonds linear in proteins?

    PubMed

    Nanda, Vikas; Schmiedekamp, Ann

    2008-02-01

    Proteins fold and maintain structure through the collective contributions of a large number of weak, noncovalent interactions. The hydrogen bond is one important category of forces that acts on very short distances. As our knowledge of protein structure continues to expand, we are beginning to appreciate the role that weak carbon-donor hydrogen bonds play in structure and function. One property that differentiates hydrogen bonds from other packing forces is propensity for forming a linear donor-hydrogen-acceptor orientation. To ascertain if carbon-donor hydrogen bonds are able to direct acceptor linearity, we surveyed the geometry of interactions specifically involving aromatic sidechain ring carbons in a data set of high resolution protein structures. We found that while donor-acceptor distances for most carbon donor hydrogen bonds were tighter than expected for van der Waals packing, only the carbons of histidine showed a significant bias for linear geometry. By categorizing histidines in the data set into charged and neutral sidechains, we found only the charged subset of histidines participated in linear interactions. B3LYP/6-31G**++ level optimizations of imidazole and indole-water interactions at various fixed angles demonstrates a clear orientation dependence of hydrogen bonding capacity for both charged and neutral sidechains. We suggest that while all aromatic carbons can participate in hydrogen bonding, only charged histidines are able to overcome protein packing forces and enforce linear interactions. The implications for protein modeling and design are discussed. PMID:17705268

  10. Characteristics of hydrogen bond revealed from water clusters

    NASA Astrophysics Data System (ADS)

    Song, Yan; Chen, Hongshan; Zhang, Cairong; Zhang, Yan; Yin, Yuehong

    2014-09-01

    The hydrogen bond network is responsible for the exceptional physical and chemical properties of water, however, the description of hydrogen bond remains a challenge for the studies of condensed water. The investigation of structural and binding properties of water clusters provides a key for understanding the H-bonds in bulk water. In this paper, a new set of geometric parameters are defined to describe the extent of the overlap between the bonding orbital of the donor OH and the nonbonding orbital of the lone-pair of the acceptor molecule. This orbital overlap plays a dominant role for the strength of H-bonds. The dependences of the binding energy of the water dimer on these parameters are studied. The results show that these parameters properly describe the H-bond strength. The ring, book, cage and prism isomers of water hexamer form 6, 7, 8 and 9 H-bonds, and the strength of the bonding in these isomers changes markedly. The internally-solvated and the all-surface structures of (H2O) n for n = 17, 19 and 21 are nearly isoenergetic. The internally-solvated isomers form fewer but stronger H-bonds. The hydrogen bonding in the above clusters are investigated in detail. The geometric parameters can well describe the characters of the H-bonds, and they correlate well with the H-bond strength. For the structures forming stronger H-bonds, the H-bond lengths are shorter, the angle parameters are closer to the optimum values, and their rms deviations are smaller. The H-bonds emanating from DDAA and DDA molecules as H-donor are relatively weak. The vibrational spectra of (H2O) n ( n = 17, 19 and 21) are studied as well. The stretching vibration of the intramolecular OH bond is sensitive to its bonding environment. The H-bond strength judged from the geometric parameters is in good agreement with the bonding strength judged from the stretching frequencies.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  12. 4-Oxocyclohexanecarboxylic acid: hydrogen bonding in the monohydrate of a delta-keto acid.

    PubMed

    Barcon, Alan; Brunskill, Andrew P J; Thompson, Hugh W; Lalancette, Roger A

    2004-02-01

    The title monohydrate, C(7)H(10)O(3).H(2)O, aggregates as a complex hydrogen-bonding network, in which the water molecule accepts a hydrogen bond from the carboxyl group of one molecule and donates hydrogen bonds to ketone and carboxyl C=O functions in two additional molecules, yielding a sheet-like structure of parallel ribbons. The keto acid adopts a chiral conformation through rotation of the carboxyl group by 62.50 (15) degrees relative to the plane defined by its point of attachment and the ketone C and O atoms. Two C-H.O close contacts exist in the structure. PMID:14767139

  13. Dynamics of Hydrogen-Bonded Supramolecular Polymers

    NASA Astrophysics Data System (ADS)

    Buhler, Eric; Candau, Jean; Kolomiets, Elena; Lehn, Jean-Marie

    2010-03-01

    Supramolecular polymers formed from molecular recognition directed association between monomers bearing complementary hydrogen bonding groups were studied by rheology, small-angle neutron and light scattering experiments. The semiflexible fibers consist of few aggregated monomolecular wires. At T= 25 C the formation of branched aggregates occurs around the crossover concentration, C^*, between the dilute and semi-dilute regimes, whereas the classical behaviour of equilibrium polymers is observed at T=65 C. For semi-dilute solutions the steady-state flow curves showed a shear banding type instability, namely the occurrence of a stress plateau σp above a critical shear rate γ̂c. The values of σp and γ̂c were found to be of the same order of magnitude as those of the elastic plateau modulus and the inverse stress relaxation time, respectively. The above features are in agreement with the theoretical predictions based on the reptation model. Dynamic light scattering experiments showed the presence in the autocorrelation function of the concentration fluctuations of a slow viscoelastic relaxation process that is likely to be of Rouse type.

  14. Hydrogen-Bonding Surfaces for Ice Mitigation

    NASA Technical Reports Server (NTRS)

    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.

  15. Synthesis and characterization of hydrogen-bond acidic functionalized graphene

    NASA Astrophysics Data System (ADS)

    Yang, Liu; Han, Qiang; Pan, Yong; Cao, Shuya; Ding, Mingyu

    2014-05-01

    Hexafluoroisopropanol phenyl group functionalized materials have great potential in the application of gas-sensitive materials for nerve agent detection, due to the formation of strong hydrogen-bonding interactions between the group and the analytes. In this paper, take full advantage of ultra-large specific surface area and plenty of carbon-carbon double bonds and hexafluoroisopropanol phenyl functionalized graphene was synthesized through in situ diazonium reaction between -C=C- and p-hexafluoroisopropanol aniline. The identity of the as-synthesis material was confirmed by transmission electron microscopy, Raman spectroscopy, ultraviolet visible spectroscopy, X-ray photoelectron spectroscopy and thermo gravimetric analysis. The synthesis method is simply which retained the excellent physical properties of original graphene. In addition, the novel material can be assigned as an potential candidate for gas sensitive materials towards organophosphorus nerve agent detection.

  16. Direct observation of intermolecular interactions mediated by hydrogen bonding

    NASA Astrophysics Data System (ADS)

    De Marco, Luigi; Thämer, Martin; Reppert, Mike; Tokmakoff, Andrei

    2014-07-01

    Although intermolecular interactions are ubiquitous in physicochemical phenomena, their dynamics have proven difficult to observe directly, and most experiments rely on indirect measurements. Using broadband two-dimensional infrared spectroscopy (2DIR), we have measured the influence of hydrogen bonding on the intermolecular vibrational coupling between dimerized N-methylacetamide molecules. In addition to strong intramolecular coupling between N-H and C=O oscillators, cross-peaks in the broadband 2DIR spectrum appearing upon dimerization reveal strong intermolecular coupling that changes the character of the vibrations. In addition, dimerization changes the effects of intramolecular coupling, resulting in Fermi resonances between high and low-frequency modes. These results illustrate how hydrogen bonding influences the interplay of inter- and intramolecular vibrations, giving rise to correlated nuclear motions and significant changes in the vibrational structure of the amide group. These observations have direct impact on modeling and interpreting the IR spectra of proteins. In addition, they illustrate a general approach to direct molecular characterization of intermolecular interactions.

  17. Direct observation of intermolecular interactions mediated by hydrogen bonding

    SciTech Connect

    De Marco, Luigi; Reppert, Mike; Thämer, Martin; Tokmakoff, Andrei

    2014-07-21

    Although intermolecular interactions are ubiquitous in physicochemical phenomena, their dynamics have proven difficult to observe directly, and most experiments rely on indirect measurements. Using broadband two-dimensional infrared spectroscopy (2DIR), we have measured the influence of hydrogen bonding on the intermolecular vibrational coupling between dimerized N-methylacetamide molecules. In addition to strong intramolecular coupling between N–H and C=O oscillators, cross-peaks in the broadband 2DIR spectrum appearing upon dimerization reveal strong intermolecular coupling that changes the character of the vibrations. In addition, dimerization changes the effects of intramolecular coupling, resulting in Fermi resonances between high and low-frequency modes. These results illustrate how hydrogen bonding influences the interplay of inter- and intramolecular vibrations, giving rise to correlated nuclear motions and significant changes in the vibrational structure of the amide group. These observations have direct impact on modeling and interpreting the IR spectra of proteins. In addition, they illustrate a general approach to direct molecular characterization of intermolecular interactions.

  18. 48 CFR 28.106-3 - Additional bond and security.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... security. 28.106-3 Section 28.106-3 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION... Additional bond and security. (a) When additional bond coverage is required and is secured in whole or in... described in 28.204 in lieu of corporate or individual surety, agencies shall use Standard Form...

  19. 48 CFR 28.106-3 - Additional bond and security.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... security. 28.106-3 Section 28.106-3 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION... Additional bond and security. (a) When additional bond coverage is required and is secured in whole or in... described in 28.204 in lieu of corporate or individual surety, agencies shall use Standard Form...

  20. The role of hydrogen bonding in tethered polymer layers

    PubMed Central

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

    2009-01-01

    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 ethylene oxide (PEO) and the predictions are compared with equivalent polymer layers that do not form hydrogen bonds. It is found that increasing the temperature lowers the solubility of the PEO and results in a collapse of the layer at high enough temperatures. The properties of the layer and their temperature dependence are shown to be the result of the coupling between the conformational entropy of the chains, the ability of the polymer to form hydrogen bonds, and the intermolecular interactions. The structural and thermodynamic properties of the PEO layers, such as the lateral pressure-area isotherms and polymer chemical potentials, are studied as a function of temperature and type of tethering surface. The possibility of phase separation of the PEO layer at high enough temperature is predicted, due to the reduced solubility induced by breaking of polymer-water hydrogen bonds. A discussion of the advantages and limitations of the theory, together with how to apply the approach to different hydrogen bonding polymers is presented. PMID:19367906

  1. Sugar-polymer hydrogen bond interactions in lyophilized amorphous mixtures.

    PubMed

    Taylor, L S; Zografi, G

    1998-12-01

    The objective of this work was to investigate hydrogen bonding interactions between a variety of glass-forming sugars and a model polymer, poly(vinylpyrrolidone) (PVP), in binary amorphous solid solutions, produced by lyophilization. The glass transition temperatures of the sugars and sugar-PVP colyophilized mixtures were assessed using differential scanning calorimetry. The hydrogen bonding interactions between each sugar and PVP were monitored using FT-Raman spectroscopy. Sucrose was found to hydrogen bond to a greater extent with PVP at a particular sugar:polymer ratio than the other disaccharides studied including trehalose and the trisaccharide raffinose. Maltodextrins showed a decreased tendency to hydrogen bond with the polymer compared to the lower molecular weight sugars. The extent of hydrogen bonding was found to correlate inversely with the glass transition temperature of the sugar, with the tendency to hydrogen bond decreasing as the Tg increased. The importance of hydrogen bonding interactions to the thermodynamics of mixing in amorphous solids is discussed. PMID:10189276

  2. Complexes between hypohalous acids and phosphine derivatives. Pnicogen bond versus halogen bond versus hydrogen bond

    NASA Astrophysics Data System (ADS)

    Li, Qingzhong; Zhu, Hongjie; Zhuo, Hongying; Yang, Xin; Li, Wenzuo; Cheng, Jianbo

    2014-11-01

    The complexes of HOBr:PH2Y (Y = H, F, Cl, Br, CH3, NH2, OH, and NO2), HOCl:PH2F, and HOI:PH2F have been investigated with ab initio calculations at the MP2/aug-cc-pVTZ level. Four types of structures (1, 2, 3a, and 3b) were observed for these complexes. 1 is stabilized by an O⋯P pnicogen bond, 2 by a P⋯X halogen bond, 3a by a H⋯P hydrogen bond and a P⋯X pnicogen bond, and 3b by H⋯P and H⋯Br hydrogen bonds. Their relative stability is related to the halogen X of HOX and the substituent Y of PH2Y. These structures can compete with interaction energy of -10.22 ∼ -29.40 kJ/mol. The Hsbnd O stretch vibration shows a small red shift in 1, a small irregular shift in 2, but a prominent red shift in 3a and 3b. The Xsbnd O stretch vibration exhibits a smaller red shift in 1, a larger red shift in 2, but an insignificant blue shift in 3a and 3b. The Psbnd Y stretch vibration displays a red shift in 1 but a blue shift in 2, 3a, and 3b. The formation mechanism, stability, and properties of these structures have been analyzed with molecular electrostatic potentials, orbital interactions, and non-covalent interaction index.

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

    PubMed

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

    2016-08-10

    The dihydrogen bond-an interaction between a transition-metal or main-group hydride (M-H) and a protic hydrogen moiety (H-X)-is arguably the most intriguing type of hydrogen bond. It was discovered in the mid-1990s and has been intensively explored since then. Herein, we collate up-to-date experimental and computational studies of the structural, energetic, and spectroscopic parameters and natures of dihydrogen-bonded complexes of the form M-H···H-X, as such species are now known for a wide variety of hydrido compounds. Being a weak interaction, dihydrogen bonding entails the lengthening of the participating bonds as well as their polarization (repolarization) as a result of electron density redistribution. Thus, the formation of a dihydrogen bond allows for the activation of both the MH and XH bonds in one step, facilitating proton transfer and preparing these bonds for further transformations. The implications of dihydrogen bonding in different stoichiometric and catalytic reactions, such as hydrogen exchange, alcoholysis and aminolysis, hydrogen evolution, hydrogenation, and dehydrogenation, are discussed. PMID:27285818

  4. Oligo(p-phenylene-ethynylene)s with backbone conformation controlled by competitive intramolecular hydrogen bonds.

    PubMed

    Hu, Wei; Yan, Qifan; Zhao, Dahui

    2011-06-14

    A series of conjugated oligo(p-phenylene-ethynylene) (OPE) molecules with backbone conformations (that is, the relative orientations of the contained phenylene units) controlled by competitive intramolecular hydrogen bonds to be either co-planar or random were synthesised and studied. In these oligomers, carboxylate and amido substituents were attached to alternate phenylene units in the OPE backbone. These functional groups were able to form intramolecular hydrogen bonds between neighbouring phenylene units. Thereby, all phenylene units in the backbone were confined in a co-planar conformation. This planarised structure featured a more extended effective conjugation length than that of regular OPEs with phenylene units adopting random orientation due to a low rotational-energy barrier. However, if a tri(ethylene glycol) (Tg) side chain was appended to the amido group, it enabled another type of intramolecular hydrogen bond, formed by the Tg chain folding back and the contained ether oxygen atom competing with the ester carbonyl group as the hydrogen-bond acceptor. The outcome of this competition was proven to depend on the length of the alkylene linker joining the ether oxygen atom to the amido group. Specifically, if the Tg chain folded back to form a five-membered cyclic structure, this hydrogen-bonding motif was sufficiently robust to overrule the hydrogen bonds between adjacent phenylene units. Consequently, the oligomers assumed non-planar conformations. However, if the side chain formed a six-membered ring by hydrogen bonding with the amido NH group, such a motif was much less stable and yielded in the competition with the ester carbonyl group from the adjacent phenylene unit. Thus, the hydrogen bonds between the phenylene units remained, and the co-planar conformation was manifested. In our system, the hydrogen bonds formed by the back-folded Tg chain and amido NH group relied on a single oxygen atom as the hydrogen-bond acceptor. The additional oxygen

  5. Hydrogen bonding tunes the early stage of hydrogen-atom abstracting reaction.

    PubMed

    Yang, Yang; Liu, Lei; Chen, Junsheng; Han, Keli

    2014-09-01

    The spontaneous and collision-assisted hydrogen-atom abstracting reaction (HA) dynamics of triplet benzil are investigated through the combination of transient absorption spectroscopy with TD-DFT calculations. HA dynamics exhibit a remarkable dependence on the hydrogen donor properties. The effects of the triplet-state hydrogen bonding on the reaction dynamics are illustrated. In particular, it is experimentally observed that strengthened triplet-state hydrogen bonding could accelerate the HA, whereas weakened triplet-state hydrogen bonding would postpone the HA. The triplet-state hydrogen bonding has great influences on the early stage of the HA reaction, while the bond dissociation energy of the hydrogen donors determines the subsequent reaction pathways. Protic solvents could sustain longer lifetimes of the excited-state intermediate formed after HA than non-protic solvents by 10 μs. This investigation provides insights into the HA dynamics and guidance to improve the product efficiency of photochemical reactions. PMID:25036436

  6. Quantum effects in a simple ring with hydrogen bonds.

    PubMed

    Kariev, Alisher M; Green, Michael E

    2015-05-14

    Complexes containing multiple arginines are common in proteins. The arginines are typically salt-bridged or hydrogen-bonded, so that their charges do not repel. Here we present a quantum calculation of a ring in which the components of a salt bridge composed of a guanidinium, the arginine side chain, and a carboxylic acid are separated by water molecules. When one water molecule is displaced from the ring, atomic charges of the other water molecule, as well as other properties, are significantly affected. The exchange and correlation energy differences between optimized and displaced rings are larger than thermal energy at room temperature, and larger than the sum of other energy differences. This suggests that calculations on proteins and other systems where such a ring may occur must take quantum effects into account; charges on certain atoms shift as substituents are added to the system: another water molecule, an -OH, or -CN bonded to either moiety. Also, charge shifts accompany proton shifts from the acid to guanidinium to ionize the salt bridge. The consequences of moving one water out of the ring give evidence for electron delocalization. Bond order and atomic charges are determined using natural bond orbital calculations. The geometry of the complex changes with ionization as well as the -OH and -CN additions but not in a simple manner. These results help in understanding the role of groups of arginines in salt-bridged clusters in proteins. PMID:25906287

  7. Stereochemistry of enzymatic water addition to C=C bonds.

    PubMed

    Chen, Bi-Shuang; Otten, Linda G; Hanefeld, Ulf

    2015-01-01

    Water addition to carbon-carbon double bonds using hydratases is attracting great interest in biochemistry. Most of the known hydratases are involved in primary metabolism and to a lesser extent in secondary metabolism. New hydratases have recently been added to the toolbox, both from natural sources or artificial metalloenzymes. In order to comprehensively understand how the hydratases are able to catalyse the water addition to carbon-carbon double bonds, this review will highlight the mechanistic and stereochemical studies of the enzymatic water addition to carbon-carbon double bonds, focusing on the syn/anti-addition and stereochemistry of the reaction. PMID:25640045

  8. Hydrogen-Bond Networks: Strengths of Different Types of Hydrogen Bonds and An Alternative to the Low Barrier Hydrogen-Bond Proposal

    SciTech Connect

    Shokri, Alireza; Wang, Yanping; O'Doherty, George A.; Wang, Xue B.; Kass, Steven R.

    2013-11-27

    We report quantifying the strengths of different types of hydrogen bonds in hydrogen bond networks (HBNs) via measurement of the adiabatic electron detachment energy of the conjugate base of a small covalent polyol model compound (i.e., (HOCH2CH2CH(OH)CH2)2CHOH) in the gas phase and the pKa of the corresponding acid in DMSO. The latter result reveals that the hydrogen bonds to the charged center and those that are one solvation shell further away (i.e., primary and secondary) provide 5.3 and 2.5 pKa units of stabilization per hydrogen bond in DMSO. Computations indicate that these energies increase to 8.4 and 3.9 pKa units in benzene and that the total stabilizations are 16 (DMSO) and 25 (benzene) pKa units. Calculations on a larger linear heptaol (i.e., (HOCH2CH2CH(OH)CH2CH(OH)CH2)2CHOH) reveal that the terminal hydroxyl groups each contribute 0.6 pKa units of stabilization in DMSO and 1.1 pKa units in benzene. All of these results taken together indicate that the presence of a charged center can provide a powerful energetic driving force for enzyme catalysis and conformational changes such as in protein folding due to multiple hydrogen bonds in a HBN.

  9. Hydrogen bond cooperativity and anticooperativity within the water hexamer.

    PubMed

    Guevara-Vela, José Manuel; Romero-Montalvo, Eduardo; Mora Gómez, Víctor Arturo; Chávez-Calvillo, Rodrigo; García-Revilla, Marco; Francisco, Evelio; Pendás, Ángel Martín; Rocha-Rinza, Tomás

    2016-07-20

    The hydrogen bond (HB), arguably the most important non-covalent interaction in chemistry, is getting renewed attention particularly in materials engineering. We address herein HB non-additive features by examining different structures of the water hexamer (cage, prism, book, bag and ring). To that end, we rely on the interacting quantum atoms (IQA) topological energy partition, an approach that has been successfully used to study similar effects in smaller water clusters (see Chem. - Eur. J., 19, 14304). Our IQA interaction energies, , are used to classify the strength of HBs in terms of the single/double character of the donor and acceptor H2O molecules involved in the interaction. The strongest hydrogen bonds on this new scale entail double donors and acceptors that show larger values of than those observed in homodromic cycles, paradigms of cooperative effects. Importantly, this means that besides the traditional HB anticooperativity ascribed to double acceptors and donors, the occurrence of these species is also related to HB strengthening. Overall, we hope that the results of this research will lead to a further understanding of the HB non-additivity in intramolecular and intermolecular interactions. PMID:27149337

  10. 29 CFR 2580.412-20 - Use of existing bonds, separate bonds and additional bonding.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... bonding. 2580.412-20 Section 2580.412-20 Labor Regulations Relating to Labor (Continued) EMPLOYEE BENEFITS SECURITY ADMINISTRATION, DEPARTMENT OF LABOR TEMPORARY BONDING RULES UNDER THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF 1974 TEMPORARY BONDING RULES General Bond Rules § 2580.412-20 Use of existing...

  11. Hydrogen bonding in the crystal structure of the molecular salt of pyrazole–pyrazolium picrate

    PubMed Central

    Su, Ping; Song, Xue-gang; Sun, Ren-qiang; Xu, Xing-man

    2016-01-01

    The asymmetric unit of the title organic salt [systematic name: 1H-pyrazol-2-ium 2,4,6-tri­nitro­phenolate–1H-pyrazole (1/1)], H(C3H4N2)2 +·C6H2N3O7 −, consists of one picrate anion and one hydrogen-bonded dimer of a pyrazolium monocation. The H atom involved in the dimer N—H⋯N hydrogen bond is disordered over both symmetry-unique pyrazole mol­ecules with occupancies of 0.52 (5) and 0.48 (5). In the crystal, the component ions are linked into chains along [100] by two different bifurcated N—H⋯(O,O) hydrogen bonds. In addition, weak C—H⋯O hydrogen bonds link inversion-related chains, forming columns along [100]. PMID:27308060

  12. Intramolecular hydrogen bonding and calixarene-like structures in p-cresol/formaldehyde resins

    NASA Astrophysics Data System (ADS)

    Opaprakasit, P.; Scaroni, A.; Painter, P.

    2001-08-01

    The nature of the strong hydrogen bonds found in p-cresol/formaldehyde (PCF) resins, compared to ordinary phenolic compounds, is studied. The evidence from FTIR spectroscopy indicates that this strong interaction is due to intramolecular hydrogen bonding from "calixarene-like" structures. The formation of this structure in PCF is enabled by its "linear" (all- ortho-linkage) structure, which is not present in branched resins. Additionally, a transition is observed at around 175 to 200°C where the intramolecular hydrogen bonded structure is lost. This structure cannot be recovered upon cooling or annealing due to restrictions on conformational rotations that are coupled to a new pattern of intermolecular hydrogen bonding. However, the structure is reformed by dissolving the resin in solution and casting new films.

  13. Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond.

    PubMed

    Arunan, Elangannan; Mani, Devendra

    2015-01-01

    In this discussion, we show that a static definition of a 'bond' is not viable by looking at a few examples for both inter- and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan, Phys. Chem. Chem. Phys. 2009, 11, 8974) which showed a practical way to differentiate 'hydrogen bonding' from 'van der Waals interaction'. We report results from ab initio and atoms in molecules theoretical calculations for a series of Rg∙∙∙HX complexes (Rg=He/Ne/Ar and X=F/Cl/Br) and ethane-1,2-diol. Results for the Rg∙∙∙HX/DX complexes show that Rg∙∙∙DX could have a 'deuterium bond' even when Rg∙∙∙HX is not 'hydrogen bonded', according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an 'intra-molecular hydrogen bond' can appear during a normal mode vibration which is dominated by the OO stretching, though a 'bond' is not found in the equilibrium structure. This dynamical 'bond' formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration 'breaks' an existing bond and in the later case, a vibration leads to 'bond' formation. In both cases, the molecule/complex stays bound irrespective of what happens to this 'hydrogen bond'. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunan et al. Pure. Appl. Chem. 2011, 83 1637) and justify the inclusive nature of the definition. PMID:25627627

  14. Tunnelling readout of hydrogen-bonding-based recognition.

    PubMed

    Chang, Shuai; He, Jin; Kibel, Ashley; Lee, Myeong; Sankey, Otto; Zhang, Peiming; Lindsay, Stuart

    2009-05-01

    Hydrogen bonding has a ubiquitous role in electron transport and in molecular recognition, with DNA base pairing being the best-known example. Scanning tunnelling microscope images and measurements of the decay of tunnel current as a molecular junction is pulled apart by the scanning tunnelling microscope tip are sensitive to hydrogen-bonded interactions. Here, we show that these tunnel-decay signals can be used to measure the strength of hydrogen bonding in DNA base pairs. Junctions that are held together by three hydrogen bonds per base pair (for example, guanine-cytosine interactions) are stiffer than junctions held together by two hydrogen bonds per base pair (for example, adenine-thymine interactions). Similar, but less pronounced effects are observed on the approach of the tunnelling probe, implying that attractive forces that depend on hydrogen bonds also have a role in determining the rise of current. These effects provide new mechanisms for making sensors that transduce a molecular recognition event into an electronic signal. PMID:19421214

  15. Hydrogen-bonded side chain liquid crystalline block copolymer: Molecular design, synthesis, characterization and applications

    NASA Astrophysics Data System (ADS)

    Chao, Chi-Yang

    combinations were carried out to investigate the interplay between morphology, mesophase behavior and blend composition (molar ratios of proton acceptors to proton donors). A critical composition for mesophase formation was identified and the characteristics of the H-bonded complexes below the critical blend ratios were very different than those above. Hydrogen bonding was also used to direct microphase separation of miscible poly(hydroxystyrene-b-methyl methacrylate) diblock copolymer by adopting imidazolyl additives able to hydrogen bond with poly(hydroxystyrene). The miscibility between PHS and PMMA segments was diminished significantly by introducing small quantities of H-binding additives. The critical blend ratio for microphase separation was determined more by the molecular structure of the additives than the number of hydrogen bonds formed between PHS and additives.

  16. Oxidative addition of carbon-carbon bonds to gold.

    PubMed

    Joost, Maximilian; Estévez, Laura; Miqueu, Karinne; Amgoune, Abderrahmane; Bourissou, Didier

    2015-04-20

    The oxidative addition of strained CC bonds (biphenylene, benzocyclobutenone) to DPCb (diphosphino-carborane) gold(I) complexes is reported. The resulting cationic organogold(III) complexes have been isolated and fully characterized. Experimental conditions can be adjusted to obtain selectively acyl gold(III) complexes resulting from oxidative addition of either the C(aryl)C(O) or C(alkyl)C(O) bond of benzocyclobutenone. DFT calculations provide mechanistic insight into this unprecedented transformation. PMID:25727203

  17. Anthrone and related hydroxyarenes: tautomerization and hydrogen bonding.

    PubMed

    Korth, Hans-Gert; Mulder, Peter

    2013-08-01

    The keto-enolization of hydroxyl-substituted naphthols and 9-anthrols has been investigated by means of CBS-QB3 calculations. An excellent agreement between experiment and theory is found for the energetics for the anthrone (5) ⇌ anthrol (6) equilibrium, with an enthalpy of tautomerization, Δ(t)H, of 3.8 kcal mol(-1). In contrast, 1-naphthol is the preferred tautomer with a Δ(t)H = -9.0 kcal mol(-1). Substitution of the hydrogens at the adjacent carbons by hydroxyl groups leads to the formation of strong intramolecular hydrogen bonds within a six-membered ring in the enones and the enols. Due to the difference in the intramolecular hydrogen bond enthalpy, Δ(HB)H(intra), the equilibrium shifts further to the enone. Thus, for 1,8-dihydroxy-anthrone (anthralin, dithranol) Δ(t)H increases to 12.7 kcal mol(-1) with an enol/enone ratio of 10(-10). The solvent effect on the 5 ⇌ 6 equilibrium has been quantified by considering the formation of intermolecular hydrogen bond(s), leading to an acidity parameter α₂(H) for anthrol of 0.42. It is shown that the hydrogen bond donating ability of bulk methanol is greatly attenuated through the formation of cyclic oligomers. The benzylic and phenolic bond dissociation enthalpies for anthrone up to anthralin suggest some antioxidant potency but the precise (radical) mechanism of action remains uncertain. PMID:23815684

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

    PubMed Central

    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

  19. Hydrogen bonding and vapor pressure isotope effect of deuterioisomeric methanethiols

    SciTech Connect

    Wolff, H.; Szydlowski, J.; Dill-Staffenberger, L.

    1981-04-16

    Wilson parameters, activity coefficients, association constants, and other thermodynamic functions which are derived from isothermal vapor pressure measurements between 223 and 293 K for binary mixtures of CH/sub 3/SH, CH/sub 3/SD, CS/sub 3/SH, and CD/sub 3/SD with n-hexane show the weakness of the hydrogen and the deuterium bonds of methanethiol. As far as these functions depend on the association model used for the calculation, the relation of their values to those obtained for the corresponding amines and alcohols under the same conditions attests the weak methanethiol association. While for the more strongly associated methylamines and methanols a greater energy of the deuterium bond compared to the hydrogen bond has clearly been observed, the differences between the thermodynamic functions of the systems with the SH compounds and of those with the SD compounds are insignificant. This observation as well as the fact that the vapor pressure ratios P-(CH/sub 3/SD)/P(CH/sub 3/SH) are only slightly greater than unity, that the ratios P(CD/sub 3/SD)/P(CH/sub 3/SH) are even greater than P(CD/sub 3/SH)/P(CH/sub 3/SH), and that the changes of these ratios with temperature and dilution are small in comparison to the strong increase of the corresponding quotients of the methylamines and the methanols are the consequence of the weak methanethiol association. P(CH/sub 3/SD)/P(CH/sub 3/SH), P(CD/sub 3/SH)/P(CH/sub 3/SH), and P(CD/sub 3/SD)/P(CH/sub 3/SH) are represented by equations of the type ln P/sub D/ P/sub H/ = -A/T/sup 2/ + B/T where A and B are nearly additive. The low values of A and B for CH/sub 3/SD/CH/sub 3/SH in comparison to the high values for CH/sub 3/ND/sub 2//CH/sub 3/NH/sub 2/ and CH/sub 3/OD/CH/sub 3/OH reflect the weakness of the methanethiol hydrogen bonds. The constants can be related to the thermochemical and the spectroscopic data reported in the literature.

  20. Self-assembled multiwalled carbon nanotube films assisted by ureidopyrimidinone-based multiple hydrogen bonds.

    PubMed

    Wang, Sumin; Guo, Hao; Wang, Xiaomin; Wang, Qiguan; Li, Jinhua; Wang, Xinhai

    2014-11-01

    Self-assembled functionalized multiwalled carbon nanotube (MWNT) films were successfully constructed, linked by a kind of strong binding strength from the self-complementary hydrogen-bonding array of ureidopyrimidinone-based modules (UPM) attached. Employing the feasible reaction of isocyanate containing ureidopyrimidinone with amine modified MWNTs, the UPMs composed of ureidopyrimidinone and ureido were attached to MWNTs with the content as low as 0.6 mmol/g MWNTs. Upon multiple hydrogen-bonding interactions from incorporation of the AADD (A, hydrogen-bonding acceptor; D, hydrogen-bonding donor) quadruple hydrogen bonds of ureidopyrimidinone and the double hydrogen bonds of ureido group, UPM functionalized MWNTs (MWNT-UPM) can be well dispersed in the polar solvent of N,N-dimethylformamide (DMF), while they tend to self-assemble to give a self-supported film in the apolar solvent of CHCl3. In addition, by using the multiple hydrogen-bonding interactions as the driving force, the layer-by-layer (LBL) MWNT-UPM films with high coverage on solid slides can be processed. Because of the self-association of MWNT-UPM in apolar solvent, it was found that the LBL assembly of MWNT-UPM was more favorable in the polar solvent of DMF than in the apolar solvent of CHCl3. Moreover, the hydrogen-bonding linked MWNT-UPM films showed good stability upon soaking in different solvents. Furthermore, the as-prepared LBL films showed electrochemical active behaviors, exhibiting a remarkable catalytic effect on the reduction of nifedipine. PMID:25296167

  1. A rheo-optic study of hydrogen-bonded polymers

    SciTech Connect

    Van Buskirk, C.S.

    1988-01-01

    The influence of hydrogen bonds on polymer mechanical properties was examined using rheo-optic techniques. To isolate the hydrogen bond effect, poly(vinyl alcohol) (PVOH), which has a high hydrogen bond density, was studied during stress relaxation, a process dominated by intermolecular hydrogen bonds. To vary the degree and strength of hydrogen bonding, copolymers containing 2.7, 5.7, and 12.8% poly (vinyl acetate) were prepared by reacetylation of PVOH. Samples were also annealed. IR spectroscopy was used to measure samples' molecular response during stress relaxation. Samples were subjected to deuterium exchange reaction before testing, amorphous regions undergo this exchange process preferentially to crystalline regions. Because IR vibration is a function of mass, deuteration resulted in separation of crystalline and amorphous response to stress in the spectra: OH stretching frequency represented crystalline response, OD the amorphous. Prior to rheo-optic testing, polymers were characterized by differential scanning calorimetry. Analysis of these data lead to the identification of a previously improperly assigned endotherm near 410 K. Three types of stress relaxation tests were performed: high strain level, low strain level, and strain and recovery sequences. Correlations between stress and IR peak position and band distribution were found during the application of large strain, though during subsequent relaxation these correlations were not as pronounced. Results indicate that stress relaxation occurs by a redistribution of hydrogen bond strengths, and that stress is borne differently in crystalline and amorphous regions. Strain and recovery test results emphasized the correlation between stress and hydrogen bond strengths. These data indicated crystalline response to stress is stiff, whereas amorphous response is viscous.

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

    SciTech Connect

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

    2015-09-15

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

  3. Enzyme:substrate hydrogen bond shortening during the acylation phase of serine protease catalysis.

    PubMed

    Fodor, Krisztián; Harmat, Veronika; Neutze, Richard; Szilágyi, László; Gráf, László; Katona, Gergely

    2006-02-21

    Atomic resolution (hydrogen bonds between the enzyme and the substrate changed during catalysis. The well-conserved hydrogen bonds of antiparallel beta-sheet between the enzyme and the substrate become significantly shorter in the transition from a Michaelis complex analogue (Pontastacus leptodactylus (narrow-fingered crayfish) trypsin (CFT) in complex with Schistocerca gregaria (desert locust) trypsin inhibitor (SGTI) at 1.2 A resolution) to an acyl-enzyme intermediate (N-acetyl-Asn-Pro-Ile acyl-enzyme intermediate of porcine pancreatic elastase at 0.95 A resolution) presumably synchronously with the nucleophilic attack on the carbonyl carbon atom of the scissile peptide bond. This is interpreted as an active mechanism that utilizes the energy released from the stronger hydrogen bonds to overcome the energetic barrier of the nucleophilic attack by the hydroxyl group of the catalytic serine. In the CFT:SGTI complex this hydrogen bond shortening may be hindered by the 27I-32I disulfide bridge and Asn-15I of SGTI. The position of the catalytic histidine changes slightly as it adapts to the different nucleophilic attacker during the transition from the Michaelis complex to the acyl-enzyme state, and simultaneously its interaction with Asp-102 and Ser-214 becomes stronger. The oxyanion hole hydrogen bonds provide additional stabilization for acyl-ester bond in the acyl-enzyme than for scissile peptide bond of the Michaelis complex. Significant deviation from planarity is not observed in the reactive bonds of either the Michaelis complex or the acyl-enzyme. In the Michaelis complex the electron distribution of the carbonyl bond is distorted toward the oxygen atom compared to other peptide bonds in the structure, which indicates the polarization effect of the oxyanion hole. PMID:16475800

  4. Hydrogen bonding in the ethanol-water dimer.

    PubMed

    Finneran, Ian A; Carroll, P Brandon; Allodi, Marco A; Blake, Geoffrey A

    2015-10-01

    We report the first rotational spectrum of the ground state of the isolated ethanol-water dimer using chirped-pulse Fourier transform microwave spectroscopy between 8-18 GHz. With the aid of isotopic substitutions, and ab initio calculations, we identify the measured conformer as a water-donor/ethanol-acceptor structure. Ethanol is found to be in the gauche conformation, while the monomer distances and orientations likely reflect a cooperation between the strong (O-HO) and weak (C-HO) hydrogen bonds that stabilizes the measured conformer. No other conformers were assigned in an argon expansion, confirming that this is the ground-state structure. This result is consistent with previous vibrationally-resolved Raman and infrared work, but sheds additional light on the structure, due to the specificity of rotational spectroscopy. PMID:26325657

  5. Non-conventional hydrogen bonds: pterins-metal anions.

    PubMed

    Vargas, Rubicelia; Martínez, Ana

    2011-07-28

    In this paper, we present an analysis of the interaction of metal ions (Cu, Ag and Au) with three different pterins (pterin, isoxanthopterin and sepiapterin) to provide insights concerning the formation of conventional and non-conventional H bonds. Density functional theory calculations were performed in order to reveal the optimized structures of pterin molecules, dimers and tetramers compounds, both with and without metal anions (M). The interaction with small metal clusters (M(3)) is also considered. The formation of different systems is characterized in terms of the structural parameters and hydrogen binding energies (HBE). The HBE values for pterin-M systems presented in this study lie between 22 and 60 kcal mol(-1) and can therefore be classified as strong conventional and strong non-conventional hydrogen bonds. The HBE with small metal clusters (pterin-M(3)) are smaller than the HBE with metal atoms. Vertical electron detachment energies (VEDEs) are also reported in order to analyze the influence of the hydrogen bond on electronic properties. A direct correlation between VEDEs and HBE was found for pterin-M and pterin-M(3) complexes; i.e. as the VEDEs increase, the HBE also augment. The only exception is with Ag(3). The main conclusion derived from this study is that the strong non-conventional hydrogen bonds formed between pterins, dimers and tetramers do not affect the formation of conventional hydrogen bonds between pterins but they do influence the VEDEs. PMID:21695329

  6. Hydrogen-bonding patterns in pyrimethaminium pyridine-3-sulfonate

    PubMed Central

    Nirmalram, Jeyaraman Selvaraj; Thomas Muthiah, Packianathan

    2010-01-01

    In the asymmetric unit of the title salt [systematic name: 2,4-diamino-5-(4-chloro­phen­yl)-6-ethyl­pyrimidin-1-ium pyri­dine-3-sulfonate], C12H14N4Cl+·C5H4NSO3 −, there are two independent pyrimethaminium cations and two 3-pyridine sulfonate anions. Each sulfonate group inter­acts with the corresponding protonated pyrimidine ring through two N—H⋯O hydrogen bonds, forming a cyclic hydrogen-bonded bimolecular R 2 2(8) motif. Even though the primary mode of association is the same, the next higher level of supra­molecular architectures are different due to different hydrogen-bonded networks. In one of the independent molecules in the asymmetric unit, the pyrimethamine cation is paired centrosymmetrically through N—H⋯N hydrogen bonds, generating an R 2 2(8) ring motif. In the other molecule, the pyrimethamine cation does not form any base pairs; instead it forms hydrogen bonds with the 3-pyridine sulfonate anion. The structure is further stabilized by C—H⋯O, C—H⋯N and π–π stacking [centroid–centroid distance = 3.9465 (13) Å] inter­actions. PMID:21588411

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

    PubMed Central

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

    2014-01-01

    Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism. PMID:24875276

  8. How Cellulose Stretches: Synergism between Covalent and Hydrogen Bonding

    PubMed Central

    2014-01-01

    Cellulose is the most familiar and most abundant strong biopolymer, but the reasons for its outstanding mechanical performance are not well understood. Each glucose unit in a cellulose chain is joined to the next by a covalent C–O–C linkage flanked by two hydrogen bonds. This geometry suggests some form of cooperativity between covalent and hydrogen bonding. Using infrared spectroscopy and X-ray diffraction, we show that mechanical tension straightens out the zigzag conformation of the cellulose chain, with each glucose unit pivoting around a fulcrum at either end. Straightening the chain leads to a small increase in its length and is resisted by one of the flanking hydrogen bonds. This constitutes a simple form of molecular leverage with the covalent structure providing the fulcrum and gives the hydrogen bond an unexpectedly amplified effect on the tensile stiffness of the chain. The principle of molecular leverage can be directly applied to certain other carbohydrate polymers, including the animal polysaccharide chitin. Related but more complex effects are possible in some proteins and nucleic acids. The stiffening of cellulose by this mechanism is, however, in complete contrast to the way in which hydrogen bonding provides toughness combined with extensibility in protein materials like spider silk. PMID:24568640

  9. Influencing factors of hydrogen bonding intensity in beer.

    PubMed

    Liu, Chunfeng; Dong, Jianjun; Yin, Xiangsheng; Li, Qi; Gu, Guoxian

    2014-11-01

    The hydrogen bonding was prone to be formed by many components in beer. Different sorts of flavor substances can affect the Chemical Shift due to their different concentrations in beer. Several key factors including 4 alcohols, 2 esters, 6 ions, 9 acids, 7 polyphenols, and 2 gravity indexes (OG and RG) were determined in this research. They could be used to investigate the relationship between hydrogen bonding intensity and the flavor components in bottled larger beers through the Correlation Analysis, Principal Component Analysis and Multiple Regression Analysis. Results showed that ethanol content was the primary influencing factor, and its correlation coefficient was 0.629 for Correlation Analysis. Some factors had a positive correlation with hydrogen bonding intensity, including the content of original gravity, ethanol, isobutanol, Cl(-), K(+), pyruvic acid, lactic acid, gallic acid, vanillic acid, and Catechin in beer. A mathematic model of hydrogen bonding Chemical Shift and the content of ethanol, pyruvic acid, K(+), and gallic acid was obtained through the Principal Component Analysis and Multiple Regression Analysis , with the adjusted R(2) being 0.779 (P = 0.001). Ethanol content was proved to be the most important factor which could impact on hydrogen bonding association in beer by Principal Component Analysis. And then, a multiple non-linearity model could be obtained as follows: [Formula: see text]. The average error was 1.23 % in the validated experiment. PMID:26396290

  10. Universality in hydrogen-bond networks

    NASA Astrophysics Data System (ADS)

    Nadler, Walter; Krausche, Thomas

    1991-12-01

    We present several lattice models for water that belong to the universality class of Angell's independent bond model. The relevance for real water, the relationship to percolation models for water, and the possible use of these models in simulations of protein-sovlent systems is discussed.

  11. Water's hydrogen bonds in the hydrophobic effect: a simple model.

    PubMed

    Xu, Huafeng; Dill, Ken A

    2005-12-15

    We propose a simple analytical model to account for water's hydrogen bonds in the hydrophobic effect. It is based on computing a mean-field partition function for a water molecule in the first solvation shell around a solute molecule. The model treats the orientational restrictions from hydrogen bonding, and utilizes quantities that can be obtained from bulk water simulations. We illustrate the principles in a 2-dimensional Mercedes-Benz-like model. Our model gives good predictions for the heat capacity of hydrophobic solvation, reproduces the solvation energies and entropies at different temperatures with only one fitting parameter, and accounts for the solute size dependence of the hydrophobic effect. Our model supports the view that water's hydrogen bonding propensity determines the temperature dependence of the hydrophobic effect. It explains the puzzling experimental observation that dissolving a nonpolar solute in hot water has positive entropy. PMID:16375338

  12. Dynamical Crossover in Hot Dense Water: The Hydrogen Bond Role.

    PubMed

    Ranieri, Umbertoluca; Giura, Paola; Gorelli, Federico A; Santoro, Mario; Klotz, Stefan; Gillet, Philippe; Paolasini, Luigi; Koza, Michael Marek; Bove, Livia E

    2016-09-01

    We investigate the terahertz dynamics of liquid H2O as a function of pressure along the 450 K isotherm, by coupled quasielastic neutron scattering and inelastic X-ray scattering experiments. The pressure dependence of the single-molecule dynamics is anomalous in terms of both microscopic translation and rotation. In particular, the Stokes-Einstein-Debye equations are shown to be violated in hot water compressed to the GPa regime. The dynamics of the hydrogen bond network is only weakly affected by the pressure variation. The time scale of the structural relaxation driving the collective dynamics increases by a mere factor of 2 along the investigated isotherm, and the structural relaxation strength turns out to be almost pressure independent. Our results point at the persistence of the hydrogen bond network in hot dense water up to ice VII crystallization, thus questioning the long-standing perception that hydrogen bonds are broken in liquid water under the effect of compression. PMID:27479235

  13. Exploring the Potential of Diarylacetylenediols as Hydrogen Bonding Catalysts

    PubMed Central

    Türkmen, Yunus E.; Rawal, Viresh H.

    2014-01-01

    In the course of a search for new classes of hydrogen bonding catalysts, we have examined diarylacetylenediols as potential catalysts for the Diels-Alder reaction. General and efficient methods have been developed for the preparation of these diols. Their structures were systematically modified and increased activity was observed for those possessing an electron-withdrawing group on the aryl groups. The electron-deficient diarylacetylenediol catalysts, while more active, undergo spontaneous cyclization to the corresponding benzo[b]furans. A mechanism is postulated to explain this facile transformation. Computational studies performed on 2-ethynylphenol help to explain the effect of the alkyne on the conformation and hydrogen bond donating ability of the adjacent OH group. Finally, the crystal structure of one of the diols is reported, and it displays an intricate network of intermolecular hydrogen bonds. PMID:23869597

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

    NASA Astrophysics Data System (ADS)

    Smedley, Sarah Black

    qualitative observations that can be made with pure D2O or H2O. The theory and experimental practice of determining the hydrogen bonding distribution of water in a range of proton exchange membranes bearing aromatic sulfonate and perfluorosulfonate groups using this OD stretch technique is discussed. To further understand how the acidity of the sulfonate can be altered and how the acidity affects the hydrogen bonding network of water in a polymer membrane, various polymers with small chemical differences in the perfluorosulfonate sidechain were studied. In addition to the vibrational spectroscopy measurements using HOD as a probe, the partial charges of the sulfonate groups were calculating using DMol3 DFT calculations. The calculations and the experimentally determined peak position of the OD stretch both correlated to give a ranking of acidity for the various sidechains. Three sulfonated poly(arylene sulfone) based polymers were studied using FTIR and DFT calculations to better understand how the acidity of the sulfonate groups were affected by the placement on the backbone. By increasing the number of sulfone groups, which have electron withdrawing properties, flanking the sulfonated aromatic ring, the acidity was increased. The charge density of a sulfonate group flanked by two sulfone groups was -1.626 (in units of fundamental charge), while the charge density of a sulfonate group flanked by one sulfone group increased to -1.703. Additionally, if the subsequent ring was unsulfonated, the charge density further increased to -1.737, indicating that some stability is gained by both available rings being sulfonated. The differences in charge density are reflected in the water uptake and conductivity measurements, where the samples with the lowest charge density had the highest water uptake and conductivity. The deconvoluted OD peak revealed that the sample with two sulfone groups flanking the sulfonated aromatic ring contains the highest amount of bulk-like water, which led

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

    SciTech Connect

    Kumar, Nitin; Neogi, Sanghamitra; Kent, Paul R; Bandura, Andrei V.; Wesolowski, David J; Cole, David R; Sofo, Jorge O.

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  17. A statistical model of hydrogen bond networks in liquid alcohols

    NASA Astrophysics Data System (ADS)

    Sillrén, Per; Bielecki, Johan; Mattsson, Johan; Börjesson, Lars; Matic, Aleksandar

    2012-03-01

    We here present a statistical model of hydrogen bond induced network structures in liquid alcohols. The model generalises the Andersson-Schulz-Flory chain model to allow also for branched structures. Two bonding probabilities are assigned to each hydroxyl group oxygen, where the first is the probability of a lone pair accepting an H-bond and the second is the probability that given this bond also the second lone pair is bonded. The average hydroxyl group cluster size, cluster size distribution, and the number of branches and leaves in the tree-like network clusters are directly determined from these probabilities. The applicability of the model is tested by comparison to cluster size distributions and bonding probabilities obtained from Monte Carlo simulations of the monoalcohols methanol, propanol, butanol, and propylene glycol monomethyl ether, the di-alcohol propylene glycol, and the tri-alcohol glycerol. We find that the tree model can reproduce the cluster size distributions and the bonding probabilities for both mono- and poly-alcohols, showing the branched nature of the OH-clusters in these liquids. Thus, this statistical model is a useful tool to better understand the structure of network forming hydrogen bonded liquids. The model can be applied to experimental data, allowing the topology of the clusters to be determined from such studies.

  18. A statistical model of hydrogen bond networks in liquid alcohols.

    PubMed

    Sillrén, Per; Bielecki, Johan; Mattsson, Johan; Börjesson, Lars; Matic, Aleksandar

    2012-03-01

    We here present a statistical model of hydrogen bond induced network structures in liquid alcohols. The model generalises the Andersson-Schulz-Flory chain model to allow also for branched structures. Two bonding probabilities are assigned to each hydroxyl group oxygen, where the first is the probability of a lone pair accepting an H-bond and the second is the probability that given this bond also the second lone pair is bonded. The average hydroxyl group cluster size, cluster size distribution, and the number of branches and leaves in the tree-like network clusters are directly determined from these probabilities. The applicability of the model is tested by comparison to cluster size distributions and bonding probabilities obtained from Monte Carlo simulations of the monoalcohols methanol, propanol, butanol, and propylene glycol monomethyl ether, the di-alcohol propylene glycol, and the tri-alcohol glycerol. We find that the tree model can reproduce the cluster size distributions and the bonding probabilities for both mono- and poly-alcohols, showing the branched nature of the OH-clusters in these liquids. Thus, this statistical model is a useful tool to better understand the structure of network forming hydrogen bonded liquids. The model can be applied to experimental data, allowing the topology of the clusters to be determined from such studies. PMID:22401459

  19. Thermodynamics of hydrogen bond and hydrophobic interactions in cyclodextrin complexes.

    PubMed Central

    Ross, P D; Rekharsky, M V

    1996-01-01

    Values of K, delta G(o), delta H(o), delta S(o) and delta C(po) for the binding reaction of small organic ligands forming 1:1 complexes with either alpha- or beta-cyclodextrin were obtained by titration calorimetry from 15 degrees C to 45 degrees C. A hydrogen bond or hydrophobic interaction was introduced by adding a single functional group to the ligand. The thermodynamics of binding with and without the added group are compared to estimate the contribution of the hydrogen bond or hydrophobic interaction. A change in the environment of a functional group is required to influence the binding thermodynamics, but molecular size-dependent solute-solvent interactions have no effect. For phenolic O-H-O hydrogen bond formation, delta H(o) varies from -2 to -1.4 kcal mol(-1) from 15 degrees C to 45 degrees C, and delta C(p) is increased by 18 cal K(-1) mol(-1). The hydrophobic interaction has an opposite effect: in alpha-cyclodextrin, delta C(po) = -13.3 cal K(-1) mol(-1) per ligand -CH(2)-, identical to values found for the transfer of a -CH(2)-group from water to a nonpolar environment. At room temperature, the hydrogen bond and the -CH(2)-interaction each contribute about -600 cal mol(-1) to the stability (delta G(o)) of the complex. With increased temperature, the hydrogen bond stability decreases (i.e., hydrogen bonds "melt"), but the stability of the hydrophobic interaction remains essentially constant. PMID:8889190

  20. Aqueous hydrogen bonding probed with polarization and matrix isolation spectroscopy

    NASA Astrophysics Data System (ADS)

    Shultz, Mary Jane; Bisson, Patrick; Buch, Victoria; Groenzin, Henning; Li, Irene

    2010-05-01

    A major challenge in hydrogen-bond research is interpreting the vibrational spectrum of water, arguably the most fundamental hydrogen bonding system. This challenge remains despite over a half century of progress in vibrational spectroscopy, largely due to a combination of the huge oscillator strength and the enormous width of the hydrogen-bond region. Lack of assignment of the resonances in the hydrogen-bond region hinders investigation of interactions between water and solutes. This lack-of-interpretation issue is an even more significant problem for studies of the aqueous interface. Numerous solutes are known to have an effect, some very dramatic, on the shape of the surface spectrum. These effects, however, are but tantalizing teasers because lack of interpretation means that the changes cannot be used to diagnose the effect of solutes or impinging gas-phase molecules on the surface. In the reported work two techniques are used to probe the origin of vibrational resonances in the H-bonded region: the surface sensitive technique sum frequency generation (SFG) and room-temperature matrix isolation spectroscopy (RT-MIS). A polarization technique called polarization angle null (PAN) has been developed that extends SFG and enables identification of resonances. The result of applying PAN-SFG to single crystal, I h ice is identification of at least nine underlying resonances and assignment of two of these. One resonance is correlated with the crystal temperature and is a sensitive probe for interactions that disrupt long range order on the surface - it is a morphology reporter. The second is associated with weakly bonded, double-donor water molecules. This resonance is sensitive to interaction of hydrogen bond donors, i.e. acids, with the surface. Both modes are more correctly pictured as collective modes. These two assignments are the first definitive assignments in the hydrogen-bond region for the aqueous surface. The effect of salts on the vibrational spectrum of

  1. Hydrogen bonding in bulk heterojunction solar cells: A case study

    PubMed Central

    Xiao, Zeyun; Sun, Kuan; Subbiah, Jegadesan; Ji, Shaomin; Jones, David J.; Wong, Wallace W. H.

