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Sample records for hydrogen bond lifetimes

  1. 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

  2. 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.

  3. 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

  4. 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.

  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. 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

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. Effect of Superalloy Substrate and Bond Coating on TBC Lifetime

    SciTech Connect

    Pint, Bruce A; Haynes, James A; Zhang, Ying

    2010-01-01

    Several different single-crystal superalloys were coated with different bond coatings to study the effect of composition on the cyclic oxidation lifetime of an yttria-stabilized zirconia (YSZ) top coating deposited by electron beam physical vapor deposition from a commercial source. Three different superalloys were coated with a 7 {micro}m Pt layer that was diffused into the surface prior to YSZ deposition. One of the superalloys, N5, was coated with a low activity, Pt-modified aluminide coating and Pt-diffusion coatings with 3 and 7 {micro}m of Pt. Three coatings of each type were furnace cycled to failure in 1 h cycles at 1150 C to assess average coating lifetime. The 7 {micro}m Pt diffusion coating on N5 had an average YSZ coating lifetime >50% higher than a Pt-modified aluminide coating on N5. Without a YSZ coating, the Pt-modified aluminide coating on N5 showed the typical surface deformation during cycling, however, the deformation was greatly reduced when constrained by the YSZ coating. The 3 {micro}m Pt diffusion coating had a similar average lifetime as the Pt-modified aluminide coating but a much wider scatter. The Pt diffusion bond coating on superalloy X4 containing Ti exhibited the shortest YSZ coating lifetime, this alloy-coating combination also showed the worst alumina scale adhesion without a YSZ coating. The third generation superalloy N6 exhibited the longest coating lifetime with a 7 {micro}m Pt diffusion coating.

  13. 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

  14. 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.

  15. 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...

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. Geometric phases causing lifetime modifications of metastable states of hydrogen

    NASA Astrophysics Data System (ADS)

    Trappe, Martin-Isbjörn; Augenstein, Peter; DeKieviet, Maarten; Gasenzer, Thomas; Nachtmann, Otto

    2016-04-01

    Externally applied electromagnetic fields in general have an influence on the width of atomic spectral lines. The decay rates of atomic states can also be affected by the geometry of an applied field configuration giving rise to an imaginary geometric phase. A specific chiral electromagnetic field configuration is presented which geometrically modifies the lifetimes of metastable states of hydrogen. We propose to extract the relevant observables in a realistic longitudinal atomic beam spin-echo apparatus which allows the initial and final fluxes of the metastable atoms to be compared with each other interferometrically. A geometry-induced change in lifetimes at the 5%-level is found, an effect large enough to be observed in an available experiment.

  1. 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.

  2. 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.

  3. 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.

  4. 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/

  5. 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.

  6. Effects of cellular viscoelasticity in lifetime extraction of single receptor-ligand bonds.

    PubMed

    Gupta, V K

    2015-06-01

    Single-molecule force spectroscopy is widely used to determine kinetic parameters of dissociation by analyzing bond rupture data obtained via applying mechanical force to cells, capsules, and beads that are attached to an intermolecular bond. The bond rupture data are obtained in experiments either at a constant force or at a constant loading rate. We explore the effect of cellular viscoelasticity in constant-force experiments. Specifically, we perform Monte Carlo simulations of bond rupture at a given constant force to obtain the bond lifetime as a function of force in the absence and in the presence of bond force modulation due to cellular viscoelasticity, to explore its effect on the bond lifetime. PMID:26172730

  7. Effects of cellular viscoelasticity in lifetime extraction of single receptor-ligand bonds

    NASA Astrophysics Data System (ADS)

    Gupta, V. K.

    2015-06-01

    Single-molecule force spectroscopy is widely used to determine kinetic parameters of dissociation by analyzing bond rupture data obtained via applying mechanical force to cells, capsules, and beads that are attached to an intermolecular bond. The bond rupture data are obtained in experiments either at a constant force or at a constant loading rate. We explore the effect of cellular viscoelasticity in constant-force experiments. Specifically, we perform Monte Carlo simulations of bond rupture at a given constant force to obtain the bond lifetime as a function of force in the absence and in the presence of bond force modulation due to cellular viscoelasticity, to explore its effect on the bond lifetime.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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

  4. Femtosecond two-dimensional infrared spectroscopy of synthetic hydrogen-bonded wires: From homogeneous to inhomogeneous dynamics

    NASA Astrophysics Data System (ADS)

    Knop, Stephan; Olschewski, Martin; Vöhringer, Peter

    2013-03-01

    Femtosecond two-dimensional infrared (2DIR) spectroscopy was carried out on stereo-selectively synthesized poly-alcohols featuring a quasi-linear array of hydrogen-bonds. From the 2DIR spectra pump-frequency-dependent vibrational lifetimes are extracted, which in turn reflect the strength of the coupling between the hydroxyls constituting the H-bonded chain. The line-broadening dynamics reflect uniquely the conformational control of the scaffold supporting the H-bond wire and the resulting structural flexibility of the hydrogen-bond network.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. 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

