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Sample records for hydrogen bonding

  1. Hydrogen multicentre bonds.

    PubMed

    Janotti, Anderson; Van de Walle, Chris G

    2007-01-01

    The concept of a chemical bond stands out as a major development in the process of understanding how atoms are held together in molecules and solids. Lewis' classical picture of chemical bonds as shared-electron pairs evolved to the quantum-mechanical valence-bond and molecular-orbital theories, and the classification of molecules and solids in terms of their bonding type: covalent, ionic, van der Waals and metallic. Along with the more complex hydrogen bonds and three-centre bonds, they form a paradigm within which the structure of almost all molecules and solids can be understood. Here, we present evidence for hydrogen multicentre bonds-a generalization of three-centre bonds-in which a hydrogen atom equally bonds to four or more other atoms. When substituting for oxygen in metal oxides, hydrogen bonds equally to all the surrounding metal atoms, becoming fourfold coordinated in ZnO, and sixfold coordinated in MgO. These multicentre bonds are remarkably strong despite their large hydrogen-metal distances. The calculated local vibration mode frequency in MgO agrees with infrared spectroscopy measurements. Multicoordinated hydrogen also explains the dependence of electrical conductivity on oxygen partial pressure, resolving a long-standing controversy on the role of point defects in unintentional n-type conductivity of ZnO (refs 8-10).

  2. Hydroperoxides as Hydrogen Bond Donors

    NASA Astrophysics Data System (ADS)

    Møller, Kristian H.; Tram, Camilla M.; Hansen, Anne S.; Kjaergaard, Henrik G.

    2016-06-01

    Hydroperoxides are formed in the atmosphere following autooxidation of a wide variety of volatile organics emitted from both natural and anthropogenic sources. This raises the question of whether they can form hydrogen bonds that facilitate aerosol formation and growth. Using a combination of Fourier transform infrared spectroscopy, FT-IR, and ab initio calculations, we have compared the gas phase hydrogen bonding ability of tert-butylhydroperoxide (tBuOOH) to that of tert-butanol (tBuOH) for a series of bimolecular complexes with different acceptors. The hydrogen bond acceptor atoms studied are nitrogen, oxygen, phosphorus and sulphur. Both in terms of calculated redshifts and binding energies (BE), our results suggest that hydroperoxides are better hydrogen bond donors than the corresponding alcohols. In terms of hydrogen bond acceptor ability, we find that nitrogen is a significantly better acceptor than the other three atoms, which are of similar strength. We observe a similar trend in hydrogen bond acceptor ability with other hydrogen bond donors including methanol and dimethylamine.

  3. Hydrogen bonded arrays: the power of multiple hydrogen bonds.

    PubMed

    Shokri, Alireza; Schmidt, Jacob; Wang, Xue-Bin; Kass, Steven R

    2012-02-01

    Hydrogen bond interactions in small covalent model compounds (i.e., deprotonated polyhydroxy alcohols) were measured by negative ion photoelectron spectroscopy. The experimentally determined vertical and adiabatic electron detachment energies for (HOCH(2)CH(2))(2)CHO(-)(2a), (HOCH(2)CH(2))(3)CO(-) (3a), and (HOCH(2)CH(2)CH(OH)CH(2))(3)CO(-) (4a)reveal that hydrogen-bonded networks can provide enormous stabilizations and that a single charge center not only can be stabilized by up to three hydrogen bonds but also can increase the interaction energy between noncharged OH groups by 5.8 kcal mol(-1) or more per hydrogen bond. This can lead to pK(a) values that are very different from those in water and can provide some of the impetus for catalytic processes.

  4. Hydrogen Bonded Arrays: The Power of Multiple Hydrogen Bonds

    SciTech Connect

    Shokri, Alireza; Schmidt, Jacob C.; Wang, Xue B.; Kass, Steven R.

    2012-02-01

    Hydrogen bond interactions in small covalent model compounds (i.e. deprotonated polyhydroxy alcohols) were measured by negative ion photoelectron spectroscopy. The experimentally determined vertical and adiabatic electron detachment energies for (HOCH2CH2)2CHO (2a), (HOCH2CH2) 3CO (3a) and (HOCH2CH2CH(OH)CH2)3CO (4a) reveal that hydrogen-bonded networks can provide enormous stabilizations, and that a single charge center not only can be stabilized by up to 3 hydrogen bonds but it can increase the interaction energy between non-charged OH groups by 5.8 kcal mol1 or more per hydrogen bond. This can lead to pKa values that are very different than in water, and provide some of the impetus for catalytic processes.

  5. Semiquantal analysis of hydrogen bond

    NASA Astrophysics Data System (ADS)

    Ando, Koji

    2006-07-01

    The semiquantal time-dependent Hartree (SQTDH) theory is applied to the coupled Morse and modified Lippincott-Schroeder (LS) model potentials of hydrogen bond. The structural correlation between the heavy atoms distance and the proton position, the geometric isotope effect, the energy of hydrogen bond formation, and the proton vibrational frequency shift are examined in a broad range of structural parameters. In particular, the geometric isotope effect is found to depend notably on the choice of the potential model, for which the LS potential gives the isotope shift of the heavy atoms distance in the range of 0.02-0.04Å, in quantitative agreement with the experimental findings from assortment of hydrogen bonding crystals. The fourth-order expansion approximation to the semiquantal extended potential was confirmed to be highly accurate in reproducing the full SQTDH results. The approximation is computationally efficient and flexible enough to be applied to general models of hydrogen bond.

  6. Hydrogen bonding in ionic liquids.

    PubMed

    Hunt, Patricia A; Ashworth, Claire R; Matthews, Richard P

    2015-03-07

    Ionic liquids (IL) and hydrogen bonding (H-bonding) are two diverse fields for which there is a developing recognition of significant overlap. Doubly ionic H-bonds occur when a H-bond forms between a cation and anion, and are a key feature of ILs. Doubly ionic H-bonds represent a wide area of H-bonding which has yet to be fully recognised, characterised or explored. H-bonds in ILs (both protic and aprotic) are bifurcated and chelating, and unlike many molecular liquids a significant variety of distinct H-bonds are formed between different types and numbers of donor and acceptor sites within a given IL. Traditional more neutral H-bonds can also be formed in functionalised ILs, adding a further level of complexity. Ab initio computed parameters; association energies, partial charges, density descriptors as encompassed by the QTAIM methodology (ρBCP), qualitative molecular orbital theory and NBO analysis provide established and robust mechanisms for understanding and interpreting traditional neutral and ionic H-bonds. In this review the applicability and extension of these parameters to describe and quantify the doubly ionic H-bond has been explored. Estimating the H-bonding energy is difficult because at a fundamental level the H-bond and ionic interaction are coupled. The NBO and QTAIM methodologies, unlike the total energy, are local descriptors and therefore can be used to directly compare neutral, ionic and doubly ionic H-bonds. The charged nature of the ions influences the ionic characteristics of the H-bond and vice versa, in addition the close association of the ions leads to enhanced orbital overlap and covalent contributions. The charge on the ions raises the energy of the Ylp and lowers the energy of the X-H σ* NBOs resulting in greater charge transfer, strengthening the H-bond. Using this range of parameters and comparing doubly ionic H-bonds to more traditional neutral and ionic H-bonds it is clear that doubly ionic H-bonds cover the full range of weak

  7. 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.

  8. Hydrogen-bonded sheets in benzylmethylammonium hydrogen maleate.

    PubMed

    Santacruz, Lynay; Abonia, Rodrigo; Cobo, Justo; Low, John N; Glidewell, Christopher

    2007-10-01

    In the title compound, C(8)H(12)N(+).C(4)H(3)O(4)(-), there is a short and almost linear but asymmetric O-H...O hydrogen bond in the anion. The ions are linked into C(2)(2)(6) chains by two short and nearly linear N-H...O hydrogen bonds and the chains are further weakly linked into sheets by a single C-H...O hydrogen bond.

  9. Hydrogen bonding. Part 25. The nature of the hydrogen bond in hydroxytropenylium chloride (tropone hydrochloride)

    NASA Astrophysics Data System (ADS)

    Harmon, Kenneth M.; Cross, Joan E.; Toccalino, Patricia L.

    1988-08-01

    Hydroxytropenylium iodide and bromide contain normal electrostatic OH⋯X - hydrogen bonds. Hydroxytropenylium chloride, however, contains a hydrogen bond intermediate between the normal electrostatic type and the very strong covalent type, similar to the hydrogen bonds found in choline fluoride or the Type I C∞v hydrogen dihalide ions. Infrared comparisons with compounds previously studied demonstrate that the hydroxytropenylium ion is a stronger hydrogen bond donor than either choline cation or protonated betaine cation, and suggest that hydroxytropenylium fluoride, if it can be prepared, should contain a three-center covalent hydrogen bond.

  10. Hydrogen Bonds in Excited State Proton Transfer

    NASA Astrophysics Data System (ADS)

    Horke, D. A.; Watts, H. M.; Smith, A. D.; Jager, E.; Springate, E.; Alexander, O.; Cacho, C.; Chapman, R. T.; Minns, R. S.

    2016-10-01

    Hydrogen bonding interactions between biological chromophores and their surrounding protein and solvent environment significantly affect the photochemical pathways of the chromophore and its biological function. A common first step in the dynamics of these systems is excited state proton transfer between the noncovalently bound molecules, which stabilizes the system against dissociation and principally alters relaxation pathways. Despite such fundamental importance, studying excited state proton transfer across a hydrogen bond has proven difficult, leaving uncertainties about the mechanism. Through time-resolved photoelectron imaging measurements, we demonstrate how the addition of a single hydrogen bond and the opening of an excited state proton transfer channel dramatically changes the outcome of a photochemical reaction, from rapid dissociation in the isolated chromophore to efficient stabilization and ground state recovery in the hydrogen bonded case, and uncover the mechanism of excited state proton transfer at a hydrogen bond, which follows sequential hydrogen and charge transfer processes.

  11. Hydrogen bond dynamics in bulk alcohols.

    PubMed

    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.

  12. Hydrogen bond dynamics in bulk alcohols

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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.

  13. 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...

  14. 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.

  15. Carboxylic Acid to Thioamide Hydrogen Bonding

    PubMed Central

    Datta, Suchitra; Lightner, David A.

    2009-01-01

    The lactam groups of dipyrrinones avidly engage in amide-amide hydrogen bonding to form dimeric association complexes in nonpolar solvents (in CHCl3, KD ~25,000 M-1 at 22°C). The corresponding thioamides (dipyrrinthiones), prepared from dipyrrinones by reaction with Lawesson’s reagent, also form intermolecularly hydrogen-bonded dimers in nonpolar solvents, albeit with much weaker association constants (in CHCl3, KD ~200 M-1 at 22°C). When a carboxylic acid group is tethered to C(9) of the dipyrrinone, as in the hexanoic acid of [6]-semirubin, tight intramolecular hydrogen bonding between the carboxylic acid group and the lactam moiety (intramolecular Kassoc ≫25,000) is found in CHCl3 with no evidence of dimers. In contrast, the analogous dipyrrinthione, [6]-thiosemirubin, eschews intramolecular hydrogen bonds, as determined using NMR spectroscopy and vapor pressure osmometry, preferring to form intermolecularly hydrogen-bonded dimers of the thioamide-thioamide type. PMID:20049064

  16. 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.

  17. 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.

  18. 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.

  19. Looking at hydrogen bonds in cellulose.

    PubMed

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

    2010-11-01

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

  20. Hydrogen bonded network properties in liquid formamide

    NASA Astrophysics Data System (ADS)

    Bakó, Imre; Megyes, Tünde; Bálint, Szabolcs; Chihaia, Viorel; Bellissent-Funel, Marie-Claire; Krienke, Hartmut; Kopf, Andreas; Suh, Soong-Hyuck

    2010-01-01

    Molecular dynamics simulations have been performed for liquid formamide using two different types of potential model (OPLS, Cordeiro). The structural results obtained from simulation were compared to experimental (x-ray and neutron diffraction measurements) outcomes. A generally good agreement for both models examined has been found, but in the hydrogen bonded region (2.9 Å) the Cordeiro model shows a slightly better fit. Besides the evaluation of partial radial distribution functions, orientational correlation functions and energy distribution functions, describing the hydrogen bonded structure, have been calculated based on the statistical analysis of configurations, resulting into a new insight in the clustering properties and topology of hydrogen bonded network. It has been shown that in liquid formamide exists a continuous hydrogen bonded network and from the analysis of the distribution of small rings revealed the ring size distribution in liquid formamide. Our study resulted that the ring size distribution of the hydrogen bonded liquid formamide shows a broad distribution with a maximum around 11. It has been found that the topology in formamide is significantly different than in water.

  1. 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.

  2. Bifunctional hydrogen bonds in monohydrated cycloether complexes.

    PubMed

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

    2010-03-04

    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.

  3. On how hydrogen bonds affect foam stability.

    PubMed

    Stubenrauch, Cosima; Hamann, Martin; Preisig, Natalie; Chauhan, Vinay; Bordes, Romain

    2017-02-08

    Do intermolecular H-bonds between surfactant head groups play a role for foam stability? From the literature on the foam stability of various surfactants with C12 alkyl chains but different head groups a clear picture emerges: stable foams are only generated when hydrogen bonds can form between the head groups, i.e. when the polar head group has a hydrogen bond donor and a proton acceptor. Stable foams can therefore be generated with surfactants having a sugar unit, a glycine, an amine oxide (at pH~5), or a carboxylic acid (at pH~pKa) as polar head group. On the other hand, aqueous foams stabilized with surfactants having oligo(ethylene oxide), phosphine oxide, quaternary ammonium, sulfate, sarcosine, amine oxide (at pH≠5), or carboxylic acid (at pH≠pKa) are not very stable. These observations suggest that hydrogen bonds between neighbouring molecules at the surface enhance foam stability. Formation of hydrogen bonds between surfactant head groups gives rise to a short-range attractive interaction that may restrict the surfactant's mobility while providing a more elastic surfactant layer which can counteract deformations. To support our hypothesis we carried out a systematic foaming study of two types of surfactants, one of them being capable of forming H-bonds and the other one not. Generating foams of all surfactants mentioned above with the same foaming conditions we found that stable foams are obtained when the head group is capable of forming intersurfactant H-bonds. The outcome of this study constitutes a new step towards the implementation of H-bonds in the future design of surfactants.

  4. Estimation on the individual hydrogen-bond strength in molecules with multiple hydrogen bonds.

    PubMed

    Dong, Hao; Hua, Weijie; Li, Shuhua

    2007-04-19

    A simple atom-replacement approach is proposed for estimating the individual contributions of each intermolecular hydrogen bond (HB) in multiple hydrogen-bonded systems. The approach is validated by calculations on the homodimer of formylformamide and then applied to nucleic acid base pairs (adenine-thymine and guanine-cytosine) and some quadruply hydrogen-bonded dimers. With the help of this method, it is easy to distinguish the relative strength of each HB, and identify the main factors contributing to the total binding energies of multiple HBs.

  5. 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.

  6. 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.

  7. Intramolecular hydrogen bonding in medicinal chemistry.

    PubMed

    Kuhn, Bernd; Mohr, Peter; Stahl, Martin

    2010-03-25

    The formation of intramolecular hydrogen bonds has a very pronounced effect on molecular structure and properties. We study both aspects in detail with the aim of enabling a more rational use of this class of interactions in medicinal chemistry. On the basis of exhaustive searches in crystal structure databases, we derive propensities for intramolecular hydrogen bond formation of five- to eight-membered ring systems of relevance in drug discovery. A number of motifs, several of which are clearly underutilized in drug discovery, are analyzed in more detail by comparing small molecule and protein-ligand X-ray structures. To investigate effects on physicochemical properties, sets of closely related structures with and without the ability to form intramolecular hydrogen bonds were designed, synthesized, and characterized with respect to membrane permeability, water solubility, and lipophilicity. We find that changes in these properties depend on a subtle balance between the strength of the hydrogen bond interaction, geometry of the newly formed ring system, and the relative energies of the open and closed conformations in polar and unpolar environments. A number of general guidelines for medicinal chemists emerge from this study.

  8. Multiple hydrogen bonds in cytosinium zoledronate trihydrate.

    PubMed

    Sridhar, Balasubramanian; Ravikumar, Krishnan

    2011-03-01

    The asymmetric unit of the title compound [systematic name: 4-amino-2-oxo-2,3-dihydropyrimidin-1-ium 1-hydroxy-2-(1H,3H-imidazol-3-ium-1-yl)ethylidenediphosphonate trihydrate], C(4)H(6)N(3)O(+)·C(5)H(9)N(2)O(7)P(2)(-)·3H(2)O, contains one cytosinium cation, one zoledronate anion and three water molecules. The zoledronate anion has a zwitterionic character, in which each phosphonate group is singly deprotonated and an imidazole N atom is protonated. Furthermore, proton transfer takes place from one of the phosphonic acid groups of the zoledronate anion to one of the N atoms of the cytosinium cation. The cytosinium cation forms a C(6) chain, while the zoledronate anion forms a rectangular-shaped centrosymmetric dimer through N-H...O hydrogen bonds. The cations and anions are held together by N-H...O and O-H...O hydrogen bonds to form a one-dimensional polymeric tape. The three water molecules play a crucial role in hydrogen bonding, resulting in a three-dimensional hydrogen-bonded network.

  9. 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.

  10. Unusual hydrogen bonding in L-cysteine hydrogen fluoride.

    PubMed

    Minkov, V S; Ghazaryan, V V; Boldyreva, E V; Petrosyan, A M

    2015-08-01

    L-Cysteine hydrogen fluoride, or bis(L-cysteinium) difluoride-L-cysteine-hydrogen fluoride (1/1/1), 2C3H8NO2S(+)·2F(-)·C3H7NO2S·HF or L-Cys(+)(L-Cys···L-Cys(+))F(-)(F(-)...H-F), provides the first example of a structure with cations of the 'triglycine sulfate' type, i.e. A(+)(A···A(+)) (where A and A(+) are the zwitterionic and cationic states of an amino acid, respectively), without a doubly charged counter-ion. The salt crystallizes in the monoclinic system with the space group P2(1). The dimeric (L-Cys···L-Cys(+)) cation and the dimeric (F(-)···H-F) anion are formed via strong O-H···O or F-H···F hydrogen bonds, respectively, with very short O···O [2.4438 (19) Å] and F···F distances [2.2676 (17) Å]. The F···F distance is significantly shorter than in solid hydrogen fluoride. Additionally, there is another very short hydrogen bond, of O-H···F type, formed by a L-cysteinium cation and a fluoride ion. The corresponding O···F distance of 2.3412 (19) Å seems to be the shortest among O-H···F and F-H···O hydrogen bonds known to date. The single-crystal X-ray diffraction study was complemented by IR spectroscopy. Of special interest was the spectral region of vibrations related to the above-mentioned hydrogen bonds.

  11. Halogen bonds in crystal engineering: like hydrogen bonds yet different.

    PubMed

    Mukherjee, Arijit; Tothadi, Srinu; Desiraju, Gautam R

    2014-08-19

    The halogen bond is an attractive interaction in which an electrophilic halogen atom approaches a negatively polarized species. Short halogen atom contacts in crystals have been known for around 50 years. Such contacts are found in two varieties: type I, which is symmetrical, and type II, which is bent. Both are influenced by geometric and chemical considerations. Our research group has been using halogen atom interactions as design elements in crystal engineering, for nearly 30 years. These interactions include halogen···halogen interactions (X···X) and halogen···heteroatom interactions (X···B). Many X···X and almost all X···B contacts can be classified as halogen bonds. In this Account, we illustrate examples of crystal engineering where one can build up from previous knowledge with a focus that is provided by the modern definition of the halogen bond. We also comment on the similarities and differences between halogen bonds and hydrogen bonds. These interactions are similar because the protagonist atoms-halogen and hydrogen-are both electrophilic in nature. The interactions are distinctive because the size of a halogen atom is of consequence when compared with the atomic sizes of, for example, C, N, and O, unlike that of a hydrogen atom. Conclusions may be drawn pertaining to the nature of X···X interactions from the Cambridge Structural Database (CSD). There is a clear geometric and chemical distinction between type I and type II, with only type II being halogen bonds. Cl/Br isostructurality is explained based on a geometric model. In parallel, experimental studies on 3,4-dichlorophenol and its congeners shed light on the nature of halogen···halogen interactions and reveal the chemical difference between Cl and Br. Variable temperature studies also show differences between type I and type II contacts. In terms of crystal design, halogen bonds offer a unique opportunity in the strength, atom size and interaction gradation; this may be

  12. Formaldoxime hydrogen bonded complexes with ammonia and hydrogen chloride.

    PubMed

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

    2015-02-05

    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.

  13. The nature of hydrogen bonding in protic ionic liquids.

    PubMed

    Hayes, Robert; Imberti, Silvia; Warr, Gregory G; Atkin, Rob

    2013-04-22

    The size, direction, strength, and distribution of hydrogen bonds in several protic ionic liquids (PILs) has been elucidated using neutron diffraction and computer simulation. There is significant variation in PIL hydrogen bond interactions ranging from short and linear to long and bi-/trifurcated. The nature of the PIL's hydrogen bonds reflects its macroscopic properties.

  14. 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.

  15. 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.

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

    PubMed

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

    2014-12-18

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

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

    PubMed

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

    2016-12-01

    In this work, we report QSPR modeling of the free energy ΔG of 1 : 1 hydrogen bond complexes of different H-bond acceptors and donors. The modeling was performed on a large and structurally diverse set of 3373 complexes featuring a single hydrogen bond, for which ΔG was measured at 298 K in CCl4 . The models were prepared using Support Vector Machine and Multiple Linear Regression, with ISIDA fragment descriptors. The marked atoms strategy was applied at fragmentation stage, in order to capture the location of H-bond donor and acceptor centers. Different strategies of model validation have been suggested, including the targeted omission of individual H-bond acceptors and donors from the training set, in order to check whether the predictive ability of the model is not limited to the interpolation of H-bond strength between two already encountered partners. Successfully cross-validating individual models were combined into a consensus model, and challenged to predict external test sets of 629 and 12 complexes, in which donor and acceptor formed single and cooperative H-bonds, respectively. In all cases, SVM models outperform MLR. The SVM consensus model performs well both in 3-fold cross-validation (RMSE=1.50 kJ/mol), and on the external test sets containing complexes with single (RMSE=3.20 kJ/mol) and cooperative H-bonds (RMSE=1.63 kJ/mol).

  18. Hydrogen bonding. Part 15. Infrared study of hydrogen bonding in betaine hydrate and betaine hydrofluoride

    NASA Astrophysics Data System (ADS)

    Harmon, Kenneth M.; Avci, Günsel F.

    1984-07-01

    Infrared spectroscopy at 300 and 10 K. deuterium labeling, internal coordinate analysis, and comparison with the spectra of compounds of known structure have been used to elucidate the nature of bound water in betaine hydrate. All evidence is consonant with a structure in which two carboxylate oxygens, one from each of two betaines, are mutually bridged by two water molecules to give a dimeric water—anion unit of D2h symmetry. The infrared spectrum of betaine hydrofluoride shows the presence of a very strong OHF hydrogen bond in this compound, in contrast to the normal OH⋯Cl hydrogen bond in betaine hydrochloride.

  19. Nature of hydrogen bonding in charged hydrogen-bonded complexes and imidazolium-based ionic liquids.

    PubMed

    Izgorodina, Ekaterina I; MacFarlane, Douglas R

    2011-12-15

    The nature of hydrogen bonding was compared in neutral complexes and negatively charged complexes consisting of either the HF molecule or the halide anion (fluoride and chloride) and the C-H bond in the methane molecule with a varying degree of fluorination (such as CH(4), CH(2)F(2), and CHF(3)). Both linear (C(3v) symmetry) and nonlinear (C(2v) symmetry) hydrogen-bonded complexes were studied. Symmetry-adapted perturbation theory was used to decompose interaction energies into fundamental components such as Coulomb, repulsion, induction and dispersion to analyze the interplay among these forces in stabilizing hydrogen bonding. In the linear charged complexes, both Coulomb attraction and induction significantly contributed to the stabilization of hydrogen bonding. In the nonlinear charged complexes, mainly Coulomb attraction contributed to the HB complex stabilization, with the inductive forces playing a less important role. Contrary to the neutral complexes, dispersion forces played only a marginal role in the charged complexes. Interplay between the fundamental forces was also investigated in the ion pairs of the imidazolium-based ionic liquid, [C(2)mim]Cl, that were categorized as either (1) typical ion-ion interaction, with the anion interacting from above or below the imidazolium plane; or (2) hydrogen-bonding interaction, with the anion interacting with the C2-H bond of the imidazolium cation. Both types of interactions were found to induce similar charge transfers, and the analysis of the energetic components revealed only a slight difference in the ion pairs studied: (1) both interactions were electrostatically driven, between 86% and 88% of the overall attractive energy, with the electrostatic component being slightly lower in the hydrogen-bonded ion pairs by ~8 kJ mol(-1); and (2) dispersion forces were found to be stronger in the typical ion-ion interactions by ~15 kJ mol(-1) and could be possible only due to the fact that the anion was able to move

  20. Polarization-induced σ-holes and hydrogen bonding.

    PubMed

    Hennemann, Matthias; Murray, Jane S; Politzer, Peter; Riley, Kevin E; Clark, Timothy

    2012-06-01

    The strong collinear polarizability of the A-H bond in A-H···B hydrogen bonds is shown to lead to an enhanced σ-hole on the donor hydrogen atom and hence to stronger hydrogen bonding. This effect helps to explain the directionality of hydrogen bonds, the well known cooperative effect in hydrogen bonding, and the occurrence of blue-shifting. The latter results when significant additional electron density is shifted into the A-H bonding region by the polarization effect. The shift in the A-H stretching frequency is shown to depend essentially linearly on the calculated atomic charge on the donor hydrogen for all donors in which A belongs to the same row of the periodic table. A further result of the polarization effect, which is also expected for other σ-hole bonds, is that the strength of the non-covalent interaction depends strongly on external electric fields.

  1. Nuclear quantum effects and hydrogen bonding in liquids.

    PubMed

    Raugei, Simone; Klein, Michael L

    2003-07-30

    We have employed ab initio path integral molecular dynamics simulations to investigate the role of nuclear quantum effects on the strength of hydrogen bonds in liquid hydrogen fluoride. Nuclear quantum effects are shown to be responsible for a stronger hydrogen bond and an enhanced dipole-dipole interaction, which lead, in turn, to a shortening of the H...F intrachain distance. The simulation results are analyzed in terms of the electronic density shifts with respect to a purely classical treatment of the nuclei. The observed enhanced hydrogen-bond interaction, which arises from a coupling of intra- and intermolecular effects, should be a general phenomenon occurring in all hydrogen-bonded systems.

  2. Hydrogen Bonding Characteristics of Crystalline Water in Inorganic Crystals

    NASA Astrophysics Data System (ADS)

    Zhang, Fangfang; Li, Keyan; Xue, Dongfeng

    From the chemical bond viewpoint, the microscopic characterstatics of hydrogen bonds in Mi—OH2⋯O (M is the metal cation coordinated to water molecule and i is the number of M) systems were comprehensively studied. It is shown that the original O—OH and H⋯O bond lengths of each hydrogen bonding system are evidently influenced by the crystalline environment and strongly dependent on the corresponding average bond lengths of each system, bar d{O - {H}} and bar d{H ... {O}}. Furthermore, the hydrogen bonding capability of water molecules coordinated to various metal cations was properly estimated and found to be related to the ionic electronegativities of these metal cations. The current work provides a useful route to calculating hydrogen bond valences within reasonable accuracy and sheds light on the rational utilization of hydrogen bonds in crystal design.

  3. Diverse world of unconventional hydrogen bonds.

    PubMed

    Belkova, Natalia V; Shubina, Elena S; Epstein, Lina M

    2005-08-01

    This Account presents our view of unconventional intermolecular hydrogen bonds (HBs) for organometallic complexes and transition-metal or main-group hydrides. Over the past decade, low-temperature spectroscopic (IR, UV, and NMR) studies combined with theoretical calculations have disclosed the static and dynamic features of different HBs. Their guiding role in the proton-transfer processes was determined, as well as the energetic characteristics of HB intermediates and the activation barriers. Nevertheless, there is still much to explore in terms of the prediction of HB properties and control of protonation/deprotonation processes.

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

    PubMed

    Henchman, Richard H

    2016-09-28

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

  5. 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.

  6. 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.

  7. HYDROGEN-BONDED DIMERS OF ADENINE AND URACIL DERIVATIVES.

    PubMed

    HAMLIN, R M; LORD, R C; RICH, A

    1965-06-25

    In concentrated solutions of either 9-ethyladenine or 1-cyclohexyluracil in deuterochloroform, absorption bands in the infrared spectrum demonstrate hydrogen bonding of the adenine and uracil derivatives with themselves. In dilute solutions, there is very little hydrogen bonding. However, when dilute solutions of 9-ethyladenine and 1-cyclohexyluracil are mixed, a series of bands appear which show that these molecules are hydrogen-bonding with each other much more strongly than with themselves. A study of the stoichiometry of this association indicates formation of 1:1 hydrogen-bonded pairs in solution.

  8. Routes to Hydrogen Bonding Chain-End Functionalized Polymers.

    PubMed

    Bertrand, Arthur; Lortie, Frédéric; Bernard, Julien

    2012-12-21

    The contribution of supramolecular chemistry to polymer science opens new perspectives for the design of polymer materials exhibiting valuable properties and easier processability due to the dynamic nature of non-covalent interactions. Hydrogen bonding polymers can be used as supramolecular units for yielding larger assemblies that possess attractive features, arising from the combination of polymer properties and the responsiveness of hydrogen bonds. The post-polymerization modification of reactive end-groups is the most common procedure for generating such polymers. Examples of polymerizations mediated by hydrogen bonding-functionalized precursors have also recently been reported. This contribution reviews the current synthetic routes toward hydrogen bonding sticker chain-end functionalized polymers.

  9. Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol

    PubMed Central

    Zhao, Hailiang; Tang, Shanshan; Xu, Xiang; Du, Lin

    2016-01-01

    Amides are important atmospheric organic–nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N-methylformamide, N,N-dimethylformamide, acetamide, N-methylacetamide and N,N-dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH–amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O–H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components. PMID:28042825

  10. Hydrogen bonding in the hexagonal ice surface.

    PubMed

    Barnett, Irene Li; Groenzin, Henning; Shultz, Mary Jane

    2011-06-16

    A recently developed technique in sum frequency generation spectroscopy, polarization angle null (or PAN-SFG), is applied to two orientations of the prism face of hexagonal ice. It is found that the vibrational modes of the surface are similar in different faces. As in the basal face, the prism face of ice contains five dominant resonances: 3096, 3146, 3205, 3253, and 3386 cm(-1). On the basal face, the reddest resonance occurs at 3098 cm(-1); within the bandwidth, the same as the prism face. On both the prism and basal faces, this mode contains a significant quadrupole component and is assigned to the bilayer stitching hydrogen bonds. The bluest of the resonances, 3386 cm(-1), occurs slightly blue-shifted at 3393 cm(-1) in the basal face. The prism face has two orientations: one with the optic or c axis in the input plane (the plane formed by the surface normal and the interrogating beam propagation) and one with the c axis perpendicular to the input plane. The 3386 cm(-1) mode has significant intensity only with the c axis in the input plane. On the basis of these orientation characteristics, the 3386 cm(-1) mode is assigned to double-donor molecules in either the top half bilayer or in the lower half bilayer. On the basis of frequency considerations, it is assigned to double-donor molecules in the top half bilayer. These are water molecules containing a nonbonded lone pair. In addition to identification of the components of the broad hydrogen-bonded region, PAN-SFG measures the tangential vs longitudinal content of the vibrational modes. In accord with previous suggestions, the lower frequency modes are predominantly tangential, whereas the higher frequency modes are mainly longitudinal. On the prism face, the 3386 cm(-1) mode is entirely longitudinal.

  11. 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.

  12. Helical polymers based on intramolecularly hydrogen-bonded aromatic polyamides.

    PubMed

    Lu, Yi-Xuan; Shi, Zhu-Ming; Li, Zhan-Ting; Guan, Zhibin

    2010-12-21

    Inspired by arylamide-based oligomeric foldermers that are stabilized by intramolecular hydrogen bonding, a series of polyamides with intramolecular hydrogen-bonding motifs were synthesized via polycondensation reactions. These polymers can fold into helical conformation different from their linear control. The chirality of helical conformation can further be tuned via acid-base complexation using chiral residues.

  13. How Do Organic Chemistry Students Understand and Apply Hydrogen Bonding?

    ERIC Educational Resources Information Center

    Henderleiter, J.; Smart, R.; Anderson, J.; Elian, O.

    2001-01-01

    Examines how students completing a two-semester organic sequence understand, explain, and apply hydrogen bonding to determine the physical attributes of molecules. Suggests that some students completing what is typically their second year of college-level chemistry still possess misconceptions about hydrogen bonds. (Contains 21 references.) (ASK)

  14. 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.

  15. Nanostructure, hydrogen bonding and rheology in choline chloride deep eutectic solvents as a function of the hydrogen bond donor.

    PubMed

    Stefanovic, Ryan; Ludwig, Michael; Webber, Grant B; Atkin, Rob; Page, Alister J

    2017-01-25

    Deep eutectic solvents (DESs) are a mixture of a salt and a molecular hydrogen bond donor, which form a eutectic liquid with a depressed melting point. Quantum mechanical molecular dynamics (QM/MD) simulations have been used to probe the 1 : 2 choline chloride-urea (ChCl : U), choline chloride-ethylene glycol (ChCl : EG) and choline chloride-glycerol (ChCl : Gly) DESs. DES nanostructure and interactions between the ions is used to rationalise differences in DES eutectic point temperatures and viscosity. Simulations show that the structure of the bulk hydrogen bond donor is largely preserved for hydroxyl based hydrogen bond donors (ChCl:Gly and ChCl:EG), resulting in a smaller melting point depression. By contrast, ChCl:U exhibits a well-established hydrogen bond network between the salt and hydrogen bond donor, leading to a larger melting point depression. This extensive hydrogen bond network in ChCl:U also leads to substantially higher viscosity, compared to ChCl:EG and ChCl:Gly. Of the two hydroxyl based DESs, ChCl:Gly also exhibits a higher viscosity than ChCl:EG. This is attributed to the over-saturation of hydrogen bond donor groups in the ChCl:Gly bulk, which leads to more extensive hydrogen bond donor self-interaction and hence higher cohesive forces within the bulk liquid.

  16. Hydrogen Bonding and Vibrational Spectroscopy: A Theoretical Study

    NASA Technical Reports Server (NTRS)

    Chaban, Galina M.

    2005-01-01

    Effects of hydrogen bonding on vibrational spectra are studied for several hydrogen-bonded complexes, in which hydrogen bonding ranges from weak (<5 kcal/mol) to very strong (>25 kcal/mol). The systems studied include complexes of inorganic acids and salts with water and ammonia, as well as complexes of several organic molecules (nitriles and amino acids) with water. Since anharmonic effects are very strong in hydrogen-bonded systems, anharmonic vibrational frequencies and infrared intensities are computed using the correlation-corrected vibrational self-consistent field (CC-VSCF) method with ab initio potential surfaces at the MP2 and CCSD(T) levels. The most common spectral effects induced by hydrogen bonding are red shifts of stretching vibrational frequencies ranging from approx.200/cm to over 2000/cm and significant increases of infrared intensities for those bonds that participate in hydrogen bonding. However, some systems (e.g. nitrile-water complexes) exhibit shifts in the opposite direction (to the blue) upon formation of hydrogen bonds.

  17. 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

    2016-05-05

    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.

  18. 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.

  19. 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.

  20. Effect of hydrogen bonds on optical nonlinearities of inorganic crystals

    NASA Astrophysics Data System (ADS)

    Xue, Dongfeng; Zhang, Siyuan

    1999-03-01

    This work probes the role of hydrogen bonds (such as O-H⋯O and N-H⋯O) in some inorganic nonlinear optical (NLO) crystals, such as HIO 3, NH 4H 2PO 4 (ADP), K[B 5O 6(OH) 4]·2H 2O (KB 5) and K 2La(NO 3) 5·2H 2O (KLN), from the chemical bond standpoint. Second order NLO behaviors of these four typical inorganic crystals have been quantitatively studied, results show hydrogen bonds play a very important role in NLO contributions to the total nonlinearity. Conclusions derived here concerning the effect of hydrogen bonds on optical nonlinearities of inorganic crystals have important implications with regard to the utilization of hydrogen bonds in the structural design of inorganic NLO crystals.

  1. The influence of hydrogen bonding on partition coefficients.

    PubMed

    Borges, Nádia Melo; Kenny, Peter W; Montanari, Carlos A; Prokopczyk, Igor M; Ribeiro, Jean F R; Rocha, Josmar R; Sartori, Geraldo Rodrigues

    2017-02-01

    This Perspective explores how consideration of hydrogen bonding can be used to both predict and better understand partition coefficients. It is shown how polarity of both compounds and substructures can be estimated from measured alkane/water partition coefficients. When polarity is defined in this manner, hydrogen bond donors are typically less polar than hydrogen bond acceptors. Analysis of alkane/water partition coefficients in conjunction with molecular electrostatic potential calculations suggests that aromatic chloro substituents may be less lipophilic than is generally believed and that some of the effect of chloro-substitution stems from making the aromatic π-cloud less available to hydrogen bond donors. Relationships between polarity and calculated hydrogen bond basicity are derived for aromatic nitrogen and carbonyl oxygen. Aligned hydrogen bond acceptors appear to present special challenges for prediction of alkane/water partition coefficients and this may reflect 'frustration' of solvation resulting from overlapping hydration spheres. It is also shown how calculated hydrogen bond basicity can be used to model the effect of aromatic aza-substitution on octanol/water partition coefficients.

  2. The influence of hydrogen bonding on partition coefficients

    NASA Astrophysics Data System (ADS)

    Borges, Nádia Melo; Kenny, Peter W.; Montanari, Carlos A.; Prokopczyk, Igor M.; Ribeiro, Jean F. R.; Rocha, Josmar R.; Sartori, Geraldo Rodrigues

    2017-01-01

    This Perspective explores how consideration of hydrogen bonding can be used to both predict and better understand partition coefficients. It is shown how polarity of both compounds and substructures can be estimated from measured alkane/water partition coefficients. When polarity is defined in this manner, hydrogen bond donors are typically less polar than hydrogen bond acceptors. Analysis of alkane/water partition coefficients in conjunction with molecular electrostatic potential calculations suggests that aromatic chloro substituents may be less lipophilic than is generally believed and that some of the effect of chloro-substitution stems from making the aromatic π-cloud less available to hydrogen bond donors. Relationships between polarity and calculated hydrogen bond basicity are derived for aromatic nitrogen and carbonyl oxygen. Aligned hydrogen bond acceptors appear to present special challenges for prediction of alkane/water partition coefficients and this may reflect `frustration' of solvation resulting from overlapping hydration spheres. It is also shown how calculated hydrogen bond basicity can be used to model the effect of aromatic aza-substitution on octanol/water partition coefficients.

  3. The influence of hydrogen bonding on partition coefficients

    NASA Astrophysics Data System (ADS)

    Borges, Nádia Melo; Kenny, Peter W.; Montanari, Carlos A.; Prokopczyk, Igor M.; Ribeiro, Jean F. R.; Rocha, Josmar R.; Sartori, Geraldo Rodrigues

    2017-02-01

    This Perspective explores how consideration of hydrogen bonding can be used to both predict and better understand partition coefficients. It is shown how polarity of both compounds and substructures can be estimated from measured alkane/water partition coefficients. When polarity is defined in this manner, hydrogen bond donors are typically less polar than hydrogen bond acceptors. Analysis of alkane/water partition coefficients in conjunction with molecular electrostatic potential calculations suggests that aromatic chloro substituents may be less lipophilic than is generally believed and that some of the effect of chloro-substitution stems from making the aromatic π-cloud less available to hydrogen bond donors. Relationships between polarity and calculated hydrogen bond basicity are derived for aromatic nitrogen and carbonyl oxygen. Aligned hydrogen bond acceptors appear to present special challenges for prediction of alkane/water partition coefficients and this may reflect `frustration' of solvation resulting from overlapping hydration spheres. It is also shown how calculated hydrogen bond basicity can be used to model the effect of aromatic aza-substitution on octanol/water partition coefficients.

  4. Hydrogen bonding definitions and dynamics in liquid water.

    PubMed

    Kumar, R; Schmidt, J R; Skinner, J L

    2007-05-28

    X-ray and neutron diffractions, vibrational spectroscopy, and x-ray Raman scattering and absorption experiments on water are often interpreted in terms of hydrogen bonding. To this end a number of geometric definitions of hydrogen bonding in water have been developed. While all definitions of hydrogen bonding are to some extent arbitrary, those involving one distance and one angle for a given water dimer are unnecessarily so. In this paper the authors develop a systematic procedure based on two-dimensional potentials of mean force for defining cutoffs for a given pair of distance and angular coordinates. They also develop an electronic structure-based definition of hydrogen bonding in liquid water, related to the electronic occupancy of the antibonding OH orbitals. This definition turns out to be reasonably compatible with one of the distance-angle geometric definitions. These two definitions lead to an estimate of the number of hydrogen bonds per molecule in liquid simple point charge/extended (SPC/E) water of between 3.2 and 3.4. They also used these and other hydrogen-bond definitions to examine the dynamics of local hydrogen-bond number fluctuations, finding an approximate long-time decay constant for SPC/E water of between 0.8 and 0.9 ps, which corresponds to the time scale for local structural relaxation.

  5. CH-π hydrogen bonds in biological macromolecules.

    PubMed

    Nishio, Motohiro; Umezawa, Yoji; Fantini, Jacques; Weiss, Manfred S; Chakrabarti, Pinak

    2014-07-07

    This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.

  6. 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.

  7. Hydrogen multicenter bond in oxide and nitride semiconductors

    NASA Astrophysics Data System (ADS)

    Janotti, Anderson

    2009-03-01

    Hydrogen is a very reactive atom, occurring in virtually all organic and in many inorganic compounds. It can form a purely covalent bond, in which two hydrogen atoms share a pair of electrons in a two-electron two-center bond, as well as polar covalent bonds, such as in an H2O molecule. In solids, hydrogen is usually considered as an interstitial impurity. In elemental semiconductors, such as silicon, hydrogen forms a three-center bond when located at the bond center. In compound semiconductors, hydrogen bonds to the anionic species in p-type material, and to the cationic species in n-type. Thus far, hydrogen in solids has been found to form chemical bonds with one, two, or at most three other atoms. Higher coordination numbers are exceedingly rare and have been reported only for clusters. In this talk we will show that hydrogen is capable of forming multicenter bonds in solids, occupying substitutional sites. As examples, we discuss substitutional hydrogen impurities in oxides (ZnO, MgO, SnO2, TiO2) [1,2] and nitrides (InN, AlN, GaN) [3]. Based on first-principles calculations we show that hydrogen replaces oxygen (nitrogen) and forms genuine chemical bonds with multiple metal atoms, in truly multicoordinated configurations. These multicenter bonds are surprisingly strong despite the large hydrogen-metal distances when compared to typical values in hydrogen two-center bonds. Hydrogen in the multicenter bond configuration is a shallow donor in a number of materials. In conducting oxides, it provides a consistent explanation for the observed dependence of electrical conductivity on oxygen partial pressure, thus resolving a long-standing controversy on the role of point defects in unintentional n-type conductivity [1,2]. [4pt] [1] A. Janotti and C. G Van de Walle, Nature Materials 6, 44 (2007). [0pt] [2] A. K. Singh, A. Janotti, M. Scheffler, and C. G. Van de Walle, Phys. Rev. Lett. 101, 055502 (2008). [0pt] [3] A. Janotti and C. G. Van de Walle, Appl. Phys. Lett. 92

  8. 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.

  9. 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.

  10. Hydrogen-bond networks: strengths of different types of hydrogen bonds and an alternative to the low barrier hydrogen-bond proposal.

    PubMed

    Shokri, Alireza; Wang, Yanping; O'Doherty, George A; Wang, Xue-Bin; 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.

  11. Counting peptide-water hydrogen bonds in unfolded proteins.

    PubMed

    Gong, Haipeng; Porter, Lauren L; Rose, George D

    2011-02-01

    It is often assumed that the peptide backbone forms a substantial number of additional hydrogen bonds when a protein unfolds. We challenge that assumption in this article. Early surveys of hydrogen bonding in proteins of known structure typically found that most, but not all, backbone polar groups are satisfied, either by intramolecular partners or by water. When the protein is folded, these groups form approximately two hydrogen bonds per peptide unit, one donor or acceptor for each carbonyl oxygen or amide hydrogen, respectively. But when unfolded, the backbone chain is often believed to form three hydrogen bonds per peptide unit, one partner for each oxygen lone pair or amide hydrogen. This assumption is based on the properties of small model compounds, like N-methylacetamide, or simply accepted as self-evident fact. If valid, a chain of N residues would have approximately 2N backbone hydrogen bonds when folded but 3N backbone hydrogen bonds when unfolded, a sufficient difference to overshadow any uncertainties involved in calculating these per-residue averages. Here, we use exhaustive conformational sampling to monitor the number of H-bonds in a statistically adequate population of blocked polyalanyl-six-mers as the solvent quality ranges from good to poor. Solvent quality is represented by a scalar parameter used to Boltzmann-weight the population energy. Recent experimental studies show that a repeating (Gly-Ser) polypeptide undergoes a denaturant-induced expansion accompanied by breaking intramolecular peptide H-bonds. Results from our simulations augment this experimental finding by showing that the number of H-bonds is approximately conserved during such expansion⇋compaction transitions.

  12. 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

  13. Hirshfeld atom refinement for modelling strong hydrogen bonds.

    PubMed

    Woińska, Magdalena; Jayatilaka, Dylan; Spackman, Mark A; Edwards, Alison J; Dominiak, Paulina M; Woźniak, Krzysztof; Nishibori, Eiji; Sugimoto, Kunihisa; Grabowsky, Simon

    2014-09-01

    High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of Z' > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O-H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.

  14. Patterned polymeric multilayered assemblies through hydrogen bonding and metal coordination.

    PubMed

    Piñón, Victor; Weck, Marcus

    2012-02-14

    Patterned polymeric multilayered assemblies were formed using a combination of metal coordination and hydrogen bonding interactions. We proved that the hydrogen bonding interaction between diamidopyridine and thymine can be employed for polymeric multilayer assemblies. We then combined this strategy along with a second supramolecular interaction, metal coordination. These interactions proved to be orthogonal to one another on the surface, making each discrete region individually responsive to external stimuli.

  15. Crystal engineering of analogous and homologous organic compounds: hydrogen bonding patterns in trimethoprim hydrogen phthalate and trimethoprim hydrogen adipate

    PubMed Central

    Muthiah, Packianathan Thomas; Francis, Savarimuthu; Rychlewska, Urszula; Warżajtis, Beata

    2006-01-01

    Background Trimethoprim [2,4-diamino-5-(3',4',5'-trimethoxybenzyl)pyrimidine] is an antifolate drug. It selectively inhibits the bacterial dihydrofolate reductase (DHFR) enzyme. Results In the crystal structures of trimethoprim (TMP)-hydrogen phthalate (1) and trimethoprim-hydrogen adipate (2), one of the N atoms of the pyrimidine ring is protonated and it interacts with the deprotonated carboxylate oxygens through a pair of nearly parallel N-H...O hydrogen bonds to form a fork-like interaction. In the compound 1, the pyrimidine moieties of the TMP cations are centrosymmetrically paired through a pair of N-H...N hydrogen bonds involving 4-amino group and the N (N3) atom of the pyrimidine rings to form a 8-membered hydrogen bonded ring [R22(8)]. The 4-amino group of one TMP moiety and 2-amino group of another TMP moiety (both moieties are members of a base pair) are bridged by the carbonyl oxygen of the phthalate moiety through N-H...O hydrogen bonds forming 8-membered hydrogen-bonded ring [R22(8)]. The characteristic hydrogen-bonded rings observed in the structure aggregate into a supramolecular ladder consisting of a pair of chains, each of which is built up of alternate TMP and hydrogen phthalate ions. In the compound 2, two TMP cations and two hydrogen adipate anions are arranged about an inversion center so that the complementary DDAA (D = donor, A = acceptor) arrays of quadruple hydrogen-bonding patterns are formed. The head-to-tail arrangement of the hydrogen adipate ions leads to a hydrogen-bonded supramolecular chain. From crystal engineering point of view, it is interesting to note that the compound 1 has a hydrogen-bonded network remarkably identical with its aliphatic analogue, trimethoprim hydrogen maleate. Similarly the compound 2, resembles its homolog trimethoprim hydrogen glutarate. Conclusion In the crystal structure of trimethoprim hydrogen phthalate, the hydrogen-bonded network is remarkably identical with its aliphatic analogue, trimethoprim

  16. How are hydrogen bonds modified by metal binding?

    PubMed

    Husberg, Charlotte; Ryde, Ulf

    2013-06-01

    We have used density functional theory calculations to investigate how the hydrogen-bond strength is modified when a ligand is bound to a metal using over 60 model systems involving six metals and eight ligands frequently encountered in metalloproteins. We study how the hydrogen-bond geometry and energy vary with the nature of metal, the oxidation state, the coordination number, the ligand involved in the hydrogen bond, other first-sphere ligands, and different hydrogen-bond probe molecules. The results show that, in general, the hydrogen-bond strength is increased for neutral ligands and decreased for negatively charged ligands. The size of the effect is mainly determined by the net charge of the metal complex, and all effects are typically decreased when the model is solvated. In water solution, the hydrogen-bond strength can increase by up to 37 kJ/mol for neutral ligands, and that of negatively charged ligands can increase (for complexes with a negative net charge) or decrease (for positively charged complexes). If the net charge of the complex does not change, there is normally little difference between different metals or different types of complexes. The only exception is observed for sulphur-containing ligands (Met and Cys) and if the ligand is redox-active (e.g. high-valence Fe-O complexes).

  17. How many hydrogen-bonded α-turns are possible?

    PubMed

    Schreiber, Anette; Schramm, Peter; Hofmann, Hans-Jörg

    2011-06-01

    The formation of α-turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated α-turns with a hydrogen bond between the first and fifth amino acid employing the methods of ab initio MO theory in vacuum (HF/6-31G*, B3LYP/6-311 + G*) and in solution (CPCM/HF/6-31G*). Only few α-turn structures with glycine and alanine backbones fulfill the geometry criteria for the i←(i + 4) hydrogen bond satisfactorily. The most stable representatives agree with structures found in the Protein Data Bank. There is a general tendency to form additional hydrogen bonds for smaller pseudocycles corresponding to β- and γ-turns with better hydrogen bond geometries. Sometimes, this competition weakens or even destroys the i←(i + 4) hydrogen bond leading to very stable double β-turn structures. This is also the reason why an "ideal" α-turn with three central amino acids having the perfect backbone angle values of an α-helix could not be localized. There are numerous hints for stable α-turns with a distance between the C(α)-atoms of the first and fifth amino acid smaller than 6-7 Å, but without an i←(i + 4) hydrogen bond.

  18. Multiple hydrogen bonds. Mass spectra of hydrogen bonded heterodimers. A comparison of ESI- and REMPI-ReTOF-MS.

    PubMed

    Taubitz, Jörg; Lüning, Ulrich; Grotemeyer, Jürgen

    2004-11-07

    Resonance enhanced multi-photon ionization-reflectron time of flight mass spectrometry is the analytical method of choice to observe hydrogen bonded supramolecules in the gas phase when protonation of basic centers competes with cluster formation.