    2014-01-01

    Small molecules with dithieno[3,2-b;2′,3′-d]thiophene as central building block and octyl cyanoacetate and octyl cyanoacetamide as different terminal building blocks have been designed and synthesized. The amide containing small molecule can form intermolecular hydrogen bonding between N-H…O = C of the amide group. The photovoltaic properties and active layer morphologies of the two molecules in bulk heterojunction solar cells are compared to study the influence of hydrogen bonding on the active layer morphology. New methanofullerene compound containing amide group has also been synthesized and compared with conventional fullerene electron acceptors. PMID:25027678

  2. Disentangling the Puzzle of Hydrogen Bonding in Vitamin C.

    PubMed

    Peña, Isabel; Daly, Adam M; Cabezas, Carlos; Mata, Santiago; Bermúdez, Celina; Niño, Amaya; López, Juan C; Grabow, Jens-Uwe; Alonso, José L

    2013-01-01

    Fast-passage Fourier transform microwave spectroscopy in combination with a laser ablation source has been successfully applied to probe vitamin C (l-ascorbic acid) in the gas phase. Its ethyldiol side chain and two hydroxyl groups around the γ-lactone ring provide five internal rotation axes, enabling vitamin C to assume a wide variety of nonplanar 3D cooperative hydrogen bond networks that can also include the keto and ether functions. The rotational constants extracted from the analysis of the spectrum unequivocally identify the existence of three dominant conformers stabilized by different intramolecular hydrogen bonding motifs forming five-, six-, or seven-membered rings. PMID:26291213

  3. Hydrogen bonds in Zif268 proteins - a theoretical perspective.

    PubMed

    Palanivel, Umadevi; Lakshmipathi, Senthilkumar

    2016-08-01

    The aim of the work was to elucidate the presence of different hydrogen bond (H-bond) in five Zif268 proteins (1A1F, 1A1G, 1A1H, 1A1I and 1A1K). For this purpose, we have performed the QM/MM and molecular dynamics (MD) studies, the results of which reveal that H-bonds depend on the amino acid sequence and orientation of the H-bond donor atoms. Further, high specificity of Arg and Asn is observed for guanine and adenine, respectively. Furthermore, both conventional and non-conventional hydrogen bond also exists in the proteins, among them N-H⋯O H-bonds are the strongest. Besides, the non-conventional bonds play a role in the protein folding and DNA stacking. From the QSAR properties, amino acids such as asparagine and aspartic acids are the major reactive sites in the Zif268 protein. The electron affinities of Zif268 proteins are high, so the charge transfer occurs from the DNA to the protein molecules. NBO analysis indicates the majority of charge transfer occurs from DNA to the corresponding anti-bonding orbital of the peptides. Root mean square deviation and Rg (radius of gyration) show that 1A1F is more compact and in native state during MD simulation. The minimum Rg leads to the large number of hydrogen bonds formation in 1A1F. Higher solvent accessible surface area in 1A1I indicates that the cavity inside the protein is large. PMID:26300286

  4. Low-barrier hydrogen bonds and enzymatic catalysis.

    PubMed

    Cleland, W W

    2000-10-01

    Short, strong (low barrier) hydrogen bonds occur when the pK values of the atoms sharing the proton are similar. The overall distance is 2.5 A or less, the deuterium fractionation factor is less than 0.5, the proton NMR chemical shift can approach 20 ppm, and deuterium or tritium substitution causes an up-field change in the chemical shift. Such bonds can have deltaH values of 25 kcal/mol in the gas phase, and at least half that in water or other high-dielectric medium. The strength of the hydrogen bond in an active site drops by approximately 1 kcal/mol for each pH unit mismatch in pKs. When a weak hydrogen bond in the initial enzyme-substrate complex is converted into a low-barrier one by alteration of the pK of the substrate or catalytic group so that the pKs match, the increase in hydrogen bond strength can be used to help catalyze the reaction. A well-established example of this is the reaction catalyzed by serine proteases. The pK of neutral histidine is 14, while that of aspartate is approximately 6. Proton transfer from serine to permit attack on bound substrate produces protonated histidine, with a pK now matching that of aspartate. Studies with trifluoromethyl ketone inhibitors that form tetrahedral adducts show up to five orders of magnitude in binding strength as the result of formation of a low-barrier hydrogen bond between aspartate and histidine. Other enzymes whose mechanisms appear to involve low-barrier hydrogen bonds include liver alcohol dehydrogenase, steroid isomerase, triose-P isomerase, aconitase, citrate synthase, and zinc proteases. It is likely that low-barrier hydrogen bonds form at the transition state of any reaction involving general-acid or general-base catalysis, as at that point the pKs of the catalytic group and reactant will be equal. PMID:11051090

  5. Superprotonics—crystals with rearranging hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Makarova, I. P.

    2015-03-01

    Interest in superprotonic crystals M m H n ( XO4)( m + n)/2 ( M = K, Rb, Cs, NH4; X = S, Se, P, As) is associated with the solution of the fundamental problem of modern condensed state physics, i.e., with the determination of the effect of the hydrogen subsystem on physicochemical properties of materials, including phase transitions. From the viewpoint of practical applications, these crystals are promising materials for developing various electrochemical devices, including fuel cell, and are actively studied for the purpose of stabilizing superprotonic phases. Based on experimental data, conclusions are drawn about structural mechanisms of variations in physical properties of a number of crystals of this family.

  6. Adhesion between silica surfaces due to hydrogen bonding

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  7. Crystalline hydrogen-bonded nanocolumns of cyclic thiourea octamers

    SciTech Connect

    Custelcean, Radu; Engle, Nancy L; Bonnesen, Peter V

    2007-01-01

    A bis(thiourea) containing the 1,3-dimethyl-adamantane linker and t-Bu end groups self-assembles in the solid state into crystalline columnar aggregates made of hydrogen-bonded cyclic thiourea octamers with 2 nm diameters.

  8. Crystal Engineering with Urea and Thiourea Hydrogen-Bonding Groups

    SciTech Connect

    Custelcean, Radu

    2008-01-01

    The utilization of N,N{prime}-disubstituted ureas and thioureas as design elements in the synthesis of crystalline organic solids is reviewed. These hydrogen-bonding units are versatile yet predictable building blocks that can be rationally employed in both crystal assembly and functionalization.

  9. Hydrogen Bonding Slows Down Surface Diffusion of Molecular Glasses.

    PubMed

    Chen, Yinshan; Zhang, Wei; Yu, Lian

    2016-08-18

    Surface-grating decay has been measured for three organic glasses with extensive hydrogen bonding: sorbitol, maltitol, and maltose. For 1000 nm wavelength gratings, the decay occurs by viscous flow in the entire range of temperature studied, covering the viscosity range 10(5)-10(11) Pa s, whereas under the same conditions, the decay mechanism transitions from viscous flow to surface diffusion for organic glasses of similar molecular sizes but with no or limited hydrogen bonding. These results indicate that extensive hydrogen bonding slows down surface diffusion in organic glasses. This effect arises because molecules can preserve hydrogen bonding even near the surface so that the loss of nearest neighbors does not translate into a proportional decrease of the kinetic barrier for diffusion. This explanation is consistent with a strong correlation between liquid fragility and the surface enhancement of diffusion, both reporting resistance of a liquid to dynamic excitation. Slow surface diffusion is expected to hinder any processes that rely on surface transport, for example, surface crystal growth and formation of stable glasses by vapor deposition. PMID:27404465

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

    PubMed

    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. PMID:25890437

  11. Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis.

    PubMed

    Park, In-Hee; Venable, John D; Steckler, Caitlin; Cellitti, Susan E; Lesley, Scott A; Spraggon, Glen; Brock, Ansgar

    2015-09-28

    Hydrogen exchange (HX) studies have provided critical insight into our understanding of protein folding, structure, and dynamics. More recently, hydrogen exchange mass spectrometry (HX-MS) has become a widely applicable tool for HX studies. The interpretation of the wealth of data generated by HX-MS experiments as well as other HX methods would greatly benefit from the availability of exchange predictions derived from structures or models for comparison with experiment. Most reported computational HX modeling studies have employed solvent-accessible-surface-area based metrics in attempts to interpret HX data on the basis of structures or models. In this study, a computational HX-MS prediction method based on classification of the amide hydrogen bonding modes mimicking the local unfolding model is demonstrated. Analysis of the NH bonding configurations from molecular dynamics (MD) simulation snapshots is used to determine partitioning over bonded and nonbonded NH states and is directly mapped into a protection factor (PF) using a logistics growth function. Predicted PFs are then used for calculating deuteration values of peptides and compared with experimental data. Hydrogen exchange MS data for fatty acid synthase thioesterase (FAS-TE) collected for a range of pHs and temperatures was used for detailed evaluation of the approach. High correlation between prediction and experiment for observable fragment peptides is observed in the FAS-TE and additional benchmarking systems that included various apo/holo proteins for which literature data were available. In addition, it is shown that HX modeling can improve experimental resolution through decomposition of in-exchange curves into rate classes, which correlate with prediction from MD. Successful rate class decompositions provide further evidence that the presented approach captures the underlying physical processes correctly at the single residue level. This assessment is further strengthened in a comparison of

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

    NASA Astrophysics Data System (ADS)

    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

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

    PubMed

    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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

    Aakeröy, Christer B.; Spartz, Christine L.; Dembowski, Sean; Dwyre, Savannah; Desper, John

    2015-01-01

    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. PMID:26306192

  16. TD-DFT study on electron transfer mobility and intramolecular hydrogen bond of substituted indigo derivatives

    NASA Astrophysics Data System (ADS)

    Ma, Chi; Li, Hui; Yang, Yonggang; Li, Donglin; Liu, Yufang

    2015-10-01

    The density functional theory (DFT) and time-dependent density functional theory (TDDFT) method were carried out to investigate the ground and excited states of indigo and its derivative molecules. The results demonstrate that the intramolecular hydrogen bond I is weakened and the intramolecular hydrogen bond II is strengthened upon photo-excitation to the S1 state. In the absorption spectra, the substitution at R4R4, of indigo causes a significant redshift. In addition, the halogen substitution obviously increases the electron transfer mobility of indigo. It is proved that the halogen substitution may be a new method to design high performance organic semiconductors.

  17. The effects of dissolved halide anions on hydrogen bonding in liquid water.

    PubMed

    Smith, Jared D; Saykally, Richard J; Geissler, Phillip L

    2007-11-14

    It is widely believed that the addition of salts to water engenders structural changes in the hydrogen-bond network well beyond the adjacent shell of solvating molecules. Classification of many ions as "structure makers" and "structure breakers" has been based in part on corresponding changes in the vibrational spectra (Raman and IR). Here we show that changes in O-H vibrational spectra induced by the alkali halides in liquid water result instead from the actions of ions' electric fields on adjacent water molecules. Computer simulations that accurately reproduce our experimental measurements suggest that the statistics of hydrogen-bond strengths are only weakly modified beyond this first solvation shell. PMID:17958418

  18. Liquid state of hydrogen bond network in ice

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  19. Transition metal activation and functionalization of carbon-hydrogen bonds

    SciTech Connect

    Jones, W.D.

    1992-06-01

    We are investigating the fundamental thermodynamic and kinetic factors that influence carbon-hydrogen bond activation at homogeneous transition metal centers and the conversion of hydrocarbons into functionalized products of potential use to the chemical industry. Advances have been made in both understanding the interactions of hydrocarbons with metals and in the functionalization of hydrocarbons. We have found that RhCl(PR{sub 3}){sub 2}(CNR) complexes can catalyze the insertion of isonitriles into the C-H bonds or arenes upon photolysis. The mechanism of these reactions was found to proceed by way of initial phosphine dissociation, followed by C-H activation and isonitrile insertion. We have also examined reactions of a series of arenes with (C{sub 5}Me{sub 5})Rh(PMe{sub 3})PhH and begun to map out the kinetic and thermodynamic preferences for arene coordination. The effects of resonance, specifically the differences in the Hueckel energies of the bound vs free ligand, are now believed to fully control the C-H activation/{eta}{sup 2}-coordination equilibria. We have begun to examine the reactions of rhodium isonitrile pyrazolylborates for alkane and arene C-H bond activation. A new, labile, carbodiimide precursor has been developed for these studies. We have completed studies of the reactions of (C{sub 5}Me{sub 5})Rh(PMe{sub 3})H{sub 2} with D{sub 2} and PMe{sub 3} that indicate that both {eta}{sup 5} {yields} {eta}{sup 3} ring slippage and metal to ring hydride migration occur more facilely than thermal reductive elimination of H{sub 2}. We have examined the reactions of heterocycles with (C{sub 5}Me{sub 5})Rh(PMe{sub 3})PhH and found that pyrrole and furan undergo C-H or N-H activation. Thiophene, however, undergoes C-S bond oxidative addition, and the mechanism of activation has been shown to proceed through sulfur coordination prior to C-S insertion.

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

    NASA Astrophysics Data System (ADS)

    Taneri, Sencer

    2013-05-01

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

  1. Strengthening of N-H...Co hydrogen bonds upon increasing the basicity of the hydrogen bond acceptor (Co)

    SciTech Connect

    Zhao, D.; Ladipo, F.T.; Braddock-Wilking, J.; Brammer, L.

    1996-03-05

    Low temperature crystal structures of (DABCO)H{sup +}Co(CO){sub 4}{sup -} (1) and (DABCO)H{sup +}Co(CO){sub 3}PPh{sub 3}{sup -} (2) (DABCO = 1,4-diazabicyclooctane) indicate that both salts exhibit N-H...Co hydrogen bonding. IR and NMR data indicate that these hydrogen bonded species persist in nonpolar solvents such as toluene, but exist as solvent separated ions in more polar solvents. Replacement of the axial CO ligand by PPh{sub 3} leads to a shortening of the N...Co separation in the solid state from 3.437(3) to 3.294(6) A. This change is accompanied by an increase in the angle between the equatorial carbonyl ligands. Thus, the crystallographic results suggest a strengthening of the N-H...Co hydrogen bond upon increasing the basicity of the metal center, the first observation of this type in the solid state. This assertion is supported by variable-temperature {sup 1}H and {sup 13}C NMR data in toluene-d{sub 8} solution which, discussed in the light of ab initio calculations, indicate that the barrier to a fluxional process involving cleavage of the N-H...Co hydrogen bond is greater in 2 than in 1. The crystal structures of 1 and 2 have been determined by X-ray diffraction at 135(5) and 123(5) K, respectively. 19 refs., 2 figs., 5 tabs.

  2. Hydrogen bonded and stacked geometries of the temozolomide dimer.

    PubMed

    Kasende, Okuma Emile; Muya, Jules Tshishimbi; de Paul N Nziko, Vincent; Scheiner, Steve

    2016-04-01

    Dispersion-corrected density functional theory (DFT) and MP2 quantum chemical methods are used to examine homodimers of temozolomide (TMZ). Of the 12 dimer configurations found to be minima, the antarafacial stacked dimer is the most favored, it is lower in energy than coplanar dimers which are stabilized by H-bonds. The comparison between B3LYP and B3LYP-D binding energies points to dispersion as a primary factor in stabilizing the stacked geometries. CO(π) → CO(π*) charge transfers between amide groups in the global minimum are identified by NBO, as well as a pair of weak CH∙∙N H-bonds. AIM analysis of the electron density provides an alternative description which includes N∙∙O, N∙∙N, and C∙∙C noncovalent bonds. Graphical Abstract Hydrogen bonded and stacked geometries of the temozolomide dimerᅟ. PMID:26971506

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

    NASA Astrophysics Data System (ADS)

    Smedley, Sarah Black

    qualitative observations that can be made with pure D2O or H2O. The theory and experimental practice of determining the hydrogen bonding distribution of water in a range of proton exchange membranes bearing aromatic sulfonate and perfluorosulfonate groups using this OD stretch technique is discussed. To further understand how the acidity of the sulfonate can be altered and how the acidity affects the hydrogen bonding network of water in a polymer membrane, various polymers with small chemical differences in the perfluorosulfonate sidechain were studied. In addition to the vibrational spectroscopy measurements using HOD as a probe, the partial charges of the sulfonate groups were calculating using DMol3 DFT calculations. The calculations and the experimentally determined peak position of the OD stretch both correlated to give a ranking of acidity for the various sidechains. Three sulfonated poly(arylene sulfone) based polymers were studied using FTIR and DFT calculations to better understand how the acidity of the sulfonate groups were affected by the placement on the backbone. By increasing the number of sulfone groups, which have electron withdrawing properties, flanking the sulfonated aromatic ring, the acidity was increased. The charge density of a sulfonate group flanked by two sulfone groups was -1.626 (in units of fundamental charge), while the charge density of a sulfonate group flanked by one sulfone group increased to -1.703. Additionally, if the subsequent ring was unsulfonated, the charge density further increased to -1.737, indicating that some stability is gained by both available rings being sulfonated. The differences in charge density are reflected in the water uptake and conductivity measurements, where the samples with the lowest charge density had the highest water uptake and conductivity. The deconvoluted OD peak revealed that the sample with two sulfone groups flanking the sulfonated aromatic ring contains the highest amount of bulk-like water, which led

  4. Displacement of the proton in hydrogen-bonded complexes of hydrogen fluoride by beryllium and magnesium ions

    SciTech Connect

    McDowell, Sean A. C.

    2009-05-14

    The displacement of the proton by a beryllium ion and by a magnesium ion from hydrogen-bonded complexes of hydrogen fluoride, of varying hydrogen bond strengths, was investigated theoretically using ab initio methods. Stable metal-containing species were obtained from all of the hydrogen-bonded complexes regardless of the strength of the hydrogen bond. It was found that the beryllium ion was energetically very effective in displacing the proton from hydrogen bonds, whereas the magnesium ion was unable to do so. The high stability of the beryllium-containing complexes is mainly due to the strong electrostatic bonding between the beryllium and fluoride atoms. This work supports the recent finding from a multidisciplinary bioinorganic study that beryllium displaces the proton in many strong hydrogen bonds.

  5. Using neutrons and X-rays to study the effect of temperature on the short hydrogen bond in potassium hydrogen phthalate

    NASA Astrophysics Data System (ADS)

    Harte, Suzanne M.; Parkin, Andrew; Goeta, Andrés; Wilson, Chick C.

    2005-05-01

    Potassium hydrogen phthalate has been investigated at several temperatures by both neutron and X-ray single crystal diffraction methods. Previous studies have shown that medium-to-strong hydrogen bonds will frequently undergo changes in the behaviour of the hydrogen atom as temperature is increased. Observed effects include proton migration and disorder over two positions. No evidence for either effect is observed for the short hydrogen bond in potassium hydrogen phthalate between 30 and 300 K, in either the X-ray or neutron data. In addition to demonstrating the robust nature of the geometry of this interaction with respect to temperature, the study has shown once again that X-ray diffraction coupled with simple Fourier imaging methods can reliably screen such hydrogen bonds.

  6. Communication: Hydrogen bonding interactions in water-alcohol mixtures from X-ray absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Lam, Royce K.; Smith, Jacob W.; Saykally, Richard J.

    2016-05-01

    While methanol and ethanol are macroscopically miscible with water, their mixtures exhibit negative excess entropies of mixing. Despite considerable effort in both experiment and theory, there remains significant disagreement regarding the origin of this effect. Different models for the liquid mixture structure have been proposed to address this behavior, including the enhancement of the water hydrogen bonding network around the alcohol hydrophobic groups and microscopic immiscibility or clustering. We have investigated mixtures of methanol, ethanol, and isopropanol with water by liquid microjet X-ray absorption spectroscopy on the oxygen K-edge, an atom-specific probe providing details of both inter- and intra-molecular structure. The measured spectra evidence a significant enhancement of hydrogen bonding originating from the methanol and ethanol hydroxyl groups upon the addition of water. These additional hydrogen bonding interactions would strengthen the liquid-liquid interactions, resulting in additional ordering in the liquid structures and leading to a reduction in entropy and a negative enthalpy of mixing, consistent with existing thermodynamic data. In contrast, the spectra of the isopropanol-water mixtures exhibit an increase in the number of broken alcohol hydrogen bonds for mixtures containing up to 0.5 water mole fraction, an observation consistent with existing enthalpy of mixing data, suggesting that the measured negative excess entropy is a result of clustering or micro-immiscibility.

  7. Communication: Hydrogen bonding interactions in water-alcohol mixtures from X-ray absorption spectroscopy.

    PubMed

    Lam, Royce K; Smith, Jacob W; Saykally, Richard J

    2016-05-21

    While methanol and ethanol are macroscopically miscible with water, their mixtures exhibit negative excess entropies of mixing. Despite considerable effort in both experiment and theory, there remains significant disagreement regarding the origin of this effect. Different models for the liquid mixture structure have been proposed to address this behavior, including the enhancement of the water hydrogen bonding network around the alcohol hydrophobic groups and microscopic immiscibility or clustering. We have investigated mixtures of methanol, ethanol, and isopropanol with water by liquid microjet X-ray absorption spectroscopy on the oxygen K-edge, an atom-specific probe providing details of both inter- and intra-molecular structure. The measured spectra evidence a significant enhancement of hydrogen bonding originating from the methanol and ethanol hydroxyl groups upon the addition of water. These additional hydrogen bonding interactions would strengthen the liquid-liquid interactions, resulting in additional ordering in the liquid structures and leading to a reduction in entropy and a negative enthalpy of mixing, consistent with existing thermodynamic data. In contrast, the spectra of the isopropanol-water mixtures exhibit an increase in the number of broken alcohol hydrogen bonds for mixtures containing up to 0.5 water mole fraction, an observation consistent with existing enthalpy of mixing data, suggesting that the measured negative excess entropy is a result of clustering or micro-immiscibility. PMID:27208929

  8. Rheology of miscible polymer blends with hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Yang, Zhiyi

    Poly(4-vinylphenol) (PVPh) was blended with four different polymers: poly(vinyl methyl ether) (PVME), poly(vinyl acetate) (PVAc), poly(2-vinylpyridine) (P2VP), and poly(4-vinylpyridine) (P4VP) by solvent casting. The miscibility of these four PVPh-based blend systems was investigated using differential scanning calorimetry (DSC) and the composition-dependent glass transition temperature (Tg) was predicted by a thermodynamic theory. The hydrogen bonds between phenolic group in PVPh and ether group, carbonyl group or pyridine group was confirmed by Fourier transform infrared (FTIR) spectroscopy. The fraction of hydrogen bonds was calculated by the Coleman-Graf-Painter association model. Linear dynamic viscoelasticity of four PVPh-based miscible polymer blends with hydrogen bonding was investigated. Emphasis was placed on investigating how the linear dynamic viscoelasticity of miscible polymer blends with specific interaction might be different from that of miscible polymer blends without specific interaction. We have found that an application of time-temperature superposition (TTS) to the PVPh-based miscible blends with intermolecular hydrogen bonding is warranted even when the difference in the component glass transition temperatures is as large as about 200°C, while TTS fails for miscible polymer blends without specific interactions. On the basis of such an observation, we have concluded that hydrogen bonding suppressed concentration fluctuations in PVPh-based miscible blends. It has been found that both the intra-association (self-association) of the phenoxy hydroxyl groups in PVPh and inter-association (intermolecular interactions) between the constituent components have a profound influence on the frequency dependence of dynamic moduli in the terminal region of the PVPh-based miscible blend systems investigated. Hydrogenated functional polynorbornenes (HFPNBs) were synthesized and they were used to investigate the miscibility and rheology of HFPNB

  9. Structure and hydrogen bonding in ortho-hydroxy Ketimines

    NASA Astrophysics Data System (ADS)

    Filarowski, A.; Koll, A.; Głowiak, T.

    2003-01-01

    Two ortho-hydroxy Ketimines (2,2'-dihydroxybenzophenone- N-methyl-imine ( 1) and 2,2'-dihydroxy-4-methoxy-benzophenone- N-methyl-imine ( 2)) were synthesized with the hydrogen atom replaced in the azomethine group by the ortho-hydroxyphenyl substituent. The crystal structures were determined, which contain two types of hydrogen bonds; the intra-molecular O⋯N ( d(ON)=2.540 Å, d(ON)=2.502 Å for compound 1, d(ON)=2.559 Å for compound 2, and intermolecular O⋯O ( d(OO)=2.632 Å, d(OO)=2.582 Å for compound 1 and d(OO)=2.581 Å for compound 2. FT-IR spectra of compounds 1 and 2 in solid state as function of temperature were recorded. Relation between the intra-molecular and intermolecular hydrogen bonds was discussed. Influence of methoxy group substituted in phenol ring on the hydrogen bond properties has been investigated.

  10. Herringbone array of hydrogen-bonded ribbons in 2-ethoxybenzamide from high-resolution X-ray powder diffraction.

    PubMed

    Pagola, Silvina; Stephens, Peter W

    2009-11-01

    In 2-ethoxybenzamide, C(9)H(11)NO(2), the amide substituents are linked into centrosymmetric head-to-head hydrogen-bonded dimers. Additional hydrogen bonds between adjacent dimers give rise to ribbon-like packing motifs, which extend along the c axis and possess a third dimension caused by twisting of the 2-ethoxyphenyl substituent with respect to the hydrogen-bonded amide groups. The ribbons are arranged in a T-shaped herringbone pattern and cohesion between them is achieved by van der Waals forces. PMID:19893241

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

    PubMed

    O'Neal, Kristi L; Weber, Stephen G

    2009-01-01

    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. PMID:19195102

  12. Alternative strategy for adjusting the association specificity of hydrogen-bonded duplexes.

    PubMed

    Zhang, Penghui; Chu, Hongzhu; Li, Xianghui; Feng, Wen; Deng, Pengchi; Yuan, Lihua; Gong, Bing

    2011-01-01

    A strategy for creating new association specificity of hydrogen-bonded duplexes by varying the spacings between neighboring hydrogen bonds is described. Incorporation of naphthalene-based residues has provided oligoamide strands that pair into duplexes sharing the same H-bonding sequences (e.g., DDAA) but differing in the spacings between their intermolecular hydrogen bonds, leading to homo- or heteroduplexes. The ability to manipulate association-specificity as demonstrated by this work may be extended to other multiple hydrogen bonded systems, thereby further enhancing the diversity of multiple hydrogen-bonded association units for constructing supramolecular structures. PMID:21133401

  13. Effect of quantum nuclear motion on hydrogen bonding

    SciTech Connect

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

    2014-05-07

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

  14. Unexpectedly lengthened N--H{hor_ellipsis}Co hydrogen bonds?

    SciTech Connect

    Brammer, L.; Mareque Rivas, J.C.; Zhao, D.

    1998-10-19

    Low-temperature crystal structures of QuinH{sup +}Co(CO){sub 4}{sup {minus}}, 1 (QuinH{sup +} = quinuclidinium), (DABCO)H{sup +}Co(CO){sub 3}P-(p-tolyl){sub 3}{sup {minus}}, 2, and (DABCO)H{sup +}Co(CO){sub 3}PPh{sub 2}(p-tolyl){sup {minus}}, 3 (DABCO = 1,4-diazabicyclooctane), 2 and 3 as their acetonitrile solvates, demonstrate that these salts exhibit intermolecular N--H{hor_ellipsis}Co hydrogen bonding between the cation and anion components. NMR and IR data demonstrate the persistence of these interactions in toluene solution. Such solution-state data, which examine solvated ion pairs, suggest little difference between these salts and the corresponding previously reported salts (DABCO)H{sup +}Co(CO){sub 3}L{sup {minus}} (4, L = CO; 5, L = PPh{sub 3}). However, in the solid state, the N--H{hor_ellipsis}Co hydrogen bonds in 1--3 are some 0.1--0.15 {angstrom} longer than would be predicted from consideration of the structures of 4 and 5 and the aforementioned similarity to 4 and 5 in solution. In previous reports the authors have shown that major steric or electronic changes to the anion or cation have resulted in substantial changes (0.15--0.3 {angstrom}) in the N{hor_ellipsis}Co [H{hor_ellipsis}] separation for N--H{hor_ellipsis}Co hydrogen bonds in related R{sub 3}NH{sup +}Co(CO){sub 3}L{sup {minus}} (L = CO, PR{sub 3}) salts. In this report, the authors present examples in which small changes are made to the anion or cation remote from the N--H{hor_ellipsis}Co hydrogen bond. In the solid state, the effect of these small changes on this hydrogen bond is subsumed by the effect of changes in the supramolecular structure. This clearly indicates the sensitivity of the geometry of these hydrogen bonds to the overall balance of intermolecular interactions in the solid state and as such is pertinent to current interest in weak (intermolecular) interactions for which characterization by X-ray crystallography is important.

  15. Formation of C-C bonds via ruthenium-catalyzed transfer hydrogenation().

    PubMed

    Moran, Joseph; Krische, Michael J

    2012-01-01

    Ruthenium-catalyzed transfer hydrogenation of diverse π-unsaturated reactants in the presence of aldehydes provides products of carbonyl addition. Dehydrogenation of primary alcohols in the presence of the same π-unsaturated reactants provides identical products of carbonyl addition. In this way, carbonyl addition is achieved from the alcohol or aldehyde oxidation level in the absence of stoichiometric organometallic reagents or metallic reductants. In this account, the discovery of ruthenium-catalyzed C-C bond-forming transfer hydrogenations and the recent development of diastereo- and enantioselective variants are discussed. PMID:23430602

  16. Formation of C–C bonds via ruthenium-catalyzed transfer hydrogenation*

    PubMed Central

    Moran, Joseph; Krische, Michael J.

    2013-01-01

    Ruthenium-catalyzed transfer hydrogenation of diverse π-unsaturated reactants in the presence of aldehydes provides products of carbonyl addition. Dehydrogenation of primary alcohols in the presence of the same π-unsaturated reactants provides identical products of carbonyl addition. In this way, carbonyl addition is achieved from the alcohol or aldehyde oxidation level in the absence of stoichiometric organometallic reagents or metallic reductants. In this account, the discovery of ruthenium-catalyzed C–C bond-forming transfer hydrogenations and the recent development of diastereo- and enantioselective variants are discussed. PMID:23430602

  17. Dynamic Ordering and Phase Segregation in Hydrogen-Bonded Polymers.

    PubMed

    Chen, Senbin; Binder, Wolfgang H

    2016-07-19

    Hydrogen bonds (H-bonds) constitute highly relevant structural units of molecular self-assembly. They bridge biological and synthetic sciences, implementing dynamic properties into materials and molecules, not achieved via purely covalent bonds. Phase segregation on the other hand represents another important assembly principle, responsible for, e.g., cell compartimentation, membrane-formation, and microphase segregation in polymers. Yet, despite the expanding elegant synthetic strategies of supramolecular polymers, the investigation of phase behavior of macromolecules driven by H-bonding forces still remains in its infancy. Compared to phase segregation arising from covalently linked block copolymers, the generation of phase segregated nanostructures via supramolecular polymers facilitates the design of novel functional materials, such as those with stimuli-responsive, self-healing, and erasable-material properties. We here discuss the phase segregation of H-bonding polymers in both the solution and solid state, wherein the molecular recognition elements are based on multiple H-bonding moieties, such as thymine/2,6-diamino-pyridine (THY/DAP), thymine/diamino triazine (THY/DAT), and barbiturate/Hamilton wedge (Ba/HW) elements. The specific aggregation of a series of different H-bonding polymers in solution, both linear and dendritic polymers, bearing heterocomplementary H-bonding moieties are described, in particular focusing on the issue of phase segregation. The exploitation of H-bonded supramolecular dendrons with segregating polymer chains leads to the formation of three-phase segregated hierarchical micelles in solution, purely linking the components via H-bonds, in turn displaying a versatile spectrum of segregated morphologies. We also focus on segregation effects of H-bonded amorphous and crystalline polymers: thus the formation of nanostructures, such as disordered micelles and well-ordered body centered cubic (BCC) packed spheres from telechelic polymers

  18. Car-Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate

    NASA Astrophysics Data System (ADS)

    Pirc, Gordana; Stare, Jernej; Mavri, Janez

    2010-06-01

    We studied proton dynamics of a short hydrogen bond of the crystalline sodium hydrogen bissulfate, a hydrogen-bonded ferroelectric system. Our approach was based on the established Car-Parrinello molecular dynamics (CPMD) methodology, followed by an a posteriori quantization of the OH stretching motion. The latter approach is based on snapshot structures taken from CPMD trajectory, calculation of proton potentials, and solving of the vibrational Schrödinger equation for each of the snapshot potentials. The so obtained contour of the OH stretching band has the center of gravity at about 1540 cm-1 and a half width of about 700 cm-1, which is in qualitative agreement with the experimental infrared spectrum. The corresponding values for the deuterated form are 1092 and 600 cm-1, respectively. The hydrogen probability densities obtained by solving the vibrational Schrödinger equation allow for the evaluation of potential of mean force along the proton transfer coordinate. We demonstrate that for the present system the free energy profile is of the single-well type and features a broad and shallow minimum near the center of the hydrogen bond, allowing for frequent and barrierless proton (or deuteron) jumps. All the calculated time-averaged geometric parameters were in reasonable agreement with the experimental neutron diffraction data. As the present methodology for quantization of proton motion is applicable to a variety of hydrogen-bonded systems, it is promising for potential use in computational enzymology.

  19. A molecular dynamics study of ethanol-water hydrogen bonding in binary structure I clathrate hydrate with CO2

    NASA Astrophysics Data System (ADS)

    Alavi, Saman; Ohmura, Ryo; Ripmeester, John A.

    2011-02-01

    Guest-host hydrogen bonding in clathrate hydrates occurs when in addition to the hydrophilic moiety which causes the molecule to form hydrates under high pressure-low temperature conditions, the guests contain a hydrophilic, hydrogen bonding functional group. In the presence of carbon dioxide, ethanol clathrate hydrate has been synthesized with 10% of large structure I (sI) cages occupied by ethanol. In this work, we use molecular dynamics simulations to study hydrogen bonding structure and dynamics in this binary sI clathrate hydrate in the temperature range of 100-250 K. We observe that ethanol forms long-lived (>500 ps) proton-donating and accepting hydrogen bonds with cage water molecules from both hexagonal and pentagonal faces of the large cages while maintaining the general cage integrity of the sI clathrate hydrate. The presence of the nondipolar CO2 molecules stabilizes the hydrate phase, despite the strong and prevalent alcohol-water hydrogen bonding. The distortions of the large cages from the ideal form, the radial distribution functions of the guest-host interactions, and the ethanol guest dynamics are characterized in this study. In previous work through dielectric and NMR relaxation time studies, single crystal x-ray diffraction, and molecular dynamics simulations we have observed guest-water hydrogen bonding in structure II and structure H clathrate hydrates. The present work extends the observation of hydrogen bonding to structure I hydrates.

  20. Supramolecular Archimedean Cages Assembled with 72 Hydrogen Bonds

    SciTech Connect

    Liu, Yuzhou; Hu, Chunhua; Comotti, Angiolina; Ward, Michael D.

    2011-12-09

    Self-assembly of multiple components into well-defined and predictable structures remains one of the foremost challenges in chemistry. Here, we report on the rational design of a supramolecular cage assembled from 20 ions of three distinct species through 72 hydrogen bonds. The cage is constructed from two kinds of hexagonal molecular tiles, a tris(guanidinium)nitrate cluster and a hexa(4-sulfonatophenyl)benzene, joined at their edges through complementary and metrically matched N-H {hor_ellipsis} O-S hydrogen bonds to form a truncated octahedron, one of the Archimedean polyhedra. The truncated octahedron, with an interior volume of 2200 cubic angstroms, serves as the composite building unit of a body-centered cubic zeolite-like framework, which exhibits an ability to encapsulate a wide range of differently charged species, including organic molecules, transition metal complexes, and 'ship-in-a-bottle' nanoclusters not observed otherwise.

  1. On Dipole Moments and Hydrogen Bond Identification in Water Clusters.

    PubMed

    Bakó, Imre; Mayer, István

    2016-06-30

    It is demonstrated that the localized orbitals calculated for a water cluster have small delocalization tails along the hydrogen bonds, that are crucial in determining the resulting dipole moments of the system. (By cutting them, one gets much smaller dipole moments for the individual monomers-close to the values one obtains by using a Bader-type analysis.) This means that the individual water monomers can be delimited only in a quite fuzzy manner, and the electronic charge density in a given point cannot be assigned completely to that or another molecule. Thus, one arrives to the brink of breaking the concept of a water cluster consisting of individual molecules. The analysis of the tails of the localized orbitals can also be used to identify the pairs of water molecules actually forming hydrogen bonds. PMID:27280888

  2. Contribution of Hydrogen Bonds to Paper Strength Properties.

    PubMed

    Przybysz, Piotr; Dubowik, Marcin; Kucner, Marta Anna; Przybysz, Kazimierz; Przybysz Buzała, Kamila

    2016-01-01

    The objective of this work was to investigate the influence of hydrogen bonds between fibres on static and dynamic strength properties of paper. A commercial bleached pinewood kraft pulp was soaked in water, refined in a PFI, and used to form paper webs in different solvents, such as water, methanol, ethanol, n-propanol and n-butanol, to determine the effect of their dipole moment on static and dynamic strength properties of resulting paper sheets. Paper which was formed in water, being the solvent of the highest dipole moment among the tested ones, showed the highest breaking length and tear resistance. When paper webs were formed in n-butanol, which was the least polar among the solvents, these parameters were reduced by around 75%. These results provide evidence of the importance of water in paper web formation and strong impact of hydrogen bonds between fibres on strength properties of paper. PMID:27228172

  3. Contribution of Hydrogen Bonds to Paper Strength Properties

    PubMed Central

    Przybysz, Piotr; Dubowik, Marcin; Kucner, Marta Anna; Przybysz, Kazimierz; Przybysz Buzała, Kamila

    2016-01-01

    The objective of this work was to investigate the influence of hydrogen bonds between fibres on static and dynamic strength properties of paper. A commercial bleached pinewood kraft pulp was soaked in water, refined in a PFI, and used to form paper webs in different solvents, such as water, methanol, ethanol, n-propanol and n-butanol, to determine the effect of their dipole moment on static and dynamic strength properties of resulting paper sheets. Paper which was formed in water, being the solvent of the highest dipole moment among the tested ones, showed the highest breaking length and tear resistance. When paper webs were formed in n-butanol, which was the least polar among the solvents, these parameters were reduced by around 75%. These results provide evidence of the importance of water in paper web formation and strong impact of hydrogen bonds between fibres on strength properties of paper. PMID:27228172

  4. Hydrophobicity and hydrogen-bonded network in liquid water

    NASA Astrophysics Data System (ADS)

    Li, Je-Luen; Wingreen, Ned; Tang, Chao; Car, Roberto

    2004-03-01

    Hydrophobicity is the main driving force behind numerous important biological processes at molecular level, including protein folding and the formation of biological membranes. Yet few experimental probes can measure the local water structure around a hydrophobic solute, and our understanding of the detailed structure of hydrophobic hydration has to rely on molecular dynamics simulation. As a model system, several groups studied two methane molecules in liquid water and obtained the potential of mean force using Lennard-Jones potential and various water models. However, hydrophobic effect critically depends on the description of hydrogen-bonded network, and classical simulations may not be sufficient to descirbe the forming and breaking of hydrogen bonds. In this work, we apply ab initio molecular dynamics simulations to study this model system. Besides the potential of mean force between 2 methanes in water, the role of the local water structure will be highlighted.

  5. Influence of hydrogen bonds and temperature on dielectric properties.

    PubMed

    Ortiz de Urbina, Jordi; Sesé, Gemma

    2016-07-01

    Dielectric properties are evaluated by means of molecular dynamics simulations on two model systems made up of dipolar molecules. One of them mimics methanol, whereas the other differs from the former only in the ability to form hydrogen bonds. Static dielectric properties such as the permittivity and the Kirkwood factor are evaluated, and results are analyzed by considering the distribution of relative orientations between molecular dipoles. Dipole moment-time correlation functions are also evaluated. The relevance of contributions associated with autocorrelations of molecular dipoles and with cross-correlations between dipoles belonging to different molecules has been investigated. For methanol, the Debye approximation for the overall dipole moment correlation function is not valid at room temperature. The model applies when hydrogen bonds are suppressed, but it fails upon cooling the nonassociated liquid. Important differences between relaxation times associated with dipole auto- versus cross-correlations as well as their relative relevance are at the root of the Debye model breakdown. PMID:27575177

  6. Infrared intensities and charge mobility in hydrogen bonded complexes

    NASA Astrophysics Data System (ADS)

    Galimberti, Daria; Milani, Alberto; Castiglioni, Chiara

    2013-08-01

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

  7. Influence of hydrogen bonds and temperature on dielectric properties

    NASA Astrophysics Data System (ADS)

    Ortiz de Urbina, Jordi; Sesé, Gemma

    2016-07-01

    Dielectric properties are evaluated by means of molecular dynamics simulations on two model systems made up of dipolar molecules. One of them mimics methanol, whereas the other differs from the former only in the ability to form hydrogen bonds. Static dielectric properties such as the permittivity and the Kirkwood factor are evaluated, and results are analyzed by considering the distribution of relative orientations between molecular dipoles. Dipole moment-time correlation functions are also evaluated. The relevance of contributions associated with autocorrelations of molecular dipoles and with cross-correlations between dipoles belonging to different molecules has been investigated. For methanol, the Debye approximation for the overall dipole moment correlation function is not valid at room temperature. The model applies when hydrogen bonds are suppressed, but it fails upon cooling the nonassociated liquid. Important differences between relaxation times associated with dipole auto- versus cross-correlations as well as their relative relevance are at the root of the Debye model breakdown.

  8. Singlet Halophenylcarbenes as Strong Hydrogen-Bond Acceptors.

    PubMed

    Richter, Geneviève; Mendez-Vega, Enrique; Sander, Wolfram

    2016-05-26

    Chlorophenylcarbene and fluorophenylcarbene were generated in water-doped argon matrices at cryogenic temperatures by photolysis of the corresponding matrix-isolated diazirines. When diffusion of H2O in solid argon was induced by annealing of the matrices at temperatures above 20 K, hydrogen-bonded complexes between the carbenes and water were formed. UV photolysis of these complexes resulted in the formation of benzaldehyde and hydrogen halides HX. The same products were obtained after photolysis of the diazirines in amorphous water ice. Obviously, the primary insertion product of the carbenes into H-OH is unstable under these conditions, and benzaldehyde is formed via secondary photolysis. The stable primary photochemical insertion product of chlorophenylcarbene into an O-H bond was observed in the reaction of the carbene with methanol. PMID:27120093

  9. Rotational Spectra of Hydrogen Bonded Networks of Amino Alcohols

    NASA Astrophysics Data System (ADS)

    Zhang, Di; Zwier, Timothy S.

    2014-06-01

    The rotational spectra of several different amino alcohols including D/L-allo-threoninol, 2-amino-1,3-propanediol and 1,3-diamino-2-propanol over the 6.5-18.5 GHz range have been investigated under jet-cooled conditions using chirped-pulsed Fourier transform microwave spectroscopy. Despite the small size of these molecules, a great variety of conformations have been observed in the molecular expansion. While the NH2 group is typically thought of as a H-bond acceptor, it often acts both as acceptor and donor in forming H-bonded networks. With three adjacent H-bonding substituents (a combination of OH and NH2 groups), many different hydrogen bonding patterns are possible, including H-bonded chains and H-bonded cycles. Since many of these structures differ primarily by the relative orientation of the H-atoms, the analysis of these rotational spectra are challenging. Only through an exhaustive conformational search and the comparison with the experimental rotational constants, nuclear quadrupolar splittings, and line strengths are we able to understand the complex nature of these interactions. The ways in which the presence and number of NH2 groups affects the relative energies, and distorts the structures will be explored.

  10. Hydrogen-bonded diketopyrrolopyrrole (DPP) pigments as organic semiconductors

    PubMed Central

    Głowacki, Eric Daniel; Coskun, Halime; Blood-Forsythe, Martin A.; Monkowius, Uwe; Leonat, Lucia; Grzybowski, Marek; Gryko, Daniel; White, Matthew Schuette; Aspuru-Guzik, Alán; Sariciftci, Niyazi Serdar

    2014-01-01

    Diketopyrrolopyrroles (DPPs) have recently gained attention as building-blocks for organic semiconducting polymers and small molecules, however the semiconducting properties of their hydrogen-bonded (H-bonded) pigment forms have not been explored. Herein we report on the performance of three archetypical H-bonded DPP pigments, which show ambipolar carrier mobilities in the range 0.01–0.06 cm2/V s in organic field-effect transistors. Their semiconducting properties are correlated with crystal structure, where an H-bonded crystal lattice supports close and relatively cofacial π–π stacking. To better understand transport in these systems, density functional theory calculations were carried out, indicating theoretical maximum ambipolar mobility values of ∼0.3 cm2/V s. Based on these experimental and theoretical results, H-bonded DPPs represent a viable alternative to more established DPP-containing polymers and small molecules where H-bonding is blocked by N-alkylation. PMID:25642158

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

    ERIC Educational Resources Information Center

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

    2009-01-01

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

  12. Hydrogen Bonding in Aqueous Solutions of PEO: Theoretical Insights

    NASA Astrophysics Data System (ADS)

    Dormidontova, Elena E.

    2004-03-01

    Polyethylene oxide (PEO) is one of the polymers for which solubility in water and biocompatibility is primarily based on hydrogen bonding. To understand the hierarchy of multiple interactions taking place in aqueous solutions of PEO we apply a statistical mean-field-like approach. In particular, we consider the competition of polymer-water, water-water and polymer-polymer (if end-groups allow) hydrogen bonding. We found that the overall degree of association between polymer and solvent (polymer hydration) considerably decreases with an increase of temperature or polymer content. For hydroxyl-terminated PEO the contribution of hydration via end-groups becomes noticeable especially for short chains in poor hydration conditions (high temperature, low water content). We also considered the possibility of physical crosslinking of PEO either via direct PEO-PEO hydrogen bonds or via a single water molecule acting as a crosslinking agent. We found that the degree of crosslinking considerably increases with chain length and is enhanced for hydroxyl terminated chains. With a temperature increase the re-arrangements of donor (acceptor) groups from intra-species to inter-species hydrogen bonding occurs leading to a decrease in polymer solubility (increase in the second virial coefficient, A_2). The predicted phase diagram for aqueous solutions of PEO features closed-loop phase-coexistence regions in good agreement with experimental observations. Comparing the critical points (UCST and LCST) for polymer chains terminated by different end-groups we found that while all curves merge in the long chain limit, for shorter chain lengths curves deviate from each other considerably, reaching double critical points (where the UCST merges with the LCST) at different N.

  13. Protonic transport through solitons in hydrogen-bonded systems

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  14. Protic Acid Hydrogen Bonding in Chlorofluoroethylenes: the Hydrogen Fluoride-Vinyl Chloride Complex

    NASA Astrophysics Data System (ADS)

    Leung, Helen O.; Marshall, Mark D.

    2012-06-01

    Our studies of intermolecular complexes formed in the gas phase between protic acids (HX) and chlorofluoroethylene complexes to date have demonstrated a preference for HX binding to a F atom over hydrogen bond formation with the Cl atom. Ab initio calculations suggest that this may not be true for species with an increased degree of halogen substitution on the ethylene. To characterize the nature of hydrogen bond formation with the less electronegative, but more polarizable Cl atom, we have obtained the microwave spectrum of HF-vinyl chloride complex. Analysis of the spectra for the 35Cl and 37Cl isotopologues demonstrate that the complex is planar and provides structural parameters for this species. This allows comparisons to be made between the HX hydrogen bond to Cl and that to F.

  15. Unusual molecular hydrogen complex of rhenium: A long hydrogen-hydrogen bond and inertness to substitution

    SciTech Connect

    Kim, Youhyuk; Deng, Haibin; Meek, D.W.; Wojcicki, A. )

    1990-03-28

    Since the discovery of M(H{sub 2})(CO){sub 3}(PR{sub 3}){sub 2} (M = Mo, W; R = i-Pr or Cy) by Kubas and co-workers, transition-metal polyhydrido complexes have been the subject of intensive research and close scrutiny with respect to the nature of metal-hydrogen bonding, e.g., M-(H){sub 3} (classical), H-M-(H{sub 2}) (nonclassical), or possibly M-(H{sub 3}). In this context, the question of the bonding in the rhenium pentahydrides ReH{sub 5}L{sub 3} has been particularly intriguing, since initially {sup 1}H NMR (T{sub 1} values) and x-ray results pointed to different conclusions when L = PPh{sub 3}. Here the authors report that protonation of an analogous rhenium pentahydride containing a tridentate phosphine ligand, viz., ReH{sub 5}(Cyttp) (1, Cyttp = PhP(CH{sub 2}CH{sub 2}CH{sub 2}PCy{sub 2}){sub 2}), affords an unusual dihydrogen complex, (Re(H{sub 2})H{sub 4}(Cyttp))SbF{sub 6} (2).

  16. Hydrogen Embrittlement Susceptibility and Hydrogen-Induced Additive Stress of 7050 Aluminum Alloy Under Various Aging States

    NASA Astrophysics Data System (ADS)

    Qi, W. J.; Song, R. G.; Qi, X.; Li, H.; Wang, Z. X.; Wang, C.; Jin, J. R.

    2015-09-01

    Hydrogen embrittlement susceptibility of 7050 aluminum alloy under various aging states has been investigated by means of cathodic hydrogen permeation, slow strain rate test, hydrogen determinator, x-ray diffraction, and scanning electron microscope, and effect of hydrogen on atomic binding force of charged alloy has been calculated by free electron theory in this paper. Simultaneously, hydrogen-induced additive stress (σad) of 7050 aluminum alloy hydrogen charged with different current densities under various aging states have been investigated by flowing stress differential method. The results showed that hydrogen concentration of examined alloy increased with increasing charging time or current density under the same aging state. Hydrogen segregation occurred at grain boundaries which enlarged the crystal lattice constant, meanwhile, it reduced the average bonding energy and interatomic bonding force of the grain boundary atoms, thus resulting in hydrogen embrittlement; moreover, σad of 7050 aluminum alloy increased linearly with increasing hydrogen concentration under the same aging state, i.e., under aged: σad = -1.61 + 9.93 × 105 C H, peak aged: σad = -1.55 + 9.67 × 105 C H, over aged: σad = -0.16 + 9.35 × 105 C H, correspondingly, σad increased the susceptibility to hydrogen embrittlement ( I HE) further. Under the same charging condition, aging states had a great influence on σad and I HE, the under-aged state alloy was of the highest, the over-aged state alloy was of the lowest, and peak-aged was in the middle.

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

    PubMed

    Sen, Ibrahim; Kara, Hulya; Azizoglu, Akın

    2016-10-01

    N-(p-benzoyl)-anthranilic acid (BAA) derivatives have been synthesized with different substituents (X: Br, Cl, OCH3, CH3), and their crystal structures have been analyzed in order to understand the variations in their molecular geometries with respect to the substituents by using (1)H NMR, (13)C NMR, IR and X-ray single-crystal diffraction. The carboxylic acid group forms classic OH⋯O hydrogen bonded dimers in a centrosymmetric R2(2)(8) ring motifs for BAA-Br and BAA-Cl. However, no carboxylic acid group forms classic OH⋯O hydrogen bonded dimers in BAA-OCH3 and BAA-CH3. The asymmetric unit consists of two crystallographically independent molecules in BAA-OCH3. DFT computations show that the interaction energies between monomer and dimer are in the range of 0.5-3.8kcal/mol with the B3LYP/6-31+G*, B3LYP/6-31++G*, B3LYP/6-31++G**, and B3LYP/AUG-cc-pVDZ levels of theory. The presence of different hydrogen bond patterns is also governed by the substrate. For monomeric compounds studied herein, theoretical calculations lead to two low-energy conformers; trans (a) and cis (b). Former one is more stable than latter by about 4kcal/mol. PMID:27239947

  18. Hydrophobic interactions and hydrogen bonds in β-sheet formation

    NASA Astrophysics Data System (ADS)

    Narayanan, Chitra; Dias, Cristiano L.

    2013-09-01

    In this study, we investigate interactions of extended conformations of homodimeric peptides made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains using all-atom molecular dynamics simulations to decipher driving forces for β-sheet formation. We make use of a periodic boundary condition setup in which individual peptides are infinitely long and stretched. Dimers adopt β-sheet conformations at short interpeptide distances (ξ ˜ 0.5 nm) and at intermediate distances (˜0.8 nm), valine and leucine homodimers assume cross-β-like conformations with side chains interpenetrating each other. These two states are identified as minima in the potential of mean force. While the number of interpeptide hydrogen bonds increases with decreasing interpeptide distance, the total hydrogen bond number in the system does not change significantly, suggesting that formation of β-sheet structures from extended conformations is not driven by hydrogen bonds. This is supported by an increase in electrostatic energy at short interpeptide distances. A remarkable correlation between the volume of the system and the total electrostatic energy is observed, further reinforcing the idea that excluding water in proteins comes with an enthalpic penalty. We also discuss microscopic mechanisms accounting for β-sheet formation based on computed enthalpy and entropy and we show that they are different for peptides with small and large side chains.

  19. Hydrogen bonding, structure, and dynamics of benzonitrile-water

    NASA Astrophysics Data System (ADS)

    Melandri, Sonia; Consalvo, Daniela; Caminati, Walther; Favero, Paolo G.

    1999-09-01

    Rotational transitions with high quantum numbers J and K of the 1:1 complex of benzonitrile with H2O and D2O have been investigated in the frequency range 60-78 GHz with the free jet absorption microwave technique to get detailed information on the unusual hydrogen bond and on the dynamics of the large amplitude motions of the water moiety. With respect to previous microwave studies [V. Storm, D. Consalvo, and H. Dreizler, Z. Naturforsch. A 52, 293 (1997); R. M. Helm, H.-P. Vogel, H. J. Neusser, V. Storm, D. Consalvo, and H. Dreizler, 52, 655 (1997); V. Storm, H. Dreizler, and D. Consalvo, Chem. Phys. 239, 109 (1998)] the position of the water oxygen has been confirmed and the planar configuration of the complex has been determined. The distance of the oxygen atom to the ortho hydrogen is 2.48 Å, the angle to the ortho C-H bond is 144° and the angle between the free hydrogen atom of water with the same C-H bond is 164°. A coupled analysis of the 0+ and 0- states observed for the normal species was performed and the experimental data were reproduced by a flexible model which allowed the determination of the barrier to internal rotation of water [V2=287(20) cm-1] and the structural relaxation associated with the dynamic process.

