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Sample records for additional hydrogen bond

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

    PubMed Central

    Klare, Helge; Neudörfl, Jörg M

    2014-01-01

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

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

    PubMed

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

    2016-05-01

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

  3. Hydrogen bonding in ionic liquids.

    PubMed

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

    2015-03-01

    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

  4. 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.

  5. Photoinduced hydrogen-bonding dynamics.

    PubMed

    Chu, Tian-Shu; Xu, Jinmei

    2016-09-01

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

  6. 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.

  7. 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.

  8. 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.

  9. "Additive" cooperativity of hydrogen bonds in complexes of catechol with proton acceptors in the gas phase: FTIR spectroscopy and quantum chemical calculations.

    PubMed

    Varfolomeev, Mikhail A; Klimovitskii, Alexander E; Abaidullina, Dilyara I; Madzhidov, Timur I; Solomonov, Boris N

    2012-06-01

    Experimental study of hydrogen bond cooperativity in hetero-complexes in the gas phase was carried out by IR-spectroscopy method. Stretching vibration frequencies of O-H groups in phenol and catechol molecules as well as of their complexes with nitriles and ethers were determined in the gas phase using a specially designed cell. O-H groups experimental frequency shifts in the complexes of catechol induced by the formation of intermolecular hydrogen bonds are significantly higher than in the complexes of phenol due to the hydrogen bond cooperativity. It was shown that the cooperativity factors of hydrogen bonds in the complexes of catechol with nitriles and ethers in the gas phase are approximately the same. Quantum chemical calculations of the studied systems have been performed using density functional theory (DFT) methods. It was shown, that theoretically obtained cooperativity factors of hydrogen bonds in the complexes of catechol with proton acceptors are in good agreement with experimental values. Cooperative effects lead to a strengthening of intermolecular hydrogen bonds in the complexes of catechol on about 30%, despite the significant difference in the proton acceptor ability of the bases. The analysis within quantum theory of atoms in molecules was carried out for the explanation of this fact.

  10. Facile and Promising Method for Michael Addition of Indole and Pyrrole to Electron-Deficient trans-β-Nitroolefins Catalyzed by a Hydrogen Bond Donor Catalyst Feist's Acid and Preliminary Study of Antimicrobial Activity

    PubMed Central

    Al Majid, Abdullah M. A.; Islam, Mohammad Shahidul; Barakat, Assem; Al-Agamy, Mohamed H. M.; Naushad, Mu.

    2014-01-01

    The importance of cooperative hydrogen-bonding effects has been demonstrated using novel 3-methylenecyclopropane-1,2-dicarboxylic acid (Feist's acid (FA)) as hydrogen bond donor catalysts for the addition of indole and pyrrole to trans-β-nitrostyrene derivatives. Because of the hydrogen bond donor (HBD) ability, Feist's acid (FA) has been introduced as a new class of hydrogen bond donor catalysts for the activation of nitroolefin towards nucleophilic substitution reaction. It has effectively catalyzed the Michael addition of indoles and pyrrole to β-nitroolefins under optimum reaction condition to furnish the corresponding Michael adducts in good to excellent yields (up to 98%). The method is general, atom-economical, convenient, and eco-friendly and could provide excellent yields and regioselectivities. Some newly synthesized compounds were for examined in vitro antimicrobial activity and their preliminary results are reported. PMID:24574906

  11. Hydrogen bonding in peptide secondary structures

    NASA Astrophysics Data System (ADS)

    Varga, Zoltán; Kovács, Attila

    Hydrogen bonding interactions in various peptide secondary structures (β-sheet, 27-ribbon, 310-helix, α-helix, π-helix, β-turn II, and γ-turn) have been investigated in small oligopeptides by quantum chemical calculations at the B3LYP/6-31G** level. Besides the primary O...HN interactions, the optimized structures revealed the importance of N...HN hydrogen bonding in several structures. The effect of substitution on the energy and structural properties was investigated comparing the properties of glycine, alanine, valine, and serine. The aliphatic substituents generally weaken the hydrogen bonds, the strongest effects being observed in crowded valine conformers. Additional hydrogen bonding interactions introduced by the OH group of serine can both strengthen (by polarizing the amide moiety through N...H interaction) and weaken (constraining the CO oxygen by O...HO interaction) the backbone hydrogen bonds. The effect of water as a polarizable medium on the energy properties was assessed by the COSMO model.

  12. Extended hydrogen-bonded structures of phosphatidylethanolamine.

    PubMed

    Sen, A; Yang, P W; Mantsch, H H; Hui, S W

    1988-06-01

    The structure of phosphatidylethanolamine in pure dry hexane was studied. Viscosity measurements show that the hexane solution of PE has a very high viscosity, while freeze fracture electron microscopy revealed extensive fibre-like structures. These extended structures are disrupted by the addition of small amounts of water or organic solvents which are capable of hydrogen-bonding. The Fourier transform infrared spectra of the lipid solutions in dry and hydrated hexane show considerable differences in the phosphate and ethanolamine absorption bands, and demonstrate that the viscous fibre-like structures formed by phosphatidylethanolamine in dry hexane consist of extended intermolecular hydrogen-bonds, similar to those found in the solid lipid, with the ammonium group as the hydrogen-donor and the phosphate group as the hydrogen-acceptor. The high viscosity is not observed in hexane solution of phosphatidylcholine.

  13. Hydrogen bond and halogen bond inside the carbon nanotube

    NASA Astrophysics Data System (ADS)

    Wang, Weizhou; Wang, Donglai; Zhang, Yu; Ji, Baoming; Tian, Anmin

    2011-02-01

    The hydrogen bond and halogen bond inside the open-ended single-walled carbon nanotubes have been investigated theoretically employing the newly developed density functional M06 with the suitable basis set and the natural bond orbital analysis. Comparing with the hydrogen or halogen bond in the gas phase, we find that the strength of the hydrogen or halogen bond inside the carbon nanotube will become weaker if there is a larger intramolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom donor to the antibonding orbital of the X-H or X-Hal bond involved in the formation of the hydrogen or halogen bond and will become stronger if there is a larger intermolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom acceptor to the antibonding orbital of the X-H or X-Hal bond. According to the analysis of the molecular electrostatic potential of the carbon nanotube, the driving force for the electron-density transfer is found to be the negative electric field formed in the carbon nanotube inner phase. Our results also show that the X-H bond involved in the formation of the hydrogen bond and the X-Hal bond involved in the formation of the halogen bond are all elongated when encapsulating the hydrogen bond and halogen bond within the carbon nanotube, so the carbon nanotube confinement may change the blue-shifting hydrogen bond and the blue-shifting halogen bond into the red-shifting hydrogen bond and the red-shifting halogen bond. The possibility to replace the all electron nanotube-confined calculation by the simple polarizable continuum model is also evaluated.

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

    PubMed

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

    2016-03-18

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

  15. Redox-controlled hydrogen bonding: turning a superbase into a strong hydrogen-bond donor.

    PubMed

    Wild, Ute; Neuhäuser, Christiane; Wiesner, Sven; Kaifer, Elisabeth; Wadepohl, Hubert; Himmel, Hans-Jörg

    2014-05-12

    Herein the synthesis, structures and properties of hydrogen-bonded aggregates involving redox-active guanidine superbases are reported. Reversible hydrogen bonding is switched on by oxidation of the hydrogen-donor unit, and leads to formation of aggregates in which the hydrogen-bond donor unit is sandwiched by two hydrogen-bond acceptor units. Further oxidation (of the acceptor units) leads again to deaggregation. Aggregate formation is associated with a distinct color change, and the electronic situation could be described as a frozen stage on the way to hydrogen transfer. A further increase in the basicity of the hydrogen-bond acceptor leads to deprotonation reactions.

  16. Water lubricates hydrogen-bonded molecular machines

    NASA Astrophysics Data System (ADS)

    Panman, Matthijs R.; Bakker, Bert H.; den Uyl, David; Kay, Euan R.; Leigh, David A.; Buma, Wybren Jan; Brouwer, Albert M.; Geenevasen, Jan A. J.; Woutersen, Sander

    2013-11-01

    The mechanical behaviour of molecular machines differs greatly from that of their macroscopic counterparts. This applies particularly when considering concepts such as friction and lubrication, which are key to optimizing the operation of macroscopic machinery. Here, using time-resolved vibrational spectroscopy and NMR-lineshape analysis, we show that for molecular machinery consisting of hydrogen-bonded components the relative motion of the components is accelerated strongly by adding small amounts of water. The translation of a macrocycle along a thread and the rotation of a molecular wheel around an axle both accelerate significantly on the addition of water, whereas other protic liquids have much weaker or opposite effects. We tentatively assign the superior accelerating effect of water to its ability to form a three-dimensional hydrogen-bond network between the moving parts of the molecular machine. These results may indicate a more general phenomenon that helps explain the function of water as the ‘lubricant of life’.

  17. Water lubricates hydrogen-bonded molecular machines.

    PubMed

    Panman, Matthijs R; Bakker, Bert H; den Uyl, David; Kay, Euan R; Leigh, David A; Buma, Wybren Jan; Brouwer, Albert M; Geenevasen, Jan A J; Woutersen, Sander

    2013-11-01

    The mechanical behaviour of molecular machines differs greatly from that of their macroscopic counterparts. This applies particularly when considering concepts such as friction and lubrication, which are key to optimizing the operation of macroscopic machinery. Here, using time-resolved vibrational spectroscopy and NMR-lineshape analysis, we show that for molecular machinery consisting of hydrogen-bonded components the relative motion of the components is accelerated strongly by adding small amounts of water. The translation of a macrocycle along a thread and the rotation of a molecular wheel around an axle both accelerate significantly on the addition of water, whereas other protic liquids have much weaker or opposite effects. We tentatively assign the superior accelerating effect of water to its ability to form a three-dimensional hydrogen-bond network between the moving parts of the molecular machine. These results may indicate a more general phenomenon that helps explain the function of water as the 'lubricant of life'.

  18. 30 CFR 256.53 - Additional bonds.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 2 2010-07-01 2010-07-01 false Additional bonds. 256.53 Section 256.53 Mineral Resources MINERALS MANAGEMENT SERVICE, DEPARTMENT OF THE INTERIOR OFFSHORE LEASING OF SULPHUR OR OIL AND GAS IN THE OUTER CONTINENTAL SHELF Bonding § 256.53 Additional bonds. (a) This paragraph explains...

  19. Hydrogen-bonded polymer blends

    NASA Astrophysics Data System (ADS)

    Guigley, Kevin Scott

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

  20. 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...

  1. Hydrogen bond dynamics in bulk alcohols

    SciTech Connect

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

    2015-06-07

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

  2. Persistent hydrogen bonding in polymorphic crystal structures.

    PubMed

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

    2009-02-01

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

  3. 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.

  4. 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.

  5. Anharmonic Vibrational Spectra of Hydrogen Bonded Clusters

    NASA Astrophysics Data System (ADS)

    Xantheas, Sotiris S.