  14. Hydrogen-bonded semiconducting pigments for air-stable field-effect transistors.

    PubMed

    Głowacki, Eric Daniel; Irimia-Vladu, Mihai; Kaltenbrunner, Martin; Gsiorowski, Jacek; White, Matthew S; Monkowius, Uwe; Romanazzi, Giuseppe; Suranna, Gian Paolo; Mastrorilli, Piero; Sekitani, Tsuyoshi; Bauer, Siegfried; Someya, Takao; Torsi, Luisa; Sariciftci, Niyazi Serdar

    2013-03-20

    Extensive intramolecular π-conjugation is considered to be requisite in the design of organic semiconductors. Here, two inkjet pigments, epindolidione and quinacridone, that break this design rule are explored. These molecules afford intermolecular π-stacking reinforced by hydrogen-bonding bridges. Air-stable organic field effect transistors are reported that support mobilities up to 1.5 cm(2)/Vs with T80 lifetimes comparable with the most stable reported organic semiconducting materials. PMID:23239229

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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

  5. Pt and Hf Additions to NiAl Bond Coats and Their Effect on the Lifetime of Thermal Barrier Coatings

    NASA Technical Reports Server (NTRS)

    Nesbitt, J. A.; Gleeson, B.; Sordelet, D.; Barrett, C. A.

    2003-01-01

    The lifetimes of thermal barrier coatings (TBC's) with various NiAlPt(HfZr) bond coats were determined by cyclic oxidation testing at 1163 C (2125 F). The bond coats were sprayed from powders by low pressure plasma spraying onto Rene N5 superalloy substrates. Yttria stabilized zirconia (8YSZ) top coats were applied by air plasma spraying. Surprisingly, there was not a strong correlation between TBC lifetime and Pt or Hf content although Zr additions decreased lifetimes. TBC failure morphologies and bond coat microstructures were examined and are discussed with respect to the bond coat compositions.

  6. 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.

  7. 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

  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. 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

  10. Stable Blue Phosphorescence Iridium(III) Cyclometalated Complexes Prompted by Intramolecular Hydrogen Bond in Ancillary Ligand.

    PubMed

    Yi, Seungjun; Kim, Jin-Hyoung; Cho, Yang-Jin; Lee, Jiwon; Choi, Tae-Sup; Cho, Dae Won; Pac, Chyongjin; Han, Won-Sik; Son, Ho-Jin; Kang, Sang Ook

    2016-04-01

    Improvement of the stability of blue phosphorescent dopant material is one of the key factors for real application of organic light-emitting diodes (OLEDs). In this study, we found that the intramolecular hydrogen bonding in an ancillary ligand from a heteroleptic Ir(III) complex can play an important role in the stability of blue phosphorescence. To rationalize the role of intramolecular hydrogen bonding, a series of Ir(III) complexes is designed and prepared: Ir(dfppy)2(pic-OH) (1a), Ir(dfppy)2(pic-OMe) (1b), Ir(ppy)2(pic-OH) (2a), and Ir(ppy)2(pic-OMe) (2b). The emission lifetime of Ir(dfppy)2(pic-OH) (1a) (τem = 3.19 μs) in dichloromethane solution was found to be significantly longer than that of Ir(dfppy)2(pic-OMe) (1b) (τem = 0.94 μs), because of a substantial difference in the nonradiative decay rate (knr = 0.28 × 10(5) s(-1) for (1a) vs 2.99 × 10(5) s(-1) for (1b)). These results were attributed to the intramolecular OH···O═C hydrogen bond of the 3-hydroxy-picolinato ligand. Finally, device lifetime was significantly improved when 1a was used as the dopant compared to FIrpic, a well-known blue dopant. Device III (1a as dopant) achieved an operational lifetime of 34.3 h for an initial luminance of 400 nits compared to that of device IV (FIrpic as dopant), a value of 20.1 h, indicating that the intramolecular hydrogen bond in ancillary ligand is playing an important role in device stability. PMID:26991672

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. Fast Interconversion of Hydrogen Bonding at the Hematite (001)-Liquid Water Interface.

    PubMed

    von Rudorff, Guido Falk; Jakobsen, Rasmus; Rosso, Kevin M; Blumberger, Jochen

    2016-04-01

    The interface between transition-metal oxides and aqueous solutions plays an important role in biogeochemistry and photoelectrochemistry, but the atomistic structure is often elusive. Here we report on the surface geometry, solvation structure, and thermal fluctuations of the hydrogen bonding network at the hematite (001)-water interface as obtained from hybrid density functional theory-based molecular dynamics. We find that the protons terminating the surface form binary patterns by either pointing in-plane or out-of-plane. The patterns exist for about 1 ps and spontaneously interconvert in an ultrafast, solvent-driven process within 50 fs. This results in only about half of the terminating protons pointing toward the solvent and being acidic. The lifetimes of all hydrogen bonds formed at the interface are shorter than those in pure liquid water. The solvation structure reported herein forms the basis for a better fundamental understanding of electron transfer coupled to proton transfer reactions at this important interface. PMID:26954334

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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

  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. 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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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.