  20. Quinacridone on Ag(111): Hydrogen Bonding versus Chirality

    PubMed Central

    2014-01-01

    Quinacridone (QA) has recently gained attention as an organic semiconductor with unexpectedly high performance in organic devices. The strong intermolecular connection via hydrogen bonds is expected to promote good structural order. When deposited on a substrate, another relevant factor comes into play, namely the 2D-chirality of the quinacridone molecules adsorbed on a surface. Scanning tunneling microscopy (STM) images of monolayer quinacridone on Ag(111) deposited at room temperature reveal the formation of quasi-one-dimensional rows of parallel quinacridone molecules. These rows are segmented into short stacks of a few molecules in which adjacent, flat-lying molecules of a single handedness are linked via hydrogen bonds. After annealing to a temperature of T = 550–570 K, which is close to the sublimation temperature of bulk quinacridone, the structure changes into a stacking of heterochiral quinacridone dimers with a markedly different intermolecular arrangement. Electron diffraction (LEED) and photoelectron emission microscopy (PEEM) data corroborate the STM findings. These results illustrate how the effects of hydrogen bonding and chirality can compete and give rise to very different (meta)stable structures of quinacridone on surfaces. PMID:24883168

  1. Analysis of nuclear quantum effects on hydrogen bonding.

    PubMed

    Swalina, Chet; Wang, Qian; Chakraborty, Arindam; Hammes-Schiffer, Sharon

    2007-03-22

    The impact of nuclear quantum effects on hydrogen bonding is investigated for a series of hydrogen fluoride (HF)n clusters and a partially solvated fluoride anion, F-(H2O). The nuclear quantum effects are included using the path integral formalism in conjunction with the Car-Parrinello molecular dynamics (PICPMD) method and using the second-order vibrational perturbation theory (VPT2) approach. For the HF clusters, a directional change in the impact of nuclear quantum effects on the hydrogen-bonding strength is observed as the clusters evolve toward the condensed phase. Specifically, the inclusion of nuclear quantum effects increases the F-F distances for the (HF)n=2-4 clusters and decreases the F-F distances for the (HF)n>4 clusters. This directional change occurs because the enhanced electrostatic interactions between the HF monomers become more dominant than the zero point energy effects of librational modes as the size of the HF clusters increases. For the F-(H2O) system, the inclusion of nuclear quantum effects decreases the F-O distance and strengthens the hydrogen bonding interaction between the fluoride anion and the water molecule because of enhanced electrostatic interactions. The vibrationally averaged 19F shielding constant for F-(H2O) is significantly lower than the value for the equilibrium geometry, indicating that the electronic density on the fluorine decreases as a result of the quantum delocalization of the shared hydrogen. Deuteration of this system leads to an increase in the vibrationally averaged F-O distance and nuclear magnetic shielding constant because of the smaller degree of quantum delocalization for deuterium. PMID:17388289

  2. Hydrogen bonds of anti-HIV active aminophenols

    NASA Astrophysics Data System (ADS)

    Belkov, M. V.; Ksendzova, G. A.; Skornyakov, I. V.; Sorokin, V. L.; Tolstorozhev, G. B.; Shadyro, O. I.

    2011-05-01

    Analysis of IR-Fourier spectra from solutions and crystals of antiviral sulfo-containing aminophenols has shown that various types of intramolecular and intermolecular interactions can occur in molecules of these compounds. Three types of intramolecular hydrogen bonds (O-HṡṡṡN, O-HṡṡṡO=S=O, and N-HṡṡṡO=S=O) are formed in CCl4 solutions of the sulfo-containing aminophenols. The formation of intermolecular H-bonds involving the NH- and OH-groups and the preservation of the intramolecular O-HṡṡṡO=S=O H-bond are characteristic of the anti-HIV active aminophenol crystals. Spectral attributes are determined in order to distinguish between the anti-HIV active and inactive sulfo-containing aminophenols.

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

    USGS Publications Warehouse

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

    2001-01-01

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

  4. Strong Ionic Hydrogen Bonding Causes a Spectral Isotope Effect in Photoactive Yellow Protein

    PubMed Central

    Kaledhonkar, Sandip; Hara, Miwa; Stalcup, T. Page; Xie, Aihua; Hoff, Wouter D.

    2013-01-01

    Standard hydrogen bonds are of great importance for protein structure and function. Ionic hydrogen bonds often are significantly stronger than standard hydrogen bonds and exhibit unique properties, but their role in proteins is not well understood. We report that hydrogen/deuterium exchange causes a redshift in the visible absorbance spectrum of photoactive yellow protein (PYP). We expand the range of interpretable isotope effects by assigning this spectral isotope effect (SIE) to a functionally important hydrogen bond at the active site of PYP. The inverted sign and extent of this SIE is explained by the ionic nature and strength of this hydrogen bond. These results show the relevance of ionic hydrogen bonding for protein active sites, and reveal that the inverted SIE is a novel, to our knowledge, tool to probe ionic hydrogen bonds. Our results support a classification of hydrogen bonds that distinguishes the properties of ionic hydrogen bonds from those of both standard and low barrier hydrogen bonds, and show how this classification helps resolve a recent debate regarding active site hydrogen bonding in PYP. PMID:24314088

  5. Weak hydrogen bonding yields rigid, tough, and elastic hydrogels

    NASA Astrophysics Data System (ADS)

    Sheiko, Sergei; Hu, Xiaobo; Vatankhah-Varnosfaderani, Mohammad; Zhou, Jing; Li, Qiaoxi; Dobrynin, Andrey

    Unlike living tissues, synthetic hydrogels are inherently soft and brittle, particularly when built of hydrogen bonds. It remains challenging to design hydrogels that combine high rigidity, strength at break, extensibility, high elasticity. Through free-radical copolymerization of N , N -dimethylacrylamide and methacrylic acid, we have designed a network system based on tunable composition of covalent bonds (permanent cross-links) and hydrogen bonds (sacrificial and recoverable crosslinks) with the following rationale: 1) Maintain a high total number of cross-links to ensure high modulus; 2) Introduce a high fraction of H-bonding to ensure high energy dissipation; and 3) Incorporate a small fraction of permanent cross-links to ensure shape control. By tuning the chemical composition and microstructure we have obtained materials with superb mechanical properties. The hydrogels contain 70 wt% water (similar to living cartilage, skin, and ligaments), while display modulus of 28 MPa, strength of 2 MPa, fracture energy of 9300 J .m-2, extensibility of 800%, excellent fatigue-resistance, and great elasticity allowing for complete and fast strain recovery. The results agreed with theoretical predictions for modulus relaxation of dual networks with dynamic and permanent crosslinks. We gratefully acknowledge funding from the National Science Foundation (DMR 1122483, DMR 1407645, and DMR 1436201).

  6. Matrix effects on hydrogen-bonded complexes trapped in low-temperature matrices

    NASA Astrophysics Data System (ADS)

    Barnes, Austin J.; Mielke, Zofia

    2012-09-01

    There are several different possible matrix effects on hydrogen-bonded complexes trapped in low-temperature matrices: hydrogen-bonded complexes may be stabilised (compared with the gas phase) as a result of being trapped in a low-temperature matrix; metastable hydrogen-bonded complexes may be trapped in matrices; the matrix may influence the extent of proton transfer in a hydrogen-bonded complex; the matrix may influence the structure of a hydrogen-bonded complex. Each of these possible effects is examined in turn using selected examples from the literature as well as our own work.

  7. An ab initio molecular dynamics study on hydrogen bonds between water molecules

    NASA Astrophysics Data System (ADS)

    Pan, Zhang; Chen, Jing; Lü, Gang; Geng, Yi-Zhao; Zhang, Hui; Ji, Qing

    2012-04-01

    The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance dHṡṡṡH between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance rOṡṡṡH between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When dHṡṡṡH and rOṡṡṡH are small (e.g., dHṡṡṡH < 2.0 Å and rOṡṡṡH < 1.62 Å), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They

  8. Intramolecular hydrogen bonds in crystals of thiophosphorylbenzopyrane derivatives X-ray and FT-IR studies

    NASA Astrophysics Data System (ADS)

    Rybarczyk-Pirek, Agnieszka J.; Dubis, Alina T.; Grabowski, Sławomir J.; Nawrot-Modranka, Jolanta

    2006-01-01

    The crystal structures of two new benzopyrane derivatives are analyzed and compared with previous X-ray investigations on related compounds. A particular attention is focused on intramolecular interactions. For the chromone derivatives ( 1 and 3) only one kind of interaction is possible, i.e., N-H⋯O, whereas for the coumarine derivatives ( 2 and 4) two types of intramolecular hydrogen bonding are observed - N-H⋯O and O-H⋯N. Two types of H-bond for coumarine derivatives are the result of the existence of two tautomeric forms - enamine and iminoenol. Combined spectroscopic, NMR and IR measurements confirm such tautomeric equilibrium in solution. The influence of the additional intermolecular hydrogen bonds on the stabilization of tautomeric forms in crystals is also discussed here.

  9. Molecular Recognition in Glycolaldehyde, the Simplest Sugar: Two Isolated Hydrogen Bonds Win Over One Cooperative Pair

    PubMed Central

    Altnöder, Jonas; Lee, Juhyon J; Otto, Katharina E; Suhm, Martin A

    2012-01-01

    Carbohydrates are used in nature as molecular recognition tools. Understanding their conformational behavior upon aggregation helps in rationalizing the way in which cells and bacteria use sugars to communicate. Here, the simplest α-hydroxy carbonyl compound, glycolaldehyde, was used as a model system. It was shown to form compact polar C2-symmetric dimers with intermolecular O–H⋅⋅⋅O=C bonds, while sacrificing the corresponding intramolecular hydrogen bonds. Supersonic jet infrared (IR) and Raman spectra combined with high-level quantum chemical calculations provide a consistent picture for the preference over more typical hydrogen bond insertion and addition patterns. Experimental evidence for at least one metastable dimer is presented. A rotational spectroscopy investigation of these dimers is encouraged, also in view of astrophysical searches. The binding motif competition of aldehydic sugars might play a role in chirality recognition phenomena of more complex derivatives in the gas phase. PMID:24551516

  10. The gold-hydrogen bond, Au-H, and the hydrogen bond to gold, Au∙∙∙H-X.

    PubMed

    Schmidbaur, Hubert; Raubenheimer, Helgard G; Dobrzańska, Liliana

    2014-01-01

    In the first part of this review, the characteristics of Au-H bonds in gold hydrides are reviewed including the data of recently prepared stable organometallic complexes with gold(I) and gold(III) centers. In the second part, the reports are summarized where authors have tried to provide evidence for hydrogen bonds to gold of the type Au∙∙∙H-X. Such interactions have been proposed for gold atoms in the Au(-I), Au(0), Au(I), and Au(III) oxidation states as hydrogen bonding acceptors and H-X units with X = O, N, C as donors, based on both experimental and quantum chemistry studies. To complement these findings, the literature was screened for examples with similar molecular geometries, for which such bonding has not yet been considered. In the discussion of the results, the recently issued IUPAC definitions of hydrogen bonding and the currently accepted description of agostic interactions have been used as guidelines to rank the Au∙∙∙H-X interactions in this broad range of weak chemical bonding. From the available data it appears that all the intra- and intermolecular Au∙∙∙H-X contacts are associated with very low binding energies and non-specific directionality. To date, the energetics have not been estimated, because there are no thermochemical and very limited IR/Raman and temperature-dependent NMR data that can be used as reliable references. Where conspicuous structural or spectroscopic effects have been observed, explanations other than hydrogen bonding Au∙∙∙H-X can also be advanced in most cases. Although numerous examples of short Au∙∙∙H-X contacts exist in the literature, it seems, at this stage, that these probably make only very minor contributions to the energy of a given system and have only a marginal influence on molecular conformations which so far have most often attracted researchers to this topic. Further, more dedicated investigations will be necessary before well founded conclusions can be drawn. PMID:23999756

  11. "Zwitterionic Proton Sponge" Hydrogen Bonding Investigations on the Basis of Car-Parrinello Molecular Dynamics.

    PubMed

    Jezierska, Aneta; Panek, Jarosław J

    2015-06-22

    1,8-Bis(dimethylamino)-4,5-dihydroxynaphthalene has been investigated on the basis of static DFT computations and Car-Parrinello molecular dynamics. The simulations were performed in the gas phase and in the solid state. The studied "zwitterionic proton sponge" possesses two, short intramolecular hydrogen bonds (O-H···O and N-H···N) classified as Low Barrier Hydrogen Bonds (LBHBs); therefore, the system studied is strongly anharmonic. In addition, the compound exists as a "zwitterion" in solution and in the solid state, thus the intramolecular hydrogen bonds belong to the class of charge-assisted interactions. The applied quantum-chemical methods enabled investigations of metric and spectroscopic parameters of the molecule. The time-evolution investigations of the H-bonding showed a strong delocalization of the bridge protons and their high mobility, reflected in the low barriers on the free energy surfaces. Frequent proton transfer phenomena were noticed. The power spectra of atomic velocity were computed to analyze the vibrational features associated with O-H and N-H stretching. A broad absorption was indicated for both hydrogen bridges. For the first time, Car-Parrinello molecular dynamics results are reported for the compound, and they indicate a broad, shallow but not barrierless, potential well for each of the bridge protons. PMID:25965324

  12. Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential

    PubMed Central

    Levy-Moonshine, Ami; Amir, El-ad David; Keasar, Chen

    2009-01-01

    Motivation: The roughness of energy landscapes is a major obstacle to protein structure prediction, since it forces conformational searches to spend much time struggling to escape numerous traps. Specifically, beta-sheet formation is prone to stray, since many possible combinations of hydrogen bonds are dead ends in terms of beta-sheet assembly. It has been shown that cooperative terms for backbone hydrogen bonds ease this problem by augmenting hydrogen bond patterns that are consistent with beta sheets. Here, we present a novel cooperative hydrogen-bond term that is both effective in promoting beta sheets and computationally efficient. In addition, the new term is differentiable and operates on all-atom protein models. Results: Energy optimization of poly-alanine chains under the new term led to significantly more beta-sheet content than optimization under a non-cooperative term. Furthermore, the optimized structure included very few non-native patterns. Availability: The new term is implemented within the MESHI package and is freely available at http://cs.bgu.ac.il/∼meshi. Contact: chen.keasar@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19628506

  13. Sulfates of organic diamines: hydrogen-bonded structures and properties

    NASA Astrophysics Data System (ADS)

    Jayaraman, K.; Choudhury, A.; Rao, C. N. R.

    2002-03-01

    In order to investigate the supramolecular hydrogen-bonded networks and other structural features exhibited by compounds containing an organic cation and an inorganic anion, sulfates of the organic diamines, ethylenediamine ( I), 1,3-diaminopropane ( II), piperazine ( III), and 1,4-diazabicyclo[2.2.2]octane (DABCO) ( IV) have been prepared investigated by X-ray crystallography. While II, III, and IV crystallize in the centrosymmetric space group, Pbca, P2 1/n, Pbcn, respectively, I crystallizes in the non-centrosymmetric space group, P4 1 exhibiting chirality and weak NLO properties. I- IV exhibit different types of supramolecular H-bonded networks involving the organic cation and the SO 2-4 anion. The nature and strength of the H-bonding network vary from one compound to another, with the strongest network found in piperazinium sulfate, III, and the weakest in II. While in III, water molecules form part of the H-bonded network, they are present as guest molecules in the channels of IV. Thermal stability of the compounds as well as the infrared spectra reflect the stabilities of these H-bonded solids.

  14. Hydrogen bond perturbation in hen egg white lysozyme by external electromagnetic fields: A nonequilibrium molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Solomentsev, Gleb Y.; English, Niall J.; Mooney, Damian A.

    2010-12-01

    Nonequilibrium molecular dynamics simulations of a charge-neutral mutant of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of external microwave fields (2.45 to 100 GHz) of an rms electric field intensity of 0.05 V Å-1. A systematic study was carried out of the distributions of persistence times and energies of each intraprotein hydrogen bond in between breakage and reformation, in addition to overall persistence over 20 ns simulations, vis-à-vis equilibrium, zero-field conditions. It was found that localized translational motion for formally charged residues led to greater disruption of associated hydrogen bonds, although induced rotational motion of strongly dipolar residues also led to a degree of hydrogen bond perturbation. These effects were most apparent in the solvent exposed exterior of hen egg white lysozyme, in which the intraprotein hydrogen bonds tend to be weaker.

  15. Exhaustive Metropolis Monte Carlo sampling and analysis of polyalanine conformations adopted under the influence of hydrogen bonds.

    PubMed

    Podtelezhnikov, Alexei A; Wild, David L

    2005-10-01

    We propose a novel Metropolis Monte Carlo procedure for protein modeling and analyze the influence of hydrogen bonding on the distribution of polyalanine conformations. We use an atomistic model of the polyalanine chain with rigid and planar polypeptide bonds, and elastic alpha carbon valence geometry. We adopt a simplified energy function in which only hard-sphere repulsion and hydrogen bonding interactions between the atoms are considered. Our Metropolis Monte Carlo procedure utilizes local crankshaft moves and is combined with parallel tempering to exhaustively sample the conformations of 16-mer polyalanine. We confirm that Flory's isolated-pair hypothesis (the steric independence between the dihedral angles of individual amino acids) does not hold true in long polypeptide chains. In addition to 3(10)- and alpha-helices, we identify a kink stabilized by 2 hydrogen bonds with a shared acceptor as a common structural motif. Varying the strength of hydrogen bonds, we induce the helix-coil transition in the model polypeptide chain. We compare the propensities for various hydrogen bonding patterns and determine the degree of cooperativity of hydrogen bond formation in terms of the Hill coefficient. The observed helix-coil transition is also quantified according to Zimm-Bragg theory. PMID:16049911

  16. Effect of the Hydrogen Bond on Photochemical Synthesis of Silver Nanoparticles.

    PubMed

    Zhao, Feng-jiao; Liu, Lei; Yang, Yang; Zhang, Rui-ling; Ren, Guang-hua; Xu, Da-li; Zhou, Pan-wang; Han, Ke-li

    2015-12-17

    The effect of a hydrogen bond on the photochemical synthesis of silver nanoparticles has been investigated via experimental and theoretical methods. In a benzophenone system, the photochemical synthesis process includes two steps, which are that hydrogen abstraction reaction and the following reduction reaction. We found that for the first step, an intermolecular hydrogen bond enhances the proton transfer. The efficiency of hydrogen abstraction increases with the hydrogen bond strength. For the second step, the hydrogen-bonded ketyl radical complex shows higher reducibility than the ketyl radical. The inductively coupled plasma-optical emission spectroscopy (ICP-OES) measurement exhibits a 2.49 times higher yield of silver nanoparticles in the hydrogen bond ketyl radical complex system than that for the ketyl radical system. Theoretical calculations show that the hydrogen bond accelerates electron transfer from the ketyl radical to the silver ion by raising the SOMO energy of the ketyl radical; thus, the SOMO-LUMO interaction is more favorable. PMID:26562362

  17. Infrared Spectroscopy of Hydrogen-Bonded Clusters of Protonated Histidine

    NASA Astrophysics Data System (ADS)

    Kondo, Makoto; Kasahara, Yasutoshi; Ishikawa, Haruki

    2015-06-01

    Histidine(His), one of the essential amino acids, is involved in active sites in many enzyme proteins, and known to play fundamental roles in human body. Thus, to gain detailed information about intermolecular interactions of His as well as its structure is very important. In the present study, we have recorded IR spectra of hydrogen-bonded clusters of protonated His (HisH^+) in the gas phase to discuss the relation between the molecular structure and intermolecular interaction of HisH^+. Clusters of HisH^+-(MeOH)_n (n = 1, 2) were generated by an electrospray ionization of the MeOH solution of L-His hydrochloride monohydrate. IR photodissociation spectra of HisH^+-(MeOH)1,2 were recorded. By comparing with the results of the DFT calculations, we determined the structures of these clusters. In the case of n = 1 cluster, MeOH is bonded to the imidazole ring as a proton acceptor. The most of vibrational bands observed were well explained by this isomer. However, a free NH stretch band of the imidazole ring was also observed in the spectrum. This indicates an existence of an isomer in which MeOH is bounded to the carboxyl group of HisH^+. Furthermore, it is found that a protonated position of His is influenced by a hydrogen bonding position of MeOH. In the case of n = 2 cluster, one MeOH molecule is bonded to the amino group, while the other MeOH molecule is separately bonded to the carboxyl group in the most stable isomer. However, there is a possibility that other conformers also exist in our experimental condition. The details of the experimental and theoretical results will be presented in the paper.

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

    PubMed

    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. PMID:18837495

  19. Resonance Character of Hydrogen-bonding Interactions in Water and Other H-bonded Species.

    PubMed

    Weinhold, F

    2005-01-01

    Hydrogen bonding underlies the structure of water and all biochemical processes in aqueous medium. Analysis of modern ab initio wave functions in terms of natural bond orbitals (NBOs) strongly suggests the resonance-type "charge transfer" (CT) character of H-bonding, contrary to the widely held classical-electrostatic viewpoint that underlies current molecular dynamics (MD) modeling technology. Quantum cluster equilibrium (QCE) theory provides an alternative ab initio-based picture of liquid water that predicts proton-ordered two-coordinate H-bonding patterns, dramatically different from the ice-like picture of electrostatics-based MD simulations. Recent X-ray absorption and Raman scattering experiments of Nilsson and co-workers confirm the microstructural two-coordinate picture of liquid water. We show how such cooperative "unsaturated" ring/chain topologies arise naturally from the fundamental resonance-CT nature of B:cdots, three dots, centeredHA hydrogen bonding, which is expressed in NBO language as n(B)-->sigma(AH)(*) intermolecular delocalization from a filled lone pair n(B) of the Lewis base (B:) into the proximal antibond sigma(AH)(*) of the Lewis acid (HA). Stabilizing n(O)-->sigma(OH)(*) orbital delocalization, equivalent to partial mixing of resonance structures H(2)O:cdots, three dots, centeredHOH H(3)O(+) cdots, three dots, centered(-):OH, is thereby seen to be the electronic origin of general enthalpic and entropic propensities that favor relatively small cyclic clusters such as water pentamers W(5c) in the QCE liquid phase. We also discuss the thermodynamically competitive three-coordinate clusters (e.g., icosahedral water buckyballs, W(24)), which appear to play a role in hydrophobic solvation phenomena. We conclude with suggestions for incorporating resonance-CT aspects of H-bonding into empirical MD simulation potentials in a computationally tractable manner. PMID:16581375

  20. Communication: Frequency shifts of an intramolecular hydrogen bond as a measure of intermolecular hydrogen bond strengths

    NASA Astrophysics Data System (ADS)

    Gu, Quanli; Trindle, Carl; Knee, J. L.

    2012-09-01

    Infrared-ultraviolet double resonance spectroscopy has been applied to study the infrared spectra of the supersonically cooled gas phase complexes of formic acid, acetic acid, propionic acid, formamide, and water with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. In these complexes each binding partner to 9HFCA can function as both proton donor and acceptor. Relative to its frequency in free 9HFCA, the 9-hydroxy (9OH) stretch is blue shifted in complexes with formic, acetic, and propionic acids, but is red shifted in the complexes with formamide and water. Density functional calculations on complexes of 9HFCA to a variety of H bonding partners with differing proton donor and acceptor abilities reveal that the quantitative frequency shift of the 9OH can be attributed to the balance struck between two competing intermolecular H bonds. More extensive calculations on complexes of glycolic acid show excellent consistency with the experimental frequency shifts.

  1. Collective vibrational effects in hydrogen bonded liquid amides and proteins studied by isotopic substitution

    NASA Astrophysics Data System (ADS)

    Nielsen, O. F.; Johansson, C.; Christensen, D. H.; Hvidt, S.; Flink, J.; Høime Hansen, S.; Poulsen, F.

    2000-09-01

    Raman spectroscopy is used to study the fast dynamics of simple liquid amides and proteins. Raman spectra in the visible region of liquid amides are obtained with a triple additive scanning monochromator, whereas FT-Raman technique is used in the near-IR region in order to avoid fluorescence from impurities in the proteins. Raman spectra are shown in the amide-I region of HCONHCH 3 ( N-methylformamide with all isotopes in their natural abundance), H 13CONHCH 3, HC 18ONHCH 3, human growth hormone, frog tropomyosin and chymotrypsin inhibitor 2 including C-13 and N-15 enriched samples of the latter. Resonance energy transfer (RET) between amide molecules gives rise to a non-coincidence effect of the anisotropic and the isotropic components of the amide-I band. This effect influences the band position in mixtures of liquid amide isotopomers. A further spectral feature caused by collective vibrational modes in the hydrogen bonded liquid amides is named coalescence of bands in mixtures of isotopomers (CBMI). The result of this effect is that only one band is found in mixtures of isotopomers where bands at different frequencies are observed for each of the isotopomers. A similar effect may account for the observation of protein amide-I bands with frequencies dependent only on the secondary structure of the protein and not on the amino acid residues. RET and CBMI are due to a collectivity of vibrational modes in different amide molecules. This collectivity may be related to a cooperativity of hydrogen bonds. A low-frequency band around 100 cm -1 is observed in hydrogen bonded liquid amides and proteins. Isotopic substitution shows that the mode corresponding to this band involves displacements of atoms in hydrogen bonds. This mode may drive a breaking of the hydrogen bond.

  2. Synthesis of substituted β-diketiminate gallium hydrides via oxidative addition of H-O bonds.

    PubMed

    Herappe-Mejía, Eduardo; Trujillo-Hernández, Karla; Carlos Garduño-Jiménez, Juan; Cortés-Guzmán, Fernando; Martínez-Otero, Diego; Jancik, Vojtech

    2015-10-14

    Oxidative addition of LGa into the OH bonds from HCCCH2OH, Ph2Si(OH)2, (nBuO)2P(O)(OH) and 4-MeC6H4S(O)2(OH) results in the formation of four compounds of the general formula LGa(H)(O-X). The correlation of the Ga-O bond length and the strength of the Ga-H bond depending on the acidity of the OH group in the starting materials has been demonstrated. The molecular structures of all four compounds have been determined using single crystal X-ray diffraction experiments. DFT calculations were performed on the reacting complex of LGa with propargyl alcohol and show an OHGa hydrogen bond as the first interaction between the reagents. This reacting complex changes into a D-A complex where the oxygen atom of the propargyl alcohol coordinates to the gallium atom and in a concerted reaction the oxidative addition product is formed. PMID:26351779

  3. Formation of hydrogen-bonded chains through inter- and intra-molecular hydrogen bonds by a strong base of guanidine-like character and 2,2'-biphenols

    NASA Astrophysics Data System (ADS)

    Brzezinski, B.; Wojciechowski, G.; Bartl, F.; Zundel, G.

    2000-11-01

    2,2'-Biphenol mixtures with 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene (MTBD) were studied by FTIR spectroscopy. In chloroform, a proton transfer from 2,2'-biphenol to MTBD occurs. In this solution the protonated MTBD molecules are hydrogen-bonded to the 2,2'-biphenol-2,2'-biphenolate chains. In acetonitrile, after the proton transfer, the complexes dissociate and hence protonated MTBD molecules and hydrogen-bonded 2,2'-biphenol-2,2'-biphenolate chains are present. The hydrogen bonds and the hydrogen-bonded chains show large proton polarizability. In the systems intra- as well as inter-molecular hydrogen bonds are formed.

  4. Topological properties of hydrogen bonds and covalent bonds from charge densities obtained by the maximum entropy method (MEM)

    PubMed Central

    Netzel, Jeanette; van Smaalen, Sander

    2009-01-01

    Charge densities have been determined by the Maximum Entropy Method (MEM) from the high-resolution, low-temperature (T ≃ 20 K) X-ray diffraction data of six different crystals of amino acids and peptides. A comparison of dynamic deformation densities of the MEM with static and dynamic deformation densities of multipole models shows that the MEM may lead to a better description of the electron density in hydrogen bonds in cases where the multipole model has been restricted to isotropic displacement parameters and low-order multipoles (l max = 1) for the H atoms. Topological properties at bond critical points (BCPs) are found to depend systematically on the bond length, but with different functions for covalent C—C, C—N and C—O bonds, and for hydrogen bonds together with covalent C—H and N—H bonds. Similar dependencies are known for AIM properties derived from static multipole densities. The ratio of potential and kinetic energy densities |V(BCP)|/G(BCP) is successfully used for a classification of hydrogen bonds according to their distance d(H⋯O) between the H atom and the acceptor atom. The classification based on MEM densities coincides with the usual classification of hydrogen bonds as strong, intermediate and weak [Jeffrey (1997) ▶. An Introduction to Hydrogen Bonding. Oxford University Press]. MEM and procrystal densities lead to similar values of the densities at the BCPs of hydrogen bonds, but differences are shown to prevail, such that it is found that only the true charge density, represented by MEM densities, the multipole model or some other method can lead to the correct characterization of chemical bonding. Our results do not confirm suggestions in the literature that the promolecule density might be sufficient for a characterization of hydrogen bonds. PMID:19767685

  5. Intramolecular hydrogen bonds in sulfur-containing aminophenols

    NASA Astrophysics Data System (ADS)

    Belkov, M. V.; Harbachova, A. N.; Ksendzova, G. A.; Polozov, G. I.; Skornyakov, I. V.; Sorokin, V. L.; Tolstorozhev, G. B.; Shadyro, O. I.

    2010-07-01

    IR Fourier spectroscopy methods have been adopted to study intramolecular interactions that occur in CCl4 solutions of antiviral derivatives of aminophenol. Analysis of the IR spectra showed that intramolecular bonds O-H···N, O-H···O=C, N-H···O=S=O, and O-H···O=S=O can occur in these compounds depending on the substituent on the amino group. Not only the presence of intramolecular O-H···N, O-H···O=S=O, and N- H···O=S=O hydrogen bonds in 2-amino-4,6-di-tert-butylphenol derivatives containing a sulfonamide fragment but also conformational equilibrium among these types of intramolecular interactions are essential for the manifestation of high efficiency in suppressing HIV-infection in cell culture.

  6. Spectroscopic investigation and hydrogen-bonding analysis of triazinones.

    PubMed

    Dhas, Devadhas Arul; Joe, Isaac Hubert; Roy, Solomon Dawn Dharma; Balachandran, Sreedharan

    2012-08-01

    NIR FT-Raman, FTIR and UV-vis spectra of the herbicide metamitron were recorded and analyzed. The aromaticities, equilibrium geometries, bonding features, electrostatic potentials, and harmonic vibrational wavenumbers of the monomers and dimers of triazinone derivatives were also investigated with the aid of BLYP/6-311 G(df, p) density functional theory. Features in the vibrational spectra were assigned with the aid of the VEDA.4 program. The calculated results were a good match to the experimental data obtained from FTIR, Raman, and electronic absorption spectra. Mulliken population analysis was performed on the atomic charges and the HOMO-LUMO energies were also calculated. NBO analysis highlighted the intra- and intermolecular N-H…O and C-H…O hydrogen bonds in the crystal structures of the triazinones. The solvent effect was calculated using time-dependent density functional theory in combination with the polarizable continuum model. PMID:22350295

  7. Bonding changes in hot fluid hydrogen at megabar pressures

    PubMed Central

    Subramanian, Natarajan; Goncharov, Alexander F.; Struzhkin, Viktor V.; Somayazulu, Maddury; Hemley, Russell J.

    2011-01-01

    Raman spectroscopy in laser-heated diamond anvil cells has been employed to probe the bonding state and phase diagram of dense hydrogen up to 140 GPa and 1,500 K. The measurements were made possible as a result of the development of new techniques for containing and probing the hot, dense fluid, which is of fundamental importance in physics, planetary science, and astrophysics. A pronounced discontinuous softening of the molecular vibron was found at elevated temperatures along with a large broadening and decrease in intensity of the roton bands. These phenomena indicate the existence of a state of the fluid having significantly modified intramolecular bonding. The results are consistent with the existence of a pressure-induced transformation in the fluid related to the presence of a temperature maximum in the melting line as a function of pressure. PMID:21447715

  8. Enzymatic Functionalization of Carbon-Hydrogen Bonds1

    PubMed Central

    Lewis, Jared C.; Coelho, Pedro S.

    2010-01-01

    The development of new catalytic methods to functionalize carbon-hydrogen (C-H) bonds continues to progress at a rapid pace due to the significant economic and environmental benefits of these transformations over traditional synthetic methods. In nature, enzymes catalyze regio- and stereoselective C-H bond functionalization using transformations ranging from hydroxylation to hydroalkylation under ambient reaction conditions. The efficiency of these enzymes relative to analogous chemical processes has led to their increased use as biocatalysts in preparative and industrial applications. Furthermore, unlike small molecule catalysts, enzymes can be systematically optimized via directed evolution for a particular application and can be expressed in vivo to augment the biosynthetic capability of living organisms. While a variety of technical challenges must still be overcome for practical application of many enzymes for C-H bond functionalization, continued research on natural enzymes and on novel artificial metalloenzymes will lead to improved synthetic processes for efficient synthesis of complex molecules. In this critical review, we discuss the most prevalent mechanistic strategies used by enzymes to functionalize non-acidic C-H bonds, the application and evolution of these enzymes for chemical synthesis, and a number of potential biosynthetic capabilities uniquely enabled by these powerful catalysts. PMID:21079862

  9. Hydrogen-Bonding-Supported Self-Healing Antifogging Thin Films

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaojie; He, Junhui

    2015-03-01

    Inspired by the repair of DNA through efficient reformation of hydrogen bonds (H-bonds), herein we report a facile one-step approach to construction of self-healing antifogging thin films on the basis of partly cross-linked poly(vinyl alcohol)(PVA) and poly(acrylic acid)(PAA). By designing the molar ratio of hydroxyl groups to carboxyl groups, the cross-linked polymer thin films maintain abundant free hydroxyl groups to present excellent antifogging property, which is derived from the hydrophilicity and hygroscopicity of the thin films. The thin films showed smart intrinsic self-healing characteristics towards wounds caused by external forces, which is attributed to sufficient free hydroxyl groups at the scratched interfaces to reform H-bonds across the interfaces and a sufficient chain mobility that is indispensable for chain diffusion across the interfaces and hydroxyl groups association to form H-bonds. No synthetic surfaces reported so far possess all the unique characteristics of the polymer thin films: intrinsic self-healing, long-term antifogging, excellent mechanical property, high transmittance and large-scale feasibility.

  10. Chemical bonding of hydrogen molecules to transition metal complexes

    SciTech Connect

    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.

  11. Hydrogen-bonding-supported self-healing antifogging thin films.

    PubMed

    Zhang, Xiaojie; He, Junhui

    2015-01-01

    Inspired by the repair of DNA through efficient reformation of hydrogen bonds (H-bonds), herein we report a facile one-step approach to construction of self-healing antifogging thin films on the basis of partly cross-linked poly(vinyl alcohol)(PVA) and poly(acrylic acid)(PAA). By designing the molar ratio of hydroxyl groups to carboxyl groups, the cross-linked polymer thin films maintain abundant free hydroxyl groups to present excellent antifogging property, which is derived from the hydrophilicity and hygroscopicity of the thin films. The thin films showed smart intrinsic self-healing characteristics towards wounds caused by external forces, which is attributed to sufficient free hydroxyl groups at the scratched interfaces to reform H-bonds across the interfaces and a sufficient chain mobility that is indispensable for chain diffusion across the interfaces and hydroxyl groups association to form H-bonds. No synthetic surfaces reported so far possess all the unique characteristics of the polymer thin films: intrinsic self-healing, long-term antifogging, excellent mechanical property, high transmittance and large-scale feasibility. PMID:25784188

  12. Sh-Stretching Intensities and Intramolecular Hydrogen Bonding in Alkanethiols

    NASA Astrophysics Data System (ADS)

    Miller, B. J.; Lane, J. R.; Sodergren, A. H.; Kjaergaard, H. G.; Dunn, M. E.; Vaida, V.

    2009-06-01

    The SH-stretching overtone transitions of tert-butylthiol and ethanethiol are observed using FT-IR, NIR and photoacoustic spectroscopies. The intensities of these are compared with OH-stretching overtones from the corresponding alcohols. We explain the paucity of SH-stretching intensity using an anharmonic oscillator local mode model. SH- and OH-stretching overtone spectra of 1,2-ethanedithiol and 2-mercaptoethanol are recorded to observe the different effects that hydrogen bonding involving SH - - - S, SH - - - O and OH - - - S have on the spectra. We discuss these effects with the help of high level ab initio calculations.

  13. Anharmonicity and hydrogen bonding in electrooptic sucrose crystal

    NASA Astrophysics Data System (ADS)

    Szostak, M. M.; Giermańska, J.

    1990-03-01

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

  14. Well-defined polymeric materials incorporating strong hydrogen bonding groups

    NASA Astrophysics Data System (ADS)

    Feldman, Kathleen E.

    The field of supramolecular chemistry has drastically grown in recent years, and in particular the development of new strongly hydrogen bonding groups has yielded numerous fundamental and practical advances allowing for the design of materials with unique combinations of macroscopic properties. For polymers whose properties typically are rather insensitive to temperature (other than e.g. when passing through the glass transition), the incorporation of hydrogen bonding groups into their structures can provide a new handle with which to tune their structural, mechanical, and thermal behavior. Limited fundamental studies exist, however, in which the combined effects of the polymer behavior and supramolecular interactions are characterized. In this work new chemistry has been developed to allow the synthesis of well-defined polymers containing quadruple hydrogen bonding groups which bind either through a complementary or self-complementary interaction. The MHB groups can be incorporated either at the chain end or along the backbone, and through simple blending a number of different architectures can be obtained. In the simplest case, two chemically distinct homopolymers with MHB groups attached at a single chain end were mixed to produce supramolecular copolymers analogous to traditional diblocks. The nature of the hydrogen bonding groups was found to be highly influential in determining the bulk microstructure. In analyzing the phase behavior of such blends, a new polymer system was discovered to display lower critical ordering behavior and its temperature dependent Flory-Huggins c parameter was measured. By randomly incorporating strongly self-complementary MHB groups as side chains rather than end groups, a new class of thermoplastic elastomers was developed which are unentangled and contain no glassy or crystalline domains, yet show dynamical properties in some ways typical of polymer networks. The study of ABA triblock copolymer-like architectures in which the MHB

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

    NASA Astrophysics Data System (ADS)

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

    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 Tg.

  16. Modelling OH⋯O hydrogen bonds in carbohydrates

    NASA Astrophysics Data System (ADS)

    Jeffrey, G. A.

    1990-09-01

    Hydrogen-bonding is particularly significant in the molecular modelling of the molecules of glycobiology because of the large number of OH⋯O functional groups for each carbohydrate monomer in these oligo- and macromolecules. This requires appropriate parameterization of the electrostatic interactions, which is considered to be the least well-developed component of molecular mechanics and dynamics formulations. Oligo- and polysaccharides are more difficult to model, in this respect, than oligo- and polypeptides and nucleotides because of the orientational freedom of the hydroxyl groups. The extension of present methods to carbohydrates is discussed.

  17. Electrons and Hydrogen-Bond Connectivity in Liquid Water

    SciTech Connect

    Fernandez-Serra, M.V.; Artacho, Emilio

    2006-01-13

    The network connectivity in liquid water is revised in terms of electronic signatures of hydrogen bonds (HBs) instead of geometric criteria, in view of recent x-ray absorption studies. The analysis is based on ab initio molecular-dynamics simulations at ambient conditions. Even if instantaneous threadlike structures are observed in the electronic network, they continuously reshape in oscillations reminiscent of the r and t modes in ice ({tau}{approx}170 fs). However, two water molecules initially joined by a HB remain effectively bound over many periods regardless of its electronic signature.

  18. Strength and nature of hydrogen bonding interactions in mono- and di-hydrated formamide complexes.

    PubMed

    Angelina, Emilio L; Peruchena, Nélida M

    2011-05-12

    In this work, mono- and di-hydrated complexes of the formamide were studied. The calculations were performed at the MP2/6-311++G(d,p) level of approximation. The atoms in molecules theory (AIM), based on the topological properties of the electronic density distribution, was used to characterize the different types of bonds. The analysis of the hydrogen bonds (H-bonds) in the most stable mono- and di-hydrated formamide complexes shows a mutual reinforcement of the interactions, and some of these complexes can be considered as "bifunctional hydrogen bonding hydration complexes". In addition, we analyzed how the strength and the nature of the interactions, in mono-hydrated complexes, are modified by the presence of a second water molecule in di-hydrated formamide complexes. Structural changes, cooperativity, and electron density redistributions demonstrate that the H-bonds are stronger in the di-hydrated complexes than in the corresponding mono-hydrated complexes, wherein the σ- and π-electron delocalization were found. To explain the nature of such interactions, we carried out the atoms in molecules theory in conjunction with reduced variational space self-consistent field (RVS) decomposition analysis. On the basis of the local Virial theorem, the characteristics of the local electron energy density components at the bond critical points (BCPs) (the 1/4∇ (2)ρ(b) component of electron energy density and the kinetic energy density) were analyzed. These parameters were used in conjunction with the electron density and the Laplacian of the electron density to analyze the characteristics of the interactions. The analysis of the interaction energy components for the systems considered indicates that the strengthening of the hydrogen bonds is manifested by an increased contribution of the electrostatic energy component represented by the kinetic energy density at the BCP. PMID:21506592

  19. Structure and energetics of hydrogen-bonded networks of methanol on close packed transition metal surfaces

    NASA Astrophysics Data System (ADS)

    Murphy, Colin J.; Carrasco, Javier; Lawton, Timothy J.; Liriano, Melissa L.; Baber, Ashleigh E.; Lewis, Emily A.; Michaelides, Angelos; Sykes, E. Charles H.

    2014-07-01

    Methanol is a versatile chemical feedstock, fuel source, and energy storage material. Many reactions involving methanol are catalyzed by transition metal surfaces, on which hydrogen-bonded methanol overlayers form. As with water, the structure of these overlayers is expected to depend on a delicate balance of hydrogen bonding and adsorbate-substrate bonding. In contrast to water, however, relatively little is known about the structures methanol overlayers form and how these vary from one substrate to another. To address this issue, herein we analyze the hydrogen bonded networks that methanol forms as a function of coverage on three catalytically important surfaces, Au(111), Cu(111), and Pt(111), using a combination of scanning tunneling microscopy and density functional theory. We investigate the effect of intermolecular interactions, surface coverage, and adsorption energies on molecular assembly and compare the results to more widely studied water networks on the same surfaces. Two main factors are shown to direct the structure of methanol on the surfaces studied: the surface coverage and the competition between the methanol-methanol and methanol-surface interactions. Additionally, we report a new chiral form of buckled hexamer formed by surface bound methanol that maximizes the interactions between methanol monomers by sacrificing interactions with the surface. These results serve as a direct comparison of interaction strength, assembly, and chirality of methanol networks on Au(111), Cu(111), and Pt(111) which are catalytically relevant for methanol oxidation, steam reforming, and direct methanol fuel cells.

  20. Tetrakis(pyridine)tetrachloro(. mu. -chloro)(. mu. -hydrido)ditungsten (W-W) and its 4-ethylpyridine homologue. Compounds derived from a quadruply bonded dimer by ligand exchange and oxidative addition of hydrogen chloride

    SciTech Connect

    Carlin, R.T.; McCarley, R.E. )

    1989-06-28

    Reaction of W{sub 2}(mhp){sub 4} (mhp = anion of 6-methyl-2-hydroxypyridine) with (CH{sub 3}){sub 3}SiCl and pyridine in the presence of methanol provides the light brown compound W{sub 2}HCl{sub 5}(NC{sub 5}H{sub 5}){sub 4}. The 4-ethylpyridine adduct W{sub 2}HCl{sub 5}(NC{sub 5}H{sub 4}C{sub 2}H{sub 5}){sub 4} is obtained by ligand exchange at 100{degree}C. Brown crystals of the latter are monoclinic, space group C2/c, with a = 11.883 (3) {angstrom}, b = 13.213 (3) {angstrom}, c = 21.727 (4) {angstrom}, {beta} = 96.39 (3){degree}, and Z = 4. Structure refinement revealed an edge-shared bioctahedral arrangement with one H atom and one Cl atom in bridging positions between the metal atoms. The Cl atoms all occupy positions in the equatorial plane, and the 4-ethylpyridine ligands occupy the axial positions of the dimer. The short W-W distance, 2.516 (2) {angstrom}, is consistent with a W-W multiple bond. Comparison of the infrared spectra of the hydride and deuteride derivatives confirms the presence of a bridging H atom and indicates an isostructural arrangement for the pyridine and 4-ethylpyridine derivatives, as do electronic reflectance spectra. 33 refs., 4 figs., 4 tabs.

  1. Sum frequency generation of hydrogen-bonding liquid surfaces

    NASA Astrophysics Data System (ADS)

    Baldelli, Steve

    The surface-specific vibrational spectroscopy sum frequency generation (SFG) is used to examine the physical/chemical environment of molecules at the liquid/air interface. In glycerol/water mixtures, glycerol is found to partition to the surface in excess compared to the bulk concentration. Further, it is discovered that the free OH peak of water (an OH group projecting out of the liquid into the vapor) can be used as an indicator of the surface coverage of water at the surface. Solutions of alkali sulfate salts also affect the surface structure of water. These ions increase the ordered structure of water at the interface by increasing the oriented hydrogen-bond network. This order-increasing effect is found to occur to a greater extent for sulfuric acid solutions. A model based on ion association and a sub-surface electric double-layer is used to describe these results. A correlation between the surface coverage of water and the extent of dissociation of the acid is discovered; i.e., increasing acid association decreases the surface coverage of water. Finally, solutions of HCl/water are investigated. In these systems, the electrolytic nature of HCl is found to increase the hydrogen-bonded order of the interfacial water molecules. Further, despite the polar nature of HCl, no molecular HCl is detected on any surface despite surface tension measurements indicating an excess of HCl at the surface. The neat HCl liquid surface is the only system where molecular HCl is observed.

  2. Hydrogen bond competition in the ethanol-methanol dimer.

    PubMed

    Finneran, Ian A; Carroll, P Brandon; Mead, Griffin J; Blake, Geoffrey A

    2016-08-10

    Previous theoretical work on the ethanol-methanol dimer has been inconclusive in predicting the preferred hydrogen bond donor/acceptor configuration. Here, we report the microwave spectrum of the dimer using a chirped pulse Fourier transform microwave spectrometer from 8-18 GHz. In an argon-backed expansion, 50 transitions have been assigned to a trans-ethanol-acceptor/methanol-donor structure that is likely stabilized by a secondary weak C-HO hydrogen bond. A higher energy conformer was observed in a helium-backed expansion and tentatively assigned to a gauche-ethanol-acceptor/methanol-donor structure. No ethanol-donor/methanol-acceptor dimers have been found, suggesting such interactions are energetically disfavored. A preliminary analysis of the A-E splitting due to the internal rotation of the methanol methyl group in the ground state species is also presented. We find evidence of the Ubbelohde effect in the measured A-E splittings of three deuterated isotopologues and the normal species of this conformer. PMID:27472828

  3. Combined Electrostatics and Hydrogen Bonding Determine PIP2 Intermolecular Interactions

    PubMed Central

    Levental, Ilya; Cebers, Andrejs; Janmey, Paul A.

    2010-01-01

    Membrane lipids are active contributors to cell function as key mediators in signaling pathways of inflammation, apoptosis, migration, and proliferation. Recent work on multimolecular lipid structures suggests a critical role for lipid organization in regulating the function of both lipids and proteins. Of particular interest in this context are the polyphosphoinositides (PPI’s), specifically phosphatidylinositol (4,5) bisphosphate (PIP2). The cellular functions of PIP2 are numerous but the factors controlling targeting of PIP2 to specific proteins and organization of PIP2 in the inner leaflet of the plasma membrane remain poorly understood. To analyze the organization of PIP2 in a simplified planar system, we used Langmuir monolayers to study the effects of subphase conditions on monolayers of purified naturally derived PIP2 and other anionic or zwitterionic phospholipids. We report a significant molecular area expanding effect of subphase monovalent salts on PIP2 at biologically relevant surface densities. This effect is shown to be specific to PIP2 and independent of subphase pH. Chaotropic agents (e.g. salts, trehalose, urea, temperature) that disrupt water structure and the ability of water to mediate intermolecular hydrogen bonding also specifically expanded PIP2 monolayers. These results suggest a combination of water-mediated hydrogen bonding and headgroup charge in determining the organization of PIP2, and may provide an explanation for the unique functionality of PIP2 compared to other anionic phospholipids. PMID:18572937

  4. Friction and Hydration Repulsion Between Hydrogen-Bonding Surfaces

    NASA Astrophysics Data System (ADS)

    Netz, Roland

    2012-02-01

    The dynamics and statics of polar surfaces are governed by the hydrogen-bonding network and the interfacial water layer properties. Insight can be gained from all-atomistic simulations with explicit water that reach the experimentally relevant length and time scales. Two connected lines of work will be discussed: 1) On surfaces, the friction coefficient of bound peptides is very low on hydrophobic substrates, which is traced back to the presence of a depletion layer between substrate and water that forms a lubrication layer. Conversely, friction forces on hydrophilic substrates are large. A general friction law is presented and describes the dynamics of hydrogen-bonded matter in the viscous limit. 2) The so-called hydration repulsion between polar surfaces in water is studied using a novel simulation technique that allows to efficiently determine the interaction pressure at constant water chemical potential. The hydration repulsion is shown to be caused by a mixture of water polarization effects and the desorption of interfacial water.

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

    NASA Astrophysics Data System (ADS)

    Wang, Yuhao; Sukhishvili, Svetlana

    2015-03-01

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

  6. Water’s dual nature and its continuously changing hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Henchman, Richard H.

    2016-09-01

    A model is proposed for liquid water that is a continuum between the ordered state with predominantly tetrahedral coordination, linear hydrogen bonds and activated dynamics and a disordered state with a continuous distribution of multiple coordinations, multiple types of hydrogen bond, and diffusive dynamics, similar to that of normal liquids. Central to water’s heterogeneous structure is the ability of hydrogen to donate to either one acceptor in a conventional linear hydrogen bond or to multiple acceptors as a furcated hydrogen. Linear hydrogen bonds are marked by slow, activated kinetics for hydrogen-bond switching to more crowded acceptors and sharp first peaks in the hydrogen-oxygen radial distribution function. Furcated hydrogens, equivalent to free, broken, dangling or distorted hydrogens, have barrierless, rapid kinetics and poorly defined first peaks in their hydrogen-oxygen radial distribution function. They involve the weakest donor in a local excess of donors, such that barrierless whole-molecule vibration rapidly swaps them between the linear and furcated forms. Despite the low number of furcated hydrogens and their transient existence, they are readily created in a single hydrogen-bond switch and free up the dynamics of numerous surrounding molecules, bringing about the disordered state. Hydrogens in the ordered state switch with activated dynamics to make the non-tetrahedral coordinations of the disordered state, which can also combine to make the ordered state. Consequently, the ordered and disordered states are both connected by diffusive dynamics and differentiated by activated dynamics, bringing about water’s continuous heterogeneity.

  7. On the nature of hydrogen bonding between the phosphatidylcholine head group and water and dimethylsulfoxide

    NASA Astrophysics Data System (ADS)

    Dabkowska, Aleksandra P.; Lawrence, M. Jayne; McLain, Sylvia E.; Lorenz, Christian D.

    2013-01-01

    Molecular dynamics simulations are used to provide a detailed investigation of the hydrogen bond networks around the phosphatidylcholine (PC) head group in 1,2-dipropionyl-sn-glycero-3-phosphocholine in pure water, 10 mol.% and 30 mol.% dimethylsulfoxide (DMSO)-water solutions. Specifically, it is observed that DMSO replaces those water molecules that are within the first solvation shell of the choline, phosphate and ester groups of the PC head group, but are not hydrogen-bonded to the group. The effect of the presence of DMSO on the hydrogen bond network around the PC head groups of the lipid changes with the concentration of DMSO. In comparison to the hydrogen bond network observed in the pure water system, the number of hydrogen-bonded chains of solvent molecules increases slightly for the 10 mol.% DMSO system, while, in the 30 mol.% DMSO system, the number of hydrogen-bonded chains of solvent molecules decreases.

  8. Hydrogen Bond Migration between Molecular Sites Observed with Ultrafast 2D IR Chemical Exchange Spectroscopy

    PubMed Central

    Rosenfeld, Daniel E.; Kwak, Kyungwon; Gengeliczki, Zsolt

    2010-01-01

    Hydrogen bonded complexes between phenol and phenylacetylene are studied using ultrafast two-dimensional infrared (2D IR) chemical exchange spectroscopy. Phenylacetylene has two possible π hydrogen bonding acceptor sites (phenyl or acetylene) that compete for hydrogen bond donors in solution at room temperature. The OD stretch frequency of deuterated phenol is sensitive to which acceptor site it is bound. The appearance of off-diagonal peaks between the two vibrational frequencies in the 2D IR spectrum reports on the exchange process between the two competitive hydrogen bonding sites of phenol-phenylacetylene complexes in the neat phenylacetylene solvent. The chemical exchange process occurs in ∼5 ps, and is assigned to direct hydrogen bond migration along the phenylacetylene molecule. Other non-migration mechanisms are ruled out by performing 2D IR experiments on phenol dissolved in the phenylacetylene/carbon tetrachloride mixed solvent. The observation of direct hydrogen bond migration can have implications for macromolecular systems. PMID:20121275

  9. Thwarting Crystallization through Hydrogen Bonding in Triazine Molecular Glasses

    NASA Astrophysics Data System (ADS)

    Laventure, Audrey; Soldera, Armand; Lebel, Olivier; Pellerin, Christian

    2015-03-01

    Using irregular shaped molecules interacting weakly with each other is the most intuitive choice to generate amorphous molecular materials. In contrast, H-bonds are commonly used in crystal engineering to create predictable ordered and well-packed structures. In spite of this fact, Lebel et al. have demonstrated that H-bonds can be used efficiently to thwart crystallization by inducing the self-assembly of aggregates that pack poorly. Since 2006, libraries of triazine derivatives with a variety of different substituents capable of forming molecular glasses have been synthesized and studied. Their outstanding glass-forming ability (with critical cooling rates lower than 0.5 °C/min) and their wide range of Tg (from below ambient temperature up to 160 °C) make them an attractive amorphous model system to deepen our understanding of the relationship between microscopic features and macroscopic behavior of glasses. In this presentation, we will show that variable-temperature infrared spectroscopy is a tool of choice to probe the vitreous state of these compounds. We take advantage of the selectivity of this technique to correlate their molecular features to their thermal properties. Quantitative monitoring of hydrogen bonds during vitrification will be addressed.