  19. How strong are hydrogen bonds in metalla-beta-diketones?

    PubMed

    Steinborn, Dirk; Schwieger, Sebastian

    2007-01-01

    The energies of the kinetically inert, electronically saturated Lukehart-type metalla-beta-diketone [Re{(COMe)2H}(CO)4] (9 a) and of the kinetically labile, electronically unsaturated platina-beta-diketones [Pt{(COMe)2H}Cl2]- (10 a), [Pt2{(COMe)2H}2(micro-Cl)2] (11 a), and [Pt{(COMe)2H}(bpy)]+ (12 a) have been calculated by DFT at the B3LYP/6-311++G(d,p) level using effective core potentials with consideration of relativistic effects for the transition metals. Analogously, energies of the requisite open (non-hydrogen-bonded) equilibrium conformers (9 b, 10 c, 11 b, 12 b) and energies which were obtained from the hydrogen-bonded conformers by rigid rotation of the OH group around the C--O bond by 180 degrees followed by relaxation of all bond lengths and angles (9 c, 10 d, 11 c, 12 d) have been calculated. These energies were found to be higher by 14.7/27.2 (9 b/9 c), 20.7/27.2 (10 c/10 d), 19.2/25.7 (11 b/11 c), and 9.4/19.6 kcal mol(-1) (12 b/12 d) than those of the intramolecularly O--HO hydrogen-bonded metalla-beta-diketones 9 a, 10 a, 11 a, and 12 a, respectively. In acetylacetone (Hacac), the generic organic analogue of metalla-beta-diketones, the energies of the most stable non-hydrogen-bonded enol isomer (6 b) and of the conformer derived from the H-bonded form by rigid rotation of the OH group by 180 degrees followed by subsequent relaxation of all bond lengths and angles (6 k) were found to be 10.9/16.1 kcal mol(-1) (6 b/6 k) higher compared to the intramolecularly O--HO bonded isomer 6 a. Thus, the hydrogen bonds in metalla-beta- diketones must be regarded as strong and were found to be up to twice as strong as that in acetylacetone. A linear relationship was found between the hydrogen-bond energies based on the rigidly rotated structures and the OO separation in the hydrogen-bonded structures. Furthermore, these energies were also found to be correlated with the electron densities at the OH bond critical points (rhobcp) in the O--HO bonds of metalla

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

    NASA Astrophysics Data System (ADS)

    Moriarty, Philip

    2014-03-01

    Hydrogen-bonding underpins the structure, properties, and dynamics of a vast array of systems spanning a wide variety of scientific fields. From the striking complexity of the phase diagram of H2O and the elegance of base pair interactions in DNA, to the directionality inherent in supramolecular self-assembly at surfaces, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the H-bond, including the magnitude of the force and binding energy, force constant, and decay length associated with the interaction, have been vigorously debated for many decades. I will discuss how dynamic force microscopy (DFM) using a qPlus sensor can quantitatively map the tip-sample force-field for naphthalene tetracarboxylic diimide (NTCDI) molecules hydrogen-bonded in 2D assemblies. A comparison of experimental images and force spectra with their simulated counterparts from density functional theory calculations shows that image contrast due to intermolecular hydrogen bonds arises fundamentally from charge density depletion due to strong tip-sample interactions. Interpretation of DFM images of hydrogen bonds 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.

  1. "Union is strength": how weak hydrogen bonds become stronger.

    PubMed

    Melandri, Sonia

    2011-08-21

    Recently reported rotational spectroscopic studies on small dimers and oligomers bound by weak hydrogen bonds show that the driving forces, the spatial arrangement and the dynamical features displayed are very different from those involved in stronger and conventional hydrogen bonds. The very small binding energies (similar to those of van der Waals interactions) imply that the stabilization of the dimer is often obtained by networks of weak hydrogen bonds. Even in the presence of multiple bonds the partner molecules show a high degree of internal freedom within the complex. This paper analyses several examples of molecular adducts bound by weak hydrogen bonds formed in free jet expansions and recently characterized by rotational spectroscopy. They include weakly bound complexes of weak donors with strong acceptors (C-H···O,N, S-H···O,N), strong donors (O-H, N-H) with weak acceptors such as the halogen atoms and π systems but also the elusive interactions between weak donors and weak acceptors (C-H···π and C-H···halogen). Examples are also given where rotational spectroscopy highlights that weak hydrogen bonds are extremely important in chiral recognition phenomena and as driving forces of the conformational landscape of important biomolecules.

  2. Physical meaning of the QTAIM topological parameters in hydrogen bonding.

    PubMed

    Duarte, Darío J R; Angelina, Emilio L; Peruchena, Nélida M

    2014-11-01

    This work examined the local topological parameters of charge density at the hydrogen bond (H-bond) critical points of a set of substituted formamide cyclic dimers and enolic tautomers. The analysis was performed not only on the total electron density of the hydrogen bonded complexes but also on the intermediate electron density differences derived from the Morokuma energy decomposition scheme. Through the connection between these intermediate electron density differences and the corresponding differences in topological parameters, the meaning of topological parameters variation due to hydrogen bonding (H-bonding) becomes evident. Thus, for example, we show in a plausible way that the potential energy density differences at the H-bond critical point properly describe the electrostatics of H-bonding, and local kinetic energy density differences account for the localization/delocalization degree of the electrons at that point. The results also support the idea that the total electronic energy density differences at the H-bond critical point describe the strength of the interaction rather than its covalent character as is commonly considered.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

    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.

  5. 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

  6. Vibrational states and optical transitions in hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Johannsen, P. G.

    1998-03-01

    Proton energies in hydrogen bonds are mostly calculated using a double Morse potential (the DMP model). This form, however, does not reproduce the experimentally observed correlation between the proton stretching frequency and the bond length in an extended bond-length region sufficiently well. An alternative potential is proposed in the present paper. The quantum states of this non-symmetric double-well potential are calculated numerically using the Numerov (Fox-Goodwin) algorithm. It is shown that the optical spectra of hydrogen bonds in various substances can be well approximated on the basis of the transition frequencies and intensities predicted by the present model. For weakly interacting OH impurities in 0953-8984/10/10/008/img1, the overtone spectrum and line intensities are well reproduced, whereas the line broadenings and the decrease of the fundamental stretching frequencies in intermediate and strong hydrogen bonds are traced back to the influence of the reduced height of the central barrier. The model is also extrapolated to the range of symmetric hydrogen bonds, and the calculated transition frequencies are discussed with respect to most recent infra-red experiments on ice under strong compression. A possible artificial infra-red signal from strained diamond anvils is thereby noted.

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

    PubMed Central

    Bower, John F.; Krische, Michael J.

    2011-01-01

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

  8. 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.

  9. 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

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

    PubMed

    Koenig, S; Müller, L; Smith, D K

    2001-03-02

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

  11. 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.

  12. 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.

  13. Strengths of hydrogen bonds involving phosphorylated amino acid side chains.

    PubMed

    Mandell, Daniel J; Chorny, Ilya; Groban, Eli S; Wong, Sergio E; Levine, Elisheva; Rapp, Chaya S; Jacobson, Matthew P

    2007-01-31

    Post-translational phosphorylation plays a key role in regulating protein function. Here, we provide a quantitative assessment of the relative strengths of hydrogen bonds involving phosphorylated amino acid side chains (pSer, pAsp) with several common donors (Arg, Lys, and backbone amide groups). We utilize multiple levels of theory, consisting of explicit solvent molecular dynamics, implicit solvent molecular mechanics, and quantum mechanics with a self-consistent reaction field treatment of solvent. Because the approximately 6 pKa of phosphate suggests that -1 and -2 charged species may coexist at physiological pH, hydrogen bonds involving both protonated and deprotonated phosphates for all donor-acceptor pairs are considered. Multiple bonding geometries for the charged-charged interactions are also considered. Arg is shown to be capable of substantially stronger salt bridges with phosphorylated side chains than Lys. A pSer hydrogen-bond acceptor tends to form more stable interactions than a pAsp acceptor. The effect of phosphate protonation state on the strengths of the hydrogen bonds is remarkably subtle, with a more pronounced effect on pAsp than on pSer.

  14. Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media.

    PubMed

    van der Spoel, David; van Maaren, Paul J; Larsson, Per; Tîmneanu, Nicusor

    2006-03-09

    The thermodynamics of hydrogen bond breaking and formation was studied in solutions of alcohol (methanol, ethanol, 1-propanol) molecules. An extensive series of over 400 molecular dynamics simulations with an aggregate length of over 900 ns was analyzed using an analysis technique in which hydrogen bond (HB) breaking is interpreted as an Eyring process, for which the Gibbs energy of activation DeltaG can be determined from the HB lifetime. By performing simulations at different temperatures, we were able to determine the enthalpy of activation DeltaH and the entropy of activation TDeltaS for this process from the Van't Hoff relation. The equilibrium thermodynamics was determined separately, based on the number of donor hydrogens that are involved in hydrogen bonds. Results (DeltaH) are compared to experimental data from Raman spectroscopy and found to be in good agreement for pure water and methanol. The DeltaG as well as the DeltaG are smooth functions of the composition of the mixtures. The main result of the calculations is that DeltaG is essentially independent of the environment (around 5 kJ/mol), suggesting that buried hydrogen bonds (e.g., in proteins) do not contribute significantly to protein stability. Enthalpically HB formation is a downhill process in all substances; however, for the alcohols there is an entropic barrier of 6-7 kJ/mol, at 298.15 K, which cannot be detected in pure water.

  15. Light-induced hydrogen evolution from hydrogenated amorphous silicon: Hydrogen diffusion by formation of bond centered hydrogen

    NASA Astrophysics Data System (ADS)

    Tanimoto, H.; Arai, H.; Mizubayashi, H.; Yamanaka, M.; Sakata, I.

    2014-02-01

    The light-induced hydrogen evolution (LIHE) from amorphous (a-) Si:H by the order of at. % is observed during white light soaking (WLS) of 100-400 mW/cm2 at 350-500 K or ultra violet light soaking (UVLS) of 30-120 mW/cm2 at 305-320 K in a vacuum. The thermal desorption spectroscopy indicates that LIHE originated from bonded hydrogen takes place through the diffusion of light-induced mobile hydrogen (LIMH) with the activation energy of 0.5 eV. LIMH is assigned to bond centered hydrogen and the hydrogen diffusion process becomes prominent when LIMH can leave from a-Si:H such under light soaking in a vacuum above room temperature. For H2 in microvoids, the hydrogen evolution rate is governed by the surface barrier and its activation energy of 1.0 eV in dark decreases to 0.4 eV under WLS or UVLS.

  16. Microstructure and hydrogen bonding in water-acetonitrile mixtures.

    PubMed

    Mountain, Raymond D

    2010-12-16

    The connection of hydrogen bonding between water and acetonitrile in determining the microheterogeneity of the liquid mixture is examined using NPT molecular dynamics simulations. Mixtures for six, rigid, three-site models for acetonitrile and one water model (SPC/E) were simulated to determine the amount of water-acetonitrile hydrogen bonding. Only one of the six acetonitrile models (TraPPE-UA) was able to reproduce both the liquid density and the experimental estimates of hydrogen bonding derived from Raman scattering of the CN stretch band or from NMR quadrupole relaxation measurements. A simple modification of the acetonitrile model parameters for the models that provided poor estimates produced hydrogen-bonding results consistent with experiments for two of the models. Of these, only one of the modified models also accurately determined the density of the mixtures. The self-diffusion coefficient of liquid acetonitrile provided a final winnowing of the modified model and the successful, unmodified model. The unmodified model is provisionally recommended for simulations of water-acetonitrile mixtures.

  17. Alternation and tunable composition in hydrogen bonded supramolecular copolymers.

    PubMed

    Felder, Thorsten; de Greef, Tom F A; Nieuwenhuizen, Marko M L; Sijbesma, Rint P

    2014-03-07

    Sequence control in supramolecular copolymers is limited by the selectivity of the associating monomer end groups. Here we introduce the use of monomers with aminopyrimidinone and aminohydroxynaphthyridine quadruple hydrogen bonding end groups, which both homodimerize, but form even stronger heterodimers. These features allow the formation of supramolecular copolymers with a tunable composition and a preference for alternating sequences.

  18. Hydrogen bonding in water clusters and their ionized counterparts.

    PubMed

    Neela, Y Indra; Mahadevi, A Subha; Sastry, G Narahari

    2010-12-30

    Ab initio and DFT computations were carried out on four distinct hydrogen-bonded arrangements of water clusters (H(2)O)(n), n = 2-20, represented as W1D, W2D, W2DH, and W3D. The variation in the strength of hydrogen bond as a function of the chain length is studied. In all the four cases, there is a substantial cooperative interaction, albeit in different degrees. The effect of basis set superposition error (BSSE) on the complexation energy of water clusters has been analyzed. Atoms in molecules (AIM) analysis performed to evaluate the nature of the hydrogen bonding shows a high correlation between hydrogen bond strength and the trends in complexation energy. Solvated water clusters exhibit lower complexation energies compared to corresponding gas-phase geometries on PCM (polarized continuum model) optimization. The feasibility of stripping an electron or addition of an electron increases dramatically as the cluster size increases. Although W3D caged structures are stable for neutral clusters, the helical W2DH arrangement appeared to be an optimal choice for its ionized counterparts.

  19. Crystal engineering with urea and thiourea hydrogen-bonding groups.

    PubMed

    Custelcean, Radu

    2008-01-21

    The utilization of N,N'-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.

  20. 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.

  1. Watson-Crick hydrogen bonding of unlocked nucleic acids.

    PubMed

    Langkjær, Niels; Wengel, Jesper; Pasternak, Anna

    2015-11-15

    We herein describe the synthesis of two new unlocked nucleic acid building blocks containing hypoxanthine and 2,6-diaminopurine as nucleobase moieties and their incorporation into oligonucleotides. The modified oligonucleotides were used to examine the thermodynamic properties of UNA against unmodified oligonucleotides and the resulting thermodynamic data support that the hydrogen bonding face of UNA is Watson-Crick like.

  2. Hydrogen bonding in protic ionic liquids: reminiscent of water.

    PubMed

    Fumino, Koichi; Wulf, Alexander; Ludwig, Ralf

    2009-01-01

    Similarities and differences: Far-infrared spectra of protic ionic liquids could be assigned to intermolecular bending and stretching modes of hydrogen bonds. The characteristics of the low-frequency spectra resemble those of water. Both liquids form three-dimensional network structures, but only water is capable of building tetrahedral configurations. EAN: ethylammonium nitrate, PAN: propylammonium nitrate, DMAN: dimethylammonium nitrate.

  3. 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

  4. 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

  5. An alternative near-neighbor definition of hydrogen bonding in water.

    PubMed

    Hammerich, A D; Buch, V

    2008-03-21

    A definition of hydrogen bonding in water is proposed in which an H...O pair forms a hydrogen bond if (a) an oxygen atom is the nearest nonchemically bonded neighbor of a hydrogen atom; and (b) the hydrogen is the first or the second intermolecular near-neighbor of the oxygen. Unlike the commonly employed hydrogen-bond definitions, this definition does not depend on the choice of geometric or energetic cutoffs applied to continuous distributions of properties. With the present definition, the distribution of O...H bond lengths decays smoothly to zero in a physically reasonable range. After correction for the presence of intermittent hydrogen bonds, this definition appears to provide a more stable description of hydrogen bonds and coordination shells than the more conventional cutoff-based definition. "Partial" H bonds satisfying only one of the two bonding requirements serve as transition states in the H-bond network evolution.

  6. Liquid state of a 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

    It is theoretically shown that the Coulomb interaction between violations of the Bernal-Fowler rules leads to a temperature-induced stepwise 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.

  7. 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.

  8. Association by hydrogen bonding of mononucleotides in aqueous solution.

    PubMed

    Raszka, M; Kaplan, N O

    1972-08-01

    Evidence for hydrogen bonding between 5'-ribonucleotides in water has been obtained from a 220-MHz proton magnetic resonance study of nitrogenous protons. The amino groups of GMP, AMP, and CMP exhibit proton resonance lines which are somewhat broadened by proton exchange with the solvent at 0 degrees ; their downfield Shifts in mixtures of mononucleotides provide the basis for the following order of base-pairing tendencies: GMP.CMP > AMP.UMP. Hydrogen bonding is also observed in other pairs of mononucleotides, notably GMP.UMP, AMP.CMP, and CMP.UMP, to a lesser extent in GMP.IMP, CMP.XMP, and possibly in CMP.IMP. In agreement with previous reports, hydrophobic interactions of mononucleotides have also been observed; base pairing occurs in addition to vertical stacking of these bases, their hydrogen bonding to water, or self-association. Only CMP shows clear evidence of self-association via hydrogen bonding in water; the evidence for GMP is less direct, and that for AMP is negative. This lack of observable self-association may occur as a result of competition from strong stacking interactions. Only CMP shows restricted rotation of the amino group at 0 degrees and neutral pH. As expected, higher temperatures increase the rate of rotation of the amino group for CMP, as well as accelerate the rate of proton exchange between water and the amino protons of mononucleotides.High-resolution proton magnetic resonance spectroscopy could prove to be a valuable tool in mapping out the specificities conferred by hydrogen bonding between biomolecules in aqueous solution.

  9. Short intramolecular hydrogen bonds: derivatives of malonaldehyde with symmetrical substituents.

    PubMed

    Hargis, Jacqueline C; Evangelista, Francesco A; Ingels, Justin B; Schaefer, Henry F

    2008-12-24

    A systematic study of various derivatives of malonaldehyde has been carried out to explore very short hydrogen bonds (r(OO) < 2.450 A). Various electron-withdrawing groups, including CN, NO(2), and BH(2), have been attached to the central carbon atom, C(2). To C(1) and C(3), strong electron donors and/or sterically hindered substituents were used to strengthen the intramolecular hydrogen bond, including but not limited to NH(2), N(CH(3))(2), and C(CH(3))(3). Seven molecules (Figure 2 ) were found to have extremely short intramolecular hydrogen bonds. The chemical systems investigated are intriguing due to their low energetic barriers for the intramolecular hydrogen atom transfers. Classical barriers were predicted using correlated methods including second-order perturbation theory and coupled cluster theory in conjunction with the Dunning hierarchy of correlation consistent basis sets, cc-pVXZ (X = D, T, Q, 5). Focal point analyses allowed for the barriers to be evaluated at the CBS limit including core correlation and zero-point vibrational energy corrections. B3LYP energies are benchmarked against highly accurate correlated energies for intramolecular hydrogen bonded systems. The focal point extrapolated method, including coupled cluster full triple excitation contributions, gives a hydrogen transfer barrier for malonaldehyde of approximately 4 kcal mol(-1). We describe two compounds with extremely low classical barriers, nitromalonamide (0.43 kcal mol(-1)) and 2-borylmalonamide (0.60 kcal mol(-1)). An empirical relationship was drawn between the B3LYP energetic barriers and the predicted coupled cluster barriers at the CBS limit. By relating these two quantities, barrier heights may be estimated for systems too large to presently use highly correlated electronic structure methods.

  10. 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.

  11. 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.

  12. A Study about Regioisomeric Hydroquinones with Multiple Intramolecular Hydrogen Bonding.

    PubMed

    Martínez-Cifuentes, Maximiliano; Cardona, Wilson; Saitz, Claudio; Weiss-López, Boris; Araya-Maturana, Ramiro

    2017-04-07

    A theoretical exploration about hydrogen bonding in a series of synthetic regioisomeric antitumor tricyclic hydroquinones is presented. The stabilization energy for the intramolecular hydrogen bond (IHB) formation in four structurally different situations were evaluated: (a) IHB between the proton of a phenolic hydroxyl group and an ortho-carbonyl group (forming a six-membered ring); (b) between the oxygen atom of a phenolic hydroxyl group and the proton of an hydroxyalkyl group (seven membered ring); (c) between the proton of a phenolic hydroxyl group with the oxygen atom of the hydroxyl group of a hydroxyalkyl moiety (seven-membered ring); and (d) between the proton of a phenolic hydroxyl group and an oxygen atom directly bonded to the aromatic ring in ortho position (five-membered ring). A conformational analysis for the rotation around the hydroxyalkyl substituent is also performed. It is observed that there is a correspondence between the conformational energies and the IHB. The strongest intramolecular hydrogen bonds are those involving a phenolic proton and a carbonyl oxygen atom, forming a six-membered ring, and the weakest are those involving a phenolic proton with the oxygen atom of the chromenone, forming five-membered rings. Additionally, the synthesis and structural assignment of two pairs of regioisomeric hydroquinones, by 2D-NMR experiments, are reported. These results can be useful in the design of biologically-active molecules.

  13. Exploring the Relationships Between Anharmonicity and OH Bond Lengths in Hydrogen Bonded Complexes

    NASA Astrophysics Data System (ADS)

    McCoy, Anne B.; Xantheas, Sotiris

    2016-06-01

    In this talk we explore the effects of anharmonicity on the zero-point averaged OH bond lengths in hydrogen bonded complexes. Clusters with as many as six HF molecules or water molecules are explored as well as protonated water clusters and complexes of water clusters with F^-, Cl^-, Br^- and OH^-. It is shown that there is a universal correlation between the vibrationally averaged OH or HF bond length and the anharmonc OH or HF stretch frequency. This relationship provides an extension to previously investigated correlations between the equilibrium bond lengths and harmonic frequencies and allows one to anticipate OH or HF bond lengths based on measured frequencies. In addition, differences between the R_z and R_0 structures are discussed within the context of these weakly bound complexes.

  14. 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

    2011-01-07

    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.

  15. Control of redox reactivity of flavin and pterin coenzymes by metal ion coordination and hydrogen bonding.

    PubMed

    Fukuzumi, Shunichi; Kojima, Takahiko

    2008-03-01

    The electron-transfer activities of flavin and pterin coenzymes can be fine-tuned by coordination of metal ions, protonation and hydrogen bonding. Formation of hydrogen bonds with a hydrogen-bond receptor in metal-flavin complexes is made possible depending on the type of coordination bond that can leave the hydrogen-bonding sites. The electron-transfer catalytic functions of flavin and pterin coenzymes are described by showing a number of examples of both thermal and photochemical redox reactions, which proceed by controlling the electron-transfer reactivity of coenzymes with metal ion binding, protonation and hydrogen bonding.

  16. Spectroscopic Evidences for Strong Hydrogen Bonds with Selenomethionine in Proteins.

    PubMed

    Mundlapati, V Rao; Sahoo, Dipak Kumar; Ghosh, Sanat; Purame, Umesh Kumar; Pandey, Shubhant; Acharya, Rudresh; Pal, Nitish; Tiwari, Prince; Biswal, Himansu S

    2017-02-16

    Careful protein structure analysis unravels many unknown and unappreciated noncovalent interactions that control protein structure; one such unrecognized interaction in protein is selenium centered hydrogen bonds (SeCHBs). We report, for the first time, SeCHBs involving the amide proton and selenium of selenomethionine (Mse), i.e., amide-N-H···Se H-bonds discerned in proteins. Using mass selective and conformer specific high resolution vibrational spectroscopy, gold standard quantum chemical calculations at CCSD(T), and in-depth protein structure analysis, we establish that amide-N-H···Se and amide-N-H···Te H-bonds are as strong as conventional amide-NH···O and amide-NH···O═C H-bonds despite smaller electronegativity of selenium and tellurium than oxygen. It is in fact, electronegativity, atomic charge, and polarizability of the H-bond acceptor atoms are at play in deciding the strength of H-bonds. The amide-N-H···Se and amide-N-H···Te H-bonds presented here are not only new additions to the ever expanding world of noncovalent interactions, but also are of central importance to design new force-fields for better biomolecular structure simulations.

  17. Local modes in a DNA polymer with hydrogen bond defect.

    PubMed Central

    Saxena, V K; Van Zandt, L L

    1994-01-01

    Vibrations of a homopolymer DNA with localized hydrogen bond defects have been examined using the recently developed decaying mode theory for long-chain polymers with local structural defects. For a poly(dA)-poly(dT) homopolymer having perturbed hydrogen bonds in one base pair, a localized mode at 63.2 cm-1 has been found. This mode has a very nearly pure H-bond stretch or "breathing" character, although the backbones do not separate. This agrees in frequency with a similar result found by other authors using a different approach. We search the full microwave frequency range for other local modes for several models of weakened H bonds. Besides the local mode with breathing characteristics, local modes with other characteristic motions were found, but only for asymmetrically perturbed bonds. We find in general that local modes are not very robust, requiring quite specific, narrow ranges in parameter space. They are also not abundant, there being only three in our most prolific model. PMID:7696483

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

    NASA Astrophysics Data System (ADS)

    Pirc, Gordana; Stare, Jernej; Mavri, Janez

    2010-06-01

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

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

    PubMed

    Pirc, Gordana; Stare, Jernej; Mavri, Janez

    2010-06-14

    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 Schrodinger 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 Schrodinger 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.

  20. Discrimination of hydrogen-bonded complexes with axial chirality

    NASA Astrophysics Data System (ADS)

    Alkorta, Ibon; Elguero, José

    2002-10-01

    The chiral self-discrimination of twelve molecules showing axial chirality has been studied. They included peroxides, hydrazines, carboxylic acids, amides, and allenes. The homo and heterochiral dimers of the selected compounds, that present two hydrogen bonds, have been studied by means of density functional theory (B3LYP/6-31+G**) and ab initio (MP2/6-31+G** and MP2/6-311++G**) methods. The energetic differences found for the complexes of each compound have been rationalized based on their electron density maps and the natural bond orbital analysis. In some cases, intermolecular oxygen-oxygen interactions have been found and interpreted as additional stabilizing contacts.

  1. Hydrogen-hydrogen bonds in highly branched alkanes and in alkane complexes: A DFT, ab initio, QTAIM, and ELF study.

    PubMed

    Monteiro, Norberto K V; Firme, Caio L

    2014-03-06

    The hydrogen-hydrogen (H-H) bond or hydrogen-hydrogen bonding is formed by the interaction between a pair of identical or similar hydrogen atoms that are close to electrical neutrality and it yields a stabilizing contribution to the overall molecular energy. This work provides new, important information regarding hydrogen-hydrogen bonds. We report that stability of alkane complexes and boiling point of alkanes are directly related to H-H bond, which means that intermolecular interactions between alkane chains are directional H-H bond, not nondirectional induced dipole-induced dipole. Moreover, we show the existence of intramolecular H-H bonds in highly branched alkanes playing a secondary role in their increased stabilities in comparison with linear or less branched isomers. These results were accomplished by different approaches: density functional theory (DFT), ab initio, quantum theory of atoms in molecules (QTAIM), and electron localization function (ELF).

  2. The pnicogen bond: its relation to hydrogen, halogen, and other noncovalent bonds.

    PubMed

    Scheiner, Steve

    2013-02-19

    Among a wide range of noncovalent interactions, hydrogen (H) bonds are well known for their specific roles in various chemical and biological phenomena. When describing conventional hydrogen bonding, researchers use the notation AH···D (where A refers to the electron acceptor and D to the donor). However, the AH molecule engaged in a AH···D H-bond can also be pivoted around by roughly 180°, resulting in a HA···D arrangement. Even without the H atom in a bridging position, this arrangement can be attractive, as explained in this Account. The electron density donated by D transfers into a AH σ* antibonding orbital in either case: the lobe of the σ* orbital near the H atom in the H-bonding AH···D geometry, or the lobe proximate to the A atom in the HA···D case. A favorable electrostatic interaction energy between the two molecules supplements this charge transfer. When A belongs to the pnictide family of elements, which include phosphorus, arsenic, antimony, and bismuth, this type of interaction is called a pnicogen bond. This bonding interaction is somewhat analogous to the chalcogen and halogen bonds that arise when A is an element in group 16 or 17, respectively, of the periodic table. Electronegative substitutions, such as a F for a H atom opposite the electron donor atom, strengthen the pnicogen bond. For example, the binding energy in FH(2)P···NH(3) greatly exceeds that of the paradigmatic H-bonding water dimer. Surprisingly, di- or tri-halogenation does not produce any additional stabilization, in marked contrast to H-bonds. Chalcogen and halogen bonds show similar strength to the pnicogen bond for a given electron-withdrawing substituent. This insensitivity to the electron-acceptor atom distinguishes these interactions from H-bonds, in which energy depends strongly upon the identity of the proton-donor atom. As with H-bonds, pnicogen bonds can extract electron density from the lone pairs of atoms on the partner molecule, such as N, O, and

  3. Contribution of Hydrogen Bonds to Paper Strength Properties

    PubMed Central

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

    2016-01-01

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

  4. Supramolecular Archimedean cages assembled with 72 hydrogen bonds.

    PubMed

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

    2011-07-22

    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···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.

  5. 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.

  6. Chiral Squaramide Derivatives are Excellent Hydrogen Bond Donor Catalysts

    PubMed Central

    Malerich, Jeremiah P.; Hagihara, Koji; Rawal, Viresh H.

    2009-01-01

    Thioureas represent the dominant platform for hydrogen bond promoted asymmetric catalysts. A large number of reactions, reported in scores of publications, have been successfully promoted by chiral thioureas. The present paper reports the use of squaramides as a highly effective new scaffold for the development of chiral hydrogen bond donor catalysts. squaramide catalysts are very simple to prepare. The (-)-cinchonine modified squaramide (5), easily prepared through a two step process from methyl squarate, was shown to be an effective catalyst, even at catalyst loadings as low as 0.1 mol%, for the conjugate addition reactions of 1,3-dicarbonyl compounds to β-nitrostyrenes. The addition products were obtained in high yields and excellent enantioselectivities. PMID:18847268

  7. Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing

    NASA Astrophysics Data System (ADS)

    Alexandrov, B. S.; Stanev, V. G.; Bishop, A. R.; Rasmussen, K. Ø.

    2012-12-01

    We study the effects of the anharmonic strand-separation dynamics of double-stranded DNA on the infrared spectra of the intramolecular base-pairing hydrogen bonds. Using the extended Peyrard-Bishop-Dauxois model for the DNA breathing dynamics coupled with the Lippincott-Schroeder potential for N-H⋯N and N-H⋯O hydrogen bonding, we identify a high-frequency (˜96 THz) feature in the infrared spectra. We show that this sharp peak arises as a result of the anharmonic base-pair breathing dynamics of DNA. In addition, we study the effects of friction on the infrared spectra. For higher temperatures (˜300 K), where the anharmonicity of DNA dynamics is pronounced, the high-frequency peak is always present irrespective of the friction strength.

  8. Nuclear quantum effects and hydrogen bond fluctuations in water.

    PubMed

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

    2013-09-24

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

  9. Hydrogen bonding in selected vanadates: a Raman and infrared spectroscopy study.

    PubMed

    Frost, Ray L; Erickson, Kristy L; Weier, Matt L

    2004-08-01

    Water plays an important role in the stability of minerals containing the deca and hexavanadates ions. A selection of minerals including pascoite, huemulite, barnesite, hewettite, metahewettite, hummerite has been analysed. Infrared spectroscopy combined with Raman spectroscopy has enabled the spectra of the water HOH stretching bands to be determined. The use of the Libowitsky type function allows for the estimation of hydrogen bond distances to be determined. The strength of the hydrogen bonds can be assessed by these hydrogen bond distances. An arbitrary value of 2.74A was used to separate the hydrogen bonds into two categories such that bond distances less than this value are considered as strong hydrogen bonds whereas hydrogen bond distances greater than this value are considered relatively weaker. Importantly infrared spectroscopy enables the estimation of hydrogen bond distances using an empirical function.

  10. Hydrated alizarin complexes: hydrogen bonding and proton transfer.

    PubMed

    Huh, Hyun; Cho, Sung Haeng; Heo, Jiyoung; Kim, Nam Joon; Kim, Seong Keun

    2012-07-07

    We investigated the hydrogen bonding structures and proton transfer for the hydration complexes of alizarin (Az) produced in a supersonic jet using fluorescence excitation (FE), dispersed laser induced fluorescence (LIF), visible-visible hole burning (HB), and fluorescence detected infrared (FDIR) spectroscopy. The FDIR spectrum of bare Az with two O-H groups exhibits two vibrational bands at 3092 and 3579 cm(-1), which, respectively, correspond to the stretching vibration of O1-H1 that forms a strong intramolecular hydrogen bond with the C9=O9 carbonyl group and the stretching vibration of O2-H2 that is weakly hydrogen-bonded to O1-H1. For the 1:1 hydration complex Az(H(2)O)(1), we identified three conformers. In the most stable conformer, the water molecule forms hydrogen bonds with the O1-H1 and O2-H2 groups of Az as a proton donor and proton acceptor, respectively. In the other conformers, the water binds to the C10=O10 group in two nearly isoenergetic configurations. In contrast to the sharp vibronic peaks in the FE spectra of Az and Az(H(2)O)(1), only broad, structureless absorption was observed for Az(H(2)O)(n) (n≥ 2), indicating a facile decay process, possibly due to proton transfer in the electronic excited state. The FDIR spectrum with the wavelength of the probe laser fixed at the broad band exhibited a broad vibrational band near the O2-H2 stretching vibration frequency of the most stable conformer of Az(H(2)O)(1). With the help of theoretical calculations, we suggest that the broad vibrational band may represent the occurrence of proton transfer by tunnelling in the electronic ground state of Az(H(2)O)(n) (n≥ 2) upon excitation of the O2-H2 vibration.

  11. Probing the hydrogen bonding structure in the Rieske protein.

    PubMed

    El Khoury, Youssef; Trivella, Aurélien; Gross, Julien; Hellwig, Petra

    2010-10-25

    The use of the far-infrared spectral range presents a novel approach for analysis of the hydrogen bonding in proteins. Here it is presented for the analysis of Fe--S vibrations (500-200 cm(-1)) and of the intra- and intermolecular hydrogen bonding signature (300-50 cm(-1)) in the Rieske protein from Thermus thermophilus as a function of temperature and pH. Three pH values were adequately chosen in order to study all the possible protonation states of the coordinating histidines. The Fe--S vibrations showed pH-dependent shifts in the FIR spectra in line with the change of protonation state of the histidines coordinating the [2Fe--2S] cluster. Measurements of the low-frequency signals between 300 and 30 K demonstrated the presence of a distinct overall hydrogen bonding network and a more rigid structure for a pH higher than 10. To further support the analysis, the redox-dependent shifts of the secondary structure were investigated by means of an electrochemically induced FTIR difference spectroscopic approach in the mid infrared. The results confirmed a clear pH dependency and an influence of the immediate environment of the cluster on the secondary structure. The results support the hypothesis that structure-mediated changes in the environment of iron--sulfur centers play a critical role in regulating enzymatic catalysis. The data point towards the role of the overall internal hydrogen bonding organization for the geometry and the electronic properties of the cluster.

  12. 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…

  13. Protonic transport through solitons in hydrogen-bonded systems

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  14. Comparative study of halogen- and hydrogen-bond interactions between benzene derivatives and dimethyl sulfoxide.

    PubMed

    Zheng, Yan-Zhen; Deng, Geng; Zhou, Yu; Sun, Hai-Yuan; Yu, Zhi-Wu

    2015-08-24

    The halogen bond, similar to the hydrogen bond, is an important noncovalent interaction and plays important roles in diverse chemistry-related fields. Herein, bromine- and iodine-based halogen-bonding interactions between two benzene derivatives (C6 F5 Br and C6 F5 I) and dimethyl sulfoxide (DMSO) are investigated by using IR and NMR spectroscopy and ab initio calculations. The results are compared with those of interactions between C6 F5 Cl/C6 F5 H and DMSO. First, the interaction energy of the hydrogen bond is stronger than those of bromine- and chlorine-based halogen bonds, but weaker than iodine-based halogen bond. Second, attractive energies depend on 1/r(n) , in which n is between three and four for both hydrogen and halogen bonds, whereas all repulsive energies are found to depend on 1/r(8.5) . Third, the directionality of halogen bonds is greater than that of the hydrogen bond. The bromine- and iodine-based halogen bonds are strict in this regard and the chlorine-based halogen bond only slightly deviates from 180°. The directional order is iodine-based halogen bond>bromine-based halogen bond>chlorine-based halogen bond>hydrogen bond. Fourth, upon the formation of hydrogen and halogen bonds, charge transfers from DMSO to the hydrogen- and halogen-bond donors. The CH3 group contributes positively to stabilization of the complexes.

  15. 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.

  16. The hydrogen-bond collective dynamics in liquid methanol

    NASA Astrophysics Data System (ADS)

    Bellissima, Stefano; de Panfilis, Simone; Bafile, Ubaldo; Cunsolo, Alessandro; González, Miguel Angel; Guarini, Eleonora; Formisano, Ferdinando

    2016-12-01

    The relatively simple molecular structure of hydrogen-bonded (HB) systems is often belied by their exceptionally complex thermodynamic and microscopic behaviour. For this reason, after a thorough experimental, computational and theoretical scrutiny, the dynamics of molecules in HB systems still eludes a comprehensive understanding. Aiming at shedding some insight into this topic, we jointly used neutron Brillouin scattering and molecular dynamics simulations to probe the dynamics of a prototypical hydrogen-bonded alcohol, liquid methanol. The comparison with the most thoroughly investigated HB system, liquid water, pinpoints common behaviours of their THz microscopic dynamics, thereby providing additional information on the role of HB dynamics in these two systems. This study demonstrates that the dynamic behaviour of methanol is much richer than what so far known, and prompts us to establish striking analogies with the features of liquid and supercooled water. In particular, based on the strong differences between the structural properties of the two systems, our results suggest that the assignment of some dynamical properties to the tetrahedral character of water structure should be questioned. We finally highlight the similarities between the characteristic decay times of the time correlation function, as obtained from our data and the mean lifetime of hydrogen bond known in literature.

  17. The hydrogen-bond collective dynamics in liquid methanol

    PubMed Central

    Bellissima, Stefano; De Panfilis, Simone; Bafile, Ubaldo; Cunsolo, Alessandro; González, Miguel Angel; Guarini, Eleonora; Formisano, Ferdinando

    2016-01-01

    The relatively simple molecular structure of hydrogen-bonded (HB) systems is often belied by their exceptionally complex thermodynamic and microscopic behaviour. For this reason, after a thorough experimental, computational and theoretical scrutiny, the dynamics of molecules in HB systems still eludes a comprehensive understanding. Aiming at shedding some insight into this topic, we jointly used neutron Brillouin scattering and molecular dynamics simulations to probe the dynamics of a prototypical hydrogen-bonded alcohol, liquid methanol. The comparison with the most thoroughly investigated HB system, liquid water, pinpoints common behaviours of their THz microscopic dynamics, thereby providing additional information on the role of HB dynamics in these two systems. This study demonstrates that the dynamic behaviour of methanol is much richer than what so far known, and prompts us to establish striking analogies with the features of liquid and supercooled water. In particular, based on the strong differences between the structural properties of the two systems, our results suggest that the assignment of some dynamical properties to the tetrahedral character of water structure should be questioned. We finally highlight the similarities between the characteristic decay times of the time correlation function, as obtained from our data and the mean lifetime of hydrogen bond known in literature. PMID:27996056

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

    NASA Astrophysics Data System (ADS)

    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 1H NMR, 13C NMR, IR and X-ray single-crystal diffraction. The carboxylic acid group forms classic Osbnd H ⋯ O hydrogen bonded dimers in a centrosymmetric R22(8) ring motifs for BAA-Br and BAA-Cl. However, no carboxylic acid group forms classic Osbnd H ⋯ 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 0.5-3.8 kcal/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 4 kcal/mol.

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

    PubMed

    Sen, Ibrahim; Kara, Hulya; Azizoglu, Akın

    2016-10-05

    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.

  20. The hydrogen-bond collective dynamics in liquid methanol

    DOE PAGES

    Bellissima, Stefano; Cunsolo, Alessandro; DePanfilis, Simone; ...

    2016-12-20

    The relatively simple molecular structure of hydrogen-bonded (HB) systems is often belied by their exceptionally complex thermodynamic and microscopic behaviour. For this reason, after a thorough experimental, computational and theoretical scrutiny, the dynamics of molecules in HB systems still eludes a comprehensive understanding. Aiming at shedding some insight into this topic, we jointly used neutron Brillouin scattering and molecular dynamics simulations to probe the dynamics of a prototypical hydrogen-bonded alcohol, liquid methanol. The comparison with the most thoroughly investigated HB system, liquid water, pinpoints common behaviours of their THz microscopic dynamics, thereby providing additional information on the role of HBmore » dynamics in these two systems. This study demonstrates that the dynamic behaviour of methanol is much richer than what so far known, and prompts us to establish striking analogies with the features of liquid and supercooled water. In particular, based on the strong differences between the structural properties of the two systems, our results suggest that the assignment of some dynamical properties to the tetrahedral character of water structure should be questioned. We finally highlight the similarities between the characteristic decay times of the time correlation function, as obtained from our data and the mean lifetime of hydrogen bond known in literature.« less

  1. The hydrogen-bond collective dynamics in liquid methanol

    SciTech Connect

    Bellissima, Stefano; Cunsolo, Alessandro; DePanfilis, Simone; Bafile, Ubaldo; Gonzalez, Miguel Angel; Guarini, Eleonora; Formisano, Ferdinando

    2016-12-20

    The relatively simple molecular structure of hydrogen-bonded (HB) systems is often belied by their exceptionally complex thermodynamic and microscopic behaviour. For this reason, after a thorough experimental, computational and theoretical scrutiny, the dynamics of molecules in HB systems still eludes a comprehensive understanding. Aiming at shedding some insight into this topic, we jointly used neutron Brillouin scattering and molecular dynamics simulations to probe the dynamics of a prototypical hydrogen-bonded alcohol, liquid methanol. The comparison with the most thoroughly investigated HB system, liquid water, pinpoints common behaviours of their THz microscopic dynamics, thereby providing additional information on the role of HB dynamics in these two systems. This study demonstrates that the dynamic behaviour of methanol is much richer than what so far known, and prompts us to establish striking analogies with the features of liquid and supercooled water. In particular, based on the strong differences between the structural properties of the two systems, our results suggest that the assignment of some dynamical properties to the tetrahedral character of water structure should be questioned. We finally highlight the similarities between the characteristic decay times of the time correlation function, as obtained from our data and the mean lifetime of hydrogen bond known in literature.

  2. Optimization of hydrogen bonds for combined DNA/collagen complex.

    PubMed

    Pidaparti, Ramana M; Svintradze, David V; Shan, Yingfeng; Yokota, Hiroki

    2009-01-21

    Many natural and biological systems including collagen and DNA polymers are formed by a process of molecular self-assembly. In this paper, we developed two novel structural models and built heterogeneous DNA/collagen complexes through a preferable arrangement of multiple hydrogen bonds (H-bonds) between DNA and collagen molecules. The simulation results based on three sets of criteria indicate that one of the models with five collagen molecules, which are positioned around each strand of DNA molecules emerged to form a suitable polymer complex with the maximum number of H-bonds. Our predictions quantitatively validated and agreed with the molecular structure reported by Mrevlishvili and Svintradze [2005. Int. J. Biol. Macromol. 36, 324-326].

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

    USGS Publications Warehouse

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

    2001-01-01

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

  4. 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).

  5. An extremely stable, self-complementary hydrogen-bonded duplex

    SciTech Connect

    Zeng, Huang; Yang, Xiaowu; Brown, A L.; Martinovic, Suzana; Smith, Richard D.; Gong, Bing

    2003-07-30

    This paper describes the design, synthesis and characterization of a self-complementary six-H-bonded duplex with an association constant greater than 10{sup 9}/M in CHCl3. Numerous unnatural self-assembly systems have been developed in recent years. Most of these previously described systems are case-dependent, i.e., the individual components carry the information that defines only the formation of the specific assembly. An alternative approach involves the design of highly specific and highly stable recognition units (modules)that are compatible with a variety of structural components. Such recognition modules or ''molecular glues'' then direct the assembly of these structural components. In this regard,hydrogen-bonded complexes based on rigid heterocycles with multiple H-bonding donor (D) and acceptor (A) sites have received the most attention in recent years. Other complexes, most based on H-bonding interactions, have also been reported. Highly stable, self-complementary H-bonded complexes are particularly attractive for developing supramolecular homopolymers of very high molecular weights. In spite of the intriguing perspective, only a very small number of self-complementary H-bonded complexes with high stabilities are known. The best known examples involve two pairs of quadruply H-bonded, self-complementary complexes, both based on the AADD-DDAA array, and with association constants greater than 10{sup 7}/M. We report here the design and characterization of our first six-H-bonded, self-complementary duplex that contains the AADADD-DDADAA array.

  6. Toward the development of the potential with angular distortion for halogen bond: a comparison of potential energy surfaces between halogen bond and hydrogen bond.

    PubMed

    Wang, Lili; Gao, Jun; Bi, Fuzhen; Song, Bo; Liu, Chengbu

    2014-10-02

    As noncovalent intermolecular interactions, hydrogen bond (HB) and halogen bond (XB) are attracting increasing attention. In this work, the potential energy surfaces (PESs) of hydrogen and halogen bonds are compared. Twelve halogen-bonded and three hydrogen-bonded models are scanned for analysis using the MP2 level of theory. This work indicates that potential energy surfaces of both HB and XB have angular distortion. The potential well of XB is narrower than that of HB. With the elongation of the bond length, the potential energy surfaces get flatter. The best fitting functions for angular distortion and the flattening character of angular terms are also combined into a modified Buckingham potential. The testing results show that the essential features of the PES, including angular distortion and flattening character, have been reproduced. These results provide a better understanding of halogen and hydrogen bonds and the optimization of halogen bond force fields.

  7. Are non-linear C-H⋯O contacts hydrogen bonds or Van der Waals interactions?. Establishing the limits between hydrogen bonds and Van der Waals interactions

    NASA Astrophysics Data System (ADS)

    Novoa, Juan J.; Lafuente, Pilar; Mota, Fernando

    1998-07-01

    The hydrogen bond nature of angular C-H⋯O contacts is examined to determine when these contacts are better classified as hydrogen bonds or as Van der Waals bonds. To classify the bond we propose to look at the nature of the intermolecular bond critical point present in the electron density of the complex containing the bond. The physics behind this approach is explained using a qualitative orbital overlap model aimed at describing the main changes in the electronic density of the complex produced by the C-H⋯O bending.

  8. Hydrogen-Bonding Polarizable Intermolecular Potential Model for Water.

    PubMed

    Jiang, Hao; Moultos, Othonas A; Economou, Ioannis G; Panagiotopoulos, Athanassios Z

    2016-12-08

    A polarizable intermolecular potential model with short-range directional hydrogen-bonding interactions was developed for water. The model has a rigid geometry, with bond lengths and angles set to experimental gas-phase values. Dispersion interactions are represented by the Buckingham potential assigned to the oxygen atom, whereas electrostatic interactions are modeled by Gaussian charges. Polarization is handled by a Drude oscillator site, using a negative Gaussian charge attached to the oxygen atom by a harmonic spring. An explicit hydrogen-bonding term is included in the model to account for the effects of charge transfer. The model parameters were optimized to density, configurational energy, pair correlation function, and the dielectric constant of water under ambient conditions, as well as the minimum gas-phase dimer energy. Molecular dynamics and Gibbs ensemble Monte Carlo simulations were performed to evaluate the new model with respect to the thermodynamic and transport properties over a wide range of temperature and pressure conditions. Good agreement between model predictions and experimental data was found for most of the properties studied. The new model yields better performance relative to the majority of existing models and outperforms the BK3 model, which is one of the best polarizable models, for vapor-liquid equilibrium properties, whereas the new model is not better than the BK3 model for representation of other properties. The model can be efficiently simulated with the thermalized Drude oscillator algorithm, resulting in computational costs only 3 times higher than those of the nonpolarizable TIP4P/2005 model, whereas having significantly improved properties. Because it involves only a single Drude oscillator site, the new model is significantly faster than polarizable models with multiple sites. With the explicit inclusion of hydrogen-bond interactions, the model may provide a better description of the phase behavior of aqueous mixtures.

  9. 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.

  10. Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system.

    PubMed

    Liu, Cui; Zhao, Dong-Xia; Yang, Zhong-Zhi

    2012-02-05

    The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field.

  11. A new quadruple hydrogen-bonding module with a DDAA array: formation of a stable homodimer without competition from undesired hydrogen-bonded dimers.

    PubMed

    Hisamatsu, Yosuke; Shirai, Naohiro; Ikeda, Shin-ichi; Odashima, Kazunori

    2009-10-01

    A new DDAA hydrogen-bonding module (UImp-2), based on a ureidoimidazo[1,2-a]pyrimidine structure, forms a highly stable homodimer (K(dim) > 1.1 x 10(5) M(-1) in CDCl(3)) without competition from undesired hydrogen-bonded dimers.

  12. 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.

  13. Metal fluorides form strong hydrogen bonds and halogen bonds: measuring interaction enthalpies and entropies in solution.

    PubMed

    Libri, Stefano; Jasim, Naseralla A; Perutz, Robin N; Brammer, Lee

    2008-06-25

    The organometallic compound trans-(tetrafluoropyrid-2-yl)bis(triethylphosphine)-fluoronickel(II) (NiF) is shown to serve as a strong hydrogen bond and halogen bond acceptor in solution via intermolecular interactions with the fluoride ligand. The nature of the interactions has been confirmed by multinuclear NMR spectroscopy. Experimental binding constants, enthalpies, and entropies of interaction with hydrogen-bond-donor indole and halogen-bond-donor iodopentafluorobenzene have been determined by 19F NMR titration. In toluene-d8 solution indole forms a 1:1 and 2:1 complex with NiF (K1 = 57.9(3), K2 = 0.58(4)). Interaction enthalpies and entropies are -23.4(2) kJ mol-1 and -44.5(8) J mol-1 K-1, respectively, for the 1:1 complex; -14.8(8) kJ mol-1 and -53(3) J mol-1 K-1, respectively, for the 2:1 complex. In toluene-d8 solution iodopentafluorobenzene forms only a 1:1 complex (K1 = 3.41(9)) with enthalpy and entropy of interaction of -16(1) kJ mol-1 and -42(4) J mol-1 K-1, respectively. A marked solvent effect was observed for the halogen bond interaction. NMR titrations in heptane solution indicated formation of both 1:1 and 2:1 complexes of iodopentafluorobenzene with NiF (K1 = 21.8(2), K2 = 0.22(4)). Interaction enthalpies and entropies are -26(1) kJ mol-1 and -63(4) J mol-1 K-1, respectively, for the 1:1 complex; -21(1) kJ mol-1 and -83(5) J mol-1 K-1, respectively, for the 2:1 complex. There is a paucity of such experimental energetic data particularly for halogen bonds despite substantial structural data. These measurements demonstrate that halogen bonds are competitive with hydrogen bonds as intermolecular interactions and provide a suitable benchmark for theoretical calculations and quantitative input into design efforts in supramolecular chemistry and crystal engineering.

  14. 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.

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

    PubMed

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

    2012-09-07

    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.

  16. A new polymorph of triphenylmethylamine: the effect of hydrogen bonding.

    PubMed

    Khrustalev, Victor N; Borisova, Irina V; Zemlyansky, Nikolai N; Antipin, M Yu

    2009-02-01

    Crystallization of the hexane reaction mixture after treatment of LiGe(OCH(2)CH(2)NMe(2))(3) with Ph(3)CN(3) gives rise to a new triclinic (space group P\\overline{1}) polymorph of triphenylmethylamine, C(19)H(17)N, (I), containing dimers formed by N-H...N hydrogen bonds, whereas the structure of the known orthorhombic (space group P2(1)2(1)2(1)) polymorph of this compound, (II), consists of isolated molecules. While the dimers in (I) lie across crystallographic inversion centres, the molecules are not truly related by them. The centrosymmetric structure is due to the statistical disordering of the amino H atoms participating in the N-H...N hydrogen-bonding interactions, and thus the inversion centre is superpositional. The conformations and geometric parameters of the molecules in (I) and (II) are very similar. It was found that the polarity of the solvent does not affect the capability of triphenylmethylamine to crystallize in the different polymorphic modifications. The orthorhombic polymorph, (II), is more thermodynamically stable under normal conditions than the triclinic polymorph, (I). The experimental data indicate the absence of a phase transition in the temperature interval 120-293 K. The densities of (I) (1.235 Mg m(-3)) and (II) (1.231 Mg m(-3)) at 120 K are practically equal. It would seem that either the kinetic factors or the effects of the other products of the reaction facilitating the hydrogen-bonded dimerization of triphenylmethylamine molecules are the determining factor for the isolation of the triclinic polymorph (I) of triphenylmethylamine.

  17. 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.

  18. 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

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

    PubMed

    Zhang, Xiaojie; He, Junhui

    2015-03-18

    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.

  20. 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.

  1. 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.

  2. Hydrogen and dihydrogen bonding of transition metal hydrides

    NASA Astrophysics Data System (ADS)

    Jacobsen, Heiko

    2008-04-01

    Intermolecular interactions between a prototypical transition metal hydride WH(CO) 2NO(PH 3) 2 and a small proton donor H 2O have been studied using DFT methodology. The hydride, nitrosyl and carbonyl ligand have been considered as site of protonation. Further, DFT-D calculations in which empirical corrections for the dispersion energy are included, have been carried out. A variety of pure and hybrid density functionals (BP86, PW91, PBE, BLYP, OLYP, B3LYP, B1PW91, PBE0, X3LYP) have been considered, and our calculations indicate the PBE functional and its hybrid variation are well suited for the calculation of transition metal hydride hydrogen and dihydrogen bonding. Dispersive interactions make up for a sizeable portion of the intermolecular interaction, and amount to 20-30% of the bond energy and to 30-40% of the bond enthalpy. An energy decomposition analysis reveals that the H⋯H bond of transition metal hydrides contains both covalent and electrostatic contributions.

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

    PubMed Central

    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

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

    PubMed

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

    2017-04-07

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

  5. Hydrogen bonding in a mixture of protic ionic liquids: a molecular dynamics simulation study.

    PubMed

    Paschek, Dietmar; Golub, Benjamin; Ludwig, Ralf

    2015-04-07

    We report results of molecular dynamics (MD) simulations characterising the hydrogen bonding in mixtures of two different protic ionic liquids sharing the same cation: triethylammonium-methylsulfonate (TEAMS) and triethylammonium-triflate (TEATF). The triethylammonium-cation acts as a hydrogen-bond donor, being able to donate a single hydrogen-bond. Both, the methylsulfonate- and the triflate-anions can act as hydrogen-bond acceptors, which can accept multiple hydrogen bonds via their respective SO3-groups. In addition, replacing a methyl-group in the methylsulfonate by a trifluoromethyl-group in the triflate significantly weakens the strength of a hydrogen bond from an adjacent triethylammonium cation to the oxygen-site in the SO3-group of the anion. Our MD simulations show that these subtle differences in hydrogen bond strength significantly affect the formation of differently-sized hydrogen-bonded aggregates in these mixtures as a function of the mixture-composition. Moreover, the reported hydrogen-bonded cluster sizes can be predicted and explained by a simple combinatorial lattice model, based on the approximate coordination number of the ions, and using statistical weights that mostly account for the fact that each anion can only accept three hydrogen bonds.