    2006-03-01

    We report anharmonic vibrational spectra for a variety of hydrogen bonded clusters such as (H2O)n and (HF)n, n=1-5. We investigate the convergence of the hydrogen bonded frequencies with basis set and level of electron correlation and compare with the available experimental data. For this purpose we employ the correlation-consistent basis sets up to quintuple zeta (5z) quality and compute the spectra at the second order Møller-Plesset (MP2) and Coupled Cluster plus Single and Double with perturbative estimate of Triple excitations [CCSD(T)]. The correlation between the calculated elongations in the hydrogen bonding stretches and the corresponding computed/observed vibrational frequencies suggest an extension of Badger's rule for these hydrogen bonded systems.

  6. 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

  7. Intramolecular Hydrogen Bonding in Substituted Aminoalcohols.

    PubMed

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

    2016-08-18

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

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

    PubMed

    Beck, John Frederick; Mo, Yirong

    2007-01-15

    Block-localized wave function (BLW) method, which is a variant of the ab initio valence bond (VB) theory, was employed to explore the nature of resonance-assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between pi delocalization and hydrogen-bonding interactions. We examined the dimers of formic acid, formamide, 4-pyrimidinone, 2-pyridinone, 2-hydroxpyridine, and 2-hydroxycyclopenta-2,4-dien-1-one. In addition, we studied the interactions in beta-diketone enols with a simplified model, namely the hydrogen bonds of 3-hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of pi resonance, were decomposed into the Hitler-London energy (DeltaEHL), polarization energy (DeltaEpol), charge transfer energy (DeltaECT), and electron correlation energy (DeltaEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of pi conjugation on hydrogen bonding interactions. Although it has been proposed that resonance-assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole-dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term "resonance-assisted binding (RAB)" instead of "resonance-assisted hydrogen bonding (RHAB)" to highlight the electrostatic, which is a long-range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs. PMID:17143867

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

    PubMed

    Bower, John F; Krische, Michael J

    2011-01-01

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

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

    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

  11. 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. PMID:20842396

  12. Hydrogen bonded network properties in liquid formamide.

    PubMed

    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 A) 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.

  13. 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.

  14. Bifunctional hydrogen bonds in monohydrated cycloether complexes.

    PubMed

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

    2010-03-01

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

  15. Bifunctional hydrogen bonds in monohydrated cycloether complexes.

    PubMed

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

    2010-03-01

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

  16. Comparison of supramolecular hydrogen bonded liquid crystals

    NASA Astrophysics Data System (ADS)

    Pongali Sathya Prabu, N.; Vijayakumar, V. N.; Madhu Mohan, M. L. N.

    2012-01-01

    Supramolecular hydrogen bonded liquid crystals are formed by methoxy hydroquinone (MHQ) and alkyloxy benzoic acids are isolated and characterised. MHQ formed double hydrogen bonds with p-n-alkyloxy benzoic acids. Fourier Transform-Infrared studies confirm the hydrogen bond formation in the complex. Polarising Optical Microscopic (POM) studies revealed the textural information, while the transition and enthalpy values are experimentally deduced from Differential Scanning Calorimetry (DSC) studies. Phase diagram has been constructed from the POM and DSC data, respectively. Experimental data of optical tilt angle in Smectic C phase have been fitted to a power law and it has been observed that the temperature variation of the tilt angle follows Mean Field theory prediction. Present homologous are compared with hydroquinone alkyloxy benzoic acids complexes and the influence of methyl group on the occurrence of phases and its transition temperatures are discussed.

  17. On the nature of blueshifting hydrogen bonds.

    PubMed

    Mo, Yirong; Wang, Changwei; Guan, Liangyu; Braïda, Benoît; Hiberty, Philippe C; Wu, Wei

    2014-07-01

    The block-localized wave function (BLW) method can derive the energetic, geometrical, and spectral changes with the deactivation of electron delocalization, and thus provide a unique way to elucidate the origin of improper, blueshifting hydrogen bonds versus proper, redshifting hydrogen bonds. A detailed analysis of the interactions of F(3)CH with NH(3) and OH(2) shows that blueshifting is a long-range phenomenon. Since among the various energy components contributing to hydrogen bonds, only the electrostatic interaction has long-range characteristics, we conclude that the contraction and blueshifting of a hydrogen bond is largely caused by electrostatic interactions. On the other hand, lengthening and redshifting is primarily due to the short-range n(Y)→σ*(X-H) hyperconjugation. The competition between these two opposing factors determines the final frequency change direction, for example, redshifting in F(3)CH⋅⋅⋅NH(3) and blueshifting in F(3)CH⋅⋅⋅OH(2). This mechanism works well in the series F(n)Cl(3)-n CH⋅⋅⋅Y (n=0-3, Y=NH(3), OH(2), SH(2)) and other systems. One exception is the complex of water and benzene. We observe the lengthening and redshifting of the O-H bond of water even with the electron transfer between benzene and water completely quenched. A distance-dependent analysis for this system reveals that the long-range electrostatic interaction is again responsible for the initial lengthening and redshifting.

  18. New supramolecular architectures using hydrogen bonding

    SciTech Connect

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

    1993-12-31

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

  19. 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.

  20. Recodable surfaces based on switchable hydrogen bonds.

    PubMed

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

    2016-07-01

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

  1. Modeling the Hydrogen Bond within Molecular Dynamics

    ERIC Educational Resources Information Center

    Lykos, Peter

    2004-01-01

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

  2. Hydrogen bonds in methane-water clusters.

    PubMed

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

    2016-08-24

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

  3. 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.

  4. Bond additivity corrections for quantum chemistry methods

    SciTech Connect

    C. F. Melius; M. D. Allendorf

    1999-04-01

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

  5. 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

  6. 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

  7. Tunneling spectroscopy measurements on hydrogen-bonded supramolecular polymers

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2011-10-28

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

  10. Formaldoxime hydrogen bonded complexes with ammonia and hydrogen chloride

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

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

    PubMed

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

    2015-02-01

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

  12. Dynamic heterogeneity in hydrogen-bonded polymers

    SciTech Connect

    Muresan, Adrian S.; Jeu, Wim H. de; Dubbeldam, Johan L. A.; Schoot, Paul van der; Kautz, Holger; Sijbesma, Rint P.; Monkenbusch, Michael

    2006-09-15

    We report on neutron spin echo experiments on hydrogen-bonded polymers and compare the experimentally found dynamical structure factor with theoretical predictions. Surprisingly, we find that in the melt phase the expected scaling of the Rouse dynamics is not satisfied. We propose an explanation based upon the large spatial volume occupied by the connecting groups. When the effects of these bulky groups on the local friction are taken into account, the usual scaling behavior is restored.

  13. 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.

  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. AAA-DDD triple hydrogen bond complexes.

    PubMed

    Blight, Barry A; Camara-Campos, Amaya; Djurdjevic, Smilja; Kaller, Martin; Leigh, David A; McMillan, Fiona M; McNab, Hamish; Slawin, Alexandra M Z

    2009-10-01

    Experiment and theory both suggest that the AAA-DDD pattern of hydrogen bond acceptors (A) and donors (D) is the arrangement of three contiguous hydrogen bonding centers that results in the strongest association between two species. Murray and Zimmerman prepared the first example of such a system (complex 3*2) and determined the lower limit of its association constant (K(a)) in CDCl(3) to be 10(5) M(-1) by (1)H NMR spectroscopy (Murray, T. J. and Zimmerman, S. C. J. Am. Chem. Soc. 1992, 114, 4010-4011). The first cationic AAA-DDD pair (3*4(+)) was described by Bell and Anslyn (Bell, D. A. and Anslyn, E. A. Tetrahedron 1995, 51, 7161-7172), with a K(a) > 5 x 10(5) M(-1) in CH(2)Cl(2) as determined by UV-vis spectroscopy. We were recently able to quantify the strength of a neutral AAA-DDD arrangement using a more chemically stable AAA-DDD system, 6*2, which has an association constant of 2 x 10(7) M(-1) in CH(2)Cl(2) (Djurdjevic, S., Leigh, D. A., McNab, H., Parsons, S., Teobaldi, G. and Zerbetto, F. J. Am. Chem. Soc. 2007, 129, 476-477). Here we report on further AA(A) and DDD partners, together with the first precise measurement of the association constant of a cationic AAA-DDD species. Complex 6*10(+)[B(3,5-(CF(3))(2)C(6)H(3))(4)(-)] has a K(a) = 3 x 10(10) M(-1) at RT in CH(2)Cl(2), by far the most strongly bound triple hydrogen bonded system measured to date. The X-ray crystal structure of 6*10(+) with a BPh(4)(-) counteranion shows a planar array of three short (NH...N distances 1.95-2.15 A), parallel (but staggered rather than strictly linear; N-H...N angles 165.4-168.8 degrees), primary hydrogen bonds. These are apparently reinforced, as theory predicts, by close electrostatic interactions (NH-*-N distances 2.78-3.29 A) between each proton and the acceptor atoms of the adjacent primary hydrogen bonds.

  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. Molecularly Tuning the Radicaloid N-H···O═C Hydrogen Bond.

    PubMed

    Lu, Norman; Chung, Wei-Cheng; Ley, Rebecca M; Lin, Kwan-Yu; Francisco, Joseph S; Negishi, Ei-Ichi

    2016-03-01

    Substituent effects on the open shell N-H···O═C hydrogen-bond has never been reported. This study examines how 12 functional groups composed of electron donating groups (EDG), halogen atoms and electron withdrawing groups (EWG) affect the N-H···O═C hydrogen-bond properties in a six-membered cyclic model system of O═C(Y)-CH═C(X)N-H. It is found that group effects on this open shell H-bonding system are significant and have predictive trends when X = H and Y is varied. When Y is an EDG, the N-H···O═C hydrogen-bond is strengthened; and when Y is an EWG, the bond is weakened; whereas the variation in electronic properties of X group do not exhibit a significant impact upon the hydrogen bond strength. The structural impact of the stronger N-H···O═C hydrogen-bond are (1) shorter H and O distance, r(H···O) and (2) a longer N-H bond length, r(NH). The stronger N-H···O═C hydrogen-bond also acts to pull the H and O in toward one another which has an effect on the bond angles. Our findings show that there is a linear relationship between hydrogen-bond angle and N-H···O═C hydrogen-bond energy in this unusual H-bonding system. In addition, there is a linear correlation of the r(H···O) and the hydrogen bond energy. A short r(H···O) distance corresponds to a large hydrogen bond energy when Y is varied. The observed trends and findings have been validated using three different methods (UB3LYP, M06-2X, and UMP2) with two different basis sets.