  10. Supramolecular polymerisation in water; elucidating the role of hydrophobic and hydrogen-bond interactions.

    PubMed

    Leenders, Christianus M A; Baker, Matthew B; Pijpers, Imke A B; Lafleur, René P M; Albertazzi, Lorenzo; Palmans, Anja R A; Meijer, E W

    2016-03-21

    Understanding the self-assembly of small molecules in water is crucial for the development of responsive, biocompatible soft materials. Here, a family of benzene-1,3,5-tricarboxamide (BTA) derivatives that comprise a BTA moiety connected to an amphiphilic chain is synthesised with the aim to elucidate the role of hydrophobic and hydrogen-bonding interactions in the self-assembly of these BTAs. The amphiphilic chain consists of an alkyl chain with a length of 10, 11, or 12 methylene units, connected to a tetraethylene glycol (at the periphery). The results show that an undecyl spacer is the minimum length required for these BTAs to self-assemble into supramolecular polymers. Interestingly, exchange studies reveal only minor differences in exchange rates between BTAs containing undecyl or dodecyl spacers. Additionally, IR spectroscopy provides the first experimental evidence that hydrogen-bonding is operative and contributes to the stabilisation of the supramolecular polymers in water. PMID:26892482

  11. Mesoscopic model parametrization of hydrogen bonds and stacking interactions of RNA from melting temperatures

    PubMed Central

    Weber, Gerald

    2013-01-01

    Information about molecular interactions in DNA can be obtained from experimental melting temperature data by using mesoscopic statistical physics models. Here, we extend the technique to RNA and show that the new parameters correctly reproduce known properties such as the stronger hydrogen bonds of AU base pairs. We also were able to calculate a complete set of elastic constants for all 10 irreducible combinations of nearest neighbours (NNs). We believe that this is particularly useful as experimentally derived information about RNA elasticity is relatively scarce. The melting temperature prediction using the present model improves over those from traditional NN model, providing thus an alternative way to calculate these temperatures for RNA. Additionally, we calculated the site-dependent base pair oscillation to explain why RNA shows larger oscillation amplitudes despite having stronger AU hydrogen bonds. PMID:23087379

  12. Hydrogen bonding in DPD: application to low molecular weight alcohol-water mixtures.

    PubMed

    Kacar, Gokhan; de With, Gijsbertus

    2016-04-14

    In this work we propose a computational approach to mimic hydrogen bonding in a widely used coarse-grained simulation method known as dissipative particle dynamics (DPD). The conventional DPD potential is modified by adding a Morse potential term to represent hydrogen bonding attraction. Morse potential parameters are calculated by a mapping of energetic and structural properties to those of atomistic scale simulations. By the addition of hydrogen bonding to DPD and with the proposed parameterization, the volumetric mixing behavior of low molecular weight alcohols and water is studied and experimentally observed negative volume excess is successfully predicted, contrary to the conventional DPD implementation. Moreover, the density-dependent DPD parameterization employed provides the asymmetrical shapes of the excess volume curves. In addition, alcohol surface enrichment at the air interface and self-assembly in the bulk is studied. The surface concentrations of alcohols at the air interface compare favorably with the experimental observations at all bulk-phase alcohol fractions and, in consonance with experiment, some clustering is observed. PMID:26986630

  13. Urea, but not guanidinium, destabilizes proteins by forming hydrogen bonds to the peptide group.

    PubMed

    Lim, Woon Ki; Rösgen, Jörg; Englander, S Walter

    2009-02-24

    The mechanism by which urea and guanidinium destabilize protein structure is controversial. We tested the possibility that these denaturants form hydrogen bonds with peptide groups by measuring their ability to block acid- and base-catalyzed peptide hydrogen exchange. The peptide hydrogen bonding found appears sufficient to explain the thermodynamic denaturing effect of urea. Results for guanidinium, however, are contrary to the expectation that it might H-bond. Evidently, urea and guanidinium, although structurally similar, denature proteins by different mechanisms. PMID:19196963

  14. Characterization of intramolecular hydrogen bonds by atomic charges and charge fluxes.

    PubMed

    Baranović, Goran; Biliškov, Nikola; Vojta, Danijela

    2012-08-16

    The electronic charge redistribution and the infrared intensities of the two types of intramolecular hydrogen bonds, O-H···O and O-H···π, of o-hydroxy- and o-ethynylphenol, respectively, together with a set of related intermolecular hydrogen bond complexes are described in terms of atomic charges and charge fluxes derived from atomic polar tensors calculated at the B3LYP/cc-pVTZ level of theory. The polarizable continuum model shows that both the atomic charges and charge fluxes are strongly dependent on solvent. It is shown that their values for the OH bond in an intramolecular hydrogen bond are not much different from those for the "free" OH bond, but the changes are toward the values found for an intermolecular hydrogen bond. The intermolecular hydrogen bond is characterized not only by the decreased atomic charge but also by the enlarged charge flux term of the same sign producing thus an enormous increase in IR intensity. The overall behavior of the charges and fluxes of the hydrogen atom in OH and ≡CH bonds agree well with the observed spectroscopic characteristics of inter- and intramolecular hydrogen bonding. The main reason for the differences between the two types of the hydrogen bond lies in the molecular structure because favorable linear proton donor-acceptor arrangement is not possible to achieve within a small molecule. The calculated intensities (in vacuo and in polarizable continuum) are only in qualitative agreement with the measured data. PMID:22809455

  15. A theoretical study on the hydrogen-bonding interactions between flavonoids and ethanol/water.

    PubMed

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

    2016-04-01

    Ethanol and water are the solvents most commonly used to extract flavonoids from propolis. Do hydrogen-bonding interactions exist between flavonoids and ethanol/water? In this work, this question was addressed by using density functional theory (DFT) to provide information on the hydrogen-bonding interactions between flavonoids and ethanol/water. Chrysin and Galangin were chosen as the representative flavonoids. The investigated complexes included chrysin-H2O, chrysin-CH3CH2OH, galangin-H2O and galangin-CH3CH2OH dyads. Molecular geometries, hydrogen-bond binding energies, charges of monomers and dyads, and topological analysis were studied at the B3LYP/M062X level of theory with the 6-31++G(d,p) basis set. The main conclusions were: (1) nine and ten optimized hydrogen-bond geometries were obtained for chrysin-H2O/CH3CH2OH and galangin-H2O/CH3CH2OH complexes, respectively. (2) The hydrogen atoms except aromatic H1 and H5 and all of the oxygen atoms can form hydrogen-bonds with H2O and CH3CH2OH. Ethanol and water form strong hydrogen-bonds with the hydroxyl, carbonyl and ether groups in chrysin/galangin and form weak hydrogen-bonds with aromatic hydrogen atoms. Except in structures labeled A and B, chrysin and galangin interact more strongly with H2O than CH3CH2OH. (3) When chrysin and galangin form hydrogen-bonds with H2O and CH3CH2OH, charge transfers from the hydrogen-bond acceptor (H2O and CH3CH2OH in structures A, B, G, H, I, J) to the hydrogen-bond donor (chrysin and galangin in structure A, B, G, H, I, J). The stronger hydrogen-bond makes the hydrogen-bond donor lose more charge (A> B> G> H> I> J). (4) Most of the hydrogen-bonds in chrysin/galangin-H2O/CH3CH2OH complexes may be considered as electrostatic dominant, while C-O2···H in structures labeled E and C-O5···H in structures labeled J are hydrogen-bonds combined of electrostatic and covalent characters. H9, H7, and O4 are the preferred hydrogen-bonding sites. PMID:27029620

  16. Quantum hydrogen-bond symmetrization in the superconducting hydrogen sulfide system

    NASA Astrophysics Data System (ADS)

    Errea, Ion; Calandra, Matteo; Pickard, Chris J.; Nelson, Joseph R.; Needs, Richard J.; Li, Yinwei; Liu, Hanyu; Zhang, Yunwei; Ma, Yanming; Mauri, Francesco

    2016-04-01

    The quantum nature of the proton can crucially affect the structural and physical properties of hydrogen compounds. For example, in the high-pressure phases of H2O, quantum proton fluctuations lead to symmetrization of the hydrogen bond and reduce the boundary between asymmetric and symmetric structures in the phase diagram by 30 gigapascals (ref. 3). Here we show that an analogous quantum symmetrization occurs in the recently discovered sulfur hydride superconductor with a superconducting transition temperature Tc of 203 kelvin at 155 gigapascals—the highest Tc reported for any superconductor so far. Superconductivity occurs via the formation of a compound with chemical formula H3S (sulfur trihydride) with sulfur atoms arranged on a body-centred cubic lattice. If the hydrogen atoms are treated as classical particles, then for pressures greater than about 175 gigapascals they are predicted to sit exactly halfway between two sulfur atoms in a structure with symmetry. At lower pressures, the hydrogen atoms move to an off-centre position, forming a short H–S covalent bond and a longer H···S hydrogen bond in a structure with R3m symmetry. X-ray diffraction experiments confirm the H3S stoichiometry and the sulfur lattice sites, but were unable to discriminate between the two phases. Ab initio density-functional-theory calculations show that quantum nuclear motion lowers the symmetrization pressure by 72 gigapascals for H3S and by 60 gigapascals for D3S. Consequently, we predict that the phase dominates the pressure range within which the high Tc was measured. The observed pressure dependence of Tc is accurately reproduced in our calculations for the phase, but not for the R3m phase. Therefore, the quantum nature of the proton fundamentally changes the superconducting phase diagram of H3S.

  17. Quantum hydrogen-bond symmetrization in the superconducting hydrogen sulfide system.

    PubMed

    Errea, Ion; Calandra, Matteo; Pickard, Chris J; Nelson, Joseph R; Needs, Richard J; Li, Yinwei; Liu, Hanyu; Zhang, Yunwei; Ma, Yanming; Mauri, Francesco

    2016-04-01

    The quantum nature of the proton can crucially affect the structural and physical properties of hydrogen compounds. For example, in the high-pressure phases of H2O, quantum proton fluctuations lead to symmetrization of the hydrogen bond and reduce the boundary between asymmetric and symmetric structures in the phase diagram by 30 gigapascals (ref. 3). Here we show that an analogous quantum symmetrization occurs in the recently discovered sulfur hydride superconductor with a superconducting transition temperature Tc of 203 kelvin at 155 gigapascals--the highest Tc reported for any superconductor so far. Superconductivity occurs via the formation of a compound with chemical formula H3S (sulfur trihydride) with sulfur atoms arranged on a body-centred cubic lattice. If the hydrogen atoms are treated as classical particles, then for pressures greater than about 175 gigapascals they are predicted to sit exactly halfway between two sulfur atoms in a structure with Im3m symmetry. At lower pressures, the hydrogen atoms move to an off-centre position, forming a short H-S covalent bond and a longer H···S hydrogen bond in a structure with R3m symmetry. X-ray diffraction experiments confirm the H3S stoichiometry and the sulfur lattice sites, but were unable to discriminate between the two phases. Ab initio density-functional-theory calculations show that quantum nuclear motion lowers the symmetrization pressure by 72 gigapascals for H3S and by 60 gigapascals for D3S. Consequently, we predict that the Im3m phase dominates the pressure range within which the high Tc was measured. The observed pressure dependence of Tc is accurately reproduced in our calculations for the phase, but not for the R3m phase. Therefore, the quantum nature of the proton fundamentally changes the superconducting phase diagram of H3S. PMID:27018657

  18. Shape of the proton potential in an intramolecular hydrogen-bonded system

    NASA Astrophysics Data System (ADS)

    Wojciechowski, Grzegorz; Brzezinski, Bogumil

    2001-09-01

    5,5'-dibromo-3-diethylaminomethyl-2,2'-biphenol N-oxide was studied by IR and NMR spectroscopy in chloroform and acetonitrile solutions. Two intramolecular hydrogen bonds are present in these molecules. The NO⋯H +⋯O - bond formed between the OH and the N-oxide groups is very strong. The proton potential is flat and broad and has probably no barrier. This hydrogen bond shows only slight proton polarizability. The other hydrogen bond formed between two hydroxyl groups OH⋯O -⇌ -O⋯HO is weaker and show large proton polarizability. The proton motions in both hydrogen bonds are not coupled and therefore these hydrogen bonds are not cooperative.

  19. Effect of the Hydrogen Bond in Photoinduced Water Dissociation: A Double-Edged Sword.

    PubMed

    Yang, Wenshao; Wei, Dong; Jin, Xianchi; Xu, Chenbiao; Geng, Zhenhua; Guo, Qing; Ma, Zhibo; Dai, Dongxu; Fan, Hongjun; Yang, Xueming

    2016-02-18

    Photoinduced water dissociation on rutile-TiO2 was investigated using various methods. Experimental results reveal that the water dissociation occurs via transferring an H atom to a bridge bonded oxygen site and ejecting an OH radical to the gas phase during irradiation. The reaction is strongly suppressed as the water coverage increases. Further scanning tunneling microscopy study demonstrates that hydrogen bonds between water molecules have a dramatic effect on the reaction. Interestingly, a single hydrogen bond in water dimer enhances the water dissociation reaction, while one-dimensional hydrogen bonds in water chains inhibit the reaction. Density functional theory calculations indicate that the effect of hydrogen bonds on the OH dissociation energy is likely the origin of this remarkable behavior. The results suggest that avoiding a strong hydrogen bond network between water molecules is crucial for water splitting. PMID:26810945

  20. A model of phase transitions in double-well Morse potential: Application to hydrogen bond

    NASA Astrophysics Data System (ADS)

    Goryainov, S. V.

    2012-11-01

    A model of phase transitions in double-well Morse potential is developed. Application of this model to the hydrogen bond is based on ab initio electron density calculations, which proved that the predominant contribution to the hydrogen bond energy originates from the interaction of proton with the electron shells of hydrogen-bonded atoms. This model uses a double-well Morse potential for proton. Analytical expressions for the hydrogen bond energy and the frequency of O-H stretching vibrations were obtained. Experimental data on the dependence of O-H vibration frequency on the bond length were successfully fitted with model-predicted dependences in classical and quantum mechanics approaches. Unlike empirical exponential function often used previously for dependence of O-H vibration frequency on the hydrogen bond length (Libowitzky, Mon. Chem., 1999, vol.130, 1047), the dependence reported here is theoretically substantiated.

  1. Hydrogen bond cooperativity and the three-dimensional structures of water nonamers and decamers.

    PubMed

    Pérez, Cristóbal; Zaleski, Daniel P; Seifert, Nathan A; Temelso, Berhane; Shields, George C; Kisiel, Zbigniew; Pate, Brooks H

    2014-12-22

    Broadband rotational spectroscopy of water clusters produced in a pulsed molecular jet expansion has been used to determine the oxygen atom geometry in three isomers of the nonamer and two isomers of the decamer. The isomers for each cluster size have the same nominal geometry but differ in the arrangement of their hydrogen bond networks. The nearest neighbor OO distances show a characteristic pattern for each hydrogen bond network isomer that is caused by three-body effects that produce cooperative hydrogen bonding. The observed structures are the lowest energy cluster geometries identified by quantum chemistry and the experimental and theoretical OO distances are in good agreement. The cooperativity effects revealed by the hydrogen bond OO distance variations are shown to be consistent with a simple model for hydrogen bonding in water that takes into account the cooperative and anticooperative bonding effects of nearby water molecules. PMID:25348841

  2. Quantification of Electrophilic Activation by Hydrogen-Bonding Organocatalysts

    PubMed Central

    2015-01-01

    A spectrophotometric sensor is described that provides a useful assessment of the LUMO-lowering provided by catalysts in Diels–Alder and Friedel–Crafts reactions. A broad range of 33 hydrogen-bonding catalysts was assessed with the sensor, and the relative rates in the above reactions spanned 5 orders of magnitude as determined via 1H- and 2H NMR spectroscopic measurements, respectively. The differences between the maximum wavelength shift of the sensor with and without catalyst (Δλmax–1) were found to correlate linearly with ln(krel) values for both reactions, even though the substrate feature that interacts with the catalyst differs significantly (ketone vs nitro). The sensor provides an assessment of both the inherent reactivity of a catalyst architecture as well as the sensitivity of the reaction to changes within an architecture. In contrast, catalyst pKa values are a poor measure of reactivity, although correlations have been identified within catalyst classes. PMID:25325850

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

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

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

  4. Hydrogen bonding in the benzene-ammonia dimer

    NASA Technical Reports Server (NTRS)

    Rodham, David A.; Suzuki, Sakae; Suenram, Richard D.; Lovas, Frank J.; Dasgupta, Siddharth; Goddard, William A., III; Blake, Geoffrey A.

    1993-01-01

    High-resolution optical and microwave spectra of the gas-phase benzene-ammonia dimer were obtained, showing that the ammonia molecule resides above the benzene plane and undergoes free, or nearly free, internal rotation. To estimate the binding energy (De) and other global properties of the intermolecular potential, theoretical calculations were performed for the benzene-ammonia dimer, using the Gaussian 92 (Fritsch, 1992) program at the MP2/6-31G** level. The predicted De was found to be at the lowest end of the range commonly accepted for hydrogen bonding and considerably below that of C6H6-H2O, consistent with the gas-phase acidities of ammonia and water. The observed geometry greatly resembles the amino-aromatic interaction found naturally in proteins.

  5. Ultrafast internal dynamics of flexible hydrogen-bonded supramolecular complexes.

    PubMed

    Olschewski, Martin; Knop, Stephan; Seehusen, Jaane; Lindner, Jörg; Vöhringer, Peter

    2011-02-24

    Supramolecular chemistry is intimately linked to the dynamical interplay between intermolecular forces and intramolecular flexibility. Here, we studied the ultrafast equilibrium dynamics of a supramolecular hydrogen-bonded receptor-substrate complex, 18-crown-6 monohydrate, using Fourier transform infrared (FTIR) and two-dimensional infrared (2DIR) spectroscopy in combination with numerical simulations based on molecular mechanics, density functional theory, and transition state theory. The theoretical calculations suggest that the flexibility of the macrocyclic crown ether receptor is related to an ultrafast crankshaft isomerization occurring on a time scale of several picoseconds and that the OH stretching vibrations of the substrate can serve as internal probes for the receptor's flexibility. The importance of population transfer among the vibrational modes of a given binding motif and of chemical exchange between spectroscopically distinguishable binding motifs for shaping the two-dimensional infrared spectrum and its temporal evolution is discussed. PMID:21271721

  6. Hydrogen-bonded aggregates in precise acid copolymers

    SciTech Connect

    Lueth, Christopher A.; Bolintineanu, Dan S.; Stevens, Mark J. Frischknecht, Amalie L.

    2014-02-07

    We perform atomistic molecular dynamics simulations of melts of four precise acid copolymers, two poly(ethylene-co-acrylic acid) (PEAA) copolymers, and two poly(ethylene-co-sulfonic acid) (PESA) copolymers. The acid groups are spaced by either 9 or 21 carbons along the polymer backbones. Hydrogen bonding causes the acid groups to form aggregates. These aggregates give rise to a low wavevector peak in the structure factors, in agreement with X-ray scattering data for the PEAA materials. The structure factors for the PESA copolymers are very similar to those for the PEAA copolymers, indicating a similar distance between aggregates which depends on the spacer length but not on the nature of the acid group. The PEAA copolymers are found to form more dimers and other small aggregates than do the PESA copolymers, while the PESA copolymers have both more free acid groups and more large aggregates.

  7. Hydroxyl-proton hydrogen bonding in the heparin oligosaccharide Arixtra in aqueous solution.

    PubMed

    Beecher, Consuelo N; Young, Robert P; Langeslay, Derek J; Mueller, Leonard J; Larive, Cynthia K

    2014-01-16

    Heparin is best known for its anticoagulant activity, which is mediated by the binding of a specific pentasaccharide sequence to the protease inhibitor antithrombin-III (AT-III). Although heparin oligosaccharides are thought to be flexible in aqueous solution, the recent discovery of a hydrogen bond between the sulfamate (NHSO3(-)) proton and the adjacent 3-O-sulfo group of the 3,6-O-sulfated N-sulfoglucosamine residue of the Arixtra (fondaparinux sodium) pentasaccharide demonstrates that definable elements of local structure are accessed. Molecular dynamics simulations of Arixtra suggest the presence of additional hydrogen bonds involving the C3-OH groups of the glucuronic acid and 2-O-sulfo-iduronic acid residues. NMR measurements of temperature coefficients, chemical shift differences, and solvent exchange rate constants provide experimental confirmation of these hydrogen bonds. We note that the extraction of rate constants from cross-peak buildup curves in 2D exchange spectroscopy is complicated by the presence of radiation damping in aqueous solution. A straightforward model is presented that explicitly takes into account the effects of radiation damping on the water proton relaxation and is sufficiently robust to provide an accurate measure of the proton exchange rate between the analyte hydroxyl protons and water. PMID:24354321

  8. Structural influence on the solid state intermolecular hydrogen bonding of substituted thioureas

    NASA Astrophysics Data System (ADS)

    Venkatachalam, T. K.; Sudbeck, E.; Uckun, F. M.

    2005-09-01

    Several thiourea derivatives have been found to possess biological activity. In particular, phenethyl thiazolyl thiourea derivatives with a heterocyclic ring exhibit potent antiviral activity. These thiourea derivatives were also found to inhibit RT, the reverse transcriptase enzyme, by binding the non-nucleoside inhibitor site of RT. To better understand the nature of the binding of these compounds a detailed crystal structure analysis on these thiourea compounds was undertaken. Here, we report, the results of our X-ray crystal structure study of substituted thiourea compounds. Comparison of the hydrogen bonding characteristics exhibited by structurally distinct thiourea analogs was informative concerning their inter- and intramolecular hydrogen bonding. Additionally, we found that among the thioureas studied, the 2,5-dimethoxy substituted phenethyl thiourea had strong intramolecular hydrogen bonding forming a nine-member ring in the crystal lattice that was absent in the other methoxy substituted phenethyl thioureas examined. Comparison of the structures demonstrated that the presence of a heterocyclic nitrogen atom in the ring results in the formation of a stable six-member ring rather than a nine-member ring.

  9. Hydrogen bonds and a hydrogen-bonded chain in mannich bases of 5,5'-dinitro-2,2'-biphenol-FT-IR and 1H NMR studies

    NASA Astrophysics Data System (ADS)

    Brzezinski, Bogumil; Urjasz, Hanna; Bartl, Franz; Zundel, Georg

    1997-11-01

    5,5'-Dinitro-3-diethylaminomethyl-2,2'-biphenol ( 1) and 5,5'-dinitro-3,3' bis(diethylaminomethyl)-2,2'-biphenol ( 2) as well as 5,5'-dinitro-2,2'-biphenol ( 3) were synthesized and studied by FT-IR and 1H NMR spectroscopy in acetonitrile or acetonitrile-d 3 solutions, respectively. With compound 1 a hydrogen-bonded system with large proton polarizability is found. In the hydrogen bonds in compound 2 the protons are localized at the N atoms. These hydrogen bonds show no proton polarizability. In the protonated compound 2 a very strong homoconjugated -O⋯H +⋯O - hydrogen bond with large proton polarizability is found, whereas two other protons are localized at the N atoms. The deviation of the results obtained with other derivatives of 2,2'-biphenols are caused by the larger acidity of the nitro groups.

  10. A Transferable Coarse-Grained Model for Hydrogen Bonding Liquids

    PubMed Central

    Golubkov, Pavel A.; Wu, Johnny C.; Ren, Pengyu

    2008-01-01

    We present here a recent development of a generalized coarse-grained model for use in molecular simulations. In this model, interactions between coarse-grained particles consist of both van der Waals and explicit electrostatic components. As a result, the coarse-grained model offers the transferability that is lacked by most current effectivepotential based approaches. The previous center-of-mass framework1 is generalized here to include arbitrary off-center interaction sites for both Gay-Berne and multipoles. The new model has been applied to molecular dynamic simulations of neat methanol liquid. By placing a single point multipole at the oxygen atom rather than at the center of mass of methanol, there is a significant improvement in the ability to capture hydrogen-bonding. The critical issue of transferability of the coarse-grained model is verified on methanol-water mixtures, using parameters derived from neat liquids without any modification. The mixture density and internal energy from coarse-grained molecular dynamics simulations show good agreement with experimental measurements, on a par with what has been obtained from more detailed atomic models. By mapping the dynamics trajectory from the coarse-grained simulation into the all-atom counterpart, we are able to investigate atomic .level structure and interaction. Atomic radial distribution functions of neat methanol, neat water and mixtures compare favorably to experimental measurements. Furthermore, hydrogen-bonded 6- and 7-molecule chains of water and methanol observed in the mixture are in agreement with previous atomic simulations. PMID:18688358

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

    PubMed

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

    2016-09-01

    Cryptochrome (CRY) is the principal light sensor of the insect circadian clock. Photoreduction of the Drosophila CRY (dCRY) flavin cofactor to the anionic semiquinone (ASQ) restructures a C-terminal tail helix (CTT) that otherwise inhibits interactions with targets that include the clock protein Timeless (TIM). All-atom molecular dynamics (MD) simulations indicate that flavin reduction destabilizes the CTT, which undergoes large-scale conformational changes (the CTT release) on short (25 ns) timescales. The CTT release correlates with the conformation and protonation state of conserved His378, which resides between the CTT and the flavin cofactor. Poisson-Boltzmann calculations indicate that flavin reduction substantially increases the His378 pKa Consistent with coupling between ASQ formation and His378 protonation, dCRY displays reduced photoreduction rates with increasing pH; however, His378Asn/Arg variants show no such pH dependence. Replica-exchange MD simulations also support CTT release mediated by changes in His378 hydrogen bonding and verify other responsive regions of the protein previously identified by proteolytic sensitivity assays. His378 dCRY variants show varying abilities to light-activate TIM and undergo self-degradation in cellular assays. Surprisingly, His378Arg/Lys variants do not degrade in light despite maintaining reactivity toward TIM, thereby implicating different conformational responses in these two functions. Thus, the dCRY photosensory mechanism involves flavin photoreduction coupled to protonation of His378, whose perturbed hydrogen-bonding pattern alters the CTT and surrounding regions. PMID:27551082

  12. Hydrogen bonding-assisted thermal conduction in β-sheet crystals of spider silk protein

    NASA Astrophysics Data System (ADS)

    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

  13. Cocrystals of 5-fluorocytosine. I. Coformers with fixed hydrogen-bonding sites.

    PubMed

    Tutughamiarso, Maya; Wagner, Guido; Egert, Ernst

    2012-08-01

    The antifungal drug 5-fluorocytosine (4-amino-5-fluoro-1,2-dihydropyrimidin-2-one) was cocrystallized with five complementary compounds in order to better understand its drug-receptor interaction. The first two compounds, 2-aminopyrimidine (2-amino-1,3-diazine) and N-acetylcreatinine (N-acetyl-2-amino-1-methyl-5H-imidazol-4-one), exhibit donor-acceptor sites for R(2)(2)(8) heterodimer formation with 5-fluorocytosine. Such a heterodimer is observed in the cocrystal with 2-aminopyrimidine (I); in contrast, 5-fluorocytosine and N-acetylcreatinine [which forms homodimers in its crystal structure (II)] are connected only by a single hydrogen bond in (III). The other three compounds 6-aminouracil (6-amino-2,4-pyrimidinediol), 6-aminoisocytosine (2,6-diamino-3H-pyrimidin-4-one) and acyclovir [acycloguanosine or 2-amino-9-[(2-hydroxyethoxy)methyl]-1,9-dihydro-6H-purin-6-one] possess donor-donor-acceptor sites; therefore, they can interact with 5-fluorocytosine to form a heterodimer linked by three hydrogen bonds. In the cocrystals with 6-aminoisocytosine (Va)-(Vd), as well as in the cocrystal with the antiviral drug acyclovir (VII), the desired heterodimers are observed. However, they are not formed in the cocrystal with 6-aminouracil (IV), where the components are connected by two hydrogen bonds. In addition, a solvent-free structure of acyclovir (VI) was obtained. A comparison of the calculated energies released during dimer formation helped to rationalize the preference for hydrogen-bonding interactions in the various cocrystal structures. PMID:22810913

  14. Spectroscopy of selected copper group minerals: Chalcophyllite and chenevixite-implications for hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; Reddy, B. Jagannadha; Keeffe, Eloise C.

    2010-10-01

    NIR and IR spectroscopy has been applied for detection of chemical species and the nature of hydrogen bonding in arsenate complexes. The structure and spectral properties of copper(II) arsenate minerals: chalcophyllite and chenevixite are compared with copper(II) sulphate minerals: devilline, chalcoalumite and caledonite. Split NIR bands in the electronic spectrum of two ranges 11,700-8500 cm -1 and 8500-7200 m -1 confirm distortion of octahedral symmetry for Cu(II) in the arsenate complexes. The observed bands with maxima at 9860 and 7750 cm -1 are assigned to Cu(II) transitions 2B 1g → 2B 2g and 2B 1g → 2A 1g. Overlapping bands in the NIR region 4500-4000 cm -1 is the effect of multi-anions OH -, (AsO 4) 3- and (SO 4) 2-. The observation of broad and diffuse bands in the range 3700-2900 cm -1 confirms strong hydrogen bonding in chalcophyllite relative to chenevixite. The position of the water bending vibrations indicates the water is strongly hydrogen bonded in the mineral structure. The strong absorption feature centred at 1644 cm -1 in chalcophyllite indicates water is strongly hydrogen bonded in the mineral structure. The H 2O-bending vibrations shift to low wavenumbers in chenevixite and an additional band observed at 1390 cm -1 is related to carbonate impurity. The characterisation of IR spectra by ν3 antisymmetric stretching vibrations of (SO 4) 2- and (AsO 4) 3 ions near 1100 and 800 cm -1 respectively is the result of isomorphic substitution for arsenate by sulphate in both the minerals of chalcophyllite and chenevixite.

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

    PubMed

    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. PMID:25947291

  16. Hydrogen-Bond and Supramolecular-Contact Mediated Fluorescence Enhancement of Electrochromic Azomethines.

    PubMed

    Wałęsa-Chorab, Monika; Tremblay, Marie-Hélène; Skene, William G

    2016-08-01

    An electronic push-pull fluorophore consisting of an intrinsically fluorescent central fluorene capped with two diaminophenyl groups was prepared. An aminothiophene was conjugated to the two flanking diphenylamines through a fluorescent quenching azomethine bond. X-ray crystallographic analysis confirmed that the fluorophore formed multiple intermolecular supramolecular bonds. It formed two hydrogen bonds involving a terminal amine, resulting in an antiparallel supramolecular dimer. Hydrogen bonding was also confirmed by FTIR and NMR spectroscopic analyses, and further validated theoretically by DFT calculations. Intrinsic fluorescence quenching modes could be reduced by intermolecular supramolecular contacts. These contacts could be engaged at high concentrations and in thin films, resulting in fluorescence enhancement. The fluorescence of the fluorophore could also be restored to an intensity similar to its azomethine-free counterpart with the addition of water in >50 % v/v in tetrahydrofuran (THF), dimethyl sulfoxide (DMSO), and acetonitrile. The fluorophore also exhibited reversible oxidation and its color could be switched between yellow and blue when oxidized. Reversible electrochemically mediated fluorescence turn-off on turn-on was also possible. PMID:27388588

  17. Density functional studies on hydrogen-bonded clusters of hydrogen halides and the interaction on halide anions

    NASA Astrophysics Data System (ADS)

    Nirmala, V.; Kolandaivel, P.

    Density functional theory (DFT) calculations have been performed to study the structures and stability of X-·(HX)n=2-5 clusters where X = F, Cl, Br at B3LYP/6-311++G** level of theory. The presence of halide ions in these clusters disintegrates the hydrogen halide clusters. All the hydrogen halides are then hydrogen bonded to the centrally placed halide ions, thereby forming multiple hydrogen bonds. The interaction energies have been corrected for the basis set superposition error (BSSE) using Boy's counterpoise correction method. Evidence for the destruction of hydrogen bonds in hydrogen halide clusters due to the presence of halide ions is further obtained from topological analysis and natural bond orbital analysis. The chemical hardness and chemical potential have been calculated for all the anion clusters. The above analysis reveals that hydrogen bonding in these systems is not an essentially electrostatic interaction. The nature of the stabilization interactions operative in these multiple hydrogen-bonded clusters has been explained in terms of many-body contribution to interaction energies. From these studies, an attempt has been made to understand the nature of the molecular properties resulting from different electronegativities of the halogens.

  18. Breaking the low barrier hydrogen bond in a serine protease.

    PubMed Central

    Kidd, R. D.; Sears, P.; Huang, D. H.; Witte, K.; Wong, C. H.; Farber, G. K.

    1999-01-01

    The serine protease subtilisin BPN' is a useful catalyst for peptide synthesis when dissolved in high concentrations of a water-miscible organic co-solvent such as N,N-dimethylformamide (DMF). However, in 50% DMF, the k(cat) for amide hydrolysis is two orders of magnitude lower than in aqueous solution. Surprisingly, the k(cat) for ester hydrolysis is unchanged in 50% DMF. To explain this alteration in activity, the structure of subtilisin 8397+1 was determined in 20, 35, and 50% (v/v) DMF to 1.8 A resolution. In 50% DMF, the imidazole ring of His64, the central residue of the catalytic triad, has rotated approximately 180 degrees around the Cbeta-Cgamma bond. Two new water molecules in the active site stabilize the rotated conformation. This rotation places His64 in an unfavorable geometry to interact with the other members of the catalytic triad, Ser221 and Asp32. NMR experiments confirm that the characteristic resonance due to the low barrier hydrogen bond between the His64 and Asp32 is absent in 50% DMF. These experiments provide a clear structural basis for the change in activity of serine proteases in organic co-solvents. PMID:10048334

  19. Structure, hydrogen bonding and thermal expansion of ammonium carbonate monohydrate.

    PubMed

    Fortes, A Dominic; Wood, Ian G; Alfè, Dario; Hernández, Eduardo R; Gutmann, Matthias J; Sparkes, Hazel A

    2014-12-01

    We have determined the crystal structure of ammonium carbonate monohydrate, (NH4)2CO3·H2O, using Laue single-crystal diffraction methods with pulsed neutron radiation. The crystal is orthorhombic, space group Pnma (Z = 4), with unit-cell dimensions a = 12.047 (3), b = 4.453 (1), c = 11.023 (3) Å and V = 591.3 (3) Å(3) [ρcalc = 1281.8 (7) kg m(-3)] at 10 K. The single-crystal data collected at 10 and 100 K are complemented by X-ray powder diffraction data measured from 245 to 273 K, Raman spectra measured from 80 to 263 K and an athermal zero-pressure calculation of the electronic structure and phonon spectrum carried out using density functional theory (DFT). We find no evidence of a phase transition between 10 and 273 K; above 273 K, however, the title compound transforms first to ammonium sesquicarbonate monohydrate and subsequently to ammonium bicarbonate. The crystallographic and spectroscopic data and the calculations reveal a quite strongly hydrogen-bonded structure (EHB ≃ 30-40 kJ mol(-1)), on the basis of H...O bond lengths and the topology of the electron density at the bond critical points, in which there is no free rotation of the ammonium cation at any temperature. The barrier to free rotation of the ammonium ions is estimated from the observed librational frequency to be ∼ 36 kJ mol(-1). The c-axis exhibits negative thermal expansion, but the thermal expansion behaviour of the a and b axes is ormal. PMID:25449618

  20. Structure, hydrogen bonding and thermal expansion of ammonium carbonate monohydrate

    PubMed Central

    Fortes, A. Dominic; Wood, Ian G.; Alfè, Dario; Hernández, Eduardo R.; Gutmann, Matthias J.; Sparkes, Hazel A.

    2014-01-01

    We have determined the crystal structure of ammonium carbonate monohydrate, (NH4)2CO3·H2O, using Laue single-crystal diffraction methods with pulsed neutron radiation. The crystal is orthorhombic, space group Pnma (Z = 4), with unit-cell dimensions a = 12.047 (3), b = 4.453 (1), c = 11.023 (3) Å and V = 591.3 (3) Å3 [ρcalc = 1281.8 (7) kg m−3] at 10 K. The single-crystal data collected at 10 and 100 K are complemented by X-ray powder diffraction data measured from 245 to 273 K, Raman spectra measured from 80 to 263 K and an athermal zero-pressure calculation of the electronic structure and phonon spectrum carried out using density functional theory (DFT). We find no evidence of a phase transition between 10 and 273 K; above 273 K, however, the title compound transforms first to ammonium sesquicarbonate monohydrate and subsequently to ammonium bicarbonate. The crystallographic and spectroscopic data and the calculations reveal a quite strongly hydrogen-bonded structure (E HB ≃ 30–40 kJ mol−1), on the basis of H⋯O bond lengths and the topology of the electron density at the bond critical points, in which there is no free rotation of the ammonium cation at any temperature. The barrier to free rotation of the ammonium ions is estimated from the observed librational frequency to be ∼ 36 kJ mol−1. The c-axis exhibits negative thermal expansion, but the thermal expansion behaviour of the a and b axes is ormal. PMID:25449618

  1. 27 CFR 19.959 - Additional provisions with respect to bonds.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Additional provisions with respect to bonds. 19.959 Section 19.959 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND... Bonds § 19.959 Additional provisions with respect to bonds. Subpart H of this part contains...

  2. Hydrogen bond symmetrization and equation of state of phase D

    SciTech Connect

    Hushur, Anwar; Manghnani, Murli H.; Smyth, Joseph R.; Williams, Quentin; Hellebrand, Eric; Lonappan, Dayana; Ye, Yu; Dera, Przemyslaw; Frost, Daniel J.

    2012-10-09

    We have synthesized phase D at 24 GPa and at temperatures of 1250-1100 C in a multianvil press under conditions of high silica activity. The compressibility of this high-silica-activity phase D (Mg{sub 1.0}Si{sub 1.7}H{sub 3.0}O{sub 6}) has been measured up to 55.8 GPa at ambient temperature by powder X-ray diffraction. The volume (V) decreases smoothly with increasing pressure up to 40 GPa, consistent with the results reported in earlier studies. However, a kink is observed in the trend of V versus pressure above {approx}40 GPa, reflecting a change in the compression behavior. The data to 30 GPa fit well to a third-order Birch-Murnaghan equation of state (EoS), yielding V{sub o} = 85.1 {+-} 0.2 {angstrom}{sup 3}; K{sub o} = 167.9 {+-} 8.6 GPa; and K{prime}{sub o} = 4.3 {+-} 0.5, similar to results for Fe-Al-free phase D reported by Frost and Fei (1999). However, these parameters are larger than those reported for Fe-Al-bearing phase D and for Fe-Al-free phase D. The abnormal volume change in this study may be attributed to the reported hydrogen bond symmetrization in phase D. Fitting a third-order Birch-Murnaghan EoS to the data below 30 GPa yields a bulk modulus K{sub o} = 173 (2) GPa for the hydrogen-off-centered (HOC) phase and K{sub o} = 212 (15) GPa for the data above 40 GPa for the hydrogen-centered (HC) phase, assuming K{prime}{sub o} is 4. The calculated bulk modulus K{sub o} of the HC phase is 18% larger than the bulk modulus K{sub o} of the HOC phase.

  3. Second sphere control of spin state: Differential tuning of axial ligand bonds in ferric porphyrin complexes by hydrogen bonding.

    PubMed

    Mittra, Kaustuv; Sengupta, Kushal; Singha, Asmita; Bandyopadhyay, Sabyasachi; Chatterjee, Sudipta; Rana, Atanu; Samanta, Subhra; Dey, Abhishek

    2016-02-01

    An iron porphyrin with a pre-organized hydrogen bonding (H-Bonding) distal architecture is utilized to avoid the inherent loss of entropy associated with H-Bonding from solvent (water) and mimic the behavior of metallo-enzyme active sites attributed to H-Bonding interactions of active site with the 2nd sphere residues. Resonance Raman (rR) data on these iron porphyrin complexes indicate that H-Bonding to an axial ligand like hydroxide can result in both stronger or weaker Fe(III)-OH bond relative to iron porphyrin complexes. The 6-coordinate (6C) complexes bearing water derived axial ligands, trans to imidazole or thiolate axial ligand with H-Bonding stabilize a low spin (LS) ground state (GS) when a complex without H-Bonding stabilizes a high spin (HS) ground state. DFT calculations reproduce the trend in the experimental data and provide a mechanism of how H-Bonding can indeed lead to stronger metal ligand bonds when the axial ligand donates an H-Bond and lead to weaker metal ligand bonds when the axial ligand accepts an H-Bond. The experimental and computational results explain how a weak Fe(III)-OH bond (due to H-Bonding) can lead to the stabilization of low spin ground state in synthetic mimics and in enzymes containing iron porphyrin active sites. H-Bonding to a water ligand bound to a reduced ferrous active site can only strengthen the Fe(II)-OH2 bond and thus exclusion of water and hydrophilic residues from distal sites of O2 binding/activating heme proteins is necessary to avoid inhibition of O2 binding by water. These results help demonstrate the predominant role played by H-Bonding and subtle changes in its orientation in determining the geometric and electronic structure of iron porphyrin based active sites in nature. PMID:26638009

  4. Hydrogen-bonds structure in poly(2-hydroxyethyl methacrylate) studied by temperature-dependent infrared spectroscopy

    PubMed Central

    Morita, Shigeaki

    2014-01-01

    Hydrogen-bonds structure in poly(2-hydroxyethyl methacrylate) (PHEMA) were investigated by means of temperature-dependent infrared (IR) spectroscopy. Spectral variations involved with the OH…OH and C=O…HO types of hydrogen-bonds were found around the glass transition temperature of 80°C. Hydrogen-bonds among the hydroxyl groups gradually dissociate with increasing temperature. In contrast, discontinuous variation in the carbonyl bands was observed around the glass transition temperature. An association of the C=O…HO type of hydrogen-bond with increasing temperature above the glass transition temperature was revealed. These were concluded from the present study that hydrogen-bonds among the hydroxyl groups in each side chain terminal suppress the main chain mobility in the polymer matrix below the glass transition temperature, while the dissociation of the OH…OH type of hydrogen-bonds induces the association of the C=O…HO type of hydrogen-bond. As a result, the mobility of the main chain is induced by the change in hydrogen-bonds structure at the glass transition temperature. PMID:24790979

  5. Fluorescence and picosecond laser photolysis studies on the deactivation processes of excited hydrogen bonding systems

    NASA Astrophysics Data System (ADS)

    Ikeda, Noriaka; Okada, Tadashi; Mataga, Noboru

    1980-01-01

    The fluorescence quenching reaction of 2-naphthylamine and 1-pyrenol due to hydrogen bonding interaction with pyndine has been investigated Absorption spectra due to the state formed by charge transfer from excited naphthylamine to hydrogen bonded pyridine have been observed by means of picosecond laser photolysis.

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

    ERIC Educational Resources Information Center

    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…

  7. Hydrogen-Bonds Structure in Poly(2-Hydroxyethyl Methacrylate) Studied by Temperature-Dependent Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Morita, Shigeaki

    2014-03-01

    Hydrogen-bonds structure in poly(2-hydroxyethyl methacrylate) (PHEMA) were investigated by means of temperature-dependent infrared (IR) spectroscopy. Spectral variations involved with the OH•••OH and C=O•••HO types of hydrogen-bonds were found around the glass transition temperature of 80 °C. Hydrogen-bonds among the hydroxyl groups gradually dissociate with increasing temperature. In contrast, discontinuous variation in the carbonyl bands was observed around the glass transition temperature. An association of the C=O•••HO type of hydrogen-bond with increasing temperature above the glass transition temperature was revealed. These were concluded from the present study that hydrogen-bonds among the hydroxyl groups in each side chain terminal suppress the main chain mobility in the polymer matrix below the glass transition temperature, while the dissociation of the OH•••OH type of hydrogen-bonds induces the association of the C=O•••HO type of hydrogen-bond. As a result, the mobility of the main chain is induced by the change in hydrogen-bonds structure at the glass transition temperature.

  8. Hydrogen-Bonding Catalysis of Tetraalkylammonium Salts in an Aza-Diels-Alder Reaction.

    PubMed

    Kumatabara, Yusuke; Kaneko, Shiho; Nakata, Satoshi; Shirakawa, Seiji; Maruoka, Keiji

    2016-08-01

    A piperidine-derived tetraalkylammonium salt with a non-coordinating counteranion worked as an effective hydrogen-bonding catalyst in an aza-Diels-Alder reaction of imines and a Danishefsky diene. The hydrogen-bonding interaction between the ammonium salt and an imine was observed as part of a (1) H NMR titration study. PMID:27311924

  9. Water templated hydrogen-bonded network of pyridine amide appended carbamate in solid state

    NASA Astrophysics Data System (ADS)

    Ghosh, Kumaresh; Adhikari, Suman; Fröhlich, Roland

    2006-03-01

    The pyridine amide appended carbamates 1 and 2 have been synthesized and their hydrogen-bonded self-assemblies in solid state have been described. The self-association pattern is dependent on the nature the anchored group of the carbamate moiety and influenced by water inclusion. Inclusion of water molecule gives a ladder type hydrogen bonded assemblies with cavities.

  10. The Contrasting Character of Early and Late Transition Metal Fluorides as Hydrogen Bond Acceptors.

    PubMed

    Smith, Dan A; Beweries, Torsten; Blasius, Clemens; Jasim, Naseralla; Nazir, Ruqia; Nazir, Sadia; Robertson, Craig C; Whitwood, Adrian C; Hunter, Christopher A; Brammer, Lee; Perutz, Robin N

    2015-09-16

    The association constants and enthalpies for the binding of hydrogen bond donors to group 10 transition metal complexes featuring a single fluoride ligand (trans-[Ni(F)(2-C5NF4)(PR3)2], R = Et 1a, Cy 1b, trans-[Pd(F)(4-C5NF4)(PCy3)2] 2, trans-[Pt(F){2-C5NF2H(CF3)}(PCy3)2] 3 and of group 4 difluorides (Cp2MF2, M = Ti 4a, Zr 5a, Hf 6a; Cp*2MF2, M = Ti 4b, Zr 5b, Hf 6b) are reported. These measurements allow placement of these fluoride ligands on the scales of organic H-bond acceptor strength. The H-bond acceptor capability β (Hunter scale) for the group 10 metal fluorides is far greater (1a 12.1, 1b 9.7, 2 11.6, 3 11.0) than that for group 4 metal fluorides (4a 5.8, 5a 4.7, 6a 4.7, 4b 6.9, 5b 5.6, 6b 5.4), demonstrating that the group 10 fluorides are comparable to the strongest organic H-bond acceptors, such as Me3NO, whereas group 4 fluorides fall in the same range as N-bases aniline through pyridine. Additionally, the measurement of the binding enthalpy of 4-fluorophenol to 1a in carbon tetrachloride (-23.5 ± 0.3 kJ mol(-1)) interlocks our study with Laurence's scale of H-bond basicity of organic molecules. The much greater polarity of group 10 metal fluorides than that of the group 4 metal fluorides is consistent with the importance of pπ-dπ bonding in the latter. The polarity of the group 10 metal fluorides indicates their potential as building blocks for hydrogen-bonded assemblies. The synthesis of trans-[Ni(F){2-C5NF3(NH2)}(PEt3)2], which exhibits an extended chain structure assembled by hydrogen bonds between the amine and metal-fluoride groups, confirms this hypothesis. PMID:26302048

  11. Hydrogen bonding in the mechanism of GDP-mannose mannosyl hydrolase

    NASA Astrophysics Data System (ADS)

    Mildvan, A. S.; Xia, Z.; Azurmendi, H. F.; Legler, P. M.; Balfour, M. R.; Lairson, L. L.; Withers, S. G.; Gabelli, S. B.; Bianchet, M. A.; Amzel, L. M.

    2006-06-01

    GDP-mannose mannosyl hydrolase (GDPMH) from E. coli catalyzes the hydrolysis of GDP-α- D-sugars to GDP and β- D-sugars by nucleophilic substitution with inversion at the anomeric C1 of the sugar, with general base catalysis by His-124. The 1.3 Å X-ray structure of the GDPMH-Mg 2+-GDP complex was used to model the complete substrate, GDP-mannose into the active site. The substrate is linked to the enzyme by 12 hydrogen bonds, as well as by the essential Mg 2+. In addition, His-124 was found to participate in a hydrogen bonded triad: His-124-NδH⋯Tyr-127-OH⋯Pro-120(C dbnd6 O). The contributions of these hydrogen bonds to substrate binding and to catalysis were investigated by site-directed mutagenesis. The hydrogen bonded triad detected in the X-ray structure was found to contribute little to catalysis since the Y127F mutation of the central residue shows only 2-fold decreases in both kcat and Km. The GDP leaving group is activated by the essential Mg 2+ which contributes at least 10 5-fold to kcat, and by nine hydrogen bonds, including those from Tyr-103, Arg-37, Arg-52, and Arg-65 (via an intervening water), each of which contribute factors to kcat ranging from 24- to 309-fold. Both Arg-37 and Tyr-103 bind the β-phosphate of the leaving GDP and are only 5.0 Å apart. Accordingly, the R37Q/Y103F double mutant shows partially additive effects of the two single mutants on kcat, indicating cooperativity of Arg-37 and Tyr-103 in promoting catalysis. The extensive activation of the GDP leaving group suggests a mechanism with dissociative character with a cationic oxocarbenium-like transition state and a half-chair conformation of the sugar ring, as found with glycosidase enzymes. Accordingly, Asp-22 which contributes 10 2.1- to 10 2.6-fold to kcat, is positioned to both stabilize a developing cationic center at C1 and to accept a hydrogen bond from the C2-OH of the mannosyl group, and His-88, which contributes 10 2.3-fold to kcat, is positioned to accept

  12. Induced Circular Dichroism in Phosphine Gold(I) Aryl Acetylide Urea Complexes through Hydrogen-Bonded Chiral Co-Assemblies.

    PubMed

    Dubarle-Offner, Julien; Moussa, Jamal; Amouri, Hani; Jouvelet, Benjamin; Bouteiller, Laurent; Raynal, Matthieu

    2016-03-14

    Phosphine gold(I) aryl acetylide complexes equipped with a central bis(urea) moiety form 1D hydrogen-bonded polymeric assemblies in solution that do not display any optical activity. Chiral co-assemblies are formed by simple addition of an enantiopure (metal-free) complementary monomer. Although exhibiting an intrinsically achiral linear geometry, the gold(I) aryl acetylide fragment is located in the chiral environment displayed by the hydrogen-bonded co-assemblies, as demonstrated by induced circular dichroism (ICD). PMID:26780877

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

    SciTech Connect

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

    2014-12-07

    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.

  14. Hydrogen addition reactions of aliphatic hydrocarbons in comets

    NASA Astrophysics Data System (ADS)

    Kobayashi, Hitomi; Watanabe, N.; Watanabe, Y.; Fukushima, T.; Kawakita, H.

    2013-10-01

    Comets are thought as remnants of early solar nebula. Their chemical compositions are precious clue to chemical and physical evolution of the proto-planetary disk. Some hydrocarbons such as C2H6, C2H2 and CH4 in comets have been observed by using near-infrared spectroscopy. Although the compositions of C2H6 were about 1% relative to the water in normal comets, there are few reports on the detection of C2H6 in ISM. Some formation mechanisms of C2H6 in ISM have been proposed, and there are two leading hypotheses; one is the dimerizations of CH3 and another is the hydrogen addition reactions of C2H2 on cold icy grains. To evaluate these formation mechanisms for cometary C2H6 quantitatively, it is important to search the C2H4 in comets, which is the intermediate product of the hydrogen addition reactions toward C2H6. However, it is very difficult to detect the C2H4 in comets in NIR (3 microns) regions because of observing circumstances. The hydrogen addition reactions of C2H2 at low temperature conditions are not well characterized both theoretically and experimentally. For example, there are no reports on the reaction rate coefficients of those reaction system. To determine the production rates of those hydrogen addition reactions, we performed the laboratory experiments of the hydrogenation of C2H2 and C2H4. We used four types of the initial composition of the ices: pure C2H4, pure C2H2, C2H2 on amorphous solid water (ASW) and C2H4 on ASW at three different temperatures of 10, 20, and 30K. We found 1) reactions are more efficient when there are ASW in the initial compositions of the ice; 2) hydrogenation of C2H4 occur more rapid than that of C2H2.

  15. Cinchona Urea-Catalyzed Asymmetric Sulfa-Michael Reactions: The Brønsted Acid-Hydrogen Bonding Model.

    PubMed

    Grayson, Matthew N; Houk, K N

    2016-07-27

    The cinchona alkaloid-derived urea-catalyzed asymmetric conjugate addition of aromatic thiols to cycloalkenones was studied using density functional theory (DFT). Deprotonation of the thiol gives a protonated amine that activates the electrophile by Brønsted acid catalysis, while the urea group binds the nucleophilic thiolate by hydrogen bonding. These results demonstrate the generality of the Brønsted acid-hydrogen bonding transition state (TS) model for cinchona alkaloid catalysis that we recently showed to be favored over Wynberg's widely accepted ion pair-hydrogen bonding model and represent the first detailed mechanistic study of a cinchona urea-catalyzed reaction. The conformation of the catalyst methoxy group has a strong effect on the TS, an effect overlooked in previous mechanistic studies of reactions catalyzed by cinchona alkaloids. PMID:27396591

  16. Improved actuated strain of dielectric elastomer through disruption of hydrogen bonds of thermoplastic polyurethane by adding diaminonaphthalene

    NASA Astrophysics Data System (ADS)

    Ning, Nanying; Yan, Bingyue; Liu, Suting; Yao, Yang; Zhang, Liqun; Chan, Tung W.; Nishi, Toshio; Tian, Ming

    2015-03-01

    We used a novel and simple approach to increase the actuated strain at low electric field of thermoplastic polyurethane (TPU) through the disruption of the hydrogen bonds of TPU by adding diaminonaphthalene (DAN) into the matrix. DAN as proton donors disrupted the original N-H/C=O hydrogen bonds between the TPU chains, improving the polarizability of the chains, thus increasing the dielectric constant of TPU. Meanwhile, DAN greatly decreased the elastic modulus of TPU by disrupting the hydrogen bonds of TPU. The simultaneous increase in dielectric constant and decrease in elastic modulus resulted in a 330% increase in electromechanical sensitivity at 103 Hz and a 500% increase in actuated strain at the low electric field of 20 V μm-1, facilitating the application of dielectric elastomers (DEs) in the biological and medical fields, where a low electric field is required. In addition, our DAN/TPU DE exhibited good mechanical strength.

  17. Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes.

    PubMed

    Chakrabarti, Shaon; Hinczewski, Michael; Thirumalai, D

    2014-06-24

    Mechanical forces acting on cell adhesion receptor proteins regulate a range of cellular functions by formation and rupture of noncovalent interactions with ligands. Typically, force decreases the lifetimes of intact complexes ("slip bonds"), making the discovery that these lifetimes can also be prolonged ("catch bonds") a surprise. We created a microscopic analytic theory by incorporating the structures of selectin and integrin receptors into a conceptual framework based on the theory of stochastic equations, which quantitatively explains a wide range of experimental data (including catch bonds at low forces and slip bonds at high forces). Catch bonds arise due to force-induced remodeling of hydrogen bond networks, a finding that also accounts for unbinding in structurally unrelated integrin-fibronectin and actomyosin complexes. For the selectin family, remodeling of hydrogen bond networks drives an allosteric transition resulting in the formation of the maximum number of hydrogen bonds determined only by the structure of the receptor and independent of the ligand. A similar transition allows us to predict the increase in the number of hydrogen bonds in a particular allosteric state of α5β1 integrin-fibronectin complex, a conformation which is yet to be crystallized. We also make a testable prediction that a single point mutation (Tyr51Phe) in the ligand associated with selectin should dramatically alter the nature of the catch bond compared with the wild type. Our work suggests that nature uses a ductile network of hydrogen bonds to engineer function over a broad range of forces. PMID:24927549

  18. Neutron diffraction of. cap alpha. ,. beta. and. gamma. cyclodextrins: hydrogen bonding patterns

    SciTech Connect

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

    1983-01-01

    Cyclodextrins (CD's) are torus-shaped molecules composed of six (..cap alpha..), seven (..beta..) or eight (..gamma..) (1 ..-->.. 4) linked glucoses. ..cap alpha..-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 ..cap alpha..-CD complex formation has been proposed. Circular hydrogen bond networks have also been found for ..cap alpha..-CD due to the energetically favored cooperative effect. ..beta..-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. ..gamma..-CD with a disordered water structure similar to ..beta..-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.