  6. 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.

  7. Hydrogen-bonded clusters of ferrocenecarboxylic acid on Au(111).

    PubMed

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

    2014-09-14

    Self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH) contain two fundamental units, both stabilized by intermolecular hydrogen bonding: dimers and cyclic five-membered catemers. At surface coverages below a full monolayer, however, there is a significantly more varied structure that includes double-row clusters containing two to twelve FcCOOH molecules. Statistical analysis shows a distribution of cluster sizes that is sharply peaked compared to a binomial distribution. This rules out simple nucleation-and-growth mechanisms of cluster formation, and strongly suggests that clusters are formed in solution and collapse into rows when deposited on the Au(111) surface.

  8. 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.

  9. Change in hydrogen bonding structures of a hydrogel with dehydration

    NASA Astrophysics Data System (ADS)

    Naohara, Ryo; Narita, Kentaro; Ikeda-Fukazawa, Tomoko

    2017-02-01

    To investigate the mechanisms of structural changes in polymer network and water during dehydration, X-ray diffraction of poly-N,N-dimethylacrylamide (PDMAA) hydrogels was measured. The variation process in the individual structures of water and PDMAA were analyzed by decomposition of the diffraction patterns to separate the respective contributions. The results show that the short-range structures of PDMAA expand during dehydration, whereas the network structure as a whole shrinks. The average length of the hydrogen bonds between water molecules increases with the process. The present results provide a direct evidence of the structural changes of water and polymer in the hydrogel during dehydration.

  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 versus hyperconjugation in condensed-phase carbocations.

    PubMed

    Reed, Christopher A; Stoyanov, Evgenii S; Tham, Fook S

    2013-06-21

    Hyperconjugative stabilization of positive charge in tertiary carbocations is the textbook explanation for their stability and low frequency νCH bands in their IR spectra have long been taken as confirming evidence. While this is substantiated in the gas phase by the very close match of the IR spectrum of argon-tagged t-butyl cation with that calculated under C(s) symmetry, the situation in condensed phases is much less clear. The congruence of νCH(max) of t-Bu(+) in superacid media (2830 cm(-1)) with that in the gas phase (2834 cm(-1)) has recently been shown to be accidental. Rather, νCH(max) varies considerably as a function of counterion in a manner that reveals the presence of significant C-H···anion hydrogen bonding. This paper addresses the question of the relative importance of hyperconjugation versus H-bonding. We show by assigning IR spectra in the νCH region to specific C-H bonds in t-butyl cation that the low frequency νCH(max) band in the IR spectrum of t-butyl cation, long taken as direct evidence for hyperconjugation, appears to be due mostly to H-bonding. The appearance of similar low frequency νCH bands in the IR spectra of secondary alkyl carboranes such as i-Pr(CHB11Cl11), which have predominant sp(3) centres rather than sp(2) centres (and are therefore less supportive of hyperconjugation), also suggests the dominance of H-bonding over hyperconjugation.

  12. Hydrogen Bonding and Related Properties in Liquid Water: A Car-Parrinello Molecular Dynamics Simulation Study.

    PubMed

    Guardia, Elvira; Skarmoutsos, Ioannis; Masia, Marco

    2015-07-23

    The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the local hydrogen-bonding network on the local tetrahedral structure and entropy. The investigation of the dynamics of the local hydrogen-bonding network in liquid water has shown that this network is very labile, and the hydrogen bonds break and reform very rapidly. Nevertheless, it has been found that the hydrogen-bonding states associated with the formation of four hydrogen bonds by a water molecule exhibit the largest survival probability and corresponding lifetime. The reorientational motions of water molecules have also been found to be strongly dependent on their initial hydrogen-bonding state. Finally, the dependence of the librational and vibrational modes of water molecules on the local hydrogen-bonding network has been carefully examined, revealing a significant effect upon the libration and bond-stretching peak frequencies. The calculated low frequency peaks come in agreement with previously reported interpretations of the experimental low-frequency Raman spectrum of liquid water.

  13. 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.

  14. Insights into hydrogen bonding via ice interfaces and isolated water

    NASA Astrophysics Data System (ADS)

    Shultz, Mary Jane; Bisson, Patrick; Vu, Tuan Hoang

    2014-11-01

    Water in a confined environment has a combination of fewer available configurations and restricted mobility. Both affect the spectroscopic signature. In this work, the spectroscopic signature of water in confined environments is discussed in the context of competing models for condensed water: (1) as a system of intramolecular coupled molecules or (2) as a network with intermolecular dipole-dipole coupled O-H stretches. Two distinct environments are used: the confined asymmetric environment at the ice surface and the near-isolated environment of water in an infrared transparent matrix. Both the spectroscopy and the environment are described followed by a perspective discussion of implications for the two competing models. Despite being a small molecule, water is relatively complex; perhaps not surprisingly the results support a model that blends inter- and intramolecular coupling. The frequency, and therefore the hydrogen-bond strength, appears to be a function of donor-acceptor interaction and of longer-range dipole-dipole alignment in the hydrogen-bonded network. The O-H dipole direction depends on the local environment and reflects intramolecular O-H stretch coupling.

  15. 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.

  16. Infrared intensities and charge mobility in hydrogen bonded complexes

    SciTech Connect

    Galimberti, Daria; Milani, Alberto; Castiglioni, Chiara

    2013-08-21

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

  17. Insights into hydrogen bonding via ice interfaces and isolated water.

    PubMed

    Shultz, Mary Jane; Bisson, Patrick; Vu, Tuan Hoang

    2014-11-14

    Water in a confined environment has a combination of fewer available configurations and restricted mobility. Both affect the spectroscopic signature. In this work, the spectroscopic signature of water in confined environments is discussed in the context of competing models for condensed water: (1) as a system of intramolecular coupled molecules or (2) as a network with intermolecular dipole-dipole coupled O-H stretches. Two distinct environments are used: the confined asymmetric environment at the ice surface and the near-isolated environment of water in an infrared transparent matrix. Both the spectroscopy and the environment are described followed by a perspective discussion of implications for the two competing models. Despite being a small molecule, water is relatively complex; perhaps not surprisingly the results support a model that blends inter- and intramolecular coupling. The frequency, and therefore the hydrogen-bond strength, appears to be a function of donor-acceptor interaction and of longer-range dipole-dipole alignment in the hydrogen-bonded network. The O-H dipole direction depends on the local environment and reflects intramolecular O-H stretch coupling.

  18. Detection by high pressure infrared spectrometry of hydrogen-bonding between water and triacetyl glycerol.

    PubMed

    Mushayakarara, E C; Wong, P T; Mantsch, H H

    1986-01-14

    The barotropic behavior of neat and aqueous 1,2,3-triacetyl glycerol was investigated by FT-IR spectroscopy over the pressure range 0.001 to 35 kbar. The infrared spectrum in the presence of water shows bands characteristic of hydrogen bonded carbonyl groups. An increase in hydrostatic pressure leads to a strengthening of the intermolecular hydrogen bond between water and the lipid ester C = O groups. The pressure-induced formation of ice VI at 9 kbar does not affect this hydrogen bond, however, the formation, at 20 kbar, of ice VII in which the water/water hydrogen bonds are stronger than the lipid C = O/water hydrogen bonds, frees the lipid carbonyl groups from the hydrogen-bonding to water.

  19. The single donator-single acceptor hydrogen bonding structure in water probed by Raman spectroscopy.

    PubMed

    Sun, Qiang

    2010-02-07

    In this work, the Raman spectra of aqueous C(12)E(5) solutions are recorded and utilized to demonstrate the existence of single donator-single acceptor (DA) hydrogen bonding in water. From Raman OH stretching bands of aqueous C(12)E(5) solutions, the relative intensity of 3430 cm(-1) subband increases with C(12)E(5) concentrations. For confined water, the DA hydrogen bonding can be expected to be the important hydrogen bonding species. Therefore, the 3430 cm(-1) component can be ascribed to OH vibration engaged in DA hydrogen bonding. This is in agreement with our recent explanation on Raman OH stretching band of water. For water at ambient conditions, the double donor-double acceptor (DDAA) and DA should be the dominant hydrogen bonding species, the ratio of DDAA to DA can be approximately to be 0.75:1, and the mean hydrogen bonding can be determined to be 2.75.

  20. The single donator-single acceptor hydrogen bonding structure in water probed by Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Sun, Qiang

    2010-02-01

    In this work, the Raman spectra of aqueous C12E5 solutions are recorded and utilized to demonstrate the existence of single donator-single acceptor (DA) hydrogen bonding in water. From Raman OH stretching bands of aqueous C12E5 solutions, the relative intensity of 3430 cm-1 subband increases with C12E5 concentrations. For confined water, the DA hydrogen bonding can be expected to be the important hydrogen bonding species. Therefore, the 3430 cm-1 component can be ascribed to OH vibration engaged in DA hydrogen bonding. This is in agreement with our recent explanation on Raman OH stretching band of water. For water at ambient conditions, the double donor-double acceptor (DDAA) and DA should be the dominant hydrogen bonding species, the ratio of DDAA to DA can be approximately to be 0.75:1, and the mean hydrogen bonding can be determined to be 2.75.

  1. FTIR study of hydrogen bonds in coal under drop weight impact testing.

    PubMed

    Li, Cheng-Wu; Wang, Jin-Gui; Xie, Bei-Jing; Dong, Li-Hui; Sun, Ying-Feng; Cao, Xu

    2014-11-01

    There are many hydrogen bonds in coal, which affect the chemical structure and properties of coal. FTIR has been applied to the characterization study of the hydrogen bonds of Dongpang coals, which were under drop weight impact. There exists five kinds of hydrogen bonds in the coal: free OH groups, OH...π, OH...OH, cyclic OH tetramers and OH...N. Absorption strength of intermolecular hydrogen bonds markedly declined after impact. Free OH groups mechanical-power chemical reacted in drop weight impact testing. The infrared spectrum were curve-resolved into their component bands. The absorption strength of various hydrogen bonds decreased with the increase of impact energy, but the trend was slowing. By statistical relationship between then, we find then complying with power function relationship. By comparing the exponents of fitted equations, we concluded that failure sensitivity sequence of hydrogen bonds to the impact: free OH groups > cyclic OH tetramers > OH...N > OH...π > OH...OH.

  2. 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.

  3. Reactions of the cumyloxyl and benzyloxyl radicals with strong hydrogen bond acceptors. Large enhancements in hydrogen abstraction reactivity determined by substrate/radical hydrogen bonding.

    PubMed

    Salamone, Michela; DiLabio, Gino A; Bietti, Massimo

    2012-12-07

    A kinetic study on hydrogen abstraction from strong hydrogen bond acceptors such as DMSO, HMPA, and tributylphosphine oxide (TBPO) by the cumyloxyl (CumO(•)) and benzyloxyl (BnO(•)) radicals was carried out in acetonitrile. The reactions with CumO(•) were described in terms of a direct hydrogen abstraction mechanism, in line with the kinetic deuterium isotope effects, k(H)/k(D), of 2.0 and 3.1 measured for reaction of this radical with DMSO/DMSO-d(6) and HMPA/HMPA-d(18). Very large increases in reactivity were observed on going from CumO(•) to BnO(•), as evidenced by k(H)(BnO(•))/k(H)(CumO(•)) ratios of 86, 4.8 × 10(3), and 1.6 × 10(4) for the reactions with HMPA, TBPO, and DMSO, respectively. The k(H)/k(D) of 0.91 and 1.0 measured for the reactions of BnO(•) with DMSO/DMSO-d(6) and HMPA/HMPA-d(18), together with the k(H)(BnO(•))/k(H)(CumO(•)) ratios, were explained on the basis of the formation of a hydrogen-bonded prereaction complex between the benzyloxyl α-C-H and the oxygen atom of the substrates followed by hydrogen abstraction. This is supported by theoretical calculations that show the formation of relatively strong prereaction complexes. These observations confirm that in alkoxyl radical reactions specific hydrogen bond interactions can dramatically influence the hydrogen abstraction reactivity, pointing toward the important role played by structural and electronic effects.

  4. DFT and AIM studies of intramolecular hydrogen bonds in dicoumarols

    NASA Astrophysics Data System (ADS)

    Trendafilova, Natasha; Bauer, Günther; Mihaylov, Tzvetan

    2004-07-01

    Density functional calculations with Becke's three parameter hybrid method using the correlation functional of Lee, Yang and Parr (B3LYP) were carried out for 3,3 '-benzylidenebis(4-hydroxycoumarin) (phenyldicoumarol, PhDC), 3,3 '-methylenebis(4-hydroxycoumarin) (dicoumarol, DC) and the parent compound, 4-hydroxycoumarin (4-HC). Different basis sets were tested in the course of the calculations: 6-31G*, 6-31+G** and 6-311G*. In full agreement with available X-ray data, B3LYP/6-31G* calculations of the lowest-energy conformer, PhDC showed two O-H⋯O asymmetrical intramolecular hydrogen bonds with O⋯O distances 2.638 and 2.696 Å. The HB energies in PhDC were estimated of -55.46 and -52.32 kJ/mol, respectively. The values obtained correlated with the calculated and experimental O⋯O distances and predicted difference in the hydrogen bonding strengths in PhDC. The total HB energy in PhDC was calculated of -107.73 kJ/mol. At the same level of theory, both O⋯O intramolecular distances in DC were calculated identical (2.696 Å) and thus two symmetrical hydrogen bondings were obtained. The single HB strength was estimated of -50.89 kJ/mol and the total one of -101.79 kJ/mol. The electron density ( ρb) and Laplacian (∇ 2ρb) properties, estimated by AIM calculations, showed that both O⋯H bonds have low ρb and positive ∇ 2ρb values (consistent with electrostatic character of the HBs), whereas both O-H bonds have covalent character (∇ 2ρb<0). Natural population analysis data for PhDC, DC and 4-HC were used to predict electrostatic interactions in the exocyclic rings. The calculated oxygen natural charges were found to correlate with the O⋯O distances in PhDC and DC. On the basis of the calculated bond ellipticity, the π-delocalization in the exocyclic rings of PhDC and DC was estimated. The results thus obtained helped to describe the nature of the intramolecular O⋯H-O bonds and the forces driving their formation

  5. Three Hydrogen Bond Donor Catalysts: Oxyanion Hole Mimics and Transition State Analogues

    SciTech Connect

    Beletskiy, Evgeny V.; Schmidt, Jacob C.; Wang, Xue B.; Kass, Steven R.

    2012-11-14

    Enzymes and their mimics use hydrogen bonds to catalyze chemical transformations. Small molecule transition state analogs of oxyanion holes are characterized by gas phase IR and photoelectron spectroscopy and their binding constants in acetonitrile. As a result, a new class of hydrogen bond catalysts is proposed (OH donors that can contribute three hydrogen bonds to a single functional group) and demonstrated in a Friedel-Crafts reaction.

  6. Mechanisms of hydrogen bond formation between ionic liquids and cellulose and the influence of water content.

    PubMed

    Rabideau, Brooks D; Ismail, Ahmed E

    2015-02-28

    We study the dynamics of the formation of multiple hydrogen bonds between ionic liquid anions and cellulose using molecular dynamics simulations. We examine fifteen different ionic liquids composed of 1-alkyl-3-methylimidazolium cations ([Cnmim], n = 1, 2, 3, 4, 5) paired with either chloride, acetate or dimethylphosphate. We map the transitions of anions hydrogen bonded to cellulose into different bonding states. We find that increased tail length in the ionic liquids has only a very minor effect on these transitions, tending to slow the dynamics of the transitions and increasing the hydrogen bond lifetimes. Each anion can form up to four hydrogen bonds with cellulose. We find that this hydrogen bond "redundancy" leads to multiply bonded anions having lifetimes three to four times that of singly bound anions. Such redundant hydrogen bonds account for roughly half of all anion-cellulose hydrogen bonds. Additional simulations for [C2mim]Cl, [C2mim]Ac and [C2mim]DMP were performed at different water concentrations between 70 mol% and 90 mol%. It was found that water crowds the hydrogen bond-accepting sites of the anions, preventing interactions with cellulose. The more water that is present in the system, the more crowded these sites become. Thus, if a hydrogen bond between an anion and cellulose breaks, the likelihood that it will be replaced by a nearby water molecule increases as well. We show that the formation of these "redundant" hydrogen bonding states is greatly affected by the presence of water, leading to steep drops in hydrogen bonding between the anions and cellulose.

  7. HBonanza: A Computer Algorithm for Molecular-Dynamics-Trajectory Hydrogen-Bond Analysis

    PubMed Central

    Durrant, Jacob D.; McCammon, J. Andrew

    2011-01-01

    In the current work, we present a hydrogen-bond analysis of 2,673 ligand-receptor complexes that suggests the total number of hydrogen bonds formed between a ligand and its protein receptor is a poor predictor of ligand potency; furthermore, even that poor prediction does not suggest a statistically significant correlation between hydrogen-bond formation and potency. While we are not the first to suggest that hydrogen bonds on average do not generally contribute to ligand binding affinities, this additional evidence is nevertheless interesting. The primary role of hydrogen bonds may instead be to ensure specificity, to correctly position the ligand within the active site, and to hold the protein active site in a ligand-friendly conformation. We also present a new computer program called HBonanza (hydrogen-bond analyzer) that aids the analysis and visualization of hydrogen-bond networks. HBonanza, which can be used to analyze single structures or the many structures of a molecular dynamics trajectory, is open source and python implemented, making it easily editable, customizable, and platform independent. Unlike many other freely available hydrogen-bond analysis tools, HBonanza provides not only a text-based table describing the hydrogen-bond network, but also a Tcl script to facilitate visualization in VMD, a popular molecular visualization program. Visualization in other programs is also possible. A copy of HBonanza can be obtained free of charge from http://www.nbcr.net/hbonanza. PMID:21880522

  8. 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.

  9. Hydrogen bonding Part 39. Hydrogen bonding by α-CH in quaternary ammonium salts and the possible role of CH⋯B hydrogen bonds in acetylcholine—receptor interactions

    NASA Astrophysics Data System (ADS)

    Harmon, Kenneth M.; De Santis, Nancy J.; Brandt, Dale O.

    1992-01-01

    Correlation of IR spectral properties with crystallographic data for tetramethylammonium ion salts shows that CH⋯B hydrogen bonding in quaternary ammonium ions salts can be assumed to be present when ( rC⋯B)( rvdwB+0.95Å)<1.00 Å. The value 0.95 Å is the average CH bond length shown by α-CH (HCN + for a variety of quaternary ammonium ions. This approach allows estimation of the presence or absence of CH⋯B hydrogen bonding is salts where hydrogens have not been located in diffraction studies. Application to choline chloride and acetylcholine chloride, bromide and iodide demostrates that CH-to-anion hydrogen bonding is present is these salts. Since tetramethylammonium ion shows CH⋯O hydrogen bonding with even the very weak acceptor ClO -4, it is likely that hydrogen bonding from the (CH 3) 3N +CH 2- group of acetylcholine to groups such as phosphate of carboxylate will play a role in the binding of acetylcholine to the anionic site of the receptor.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

  13. Interplay of hydrogen bonds and n→π* interactions in proteins.

    PubMed

    Bartlett, Gail J; Newberry, Robert W; VanVeller, Brett; Raines, Ronald T; Woolfson, Derek N

    2013-12-11

    Protein structures are stabilized by multiple weak interactions, including the hydrophobic effect, hydrogen bonds, electrostatic effects, and van der Waals interactions. Among these interactions, the hydrogen bond is distinct in having its origins in electron delocalization. Recently, another type of electron delocalization, the n→π* interaction between carbonyl groups, has been shown to play a role in stabilizing protein structure. Here we examine the interplay between hydrogen bonding and n→π* interactions. To address this issue, we used data available from high-resolution protein crystal structures to interrogate asparagine side-chain oxygen atoms that are both acceptors of a hydrogen bond and donors of an n→π* interaction. Then we employed natural bond orbital analysis to determine the relative energetic contributions of the hydrogen bonds and n→π* interactions in these systems. We found that an n→π* interaction is worth ~5-25% of a hydrogen bond and that stronger hydrogen bonds tend to attenuate or obscure n→π* interactions. Conversely, weaker hydrogen bonds correlate with stronger n→π* interactions and demixing of the orbitals occupied by the oxygen lone pairs. Thus, these two interactions conspire to stabilize local backbone-side-chain contacts, which argues for the inclusion of n→π* interactions in the inventory of non-covalent forces that contribute to protein stability and thus in force fields for biomolecular modeling.

  14. Hydrogen bonding in 1-butyl- and 1-ethyl-3-methylimidazolium chloride ionic liquids.

    PubMed

    Skarmoutsos, Ioannis; Dellis, Dimitris; Matthews, Richard P; Welton, Tom; Hunt, Patricia A

    2012-04-26

    A detailed investigation of hydrogen bonding in the pure ionic liquids [C4C1im]Cl and [C2C1im]Cl has been carried out using primarily molecular dynamics techniques. Analyses of the individual atom-atom pair radial distribution functions, and in particular those for C···Cl(-), have revealed that hydrogen bonding to the first methylene or methyl units of the substituent groups is important. Multiple geometric criteria for defining a hydrogen bond have been applied, and in particular the choice of the cutoff angle has been carefully examined. The interpretation of hydrogen bonding within these ionic liquids is highly angle dependent, and justification is provided for why it may be appropriate to employ a wider angle criteria than the 30° used for water or alcohol systems. The different types of hydrogen bond formed are characterized, and "top" conformations where the Cl anion resides above (or below) the imidazolium ring are investigated. The number of hydrogen bonds undertaken by each hydrogen atom (and the chloride anion) is quantified, and the propensity to form zero, one, or two hydrogen bonds is established. The effects of an increase in temperature on the static hydrogen bonding are also briefly examined.

  15. 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.

  16. 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.

  17. Hydrogen bonded OH-stretching vibration in the water dimer.

    PubMed

    Schofield, Daniel P; Lane, Joseph R; Kjaergaard, Henrik G

    2007-02-01

    We have calculated the frequencies and intensities of the hydrogen-bonded OH-stretching transitions in the water dimer complex. The potential-energy curve and dipole-moment function are calculated ab initio at the coupled cluster with singles, doubles, and perturbative triples level of theory with correlation-consistent Dunning basis sets. The vibrational frequencies and wavefunctions are found from a numerical solution to a one-dimensional Schrödinger equation. The corresponding transition intensities are found from numerical integration of these vibrational wavefunctions with the ab initio calculated dipole moment function. We investigate the effect of counterpoise correcting both the potential-energy surface and dipole-moment function. We find that the effect of using a numeric potential is significant for higher overtones and that inclusion of a counterpoise correction for basis set superposition error is important.

  18. 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.

  19. 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

    2016-09-06

    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.

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

    PubMed Central

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

    2016-01-01

    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

  1. Selective perrhenate recognition in pure water by halogen bonding and hydrogen bonding alpha-cyclodextrin based receptors.

    PubMed

    Cornes, Stuart P; Sambrook, Mark R; Beer, Paul D

    2017-03-20

    Alpha-cyclodextrin based anion receptors functionalised with pendant arms containing halogen and hydrogen bond donor motifs display selective association of perrhenate in aqueous media at neutral pH. NMR and ITC anion binding investigations reveal the halogen bonding receptor to be the superior host.

  2. Friedel-Crafts reaction of benzyl fluorides: selective activation of C-F bonds as enabled by hydrogen bonding.

    PubMed

    Champagne, Pier Alexandre; Benhassine, Yasmine; Desroches, Justine; Paquin, Jean-François

    2014-12-08

    A Friedel-Crafts benzylation of arenes with benzyl fluorides has been developed. The reaction produces 1,1-diaryl alkanes in good yield under mild conditions without the need for a transition metal or a strong Lewis acid. A mechanism involving activation of the C-F bond through hydrogen bonding is proposed. This mode of activation enables the selective reaction of benzylic C-F bonds in the presence of other benzylic leaving groups.

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

    PubMed

    Jouypazadeh, Hamidreza; Farrokhpour, Hossein; Solimannejad, Mohammad

    2017-05-01

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

  4. 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.

  5. Bimodal dynamics of mechanically constrained hydrogen bonds revealed by vibrational photon echoes

    NASA Astrophysics Data System (ADS)

    Bodis, Pavol; Yeremenko, Sergiy; Berná, José; Buma, Wybren J.; Leigh, David A.; Woutersen, Sander

    2011-04-01

    We have investigated the dynamics of the hydrogen bonds that connect the components of a [2]rotaxane in solution. In this rotaxane, the amide groups in the benzylic-amide macrocycle and the succinamide thread are connected by four equivalent N-HṡṡṡO=C hydrogen bonds. The fluctuations of these hydrogen bonds are mirrored by the frequency fluctuations of the NH-stretch modes, which are probed by means of three-pulse photon-echo peak shift spectroscopy. The hydrogen-bond fluctuations occur on three different time scales, with time constants of 0.1, 0.6, and ⩾200 ps. Comparing these three time scales to the ones found in liquid formamide, which contains the same hydrogen-bonded amide motif but without mechanical constraints, we find that the faster two components, which are associated with small-amplitude fluctuations in the strength of the N-HṡṡṡO=C hydrogen bonds, are very similar in the liquid and the rotaxane. However, the third component, which is associated with the breaking and subsequent reformation of hydrogen bonds, is found to be much slower in the rotaxane than in the liquid. It can be concluded that the mechanical bonding in a rotaxane does not influence the amplitude and time scale of the small-amplitude fluctuations of the hydrogen bonds, but strongly slows down the complete dissociation of these hydrogen bonds. This is probably because in a rotaxane breaking of the macrocycle-axle contacts is severely hindered by the mechanical constraints. The hydrogen-bond dynamics in rotaxane-based molecular machines can therefore be regarded as liquidlike on a time scale 1 ps and less, but structurally frozen on longer (up to at least 200 ps) time scales.

  6. Hydrogen-bonding Interactions between Apigenin and Ethanol/Water: A Theoretical Study

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    In this work, hydrogen-bonding interactions between apigenin and water/ethanol were investigated from a theoretical perspective using quantum chemical calculations. Two conformations of apigenin molecule were considered in this work. The following results were found. (1) For apigenin monomer, the molecular structure is non-planar, and all of the hydrogen and oxygen atoms can be hydrogen-bonding sites. (2) Eight and seven optimized geometries are obtained for apigenin (I)–H2O/CH3CH2OH and apigenin (II)–H2O/CH3CH2OH complexes, respectively. In apigenin, excluding the aromatic hydrogen atoms in the phenyl substituent, all other hydrogen atoms and the oxygen atoms form hydrogen-bonds with H2O and CH3CH2OH. (3) In apigenin–H2O/CH3CH2OH complexes, the electron density and the E(2) in the related localized anti-bonding orbital are increased upon hydrogen-bond formation. These are the cause of the elongation and red-shift of the X‑H bond. The sum of the charge change transfers from the hydrogen-bond acceptor to donor. The stronger interaction makes the charge change more intense than in the less stable structures. (4) Most of the hydrogen-bonds in the complexes are electrostatic in nature. However, the C4‑O5···H, C9‑O4···H and C13‑O2···H hydrogen-bonds have some degree of covalent character. Furthermore, the hydroxyl groups of the apigenin molecule are the preferred hydrogen-bonding sites.

  7. Hydrogen-bonding Interactions between Apigenin and Ethanol/Water: A Theoretical Study

    PubMed Central

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

    2016-01-01

    In this work, hydrogen-bonding interactions between apigenin and water/ethanol were investigated from a theoretical perspective using quantum chemical calculations. Two conformations of apigenin molecule were considered in this work. The following results were found. (1) For apigenin monomer, the molecular structure is non-planar, and all of the hydrogen and oxygen atoms can be hydrogen-bonding sites. (2) Eight and seven optimized geometries are obtained for apigenin (I)–H2O/CH3CH2OH and apigenin (II)–H2O/CH3CH2OH complexes, respectively. In apigenin, excluding the aromatic hydrogen atoms in the phenyl substituent, all other hydrogen atoms and the oxygen atoms form hydrogen-bonds with H2O and CH3CH2OH. (3) In apigenin–H2O/CH3CH2OH complexes, the electron density and the E(2) in the related localized anti-bonding orbital are increased upon hydrogen-bond formation. These are the cause of the elongation and red-shift of the X−H bond. The sum of the charge change transfers from the hydrogen-bond acceptor to donor. The stronger interaction makes the charge change more intense than in the less stable structures. (4) Most of the hydrogen-bonds in the complexes are electrostatic in nature. However, the C4−O5···H, C9−O4···H and C13−O2···H hydrogen-bonds have some degree of covalent character. Furthermore, the hydroxyl groups of the apigenin molecule are the preferred hydrogen-bonding sites. PMID:27698481

  8. Insights into the spontaneity of hydrogen bond formation between formic acid and phthalimide derivatives.

    PubMed

    Júnior, Rogério V A; Moura, Gustavo L C; Lima, Nathalia B D

    2016-11-01

    We evaluated a group of phthalimide derivatives, which comprise a convenient test set for the study of the multiple factors involved in the energetics of hydrogen bond formation. Accordingly, we carried out quantum chemical calculations on the hydrogen bonded complexes formed between a sample of phthalimide derivatives with formic acid with the intent of identifying the most important electronic and structural factors related to how their strength and spontaneity vary across the series. The geometries of all species considered were fully optimized at DFT B3LYP/6-31++G(d,p), RM1, RM1-DH2, and RM1-D3H4 level, followed by frequency calculations to determine their Gibbs free energies of hydrogen bond formation using Gaussian 2009 and MOPAC 2012. Our results indicate that the phthalimide derivatives that form hydrogen bond complexes most favorably, have in their structures only one C=O group and at least one NH group. On the other hand, the phthalimide derivatives predicted to form hydrogen bonds least favorably, possess in their structures two carbonyl groups, C=O, and no NH group. The ability to donate electrons and simultaneously receive one acidic hydrogen is the most important property related to the spontaneity of hydrogen bond formation. We further chose two cyclic compounds, phthalimide and isoindolin-1-one, in which to study the main changes in molecular, structural and spectroscopic properties as related to the formation of hydrogen bonds. Thus, the greatest ability of the isoindolin-1-one compound in forming hydrogen bonds is evidenced by the larger effect on the structural, vibrational, and chemical shifts properties associated with the O-H group. In summary, the electron-donating ability of the hydrogen bond acceptor emerged as the most important property differentiating the spontaneity of hydrogen bond formation in this group of complexes.

  9. Backscattering interferometry: an alternative approach for the study of hydrogen bonding interactions in organic solvents.

    PubMed

    Pesciotta, Esther N; Bornhop, Darryl J; Flowers, Robert A

    2011-05-20

    Intermolecular interactions involving hydrogen bonds are responsible for catalysis and recognition. Traditional methods used to study hydrogen-bonding interactions are generally limited to relatively large volumes and high substrate concentrations. Backscattering Interferometry (BSI) provides a microfluidic platform to study these interactions in nonaqueous media at micromolar to nanomolar concentrations in picoliter volumes by monitoring changes in the refractive index.

  10. 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…

  11. Origin of hydrophobicity and enhanced water hydrogen bond strength near purely hydrophobic solutes

    PubMed Central

    Grdadolnik, Joze; Merzel, Franci; Avbelj, Franc

    2017-01-01

    Hydrophobicity plays an important role in numerous physicochemical processes from the process of dissolution in water to protein folding, but its origin at the fundamental level is still unclear. The classical view of hydrophobic hydration is that, in the presence of a hydrophobic solute, water forms transient microscopic “icebergs” arising from strengthened water hydrogen bonding, but there is no experimental evidence for enhanced hydrogen bonding and/or icebergs in such solutions. Here, we have used the redshifts and line shapes of the isotopically decoupled IR oxygen–deuterium (O-D) stretching mode of HDO water near small purely hydrophobic solutes (methane, ethane, krypton, and xenon) to study hydrophobicity at the most fundamental level. We present unequivocal and model-free experimental proof for the presence of strengthened water hydrogen bonds near four hydrophobic solutes, matching those in ice and clathrates. The water molecules involved in the enhanced hydrogen bonds display extensive structural ordering resembling that in clathrates. The number of ice-like hydrogen bonds is 10–15 per methane molecule. Ab initio molecular dynamics simulations have confirmed that water molecules in the vicinity of methane form stronger, more numerous, and more tetrahedrally oriented hydrogen bonds than those in bulk water and that their mobility is restricted. We show the absence of intercalating water molecules that cause the electrostatic screening (shielding) of hydrogen bonds in bulk water as the critical element for the enhanced hydrogen bonding around a hydrophobic solute. Our results confirm the classical view of hydrophobic hydration. PMID:28028244

  12. Efficient electronic communication between two identical ferrocene centers in a hydrogen-bonded dimer.

    PubMed

    Sun, Hao; Steeb, Jennifer; Kaifer, Angel E

    2006-03-08

    A novel ferrocene derivative that contains a donor-donor-acceptor-acceptor (DDAA) hydrogen bonding motif forms highly stable, noncovalent dimers in chloroform and dichloromethane solutions. Its voltammetric behavior and the observation of an intervalence charge-transfer band reveal that the two equivalent ferrocene centers in the hydrogen-bonded dimer exhibit a surprisingly efficient level of electronic communication.

  13. DFT study of hydrogen-bonded dimers and tetramer of glyoxilic acid oxime

    NASA Astrophysics Data System (ADS)

    Georgieva, Ivelina; Binev, Daniel; Trendafilova, Natasha; Bauer, Günther

    2003-01-01

    DFT study of hydrogen-bonded dimers and tetramer of glyoxilic acid oxime (GAO) has been performed at B3LYP/6-31G* and B3LYP/6-31++G** levels of the theory. The N⋯HO and O⋯HO hydrogen bondings in the self-assembling structures studied have been estimated from intermolecular distances, enthalpy of stabilization, hydrogen-bonding energies and AIM electron density at the hydrogen bond critical points. The calculated hydrogen-bonding energies of various GAO dimers suggested a cooperative interaction in the cyclic dimers and tetramer. The comparative study of chain aggregate with both head-to-head and tail-to-tail bondings and chain aggregate only with head-to-tail bondings, showed that the latter is enthalpically preferred in agreement with the crystal structure of GAO. Harmonic frequencies for the monomer, five dimers and tetramer have been calculated and discussed as to the changes in the most sensitive to the complexation vibrations and as to the strengths of the O⋯HO and N⋯HO hydrogen bondings. Vibrational analysis at B3LYP/6-31G* level confirmed the suggestion for a cooperativity in the cyclic H-bonded complexes. Natural population analysis was performed to predict electrostatic interactions in the cyclic H-bonded complexes. The π-delocalization was estimated on the basis of the calculated AIM ellipticity.

  14. Understanding hydrogen atom transfer: from bond strengths to Marcus theory.

    PubMed

    Mayer, James M

    2011-01-18

    Hydrogen atom transfer (HAT), a key step in many chemical, environmental, and biological processes, is one of the fundamental chemical reactions: A-H + B → A + H-B. Traditional HAT involves p-block radicals such as tert-BuO(•) abstracting H(•) from organic molecules. More recently, the recognition that transition metal species undergo HAT has led to a broader perspective, with HAT viewed as a type of proton-coupled electron transfer (PCET). When transition metal complexes oxidize substrates by removing H(•) (e(-) + H(+)), typically the electron transfers to the metal and the proton to a ligand. Examples with iron-imidazolinate, vanadium-oxo, and many other complexes are discussed. Although these complexes may not "look like" main group radicals, they have the same pattern of reactivity. For instance, their HAT rate constants parallel the A-H bond strengths within a series of similar reactions. Like main group radicals, they abstract H(•) much faster from O-H bonds than from C-H bonds of the same strength, showing that driving force is not the only determinant of reactivity. This Account describes our development of a conceptual framework for HAT with a Marcus theory approach. In the simplest model, the cross relation uses the self-exchange rate constants (k(AH/A) for AH + A) and the equilibrium constant to predict the rate constant for AH + B: k(AH/B) = (k(AH/A)k(BH/B)K(eq)f)(1/2). For a variety of transition metal oxidants, k(AH/B) is predicted within one or two orders of magnitude with only a few exceptions. For 36 organic reactions of oxyl radicals, k(AH/B) is predicted with an average deviation of a factor of 3.8, and within a factor of 5 for all but six of the reactions. These reactions involve both O-H or C-H bonds, occur in either water or organic solvents, and occur over a range of 10(28) in K(eq) and 10(13) in k(AH/B). The treatment of organic reactions includes the well-established kinetic solvent effect on HAT reactions. This is one of a number

  15. DFT study of hydrogen bonding and IR spectra of calix[6]arene

    NASA Astrophysics Data System (ADS)

    Furer, V. L.; Potapova, L. I.; Kovalenko, V. I.

    2017-01-01

    IR and far IR spectra of calix[6]arene were recorded at various temperatures, between 16 and 180 °C and spectra of solutions and crystalline solids were obtained. Density functional calculations (DFT) gave vibrational frequencies and infrared intensities for the compressed cone conformation. Complete assignments were made for experimental IR spectrum of the compressed cone conformer. DFT calculations, in conjunction with experimental data give a better understanding of the effect of hydrogen bonding on the typical bands of calixarenes. Method of FTIR spectroscopy shows that a cyclic cooperative intramolecular hydrogen bond is implemented in calix[6]arene. Weakening of the cooperative hydrogen bond in calixarenes is caused by the mutual influence of covalent and hydrogen-bonded macrocycles on each other. Analysis of IR spectra changes during heating showed that calix[6]arene remains in the compressed cone conformation. In a molecule of calix[6]arene six oxygen atoms form a "boat" conformation with three pairs of hydrogen bonds.

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

    SciTech Connect

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

    1983-01-01

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

  17. 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.

  18. 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.

  19. Hydrogen bonding in the protic ionic liquid triethylammonium nitrate explored by density functional tight binding simulations

    NASA Astrophysics Data System (ADS)

    Zentel, Tobias; Kühn, Oliver

    2016-12-01

    The applicability of the density functional based tight binding (DFTB) method to the description of hydrogen bond dynamics and infrared (IR) spectroscopy is addressed for the exemplary protic ionic liquid triethylammonium nitrate. Potential energy curves for proton transfer in gas and liquid phases are shown to be comparable to the high level coupled cluster theory in the thermally accessible range of bond lengths. Geometric correlations in the hydrogen bond dynamics are analyzed for a cluster of six ion pairs. Comparing DFTB and DFT data lends further support for the reliability of the DFTB method. Therefore, DFTB bulk simulations are performed to quantify the extent of geometric correlations in terms of Pauling's bond order model. Further, IR absorption spectra are obtained using DFTB and analyzed putting emphasis on the signatures of hydrogen bonding in the NH-stretching and far IR hydrogen bond range.

  20. 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

  1. 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.

  2. Evidences for Cooperative Resonance-Assisted Hydrogen Bonds in Protein Secondary Structure Analogs

    PubMed Central

    Zhou, Yu; Deng, Geng; Zheng, Yan-Zhen; Xu, Jing; Ashraf, Hamad; Yu, Zhi-Wu

    2016-01-01

    Cooperative behaviors of the hydrogen bonding networks in proteins have been discovered for a long time. The structural origin of this cooperativity, however, is still under debate. Here we report a new investigation combining excess infrared spectroscopy and density functional theory calculation on peptide analogs, represented by N-methylformamide (NMF) and N-methylacetamide (NMA). Interestingly, addition of the strong hydrogen bond acceptor, dimethyl sulfoxide, to the pure analogs caused opposite effects, namely red- and blue-shift of the N−H stretching infrared absorption in NMF and NMA, respectively. The contradiction can be reconciled by the marked lowering of the energy levels of the self-associates between NMA molecules due to a cooperative effect of the hydrogen bonds. On the contrary, NMF molecules cannot form long-chain cooperative hydrogen bonds because they tend to form dimers. Even more interestingly, we found excellent linear relationships between changes on bond orders of N−H/N−C/C = O and the hydrogen bond energy gains upon the formation of hydrogen bonding multimers in NMA, suggesting strongly that the cooperativity originates from resonance-assisted hydrogen bonds. Our findings provide insights on the structures of proteins and may also shed lights on the rational design of novel molecular recognition systems. PMID:27849028

  3. Evidences for Cooperative Resonance-Assisted Hydrogen Bonds in Protein Secondary Structure Analogs

    NASA Astrophysics Data System (ADS)

    Zhou, Yu; Deng, Geng; Zheng, Yan-Zhen; Xu, Jing; Ashraf, Hamad; Yu, Zhi-Wu

    2016-11-01

    Cooperative behaviors of the hydrogen bonding networks in proteins have been discovered for a long time. The structural origin of this cooperativity, however, is still under debate. Here we report a new investigation combining excess infrared spectroscopy and density functional theory calculation on peptide analogs, represented by N-methylformamide (NMF) and N-methylacetamide (NMA). Interestingly, addition of the strong hydrogen bond acceptor, dimethyl sulfoxide, to the pure analogs caused opposite effects, namely red- and blue-shift of the N‑H stretching infrared absorption in NMF and NMA, respectively. The contradiction can be reconciled by the marked lowering of the energy levels of the self-associates between NMA molecules due to a cooperative effect of the hydrogen bonds. On the contrary, NMF molecules cannot form long-chain cooperative hydrogen bonds because they tend to form dimers. Even more interestingly, we found excellent linear relationships between changes on bond orders of N‑H/N‑C/C = O and the hydrogen bond energy gains upon the formation of hydrogen bonding multimers in NMA, suggesting strongly that the cooperativity originates from resonance-assisted hydrogen bonds. Our findings provide insights on the structures of proteins and may also shed lights on the rational design of novel molecular recognition systems.

  4. Correlation of the bond-length change and vibrational frequency shift in model hydrogen-bonded complexes of pyrrole

    NASA Astrophysics Data System (ADS)

    McDowell, Sean A. C.

    2017-04-01

    An MP2 computational study of model hydrogen-bonded pyrrole⋯YZ (YZ = NH3, NCH, BF, CO, N2, OC, FB) complexes was undertaken in order to examine the variation of the Nsbnd H bond length change and its associated vibrational frequency shift. The chemical hardness of Y, as well as the YZ dipole moment, were found to be important parameters in modifying the bond length change/frequency shift. The basis set effect on the computed properties was also assessed. A perturbative model, which accurately reproduced the ab initio Nsbnd H bond length changes and frequency shifts, was useful in rationalizing the observed trends.

  5. Adaptive polymeric nanomaterials utilizing reversible covalent and hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Neikirk, Colin

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

  6. C-H…O hydrogen bonds in FK506-binding protein-ligand interactions.

    PubMed

    Rajan, Sreekanth; Baek, Kwanghee; Yoon, Ho Sup

    2013-11-01

    Hydrogen bonds are important interaction forces observed in protein structures. They can be classified as stronger or weaker depending on their energy, thereby reflecting on the type of donor. The contribution of weak hydrogen bonds is deemed as an important factor toward structure stability along with the stronger bonds. One such bond, the C-H…O type hydrogen bond, is shown to make a contribution in maintaining three dimensional structures of proteins. Apart from their presence within protein structures, the role of these bonds in protein-ligand interactions is also noteworthy. In this study, we present a statistical analysis on the presence of C-H…O hydrogen bonds observed between FKBPs and their cognate ligands. The FK506-binding proteins (FKBPs) carry peptidyl cis-trans isomerase activity apart from the immunosuppressive property by binding to the immunosuppressive drugs FK506 or rapamycin. Because the active site of FKBPs is lined up by many hydrophobic residues, we speculated that the prevalence of C-H…O hydrogen bonds will be considerable. In a total of 25 structures analyzed, a higher frequency of C-H…O hydrogen bonds is observed in comparison with the stronger hydrogen bonds. These C-H…O hydrogen bonds are dominated by a highly conserved donor, the C(α/β) of Val55 and an acceptor, the backbone oxygen of Glu54. Both these residues are positioned in the β4-α1 loop, whereas the other residues Tyr26, Phe36 and Phe99 with higher frequencies are lined up at the opposite face of the active site. These preferences could be implicated in FKBP pharmacophore models toward enhancing the ligand affinity. This study could be a prelude to studying other proteins with hydrophobic pockets to gain better insights into ligand recognition.

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

    PubMed

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

    2015-09-28

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

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

    PubMed

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

    2015-09-03

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

  9. Competitive pi interactions and hydrogen bonding within imidazolium ionic liquids.

    PubMed

    Matthews, Richard P; Welton, Tom; Hunt, Patricia A

    2014-02-21

    In this paper we have explored the structural and energetic landscape of potential π(+)-π(+) stacked motifs, hydrogen-bonding arrangements and anion-π(+) interactions for gas-phase ion pair (IP) conformers and IP-dimers of 1,3-dimethylimidazolium chloride, [C1C1im]Cl. We classify cation-cation ring stacking as an electron deficient π(+)-π(+) interaction, and a competitive anion on-top IP motif as an anion-donor π(+)-acceptor interaction. 21 stable IP-dimers have been obtained within an energy range of 0-126 kJ mol(-1). The structures have been found to exhibit a complex interplay of structural features. We have found that low energy IP-dimers are not necessarily formed from the lowest energy IP conformers. The sampled range of IP-dimers exhibits new structural forms that cannot be recovered by examining the ion-pairs alone, moreover the IP-dimers are recovering additional key features of the local liquid structure. Including dispersion is shown to impact both the relative energy ordering and the geometry of the IPs and IP-dimers, however the impact is found to be subtle and dependent on the underlying functional.

  10. 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

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

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

    SciTech Connect

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

    2010-05-01

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

  13. Effects of hydrogen bond on 2-aminopyridine and its derivatives complexes in methanol solvent.

    PubMed

    Zhao, Jinfeng; Song, Peng; Cui, Yanling; Liu, Xuemei; Sun, Shaowu; Hou, Siyao; Ma, Fengcai

    2014-10-15

    In the present work, the time-dependent density functional theory (TD-DFT) method was adopted to investigate the excited state hydrogen-bond dynamics of 2-aminopyridine monomer (2AP) and its derivatives in hydrogen donating methanol solvent. The calculated steady-state absorption and fluorescence spectra agree well with the experimental results. Theoretical results state that the bond lengths of both O-H and N-H bands are lengthened, while the intermolecular hydrogen bond lengths are shortened in the excited state. Further, the intermolecular hydrogen bonds are proved to be strengthened according to the calculated binding energy. As a reasonable explanation, the hydrogen bonds binding energy increases with multiple hydrogen-bonding interactions in the electronically excited state. In addition, the hydrogen bonding dynamics in the excited state were visualized by the spectral shifts of vibrational modes. The calculated infrared spectra of both O-H and N-H stretching vibrational regions revealed that the O-H and N-H stretching bands red-shift.

  14. Cooperatively enhanced ionic hydrogen bonds in Cl-(CH3OH)(1-3)Ar clusters.

    PubMed

    Beck, Jordan P; Lisy, James M

    2010-09-23

    Infrared predissociation (IRPD) spectra of Cl−(CH3OH)1-3Ar and Cl-(CH3OD)1-3Ar were obtained in the OH and CH stretching regions. The use of methanol-d1 was necessary to distinguish between CH stretches and hydrogen-bonded OH features. The spectra of Cl-(CH3OH)2-3Ar show intense features at frequencies lower than the CH stretches, indicating structures with very strong hydrogen bonds. These strong hydrogen bonds arise from structures in which a Cl-···methanol ionic hydrogen bond is cooperatively enhanced by the presence of a second shell and, in the case of Cl-(CH3OH)3Ar, a third shell methanol. The strongest hydrogen bond is observed in the Cl-(CH3OH)3Ar spectrum at 2733 cm-1, shifted a remarkable -948 cm-1 from the neutral, gas-phase methanol value. Harmonic, ab initio frequency calculations are not adequate in describing these strong hydrogen bonds. Therefore, we describe a simple computational approach to better approximate the hydrogen bond frequencies. Overall, the results of this study indicate that high-energy isomers are very efficiently trapped using our experimental method of introducing Cl- into neutral, cold methanol-argon clusters.

  15. Hydrogen bond formation in regioselectively functionalized 3-mono-O-methyl cellulose.

    PubMed

    Kondo, Tetsuo; Koschella, Andreas; Heublein, Brigitte; Klemm, Dieter; Heinze, Thomas

    2008-10-13

    The hydrogen bond systems of cellulose and its derivatives are one of the most important factors regarding their physical- and chemical properties such as solubility, crystallinity, gel formation, and resistance to enzymatic degradation. In this paper, it was attempted to clarify the intra- and intermolecular hydrogen bond formation in regioselectively functionalized 3-mono-O-methyl cellulose (3MC). First, the 3MC was synthesized and the cast film thereof was characterized in comparison to 2,3-di-O-methyl cellulose, 6-mono-O-methyl cellulose, and 2,3,6-tri-O-methyl cellulose by means of wide angle X-ray diffraction (WAXD) and (13)C cross polarization/magic angle spinning NMR spectroscopy. Second, the hydrogen bonds in the 3MC film were analyzed by means of FTIR spectroscopy in combination with a curve fitting method. After deconvolution, the resulting two main bands (Fig. 3) indicated that instead of intramolecular hydrogen bonds between position OH-3 and O-5 another intramolecular hydrogen bond between OH-2 and OH-6 may exist. The large deconvoluted band at 3340cm(-1) referred to strong interchain hydrogen bonds involving the hydroxyl groups at C-6. The crystallinity of 54% calculated from the WAXD supports also the dependency of the usually observed crystallization in cellulose of the hydroxyl groups at C-6 to engage in interchain hydrogen bonding.

  16. Hydrogen bonding: part 78. Ab initio molecular orbital study of intra- and intermolecular hydrogen bonding in choline and betaine and their compounds with HF and H 2O

    NASA Astrophysics Data System (ADS)

    Harmon, K. M.; Avci, G. F.; Madeira, S. L.; Mounts, P. A.; Thiel, A. C.

    2001-10-01

    We previously prepared several compounds of the zwitterions [(CH 3) 3NCH 2CH 2O] 0 (deprotonated choline, herein named cholaine) and [(CH 3) 3NCH 2CO 2] 0 (betaine) and proposed structures based on infrared spectroscopy. We now examine these compounds with use of ab initio molecular orbital methods to further elucidate possible structure. These calculations demonstrate that: (1) cholaine and betaine both have internal CHO hydrogen bonds, and these are retained in some form in all other compounds. (2) Cholaine hydrate and hydrofluoride and betaine hydrofluoride monomers have covalent three-center hydrogen bonds between H 2O or HF and negative zwitterion oxygen, and additional CHX hydrogen bonds to H 2O oxygen or HF fluorine. (3) Cholaine monohydrate and cholaine hydrofluoride monohydrate form dimers of Ci symmetry which contain planar C2 h (H 2O·O) 2 and (HOH·F) 2 clusters. (4) Cholaine hydrofluoride forms head-to-tail dimers bound by intermolecular CHX hydrogen bonds; this arrangement could lead to extended linear structures in the solid state. (5) Betaine hydrofluoride, in contrast, forms a tightly bound discrete dimeric unit in which two molecules join in a head-to-head manner held together by five intermolecular hydrogen bonds and by the mutual proximities of negative fluorides to positive nitrogens.

  17. Nuclear quantum effect on intramolecular hydrogen bond of hydrogen maleate anion: An ab initio path integral molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Kawashima, Yukio; Tachikawa, Masanori

    2013-05-01

    Ab initio path integral molecular dynamics simulation was performed to understand the nuclear quantum effect on the hydrogen bond of hydrogen malonate anion. Static calculation predicted the proton transfer barrier as 0.12 kcal/mol. Conventional ab initio molecular dynamics simulation at 300 K found proton distribution with a double peak on the proton transfer coordinate. Inclusion of thermal effect alone elongates the hydrogen bond length, which increases the barrier height. Inclusion of nuclear quantum effect washes out this barrier, and distributes a single broad peak in the center. H/D isotope effect on the proton transfer is also discussed.

  18. Determining the Energetics of the Hydrogen Bond through FTIR: A Hands-On Physical Chemistry Lab Experiment

    ERIC Educational Resources Information Center

    Guerin, Abby C.; Riley, Kristi; Rupnik, Kresimir; Kuroda, Daniel G.