  18. Molecularly Tuning the Radicaloid N-H···O═C Hydrogen Bond.

    PubMed

    Lu, Norman; Chung, Wei-Cheng; Ley, Rebecca M; Lin, Kwan-Yu; Francisco, Joseph S; Negishi, Ei-Ichi

    2016-03-01

    Substituent effects on the open shell N-H···O═C hydrogen-bond has never been reported. This study examines how 12 functional groups composed of electron donating groups (EDG), halogen atoms and electron withdrawing groups (EWG) affect the N-H···O═C hydrogen-bond properties in a six-membered cyclic model system of O═C(Y)-CH═C(X)N-H. It is found that group effects on this open shell H-bonding system are significant and have predictive trends when X = H and Y is varied. When Y is an EDG, the N-H···O═C hydrogen-bond is strengthened; and when Y is an EWG, the bond is weakened; whereas the variation in electronic properties of X group do not exhibit a significant impact upon the hydrogen bond strength. The structural impact of the stronger N-H···O═C hydrogen-bond are (1) shorter H and O distance, r(H···O) and (2) a longer N-H bond length, r(NH). The stronger N-H···O═C hydrogen-bond also acts to pull the H and O in toward one another which has an effect on the bond angles. Our findings show that there is a linear relationship between hydrogen-bond angle and N-H···O═C hydrogen-bond energy in this unusual H-bonding system. In addition, there is a linear correlation of the r(H···O) and the hydrogen bond energy. A short r(H···O) distance corresponds to a large hydrogen bond energy when Y is varied. The observed trends and findings have been validated using three different methods (UB3LYP, M06-2X, and UMP2) with two different basis sets. PMID:26855203

  19. Hydrogen bonding at the aerosol interface

    SciTech Connect

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

    1995-01-12

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

  20. Negligible Isotopic Effect on Dissociation of Hydrogen Bonds.

    PubMed

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

    2016-03-31

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

  1. Hydrogen Bond Nanoscale Networks Showing Switchable Transport Performance

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

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

  2. Interpretation of Spectroscopic Markers of Hydrogen Bonds.

    PubMed

    Scheiner, Steve

    2016-07-18

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

  3. Pyranose sulfamates: conformation and hydrogen bonding

    NASA Astrophysics Data System (ADS)

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

    1999-01-01

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

  4. Vibrational spectroscopic properties of hydrogen bonded acetonitrile studied by DFT.

    PubMed

    Alía, Jose M; Edwards, Howell G M

    2005-09-01

    Vibrational properties (band position, Infrared and Raman intensities) of the acetonitrile C[triple bond]N stretching mode were studied in 27 gas-phase medium intensity (length range: = 1.71-2.05 angstroms; -deltaE range = 13-48 kJ/mol) hydrogen-bonded 1:1 complexes of CH3CN with organic and inorganic acids using density functional theory (DFT) calculations [B3LYP-6-31++G(2d,2p)]. Furthermore, general characteristics of the hydrogen bonds and vibrational changes in the OH stretching band of the acids were also considered. Experimentally observed blue-shifts of the C[triple bond]N stretching band promoted by the hydrogen bonding, which shortens the triple bond length, are very well reproduced and quantitatively depend on the hydrogen bond length. Both predicted enhancement of the infrared and Raman nu(C[triple bond]N) band intensities are in good agreement with the experimental results. Infrared band intensity increase is a direct function of the hydrogen bond energy. However, the predicted increase in the Raman band intensity increase is a more complex function, depending simultaneously on the characteristics of both the hydrogen bond (C[triple bond]N bond length) and the H-donating acid polarizability. Accounting for these two parameters, the calculated nu(C[triple bond]N) Raman intensities of the complexes are explained with a mean error of +/- 2.4%.

  5. 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

  6. Molecular orbital analysis of the hydrogen bonded water dimer.

    PubMed

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

    2016-02-24

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

  7. 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.

  8. Hydrogen bonds in concreto and in computro

    NASA Astrophysics Data System (ADS)

    Stouten, Pieter F. W.; Kroon, Jan

    1988-07-01

    Molecular dynamics simulations of liquid water and liquid methanol have been carried out. For both liquids an effective pair potential was used. The models were fitted to the heat of vaporization, pressure and various radial distribution functions resulting from diffraction experiments on liquids. In both simulations 216 molecules were put in a cubic periodical ☐. The system was loosely coupled to a temperature bath and to a pressure bath. Following an initial equilibration period relevant data were sampled during 15 ps. The distributions of oxygen—oxygen distances in hydrogen bonds obtained from the two simulations are essentially the same. The distribution obtained from crystal data is somewhat different: the maximum has about the same position, but the curve is much narrower, which can be expected merely from the fact that diffraction experiments only supply average atomic positions and hence average interatomic distances. When thermal motion is taken into account a closer likeness is observed.

  9. Hydrogen-Bonded Liquid Crystal Nanocomposites.

    PubMed

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

    2016-08-23

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

  10. 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.

  11. 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)

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

    PubMed Central

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

    2013-01-01

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

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

    SciTech Connect

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

    2006-10-23

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

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

    NASA Astrophysics Data System (ADS)

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

    1994-06-01

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

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

    PubMed

    Nose, Akira; Hojo, Masashi

    2006-10-01

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

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

    PubMed

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

    2010-04-01

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

  17. 30 CFR 556.53 - Additional bonds.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Resources BUREAU OF OCEAN ENERGY MANAGEMENT, DEPARTMENT OF THE INTERIOR OFFSHORE LEASING OF SULPHUR OR OIL... what bonds the lessee must provide before lease exploration activities commence. (1)(i) You must... of the lease by the earliest of: (A) The date you submit a proposed Exploration Plan (EP)...

  18. 30 CFR 556.53 - Additional bonds.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Resources BUREAU OF OCEAN ENERGY MANAGEMENT, DEPARTMENT OF THE INTERIOR OFFSHORE LEASING OF SULPHUR OR OIL... what bonds the lessee must provide before lease exploration activities commence. (1)(i) You must... of the lease by the earliest of: (A) The date you submit a proposed Exploration Plan (EP)...

  19. 30 CFR 556.53 - Additional bonds.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Resources BUREAU OF OCEAN ENERGY MANAGEMENT, DEPARTMENT OF THE INTERIOR OFFSHORE LEASING OF SULPHUR OR OIL... what bonds the lessee must provide before lease exploration activities commence. (1)(i) You must... of the lease by the earliest of: (A) The date you submit a proposed Exploration Plan (EP)...

  20. Molecular orbital analysis of the hydrogen bonded water dimer

    PubMed Central

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

    2016-01-01

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

  1. 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.

  2. 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.

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

    PubMed

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

    2016-05-01

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

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

    PubMed

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

    2016-05-01

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

  5. 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.

  6. 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.

  7. Structures, stability and hydrogen bonding in inositol conformers.

    PubMed

    Siddiqui, Nazia; Singh, Vijay; Deshmukh, Milind M; Gurunath, Ramanathan

    2015-07-28

    Various ab initio calculations using the density-functional (DFT), the second order Möller-Plesset perturbation (MP2) and self-consistent reaction field (SCRF) theories were performed on thirteen theoretically possible inositol stereoisomers. Gas phase calculations reveal that the myo- and neo-isomers of inositol (bearing one and two axial hydroxyl groups, respectively) are marginally more stable (by 0.5 kcal mol(-1)) than the all equatorially substituted scyllo-inositol. The calculations when done in different polar solvents show that the scyllo-inositol becomes the most stable inositol isomer, a fact attributed to weaker intramolecular hydrogen bonds. The individual hydrogen bond energy in all the isomers of inositol was also estimated using the molecular tailoring approach (MTA). The calculated hydrogen bond energies in these isomers are in excellent agreement with reported O-H···O hydrogen bond distances and ν(O-H) stretching frequencies. The estimated H-bond energy values suggest that the order of the intramolecular hydrogen bond strength follows: axial-axial > equatorial-axial > axial-equatorial > equatorial-equatorial hydrogen bonds. The intramolecular hydrogen bonds in the scyllo isomer are much weaker than those in other conformers, thus making this isomer more stable in polar solvents.

  8. 4-Oxocyclohexanecarboxylic acid: hydrogen bonding in the monohydrate of a delta-keto acid.

    PubMed

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

    2004-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  10. 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.

  11. Dynamics of Hydrogen-Bonded Supramolecular Polymers

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

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

  12. Functional group accessibility in hydrogen bonded polymer blends

    NASA Astrophysics Data System (ADS)

    Pehlert, George James

    Intramolecular screening and functional group accessibility are important concepts in hydrogen bonded polymer blends. Intramolecular screening results from the fact that the units in a polymer are linked together via covalent bonds (chain connectivity). This linking together of the units results in an increase in the number of same chain contacts (self-association) due to the chains bending back upon themselves, both locally and through long range effects. Because of this effect, the number of interchain contacts (interassociation) in a polymer blend is significantly lower than that observed in an analogous low molecular weight mixture. In addition to intramolecular screening, evidence has been found showing that the accessibility of functional groups is affected by factors such as the functional groups being too close to one another along the (co)polymer chain and steric shielding due to the presence of bulky or long chain side groups. The effect of these factors on the scaling and transferability of self-association and interassociation equilibrium constants is discussed, together with ramifications in terms of the predictions of miscibility windows and maps (using the association model) for hydrogen bonded polymer blends.

  13. Comparison of cationic, anionic and neutral hydrogen bonded dimers.

    PubMed

    Lee, Han Myoung; Kumar, Anupriya; Kołaski, Maciej; Kim, Dong Young; Lee, Eun Cheol; Min, Seung Kyu; Park, Mina; Choi, Young Cheol; Kim, Kwang S

    2010-06-21

    Short Strong Hydrogen Bonds (SSHBs) play an important role in many fields of physics, chemistry and biology. Since it is known that SSHBs exist in many biological systems, the role of hydrogen bonding motifs has been particularly interesting in enzyme catalysis, bio-metabolism, protein folding and proton transport phenomena. To explore the characteristic features of neutral, anionic and cationic hydrogen bonds, we have carried out theoretical studies of diverse homogeneous and heterogeneous hydrogen bonded dimers including water, peroxides, alcohols, ethers, aldehydes, ketones, carboxylic acids, anhydrides, and nitriles. Geometry optimization and harmonic frequency calculations are performed at the levels of Density Functional Theory (DFT) and Møller-Plesset second order perturbation (MP2) theory. First principles Car-Parrinello molecular dynamics (CPMD) simulations are performed to obtain IR spectra derived from velocity- and dipole-autocorrelation functions. We find that the hydrogen bond energy is roughly inversely proportional to the fourth power of the r(O/N-H) distance. Namely, the polarization of the proton accepting O/N atom by the proton-donating H atom reflects most of the binding energy in these diverse cation/anion/neutral hydrogen bonds. The present study gives deeper insight into the nature of hydrogen-bonded dimers including SSHBs. PMID:20405079

  14. Direct observation of intermolecular interactions mediated by hydrogen bonding

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  15. 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.

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

    PubMed

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

    2016-08-10

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

  17. 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.

  18. 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.