  19. Hydrogen bond disruption in DNA base pairs from (14)C transmutation.

    PubMed

    Sassi, Michel; Carter, Damien J; Uberuaga, Blas P; Stanek, Christopher R; Mancera, Ricardo L; Marks, Nigel A

    2014-09-01

    Recent ab initio molecular dynamics simulations have shown that radioactive carbon does not normally fragment DNA bases when it decays. Motivated by this finding, density functional theory and Bader analysis have been used to quantify the effect of C → N transmutation on hydrogen bonding in DNA base pairs. We find that (14)C decay has the potential to significantly alter hydrogen bonds in a variety of ways including direct proton shuttling (thymine and cytosine), thermally activated proton shuttling (guanine), and hydrogen bond breaking (cytosine). Transmutation substantially modifies both the absolute and relative strengths of the hydrogen bonding pattern, and in two instances (adenine and cytosine), the density at the critical point indicates development of mild covalent character. Since hydrogen bonding is an important component of Watson-Crick pairing, these (14)C-induced modifications, while infrequent, may trigger errors in DNA transcription and replication. PMID:25127298

  20. Analysis of hydrogen-bond interaction potentials from the electron density: Integration of NCI regions

    PubMed Central

    Contreras-García, Julia; Yang, Weitao; Johnson, Erin R.

    2013-01-01

    Hydrogen bonds are of crucial relevance to many problems in chemistry biology and materials science. The recently-developed NCI (Non-Covalent Interactions) index enables real-space visualization of both attractive (van der Waals and hydrogen-bonding) and repulsive (steric) interactions based on properties of the electron density It is thus an optimal index to describe the interplay of stabilizing and de-stabilizing contributions that determine stable minima on hydrogen-bonding potential-energy surfaces (PESs). In the framework of density-functional theory energetics are completely determined by the electron density Consequently NCI will be shown to allow quantitative treatment of hydrogen-bond energetics. The evolution of NCI regions along a PES follows a well-behaved pattern which, upon integration of the electron density is capable of mimicking conventional hydrogen-bond interatomic potentials. PMID:21786796

  1. Nuclear quantum effects of hydrogen bonds probed by tip-enhanced inelastic electron tunneling.

    PubMed

    Guo, Jing; Lü, Jing-Tao; Feng, Yexin; Chen, Ji; Peng, Jinbo; Lin, Zeren; Meng, Xiangzhi; Wang, Zhichang; Li, Xin-Zheng; Wang, En-Ge; Jiang, Ying

    2016-04-15

    We report the quantitative assessment of nuclear quantum effects on the strength of a single hydrogen bond formed at a water-salt interface, using tip-enhanced inelastic electron tunneling spectroscopy based on a scanning tunneling microscope. The inelastic scattering cross section was resonantly enhanced by "gating" the frontier orbitals of water via a chlorine-terminated tip, so the hydrogen-bonding strength can be determined with high accuracy from the red shift in the oxygen-hydrogen stretching frequency of water. Isotopic substitution experiments combined with quantum simulations reveal that the anharmonic quantum fluctuations of hydrogen nuclei weaken the weak hydrogen bonds and strengthen the relatively strong ones. However, this trend can be completely reversed when a hydrogen bond is strongly coupled to the polar atomic sites of the surface. PMID:27081066

  2. Structure and hydrogen bond dynamics of water-dimethyl sulfoxide mixtures by computer simulations

    NASA Astrophysics Data System (ADS)

    Luzar, Alenka; Chandler, David

    1993-05-01

    We have used two different force field models to study concentrated dimethyl sulfoxide (DMSO)-water solutions by molecular dynamics. The results of these simulations are shown to compare well with recent neutron diffraction experiments using H/D isotope substitution [A. K. Soper and A. Luzar, J. Chem. Phys. 97, 1320 (1992)]. Even for the highly concentrated 1 DMSO : 2 H2O solution, the water hydrogen-hydrogen radial distribution function, gHH(r), exhibits the characteristic tetrahedral ordering of water-water hydrogen bonds. Structural information is further obtained from various partial atom-atom distribution functions, not accessible experimentally. The behavior of water radial distribution functions, gOO(r) and gOH(r) indicate that the nearest neighbor correlations among remaining water molecules in the mixture increase with increasing DMSO concentration. No preferential association of methyl groups on DMSO is detected. The pattern of hydrogen bonding and the distribution of hydrogen bond lifetimes in the simulated mixtures is further investigated. Molecular dynamics results show that DMSO typically forms two hydrogen bonds with water molecules. Hydrogen bonds between DMSO and water molecules are longer lived than water-water hydrogen bonds. The hydrogen bond lifetimes determined by reactive flux correlation function approach are about 5 and 3 ps for water-DMSO and water-water pairs, respectively, in 1 DMSO : 2 H2O mixture. In contrast, for pure water, the hydrogen bond lifetime is about 1 ps. We discuss these times in light of experimentally determined rotational relaxation times. The relative values of the hydrogen bond lifetimes are consistent with a statistical (i.e., transition state theory) interpretation.

  3. Anionic complexes of F- and Cl- with substituted methanes: Hydrogen, halogen, and tetrel bonds

    NASA Astrophysics Data System (ADS)

    Del Bene, Janet E.; Alkorta, Ibon; Elguero, José

    2016-07-01

    Ab initio MP2/aug‧-cc-pVTZ calculations have been carried out to investigate the anionic complexes X-:CX(FnH3-n), for X = F, Cl, and n = 0-3. These complexes are stabilized by tetrel, hydrogen, and halogen bonds. Hydrogen-bonded complexes are the most stable complexes and halogen-bonded complexes are the least stable, with one exception. Charge-transfer across intermolecular bonds stabilizes all complexes, and occurs from the anion lone-pair to a σ∗ orbital of the substituted methane. EOM-CCSD spin-spin coupling constants 1tJ(X-C) across intermolecular tetrel bonds, 2hJ(C-X) across hydrogen bonds, and 1xJ(Cl-Cl) and 2xJ(C-Cl) across halogen bonds correlate with intermolecular distances.

  4. Carbon-donated hydrogen bonding: Electrostatics, frequency shifts, directionality, and bifurcation

    NASA Astrophysics Data System (ADS)

    Compaan, Katherine; Vergenz, Robert; Schleyer, Paul Von Rague; Arreguin, Isis

    Structure, energies, electrostatics, and vibrational modes were calculated ab initio for dimethyl sulfoxide (DMSO) and its 1:1 hydrogen bonded complex with chloride ion at the MP2/6-311+G** level. The interaction energy is -71.476 kJ/mole. On average, the C bond H stretching frequencies decreased by 35 cm-1, whereas their intensities increased by a factor of 19. Methyl torsion frequencies increased by 50-80 cm-1. We review the past and present understanding of hydrogen bonding, and apply these perspectives to analyze properties of the complex. The stretching shifts conform to the established spectral criteria for hydrogen bonding. The bifurcated geometry of the complex and its electrostatic character are fully consistent with trends observed in classically defined hydrogen bonds. All of the established definitions and criteria for identifying hydrogen bonding have been challenged. By any of the most well-established criteria, the DMSO/Cl- complex is hydrogen bonded. We propose a generally applicable working definition of hydrogen bonding to clarify and unify understanding of this interaction.

  5. Ruthenium-Catalyzed Transfer Hydrogenation for C-C Bond Formation: Hydrohydroxyalkylation and Hydroaminoalkylation via Reactant Redox Pairs.

    PubMed

    Perez, Felix; Oda, Susumu; Geary, Laina M; Krische, Michael J

    2016-06-01

    Merging the chemistry of transfer hydrogenation and carbonyl or imine addition, a broad new family of redox-neutral or reductive hydrohydroxyalkylations and hydroaminomethylations have been developed. In these processes, hydrogen redistribution between alcohols and π-unsaturated reactants is accompanied by C-C bond formation, enabling direct conversion of lower alcohols to higher alcohols. Similarly, hydrogen redistribution between amines to π-unsaturated reactants results in direct conversion of lower amines to higher amines. Alternatively, equivalent products of hydrohydroxyalkylation and hydroaminomethylation may be generated through the reaction of carbonyl compounds or imines with π-unsaturated reactants under the conditions of 2-propanol-mediated reductive coupling. Finally, using vicinally dioxygenated reactants, that is, diol, ketols, or diones, successive transfer hydrogenative coupling occurs to generate 2 C-C bonds, resulting in products of formal [4+2] cycloaddition. PMID:27573275

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

    PubMed

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

    2016-05-20

    Sodium alginate/Antarctic krill protein composite material (SA/AKP) was successfully obtained by blending method. The hydrogen bonds of SA/AKP composite material were analyzed by Fourier transform infrared spectroscopy (FT-IR) and Nuclear magnetic resonance hydrogen spectrum (HNMR). Experiment manifested the existence of intermolecular and intramolecular hydrogen bonds in SA/AKP system; strength of intermolecular hydrogen bond enhanced with the increase of AKP in the composite material and the interaction strength of hydrogen bonding followed the order: OH…Ether O>OH…π>OH…N. The percentage of intermolecular hydrogen bond decreased with increase of pH. At the same time, the effect of hydrogen bonds on properties of the composite material was discussed. The increase of intermolecular hydrogen bonding led to the decrease of crystallinity, increase of apparent viscosity and surface tension, as well as obvious decrease of heat resistance of SA/AKP composite material. SA/AKP fiber SEM images and energy spectrum showed that crystallized salt was separated from the fiber, which possibly led to the fibrillation of the composite fibers. PMID:26917400

  7. Intramolecular hydrogen bond in biologically active o-carbonyl hydroquinones.

    PubMed

    Martínez-Cifuentes, Maximiliano; Weiss-López, Boris E; Santos, Leonardo S; Araya-Maturana, Ramiro

    2014-01-01

    Intramolecular hydrogen bonds (IHBs) play a central role in the molecular structure, chemical reactivity and interactions of biologically active molecules. Here, we study the IHBs of seven related o-carbonyl hydroquinones and one structurally-related aromatic lactone, some of which have shown anticancer and antioxidant activity. Experimental NMR data were correlated with theoretical calculations at the DFT and ab initio levels. Natural bond orbital (NBO) and molecular electrostatic potential (MEP) calculations were used to study the electronic characteristics of these IHB. As expected, our results show that NBO calculations are better than MEP to describe the strength of the IHBs. NBO energies (∆Eij(2)) show that the main contributions to energy stabilization correspond to LP-->σ* interactions for IHBs, O1…O2-H2 and the delocalization LP-->π* for O2-C2=Cα(β). For the O1…O2-H2 interaction, the values of ∆Eij(2) can be attributed to the difference in the overlap ability between orbitals i and j (Fij), instead of the energy difference between them. The large energy for the LP O2-->π* C2=Cα(β) interaction in the compounds 9-Hydroxy-5-oxo-4,8, 8-trimethyl-l,9(8H)-anthracenecarbolactone (VIII) and 9,10-dihydroxy-4,4-dimethylanthracen-1(4H)-one (VII) (55.49 and 60.70 kcal/mol, respectively) when compared with the remaining molecules (all less than 50 kcal/mol), suggests that the IHBs in VIII and VII are strongly resonance assisted. PMID:24995921

  8. Adaptive polymeric nanomaterials utilizing reversible covalent and hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Neikirk, Colin

    Adaptive materials based on stimuli responsive and reversible bonding moieties are a rapidly developing area of materials research. Advances in supramolecular chemistry are now being adapted to novel molecular architectures including supramolecular polymers to allow small, reversible changes in molecular and nanoscale structure to affect large changes in macroscale properties. Meanwhile, dynamic covalent chemistry provides a complementary approach that will also play a role in the development of smart adaptive materials. In this thesis, we present several advances to the field of adaptive materials and also provide relevant insight to the areas of polymer nanocomposites and polymer nanoparticles. First, we have utilized the innate molecular recognition and binding capabilities of the quadruple hydrogen bonding group ureidopyrimidinone (UPy) to prepare supramolecular polymer nanocomposites based on supramolecular poly(caprolactone) which show improved mechanical properties, but also an increase in particle aggregation with nanoparticle UPy functionalization. We also present further insight into the relative effects of filler-filler, filler-matrix, and matrix-matrix interactions using a UPy side-chain functional poly(butyl acrylate). These nanocomposites have markedly different behavior depending on the amount of UPy sidechain functionality. Meanwhile, our investigations of reversible photo-response showed that coumarin functionality in polymer nanoparticles not only facilitates light mediated aggregation/dissociation behavior, but also provides a substantial overall reduction in particle size and improvement in nanoparticle stability for particles prepared by Flash NanoPrecipitation. Finally, we have combined these stimuli responsive motifs as a starting point for the development of multiresponsive adaptive materials. The synthesis of a library of multifunctional materials has provided a strong base for future research in this area, although our initial

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

    PubMed

    Zhou, Pan-Pan; Qiu, Wen-Yuan

    2009-08-01

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

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

    NASA Astrophysics Data System (ADS)

    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.

  11. Vibronic spectroscopy of jet-cooled hydrogen-bonded clusters

    NASA Astrophysics Data System (ADS)

    Gerhards, M.; Kimpfel, B.; Pohl, M.; Schmitt, M.; Kleinermanns, K.

    1992-07-01

    Mass-selected, two-photon resonant ionisation spectra of supersonically cooled p-cresol · (H 2O) n and phenol · (H 2O) n are reported. Cluster spectra with one, two and three water molecules attached can be unambiguously assigned. A monotonic shift of the electronic spectra with increasing cluster size is not observed here. The spectrum of p-cresol · (H 2O) 1, is red-shifted relative to the free p-cresol spectrum, while the p-cresol · (H 2O) 2,3 electronic origins are blue-shifted relative to p-cresol · (H 2O) 1 but still lie on the red side of the monomer. Simple, highest occupied molecular orbital—lowest unoccupied molecular orbital (HOMO—LUMO) considerations based on an initio calculations show that this can be explained by the inductive effect exerted on the O-atom of p-cresol, which acts as proton donor and acceptor in the H-bonding. The blue shift of n-π* transitions of H-bonded chromophores with carbonyl groups like CH 2O · (H 2O) 1 can be explained similarly. Vibrational spectra of supersonically cooled complexes of p-cresol with H 2O and CH 3OH were further analysed by dispersed fluorescence and stimulated emission, detected by two-colour ionisation dip. In p-cresol · (H 2O) 1, progressions of the intermolecular cluster stretch vibration and its combination bands with intramolecular cluster vibrations were observed with similar frequencies in the S 0 and S 1 states. In p-cresol · (H 2O) 3, further intense intermolecular bands arise, namely the hydrogen-bridge bending and torsion vibrations. This can be attributed to the lower symmetry of these clusters. Ab initio quantum chemical calculations show p-cresol · (H 2O) 3 to have a higher H-bond stretch frequency than p-cresol · (H 2O) 1, because its (unsymmetric) cyclic structure is more rigid. A characteristic pattern of CH 3 torsional bands in p-cresol is observed with complex structures due the CH 3 torsion—overall rotation interaction. Although their appearance is similar, the spacing of

  12. Bifurcated hydrogen bonds stabilize fibrils of poly(L-glutamic) acid.

    PubMed

    Fulara, Aleksandra; Dzwolak, Wojciech

    2010-06-24

    Model fibrillating homopolypeptides have been providing many insightful analogies to the clinically important phenomena of protein misfolding and amyloidogenesis. Here we show that the beta(2) structural variant of poly(l-glutamic) acid forms fibrils with an amyloid-like morphology, ability to enhance fluorescence of thioflavin T, and seeding properties. The beta(2) fibrils are formed upon heating of aqueous solutions of alpha-helical poly(l-glutamic) acid, which leads to a significant increase of pD (pH) of unbuffered samples and a concomitant precipitation of fibrils with unusual infrared traits: amide I' band being dramatically red-shifted to 1596 cm(-1), and the -COOD stretching band split into two peaks around 1730 and 1719 cm(-1). We are proposing that formation of three-center hydrogen bonds involving bifurcated peptide carbonyl acceptors (>C=O) and main chains' NH, as well as side chains' -COOH proton donors is likely to underlie the observed infrared characteristics of beta(2) fibrils. Such bonds provide additional conformational constraints in a tightly packed environment around glutamate side chains resulting in the decreased overall acidity of the polypeptide. The presence of bifurcated hydrogen bonds in amyloid fibrils may be an overlooked factor in fibrils' robustness, thermodynamic stability and the ability to propagate their own growth. PMID:20509699

  13. Acid-Base Formalism Extended to Excited State for O-H···S Hydrogen Bonding Interaction.

    PubMed

    Bhattacharyya, Surjendu; Roy, Ved Prakash; Wategaonkar, Sanjay

    2016-09-01

    scaled with the pKa of the donor, similar to that observed in the O-H···O interaction. However, the two classes of H-bonds follow different correlations. In addition we also discuss the nuances associated with the similarity and differences in the hydrogen bonding properties of the two classes in the ground electronic state as well as in the excited state. PMID:27529293

  14. Preorganized Hydrogen Bond Donor Catalysts: Acidities and Reactivities.

    PubMed

    Samet, Masoud; Kass, Steven R

    2015-08-01

    Measured DMSO pKa values for a series of rigid tricyclic adamantane-like triols containing 0-3 trifluoromethyl groups (i.e., 3(0)-3(3)) are reported. The three compounds with CF3 substituents are similar or more acidic than acetic acid (pKa = 13.5 (3(1)), 9.5 (3(2)), 7.3 (3(3)) vs 12.6 (HOAc)), and the resulting hydrogen bond network enables a remote γ-trifluoromethyl group to enhance the acidity as well as one located at the α-position. Catalytic abilities of 3(0)-3(3) were also examined. In a nonpolar environment a rate enhancement of up to 100-fold over flexible acyclic analogs was observed presumably due to an entropic advantage of the locked-in structure. Gas-phase acidities are found to correlate with the catalytic activity better than DMSO pKa values and appear to be a better measure of acidities in low dielectric constant media. These trends are reduced or reversed in polar solvents highlighting the importance of the reaction environment. PMID:26140305

  15. Ab initio SCF calculations on hydrogen bonded cresol isomers

    NASA Astrophysics Data System (ADS)

    Pohl, M.; Kleinermanns, K.

    1988-12-01

    Ab initio GAUSSIAN 80 calculations with two different basis sets (STO-3G and 4 31 G*) were performed on hydrogen bonded cresol isomers for comparison with experimental data from free jet fluorescence excitation spectroscopy. For m-cresol, the calculated barriers for hindered internal rotation of the OH-group and the CH3-group are in good agreement with experiment. The calculations show the trans-linear configuration of p-cresol· B-clusters ( B = H2O, CH3OH) to be more stable than the all-planar configuration. This agrees with CI calculations and microwave spectroscopic investigations of the water dimer. Calculations of both the intermolecular stretch and bend frequencies of p-cresol· B-clusters show little dependence on the all-planar or trans-linear configuration but a strong dependence on the choice of the basis set. With the minimal basis set STO-3G, the vibrational energies are generally too high. The agreement between the calculated vibrational frequencies from the 4 31 G* basis set and the experimental values is fair.

  16. Intermolecular hydrogen bonded and self-assembled β-pleated sheet structures of β-sulfidocarbonyls

    NASA Astrophysics Data System (ADS)

    Hussain, Sahid; Das, Gopal; Chaudhuri, Mihir K.

    2007-06-01

    The three crystal structures of β-sulfidocarbonyls 1, 2 and 3 synthesized from the reaction of acryl amide with cystiene, 1,2-dithiol and 1,3-dithiols, respectively, in water catalyzed by borax, have been determined at 273 K. The characteristic features of the structures are self-assembly through intermolecular hydrogen bonding leading to infinite chains of molecules in one direction, in addition to the stacking of layers of such molecular chains in the perpendicular direction ultimately giving rise to β-pleated sheets of 3D molecular network involving N-H⋯O, C-H⋯O and C-H⋯S bonding in the crystal lattice.

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

    SciTech Connect

    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.

  18. Shape of the proton potential in an intramolecular hydrogen-bonded system. Part II

    NASA Astrophysics Data System (ADS)

    Wojciechowski, Grzegorz; Ratajczak-Sitarz, Małgorzata; Katrusiak, Andrzej; Brzezinski, Bogumil

    2002-06-01

    The crystals of 5,5'-dibromo-3-diethylaminomethyl-2,2'-biphenol N-oxide were studied by X-ray and FT-IR spectroscopy. Within this molecule two short OHO intramolecular hydrogen bonds are formed. The NO⋯H +⋯O - bond between the OH and the N-oxide groups is very strong, of 2.419(7) Å between the oxygen atoms. The proton potential of this hydrogen bond is flat, broad and has probably no barrier—consequently it could not be located from X-ray diffraction data. The other hydrogen bond formed between two hydroxyl groups appears asymmetrical from FT-IR spectra, and shows also relatively limited proton polarizability. The molecular conformation is non-planar, due to strong overcrowding effect between the oxygen atoms involved in the hydrogen bonds.

  19. Addition of antibacterial agents to MMA-TBB dentin bonding systems--influence on tensile bond strength and antibacterial effect.

    PubMed

    Kudou, Y; Obara, K; Kawashima, T; Kubota, M; Abe, S; Endo, T; Komatsu, M; Okuda, R

    2000-03-01

    To produce a bonding system which has both high bond strength and antibacterial properties, an antibacterial agent (vancomycin: VCM or metronidazol: MN) was added to the PMMA powder of 4-META/MMA-TBB resin (CB). The influence of the addition of an antibacterial agent on tensile bond strength to dentin and the antibacterial effect were investigated in this study. Forty-seven freshly extracted bovine first or second incisors were used to measure the tensile bond strength to dentin. The bond strengths to bovine dentin were not significantly decreased by addition of VCM (1%, 2%, 5%), or MN (1%) to CB (p < 0.05). The antibacterial effect of CB containing antibacterial agent on six strains of bacteria was investigated by the agar plate diffusion method, analyzing the appearance of the inhibition zone around a resin disk following anaerobic culturing. The resin disks containing VCM showed antibacterial effects on all of the strains examined; the widths of the inhibition zones were 4-15 mm. The resin disks containing MN showed antibacterial effects on three strains; the widths of the inhibition zones were 0-4 mm. It was thus possible to produce a bonding system with both antibacterial effect and high tensile bond strength by addition of VCM to PMMA powder. PMID:11219091

  20. Crystalline Metaphosphate Acid Salts: Synthesis in Organic Media, Structures, Hydrogen-Bonding Capability, and Implication of Superacidity.

    PubMed

    Chakarawet, Khetpakorn; Knopf, Ioana; Nava, Matthew; Jiang, Yanfeng; Stauber, Julia M; Cummins, Christopher C

    2016-06-20

    Metaphosphate acids cannot be thoroughly studied in aqueous media because their acidity is leveled by the solvent, and the resulting metaphosphates are susceptible to acid-catalyzed hydrolysis. Exploration of metaphosphate acid chemistry has now been made possible with the development of a general synthetic method for organic media soluble metaphosphate acids. Protonation of the [PPN](+) salts ([PPN](+) = [N(PPh3)2](+)) of tri-, tetra-, and hexametaphosphates results in five new metaphosphate acids, [PPN]2[P3O9H] (2), [PPN]4[(P4O12)3H8] (3), [PPN]4[P6O18H2]·2H2O (4), [PPN]3[P6O18H3] (5), and [PPN]2[P6O18H2(H3O)2] (6), obtained in yields of 80, 71, 66, 88, and 76%, respectively. Additionally, our synthetic method can be extended to pyrophosphate to produce [PPN][P2O7H3] (7) in 77% yield. The structural configurations of these oxoacids are dictated by strong hydrogen bonds and the anticooperative effect. Intramolecular hydrogen bonds are observed in 2, 4, and 5 and the previously reported [PPN]2[P4O12H2] (1), while intermolecular hydrogen bonds are observed in 3, 6, and 7. The hydrogen bonds in 3-7 possess short distances and are classified as low-barrier hydrogen bonds. Gas-phase acidity computations reveal that the parent tri- and tetrametaphosphoric acids are superacids. Their remarkable acidity is attributable to the stabilization of their corresponding conjugate bases via intramolecular hydrogen bonding. PMID:27267865

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

    SciTech Connect

    Tolk, Norman H.; Feldman, L. C.; Luepke, G.

    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

  2. Effect of the intramolecular hydrogen bond on the spectral and optical properties in chitosan oligosaccharide

    NASA Astrophysics Data System (ADS)

    Li, Xin; Yang, Mengshi; Shi, Xiao; Chu, Xiuxiang; Chen, Liang; Wu, Qiang; Wang, Yueyue

    2015-05-01

    The geometric structures, hydrogen bond types, IR spectra and nonlinear optical properties of chitosan oligosaccharide (degree of polymerization 2-5) are studied by density-functional theory (DFT) at B3LYP/6-31+G(d) level. We have analyzed the statistics of relationship between IR spectra and bond lengths, and angles of amino, hydroxyl. The results show that: (1) the active groups C3-OH, C6-OH and -NH2 can form intramolecular hydrogen bond in chitosan oligosaccharide; (2) the IR spectra of three active groups have size effect in growth process, however, its IR intensity increases significantly and IR frequencies are red shifted obviously when the active hydroxyl form hydrogen bonds, because the bond length of active hydroxyl becomes longer; (3) the effect of hydrogen bond on intensity and frequency of the three vibration mode of amino is the main factor and complication. The paper also provides the nonlinear optical properties of chitosan oligosaccharide. The reason why hydrogen bond can make an appreciable difference to IR spectra, and the nonlinear optical properties of chitosan oligosaccharide are discussed. This research has important significance in the characterization of chitosan oligosaccharide, the properties of chitosan material and hydrogen bond by infrared spectroscopy.

  3. Experimental evidence of O-H—S hydrogen bonding in supersonic jet

    NASA Astrophysics Data System (ADS)

    Biswal, Himansu S.; Chakraborty, Shamik; Wategaonkar, Sanjay

    2008-11-01

    Experimental evidence is presented for the O-H—S hydrogen bonding in the complexes of simple model compounds of methionine (dimethyl sulphide) and tyrosine (phenol, p-cresol, and 2-naphthol). The complexes were formed in the supersonic jet and were detected using resonantly enhanced multiphoton ionization spectroscopy. In all the complexes, the band origins for the S1-S0 electronic transition were redshifted relative to that of their respective monomers. The resonant ion depletion IR spectra of all the complexes show redshifts of 123-140 cm-1 in the O-H stretching frequency, indicating that the OH group acts as the hydrogen bond donor and sulfur as an acceptor. The density functional theory calculations also predict the stable structures in support of this and predict the redshifted O-H stretching frequency in the complex. The atoms-in-molecules and natural bond orbital calculations confirm the O-H—S hydrogen bonding interaction. The significant finding of this study is that the magnitudes of redshifts in the O-H stretch in the O-H—S hydrogen bonded complexes reported here are comparable to those reported for the O-H—O hydrogen bonded complexes where H2O acts as the H-bond acceptor, which suggests that the OH-S interaction is perhaps as strong as the OH-O interaction. To the best of our knowledge, this is the first such report on the O-H—S hydrogen bonded complexes.

  4. FTIR studies of hydrogen bonding between α,β-unsaturated esters and alcohols

    NASA Astrophysics Data System (ADS)

    Tonge, P. J.; Fausto, R.; Carey, P. R.

    1996-06-01

    The enthalpy (and entropy) of hydrogen bond formation has been measured between the ester carbonyl groups of the two α,β-unsaturated esters thienylacryloyl (TAOMe) and 5-methylthienylacryloyl (5MeTAOMe) methyl ester and the hydrogen bond donors ethanol, phenol and 3,5-dichlorophenol in CCl 4. For the esters, the hydrogen bonding strengths were measured by quantitating the amount of bound and unbound donor, using the OH stretching region, as a function of temperature and applying the van't Hoff equation. The decrease in νCO of the ester carbonyl group upon hydrogen bond formation ΔνCO has also been measured and correlated with the enthalpy of hydrogen bond formation. A linear correlation is observed between the enthalpy of hydrogen bond formation - ΔH and ΔνCO, with - ΔH = 1.36 ΔνCO - 16.1, where ΔH is measured in kJ mol -1 and Δν in cm -1. Comparison with data for other carbonyl acceptor compounds indicates that the carbonyl group of the above α,β-unsaturated esters is more readily polarized than the carbonyl group of saturated esters or ketones. The quantitative relationship between - ΔH and ΔνCO derived here has been used to determine the change in the enthalpy of hydrogen bond formation between substrate and enzyme groups in a series of acylserine proteases.

  5. An experimental and theoretical study of a hydrogen-bonded complex: O-phenylenediamine with 2,6-pyridinedicarboxylic acid

    NASA Astrophysics Data System (ADS)

    Ghasemi, Khaled; Rezvani, Ali Reza; Habibi-Khorassani, Sayyed Mostafa; Shahraki, Mehdi; Shokrollahi, Ardeshir; Moghimi, Abolghasem; Tamandani, Halimeh Kord; Gavahi, Sara

    2015-11-01

    The hydrogen-bonded complex, [(OPDH)+(dipicH)-.H2O], between o-phenylenediamine (OPD) and 2,6-pyridinedicarboxylic acid (dipicH2) has been characterized in water by the 1H, 13C NMR and IR spectroscopies. The crystal structure showed that the edge to face C-H⋯π and C-O⋯π stacking interactions between the dipicH2 and OPD rings play an extra significant role in the formation of the hydrogen-bonded complex and supported the H-bonding interactions. The proton transfer also investigated theoretically in gas phase and thermodynamic parameters such as ΔH‡, ΔG‡, ΔS‡ were calculated for this process. Moreover, intramolecular hydrogen-bonding interaction has been recognized by calculating the electron density ρ(r) and Laplacian ∇2ρ(r) at the bond critical point (BCP) using Atoms-In-Molecule (AIM) method and also the interaction between electron acceptor (σ*) of OH with the lone pair of the nitrogen atom as an electron donor using Natural Bond Orbital (NBO) analysis. In addition, the protonation constants of dipicH2 and OPD and the equilibrium constants for the dipic-OPD (1:1) proton transfer system were obtained by the potentiometric pH titration method using the Hyperquad 2008 program. The stoichiometry of the proton transfer species in the solution confirmed the solid state result.

  6. Covalency of hydrogen bonds in liquid water can be probed by proton nuclear magnetic resonance experiments

    PubMed Central

    Elgabarty, Hossam; Khaliullin, Rustam Z.; Kühne, Thomas D.

    2015-01-01

    The concept of covalency is widely used to describe the nature of intermolecular bonds, to explain their spectroscopic features and to rationalize their chemical behaviour. Unfortunately, the degree of covalency of an intermolecular bond cannot be directly measured in an experiment. Here we established a simple quantitative relationship between the calculated covalency of hydrogen bonds in liquid water and the anisotropy of the proton magnetic shielding tensor that can be measured experimentally. This relationship enabled us to quantify the degree of covalency of hydrogen bonds in liquid water using the experimentally measured anisotropy. We estimated that the amount of electron density transferred between molecules is on the order of 10  m while the stabilization energy due to this charge transfer is ∼15 kJ mol−1. The physical insight into the fundamental nature of hydrogen bonding provided in this work will facilitate new studies of intermolecular bonding in a variety of molecular systems. PMID:26370179

  7. Covalency of hydrogen bonds in liquid water can be probed by proton nuclear magnetic resonance experiments.

    PubMed

    Elgabarty, Hossam; Khaliullin, Rustam Z; Kühne, Thomas D

    2015-01-01

    The concept of covalency is widely used to describe the nature of intermolecular bonds, to explain their spectroscopic features and to rationalize their chemical behaviour. Unfortunately, the degree of covalency of an intermolecular bond cannot be directly measured in an experiment. Here we established a simple quantitative relationship between the calculated covalency of hydrogen bonds in liquid water and the anisotropy of the proton magnetic shielding tensor that can be measured experimentally. This relationship enabled us to quantify the degree of covalency of hydrogen bonds in liquid water using the experimentally measured anisotropy. We estimated that the amount of electron density transferred between molecules is on the order of 10  m while the stabilization energy due to this charge transfer is ∼15 kJ mol(-1). The physical insight into the fundamental nature of hydrogen bonding provided in this work will facilitate new studies of intermolecular bonding in a variety of molecular systems. PMID:26370179

  8. Diels-Alder attachment of a planar organic molecule to a dangling bond dimer on a hydrogenated semiconductor surface.

    PubMed

    Godlewski, Szymon; Kawai, Hiroyo; Engelund, Mads; Kolmer, Marek; Zuzak, Rafal; Garcia-Lekue, Aran; Novell-Leruth, Gerard; Echavarren, Antonio M; Sanchez-Portal, Daniel; Joachim, Christian; Saeys, Mark

    2016-06-22

    Construction of single-molecule electronic devices requires the controlled manipulation of organic molecules and their properties. This could be achieved by tuning the interaction between the molecule and individual atoms by local "on-surface" chemistry, i.e., the controlled formation of chemical bonds between the species. We demonstrate here the reversible attachment of a planar conjugated polyaromatic molecule to a pair of unpassivated dangling bonds on a hydrogenated Ge(001):H surface via a Diels-Alder [4+2] addition using the tip of a scanning tunneling microscope (STM). Due to the small stability difference between the covalently bonded and a nearly undistorted structure attached to the dangling bond dimer by long-range dispersive forces, we show that at cryogenic temperatures the molecule can be switched between both configurations. The reversibility of this covalent bond forming reaction may be applied in the construction of complex circuits containing organic molecules with tunable properties. PMID:27271337

  9. Two-dimensional interlocked pentagonal bilayer ice: how do water molecules form a hydrogen bonding network?

    PubMed

    Zhu, Weiduo; Zhao, Wen-Hui; Wang, Lu; Yin, Di; Jia, Min; Yang, Jinlong; Zeng, Xiao Cheng; Yuan, Lan-Feng

    2016-06-01

    The plethora of ice structures observed both in bulk and under nanoscale confinement reflects the extraordinary ability of water molecules to form diverse forms of hydrogen bonding networks. An ideal hydrogen bonding network of water should satisfy three requirements: (1) four hydrogen bonds connected with every water molecule, (2) nearly linear hydrogen bonds, and (3) tetrahedral configuration for the four hydrogen bonds around an O atom. However, under nanoscale confinement, some of the three requirements have to be unmet, and the selection of the specific requirement(s) leads to different types of hydrogen bonding structures. According to molecular dynamics (MD) simulations for water confined between two smooth hydrophobic walls, we obtain a phase diagram of three two-dimensional (2D) crystalline structures and a bilayer liquid. A new 2D bilayer ice is found and named the interlocked pentagonal bilayer ice (IPBI), because its side view comprises interlocked pentagonal channels. The basic motif in the top view of IPBI is a large hexagon composed of four small pentagons, resembling the top view of a previously reported "coffin" bilayer ice [Johnston, et al., J. Chem. Phys., 2010, 133, 154516]. First-principles optimizations suggest that both bilayer ices are stable. However, there are fundamental differences between the two bilayer structures due to the difference in the selection among the three requirements. The IPBI sacrifices the linearity of hydrogen bonds to retain locally tetrahedral configurations of the hydrogen bonds, whereas the coffin structure does the opposite. The tradeoff between the conditions of an ideal hydrogen bonding network can serve as a generic guidance to understand the rich phase behaviors of nanoconfined water. PMID:27063210

  10. Dynamics of supercritical methanol of varying density from first principles simulations: Hydrogen bond fluctuations, vibrational spectral diffusion, and orientational relaxation

    NASA Astrophysics Data System (ADS)

    Yadav, Vivek Kumar; Chandra, Amalendu

    2013-06-01

    A first principles study of the dynamics of supercritical methanol is carried out by means of ab initio molecular dynamics simulations. In particular, the fluctuation dynamics of hydroxyl stretch frequencies, hydrogen bonds, dangling hydroxyl groups, and orientation of methanol molecules are investigated for three different densities at 523 K. Apart from the dynamical properties, various equilibrium properties of supercritical methanol such as the local density distributions and structural correlations, hydrogen bonding aspects, frequency-structure correlations, and dipole distributions of methanol molecules are also investigated. In addition to the density dependence of various equilibrium and dynamical properties, their dependencies on dispersion interactions are also studied by carrying out additional simulations using a dispersion corrected density functional for all the systems. It is found that the hydrogen bonding between methanol molecules decreases significantly as we move to the supercritical state from the ambient one. The inclusion of dispersion interactions is found to increase the number of hydrogen bonds to some extent. Calculations of the frequency-structure correlation coefficient reveal that a statistical correlation between the hydroxyl stretch frequency and the nearest hydrogen-oxygen distance continues to exist even at supercritical states of methanol, although it is weakened with increase of temperature and decrease of density. In the supercritical state, the frequency time correlation function is found to decay with two time scales: One around or less than 100 fs and the other in the region of 250-700 fs. It is found that, for supercritical methanol, the times scales of vibrational spectral diffusion are determined by an interplay between the dynamics of hydrogen bonds, dangling OD groups, and inertial rotation of methanol molecules and the roles of these various components are found to vary with density of the supercritical solvent. Effects

  11. Investigation of hydrogen bond in binary mixture (pyridine + propionic acid) by spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Chen, Yuan-Zheng; Liu, Tian-Yuan; Qu, Guan-Nan; Sun, Shang; Gao, Shu-Qin; Zhou, Mi; Sun, Chen-Lin; Li, Zuo-Wei

    2011-11-01

    This Letter analyzed the hydrogen bond between pyridine and propionic acid using Raman and infrared spectra as a function of concentrations. The wavenumber shift and line width change were investigated to analyze the effects of hydrogen bond on the ring breathing mode and the triangle mode of pyridine. Density functional theory (DFT) at the B3LYP/6-31++G (d,p) level was performed on the binary solution. The simulated vibrational Raman spectra obtained the experimentally observed spectral features about the blue-shifted of the ring breathing mode. Furthermore, the effect of the hydrogen bond on Fermi Resonance (FR) was discussed.

  12. Self-complementary quadruply hydrogen-bonded duplexes based on imide and urea units.

    PubMed

    Li, Xianghui; Fang, Yuyu; Deng, Pengchi; Hu, Jinchuan; Li, Tian; Feng, Wen; Yuan, Lihua

    2011-09-01

    The quadruply hydrogen-bonded duplexes based on an imide-urea structure preorganized by three-center hydrogen bonds were found to associate via bifurcated hydrogen bonds. (1)H NMR dilution experiments revealed the high stability of the homodimer in apolar solvent (K(dim) > 10(5) M(-1) in CDCl(3)) and enhancement of association ability due to electron-withdrawing substituent effects. The ready synthetic availability and adjustable association affinity via electronic effects may render these association units potentially applicable in constructing supramolecular architectures. PMID:21819056

  13. Intra- and intermolecular hydrogen bonds in ethylene glycol, monoethanolamine, and ethylenediamine

    NASA Astrophysics Data System (ADS)

    Krest'yaninov, M. A.; Titova, A. G.; Zaichikov, A. M.

    2014-12-01

    The structures of ethylene glycol, aminoethanol, ethylenediamine, and their dimers with the formation of hydrogen bonds of different types are optimized by density functional theory (DFT) using hybrid functional B3LYP in the basis of 6-31++G( d,p), 6-311++G(2 d,2 p) and aug-CC-pVTZ. Energies of interactions, hydrogen bond parameters, and oscillation frequency are calculated, and NBO analysis is performed. The types of hydrogen bonds formed in dimers of 1,2-disubstituted ethanes X-CH2-CH2-Y (X, Y = OH, NH2) are established.

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

    NASA Astrophysics Data System (ADS)

    Takahashi, Masae; Ishikawa, Yoichi

    2013-06-01

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

  15. Systematic Construction of Ternary Cocrystals by Orthogonal and Robust Hydrogen and Halogen Bonds.

    PubMed

    Topić, Filip; Rissanen, Kari

    2016-05-25

    A carefully designed strategy is presented for the construction of ternary cocrystals, based on the orthogonality of two supramolecular interaction modes: hydrogen bonding between crown ethers and thioureas and the halogen bonding between thioureas and perfluorohalocarbons. Tested on a set comprising two crown ethers, two thioureas and five halogen bond donors, the strategy resulted in a high, 75% success rate, with 15/20 component combinations yielding at least one cocrystal. Crystal structure analysis revealed the interplay between the hydrogen and halogen bonding motifs, also shedding light on the variables affecting their formation. PMID:27145122

  16. Investigation of the H-Cu and Cu-Cu bonds in hydrogenated Cu

    NASA Astrophysics Data System (ADS)

    Shuttleworth, I. G.

    2013-01-01

    The pure and hydrogenated copper system CuHn (n=0, 0.25, 0.50, 0.75 and 1) has been investigated using LCAO-DFT. The average H-Cu (Cu-Cu) bonding interaction increases (decreases) with n whilst concurrent orbital-resolved studies of the H-Cu interactions showed that the (non-)directional H-Cu bonds become more (less) bonding. This preference for directional bonds is reflected in the Cu-Cu interactions. CuH0.25 is shown to have an unusually localized electronic structure compared to the more hydrogenated systems, and the origins of this structure are discussed.

  17. Electron-Withdrawing Trifluoromethyl Groups in Combination with Hydrogen Bonds in Polyols: Brønsted Acids, Hydrogen-Bond Catalysts, and Anion Receptors

    SciTech Connect

    Shokri, Alireza; Wang, Xue B.; Kass, Steven R.

    2013-06-26

    Electron withdrawing trifluoromethyl groups were characterized in combination with hydrogen bond interactions in three polyols (i.e., CF3CH(OH)CH2CH(OH)CF3, 1; (CF3)2C(OH)C(OH)(CF3)2, 2; ((CF3)2C(OH)CH2)2CHOH, 3) by pKa measurements in DMSO and H2O, negative ion photoelectron spectroscopy and binding constant determinations with Cl–. Their catalytic behavior in several reactions were also examined and compared to a BrØnsted acid (HOAc) and a commonly employed thiourea ((3,5-(CF3)3C6H3NH)2CS). The combination of inductive stabilization and hydrogen bonds was found to afford potent acids which are effective catalysts. It also appears that hydrogen bonds can transmit the inductive effect over distance even in an aqueous environment, and this has far reaching implications.

  18. The Variable Transition State in Polar Additions to Pi Bonds

    ERIC Educational Resources Information Center

    Weiss, Hilton M.

    2010-01-01

    A vast majority of polar additions of Bronsted acids to alkynes involve a termolecular transition state. With strong acids, considerable positive charge is developed on carbon and Markovnikov addition predominates. In less acidic solutions, however, the reaction is much slower and the transition state more closely resembles the olefinic product.…

  19. Hydrogen bonding at C=Se acceptors in selenoureas, selenoamides and selones.

    PubMed

    Bibelayi, Dikima; Lundemba, Albert S; Allen, Frank H; Galek, Peter T A; Pradon, Juliette; Reilly, Anthony M; Groom, Colin R; Yav, Zéphyrin G

    2016-06-01

    In recent years there has been considerable interest in chalcogen and hydrogen bonding involving Se atoms, but a general understanding of their nature and behaviour has yet to emerge. In the present work, the hydrogen-bonding ability and nature of Se atoms in selenourea derivatives, selenoamides and selones has been explored using analysis of the Cambridge Structural Database and ab initio calculations. In the CSD there are 70 C=Se structures forming hydrogen bonds, all of them selenourea derivatives or selenoamides. Analysis of intramolecular geometries and ab initio partial charges show that this bonding stems from resonance-induced C(δ+)=Se(δ-) dipoles, much like hydrogen bonding to C=S acceptors. C=Se acceptors are in many respects similar to C=S acceptors, with similar vdW-normalized hydrogen-bond lengths and calculated interaction strengths. The similarity between the C=S and C=Se acceptors for hydrogen bonding should inform and guide the use of C=Se in crystal engineering. PMID:27240763

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

    PubMed

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

    2016-03-01

    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. PMID:26852414

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

    PubMed

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

    2016-04-21

    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 (HO2C(CH2)nCO2(-)[HO2C(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 the previously studied HSO4(-)[HO2C(CH2)2CO2H] complex (J. Phys. Chem. Lett. 2013, 4, 779-785) shows that HO2C(CH2)2CO2(-)[HO2C(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 homogeneous complexes by involving dicarboxylic acids themselves. PMID:27032015

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

    NASA Astrophysics Data System (ADS)

    Xin-Jun, Zhao; Zhi-Fu, Gao

    2016-07-01

    By employing molecular theory, we systematically investigate the shift of solubility of poly(N-isopropylacrylamide) (PNIPAM) brushes in sodium halide solutions. After considering PNIPAM–water hydrogen bonds, water–anion hydrogen bonds, and PNIPAM–anion bonds and their explicit coupling to the PNIPAM conformations, we find that increasing temperature lowers the solubility of PNIPAM, and results in a collapse of the layer at high enough temperatures. The combination of the three types of bonds would yield a decrease in the solubility of PNIPAM following the Hofmeister series: NaCl>NaBr>NaI. PNIPAM–water hydrogen bonds are affected by water–anion hydrogen bonds and PNIPAM–anion bonds. The coupling of polymer conformations and the competition among the three types of bonds are essential for describing correctly a decrease in the solubility of PNIPAM brushes, which is determined by the free energy associated with the formation of the three types of bonds. Our results agree well with the experimental observations, and would be very important for understanding the shift of the lower critical solution temperature of PNIPAM brushes following the Hofmeister series. Project supported by the National Natural Science Foundation of China (Grant Nos. 21264016, 11464047, and 21364016) and the Joint Funds of Xinjiang Natural Science Foundation, China (Grant No. 2015211C298).

  3. Competition between hydrogen and halogen bonding in halogenated 1-methyluracil: Water systems.

    PubMed

    Hogan, Simon W L; van Mourik, Tanja

    2016-03-30

    The competition between hydrogen- and halogen-bonding interactions in complexes of 5-halogenated 1-methyluracil (XmU; X = F, Cl, Br, I, or At) with one or two water molecules in the binding region between C5-X and C4O4 is investigated with M06-2X/6-31+G(d). In the singly-hydrated systems, the water molecule forms a hydrogen bond with C4O4 for all halogens, whereas structures with a halogen bond between the water oxygen and C5-X exist only for X = Br, I, and At. Structures with two waters forming a bridge between C4O and C5-X (through hydrogen- and halogen-bonding interactions) exist for all halogens except F. The absence of a halogen-bonded structure in singly-hydrated ClmU is therefore attributed to the competing hydrogen-bonding interaction with C4O4. The halogen-bond angle in the doubly-hydrated structures (150-160°) is far from the expected linearity of halogen bonds, indicating that significantly non-linear halogen bonds may exist in complex environments with competing interactions. © 2016 Wiley Periodicals, Inc. PMID:26773851

  4. Applications of 2D IR spectroscopy to peptides, proteins, and hydrogen-bond dynamics

    PubMed Central

    Kim, Yung Sam; Hochstrasser, Robin M.

    2010-01-01

    Following a survey of 2D IR principles this Feature Article describes recent experiments on the hydrogen-bond dynamics of small ions, amide-I modes, nitrile probes, peptides, reverse transcriptase inhibitors, and amyloid fibrils. PMID:19351162

  5. Molecular Dynamics Study of Hsp90 and ADP: Hydrogen Bond Analysis for ADP Dissociation

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Kazutomo; Saito, Hiroaki; Nagao, Hidemi

    The contacts between the N-terminal domain of heat shock protein 90 (N-Hsp90) and ADP involve both direct and water-mediated hydrogen bonds in X-ray crystallographic structure. We perform all-atom molecular dynamics (MD) simulations of N-Hsp90 and ADP to investigate the changes of the hydrogen bond lengths during ADP dissociation. We show the difference between the hydrogen bonds in the crystal structure and MD simulations. Moreover, the N6 group of ADP does not contact with the Cγ group of Asp93, and the hydrogen bonds between Asn51 side chain and ADP are stable in the early step of ADP dissociation.

  6. Hydrogen bonding in liquid methanol, methylamine, and methanethiol studied by molecular-dynamics simulations

    NASA Astrophysics Data System (ADS)

    Kosztolányi, T.; Bakó, I.; Pálinkás, G.

    2003-03-01

    Molecular-dynamics computer simulations have been carried out on liquid methanol, methylamine, and methanethiol. The local structure of the liquids was studied based on radial distribution functions and the density projections of the neighboring molecules obtained on the basis of simulated molecular configurations. The extent of hydrogen bonding was investigated by direct analysis of the connectivity of molecules forming hydrogen-bonded clusters in these liquids. By this analysis, the methanol molecules were found to form linear chainlike structures. The local structure of hydrogen-bonded molecules of methylamine proved to be rather space filling due to the great extent of chain branching. Methanethiol molecules also proved to form hydrogen bonds forming small compact clusters. No evidence was found, however, for the clustering of hydrophobic methyl groups in any of the liquids. The quality of simulations was checked by derivation of neutron total and composite radial distribution functions and by comparison of those with available experimental data.

  7. Identification of intramolecular hydrogen bonds as the origin of malfunctioning of multitopic receptors

    NASA Astrophysics Data System (ADS)

    Dolenský, Bohumil; Konvalinka, Roman; Jakubek, Milan; Král, Vladimír

    2013-03-01

    Several trisamides of N,N-bis(2-aminoethyl)ethane-1,2-amine are prepared as potential saccharide receptors. Surprisingly low or even nil affinity to n-octyl-glucose is found by 1H NMR titration, and explained as a consequence of intramolecular hydrogen bonds of trisamides, (Rsbnd COsbnd NHsbnd C2H4)3N. The hydrogen bonds are identified by combination of 1H NMR and infrared spectra, and 1H NMR temperature coefficients. Results demonstrate that even small molecule can has a rather strong secondary structure, which can cause their malfunctioning in certain applications. Results also point out that the amide temperature coefficients should not be used as the only parameter for the consideration a hydrogen bond is intermolecular or intramolecular, particularly, in the case of furcated hydrogen bonds, and in the cases were a couple of signals are averaged.

  8. Hydrogen-bond acidic functionalized carbon nanotubes (CNTs) with covalently-bound hexafluoroisopropanol groups

    SciTech Connect

    Fifield, Leonard S.; Grate, Jay W.

    2010-06-01

    Fluorinated hydrogen-bond acidic groups are directly attached to the backbone of single walled carbon nanotubes (SWCNTs) without the introduction of intermediate electron donating surface groups. Hexafluoroalcohol functional groups are exceptionally strong hydrogen bond acids, and are added to the nanotube surface using the aryl diazonium approach to create hydrogen-bond acidic carbon nanotube (CNT) surfaces. These groups can promote strong hydrogen-bonding interactions with matrix materials in composites or with molecular species to be concentrated and sensed. In the latter case, this newly developed material is expected to find useful application in chemical sensors and in CNT-based preconcentrator devices for the detection of pesticides, chemical warfare agents and explosives.

  9. Instability of bell-shaped solitary waves in a two-component hydrogen-bonded chain

    NASA Astrophysics Data System (ADS)

    Machnikowski, Paweł; Radosz, Andrzej

    1998-06-01

    Bell-shaped solitons found in a chain of asymmetric double-well hydrogen bonds are unstable, unlike ordinary solitons or kinks. A proof of their instability for low velocities based on a perturbation approach is proposed.

  10. (+)-Gibberellin C: hydrogen-bonding pattern of the monohydrate of a non-racemic pentacyclic diterpenoid.

    PubMed

    Thompson, H W; Brunskill, A P; Lalancette, R A

    2000-12-01

    In the monohydrate of the title compound, (+)-2beta, 4aalpha-dihydroxy-1,7-dimethyl-8-oxo-4bbeta,7alpha- gibbane-1alpha, 10beta-dicarboxylic acid-1,4a-lactone, C(19)H(24)O(6).H(2)O, intermolecular hydrogen bonding progresses helically along b from carboxyl to ketone [O...O = 2.694 (5) A]. The carboxyl and lactone carbonyl groups in translationally related molecules within a helix both accept hydrogen bonds from the same water of hydration. The oxygen of this water in turn accepts a hydrogen bond from the hydroxyl group of a third screw-related molecule in an adjacent counterdirectionally oriented helix, yielding a complex three-dimensional hydrogen-bonding array. Intermolecular O...H-C close contacts were found to the carboxyl and lactone carbonyls, the hydroxyl, and the water. PMID:11119009

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

    PubMed Central

    Wang, Lu; Fried, Stephen D.; Boxer, Steven G.; Markland, Thomas E.

    2014-01-01

    Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds. PMID:25503367

  12. Hydrogen bonded C-H···Y (Y = O, S, Hal) molecular complexes: A natural bond orbital analysis

    NASA Astrophysics Data System (ADS)

    Isaev, A. N.

    2016-03-01

    Hydrogen bonded C-H···Y complexes formed by H2O, H2S molecules, hydrogen halides, and halogen-ions with methane, halogen substituted methane as well as with the C2H2 and NCH molecules were studied at the MP2/aug-cc-pVDZ level. The structure of NBOs corresponding to lone pair of acceptor Y, n Y, and vacant anti-σ-bond C-H of proton donor was analyzed and estimates of second order perturbation energy E(2) characterizing donor-acceptor n Y → σ C-H * charge-transfer interaction were obtained. Computational results for complexes of methane and its halogen substituted derivatives show that for each set of analogous structures, the EnY→σ*C-H (2) energy tends to grow with an increase in the s-component percentage in the lone pair NBO of acceptor Y. Calculations for different C···Y distances show that the equilibrium geometries of complexes lie in the region where the E(2) energy is highest and it changes symbatically with the length of the covalent E-H bond when the R(C···Y) distance is varied. The performed analysis allows us to divide the hydrogen bonded complexes into two groups, depending on the pattern of overlapping for NBOs of the hydrogen bridge.