    2016-01-01

    Hydrogen bonds are very important chemical structures that are responsible for many unique and important properties of solvents, such as the solvation power of water. These distinctive features are directly related to the stabilization energy conferred by hydrogen bonds to the solvent. Thus, the characterization of hydrogen bond energetics has…

  19. Correlation of structural order, anomalous density, and hydrogen bonding network of liquid water.

    PubMed

    Bandyopadhyay, Dibyendu; Mohan, S; Ghosh, S K; Choudhury, Niharendu

    2013-07-25

    We use extensive molecular dynamics simulations employing different state-of-the-art force fields to find a common framework for comparing structural orders and density anomalies as obtained from different water models. It is found that the average number of hydrogen bonds correlates well with various order parameters as well as the temperature of maximum densities across the different models, unifying apparently disparate results from different models and emphasizing the importance of hydrogen bonding in determining anomalous properties and the structure of water. A deeper insight into the hydrogen bond network of water reveals that the solvation shell of a water molecule can be defined by considering only those neighbors that are hydrogen-bonded to it. On the basis of this view, the origin of the appearance of a non-tetrahedral peak at a higher temperature in the distribution of tetrahedral order parameters has been explained. It is found that a neighbor that is hydrogen-bonded to the central molecule is tetrahedrally coordinated even at higher temperatures. The non-tetrahedral peak at a higher temperature arises due to the strained orientation of the neighbors that are non-hydrogen-bonded to the central molecule. With the new definition of the solvation shell, liquid water can be viewed as an instantaneously changing random hydrogen-bonded network consisting of differently coordinated hydrogen-bonded molecules with their distinct solvation shells. The variation of the composition of these hydrogen-bonded molecules against temperature accounts for the density anomaly without introducing the concept of large-scale structural polyamorphism in water.

  20. Molecular tuning of the closed shell C-H···F-C hydrogen bond.

    PubMed

    Lu, Norman; Ley, Rebecca M; Cotton, Charles E; Chung, Wei-Cheng; Francisco, Joseph S; Negishi, Ei-ichi

    2013-08-29

    The existence of the rare six-membered and intramolecular C-H···F-C hydrogen-bond has been experimentally proven in the gas phase and in the solid state recently. However, the effect of the substituents on this C-H···F-C hydrogen-bond system has never been reported. In view of the importance of this type of C-H···F-C H-bonding whose weak interaction has been found critical in nanotechnology and biological systems, the nine functional groups composed of electron donating and electron withdrawing groups are inserted into this C-H···F-C interaction to study the group effect on the hydrogen bonding. Group effects on this C-H···F-C H-bonding system have been found, and their effects on the H-bonding system have been found to be tunable.

  1. Empirical corrections for anharmonic zero-point vibrations of hydrogen and deuterium in geometric hydrogen bond correlations

    NASA Astrophysics Data System (ADS)

    Limbach, Hans-Heinrich; Pietrzak, Mariusz; Benedict, Hans; Tolstoy, Peter M.; Golubev, Nikolai S.; Denisov, Gleb S.

    2004-11-01

    In this paper, empirical corrections for anharmonic ground-state vibrations of hydrogen and deuterium in the hydrogen bridges A-L⋯B, L=H, D are introduced into the geometric hydrogen bond correlation analysis based on the empirical Pauling valence bond orders. The method is verified using the examples of the hydrogen bonded anions in [(CO) 5Cr-CN⋯H⋯NC-Cr(CO) 5] - As(Ph) 4+ ( 1h), in [(CO) 5Cr-CN⋯H⋯NC-Cr(CO) 5] - N( n-propyl) 4+ ( 2h), in the model system [CN⋯H⋯NC] - Li + ( 3h), and their deuterated isotopologs ( 1d, 2d and 3d) studied previously by dipolar NMR and theoretical methods by H. Benedict et al. [J. Am. Chem. Soc. 120 (1998) 2939]. The new corrections are able to describe isotope effects on hydrogen bond geometries from the weak to the strong hydrogen bond regime, taking into account single and double-well situations.

  2. The Effect of Axial Mg{sup 2+} Ligation and Peripheral Hydrogen Bonding on Chlorophyll a

    SciTech Connect

    Sun, Yuming; Wang, Hezhou; Zhao, Fuli; Sun, Jinzuo

    2004-03-21

    Model systems of the chlorophyll a (Chla) molecule were studied using density functional theory. Dependence of structure variation of Chla on the polarity of ligand was described. The hydrogen bonding (H-bond) donated to the 13{sup 1}-keto carbonyl oxygen favors the ionic resonance structure of the 13{sup 1}-keto carbonyl bond. Such a H-bond causes spin density redistribution in anion, and charge transfer in cation from donor of H-bond to the porphyrin plane of Chla because of orbital admixing, which indicates that the spin density of chlorophyll cation could be easily regulated by its peripheral H-bond.

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

    NASA Astrophysics Data System (ADS)

    Takahashi, Masae; Ishikawa, Yoichi

    2013-06-01

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

  4. A combined deuterium NMR and quantum chemical investigation of inequivalent hydrogen bonds in organic solids.

    PubMed

    Webber, Renee; Penner, Glenn H

    2012-01-01

    Deuterium magic angle spinning (MAS) NMR spectroscopy and quantum chemical calculations are used to investigate organic solids in which inequivalent hydrogen bonds are present. The use of (2)H MAS allows one to measure the chemical shift, δ, quadrupolar coupling constant, C(Q), and asymmetry in the quadrupolar interaction, η(Q), for each type of hydrogen bond present in the system. Quantum chemical calculations of the magnetic shielding (σ, which can be related to δ) and the electric field gradient (EFG, which can be related to C(Q)) are compared to the experimental results and are discussed with respect to the relative strengths of the hydrogen bonds within each system.

  5. Hydrogen bond lifetime for water in classic and quantum molecular dynamics

    NASA Astrophysics Data System (ADS)

    Antipova, M. L.; Petrenko, V. E.

    2013-07-01

    The lifetime of hydrogen bonds in water at T = 298 K and p = 0.1 MPa is computed by means of classic molecular dynamics with eight different potentials of pair lifetime interaction and Car-Parinello molecular dynamics. The results obtained using various computational techniques for hydrogen bond life-times are compared. It is shown that they can differ from one another by several times. The dependence for the hydrogen bond lifetime computed in our numerical experiment upon the method of its determination is found.

  6. Hydrogen bonds in ethylene glycol, monoethanolamine, and ethylenediamine complexes with water

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

    The structures of ethylene glycol, aminoethanol, and ethylenediamine complexes with water and the formation of hydrogen bonds of different types are optimized using the B3LYP hybrid functional and the aug-CC-pVTZ basis. The parameters of the hydrogen bonds, their energies of interaction, and their oscillation frequencies are calculated, and NBO and QTAIM analyses are performed. The order of hydrogen bonds according to strength is obtained: O-HW···N > O-HW···O > O-H···OW.

  7. Deactivation of 6-Aminocoumarin Intramolecular Charge Transfer Excited State through Hydrogen Bonding

    PubMed Central

    Krystkowiak, Ewa; Dobek, Krzysztof; Maciejewski, Andrzej

    2014-01-01

    This paper presents results of the spectral (absorption and emission) and photophysical study of 6-aminocoumarin (6AC) in various aprotic hydrogen-bond forming solvents. It was established that solvent polarity as well as hydrogen-bonding ability influence solute properties. The hydrogen-bonding interactions between S1-electronic excited solute and solvent molecules were found to facilitate the nonradiative deactivation processes. The energy-gap dependence on radiationless deactivation in aprotic solvents was found to be similar to that in protic solvents. PMID:25244014

  8. Coupling of complex aromatic ring vibrations to solvent through hydrogen bonds: effect of varied on-ring and off-ring hydrogen-bonding substitutions.

    PubMed

    Nucci, Nathaniel V; Scott, J Nathan; Vanderkooi, Jane M

    2008-04-03

    In this study, we examine the coupling of a complex ring vibration to solvent through hydrogen-bonding interactions. We compare phenylalanine, tyrosine, l-dopa, dopamine, norepinephrine, epinephrine, and hydroxyl-dl-dopa, a group of physiologically important small molecules that vary by single differences in H-bonding substitution. By examination of the temperature dependence of infrared absorptions of these molecules, we show that complex, many-atom vibrations can be coupled to solvent through hydrogen bonds and that the extent of that coupling is dependent on the degree of both on- and off-ring H-bonding substitution. The coupling is seen as a temperature-dependent frequency shift in infrared spectra, but the determination of the physical origin of that shift is based on additional data from temperature-dependent optical experiments and ab initio calculations. The optical experiments show that these small molecules are most sensitive to their immediate H-bonding environment rather than to bulk solvent properties. Ab initio calculations demonstrate H-bond-mediated vibrational coupling for the system of interest and also show that the overall small molecule solvent dependence is determined by a complex interplay of specific interactions and bulk solvation characteristics. Our findings indicate that a full understanding of biomolecule vibrational properties must include consideration of explicit hydrogen-bonding interactions with the surrounding microenvironment.

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

    SciTech Connect

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

    2013-06-26

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

  10. Thermodynamics of hydrogen bond patterns in supramolecular assemblies of water molecules.

    PubMed

    Henry, Marc

    2002-07-02

    The PACHA (Partial Atomic Charges and Hardnesses Analysis) formalism is applied to various supramolecular assemblies of water molecules. After a detailed study of all available crystal structures for ice polymorphs, we shown that the hydrogen bond strength is roughly constant below 1 GPa and considerably weakened above that value. New hydrogen bond patterns are proposed for ice IV, V, and VI after (EB) (electrostatic balance) minimization. For other polymorphs, there is an almost perfect coincidence between experimental and predicted hydrogen bond patterns. The evolution of hydrogen bond energy as a function of molecular geometry in water clusters with up to 280 water molecules and in large supramolecular compounds is quantitatively described. Intermolecular hydrogen bonds are found to lie between -9 and -32 kJ mol-1, the stronger interaction occurs within the spherical fully disordered water droplet buried at the heart of Müller's superfullerene keplerate. The weakest one occurs in a chiral molecular snub cube built from six calix[4]resorcinarene and eight water molecules. Intramolecular hydrogen bonds are found in the range -10-100 kJ mol-1 and can thus be considerably stronger than intermolecular bonds. Finally, through the investigation of a clathrate type I compound, it was possible to obtain a deep insight of the host-guest interactions and self-assembly rules of water cages in these materials.

  11. Proximal Pocket Hydrogen Bonds Significantly Influence the Mechanism of Chloroperoxidase Compound I Formation.

    PubMed

    Pardillo, Armando D; Morozov, Alexander N; Chatfield, David C

    2015-10-01

    The influence of backbone hydrogen bonds to the sulfur atom of the proximal thiolate (NH···S hydrogen bonds) on the formation of compound I in chloroperoxidase is investigated with DFT calculations. Reaction profiles for the transformation of the ferric resting state into compound I in the presence of a peroxide substrate are calculated for a model system incorporating the heme and key proximal and distal amino acid residues. We find that NH···S hydrogen bonds (1) reduce the barrier for the formation of compound 0 by 7.6 kcal/mol, (2) increase the stability of compound 0 by 5.2 kcal/mol, (3) reduce the stability of compound I relative to compound 0 by 6.2 kcal/mol, and (4) reduce the stability of protonated compound 0, favoring a hybrid homo-heterolytic relative to a classic heterolytic mechanism for O-O bond scission. In general, the influence of the NH···S hydrogen bonds can be traced to a reduction in the pKa of the heme-bound substrate. We find that the hydrogen bond networks on the proximal and distal sides of the heme function together to modulate the mechanism of reaction. These results confirm and extend long-standing theories that the NH···S hydrogen bonds in heme thiolate proteins influence reactivity by tuning the thiolate "push" effect.

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

    SciTech Connect

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

    2016-03-31

    Dicarboxylic acids represent an important class of water-soluble organic compounds found in the atmosphere. In this work we are studying properties of dicarboxylic acid homodimer complexes (HO2(CH2)nCO2-[HO2(CH2)nCO2H], n = 0-12), as potentially important intermediates in aerosol formation processes. Our approach is based on experimental data from negative ion photoelectron spectra of the dimer complexes combined with updated measurements of the corresponding monomer species. These results are analyzed with quantum-mechanical calculations, which provide further information about equilibrium structures, thermochemical parameters associated with the complex formation, and evaporation rates. We find that upon formation of the dimer complexes the electron binding energies increase by 1.3–1.7 eV (30.0–39.2 kcal/mol), indicating increased stability of the dimerized complexes. Calculations indicate that these dimer complexes are characterized by the presence of strong intermolecular hydrogen bonds with high binding energies and are thermodynamically favorable to form with low evaporation rates. Comparison with previously studied HSO4-[HO2(CH2)2CO2H] complex (J. Phys. Chem. Lett. 2013, 4, 779-785) shows that HO2(CH2)2CO2-[HO2(CH2)2CO2H] has very similar thermochemical properties. These results imply that dicarboxylic acids not only can contribute to the heterogeneous complexes formation involving sulfuric acid and dicarboxylic acids, but also can promote the formation of homogenous complexes by involving dicarboxylic acids themselves.

  13. Head-to-tail intermolecular hydrogen bonding of OH and NH groups with fluoride.

    PubMed

    Ashokkumar, Pichandi; Ramakrishnan, Vayalakkavoor T; Ramamurthy, Perumal

    2011-02-07

    To explore the anion-recognition ability of the phenolic hydroxyl group and the amino hydrogen, we synthesized three different acridinedione (ADD) based anion receptors, 1, 2 and 3, having OH, NH, and combination of OH and NH groups, respectively. Absorption, emission and (1)H NMR spectral studies revealed that receptor 1, having only a phenolic OH group, shows selective deprotonation of the hydroxyl proton towards F(-), which results in an "ON-OFF"-type signal in the fluorescence spectral studies. Receptor 2, which only has an amino hydrogen, also shows deprotonation of the amino hydrogen with F(-), whereas receptor 3 (having both OH and NH groups) shows head-to-tail intermolecular hydrogen bonding of OH and NH groups with F(-) prior to deprotonation. The observation of hydrogen bonding of the OH and NH groups in a combined solution of 1 and 2 with F(-) in a head-to-tail hetero-intermolecular fashion, and the absence of head-to-head and tail-to-tail intermolecular hydrogen bonding in 1 and 2 with F(-), prove that the difference in the acidity of the OH and NH protons leads to the formation of an intermolecular hydrogen-bonding complex with F(-) prior to deprotonation. The presence of this hydrogen-bonding complex was confirmed by absorption spectroscopy, 3D emission contour studies, and (1)H NMR titration.

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

    SciTech Connect

    Fifield, Leonard S.; Grate, Jay W.

    2010-06-01

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

  15. Hydrogen bonding. Part 20. Infrared study of the high temperature β-form of choline chloride

    NASA Astrophysics Data System (ADS)

    Harmon, Kenneth M.; Avci, Günsel F.

    1986-02-01

    Infrared spectral studies of β-choline chloride at 95°C clearly demonstrate the presence of OH … Cl hydrogen bonding. This observation contradicts an earlier conclusion, based on X-ray structural studies, that such hydrogen bonding could not occur in this high-temperature form of choline chloride. A moderate reinterpretation of the X-ray data may reconcile these contradictory conclusions. Unlike α-choline chloride, β-choline chloride does not show CH … Cl hydrogen bonding. It is possible that loss of CH … Cl hydrogen bonding is a factor in the marked difference in radiation sensitivity of the α- and β-forms.

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

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Kazutomo; Saito, Hiroaki; Nagao, Hidemi

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

  17. Supramolecular Construction of Multifluorescent Gels: Interfacial Assembly of Discrete Fluorescent Gels through Multiple Hydrogen Bonding.

    PubMed

    Ji, Xiaofan; Shi, Bingbing; Wang, Hu; Xia, Danyu; Jie, Kecheng; Wu, Zi Liang; Huang, Feihe

    2015-12-22

    Multifluorescent supramolecular gels with complex structures are constructed from discrete fluorescent gels, which serve as the building blocks, through hydrogen bonding interactions at interfaces. The multifluorescent gel can realize rapid healing within only ≈100 s.

  18. [Intermolecular hydrogen bond between protein and flavonoid and its contribution to the stability of the flavonoids].

    PubMed

    Fang, Ru; Leng, Xiao-jing; Wu, Xia; Li, Qi; Hao, Rui-fang; Ren, Fa-zheng; Jing, Hao

    2012-01-01

    The interactions between three proteins (BSA, lysozyme and myoglobin) and three flavonoids (quercetin, kaempferol and rutin) were analyzed, using three-dimensional fluorescence spectrometry in combination with UV-Vis spectrometry and Fourier transform infrared (FTIR) spectroscopy. The stabilities of unbound flavonoids and protein-bound flavonoids were compared. The correlation between the interaction and stability was analyzed. The results showed that the hydrophobic interaction was the main binding code in all proteins and flavonoids systems. However, the hydrogen bond has been involved merely in the BSA system. The stability of all three flavonoids (quercetin, kaempferol and rutin) was improved by BSA. There was a great correlation between the hydrogen bonding and the stability of the flavonoids in the presence of BSA. It suggested that the protection of BSA on the flavonoids was due to the intermolecular hydrogen bonding between BSA and flavonoid, and the stronger hydrogen bonding resulted in more protection.

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

    NASA Astrophysics Data System (ADS)

    Du, Lin; Tang, Shanshan; Hansen, Anne S.; Frandsen, Benjamin N.; Maroun, Zeina; Kjaergaard, Henrik G.

    2017-01-01

    The Osbnd H⋯O and Osbnd H⋯S hydrogen bonds were investigated by gas phase FTIR spectroscopy of alcohol-dimethylether and alcohol-dimethylsulfide complexes, with alcohols of increasing hydrogen bond donor strength; methanol (MeOH), ethanol (EtOH) and 2,2,2-trifluoroethanol (TFE). The TFE complexes are more stable and form stronger hydrogen bonds compared to complexes with MeOH and EtOH, which are comparable, and only for the stronger hydrogen bond donor (TFE) are the small differences in acceptor molecules highlighted. The equilibrium constant for complex formation was determined from the experimental and calculated intensity of the OH-stretching transition. The interactions are illustrated by theoretical calculations and topological analysis.

  20. Dinuclear complexes formed by hydrogen bonds: synthesis, structure and magnetic and electrochemical properties.

    PubMed

    Williams, Alan Francis; Granelli, Matteo; Downward, Alan M; Huber, Robin; Guenée, Laure; Besnard, Céline; Krämer, Karl W; Decurtins, Silvio; Liu, Shi-Xia; Thompson, Laurence K

    2017-03-20

    The synthesis is reported of a series of homo- and hetero-dinuclear octahedral complexes of the ligand 1, 1,2-bis(1-methyl-benzimidazol-2-yl) ethanol, where the two metal centres are linked by hydrogen bonds between coordinated alcohols and coordinated alkoxides. Homonuclear divalent M(II)M(II), mixed valent M(II)M(III) and heteronuclear M(II)M'(III) species are prepared. The complexes have been characterised by X-ray crystallography and show unusually short O…O distances for the hydrogen bonds. Magnetic measurements show the hydrogen bond bridges can lead to ferromagnetic or antiferromagnetic coupling. The electrochemistry of the dinuclear species is significantly different from the mononuclear systems: the latter show irreversible waves in cyclic voltammograms as a result of the need to couple proton and electron transfer. The dinuclear species, in contrast, show reversible waves which are attributed to rapid intramolecular proton transfer facilitated by the hydrogen bonded structure.

  1. Microwave Measurements of Maleimide and its Doubly Hydrogen Bonded Dimer with Formic ACID*

    NASA Astrophysics Data System (ADS)

    Pejlovas, Aaron M.; Kang, Lu; Kukolich, Stephen G.

    2016-06-01

    The microwave spectra were measured for the maleimide monomer and the maleimide-formic acid doubly hydrogen bonded dimer using a pulsed-beam Fourier transform microwave spectrometer. Many previously studied doubly hydrogen bonded dimers are formed between oxygen containing species, so it is important to also characterize and study other dimers containing nitrogen, as hydrogen bonding interactions with nitrogen are found in biological systems such as in DNA. The transition state of the dimer does not exhibit C_2_V symmetry, so the tunneling motion was not expected to be observed based on the symmetry, but it would be very important to also observe the tunneling process for an asymmetric dimer. Single-line b-type transitions were observed, so the tunneling motion was not observed in our microwave spectra. The hydrogen bond lengths were determined using a nonlinear least squares fitting program. *Supported by the NSF CHE-1057796

  2. Coupling between inter-helical hydrogen bonding and water dynamics in a proton transporter.

    PubMed

    del Val, Coral; Bondar, Luiza; Bondar, Ana-Nicoleta

    2014-04-01

    Long-distance proton transfers by proton pumps occurs in discrete steps that may involve the direct participation of protein sidechains and water molecules, and coupling of protonation changes to structural rearrangements of the protein matrix. Here we explore the role of inter-helical hydrogen bonding in long-distance protein conformational coupling and dynamics of internal water molecules. From molecular dynamics simulations of wild type and nine different bacteriorhodopsin mutants we find that both intra- and inter-helical hydrogen bonds are important determinants of the local protein structure, dynamics, and water interactions. Based on molecular dynamics and bioinformatics analyses, we identify an aspartate/threonine inter-helical hydrogen-bonding motif involved in controlling the local conformational dynamics. Perturbation of inter-helical hydrogen bonds can couple to rapid changes in water dynamics.

  3. N-heteroquinones: quadruple weak hydrogen bonds and n-channel transistors.

    PubMed

    Tang, Qin; Liang, Zhixiong; Liu, Jing; Xu, Jianbin; Miao, Qian

    2010-05-07

    This study demonstrates that the easily synthesized N-heteroquinones, having unusual quadruple weak hydrogen bonds of a DDAA-AADD pattern, can function as n-type organic semiconductors in OTFTs with high electron mobility.

  4. Double hydrogen bond mediating self-assembly structure of cyanides on metal surface

    NASA Astrophysics Data System (ADS)

    Wang, Zhongping; Xiang, Feifei; Lu, Yan; Wei, Sheng; Li, Chao; Liu, Xiaoqing; Liu, Lacheng; Wang, Li

    2016-10-01

    Cyanides with different numbers of -C≡N, 1,2,4,5-Tetracyanobenzene (TCNB) and 2,3-Dicyanonaphthalene (2,3-DCN) deposited on Ag(111) and Ag(110) surfaces, have been investigated by room temperature scanning tunneling microscopy (RTSTM), respectively. High resolution STM images show double hydrogen bond is the main driving force to form variety of self-assembly structures, indicating the double hydrogen bond affects the electron distribution of cyanides and leads to a more stable structure with lower energy. In addition, the difference between Ag(111) and Ag(110) surfaces in their lattice structure induces a bigger assembly structural change of 2,3-DCN than that of 1,2,4,5-TCNB, which confirms the fact that the opposite double hydrogen bond formation formed by 1,2,4,5-TCNB is more stable than the neighboring double hydrogen bond formation formed by molecule 2,3-DCN.

  5. Isotope effects on chemical shifts in the study of intramolecular hydrogen bonds.

    PubMed

    Hansen, Poul Erik

    2015-01-30

    The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between "static" and tautomeric systems. Isotope effects on chemical shifts are particularly useful in such studies. All kinds of intramolecular hydrogen bonded systems will be treated, typical hydrogen bond donors: OH, NH, SH and NH+, typical acceptors C=O, C=N, C=S C=N-. The paper will be deal with both secondary and primary isotope effects on chemical shifts. These two types of isotope effects monitor the same hydrogen bond, but from different angles.

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

    NASA Astrophysics Data System (ADS)

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

    2003-03-01

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

  7. Hydrogen bonding in the crystal structure of the molecular salt of pyrazole-pyrazolium picrate.

    PubMed

    Su, Ping; Song, Xue-Gang; Sun, Ren-Qiang; Xu, Xing-Man

    2016-06-01

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

  8. SN2-like reaction in hydrogen-bonded complexes: a theoretical study.

    PubMed

    Wang, Weizhou; Zhang, Yu; Huang, Kaixun

    2005-10-20

    S(N)2-like reactions in hydrogen-bonded complexes have been investigated in this paper at a correlated MP2(full)/6-311++G(3df,3pd) level, employing FH...NH(3)...HF and ClH...NH(3)...HCl as model systems. The unconventional F(Cl)-H...N noncovalent bond and the conventional F(Cl)-H...N hydrogen bond can coexist in one complex which is taken as the reactant of the S(N)2-like reaction. The S(N)2-like reaction occurs along with the inversion of NH(3) and the interconversion of the unconventional F(Cl)-H...N noncovalent bond and the conventional F(Cl)-H...N hydrogen bond. In comparison with that of the isolated NH(3), the inversion barriers of the two complexes both are significantly reduced. The effect of carbon nanotube confinement on the inversion barrier is also discussed.

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

    NASA Astrophysics Data System (ADS)

    Wójcik, Marek J.

    1981-11-01

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

  10. Ranking relative hydrogen-bond strengths in hydroxybenzoic acids for crystal-engineering purposes.

    PubMed

    Aakeröy, Christer B; Epa, Kanishka; Forbes, Safiyyah; Schultheiss, Nathan; Desper, John

    2013-10-25

    Systematic co-crystallizations resulting in a total of six new crystal structures involving either 3-hydroxy- or 4-hydroxybenzoic acid, complemented by calculated molecular electrostatic potential surfaces and existing structural data, have shown that in a competitive molecular recognition situation, the -OH moiety is a more effective hydrogen-bond donor than the -COOH moiety which, in turn, highlights that electrostatic charge can offer more useful guidance than acidity for predicting competitive hydrogen-bond preferences.

  11. Structure of hydrogen-bonded associates in supercritical water under low and high pressures

    NASA Astrophysics Data System (ADS)

    Antipova, M. L.; Gurina, D. L.; Petrenko, V. E.

    2013-03-01

    The character and structural features of hydrogen-bonded associates in sub- and supercritical water are studied by analyzing distributions of the dipole moments of water molecules at P = 40, 80, and 100 MPa and T = 373-773 K, calculated using Car-Parrinello molecular dynamics. The main types of hydrogen-bonded structures and their changes upon isobaric heating are determined. It is shown that clusters with tetrahedral configurations exist in supercritical water only under high pressure.

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

    PubMed

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

    2014-11-04

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

  13. A Preorganized Hydrogen Bond Network and Its Effect on Anion Stability

    SciTech Connect

    Samet, Masoud; Wang, Xue B.; Kass, Steven R.

    2014-08-07

    Rigid tricyclic locked in all axial 1,3,5-cyclohexanetriol derivatives with 0–3 trifluoromethyl groups were synthesized and photoelectron spectra of their conjugate bases and chloride anion clusters are reported along with density functional computations. The resulting vertical and adiabatic detachment energies provide measures of the anion stabilization due to the hydrogen bond network and inductive effects. The latter mechanism is found to be transmitted through space via hydrogen bonds

  14. Influence of molecular interactions on the stability of hydrogen-bonded dimers of carboxylic acids

    NASA Astrophysics Data System (ADS)

    Kolbe, Alfred; Plass, Monika; Kresse, Horst; Kolbe, Adelheid; Drabowicz, Jozef; Zurawinski, Remiguisz

    1997-12-01

    Possibilities to change the molecular arrangement of hydrogen bonded dimers of carboxylic acids by offering other acceptor groups are investigated in different species of molecules, namely in amino acid conjugates, in sulfinyl- and phosphinyl-carboxylic acids and in some p- n-alkoxybenzoic acids. As a result it was found that the carboxylic dimers are rather easily broken by lattice forces, by forming other intra- and intermolecular hydrogen bonds to stronger acceptor groups, and by increasing the temperature.

  15. Hydrogen bonding motifs of protein side chains: descriptions of binding of arginine and amide groups.

    PubMed Central

    Shimoni, L.; Glusker, J. P.

    1995-01-01

    The modes of hydrogen bonding of arginine, asparagine, and glutamine side chains and of urea have been examined in small-molecule crystal structures in the Cambridge Structural Database and in crystal structures of protein-nucleic acid and protein-protein complexes. Analysis of the hydrogen bonding patterns of each by graph-set theory shows three patterns of rings (R) with one or two hydrogen bond acceptors and two donors and with eight, nine, or six atoms in the ring, designated R2(2)(8), R2(2)(9), and R1(2)(6). These three patterns are found for arginine-like groups and for urea, whereas only the first two patterns R2(2)(8) and R2(2)(9) are found for asparagine- and glutamine-like groups. In each case, the entire system is planar within 0.7 A or less. On the other hand, in macromolecular crystal structures, the hydrogen bonding patterns in protein-nucleic acid complexes between the nucleic acid base and the protein are all R2(2)(9), whereas hydrogen bonding between Watson-Crick-like pairs of nucleic acid bases is R2(2)(8). These two hydrogen bonding arrangements [R2(2)(9)] and R2(2)(8)] are predetermined by the nature of the groups available for hydrogen bonding. The third motif identified, R1(2)(6), involves hydrogen bonds that are less linear than in the other two motifs and is found in proteins. PMID:7773178

  16. Cosolvent Effects on Solute-Solvent Hydrogen-Bond Dynamics: Ultrafast 2D IR Investigations.

    PubMed

    Kashid, Somnath M; Jin, Geun Young; Bagchi, Sayan; Kim, Yung Sam

    2015-12-10

    Cosolvents strongly influence the solute-solvent interactions of biomolecules in aqueous environments and have profound effects on the stability and activity of several proteins and enzymes. Experimental studies have previously reported on the hydrogen-bond dynamics of water molecules in the presence of a cosolvent, but understanding the effects from a solute's perspective could provide greater insight into protein stability. Because carbonyl groups are abundant in biomolecules, the current study used 2D IR spectroscopy and molecular dynamics simulations to compare the hydrogen-bond dynamics of the solute's carbonyl group in aqueous solution, with and without the presence of DMSO as a cosolvent. 2D IR spectroscopy was used to quantitatively estimate the time scales of the hydrogen-bond dynamics of the carbonyl group in neat water and 1:1 DMSO/water solution. The 2D IR results show spectral signatures of a chemical exchange process: The presence of the cosolvent was found to lower the hydrogen-bond exchange rate by a factor of 5. The measured exchange rates were 7.50 × 10(11) and 1.48 × 10(11) s(-1) in neat water and 1:1 DMSO/water, respectively. Molecular dynamics simulations predict a significantly shorter carbonyl hydrogen-bond lifetime in neat water than in 1:1 DMSO/water and provide molecular insights into the exchange mechanism. The binding of the cosolvent to the solute was found to be accompanied by the release of hydrogen-bonded water molecules to the bulk. The widely different hydrogen-bond lifetimes and exchange rates with and without DMSO indicate a significant change in the ultrafast hydrogen-bond dynamics in the presence of a cosolvent, which, in turn, might play an important role in the stability and activity of biomolecules.

  17. Quantum Calculations On Hydrogen Bonds In Certain Water Clusters Show Cooperative Effects

    PubMed Central

    ZNAMENSKIY, VASILIY S.; GREEN, MICHAEL E.

    2008-01-01

    Water molecules in clefts and small clusters are in a significantly different environment than in bulk water. We have carried out ab initio calculations that demonstrate this in a series of clusters, showing that cooperative effects must be taken into account in the treatment of hydrogen bonds and water clusters in such bounded systems. Hydrogen bonds between water molecules in simulations are treated most frequently by using point charge water potentials, such as TIP3P or SPC, sometimes with a polarizable extension. These produce excellent results in bulk water, for which they are calibrated. Clefts are different from bulk; it is necessary to look at smaller systems, and investigate the effect of limited numbers of neighbors. We start with a study of isolated clusters of water with varying numbers of neighbors of a hydrogen bonded pair of water molecules. The cluster as a whole is in vacuum. The clusters are defined so as to provide the possible arrangements of nearest neighbors of a central hydrogen bonded pair of water molecules. We then scan the length and angles of the central hydrogen bond of the clusters, using density functional theory, for each possible arrangement of donor and acceptor hydrogen bonds on the central hydrogen bonding pair; the potential of interaction of two water molecules varies with the number of donor and of acceptor neighbors. This also involves changes in charge on the water molecules as a function of bond length, and changes in energy and length as a function of number of neighboring donor and acceptor molecules. Energy varies by approximately 6 kBT near room temperature from the highest to the lowest energy when bond length alone is varied, enough to seriously affect simulations. PMID:19169381

  18. Hydrogen bonding. Part 69. Inter- and intramolecular hydrogen bonding effects on the structure, solubility, and reactivity of 4,5-dicarboxyimidazoles

    NASA Astrophysics Data System (ADS)

    Harmon, Kenneth M.; Gill, Stacee H.; Rasmussen, Paul G.; Hardgrove, George L., Jr.

    1999-03-01

    1-Methyl-4,5-dicarboxyimidazole (H 2MDCI) and 4,5-dicarboxyimidazole (H 2DCI) are both zwitterionic, with one acidic hydrogen on a ring nitrogen and one in an O-H-O hydrogen bond between carboxylate groups. H 2MDCI is relatively soluble in H 2O, and further diacid is taken into saturated aqueous solution in the presence of F - with removal of O-H-O hydrogen and formation of HMDCI - and HF 2-. In contrast, H 2DCI is almost completely insoluble in H 2O and, unlike other similar dicarboxylic acids we have studied, is completely unaffected by added F -. We have used titrametric analysis, molecular modeling, infrared spectra, molecular orbital calculations and X-ray crystallography to elucidate the properties of H 2DCI and H 2MDCI. The crystal structure of H 2MDCI was solved in the P2 1/c space group with Z = 4, a = 4.6402(5), b = 15.070(2), c = 9.6786(11), β = 94.928(2)° and V = 674.32(13) Å 3. The structure shows two hydrogen bonds, one intramolecular and one intermolecular per molecule. The reduced solubility of H 2DCI arises from facile formation of four N-H ⋯O intermolecular hydrogen bonds by each molecule (2 donor and 2 acceptor). The failure of H 2DCI to react with F - is ascribed to lowered acidity of H 2DCI, relative to that of structurally quite similar H 2MDCI, which in turn results, in part, from the presence of a symmetric O-H-O hydrogen bond in the C2v H 2DCI zwitterion, which is stronger than the unsymmetrical O-H-O bond in the Cs zwitterion of H 2MDCI.

  19. Hydrogen-bonding molecular ruler surfactants as probes of specific solvation at liquid/liquid interfaces.

    PubMed

    Siler, A Renee; Brindza, Michael R; Walker, Robert A

    2009-10-01

    Resonance-enhanced, second harmonic generation (SHG) is used to measure the electronic structure of solutes sensitive to specific solvation adsorbed to liquid/liquid and liquid/solid interfaces. Here, specific solvation refers to solvent-solute interactions that are directional and localized. N-methyl-p-methoxyaniline (NMMA) is a solute whose first allowed electronic transition wavelength remains almost constant (approximately 315 nm) in non-hydrogen-bonding solvents regardless of solvent polarity. However, in hydrogen-bond-accepting solvents such as dimethylsulfoxide, NMMA's absorbance shifts to longer wavelengths (320 nm), whereas in hydrogen-bond-donating solvents (e.g., water), the absorbance shifts to shorter wavelengths (approximately 300 nm). SHG experiments show that at alkane/silica interfaces, surface silanol groups serve as moderately strong hydrogen-bond donors as evidenced by NMMA's absorbance of 307 nm. At the carbon tetrachloride/water interface, NMMA absorbance also shifts to slightly shorter wavelengths (298 nm) implying that water molecules at this liquid/liquid interface are donating strong hydrogen bonds to the adsorbed NMMA solutes. In contrast, experiments using newly developed molecular ruler surfactants with NMMA as a model hydrophobic solute and a hydrophilic, cationic headgroup imply that, as NMMA migrates across an aqueous/alkane interface, it carries with it water that functions as a hydrogen-bond-accepting partner.

  20. Pressure-induced localisation of the hydrogen-bond network in KOH-VI

    SciTech Connect

    Hermann, Andreas Nelmes, Richard J.; Loveday, John S.; Guthrie, Malcolm

    2015-12-28

    Using a combination of ab initio crystal structure prediction and neutron diffraction techniques, we have solved the full structure of KOH-VI at 7 GPa. Rather than being orthorhombic and proton-ordered as had previously be proposed, we find that this high-pressure phase of potassium hydroxide is tetragonal (space group I4/mmm) and proton disordered. It has an unusual hydrogen bond topology, where the hydroxyl groups form isolated hydrogen-bonded square planar (OH){sub 4} units. This structure is stable above 6.5 GPa and, despite being macroscopically proton-disordered, local ice rules enforce microscopic order of the hydrogen bonds. We suggest the use of this novel type of structure to study concerted proton tunneling in the solid state, while the topology of the hydrogen bond network could conceivably be exploited in data storage applications based solely on the manipulations of hydrogen bonds. The unusual localisation of the hydrogen bond network under applied pressure is found to be favored by a more compact packing of the constituents in a distorted cesium chloride structure.

  1. NMR Spectroscopic Characterization of Charge Assisted Strong Hydrogen Bonds in Brønsted Acid Catalysis

    PubMed Central

    2016-01-01

    Hydrogen bonding plays a crucial role in Brønsted acid catalysis. However, the hydrogen bond properties responsible for the activation of the substrate are still under debate. Here, we report an in depth study of the properties and geometries of the hydrogen bonds in (R)-TRIP imine complexes (TRIP: 3,3′-Bis(2,4,6-triisopropylphenyl)-1,1′-binaphthyl-2,2′-diylhydrogen phosphate). From NMR spectroscopic investigations 1H and 15N chemical shifts, a Steiner–Limbach correlation, a deuterium isotope effect as well as quantitative values of 1JNH,2hJPH and 3hJPN were used to determine atomic distances (rOH, rNH, rNO) and geometry information. Calculations at SCS-MP2/CBS//TPSS-D3/def2-SVP-level of theory provided potential surfaces, atomic distances and angles. In addition, scalar coupling constants were computed at TPSS-D3/IGLO-III. The combined experimental and theoretical data reveal mainly ion pair complexes providing strong hydrogen bonds with an asymmetric single well potential. The geometries of the hydrogen bonds are not affected by varying the steric or electronic properties of the aromatic imines. Hence, the strong hydrogen bond reduces the degree of freedom of the substrate and acts as a structural anchor in the (R)-TRIP imine complex. PMID:27936674

  2. Hydrogen Bonding between Solutes in Solvents Octan-1-ol and Water

    PubMed Central

    Abraham, Michael H.; Gola, Joelle M. R.; Cometto-Muñiz, J. Enrique; Acree, William E.

    2010-01-01

    1:1 Equilibrium constants, K, for the association of hydrogen bond bases and hydrogen bond acids have been determined using solvent octan-1-ol at 298 K for 30 acid-base combinations. The values of K are much smaller than those found for aprotic, rather non-polar solvents. It is shown that the log K values can satisfactorily be correlated against αH2*βH2, where αH2 and βH2 are the 1:1 hydrogen bond acidities and basicities of solutes. The slope of the plot, 2.938, is much smaller than those for log K values in the non-polar organic solvents previously studied. An analysis of literature data on 1:1 hydrogen bonding in water yields a negative slope for a plot of log K against αH2*βH2, thus showing how the use of very strong hydrogen bond acids and bases does not lead to larger values of log K for 1:1 hydrogen bonding in water. It is suggested that for simple 1:1 association between mono-functional solutes in water, log K cannot be larger than about −0.1 log units. Descriptors have been obtained for the complex between 2,2,2-trifluoroethanol and propanone, and used to analyze solvent effects on the two reactants, the complex, and the complexation constant. PMID:20954704

  3. Classification of hydrogen bond flips in small water polyhedra applied to concerted proton tunneling.

    PubMed

    Kirov, M V

    2016-10-05

    Recently a new mechanism of proton tunneling in a prism-like water hexamer was revealed [Richardson et al., Science, 2016, 351, 1310]. The tunneling motion involves the concerted breaking of two hydrogen bonds and rotations of two nearest water molecules. Eventually, this structural transformation means flipping one of the hydrogen bonds without the creation of defects in the hydrogen bond network. On the surface of polyhedral water clusters, there are five essentially different types of hydrogen bonds, and only two of them can be changed in this manner. In this article, the topological classification of such transformations for five small water polyhedra: triangular, pentagonal, and hexagonal prisms as well as cube and polyhedron 4(4)5(4), consisting of four square and four pentagonal faces, is presented. Our classification includes the enumeration of all possible one-bond-flips with consideration of the types of hydrogen bonds on the polyhedral surface. Attention is paid to the most stable proton configurations which can be studied in experiments. It was established that a number of one-bond-flip transitions between the low energy configurations are possible in clusters in the shape of triangular and pentagonal prisms.

  4. Infrared spectral evidence and DFT calculations of hydrogen-bonding and molecular structures of acetogenins

    NASA Astrophysics Data System (ADS)

    Afonso, Sabrina; Silva, Fabiano B.; Silva, Arnaldo F.; Scarminio, Ieda S.; Bruns, Roy E.

    2017-02-01

    FTIR spectra have been measured for 31 different five component - simplex centroid design solvent mixture extracts of shaded and sun-exposed Annonaceous leaves harvested in all four seasons. The spectral frequencies are characteristic of anonnaceous acetogenins known to be a major component of these leaves. Osbnd H stretching spectral bands in the 3100-3600 cm-1 region provide evidence of notable intensity changes for the shaded and sun-exposed leaves. Chemometric principal component analysis involving 264 spectra show that shaded samples tend to have more intense Osbnd H stretching bands than those grown in the sun. B3LYP density functional calculations indicate significant Osbnd H stretching band changes in this region owing to hydrogen bond formation. Weak Osbnd H intensity enhancements, around 40 km mol-1, occur when an Osbnd H group forms a hydrogen bond with the oxygen atom of an adjacent tetrahydrofuran ring oxygen atom. Much more intense enhancements, 400-500 km mol-1, are predicted to occur for acetogenins with two tetrahydrofuran rings for which the Osbnd H group hydrogen bonds with its fartherest removed tetrahydrofuran ring oxygen. Whereas weak or moderate H-bond stretching intensities are obtained for acetogenins with slightly bent carbon chain structures the strongest hydrogen bond intensities are calculated for molecules with a 45° V-type backbone structure. These important structural modifications as well as significant changes in bond lengths and angles owing to hydrogen bonding are detailed.

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

    SciTech Connect

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

    2015-07-28

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

  6. On the physical origin of the cation-anion intermediate bond in ionic liquids Part I. Placing a (weak) hydrogen bond between two charges.

    PubMed

    Lehmann, Sebastian B C; Roatsch, Martin; Schöppke, Matthias; Kirchner, Barbara

    2010-07-21

    The intermediate bond forces in ionic liquids are investigated from static quantum chemical calculations at various methods and two basis sets. The experimentally observed red-shift of the donor-proton bond stretching frequency due to a bond elongation is confirmed by all methods. Comparing Hartree-Fock to second-order Møller-Plesset perturbation theory, the Hartree-Fock method gives in many cases an erroneous description of the geometries. Furthermore, the Hartree-Fock interaction energies can deviate up to 60 kJ mol(-1) from Møller-Plesset perturbation theory indicating the importance of dispersion interaction. While the usual trends of decreasing stability or interaction energies with increasing ion sizes are found, the geometries involving hydrogen atoms do not change this order of total interaction energies. Therefore, the hydrogen bond is not the most important interaction for ion pairs with regard to the total interaction energy. On the other hand, the different established analysis methods give rise to hydrogen bonding in several ion pairs. Charge analysis reveals the hydrogen-bonding character of the ion pair and shows, depending on the type of ions combined and further on the type of conformers considered, that a hydrogen bond can be present. The possibility of hydrogen bonding is also shown by an analysis of the frontier orbitals. Calculating potential energy surfaces and observing from this the change in the donor proton bond indicates that regular hydrogen bonds are possible in ion pairs of ionic liquids. Thereby, the maximum of bond elongation exceeds the one of a usual hydrogen bond by far. The more salt-like hydrogen-bonded ion pair [NH(4)][BF(4)] exhibits a steeper maximum than the more ionic liquid like ion pair [EtNH(3)][BF(4)]. The fact that imidazolium-based ionic liquids as [Emim][Cl] can display two faces, hydrogen bonding and purely ionic bonding, points to a disturbing rather than stabilizing role of hydrogen bonding on the interaction of

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    a-type rotational spectra of the hydrogen-bonded complex formed from pyridine and acetylene are reported. Rotational and 14N hyperfine constants indicate that the complex is planar with an acetylenic hydrogen directed toward the nitrogen. However, unlike the complexes of pyridine with HCl and HBr, the acetylene moiety in HCCH—NC5H5 does not lie along the symmetry axis of the nitrogen lone pair, but rather, forms an average angle of 46° with the C2 axis of the pyridine. The a-type spectra of HCCH—NC5H5 and DCCD—NC5H5 are doubled, suggesting the existence of a low lying pair of tunneling states. This doubling persists in the spectra of HCCD—NC5H5, DCCH—NC5H5, indicating that the underlying motion does not involve interchange of the two hydrogens of the acetylene. Single 13C substitution in either the ortho- or meta-position of the pyridine eliminates the doubling and gives rise to separate sets of spectra that are well predicted by a bent geometry with the 13C on either the same side ("inner") or the opposite side ("outer") as the acetylene. High level ab initio calculations are presented which indicate a binding energy of 1.2 kcal/mol and a potential energy barrier of 44 cm-1 in the C2v configuration. Taken together, these results reveal a complex with a bent hydrogen bond and large amplitude rocking of the acetylene moiety. It is likely that the bent equilibrium structure arises from a competition between a weak hydrogen bond to the nitrogen (an n-pair hydrogen bond) and a secondary interaction between the ortho-hydrogens of the pyridine and the π electron density of the acetylene.

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

    NASA Astrophysics Data System (ADS)

    Chao, Chi-Yang

    Block copolymers can self-assemble into highly regular, microphase-separated morphologies with dimensions at nanometer length scales. Potential applications such as optical wavelength photonic crystals, templates for nanolithographic patterning, or nanochannels for biomacromolecular separation take advantage of the well-ordered, controlled size microdomains of block copolymers. Side-chain liquid crystalline block copolymers (SCLCBCPs) are drawing increasing attention since the incorporation of liquid crystallinity turns their well-organized microstructures into dynamic functional materials. As a special type of block copolymer, hydrogen-bonded SCLCBCPs are unique, compositionally tunable materials with multiple dynamic functionalities that can readily respond to thermal, electrical and mechanical fields. Hydrogen-bonded SCLCBCPs were synthesized and assembled from host poly(styrene- b-acrylic acid) diblock copolymers with narrow molecular weight distributions as proton donors and guest imidazole functionalized mesogenic moieties as proton acceptors. In these studies non-covalent hydrogen bonding is employed to connect mesogenic side groups to a block copolymer backbone, both for its dynamic character as well as for facile materials preparation. The homogeneity and configuration of the hydrogen-bonded complexes were determined by both the molecular architecture of imidazolyl side groups and the process conditions. A one-dimensional photonic crystal composed of high molecular weight hydrogen-bonded SCLCBCP, with temperature dependent optical wavelength stop bands was successfully produced. The microstructures of hydrogen-bonded complexes could be rapidly aligned in an AC electric field at temperatures below the order-disorder transition but above their glass transitions. Remarkable dipolar properties of the mesogenic groups and thermal dissociation of hydrogen bonds are key elements to fast orientation switching. Studies of a wide range of mesogen and polymer

  9. The Influence of Hydrogen Bonding on Sphingomyelin/Colipid Interactions in Bilayer Membranes

    PubMed Central

    Yasuda, Tomokazu; Al Sazzad, Md. Abdullah; Jäntti, Niklas Z.; Pentikäinen, Olli T.; Slotte, J. Peter

    2016-01-01

    The phospholipid acyl chain composition and order, the hydrogen bonding, and properties of the phospholipid headgroup all influence cholesterol/phospholipid interactions in hydrated bilayers. In this study, we examined the influence of hydrogen bonding on sphingomyelin (SM) colipid interactions in fluid uni- and multilamellar vesicles. We have compared the properties of oleoyl or palmitoyl SM with comparable dihydro-SMs, because the hydrogen bonding properties of SM and dihydro-SM differ. The association of cholestatrienol, a fluorescent cholesterol analog, with oleoyl sphingomyelin (OSM) was significantly stronger than its association with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, in bilayers with equal acyl chain order. The association of cholestatrienol with dihydro-OSM, which lacks a trans double bond in the sphingoid base, was even stronger than the association with OSM, suggesting an important role for hydrogen bonding in stabilizing sterol/SM interactions. Furthermore, with saturated SM in the presence of 15 mol % cholesterol, cholesterol association with fluid dihydro-palmitoyl SM bilayers was stronger than seen with palmitoyl SM under similar conditions. The different hydrogen bonding properties in OSM and dihydro-OSM bilayers also influenced the segregation of palmitoyl ceramide and dipalmitoylglycerol into an ordered phase. The ordered, palmitoyl ceramide-rich phase started to form above 2 mol % in the dihydro-OSM bilayers but only above 6 mol % in the OSM bilayers. The lateral segregation of dipalmitoylglycerol was also much more pronounced in dihydro-OSM bilayers than in OSM bilayers. The results show that hydrogen bonding is important for sterol/SM and ceramide/SM interactions, as well as for the lateral segregation of a diglyceride. A possible molecular explanation for the different hydrogen bonding in SM and dihydro-SM bilayers is presented and discussed. PMID:26789766

  10. Outline of a transition-state hydrogen-bond theory

    NASA Astrophysics Data System (ADS)

    Gilli, Paola; Bertolasi, Valerio; Pretto, Loretta; Gilli, Gastone

    2006-06-01

    Though the H-bond is well characterized as a D-H⋯:A three-center-four-electron interaction, the formulation of a general H-bond theory has turned out to be a rather formidable problem because of the extreme variability of the bonds formed (for instance, O-H⋯O energies range from 0.1 to 31 kcal mol -1). This paper surveys our previous contributions to the problem, including: (a) the H-bond chemical leitmotifs (CLs), showing that there are only four classes of strong H-bonds and one of moderately strong ones; (b) the PA/pK a equalization principle , showing that the four CLs forming strong H-bonds are actually molecular devices apt to equalize the acid-base properties (PA or p Ka) of the H-bond donor and acceptor groups; (c) the driving variable of the H-bond strength, which remains so identified as the difference Δp Ka=p KAH(D-H)-p KBH(A-H +) or, alternatively, ΔPA=PA(D -)-PA(A); and, in particular, (d) the transition-state H-bond theory (TSHBT), which interprets the H-bond as a stationary point along the complete proton transfer pathway going from D-H⋯A to D⋯H-A via the D⋯H⋯A transition state. TSHBT is verified in connection with a series of seven 1-(X-phenylazo)-2-naphthols, a class of compounds forming a strong intramolecular resonance-assisted H-bond (RAHB), which is switched from N-H⋯O to N⋯H-O by the decreasing electron-withdrawing properties of the substituent X. The system is studied in terms of: (i) variable-temperature X-ray crystallography; (ii) DFT emulation of stationary points and full PT pathways; (iii) Marcus rate-equilibrium analysis correlated with substituent LFER Hammett parameters.

  11. The quantum nature of the hydrogen bond: insight from path-integral molecular dynamics

    NASA Astrophysics Data System (ADS)

    Walker, Brent; Li, Xin-Zheng; Michaelides, Angelos

    2011-03-01

    Hydrogen (H) bonds are weak, generally intermolecular bonds, that hold together much of soft matter, the condensed phases of water, network liquids, and many ferroelectric crystals. The small mass of H means H-bonds are inherently quantum mechanical; effects such as zero point motion and tunneling should be considered, although often are not. In particular, a consistent picture of quantum nuclear effects on the strength of H-bonds and consequently the structure of H-bonded systems is still absent. Here, we report ab initio path-integral molecular dynamics studies on the quantum nature of the H-bond. Systematic examination of a range of H-bonded systems shows that quantum nuclei weaken weak H-bonds but strengthen relatively strong ones. This correlation arises from a competition between anharmonic intermolecular bond bending and intramolecular bond stretching. A simple rule of thumb enables predictions to be made for H-bonded bonded materials in general with merely classical knowledge (e.g. H-bond strength or H-bond length). Our work rationalizes the contrasting influence of quantum nuclear dynamics on a wide variety of materials, including liquid water and HF, and highlights the need for flexible molecules in force-field based studies of quantum nuclear dynamics.

  12. Structural and medium effects on the reactions of the cumyloxyl radical with intramolecular hydrogen bonded phenols. The interplay between hydrogen-bonding and acid-base interactions on the hydrogen atom transfer reactivity and selectivity.

    PubMed

    Salamone, Michela; Amorati, Riccardo; Menichetti, Stefano; Viglianisi, Caterina; Bietti, Massimo

    2014-07-03

    A time-resolved kinetic study on the reactions of the cumyloxyl radical (CumO(•)) with intramolecularly hydrogen bonded 2-(1-piperidinylmethyl)phenol (1) and 4-methoxy-2-(1-piperidinylmethyl)phenol (2) and with 4-methoxy-3-(1-piperidinylmethyl)phenol (3) has been carried out. In acetonitrile, intramolecular hydrogen bonding protects the phenolic O-H of 1 and 2 from attack by CumO(•) and hydrogen atom transfer (HAT) exclusively occurs from the C-H bonds that are α to the piperidine nitrogen (α-C-H bonds). With 3 HAT from both the phenolic O-H and the α-C-H bonds is observed. In the presence of TFA or Mg(ClO4)2, protonation or Mg(2+) complexation of the piperidine nitrogen removes the intramolecular hydrogen bond in 1 and 2 and strongly deactivates the α-C-H bonds of the three substrates. Under these conditions, HAT to CumO(•) exclusively occurs from the phenolic O-H group of 1-3. These results clearly show that in these systems the interplay between intramolecular hydrogen bonding and Brønsted and Lewis acid-base interactions can drastically influence both the HAT reactivity and selectivity. The possible implications of these findings are discussed in the framework of the important role played by tyrosyl radicals in biological systems.