  19. An AAAA-DDDD quadruple hydrogen-bond array

    NASA Astrophysics Data System (ADS)

    Blight, Barry A.; Hunter, Christopher A.; Leigh, David A.; McNab, Hamish; Thomson, Patrick I. T.

    2011-03-01

    Secondary electrostatic interactions between adjacent hydrogen bonds can have a significant effect on the stability of a supramolecular complex. In theory, the binding strength should be maximized if all the hydrogen-bond donors (D) are on one component and all the hydrogen-bond acceptors (A) are on the other. Here, we describe a readily accessible AAAA-DDDD quadruple hydrogen-bonding array that exhibits exceptionally strong binding for a small-molecule hydrogen-bonded complex in a range of different solvents (Ka > 3 × 1012 M-1 in CH2Cl2, 1.5 × 106 M-1 in CH3CN and 3.4 × 105 M-1 in 10% v/v DMSO/CHCl3). The association constant in CH2Cl2 corresponds to a binding free energy (ΔG) in excess of -71 kJ mol-1 (more than 20% of the thermodynamic stability of a carbon-carbon covalent bond), which is remarkable for a supramolecular complex held together by just four intercomponent hydrogen bonds.

  20. An AAAA–DDDD quadruple hydrogen-bond array.

    PubMed

    Blight, Barry A; Hunter, Christopher A; Leigh, David A; McNab, Hamish; Thomson, Patrick I T

    2011-03-01

    Secondary electrostatic interactions between adjacent hydrogen bonds can have a significant effect on the stability of a supramolecular complex. In theory, the binding strength should be maximized if all the hydrogen-bond donors (D) are on one component and all the hydrogen-bond acceptors (A) are on the other. Here, we describe a readily accessible AAAA–DDDD quadruple hydrogen-bonding array that exhibits exceptionally strong binding for a small-molecule hydrogen-bonded complex in a range of different solvents (K(a) > 3 × 10(12) M(-1) in CH2Cl2, 1.5 × 10(6) M(-1) in CH3CN and 3.4 × 10(5) M(-1) in 10% v/v DMSO/CHCl3). The association constant in CH2Cl2 corresponds to a binding free energy (ΔG) in excess of –71 kJ mol(-1) (more than 20% of the thermodynamic stability of a carbon–carbon covalent bond), which is remarkable for a supramolecular complex held together by just four intercomponent hydrogen bonds.

  1. 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.

  2. Stereoelectronic requirements for optimal hydrogen-bond-catalyzed enolization.

    PubMed

    Pápai, Imre; Hamza, Andrea; Pihko, Petri M; Wierenga, Rik K

    2011-03-01

    Protein crystallographic analysis of the active sites of enolizing enzymes and structural analysis of hydrogen-bonded carbonyl compounds in small molecule crystal structures, complemented by quantum chemical calculations on related model enolization reactions, suggest a new stereoelectronic model that accounts for the observed out-of-plane orientation of hydrogen-bond donors (HBDs) in the oxyanion holes of enolizing enzymes. The computational results reveal that the lone-pair directionality of HBDs characteristic for hydrogen-bonded carbonyls is reduced upon enolization, and the enolate displays almost no directional preference for hydrogen bonding. Positioning the HBDs perpendicular to the carbonyl plane induces strain in the catalyst-substrate complex, which is released upon enolization, resulting in more favorable kinetics and thermodynamics than the in-plane arrangement of HBDs. PMID:21308811

  3. Hydrogen bonding in phenol, water, and phenol-water clusters.

    PubMed

    Parthasarathi, R; Subramanian, V; Sathyamurthy, N

    2005-02-10

    Structure, stability, and hydrogen-bonding interaction in phenol, water, and phenol-water clusters have been investigated using ab initio and density functional theoretical (DFT) methods and using various topological features of electron density. Calculated interaction energies at MP2/6-31G level for clusters with similar hydrogen-bonding pattern reveal that intermolecular interaction in phenol clusters is slightly stronger than in water clusters. However, fusion of phenol and water clusters leads to stability that is akin to that of H(2)O clusters. The presence of hydrogen bond critical points (HBCP) and the values of rho(r(c)) and nabla(2)rho(r(c)) at the HBCPs provide an insight into the nature of closed shell interaction in hydrogen-bonded clusters. It is shown that the calculated values of total rho(r(c)) and nabla(2)rho(r(c)) of all the clusters vary linearly with the interaction energy.

  4. Metal-hydrogen bridge bonding of hydrocarbons on metal surfaces

    PubMed Central

    Gavin, Robert M.; Reutt, Janice; Muetterties, Earl L.

    1981-01-01

    Molecular orbital studies implicate multicenter metal-hydrogen-carbon interactions as contributors to the bonding of chemisorbed hydrocarbons on clean metal surfaces. The most stable geometries appear to be those that achieve the maximum multicenter bonding to the coordinately unsaturated metal atoms in the vicinity of the anchoring metal-carbon interaction. Energy differences between possible surface sites are of the same magnitude as stabilization energies for three-center bonding of hydrogen atoms to the metal surface. Accordingly, secondary interactions of hydrogen with neighboring metal atoms may be significant determining factors in surface structures. The model predictions are compared with known structures and are used to propose a mechanism for hydrocarbon reactions on metal surfaces. These metal-hydrogen-carbon interactions are presumed to be intermediate points or states in C—H bond-breaking processes. PMID:16593041

  5. Is electrostatics sufficient to describe hydrogen-bonding interactions?

    PubMed

    Hoja, Johannes; Sax, Alexander F; Szalewicz, Krzysztof

    2014-02-17

    The stability and geometry of a hydrogen-bonded dimer is traditionally attributed mainly to the central moiety A-H⋅⋅⋅B, and is often discussed only in terms of electrostatic interactions. The influence of substituents and of interactions other than electrostatic ones on the stability and geometry of hydrogen-bonded complexes has seldom been addressed. An analysis of the interaction energy in the water dimer and several alcohol dimers--performed in the present work by using symmetry-adapted perturbation theory--shows that the size and shape of substituents strongly influence the stabilization of hydrogen-bonded complexes. The larger and bulkier the substituents are, the more important the attractive dispersion interaction is, which eventually becomes of the same magnitude as the total stabilization energy. Electrostatics alone are a poor predictor of the hydrogen-bond stability trends in the sequence of dimers investigated, and in fact, dispersion interactions predict these trends better. PMID:24453112

  6. Glycine hydrogen fluoride: Remarkable hydrogen bonding in the dimeric glycine glycinium cation

    NASA Astrophysics Data System (ADS)

    Fleck, M.; Ghazaryan, V. V.; Petrosyan, A. M.

    2010-12-01

    Crystals of glycine hydrogen fluoride (Gly·HF) were prepared from an aqueous solution containing stoichiometric quantities of the components. The crystal structure of Gly·HF was determined, IR and Raman spectra were registered and are discussed. Gly·HF crystallizes in the orthorhombic space group Pbca with Z = 32. The most remarkable feature of the structure is the existence of symmetric dimeric glycine-glycinium cations with short hydrogen bonds (O⋯O distance of 2.446 Å), charge-counterbalanced by hydrogen bifluoride (F sbnd H⋯F) - anions - in addition to the expected glycinium cations and fluoride anions. These results were compared with previously published data on crystals grown in the system glycine-HF-H 2O.

  7. Correlation effects in hydrogen-bonded polymer blends

    SciTech Connect

    Veytsman, B.; Painter, P. )

    1993-12-01

    In hydrogen-bonded polymer blends there are long range correlations that are a result of the combined covalent and hydrogen-bond connections. A mean field description of these mixtures is presented which indicates that there should be an infinite correlation length above some percolation threshold. There are various consequences of the compositional heterogeneities or clustering that results from these effects and these are discussed in this paper.

  8. 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.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    Arunan, Elangannan; Mani, Devendra

    2015-01-01

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

  11. Competition between hydrogen bonds and halogen bonds in complexes of formamidine and hypohalous acids.

    PubMed

    An, Xiulin; Zhuo, Hongying; Wang, Yingying; Li, Qingzhong

    2013-10-01

    Quantum chemical calculations have been per-formed for the complexes of formamidine (FA) and hypohalous acid (HOX, X = F, Cl, Br, I) to study their structures, properties, and competition of hydrogen bonds with halogen bonds. Two types of complexes are formed mainly through a hydrogen bond and a halogen bond, respectively, and the cyclic structure is more stable. For the F, Cl, and Br complexes, the hydrogen-bonded one is more stable than the halogen-bonded one, while the halogen-bonded structure is favorable for the I complexes. The associated H-O and X-O bonds are elongated and exhibit a red shift, whereas the distant ones are contracted and display a blue shift. The strength of hydrogen and halogen bonds is affected by F and Li substitutents and it was found that the latter tends to smooth differences in the strength of both types of interactions. The structures, properties, and interaction nature in these complexes have been understood with natural bond orbital (NBO) and atoms in molecules (AIM) theories.

  12. Triplet-Triplet Energy Transfer Study in Hydrogen Bonding Systems.

    PubMed

    Wang, Zhijia; Zhao, Jianzhang; Guo, Song

    2015-01-01

    The 2,6-diiodoBodipy-styrylBodipy hydrogen bonding system was prepared to study the effect of hydrogen bonding on the triplet-triplet-energy-transfer (TTET) process. 2,6-DiiodoBodipy linked with N-acetyl-2,6-diaminopyridine (D-2) was used as the triplet energy donor, and the styrylBodipy connected with thymine (A-1) was used as triplet energy acceptor, thus the TTET process was established upon photoexcitation. The photophysical processes of the hydrogen bonding system were studied with steady-state UV-vis absorption spectroscopy, fluorescence spectroscopy, fluorescence lifetime measurement and nanosecond time-resolved transient absorption spectroscopies. The TTET of the intramolecular/hydrogen bonding/intermolecular systems were compared through nanosecond transient absorption spectroscopy. The TTET process of the hydrogen bonding system is faster and more efficient (kTTET = 6.9 × 10(4) s(-1), ΦTTET = 94.0%) than intermolecular triplet energy transfer (kTTET = 6.0 × 10(4) s(-1), ΦTTET = 90.9%), but slower and less efficient than intramolecular triplet energy transfer (kTTET > 10(8) s(-1)). These results are valuable for designing self-assembly triplet photosensitizers and for the study of the TTET process of hydrogen bonding systems.

  13. A probabilistic approach to the effect of hydrogen bonding on the hydrophobic attraction.

    PubMed

    Djikaev, Y S; Ruckenstein, Eli

    2009-03-28

    Water molecules, belonging to the first hydration shell around a hydrophobic particle, form fewer hydrogen bonds than bulk molecules. On the other hand, the former (boundary) bonds may be slightly stronger than the latter. When two hydrophobic particles are sufficiently close to each other, the disruption of water-water hydrogen bonds in their first hydration layers can give rise to an additional contribution to their overall interaction potential. Here we present a probabilistic approach to studying this phenomenon. The proposed method allows one to determine the average number of hydrogen bonds per water molecule in the first hydration shell. Numerical evaluations show that in the interplay between a decrease in the number of boundary bonds per water molecule and the enhancement of such a bond the former effect is clearly predominant. As a result, the disruption of boundary hydrogen bonds, which occurs when the first two hydration shells of two particles overlap, leads to an attractive contribution to the overall particle interaction. This contribution is naturally short range, appearing only when the separation between the two particles becomes smaller than four lengths of a hydrogen bond. It is greater than the overall van der Waals interaction potential of the same hydrophobic particles (with typical Hamaker constants) by at least an order of magnitude.