  13. Hydrogen Peroxide Coordination to Cobalt(II) Facilitated by Second-Sphere Hydrogen Bonding.

    PubMed

    Wallen, Christian M; Palatinus, Lukáš; Bacsa, John; Scarborough, Christopher C

    2016-09-19

    M(H2 O2 ) adducts have been postulated as intermediates in biological and industrial processes; however, only one observable M(H2 O2 ) adduct has been reported, where M is redox-inactive zinc. Herein, direct solution-phase detection of an M(H2 O2 ) adduct with a redox-active metal, cobalt(II), is described. This Co(II) (H2 O2 ) compound is made observable by incorporating second-sphere hydrogen-bonding interactions between bound H2 O2 and the supporting ligand, a trianionic trisulfonamido ligand. Thermodynamics of H2 O2 binding and decay kinetics of the Co(II) (H2 O2 ) species are described, as well as the reaction of this Co(II) (H2 O2 ) species with Group 2 cations. PMID:27560462

  14. Suppression of hydrogenated carbon film deposition and hydrogen isotope retention by nitrogen addition into cold remote H/D and CH4 mixture plasmas

    NASA Astrophysics Data System (ADS)

    Iida, K.; Notani, M.; Uesugi, Y.; Tanaka, Y.; Ishijima, T.

    2015-08-01

    Control of tritium retention and its removal from the first wall of future fusion devices are one of the most crucial issues for safety and effective use for fuel. Nitrogen addition into remote edge plasmas has been considered and tested as an effective method for suppression of carbon film deposition and reduction of hydrogen isotope absorption in the deposited films. In this paper we have investigated the scavenger effects of nitrogen injected into low temperature D2/CH4 plasmas on hydrogenated carbon film growth using a small helical device. The result of the deposition shows that the key reactive particles with CN and ND(H) bonds to suppression of hydrogenated carbon film growth and hydrogen isotope absorption are much slowly generated compared with hydrocarbon particles such as CD(H)x and C2D(H)x. This may be due to the slow atomic nitrogen diffusion into hydrogenated carbon layer and the chemical equilibrium between nitrogen absorption.

  15. Highly Extensible Supramolecular Elastomers with Large Stress Generation Capability Originating from Multiple Hydrogen Bonds on the Long Soft Network Strands.

    PubMed

    Hayashi, Mikihiro; Noro, Atsushi; Matsushita, Yushu

    2016-04-01

    Highly extensible supramolecular elastomers are prepared from ABA triblock-type copolymers bearing glassy end blocks and a long soft middle block with multiple hydrogen bonds. The copolymer used is polystyrene-b-[poly(butyl acrylate)-co-polyacrylamide]-b-polystyrene (S-Ba-S), which is synthesized via reversible addition-fragmentation chain transfer (RAFT) polymerization. Tensile tests reveal that the breaking elongation (εb ) increases with an increase in the middle block molecular weight (Mmiddle ). Especially, the largest S-Ba-S with Mmiddle of 3140k, which is synthesized via high-pressure RAFT polymerization, achieves εb of over 2000% with a maximum tensile stress of 3.6 MPa, while the control sample without any middle block hydrogen bonds, polystyrene-b-poly(butyl acrylate)-b-polystyrene with Mmiddle of 2780k, is merely a viscous material due to the large volume fraction of soft block. Thus, incorporation of hydrogen bonds into the large molecular weight soft middle block is found to be beneficial to prepare supramolecular elastomers attaining high extensibility and sufficiently large stress generation ability simultaneously. This outcome is probably due to concerted combination of entropic changes and internal potential energy changes originating from the dissociation of multiple hydrogen bonds by elongation. PMID:26914643

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

    PubMed Central

    Mohana, Marimuthu; Muthiah, Packianathan Thomas; Sanjeewa, Liurukara D.; McMillen, Colin D.

    2016-01-01

    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 [R 2 2(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 R 6 6(24) and R 4 4(15) ring motifs. The crystal structure is further strengthened by C—H⋯F, C—F⋯π and π–π stacking inter­actions. PMID:27375887

  17. Quantum Calculations on Hydrogen Bonds in Certain Water Clusters Show Cooperative Effects

    SciTech Connect

    Znamenskiy, Vasiliy S.; Green, Michael E.

    2007-01-09

    Water molecules in clefts and small clusters are in a significantly different environment than those in bulk water. We have carried out ab initio calculations that demonstrate this in a series of clusters, showing that cooperative effects must be taken into account in the treatment of hydrogen bonds and water clusters in such bounded systems. Hydrogen bonds between water molecules in simulations are treated most frequently by using point-charge water potentials, such as TIP3P or SPC, sometimes with a polarizable extension. These produce excellent results in bulk water, for which they are calibrated. Clefts are different from bulk; it is necessary to look at smaller systems and investigate the effect of limited numbers of neighbors. We start with a study of isolated clusters of water with varying numbers of neighbors of a hydrogen-bonded pair of water molecules. The cluster as a whole is in a vacuum. The clusters are defined so as to provide the possible arrangements of nearest neighbors of a central hydrogen-bonded pair of water molecules. We then scan the length and angles of the central hydrogen bond of the clusters, using density functional theory, for each possible arrangement of donor and acceptor hydrogen bonds on the central hydrogen-bonding pair; the potential of interaction of two water molecules varies with the number of donor and acceptor neighbors. This also involves changes in charge on the water molecules as a function of bond length and changes in energy and length as a function of the number of neighboring donor and acceptor molecules. The energy varies by approximately 6 kBT near room temperature from the highest to the lowest energy when bond length alone is varied, enough to seriously affect simulations.

  18. Quantum Calculations on Hydrogen Bonds in Certain Water Clusters Show Cooperative Effects.

    SciTech Connect

    Znamenskiy, Vasiliy S.; Green, Michael E.

    2006-12-08

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Water molecules in clefts and small clusters are in a significantly different environment than those in bulk water. We have carried out ab initio calculations that demonstrate this in a series of clusters, showing that cooperative effects must be taken into account in the treatment of hydrogen bonds and water clusters in such bounded systems. Hydrogen bonds between water molecules in simulations are treated most frequently by using point-charge water potentials, such as TIP3P or SPC, sometimes with a polarizable extension. These produce excellent results in bulk water, for which they are calibrated. Clefts are different from bulk; it is necessary to look at smaller systems and investigate the effect of limited numbers of neighbors. We start with a study of isolated clusters of water with varying numbers of neighbors of a hydrogen-bonded pair of water molecules. The cluster as a whole is in a vacuum. The clusters are defined so as to provide the possible arrangements of nearest neighbors of a central hydrogen-bonded pair of water molecules. We then scan the length and angles of the central hydrogen bond of the clusters, using density functional theory, for each possible arrangement of donor and acceptor hydrogen bonds on the central hydrogen-bonding pair; the potential of interaction of two water molecules varies with the number of donor and acceptor neighbors. This also involves changes in charge on the water molecules as a function of bond length and changes in energy and length as a function of the number of neighboring donor and acceptor molecules. The energy varies by approximately 6 kBT near room temperature from the highest to the lowest energy when bond length alone is

  19. A Preorganized Hydrogen Bond Network and Its Effect on Anion Stability

    SciTech Connect

    Samet, Masoud; Wang, Xue B.; Kass, Steven R.

    2014-08-07

    Rigid tricyclic locked in all axial 1,3,5-cyclohexanetriol derivatives with 0–3 trifluoromethyl groups were synthesized and photoelectron spectra of their conjugate bases and chloride anion clusters are reported along with density functional computations. The resulting vertical and adiabatic detachment energies provide measures of the anion stabilization due to the hydrogen bond network and inductive effects. The latter mechanism is found to be transmitted through space via hydrogen bonds

  20. Hydrogen bonding motifs of protein side chains: descriptions of binding of arginine and amide groups.

    PubMed Central

    Shimoni, L.; Glusker, J. P.

    1995-01-01

    The modes of hydrogen bonding of arginine, asparagine, and glutamine side chains and of urea have been examined in small-molecule crystal structures in the Cambridge Structural Database and in crystal structures of protein-nucleic acid and protein-protein complexes. Analysis of the hydrogen bonding patterns of each by graph-set theory shows three patterns of rings (R) with one or two hydrogen bond acceptors and two donors and with eight, nine, or six atoms in the ring, designated R2(2)(8), R2(2)(9), and R1(2)(6). These three patterns are found for arginine-like groups and for urea, whereas only the first two patterns R2(2)(8) and R2(2)(9) are found for asparagine- and glutamine-like groups. In each case, the entire system is planar within 0.7 A or less. On the other hand, in macromolecular crystal structures, the hydrogen bonding patterns in protein-nucleic acid complexes between the nucleic acid base and the protein are all R2(2)(9), whereas hydrogen bonding between Watson-Crick-like pairs of nucleic acid bases is R2(2)(8). These two hydrogen bonding arrangements [R2(2)(9)] and R2(2)(8)] are predetermined by the nature of the groups available for hydrogen bonding. The third motif identified, R1(2)(6), involves hydrogen bonds that are less linear than in the other two motifs and is found in proteins. PMID:7773178

  1. Oligo(p-phenyleneethynylene)s with hydrogen-bonded coplanar conformation.

    PubMed

    Hu, Wei; Zhu, Ningbo; Tang, Wen; Zhao, Dahui

    2008-07-01

    A series of monodispersed oligo( p-phenyleneethynylene)s were synthesized bearing intramolecular hydrogen bonds between side chains of adjacent phenylene units in the backbone. Thus, all repeating units of the molecules are constrained in a coplanar orientation. Such planarized conformation is considered favorable for single-molecule conductance. Photophysical characterization results show narrowed bandgaps and extended conjugation lengths, consistent with a rigid, planar backbone framework as a result of intramolecular hydrogen bonding. PMID:18507389

  2. Silicon layer transfer by hydrogen implantation combined with wafer bonding in ultrahigh vacuum

    NASA Astrophysics Data System (ADS)

    Fecioru, Alin Mihai; Senz, Stephan; Scholz, Roland; Gösele, Ulrich

    2006-11-01

    A layer transfer method was developed by combining in situ photothermal activation of hydrogen passivated surfaces, ultrahigh vacuum bonding, and hydrogen-implantation induced splitting. Structural and electrical investigations showed that ultrathin, single crystalline silicon layers can be transferred to appropriate substrates without the involvement of an intermediate layer such as an oxide or solder. Significant current flow across such produced silicon-silicon bonded interfaces was observed, making this approach very attractive for material integration.

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

    PubMed

    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. PMID:27417325

  4. How Alcohol Chain-Length and Concentration Modulate Hydrogen Bond Formation in a Lipid Bilayer

    PubMed Central

    Dickey, Allison N.; Faller, Roland

    2007-01-01

    Molecular dynamics simulations are used to measure the change in properties of a hydrated dipalmitoylphosphatidylcholine bilayer when solvated with ethanol, propanol, and butanol solutions. There are eight oxygen atoms in dipalmitoylphosphatidylcholine that serve as hydrogen bond acceptors, and two of the oxygen atoms participate in hydrogen bonds that exist for significantly longer time spans than the hydrogen bonds at the other six oxygen atoms for the ethanol and propanol simulations. We conclude that this is caused by the lipid head group conformation, where the two favored hydrogen-bonding sites are partially protected between the head group choline and the sn-2 carbonyl oxygen. We find that the concentration of the alcohol in the ethanol and propanol simulations does not have a significant influence on the locations of the alcohol/lipid hydrogen bonds, whereas the concentration does impact the locations of the butanol/lipid hydrogen bonds. The concentration is important for all three alcohol types when the lipid chain order is examined, where, with the exception of the high-concentration butanol simulation, the alcohol molecules having the longest hydrogen-bonding relaxation times at the favored carbonyl oxygen acceptor sites also have the largest order in the upper chain region. The lipid behavior in the high-concentration butanol simulation differs significantly from that of the other alcohol concentrations in the order parameter, head group rotational relaxation time, and alcohol/lipid hydrogen-bonding location and relaxation time. This appears to be the result of the system being very near to a phase transition, and one occurrence of lipid flip-flop is seen at this concentration. PMID:17218462

  5. A supramolecular photoswitch constructed by intermolecular hydrogen bond between BTEPy and TTF COOH

    NASA Astrophysics Data System (ADS)

    Feng, Yanli; Zhang, Qiong; Tan, Wenjuan; Zhang, Deqing; Tu, Yaoquan; Ågren, Hans; Tian, He

    2008-04-01

    A novel supramolecular photoswitch containing bisthienylethene-pyridine (BTEPy) and carboxyl attached tetrathiafluvalene (TTF-COOH) was constructed via intermolecular hydrogen bond. FT-IR spectra, XPS characterizations, 1H NMR and theoretical calculation were carried out to verify the formation of the intermolecular hydrogen bond. The supramolecular self-assemblies BTEPy · 2TTF show good photochromic properties. A molecular switch with UV/vis light as inputs and electrochemical signals as outputs was obtained.

  6. Unconventional hydrogen bonding to organic ions in the gas phase: Stepwise association of hydrogen cyanide with the pyridine and pyrimidine radical cations and protonated pyridine

    NASA Astrophysics Data System (ADS)

    Hamid, Ahmed M.; El-Shall, M. Samy; Hilal, Rifaat; Elroby, Shaaban; Aziz, Saadullah G.

    2014-08-01

    Equilibrium thermochemical measurements using the ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes for the stepwise association of HCN molecules with the pyridine and pyrimidine radical cations forming the C5H5N+.(HCN)n and C4H4N2+.(HCN)n clusters, respectively, with n = 1-4. For comparison, the binding of 1-4 HCN molecules to the protonated pyridine C5H5NH+(HCN)n has also been investigated. The binding energies of HCN to the pyridine and pyrimidine radical cations are nearly equal (11.4 and 12.0 kcal/mol, respectively) but weaker than the HCN binding to the protonated pyridine (14.0 kcal/mol). The pyridine and pyrimidine radical cations form unconventional carbon-based ionic hydrogen bonds with HCN (CHδ+⋯NCH). Protonated pyridine forms a stronger ionic hydrogen bond with HCN (NH+⋯NCH) which can be extended to a linear chain with the clustering of additional HCN molecules (NH+⋯NCH..NCH⋯NCH) leading to a rapid decrease in the bond strength as the length of the chain increases. The lowest energy structures of the pyridine and pyrimidine radical cation clusters containing 3-4 HCN molecules show a strong tendency for the internal solvation of the radical cation by the HCN molecules where bifurcated structures involving multiple hydrogen bonding sites with the ring hydrogen atoms are formed. The unconventional H-bonds (CHδ+⋯NCH) formed between the pyridine or the pyrimidine radical cations and HCN molecules (11-12 kcal/mol) are stronger than the similar (CHδ+⋯NCH) bonds formed between the benzene radical cation and HCN molecules (9 kcal/mol) indicating that the CHδ+ centers in the pyridine and pyrimidine radical cations have more effective charges than in the benzene radical cation.

  7. Interplay of olefin metathesis and multiple hydrogen bonding interactions: covalently cross-linked zippers.

    PubMed

    Zeng, Jisen; Wang, Wei; Deng, Pengchi; Feng, Wen; Zhou, Jingjing; Yang, Yuanyou; Yuan, Lihua; Yamato, Kazuhiro; Gong, Bing

    2011-08-01

    Hydrogen-bonded zippers bearing terminal alkene groups were treated with Grubbs' catalyst, leading to covalently cross-linked zippers without violating H-bonding sequence specificity. The yield of a cross-linked zipper depended on the stability of its H-bonded precursor, with a weakly associating pair giving reasonable yields only at high concentrations while strongly associating pairs showed nearly quantitative yields. The integration of thermodynamic (H-bonding) and kinetic (irreversible C═C bond formation) processes suggests the possibility of developing many different covalent association units for constructing molecular structures based on a self-assembling way. PMID:21699249

  8. Knowledge-based model of hydrogen-bonding propensity in organic crystals.

    PubMed

    Galek, Peter T A; Fábián, László; Motherwell, W D Samuel; Allen, Frank H; Feeder, Neil

    2007-10-01

    A new method is presented to predict which donors and acceptors form hydrogen bonds in a crystal structure, based on the statistical analysis of hydrogen bonds in the Cambridge Structural Database (CSD). The method is named the logit hydrogen-bonding propensity (LHP) model. The approach has a potential application in identifying both likely and unusual hydrogen bonding, which can help to rationalize stable and metastable crystalline forms, of relevance to drug development in the pharmaceutical industry. Whilst polymorph prediction techniques are widely used, the LHP model is knowledge-based and is not restricted by the computational issues of polymorph prediction, and as such may form a valuable precursor to polymorph screening. Model construction applies logistic regression, using training data obtained with a new survey method based on the CSD system. The survey categorizes the hydrogen bonds and extracts model parameter values using descriptive structural and chemical properties from three-dimensional organic crystal structures. LHP predictions from a fitted model are made using two-dimensional observables alone. In the initial cases analysed, the model is highly accurate, achieving approximately 90% correct classification of both observed hydrogen bonds and non-interacting donor-acceptor pairs. Extensive statistical validation shows the LHP model to be robust across a range of small-molecule organic crystal structures. PMID:17873446

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

    SciTech Connect

    Hermann, Andreas Nelmes, Richard J.; Loveday, John S.; Guthrie, Malcolm

    2015-12-28

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

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

    PubMed

    Hermann, Andreas; Guthrie, Malcolm; Nelmes, Richard J; Loveday, John S

    2015-12-28

    Using a combination of ab initio crystal structure prediction and neutron diffraction techniques, we have solved the full structure of KOH-VI at 7 GPa. Rather than being orthorhombic and proton-ordered as had previously be proposed, we find that this high-pressure phase of potassium hydroxide is tetragonal (space group I4/mmm) and proton disordered. It has an unusual hydrogen bond topology, where the hydroxyl groups form isolated hydrogen-bonded square planar (OH)4 units. This structure is stable above 6.5 GPa and, despite being macroscopically proton-disordered, local ice rules enforce microscopic order of the hydrogen bonds. We suggest the use of this novel type of structure to study concerted proton tunneling in the solid state, while the topology of the hydrogen bond network could conceivably be exploited in data storage applications based solely on the manipulations of hydrogen bonds. The unusual localisation of the hydrogen bond network under applied pressure is found to be favored by a more compact packing of the constituents in a distorted cesium chloride structure. PMID:26723701

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

    NASA Astrophysics Data System (ADS)

    Hermann, Andreas; Guthrie, Malcolm; Nelmes, Richard J.; Loveday, John S.

    2015-12-01

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

  12. Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization

    NASA Astrophysics Data System (ADS)

    Duan, Li L.; Mei, Ye; Zhang, Qing G.; Zhang, John Z. H.

    2009-03-01

    Molecular dynamics (MD) simulation has been carried out to study dynamical stability of intra-protein hydrogen bonds based on two set of atomic charges, the standard AMBER charge and the polarized protein-specific charge (PPC). The latter is derived from quantum mechanical calculation for protein in solution using a recently developed molecular fractionation with conjugate caps-Poisson-Boltzmann (MFCC-PB) approach and therefore includes electronic polarization effect of the protein at native structure. MD simulations are performed for a number of benchmark proteins containing helix and/or beta sheet secondary structures. The computational result shows that occupancy percentage of hydrogen bonds averaged over simulation time, as well as the number of hydrogen bonds as a function of simulation time, is consistently higher under PPC than AMBER charge. In particular, some intra-protein hydrogen bonds are found broken during MD simulation using AMBER charge but they are stable using PPC. The breaking of some intra-protein hydrogen bonds in AMBER simulation is responsible for deformation or denaturing of some local structures of proteins during MD simulation. The current study provides strong evidence that hydrogen bonding is dynamically more stable using PPC than AMBER charge, highlighting the stabilizing effect of electronic polarization on protein structure.

  13. Hydrogen Bonding in Liquid Water and in the Hydration Shell of Salts.

    PubMed

    Dagade, Dilip H; Barge, Seema S

    2016-03-16

    A near-IR spectral study on pure water and aqueous salt solutions is used to investigate stoichiometric concentrations of different types of hydrogen-bonded water species in liquid water and in water comprising the hydration shell of salts. Analysis of the thermodynamics of hydrogen-bond formation signifies that hydrogen-bond making and breaking processes are dominated by enthalpy with non-negligible heat capacity effects, as revealed by the temperature dependence of standard molar enthalpies of hydrogen-bond formation and from analysis of the linear enthalpy-entropy compensation effects. A generalized method is proposed for the simultaneous calculation of the spectrum of water in the hydration shell and hydration number of solutes. Resolved spectra of water in the hydration shell of different salts clearly differentiate hydrogen bonding of water in the hydration shell around cations and anions. A comparison of resolved liquid water spectra and resolved hydration-shell spectra of ions highlights that the ordering of absorption frequencies of different kinds of hydrogen-bonded water species is also preserved in the bound state with significant changes in band position, band width, and band intensity because of the polarization of water molecules in the vicinity of ions. PMID:26749515

  14. Variation of geometries and electron properties along proton transfer in strong hydrogen-bond complexes

    NASA Astrophysics Data System (ADS)

    Pacios, L. F.; Gálvez, O.; Gómez, P. C.

    2005-06-01

    Proton transfer in hydrogen-bond systems formed by 4-methylimidazole in both neutral and protonated cationic forms and by acetate anion are studied by means of MP2/6-311++G(d,p) ab initio calculations. These two complexes model the histidine (neutral and protonated)-aspartate diad present in the active sites of enzymes the catalytic mechanism of which involves the formation of strong hydrogen bonds. We investigate the evolution of geometries, natural bond orbital populations of bonds and electron lone pairs, topological descriptors of the electron density, and spatial distributions of the electron localization function along the process N-H ⋯O→N⋯H⋯O→N⋯H-O, which represents the stages of the H-transfer. Except for a sudden change in the population of electron lone pairs in N and O at the middle N...H...O stage, all the properties analyzed show a smooth continuous behavior along the covalent → hydrogen bond transit inherent to the transfer, without any discontinuity that could identify a formation or breaking of the hydrogen bond. This way, the distinction between covalent or hydrogen-bonding features is associated to subtle electron rearrangement at the intermolecular space.

  15. Blue shifted hydrogen bond in 3-methylindole.CHX(3) complexes (X = Cl, F).

    PubMed

    Shirhatti, Pranav R; Wategaonkar, Sanjay

    2010-07-01

    Although the first experimental report on the blue shifted hydrogen bond in gas phase appeared about a decade ago, not many examples have been reported in the literature thereafter. Computational studies on systems exhibiting such blue shifted hydrogen bond however have been abundant since then. Many of these theoretical predictions remain to be verified experimentally. In this work we present an example of blue shifted hydrogen bond observed in the weakly bound complexes of 3-methylindole and CHX(3) (X = F, Cl). The complexes were prepared using the supersonic jet expansion method and studied using the laser spectroscopic methods. The key findings were that these complexes exhibit C-Hpi type hydrogen bonding interaction and the CH is bound to the phenyl part of the aromatic plane. The CH stretch was found to be blue shifted by 2 and 16 cm(-1) in the case of CHCl(3) and CHF(3), respectively. Ab initio calculations along with atoms-in-molecule analysis and natural bond orbital analysis support the experimental findings. The computed results at the DFT/MP2 level also indicated that the IR intensity of the H-bond donor CH-stretch increases by two to three orders of magnitude for the CHCl(3) complex whereas for the fluoroform complex the same decreases by an order of magnitude, which are consistent with the trend reported in the case of C-HO type of blue shifting hydrogen bonds. PMID:20407683

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent, it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor 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.

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

    PubMed

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

    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. PMID:26233131

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

    SciTech Connect

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

    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. Recent advances in the gold-catalyzed additions to C–C multiple bonds

    PubMed Central

    Huang, He; Zhou, Yu

    2011-01-01

    Summary C–O, C–N and C–C bonds are the most widespread types of bonds in nature, and are the cornerstone of most organic compounds, ranging from pharmaceuticals and agrochemicals to advanced materials and polymers. Cationic gold acts as a soft and carbophilic Lewis acid and is considered one of the most powerful activators of C–C multiple bonds. Consequently, gold-catalysis plays an important role in the development of new strategies to form these bonds in more convenient ways. In this review, we highlight recent advances in the gold-catalyzed chemistry of addition of X–H (X = O, N, C) bonds to C–C multiple bonds, tandem reactions, and asymmetric additions. This review covers gold-catalyzed organic reactions published from 2008 to the present. PMID:21804887

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

    PubMed

    Saluja, Hardeep; Mehanna, Ahmed; Panicucci, Riccardo; Atef, Eman

    2016-01-01

    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. PMID:27258248

  1. Energetic multifunctionalized nitraminopyrazoles and their ionic derivatives: ternary hydrogen-bond induced high energy density materials.

    PubMed

    Yin, Ping; Parrish, Damon A; Shreeve, Jean'ne M

    2015-04-15

    Diverse functionalization was introduced into the pyrazole framework giving rise to a new family of ternary hydrogen-bond induced high energy density materials. By incorporating extended cationic interactions, nitramine-based ionic derivatives exhibit good energetic performance and enhanced molecular stability. Performance parameters including heats of formation and detonation properties were calculated by using Gaussian 03 and EXPLO5 v6.01 programs, respectively. It is noteworthy to find that 5-nitramino-3,4-dinitropyrazole, 4, has a remarkable measured density of 1.97 g cm(-3) at 298 K, which is consistent with its crystal density (2.032 g cm(-3), 150 K), and ranks highest among azole-based CHNO compounds. Energetic evaluation indicates that, in addition to the molecular compound 4, some ionic derivatives, 9, 11, 12, 17, 19, and 22, also have high densities (1.83-1.97 g cm(-3)), excellent detonation pressures and velocities (P, 35.6-41.6 GPa; vD, 8880-9430 m s(-1)), as well as acceptable impact and friction sensitivities (IS, 4-30 J; FS, 40-240 N). These attractive features highlight the application potential of nitramino hydrogen-bonded interactions in the design of advanced energetic materials. PMID:25807076

  2. Accurate hydrogen bond energies within the density functional tight binding method.

    PubMed

    Domínguez, A; Niehaus, T A; Frauenheim, T

    2015-04-01

    The density-functional-based tight-binding (DFTB) approach has been recently extended by incorporating one-center exchange-like terms in the expansion of the multicenter integrals. This goes beyond the Mulliken approximation and leads to a scheme which treats in a self-consistent way the fluctuations of the whole dual density matrix and not only its diagonal elements (Mulliken charges). To date, only the performance of this new formalism to reproduce excited-state properties has been assessed (Domínguez et al. J. Chem. Theory Comput., 2013, 9, 4901-4914). Here we study the effect of our corrections on the computation of hydrogen bond energies for water clusters and water-containing systems. The limitations of traditional DFTB to reproduce hydrogen bonds has been acknowledged often. We compare our results for a set of 22 small water clusters and water-containing systems as well as for five water hexadecamers to those obtained with the DFTB3 method. Additionally, we combine our extension with a third-order energy expansion in the charge fluctuations. Our results show that the new formalisms significantly improve upon original DFTB. PMID:25763597

  3. Hydrogen bonding and orientation effects on the accommodation of methylamine at the air-water interface.

    PubMed

    Hoehn, Ross D; Carignano, Marcelo A; Kais, Sabre; Zhu, Chongjing; Zhong, Jie; Zeng, Xiao C; Francisco, Joseph S; Gladich, Ivan

    2016-06-01

    Methylamine is an abundant amine compound detected in the atmosphere which can affect the nature of atmospheric aerosol surfaces, changing their chemical and optical properties. Molecular dynamics simulation results show that methylamine accommodation on water is close to unity with the hydrophilic head group solvated in the interfacial environment and the methyl group pointing into the air phase. A detailed analysis of the hydrogen bond network indicates stronger hydrogen bonds between water and the primary amine group at the interface, suggesting that atmospheric trace gases will likely react with the methyl group instead of the solvated amine site. These findings suggest new chemical pathways for methylamine acting on atmospheric aerosols in which the methyl group is the site of orientation specific chemistry involving its conversion into a carbonyl site providing hydrophilic groups for uptake of additional water. This conversion may explain the tendency of aged organic aerosols to form cloud condensation nuclei. At the same time, formation of NH2 radical and formaldehyde is suggested to be a new source for NH2 radicals at aerosol surfaces, other than by reaction of absorbed NH3. The results have general implications for the chemistry of other amphiphilic organics, amines in particular, at the surface of atmospherically relevant aerosols. PMID:27276960

  4. Hydrogen bonding and orientation effects on the accommodation of methylamine at the air-water interface

    NASA Astrophysics Data System (ADS)

    Hoehn, Ross D.; Carignano, Marcelo A.; Kais, Sabre; Zhu, Chongjing; Zhong, Jie; Zeng, Xiao C.; Francisco, Joseph S.; Gladich, Ivan

    2016-06-01

    Methylamine is an abundant amine compound detected in the atmosphere which can affect the nature of atmospheric aerosol surfaces, changing their chemical and optical properties. Molecular dynamics simulation results show that methylamine accommodation on water is close to unity with the hydrophilic head group solvated in the interfacial environment and the methyl group pointing into the air phase. A detailed analysis of the hydrogen bond network indicates stronger hydrogen bonds between water and the primary amine group at the interface, suggesting that atmospheric trace gases will likely react with the methyl group instead of the solvated amine site. These findings suggest new chemical pathways for methylamine acting on atmospheric aerosols in which the methyl group is the site of orientation specific chemistry involving its conversion into a carbonyl site providing hydrophilic groups for uptake of additional water. This conversion may explain the tendency of aged organic aerosols to form cloud condensation nuclei. At the same time, formation of NH2 radical and formaldehyde is suggested to be a new source for NH2 radicals at aerosol surfaces, other than by reaction of absorbed NH3. The results have general implications for the chemistry of other amphiphilic organics, amines in particular, at the surface of atmospherically relevant aerosols.

  5. Experimental and theoretical study of the exited state of aminostyryl terpyridine derivatives: Hydrogen-bonding effects

    NASA Astrophysics Data System (ADS)

    Song, Peng; Sun, Shi-Guo; Wang, Sha; Ma, Feng-Cai; Xu, Yong-Qian; Peng, Xiao-Jun

    2011-10-01

    The synthesis, structure and photophysical behavior of the aminostyryl terpyridine derivatives, named 4'-(4-{2-[4-(N,N-dimethylaniline)]vinyl}phenyl)-2,2':6',2″-terpyridine (M 1) and the related model compounds 4'-(4-{2-[4-(N,N-diphenylammino)phenyl]vinyl}phenyl)-2,2':6',2″-terpyridine (M 2), respectively, are reported. Large solvatochromic shifts of the first excited-state fluorescence maximum suggest the intramolecular charge transfer characters for both compounds. In addition, with N, N-dimethyl substituents, its fluorescence is quenched a lot in protic solvents. This is consisted with the decay of its S 1 state, through nonradiative internal conversion, to the ground state, which is facilitated by the formation of the hydrogen bond between M 1 and alcohols. Whereas, the introduction of N, N-diphenyl substituents has been proved to be a hydrogen-bond-free case with the unchanged Φf. Furthermore, the formation of TICT state via diffusive twisting motion of the dimethyl/phenylamino group is the major relaxation process, which is proved by the ultrafast relaxation dynamics experiment and theoretically conformational optimization of the first excited-state of both the compounds.

  6. Hydrogen-Bond Basic Siloxane Phosphonate Polymers for Surface Acoustic Wave (Saw) Sensors

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A surface acoustic wave (SAW) sensor coated with a novel hydrogen-bond basic siloxane phosphonate SAW polymer gave excellent initial response and long-term performance when tested against phenol vapor and compared with polyethyleneimine (PEI), a conventional hydrogent-bond basic SAW polymer....

  7. The effect of cooperative hydrogen bonding on the OH stretching-band shift for water clusters studied by matrix-isolation infrared spectroscopy and density functional theory.

    PubMed

    Ohno, Keiichi; Okimura, Mari; Akai, Nobuyuki; Katsumoto, Yukiteru

    2005-08-21

    Infrared spectra of the water clusters have been measured in the N2 + O2 matrix. The aggregation process of water in the matrix has been monitored by annealing the deposited samples up to 40 K and UV irradiation. The monomer, dimer, cyclic trimer and cyclic pentamer are found as water clusters in the matrix. For the hexamer, several structures such as chair, cage, prism, bag 1 and/or book 1 are likely to exist. By UV irradiation, the cyclic pentamer is predominantly formed from the monomer and dimer. On the other hand, by annealing the deposited sample, several hexamers are formed. The theoretical calculation for water clusters has revealed that the formation of one hydrogen bonding in a hydrogen-bonded chain cooperatively enhances or diminishes the strength of another hydrogen bond. Both proton donor (D) and acceptor (A) participating in a hydrogen-bonding pair DA are capable of forming hydrogen bonding with the other water molecules; D can additionally accept two protons and donate one proton, and A can additionally donate two protons and accept one proton. We have proposed the classification of hydrogen-bonding patterns considering the cooperativity, denoting as d'a'DAd''a'', where d and a are integers indicating the number of proton donors and acceptors to D (the single prime) and A (the double prime), respectively. Then, a magnitude given by MOH = -d' + a' + d'' - a'' has been introduced, which is very useful for connecting the hydrogen-bonding patterns to their OH wavenumbers. As a result, it is revealed that the OH stretching bands of water clusters are characterized by eight indicators (free and MOH = -2, -1, 0, 1, 2, 3 and 4). The classification proposed here is applicable to the OH band analysis for the hydrogen-bonded water and alcohols in a condensed phase. PMID:16186903

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

    PubMed

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

    2015-09-14

    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-NC5H5 does not lie along the symmetry axis of the nitrogen lone pair, but rather, forms an average angle of 46° with the C2 axis of the pyridine. The a-type spectra of HCCH-NC5H5 and DCCD-NC5H5 are doubled, suggesting the existence of a low lying pair of tunneling states. This doubling persists in the spectra of HCCD-NC5H5, DCCH-NC5H5, 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 C2v 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. PMID:26374037

  9. Outline of a transition-state hydrogen-bond theory

    NASA Astrophysics Data System (ADS)

    Gilli, Paola; Bertolasi, Valerio; Pretto, Loretta; Gilli, Gastone

    2006-06-01

    Though the H-bond is well characterized as a D-H⋯:A three-center-four-electron interaction, the formulation of a general H-bond theory has turned out to be a rather formidable problem because of the extreme variability of the bonds formed (for instance, O-H⋯O energies range from 0.1 to 31 kcal mol -1). This paper surveys our previous contributions to the problem, including: (a) the H-bond chemical leitmotifs (CLs), showing that there are only four classes of strong H-bonds and one of moderately strong ones; (b) the PA/pK a equalization principle , showing that the four CLs forming strong H-bonds are actually molecular devices apt to equalize the acid-base properties (PA or p Ka) of the H-bond donor and acceptor groups; (c) the driving variable of the H-bond strength, which remains so identified as the difference Δp Ka=p KAH(D-H)-p KBH(A-H +) or, alternatively, ΔPA=PA(D -)-PA(A); and, in particular, (d) the transition-state H-bond theory (TSHBT), which interprets the H-bond as a stationary point along the complete proton transfer pathway going from D-H⋯A to D⋯H-A via the D⋯H⋯A transition state. TSHBT is verified in connection with a series of seven 1-(X-phenylazo)-2-naphthols, a class of compounds forming a strong intramolecular resonance-assisted H-bond (RAHB), which is switched from N-H⋯O to N⋯H-O by the decreasing electron-withdrawing properties of the substituent X. The system is studied in terms of: (i) variable-temperature X-ray crystallography; (ii) DFT emulation of stationary points and full PT pathways; (iii) Marcus rate-equilibrium analysis correlated with substituent LFER Hammett parameters.

  10. Selective Breaking of Hydrogen Bonds of Layered Carbon Nitride for Visible Light Photocatalysis.

    PubMed

    Kang, Yuyang; Yang, Yongqiang; Yin, Li-Chang; Kang, Xiangdong; Wang, Lianzhou; Liu, Gang; Cheng, Hui-Ming

    2016-08-01

    Selective breaking of the hydrogen bonds of graphitic carbon nitride can introduce favorable features, including increased band tails close to the band edges and the creation of abundant pores. These features can simultaneously improve the three basic processes of photocatalysis. As a consequence, the photocatalytic hydrogen-generation activity of carbon nitride under visible light is drastically increased by tens of times. PMID:27167996

  11. The Influence of Hydrogen Bonding on Sphingomyelin/Colipid Interactions in Bilayer Membranes.

    PubMed

    Yasuda, Tomokazu; Al Sazzad, Md Abdullah; Jäntti, Niklas Z; Pentikäinen, Olli T; Slotte, J Peter

    2016-01-19

    The phospholipid acyl chain composition and order, the hydrogen bonding, and properties of the phospholipid headgroup all influence cholesterol/phospholipid interactions in hydrated bilayers. In this study, we examined the influence of hydrogen bonding on sphingomyelin (SM) colipid interactions in fluid uni- and multilamellar vesicles. We have compared the properties of oleoyl or palmitoyl SM with comparable dihydro-SMs, because the hydrogen bonding properties of SM and dihydro-SM differ. The association of cholestatrienol, a fluorescent cholesterol analog, with oleoyl sphingomyelin (OSM) was significantly stronger than its association with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, in bilayers with equal acyl chain order. The association of cholestatrienol with dihydro-OSM, which lacks a trans double bond in the sphingoid base, was even stronger than the association with OSM, suggesting an important role for hydrogen bonding in stabilizing sterol/SM interactions. Furthermore, with saturated SM in the presence of 15 mol % cholesterol, cholesterol association with fluid dihydro-palmitoyl SM bilayers was stronger than seen with palmitoyl SM under similar conditions. The different hydrogen bonding properties in OSM and dihydro-OSM bilayers also influenced the segregation of palmitoyl ceramide and dipalmitoylglycerol into an ordered phase. The ordered, palmitoyl ceramide-rich phase started to form above 2 mol % in the dihydro-OSM bilayers but only above 6 mol % in the OSM bilayers. The lateral segregation of dipalmitoylglycerol was also much more pronounced in dihydro-OSM bilayers than in OSM bilayers. The results show that hydrogen bonding is important for sterol/SM and ceramide/SM interactions, as well as for the lateral segregation of a diglyceride. A possible molecular explanation for the different hydrogen bonding in SM and dihydro-SM bilayers is presented and discussed. PMID:26789766

  12. A canonical approach to multi-dimensional van der Waals, hydrogen-bonded, and halogen-bonded potentials

    NASA Astrophysics Data System (ADS)

    Walton, Jay R.; Rivera-Rivera, Luis A.; Lucchese, Robert R.; Bevan, John W.

    2016-05-01

    A canonical approach is used to investigate prototypical multi-dimensional intermolecular interaction potentials characteristic of categories in van der Waals, hydrogen-bonded, and halogen-bonded intermolecular interactions. It is demonstrated that well-characterized potentials in Ar·HI, OC·HI, OC·HF, and OC·BrCl, can be canonically transformed to a common dimensionless potential with relative error less than 0.010. The results indicate common intrinsic bonding properties despite other varied characteristics in the systems investigated. The results of these studies are discussed in the context of the previous statement made by Slater (1972) concerning fundamental bonding properties in the categories of interatomic interactions analyzed.

  13. Neutron diffraction of alpha, beta and gamma cyclodextrins: Hydrogen bonding patterns

    SciTech Connect

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

    1984-08-01

    Cyclodextrins (CD's) have proved useful as model systems for the study of hydrogen bonding. They are torus-shaped molecules composed of six(alpha), seven(beta) or eight(gamma) (1----4) linked glucoses. Because of their particular geometry, they are able to act as a host to form inclusion complexes with guest molecules very much like enzymes. Cyclodextrins have been shown to exert catalytic activity on suitable included-substrate molecules; they catalyze the hydrolysis of phenylacetates, of organic pyrophosphates and of penicillin derivatives. They also accelerate aromatic chlorinations and diazo coupling by means of their primary and/or secondary hydroxyl groups, so that the rates of hydrolysis are enhanced by up to a factor of 400. In order to understand the hydrogen bonding in these enzyme models, neutron diffraction data were collected to unambiguously determine the hydrogen atom positions, which could not be done from the x-ray diffraction data. alpha-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 alpha-CD complex formation has been proposed. Circular hydrogen bond networks have also been found for alpha-CD due to the energetically favored cooperative effect. beta-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 in equilibrium O...H-O. gamma-CD with a disordered water structure similar to beta-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. 33 references.

  14. Charged versus Neutral Hydrogen-Bonded Complexes: Is There a Difference in the Nature of the Hydrogen Bonds?

    PubMed

    Alkorta, Ibon; Mata, Ignasi; Molins, Elies; Espinosa, Enrique

    2016-06-27

    A theoretical study on some carboxylic acid dimers formed by positively or negatively charged molecules has been carried out by using DFT methods. The resulting dimers possess either a charge of +2 or -2. In addition, the corresponding neutral complexes have also been considered. The electron density distribution described by the atoms in molecules and the natural bond orbital methods, as well as the electric field maps of the systems, have been analyzed and compared without finding significant differences between the neutral and ionic complexes. The interaction energy along the dissociation path of the charged dimers shows both a local minimum and a local maximum, defining a stability region between them. When this energetic profile is recalculated by removing the repulsion between the charged groups, it resembles to those of the neutral molecules. Hence, the characteristics of the charged dimers are similar to those of the neutral ones: the addition of a repulsion term for the charged groups permits to retrieve the energetic profiles dependence with the distance in the charged system. The interacting quantum atom (IQA) method has been used to calculate the interaction energy terms, including the classic Coulombic term between the whole molecules and the corresponding of the carboxylic acid groups. The IQA results show repulsive electrostatic interactions when the whole molecules are considered in the ionic complexes, but attractive ones between the carboxylic groups in both neutral and ionic complexes. PMID:27225820

  15. Hydrogen-bonded complexes upon spatial confinement: structural and energetic aspects.

    PubMed

    Lipkowski, Paweł; Kozłowska, Justyna; Roztoczyńska, Agnieszka; Bartkowiak, Wojciech

    2014-01-28

    In the present study we consider structural and energetic aspects of spatial confinement of the H-bonded systems. The model dimeric systems: HF···HF, HCN···HCN and HCN···HCCH have been chosen for a case study. Two-dimensional harmonic oscillator potential, mimicking a cylindrical confinement, was applied in order to render the impact of orbital compression on the analyzed molecular complexes. The calculations have been performed employing the MP2 method as well as the Kohn-Sham formulation of density functional theory. In the latter case, two exchange-correlation potentials have been used, namely B3LYP and M06-2X. The geometries of studied complexes have been optimized (without any constraints) in the presence of the applied model confining potential. A thorough analysis of topological parameters characterizing hydrogen bonds upon orbital compression has been performed within the Quantum Theory of Atoms in Molecules (QTAIM). Furthermore, an energetic analysis performed for the confined H-bonded complexes has shown a different trend in the interaction energy changes. Additionally, a variational-perturbational decomposition scheme was applied to study the interaction energy components in the presence of spatial confinement. PMID:24296646

  16. Metal-and hydrogen-bonding competition during water absorption on Pd(111) and Ru(0001)

    SciTech Connect

    Tatarkhanov, Mouslim; Ogletree, D. Frank; Rose, Franck; Mitsui, Toshiyuki; Fomin, Evgeny; Rose, Mark; Cerda, Jorge I.; Salmeron, Miquel

    2009-09-03

    The initial stages of water adsorption on the Pd(111) and Ru(0001) surfaces have been investigated experimentally by Scanning Tunneling Microscopy in the temperature range between 40 K and 130 K, and theoretically with Density Functional Theory (DFT) total energy calculations and STM image simulations. Below 125 K water dissociation does not occur at any appreciable rate and only molecular films are formed. Film growth starts by the formation of flat hexamer clusters where the molecules bind to the metal substrate through the O-lone pair while making H-bonds with neighboring molecules. As coverage increases, larger networks of linked hexagons are formed with a honeycomb structure, which requires a fraction of the water molecules to have their molecular plane perpendicular to the metal surface with reduced water-metal interaction. Energy minimization favors the growth of networks with limited width. As additional water molecules adsorb on the surface they attach to the periphery of existing islands, where they interact only weakly with the metal substrate. These molecules hop along the periphery of the clusters at intermediate temperatures. At higher temperatures they bind to the metal to continue the honeycomb growth. The water-Ru interaction is significantly stronger than the water-Pd interaction, which is consistent with the greater degree of hydrogen-bonded network formation and reduced water-metal bonding observed on Pd relative to Ru.

  17. Structure and hydrogen bonding in plasma deposited polymorphous silicon thin films

    NASA Astrophysics Data System (ADS)

    Lebib, S.; Cabarrocas, P. Roca I.

    2004-04-01

    We present a detailed study of the structure and hydrogen bonding in silicon thin films ranging from amorphous to microcrystalline. We emphasize the results for hydrogenated polymorphous silicon films obtained under plasma conditions close to powder formation where silicon clusters and nanocrystals contribute to growth. Fourier Transform Infra-Red (FTIR) spectroscopy, Raman spectroscopy, X-Ray-Diffraction (XRD), and hydrogen evolution measurements are performed to characterize the hydrogen bonding and the structure of the films in their as-deposited state and after isochronal annealing at increasing temperature in the range of 300 to 600 °C. While Raman spectroscopy and XRD give an average information on the structure of the films, without clear evidence of the presence of crystallites in the polymorphous films, infrared spectroscopy and hydrogen evolution measurements which probe the local hydrogen related structure are shown to be perfectly adapted to characterize polymorphous silicon films. In particular, IR spectroscopy measurements, reveal the presence of a stretching band at 2030 cm^{-1}, associated with a peak at 873 cm^{-1} in the bending region and a downward shift in the Si-H wagging mode from 640 cm^{-1} to 622 cm^{-1}. We attribute the 2030 cm^{-1} mode to the presence of hydrogen bonded at the surface of the plasma produced silicon clusters and nanocrystals. This assignment is supported by hydrogen evolution measurements in which a sharp low-temperature hydrogen evolution peak appears at around 420 °C followed by up to five peaks at higher temperatures. This particular hydrogen bonding in polymorphous silicon films is also supported by isochronal annealing studies which show that the bands at 2030 cm^{-1} and 873 cm^{-1} vanish at annealing temperatures corresponding to the low temperature hydrogen evolution peak. Based on these results and their correlation with the hydrogen-related material structure, we propose a picture for the structure of

  18. In situ ESR study to detect the diffusion of free H and creation of dangling bonds in hydrogenated amorphous silicon

    NASA Astrophysics Data System (ADS)

    Das, U. K.; Yasuda, T.; Yamasaki, S.

    2001-06-01

    In situ electron spin resonance (ESR) was studied during exposure of hydrogenated amorphous silicon (a-Si:H) films to atomic hydrogen (H) generated by a remote plasma. A high diffusion coefficient of free atomic H (>10-10 cm2 s-1) is observed in a-Si:H films at the very initial stage of H treatment. The H creates additional dangling bonds (~1013 cm-2) during in-diffusion. The diffusion mechanism of such free H is a self-limiting process. The dangling bonds created at the very initial stage of H exposure act as the trapping sites for the impinging H atoms. Consequently, the effective diffusion coefficient (Deff) reduces with H treatment time. The Deff for plasma in-diffusion of H with a relatively wide time span reported in literature is considered to be the resultant of the diffusion coefficient of free H and the bonded H. The characteristic depth of dangling-bond distribution decreases with increasing H treatment temperature. The activated rate constants of db creation reactions dominate over the activated free-H diffusion to determine the distribution of additional dangling bonds at different treatment temperatures.

  19. 42 CFR 489.66 - Additional requirements of the surety bond.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    .... (e) The bond must provide the Surety's name, street address or post office box number, city, state... 42 Public Health 5 2011-10-01 2011-10-01 false Additional requirements of the surety bond. 489.66... SERVICES (CONTINUED) STANDARDS AND CERTIFICATION PROVIDER AGREEMENTS AND SUPPLIER APPROVAL Surety...

  20. 42 CFR 489.66 - Additional requirements of the surety bond.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    .... (e) The bond must provide the Surety's name, street address or post office box number, city, state... 42 Public Health 5 2010-10-01 2010-10-01 false Additional requirements of the surety bond. 489.66... SERVICES (CONTINUED) STANDARDS AND CERTIFICATION PROVIDER AGREEMENTS AND SUPPLIER APPROVAL Surety...

  1. Hydrogen bonding and solution state structure of salicylaldehyde-4-phenylthiosemicarbazone: A combined experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Novak, Predrag; Pičuljan, Katarina; Hrenar, Tomica; Biljan, Tomislav; Meić, Zlatko

    2009-02-01

    Hydrogen bonding in salicylaldehyde-4-phenylthiosemicarbazone ( 1) has been studied by using experimental (NMR, Raman and UV spectroscopies) and quantum chemical (DFT) methods. It has been demonstrated that 1 adopted the hydroxy-thione tautomeric form in solution as found also in the solid state and previously indicated by secondary deuterium isotope effects. Apart from the intra-molecular hydrogen bonds new interactions between 1 and solvent molecules were formed as well. Changes in NMR chemical shifts and calculations have pointed towards a formation of inter-molecular three-centered hydrogen bonds in each of the studied complexes involving OH and NH groups of 1 and associated solvent molecules. Stabilization energies of intra-molecular hydrogen bonds were found to decrease with the increase of the solvent polarity. Two-dimensional NOESY spectra indicated conformational changes in solution with respect to the structure observed in the solid state. These were accounted for by a relatively low barrier of the rotation of the N sbnd N single bond thus enabling a molecule to posses a higher conformational flexibility in solution with portions of skewed conformations. The results presented here can help in a better understanding of the role hydrogen bonds can play in bioactivity of related thiosemicarbazone derivatives and their metal complexes.

  2. Insights on hydrogen-bond lifetimes in liquid and supercooled water.

    PubMed

    Martiniano, H F M C; Galamba, N

    2013-12-19

    We study the temperature dependence of the lifetime of geometric and geometric/energetic water hydrogen-bonds (H-bonds), down to supercooled water, through molecular dynamics. The probability and lifetime of H-bonds that break either by translational or librational motions and those of energetic broken H-bonds, along with the effects of transient broken H-bonds and transient H-bonds, are considered. We show that the fraction of transiently broken energetic H-bonds increases at low temperatures and that this energetic breakdown is caused by oxygen-oxygen electrostatic repulsions upon too small amplitude librations to disrupt geometric H-bonds. Hence, differences between geometric and energetic continuous H-bond lifetimes are associated with large H-bond energy fluctuations, in opposition to moderate geometric fluctuations, within common energetic and geometric H-bond definition thresholds. Exclusion of transient broken H-bonds and transient H-bonds leads to H-bond definition-independent mean lifetimes and activation energies, ~11 kJ/mol, consistent with the reactive flux method and experimental scattering results. Further, we show that power law decay of specific temporal H-bond lifetime probability distributions is associated with librational and translational motions that occur on the time scale (~0.1 ps) of H-bond breaking /re-forming dynamics. While our analysis is diffusion-free, the effect of diffusion on H-bond probability distributions where H-bonds are allowed to break and re-form, switching acceptors in between, is shown to result in neither exponential nor power law decay, similar to the reactive flux correlation function. PMID:24279452

  3. Hydrogen-bonded glycine-HCN complexes in gas phase: structure, energetics, electric properties and cooperativity

    NASA Astrophysics Data System (ADS)

    Machado da Silva, Arnaldo; Chakrabarty, Sumana; Chaudhuri, Puspitapallab

    2015-03-01

    Twelve hydrogen-bonded complexes of glycine and hydrogen cyanide have been studied using high-level quantum-chemical calculations in gas phase. In particular, six 1:1 glycine-HCN dimers and six 1:2 glycine-HCN trimers have been considered. Besides the characteristics of the hydrogen bonds and their effect on molecular structure and energetics, several molecular electric properties have been calculated utilising two different models: MP2/6-31++G(d,p) and DFT-B3LYP/6-31++G(d,p). Although the structural parameters calculated by the two models are similar, equilibrium electronic energies of the clusters show model dependence. The lowest energy dimer is same in both the models which is ca. 3.0 kcal/mol more stable than the highest energy dimer. However, the lowest energy trimer is different in two methods. The energetic difference of stability between the highest and lowest trimer is 4.2 kcal/mol (4.4 kcal/mol) at an MP2 (B3LYP) level of calculation. The bond angles of glycine, in particular, are quite sensitive to the hydrogen-bond formation. Four out of six trimers are found to be strongly cooperative in both the models. Significant changes of dipole moments and polarisabilities of isolated glycine and hydrogen cyanide are observed due to the formation of hydrogen bonding. The Rayleigh scattering intensities of all clusters are much larger than those of their constituent monomers.

  4. Monitoring Backbone Hydrogen-Bond Formation in β-Barrel Membrane Protein Folding.

    PubMed

    Raschle, Thomas; Rios Flores, Perla; Opitz, Christian; Müller, Daniel J; Hiller, Sebastian

    2016-05-10

    β-barrel membrane proteins are key components of the outer membrane of bacteria, mitochondria and chloroplasts. Their three-dimensional structure is defined by a network of backbone hydrogen bonds between adjacent β-strands. Here, we employ hydrogen-deuterium (H/D) exchange in combination with NMR spectroscopy and mass spectrometry to monitor backbone hydrogen bond formation during folding of the outer membrane protein X (OmpX) from E. coli in detergent micelles. Residue-specific kinetics of interstrand hydrogen-bond formation were found to be uniform in the entire β-barrel and synchronized to formation of the tertiary structure. OmpX folding thus propagates via a long-lived conformational ensemble state in which all backbone amide protons exchange with the solvent and engage in hydrogen bonds only transiently. Stable formation of the entire OmpX hydrogen bond network occurs downhill of the rate-limiting transition state and thus appears cooperative on the overall folding time scale. PMID:27062600

  5. Carbon–carbon bond activation of cyclobutenones enabled by the addition of chiral organocatalyst to ketone

    PubMed Central

    Li, Bao-Sheng; Wang, Yuhuang; Jin, Zhichao; Zheng, Pengcheng; Ganguly, Rakesh; Chi, Yonggui Robin

    2015-01-01

    The activation of carbon–carbon (C–C) bonds is an effective strategy in building functional molecules. The C–C bond activation is typically accomplished via metal catalysis, with which high levels of enantioselectivity are difficult to achieve due to high reactivity of metal catalysts and the metal-bound intermediates. It remains largely unexplored to use organocatalysis for C–C bond activation. Here we describe an organocatalytic activation of C–C bonds through the addition of an NHC to a ketone moiety that initiates a C–C single bond cleavage as a key step to generate an NHC-bound intermediate for chemo- and stereo-selective reactions. This reaction constitutes an asymmetric functionalization of cyclobutenones using organocatalysts via a C–C bond activation process. Structurally diverse and multicyclic compounds could be obtained with high optical purities via an atom and redox economic process. PMID:25652912

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

    SciTech Connect

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

    2005-04-15

    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.

  7. Hydrogen Bonding between Metal-Ion Complexes and Noncoordinated Water: Electrostatic Potentials and Interaction Energies.