  13. EFFECT OF TEMPERATURE AND GLYCEROL ON THE HYDROGEN-BOND DYNAMICS OF WATER

    SciTech Connect

    Ghattyvenkatakrishna, Pavan K; Uberbacher, Edward C

    2013-01-01

    The effect of glycerol, water and glycerol-water binary mixtures on the structure and dynamics of biomolecules has been well studied. However, the effect of varying glycerol concentration and temperature on the dynamics of water has not received due attention. We have studied the effect of concentration and temperature on the hydrogen bonded network formed by water molecules. A strong correlation between the relaxation time of the network and average number of hydrogen bonds per water molecules was found. The radial distribution function of water oxygens and hydrogens clarifies the effect of concentration on the structure and clustering of water.

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

    PubMed

    Dalvit, Claudio; Invernizzi, Christian; Vulpetti, Anna

    2014-08-25

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

  15. The effect of intermolecular hydrogen bonding on the fluorescence of a bimetallic platinum complex.

    PubMed

    Zhao, Guang-Jiu; Northrop, Brian H; Han, Ke-Li; Stang, Peter J

    2010-09-02

    The bimetallic platinum complexes are known as unique building blocks and arewidely utilized in the coordination-driven self-assembly of functionalized supramolecular metallacycles. Hence, photophysical study of the bimetallic platinum complexes will be very helpful for the understanding on the optical properties and further applications of coordination-driven self-assembled supramolecular metallacycles. Herein, we report steady-state and time-resolved spectroscopic experiments as well as quantum chemistry calculations to investigate the significant intermolecular hydrogen bonding effects on the intramolecular charge transfer (ICT) fluorescence of a bimetallic platinum compound 4,4'-bis(trans-Pt(PEt(3))(2)OTf)benzophenone 3 in solution. We demonstrated that the fluorescent state of compound 3 can be assigned as a metal-to-ligand charge transfer (MLCT) state. Moreover, it was observed that the formation of intermolecular hydrogen bonds can effectively lengthen the fluorescence lifetime of 3 in alcoholic solvents compared with that in hexane solvent. At the same time, the electronically excited states of 3 in solution are definitely changed by intermolecular hydrogen bonding interactions. As a consequence, we propose a new fluorescence modulation mechanism by hydrogen bonding to explain different fluorescence emissions of 3 in hydrogen-bonding solvents and nonhydrogen-bonding solvents.

  16. Dinuclear Calcium Complexes with Intramolecularly NH.O Hydrogen-Bonded Dicarboxylate Ligands.

    PubMed

    Ueyama, Norikazu; Takeda, Jiro; Yamada, Yusuke; Onoda, Akira; Okamura Ta, Taka-aki; Nakamura, Akira

    1999-02-08

    A novel dinuclear calcium complex, [Ca(2){(2-OCO-3-CH(3)C(6)H(3)NHCO)(2)C(CH(3))(2)}(2)(CH(3)OH)(6)] (1), was synthesized as a structural model of 8-coordinated Ca(II) ions in the double calcium-binding site of thermolysin. The complex has four NH.O hydrogen bonds between the amide NH and the carboxylate oxygen anion. Two types of bridging coordination of the carboxylate ligand to Ca(II) were found in 1. The amide NH forms a strong NH.O hydrogen bond with the anionic oxygen of the two carboxylate oxygens. A ligand-exchange reaction between the dinuclear calcium complex and eight equimolar amounts of 2,4,6-trimethylbenzoic acid or 2-CH(3)-6-t-BuCONHC(6)H(3)COOH indicates that the NH.O hydrogen bond prevents the dissociation of the Ca-O bond.

  17. Compressed hydrogen-bond effects in the pressure-frozen chloroacetic acid.

    PubMed

    Gajda, Roman; Katrusiak, Andrzej

    2007-12-01

    The competing effects of squeezed OH...O bonds, destabilizing the H-atom position, and of displaced hydrogen donor and acceptor groups, favouring the ordered H-atom sites, have been tuned by pressure in the pressure-frozen dichloroacetic acid. Its structure has been determined at 0.1, 0.7, 0.9 and 1.4 GPa: in this pressure range the crystals are stable in the monoclinic space group P2(1)/n. The molecules are O-H...O hydrogen bonded into dimers, which in turn interact via a unique pattern of halogen...halogen contacts. Between 0.1 and 1.4 GPa the OH...O bond is squeezed from 2.674 (13) to 2.632 (9) A. Within the pressure range investigated the hydrogen bonds are squeezed and the shear displacement of the molecules compensate, and the H atoms remain ordered.

  18. The effects of hydrogen bonds on metal-mediated O2 activation and related processes

    PubMed Central

    Shook, Ryan L.; Borovik, A. S.

    2009-01-01

    Hydrogen bonds stabilize and direct chemistry performed by metalloenzymes. With inspiration from enzymes, we will utilize an approach that incorporates intramolecular hydrogen bond donors to determine their effects on the stability and reactivity of metal complexes. Our premise is that control of secondary coordination sphere interactions will promote new function in synthetic metal complexes. Multidentate ligands have been developed that create rigid organic structures around metal ions. These ligands place hydrogen bond (H-bond) donors proximal to the metal centers, forming specific microenvironments. One distinguishing attribute of these systems is that site-specific modulations in structure can be readily accomplished, in order to evaluate correlations with reactivity. A focus of this research is consideration of dioxygen binding and activation by metal complexes, including developing structure–function relationships in metal-assisted oxidative catalysis. PMID:19082087

  19. 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

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

    PubMed

    Polander, Brandon C; Barry, Bridgette A

    2012-04-17

    In photosystem II, oxygen evolution occurs by the accumulation of photo-induced oxidizing equivalents at the oxygen-evolving complex (OEC). The sequentially oxidized states are called the S(0)-S(4) states, and the dark stable state is S(1). Hydrogen bonds to water form a network around the OEC; this network is predicted to involve multiple peptide carbonyl groups. In this work, we tested the idea that a network of hydrogen bonded water molecules plays a catalytic role in water oxidation. As probes, we used OEC peptide carbonyl frequencies, the substrate-based inhibitor, ammonia, and the sugar, trehalose. Reaction-induced FT-IR spectroscopy was used to describe the protein dynamics associated with the S(1) to S(2) transition. A shift in an amide CO vibrational frequency (1664 (S(1)) to 1653 (S(2)) cm(-1)) was observed, consistent with an increase in hydrogen bond strength when the OEC is oxidized. Treatment with ammonia/ammonium altered these CO vibrational frequencies. The ammonia-induced spectral changes are attributed to alterations in hydrogen bonding, when ammonia/ammonium is incorporated into the OEC hydrogen bond network. The ammonia-induced changes in CO frequency were reversed or blocked when trehalose was substituted for sucrose. This trehalose effect is attributed to a displacement of ammonia molecules from the hydrogen bond network. These results imply that ammonia, and by extension water, participate in a catalytically essential hydrogen bond network, which involves OEC peptide CO groups. Comparison to the ammonia transporter, AmtB, reveals structural similarities with the bound water network in the OEC.

  1. Spectroscopic, DFT, and XRD Studies of Hydrogen Bonds in N-Unsubstituted 2-Aminobenzamides.

    PubMed

    Mphahlele, Malose Jack; Maluleka, Marole Maria; Rhyman, Lydia; Ramasami, Ponnadurai; Mampa, Richard Mokome

    2017-01-04

    The structures of the mono- and the dihalogenated N-unsubstituted 2-aminobenzamides were characterized by means of the spectroscopic (¹H-NMR, UV-Vis, FT-IR, and FT-Raman) and X-ray crystallographic techniques complemented with a density functional theory (DFT) method. The hindered rotation of the C(O)-NH₂ single bond resulted in non-equivalence of the amide protons and therefore two distinct resonances of different chemical shift values in the ¹H-NMR spectra of these compounds were observed. 2-Amino-5-bromobenzamide (ABB) as a model confirmed the presence of strong intramolecular hydrogen bonds between oxygen and the amine hydrogen. However, intramolecular hydrogen bonding between the carbonyl oxygen and the amine protons was not observed in the solution phase due to a rapid exchange of these two protons with the solvent and fast rotation of the Ar-NH₂ single bond. XRD also revealed the ability of the amide unit of these compounds to function as a hydrogen bond donor and acceptor simultaneously to form strong intermolecular hydrogen bonding between oxygen of one molecule and the NH moiety of the amine or amide group of the other molecule and between the amine nitrogen and the amide hydrogen of different molecules. DFT calculations using the B3LYP/6-311++G(d,p) basis set revealed that the conformer (A) with oxygen and 2-amine on the same side predominates possibly due to the formation of a six-membered intramolecular ring, which is assisted by hydrogen bonding as observed in the single crystal XRD structure.

  2. The importance of timescale for hydrogen bonding in imidazolium chloride ionic liquids.

    PubMed

    Skarmoutsos, Ioannis; Welton, Tom; Hunt, Patricia A

    2014-02-28

    Hydrogen bond (H-bond) dynamics have been investigated for "hot" 1-ethyl-3-methylimidazolium chloride and "cold" 1-butyl-3-methylimidazolium chloride ionic liquids (IL). While the average number of H-bonds remains constant for a ≈100 °C temperature change we show that the underlying dynamics of the H-bonding changes dramatically. H-bond dynamics are investigated based on distance and angle criteria, and on the H-bond state (zero, single or bifurcated H-bonds). Temperature effects on the cation ring reorientational dynamics are also examined. Angle deformations are found to be more important than bond stretching in determining the lifetime of individual H-bonds, and decay occurs on two time scales related to the magnitude of the deviation from linearity. Rapid angular oscillation of the anion breaks the H-bond (for the first time) and minimal temperature effects indicate that H-bonds are readily reformed even near the melting point. Intermittent H-bonds repeatedly break and reform over a longer timescale, and exhibit very strong temperature effects. In the hot IL H-bonding with ring and alkyl chain H-atoms occurs, ring reorientational dynamics is anisotropic and the corresponding lifetimes are similar to the intermittent H-bond lifetimes. In the cold IL ring H-atoms dominate the H-bonding and intermittent H-bonds last for ≈5 ns, ring reorientation occurs on a much slower timescale. The hot IL favours single H-bonds, but the individual ions often change, while the cold IL favours bifurcated H-bonds with the same co-located ions.

  3. Alternative hydrogen bond implementations produce opposite effects on collapse cooperativity of lattice homopolypeptide models.

    PubMed

    Fleury, Gustavo M N; Barbosa, Marco A A; Pereira de Araújo, Antônio F

    2007-11-01

    We use complete enumeration of self-avoiding chains of up to N=26 monomers in two-dimensional lattices to investigate the effect of alternative implementations of backbone hydrogen bonds on the cooperativity of homopolypeptide collapse. Following a recent study on protein folding models, we use the square lattice with z=3 local conformations per monomer and lattice extensions containing diagonal steps which result in z=5 or z=7 and assume that only a subset of zhhydrogen bond formation. As previously observed in heteropolymeric folding, a significant increase in cooperativity, as measured by kappa2 values, results from the coupling between hydrogen bonds and hydrophobic interactions, in such a way that hydrophobic contacts are favorable only when contacting monomers are involved in hydrogen bond formation. For some z/zh combinations the energy distribution is bimodal at the collapse transition temperature. The situation can be regarded as if all hydrophobic contacts actually decrease the energy by the same amount, 2h , with the addition of an energetic increase, epsilon2=h, as a penalty for each contacting monomer not satisfying the hydrogen bond condition. Cooperativity is little affected and might even decrease, however, when hydrogen bonds produce a decrease in energy by the same amount, epsilon1=h, for each bonding monomer. For the more general situation when the hydrogen bond effect is not equal, in modulus, to the hydrophobic interaction, i.e., epsilon2 not equalh or epsilon1 not equal h, we observe a pronounced increase in kappa2 for small epsilon2, with a maximum around epsilon2/h approximately 1.5, followed by a gradual decrease to a limiting value at large epsilon2. The opposite behavior is observed when epsilon1 is varied. The observed qualitative difference is shown to arise from opposite effects on the convexity of the total density of states of the system when subdensities corresponding to different numbers of

  4. Cooperative deformation of hydrogen bonds in beta-strands and beta-sheet nanocrystals

    NASA Astrophysics Data System (ADS)

    Qin, Zhao; Buehler, Markus J.

    2010-12-01

    Beta-sheet protein domains are stabilized by weak hydrogen bonds, yet materials such as silk—whose ultimate tensile strength is controlled primarily by this secondary structure—can exceed the ultimate tensile strength of steel. Earlier work has suggested that this is because hydrogen bonds deform cooperatively within small protein domains to reach the maximum strength. Here we study the atomistic mechanism of this concerted deformation mechanism by applying an elastic structural model, used to solve the deformation field of the chemical bonds in beta-sheet nanostructures under stretching and thereby identify the number of hydrogen bonds that deform cooperatively. Through this analysis, we predict the optimal beta-strand and beta-sheet nanocrystal size associated with reaching the maximum usage of hydrogen bonds under loading applied per unit material volume. Our results, albeit based on a simple model and analytical equations, quantitatively agree with results based on experimental and molecular-dynamics studies and provide physical insight into the underlying molecular mechanisms of weak bond cooperativity. A comparison with the size of hydrogen bond clusters in biology reveals excellent agreement with the cluster sizes predicted by our analysis, suggesting that perhaps the confinement of hydrogen bonds into nanoscale elements is a universal biological design paradigm that turns weakness to strength. The parameters used in this study could be modified and applied to other protein and polymer structures, which imply potential applications of our model in understanding the physics of deformation and failure in a broader range of biological and polymer materials, as well as in de novo biomaterial design.

  5. The two faces of hydrogen-bond strength on triple AAA-DDD arrays.

    PubMed

    Lopez, Alfredo Henrique Duarte; Caramori, Giovanni Finoto; Coimbra, Daniel Fernando; Parreira, Renato Luis Tame; da Silva, Éder Henrique

    2013-12-02

    Systems that are connected through multiple hydrogen bonds are the cornerstone of molecular recognition processes in biology, and they are increasingly being employed in supramolecular chemistry, specifically in molecular self-assembly processes. For this reason, the effects of different substituents (NO2, CN, F, Cl, Br, OCH3 and NH2) on the electronic structure, and consequently on the magnitude of hydrogen bonds in triple AAA-DDD arrays (A=acceptor, D=donor) were evaluated in the light of topological [electron localization function (ELF) and quantum theory of atoms in molecules (QTAIM)], energetic [Su-Li energy-decomposition analysis (EDA) and natural bond orbital analysis (NBO)], and geometrical analysis. The results based on local H-bond descriptors (geometries, QTAIM, ELF, and NBO) indicate that substitutions with electron-withdrawing groups on the AAA module tend to strengthen, whereas electron-donating substituents tend to weaken the covalent character of the AAA-DDD intermolecular H-bonds, and also indicate that the magnitude of the effect is dependent on the position of substitution. In contrast, Su-Li EDA results show an opposite behavior when compared to local H-bond descriptors, indicating that electron-donating substituents tend to increase the magnitude of H-bonds in AAA-DDD arrays, and thus suggesting that the use of local H-bond descriptors describes the nature of H bonds only partially, not providing enough insight about the strength of such H bonds.

  6. Cation-cation clusters in ionic liquids: Cooperative hydrogen bonding overcomes like-charge repulsion.

    PubMed

    Knorr, Anne; Ludwig, Ralf

    2015-12-02

    Direct spectroscopic evidence for H-bonding between like-charged ions is reported for the ionic liquid, 1-(2-hydroxyethyl)-3-methylimidazolium tetrafluoroborate. New infrared bands in the OH frequency range appear at low temperatures indicating the formation of H-bonded cation-cation clusters similar to those known for water and alcohols. Supported by DFT calculations, these vibrational bands can be assigned to attractive interaction between the hydroxyl groups of the cations. The repulsive Coulomb interaction is overcome by cooperative hydrogen bonding between ions of like charge. The transition energy from purely cation-anion interacting configurations to those including cation-cation H-bonds is determined to be 3-4 kJmol(-1). The experimental findings and DFT calculations strongly support the concept of anti-electrostatic hydrogen bonds (AEHBs) as recently suggested by Weinhold and Klein. The like-charge configurations are kinetically stabilized with decreasing temperatures.

  7. Hydrogen-bond-dynamics-based switching of conductivity and magnetism: a phase transition caused by deuterium and electron transfer in a hydrogen-bonded purely organic conductor crystal.

    PubMed

    Ueda, Akira; Yamada, Shota; Isono, Takayuki; Kamo, Hiromichi; Nakao, Akiko; Kumai, Reiji; Nakao, Hironori; Murakami, Youichi; Yamamoto, Kaoru; Nishio, Yutaka; Mori, Hatsumi

    2014-08-27

    A hydrogen bond (H-bond) is one of the most fundamental and important noncovalent interactions in chemistry, biology, physics, and all other molecular sciences. Especially, the dynamics of a proton or a hydrogen atom in the H-bond has attracted increasing attention, because it plays a crucial role in (bio)chemical reactions and some physical properties, such as dielectricity and proton conductivity. Here we report unprecedented H-bond-dynamics-based switching of electrical conductivity and magnetism in a H-bonded purely organic conductor crystal, κ-D3(Cat-EDT-TTF)2 (abbreviated as κ-D). This novel crystal κ-D, a deuterated analogue of κ-H3(Cat-EDT-TTF)2 (abbreviated as κ-H), is composed only of a H-bonded molecular unit, in which two crystallographically equivalent catechol-fused ethylenedithiotetrathiafulvalene (Cat-EDT-TTF) skeletons with a +0.5 charge are linked by a symmetric anionic [O···D···O](-1)-type strong H-bond. Although the deuterated and parent hydrogen systems, κ-D and κ-H, are isostructural paramagnetic semiconductors with a dimer-Mott-type electronic structure at room temperature (space group: C2/c), only κ-D undergoes a phase transition at 185 K, to change to a nonmagnetic insulator with a charge-ordered electronic structure (space group: P1). The X-ray crystal structure analysis demonstrates that this dramatic switching of the electronic structure and physical properties originates from deuterium transfer or displacement within the H-bond accompanied by electron transfer between the Cat-EDT-TTF π-systems, proving that the H-bonded deuterium dynamics and the conducting TTF π-electron are cooperatively coupled. Furthermore, the reason why this unique phase transition occurs only in κ-D is qualitatively discussed in terms of the H/D isotope effect on the H-bond geometry and potential energy curve.

  8. Critical hydrogen bonds and protonation states of pyridoxal 5'-phosphate revealed by NMR.

    PubMed

    Limbach, Hans-Heinrich; Chan-Huot, Monique; Sharif, Shasad; Tolstoy, Peter M; Shenderovich, Ilya G; Denisov, Gleb S; Toney, Michael D

    2011-11-01

    In this contribution we review recent NMR studies of protonation and hydrogen bond states of pyridoxal 5'-phosphate (PLP) and PLP model Schiff bases in different environments, starting from aqueous solution, the organic solid state to polar organic solution and finally to enzyme environments. We have established hydrogen bond correlations that allow one to estimate hydrogen bond geometries from (15)N chemical shifts. It is shown that protonation of the pyridine ring of PLP in aspartate aminotransferase (AspAT) is achieved by (i) an intermolecular OHN hydrogen bond with an aspartate residue, assisted by the imidazole group of a histidine side chain and (ii) a local polarity as found for related model systems in a polar organic solvent exhibiting a dielectric constant of about 30. Model studies indicate that protonation of the pyridine ring of PLP leads to a dominance of the ketoenamine form, where the intramolecular OHN hydrogen bond of PLP exhibits a zwitterionic state. Thus, the PLP moiety in AspAT carries a net positive charge considered as a pre-requisite to initiate the enzyme reaction. However, it is shown that the ketoenamine form dominates in the absence of ring protonation when PLP is solvated by polar groups such as water. Finally, the differences between acid-base interactions in aqueous solution and in the interior of proteins are discussed. This article is part of a special issue entitled: Pyridoxal Phosphate Enzymology.

  9. Self-assembly of hydrogen-bonded two-dimensional quasicrystals

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    The process of molecular self-assembly on solid surfaces is essentially one of crystallization in two dimensions, and the structures that result depend on the interplay between intermolecular forces and the interaction between adsorbates and the underlying substrate. Because a single hydrogen bond typically has an energy between 15 and 35 kilojoules per mole, hydrogen bonding can be a strong driver of molecular assembly; this is apparent from the dominant role of hydrogen bonding in nucleic-acid base pairing, as well as in the secondary structure of proteins. Carboxylic acid functional groups, which provide two hydrogen bonds, are particularly promising and reliable in creating and maintaining surface order, and self-assembled monolayers of benzoic acids produce structure that depends on the number and relative placement of carboxylic acid groups. Here we use scanning tunnelling microscopy to study self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH), and find that, rather than producing dimeric or linear structures typical of carboxylic acids, FcCOOH forms highly unusual cyclic hydrogen-bonded pentamers, which combine with simultaneously formed FcCOOH dimers to form two-dimensional quasicrystallites that exhibit local five-fold symmetry and maintain translational and rotational order (without periodicity) for distances of more than 400 ångströms.

  10. Conservation and Functional Importance of Carbon-Oxygen Hydrogen Bonding in AdoMet-Dependent Methyltransferases

    SciTech Connect

    Horowitz, Scott; Dirk, Lynnette M.A.; Yesselman, Joseph D.; Nimtz, Jennifer S.; Adhikari, Upendra; Mehl, Ryan A.; Scheiner, Steve; Houtz, Robert L.; Al-Hashimi, Hashim M.; Trievel, Raymond C.

    2013-09-06

    S-Adenosylmethionine (AdoMet)-based methylation is integral to metabolism and signaling. AdoMet-dependent methyltransferases belong to multiple distinct classes and share a catalytic mechanism that arose through convergent evolution; however, fundamental determinants underlying this shared methyl transfer mechanism remain undefined. A survey of high-resolution crystal structures reveals that unconventional carbon–oxygen (CH···O) hydrogen bonds coordinate the AdoMet methyl group in different methyltransferases irrespective of their class, active site structure, or cofactor binding conformation. Corroborating these observations, quantum chemistry calculations demonstrate that these charged interactions formed by the AdoMet sulfonium cation are stronger than typical CH···O hydrogen bonds. Biochemical and structural studies using a model lysine methyltransferase and an active site mutant that abolishes CH···O hydrogen bonding to AdoMet illustrate that these interactions are important for high-affinity AdoMet binding and transition-state stabilization. Further, crystallographic and NMR dynamics experiments of the wild-type enzyme demonstrate that the CH···O hydrogen bonds constrain the motion of the AdoMet methyl group, potentially facilitating its alignment during catalysis. Collectively, the experimental findings with the model methyltransferase and structural survey imply that methyl CH···O hydrogen bonding represents a convergent evolutionary feature of AdoMet-dependent methyltransferases, mediating a universal mechanism for methyl transfer.

  11. 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.

  12. The energy of the intramolecular hydrogen bond in chloro-substituted N-methyl-salicylidene imines

    NASA Astrophysics Data System (ADS)

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

    2007-11-01

    The energetic effects of the conformational rearrangement of eight Schiff bases, differently chloro-substituted, are discussed on the basis of the results of B3LYP/6-31+G(d,p) calculations. The proton transfer tautomers as well as "open"-non-hydrogen-bonded forms were considered. It was found, that the hydrogen-bonded forms have the lowest energy, but the second most stable were the proton transfer states with an O…H sbnd N intramolecular hydrogen bond. The proton transfer in Schiff bases dominates in comparison to other conformational rearrangements. This is important for the understanding of thermochromic and photochromic properties of these molecules. By using a thermodynamic cycle, the steric effects connected with chelate ring formation are estimated to be up to 5 kcal/mol, much higher than in related Mannich bases (˜1 kcal/mol) which do not form resonance assisted hydrogen bonds. Accounting these effects the "real" value of the energy of hydrogen bond formation was estimated to be 15 kcal/mol which increases with growing number of chlorine atoms up to 16.5 kcal/mol for 4,5,6-trichloro substitution.

  13. The influence of hydrogen bonding on the physical properties of ionic liquids.

    PubMed

    Fumino, Koichi; Peppel, Tim; Geppert-Rybczyńska, Monika; Zaitsau, Dzmitry H; Lehmann, Jochen K; Verevkin, Sergey P; Köckerling, Martin; Ludwig, Ralf

    2011-08-21

    Potential applications of ionic liquids depend on the properties of this class of liquid material. To a large extent the structure and properties of these Coulomb systems are determined by the intermolecular interactions among anions and cations. In particular the subtle balance between Coulomb forces, hydrogen bonds and dispersion forces is of great importance for the understanding of ionic liquids. The purpose of the present paper is to answer three questions: Do hydrogen bonds exist in these Coulomb fluids? To what extent do hydrogen bonds contribute to the overall interaction between anions and cations? And finally, are hydrogen bonds important for the physical properties of ionic liquids? All these questions are addressed by using a suitable combination of experimental and theoretical methods including newly synthesized imidazolium-based ionic liquids, far infrared spectroscopy, terahertz spectroscopy, DFT calculations, differential scanning calorimetry (DSC), viscometry and quartz-crystal-microbalance measurements. The key statement is that although ionic liquids consist solely of anions and cations and Coulomb forces are the dominating interaction, local and directional interaction such as hydrogen bonding has significant influence on the structure and properties of ionic liquids. This is demonstrated for the case of melting points, viscosities and enthalpies of vaporization. As a consequence, a variety of important properties can be tuned towards a larger working temperature range, finally expanding the range of potential applications.

  14. Disruption of hydrogen bonding between plant cell wall polymers by proteins that induce wall extension.

    PubMed Central

    McQueen-Mason, S; Cosgrove, D J

    1994-01-01

    Plant cell enlargement is controlled by the ability of the constraining cell wall to expand. This ability has been postulated to be under the control of polysaccharide hydrolases or transferases that weaken or rearrange the loadbearing polymeric networks in the wall. We recently identified a family of wall proteins, called expansins, that catalyze the extension of isolated plant cell walls. Here we report that these proteins mechanically weaken pure cellulose paper in extension assays and stress relaxation assays, without detectable cellulase activity (exo- or endo- type). Because paper derives its mechanical strength from hydrogen bonding between cellulose microfibrils, we conclude that expansins can disrupt hydrogen bonding between cellulose fibers. This conclusion is further supported by experiments in which expansin-mediated wall extension (i) was increased by 2 M urea (which should weaken hydrogen bonding between wall polymers) and (ii) was decreased by replacement of water with deuterated water, which has a stronger hydrogen bond. The temperature sensitivity of expansin-mediated wall extension suggests that units of 3 or 4 hydrogen bonds are broken by the action of expansins. In the growing cell wall, expansin action is likely to catalyze slippage between cellulose microfibrils and the polysaccharide matrix, and thereby catalyze wall stress relaxation, followed by wall surface expansion and plant cell enlargement. Images PMID:11607483

  15. Hydrogen-bonding patterns in two aroylthio­carbamates and two aroylimidothio­carbonates

    PubMed Central

    Insuasty, Henry; Castro, Edison; Sánchez, Edison; Cobo, Justo; Glidewell, Christopher

    2010-01-01

    In O-ethyl N-benzoyl­thio­carbamate, C10H11NO2S, the mol­ecules are linked into sheets by a combination of two-centre N—H⋯O and C—H⋯S hydrogen bonds and a three-centre C—H⋯(O,S) hydrogen bond. A combination of two-centre N—H⋯O and C—H⋯O hydrogen bonds links the mol­ecules of O-ethyl N-(4-methyl­benzoyl)thio­carbamate, C11H13NO2S, into chains of rings, which are linked into sheets by an aromatic π–π stacking inter­action. In O,S-diethyl N-(4-methyl­benzoyl)imidothio­carbonate, C13H17NO2S, pairs of mol­ecules are linked into centrosymmetric dimers by pairs of symmetry-related C—H⋯π(arene) hydrogen bonds, while the mol­ecules of O,S-diethyl N-(4-chloro­benzoyl)imidothio­carbonate, C12H14ClNO2S, are linked by a single C—H⋯O hydrogen bond into simple chains, pairs of which are linked by an aromatic π–π stacking inter­action to form a ladder-type structure. PMID:20203412

  16. The discovery of the hydrogen bond from p-Nitrothiophenol by Raman spectroscopy: Guideline for the thioalcohol molecule recognition tool

    PubMed Central

    Ling, Yun; Xie, Wen Chang; Liu, Guo Kun; Yan, Run Wen; Wu, De Yin; Tang, Jing

    2016-01-01

    Inter- and intra- molecular hydrogen bonding plays important role in determining molecular structure, physical and chemical properties, which may be easily ignored for molecules with a non-typical hydrogen bonding structure. We demonstrated in this paper that the hydrogen bonding is responsible for the different Raman spectra in solid and solution states of p-Nitrothiophenol (PNTP). The consistence of the theoretical calculation and experiment reveals that the intermolecular hydrogen bonding yields an octatomic ring structure (8) of PNTP in the solid state, confirmed by the characteristic S-H---O stretching vibration mode at 2550 cm−1; when it comes to the solution state, the breakage of hydrogen bond of S-H---O induced the S-H stretching vibration at 2590 cm−1. Our findings may provide a simple and fast method for identifying the intermolecular hydrogen bonding. PMID:27659311

  17. A computational study on the enhanced stabilization of aminophenol derivatives by internal hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Gomes, José R. B.; Ribeiro da Silva, Manuel A. V.

    2006-05-01

    The stabilization of aminophenol derivatives and their radicals due to internal hydrogen bonding has been analyzed by means of density functional theory and by topological electron density analysis. The calculations have been carried out at the B3LYP level of theory, using several basis sets, and by means of the CBS-4M composite approach. A strong O-H⋯NH 2 hydrogen bond is found to stabilize the aminophenol with the lone-pair of the nitrogen atom co-planar with the aromatic ring, contrasting with the optimized structure found for aniline. The effect of electron donors and electron acceptors on the strength of the internal hydrogen bond is also analyzed. For one of the species studied, 2,6-diaminophenol, the computed O-H bond dissociation enthalpy is only 300 kJ/mol, the lowest value found so far for phenol and other compounds containing the O-H bond, almost 25 kJ/mol lower than those found experimentally for pyrogallol and for vitamin E. The explanation for such a small value comes from the enhanced stabilization of the corresponding radical species by internal hydrogen bonding, combined with a decrease of the steric effects caused by rotation of the amino groups.

  18. Regulation of protein-ligand binding affinity by hydrogen bond pairing

    PubMed Central

    Chen, Deliang; Oezguen, Numan; Urvil, Petri; Ferguson, Colin; Dann, Sara M.; Savidge, Tor C.

    2016-01-01

    Hydrogen (H)-bonds potentiate diverse cellular functions by facilitating molecular interactions. The mechanism and the extent to which H-bonds regulate molecular interactions are a largely unresolved problem in biology because the H-bonding process continuously competes with bulk water. This interference may significantly alter our understanding of molecular function, for example, in the elucidation of the origin of enzymatic catalytic power. We advance this concept by showing that H-bonds regulate molecular interactions via a hitherto unappreciated donor-acceptor pairing mechanism that minimizes competition with water. On the basis of theoretical and experimental correlations between H-bond pairings and their effects on ligand binding affinity, we demonstrate that H-bonds enhance receptor-ligand interactions when both the donor and acceptor have either significantly stronger or significantly weaker H-bonding capabilities than the hydrogen and oxygen atoms in water. By contrast, mixed strong-weak H-bond pairings decrease ligand binding affinity due to interference with bulk water, offering mechanistic insight into why indiscriminate strengthening of receptor-ligand H-bonds correlates poorly with experimental binding affinity. Further support for the H-bond pairing principle is provided by the discovery and optimization of lead compounds targeting dietary melamine and Clostridium difficile toxins, which are not realized by traditional drug design methods. Synergistic H-bond pairings have therefore evolved in the natural design of high-affinity binding and provide a new conceptual framework to evaluate the H-bonding process in biological systems. Our findings may also guide wider applications of competing H-bond pairings in lead compound design and in determining the origin of enzymatic catalytic power. PMID:27051863

  19. Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity

    NASA Astrophysics Data System (ADS)

    Liu, Lan; Baergen, Alyson; Michelsen, Klaus; Kitova, Elena N.; Schnier, Paul D.; Klassen, John S.

    2014-05-01

    This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the -7 charge state) of complexes of bovine β-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)7- ions, compared with that of the (Lg + PA)7- ion, it is concluded that the -OH groups of the X-OHPA ligands participate in strong (5 - 11 kcal mol-1) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the -OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the -OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (Ka) measured for 7-OHPA [(2.3 ± 0.2) × 105 M-1] is similar to the value for the PA [(3.8 ± 0.1) × 105 M-1]; Ka for 3-OHPA [(1.1 ± 0.3) × 106 M-1] is approximately three-times larger, whereas Ka for 16-OHPA [(2.3 ± 0.2) × 104 M-1] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand -OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds.

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

    SciTech Connect

    Sigala, Paul A.; Ruben, Eliza A.; Liu, Corey W.; Piccoli, Paula M. B.; Hohenstein, Edward G.; Martinez, Todd J.; Schultz, Arthur J.; Herschiag, Daniel

    2015-05-06

    Hydrogen bonds profoundly influence the architecture and activity of biological macromolecules. Deep appreciation of hydrogen bond contributions to biomolecular function thus requires a detailed understanding of hydrogen bond structure and energetics and the relationship between these properties. Hydrogen bond formation energies (Delta G(f)) are enormously more favorable in aprotic solvents than in water, and two classes of contributing factors have been proposed to explain this energetic difference, focusing respectively on the isolated and hydrogen-bonded species: (I) water stabilizes the dissociated donor and acceptor groups much better than aprotic solvents, thereby reducing the driving force for hydrogen bond formation; and (II) water lengthens hydrogen bonds compared to aprotic environments, thereby decreasing the potential energy within the hydrogen bond. Each model has been proposed to provide a dominant contribution to Delta G(f), but incisive tests that distinguish the importance of these contributions are lacking. Here we directly test the structural basis of model II. Neutron crystallography, NMR spectroscopy, and quantum mechanical calculations demonstrate that O-H center dot center dot center dot O hydrogen bonds in crystals, chloroform, acetone, and water have nearly identical lengths and very similar potential energy surfaces despite Delta G(f) differences >8 kcal/mol across these solvents. These results rule out a substantial contribution from solvent-dependent differences in hydrogen bond structure and potential energy after association (model II) and thus support the conclusion that differences in hydrogen bond Delta G(f) are predominantly determined by solvent interactions with the dissociated groups (model I). These findings advance our understanding of universal hydrogen-bonding interactions and have important implications for biology and engineering.

  1. Access to B=S and B=Se double bonds via sulfur and selenium insertion into a B-H bond and hydrogen migration.

    PubMed

    Wang, Hao; Zhang, Jianying; Hu, Hongfan; Cui, Chunming

    2010-08-18

    Stable compounds with a boron-chalcogen (S or Se) valence double bond have been prepared via sequences involving insertion of the chalcogen into a B-H bond and subsequent hydrogen migration. X-ray diffraction studies and density functional theory calculations on the resulting compounds provide convincing evidence for the boron-chalcogen multiple bonding.

  2. Dynamics of Weak, Bifurcated and Strong Hydrogen Bonds in Lithium Nitrate Trihydrate

    SciTech Connect

    Werhahn, Jasper C.; Pandelov, S.; Xantheas, Sotiris S.; Iglev, H.

    2011-07-07

    The properties of three distinct types of hydrogen bonds, namely a weak, a bifurcated and a strong one, all present in/the LiNO3 (HDO)(D2O)2 hydrate lattice unit cell are studied using steady-state and time-resolved spectroscopy. The lifetimes of the OH stretching vibrations for the three individual bonds are 2.2 ps (weak), 1.7 ps (bifurcated), and 1.2 ps (strong), respectively. For the first time the properties of bifurcated H bonds can thus be unambiguously directly compared to those of weak and strong H bonds in the same system. The values of their OH stretching vibration lifetime, anharmonicity, red shift and bond strength lie between those for the strong and weak H bonds. The experimentally observed inhomogeneous broadening of their spectral signature is attributed to the coupling with a low frequency intermolecular wagging vibration/

  3. The Delicate Balance of Hydrogen Bond Forces in D-Threoninol

    NASA Astrophysics Data System (ADS)

    Zhang, Di; Vara, Vanesa Vaquero; Dian, Brian C.; Zwier, Timothy S.; Pratt, David W.

    2013-06-01

    The molecule of D-threoninol has been studied using CP-FTMW spectroscopy. Despite the small size of this molecule, a great variety of conformations have been observed in the molecular expansion. With 2 OH groups and one NH_2 group, many possibilities for hydrogen bonding are anticipated. The multiple ways they can interact with each other make the analysis of its rotational spectrum challenging and only through an exhaustive conformational search and the comparison with the experimental rotational parameters and line strengths are we able to understand the complex nature of these interactions. In the 7 conformations already assigned, evidences for hydrogen bonded cycles and chains are revealed with dipole moment very sensitive to the configuration of the hydrogen bond.

  4. Non-covalent synthesis of supermicelles with complex architectures using spatially confined hydrogen-bonding interactions

    PubMed Central

    Li, Xiaoyu; Gao, Yang; Boott, Charlotte E.; Winnik, Mitchell A.; Manners, Ian

    2015-01-01

    Nature uses orthogonal interactions over different length scales to construct structures with hierarchical levels of order and provides an important source of inspiration for the creation of synthetic functional materials. Here, we report the programmed assembly of monodisperse cylindrical block comicelle building blocks with crystalline cores to create supermicelles using spatially confined hydrogen-bonding interactions. We also demonstrate that it is possible to further program the self-assembly of these synthetic building blocks into structures of increased complexity by combining hydrogen-bonding interactions with segment solvophobicity. The overall approach offers an efficient, non-covalent synthesis method for the solution-phase fabrication of a range of complex and potentially functional supermicelle architectures in which the crystallization, hydrogen-bonding and solvophobic interactions are combined in an orthogonal manner. PMID:26337527

  5. Effects of hydrogen bonding on current-voltage characteristics of molecular junctions

    NASA Astrophysics Data System (ADS)

    Kula, Mathias; Jiang, Jun; Lu, Wei; Luo, Yi

    2006-11-01

    We present a first-principles study of hydrogen bonding effect on current-voltage characteristics of molecular junctions. Three model charge-transfer molecules, 2'-amino-4,4'-di(ethynylphenyl)-1-benzenethiolate (DEPBT-D), 4,4'-di(ethynylphenyl)-2'-nitro-1-benzenethiolate (DEPBT-A), and 2'-amino-4,4'-di(ethynylphenyl)-5'-nitro-1-benzenethiolate (DEPBT-DA), have been examined and compared with the corresponding hydrogen bonded complexes formed with different water molecules. Large differences in current-voltage characteristics are observed for DEPBT-D and DEPBT-A molecules with or without hydrogen bonded waters, while relatively small differences are found for DEPBT-DA. It is predicted that the presence of water clusters can drastically reduce the conductivities of the charge-transfer molecules. The underlying microscopic mechanism has been discussed.

  6. Concerted hydrogen-bond breaking by quantum tunneling in the water hexamer prism.

    PubMed

    Richardson, Jeremy O; Pérez, Cristóbal; Lobsiger, Simon; Reid, Adam A; Temelso, Berhane; Shields, George C; Kisiel, Zbigniew; Wales, David J; Pate, Brooks H; Althorpe, Stuart C

    2016-03-18

    The nature of the intermolecular forces between water molecules is the same in small hydrogen-bonded clusters as in the bulk. The rotational spectra of the clusters therefore give insight into the intermolecular forces present in liquid water and ice. The water hexamer is the smallest water cluster to support low-energy structures with branched three-dimensional hydrogen-bond networks, rather than cyclic two-dimensional topologies. Here we report measurements of splitting patterns in rotational transitions of the water hexamer prism, and we used quantum simulations to show that they result from geared and antigeared rotations of a pair of water molecules. Unlike previously reported tunneling motions in water clusters, the geared motion involves the concerted breaking of two hydrogen bonds. Similar types of motion may be feasible in interfacial and confined water.

  7. Hydrogen Bonding in 4-AMINOPHENYL Ethanol: a Combined Ir-Uv Double Resonance and Microwave Study

    NASA Astrophysics Data System (ADS)

    Bray, Caitlin; Rivera, Cara Rae; Arsenault, E. A.; Obenchain, Daniel A.; Novick, Stewart E.; Knee, Joseph L.

    2015-06-01

    Both amine and hydroxyl functional groups are present in 4-aminophenyl ethanol (4-AE), and each functional group can form hydrogen bonds with carboxylic acids, such as formic acid and acetic acid. Predicting the structures of such complexes involving 4-AE is rather complex, given the many possible conformations and their similar (and method and basis-dependent) energies. In particular, the carboxyl group, -COOH, can act as both as a hydrogen bond donor or acceptor, or both at once. In this study we report the formic acid - 4-AE hydrogen bonded complex. An infrared-ultraviolet double resonance spectrometer is used to examine the shifts in IR frequencies of 4-AE from the monomer to the complex. Fourier transform microwave spectroscopy is used to determine structures of the species. Results from both experiments are compared to DFT and ab initio results. Time permitting, results of the water complex with 4-AE will also be presented.

  8. Two-dimensional infrared spectroscopy of intermolecular hydrogen bonds in the condensed phase.

    PubMed

    Elsaesser, Thomas

    2009-09-15

    Hydrogen bonding plays a key role in the structural, physical, and chemical properties of liquids such as water and in macromolecular structures such as proteins. Vibrational spectroscopy is an important tool for understanding hydrogen bonding because it provides a way to observe local molecular geometries and their interaction with the environment. Linear vibrational spectroscopy has mapped characteristic changes of vibrational spectra and the occurrence of new bands that form upon hydrogen bonding. However, linear vibrational spectroscopy gives very limited insight into ultrafast dynamics of the underlying molecular interactions, such as the motions of hydrogen-bonded groups, energy dissipation and delocalization, and the fluctuations within hydrogen-bonded structures that occur in the ultrafast time domain. Nonlinear vibrational spectroscopy with its femtosecond time resolution can discern these dynamic processes in real time and has emerged as an important tool for unraveling molecular dynamics and for quantifying interactions that govern the vibrational and structural dynamics of hydrogen bonds. This Account reviews recent progress originating from third-order nonlinear methods of coherent multidimensional vibrational spectroscopy. Ultrafast dynamics of intermolecular hydrogen bonds are addressed for a number of prototype systems: hydrogen-bonded carboxylic acid dimers in an aprotic liquid environment, the disordered fluctuating hydrogen-bond network of liquid water, and DNA oligomers interacting with water. Cyclic carboxylic acid dimers display a rich scheme of vibrational couplings, resulting in OH stretching absorption bands with highly complex spectral envelopes. Two-dimensional spectroscopy of acetic acid dimers in a nonpolar liquid environment demonstrates that multiple Fermi resonances of the OH stretching mode with overtones and combination tones of fingerprint vibrations dominate both the 2D and linear absorption spectra. The coupling of the OH

  9. Controlling hydrolysis reaction rates with binary ionic liquid mixtures by tuning hydrogen-bonding interactions.

    PubMed

    Weber, Cameron C; Masters, Anthony F; Maschmeyer, Thomas

    2012-02-16

    The ability of a binary ionic liquid (IL) system consisting of a phosphonium transition state analogue (TSA) and 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([BMIM][NTf(2)]) to accelerate the rate of the well-studied hydrolysis of a tert-alkyl picolinium salt by influencing the solvent structure was investigated. A significant rate enhancement was observed in the presence of the TSA; however, comparison with other cations illustrated that this enhancement was not unique to the chosen TSA. Instead, the rate enhancements were correlated with the dilution of hydrogen bonding by the added cations. This phenomenon was further examined by the use of 1-butyl-2,3-dimethylimidazolium bis(trifluoromethanesulfonyl)imide ([BMMIM][NTf(2)]) as a cosolvent and the use of Reichardt's dye to measure the extent of hydrogen bonding on solutes in these systems. The rate increases are rationalized in terms of weaker hydrogen bonding from the solvent system to water.

  10. The hydrogen bond stabilizing effect in enammonium salts of captodative aminoalkenes containing a carbonyl group

    NASA Astrophysics Data System (ADS)

    Fedorov, S. V.; Rulev, A. Yu; Chipanina, N. N.; Sherstyannikova, L. V.; Turchaninov, V. K.

    2004-03-01

    Enhanced stability of enammonium salts of captodative carbonyl-containing aminoalkenes as compared to the salts of simple enamines is discussed on the basis of 1H and 13C NMR, IR, UV spectroscopy and the results quantum chemical calculations. Stabilization of the N-protonated form of captodative aminoalkenes is due to either intramolecular (NH +⋯OC) or intermolecular (NH +⋯Solv or NH +⋯X -) hydrogen bonding, whereas the C-protonated form is destabilized due to umpolung of the carbon-carbon double bond. The formation of bifurcated (three-centered) hydrogen bond between the enammonium cation and the solvent is demonstrated. The three-centered solvate complex is characterized by nonclassical dependence of the chemical shift of the bridging hydrogen atom from the proton-acceptor power of the solvent.

  11. Bio-inspired carbon nanotube-polymer composite yarns with hydrogen bond-mediated lateral interactions.

    PubMed

    Beese, Allison M; Sarkar, Sourangsu; Nair, Arun; Naraghi, Mohammad; An, Zhi; Moravsky, Alexander; Loutfy, Raouf O; Buehler, Markus J; Nguyen, SonBinh T; Espinosa, Horacio D

    2013-04-23

    Polymer composite yarns containing a high loading of double-walled carbon nanotubes (DWNTs) have been developed in which the inherent acrylate-based organic coating on the surface of the DWNT bundles interacts strongly with poly(vinyl alcohol) (PVA) through an extensive hydrogen-bond network. This design takes advantage of a toughening mechanism seen in spider silk and collagen, which contain an abundance of hydrogen bonds that can break and reform, allowing for large deformation while maintaining structural stability. Similar to that observed in natural materials, unfolding of the polymeric matrix at large deformations increases ductility without sacrificing stiffness. As the PVA content in the composite increases, the stiffness and energy to failure of the composite also increases up to an optimal point, beyond which mechanical performance in tension decreases. Molecular dynamics (MD) simulations confirm this trend, showing the dominance of nonproductive hydrogen bonding between PVA molecules at high PVA contents, which lubricates the interface between DWNTs.

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

    PubMed

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

    2017-02-15

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

  13. Controlling the subtle energy balance in protic ionic liquids: dispersion forces compete with hydrogen bonds.

    PubMed

    Fumino, Koichi; Fossog, Verlaine; Stange, Peter; Paschek, Dietmar; Hempelmann, Rolf; Ludwig, Ralf

    2015-02-23

    The properties of ionic liquids are determined by the energy-balance between Coulomb-interaction, hydrogen-bonding, and dispersion forces. Out of a set of protic ionic liquids (PILs), including trialkylammonium cations and methylsulfonate and triflate anions we could detect the transfer from hydrogen-bonding to dispersion-dominated interaction between cation and anion in the PIL [(C6 H13 )3 NH][CF3 SO3 ]. The characteristic vibrational features for both ion-pair species can be detected and assigned in the far-infrared spectra. Our approach gives direct access to the relative strength of hydrogen-bonding and dispersion forces in a Coulomb-dominated system. Dispersion-corrected density functional theory (DFT) calculations support the experimental findings. The dispersion forces could be quantified to contribute about 2.3 kJ mol(-1) per additional methylene group in the alkyl chains of the ammonium cation.

  14. Non-covalent synthesis of supermicelles with complex architectures using spatially confined hydrogen-bonding interactions

    NASA Astrophysics Data System (ADS)

    Li, Xiaoyu; Gao, Yang; Boott, Charlotte E.; Winnik, Mitchell A.; Manners, Ian

    2015-09-01

    Nature uses orthogonal interactions over different length scales to construct structures with hierarchical levels of order and provides an important source of inspiration for the creation of synthetic functional materials. Here, we report the programmed assembly of monodisperse cylindrical block comicelle building blocks with crystalline cores to create supermicelles using spatially confined hydrogen-bonding interactions. We also demonstrate that it is possible to further program the self-assembly of these synthetic building blocks into structures of increased complexity by combining hydrogen-bonding interactions with segment solvophobicity. The overall approach offers an efficient, non-covalent synthesis method for the solution-phase fabrication of a range of complex and potentially functional supermicelle architectures in which the crystallization, hydrogen-bonding and solvophobic interactions are combined in an orthogonal manner.

  15. Hydrogen-Bonding-Induced Fluorescence: Water-Soluble and Polarity-Independent Solvatochromic Fluorophores.

    PubMed

    Okada, Yohei; Sugai, Masae; Chiba, Kazuhiro

    2016-11-18

    Fluorophores with emission wavelengths that shift depending on their hydrogen-bonding microenvironment in water would be fascinating tools for the study of biological events. Herein we describe the design and synthesis of a series of water-soluble solvatochromic fluorophores, 2,5-bis(oligoethylene glycol)oxybenzaldehydes (8-11) and 2,5-bis(oligoethylene glycol)oxy-1,4-dibenzaldehydes (14-17), based on a push-pull strategy. Unlike typical examples in this class of fluorophores, the fluorescence properties of these compounds are independent of solvent polarity and become fluorescent upon intermolecular hydrogen-bonding, exhibiting high quantum yields (up to ϕ = 0.55) and large Stokes shifts (up to 134 nm). Furthermore, their emission wavelengths change depending on their hydrogen-bonding environment. The described fluorophores provide a starting point for unprecedented applications in the fields of chemical biology and medicinal chemistry.

  16. Matrix isolation infrared and DFT study of the trimethyl phosphite-hydrogen chloride interaction: hydrogen bonding versus nucleophilic substitution.

    PubMed

    Ramanathan, N; Kar, Bishnu Prasad; Sundararajan, K; Viswanathan, K S

    2012-12-13

    Trimethyl phosphite (TMPhite) and hydrogen chloride (HCl), when separately codeposited in a N(2) matrix, yielded a hydrogen bonded adduct, which was evidenced by shifts in the vibrational frequencies of the TMPhite and HCl submolecules. The structure and energy of the adducts were computed at the B3LYP level using 6-31++G** and aug-cc-pVDZ basis sets. While our computations indicated four minima for the TMPhite-HCl adducts, only one adduct was experimentally identified in the matrix at low temperatures, which interestingly was not the structure corresponding to the global minimum, but was the structure corresponding to the first higher energy local minimum. The Onsager self-consistent reaction field model was used to explain this observation. In an attempt to prepare the hydrogen bonded adduct in the gas phase and then trap it in the matrix, TMPhite and HCl were premixed prior to deposition. However, in these experiments, no hydrogen bonded adduct was observed; on the contrary, TMPhite reacted with HCl to yield CH(3)Cl, following a nucleophilic substitution, a reaction that is apparently frustrated in the matrix.

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

    SciTech Connect

    Mackenzie, Rebecca B.; Dewberry, Christopher T.; Leopold, Kenneth R. E-mail: david.tew@bristol.ac.uk; Coulston, Emma; Cole, George C.; Legon, Anthony C. E-mail: david.tew@bristol.ac.uk Tew, David P. E-mail: david.tew@bristol.ac.uk

    2015-09-14

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

  18. Performance of a nonempirical density functional on molecules and hydrogen-bonded complexes

    NASA Astrophysics Data System (ADS)

    Mo, Yuxiang; Tian, Guocai; Car, Roberto; Staroverov, Viktor N.; Scuseria, Gustavo E.; Tao, Jianmin

    2016-12-01

    Recently, Tao and Mo derived a meta-generalized gradient approximation functional based on a model exchange-correlation hole. In this work, the performance of this functional is assessed on standard test sets, using the 6-311++G(3df,3pd) basis set. These test sets include 223 G3/99 enthalpies of formation, 99 atomization energies, 76 barrier heights, 58 electron affinities, 8 proton affinities, 96 bond lengths, 82 harmonic vibrational frequencies, 10 hydrogen-bonded molecular complexes, and 22 atomic excitation energies. Our calculations show that the Tao-Mo functional can achieve high accuracy for most properties considered, relative to the local spin-density approximation, Perdew-Burke-Ernzerhof, and Tao-Perdew-Staroverov-Scuseria functionals. In particular, it yields the best accuracy for proton affinities, harmonic vibrational frequencies, hydrogen-bond dissociation energies and bond lengths, and atomic excitation energies.

  19. Indications of chemical bond contrast in AFM images of a hydrogen-terminated silicon surface

    PubMed Central

    Labidi, Hatem; Koleini, Mohammad; Huff, Taleana; Salomons, Mark; Cloutier, Martin; Pitters, Jason; Wolkow, Robert A.