  14. Hydrogen-bond reinforced vanadia nanofiber paper of high stiffness.

    PubMed

    Burghard, Zaklina; Leineweber, Andreas; van Aken, Peter A; Dufaux, Thomas; Burghard, Marko; Bill, Joachim

    2013-05-01

    Low-temperature, solution-based self-assembly of vanadia nanofibers yields a free-standing, ceramic paper with an outstanding combination of high strength, stiffness, and macroscopic flexibility. Its excellent mechanical performance results from a brick-and-mortar like architecture, which combines strong covalent bonding within the single-crystalline nanofibers with an intricate hydrogen bonding network between them. PMID:23468458

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

    NASA Astrophysics Data System (ADS)

    Chao, Chi-Yang

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

  16. Nature of the N-H...S hydrogen bond.

    PubMed

    Biswal, Himansu S; Wategaonkar, Sanjay

    2009-11-19

    The N-H...S hydrogen-bonded complexes of the model compounds of tryptophan (indole and 3-methylindole) and methionine (dimethyl sulfide, Me(2)S) have been characterized by a combination of experimental techniques like resonant two-photon ionization (R2PI), resonant ion dip infrared spectroscopy (RIDIRS), and fluorescence dip infrared spectroscopy (FDIRS) and computational methods like ab initio electronic structure calculations, atoms-in-molecules (AIM), natural bond orbital (NBO), and energy decomposition analyses. The results are compared with the N-H...O (M.H(2)O; M = indole, 3-methyl indole) sigma-type and N-H...Phi (M.benzene) pi-type hydrogen-bonded complexes. It was shown that the S(1)-S(0) band origin red shifts in the N-H...S hydrogen-bonded complexes correlated well with the polarizability of the acceptor rather than their proton affinity, contrary to the trend observed in most X-H...Y (X, Y = O, N, halogens, etc.) hydrogen-bonded systems. The red shift in the N-H stretching frequency in the N-H...S HB clusters (Me(2)S as HB acceptor) was found to be 1.8 times greater than that for the N-H...O hydrogen-bonded complexes (H(2)O as HB acceptor), although the binding energies for the two complexes were comparable. The energy decomposition analyses for all of the N-H...S hydrogen-bonded complexes showed that the correlation (or dispersion) energy has significant contribution to the total binding energy. It is pointed out that the binding energy of the N-H...S complex was also comparable to that of the indole.benzene complex, which is completely dominated by the dispersion interaction. Atoms-in-molcules (AIM) and natural bond orbital (NBO) analyses indicated a nontrivial electrostatic component in the hydrogen-bonding interaction. Greater dispersion contribution to the stabilization energy as well as greater red shifts in the N-H stretch relative to those of N-H...O hydrogen-bonded complexes makes the indole.dimethylsulfide complex unique in regard to the

  17. Addition of methanetrisulfonyl fluoride to unsaturated bonds

    SciTech Connect

    Yagupol'skii, Yu.L.; Gerus, I.I.; Savina, T.I.

    1988-06-10

    The reactions of methanetrisulfonyl fluoride, HC(SO/sub 2/F)/sub 3/ with acrylic acid derivatives lead to addition products containing the tris(fluorosulfonyl)methyl group, while methyl vinyl ketone gives an unstable adduct. The methyl ester of propiolic acid is converted to a mixture of cis- and trans-tris(fluorosulfonyl)-crotonic acid esters. The reaction of cyclohexene with methanesulfonyl fluoride leads to dimerization of the olefin and the cyclohexyl derivative is formed in low yield. Sulfonyl fluoride acts as catalyst for the conversion of cyclohexene to dimer and only a small portion of the cyclohexyl cation reacts with the weakly nucleophilic /sup /minus//C(SO/sub 2/F)/sub 3/ anion.

  18. Interaction geometries and energies of hydrogen bonds to C[double bond]O and C[double bond]S acceptors: a comparative study.

    PubMed

    Wood, Peter A; Pidcock, Elna; Allen, Frank H

    2008-08-01

    The occurrence, geometries and energies of hydrogen bonds from N-H and O-H donors to the S acceptors of thiourea derivatives, thioamides and thiones are compared with data for their O analogues - ureas, amides and ketones. Geometrical data derived from the Cambridge Structural Database indicate that hydrogen bonds to the C[double bond]S acceptors are much weaker than those to their C[double bond]O counterparts: van der Waals normalized hydrogen bonds to O are shorter than those to S by approximately 0.25 A. Further, the directionality of the approach of the hydrogen bond with respect to S, defined by the C[double bond]S...H angle, is in the range 102-109 degrees , much lower than the analogous C[double bond]O...H angle which lies in the range 127-140 degrees . Ab initio calculations using intermolecular perturbation theory show good agreement with the experimental results: the differences in hydrogen-bond directionality are closely reproduced, and the interaction energies of hydrogen bonds to S are consistently weaker than those to O, by approximately 12 kJ mol(-1), for each of the three compound classes. There are no CSD examples of hydrogen bonds to aliphatic thiones, (Csp(3))(2)C=S, consistent with the near-equality of the electronegativities of C and S. Thioureas and thioamides have electron-rich N substituents replacing the Csp(3) atoms. Electron delocalization involving C[double bond]S and the N lone pairs then induces a significant >C(delta+)[double bond]S(delta-) dipole, which enables the formation of the medium-strength C[double bond]S...H bonds observed in thioureas and thioamides.

  19. 31 CFR 315.91 - Additional requirements; bond of indemnity.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 31 Money and Finance: Treasury 2 2010-07-01 2010-07-01 false Additional requirements; bond of indemnity. 315.91 Section 315.91 Money and Finance: Treasury Regulations Relating to Money and Finance.... SAVINGS BONDS, SERIES A, B, C, D, E, F, G, H, J, AND K, AND U.S. SAVINGS NOTES Miscellaneous...

  20. 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.

  1. 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.

  2. Hydrogen bonding in the ethanol-water dimer.

    PubMed

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

    2015-10-01

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

  3. 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

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

    PubMed

    Vargas, Rubicelia; Martínez, Ana

    2011-07-28

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

  5. How cellulose stretches: synergism between covalent and hydrogen bonding.

    PubMed

    Altaner, Clemens M; Thomas, Lynne H; Fernandes, Anwesha N; Jarvis, Michael C

    2014-03-10

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

    PubMed Central

    Nirmalram, Jeyaraman Selvaraj; Thomas Muthiah, Packianathan

    2010-01-01

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

  7. Influencing factors of hydrogen bonding intensity in beer.

    PubMed

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

    2014-11-01

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

  8. Spectroscopic and theoretical evidence for the cooperativity between red-shift hydrogen bond and blue-shift hydrogen bond in DMSO aqueous solutions.

    PubMed

    Li, Qingzhong; An, Xiulin; Gong, Baoan; Cheng, Jianbo

    2008-01-01

    The cooperativity between red-shifted hydrogen bond and blue-shifting hydrogen bond in dimethyl sulfoxide aqueous solutions was studied by methods of quantum chemical calculations and infrared spectroscopy. The water molecule plays a different role in two types of hydrogen bonds: proton-donor in red-shifted hydrogen bond and proton-acceptor in blue-shifting hydrogen bond. The cooperativity is not prominent if the ring structure is formed through the OHcdots, three dots, centeredOS H-bond and CHcdots, three dots, centeredO(w) H-bond. However, if the methyl groups in the above ring structure participate in second CHcdots, three dots, centeredO(w) H-bond, the cooperativity is increased. The second CHcdots, three dots, centeredO(w) H-bond enhances OHcdots, three dots, centeredOS H-bond and weakens the first CHcdots, three dots, centeredO(w) H-bond.

  9. Intra- vs. intermolecular hydrogen bonding: dimers of alpha-hydroxyesters with methanol.

    PubMed

    Borho, Nicole; Suhm, Martin A; Le Barbu-Debus, Katia; Zehnacker, Anne

    2006-10-14

    Intermolecular hydrogen bonding competes with an intramolecular hydrogen bond when methanol binds to an alpha-hydroxyester. Disruption of the intramolecular OH...O=C contact in favour of a cooperative OH...OH...O=C sequence is evidenced by FTIR spectroscopy for the addition of methanol to the esters methyl glycolate, methyl lactate and methyl alpha-hydroxyisobutyrate in seeded supersonic jet expansions. Comparison of the OH stretching modes with quantum-chemical harmonic frequency calculations and 18O labelling of methanol unambiguously prove the insertion of methanol into the intramolecular hydrogen bond. This is in marked contrast to UV/IR hole burning studies of the homologous system methyl lactate: (+/-)-2-naphthyl-1-ethanol, where only addition complexes were found and the intramolecular hydrogen bond was conserved. This switch in hydrogen bond pattern from aliphatic to aromatic heterodimers is thought to reflect not only a kinetic propensity but also a thermodynamic preference for addition complexes when dispersion forces become more important in aromatic systems. PMID:17001413

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

    PubMed

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

    2016-09-01

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

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

    PubMed

    Xu, Huafeng; Dill, Ken A

    2005-12-15

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

  12. Density functional theory and hydrogen bonds: are we there yet?

    PubMed

    Boese, A Daniel

    2015-04-01

    Density functional theory (DFT) has become more successful at introducing dispersion interactions, and can be thus applied to a wide range of systems. Amongst these are systems that contain hydrogen bonds, which are extremely important for the biological regime. Here, the description of hydrogen-bonded interactions by DFT with and without dispersion corrections is investigated. For small complexes, for which electrostatics are the determining factor in the intermolecular interactions, the inclusion of dispersion with most functionals yields large errors. Only for larger systems, in which van der Waals interactions are more important, do dispersion corrections improve the performance of DFT for hydrogen-bonded systems. None of the studied functionals, including double hybrid functionals (with the exception of DSD-PBEP86 without dispersion corrections), are more accurate than MP2 for the investigated species.

  13. Exploring the Potential of Diarylacetylenediols as Hydrogen Bonding Catalysts

    PubMed Central

    Türkmen, Yunus E.; Rawal, Viresh H.

    2014-01-01

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

  14. Infrared Spectra and Hydrogen Bonds of Biologically Active Benzaldehydes

    NASA Astrophysics Data System (ADS)

    Tolstorozhev, G. B.; Skornyakov, I. V.; Belkov, M. V.; Shimko, A. N.; Shadyro, O. I.; Brinkevich, S. D.; Samovich, S. N.