    PubMed

    Andrić, Jelena M; Misini-Ignjatović, Majda Z; Murray, Jane S; Politzer, Peter; Zarić, Snežana D

    2016-07-01

    The hydrogen bonding of noncoordinated water molecules to each other and to water molecules that are coordinated to metal-ion complexes has been investigated by means of a search of the Cambridge Structural Database (CSD) and through quantum chemical calculations. Tetrahedral and octahedral complexes that were both charged and neutral were studied. A general conclusion is that hydrogen bonds between noncoordinated water and coordinated water are much stronger than those between noncoordinated waters, whereas hydrogen bonds of water molecule in tetrahedral complexes are stronger than in octahedral complexes. We examined the possibility of correlating the computed interaction energies with the most positive electrostatic potentials on the interacting hydrogen atoms prior to interaction and obtained very good correlation. This study illustrates the fact that electrostatic potentials computed for ground-state molecules, prior to interaction, can provide considerable insight into the interactions. PMID:26989883

  8. Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network☆

    PubMed Central

    Kaiser, Alexander; Ismailova, Oksana; Koskela, Antti; Huber, Stefan E.; Ritter, Marcel; Cosenza, Biagio; Benger, Werner; Nazmutdinov, Renat; Probst, Michael

    2014-01-01

    Molecular dynamics simulations of liquid ethylene glycol described by the OPLS-AA force field were performed to gain insight into its hydrogen-bond structure. We use the population correlation function as a statistical measure for the hydrogen-bond lifetime. In an attempt to understand the complicated hydrogen-bonding, we developed new molecular visualization tools within the Vish Visualization shell and used it to visualize the life of each individual hydrogen-bond. With this tool hydrogen-bond formation and breaking as well as clustering and chain formation in hydrogen-bonded liquids can be observed directly. Liquid ethylene glycol at room temperature does not show significant clustering or chain building. The hydrogen-bonds break often due to the rotational and vibrational motions of the molecules leading to an H-bond half-life time of approximately 1.5 ps. However, most of the H-bonds are reformed again so that after 50 ps only 40% of these H-bonds are irreversibly broken due to diffusional motion. This hydrogen-bond half-life time due to diffusional motion is 80.3 ps. The work was preceded by a careful check of various OPLS-based force fields used in the literature. It was found that they lead to quite different angular and H-bond distributions. PMID:24748697

  9. Investigation of the hydrogen bonding in ice Ih by first-principles density function methods.

    PubMed

    Zhang, P; Tian, L; Zhang, Z P; Shao, G; Li, J C

    2012-07-28

    It is a well recognized difficult task to simulate the vibrational dynamics of ices using the density functional theory (DFT), and there has thus been rather limited success in modelling the inelastic neutron scattering (INS) spectra for even the simplest structure of ice, ice Ih, particularly in the translational region below 400 cm(-1). The reason is partly due to the complex nature of hydrogen bonding (H-bond) among water-water molecules which require considerable improvement of the quantum mechanical simulation methods, and partly owing to the randomness of protons in ice structures which often requires simulation of large super-lattices. In this report, we present the first series of successful simulation results for ice Ih using DFT methods. On the basis of the recent advancement in the DFT programs, we have achieved for the first time theoretical outcomes that not only reproduce the rotational frequencies between 500 to 1200 cm(-1) for ice Ih, but also the two optic peaks at ∼240 and 320 cm(-1) in the translational region of the INS spectra [J. C. Li, J. Chem. Phys 105, 6733 (1996)]. Besides, we have also investigated the impact of pairwise configurations of H(2)O molecules on the H-bond and found that different proton arrangements of pairwise H(2)O in the ice Ih crystal lattice could not alter the nature of H-bond as significantly as suggested in an early paper [J. C. Li and D. K. Ross, Nature (London) 365, 327 (1993)], i.e., reproducing the two experimental optic peaks do not need to invoke the two H-bonds as proposed in the previous model which led to considerable debates. The results of this work suggest that the observed optic peaks may be attributed to the coupling between the two bands of H-O stretching modes in H(2)O. The current computational work is expected to shed new light on the nature of the H-bonds in water, and in addition to offer a new approach towards probing the interaction between water and biomaterials for which H-bond is essential

  10. Simulating hydrogen-bond clustering and phase behaviour of imidazole oligomers

    NASA Astrophysics Data System (ADS)

    Harvey, Jacob A.; Basak, Dipankar; Venkataraman, Dhandapani; Auerbach, Scott M.

    2012-05-01

    We have modelled structures and dynamics of hydrogen bond networks that form from imidazoles tethered to oligomeric aliphatic backbones in crystalline and glassy phases. We have studied the behaviour of oligomers containing 5 or 10 imidazole groups. These systems have been simulated over the range 100-900 K with constant-pressure molecular dynamics using the AMBER 94 forcefield, which was found to show good agreement with ab initio calculations on hydrogen bond strengths and imidazole rotational barriers. Hypothetical crystalline solids formed from packed 5-mers and 10-mers melt above 600 K, then form glassy solids upon cooling. Viewing hydrogen bond networks as clusters, we gathered statistics on cluster sizes and percolating pathways as a function of temperature, for comparison with the same quantities extracted from neat imidazole liquid. We have found that, at a given temperature, the glass composed of imidazole 5-mers shows the same hydrogen bond mean cluster size as that from the 10-mer glass, and that this size is consistently larger than that in liquid imidazole. Hydrogen bond clusters were found to percolate across the simulation cell for all glassy and crystalline solids, but not for any imidazole liquid. The apparent activation energy associated with hydrogen bond lifetimes in these glasses (9.3 kJ mol-1) is close to that for the liquid (8.7 kJ mol-1), but is substantially less than that in the crystalline solid (13.3 kJ mol-1). These results indicate that glassy oligomeric solids show a promising mixture of extended hydrogen bond clusters and liquid-like dynamics.

  11. The hydrogen bond network in I β cellulose as observed by infrared spectrometry

    NASA Astrophysics Data System (ADS)

    Maréchal, Y.; Chanzy, H.

    2000-05-01

    FT-IR spectra of I β cellulose were recorded on films made of hydrothermally treated Valonia microcrystals. Polarized spectra of these not completely disordered systems allowed to define the spectra along the cellulose c chain axis as well as along a perpendicular axis which may slightly vary from one sample to another one. Weakening and ruptures of some hydrogen bonds upon heating the samples at 115°C, as well as evaporation of D 2O molecules and H/D exchanges after immersion in a D 2O vapor were followed spectroscopically. A critical analysis of the spectra allowed to propose a detailed assignment for most of the bands at wavenumbers higher than 800 cm -1. From this analysis it appeared that the majority (more than 2/3) of C2O2H alcohols were involved in weak hydrogen bonds or perhaps even not hydrogen-bonded at all. On the other hand, the minority of C2O2H established a hydrogen bond with the O6 atom of an adjacent primary alcohol of the same chain. This particular hydrogen bond was the strongest found in these crystals. With the proposed assignment, hydroxymethyl moieties were found adopting three conformations (a dominant one and two minor) allowing the formation of different hydrogen bonds on adjacent chains. These conformations corresponded to three slightly different C4-C5-C6-O6 ( χ) dihedral angles. Most probably the primary alcohols that accept a hydrogen bond from the adjacent C2O2H alcohols were not the ones which adopt the dominant conformation.

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

    PubMed

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

    2016-04-01

    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. PMID:26979297

  13. The effect of intermolecular hydrogen bonding on the planarity of amides.

    PubMed

    Platts, James A; Maarof, Hasmerya; Harris, Kenneth D M; Lim, Gin Keat; Willock, David J

    2012-09-14

    Ab initio and density functional theory (DFT) calculations on some model systems are presented to assess the extent to which intermolecular hydrogen bonding can affect the planarity of amide groups. Formamide and urea are examined as archetypes of planar and non-planar amides, respectively. DFT optimisations suggest that appropriately disposed hydrogen-bond donor or acceptor molecules can induce non-planarity in formamide, with OCNH dihedral angles deviating by up to ca. 20° from planarity. Ab initio energy calculations demonstrate that the energy required to deform an amide molecule from the preferred geometry of the isolated molecule is more than compensated by the stabilisation due to hydrogen bonding. Similarly, the NH(2) group in urea can be made effectively planar by the presence of appropriately positioned hydrogen-bond acceptors, whereas hydrogen-bond donors increase the non-planarity of the NH(2) group. Small clusters (a dimer, two trimers and a pentamer) extracted from the crystal structure of urea indicate that the crystal field acts to force planarity of the urea molecule; however, the interaction with nearest neighbours alone is insufficient to induce the molecule to become completely planar, and longer-range effects are required. Finally, the potential for intermolecular hydrogen bonding to induce non-planarity in a model of a peptide is explored. Inter alia, the insights obtained in the present work on the extent to which the geometry of amide groups may be deformed under the influence of intermolecular hydrogen bonding provide structural guidelines that can assist the interpretation of the geometries of such groups in structure determination from powder X-ray diffraction data. PMID:22847473

  14. Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes

    PubMed Central

    Chakrabarti, Shaon; Hinczewski, Michael; Thirumalai, D.

    2014-01-01

    Mechanical forces acting on cell adhesion receptor proteins regulate a range of cellular functions by formation and rupture of noncovalent interactions with ligands. Typically, force decreases the lifetimes of intact complexes (“slip bonds”), making the discovery that these lifetimes can also be prolonged (“catch bonds”) a surprise. We created a microscopic analytic theory by incorporating the structures of selectin and integrin receptors into a conceptual framework based on the theory of stochastic equations, which quantitatively explains a wide range of experimental data (including catch bonds at low forces and slip bonds at high forces). Catch bonds arise due to force-induced remodeling of hydrogen bond networks, a finding that also accounts for unbinding in structurally unrelated integrin–fibronectin and actomyosin complexes. For the selectin family, remodeling of hydrogen bond networks drives an allosteric transition resulting in the formation of the maximum number of hydrogen bonds determined only by the structure of the receptor and independent of the ligand. A similar transition allows us to predict the increase in the number of hydrogen bonds in a particular allosteric state of α5β1 integrin–fibronectin complex, a conformation which is yet to be crystallized. We also make a testable prediction that a single point mutation (Tyr51Phe) in the ligand associated with selectin should dramatically alter the nature of the catch bond compared with the wild type. Our work suggests that nature uses a ductile network of hydrogen bonds to engineer function over a broad range of forces. PMID:24927549

  15. A low-barrier hydrogen bond in the catalytic triad of serine proteases? Theory versus experiment.

    PubMed

    Ash, E L; Sudmeier, J L; De Fabo, E C; Bachovchin, W W

    1997-11-01

    Cleland and Kreevoy recently advanced the idea that a special type of hydrogen bond (H-bond), termed a low-barrier hydrogen bond (LBHB), may account for the "missing" transition state stabilization underlying the catalytic power of many enzymes, and Frey et al. have proposed that the H-bond between aspartic acid 102 and histidine 57 in the catalytic triad of serine proteases is an example of a catalytically important LBHB. Experimental facts are here considered regarding the aspartic acid-histidine and cis-urocanic H-bonds that are inconsistent with fundamental tenets of the LBHB hypothesis. The inconsistencies between theory and experiment in these paradigm systems cast doubt on the existence of LBHBs, as currently defined, within enzyme active sites. PMID:9353195

  16. Cation-cation clusters in ionic liquids: Cooperative hydrogen bonding overcomes like-charge repulsion

    PubMed Central

    Knorr, Anne; Ludwig, Ralf

    2015-01-01

    Direct spectroscopic evidence for H-bonding between like-charged ions is reported for the ionic liquid, 1-(2-hydroxyethyl)-3-methylimidazolium tetrafluoroborate. New infrared bands in the OH frequency range appear at low temperatures indicating the formation of H-bonded cation-cation clusters similar to those known for water and alcohols. Supported by DFT calculations, these vibrational bands can be assigned to attractive interaction between the hydroxyl groups of the cations. The repulsive Coulomb interaction is overcome by cooperative hydrogen bonding between ions of like charge. The transition energy from purely cation-anion interacting configurations to those including cation-cation H-bonds is determined to be 3–4 kJmol−1. The experimental findings and DFT calculations strongly support the concept of anti-electrostatic hydrogen bonds (AEHBs) as recently suggested by Weinhold and Klein. The like-charge configurations are kinetically stabilized with decreasing temperatures. PMID:26626928

  17. Evidence of the weakness of the OH⋯F hydrogen bond from a conformational study of 3-fluoro-1-propanol by microwave spectroscopy

    NASA Astrophysics Data System (ADS)

    Caminati, Walther

    1982-03-01

    The rotational spectra of the OH and OD isotopic species have been observed for three rotamers of 3-fluoro-1-propanol. One of them (HBC form) displays an internal hydrogen bond with a distorted chair conformation of the six-membered ring. The other two rotamers have the oxygen atom gauche with respect to the C 2C 3 bond, the hydroxyl hydrogen trans with respect to the C 1C 2 bond and the fluorine atom gauche (GGT form) and trans (TGT form), respectively, with respect to the C 2C 1 bond. The energies of the vibrational ground states of the HBC and TGT forms are ˜0.4 and 1.0 kcal/mole higher than that of the GGT form, respectively (from relative intensity measurements). The hydrogen bond is therefore rather weak in this compound. With compounds capable of forming OH⋯O or OH⋯N bonds, the conformation appropriate for hydrogen bonding is normally the most stable form. Several excited states have been analyzed for the TGT and GGT rotamers in order to have additional data with respect to the potential function for the internal rotation about the C 3C 2 bond.

  18. The Effect of Hydrogen on the Bonding and Dissociation of Carbon Monoxide on AN IRON(100) Surface

    NASA Astrophysics Data System (ADS)

    Nassir, Mohamed Husain

    1993-01-01

    Adsorption and coadsorption of CO and H _2 on Fe(100) was studied using the following six methods: Temperature programmed desorption (TPD), x -ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), high resolution electron energy loss spectroscopy (HREELS), single reflection Fourier transform infrared spectroscopy (FTIR) and low-energy electron diffraction (LEED). The binding and dissociation of CO on a clean and hydrogen presaturated Fe(100) surface were investigated to provide better understanding of the first step in the Fischer-Tropsch synthesis, an important industrial catalytic reaction for converting CO and hydrogen to hydrocarbon. CO adsorbs molecularly on the clean surface in three states alpha_1, alpha_2 and alpha_3 . At temperatures above 350 K but below 440 K, CO is bound to the surface only in the highly perturbed alpha_3 state (pi -bonded geometry). The CO alpha_3 molecules are believed to occupy the 4-fold hollow sites. When the surface temperature is raised above 440 K, a fraction of the alpha_3 desorbs and the remainder dissociates. The dissociation fragments replace the CO alpha_3 molecules in the 4-fold hollow sites. These fragments recombine at higher temperatures and appear as beta CO. The bonding and dissociation of CO in the alpha_3 received more attention because it is believed that this state is a precursor to dissociation. A model describing the partitioning between desorption and dissociation is proposed in which the dissociation fragments displace the strongly bound CO in the beta -bonded state. The stoichiometry of this reaction at saturation requires that only half the original CO adsorbed in the beta-bonded CO state can dissociate. Presaturating the surface with hydrogen affects the bonding and dissociation of CO on the iron surface. One effect is to weaken CO-Fe bonds which results in a very weakly bound state (alpha^' _1). In addition to the alpha ^'_1 state, presaturating the surface with hydrogen

  19. 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.

    PubMed

    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. PMID:25127315

  20. Conformational stability and intramolecular hydrogen bonding in 1,2-ethanediol and 1,4-butanediol.

    PubMed

    Das, Prasanta; Das, Puspendu K; Arunan, E

    2015-04-23

    The gas-phase infrared spectra of 1,2-ED and 1,4-BD have been recorded at three different temperatures using a multipass gas cell of 6 m optical path length. DFT calculation has also been carried out using 6-311++G** and aug-cc-pVDZ basis sets to look for the existence of intramolecular hydrogen bonding in them from the red shift and infrared absorption intensity enhancement of the bonded O-H band compared to that of the free O-H band. Equilibrium population analysis with 10 conformers of 1,2-ED and 1,4-BD at experimental temperatures were carried out for the reconstruction of the observed vibrational spectra at that temperature using standard statistical relationships. The most abundant conformer at experimental temperatures was identified. In 1,2-ED a red shift of 45 cm(-1) in the intramolecularly interacting O-H stretching vibrational band position and no significant intensity enhancement compared to that of the free O-H have been observed. On the contrary, in one of the hydrogen-bonded conformers of 1,4-BD, a 124 cm(-1) red shift in the O-H stretching frequency and a 8.5 times intensity enhancement for the "bonded" O-H compared to that of the "free" O-H is seen. On the basis of this comparative study, we have concluded that strong intramolecular hydrogen bonding exists in 1,4-BD. But there appears to be weak intramolecular hydrogen bonding in 1,2-ED at temperatures of 303, 313, and 323 K in the gas phase. We have found that most stable hydrogen-bonded conformers of 1,4-BD are less populated than some of the non-hydrogen-bonded conformers. Even for the 1,4-BD, the relative population of the g'GG'Gt conformer, which has a strong intramolecular hydrogen bond, is less than what is predicted. Perhaps the intramolecular hydrogen bond plays a less significant role in the relative stability of the various conformers than what has been predicted from calculations and prevails in the literature. PMID:25839224

  1. Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase

    PubMed Central

    Langkilde, Annette; Kristensen, Søren M.; Lo Leggio, Leila; Mølgaard, Anne; Jensen, Jan H.; Houk, Andrew R.; Navarro Poulsen, Jens-Christian; Kauppinen, Sakari; Larsen, Sine

    2008-01-01

    An extremely low-field signal (at approximately 18 p.p.m.) in the 1H NMR spectrum of rhamnogalacturonan acetylesterase (RGAE) shows the presence of a short strong hydrogen bond in the structure. This signal was also present in the mutant RGAE D192N, in which Asp192, which is part of the catalytic triad, has been replaced with Asn. A careful analysis of wild-type RGAE and RGAE D192N was conducted with the purpose of identifying possible candidates for the short hydrogen bond with the 18 p.p.m. deshielded proton. Theor­etical calculations of chemical shift values were used in the interpretation of the experimental 1H NMR spectra. The crystal structure of RGAE D192N was determined to 1.33 Å resolution and refined to an R value of 11.6% for all data. The structure is virtually identical to the high-resolution (1.12 Å) structure of the wild-type enzyme except for the interactions involving the mutation and a disordered loop. Searches of the Cambridge Structural Database were conducted to obtain information on the donor–acceptor distances of different types of hydrogen bonds. The short hydrogen-bond inter­actions found in RGAE have equivalents in small-molecule structures. An examination of the short hydrogen bonds in RGAE, the calculated pK a values and solvent-accessibilities identified a buried carboxylic acid carboxylate hydrogen bond between Asp75 and Asp87 as the likely origin of the 18 p.p.m. signal. Similar hydrogen-bond interactions between two Asp or Glu carboxy groups were found in 16% of a homology-reduced set of high-quality structures extracted from the PDB. The shortest hydrogen bonds in RGAE are all located close to the active site and short interactions between Ser and Thr side-chain OH groups and backbone carbonyl O atoms seem to play an important role in the stability of the protein structure. These results illustrate the significance of short strong hydrogen bonds in proteins. PMID:18645234

  2. Nano breathers and molecular dynamics simulations in hydrogen-bonded chains.

    PubMed

    Kavitha, L; Muniyappan, A; Prabhu, A; Zdravković, S; Jayanthi, S; Gopi, D

    2013-01-01

    Non-linear localization phenomena in biological lattices have attracted a steadily growing interest and their existence has been predicted in a wide range of physical settings. We investigate the non-linear proton dynamics of a hydrogen-bonded chain in a semi-classical limit using the coherent state method combined with a Holstein-Primakoff bosonic representation. We demonstrate that even a weak inherent discreteness in the hydrogen-bonded (HB) chain may drastically modify the dynamics of the non-linear system, leading to instabilities that have no analog in the continuum limit. We suggest a possible localization mechanism of polarization oscillations of protons in a hydrogen-bonded chain through modulational instability analysis. This mechanism arises due to the neighboring proton-proton interaction and coherent tunneling of protons along hydrogen bonds and/or around heavy atoms. We present a detailed analysis of modulational instability, and highlight the role of the interaction strength of neighboring protons in the process of bioenergy localization. We perform molecular dynamics simulations and demonstrate the existence of nanoscale discrete breather (DB) modes in the hydrogen-bonded chain. These highly localized and long-lived non-linear breather modes may play a functional role in targeted energy transfer in biological systems. PMID:23860832

  3. Wetting Properties of Chemically Modified Surfaces: The role of hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Bekele, Selemon; Tsige, Mesfin

    2015-03-01

    Many industrial processing operations involve the spreading of a liquid on a solid material. Controlling the wetting of one material by another is of crucial importance in such applications as adhesion, coating and oil recovery. A strategy often employed to control the wettability of solid surfaces is a combination of surface patterning and chemical surface modification. In order to understand the effect of surface chemistry on the wetting process, we have carried out all-atom molecular dynamics (MD) simulations of a water droplet spreading on pure and oxidized polystyrene surfaces. Our previous results show that the contact angle generally decreases with increasing oxygen concentration and there is a correlation between the spreading and hydrogen bonding. In this talk, we will present results on the structure and dynamics of the hydrogen bonds in the interfacial region between water and the polystyrene substrate. We will discuss our findings on hydrogen bond lifetimes, time correlations functions and number of hydrogen bonds per water molecule for the hydrogen bonds around the water/polystyrene interface which are found to play a role in the spreading process. This work was supported by NSF Grant DMR0847580.

  4. Short Hydrogen Bonds and Proton Delocalization in Green Fluorescent Protein (GFP)

    PubMed Central

    2015-01-01

    Short hydrogen bonds and specifically low-barrier hydrogen bonds (LBHBs) have been the focus of much attention and controversy for their possible role in enzymatic catalysis. The green fluorescent protein (GFP) mutant S65T, H148D has been found to form a very short hydrogen bond between Asp148 and the chromophore resulting in significant spectral perturbations. Leveraging the unique autocatalytically formed chromophore and its sensitivity to this interaction we explore the consequences of proton affinity matching across this putative LBHB. Through the use of noncanonical amino acids introduced through nonsense suppression or global incorporation, we systematically modify the acidity of the GFP chromophore with halogen substituents. X-ray crystal structures indicated that the length of the interaction with Asp148 is unchanged at ∼2.45 Å while the absorbance spectra demonstrate an unprecedented degree of color tuning with increasing acidity. We utilized spectral isotope effects, isotope fractionation factors, and a simple 1D model of the hydrogen bond coordinate in order to gain insight into the potential energy surface and particularly the role that proton delocalization may play in this putative short hydrogen bond. The data and model suggest that even with the short donor–acceptor distance (∼2.45 Å) and near perfect affinity matching there is not a LBHB, that is, the barrier to proton transfer exceeds the H zero-point energy. PMID:27162964

  5. Conservation and Functional Importance of Carbon-Oxygen Hydrogen Bonding in AdoMet-Dependent Methyltransferases

    SciTech Connect

    Horowitz, Scott; Dirk, Lynnette M.A.; Yesselman, Joseph D.; Nimtz, Jennifer S.; Adhikari, Upendra; Mehl, Ryan A.; Scheiner, Steve; Houtz, Robert L.; Al-Hashimi, Hashim M.; Trievel, Raymond C.

    2013-09-06

    S-Adenosylmethionine (AdoMet)-based methylation is integral to metabolism and signaling. AdoMet-dependent methyltransferases belong to multiple distinct classes and share a catalytic mechanism that arose through convergent evolution; however, fundamental determinants underlying this shared methyl transfer mechanism remain undefined. A survey of high-resolution crystal structures reveals that unconventional carbon–oxygen (CH···O) hydrogen bonds coordinate the AdoMet methyl group in different methyltransferases irrespective of their class, active site structure, or cofactor binding conformation. Corroborating these observations, quantum chemistry calculations demonstrate that these charged interactions formed by the AdoMet sulfonium cation are stronger than typical CH···O hydrogen bonds. Biochemical and structural studies using a model lysine methyltransferase and an active site mutant that abolishes CH···O hydrogen bonding to AdoMet illustrate that these interactions are important for high-affinity AdoMet binding and transition-state stabilization. Further, crystallographic and NMR dynamics experiments of the wild-type enzyme demonstrate that the CH···O hydrogen bonds constrain the motion of the AdoMet methyl group, potentially facilitating its alignment during catalysis. Collectively, the experimental findings with the model methyltransferase and structural survey imply that methyl CH···O hydrogen bonding represents a convergent evolutionary feature of AdoMet-dependent methyltransferases, mediating a universal mechanism for methyl transfer.

  6. Hydrogen Bonds in Crystalline Imidazoles Studied by 15N NMR and ab initio MO Calculations

    NASA Astrophysics Data System (ADS)

    Ueda, Takahiro; Nagatomo, Shigenori; Masui, Hirotsugu; Nakamura, Nobuo; Hayashi, Shigenobu

    1999-07-01

    Intermolecular hydrogen bonds of the type N-H...N in crystals of imidazole and its 4-substituted and 4,5-disubstituted derivatives were studied by 15N CP/MAS NMR and an ab initio molecular orbital (MO) calculation. In the 15N CP/MAS NMR spectrum of each of the imidazole derivatives, two peaks due to the two different functional groups, >NH and =N-, were observed. The value of the 15N isotropic chemical shift for each nitrogen atom depends on both the length of the intermolecular hydrogen bond and the kind of the substituent or substituents. It was found that the difference between the experimen-tal chemical shifts of >NH and =N-varies predominantly with the hydrogen bond length but does not show any systematic dependence on the kind of substituent. The ab initio MO calculations suggest that the hydrogen bond formation influences the 15N isotropic chemical shift predominantly, and that the difference between the 15N isotropic chemical shift of >NH and =N-varies linearly with the hydrogen bond length.

  7. The effect of hydrogen bonds on diffusion mechanism of water inside single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Chen, Qu; Wang, Qi; Liu, Ying-Chun; Wu, Tao

    2014-06-01

    Nanopores can serve as a molecule channel for transport of fluid, where water diffusion differs remarkably from that of simple particles. Hydrogen bonds play an essential role in the diffusion anomaly. Detailed investigations are carried out on the systems of rigid (6, 6), (7, 7), (8, 8), (9, 9), and (10, 10) armchair carbon nanotubes, solvated with Lennard-Jones water fluids. The role of hydrogen bonds is examined by diffusivity statistics and animation snapshots. It is found that in small (6,6) CNT, hydrogen bonds tend to aggregate water into a wire and lead to rapid collective drift. Confinement can stabilize the hydrogen bond of water molecules and enhance its lifetime. In relatively smaller CNTs, the diffusion mechanism could be altered by the temperature. Moreover, in larger nanotubes hydrogen bonding network allows the water to form regional concentrated clusters. This allows water fluid in extremely low density exhibit rather slow self-diffusion motion. This fundamental study attempts to provide insights in understanding nanoscale delivery system in aqueous solution.

  8. (-)-Dioxosantadienic acid: hydrogen-bonding patterns in a bicyclic sesquiterpenoid keto acid and its monohydrate.

    PubMed

    Brunskill, A P; Lalancette, R A; Thompson, H W

    2001-09-01

    The anhydrous form, (I), of the title compound, (-)-2-(1,2,3,4,4a,7-hexahydro-4a,8-dimethyl-1,7-dioxo-2-naphthyl)propionic acid, C(15)H(18)O(4), derived from a naturally occurring sesquiterpenoid, has two molecules in the asymmetric unit, (I) and (I'), differing in the conformations of the saturated ring and the carboxyl group. The compound aggregates as carboxyl-to-ketone hydrogen-bonding catemers [O.O = 2.776 (3) and 2.775 (3) A]. Two crystallographically independent sets of single-strand hydrogen-bonding helices with opposite end-to-end orientation pass through the cell in the b direction, one consisting exclusively of molecules of (I) and the other entirely of (I'). Three C-H.O=C close contacts are found in (I). The monohydrate, C(15)H(18)O(4).H(2)O, (II), with two molecules of (I) plus two water molecules in its asymmetric unit, forms a complex three-dimensional hydrogen-bonding network including acid-to-water, water-to-acid, water-to-ketone, water-to-water and acid-to-acid hydrogen bonds, plus three C-H.O=C close contacts. In both (I) and (II), only the ketone remote from the acid is involved in hydrogen bonding. PMID:11588376

  9. Short Hydrogen Bonds and Proton Delocalization in Green Fluorescent Protein (GFP).

    PubMed

    Oltrogge, Luke M; Boxer, Steven G

    2015-06-24

    Short hydrogen bonds and specifically low-barrier hydrogen bonds (LBHBs) have been the focus of much attention and controversy for their possible role in enzymatic catalysis. The green fluorescent protein (GFP) mutant S65T, H148D has been found to form a very short hydrogen bond between Asp148 and the chromophore resulting in significant spectral perturbations. Leveraging the unique autocatalytically formed chromophore and its sensitivity to this interaction we explore the consequences of proton affinity matching across this putative LBHB. Through the use of noncanonical amino acids introduced through nonsense suppression or global incorporation, we systematically modify the acidity of the GFP chromophore with halogen substituents. X-ray crystal structures indicated that the length of the interaction with Asp148 is unchanged at ∼2.45 Å while the absorbance spectra demonstrate an unprecedented degree of color tuning with increasing acidity. We utilized spectral isotope effects, isotope fractionation factors, and a simple 1D model of the hydrogen bond coordinate in order to gain insight into the potential energy surface and particularly the role that proton delocalization may play in this putative short hydrogen bond. The data and model suggest that even with the short donor-acceptor distance (∼2.45 Å) and near perfect affinity matching there is not a LBHB, that is, the barrier to proton transfer exceeds the H zero-point energy. PMID:27162964

  10. A computational study on the enhanced stabilization of aminophenol derivatives by internal hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Gomes, José R. B.; Ribeiro da Silva, Manuel A. V.

    2006-05-01

    The stabilization of aminophenol derivatives and their radicals due to internal hydrogen bonding has been analyzed by means of density functional theory and by topological electron density analysis. The calculations have been carried out at the B3LYP level of theory, using several basis sets, and by means of the CBS-4M composite approach. A strong O-H⋯NH 2 hydrogen bond is found to stabilize the aminophenol with the lone-pair of the nitrogen atom co-planar with the aromatic ring, contrasting with the optimized structure found for aniline. The effect of electron donors and electron acceptors on the strength of the internal hydrogen bond is also analyzed. For one of the species studied, 2,6-diaminophenol, the computed O-H bond dissociation enthalpy is only 300 kJ/mol, the lowest value found so far for phenol and other compounds containing the O-H bond, almost 25 kJ/mol lower than those found experimentally for pyrogallol and for vitamin E. The explanation for such a small value comes from the enhanced stabilization of the corresponding radical species by internal hydrogen bonding, combined with a decrease of the steric effects caused by rotation of the amino groups.

  11. Toxin-induced pore formation is hindered by intermolecular hydrogen bonding in sphingomyelin bilayers.

    PubMed

    García-Linares, Sara; Palacios-Ortega, Juan; Yasuda, Tomokazu; Åstrand, Mia; Gavilanes, José G; Martínez-del-Pozo, Álvaro; Slotte, J Peter

    2016-06-01

    Sticholysin I and II (StnI and StnII) are pore-forming toxins that use sphingomyelin (SM) for membrane binding. We examined how hydrogen bonding among membrane SMs affected the StnI- and StnII-induced pore formation process, resulting in bilayer permeabilization. We compared toxin-induced permeabilization in bilayers containing either SM or dihydro-SM (lacking the trans Δ(4) double bond of the long-chain base), since their hydrogen-bonding properties are known to differ greatly. We observed that whereas both StnI and StnII formed pores in unilamellar vesicles containing palmitoyl-SM or oleoyl-SM, the toxins failed to similarly form pores in vesicles prepared from dihydro-PSM or dihydro-OSM. In supported bilayers containing OSM, StnII bound efficiently, as determined by surface plasmon resonance. However, StnII binding to supported bilayers prepared from dihydro-OSM was very low under similar experimental conditions. The association of the positively charged StnII (at pH7.0) with unilamellar vesicles prepared from OSM led to a concentration-dependent increase in vesicle charge, as determined from zeta-potential measurements. With dihydro-OSM vesicles, a similar response was not observed. Benzyl alcohol, which is a small hydrogen-bonding compound with affinity to lipid bilayer interfaces, strongly facilitated StnII-induced pore formation in dihydro-OSM bilayers, suggesting that hydrogen bonding in the interfacial region originally prevented StnII from membrane binding and pore formation. We conclude that interfacial hydrogen bonding was able to affect the membrane association of StnI- and StnII, and hence their pore forming capacity. Our results suggest that other types of protein interactions in bilayers may also be affected by hydrogen-bonding origination from SMs. PMID:26975250

  12. Regulation of protein-ligand binding affinity by hydrogen bond pairing.

    PubMed

    Chen, Deliang; Oezguen, Numan; Urvil, Petri; Ferguson, Colin; Dann, Sara M; Savidge, Tor C

    2016-03-01

    Hydrogen (H)-bonds potentiate diverse cellular functions by facilitating molecular interactions. The mechanism and the extent to which H-bonds regulate molecular interactions are a largely unresolved problem in biology because the H-bonding process continuously competes with bulk water. This interference may significantly alter our understanding of molecular function, for example, in the elucidation of the origin of enzymatic catalytic power. We advance this concept by showing that H-bonds regulate molecular interactions via a hitherto unappreciated donor-acceptor pairing mechanism that minimizes competition with water. On the basis of theoretical and experimental correlations between H-bond pairings and their effects on ligand binding affinity, we demonstrate that H-bonds enhance receptor-ligand interactions when both the donor and acceptor have either significantly stronger or significantly weaker H-bonding capabilities than the hydrogen and oxygen atoms in water. By contrast, mixed strong-weak H-bond pairings decrease ligand binding affinity due to interference with bulk water, offering mechanistic insight into why indiscriminate strengthening of receptor-ligand H-bonds correlates poorly with experimental binding affinity. Further support for the H-bond pairing principle is provided by the discovery and optimization of lead compounds targeting dietary melamine and Clostridium difficile toxins, which are not realized by traditional drug design methods. Synergistic H-bond pairings have therefore evolved in the natural design of high-affinity binding and provide a new conceptual framework to evaluate the H-bonding process in biological systems. Our findings may also guide wider applications of competing H-bond pairings in lead compound design and in determining the origin of enzymatic catalytic power. PMID:27051863

  13. Regulation of protein-ligand binding affinity by hydrogen bond pairing

    PubMed Central

    Chen, Deliang; Oezguen, Numan; Urvil, Petri; Ferguson, Colin; Dann, Sara M.; Savidge, Tor C.

    2016-01-01

    Hydrogen (H)-bonds potentiate diverse cellular functions by facilitating molecular interactions. The mechanism and the extent to which H-bonds regulate molecular interactions are a largely unresolved problem in biology because the H-bonding process continuously competes with bulk water. This interference may significantly alter our understanding of molecular function, for example, in the elucidation of the origin of enzymatic catalytic power. We advance this concept by showing that H-bonds regulate molecular interactions via a hitherto unappreciated donor-acceptor pairing mechanism that minimizes competition with water. On the basis of theoretical and experimental correlations between H-bond pairings and their effects on ligand binding affinity, we demonstrate that H-bonds enhance receptor-ligand interactions when both the donor and acceptor have either significantly stronger or significantly weaker H-bonding capabilities than the hydrogen and oxygen atoms in water. By contrast, mixed strong-weak H-bond pairings decrease ligand binding affinity due to interference with bulk water, offering mechanistic insight into why indiscriminate strengthening of receptor-ligand H-bonds correlates poorly with experimental binding affinity. Further support for the H-bond pairing principle is provided by the discovery and optimization of lead compounds targeting dietary melamine and Clostridium difficile toxins, which are not realized by traditional drug design methods. Synergistic H-bond pairings have therefore evolved in the natural design of high-affinity binding and provide a new conceptual framework to evaluate the H-bonding process in biological systems. Our findings may also guide wider applications of competing H-bond pairings in lead compound design and in determining the origin of enzymatic catalytic power. PMID:27051863

  14. Effect of pressure on the structure and dynamics of hydrogen bonds in ethylene glycol-water mixtures: Numerical simulation data

    NASA Astrophysics Data System (ADS)

    Antipova, M. L.; Gurina, D. L.; Makarov, D. M.; Egorov, G. I.; Petrenko, V. E.

    2016-03-01

    Water-ethylene glycol mixtures containing from 0.002 to 0.998 mole fractions of ethylene glycol at T = 298.15 K and P = 0.1 and 100 MPa are simulated by means of classical molecular dynamics. Such structural and dynamic characteristics of hydrogen bonds as the average number and lifetime, along with the distribution of molecules over the number of hydrogen bonds, are calculated; their changes are analyzed, depending on the mixture's composition and pressure. It is shown that the components are characterized by a high degree of interpenetration and form a uniform infinite hydrogen-bonded cluster over the range of concentrations. It is found that the higher the concentration of ethylene glycol, the greater the stability of all hydrogen bonds. It is concluded that an increase in pressure lowers the number of hydrogen bonds, while the average lifetime of the remaining hydrogen bonds grows.

  15. The Influence of Hydrogen Bonding on Hydrogen-Atom Abstraction Reactions of Dehydropyridinium Cations in the Gas Phase

    PubMed Central

    Adeuya, Anthony; Nash, John J.; Kenttämaa, Hilkka I.

    2010-01-01

    The reactions of several substituted, positively-charged dehydropyridinium cations with cyclohexane, methanol and tetrahydrofuran have been examined in a Fourier-transform ion cyclotron resonance mass spectrometer. All of the charged monoradicals react with the neutral reagents exclusively via hydrogen atom abstraction. For cyclohexane, there is a good correlation between the reaction efficiencies and the calculated electron affinities at the radical sites; that is, the greater the electron affinity of the charged monoradical at the radical site, the faster the reaction. The reaction efficiencies with methanol and tetrahydrofuran, however, do not correlate with the calculated electron affinities. Density functional theory (DFT) calculations indicate that for these reagents a stabilizing hydrogen bonding interaction exists in the hydrogen atom abstraction transition states for some of the charged monoradicals but not for others. At both the MPW1K and G3MP2B3 levels of theory, there is a good correlation between the calculated activation enthalpies and the observed reaction efficiencies although the G3MP2B3 method provides a slightly better correlation than the MPW1K method. The extent of enhancement in the reaction efficiencies caused by the hydrogen bonding interactions parallels the calculated hydrogen bond lengths in the transition states. PMID:21080694

  16. Energetics of short hydrogen bonds in photoactive yellow protein.

    PubMed

    Saito, Keisuke; Ishikita, Hiroshi

    2012-01-01

    Recent neutron diffraction studies of photoactive yellow protein (PYP) proposed that the H bond between protonated Glu46 and the chromophore [ionized p-coumaric acid (pCA)] was a low-barrier H bond (LBHB). Using the atomic coordinates of the high-resolution crystal structure, we analyzed the energetics of the short H bond by two independent methods: electrostatic pK(a) calculations and a quantum mechanical/molecular mechanical (QM/MM) approach. (i) In the QM/MM optimized geometry, we reproduced the two short H-bond distances of the crystal structure: Tyr42-pCA (2.50 Å) and Glu46-pCA (2.57 Å). However, the H atoms obviously belonged to the Tyr or Glu moieties, and were not near the midpoint of the donor and acceptor atoms. (ii) The potential-energy curves of the two H bonds resembled those of standard asymmetric double-well potentials, which differ from those of LBHB. (iii) The calculated pK(a) values for Glu46 and pCA were 8.6 and 5.4, respectively. The pK(a) difference was unlikely to satisfy the prerequisite for LBHB. (iv) The LBHB in PYP was originally proposed to stabilize the ionized pCA because deprotonated Arg52 cannot stabilize it. However, the calculated pK(a) of Arg52 and QM/MM optimized geometry suggested that Arg52 was protonated on the protein surface. The short H bond between Glu46 and ionized pCA in the PYP ground state could be simply explained by electrostatic stabilization without invoking LBHB. PMID:22173632

  17. Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity

    NASA Astrophysics Data System (ADS)

    Liu, Lan; Baergen, Alyson; Michelsen, Klaus; Kitova, Elena N.; Schnier, Paul D.; Klassen, John S.

    2014-05-01

    This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the -7 charge state) of complexes of bovine β-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)7- ions, compared with that of the (Lg + PA)7- ion, it is concluded that the -OH groups of the X-OHPA ligands participate in strong (5 - 11 kcal mol-1) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the -OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the -OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (Ka) measured for 7-OHPA [(2.3 ± 0.2) × 105 M-1] is similar to the value for the PA [(3.8 ± 0.1) × 105 M-1]; Ka for 3-OHPA [(1.1 ± 0.3) × 106 M-1] is approximately three-times larger, whereas Ka for 16-OHPA [(2.3 ± 0.2) × 104 M-1] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand -OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds.

  18. Quantitative evaluation on activated property-tunable bulk liquid water with reduced hydrogen bonds using deconvoluted Raman spectroscopy.

    PubMed

    Chen, Hsiao-Chien; Mai, Fu-Der; Yang, Kuang-Hsuan; Chen, Liang-Yih; Yang, Chih-Ping; Liu, Yu-Chuan

    2015-01-01

    Interesting properties of water with distinguishable hydrogen-bonding structure on interfacial phase or in confined environment have drawn wide attentions. However, these unique properties of water are only found within the interfacial phase and confined environment, thus, their applications are limited. In addition, quantitative evaluation on these unique properties associating with the enhancement of water's physical and chemical activities represents a notable challenge. Here we report a practicable production of free-standing liquid water at room temperature with weak hydrogen-bonded structure naming Au nanoparticles (NPs)-treated (AuNT) water via treating by plasmon-induced hot electron transfer occurred on resonantly illuminated gold NPs (AuNPs). Compared to well-known untreated bulk water (deionized water), the prepared AuNT water exhibits many distinct activities in generally physical and chemical reactions, such as high solubilities to NaCl and O2. Also, reducing interaction energy within water molecules provides lower overpotential and higher efficiency in electrolytic hydrogen production. In addition, these enhanced catalytic activities of AuNT water are tunable by mixing with deionized water. Also, most of these tunable activities are linearly proportional to its degree of nonhydrogen-bonded structure (DNHBS), which is derived from the O-H stretching in deconvoluted Raman spectrum. PMID:25471522

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

    SciTech Connect

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

    2015-05-06

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

  20. Transition metal-catalyzed process for addition of amines to carbon-carbon double bonds

    DOEpatents

    Hartwig, John F.; Kawatsura, Motoi; Loeber, Oliver

    2002-01-01

    The present invention is directed to a process for addition of amines to carbon-carbon double bonds in a substrate, comprising: reacting an amine with a compound containing at least one carbon-carbon double bond in the presence a transition metal catalyst under reaction conditions effective to form a product having a covalent bond between the amine and a carbon atom of the former carbon-carbon double bond. The transition metal catalyst comprises a Group 8 metal and a ligand containing one or more 2-electron donor atoms. The present invention is also directed to enantioselective reactions of amine compounds with compounds containing carbon-carbon double bonds, and a calorimetric assay to evaluate potential catalysts in these reactions.

  1. Intramolecular Hydrogen-Bonding Effects on the Fluorescence of PRODAN Derivatives.

    PubMed

    Alty, Isaac G; Cheek, Douglas W; Chen, Tao; Smith, David B; Walhout, Emma Q; Abelt, Christopher J

    2016-05-26

    The effects of intramolecular hydrogen-bonding on the fluorescence behavior of three derivatives of 6-propionyl-2-dimethylaminonaphthalene are reported. The H-bonding effects are revealed through comparisons with corresponding reference compounds in which the H-bond-donating hydroxyl groups are replaced with methoxy groups. In toluene, intramolecular H bonding gives rise to a dramatic increase in the fluorescence intensity but only a slight red shift in the position. This behavior is attributed to decreased efficiency in intersystem crossing due to an increase in the energy of the n → π* triplet state. The intramolecular H bond does not induce quenching in acetonitrile; however, in the presence of a very small concentration of methanol, a dual intramolecular, intermolecular H-bonding arrangement does lead to partial quenching as revealed by preferential solvation studies. PMID:27127907

  2. Dynamics of Weak, Bifurcated and Strong Hydrogen Bonds in Lithium Nitrate Trihydrate

    SciTech Connect

    Werhahn, Jasper C.; Pandelov, S.; Xantheas, Sotiris S.; Iglev, H.

    2011-07-07

    The properties of three distinct types of hydrogen bonds, namely a weak, a bifurcated and a strong one, all present in/the LiNO3 (HDO)(D2O)2 hydrate lattice unit cell are studied using steady-state and time-resolved spectroscopy. The lifetimes of the OH stretching vibrations for the three individual bonds are 2.2 ps (weak), 1.7 ps (bifurcated), and 1.2 ps (strong), respectively. For the first time the properties of bifurcated H bonds can thus be unambiguously directly compared to those of weak and strong H bonds in the same system. The values of their OH stretching vibration lifetime, anharmonicity, red shift and bond strength lie between those for the strong and weak H bonds. The experimentally observed inhomogeneous broadening of their spectral signature is attributed to the coupling with a low frequency intermolecular wagging vibration/

  3. Hydrogen Bond Formation between the Carotenoid Canthaxanthin and the Silanol Group on MCM-41 Surface.

    PubMed

    Gao, Yunlong; Xu, Dayong; Kispert, Lowell D

    2015-08-20

    The formation of one or two hydrogen bonds (H-bonds) between canthaxanthin (CAN), a dye, and the silanol group(s) on the MCM-41 surface has been studied by density functional theory (DFT) calculations and calorimetric experiments. It was found that the formation of the H-bond(s) stabilized the CAN molecule more than its radical cation (CAN(•+)). The charge distribution, bond lengths, and the HOMO and LUMO energies of CAN are also affected. The formation of the H-bond(s) explains the lower photoinduced electron transfer efficiency of CAN imbedded in Cu-MCM-41 versus that for β-carotene (CAR) imbedded in Cu-MCM-41 where complex formation with Cu(2+) dominates. These calculations show that to achieve high electron transfer efficiency for a dye-sensitized solar cell, H-bonding between the dye and the host should be avoided. PMID:26230844

  4. Hydrophobic, Non-Hydrogen-Bonding Bases and Base Pairs in DNA

    PubMed Central

    Schweitzer, Barbara A.; Kool, Eric T.

    2009-01-01

    We report the properties of hydrophobic isosteres of pyrimidines and purines in synthetic DNA duplexes. Phenyl nucleosides 1 and 2 are nonpolar isosteres of the natural thymidine nucleoside, and indole nucleoside 3 is an analog of the complementary purine 2-aminodeoxyadenosine. The nucleosides were incorporated into synthetic oligodeoxynucleotides and were paired against each other and against the natural bases. Thermal denaturation experiments were used to measure the stabilities of the duplexes at neutral pH. It is found that the hydrophobic base analogs are nonselective in pairing with the four natural bases but selective for pairing with each other rather than with the natural bases. For example, compound 2 selectively pairs with itself rather than with A, T, G, or C; the magnitude of this selectivity is found to be 6.5–9.3 °C in Tm or 1.5–1.8 kcal/mol in free energy (25 °C). All possible hydrophobic pairing combinations of 1, 2, and 3 were examined. Results show that the pairing affinity depends on the nature of the pairs and on position in the duplex. The highest affinity pairs are found to be the 1–1 and 2–2 self-pairs and the 1–2 heteropair. The best stabilization occurs when the pairs are placed at the ends of duplexes rather than internally; the internal pairs may be destabilized by imperfect steric mimicry which leads to non-ideal duplex structure. In some cases the hydrophobic pairs are significantly stabilizing to the DNA duplex; for example, when situated at the end of a duplex, the 1–1 pair is more stabilizing than a T–A pair. When situated internally, the affinity of the 1–1 pair is the same as, or slightly better than, the analogous T–T mismatch pair, which is known to have two hydrogen bonds. The studies raise the possibility that hydrogen bonds may not always be required for the formation of stable duplex DNA-like structure. In addition, the results point out the importance of solvation and desolvation in natural base pairing

  5. A direct experimental evidence for an aromatic C-H⋯O hydrogen bond by fluorescence-detected infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Venkatesan, V.; Fujii, A.; Ebata, T.; Mikami, N.

    2004-08-01

    Formation of a weak aromatic C-H⋯O hydrogen bond has been discerned both experimentally and computationally in the 1,2,4,5-tetrafluorobenzene (TFB)-water system. The intermolecular structure of the isolated TFB-water cluster in a supersonic jet was characterized using fluorescence-detected infrared spectroscopy. The formation of a weak hydrogen bond in the cluster was directly evidenced by a low-frequency shift and intensity enhancement of the hydrogen-bonded aromatic C-H stretch in the TFB moiety. This is the first direct observation of an aromatic C-H⋯O hydrogen bond in isolated gas phase clusters.

  6. Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid water.

    PubMed

    Houriez, Céline; Masella, Michel; Ferré, Nicolas

    2010-09-28

    In this study, we investigated the hydrogen-bond network patterns involving the NO moieties of five small nitroxides in liquid water by analyzing nanosecond scale molecular dynamics trajectories. To this end, we implemented two types of hydrogen-bond definitions, based on electronic structure, using Bader's atoms-in-molecules analysis and based on geometric criteria. In each definition framework, the nitroxide/water hydrogen-bond networks appear very variable from a nitroxide to another. Moreover, each definition clearly leads to a different picture of nitroxide hydration. For instance, the electronic structure-based definition predicts a number of hydrogen bonds around the nitroxide NO moiety usually larger than geometric structure-based ones. One particularly interesting result is that the strength of a nitroxide/water hydrogen bond does not depend on its linearity, leading us to question the relevance of geometric definition based on angular cutoffs to study this type of hydrogen bond. Moreover, none of the hydrogen-bond definitions we consider in the present study is able to quantitatively correlate the strength of nitroxide/water hydrogen-bond networks with the aqueous nitroxide spin properties. This clearly exhibits that the hydrogen-bonding concept is not reliable enough to draw quantitative conclusions concerning such properties. PMID:20886951

  7. Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid water

    NASA Astrophysics Data System (ADS)

    Houriez, Céline; Masella, Michel; Ferré, Nicolas

    2010-09-01

    In this study, we investigated the hydrogen-bond network patterns involving the NO moieties of five small nitroxides in liquid water by analyzing nanosecond scale molecular dynamics trajectories. To this end, we implemented two types of hydrogen-bond definitions, based on electronic structure, using Bader's atoms-in-molecules analysis and based on geometric criteria. In each definition framework, the nitroxide/water hydrogen-bond networks appear very variable from a nitroxide to another. Moreover, each definition clearly leads to a different picture of nitroxide hydration. For instance, the electronic structure-based definition predicts a number of hydrogen bonds around the nitroxide NO moiety usually larger than geometric structure-based ones. One particularly interesting result is that the strength of a nitroxide/water hydrogen bond does not depend on its linearity, leading us to question the relevance of geometric definition based on angular cutoffs to study this type of hydrogen bond. Moreover, none of the hydrogen-bond definitions we consider in the present study is able to quantitatively correlate the strength of nitroxide/water hydrogen-bond networks with the aqueous nitroxide spin properties. This clearly exhibits that the hydrogen-bonding concept is not reliable enough to draw quantitative conclusions concerning such properties.

  8. Effect of Hydrogen-Bonding Junctions on Microphase Separation in Block Copolymers

    NASA Astrophysics Data System (ADS)

    Stone, Greg; Hedrick, Jim; Nederberg, Fredrik; Balsara, Nitash

    2008-03-01

    The morphology of poly(styrene-block- trimethylene carbonate) (PS-PTMC) copolymers with and without thiourea groups at the junction between the blocks was studied by a combination of small angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). The thiourea groups are known to exhibit inter-molecular hydrogen bonding. We demonstrate that the presence of thiourea groups results in increased segregation between PS and PTMC blocks. We focus on symmetric systems with total molecular weights in the 5 kg/mol range. In conventional block copolymers without hydrogen bonding groups it is difficult to obtain strong segregation in low molecular weight systems because the product chi*N controls segregation (chi is the Flory-Huggins interaction parameter and N is the number of monomers per chain). The incorporation of hydrogen bonding groups may provide a route for the generation of patterns with small, sharply defined features using block copolymers.

  9. Role of the Uranyl Oxo Group as a Hydrogen Bond Acceptor

    SciTech Connect

    Watson, Lori A; Hay, Benjamin

    2011-01-01

    Density functional theory calculations have been used to evaluate the geometries and energetics of interactions between a number of uranyl complexes and hydrogen bond donor groups. The results reveal that although traditional hydrogen bond donors are repelled by the oxo group in the [UO{sub 2}(OH{sub 2}){sub 5}]{sup 2+} species, they are attracted to the oxo groups in [UO{sub 2}(OH{sub 2}){sub 2}(NO{sub 3}){sub 2}]{sup 0}, [UO{sub 2}(NO{sub 3}){sub 3}]{sup -}, and [UO{sub 2}Cl{sub 4}]{sup 2-} species. Hydrogen bond strength depends on the equatorial ligation and can exceed 15 kcal mol{sup -1}. The results also reveal the existence of directionality at the uranyl oxo acceptor, with a weak preference for linear U=O---H angles.