    2017-01-01

    The origin of bond-resolved atomic force microscope images remains controversial. Moreover, most work to date has involved planar, conjugated hydrocarbon molecules on a metal substrate thereby limiting knowledge of the generality of findings made about the imaging mechanism. Here we report the study of a very different sample; a hydrogen-terminated silicon surface. A procedure to obtain a passivated hydrogen-functionalized tip is defined and evolution of atomic force microscopy images at different tip elevations are shown. At relatively large tip-sample distances, the topmost atoms appear as distinct protrusions. However, on decreasing the tip-sample distance, features consistent with the silicon covalent bonds of the surface emerge. Using a density functional tight-binding-based method to simulate atomic force microscopy images, we reproduce the experimental results. The role of the tip flexibility and the nature of bonds and false bond-like features are discussed. PMID:28194036

  20. Indications of chemical bond contrast in AFM images of a hydrogen-terminated silicon surface

    NASA Astrophysics Data System (ADS)

    Labidi, Hatem; Koleini, Mohammad; Huff, Taleana; Salomons, Mark; Cloutier, Martin; Pitters, Jason; Wolkow, Robert A.

    2017-02-01

    The origin of bond-resolved atomic force microscope images remains controversial. Moreover, most work to date has involved planar, conjugated hydrocarbon molecules on a metal substrate thereby limiting knowledge of the generality of findings made about the imaging mechanism. Here we report the study of a very different sample; a hydrogen-terminated silicon surface. A procedure to obtain a passivated hydrogen-functionalized tip is defined and evolution of atomic force microscopy images at different tip elevations are shown. At relatively large tip-sample distances, the topmost atoms appear as distinct protrusions. However, on decreasing the tip-sample distance, features consistent with the silicon covalent bonds of the surface emerge. Using a density functional tight-binding-based method to simulate atomic force microscopy images, we reproduce the experimental results. The role of the tip flexibility and the nature of bonds and false bond-like features are discussed.

  1. Hydrogen Bonding Between FNO and H2O: Structure and Energetics

    NASA Astrophysics Data System (ADS)

    Ting, Melodie; Peters, Nancy J. S.

    2009-09-01

    Nitrosyl fluoride, of some interest in atmospheric chemistry, has three atoms which could potentially serve as proton acceptors in the formation of hydrogen bonds. The optimized structure of FNO and H2O was determined at the MP4/6-31G** level of calculation. In the resulting structure, the hydrogen bonds at the fluorine with an energy of 5.15 kcal/mol, contrary to the prediction that less electronegative atoms make better proton acceptors/electron donors but consistent with results of proton affinity studies and with the contribution of a resonance structure with no bond between the N and F and a negative charge on the fluorine atom. The resulting structure also shows a significant increase in the length of the NF bond from 1.51 to 1.61 Å.

  2. The properties of isolated dangling bonds on hydrogenated 2H-SiC surfaces

    NASA Astrophysics Data System (ADS)

    Tuttle, Blair R.; Pantelides, Sokrates T.

    2017-02-01

    Using state-of-the-art electronic structure methods, we calculate the properties of silicon and carbon dangling bonds at several hydrogenated SiC surfaces including polar and non-polar cases. Generally, carbon defect levels are in the lower portion of the SiC band gap whereas silicon defect levels are in the upper portion. Additionally, surface work functions and hydrogen desorption energies are calculated and compared with experimental data. Carbon dangling bonds with hetero-polar back-bonding appear consistent with constraints derived from experiments on device quality nano-porous SiC. Finally, we make superhyperfine predictions which may help identify back bonded atoms involved in defect complexes.

  3. Role of hydrogen bonds in hydrophobicity: the free energy of cavity formation in water models with and without the hydrogen bonds.

    PubMed

    Madan, B; Lee, B

    1994-08-01

    The free energies of cavity formation in water with and without hydrogen bonding potential were computed from the results of a set of Monte Carlo simulation calculations on pure liquid TIP4P water model and on the same model but with the electrostatic charges turned off (Lennard-Jones liquid). The free energies of cavity formation in the Lennard-Jones liquids are higher than or approximately equal to those in TIP4P water, depending, respectively, on whether the Lennard-Jones size parameter sigma is set equal to 3.15 A, which is the value of sigma for TIP4P water, or to 2.8 A, which is the commonly assumed value for the oxygen-oxygen distance between two hydrogen-bonded water molecules. This result indicates that changes in the hydrogen-bonded structure of water and/or in the orientational degree of freedom of water are not essential features in the production of the large free energy change upon cavity formation.

  4. Chirality Synchronization of Hydrogen-Bonded Complexes of Achiral N-Heterocycles.

    PubMed

    Buchs, Jens; Vogel, Laura; Janietz, Dietmar; Prehm, Marko; Tschierske, Carsten

    2017-01-02

    2,4-Diamino-6-phenyl-1,3,5-triazines carrying a single oligo(ethylene oxide) (EO) chain form an optically isotropic mesophase composed of a conglomerate of macroscopic chiral domains with opposite sense of chirality even though the constituent molecules are achiral. This mesophase was proposed to result from the helical packing of hydrogen-bonded triazine aggregates, providing long-range chirality synchronization. The results provide first evidence for macroscopic achiral symmetry breaking upon conglomerate formation in an amorphous isotropic phase formed by hydrogen-bonded associates of simple N-heterocycles that are related to prebiotic molecules.

  5. A triclinic polymorph of benzanilide: disordered molecules form hydrogen-bonded chains.

    PubMed

    Bowes, Katharine F; Glidewell, Christopher; Low, John N; Skakle, Janet M S; Wardell, James L

    2003-01-01

    In the P-1 polymorph of benzanilide or N-phenylbenzamide, C(13)H(11)NO, the molecules are linked into simple C(4) chains by N-H...O hydrogen bonds. The molecules exhibit orientational disorder, but the donor and acceptor in a given hydrogen bond may occur, independently, in either the major or the minor orientation, such that all four possible N-H.O combinations have very similar geometries. The structure of this P-1 polymorph can be related to that of a previously reported C2/c polymorph.

  6. Structural and vibrational properties of betainium perchlorate monohydrate crystal and character of its hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Ilczyszyn, Marek; Godzisz, Dorota; Ilczyszyn, Maria M.

    2002-06-01

    Betainium perchlorate monohydrate crystal ((CH 3) 3NCH 2COOH)(ClO 4)·H 2O) undergoes a continuous (second order) phase transition at ca. 180 K. X-ray data and vibrational spectroscopy studies at different temperatures are used for description of the phase transition mechanism, as well as of hydrogen bonds formed by water in this molecular system. Perturbation of monomer water by various surroundings (water vapour, low-temperature matrices, solvents, betaine-acid crystals) and properties of triple hydrogen bonds to water oxygen atom are discussed.

  7. Molecular Coplanarity and Self-Assembly Promoted by Intramolecular Hydrogen Bonds.

    PubMed

    Zhu, Congzhi; Mu, Anthony U; Lin, Yen-Hao; Guo, Zi-Hao; Yuan, Tianyu; Wheeler, Steven E; Fang, Lei

    2016-12-16

    Active conformational control is realized in a conjugated system using intramolecular hydrogen bonds to achieve tailored molecular, supramolecular, and solid-state properties. The hydrogen bonding functionalities are fused to the backbone and precisely preorganized to enforce a fully coplanar conformation of the π-system, leading to short π-π stacking distances, controllable molecular self-assembly, and solid-state growth of one-dimensional nano-/microfibers. This investigation demonstrates the efficiency and significance of an intramolecular noncovalent approach in promoting conformational control and self-assembly of organic molecules.

  8. NMR spectra and translational diffusion of protons in crystals with hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Timokhin, V. M.; Garmash, V. M.; Tarasov, V. P.

    2015-07-01

    Investigation of proton transport in hydrogen-bond crystals at low temperatures is currently one of important problems in the semiconductor physics. With the use of the NMR spectra of wide-band-gap hydrogen-bond crystals grown in H2O and D2O solutions, we have succeeded in finding a direct proof of the presence of protons in the mobile phase, determined their activation energy in good agreement with the spectra of thermally stimulated depolarization currents and with the infrared spectra, and, as a result, clarified the mechanism of proton transport and tunneling.

  9. Hydrogen-bond-assisted activation of allylic alcohols for palladium-catalyzed coupling reactions.

    PubMed

    Gumrukcu, Yasemin; de Bruin, Bas; Reek, Joost N H

    2014-03-01

    We report direct activation of allylic alcohols using a hydrogen-bond-assisted palladium catalyst and use this for alkylation and amination reactions. The novel catalyst comprises a palladium complex based on a functionalized monodentate phosphoramidite ligand in combination with urea additives and affords linear alkylated and aminated allylic products selectively. Detailed kinetic analysis show that oxidative addition of the allyl alcohol is the rate-determining step, which is facilitated by hydrogen bonds between the alcohol, the ligand functional group, and the additional urea additive.

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

    PubMed

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

    2014-04-17

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

  11. Microwave spectrum and intramolecular hydrogen bonding of 2-isocyanoethanol (HOCH(2)CH(2)N≡C).

    PubMed

    Møllendal, Harald; Samdal, Svein; Guillemin, Jean-Claude

    2014-05-01

    The microwave spectrum of 2-isocyanoethanol (HOCH2CH2NC) has been investigated in the 12-120 GHz spectral range. The assignment of this spectrum was severely complicated by the rapid transformation of 2-isocyanoethanol into its isomer 2-oxazoline, which has a rich and strong spectrum. This process appeared both in a gold-plated microwave cell and in a brass cell and is presumed to be catalyzed by metals or traces of base. The spectrum of one conformer was ultimately assigned. This form is stabilized by an intramolecular hydrogen bond between the hydroxyl group and the isocyano group and is the first gas-phase study ever of this kind of hydrogen bonding. The distance between the hydrogen atom of the hydroxyl group and the nitrogen and carbon atoms are as long as 256 and 298 pm, respectively, indicating that covalent contribution to the hydrogen bond is minimal. Electrostatic forces are much more important because the O-H and N≡C bonds are almost parallel and the corresponding bond moments are practically antiparallel. The microwave work has been augmented by quantum chemical calculations at the CCSD(T)/cc-pVTZ and MP2/cc-pVTZ levels of theory. Results of these calculations are generally in good agreement with experimental findings.

  12. Relativistic effects on the bonding of heavy and superheavy hydrogen halides

    NASA Astrophysics Data System (ADS)

    Saue, Trond; Faegri, Knut; Gropen, Odd

    1996-12-01

    The bonding in the hydrogen halides HI, HAt and HUus (Uus = element 117) has been studied using four-component Dirac-Hartree-Fock calculations and finite basis sets. The calculations show that the effect of spin-orbit splitting on the valence p-orbital dominates the bonding for the compound of the superheavy element, and even for the sixth row the spin-orbit interaction should be treated self-consistently for an accurate description of the electronic structure.

  13. Linear distortion of octahedral metal centres by multiple hydrogen bonds in modular ML(4) systems.

    PubMed

    Turner, David R; Hursthouse, M B; Light, M E; Steed, Jonathan W

    2004-06-21

    A series of compounds of the type [M(1)(4)(H(2)O)(2)]SO(4)[middle dot]2H(2)O containing a simple urea-based pyridyl ligand have been synthesised and characterised by X-ray crystallography. The enclathrated water exists within discrete linearly stacked cavities and causes significant distortions in the M-OH(2) bonds due to the presence of a strongly hydrogen bonded water square.

  14. Molecular deformation mechanisms in cellulose allomorphs and the role of hydrogen bonds.

    PubMed

    Djahedi, Cyrus; Berglund, Lars A; Wohlert, Jakob

    2015-10-05

    Differences in tensile properties between cellulose crystal allomorphs cannot be rationalized by simply counting hydrogen bonds. From molecular dynamics computer simulations the cooperative nature of energy contributions to axial cellulose crystal modulus becomes apparent. Using a decomposition of inter and intramolecular forces as a function of tensile strain, the three allomorphs show dramatic differences in terms of how the contributions to elastic energy are distributed between covalent bonds, angles, dihedrals, electrostatic forces, dispersion and steric forces.

  15. Intermolecular Hydrogen Bonding in Peptide and Modified Jeffamine Organogels

    NASA Astrophysics Data System (ADS)

    Savin, Daniel; Richardson, Adam

    2011-03-01

    In these studies, we present two systems whereby supramolecular assembly results in rigid organogels. First, a series of AB diblock copolymers consisting of poly(Lysine(Z)) (P(Lys(Z)) blocks were synthesized and found to form stable, rigid organogels in THF (ca. 1 - 1.5 wt.% solutions) and chloroform at room temperature. In these systems, the protecting group on the P(Lys) side-chains remains intact and gel formation results from the assembly of the solventphobic P(Lys(Z)) chains through intermolecular beta-sheet formation. The non-peptide block was found to have an effect on organogel properties due to interfacial frustration, which disrupts H-bonding. Second, Jeffamine polymers were modified in a facile way to incorporate intermolecular H-bonding groups to yield networks able to gel various solvents as well as mineral and canola oil. We present the physical and rheological properties of the organogels produced.

  16. Investigations of intramolecular hydrogen bonding in three types of Schiff bases by 2H and 3H NMR isotope effects.

    PubMed

    Schilf, Wojciech; Bloxsidge, James P; Jones, John R; Lu, Shui-Yu

    2004-06-01

    Hydrogen bonding within the structures of three Schiff bases (1-3), obtained by condensation of 4-methoxy-, 5-methoxy- and 4,6-dimethoxysalicylaldehyde with methylamine, was investigated by measuring deuterium and tritium NMR isotope effects. The primary deuterium and tritium isotope effects (delta(XH)-delta(XD/T)) and secondary one-bond nitrogen deuterium effect appear to be very useful parameters for defining the character of intramolecular hydrogen bonds. The tritium isotope effects were also determined for nitrogen-hydrogen one-bond coupling constants for both 4-methoxy and 4,6-dimethoxy derivatives. These parameters are seen to be highly sensitive to hydrogen bond characteristics and can be used to distinguish localized and tautomeric hydrogen bonds.

  17. Low temperature FTIR spectroscopy and hydrogen bonding in cytosine polycrystals

    NASA Astrophysics Data System (ADS)

    Rozenberg, M.; Shoham, G.; Reva, I.; Fausto, R.

    2004-01-01

    The FTIR spectra of both the pure NH and isotopically substituted ND (<10% and >90% D) polycrystalline cytosine were recorded in the range 400-4000 cm -1 as a function of temperature (10-300 K). For the first time, uncoupled NH(D) stretching mode bands of amine and imine groups were observed in the spectra of isotopically diluted cytosine at low temperatures. These bands correspond to the three distinct H-bonds that are present in the crystal, in agreement with the available data obtained by structural methods. At least nine bands were observed below 1000 cm -1 and, in consonance with their temperature and isotopic exchange behavior, were assigned to the NH proton out-of-the-plane bending modes. Six of these bands were found to correspond to additional "disordered" H-bonds, which could not be observed by structural methods. Empirical correlations of spectral and thermodynamic parameters enabled to estimate the contribution of the H-bonds to the sublimation enthalpy of the crystal, in agreement with independent experimental data.

  18. Kinetic solvent effects on hydrogen abstraction reactions from carbon by the cumyloxyl radical. The role of hydrogen bonding.

    PubMed

    Bietti, Massimo; Salamone, Michela

    2010-08-20

    A kinetic study of the H-atom abstraction reactions from 1,4-cyclohexadiene and triethylamine by the cumyloxyl radical has been carried out in different solvents. Negligible effects are observed with 1,4-cyclohexadiene, whereas with triethylamine a significant decrease in rate constant (k(H)) is observed on going from benzene to MeOH. A good correlation between log k(H) and the solvent hydrogen bond donor parameter alpha is observed, indicative of an H-bonding interaction between the amine lone pair and the solvent.

  19. Linking microscopic guest properties to macroscopic observables in clathrate hydrates: Guest-host hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Alavi, Saman; Susilo, Robin; Ripmeester, John A.

    2009-05-01

    Molecular dynamics simulations are used to compare microscopic structures and guest dynamics to macroscopic properties in structure II clathrate hydrates with cyclopentane, tetrahydrofuran (THF), 1,3-dioxolane, tetrahydropyran (THP), and p-dioxane as guests. Significant differences are observed between structural parameters and rotational dynamics for the different guests. The simulations show the formation of guest-host hydrogen bonds between the ether oxygen atoms of THF and THP and the cage water hydrogen atoms of the clathrate but the absence of similar hydrogen bonds in the clathrate hydrates of the other guests on the time scale of the calculations. This guest-host hydrogen bonding leads to the formation of Bjerrum L-defects in the clathrate water lattice where two adjacent water molecules have no covalently bonded hydrogen atom between them. Unlike Bjerrum defects of ice lattices, these guest-induced L-defects are not accompanied by the formation of a D-defect at an adjacent site in the water lattice. At the simulation temperature of 200 K, the guest-water hydrogen bonds in the THF clathrate are short lived (lifetime less than 1 ps) but in the THP they are longer lived (a minimum of 100 ps). A van't Hoff plot for the probability of defect formation in THF as a function of temperature gives an activation barrier of ˜8.3 kJ/mol for guest-host defect formation in the THF clathrate. The consequences of the defect formation on the thermal expansivity, isothermal compressibility, dipole-dipole correlation function, and mechanical stability of the clathrate are discussed.

  20. Biological activity predictions, crystallographic comparison and hydrogen bonding analysis of cholane derivatives.

    PubMed

    Rajnikant; Dinesh; Chand, Bhavnaish

    2007-12-01

    A total of eighteen molecules of cholane derivatives (I-XVIII) (a series of steroids) have been included to predict their pharmacological effects, specific mechanisms of action, known toxicities, drug-likeness, etc, by using the statistics of multilevel neighbourhoods of atoms (MNA) descriptors for active and inactive fragments. The biological activity spectra for substances have been correlated on SAR base (structure-activity relationships data and knowledge base), which provides the different P(a) (possibility of activity) and P(i) (possibility of inactivity). Most of the probable activities have been characterized by P(a) and P(i) values, which depict that all the molecules have high value of teratogen activity. The Lipinski's thumb rule predicts that all the cholane derivatives have stronger preponderance for "cancer-like-drug" molecules and some of their related analogous have entered in the ANCI (American National Cancer Institute) database. Some selected bond distances and bond angles of interest have been taken into account and deviation of bond distances/bond angles, vis-a-vis the substitutional group and X-H...A intra/intermolecular hydrogen bonds has been discussed in detail. X-H...A intra and intermolecular hydrogen bonds in the molecules have been described with the standard distance and angle cut-off criteria. D-theta and d-theta. scatter plots for intra- and intermolecular interactions are presented for better understanding of packing interactions existing among these derivatives. There exists only one C-H...O intramolecular bifurcated hydrogen bond. while high tendency of intermolecular bifurcated hydrogen bonds based on a defined O-H...O has been observed, in which O atom acts as a prototype donor as well as acceptor. The frequency of occurrence of C-H...O hydrogen bonds is predominant (i.e. 85.7%) in intramolecular interactions, whereas in intermolecular interactions, frequency of occurrence for O-H...O interactions is 62.9%. Solvent

  1. Hydrogen bond network topology in liquid water and methanol: a graph theory approach.

    PubMed

    Bakó, Imre; Bencsura, Akos; Hermannson, Kersti; Bálint, Szabolcs; Grósz, Tamás; Chihaia, Viorel; Oláh, Julianna

    2013-09-28

    Networks are increasingly recognized as important building blocks of various systems in nature and society. Water is known to possess an extended hydrogen bond network, in which the individual bonds are broken in the sub-picosecond range and still the network structure remains intact. We investigated and compared the topological properties of liquid water and methanol at various temperatures using concepts derived within the framework of graph and network theory (neighbour number and cycle size distribution, the distribution of local cyclic and local bonding coefficients, Laplacian spectra of the network, inverse participation ratio distribution of the eigenvalues and average localization distribution of a node) and compared them to small world and Erdős-Rényi random networks. Various characteristic properties (e.g. the local cyclic and bonding coefficients) of the network in liquid water could be reproduced by small world and/or Erdős-Rényi networks, but the ring size distribution of water is unique and none of the studied graph models could describe it. Using the inverse participation ratio of the Laplacian eigenvectors we characterized the network inhomogeneities found in water and showed that similar phenomena can be observed in Erdős-Rényi and small world graphs. We demonstrated that the topological properties of the hydrogen bond network found in liquid water systematically change with the temperature and that increasing temperature leads to a broader ring size distribution. We applied the studied topological indices to the network of water molecules with four hydrogen bonds, and showed that at low temperature (250 K) these molecules form a percolated or nearly-percolated network, while at ambient or high temperatures only small clusters of four-hydrogen bonded water molecules exist.

  2. On the hydrogen bonding between N-methylformamide and acetone and tetrahydrofuran

    NASA Astrophysics Data System (ADS)

    Almeida, Glauco G.; Borges, Alexandre; Cordeiro, João M. M.

    2014-04-01

    Liquid mixtures of N-methylformamide (NMF)-acetone (ACT) and NMF-tetrahydrofuran (THF) 20 mol% NMF have been investigated using Monte Carlo simulations, aiming to obtain new details on the hydrogen bonding donation of the peptide bond in non-aqueous media. There are strong evidences of the H-bonding between NMF and each of the solvents, but the results indicate significant differences between the H-bond interactions in each mixture. THF solvates better the amide than ACT. The NMF-THF H-bonds are more directed and the structure of the solvation shell is much more ordered in the NMF-THF mixture than in the NMF-ACT one.

  3. Hydrogen bonding and π-π interactions in imidazolium-chloride ionic liquid clusters.

    PubMed

    Matthews, Richard P; Welton, Tom; Hunt, Patricia A

    2015-06-14

    A systematic electronic structure analysis of hydrogen bonding (H-bonding), anion-π(+) and π(+)-π(+) interactions present in [C1C1im]Cl ion-pairs (IPs) and selected [C1C1im]2Cl2 IP-dimers has been carried out. Interactions have been characterised using a combination of QTAIM, NCIPLOT, NBO and qualitative MO theory. IP-dimers form non-directional charge quadrupolar arrangements due to Coulombic interactions. These are found to associate either as clusters or as loosely associated IP-IP structures. Large conformational changes are found to occur for very little cost in energy, indicating that charge screening is essentially independent of the cation ring orientation. H-bond formation is accompanied by charge transfer and polarisation of the entire [C1C1im](+) ring. Charge transfer does not follow the same trend for the CHelpG, QTAIM and NBO methods. Weak "stacked" π(+)-π(+) interactions are stabilised in the presence of anions, which locate between and at the periphery of the rings, novel strongly bent H-bonds are also present. Primary (ring; C-H···Cl(-)) H-bonds and anion-π(+) (C(2)···Cl(-)) interactions are found to decay more rapidly with distance than secondary (aliphatic; C(M)-H···Cl(-)) H-bonds. This leads to an increase in the relative importance of secondary H-bond interactions in the IP-dimers. Moreover, rotation of the methyl groups within the "stacked" π(+)-π(+) IP-dimers facilitates the formation of (stronger) linear secondary H-bonds. Thus, compared to isolated IPs, secondary H-bonds may play an increased role within the condensed phase. Overall we find that structural fluidity is facilitated by fluctuating hydrogen bond, π(+)-π(+) and anion-π(+) interactions.

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

    PubMed

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

    2017-03-14

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

  5. NMR Determination of Hydrogen Bond Thermodynamics in a Simple Diamide: A Physical Chemistry Experiment

    ERIC Educational Resources Information Center

    Morton, Janine G.; Joe, Candice L.; Stolla, Massiel C.; Koshland, Sophia R.; Londergan, Casey H.; Schofield, Mark H.

    2015-01-01

    Variable temperature NMR spectroscopy is used to determine the ?H° and ?S° of hydrogen bond formation in a simple diamide. In this two- or three-day experiment, students synthesize N,N'-dimethylmalonamide, dimethylsuccinamide, dimethylglutaramide, or dimethyladipamide from methylamine and the corresponding diester (typically in 50% recrystallized…

  6. Hydrogen-bond basicity of push-pull α,β-unsaturated enaminoketones

    NASA Astrophysics Data System (ADS)

    Vdovenko, Sergey I.; Gerus, Igor I.; Fedorenko, Elena A.; Kukhar, Valery P.

    2010-08-01

    A method is proposed for evaluating the hydrogen-bond basicity of certain conformers of two push-pull enaminoketones with the general formula R sbnd C(O) sbnd CH dbnd CH sbnd N(CH 3) 2, where R=CH 3 (DMBN); R=CF 3 (DMTBN). It has been shown, for both enaminoketones, that the ( EE) conformer has a higher basicity than the ( EZ) conformer. Moreover, the (DMBN) has one of the highest general p KHB values in the hydrogen-bond basicity scale of ketones. Substitution of the CH 3-group in (DMBN) with the CF 3-group in (DMTBN) reduces general p KHB sharply as a consequence of electron withdrawal of CF 3-group. Hydrogen bond sites are also discussed; it is shown that, in both enaminoketones, carbonyl oxygen possesses the maximal basicity, whereas nitrogen of the dimethylamino group has less basicity, and the vinyl moiety is the least basic site. Enthalpies of hydrogen bond formation (-Δ H) in absolute values, as well as the respective p KHB values, are greater for the ( EE) conformer than for the ( EZ) as a consequence of greater contribution of resonance structure in the ( EE) form. ?

  7. Proton transfer dependence on hydrogen-bonding of solvent to the water wire: a theoretical study.

    PubMed

    Mai, Binh Khanh; Park, Kisoo; Duong, My Phu Thi; Kim, Yongho

    2013-01-10

    The mechanism and dynamics of double proton transfer dependence on hydrogen-bonding of solvent molecules to the bridging water in a water wire were studied by a direct ab initio dynamics approach with variational transition-state theory including multidimensional tunneling. Long-range proton transfers in solution and within enzymes may have very different mechanisms depending on the pK(a) values of participating groups and their electrostatic interactions with their environment. For end groups that have acidic or basic pK(a) values, proton transfers by the classical Grotthuss and "proton-hole" transfer mechanisms, respectively, are energetically favorable. This study shows that these processes are facilitated by hydrogen-bond accepting and donating solvent molecule interactions with the water wire in the transition state (TS), respectively. Tunneling also depends very much on the hydrogen bonding to the water wire. All molecules hydrogen bonded to the water wire, even if they raised and narrowed energy barriers, reduced the tunneling coefficients of double proton transfer, which was attributed to the increased effective mass of transferring protons near the TS. The theoretical HH/DD KIE, including tunneling, was in good agreement with experimental KIE values. These results suggest that the classical Grotthuss and proton-hole transfer mechanisms require quite different solvent (or protein) environments near the TS for the most efficient processes.

  8. Adsorption properties of polyvinyl-alcohol-grafted particles toward genistein driven by hydrogen-bond interaction.

    PubMed

    Zhang, Yanyan; Gao, Baojiao; Xu, Zeqing

    2013-05-09

    The adsorption properties of polyvinyl alcohol (PVA)-grafted silica gel particles PVA/SiO2 toward genistein are researched in this paper. The effects of the main factors on the adsorption properties are investigated, the adsorption mechanism is explored in depth, and the adsorption thermodynamics is researched. The experimental results show that the conventional hydrogen bond is formed between the hydroxyl groups with high density on the surfaces of PVA/SiO2 and the phenolic hydroxyl groups in genistein, while π-type hydrogen bond is formed between the hydroxyl groups of PVA/SiO2 and the conjugated aromatic rings. It is the two types of hydrogen bond that make the functional composite particles PVA/SiO2 produce very strong physical adsorption toward genistein. The competitive adsorption of the solvent can have severe negative impact on the adsorption capacity of genistein. Increasing temperature will weaken the hydrogen-bond interaction between PVA/SiO2 particles and genistein. The existence of electrolytes in the protic solvent will affect the adsorption negatively. The adsorption process of PVA/SiO2 particles toward genistein is exothermic and driven by enthalpy. The adsorption isotherm data matches the Langmuir model.

  9. Usnic Acid and the Intramolecular Hydrogen Bond: A Computational Experiment for the Organic Laboratory

    ERIC Educational Resources Information Center

    Green, Thomas K.; Lane, Charles A.

    2006-01-01

    A computational experiment is described for the organic chemistry laboratory that allows students to estimate the relative strengths of the intramolecular hydrogen bonds of usnic and isousnic acids, two related lichen secondary metabolites. Students first extract and purify usnic acid from common lichens and obtain [superscript 1]H NMR and IR…

  10. Scales of Hydrogen-Bonding Workshop Held in London, England on 1-3 July 1987

    DTIC Science & Technology

    1987-07-03

    UNDERSTANDING OF THE HYDROGEN-BOND INTERACTION Pierre-Charles Maria and Jean-Francois Gal Laboratoire de Chimie Physique Organique , Universite de Nice - Parc...Faculte des Sciences 2 Rue de Ia Houssiniere 44072 Nantes cedex 03 FRANCE Dr Pierre-Charles Maria Laboratorie de Chimie Physique Organic Dr Jean

  11. Guest driven rearrangements of protonation and hydrogen bonding in decavanadate anions as their tetraalkylammonium salts.

    PubMed

    Nakamura, Setsuko; Ozeki, Tomoji

    2008-11-28

    Single crystal X-ray structure determinations of [(n-C5H11)4N]3[H3V10O28].2(CH3)2CO (TAA-acetone), [(n-C5H11)4N]8[H3V10O28]2[H4V10O28].7C4H8O2 (TAA-dioxane), [(n-C5H11)4N]3[H3V10O28] (TAAh) and [(n-C6H13)4N]2[H4V10O28].4C4H8O2 (THA-dioxane) revealed that protonation and hydrogen bond formation of decavanadate anions in their tetraalkylammonium salts are influenced by the nature of the solvent molecules incorporated as guests into the crystals. When crystallized with acetone molecules, the decavanadate anion forms a self-associated hydrogen-bonded dimer of ([H3V10O28](3-))2 to hide the protons from the aprotic protophobic acetone molecules. When crystallized with 1,4-dioxane molecules, the decavanadate anion exposes its protons to the aprotic protophilic 1,4-dioxane molecules to form a hydrogen-bond assisted solvation complex of ((C4H8O2)4...[H4V10O28)](2-)). Size effects of the tetraalkylammonium cations on crystallizing these hydrogen-bonded assemblies were also examined.

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

    PubMed

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

    2017-03-01

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

  13. Water hydrogen bond structure near highly charged interfaces is not like ice.

    PubMed

    Nihonyanagi, Satoshi; Yamaguchi, Shoichi; Tahara, Tahei

    2010-05-26

    Imaginary chi(2) spectra of HOD at air/charged surfactant/aqueous interfaces highly resemble the IR spectrum of the bulk liquid HOD, showing no indication of the "ice-like" structure. Clearly, the hydrogen bond structures at highly charged interfaces are not like ice but very similar to the structure in the bulk.

  14. Hierarchical formation of helical supramolecular polymers via stacking of hydrogen-bonded pairs in water.

    PubMed

    Brunsveld, L; Vekemans, J A J M; Hirschberg, J H K K; Sijbesma, R P; Meijer, E W

    2002-04-16

    Bifunctional ureido-s-triazines provided with penta(ethylene oxide) side chains are able to self assemble in water, leading to helical columns via cooperative stacking of the hydrogen-bonded pairs (DADA array). Monofunctional ureido-s-triazines do not form such helical architectures. The presence of a linker, covalently connecting the two ureido-s-triazine units, is essential as it generates a high local concentration of aromatic units, favorable for stacking interactions. This hydrophobic stacking of the aromatic units occurs at concentrations as low as 5 x 10(-6) M and can be visualized by using fluorescence spectroscopy. The stacking generates a hydrophobic microenvironment that allows intermolecular hydrogen bonding to occur at higher concentrations because the hydrogen bonds are shielded from competitive hydrogen bonding with water. This hierarchical process results in the formation of a helical self-assembled polymer in water at concentrations above 10(-4) M. Chiral side chains attached to the ureido-s-triazine units bias the helicity of these columns as concluded from CD spectroscopy and "Sergeants and Soldiers" experiments.

  15. Effect of hydrogen bonds on pKa values: importance of networking.

    PubMed

    Shokri, Alireza; Abedin, Azardokht; Fattahi, Alireza; Kass, Steven R

    2012-06-27

    The pK(a) of an acyclic aliphatic heptaol ((HOCH(2)CH(2)CH(OH)CH(2))(3)COH) was measured in DMSO, and its gas-phase acidity is reported as well. This tertiary alcohol was found to be 10(21) times more acidic than tert-butyl alcohol in DMSO and an order of magnitude more acidic than acetic acid (i.e., pK(a) = 11.4 vs 12.3). This can be attributed to a 21.9 kcal mol(-1) stabilization of the charged oxygen center in the conjugate base by three hydrogen bonds and another 6.3 kcal mol(-1) stabilization resulting from an additional three hydrogen bonds between the uncharged primary and secondary hydroxyl groups. Charge delocalization by both the first and second solvation shells may be used to facilitate enzymatic reactions. Acidity constants of a series of polyols were also computed, and the combination of hydrogen-bonding and electron-withdrawing substituents was found to afford acids that are predicted to be extremely acidic in DMSO (i.e., pK(a) < 0). These hydrogen bond enhanced acids represent an attractive class of Brønsted acid catalysts.

  16. Hierarchical hydrogen bonds directed multi-functional carbon nanotube-based supramolecular hydrogels.

    PubMed

    Du, Ran; Wu, Juanxia; Chen, Liang; Huang, Huan; Zhang, Xuetong; Zhang, Jin

    2014-04-09

    Supramolecular hydrogels (SMHs) are three-dimensional networks filled with a large amount of water. The crosslinking force in the 3D network is always constructed by relatively weak and dynamic non-covalent interactions, and thus SMHs usually possess extremely high susceptibility to external environment and can show extraordinary stimuli-responsive, self-healing or other attractive properties. However, the overall crosslinking force in hydrogel networks is difficult to flexibly modulate, and this leads to limited functions of the SMHs. In this regard, hierarchical hydrogen bonds, that is, the mixture of relatively strong and relatively weak hydrogen bonds, are used herein as crosslinking force for the hydrogel preparation. The ratio of strong and weak hydrogen bonds can be finely tuned to tailor the properties of resultant gels. Thus, by delicate manipulation of the overall crosslinking force in the system, a hydrogel with multiple (thermal, pH and NIR light) responsiveness, autonomous self-healing property and interesting temperature dependent, reversible adhesion behavior is obtained. This kind of hierarchical hydrogen bond manipulation is proved to be a general method for multiple-functionality hydrogel preparation, and the resultant material shows potential for a range of applications.

  17. Manifestation of hydrogen bonds of aqueous ethanol solutions in the Raman scattering spectra

    SciTech Connect

    Dolenko, T A; Burikov, S A; Patsaeva, S V; Yuzhakov, V I

    2011-03-31

    Spectra of Raman scattering of light by aqueous ethanol solutions in the range of concentrations from pure water to 96% alcohol are studied. For water, 25%, and 40% solutions of ethanol in water, as well as for 96% alcohol the Raman spectra are measured at temperatures from the freezing point to nearly the boiling point. The changes in the shape of the stretching OH band are interpreted in terms of strengthening or weakening of hydrogen bonds between the molecules in the solution. The strongest hydrogen bonding of hydroxyl groups is observed at the ethanol content from 20 to 25 volume percent, which is explained by formation of ethanol hydrates of a definite type at the mentioned concentrations of alcohol. This is confirmed by means of the method of multivariate curve resolution, used to analyse the Raman spectra of aqueous ethanol solutions. With growing temperature the weakening of hydrogen bonding occurs in all studied systems, which consists in reducing the number of OH groups, linked by strong hydrogen bonds. (laser applications and other problems in quantum electronics)

  18. Nonlinear Spectroscopy Study of Vibrational Self-Trapping in Hydrogen Bonded Crystals

    NASA Astrophysics Data System (ADS)

    Edler, Julian; Hamm, Peter

    Femtosecond pump probe spectroscopy proves that self-trapping occurs in the NH and amide I band of crystalline acetanilide (ACN). The phonon modes that mediate the self-trapping are identified. Comparison between ACN and N-methylacetamide, both model systems for proteins, shows that self-trapping is a common feature in hydrogen bonded systems.

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

    PubMed

    Jezierska, Aneta; Panek, Jarosław J

    2015-06-22

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

  20. Two-dimensional self-assembly into multicomponent hydrogen-bonded nanostructures.

    PubMed

    De Feyter, Steven; Miura, Atsushi; Yao, Sheng; Chen, Zhijian; Würthner, Frank; Jonkheijm, Pascal; Schenning, Albertus P H J; Meijer, E W; De Schryver, Frans C

    2005-01-01

    By means of scanning tunneling microscopy, we have explored the two-dimensional self-assembly of functional bicomponent hydrogen-bonding dye systems, leading to well-defined patterns, different from those of the individual components, and providing design rules to immobilize multicomponent systems at the liquid-solid interface.

  1. Spectroscopic identification of ethanol-water conformers by large-amplitude hydrogen bond librational modes

    SciTech Connect

    Andersen, J.; Wugt Larsen, R.; Heimdal, J.

    2015-12-14

    The far-infrared absorption spectra have been recorded for hydrogen-bonded complexes of water with ethanol embedded in cryogenic neon matrices at 2.8 K. The partial isotopic H/D-substitution of the ethanol subunit enabled by a dual inlet deposition procedure enables the observation and unambiguous assignment of the intermolecular high-frequency out-of-plane and the low-frequency in-plane donor OH librational modes for two different conformations of the mixed binary ethanol/water complex. The resolved donor OH librational bands confirm directly previous experimental evidence that ethanol acts as the O⋯HO hydrogen bond acceptor in the two most stable conformations. In the most stable conformation, the water subunit forces the ethanol molecule into its less stable gauche configuration upon dimerization owing to a cooperative secondary weak O⋯HC hydrogen bond interaction evidenced by a significantly blue-shift of the low-frequency in-plane donor OH librational band origin. The strong correlation between the low-frequency in-plane donor OH librational motion and the secondary intermolecular O⋯HC hydrogen bond is demonstrated by electronic structure calculations. The experimental findings are further supported by CCSD(T)-F12/aug-cc-pVQZ calculations of the conformational energy differences together with second-order vibrational perturbation theory calculations of the large-amplitude donor OH librational band origins.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  3. Hydrogen-bonding patterns in 5-fluoro-cytosine-melamine co-crystal (4/1).

    PubMed

    Mohana, Marimuthu; Muthiah, Packianathan Thomas; Sanjeewa, Liurukara D; McMillen, Colin D

    2016-04-01

    The asymmetric unit of the title compound, 4C4H4FN3O·C3H6N6, comprises of two independent 5-fluoro-cytosine (5FC) mol-ecules (A and B) and one half-mol-ecule of melamine (M). The other half of the melamine mol-ecule is generated by a twofold axis. 5FC mol-ecules A and B are linked through two different homosynthons [R 2 (2)(8) ring motif]; one is formed via a pair of N-H⋯O hydrogen bonds and the second via a pair of N-H⋯N hydrogen bonds. In addition to this pairing, the O atoms of 5FC mol-ecules A and B inter-act with the N2 amino group on both sides of the melamine mol-ecule, forming a DDAA array of quadruple hydrogen bonds and generating a supra-molecular pattern. The 5FC (mol-ecules A and B) and two melamine mol-ecules inter-act via N-H⋯O, N-H⋯N and N-H⋯O, N-H⋯N, C-H⋯F hydrogen bonds forming R 6 (6)(24) and R 4 (4)(15) ring motifs. The crystal structure is further strengthened by C-H⋯F, C-F⋯π and π-π stacking inter-actions.

  4. Extended scale for the hydrogen-bond basicity of ionic liquids.

    PubMed

    Cláudio, Ana Filipa M; Swift, Lorna; Hallett, Jason P; Welton, Tom; Coutinho, João A P; Freire, Mara G

    2014-04-14

    In the past decade, ionic liquids (ILs) have been the focus of intensive research regarding their use as potential and alternative solvents in many chemical applications. Targeting their effectiveness, recent investigations have attempted to establish polarity scales capable of ranking ILs according to their chemical behaviours. However, some major drawbacks have been found since polarity scales only report relative ranks because they depend on the set of probe dyes used, and they are sensitive to measurement conditions, such as purity levels of the ILs and procedures employed. Due to all these difficulties it is of crucial importance to find alternative and/or predictive methods and to evaluate them as a priori approaches capable of providing the chemical properties of ILs. Furthermore, the large number of ILs available makes their experimental characterization, usually achieved by a trial and error methodology, burdensome. In this context, we firstly evaluated COSMO-RS, COnductor-like Screening MOdel for Real Solvents, as an alternative tool to estimate the hydrogen-bond basicity of ILs. After demonstrating a straight-line correlation between the experimental hydrogen-bond basicity values and the COSMO-RS hydrogen-bonding energies in equimolar cation-anion pairs, an extended scale for the hydrogen-bond accepting ability of IL anions is proposed here. This new ranking of the ILs' chemical properties opens the possibility to pre-screen appropriate ILs (even those not yet synthesized) for a given task or application.

  5. High-fidelity self-assembly pathways for hydrogen-bonding molecular semiconductors

    PubMed Central

    Lin, Xu; Suzuki, Mika; Gushiken, Marina; Yamauchi, Mitsuaki; Karatsu, Takashi; Kizaki, Takahiro; Tani, Yuki; Nakayama, Ken-ichi; Suzuki, Mitsuharu; Yamada, Hiroko; Kajitani, Takashi; Fukushima, Takanori; Kikkawa, Yoshihiro; Yagai, Shiki

    2017-01-01

    The design of molecular systems with high-fidelity self-assembly pathways that include several levels of hierarchy is of primary importance for the understanding of structure-function relationships, as well as for controlling the functionality of organic materials. Reported herein is a high-fidelity self-assembly system that comprises two hydrogen-bonding molecular semiconductors with regioisomerically attached short alkyl chains. Despite the availability of both discrete cyclic and polymeric linear hydrogen-bonding motifs, the two regioisomers select one of the two motifs in homogeneous solution as well as at the 2D-confined liquid-solid interface. This selectivity arises from the high directionality of the involved hydrogen-bonding interactions, which renders rerouting to other self-assembly pathways difficult. In thin films and in the bulk, the resulting hydrogen-bonded assemblies further organize into the expected columnar and lamellar higher-order architectures via solution processing. The contrasting organized structures of these regioisomers are reflected in their notably different miscibility with soluble fullerene derivatives in the solid state. Thus, electron donor-acceptor blend films deliver a distinctly different photovoltaic performance, despite their virtually identical intrinsic optoelectronic properties. Currently, we attribute this high-fidelity control via self-assembly pathways to the molecular design of these supramolecular semiconductors, which lacks structure-determining long aliphatic chains. PMID:28225029

  6. High-fidelity self-assembly pathways for hydrogen-bonding molecular semiconductors.

    PubMed

    Lin, Xu; Suzuki, Mika; Gushiken, Marina; Yamauchi, Mitsuaki; Karatsu, Takashi; Kizaki, Takahiro; Tani, Yuki; Nakayama, Ken-Ichi; Suzuki, Mitsuharu; Yamada, Hiroko; Kajitani, Takashi; Fukushima, Takanori; Kikkawa, Yoshihiro; Yagai, Shiki

    2017-02-22

    The design of molecular systems with high-fidelity self-assembly pathways that include several levels of hierarchy is of primary importance for the understanding of structure-function relationships, as well as for controlling the functionality of organic materials. Reported herein is a high-fidelity self-assembly system that comprises two hydrogen-bonding molecular semiconductors with regioisomerically attached short alkyl chains. Despite the availability of both discrete cyclic and polymeric linear hydrogen-bonding motifs, the two regioisomers select one of the two motifs in homogeneous solution as well as at the 2D-confined liquid-solid interface. This selectivity arises from the high directionality of the involved hydrogen-bonding interactions, which renders rerouting to other self-assembly pathways difficult. In thin films and in the bulk, the resulting hydrogen-bonded assemblies further organize into the expected columnar and lamellar higher-order architectures via solution processing. The contrasting organized structures of these regioisomers are reflected in their notably different miscibility with soluble fullerene derivatives in the solid state. Thus, electron donor-acceptor blend films deliver a distinctly different photovoltaic performance, despite their virtually identical intrinsic optoelectronic properties. Currently, we attribute this high-fidelity control via self-assembly pathways to the molecular design of these supramolecular semiconductors, which lacks structure-determining long aliphatic chains.

  7. Imidazole tailored deep eutectic solvents for CO2 capture enhanced by hydrogen bonds.

    PubMed

    Cao, Lingdi; Huang, Junhua; Zhang, Xiangping; Zhang, Suojiang; Gao, Jubao; Zeng, Shaojuan

    2015-11-07

    Deep eutectic solvents (DESs) have emerged as promising alternative candidates for CO2 capture in recent years. In this work, several novel DESs were firstly prepared to enhance CO2 absorption. Structural and physical properties of DESs were investigated, as well as their absorption performance of CO2. A distinct depression in the melting point up to 80 K of DESs was observed compared with that of BMIMCl. The observed red shifts of the C2H group in an imidazolium ring and its chemical shifts downfield in NMR spectra are indicative of a hydrogen bond interaction between BMIMCl and MEA. In particular, CO2 uptake in MEA : ILs (4 : 1) at room temperature and atmospheric pressure is up to 21.4 wt%, which is higher than that of 30 wt% MEA (13%). A hydrogen bond related mechanism was proposed in which ILs act as a medium to improve CO2 uptake through hydrogen bonds. Finally, the firstly reported overall heat of CO2 absorption is slightly higher than that of 30 wt% MEA, implying that the hydrogen bonds of DESs contribute to the overall heat of CO2 absorption. This study reveals that the heat of CO2 absorption can be tailored by the proper molar ratio of MEA and ILs.

  8. Hydrogen Bond Dynamic Propensity Studies for Protein Binding and Drug Design

    PubMed Central

    2016-01-01

    We study the dynamic propensity of the backbone hydrogen bonds of the protein MDM2 (the natural regulator of the tumor suppressor p53) in order to determine its binding properties. This approach is fostered by the observation that certain backbone hydrogen bonds at the p53-binding site exhibit a dynamical propensity in simulations that differs markedly form their state-value (that is, formed/not formed) in the PDB structure of the apo protein. To this end, we conduct a series of hydrogen bond propensity calculations in different contexts: 1) computational alanine-scanning studies of the MDM2-p53 interface; 2) the formation of the complex of MDM2 with the disruptive small molecule Nutlin-3a (dissecting the contribution of the different molecular fragments) and 3) the binding of a series of small molecules (drugs) with different affinities for MDM2. Thus, the relevance of the hydrogen bond propensity analysis for protein binding studies and as a useful tool to complement existing methods for drug design and optimization will be made evident. PMID:27792778

  9. Intramolecular C-H···O hydrogen bonding in 1,4-dihydropyridine derivatives.

    PubMed

    Petrova, Marina; Muhamadejev, Ruslan; Vigante, Brigita; Cekavicus, Brigita; Plotniece, Aiva; Duburs, Gunars; Liepinsh, Edvards

    2011-09-19

    The diastereotopy of the methylene protons at positions 2 and 6 in 1,4-dihydropiridine derivatives with various substituents has been investigated. NMR spectroscopy and quantum chemistry calculations show that the CH···O intramolecular hydrogen bond is one of the factors amplifying the chemical shift differences in the 1H-NMR spectra.

  10. Detailing hydrogen bonding and deprotonation equilibria between anions and urea/thiourea derivatives.

    PubMed

    Pérez-Casas, Carol; Yatsimirsky, Anatoly K

    2008-03-21

    Spectrophotometric and 1H NMR titrations of N-methoxyethyl-N'-(4-nitrophenyl)thiourea (3) by Bu(4-)NOAc show that in DMSO deprotonation of the receptor and formation of a hydrogen-bonded complex with anion proceed simultaneously but in MeCN deprotonation requires the participation of the second acetate anion. The formation constants of hydrogen-bonded complexes were determined from titrations in the presence of added acetic acid, which suppressed deprotonation. These constants together with independently measured stability constants of (AcO)(2)H(-) complexes were employed for a rigorous numerical analysis of titration results in the absence of added acid, which allowed us to determine the equilibrium deprotonation constants as well as pKa values for 3 in both solvents. Although 3 appeared to be a weaker acid than AcOH in both solvents, it can be deprotonated by acetate in dilute solutions when the concentration of liberated acetic acid is low enough. With disubstituted N,N-bis(methoxyethyl)-N'-(4-nitrophenyl)thiourea 4 only deprotonation equilibrium is observed. In contrast, both parent urea derivatives 1 and 2 cannot be deprotonated by acetate anions. Independent of the real type of equilibrium, whether it is a deprotonation or a hydrogen bonding, titration plots always can be satisfactorily fitted to a formal 1:1 binding isotherm. A relationship between apparent "binding constants" and real equilibrium constants of hydrogen bonding association and deprotonation processes is discussed.

  11. Molecular tectonics: polymorphism and enhancement of network dimensionality by a combination of primary and secondary hydrogen bond sites.

    PubMed

    Dechambenoit, Pierre; Ferlay, Sylvie; Hosseini, Mir Wais; Kyritsakas, Nathalie

    2007-11-28

    A dicationic tecton bearing four NH and two OH groups, as primary and secondary hydrogen bond donor sites, respectively, leads, in the presence of [M(CN)(4)](2-) anions, to the formation of polymorphic 2- and 3-D hydrogen-bonded networks.

  12. Enhancement of chemical stability and crystallinity in porphyrin-containing covalent organic frameworks by intramolecular hydrogen bonds.

    PubMed

    Kandambeth, Sharath; Shinde, Digambar Balaji; Panda, Manas K; Lukose, Binit; Heine, Thomas; Banerjee, Rahul

    2013-12-02

    A strong bond: A strategy based on intramolecular hydrogen-binding interactions in 2D covalent organic frameworks (COFs) is shown to improve the crystallinity, porosity, and chemical stability of the material. The concept is validated by removing the hydrogen-bonding interaction in the methoxy analog which showed a lower stability and crystallinity.

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

    SciTech Connect

    Gasparotto, Piero; Ceriotti, Michele

    2014-11-07

    The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding – a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

  14. Tunneling and delocalization effects in hydrogen bonded systems: a study in position and momentum space.

    PubMed

    Morrone, Joseph A; Lin, Lin; Car, Roberto

    2009-05-28

    Novel experimental and computational studies have uncovered the proton momentum distribution in hydrogen bonded systems. In this work, we utilize recently developed open path integral Car-Parrinello molecular dynamics methodology in order to study the momentum distribution in phases of high pressure ice. Some of these phases exhibit symmetric hydrogen bonds and quantum tunneling. We find that the symmetric hydrogen bonded phase possesses a narrowed momentum distribution as compared with a covalently bonded phase, in agreement with recent experimental findings. The signatures of tunneling that we observe are a narrowed distribution in the low-to-intermediate momentum region, with a tail that extends to match the result of the covalently bonded state. The transition to tunneling behavior shows similarity to features observed in recent experiments performed on confined water. We corroborate our ice simulations with a study of a particle in a model one-dimensional double well potential that mimics some of the effects observed in bulk simulations. The temperature dependence of the momentum distribution in the one-dimensional model allows for the differentiation between ground state and mixed state tunneling effects.

  15. Intramolecular hydrogen bond in 3-imino-propenylamine isomers: AIM and NBO studies

    NASA Astrophysics Data System (ADS)

    Raissi, H.; Jalbout, Abraham F.; Abbasi, B.; Fazli, F.; Farzad, F.; Nadim, E.; Leon, Aned De

    The molecular structure and intramolecular hydrogen bond energy of 18 conformers of 3-imino-propenyl-amine were investigated at MP2 and B3LYP levels of theory using the standard 6-311++G** basis set. The atom in molecules or AIM theory of Bader, which is based on the topological properties of the electron density (rho), was used additionally and the natural bond orbital (NBO) analysis was also carried out. Furthermore calculations for all possible conformations of 3-imino-propenyl-amin in water solution were also carried out at B3LYP/6-311++G** and MP2/6-311++G** levels of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the imine-amine conformers of this compound are more stable than the other conformers. B3LYP method predicts the IMA-1 as global minimum. This stability is mainly due to the formation of a strong N bond H···N intramolecular hydrogen bond, which is assisted by pi-electrons resonance, and this pi-electrons are established by NH2 functional group. Hydrogen bond energies for all conformers of 3-imino-propenyl-amine were obtained from the related rotamers methods.

  16. Molecular structure, hydrogen bonding, basicity and spectroscopic properties of 3-hydroxypyridine betaine hydrochloride monohydrate

    NASA Astrophysics Data System (ADS)

    Barczyński, P.; Komasa, A.; Katrusiak, A.; Dega-Szafran, Z.; Szafran, M.