    2013-09-01

    IR-Fourier spectra of solutions and crystals of biologically active benzaldehyde derivatives were studied. Specific features of the formation of intra- and intermolecular hydrogen bonds were analyzed. Spectral signatures that characterized participation of the hydroxyl OH group and also the OCH3 and C=O groups in the formation of intramolecular hydrogen bonds of the three different types O-H···O-H, O-H···O-CH3, and O-H···O=C were revealed. Intramolecular hydrogen bonds of the types O-H···O-H and O-H···O-CH3 were absent for benzaldehyde derivatives in the crystal phase. Only hydroxyl and carbonyl groups participated in intermolecular interactions. This resulted in the formation of linear intermolecular dimers. Seven various configurations of the linear dimers were identified in solutions and crystals.

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

    PubMed

    Xu, Huafeng; Dill, Ken A

    2005-12-15

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

  16. 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.

  17. 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.

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

    PubMed

    Koenig, S; Müller, L; Smith, D K

    2001-03-01

    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.

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

    PubMed Central

    Ross, P D; Rekharsky, M V

    1996-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Smedley, Sarah Black

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2013-01-01

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

  3. On some hydrogen bond correlations at high pressures

    NASA Astrophysics Data System (ADS)

    Sikka, S. K.

    2007-09-01

    In situ high pressure neutron diffraction measured lengths of O H and H O pairs in hydrogen bonds in substances are shown to follow the correlation between them established from 0.1 MPa data on different chemical compounds. In particular, the conclusion by Nelmes et al that their high pressure data on ice VIII differ from it is not supported. For compounds in which the O H stretching frequencies red shift under pressure, it is shown that wherever structural data is available, they follow the stretching frequency versus H O (or O O) distance correlation. For compounds displaying blue shifts with pressure an analogy appears to exist with improper hydrogen bonds.

  4. AAAA-DDDD quadruple hydrogen-bond arrays featuring NH···N and CH···N hydrogen bonds.

    PubMed

    Leigh, David A; Robertson, Craig C; Slawin, Alexandra M Z; Thomson, Patrick I T

    2013-07-01

    The X-ray crystal structure of a previously reported extremely strong quadruple NH···N AAAA-DDDD hydrogen-bond array [5·4] (K(a) = 1.5 × 10(6) M(-1) in CH3CN; K(a) > 3 × 10(12) M(-1) in CH2Cl2) features four short linear hydrogen bonds. Changing the two benzimidazole groups of the DDDD unit to triazole groups replaces two of the NH···N hydrogen bonds with CH···N interactions (complex [5·6]), but only reduces the association constant in CH3CN by 2 orders of magnitude (K(a) = 2.6 × 10(4) M(-1) in CH3CN; K(a) > 1 × 10(7) M(-1) in CH2Cl2). Related complexes without the triazole groups range in K(a) from 18 to 270 M(-1) in CH3CN, suggesting that the CH···N interactions can be considered part of a strong AAAA-DDDD quadruple hydrogen-bonding array. The NH···N/CH···N AAAA-DDDD motif can be repeatedly switched "on" and "off" in CDCl3 through successive additions of acid and base.

  5. Piezoelectric hydrogen bonding: computational screening for a design rationale.

    PubMed

    Werling, Keith A; Griffin, Maryanne; Hutchison, Geoffrey R; Lambrecht, Daniel S

    2014-09-01

    Organic piezoelectric materials are promising targets in applications such as energy harvesting or mechanical sensors and actuators. In a recent paper (Werling, K. A.; et al. J. Phys. Chem. Lett. 2013, 4, 1365-1370), we have shown that hydrogen bonding gives rise to a significant piezoelectric response. In this article, we aim to find organic hydrogen bonded systems with increased piezo-response by investigating different hydrogen bonding motifs and by tailoring the hydrogen bond strength via functionalization. The largest piezo-coefficient of 23 pm/V is found for the nitrobenzene-aniline dimer. We develop a simple, yet surprisingly accurate rationale to predict piezo-coefficients based on the zero-field compliance matrix and dipole derivatives. This rationale increases the speed of first-principles piezo-coefficient calculations by an order of magnitude. At the same time, it suggests how to understand and further increase the piezo-response. Our rationale also explains the remarkably large piezo-response of 150 pm/V and more for another class of systems, the "molecular springs" (Marvin, C.; et al. J. Phys. Chem. C 2013, 117, 16783-16790.).

  6. Piezoelectric hydrogen bonding: computational screening for a design rationale.

    PubMed

    Werling, Keith A; Griffin, Maryanne; Hutchison, Geoffrey R; Lambrecht, Daniel S

    2014-09-01

    Organic piezoelectric materials are promising targets in applications such as energy harvesting or mechanical sensors and actuators. In a recent paper (Werling, K. A.; et al. J. Phys. Chem. Lett. 2013, 4, 1365-1370), we have shown that hydrogen bonding gives rise to a significant piezoelectric response. In this article, we aim to find organic hydrogen bonded systems with increased piezo-response by investigating different hydrogen bonding motifs and by tailoring the hydrogen bond strength via functionalization. The largest piezo-coefficient of 23 pm/V is found for the nitrobenzene-aniline dimer. We develop a simple, yet surprisingly accurate rationale to predict piezo-coefficients based on the zero-field compliance matrix and dipole derivatives. This rationale increases the speed of first-principles piezo-coefficient calculations by an order of magnitude. At the same time, it suggests how to understand and further increase the piezo-response. Our rationale also explains the remarkably large piezo-response of 150 pm/V and more for another class of systems, the "molecular springs" (Marvin, C.; et al. J. Phys. Chem. C 2013, 117, 16783-16790.). PMID:24576213

  7. 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.

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

    SciTech Connect

    Custelcean, Radu

    2008-01-01

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

  9. 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.

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

    PubMed

    Chen, Yinshan; Zhang, Wei; Yu, Lian

    2016-08-18

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

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

    PubMed

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

    2015-09-28

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

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

    NASA Astrophysics Data System (ADS)

    Stouten, Pieter F. W.; Van Eijck, Bouke P.; Kroon, Jan

    1991-02-01

    In the framework of our comparative research concerning hydrogen bonding in the crystalline and liquid phases we have carried out molecular dynamics (MD) simulations of liquid methanol. Six different rigid three site models are compared. Five of them had been reported in the literature and one (OM2) we developed by a fit to the experimental molar volume, heat of vaporization and neutron weighted radial distribution function. In general the agreement with experiment is satisfactory for the different models. None of the models has an explicit hydrogen bond potential, but five of the six models show a degree of hydrogen bonding comparable to experiments on liquid methanol. The analysis of the simulation hydrogen bonds indicates that there is a distinct preference of the O⋯O axis to lie in the acceptor lone pairs plane, but hardly any for the lone pair directions. Ab initio calculations and crystal structure statistics of OH⋯O hydrogen bonds agree with this observation. The O⋯O hydrogen bond length distributions are similar for most models. The crystal structures show a sharper O⋯O distribution. Explicit introduction of harmonic motion with a quite realistic root mean square amplitude of 0.08 Å to the thermally averaged crystal distribution results in a distribution comparable to OM2 although the maximum of the former is found at shorter distance. On the basis of the analysis of the static properties of all models we conclude that our OM2, Jorgenson's OPLS and Haughney, Ferrario and McDonald's HFM1 models are good candidates for simulations of liquid methanol under isothermal, isochoric conditions. Partly flexible and completely rigid OM2 are simulated at constant pressure and with fixed volume. The flexible simulations give essentially the same (correct) results under both conditions, which is not surprising because the flexible form was fitted under both conditions. Rigid OM2 has a similar potential energy but larger pressure in the

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

    PubMed 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

  14. The importance of hydrogen bonding in sphingomyelin's membrane interactions with co-lipids.

    PubMed

    Slotte, J Peter

    2016-02-01

    Sphingomyelin is an important constituent of mammalian cell membranes. Its molecular structure is N-acyl-D-erythro-sphingosylphosphorylcholine. The N-acyls in sphingomyelin often contain 16-24 carbons that are mostly saturated chains; however, the monounsaturated 24:1(Δ15c) acyl chain is also common. In addition to the more saturated nature of sphingomyelins, compared to physiologically relevant glycerophospholipids, also their hydrogen bonding properties are very different from the glycerophospholipids. Sphingomyelins form extensive intramolecular hydrogen bonds (from the 3OH of the long-chain base to phosphate oxygens of the head group), but also intermolecular hydrogen bonding involving the NH of the long-chain base are important for sphingomyelin (and sphingolipid) properties in membrane environments. Hydrogen bonding involving sphingomyelin has been shown to markedly stabilize interactions with both cholesterol and ceramide in fully hydrated bilayers. Such interactions contribute to the propensity of saturated sphingomyelin to form a liquid-ordered phase together with cholesterol, or a gel phase with saturated ceramides. The purpose of this review is to present recent experimental and computational evidence in support of the importance of hydrogen bonding for the interaction of sphingomyelin with other membrane lipids.

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

    PubMed

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

    2013-07-19

    The construction of pyridine-containing macrocyclic architectures using a nonmetallic template is described. 4,6-Dichlororesorcinol was used as an exotemplate to self-organize two aza-heterocyclic units by OH···N hydrogen bonds. Subsequent sequential double olefin metathesis/hydrogenation reactions employing a single ruthenium-alkylidene precatalyst open access to macrocyclic molecules. PMID:23829609

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

    PubMed

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

    2013-07-19

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

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

    PubMed Central

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

    2015-01-01

    As halogen bonds gain prevalence in supramolecular synthesis and materials chemistry, it has become necessary to examine more closely how such interactions compete with or complement hydrogen bonds whenever both are present within the same system. As hydrogen and halogen bonds have several fundamental features in common, it is often difficult to predict which will be the primary interaction in a supramolecular system, especially as they have comparable strength and geometric requirements. To address this challenge, a series of molecules containing both hydrogen- and halogen-bond donors were co-crystallized with various monotopic, ditopic symmetric and ditopic asymmetric acceptor molecules. The outcome of each reaction was examined using IR spectroscopy and, whenever possible, single-crystal X-ray diffraction. 24 crystal structures were obtained and subsequently analyzed, and the synthon preferences of the competing hydrogen- and halogen-bond donors were rationalized against a background of calculated molecular electrostatic potential values. It has been shown that readily accessible electrostatic potentials can offer useful practical guidelines for predicting the most likely primary synthons in these co-crystals as long as the potential differences are weighted appropriately. PMID:26306192

  18. 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.

  19. Study of the Hydrogen Bond Network in sub-and supercritical Water by Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Krishtal, S.; Kiselev, M.; Puhovski, Y.; Kerdcharoen, T.; Hannongbua, S.; Heinzinger, K.