  10. Hydrogen Bond Fluctuations Control Photochromism in a Reversibly Photo-Switchable Fluorescent Protein.

    PubMed

    Morozov, Dmitry; Groenhof, Gerrit

    2016-01-11

    Reversibly switchable fluorescent proteins (RSFPs) are essential for high-resolution microscopy of biological samples, but the reason why these proteins are photochromic is still poorly understood. To address this problem, we performed molecular dynamics simulations of the fast switching Met159Thr mutant of the RSFP Dronpa. Our simulations revealed a ground state structural heterogeneity in the chromophore pocket that consists of three populations with one, two, or three hydrogen bonds to the phenolate moiety of the chromophore. By means of non-adiabatic quantum mechanics/molecular dynamics simulations, we demonstrated that the subpopulation with a single hydrogen bond is responsible for off-switching through photo-isomerization of the chromophore, whereas two or more hydrogen bonds inhibit the isomerization and promote fluorescence instead. While rational design of new RSFPs has so far focused on structure alone, our results suggest that structural heterogeneity must be considered as well. PMID:26612709

  11. Tunable capsule space: self-assembly of hemispherical cavitands with hydrogen-bonding linkers.

    PubMed

    Yamanaka, Masamichi; Ishii, Kei; Yamada, Yoshifumi; Kobayashi, Kenji

    2006-11-10

    Fine and/or drastic tuning of capsule space has been attained by alteration of the hydrogen-bonding linker and/or hemispherical cavitand, respectively. Two molecules of tetracarboxyl-cavitand 1 or tetrakis(4-carboxyphenyl)-cavitand 2 as a hemisphere and four molecules of 2-aminopyrimidine (2-AP) or tetrahydro-2-pyrimidinone (THP) as an equatorial hydrogen-bonding linker self-assemble into a capsule [(1)2.(2-AP)4] (3), [(1)2.(THP)4] (4), [(2)2.(2-AP)4] (5), or [(2)2.(THP)4] (6), respectively, via 16 hydrogen bonds. These capsules provide isolated nanospace and can encapsulate one guest molecule (7-13) in solution. Each capsule has a different cavity size and shows particular guest selectivity on the competitive encapsulation experiments. PMID:17081009

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

    PubMed

    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

    2014-06-01

    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. PMID:24815319

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

    PubMed

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

    2016-03-18

    The nature of the intermolecular forces between water molecules is the same in small hydrogen-bonded clusters as in the bulk. The rotational spectra of the clusters therefore give insight into the intermolecular forces present in liquid water and ice. The water hexamer is the smallest water cluster to support low-energy structures with branched three-dimensional hydrogen-bond networks, rather than cyclic two-dimensional topologies. Here we report measurements of splitting patterns in rotational transitions of the water hexamer prism, and we used quantum simulations to show that they result from geared and antigeared rotations of a pair of water molecules. Unlike previously reported tunneling motions in water clusters, the geared motion involves the concerted breaking of two hydrogen bonds. Similar types of motion may be feasible in interfacial and confined water. PMID:26989250

  14. Effect of superalkali substituents on the strengths and properties of hydrogen and halogen bonds.

    PubMed

    Tian, Wenkai; Huang, Xin; Li, Qingzhong; Li, Wenzuo; Cheng, Jianbo; Gong, Baoan

    2013-03-01

    Quantum chemical calculations have been performed for the complexes Li(3)OCCX-Y (X = Cl, Br, H; Y = NH(3), H(2)O, H(2)S) and Li(3)OCN-X'Y' (X'Y' = ClF, BrCl, BrF, HF) to study the role of superalkalis in hydrogen and halogen bonds. The results show that the presence of an Li(3)O cluster in a Lewis acid weakens its acidity, while its presence in a Lewis base enhances its basicity. Furthermore, the latter effect is more prominent than the former one, and the presence of an Na(3)O cluster causes an even greater effect than Li(3)O. The strengths of hydrogen and halogen bonds were analyzed using molecular electrostatic potentials. The contributions of superalkalis to the strength of hydrogen and halogen bonds were elucidated by analyzing differences in electron density. PMID:23179773

  15. Non-covalent synthesis of supermicelles with complex architectures using spatially confined hydrogen-bonding interactions

    PubMed Central

    Li, Xiaoyu; Gao, Yang; Boott, Charlotte E.; Winnik, Mitchell A.; Manners, Ian

    2015-01-01

    Nature uses orthogonal interactions over different length scales to construct structures with hierarchical levels of order and provides an important source of inspiration for the creation of synthetic functional materials. Here, we report the programmed assembly of monodisperse cylindrical block comicelle building blocks with crystalline cores to create supermicelles using spatially confined hydrogen-bonding interactions. We also demonstrate that it is possible to further program the self-assembly of these synthetic building blocks into structures of increased complexity by combining hydrogen-bonding interactions with segment solvophobicity. The overall approach offers an efficient, non-covalent synthesis method for the solution-phase fabrication of a range of complex and potentially functional supermicelle architectures in which the crystallization, hydrogen-bonding and solvophobic interactions are combined in an orthogonal manner. PMID:26337527

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

    NASA Astrophysics Data System (ADS)

    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.

  17. Hydrogen-bond dynamics and Fermi resonance in high-pressure methane filled ice.

    PubMed

    Klug, D D; Tse, J S; Liu, Zhenxian; Hemley, Russell J

    2006-10-21

    High-pressure, variable temperature infrared spectroscopy and first-principles calculations on the methane filled ice structure (MH-III) at high pressures are used to investigate the vibrational dynamics related to pressure induced modifications in hydrogen bonding. Infrared spectroscopy of isotopically dilute solutions of H(2)O in D(2)O is employed together with first-principles calculations to characterize proton dynamics with the pressure induced shortening of hydrogen bonds. A Fermi resonance is identified and shown to dominate the infrared spectrum in the pressure region between 10 and 30 GPa. Significant differences in the effects of the Fermi resonance observed between 10 and 300 K arise from the double-well potential energy surface of the hydrogen bond and quantum effects associated with the proton dynamics. PMID:17059274

  18. Hydrogen-bond Dynamics and Fermi Resonance in High-pressure Methane Filled Ice

    SciTech Connect

    Klug,D.; Tse, J.; Liu, Z.; Hemley, R.

    2006-01-01

    High-pressure, variable temperature infrared spectroscopy and first-principles calculations on the methane filled ice structure (MH-III) at high pressures are used to investigate the vibrational dynamics related to pressure induced modifications in hydrogen bonding. Infrared spectroscopy of isotopically dilute solutions of H{sub 2}O in D{sub 2}O is employed together with first-principles calculations to characterize proton dynamics with the pressure induced shortening of hydrogen bonds. A Fermi resonance is identified and shown to dominate the infrared spectrum in the pressure region between 10 and 30 GPa. Significant differences in the effects of the Fermi resonance observed between 10 and 300 K arise from the double-well potential energy surface of the hydrogen bond and quantum effects associated with the proton dynamics.

  19. Monitoring the pH Triggered Collapse of Liposomes in the Far IR Hydrogen Bonding Continuum.

    PubMed

    Srour, Batoul; Erhard, Birgit; Süss, Regine; Hellwig, Petra

    2016-05-01

    Far infrared spectra of complex molecular structures like lipid membranes or proteins show large and broad continuum modes that include contributions of the internal hydrogen bonding of the assembled structures. Here we corroborate the pH triggered structural rearrangement in pH-sensitive liposomes with a clear shift of the far-infrared mode from 170 to 159 cm(-1). This spectral change was accompanied by the broadening of the hydrogen bonding signature by about 25 cm(-1) and correlates with the well-known hydrogen bonding dependent shifts of the ν(PO2(-))(as) vibration of the lipid headgroup in the mid infrared and with further shifts of functional group vibrations. Far infrared spectroscopy is thus a useful tool for the investigation of conformational changes in large molecular structures. PMID:27092567

  20. Probing Defects and Correlations in the Hydrogen-Bond Network of ab Initio Water.

    PubMed

    Gasparotto, Piero; Hassanali, Ali A; Ceriotti, Michele

    2016-04-12

    The hydrogen-bond network of water is characterized by the presence of coordination defects relative to the ideal tetrahedral network of ice, whose fluctuations determine the static and time-dependent properties of the liquid. Because of topological constraints, such defects do not come alone but are highly correlated coming in a plethora of different pairs. Here we discuss in detail such correlations in the case of ab initio water models and show that they have interesting similarities to regular and defective solid phases of water. Although defect correlations involve deviations from idealized tetrahedrality, they can still be regarded as weaker hydrogen bonds that retain a high degree of directionality. We also investigate how the structure and population of coordination defects is affected by approximations to the interatomic potential, finding that, in most cases, the qualitative features of the hydrogen-bond network are remarkably robust. PMID:26881726

  1. Bio-inspired carbon nanotube-polymer composite yarns with hydrogen bond-mediated lateral interactions.

    PubMed

    Beese, Allison M; Sarkar, Sourangsu; Nair, Arun; Naraghi, Mohammad; An, Zhi; Moravsky, Alexander; Loutfy, Raouf O; Buehler, Markus J; Nguyen, SonBinh T; Espinosa, Horacio D

    2013-04-23

    Polymer composite yarns containing a high loading of double-walled carbon nanotubes (DWNTs) have been developed in which the inherent acrylate-based organic coating on the surface of the DWNT bundles interacts strongly with poly(vinyl alcohol) (PVA) through an extensive hydrogen-bond network. This design takes advantage of a toughening mechanism seen in spider silk and collagen, which contain an abundance of hydrogen bonds that can break and reform, allowing for large deformation while maintaining structural stability. Similar to that observed in natural materials, unfolding of the polymeric matrix at large deformations increases ductility without sacrificing stiffness. As the PVA content in the composite increases, the stiffness and energy to failure of the composite also increases up to an optimal point, beyond which mechanical performance in tension decreases. Molecular dynamics (MD) simulations confirm this trend, showing the dominance of nonproductive hydrogen bonding between PVA molecules at high PVA contents, which lubricates the interface between DWNTs. PMID:23548065

  2. (+/-)-3-Oxocyclohexanecarboxylic and -acetic acids: contrasting hydrogen-bonding patterns in two homologous keto acids.

    PubMed

    Barcon, Alan; Brunskill, Andrew P J; Lalancette, Roger A; Thompson, Hugh W

    2002-03-01

    The crystal structures for the title compounds reveal fundamentally different hydrogen-bonding patterns. (+/-)-3-Oxocyclohexanecarboxylic acid, C(7)H(10)O(3), displays acid-to-ketone catemers having a glide relationship for successive components of the hydrogen-bonding chains which advance simultaneously by two cells in a and one in c [O...O = 2.683 (3) A and O-H...O = 166]. A pair of intermolecular close contacts exists involving the acid carbonyl group. The asymmetric unit in (+/-)-3-oxocyclohexaneacetic acid, C(8)H(12)O(3), utilizes only one of two available isoenthalpic conformers and its aggregation involves mutual hydrogen bonding by centrosymmetric carboxyl dimerization [O.O = 2.648 (3) A and O-H...O = 171]. Intermolecular close contacts exist for both the ketone and the acid carbonyl group. PMID:11870311

  3. HBNG: Graph theory based visualization of hydrogen bond networks in protein structures

    PubMed Central

    Tiwari, Abhishek; Tiwari, Vivek

    2007-01-01

    HBNG is a graph theory based tool for visualization of hydrogen bond network in 2D. Digraphs generated by HBNG facilitate visualization of cooperativity and anticooperativity chains and rings in protein structures. HBNG takes hydrogen bonds list files (output from HBAT, HBEXPLORE, HBPLUS and STRIDE) as input and generates a DOT language script and constructs digraphs using freeware AT and T Graphviz tool. HBNG is useful in the enumeration of favorable topologies of hydrogen bond networks in protein structures and determining the effect of cooperativity and anticooperativity on protein stability and folding. HBNG can be applied to protein structure comparison and in the identification of secondary structural regions in protein structures. Availability Program is available from the authors for non-commercial purposes. PMID:18084648

  4. The Delicate Balance of Hydrogen Bond Forces in D-Threoninol

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

    The molecule of D-threoninol has been studied using CP-FTMW spectroscopy. Despite the small size of this molecule, a great variety of conformations have been observed in the molecular expansion. With 2 OH groups and one NH_2 group, many possibilities for hydrogen bonding are anticipated. The multiple ways they can interact with each other make the analysis of its rotational spectrum challenging and only through an exhaustive conformational search and the comparison with the experimental rotational parameters and line strengths are we able to understand the complex nature of these interactions. In the 7 conformations already assigned, evidences for hydrogen bonded cycles and chains are revealed with dipole moment very sensitive to the configuration of the hydrogen bond.

  5. Hydrogen Bonding Between FNO and H2O: Structure and Energetics

    NASA Astrophysics Data System (ADS)

    Ting, Melodie; Peters, Nancy J. S.

    2009-09-01

    Nitrosyl fluoride, of some interest in atmospheric chemistry, has three atoms which could potentially serve as proton acceptors in the formation of hydrogen bonds. The optimized structure of FNO and H2O was determined at the MP4/6-31G** level of calculation. In the resulting structure, the hydrogen bonds at the fluorine with an energy of 5.15 kcal/mol, contrary to the prediction that less electronegative atoms make better proton acceptors/electron donors but consistent with results of proton affinity studies and with the contribution of a resonance structure with no bond between the N and F and a negative charge on the fluorine atom. The resulting structure also shows a significant increase in the length of the NF bond from 1.51 to 1.61 Å.

  6. Using equilibrium isotope effects to detect intramolecular OH/OH hydrogen bonds: structural and solvent effects.

    PubMed

    Vasquez, Thomas E; Bergset, Jon M; Fierman, Matthew B; Nelson, Alshakim; Roth, Joshua; Khan, Saeed I; O'Leary, Daniel J

    2002-03-27

    A comparative (1)H NMR study of partially deuterated 1,3- and 1,4-diols has demonstrated that intramolecular hydrogen bonds of different geometry can give rise to equilibrium isotope shifts of opposite sign in hydrogen-bond-accepting solvents such as DMSO-d(6), acetone-d(6), and THF-d(8). The sign inversion is interpreted in terms of the ability of solvent molecules to form competitive intermolecular hydrogen bonds with the diol and in terms of the limiting chemical shifts for the interior and exterior hydroxyl groups. Deuterium is shown to prefer the intermolecular solvent hydrogen bond by 10.9 +/- 0.5 cal/mol for 1,4-diol 3 dissolved in DMSO-d(6) at room temperature. Pyridine-d(5) is shown to be capable of amplifying positive (downfield) isotope shifts measured in DMSO-d(6), in some cases by as much as a factor of 3. Its use is demonstrated for the assignment of the syn or anti relative configuration of 2,4-pentanediol and for the amplification of isotope shifts used to detect intramolecular hydrogen bonds in alpha- and beta-cyclodextrin. Studies in apolar solvents such as CD(2)Cl(2) and benzene-d(6) reveal that the isotope shift is negative (upfield) for all hydrogen bond geometries studied. Larger isotope shifts are measured in benzene-d(6), and a rationale for this amplification is presented. The use of apolar solvents is particularly useful for assigning the syn or anti configuration of 2,4-pentanediol. PMID:11902884

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

    SciTech Connect

    Mackenzie, Rebecca B.; Dewberry, Christopher T.; Leopold, Kenneth R. E-mail: david.tew@bristol.ac.uk; Coulston, Emma; Cole, George C.; Legon, Anthony C. E-mail: david.tew@bristol.ac.uk Tew, David P. E-mail: david.tew@bristol.ac.uk

    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.

  8. Direct Addition Mechanism during the Catalytic Hydrogenation of Olefins over Platinum Surfaces.

    PubMed

    Dong, Yujung; Ebrahimi, Maryam; Tillekaratne, Aashani; Zaera, Francisco

    2016-07-01

    The mechanism of the hydrogenation of olefins catalyzed by metal surfaces was probed by using isotope labeling in conjunction with a high-flux effusive molecular beam setup capable of sustaining steady-state conversion under well-controlled ultrahigh vacuum (UHV). The unique conditions afforded by this instrument, namely, a single collision regime and impinging frequencies equivalent to pressures in the mTorr range, led to the clear identification of two competing pathways: a multiple H-D isotope exchange channel explained by the well-known Horiuti-Polanyi mechanism but with an unusually high probability for β-hydride elimination from the alkyl surface intermediate (versus its reductive elimination to the alkane), and a direct addition route that produces dideuterated alkanes selectively. The latter may follow an Eley-Rideal mechanism involving an adsorbate (either the olefin or the hydrogen/deuterium atoms resulting from dissociative adsorption of H2/D2) and a gas-phase molecule (the other reactant), or, alternatively, it could reflect the limited diffusion of the hydrogen atoms on the surface under catalytic conditions because of site blocking by the islands of strongly bonded carbonaceous (alkylidyne) layers present during catalysis. Regardless, our data clearly show that the distribution of alkane isotopologues obtained from the conversion of olefins with deuterium can deviate significantly from statistical expectations. PMID:27309969

  9. tert-Butyl Carbocation in Condensed Phases: Stabilization via Hyperconjugation, Polarization, and Hydrogen Bonding.

    PubMed

    Stoyanov, Evgenii S; Gomes, Gabriel dos Passos

    2015-08-13

    Despite the seeming similarity of the infrared (IR) spectra between tert-butyl cations (t-Bu(+)) in gaseous and condensed phases, there are important but so far unrecognized differences. The IR spectroscopic investigation of the hydrogen (H)-bonding of t-Bu(+) with the immediate environment together with the X-ray crystallographic data shows that one CH3 group of t-Bu(+) differs from the other two. In the Ar-tagged t-Bu(+) in vacuum, this group is predominantly polarized, showing three C-H stretch vibrations at 2913, 2965, and 3036 cm(-1) whereas the other two methyls are predominantly involved in strong hyperconjugation, yielding an intense triple IR band with a maximum at 2839 cm(-1). In a condensed phase, the bulk solvent effect promoted participation of the polarized CH3 group in additional hyperconjugation, decreasing its νCH3 frequencies by approximately 120 cm(-1), whereas frequencies of the other CH3 groups decreased by only ca. 4-10 cm(-1). This observation indicates that the influence of the condensed phase on t-Bu(+) stabilization is substantial. Thus, enhancement of H-bonding between t-Bu(+) and Anion(-) strengthens hyperconjugation and promotes further cation stabilization. PMID:26172244

  10. Hydrogen-bonding studies of amino acid side-chains with DNA base pairs

    NASA Astrophysics Data System (ADS)

    Deepa, P.; Kolandaivel, P.; Senthilkumar, K.

    2011-08-01

    The interactions of the amino acid side-chains arginine (ARG), aspartic acid (ASP), asparagine (ASN), lysine (LYS) and serine (SER) with nucleic acid base pairs have been investigated using theoretical methods. The interaction energy of the short intermolecular N-H ... N, N-H ... O, O-H ... O, O-H ... N, C-H ... O and C-H ... N hydrogen bonds present in both isolated base pairs and complexes and its role in providing stability to the complexes have been explored. The homonuclear interactions are found to be stronger than the heteronuclear interactions. An improper hydrogen bond has been observed for some of the N-H ... O and N-H ... N hydrogen-bond interactions with the contraction of the N-H bond varying from 0.001 to 0.0260 Å and the corresponding blue shift of the stretching frequency by 4-291 cm-1. Localized molecular orbital energy decomposition analysis (LMOEDA) reveals that the major contributions to the energetics are from the long-range polarization (PL) interaction, and the short-range attractive (ES, EX) and repulsive (REP) interactions. The Bader's atoms in molecules (AIM) theory shows good correlation for the electron density and its Laplacian at the bond critical points (BCP) with the N-H ... N and N-H ... O hydrogen-bond lengths in the complexes, and gives a proper explanation for the stability of the structure. The charge-transfer from the proton acceptor to the antibonding orbital of the X-H bond in the complexes was studied using natural bond orbital (NBO) analysis.

  11. The effect of additional etching and curing mechanism of composite resin on the dentin bond strength

    PubMed Central

    Lee, In-Su; Son, Sung-Ae; Hur, Bock; Kwon, Yong-Hoon

    2013-01-01

    PURPOSE The aim of this study was to evaluate the effects of additional acid etching and curing mechanism (light-curing or self-curing) of a composite resin on the dentin bond strength and compatibility of one-step self-etching adhesives. MATERIALS AND METHODS Sixteen human permanent molars were randomly divided into eight groups according to the adhesives used (All-Bond Universal: ABU, Clearfil S3 Bond: CS3), additional acid etching (additional acid etching performed: EO, no additional acid etching performed: EX), and composite resins (Filtek Z-250: Z250, Clearfil FII New Bond: CFNB). Group 1: ABU-EO-Z250, Group 2: ABU-EO-CFNB, Group 3: ABU-EX-Z250, Group 4: ABU-EX-CFNB, Group 5: CS3-EO-Z250, Group 6: CS3-EO-CFNB, Group 7: CS3-EX-Z250, Group 8: CS3-EX-CFNB. After bonding procedures, composite resins were built up on dentin surfaces. After 24-hour water storage, the teeth were sectioned to make 10 specimens for each group. The microtensile bond strength test was performed using a microtensile testing machine. The failure mode of the fractured specimens was examined by means of an optical microscope at ×20 magnification. The data was analyzed using a one-way ANOVA and Scheffe's post-hoc test (α=.05). RESULTS Additional etching groups showed significantly higher values than the no additional etching group when using All-Bond Universal. The light-cured composite resin groups showed significantly higher values than the self-cured composite resin groups in the Clearfil S3 Bond. CONCLUSION The additional acid etching is beneficial for the dentin bond strength when using low acidic one-step self-etch adhesives, and low acidic one-step self-etch adhesives are compatible with self-cured composite resin. The acidity of the one-step self-etch adhesives is an influencing factor in terms of the dentin bonding strength and incompatibility with a self-cured composite resin. PMID:24353889

  12. A molecular electrostatic potential analysis of hydrogen, halogen, and dihydrogen bonds.

    PubMed

    Mohan, Neetha; Suresh, Cherumuttathu H

    2014-03-01

    Hydrogen, halogen, and dihydrogen bonds in weak, medium and strong regimes (<1 to ∼ 60 kcal/mol) have been investigated for several intermolecular donor-acceptor (D-A) complexes at ab initio MP4//MP2 method coupled with atoms-in-molecules and molecular electrostatic potential (MESP) approaches. Electron density ρ at bond critical point correlates well with interaction energy (Enb) for each homogeneous sample of complexes, but its applicability to the entire set of complexes is not satisfactory. Analysis of MESP minimum (V(min)) and MESP at the nuclei (Vn) shows that in all D-A complexes, MESP of A becomes more negative and that of D becomes less negative suggesting donation of electrons from D to A leading to electron donor-acceptor (eDA) interaction between A and D. MESP based parameter ΔΔVn measures donor-acceptor strength of the eDA interactions as it shows a good linear correlation with Enb for all D-A complexes (R(2) = 0.976) except the strongly bound bridged structures. The bridged structures are classified as donor-acceptor-donor complexes. MESP provides a clear evidence for hydrogen, halogen, and dihydrogen bond formation and defines them as eDA interactions in which hydrogen acts as electron acceptor in hydrogen and dihydrogen bonds while halogen acts as electron acceptor in halogen bonds. PMID:24506527

  13. Hydrogen bonding and aqueous base dissolution behavior of hexafluoroisopropanol-bearing polymers

    NASA Astrophysics Data System (ADS)

    Ito, Hiroshi; Hinsberg, William D.; Rhodes, Larry F.; Chang, Chun

    2003-06-01

    The aqueous base dissolution behavior and hydrogen bonding interaction of polymers bearing hexafluoroisopropanol (HFA) as an acid group have been investigated. While pKa of HFA is similar to that of phenol, the dissolution rate of HFA polymers in aqueous base varies from one structure to another. Poly(norbornene hexafluoroisopropanol) (PNBHFA) dissolves in 0.26 tetramethylammonium hydroxide (TMAH) aqueous solution at a rate of 1,500-8,000 A/sec, which is not correlated to the number-average or weight-average molecular weight. Furthermore, PNGHFA exhibits a complex multi-stage dissolution kinetics in 0.21 N TMAH, depending on the molecular weight and molecular weight distribution. Hydrogen bonding of HFA polymers has been investigated using FTIR. Polynorbornene and polystyrene bearing HFA (PNBHFA and PSTHFA) are much less hydrogen-bonded than poly(4-hydroxystyrene)(PHOST). HFA-ester copolymers tend to have more free OH groups than a HOST/t-butyl acrylate copolymer. The carbonyl bond in 2-trifluoromethylacrylic units is less polarized and therefore less prone to hydrogen bonding with OH than C=O in (meth)acrylate units. The interaction of acid generators with the HFA group can be studied by 19F NMR. Both ionic iodonium and nonionic imidesulfonate acid generators interact strongly with HFA and inhibit the dissolution of HFA polymers in aqueous base while ionic acid generators are better dissolution inhibitors of phenolic resins.

  14. Structural and vibrational properties of betainium perchlorate monohydrate crystal and character of its hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Ilczyszyn, Marek; Godzisz, Dorota; Ilczyszyn, Maria M.

    2002-06-01

    Betainium perchlorate monohydrate crystal ((CH 3) 3NCH 2COOH)(ClO 4)·H 2O) undergoes a continuous (second order) phase transition at ca. 180 K. X-ray data and vibrational spectroscopy studies at different temperatures are used for description of the phase transition mechanism, as well as of hydrogen bonds formed by water in this molecular system. Perturbation of monomer water by various surroundings (water vapour, low-temperature matrices, solvents, betaine-acid crystals) and properties of triple hydrogen bonds to water oxygen atom are discussed.

  15. A temperature dependent infrared absorption study of strong hydrogen bonds in bis(glycinium)oxalate

    NASA Astrophysics Data System (ADS)

    Bhatt, Himal; Deo, M. N.; Murli, C.; Vishwakarma, S. R.; Chitra, R.; Sharma, Surinder M.

    2016-05-01

    We report infrared absorption studies on Bis(glycinium)oxalate, an organic complex of the simplest amino acid Glycine, under varying temperatures in the range 77 - 350 K. The measurements have been carried out in the spectral range 400 - 4000 cm-1 and the strongest O-H---O hydrogen bond, which plays a vital role in the structural stabilization, has been studied. Subtle changes in widths of modes and temperature dependent frequency variations have been observed near 250 K. The hydrogen bonding network remains stable in the entire temperature range. This is in contrast to its reported high pressure behavior.

  16. Metal-free, polyether-mediated H2-release from ammonia borane: roles of hydrogen bonding interactions in promoting dehydrogenation.

    PubMed

    Kim, Yongmin; Baek, Hyunjae; Lee, Jin Hee; Yeo, Shinyoung; Kim, Kibum; Hwang, Son-Jong; Eun, Bit; Nam, Suk Woo; Lim, Tae-Hoon; Yoon, Chang Won

    2013-12-01

    Polyetheral additives were found to be efficient promoters to enhance the rate of H2-release from ammonia borane (AB) at various temperatures. In particular, tetraethylene glycol dimethyl ether (T4EGDE, 29 wt% relative to AB + T4EGDE) exhibited significantly improved activities for AB dehydrogenation, with the material-based hydrogen storage capacity of 10.3 wt% at 125 °C within 40 min. In situ FT-IR spectroscopy indicated the formation of B-(cyclodiborazanyl)amino-borohydride (BCDB), borazine, and μ-aminodiborane as gaseous byproducts. In addition, (11)B nuclear magnetic resonance (NMR) spectroscopy further revealed that diammoniate of diborane (DADB) was initially formed to give polyaminoborane as liquid and/or solid spent-fuel, consistent with previous reports. Density Functional Theory (DFT) calculations suggested that hydrogen bonding interactions between AB and a polyetheral promoter initially played an important role in increasing the reactivity of B-H bonds of AB by transferring electron density from oxygen atoms of the promoter into B-H bonds of AB. These partially activated, hydridic B-H bonds were proposed to help promote the formation of diammoniate of diborane (DADB), which is considered as a reactive intermediate, eventually enhancing the rate of H2-release from AB. In addition, our in situ solid state (11)B magic angle spinning (MAS) NMR measurements further confirmed that the rate of DADB formation from AB with a small quantity of T4EGDE was found to be much faster than that of pristine AB even at 50 °C. This metal-free method for H2-release from AB with an added, small quantity of polyethers would be helpful to develop feasible hydrogen storage systems for long-term fuel cell applications. PMID:24068365

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

    NASA Astrophysics Data System (ADS)

    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. Tuning the mechanical properties of graphene oxide paper and its associated polymer nanocomposites by controlling cooperative intersheet hydrogen bonding.

    PubMed

    Compton, Owen C; Cranford, Steven W; Putz, Karl W; An, Zhi; Brinson, L Catherine; Buehler, Markus J; Nguyen, SonBinh T

    2012-03-27

    The mechanical properties of pristine graphene oxide paper and paper-like films of polyvinyl alcohol (PVA)-graphene oxide nanocomposite are investigated in a joint experimental-theoretical and computational study. In combination, these studies reveal a delicate relationship between the stiffness of these papers and the water content in their lamellar structures. ReaxFF-based molecular dynamics (MD) simulations elucidate the role of water molecules in modifying the mechanical properties of both pristine and nanocomposite graphene oxide papers, as bridge-forming water molecules between adjacent layers in the paper structure enhance stress transfer by means of a cooperative hydrogen-bonding network. For graphene oxide paper at an optimal concentration of ~5 wt % water, the degree of cooperative hydrogen bonding within the network comprising adjacent nanosheets and water molecules was found to optimally enhance the modulus of the paper without saturating the gallery space. Introducing PVA chains into the gallery space further enhances the cooperativity of this hydrogen-bonding network, in a manner similar to that found in natural biomaterials, resulting in increased stiffness of the composite. No optimal water concentration could be found for the PVA-graphene oxide nanocomposite papers, as dehydration of these structures continually enhances stiffness until a final water content of ~7 wt % (additional water cannot be removed from the system even after 12 h of annealing). PMID:22188595

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

    SciTech Connect

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

    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. Hydrogen bond dynamics of superheated water and methanol by ultrafast IR-pump and EUV-photoelectron probe spectroscopy.

    PubMed

    Vöhringer-Martinez, E; Link, O; Lugovoy, E; Siefermann, K R; Wiederschein, F; Grubmüller, H; Abel, B

    2014-09-28

    Supercritical water and methanol have recently drawn much attention in the field of green chemistry. It is crucial to an understanding of supercritical solvents to know their dynamics and to what extent hydrogen (H) bonds persist in these fluids. Here, we show that with femtosecond infrared (IR) laser pulses water and methanol can be heated to temperatures near and above their critical temperature Tc and their molecular dynamics can be studied via ultrafast photoelectron spectroscopy at liquid jet interfaces with high harmonics radiation. As opposed to previous studies, the main focus here is the comparison between the hydrogen bonded systems of methanol and water and their interpretation by theory. Superheated water initially forms a dense hot phase with spectral features resembling those of monomers in gas phase water. On longer timescales, this phase was found to build hot aggregates, whose size increases as a function of time. In contrast, methanol heated to temperatures near Tc initially forms a broad distribution of aggregate sizes and some gas. These experimental features are also found and analyzed in extended molecular dynamics simulations. Additionally, the simulations enabled us to relate the origin of the different behavior of these two hydrogen-bonded liquids to the nature of the intermolecular potentials. The combined experimental and theoretical approach delivers new insights into both superheated phases and may contribute to understand their different chemical reactivities. PMID:25102451

  1. Effect of additional etching and ethanol-wet bonding on the dentin bond strength of one-step self-etch adhesives

    PubMed Central

    Ahn, Joonghee; Jung, Kyoung-Hwa; Son, Sung-Ae; Hur, Bock; Kwon, Yong-Hoon

    2015-01-01

    Objectives This study examined the effects of additional acid etching on the dentin bond strength of one-step self-etch adhesives with different compositions and pH. The effect of ethanol wetting on etched dentin bond strength of self-etch adhesives was also evaluated. Materials and Methods Forty-two human permanent molars were classified into 21 groups according to the adhesive types (Clearfil SE Bond [SE, control]; G-aenial Bond [GB]; Xeno V [XV]; Beauti Bond [BB]; Adper Easy Bond [AE]; Single Bond Universal [SU]; All Bond Universal [AU]), and the dentin conditioning methods. Composite resins were placed on the dentin surfaces, and the teeth were sectioned. The microtensile bond strength was measured, and the failure mode of the fractured specimens was examined. The data were analyzed statistically using two-way ANOVA and Duncan's post hoc test. Results In GB, XV and SE (pH ≤ 2), the bond strength was decreased significantly when the dentin was etched (p < 0.05). In BB, AE and SU (pH 2.4 - 2.7), additional etching did not affect the bond strength (p > 0.05). In AU (pH = 3.2), additional etching increased the bond strength significantly (p < 0.05). When adhesives were applied to the acid etched dentin with ethanol-wet bonding, the bond strength was significantly higher than that of the no ethanol-wet bonding groups, and the incidence of cohesive failure was increased. Conclusions The effect of additional acid etching on the dentin bond strength was influenced by the pH of one-step self-etch adhesives. Ethanol wetting on etched dentin could create a stronger bonding performance of one-step self-etch adhesives for acid etched dentin. PMID:25671215

  2. Explosives sensing by using electron-rich supramolecular polymers: role of intermolecular hydrogen bonding in significant enhancement of sensitivity.

    PubMed

    Gole, Bappaditya; Song, Wentao; Lackinger, Markus; Mukherjee, Partha Sarathi

    2014-10-13

    We demonstrate here that supramolecular interactions enhance the sensitivity towards detection of electron-deficient nitro-aromatic compounds (NACs) over discrete analogues. NACs are the most commonly used explosive ingredients and are common constituents of many unexploded landmines used during World War II. In this study, we have synthesised a series of pyrene-based polycarboxylic acids along with their corresponding discrete esters. Due to the electron richness and the fluorescent behaviour of the pyrene moiety, all the compounds act as sensors for electron-deficient NACs through a fluorescence quenching mechanism. A Stern-Volmer quenching constant determination revealed that the carboxylic acids are more sensitive than the corresponding esters towards NACs in solution. The high sensitivity of the acids was attributed to supramolecular polymer formation through hydrogen bonding in the case of the acids, and the enhancement mechanism is based on an exciton energy migration upon excitation along the hydrogen-bond backbone. The presence of intermolecular hydrogen bonding in the acids in solution was established by solvent-dependent fluorescence studies and dynamic light scattering (DLS) experiments. In addition, the importance of intermolecular hydrogen bonds in solid-state sensing was further explored by scanning tunnelling microscopy (STM) experiments at the liquid-solid interface, in which structures of self-assembled monolayer of the acids and the corresponding esters were compared. The sensitivity tests revealed that these supramolecular sensors can even detect picric acid and trinitrotoluene in solution at levels as low as parts per trillion (ppt), which is much below the recommended permissible level of these constituents in drinking water. PMID:25187022

  3. Two different hydrogen bond donor ligands together: a selectivity improvement in organometallic {Re(CO)3} anion hosts.

    PubMed

    Ion, Laura; Nieto, Sonia; Pérez, Julio; Riera, Lucía; Riera, Víctor; Díaz, Jesús; López, Ramón; Anderson, Kirsty M; Steed, Jonathan W

    2011-09-01

    Rhenium(I) compounds [Re(CO)(3)(Hdmpz)(2)(ampy)]BAr'(4) and [Re(CO)(3)(N-MeIm)(2)(ampy)]BAr'(4) (Hdmpz = 3,5-dimethylpyrazole, N-MeIm = N-methylimidazole, ampy = 2-aminopyridine or 3-aminopyridine) have been prepared stepwise as the sole reaction products in good yields. The cationic complexes feature two different types of hydrogen bond donor ligands, and their anion binding behavior has been studied both in solution and in the solid state. Compounds with 2-ampy ligands are labile in the presence of nearly all of the anions tested. The X-ray structure of the complex [Re(CO)(3)(Hdmpz)(2)(ampy)](+) (2) shows that the 2-ampy ligand is metal-coordinated through the amino group, a fact that can be responsible for its labile character. The 3-ampy derivatives (coordinated through the pyridinic nitrogen atom) are stable toward the addition of several anions and are more selective anion hosts than their tris(pyrazole) or tris(imidazole) counterparts. This selectivity is higher for compound [Re(CO)(3)(N-MeIm)(2)(MeNA)]BAr'(4) (5·BAr'(4), MeNA = N-methylnicotinamide) that features an amido moiety, which is a better hydrogen bond donor than the amino group. Some of the receptor-anion adducts have been characterized in the solid state by X-ray diffraction, showing that both types of hydrogen bond donor ligands of the cationic receptor participate in the interaction with the anion hosts. DFT calculations suggest that coordination of the ampy ligands is more favorable through the amino group only for the cationic complex 2, as a consequence of the existence of a strong intramolecular hydrogen bond. In all other cases, the pyridinic coordination is clearly favored. PMID:21834508

  4. Cooperativity Assisted Shortening of Hydrogen Bonds in Crystalline Oxalic Acid Dihydrate: DFT and NBO Model Studies.

    PubMed

    Stare, Jernej; Hadži, Dušan

    2014-04-01

    The distance of ∼2.49 Å separating the carboxylic OH oxygen from the water oxygen atom in the α-polymorph of crystalline oxalic acid dihydrate is by ∼0.1 Å shorter than the average distance in carboxylic acid monohydrates. It is also by ∼0.2 Å shorter than the corresponding distance presently calculated for the heterotrimer consisting of one acid and two water molecules. The large difference between RO···O in the heterotrimer and in the crystal is attributed to the cooperative effect in the latter; this is supported by calculations carried out on clusters constituted of an increasing number of acid and water molecules. The present DFT calculations with geometry optimization include seven isolated model clusters, the largest of which contains five acid and eight water molecules. The RO···O of the short hydrogen bond shortens progressively with increasing the number of cluster constituents; in the largest cluster, it reaches 2.50 Å. This is remarkably close to both the experimental distance as well as to the distance obtained by the periodic DFT calculation. The electronic effects were studied by Natural Bond Orbital analysis, revealing an enhancement of hydrogen bonding on extending the network by increased polarization of the carbonyl group and by the increased delocalization interaction between the lone electron pair on the acceptor oxygen atom and the OH antibond orbital. The formation of circular motifs appears to be the most important factor in the cooperative shortening of the hydrogen bonds. In agreement with the measured hydrogen bond distances, inspection of the electron density reveals a notable difference in hydrogen bond shrinking tendency between the two known polymorphs of the title system. PMID:26580388

  5. Hydrogen-bond-reversal symmetry and its violation in ice nanotubes.

    PubMed

    Kirov, Mikhail V

    2016-05-01

    Recently, a new type of generalized symmetry of ice structures was introduced which takes into account the change of direction of all hydrogen bonds. The energy nonequivalence of pairs of configurations with opposite direction of all hydrogen bonds was established in the course of computer simulation of bilayer ice and other four-coordinated structures without `dangling' hydrogen atoms. In this article, the results of detailed investigations of the violation of the hydrogen-bond-reversal symmetry in ice nanotubes consisting of stacked n-membered rings are presented. A comprehensive classification of all possible hydrogen-bonding configurations and their division into two classes (antisymmetrical and non-antisymmetrical) are given. Attention is focused on the most stable configurations that have no longitudinally arranged water molecules. This restriction made the asymmetry very difficult to find. For example, it was established that the asymmetry (non-antisymmetrical configurations) in ice nanotubes with square, pentagonal and hexagonal cross sections appears only when the number of transverse rings in the unit cell is more than six. It is shown that this is related to the well known combinatorial problem of enumerating the symmetry-distinct necklaces of black and white beads. It was found that, among the ice nanotubes that had been considered, hydrogen-bond-reversal asymmetry is most conspicuous in wide nanotubes such as heptagonal and octagonal. In this case the asymmetry is observed for unit cells of any length. In order to verify the results of the symmetry analysis and to confirm the energy nonequivalence of some (non-antisymmetrical) configurations, approximate calculations of the binding energy have been performed using the package TINKER. PMID:27126117

  6. Neutron diffraction study of hydrogen-bond symmetrization in δ-AlOOD

    NASA Astrophysics Data System (ADS)

    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.

  7. Computational insights into the photocyclization of diclofenac in solution: effects of halogen and hydrogen bonding.

    PubMed

    Bani-Yaseen, Abdulilah Dawoud

    2016-08-21

    The effects of noncovalent interactions, namely halogen and hydrogen bonding, on the photochemical conversion of the photosensitizing drug diclofenac (DCF) in solution were investigated computationally. Both explicit and implicit solvent effects were qualitatively and quantitatively assessed employing the DFT/6-31+G(d) and SQM(PM7) levels of theory. Full geometry optimizations were performed in solution for the reactant DCF, hypothesized radical-based intermediates, and the main product at both levels of theories. Notably, in good agreement with previous experimental results concerning the intermolecular halogen bonding of DCF, the SQM(PM7) method revealed different values for d(ClO, Å) and ∠(C-ClO, °) for the two chlorine-substituents of DCF, with values of 2.63 Å/162° and 3.13 Å/142° for the trans and cis orientations, respectively. Employing the DFT/6-31+G(d) method with implicit solvent effects was not conclusive; however, explicit solvent effects confirmed the key contribution of hydrogen and halogen bonding in stabilizing/destabilizing the reactant and hypothesized intermediates. Interestingly, the obtained results revealed that a protic solvent such as water can increase the rate of photocyclization of DCF not only through hydrogen bonding effects, but also through halogen bonding. Furthermore, the atomic charges of atoms majorly involved in the photocyclization of DCF were calculated using different methods, namely Mulliken, Hirshfeld, and natural bond orbital (NBO). The obtained results revealed that in all cases there is a notable nonequivalency in the noncovalent intermolecular interactions of the two chlorine substituents of DCF and the radical intermediates with the solvent, which in turn may account for the discrepancy of their reactivity in different media. These computational results provide insight into the importance of halogen and hydrogen bonding throughout the progression of the photochemical conversion of DCF in solution. PMID:27424600

  8. Anticooperativity of FHF hydrogen bonds in clusters of the type F- × (HF)n, RF × (HF)n and XF × (HF)n, R = alkyl and X = H, Br, Cl, F

    NASA Astrophysics Data System (ADS)

    Kucherov, S. Yu.; Bureiko, S. F.; Denisov, G. S.

    2016-02-01

    Properties of twenty five hydrogen-bonded complexes, namely, F- × (HF)n (n = 1-6), RF × (HF)n (R = t-Bu, i-Pr, Et, Me; n = 1-3), XF × (HF)n (X = H, Br, Cl; n = 1-2), and FF…HF with the hydrogen bond energy varying in a wide range have been calculated using ab initio methods at the MP2/6-31++G** level. For the first time, the energies, geometrical parameters and vibrational frequencies are obtained for the series of clusters, where the bonding character changes from covalent to van der Waals on the variation of proton-acceptor ability of the base, and the energies are in the range of 45-1 kcal/mol. The mutual influence of multiple hydrogen bonds of F…HF type in clusters, in which a fluorine anion or an atom participates in hydrogen bond formation as the acceptor, is systematically investigated. The relative changes in the values of the considered parameters on the sequential addition of an HF molecule (anticooperativity) were determined. It was shown that non-additivity of the interaction is most strongly pronounced in the energy and vibrational frequency values, geometrical parameters of hydrogen bonds are less sensitive to the mutual influence. The anticooperative effect is more pronounced on the hydrogen bridge length R(F...F) than on the geometry of proton donor r(HF). The hydrogen bond formation and the increase of the number n of ligands lead to successive lengthening of the r(XF) bond adjacent to the hydrogen bridge. The length of an XF bond changes stronger on formation of each hydrogen bond than the HF bond length.

  9. Unconventional hydrogen bonding to organic ions in the gas phase: Stepwise association of hydrogen cyanide with the pyridine and pyrimidine radical cations and protonated pyridine

    SciTech Connect

    Hamid, Ahmed M.; El-Shall, M. Samy; Hilal, Rifaat; Elroby, Shaaban; Aziz, Saadullah G.

    2014-08-07

    Equilibrium thermochemical measurements using the ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes for the stepwise association of HCN molecules with the pyridine and pyrimidine radical cations forming the C{sub 5}H{sub 5}N{sup +·}(HCN){sub n} and C{sub 4}H{sub 4}N{sub 2}{sup +·}(HCN){sub n} clusters, respectively, with n = 1–4. For comparison, the binding of 1–4 HCN molecules to the protonated pyridine C{sub 5}H{sub 5}NH{sup +}(HCN){sub n} has also been investigated. The binding energies of HCN to the pyridine and pyrimidine radical cations are nearly equal (11.4 and 12.0 kcal/mol, respectively) but weaker than the HCN binding to the protonated pyridine (14.0 kcal/mol). The pyridine and pyrimidine radical cations form unconventional carbon-based ionic hydrogen bonds with HCN (CH{sup δ+}⋯NCH). Protonated pyridine forms a stronger ionic hydrogen bond with HCN (NH{sup +}⋯NCH) which can be extended to a linear chain with the clustering of additional HCN molecules (NH{sup +}⋯NCH··NCH⋯NCH) leading to a rapid decrease in the bond strength as the length of the chain increases. The lowest energy structures of the pyridine and pyrimidine radical cation clusters containing 3-4 HCN molecules show a strong tendency for the internal solvation of the radical cation by the HCN molecules where bifurcated structures involving multiple hydrogen bonding sites with the ring hydrogen atoms are formed. The unconventional H-bonds (CH{sup δ+}⋯NCH) formed between the pyridine or the pyrimidine radical cations and HCN molecules (11–12 kcal/mol) are stronger than the similar (CH{sup δ+}⋯NCH) bonds formed between the benzene radical cation and HCN molecules (9 kcal/mol) indicating that the CH{sup δ+} centers in the pyridine and pyrimidine radical cations have more effective charges than in the benzene radical cation.

  10. Neural Plasticity and Memory: Is Memory Encoded in Hydrogen Bonding Patterns?

    PubMed

    Amtul, Zareen; Rahman, Atta-Ur

    2016-02-01

    Current models of memory storage recognize posttranslational modification vital for short-term and mRNA translation for long-lasting information storage. However, at the molecular level things are quite vague. A comprehensive review of the molecular basis of short and long-lasting synaptic plasticity literature leads us to propose that the hydrogen bonding pattern at the molecular level may be a permissive, vital step of memory storage. Therefore, we propose that the pattern of hydrogen bonding network of biomolecules (glycoproteins and/or DNA template, for instance) at the synapse is the critical edifying mechanism essential for short- and long-term memories. A novel aspect of this model is that nonrandom impulsive (or unplanned) synaptic activity functions as a synchronized positive-feedback rehearsal mechanism by revising the configurations of the hydrogen bonding network by tweaking the earlier tailored hydrogen bonds. This process may also maintain the elasticity of the related synapses involved in memory storage, a characteristic needed for such networks to alter intricacy and revise endlessly. The primary purpose of this review is to stimulate the efforts to elaborate the mechanism of neuronal connectivity both at molecular and chemical levels. PMID:25168338

  11. Nonlinear Spectroscopy Study of Vibrational Self-Trapping in Hydrogen Bonded Crystals

    NASA Astrophysics Data System (ADS)

    Edler, Julian; Hamm, Peter

    Femtosecond pump probe spectroscopy proves that self-trapping occurs in the NH and amide I band of crystalline acetanilide (ACN). The phonon modes that mediate the self-trapping are identified. Comparison between ACN and N-methylacetamide, both model systems for proteins, shows that self-trapping is a common feature in hydrogen bonded systems.

  12. Self-sorting regioisomers through the hierarchical organization of hydrogen-bonded rosettes.

    PubMed

    Aratsu, Keisuke; Prabhu, Deepak D; Iwawaki, Hidetaka; Lin, Xu; Yamauchi, Mitsuaki; Karatsu, Takashi; Yagai, Shiki

    2016-07-01

    The self-assembly of two regioisomeric hydrogen-bonding naphthalenes was studied in mixed states in different polarity solvents. The regioisomers co-assemble to form heteromeric rosettes in chloroform. Upon injecting this solution into methylcyclohexane the heteromeric rosettes kinetically form amorphous aggregates, which over time differentiate into thermodynamically stable distinct nanostructures through self-sorting. PMID:27211509

  13. A PYP chromophore acts as a 'photoacid' in an isolated hydrogen bonded complex.

    PubMed

    Andersen, Lars H; Bochenkova, Anastasia V; Houmøller, Jørgen; Kiefer, Hjalte V; Lattouf, Elie; Stockett, Mark H

    2016-04-21

    The light-induced response of a neutral Photoactive Yellow Protein chromophore in a hydrogen-bonded complex with a proton acceptor has been studied by dual-detection action absorption spectroscopy and density functional theory. We show that the chromophore is a 'photoacid' and that ultrafast excited-state proton transfer might be operative in an isolated complex. PMID:27009407

  14. Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

    PubMed Central

    Sigala, Paul A.; Fafarman, Aaron T.; Schwans, Jason P.; Fried, Stephen D.; Fenn, Timothy D.; Caaveiro, Jose M. M.; Pybus, Brandon; Ringe, Dagmar; Petsko, Gregory A.; Boxer, Steven G.; Herschlag, Daniel

    2013-01-01

    Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated site-specific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol–Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations. PMID:23798390

  15. Adsorption of nucleobase pairs on hexagonal boron nitride sheet: hydrogen bonding versus stacking.

    PubMed

    Ding, Ning; Chen, Xiangfeng; Wu, Chi-Man Lawrence; Li, Hui

    2013-07-14

    The adsorption of hydrogen-bonded and stacked nucleobase pairs on the hexagonal boron nitride (h-BN) surface was studied by density functional theory and molecular dynamics methods. Eight types of nucleobase pairs (i.e., GG, AA, TT, CC, UU, AT, GC, and AU) were chosen as the adsorbates. The adsorption configurations, interaction energies, and electronic properties of the nucleobase pair on the h-BN surface were obtained and compared. The density of states analysis result shows that both the hydrogen-bonded and stacked nucleobase pairs were physisorbed on h-BN with minimal charge transfer. The hydrogen-bonded base pairs lying on the h-BN surface are significantly more stable than the stacked forms in both the gas and water phase. The molecular dynamics simulation result indicates that h-BN possessed high sensitivity for the nucleobases and the h-BN surface adsorption could revert the base pair interaction from stacking back to hydrogen bonding in aqueous environment. The h-BN surface could immobilize the nucleobases on its surface, which suggests the use of h-BN has good potential in DNA/RNA detection biosensors and self-assembly nanodevices. PMID:23689542

  16. Spectroscopic identification of ethanol-water conformers by large-amplitude hydrogen bond librational modes.

    PubMed

    Andersen, J; Heimdal, J; Wugt Larsen, R

    2015-12-14

    The far-infrared absorption spectra have been recorded for hydrogen-bonded complexes of water with ethanol embedded in cryogenic neon matrices at 2.8 K. The partial isotopic H/D-substitution of the ethanol subunit enabled by a dual inlet deposition procedure enables the observation and unambiguous assignment of the intermolecular high-frequency out-of-plane and the low-frequency in-plane donor OH librational modes for two different conformations of the mixed binary ethanol/water complex. The resolved donor OH librational bands confirm directly previous experimental evidence that ethanol acts as the O⋯HO hydrogen bond acceptor in the two most stable conformations. In the most stable conformation, the water subunit forces the ethanol molecule into its less stable gauche configuration upon dimerization owing to a cooperative secondary weak O⋯HC hydrogen bond interaction evidenced by a significantly blue-shift of the low-frequency in-plane donor OH librational band origin. The strong correlation between the low-frequency in-plane donor OH librational motion and the secondary intermolecular O⋯HC hydrogen bond is demonstrated by electronic structure calculations. The experimental findings are further supported by CCSD(T)-F12/aug-cc-pVQZ calculations of the conformational energy differences together with second-order vibrational perturbation theory calculations of the large-amplitude donor OH librational band origins. PMID:26671383

  17. Hydrogen-Bond Network Breakage as a First Step to Isopropanol Crystallization

    NASA Astrophysics Data System (ADS)

    Sanz, A.; Jiménez-Ruiz, M.; Nogales, A.; Martín Y Marero, D.; Ezquerra, T. A.

    2004-07-01

    Here we present an experimental study of isopropanol crystallization in real time by means of a novel setup combining simultaneously structural measurements with dynamical techniques. By coupling time resolved neutron diffraction and dielectric spectroscopy experiments we demonstrate that a breakage of the hydrogen-bond network is a precursor step for the crystallization of isopropanol.

  18. The nature of the hydrogen bond: A synthesis from the interacting quantum atoms picture

    NASA Astrophysics Data System (ADS)

    Martín Pendás, A.; Blanco, M. A.; Francisco, E.

    2006-11-01

    The interacting quantum atoms approach [IQA, as presented by Blanco et al., J. Chem. Theory Comput. 1, 1096 (2005)] is applied to standard hydrogen bonded dimers. IQA is an interpretation tool based on a real space energy decomposition scheme fully consistent with the quantum theory of atoms in molecules. It provides a partition of every physical term present in the Hamiltonian into atomic and interatomic contributions. The procedure is orbital-free and self-contained, needing neither external references nor artificial intermediate states. Binding is the result of a competition between the destabilizing deformations suffered by the interacting fragments upon interaction and the stabilizing interaction energy itself. According to IQA, there is no incompatibility between the prevalent electrostatic image of hydrogen bonded systems and that favoring important covalent contributions. Depending on how we gather the different energetic terms, we may recover electrostatic or covalent pictures from the same underlying quantum mechanical description. Our results show that the nonclassical contributions to hydrogen bonding are spatially localized, involving only the H atom and its two nearest neighbors. IQA is well suited as a comparative tool. Its thin energetic decomposition allows us to recover exactly (or to a very good approximation) the quantities of the most widely used energy decomposition schemes. Such a comparison sheds light on the virtues and faults of the different methods and on the origin of the 50years old debate regarding the covalent/electrostatic nature of the hydrogen bond.

  19. Ultrafast memory loss and energy redistribution in the hydrogen bond network of liquid H2O

    NASA Astrophysics Data System (ADS)

    Cowan, M. L.; Bruner, B. D.; Huse, N.; Dwyer, J. R.; Chugh, B.; Nibbering, E. T. J.; Elsaesser, T.; Miller, R. J. D.

    2005-03-01

    Many of the unusual properties of liquid water are attributed to its unique structure, comprised of a random and fluctuating three-dimensional network of hydrogen bonds that link the highly polar water molecules. One of the most direct probes of the dynamics of this network is the infrared spectrum of the OH stretching vibration, which reflects the distribution of hydrogen-bonded structures and the intermolecular forces controlling the structural dynamics of the liquid. Indeed, water dynamics has been studied in detail, most recently using multi-dimensional nonlinear infrared spectroscopy for acquiring structural and dynamical information on femtosecond timescales. But owing to technical difficulties, only OH stretching vibrations in D2O or OD vibrations in H2O could be monitored. Here we show that using a specially designed, ultrathin sample cell allows us to observe OH stretching vibrations in H2O. Under these fully resonant conditions, we observe hydrogen bond network dynamics more than one order of magnitude faster than seen in earlier studies that include an extremely fast sweep in the OH frequencies on a 50-fs timescale and an equally fast disappearance of the initial inhomogeneous distribution of sites. Our results highlight the efficiency of energy redistribution within the hydrogen-bonded network, and that liquid water essentially loses the memory of persistent correlations in its structure within 50fs.

  20. Viscosity of Water under Electric Field: Anisotropy Induced by Redistribution of Hydrogen Bonds.

    PubMed

    Zong, Diyuan; Hu, Han; Duan, Yuanyuan; Sun, Ying

    2016-06-01

    The viscosity of water under an external electric field of 0.00-0.90 V/nm was studied using both molecular dynamics simulations and atomistic modeling accounting for intermolecular potentials. For all temperatures investigated, the water viscosity becomes anisotropic under an electric field: the viscosity component parallel to the field increases monotonically with the field strength, E, while the viscosity perpendicular to the field first decreases and then increases with E. This anisotropy is believed to be mainly caused by the redistribution of hydrogen bonds under the electric field. The preferred orientation of hydrogen bonds along the field direction leads to an increase of the energy barrier of a water molecule to its neighboring site, and hence increases the viscosity in that direction. However, the probability of hydrogen bonds perpendicular to the electric field decreases with E, together with the increase of the average number of hydrogen bonds per molecule, causing the perpendicular component of water viscosity to first decrease and then increase with the electric field. PMID:27163345