    2007-04-01

    The effect of hydrogen bonding, inter- and intramolecular electrostatic interactions on the structure of 3-hydroxy-pyridine betaine hydrochloride monohydrate (1-carboxymethyl-3-hydroxypyridinium chloride monohydrate), 3-HO-PBH·Cl·H 2O, has been studied by X-ray diffraction, 1H and 13C NMR and FTIR spectroscopies, and by the B3LYP/6-31G(d,p) calculations. In the crystal, the Cl - anion is connected with protonated betaine via the hydrogen bond, O dbnd C sbnd O sbnd H⋯Cl - = 2.993(2) Å and with neighboring H 2O molecules via the 3.111(1) and 3.578(1) Å bonds, while the 3-OH group interacts with water molecule by the hydrogen bond of 2.566(2) Å, forming an aggregate along the [b] direction. The water molecule additionally forms hydrogen bonds of 2.888(3) Å to the C dbnd O bond of O dbnd C sbnd OH group. On recrystallization the 1:1 complex slowly converts into the 2:1 complex, bis(3-hydroxy-pyridine betaine) hydrochloride, [bis(1-carboxymethyl-3-hydroxypyridinium) chloride], [(3-HO-PB) 2H·Cl]. The geometries of 3-HO-PBH·Cl·H 2O in the gas phase (vacuum), DMSO and water solutions have been optimized by the B3LYP/6-31G(d,p) level of theory using the COSMO model. Good linear correlations between 13C and 1H experimental chemical shifts and GIAO/ B3LYP/6-31G(d,p) calculated magnetic isotropic shielding tensors ( σ) have been obtained. The FTIR spectrum of the 1:1 complex shows a broad and intense absorption in the 3100-2500 cm -1 region due to the stretching vibration of hydrogen bonds between the Cl - anion and COOH, OH substituents and H 2O molecules, and the νC dbnd O band at 1739 cm -1. The spectrum of the 2:1 complex shows an additional broad absorption in the 1900-800 cm -1 region due to the O sbnd H·O hydrogen bonds between COO groups.

  17. Influence of hydrogen bonding on the geometry of the adenine fragment

    NASA Astrophysics Data System (ADS)

    Słowikowska, Joanna Maria; Woźniak, Krzysztof

    1996-01-01

    The crystal structures of two adenine derivatives, N(6),9-dimethyl-8-butyladenine (I) and its hydrate (1 : 1) (II), have been determined by single-crystal X-ray diffraction. The geometrical features of both structures are discussed. The influence of protonation, substitution and hydrogen bond formation on the geometry of the adenine fragment was studied, based on data retrieved from the Cambridge Structural Database. Total correlation analysis showed mutual correlation between the structural parameters in the adenine ring system; partial correlation calculations for the adenine nucleoside fragments suggest intercorrelation between the parameters of the hydrogen bonding involved in base pairing and the N(adenine)-C(sugar) bond through the adenine fragment; few such correlations were found for fragments without the sugar substituent.

  18. Note: Molecular architecture dependent hydrogen-bonded motifs, entropy change, and dielectric permittivity of alcohols

    NASA Astrophysics Data System (ADS)

    Johari, G. P.

    2013-07-01

    Our previous studies showed that the static permittivity, ɛs, of some octanol isomers first increased on cooling, then decreased, and finally increased rapidly, and ɛs monotonically increased on compression such that the local minimum in ɛs vanished. Thus, while ɛs is the same at different temperatures and pressures, the density differs. To reconcile these findings with thermodynamic requirements, we propose that hydrogen bonded ring-dimers of near zero dipole moment that form on initial cooling and decrease ɛs, open to form linear-dimers on further cooling (or pressurizing). The H and O atoms at the terminals of the linear dimer form hydrogen bonds with the existing monomers and linear chains, thus extending the length of the H-bonded chains. This mechanism agrees with the enthalpy and entropy of formation of ring-dimer and linear-chain motifs.

  19. Hydrogen bonding Part 38. IR and thermodynamic study of phosphorylcholine chloride calcium salt tetrahydrate and monohydrate

    NASA Astrophysics Data System (ADS)

    Harmon, Kenneth M.; Akin, Anne C.

    1991-09-01

    Vapor pressure vs. H 2O content studies demonstrate that phosphorylcholine chloride calcium salt forms two hydrates, a monohydrate and a tetrahydrate, in the range 0-4 mol H 20 mol -1 of salt; there is no dihydrate or trihydrate. Equilibrium vapor pressure measurements show that ΔH 0 of dissociation per mol H 20 lost is greater for the tetrahydrate (16.08 kcal mol -1) than for the monohydrate (12.49 kcal mo -1); the lower stability of the tetrahydrate arises from entropy effects. The IR spectrum of the tetrahydrate is that of a framework clathrate hydrate and suggests that the -P0 3 group may act as a very weak hydrogen-bond acceptor. In the monohydrate the -P0 3 group is not involved in hydrogen bonding. Neither hydrate contains POH bonds.

  20. A multiscale approach to model hydrogen bonding: The case of polyamide

    SciTech Connect

    Gowers, Richard J. Carbone, Paola

    2015-06-14

    We present a simple multiscale model for polymer chains in which it is possible to selectively remove degrees of freedom. The model integrates all-atom and coarse-grained potentials in a simple and systematic way and allows a fast sampling of the complex conformational energy surface typical of polymers whilst maintaining a realistic description of selected atomistic interactions. In particular, we show that it is possible to simultaneously reproduce the structure of highly directional non-bonded interactions such as hydrogen bonds and efficiently explore the large number of conformations accessible to the polymer chain. We apply the method to a melt of polyamide removing from the model only the degrees of freedom associated to the aliphatic segments and keeping at atomistic resolution the amide groups involved in the formation of the hydrogen bonds. The results show that the multiscale model produces structural properties that are comparable with the fully atomistic model despite being five times faster to simulate.

  1. "Chameleonic" backbone hydrogen bonds in protein binding and as drug targets.

    PubMed

    Menéndez, C A; Accordino, S R; Gerbino, D C; Appignanesi, G A

    2015-10-01

    We carry out a time-averaged contact matrix study to reveal the existence of protein backbone hydrogen bonds (BHBs) whose net persistence in time differs markedly form their corresponding PDB-reported state. We term such interactions as "chameleonic" BHBs, CBHBs, precisely to account for their tendency to change the structural prescription of the PDB for the opposite bonding propensity in solution. We also find a significant enrichment of protein binding sites in CBHBs, relate them to local water exposure and analyze their behavior as ligand/drug targets. Thus, the dynamic analysis of hydrogen bond propensity might lay the foundations for new tools of interest in protein binding-site prediction and in lead optimization for drug design.

  2. Multiple hydrogen bonding in excited states of aminopyrazine in methanol solution: time-dependent density functional theory study.

    PubMed

    Chai, Shuo; Yu, Jie; Han, Yong-Chang; Cong, Shu-Lin

    2013-11-01

    Aminopyrazine (AP) and AP-methanol complexes have been theoretically studied by using density functional theory (DFT) and time-dependent density functional theory (TDDFT). The excited-state hydrogen bonds are discussed in detail. In the ground state the intermolecular multiple hydrogen bonds can be formed between AP molecule and protic solvents. The AP monomer and hydrogen-bonded complex of AP with one methanol are photoexcited initially to the S2 state, and then transferred to the S1 state via internal conversion. However the complex of AP with two methanol molecules is directly excited to the S1 state. From the calculated electronic excited energies and simulated absorption spectra, we find that the intermolecular hydrogen bonds are strengthened in the electronic excited states. The strengthening is confirmed by the optimized excited-state geometries. The photochemical processes in the electronic excited states are significantly influenced by the excited-state hydrogen bond strengthening.

  3. Chemical bonding in hydrogen and lithium under pressure

    SciTech Connect

    Naumov, Ivan I.; Hemley, Russell J.; Hoffmann, Roald; Ashcroft, N. W.

    2015-08-14

    Though hydrogen and lithium have been assigned a common column of the periodic table, their crystalline states under common conditions are drastically different: the former at temperatures where it is crystalline is a molecular insulator, whereas the latter is a metal that takes on simple structures. On compression, however, the two come to share some structural and other similarities associated with the insulator-to-metal and metal-to-insulator transitions, respectively. To gain a deeper understanding of differences and parallels in the behaviors of compressed hydrogen and lithium, we performed an ab initio comparative study of these systems in selected identical structures. Both elements undergo a continuous pressure-induced s-p electronic transition, though this is at a much earlier stage of development for H. The valence charge density accumulates in interstitial regions in Li but not in H in structures examined over the same range of compression. Moreover, the valence charge density distributions or electron localization functions for the same arrangement of atoms mirror each other as one proceeds from one element to the other. Application of the virial theorem shows that the kinetic and potential energies jump across the first-order phase transitions in H and Li are opposite in sign because of non-local effects in the Li pseudopotential. Finally, the common tendency of compressed H and Li to adopt three-fold coordinated structures as found is explained by the fact that such structures are capable of yielding a profound pseudogap in the electronic densities of states at the Fermi level, thereby reducing the kinetic energy. These results have implications for the phase diagrams of these elements and also for the search for new structures with novel properties.

  4. Chemical bonding in hydrogen and lithium under pressure

    SciTech Connect

    Naumov, Ivan I.; Hemley, Russell J.; Hoffmann, Roald; Ashcroft, N. W.

    2015-08-12

    Though hydrogen and lithium have been assigned a common column of the periodic table, their crystalline states under common conditions are drastically different: the former at temperatures where it is crystalline is a molecular insulator whereas the latter is a metal that takes on simple structures. On compression, however, the two come to share some structural and other similarities associated with the insulator-to-metal and metal-to-insulator transitions, respectively. To gain a deeper understanding of differences and parallels in the behaviors of compressed hydrogen and lithium, we performed an ab-initio comparative study of these systems in selected identical structures. Both elements undergo a continuous pressure-induced s-p electronic transition, though this is at a much earlier stage of development for H. The valence charge density accumulates in interstitial regions in Li but not in H in structures examined over the same range of compression. Moreover, the valence charge density distributions or electron localization functions for the same arrangement of atoms mirror each other as one proceeds from one element to the other. Application of the viral theorem shows that the kinetic and potential energies jump across the first-order phase transitions in H and Li are opposite in sign because of non-local effects in the Li pseudopotential. Finally, the common tendency of compressed H and Li to adopt three-fold coordinated structures as found is explained by the fact that such structures are capable of yielding a profound pseudogap in the electronic densities of states at the Fermi level, thereby reducing the kinetic energy. Lastly, these results have implications for the phase diagrams of these elements and also for the search for new structures with novel properties.

  5. Chemical bonding in hydrogen and lithium under pressure

    DOE PAGES

    Naumov, Ivan I.; Hemley, Russell J.; Hoffmann, Roald; ...

    2015-08-12

    Though hydrogen and lithium have been assigned a common column of the periodic table, their crystalline states under common conditions are drastically different: the former at temperatures where it is crystalline is a molecular insulator whereas the latter is a metal that takes on simple structures. On compression, however, the two come to share some structural and other similarities associated with the insulator-to-metal and metal-to-insulator transitions, respectively. To gain a deeper understanding of differences and parallels in the behaviors of compressed hydrogen and lithium, we performed an ab-initio comparative study of these systems in selected identical structures. Both elements undergomore » a continuous pressure-induced s-p electronic transition, though this is at a much earlier stage of development for H. The valence charge density accumulates in interstitial regions in Li but not in H in structures examined over the same range of compression. Moreover, the valence charge density distributions or electron localization functions for the same arrangement of atoms mirror each other as one proceeds from one element to the other. Application of the viral theorem shows that the kinetic and potential energies jump across the first-order phase transitions in H and Li are opposite in sign because of non-local effects in the Li pseudopotential. Finally, the common tendency of compressed H and Li to adopt three-fold coordinated structures as found is explained by the fact that such structures are capable of yielding a profound pseudogap in the electronic densities of states at the Fermi level, thereby reducing the kinetic energy. Lastly, these results have implications for the phase diagrams of these elements and also for the search for new structures with novel properties.« less

  6. Chemical bonding in hydrogen and lithium under pressure.

    PubMed

    Naumov, Ivan I; Hemley, Russell J; Hoffmann, Roald; Ashcroft, N W

    2015-08-14

    Though hydrogen and lithium have been assigned a common column of the periodic table, their crystalline states under common conditions are drastically different: the former at temperatures where it is crystalline is a molecular insulator, whereas the latter is a metal that takes on simple structures. On compression, however, the two come to share some structural and other similarities associated with the insulator-to-metal and metal-to-insulator transitions, respectively. To gain a deeper understanding of differences and parallels in the behaviors of compressed hydrogen and lithium, we performed an ab initio comparative study of these systems in selected identical structures. Both elements undergo a continuous pressure-induced s-p electronic transition, though this is at a much earlier stage of development for H. The valence charge density accumulates in interstitial regions in Li but not in H in structures examined over the same range of compression. Moreover, the valence charge density distributions or electron localization functions for the same arrangement of atoms mirror each other as one proceeds from one element to the other. Application of the virial theorem shows that the kinetic and potential energies jump across the first-order phase transitions in H and Li are opposite in sign because of non-local effects in the Li pseudopotential. Finally, the common tendency of compressed H and Li to adopt three-fold coordinated structures as found is explained by the fact that such structures are capable of yielding a profound pseudogap in the electronic densities of states at the Fermi level, thereby reducing the kinetic energy. These results have implications for the phase diagrams of these elements and also for the search for new structures with novel properties.

  7. Chemical bonding in hydrogen and lithium under pressure

    NASA Astrophysics Data System (ADS)

    Naumov, Ivan I.; Hemley, Russell J.; Hoffmann, Roald; Ashcroft, N. W.

    2015-08-01

    Though hydrogen and lithium have been assigned a common column of the periodic table, their crystalline states under common conditions are drastically different: the former at temperatures where it is crystalline is a molecular insulator, whereas the latter is a metal that takes on simple structures. On compression, however, the two come to share some structural and other similarities associated with the insulator-to-metal and metal-to-insulator transitions, respectively. To gain a deeper understanding of differences and parallels in the behaviors of compressed hydrogen and lithium, we performed an ab initio comparative study of these systems in selected identical structures. Both elements undergo a continuous pressure-induced s-p electronic transition, though this is at a much earlier stage of development for H. The valence charge density accumulates in interstitial regions in Li but not in H in structures examined over the same range of compression. Moreover, the valence charge density distributions or electron localization functions for the same arrangement of atoms mirror each other as one proceeds from one element to the other. Application of the virial theorem shows that the kinetic and potential energies jump across the first-order phase transitions in H and Li are opposite in sign because of non-local effects in the Li pseudopotential. Finally, the common tendency of compressed H and Li to adopt three-fold coordinated structures as found is explained by the fact that such structures are capable of yielding a profound pseudogap in the electronic densities of states at the Fermi level, thereby reducing the kinetic energy. These results have implications for the phase diagrams of these elements and also for the search for new structures with novel properties.

  8. Unconventional N-H…N Hydrogen Bonds Involving Proline Backbone Nitrogen in Protein Structures.

    PubMed

    Deepak, R N V Krishna; Sankararamakrishnan, Ramasubbu

    2016-05-10

    Contrary to DNA double-helical structures, hydrogen bonds (H-bonds) involving nitrogen as the acceptor are not common in protein structures. We systematically searched N-H…N H-bonds in two different sets of protein structures. Data set I consists of neutron diffraction and ultrahigh-resolution x-ray structures (0.9 Å resolution or better) and the hydrogen atom positions in these structures were determined experimentally. Data set II contains structures determined using x-ray diffraction (resolution ≤ 1.8 Å) and the positions of hydrogen atoms were generated using a computational method. We identified 114 and 14,347 potential N-H…N H-bonds from these two data sets, respectively, and 56-66% of these were of the Ni+1-Hi+1…Ni type, with Ni being the proline backbone nitrogen. To further understand the nature of such unusual contacts, we performed quantum chemical calculations on the model compound N-acetyl-L-proline-N-methylamide (Ace-Pro-NMe) with coordinates taken from the experimentally determined structures. A potential energy profile generated by varying the ψ dihedral angle in Ace-Pro-NMe indicates that the conformation with the N-H…N H-bond is the most stable. An analysis of H-bond-forming proline residues reveals that more than 30% of the proline carbonyl groups are also involved in n → π(∗) interactions with the carbonyl carbon of the preceding residue. Natural bond orbital analyses demonstrate that the strength of N-H…N H-bonds is less than half of that observed for a conventional H-bond. This study clearly establishes the H-bonding capability of proline nitrogen and its prevalence in protein structures. We found many proteins with multiple instances of H-bond-forming prolines. With more than 15% of all proline residues participating in N-H…N H-bonds, we suggest a new, to our knowledge, structural role for proline in providing stability to loops and capping regions of secondary structures in proteins.

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

    PubMed

    Vyalikh, Anastasia; Zesewitz, Konrad; Scheler, Ulrich

    2010-11-01

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

  10. Hydrogen bonding at the water surface revealed by isotopic dilution spectroscopy.

    PubMed

    Stiopkin, Igor V; Weeraman, Champika; Pieniazek, Piotr A; Shalhout, Fadel Y; Skinner, James L; Benderskii, Alexander V

    2011-06-08

    The air-water interface is perhaps the most common liquid interface. It covers more than 70 per cent of the Earth's surface and strongly affects atmospheric, aerosol and environmental chemistry. The air-water interface has also attracted much interest as a model system that allows rigorous tests of theory, with one fundamental question being just how thin it is. Theoretical studies have suggested a surprisingly short 'healing length' of about 3 ångströms (1 Å = 0.1 nm), with the bulk-phase properties of water recovered within the top few monolayers. However, direct experimental evidence has been elusive owing to the difficulty of depth-profiling the liquid surface on the ångström scale. Most physical, chemical and biological properties of water, such as viscosity, solvation, wetting and the hydrophobic effect, are determined by its hydrogen-bond network. This can be probed by observing the lineshape of the OH-stretch mode, the frequency shift of which is related to the hydrogen-bond strength. Here we report a combined experimental and theoretical study of the air-water interface using surface-selective heterodyne-detected vibrational sum frequency spectroscopy to focus on the 'free OD' transition found only in the topmost water layer. By using deuterated water and isotopic dilution to reveal the vibrational coupling mechanism, we find that the free OD stretch is affected only by intramolecular coupling to the stretching of the other OD group on the same molecule. The other OD stretch frequency indicates the strength of one of the first hydrogen bonds encountered at the surface; this is the donor hydrogen bond of the water molecule straddling the interface, which we find to be only slightly weaker than bulk-phase water hydrogen bonds. We infer from this observation a remarkably fast onset of bulk-phase behaviour on crossing from the air into the water phase.

  11. Molecular Simulations of Hydrogen Bond Cluster Size and Reorientation Dynamics in Liquid and Glassy Azole Systems.

    PubMed

    Sun, Qinfang; Harvey, Jacob A; Greco, Katharine V; Auerbach, Scott M

    2016-10-06

    We simulated the dynamics of azole groups (pyrazole, imidazole, 1,2,3-triazole, 1,2,4-triazole, and tetrazole) as neat liquids and tethered via linkers to aliphatic backbones to determine how tethering and varying functional groups affect hydrogen bond networks and reorientation dynamics, both factors which are thought to influence proton conduction. We used the DL_Poly_2 molecular dynamics code with the GAFF force field to simulate tethered systems over the temperature range 200-900 K and the corresponding neat liquids under liquid state temperatures at standard pressure. We computed hydrogen bond cluster sizes; orientational order parameters; orientational correlation functions associated with functional groups, linkers, and backbones; time scales; and activation energies associated with orientational randomization. All tethered systems exhibit a liquid to glassy-solid transition upon cooling from 600 to 500 K, as evidenced by orientational order parameters and correlation functions. Tethering the azoles was generally found to produce hydrogen bond cluster sizes similar to those in untethered liquids and hydrogen bond lifetimes longer than those in liquids. The simulated rates of functional group reorientation decreased dramatically upon tethering. The activation energies associated with orientational randomization agree well with NMR data for tethered imidazole systems at lower temperatures and for tethered 1,2,3-triazole systems at both low- and high-temperature ranges. Overall, our simulations corroborate the notion that tethering functional groups dramatically slows the process of reorientation. We found a linear correlation between gas-phase hydrogen bond energies and tethered functional group reorientation barriers for all azoles except for imidazole, which acts as an outlier because of both atomic charges and molecular structure.

  12. Herpes simplex virus 1 primase employs watson-crick hydrogen bonding to identify cognate nucleoside triphosphates.

    PubMed

    Ramirez-Aguilar, Kathryn A; Moore, Chad L; Kuchta, Robert D

    2005-11-29

    We utilized NTP analogues containing modified bases to probe the mechanism of NTP selection by the primase activity of the herpes simplex virus 1 helicase-primase complex. Primase readily bound NTP analogues of varying base shape, hydrophobicity, and hydrogen-bonding capacity. Remarkably, primase strongly discriminated against incorporating virtually all of the analogues, even though this enzyme misincorporates natural NTPs at frequencies as high as 1 in 7. This included analogues with bases much more hydrophobic than a natural base (e.g., 4- and 7-trifluoromethylbenzimidazole), a base of similar hydrophobicity as a natural base but with the Watson-Crick hydrogen-bonding groups in unusual positions (7-beta-d-guanine), bases shaped almost identically to the natural bases (4-aminobenzimidazole and 4,6-difluorobenzimidazole), bases shaped very differently than a natural base (e.g., 5- and 6-trifluoromethylbenzimidazole), and bases capable of forming just one Watson-Crick hydrogen bond with the template base (purine and 4-aminobenzimidazole). The only analogues that primase readily polymerized into primers (ITP and 3-deaza-ATP) were those capable of forming Watson-Crick hydrogen bonds with the template base. Thus, herpes primase appears to require the formation of Watson-Crick hydrogen bonds in order to efficiently polymerize a NTP. In contrast to primase's narrow specificity for NTP analogues, the DNA-dependent NTPase activity associated with the herpes primase-helicase complex exhibited very little specificity with respect to NTPs containing unnatural bases. The implications of these results with respect to the mechanism of the helicase-primase and current fidelity models are discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2000-09-01

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

  14. Early hydrogen-bonding events in the folding reaction of ubiquitin.

    PubMed

    Briggs, M S; Roder, H

    1992-03-15

    The formation of hydrogen-bonded structure in the folding reaction of ubiquitin, a small cytoplasmic protein with an extended beta-sheet and an alpha-helix surrounding a pronounced hydrophobic core, has been investigated by hydrogen-deuterium exchange labeling in conjunction with rapid mixing methods and two-dimensional NMR analysis. The time course of protection from exchange has been measured for 26 back-bone amide protons that form stable hydrogen bonds upon refolding and exchange slowly under native conditions. Amide protons in the beta-sheet and the alpha-helix, as well as protons involved in hydrogen bonds at the helix/sheet interface, become 80% protected in an initial 8-ms folding phase, indicating that the two elements of secondary structure form and associate in a common cooperative folding event. Somewhat slower protection rates for residues 59, 61, and 69 provide evidence for the subsequent stabilization of a surface loop. Most probes also exhibit two minor phases with time constants of about 100 ms and 10 s. Only two of the observed residues, Gln-41 and Arg-42, display significant slow folding phases, with amplitudes of 37% and 22%, respectively, which can be attributed to native-like folding intermediates containing cis peptide bonds for Pro-37 and/or Pro-38. Compared with other proteins studied by pulse labeling, including cytochrome c, ribonuclease, and barnase, the initial formation of hydrogen-bonded structure in ubiquitin occurs at a more rapid rate and slow-folding species are less prominent.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed

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

    2006-09-14

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

  17. Computational study of glucosepane-water and hydrogen bond formation: an electron topology and orbital analysis.

    PubMed

    Nash, Anthony; Saßmannshausen, Jörg; Bozec, Laurent; Birch, Helen L; de Leeuw, Nora H

    2017-04-01

    The collagen protein provides tensile strength to the extracellular matrix in addition to localising cells, proteins and protein cofactors. Collagen is susceptible to a build up of glycation modifications as a result of an exceptionally long half-life. Glucosepane is a collagen cross-linking advanced glycation end product; the structural and mechanical effects of glucosepane are still the subjects of much debate. With the prospect of an ageing population, the management and treatment of age-related diseases is becoming a pressing concern. One area of interest is the isolation of hydrated glucosepane, which has yet to be reported at an atomistic level. This study presents a series of glucosepane-water complexes within an implicit aqueous environment. Electronic structure calculations were performed using density functional theory and a high level basis set. Hydrogen bonds between glucosepane and explicit water were identified by monitoring changes to covalent bonds, calculating levels of electron donation from Natural Bonding Orbital analysis and the detection of bond critical points. Hydrogen bond strength was calculated using second-order perturbation calculations. The combined results suggest that glucosepane is very hydrophilic, with the imidazole feature being energetically more attractive to water than either hydroxyl group, although all hydrogen bonds, regardless of bond strength, were electrostatic in nature. Our results are in growing support of an earlier hypothesis that cross-links may result in an increase in interstitial water retention, which would permit the collagen fibril to swell, thereby potentially affecting the tensile and compression properties and biological function of connective tissues.

  18. Solid-State (17) O NMR Reveals Hydrogen-Bonding Energetics: Not All Low-Barrier Hydrogen Bonds Are Strong.

    PubMed

    Lu, Jiasheng; Hung, Ivan; Brinkmann, Andreas; Gan, Zhehong; Kong, Xianqi; Wu, Gang

    2017-02-22

    While NMR and IR spectroscopic signatures and structural characteristics of low-barrier hydrogen bond (LBHB) formation are well documented in the literature, direct measurement of the LBHB energy is difficult. Here, we show that solid-state (17) O NMR spectroscopy can provide unique information about the energy required to break a LBHB. Our solid-state (17) O NMR data show that the HB enthalpy of the O⋅⋅⋅H⋅⋅⋅N LBHB formed in crystalline nicotinic acid is only 7.7±0.5 kcal mol(-1) , suggesting that not all LBHBs are particularly strong.

  19. O-H···S hydrogen bonds conform to the acid-base formalism.

    PubMed

    Bhattacharyya, Surjendu; Bhattacherjee, Aditi; Shirhatti, Pranav R; Wategaonkar, Sanjay

    2013-08-29

    Hydrogen bonding interaction between the ROH hydrogen bond donor and sulfur atom as an acceptor has not been as well characterized as the O-H···O interaction. The strength of O-H···O interactions for a given donor has been well documented to scale linearly with the proton affinity (PA) of the H-bond acceptor. In this regard, O-H···O interactions conform to the acid-base formalism. The importance of such correlation is to be able to estimate molecular property of the complex from the known thermodynamic data of its constituents. In this work, we investigate the properties of O-H···S interaction in the complexes of the H-bond donor and sulfur containing acceptors of varying proton affinity. The hydrogen bonded complexes of p-Fluorophenol (FP) with four different sulfur containing acceptors and their oxygen analogues, namely H2O/H2S, MeOH/MeSH, Me2O/Me2S and tetrahydrofuran (THF)/tetrahydrothiophene (THT) were characterized in regard to its S1-S0 excitation spectra and the IR spectra. Two-color resonantly enhanced multiphoton ionization (2c-R2PI), resonant ion-dip infrared (RIDIR) spectroscopy, and IR-UV hole burning spectroscopic techniques were used to probe the hydrogen bonds in the aforementioned complexes. The spectroscopic data along with the ab initio calculations were used to deduce the strength of the O-H···S hydrogen bonding interactions in these system relative to that in the O-H···O interactions. It was found that, despite being dominated by the dispersion interaction, the O-H···S interactions conform to the acid-base formalism as in the case of more conventional O-H···O interactions. The dissociation energies and the red shifts in the O-H stretching frequencies correlated very well with the proton affinity of the acceptors. However, the O-H···S interaction did not follow the same correlation as that in the O-H···O H-bond. The energy decomposition analysis showed that the dissociation energies and the red shifts in the O

  20. Tyrosine B10 triggers a heme propionate hydrogen bonding network loop with glutamine E7 moiety

    SciTech Connect

    Ramos-Santana, Brenda J.; Lopez-Garriga, Juan

    2012-08-10

    Highlights: Black-Right-Pointing-Pointer H-bonding network loop by PheB10Tyr mutation is proposed. Black-Right-Pointing-Pointer The propionate group H-bonding network restricted the flexibility of the heme. Black-Right-Pointing-Pointer The hydrogen bonding interaction modulates the electron density of the iron. Black-Right-Pointing-Pointer Propionate H-bonding network loop explains the heme-ligand stabilization. -- Abstract: Propionates, as peripheral groups of the heme active center in hemeproteins have been described to contribute in the modulation of heme reactivity and ligand selection. These electronic characteristics prompted the question of whether the presence of hydrogen bonding networks between propionates and distal amino acids present in the heme ligand moiety can modulate physiological relevant events, like ligand binding association and dissociation activities. Here, the role of these networks was evaluated by NMR spectroscopy using the hemoglobin I PheB10Tyr mutant from Lucina pectinata as model for TyrB10 and GlnE7 hemeproteins. {sup 1}H-NMR results for the rHbICN PheB10Tyr derivative showed chemical shifts of TyrB10 OH{eta} at 31.00 ppm, GlnE7 N{sub {epsilon}1}H/N{sub {epsilon}2}H at 10.66 ppm/-3.27 ppm, and PheE11 C{sub {delta}}H at 11.75 ppm, indicating the presence of a crowded, collapsed, and constrained distal pocket. Strong dipolar contacts and inter-residues crosspeaks between GlnE7/6-propionate group, GlnE7/TyrB10 and TyrB10/CN suggest that this hydrogen bonding network loop between GlnE7, TyrB10, 6-propionate group, and the heme ligand contribute significantly to the modulation of the heme iron electron density as well as the ligand stabilization mechanism. Therefore, the network loop presented here support the fact that the electron withdrawing character of the hydrogen bonding is controlled by the interaction of the propionates and the nearby electronic environments contributing to the modulation of the heme electron density state. Thus

  1. Bidentate, Monoanionic Auxiliary-Directed Functionalization of Carbon–Hydrogen Bonds

    PubMed Central

    Daugulis, Olafs; Roane, James; Tran, Ly Dieu

    2015-01-01

    CONSPECTUS In recent years, carbon–hydrogen bond functionalization has evolved from an organometallic curiosity to mainstream applications in the synthesis of complex natural products and drugs. The use of C–H bonds as a transformable functional group is advantageous because these bonds are the most abundant functionality in organic molecules. One-step conversion of these bonds to the desired functionality shortens synthetic pathways, saving reagents, solvents, and labor. Less chemical waste is generated as well, showing that this chemistry is environmentally beneficial. This Account describes the development and use of bidentate, monoanionic auxiliaries for transition-metal-catalyzed C–H bond functionalization reactions. The chemistry was initially developed to overcome the limitations with palladium-catalyzed C–H bond functionalization assisted by monodentate directing groups. By the use of electron-rich bidentate directing groups, functionalization of unactivated sp3 C–H bonds under palladium catalysis has been developed. Furthermore, a number of abundant base-metal complexes catalyze functionalization of sp2 C–H bonds. At this point, aminoquinoline, picolinic acid, and related compounds are among the most used and versatile directing moieties in C–H bond functionalization chemistry. These groups facilitate catalytic functionalization of sp2 and sp3 C–H bonds by iron, cobalt, nickel, copper, ruthenium, rhodium, and palladium complexes. Exceptionally general reactivity is observed, enabling, among other transformations, direct arylation, alkylation, fluorination, sulfenylation, amination, etherification, carbonylation, and alkenylation of carbon–hydrogen bonds. The versatility of these auxilaries can be attributed to the following factors. First, they are capable of stabilizing high oxidation states of transition metals, thereby facilitating the C–H bond functionalization step. Second, the directing groups can be removed, enabling their use in

  2. Bidentate, monoanionic auxiliary-directed functionalization of carbon-hydrogen bonds.

    PubMed

    Daugulis, Olafs; Roane, James; Tran, Ly Dieu

    2015-04-21

    In recent years, carbon-hydrogen bond functionalization has evolved from an organometallic curiosity to a tool used in mainstream applications in the synthesis of complex natural products and drugs. The use of C-H bonds as a transformable functional group is advantageous because these bonds are the most abundant functionality in organic molecules. One-step conversion of these bonds to the desired functionality shortens synthetic pathways, saving reagents, solvents, and labor. Less chemical waste is generated as well, showing that this chemistry is environmentally beneficial. This Account describes the development and use of bidentate, monoanionic auxiliaries for transition-metal-catalyzed C-H bond functionalization reactions. The chemistry was initially developed to overcome the limitations with palladium-catalyzed C-H bond functionalization assisted by monodentate directing groups. By the use of electron-rich bidentate directing groups, functionalization of unactivated sp(3) C-H bonds under palladium catalysis has been developed. Furthermore, a number of abundant base-metal complexes catalyze functionalization of sp(2) C-H bonds. At this point, aminoquinoline, picolinic acid, and related compounds are among the most used and versatile directing moieties in C-H bond functionalization chemistry. These groups facilitate catalytic functionalization of sp(2) and sp(3) C-H bonds by iron, cobalt, nickel, copper, ruthenium, rhodium, and palladium complexes. Exceptionally general reactivity is observed, enabling, among other transformations, direct arylation, alkylation, fluorination, sulfenylation, amination, etherification, carbonylation, and alkenylation of carbon-hydrogen bonds. The versatility of these auxilaries can be attributed to the following factors. First, they are capable of stabilizing high oxidation states of transition metals, thereby facilitating the C-H bond functionalization step. Second, the directing groups can be removed, enabling their use in

  3. Large Angular Jump Mechanism Observed for Hydrogen Bond Exchange in Aqueous Perchlorate Solution

    SciTech Connect

    Ji, Minbiao; Odelius3, Michael; Gaffney1, K.J.; /aff SLAC, PULSE

    2010-06-11

    The mechanism for hydrogen bond (H-bond) switching in solution has remained subject to debate despite extensive experimental and theoretical studies. We have applied polarization-selective multidimensional vibrational spectroscopy to investigate the H-bond exchange mechanism in aqueous NaClO{sub 4} solution. The results show that a water molecule shifts its donated H-bonds between water and perchlorate acceptors by means of large, prompt angular rotation. Using a jump-exchange kinetic model, we extract an average jump angle of 49 {+-} 4{sup o}, in qualitative agreement with the jump angle observed in molecular dynamics simulations of the same aqueous NaClO{sub 4} solution.

  4. Halogen- and hydrogen-bonding catenanes for halide-anion recognition.

    PubMed

    Gilday, Lydia C; Beer, Paul D

    2014-07-01

    Halogen-bonding (XB) interactions were exploited in the solution-phase assembly of anion-templated pseudorotaxanes between an isophthalamide-containing macrocycle and bromo- or iodo-functionalised pyridinium threading components. (1)H NMR spectroscopic titration investigations demonstrated that such XB interpenetrated assemblies are more stable than analogous hydrogen bonding (HB) pseudorotaxanes. The stability of the anion-templated halogen-bonded pseudorotaxane architectures was exploited in the preparation of new halogen-bonding interlocked catenane species through a Grubbs' ring-closing metathesis (RCM) clipping methodology. The catenanes' anion recognition properties in the competitive CDCl(3)/CD(3) OD 1:1 solvent mixture revealed selectivity for the heavier halides iodide and bromide over chloride and acetate.

  5. NQR application to the study of hydrogen dynamics in hydrogen-bonded molecular dimers

    NASA Astrophysics Data System (ADS)

    Asaji, Tetsuo

    2016-12-01

    The temperature dependences of 1H NMR as well as 35Cl NQR spin-lattice relaxation times T 1 were investigated in order to study the hydrogen transfer dynamics in carboxylic acid dimers in 3,5-dichloro- and 2,6-dichlorobenzoic acids. The asymmetry energy A/ k B and the activation energy V/ k B for the hydrogen transfer were estimated to be 240 K and 900 K, and 840 K and 2500 K, respectively, for these compounds. In spite of a large asymmetric potential the quantum nature of hydrogen transfer is recognized in the slope of the temperature dependence of T 1 on the low-temperature side of the T 1 minimum. The NQR T 1 measurements was revealed to be a good probe for the hydrogen transfer dynamics.

  6. Selective Sensing of Phosphates by a New Bis-heteroleptic Ru(II) Complex through Halogen Bonding: A Superior Sensor over Its Hydrogen-Bonding Analogue.

    PubMed

    Chowdhury, Bijit; Sinha, Sanghamitra; Ghosh, Pradyut

    2016-12-12

    The selective phosphate-sensing property of a bis-heteroleptic Ru(II) complex, 1[PF6 ]2 , which has a halogen-bonding iodotriazole unit, is demonstrated and is shown to be superior to its hydrogen-bonding analogue, 2[PF6 ]2 . Complex 1[PF6 ]2 , exploiting halogen-bonding interactions, shows enhanced phosphate recognition in both acetonitrile and aqueous acetonitrile compared with its hydrogen-bonding analogue, owing to considerable amplification of the Ru(II) -center-based metal-to-ligand charge transfer (MLCT) emission response and luminescence lifetime. Detailed solution-state studies reveal a higher association constant, lower limit of detection, and greater change in lifetime for complex 1 in the presence of phosphates compared with its hydrogen-bonding analogue, complex 2. The (1) H NMR titration study with H2 PO4(-) ascertains that the binding of H2 PO4(-) occurs exclusively through halogen-bonding or hydrogen-bonding interactions in complexes 1[PF6 ]2 and 2[PF6 ]2 , respectively. Importantly, the single-crystal X-ray structure confirms the first ever report on metal-assisted second-sphere recognition of H2 PO4(-) and H2 P2 O7(2-) with 1 through a solitary C-I⋅⋅⋅anion halogen-bonding interaction.

  7. Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains

    SciTech Connect

    Daidone, Isabella; Neuweiler, H; Doose, S; Sauer, M; Smith, Jeremy C

    2010-12-01

    Characterization of the length dependence of end-to-end loop-closure kinetics in unfolded polypeptide chains provides an understanding of early steps in protein folding. Here, loop-closure in poly-glycine-serine peptides is investigated by combining single-molecule fluorescence spectroscopy with molecular dynamics simulation. For chains containing more than 10 peptide bonds loop-closing rate constants on the 20-100 nanosecond time range exhibit a power-law length dependence. However, this scaling breaks down for shorter peptides, which exhibit slower kinetics arising from a perturbation induced by the dye reporter system used in the experimental setup. The loop-closure kinetics in the longer peptides is found to be determined by the formation of intra-peptide hydrogen bonds and transient beta-sheet structure, that accelerate the search for contacts among residues distant in sequence relative to the case of a polypeptide chain in which hydrogen bonds cannot form. Hydrogen-bond-driven polypeptide-chain collapse in unfolded peptides under physiological conditions found here is not only consistent with hierarchical models of protein folding, that highlights the importance of secondary structure formation early in the folding process, but is also shown to speed up the search for productive folding events.

  8. The unique physical properties of the hydrogen bonded in dimers liquid crystals

    NASA Astrophysics Data System (ADS)

    Petrov, M.; Katranchev, B.; Rafailov, P. M.

    2017-01-01

    The dimerization of aromatic carboxylic acids, is the base of the structure formation of hydrogen bonded in dimers liquid crystals (HBDLCs), that exhibit non-conventional mesomorphism. The structural units of these LCs are amphiphilic-type molecules, which after suitable functionalization, induce supramolecular complexes, nanocomposites based on HBDLCs. The liquid crystalline character of the nanocomposites strongly dependent on intermolecular hydrogen bonds between symmetric, where the H-donors and H acceptors are contained in similar and non-symmetric HBDLCs, where the H-donors and H acceptors are contained in unlike molecules. The strength and non-covalent character of the hydrogen bonds provides both sufficient HBDLCs complex stability and bonding flexibility with a possibility to design and drive the supramolecular geometry. We investigated a series of nanocomposites produced by mixture of HBDLC (p-n-alkyloxybenzoic acid - nOBA), serving as matrices, with non-mesogenic (single walled carbon nanotubes - SWCNTs, hydroxypiridine – HOPY) and mesogenic (cholesteryl benzoate - ChB) nano-particles in various shapes and sizes. A set of new chiral ferroelectric phases were found in the nanocomposites, otherwise do not appearing in the pristine achiral HBDLCs materials. A molecular model of an unique low-temperature ferroelectric smectic phase C based on the molecular dimer ring symmetry reduction (bent dimer formation) towards to the lowest triclinic one is presented for both symmetric and nonsymmetric supramolecular liquid crystal complexes.

  9. Theoretical exploration of the cooperative effect in NMF-NMF-amino acid residue hydrogen bonding system.

    PubMed

    Li, Xichen; Liu, Wenlan; Sun, Kening; Wang, Yan; Tan, Hongwei; Chen, Guangju

    2008-09-28

    This paper presents a theoretical study of the cooperative effect in sixteen linearly-arranged trimer systems consisting of N-methylformamide dimer and an extra amino acid residue. These trimer systems, NMF-NMF-AAR, in short, have been systematically investigated by full optimization at B3LYP/cc-pVTZ level and subsequent electronic energy calculations at PBE1PBE/cc-pVTZ, HF/cc-pVTZ and MP2/cc-pVTZ, respectively. Obvious spatial transformation due to energetic factors has been found in almost all the trimers. Systematic analysis in weak interaction energy components has shown that: (1) in these trimer systems, the bonding structure and the cooperative effect combine to determine the stability of both HB1 and HB2. For HB2, the structure of the constituent amino acid residue also plays a crucial role by interfering with the neighboring moieties; (2) the large contribution of the cooperative effect to the overall hydrogen bonding energy has claimed the importance of cooperativity in our systems; (3) the non-hydrogen bonding weak interaction components are found to be non-negligible in these trimer systems; (4) moreover, the cooperative effect between these non-hydrogen bonding components is always found to be positive. The good performances of PBE1PBE and PM6 have been established by comparisons between these methods.

  10. Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water.

    PubMed Central

    Nina, M; Roux, B; Smith, J C

    1995-01-01

    The light-driven proton pump, bacteriorhodopsin (bR) contains a retinal molecule with a Schiff base moiety that can participate in hydrogen-bonding interactions in an internal, water-containing channel. Here we combine quantum chemistry and molecular mechanics techniques to determine the geometries and energetics of retinal Schiff base-water interactions. Ab initio molecular orbital calculations are used to determine potential surfaces for water-Schiff base hydrogen-bonding and to characterize the energetics of rotation of the C-C single bond distal and adjacent to the Schiff base NH group. The ab initio results are combined with semiempirical quantum chemistry calculations to produce a data set used for the parameterization of a molecular mechanics energy function for retinal. Using the molecular mechanics force field the hydrated retinal and associated bR protein environment are energy-minimized and the resulting geometries examined. Two distinct sites are found in which water molecules can have hydrogen-bonding interactions with the Schiff base: one near the NH group of the Schiff base in a polar region directed towards the extracellular side, and the other near a retinal CH group in a relatively nonpolar region, directed towards the cytoplasmic side. Images FIGURE 1 FIGURE 2 FIGURE 6 FIGURE 8 PMID:7711248

  11. Investigation on Thermal and Optical Properties of Hydrogen-Bonded Binary Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Ranjeeth kumar, T.; Sundaram, S.; Vasanthi, T.; Subhasri, P.; Chitravel, T.; Senthil, T. S.; Jayaprakasam, R.; Vijayakumar, V. N.

    2016-12-01

    A homologous series of hydrogen-bonded liquid crystals (HBLCs) are synthesized and characterized. Intermolecular hydrogen bonding occurs between 4-methoxycinnamic acid (4MCA) and p-n-alkyloxy benzoic acids (nOBA, where n = 3, 7 to 12). These binary complexes have been obtained by following well-designed synthesis route. The subsequent binary complexes have been characterized by polarizing optical thermal microscopy (POM), differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR). The present work explains the details of the association between the mesogenic phase behavior and H-bonding in the homologous series of 4MCA + nOBA. Nematic phase is interrelated with the closed dimers between acid molecules through the formation of strong hydrogen bonds. But, high concentrations are linked to the manifestation of smectic phases that disturb the local order of the nematic phase. As a result, the higher-order mesophases are observed in the present binary complex series. The inclusion of nematic LC (4MCA) in the nOBA alters the melting temperature and the clearing temperature as lower than those of the individual. Also, the wide mesophase regions of the present series are identified compared to those of the constituent mesogens. The optical tilt angle of binary mixtures for smectic C phase and thermal stability factors of the mesogenic phases have been discussed.

  12. Interdigitated hydrogen bonds: electrophile activation for covalent capture and fluorescence turn-on detection of cyanide.

    PubMed

    Jo, Junyong; Olasz, András; Chen, Chun-Hsing; Lee, Dongwhan

    2013-03-06

    Hydrogen-bonding promoted covalent modifications are finding useful applications in small-molecule chemical synthesis and detection. We have designed a xanthene-based fluorescent probe 1, in which tightly held acylguanidine and aldehyde groups engage in multiple intramolecular hydrogen bonds within the concave side of the molecule. Such an interdigitated hydrogen bond donor-acceptor (HBD-HBA) array imposes significant energy barriers (ΔG(‡) = 10-16 kcal mol(-1)) for internal bond rotations to assist structural preorganization and effectively polarizes the electrophilic carbonyl group toward a nucleophilic attack by CN(-) in aqueous environment. This covalent modification redirects the de-excitation pathways of the cyanohydrin adduct 2 to elicit a large (>7-fold) enhancement in the fluorescence intensity at λmax = 440 nm. A remarkably faster (> 60-fold) response kinetics of 1, relative to its N-substituted (and therefore "loosely held") analogue 9, provided compelling experimental evidence for the functional role of HBD-HBA interactions in the "remote" control of chemical reactivity, the electronic and steric origins of which were investigated by DFT computational and X-ray crystallographic studies.

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

    PubMed

    Slavíček, Petr; Fárník, Michal

    2011-07-14

    In this perspective article, we focus on the photochemistry of five-membered nitrogen containing heterocycles (pyrrole, imidazole and pyrazole) in clusters. These heterocycles represent paradigmatic structures for larger biologically active heterocyclic molecules and complexes. The dimers of the three molecules are also archetypes of different bonding patterns: N-H···π interaction, N-H···N hydrogen bond and double hydrogen bond. We briefly review available data on photochemistry of the title molecules in the gas phase, but primarily we focus on the new reaction channels opened upon the complexation with other heterocycles or solvent molecules. Based on ab initio calculations we discuss various possible reactions in the excited states of the clusters: (1) hydrogen dissociation, (2) hydrogen transfer between the heterocyclic units, (3) molecular ring distortion, and (4) coupled electron-proton transfer. The increasing photostability with complexity of the system can be inferred from experiments with photodissociation in these clusters. A unified view on photoinduced processes in five-membered N-heterocycles is provided. We show that even though different deactivation channels are energetically possible for the complexed heterocycles, in most cases the major result is a fast reconstruction of the ground state. The complexed or solvated heterocycles are thus inherently photostable although the stability can in principle be achieved via different reaction routes.

  14. Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints.

    PubMed

    Porter, Lauren L; Rose, George D

    2011-01-04

    A protein backbone has two degrees of conformational freedom per residue, described by its ϕ,ψ-angles. Accordingly, the energy landscape of a blocked peptide unit can be mapped in two dimensions, as shown by Ramachandran, Sasisekharan, and Ramakrishnan almost half a century ago. With atoms approximated as hard spheres, the eponymous Ramachandran plot demonstrated that steric clashes alone eliminate 3/4 of ϕ,ψ-space, a result that has guided all subsequent work. Here, we show that adding hydrogen-bonding constraints to these steric criteria eliminates another substantial region of ϕ,ψ-space for a blocked peptide; for conformers within this region, an amide hydrogen is solvent-inaccessible, depriving it of a hydrogen-bonding partner. Yet, this "forbidden" region is well populated in folded proteins, which can provide longer-range intramolecular hydrogen-bond partners for these otherwise unsatisfied polar groups. Consequently, conformational space expands under folding conditions, a paradigm-shifting realization that prompts an experimentally verifiable conjecture about likely folding pathways.

  15. Hydrogen bonding changes of internal water molecules in rhodopsin during metarhodopsin I and metarhodopsin II formation.

    PubMed Central

    Rath, P; Delange, F; Degrip, W J; Rothschild, K J

    1998-01-01

    Rhodopsin is a 7-helix, integral membrane protein found in the rod outer segments, which serves as the light receptor in vision. Light absorption by the retinylidene chromophore of rhodopsin triggers an 11-cis-->all-trans isomerization, followed by a series of protein conformational changes, which culminate in the binding and activation of the G-protein transducin by the metarhodopsin II (Meta II) intermediate. Fourier transform IR difference spectroscopy has been used to investigate the structural changes that water, as well as other OH- and NH-containing groups, undergo during the formation of the metarhodopsin I (Meta I) and Meta II intermediates. Bands associated with the OH stretch modes of water are identified by characteristic downshifts upon substitution of H2(18)O for H2O. Compared with earlier work, several negative bands associated with water molecules in unphotolysed rhodopsin were detected, which shift to lower frequencies upon formation of the Meta I and Meta II intermediates. These data indicate that at least one water molecule undergoes an increase in hydrogen bonding upon formation of the Meta I intermediate, while at least one other increases its hydrogen bonding during Meta II formation. Amino acid residue Asp-83, which undergoes a change in its hydrogen bonding during Meta II formation, does not appear to interact with any of the structurally active water molecules. Several NH and/or OH groups, which are inaccessible to hydrogen/deuterium exchange, also undergo alterations during Meta I and Meta II formation. PMID:9445403

  16. A molecular dynamics study of guest-host hydrogen bonding in alcohol clathrate hydrates.

    PubMed

    Hiratsuka, Masaki; Ohmura, Ryo; Sum, Amadeu K; Alavi, Saman; Yasuoka, Kenji

    2015-05-21

    Clathrate hydrates are typically stabilized by suitably sized hydrophobic guest molecules. However, it has been experimentally reported that isomers of amyl-alcohol C5H11OH can be enclosed into the 5(12)6(4) cages in structure II (sII) clathrate hydrates, even though the effective radii of the molecules are larger than the van der Waals radii of the cages. To reveal the mechanism of the anomalous enclathration of hydrophilic molecules, we performed ab initio and classical molecular dynamics simulations (MD) and analyzed the structure and dynamics of a guest-host hydrogen bond for sII 3-methyl-1-butanol and structure H (sH) 2-methyl-2-butanol clathrate hydrates. The simulations clearly showed the formation of guest-host hydrogen bonds and the incorporation of the O-H group of 3-methyl-1-butanol guest molecules into the framework of the sII 5(12)6(4) cages, with the remaining hydrophobic part of the amyl-alcohol molecule well accommodated into the cages. The calculated vibrational spectra of alcohol O-H bonds showed large frequency shifts due to the strong guest-host hydrogen bonding. The 2-methyl-2-butanol guests form strong hydrogen bonds with the cage water molecules in the sH clathrate, but are not incorporated into the water framework. By comparing the structures of the alcohols in the hydrate phases, the effect of the location of O-H groups in the butyl chain of the guest molecules on the crystalline structure of the clathrate hydrates is indicated.

  17. Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole.

    PubMed

    Kraut, Daniel A; Sigala, Paul A; Pybus, Brandon; Liu, Corey W; Ringe, Dagmar; Petsko, Gregory A; Herschlag, Daniel

    2006-04-01

    A longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis. Experimental evaluation of this contribution, however, has been difficult. We have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. Phenolates, analogs of the transition state and reaction intermediate, bind and accept two hydrogen bonds in an active site oxyanion hole. The binding of substituted phenolates of constant molecular shape but increasing pK(a) models the charge accumulation in the oxyanion hole during the enzymatic reaction. As charge localization increases, the NMR chemical shifts of protons involved in oxyanion hole hydrogen bonds increase by 0.50-0.76 ppm/pK(a) unit, suggesting a bond shortening of 0.02 A/pK(a) unit. Nevertheless, there is little change in binding affinity across a series of substituted phenolates (DeltaDeltaG = -0.2 kcal/mol/pK(a) unit). The small effect of increased charge localization on affinity occurs despite the shortening of the hydrogen bonds and a large favorable change in binding enthalpy (DeltaDeltaH = -2.0 kcal/mol/pK(a) unit). This shallow dependence of binding affinity suggests that electrostatic complementarity in the oxyanion hole makes at most a modest contribution to catalysis of 300-fold. We propose that geometrical complementarity between the oxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution.

  18. Fluoroolefins as peptide mimetics: a computational study of structure, charge distribution, hydration, and hydrogen bonding.

    PubMed

    Urban, Joseph J; Tillman, Brendon G; Cronin, William Andrew

    2006-09-28

    The design of peptide mimetic compounds is greatly facilitated by the identification of functionalities that can act as peptide replacements. The fluoroalkene moiety has recently been employed for that purpose. The purpose of this work is to characterize prototypical fluoroalkenes (fluoroethylene and 2-fluoro-2-butene) with respect to key properties of peptides (amides) including structure, charge distribution, hydration, and hydrogen bonding. The results are compared to those obtained for model peptides (formamide, N-methylacetamide). Calculations have been carried out at the MP2 and B3LYP levels of theory with the 6-311++G(2d,p) and 6-311++G(2d,2p) basis sets. The results suggest that the fluoroalkene is similar in steric requirements to a peptide bond but that there is less charge separation. Calculations of the hydration free energies with the PCM bulk continuum solvent model indicate that the fluoroalkene has much smaller hydration free energies than an amide but that the difference in solvation free energy for cis and trans isomers is comparable. In studies of complexes with water molecules, the fluoroalkene is found to engage in interactions that are analogous to backbone hydrogen-bonding interactions that govern many properties of natural peptides and proteins but with smaller interaction energies. In addition, key structural differences are noted when the fluoroalkene is playing the role of hydrogen-bond acceptor which may have implications in binding, aggregation, and conformational preferences in fluoroalkene peptidomimetics. The issue of cooperativity in hydrogen-bonding interactions in complexes with multiple waters has also been investigated. The fluoroalkene is found to exhibit cooperative effects that mirror those of the peptide but are smaller in magnitude. Thus, pairwise addivitity of interactions appears to more adequately describe the fluoroalkenes than the peptides they are intended to mimic.