    2001-08-01

    For 12 points along the tangent to the saturation curve at the critical point the temperature dependen­cies of the heights of the first maximum in the 0 -0 RDF, the average number of hydrogen bonds, and the self-diffusion coefficients have been calculated from MD simulations. The curves of these three properties show an inflection near the critical point. To improve the understanding of these changes in going from subcritical to supercritical water the librational spectra and the change in the fractions of wa­ter molecules with a given number of hydrogen bonds as a function of temperature have been derived from the simulations, additionally.

  20. Liquid state of hydrogen bond network in ice

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  1. Aminoboration: Addition of B–N σ Bonds across C–C π Bonds

    PubMed Central

    2016-01-01

    This communication demonstrates the first catalytic aminoboration of C–C π bonds by B–N σ bonds and its application to the synthesis of 3-borylated indoles. The regiochemistry and broad functional group compatibility of this addition reaction enable substitution patterns that are incompatible with major competing technologies. This aminoboration reaction effects the formation of C–B and C–N bonds in a single step from aminoboronic esters, which are simple starting materials available on the gram scale. This reaction generates synthetically valuable N-heterocyclic organoboron compounds as potential building blocks for drug discovery. The working mechanistic hypothesis involves a bifunctional Lewis acid/base catalysis strategy involving the combination of a carbophilic gold cation and a trifluoroacetate anion that activate the C–C π bond and the B–N σ bond simultaneously. PMID:26238962

  2. Dangling-bond defects and hydrogen passivation in germanium

    NASA Astrophysics Data System (ADS)

    Weber, Justin R.

    2008-03-01

    The application of germanium in complementary metal-oxide semiconductor (CMOS) technology is hampered by high interface-state densities, the microscopic origin of which has remained elusive. Using first-principles calculations, we have investigated the atomic and electronic structure of prototype germanium dangling-bond defects [1]. The computational approach is based on density functional theory, and in order to overcome band-gap problems we have also performed quasiparticle calculations based on the GW approach. Surprisingly, the germanium dangling bonds give rise to electronic levels below the valence-band maximum. They therefore occur exclusively in the negative charge state, explaining why they have eluded observation with electron spin resonance. The associated fixed charge is likely responsible for threshold-voltage shifts and poor performance of n-channel transistors. At silicon/silicon dioxide interfaces, hydrogen is successfully used to passivate dangling-bond defects. We have therefore also investigated the interaction of hydrogen with germanium. In contrast to silicon and other semiconductors in which hydrogen behaves as an amphoteric impurity, interstitial hydrogen in germanium is stable only in the negative charge state, i.e., it behaves exclusively as an acceptor. Passivation of dangling bonds by hydrogen will therefore be ineffective, again explaining experimental observations. Other cases where unusual interfacial defects and problems with hydrogen passivation may occur will be discussed. Work performed in collaboration with A. Janotti, P. Rinke, and C. G. Van de Walle, and supported by the Semiconductor Research Corporation. 1. J. R. Weber, A. Janotti, P. Rinke, and C. G. Van de Walle, Appl. Phys. Lett. 91, 142101 (2007).

  3. The effect of hydrogen bonding on the solvent-mediated interaction of composite plates.

    PubMed

    Djikaev, Y S; Ruckenstein, Eli

    2009-08-15

    When two solute particles in water sufficiently approach each other, the disruption of water-water hydrogen bonds in their first hydration layers gives rise to an additional contribution to their overall interaction. Here we present a probabilistic approach to examining interactions between two identical parallel plates whereof the surfaces are covered with uniformly distributed hydrophobic and hydrophilic sites. The proposed approach allows one to determine the average number of hydrogen bonds per water molecule in the first hydration shell of a plate. Because of the constraint imposed by the proximity to the plate, a water molecule forms less hydrogen bond in this shell than in the bulk medium. As a result, the water molecules prefer the latter to the former, even though a bond is stronger in the former than in the latter. The interplay of these factors results in an additional contribution to the overall plate interaction which is attractive and naturally short-range, appearing only when the distance between the plates is smaller than five lengths of a hydrogen bond. At a given distance, it monotonically increases from 0 to its maximum value as the fraction of hydrophobic surface area on a plate increases from 0 to 1. When this fraction is 0.5, this contribution can be up to two orders of magnitude larger than the van der Waals interaction (depending on the water density in the vicinity of a plate).

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

    SciTech Connect

    McDowell, Sean A. C.

    2009-05-14

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

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

    NASA Astrophysics Data System (ADS)

    Smedley, Sarah Black

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

  6. Rheology of miscible polymer blends with hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Yang, Zhiyi

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

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

    PubMed

    O'Neal, Kristi L; Weber, Stephen G

    2009-01-01

    There are only a few studies of noncovalent association in fluorous solvents and even fewer that are quantitative. A full understanding, particularly of stoichiometry and binding strength of noncovalent interactions in fluorous solvents could be very useful in improved molecular-receptor-based extractions, advancements in sensor technologies, crystal engineering, and supramolecular chemistry. This work investigates hydrogen bonding between heterocyclic bases and a perfluoropolyether with a terminal carboxylic acid group (Krytox 157FSH (1)), chiefly in FC-72 (a mixture of perfluorohexanes). In particular, we were interested in whether or not proton transfer occurs, and if so, under what conditions in H-bonded complexes. Continuous variations experiments show that in FC-72 weaker bases (pyrazine, pyrimidine, and quinazoline) form 1:1 complexes with 1, whereas stronger bases (quinoline, pyridine, and isoquinoline) form 1:3 complexes. Ultraviolet and infrared spectral signatures reveal that the 1:1 complexes are molecular (B.HA) whereas the 1:3 complexes are ionic (BH+.A-HAHA). Infrared spectra of 1:3 ionic complexes are discussed in detail. Literature and experimental data on complexes between N-heterocyclic bases and carboxylic acids in a range of solvents are compiled to compare solvent effects on proton transfer. Polar solvents support ionic hydrogen bonds at a 1:1 mol ratio. In nonpolar organic solvents, ionic hydrogen bonds are only observed in complexes with 1:2 (base/acid) stoichiometries. In fluorous solvents, a larger excess of acid, 1:3, is necessary to facilitate proton transfer in hydrogen bonds between carboxylic acids and the bases studied.

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

    PubMed

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

    2016-05-21

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

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

    PubMed

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

    2016-05-21

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

  10. 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.

  11. 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.

  12. Herringbone Array of Hydrogen-bonded Ribbons in 2-ethoxybenzamide from High-resolution X-ray Powder Diffraction

    SciTech Connect

    Pagola, S.; Stephens, P

    2009-01-01

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

  13. Effect of quantum nuclear motion on hydrogen bonding

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  14. Effect of quantum nuclear motion on hydrogen bonding.

    PubMed

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

    2014-05-01

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

  15. Effect of quantum nuclear motion on hydrogen bonding

    SciTech Connect

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

    2014-05-07

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

  16. Analysis of Proton NMR in Hydrogen Bonds in Terms of Lone-Pair and Bond Orbital Contributions.

    PubMed

    Sutter, Kiplangat; Aucar, Gustavo A; Autschbach, Jochen

    2015-12-01

    NMR spectroscopic parameters of the proton involved in hydrogen bonding are studied theoretically. The set of molecules includes systems with internal resonance-assisted hydrogen bonds, internal hydrogen bonds but no resonance stabilization, the acetic acid dimer (AAD), a DNA base pair, and the hydrogen succinate anion (HSA). Ethanol and guanine represent reference molecules without hydrogen bonding. The calculations are based on zero-point vibrationally averaged molecular structures in order to include anharmonicity effects in the NMR parameters. An analysis of the calculated NMR shielding and J-coupling is performed in terms of "chemist's orbitals", that is, localized molecular orbitals (LMOs) representing lone-pairs, atomic cores, and bonds. The LMO analysis associates some of the strong de-shielding of the protons in resonance-assisted hydrogen bonds with delocalization involving the π-backbone. Resonance is also shown to be an important factor causing de-shielding of the OH protons for AAD and HSA, but not for the DNA base pair. Nitromalonamide (NMA) and HSA have particularly strong hydrogen bonds exhibiting signs of covalency in the associated J-couplings. The analysis results show how NMR spectroscopic parameters that are characteristic for hydrogen bonded protons are influenced by the geometry and degree of covalency of the hydrogen bond as well as intra- and intermolecular resonance.

  17. Subphthalocyanines hydrogen bonded capsules featuring norbornadiene tethers: Promising fullerene receptors

    NASA Astrophysics Data System (ADS)

    Denis, Pablo A.; Yanney, Michael

    2015-11-01

    We have employed density functional theory to study new subphthalocyanine based receptors which feature the 1,4-dithiino and norbornadiene linkages. The latter linkage significantly improves the host binding capabilities with respect to subphthalocyanine based receptors. Moreover, the interaction energy of the new subphthalocyanine-norbornadiene receptor is larger than that computed for the C60H28 buckycatcher. The dimerization of the new receptor forms a hydrogen-bonded capsule. Through a combination of non-bonded interactions, this capsule can bind C60 with an unprecedented affinity. Due to the exceptional stability of this capsule, it is our hope that it can be used for other guests besides fullerenes.

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

    PubMed

    Chen, Senbin; Binder, Wolfgang H

    2016-07-19

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

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

    PubMed

    Chen, Senbin; Binder, Wolfgang H

    2016-07-19

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

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

    PubMed Central

    Moran, Joseph; Krische, Michael J.

    2013-01-01

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

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

    PubMed

    Moran, Joseph; Krische, Michael J

    2012-01-01

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

  2. Rhodium-Catalyzed Asymmetric Hydrogenation of α,β-Unsaturated Carbonyl Compounds via Thiourea Hydrogen Bonding.

    PubMed

    Wen, Jialin; Jiang, Jun; Zhang, Xumu

    2016-09-16

    The strategy of secondary interaction enables enantioselectivity for homogeneous hydrogenation. By introducing hydrogen bonding of substrates with thiourea from the ligand, α,β-unsaturated carbonyl compounds, such as amides and esters, are hydrogenated with high enantiomeric excess. The substrate scope for this chemical transformation is broad with various substituents at the β-position. Control experiments revealed that each unit of the ligand ZhaoPhos is irreplaceable. No nonlinear effect was observed for this Rh/ZhaoPhos-catalyzed asymmetric hydrogenation. PMID:27574859

  3. 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. PMID:20550407

  4. 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.

  5. 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.

  6. 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

  7. Does fluoromethane form a hydrogen bond with water?

    PubMed

    Rosenberg, Robert E

    2012-11-01

    Fluorinated organic compounds have become increasingly important in the pharmaceutical and agricultural industries. However, even the simplest aspects of these compounds are still not well understood. For instance, it is an open question as to whether fluoroorganics can form a hydrogen bond. To answer this question, this work compares the complex CH(3)F···HOH with 10 other complexes including the water dimer, the water-ammonia dimer, the methane-water dimer, and the methane dimer, among others. The features that are compared include binding energy and its electrostatic and dispersive components, geometry, vibrational frequencies, charge transfer, and topological analysis of the electron density. All of these are consistent with a hydrogen bond forming in CH(3)F···HOH. Moreover, all features of this dimer appear to be quite similar in kind, although slightly lesser in degree, than the corresponding features of the water dimer.