  13. Stretching of hydrogen-bonded OH in the lowest singlet excited electronic state of water dimer.

    PubMed

    Chipman, Daniel M

    2006-01-28

    The lowest singlet excited electronic state of water monomer in the gas phase is strictly dissociative along a OH stretch coordinate but changes its nature when the stretched OH moiety is hydrogen bonded to a neighboring water molecule. This work extends previous exploration of the water dimer excited singlet potential-energy surface, using computational methods that are reliable even at geometries well removed from the ground-state equilibrium. First, the hydrogen-bonded OH moiety is stretched far enough to establish the existence of a barrier that is sufficient to support a quasibound vibrational state of the OH oscillator near the Franck-Condon region. Second, the constraint of an icelike structure is relaxed, and it is found that a substantial fraction of liquidlike structures also supports a quasibound vibrational state. These potential-energy explorations on stretching of the hydrogen-bonded OH moiety in a water dimer are discussed as a model for understanding the initial dynamics upon excitation into the lowest excited singlet state of condensed water. The possibility is raised that the excited-state lifetime may be long enough to allow for exciton migration, which would provide a mechanism for energy transport in condensed water phases. PMID:16460160

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. Photochemistry of squaraine dyes. 6. Solvent hydrogen bonding effects on the photophysical properties of bis(benzothiazolylidene)squaraines

    SciTech Connect

    Das, S. Regional Research Lab. , Trivandrum ); Thomas, K.G.; Ramanathan, R. , Trivandrum ); George, M.V. Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore Regional Research Lab. , Trivandrum ); Kamat, P.V. )

    1993-12-23

    The photophysical properties of two bis(benzothiazolylidene)squaraine dyes have been studied in aromatic hydrocarbon and alcoholic solvents. These dyes exhibit fluorescence quantum yields of 0.06-0.52 and excited singlet lifetimes of 0.48-2.5 ns in these solvents. Although the photophysical properties of the dyes are independent of solvent polarity in the hydrocarbon solvents, in alcoholic solvents a marked hyposchromic shift in the absorption and emission spectra and a reduction in lifetimes of excited state have been observed. These effects have been correlated with the hydrogen bond donating ability of the alcoholic solvents. 17 refs., 6 figs., 2 tabs.

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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…

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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).

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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).

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  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. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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

  17. Water Hydrogen-Bonding Network Structure and Dynamics at Phospholipid Multibilayer Surface: Femtosecond Mid-IR Pump-Probe Spectroscopy.

    PubMed

    Kundu, Achintya; Błasiak, Bartosz; Lim, Joon-Hyung; Kwak, Kyungwon; Cho, Minhaeng

    2016-03-01

    The water hydrogen-bonding network at a lipid bilayer surface is crucial to understanding membrane structures and its functional activities. With a phospholipid multibilayer mimicking a biological membrane, we study the temperature dependence of water hydrogen-bonding structure, distribution, and dynamics at a lipid multibilayer surface using femtosecond mid-IR pump-probe spectroscopy. We observe two distinguished vibrational lifetime components. The fast component (0.6 ps) is associated with water interacting with a phosphate part, whereas the slow component (1.9 ps) is with bulk-like choline-associated water. With increasing temperature, the vibrational lifetime of phosphate-associated water remains constant though its relative fraction dramatically increases. The OD stretch vibrational lifetime of choline-bound water slows down in a sigmoidal fashion with respect to temperature, indicating a noticeable change of the water environment upon the phase transition. The water structure and dynamics are thus shown to be in quantitative correlation with the structural change of liquid multibilayer upon the gel-to-liquid crystal phase transition. PMID:26859047

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Smedley, Sarah Black

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

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. Magnetic tweezers measurement of the bond lifetime-force behavior of the IgG-protein A specific molecular interaction.

    PubMed

    Shang, Hao; Lee, Gil U

    2007-05-23

    The bond lifetime-force behavior of the immunoglobulin G (IgG)-protein A interaction has been studied with magnetic tweezers to characterize the physical properties of the bond under nonequilibrium conditions. Super-paramagnetic microparticles were developed that have a high and uniform magnetization to simultaneously apply a piconewton-scale tensile force to many thousands of IgG-protein A bonds. A strong and a weak slip bond were detected with an effective bond length that is characteristic of short-range, stiff intermolecular interactions. These bonds are attributed to the interaction of protein A with the constant region (Fc) and heavy chain variable domain (VH) of IgG, respectively. The IgG-VH interaction appears to be one of the weakest specific molecular interactions that has been identified with a single molecule force measurement technique. This study demonstrates that magnetic tweezers can be used to rapidly characterize very weak biomolecular interactions as well as strong biomolecular interactions with a high degree of accuracy. PMID:17465553

  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. 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.

  20. 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

  1. 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

  2. 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

  3. 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.

  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. 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

  7. 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.

  8. 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.

  9. 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…

  10. 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.