  19. New insights about the hydrogen bonds formed between acetylene and hydrogen fluoride: π ⋯ H, C ⋯ H and F ⋯ H

    NASA Astrophysics Data System (ADS)

    Silva, Denize S.; Oliveira, Boaz G.

    2017-02-01

    A theoretical study of hydrogen bond strength and bond properties in the C2H2 ⋯(HF)-T, C2H2 ⋯ 2(HF)-T, C2H2 ⋯ 2(HF), C2H2 ⋯ 3(HF) and C2H2 ⋯ 4(HF) complexes was carried out at the B3LYP/6-311 ++G(d,p) theory level. In these systems, a strength competition between the π ⋯ H and C ⋯ H interactions was examined. Specifically the F ⋯ H hydrogen bond, its properties were studied through a comparison between the hydrogen fluoride and the higher-order complexes (trimer, tetramer and pentamer). Regarding the electronic properties, the hydrogen bond strength could not be determined by the supermolecule approach. Thus, the hydrogen bond energies were computed via NBO calculations. Additionally to NBO, the ChelpG charge calculations were used to interpret the intermolecular charge transfer. The QTAIM integrations were useful to predict the covalent character of the π ⋯ H, C ⋯ H and F ⋯ H hydrogen bonds. Moreover, values of hybrid orbitals (s and p) and atomic radii were also determined in order to justify the red shifts in the stretch frequencies of the Hsbnd F bonds.

  20. The Role of Hydrogen Bonds in the Stabilization of Silver-Mediated Cytosine Tetramers.

    PubMed

    Espinosa Leal, Leonardo Andrés; Karpenko, Alexander; Swasey, Steven; Gwinn, Elisabeth G; Rojas-Cervellera, Victor; Rovira, Carme; Lopez-Acevedo, Olga

    2015-10-15

    DNA oligomers can form silver-mediated duplexes, stable in gas phase and solution, with potential for novel biomedical and technological applications. The nucleobase-metal bond primarily drives duplex formation, but hydrogen (H-) bonds may also be important for structure selection and stability. To elucidate the role of H-bonding, we conducted theoretical and experimental studies of a duplex formed by silver-mediated cytosine homopobase DNA strands, two bases long. This silver-mediated cytosine tetramer is small enough to permit accurate, realistic modeling by DFT-based quantum mechanics/molecular mechanics methods. In gas phase, our calculations found two energetically favorable configurations distinguished by H-bonding, one with a novel interplane H-bond, and the other with planar H-bonding of silver-bridged bases. Adding solvent favored silver-mediated tetramers with interplane H-bonding. Overall agreement of electronic circular dichroism spectra for the final calculated structure and experiment validates these findings. Our results can guide use of these stabilization mechanisms for devising novel metal-mediated DNA structures.

  1. How Hydrogen Bonds Affect the Growth of Reverse Micelles around Coordinating Metal Ions.

    PubMed

    Qiao, Baofu; Demars, Thomas; Olvera de la Cruz, Monica; Ellis, Ross J

    2014-04-17

    Extensive research on hydrogen bonds (H-bonds) have illustrated their critical role in various biological, chemical and physical processes. Given that existing studies are predominantly performed in aqueous conditions, how H-bonds affect both the structure and function of aggregates in organic phase is poorly understood. Herein, we investigate the role of H-bonds on the hierarchical structure of an aggregating amphiphile-oil solution containing a coordinating metal complex by means of atomistic molecular dynamics simulations and X-ray techniques. For the first time, we show that H-bonds not only stabilize the metal complex in the hydrophobic environment by coordinating between the Eu(NO3)3 outer-sphere and aggregating amphiphiles, but also affect the growth of such reverse micellar aggregates. The formation of swollen, elongated reverse micelles elevates the extraction of metal ions with increased H-bonds under acidic condition. These new insights into H-bonds are of broad interest to nanosynthesis and biological applications, in addition to metal ion separations.

  2. Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs.

    PubMed

    Takezawa, Yusuke; Shionoya, Mitsuhiko

    2012-12-18

    With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely based on highly specific molecular recognition between nucleobases through the specific hydrogen bonds in the Watson-Crick base pairing system. While the native base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative base pairing systems in recent decades. Most of these new systems were designed based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA base pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme in biological systems, metal-coordination bonding. In this Account, we provide an overview of the chemistry of metal-mediated base pairing including basic concepts, molecular design, characteristic structures and properties, and possible applications of DNA-based molecular systems. We describe several examples of artificial metal-mediated base pairs, such as Cu(2+)-mediated hydroxypyridone base pair, H-Cu(2+)-H (where H denotes a hydroxypyridone-bearing nucleoside), developed by us and other researchers. To design the metallo-base pairs we carefully chose appropriate combinations of ligand-bearing nucleosides and metal ions. As expected from their stronger bonding through metal coordination, DNA duplexes possessing metallo-base pairs exhibited higher thermal stability than natural hydrogen-bonded DNAs. Furthermore, we could also use metal-mediated base pairs to construct or induce other high-order structures. These features could lead to metal-responsive functional

  3. The nature of resonance-assisted hydrogen bonds: a quantum chemical topology perspective.

    PubMed

    Guevara-Vela, José Manuel; Romero-Montalvo, Eduardo; Costales, Aurora; Pendás, Ángel Martín; Rocha-Rinza, Tomás

    2016-10-14

    Resonance Assisted Hydrogen Bonds (RAHBs) are particularly strong H-Bonds (HBs) which are relevant in several fields of chemistry. The traditional explanation for the occurrence of these HBs is built on mesomeric structures evocative of electron delocalisation in the system. Nonetheless, there are several theoretical studies which have found no evidence of such electron delocalisation. We considered the origin of RAHBs by employing Quantum Chemical Topology tools, more specifically, the Quantum Theory of Atoms in Molecules (QTAIM) and the Interacting Quantum Atoms energy partition. Our results indicate that the π-conjugated bonds allow for a larger adjustment of electron density throughout the H-bonded system as compared with non-conjugated carbonyl molecules. This rearrangement of charge distribution is a response to the electric field due to the H atom involved in the hydrogen bonding of the considered compounds. As opposed to the usual description of RAHB interactions, these HBs lead to a larger electron localisation in the system, and concomitantly to larger QTAIM charges which in turn lead to stronger electrostatic, polarization and charge transfer components of the interaction. Overall, the results presented here offer a new perspective on the cause of strengthening of these important interactions.

  4. Theoretical Prediction of Hydrogen-Bond Basicity pKBHX Using Quantum Chemical Topology Descriptors

    PubMed Central

    2014-01-01

    Hydrogen bonding plays an important role in the interaction of biological molecules and their local environment. Hydrogen-bond strengths have been described in terms of basicities by several different scales. The pKBHX scale has been developed with the interests of medicinal chemists in mind. The scale uses equilibrium constants of acid···base complexes to describe basicity and is therefore linked to Gibbs free energy. Site specific data for polyfunctional bases are also available. The pKBHX scale applies to all hydrogen-bond donors (HBDs) where the HBD functional group is either OH, NH, or NH+. It has been found that pKBHX can be described in terms of a descriptor defined by quantum chemical topology, ΔE(H), which is the change in atomic energy of the hydrogen atom upon complexation. Essentially the computed energy of the HBD hydrogen atom correlates with a set of 41 HBAs for five common HBDs, water (r2 = 0.96), methanol (r2 = 0.95), 4-fluorophenol (r2 = 0.91), serine (r2 = 0.93), and methylamine (r2 = 0.97). The connection between experiment and computation was strengthened with the finding that there is no relationship between ΔE(H) and pKBHX when hydrogen fluoride was used as the HBD. Using the methanol model, pKBHX predictions were made for an external set of bases yielding r2 = 0.90. Furthermore, the basicities of polyfunctional bases correlate with ΔE(H), giving r2 = 0.93. This model is promising for the future of computation in fragment-based drug design. Not only has a model been established that links computation to experiment, but the model may also be extrapolated to predict external experimental pKBHX values. PMID:24460383

  5. On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules.

    PubMed

    Luisi, B; Orozco, M; Sponer, J; Luque, F J; Shakked, Z

    1998-06-26

    Crystallographic studies of duplex DNA have indicated that opposing exocyclic amino groups may form close NH⋯:N contacts. To study the nature of such interactions, we have examined the database of small molecule, high-resolution crystal structures for more accurate examples of this type of unconventional interaction. We have found cases where the amino groups in guanine and adenine bases accept hydrogen bonds from conventional donors, such as amino or hydroxyl groups. More frequently, the purine amino group was found to contact closely electropositive C-H groups. Searches of the nucleic acid structural databases also yielded several examples where the purine amino group is contacted by hydrogen bond donors in macromolecules. Ab initio calculations indicate that the hydrogen-amino contact is improved energetically when the amino group moves from the conventional geometry, where all atoms are co-planar with the base, to one in which the hydrogen atoms lie out of the plane and the nitrogen is at the apex of a pyramid, resulting in polarization of the amino group. The combined structural and theoretical data suggest that the amino group is flexible, and can accommodate close contacts, because the resulting polarization permits electropositive atoms to approach the amino group nitrogen more closely than expected for their conventional van der Waals radii. The flexibility of the amino group may permit particular DNA conformations that enforce hydrogen-amino contacts to optimize favorable stacking interactions, and it may play a role in the recognition of nucleosides. We speculate that the amino group can accept hydrogen bonds under special circumstances in macromolecules, and that this ability might play a mechanistic role in catalytic processes such as deamination or amino transfer.

  6. Theoretical prediction of hydrogen-bond basicity pKBHX using quantum chemical topology descriptors.

    PubMed

    Green, Anthony J; Popelier, Paul L A

    2014-02-24

    Hydrogen bonding plays an important role in the interaction of biological molecules and their local environment. Hydrogen-bond strengths have been described in terms of basicities by several different scales. The pKBHX scale has been developed with the interests of medicinal chemists in mind. The scale uses equilibrium constants of acid···base complexes to describe basicity and is therefore linked to Gibbs free energy. Site specific data for polyfunctional bases are also available. The pKBHX scale applies to all hydrogen-bond donors (HBDs) where the HBD functional group is either OH, NH, or NH+. It has been found that pKBHX can be described in terms of a descriptor defined by quantum chemical topology, ΔE(H), which is the change in atomic energy of the hydrogen atom upon complexation. Essentially the computed energy of the HBD hydrogen atom correlates with a set of 41 HBAs for five common HBDs, water (r2=0.96), methanol (r2=0.95), 4-fluorophenol (r2=0.91), serine (r2=0.93), and methylamine (r2=0.97). The connection between experiment and computation was strengthened with the finding that there is no relationship between ΔE(H) and pKBHX when hydrogen fluoride was used as the HBD. Using the methanol model, pKBHX predictions were made for an external set of bases yielding r2=0.90. Furthermore, the basicities of polyfunctional bases correlate with ΔE(H), giving r2=0.93. This model is promising for the future of computation in fragment-based drug design. Not only has a model been established that links computation to experiment, but the model may also be extrapolated to predict external experimental pKBHX values.

  7. Carbon-tuned bonding method significantly enhanced the hydrogen storage of BN-Li complexes.

    PubMed

    Deng, Qing-ming; Zhao, Lina; Luo, You-hua; Zhang, Meng; Zhao, Li-xia; Zhao, Yuliang

    2011-11-01

    Through first-principles calculations, we found doping carbon atoms onto BN monolayers (BNC) could significantly strengthen the Li bond on this material. Unlike the weak bond strength between Li atoms and the pristine BN layer, it is observed that Li atoms are strongly hybridized and donate their electrons to the doped substrate, which is responsible for the enhanced binding energy. Li adsorbed on the BNC layer can serve as a high-capacity hydrogen storage medium, without forming clusters, which can be recycled at room temperature. Eight polarized H(2) molecules are attached to two Li atoms with an optimal binding energy of 0.16-0.28 eV/H(2), which results from the electrostatic interaction of the polarized charge of hydrogen molecules with the electric field induced by positive Li atoms. This practical carbon-tuned BN-Li complex can work as a very high-capacity hydrogen storage medium with a gravimetric density of hydrogen of 12.2 wt%, which is much higher than the gravimetric goal of 5.5 wt % hydrogen set by the U.S. Department of Energy for 2015.

  8. Simulation of the effect of hydrogen bonds on water activity of glucose and dextran using the Veytsman model.

    PubMed

    De Vito, Francesca; Veytsman, Boris; Painter, Paul; Kokini, Jozef L

    2015-03-06

    Carbohydrates exhibit either van der Waals and ionic interactions or strong hydrogen bonding interactions. The prominence and large number of hydrogen bonds results in major contributions to phase behavior. A thermodynamic framework that accounts for hydrogen bonding interactions is therefore necessary. We have developed an extension of the thermodynamic model based on the Veytsman association theory to predict the contribution of hydrogen bonds to the behavior of glucose-water and dextran-water systems and we have calculated the free energy of mixing and its derivative leading to chemical potential and water activity. We compared our calculations with experimental data of water activity for glucose and dextran and found excellent agreement far superior to the Flory-Huggins theory. The validation of our calculations using experimental data demonstrated the validity of the Veytsman model in properly accounting for the hydrogen bonding interactions and successfully predicting water activity of glucose and dextran. Our calculations of the concentration of hydrogen bonds using the Veytsman model were instrumental in our ability to explain the difference between glucose and dextran and the role that hydrogen bonds play in contributing to these differences. The miscibility predictions showed that the Veytsman model is also able to correctly describe the phase behavior of glucose and dextran.

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

    PubMed

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

    2011-02-07

    Guest-host hydrogen bonding in clathrate hydrates occurs when in addition to the hydrophilic moiety which causes the molecule to form hydrates under high pressure-low temperature conditions, the guests contain a hydrophilic, hydrogen bonding functional group. In the presence of carbon dioxide, ethanol clathrate hydrate has been synthesized with 10% of large structure I (sI) cages occupied by ethanol. In this work, we use molecular dynamics simulations to study hydrogen bonding structure and dynamics in this binary sI clathrate hydrate in the temperature range of 100-250 K. We observe that ethanol forms long-lived (>500 ps) proton-donating and accepting hydrogen bonds with cage water molecules from both hexagonal and pentagonal faces of the large cages while maintaining the general cage integrity of the sI clathrate hydrate. The presence of the nondipolar CO(2) molecules stabilizes the hydrate phase, despite the strong and prevalent alcohol-water hydrogen bonding. The distortions of the large cages from the ideal form, the radial distribution functions of the guest-host interactions, and the ethanol guest dynamics are characterized in this study. In previous work through dielectric and NMR relaxation time studies, single crystal x-ray diffraction, and molecular dynamics simulations we have observed guest-water hydrogen bonding in structure II and structure H clathrate hydrates. The present work extends the observation of hydrogen bonding to structure I hydrates.

  10. Hydrogen bonding effects on infrared and Raman spectra of drug molecules

    NASA Astrophysics Data System (ADS)

    Bondesson, Laban; Mikkelsen, Kurt V.; Luo, Yi; Garberg, Per; Ågren, Hans

    2007-02-01

    Infrared and Raman spectra of three drug molecules, aspirin, caffeine and ibuprofen, in gas phase and in aqueous solution have been simulated using hybrid density functional theory. The long range solvent effect is modelled by the polarizable continuum model, while the short range hydrogen bonding effects are taken care of by the super-molecular approach with explicit inclusion of water molecules. The calculated spectra are found to compare well with available experimental results. The agreement obtained make grounds for proposing theoretical modeling as a tool for characterizing changes in the bonding environments of drug molecules in terms of particular variations in their IR and Raman spectra.

  11. Fluorescence study on the phase transition of hydrogen-bonding gels

    NASA Astrophysics Data System (ADS)

    Yılmaz, Yaşar

    2002-11-01

    A technique based on steady-state fluorescence measurements is introduced to study the discontinuous volume phase transition of hydrogen-bonding gel. The fluorescence light intensity of pyranine (1-Hydroxypyrene-3, 6, 8-trisulfonic acid) bonded to the gel by means of methacryl amino-propyl-trimethyl ammonium chloride was monitored during the swelling of poly(methacrylic acid-co-dimethyl acrylamide) copolymer in water as a function of temperature. A discontinuous volume phase transition around 60 °C and an additional phase around 30 °C, which may be interpreted as the freely fluctuating phase in a collapsed state, were observed when the fluorescence intensity changes.

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

    PubMed

    Blinc, Robert; Lahajnar, Gojmir; Potočnik, Anton

    2011-09-01

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

  13. Small-molecule recognition for controlling molecular motion in hydrogen-bond-assembled rotaxanes.

    PubMed

    Martinez-Cuezva, Alberto; Berna, Jose; Orenes, Raul-Angel; Pastor, Aurelia; Alajarin, Mateo

    2014-06-23

    Di(acylamino)pyridines successfully template the formation of hydrogen-bonded rotaxanes through five-component clipping reactions. A solid-state study showed the participation of the pyridine nitrogen atom in the stabilization of the mechanical bond between the thread and the benzylic amide macrocycle. The addition of external complementary binders to a series of interlocked bis(2,6-di(acylamino)pyridines) promoted restraint of the back and forward ring motion. The original translation can be restored through a competitive recognition event by the addition of a preorganized bis(di(acylamino)pyridine) that forms stronger ADA-DAD complexes with the external binders.

  14. O-H hydrogen bonding promotes H-atom transfer from α C-H bonds for C-alkylation of alcohols.

    PubMed

    Jeffrey, Jenna L; Terrett, Jack A; MacMillan, David W C

    2015-09-25

    The efficiency and selectivity of hydrogen atom transfer from organic molecules are often difficult to control in the presence of multiple potential hydrogen atom donors and acceptors. Here, we describe the mechanistic evaluation of a mode of catalytic activation that accomplishes the highly selective photoredox α-alkylation/lactonization of alcohols with methyl acrylate via a hydrogen atom transfer mechanism. Our studies indicate a particular role of tetra-n-butylammonium phosphate in enhancing the selectivity for α C-H bonds in alcohols in the presence of allylic, benzylic, α-C=O, and α-ether C-H bonds.

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

    PubMed

    Moran, Joseph; Krische, Michael J

    2012-01-01

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

  16. Ortho-substituted catechol derivatives: the effect of intramolecular hydrogen-bonding pathways on chloride anion recognition.

    PubMed

    Winstanley, Keith J; Smith, David K

    2007-04-13

    This paper reports a series of chloride anion receptors containing two catechol head groups connected through their ortho-positions via a spacer chain. The linking group chosen to attach the spacer chain to the catechol units has a major impact on the anion-binding potential of the receptor. Linking groups that are capable of forming stable six-membered intramolecular hydrogen-bonded rings with the catechol O-H groups significantly inhibit the ability of the catechol units to hydrogen bond to chloride anions. However, where the linking groups are only capable of forming five- or seven-membered intramolecular hydrogen-bonded rings, then anion binding via hydrogen bonding through the catechol O-H groups becomes a possibility. This process is solvent dependent; the presence of competitive solvent (e.g., DMSO-d6) disrupts the intramolecular hydrogen-bonding pattern and enhances anion binding relative to simple unfunctionalized catechol. The most effective receptor is that in which the hydrogen-bonding linker (-CH2CONH-) is most distant from the catechol units and can only form a seven-membered intramolecular hydrogen-bonded ring. In this case, the receptor, which contains two catechol units, is a more effective chloride anion binder than simple unfunctionalized catechol, demonstrating that the two head groups, in combination with the N-H groups in the linker, act cooperatively and enhance the degree of anion binding. In summary, this paper provides insight into the hydrogen-bonding patterns in ortho-functionalized catechols and the impact these have on the potential of the catechol O-H groups to hydrogen bond to a chloride anion.

  17. Hydrogen bonding. Part 26. Thermodynamics of dissociation and infrared spectracrystal structure correlations for betaine monohydrate and trimethylamine oxide dihydrate

    NASA Astrophysics Data System (ADS)

    Toccalino, Patricia L.; Harmon, Kenneth M.; Harmon, Jennifer

    1988-10-01

    Thermodynamic parameters for the dissociation of betaine monohydrate and trimethylamine oxide dihydrate have been determined by equilibrium vapor pressure measurements. Betaine monohydrate appears in two slightly different crystalline forms, one obtained by crystallization from water and the other by addition of water vapor to solid anhydrous betaine. Hydrogen bond energies in these hydrates are at least 8-9 kcal mol -1 per OH⋯O bond. Hydrogen bond energies in trimethylamine oxide dihydrate average at least 14 kcal mol -1 per OH⋯O bond; however, as there are two distinct types of hydrogen bonds in this hydrate, some bonds are stronger and some weaker than 14 kcal mol -1. These studies show conclusively that trimethylamine oxide monohydrate does not exist. The infrared spectrum of trimethylamine oxide dihydrate is correlated with the crystal structure.

  18. Investigation of bonded hydrogen defects in nanocrystalline diamond films grown with nitrogen/methane/hydrogen plasma at high power conditions

    NASA Astrophysics Data System (ADS)

    Tang, C. J.; Hou, Haihong; Fernandes, A. J. S.; Jiang, X. F.; Pinto, J. L.; Ye, H.

    2017-02-01

    In this work, we investigate the influence of some growth parameters such as high microwave power ranging from 3.0 to 4.0 kW and N2 additive on the incorporation of bonded hydrogen defects in nanocrystalline diamond (NCD) films grown through a small amount of pure N2 addition into conventional 4% CH4/H2 plasma using a 5 kW microwave plasma CVD system. Incorporation form and content of hydrogen point defects in the NCD films produced with pure N2 addition was analyzed by employing Fourier-transform infrared (FTIR) spectroscopy for the first time. A large amount of hydrogen related defects was detected in all the produced NCD films with N2 additive ranging from 29 to 87 μm thick with grain size from 47 nm to 31 nm. Furthermore, a specific new H related sharp absorption peak appears in all the NCD films grown with pure N2/CH4/H2 plasma at high powers and becomes stronger at powers higher than 3.0 kW and is even stronger than the 2920 cm-1 peak, which is commonly found in CVD diamond films. Based on these experimental findings, the role of high power and pure nitrogen addition on the growth of NCD films including hydrogen defect formation is analyzed and discussed.

  19. Use of H/D isotope effects to gather information about hydrogen bonding and hydrogen exchange rates.

    PubMed

    Takeda, Mitsuhiro; Miyanoiri, Yohei; Terauchi, Tsutomu; Yang, Chun-Jiun; Kainosho, Masatsune

    2014-04-01

    Polar side-chains in proteins play important roles in forming and maintaining three-dimensional structures, and thus participate in various biological functions. Until recently, most protein NMR studies have focused on the non-exchangeable protons of amino acid residues. The exchangeable protons attached to polar groups, such as hydroxyl (OH), sulfhydryl (SH), and amino (NH2) groups, have mostly been ignored, because in many cases these hydrogen atoms exchange too quickly with water protons, making NMR observations impractical. However, in certain environments, such as deep within the hydrophobic interior of a protein, or in a strong hydrogen bond to other polar groups or interacting ligands, the protons attached to polar groups may exhibit slow hydrogen exchange rates and thus become NMR accessible. To explore the structural and biological implications of the interactions involving polar side-chains, we have developed versatile NMR methods to detect such cases by observing the line shapes of (13)C NMR signals near the polar groups, which are affected by deuterium-proton isotope shifts in a mixture of H2O and D2O. These methods allow the detection of polar side-chains with slow hydrogen-deuterium exchange rates, and therefore provide opportunities to retrieve information about the polar side-chains, which might otherwise be overlooked by conventional NMR experiments. Future prospects of applications using deuterium-proton isotope shifts to retrieve missing structural and dynamic information of proteins are discussed.

  20. Note: Charge transfer in a hydrated peptide group is determined mainly by its intrinsic hydrogen-bond energetics

    SciTech Connect

    Mirkin, Noemi G.; Krimm, Samuel

    2014-01-28

    Charge transfer in a hydrogen-bonded N-methylacetamide(H{sub 2}O){sub 3} system is obtained from ωB97X-D/6-31++G** and CHelpG atomic charge calculations of individual peptide-water interactions as well as that of the entire complex. In the latter, the electron transfer to water is 0.19 e, influenced primarily by the hydrogen bonds to the C=O group. The values of such charge transfer are paralleled by the corresponding intrinsic hydrogen-bond energies. These results support the desirability of incorporating charge transfer in molecular mechanics energy functions.

  1. Spectroscopic Evidence for Clusters of Like-Charged Ions in Ionic Liquids Stabilized by Cooperative Hydrogen Bonding.

    PubMed

    Knorr, Anne; Stange, Peter; Fumino, Koichi; Weinhold, Frank; Ludwig, Ralf

    2016-02-16

    Direct spectroscopic evidence for hydrogen-bonded clusters of like-charged ions is reported for ionic liquids. The measured infrared O-H vibrational bands of the hydroxyethyl groups in the cations can be assigned to the dispersion-corrected DFT calculated frequencies of linear and cyclic clusters. Compensating the like-charge Coulomb repulsion, these cationic clusters can range up to cyclic tetramers resembling molecular clusters of water and alcohols. These ionic clusters are mainly present at low temperature and show strong cooperative effects in hydrogen bonding. DFT-D3 calculations of the pure multiply charged clusters suggest that the attractive hydrogen bonds can compete with repulsive Coulomb forces.

  2. Crystal structure and hydrogen-bonding patterns in 5-fluoro­cytosinium picrate

    PubMed Central

    Mohana, Marimuthu; Thomas Muthiah, Packianathan; McMillen, Colin D.

    2017-01-01

    In the crystal structure of the title compound, 5-fluoro­cytosinium picrate, C4H5FN3O+·C6H2N3O7 −, one N heteroatom of the 5-fluoro­cytosine (5FC) ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11)° with the ring of the picrate (PA−) anion. In the crystal, the 5FC+ cation inter­acts with the PA− anion through three-centre N—H⋯O hydrogen bonds, forming two conjoined rings having R 2 1(6) and R 1 2(6) motifs, and is extended by N—H⋯O hydrogen bonds and C—H⋯O inter­actions into a two-dimensional sheet structure lying parallel to (001). Also present in the crystal structure are weak C—F⋯π inter­actions. PMID:28316809

  3. Hydrogen-bonding networks from first-principles: exploring the guanidine crystal.

    PubMed

    Hoepfner, Veronika; Deringer, Volker L; Dronskowski, Richard

    2012-05-10

    Hydrogen bonding is among the most important interactions in molecular crystals, and examples are abundant. As a consequence of such interactions, many molecules crystallize in complex but intriguing structures, in contrast to the relatively simple packing principles of metallic or ionic solids. In this work, we present a computational approach based on plane-wave density-functional theory (DFT) and supercell techniques, aiming to understand and quantify hydrogen-bonded networks in the solid state and in two-, one-, and zero-dimensional fragments derived from the molecular crystal. With such methodology at hand, we investigate guanidine, a fitting example of a molecular crystal and an important compound for inorganic and organic chemistry alike. On the basis of our computations, we discuss the initially proposed layered structure of guanidine and identify both stabilizing and destabilizing cooperative interactions in the three crystalline dimensions.

  4. Biasing hydrogen bond donating host systems towards chemical warfare agent recognition.

    PubMed

    Hiscock, Jennifer R; Wells, Neil J; Ede, Jayne A; Gale, Philip A; Sambrook, Mark R

    2016-10-12

    A series of neutral ditopic and negatively charged, monotopic host molecules have been evaluated for their ability to bind chloride and dihydrogen phosphate anions, and neutral organophosphorus species dimethyl methylphosphonate (DMMP), pinacolyl methylphosphonate (PMP) and the chemical warfare agent (CWA) pinacolyl methylphosphonofluoridate (GD, soman) in organic solvent via hydrogen bonding. Urea, thiourea and boronic acid groups are shown to bind anions and neutral guests through the formation of hydrogen bonds, with the urea and thiourea groups typically exhibiting higher affinity interactions. The introduction of a negative charge on the host structure is shown to decrease anion affinity, whilst still allowing for high stability host-GD complex formation. Importantly, the affinity of the host for the neutral CWA GD is greater than for anionic guests, thus demonstrating the potential for selectivity reversal based on charge repulsion.

  5. Slow dielectric response of Debye-type in water and other hydrogen bonded liquids

    NASA Astrophysics Data System (ADS)

    Jansson, Helén; Bergman, Rikard; Swenson, Jan

    2010-05-01

    The slow dynamics of some hydrogen bonded glass-forming liquids has been investigated by broadband dielectric spectroscopy. We show that the polyalcohols glycerol, xylitol, and sorbitol, and mixtures of glycerol and water, and in fact, even pure water exhibit a process of Debye character at longer time-scales than the glass transition and viscosity related α-relaxation. Even if it is less pronounced, this process displays many similarities to the well-studied Debye-like process in monoalcohols. It can be observed in both the negative derivative of the real part of the permittivity or in the imaginary part of the permittivity, if the conductivity contribution is reduced. In the present study the conductivity contribution has been suppressed by use of a thin Teflon film placed between the sample and one of the electrodes. The new findings might have important implications for the structure and dynamics of hydrogen bonded liquids in general, and for water in particular.

  6. DNA terminal base pairs have weaker hydrogen bonds especially for AT under low salt concentration

    NASA Astrophysics Data System (ADS)

    Ferreira, Izabela; Amarante, Tauanne D.; Weber, Gerald

    2015-11-01

    DNA base pairs are known to open more easily at the helix terminal, a process usually called end fraying, the details of which are still poorly understood. Here, we present a mesoscopic model calculation based on available experimental data where we consider separately the terminal base pairs of a DNA duplex. Our results show an important reduction of hydrogen bond strength for terminal cytosine-guanine (CG) base pairs which is uniform over the whole range of salt concentrations, while for AT base pairs, we obtain a nearly 1/3 reduction but only at low salt concentrations. At higher salt concentrations, terminal adenine-thymine (AT) pair has almost the same hydrogen bond strength than interior bases. The calculated terminal stacking interaction parameters display some peculiarly contrasting behavior. While there is mostly no perceptible difference to internal stacking, for some cases, we observe an unusually strong dependence with salt concentration which does not appear follow any pattern or trend.

  7. Impact of hydrogen bonding on dynamics of hydroxyl-terminated polydimethylsiloxane

    SciTech Connect

    Xing, Kunyue; Chatterjee, Sabornie; Saito, Tomonori; Gainaru, Catalin P.; Sokolov, Alexei P.

    2016-04-06

    Dielectric spectroscopy, rheology, and differential scanning calorimetry were employed to study the effect of chain-end hydrogen bonding on the dynamics of hydroxylterminated polydimethylsiloxane. We demonstrate that hydrogen bonding has a strong influence on both segmental and slower dynamics in the systems with low molecular weights. In particular, the decrease in the chain length leads to an increase of the glass transition temperature, viscosity, and fragility index, at variance with the usual behavior of nonassociating polymers. The supramolecular association of hydroxylterminated chains leads to the emergence in dielectric and mechanical relaxation spectra of the so-called Debye process traditionally observed in monohydroxy alcohols. Our analysis suggests that the hydroxyl-terminated PDMS oligomers may associate in brush-like or chain-like structures, depending on the size of their covalent chains. Finally, the effective length of the linear-associated chains was estimated from the rheological measurements.

  8. Impact of hydrogen bonding on dynamics of hydroxyl-terminated polydimethylsiloxane

    DOE PAGES

    Xing, Kunyue; Chatterjee, Sabornie; Saito, Tomonori; ...

    2016-04-06

    Dielectric spectroscopy, rheology, and differential scanning calorimetry were employed to study the effect of chain-end hydrogen bonding on the dynamics of hydroxylterminated polydimethylsiloxane. We demonstrate that hydrogen bonding has a strong influence on both segmental and slower dynamics in the systems with low molecular weights. In particular, the decrease in the chain length leads to an increase of the glass transition temperature, viscosity, and fragility index, at variance with the usual behavior of nonassociating polymers. The supramolecular association of hydroxylterminated chains leads to the emergence in dielectric and mechanical relaxation spectra of the so-called Debye process traditionally observed in monohydroxymore » alcohols. Our analysis suggests that the hydroxyl-terminated PDMS oligomers may associate in brush-like or chain-like structures, depending on the size of their covalent chains. Finally, the effective length of the linear-associated chains was estimated from the rheological measurements.« less

  9. Competing hydrogen bonding in methoxyphenols: The rotational spectrum of o-vanillin

    NASA Astrophysics Data System (ADS)

    Cocinero, Emilio J.; Lesarri, Alberto; Écija, Patricia; Basterretxea, Francisco; Fernández, José A.; Castaño, Fernando

    2011-05-01

    The conformational preferences of o-vanillin have been investigated in a supersonic jet expansion using Fourier transform microwave (FT-MW) spectroscopy. Three molecular conformations were derived from the rotational spectrum. The two most stable structures are characterized by a moderate O sbnd H···O dbnd C hydrogen bond between the aldehyde and the hydroxyl groups, with the methoxy side chain either in plane (global minimum a- cis-trans) or out of plane (a- cis-gauche) with respect to the aromatic ring. In the third conformer the aldehyde group is rotated by ca. 180°, forming a O sbnd H···O hydrogen bond between the methoxy and hydroxyl groups (s- trans-trans). Rotational parameters and relative populations are provided for the three conformations, which are compared with the results of ab initio (MP2) and density-functional (B3LYP, M05-2X) theoretical predictions.

  10. Ab initio Study of Structure and Hydrogen Bonding of Cellulose Crystals and Surfaces

    NASA Astrophysics Data System (ADS)

    Davenport, James; Li, Yan

    2011-03-01

    We have studied the equilibrium structure and hydrogen bonding of cellulose crystals and surfaces using semi-empirical dispersion corrections to density functional theory (DFT+D), which has been shown to be an efficient alternative to more advanced methods for weakly bound aromatic assemblies. The predicted crystal structures for both Iα and Iβ phases agree well with experiments. The cohesive energy was decomposed into interchain and intersheet interactions and analyzed in terms of hydrogen bonding and van der Waals dispersion forces. Both interactions were found to be responsible for holding cellulose sheets together. In particular, the dispersion corrections to DFT proved to be indispensable in reproducing the equilibrium intersheet distance and binding strength. Adsorption energy and configuration of water molecules on cellulose surfaces were found to depend sensitively on the surface orientation, adsorption site and contribution from vdW interactions. This work was funded by US Department of Energy under Contract No. DE-AC02-98CH10886.

  11. Ammonia as a case study for the spontaneous ionization of a simple hydrogen-bonded compound.

    PubMed

    Palasyuk, Taras; Troyan, Ivan; Eremets, Mikhail; Drozd, Vadym; Medvedev, Sergey; Zaleski-Ejgierd, Patryk; Magos-Palasyuk, Ewelina; Wang, Hongbo; Bonev, Stanimir A; Dudenko, Dmytro; Naumov, Pavel

    2014-03-24

    Modern ab initio calculations predict ionic and superionic states in highly compressed water and ammonia. The prediction apparently contradicts state-of-the-art experimentally established phase diagrams overwhelmingly dominated by molecular phases. Here we present experimental evidence that the threshold pressure of ~120 GPa induces in molecular ammonia the process of autoionization to yet experimentally unknown ionic compound--ammonium amide. Our supplementary theoretical simulations provide valuable insight into the mechanism of autoionization showing no hydrogen bond symmetrization along the transformation path, a remarkably small energy barrier between competing phases and the impact of structural rearrangement contribution on the overall conversion rate. This discovery is bridging theory and experiment thus opening new possibilities for studying molecular interactions in hydrogen-bonded systems. Experimental knowledge on this novel ionic phase of ammonia also provides strong motivation for reconsideration of the theory of molecular ice layers formation and dynamics in giant gas planets.

  12. Hydrogen Bonding and Binding of Polybasic Residues with Negatively Charged Mixed Lipid Monolayers

    SciTech Connect

    Lorenz, C.; Feraudo, J.; Travesset, A.

    2008-01-23

    Phosphoinositides, phosphorylated products of phosphatidylinositol, are a family of phospholipids present in tiny amounts (1% or less) in the cytosolic surface of cell membranes, yet they play an astonishingly rich regulatory role, particularly in signaling processes. In this letter, we use molecular dynamics simulations on a model system of mixed lipid monolayers to investigate the interaction of phosphatidylinositol 4,5-bisphosphate (PIP{sub 2}), the most common of the phosphoinositides, with a polybasic peptide consisting of 13 lysines. Our results show that the polybasic peptide sequesters three PIP{sub 2} molecules, forming a complex stabilized by the formation of multiple hydrogen bonds between PIP{sub 2} and the Lys residues. We also show that the polybasic peptide does not sequester other charged phospholipids such as phosphatidylserine because of the inability to form long-lived stable hydrogen bonds.

  13. The role of intramolecular hydrogen bonds in nucleophilic addition reactions of ketenaminals

    NASA Astrophysics Data System (ADS)

    Isaev, A. N.

    2012-08-01

    Quantum-chemical calculations of the geometries and electronic structures of molecules of ketenaminals 3-(diaminomethylene)-2,4-pentanedione and dimethyl-2-(diaminomethylene)-malonate and calculations of the structures of intermediates in the reaction of the nucleophilic addition of the ketenaminals to the acetonitrile molecule are performed by B3LYP/6-31+G** method. Two possible scenarios of the process are shown, depending on the mutual orientation of reacting molecules. The nucleophilic addition proceeds in two stages. It is found that the rate-limiting stage of the process is the transfer of the proton of the intramolecular hydrogen bond in a ketenaminal molecule. The experimentally observed faster reaction of pyrimidine formation for the 3-(diaminomethylene)-2,4-pentanedione molecule relative to that for dimethyl-2-(diaminomethylene)-malonate is explained by the hydrogen bond being stronger and the barrier of proton transfer from the aminogroup to the ketogroup oxygen falling upon nucleophilic attack in the former molecule.

  14. A diabatic state model for double proton transfer in hydrogen bonded complexes.

    PubMed

    McKenzie, Ross H

    2014-09-14

    Four diabatic states are used to construct a simple model for double proton transfer in hydrogen bonded complexes. Key parameters in the model are the proton donor-acceptor separation R and the ratio, D1/D2, between the proton affinity of a donor with one and two protons. Depending on the values of these two parameters the model describes four qualitatively different ground state potential energy surfaces, having zero, one, two, or four saddle points. Only for the latter are there four stable tautomers. In the limit D2 = D1 the model reduces to two decoupled hydrogen bonds. As R decreases a transition can occur from a synchronous concerted to an asynchronous concerted to a sequential mechanism for double proton transfer.

  15. The IINS, IR and DFT studies of hydrogen bonds in 6-Furfuryl and 6-Benzylaminopurines

    NASA Astrophysics Data System (ADS)

    Holderna-Natkaniec, Krystyna; Natkaniec, Ireneusz; Kasperkowiak, Weronika; Sciesinska, Elzbieta; Sciesinski, Jacek; Mikuli, Edward

    2006-06-01

    FTIR and IINS spectra of 6-Furfurylaminopurine (6-FAP) and 6-Benzylaminopurine (6-BAP) taken at different temperatures have been analysed and compared with the spectra calculated by the ab initio DFT/B3LYP method and the semiempirical PM3 method in the isolated molecule approximation, for the tautomers N3-H, N7-H and N9-H, and dimers with hydrogen bonds. For 6-FAP the best agreement between the calculated and experimental (at 20 K) spectra has been found for the N9-H tautomer, whose structure was established by X-ray diffraction. For 6-BAP the analogous agreement for the N9-H tautomer structure has been poor and much better for the N7-H tautomer. The vibrational spectra calculated for dimers of the molecules studied involved in hydrogen bonds, permitted also an interpretation of the bands whose positions and FWHM in the FTIR spectra changed with temperature.

  16. Hydrogen-Bonded Organic Frameworks (HOFs): A New Class of Porous Crystalline Proton-Conducting Materials.

    PubMed

    Karmakar, Avishek; Illathvalappil, Rajith; Anothumakkool, Bihag; Sen, Arunabha; Samanta, Partha; Desai, Aamod V; Kurungot, Sreekumar; Ghosh, Sujit K

    2016-08-26

    Two porous hydrogen-bonded organic frameworks (HOFs) based on arene sulfonates and guanidinium ions are reported. As a result of the presence of ionic backbones appended with protonic source, the compounds exhibit ultra-high proton conduction values (σ) 0.75× 10(-2)  S cm(-1) and 1.8×10(-2)  S cm(-1) under humidified conditions. Also, they have very low activation energy values and the highest proton conductivity at ambient conditions (low humidity and at moderate temperature) among porous crystalline materials, such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs). These values are not only comparable to the conventionally used proton exchange membranes, such as Nafion used in fuel cell technologies, but is also the highest value reported in organic-based porous architectures. Notably, this report inaugurates the usage of crystalline hydrogen-bonded porous organic frameworks as solid-state proton conducting materials.

  17. The potential role of hydrogen bonding in aprotic and protic ionic liquids.

    PubMed

    Fumino, Koichi; Wulf, Alexander; Ludwig, Ralf

    2009-10-21

    Cohesion energies determine the phase behavior of materials. The understanding of interaction energies is in particular interesting for ionic liquids. Here we show experimentally that, in accord with theoretical work, the intermolecular cation-anion interactions in ionic liquids can be detected by far FTIR spectroscopy. The measured vibrational bands of aprotic and protic ionic liquids in the low-frequency range can be referred to the interaction strength between cations and anions in various combinations. It can be shown by DFT B3LYP calculations that these interactions are described by characteristic ratios between Coulomb forces and hydrogen bonds. These ratios can be tuned towards increasing hydrogen bond contributions which is reflected in important macroscopic properties of ionic liquids such as enthalpies of vaporization and viscosities. This opens a new path for tuning the desired properties of this new class of material.

  18. Fast Interconversion of Hydrogen Bonding at the Hematite (001)–Liquid Water Interface

    SciTech Connect

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

    2016-04-07

    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.

  19. Hydrogen Dissociation in Generalized Hartree-Fock Theory: Breaking the diatomic bond

    NASA Astrophysics Data System (ADS)

    Jerke, Jonathan; Masood, Samina; Tymczak, Cj

    Generalized Hartree Fock theory predicts molecular Hydrogen dissociation without correlation. A variational Gaussian-Sinc linear superposition is the basis of 50 calculations with 3-4 significant digits of quality. The spin singlet covalent bond spontaneously breaks into a pair of uncorrelated doublets at atomic separation of 1.22 Angstroms. Quantum spin numbers and energetic comparison with Configuration Interaction theory--correlation--point to a first order phase transition in the molecular Hydrogen bond without correlation. Welch Foundation (Grant J-1675), the ARO (Grant W911Nf-13-1-0162), the Texas Southern University High Performance Computing Center (http:/hpcc.tsu.edu/; Grant PHY-1126251) and NSF-CREST CRCN project (Grant HRD-1137732).

  20. Highly enantioselective Michael addition of nitroalkanes to chalcones using chiral squaramides as hydrogen bonding organocatalysts.

    PubMed

    Yang, Wen; Du, Da-Ming

    2010-12-03

    A series of squaramide-based organocatalysts were facilely synthesized and applied as hydrogen bonding organocatalysts in the enantioselective Michael addition of nitroalkanes to chalcones. These organocatalysts promoted the Michael addition with low catalyst loading under high temperature (80 °C), affording the desired R or S enantiomers of the products flexibly in high yields with excellent enantioselectivities (93-96% ee) by the appropriate choice of organocatalysts.

  1. Chiral Hydrogen Bond Environment Providing Unidirectional Rotation in Photoactive Molecular Motors.

    PubMed

    García-Iriepa, Cristina; Marazzi, Marco; Zapata, Felipe; Valentini, Alessio; Sampedro, Diego; Frutos, Luis Manuel

    2013-05-02

    Generation of a chiral hydrogen bond environment in efficient molecular photoswitches is proposed as a novel strategy for the design of photoactive molecular motors. Here, the following strategy is used to design a retinal-based motor presenting singular properties: (i) a single excitation wavelength is needed to complete the unidirectional rotation process (360°); (ii) the absence of any thermal step permits the process to take place at low temperatures; and (iii) the ultrafast process permits high rotational frequencies.

  2. Effect of lipid structural modifications on their intermolecular hydrogen bonding interactions and membrane functions.

    PubMed

    Boggs, J M

    1986-01-01

    The large number of different membrane lipids with various structural modifications and properties and the characteristic lipid composition of different types of membranes suggest that different lipids have specific functions in the membrane. Many of the varying properties of lipids with different polar head groups and in different ionization states can be attributed to the presence of interactive or repulsive forces between the head groups in the bilayer. The interactive forces are hydrogen bonds between hydrogen bond donating groups such as --P--OH,--OH, and--NH3+ and hydrogen bond accepting groups such as --P--O- and --COO-. These interactions increase the lipid phase transition temperature and can account for the tendency of certain lipids to go into the hexagonal phase and the dependence of this tendency on the pH and ionization state of the lipid. The presence or absence of these interactions can also affect the penetration of hydrophobic substances into the bilayer, including hydrophobic residues of membrane proteins. Evidence for this suggestion has been gathered from studies of the myelin basic protein, a water-soluble protein with a number of hydrophobic residues. In this way the lipid composition can affect the conformation and activity of membrane proteins. Since hydrogen-bonding interactions depend on the ionization state of the lipid, they can be altered by changes in the environment which affect the pK of the ionizable groups. The formation of the hexagonal phase or inverted micelles, the conformation and activity of membrane proteins, and other functions mediated by lipids could thus be regulated in this way.

  3. 35Cl NQR study of geometric isotope effect in hydrogen bonded chlorooctanes

    NASA Astrophysics Data System (ADS)

    Zdanowska-Fraçzek, M.

    1994-05-01

    35Cl NQR spectroscopy was applied to study the geometric isotope effect in a wide range of 2 : 1 salts of chloroacetic, trichloroacetic and difluorochloroacetic acids. The NQR results were correlated with IR spectroscopic studies, which provided information on the potential shape for proton motion. The NQR results were discussed on the basis of a variational correlated ground state wave function theory of a single hydrogen bond.

  4. Hydrogen-bond-assisted "gold cold fusion" for fabrication of 2D web structures.

    PubMed

    Mandal, Saikat; Shundo, Atsuomi; Acharya, Somobrata; Hill, Jonathan P; Ji, Qingmin; Ariga, Katsuhiko

    2009-07-06

    Keeping their cool: Fabrication of a 2D weblike nanonetwork of gold was successfully demonstrated through a two-step procedure including complexation of gold precursors to a weblike supramolecular assembly of surfactant followed by in situ reduction of the precursors to gold. Molecular assemblies stabilized by hydrogen bonding provided a sound template, leading to the highly integrated structure of gold through room-temperature (cold) nanostructure fusion.

  5. Highly fluorescent rigid supramolecular polymeric nanowires constructed through multiple hydrogen bonds.

    PubMed

    Luo, Jia; Lei, Ting; Wang, Lei; Ma, Yuguo; Cao, Yong; Wang, Jian; Pei, Jian

    2009-02-18

    Supramolecular polymeric nanowires 1(n) constructed by a 3D shape-persistent hexaacid 1 through multiple hydrogen bonding interactions was developed. Single molecular nanoires were also obtained from its highly dilute solution.Hexaacid 1 containing pi-conjugated chromophores successfully self-assembled to afford these nanofibers with high solid quantum efficiency (22%), which provides us a pathway to fabricate optoelectronic devices using these highly fluorescent nanofibers.

  6. Total synthesis of virgatolide B via exploitation of intramolecular hydrogen bonding.

    PubMed

    Hume, Paul A; Furkert, Daniel P; Brimble, Margaret A

    2014-06-06

    A full account of the enantioselective total synthesis of virgatolide B is reported. Key features of the synthesis include an sp(3)-sp(2) Suzuki-Miyaura cross-coupling of a β-trifluoroboratoamide with an aryl bromide, regioselective intramolecular carboalkoxylation, and a 1,3-anti-selective Mukaiyama aldol reaction. Intramolecular hydrogen bonding governed the regioselectivity of the key spiroketalization step, affording the natural product as a single regioisomer.

  7. Effect of hydrogen bonding on the vibrational dephasing time in glycerol

    NASA Technical Reports Server (NTRS)

    Dorsinville, R.; Franklin, W. M.; Ockman, N.; Alfano, R. R.

    1982-01-01

    The vibrational dephasing of the methyl CH2 symmetric stretch mode in glycerol was directly measured over an extended temperature range using picosecond coherent Raman pump and probe spectroscopy. The dephasing time was found to increase dramatically as the temperature of the supercooled liquid was lowered. This observation is attributed to the increased hydrogen bonding with decreasing temperature which hinders the dephasing of the CH2 vibration by reducing molecular motions.

  8. The Proximal Hydrogen Bond Network Modulates Bacillus subtilis Nitric-oxide Synthase Electronic and Structural Properties

    PubMed Central

    Brunel, Albane; Wilson, Adjélé; Henry, Laura; Dorlet, Pierre; Santolini, Jérôme

    2011-01-01

    Bacterial nitric-oxide synthase (NOS)-like proteins are believed to be genuine NOSs. As for cytochromes P450 (CYPs), NOS-proximal ligand is a thiolate that exerts a push effect crucial for the process of dioxygen activation. Unlike CYPs, this catalytic electron donation seems controlled by a hydrogen bond (H-bond) interaction between the thiolate ligand and a vicinal tryptophan. Variations of the strength of this H-bond could provide a direct way to tune the stability along with the electronic and structural properties of NOS. We generated five different mutations of bsNOS Trp66, which can modulate this proximal H-bond. We investigated the effects of these mutations on different NOS complexes (FeIII, FeIICO, and FeIINO), using a combination of UV-visible absorption, EPR, FTIR, and resonance Raman spectroscopies. Our results indicate that (i) the proximal H-bond modulation can selectively decrease or increase the electron donating properties of the proximal thiolate, (ii) this modulation controls the σ-competition between distal and proximal ligands, (iii) this H-bond controls the stability of various NOS intermediates, and (iv) a fine tuning of the electron donation by the proximal ligand is required to allow at the same time oxygen activation and to prevent uncoupling reactions. PMID:21310962

  9. The proximal hydrogen bond network modulates Bacillus subtilis nitric-oxide synthase electronic and structural properties.

    PubMed

    Brunel, Albane; Wilson, Adjélé; Henry, Laura; Dorlet, Pierre; Santolini, Jérôme

    2011-04-08

    Bacterial nitric-oxide synthase (NOS)-like proteins are believed to be genuine NOSs. As for cytochromes P450 (CYPs), NOS-proximal ligand is a thiolate that exerts a push effect crucial for the process of dioxygen activation. Unlike CYPs, this catalytic electron donation seems controlled by a hydrogen bond (H-bond) interaction between the thiolate ligand and a vicinal tryptophan. Variations of the strength of this H-bond could provide a direct way to tune the stability along with the electronic and structural properties of NOS. We generated five different mutations of bsNOS Trp66, which can modulate this proximal H-bond. We investigated the effects of these mutations on different NOS complexes (FeIII, FeIICO, and FeIINO), using a combination of UV-visible absorption, EPR, FTIR, and resonance Raman spectroscopies. Our results indicate that (i) the proximal H-bond modulation can selectively decrease or increase the electron donating properties of the proximal thiolate, (ii) this modulation controls the σ-competition between distal and proximal ligands, (iii) this H-bond controls the stability of various NOS intermediates, and (iv) a fine tuning of the electron donation by the proximal ligand is required to allow at the same time oxygen activation and to prevent uncoupling reactions.

  10. Enhancement in Organic Photovoltaic Efficiency through the Synergistic Interplay of Molecular Donor Hydrogen Bonding and -Stacking

    SciTech Connect

    Shewmon, Nathan; Watkins, Davita; Galindo, Johan; Zerdan, Raghida; Chen, Jihua; Keum, Jong Kahk; Roitberg, Adrian; Xue, Jiangeng; Castellano, Ronald

    2015-07-20

    For organic photovoltaic (OPV) cells based on the bulk heterojunction (BHJ) structure, it remains challenging to rationally control the degree of phase separation and percolation within blends of donors and acceptors to secure optimal charge separation and transport. Reported is a bottom-up, supramolecular approach to BHJ OPVs wherein tailored hydrogen bonding (H-bonding) interactions between π-conjugated electron donor molecules encourage formation of vertically aligned donor π-stacks while simultaneously suppressing lateral aggregation; the programmed arrangement facilitates fine mixing with fullerene acceptors and efficient charge transport. The approach is illustrated using conventional linear or branched quaterthiophene donor chromophores outfitted with terminal functional groups that are either capable or incapable of self-complementary H-bonding. When applied to OPVs, the H-bond capable donors yield a twofold enhancement in power conversion efficiency relative to the comparator systems, with a maximum externa