  8. Synthesis of non-polar/hydrogen bonding block copolymers

    NASA Astrophysics Data System (ADS)

    Montgomery, Steven J.

    Methods for the synthesis of novel block copolymers consisting of a non-polar segment and a hydrogen bonding segment were developed using a combination of living polymerization techniques. A series of well defined block copolymers was synthesized consisting of polybutadiene-block-poly(t-butyldimethylsilyloxystyrene), polybutadiene-block-poly(p-acetoxystyrene) and polybutadiene-block-poly(methyl methacrylate). The block copolymers containing t-butyldimethylsilyloxystyrene and p-acetoxystyrene may be deprotected to yield polybutadiene-block-poly(4-hydroxystyrene). Specifically, non-polar/hydrogen bonding (NP/HB) block copolymers were synthesized via two routes. The first consisted of anionic polymerization. The second involved a mechanistic transformation technique comprised of anionic and atom transfer radical polymerization techniques. The mechanistic transformation route was determined to be the superior method with regard to the molecular weight of the polymers produced, the abundance of compatible monomers, and the facile nature of the reaction technique.

  9. Influence of hydrogen bonds and temperature on dielectric properties

    NASA Astrophysics Data System (ADS)

    Ortiz de Urbina, Jordi; Sesé, Gemma

    2016-07-01

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

  10. Infrared intensities and charge mobility in hydrogen bonded complexes

    NASA Astrophysics Data System (ADS)

    Galimberti, Daria; Milani, Alberto; Castiglioni, Chiara

    2013-08-01

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

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

    PubMed

    Ortiz de Urbina, Jordi; Sesé, Gemma

    2016-07-01

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

  12. 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.

  13. Thioamides: versatile bonds to induce directional and cooperative hydrogen bonding in supramolecular polymers.

    PubMed

    Mes, Tristan; Cantekin, Seda; Balkenende, Dirk W R; Frissen, Martijn M M; Gillissen, Martijn A J; De Waal, Bas F M; Voets, Ilja K; Meijer, E W; Palmans, Anja R A

    2013-06-24

    The amide bond is a versatile functional group and its directional hydrogen-bonding capabilities are widely applied in, for example, supramolecular chemistry. The potential of the thioamide bond, in contrast, is virtually unexplored as a structuring moiety in hydrogen-bonding-based self-assembling systems. We report herein the synthesis and characterisation of a new self-assembling motif comprising thioamides to induce directional hydrogen bonding. N,N',N''-Trialkylbenzene-1,3,5-tris(carbothioamide)s (thioBTAs) with either achiral or chiral side-chains have been readily obtained by treating their amide-based precursors with P2S5. The thioBTAs showed thermotropic liquid crystalline behaviour and a columnar mesophase was assigned. IR spectroscopy revealed that strong, three-fold, intermolecular hydrogen-bonding interactions stabilise the columnar structures. In apolar alkane solutions, thioBTAs self-assemble into one-dimensional, helical supramolecular polymers stabilised by three-fold hydrogen bonding. Concentration- and temperature-dependent self-assembly studies performed by using a combination of UV and CD spectroscopy demonstrated a cooperative supramolecular polymerisation mechanism and a strong amplification of supramolecular chirality. The high dipole moment of the thioamide bond in combination with the anisotropic shape of the resulting cylindrical aggregate gives rise to sufficiently strong depolarised light scattering to enable depolarised dynamic light scattering (DDLS) experiments in dilute alkane solution. The rotational and translational diffusion coefficients, D(trans) and D(rot), were obtained from the DDLS measurements, and the average length, L, and diameter, d, of the thioBTA aggregates were derived (L = 490 nm and d = 3.6 nm). These measured values are in good agreement with the value L(w) = 755 nm obtained from fitting the temperature-dependent CD data by using a recently developed equilibrium model. This experimental verification

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

    PubMed Central

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

    2014-01-01

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

  15. Metal complexes with varying intramolecular hydrogen bonding networks

    PubMed Central

    Lacy, David C.; Mukherjee, Jhumpa; Lucas, Robie L.; Day, Victor W.; Borovik, A.S.

    2013-01-01

    Alfred Werner described the attributes of the primary and secondary coordination spheres in his development of coordination chemistry. To examine the effects of the secondary coordination sphere on coordination chemistry, a series of tripodal ligands containing differing numbers of hydrogen bond (H-bond) donors were used to examine the effects of H-bonds on Fe(II), Mn(II)–acetato, and Mn(III)–OH complexes. The ligands containing varying numbers of urea and amidate donors allowed for systematic changes in the secondary coordination spheres of the complexes. Two of the Fe(II) complexes that were isolated as their Bu4N+ salts formed dimers in the solid-state as determined by X-ray diffraction methods, which correlates with the number of H-bonds present in the complexes (i.e., dimerization is favored as the number of H-bond donors increases). Electron paramagnetic resonance (EPR) studies suggested that the dimeric structures persist in acetonitrile. The Mn(II) complexes were all isolated as their acetato adducts. Furthermore, the synthesis of a rare Mn(III)–OH complex via dioxygen activation was achieved that contains a single intramolecular H-bond; its physical properties are discussed within the context of other Mn(III)–OH complexes. PMID:24904193

  16. Rotational Spectra of Hydrogen Bonded Networks of Amino Alcohols

    NASA Astrophysics Data System (ADS)

    Zhang, Di; Zwier, Timothy S.

    2014-06-01

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

  17. 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…

  18. 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.

  19. 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.

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

    PubMed Central

    2014-01-01

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

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

    PubMed

    Sen, Ibrahim; Kara, Hulya; Azizoglu, Akın

    2016-10-01

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

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    Narayanan, Chitra; Dias, Cristiano L.

    2013-09-01

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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed

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

    2012-04-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

    Jezierska, Aneta; Panek, Jarosław J

    2015-06-22

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

  10. 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.

  11. Hydrogen bond stabilities in membrane-reconstituted alamethicin from amide-resolved hydrogen-exchange measurements.

    PubMed Central

    Dempsey, C E; Handcock, L J

    1996-01-01

    Amide-resolved hydrogen-deuterium exchange-rate constants were measured for backbone amides of alamethicin reconstituted in dioleoylphosphatidylcholine vesicles by an exchange-trapping method combined with high-resolution nuclear magnetic resonance spectroscopy. In vesicles containing alamethicin at molar ratios between 1:20 and 1:100 relative to lipid, the exchange-rate constants increased with increasing volume of the D20 buffer in which the vesicles were suspended, indicating that exchange under these conditions is dominated by partitioning of the peptide into the aqueous phase. This was supported by observation of a linear relationship between the exchange-rate constants for amides in membrane-reconstituted alamethicin and those for amides in alamethicin dissolved directly into D2O buffer. Significant protection of amides from exchange with D2O buffer in membrane-reconstituted alamethicin is interpreted in terms of stabilization by helical hydrogen bonding. Under conditions in which amide exchange occurred by partitioning of the peptide into solution, only lower limits for hydrogen-bond stabilities in the membrane were determined; all the potentially hydrogen-bonded amides of alamethicin are at least 1000-fold exchange protected in the membrane-bound state. When partitioning of alamethicin into the aqueous phase was suppressed by hydration of reconstituted vesicles in a limiting volume of water [D2O:dioleoylphosphatidylcholine:alamethicin; 220:1:0.05; (M:M:M)], the exchange-protection factors exhibited helical periodicity with highly exchange-protected, and less well-protected, amides on the nonpolar and polar helix faces, respectively. The exchange data indicate that, under the conditions studied, alamethicin adopts a stable helical structure in DOPC bilayers in which all the potentially hydrogen-bonded amides are stabilized by helical hydrogen bonds. The protection factors define the orientation of the peptide helix with respect to an aqueous phase, which is

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

    PubMed

    Podtelezhnikov, Alexei A; Wild, David L

    2005-10-01

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

  13. Theoretical study of the interplay between lithium bond and hydrogen bond in complexes involved with HLi and HCN.

    PubMed

    Li, Qingzhong; Hu, Ting; An, Xiulin; Li, Wenzuo; Cheng, Jianbo; Gong, Baoan; Sun, Jiazhong

    2009-12-21

    The lithium- and hydrogen-bonded complex of HLi-NCH-NCH is studied with ab initio calculations. The optimized structure, vibrational frequencies, and binding energy are calculated at the MP2 level with 6-311++G(2d,2p) basis set. The interplay between lithium bonding and hydrogen bonding in the complex is investigated with these properties. The effect of lithium bonding on the properties of hydrogen bonding is larger than that of hydrogen bonding on the properties of lithium bonding. In the trimer, the binding energies are increased by about 19% and 61% for the lithium and hydrogen bonds, respectively. A big cooperative energy (-5.50 kcal mol(-1)) is observed in the complex. Both the charge transfer and induction effect due to the electrostatic interaction are responsible for the cooperativity in the trimer. The effect of HCN chain length on the lithium bonding has been considered. The natural bond orbital and atoms in molecules analyses indicate that the electrostatic force plays a main role in the lithium bonding. A many-body interaction analysis has also been performed for HLi-(NCH)(N) (N=2-5) systems.

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

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

    PubMed

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

    2015-12-17

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

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

    NASA Astrophysics Data System (ADS)

    Kondo, Makoto; Kasahara, Yasutoshi; Ishikawa, Haruki

    2015-06-01

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

  17. Asymmetric hydrogen bonds in a centrosymmetric environment. III. Quantum mechanical calculations of the potential-energy surfaces for the very short hydrogen bonds in potassium hydrogen dichloromaleate.

    PubMed

    Majerz, I; Olovsson, I

    2007-10-01

    In the crystal structure of potassium hydrogen dichloromaleate there are two short hydrogen bonds of 2.44 A. The 'heavy-atom' structure is centrosymmetric (space group P1) with centers of symmetry in the middle of the O-O bonds, suggesting centered hydrogen bonds. However, earlier unconventional types of refinements of the extensive neutron data taken at 30, 90, 135, 170 and 295 K demonstrated that the H atoms are actually non-centered in the hydrogen bonds, although the environment is centrosymmetric. Traditionally it has been assumed that the hydrogen distribution adopts the same symmetry as the environment. Reviewing these unusual results it was considered of great interest to verify that the non-centered locations of the H atoms are reasonable from an energy point of view. Quantum mechanical calculations have now been carried out for the potential-energy surfaces (PES) for both the centered and non-centered locations of the H atoms. In all cases the non-centered positions are closer to the energy minima in the PES than the centered positions, and this result confirms that the structure is best described with non-centered H atoms. There is virtually perfect agreement between the quantum-mechanically derived reaction coordinates (QMRC) and the bond-order reaction coordinates (BORC) derived using Pauling's bond-order concept together with the principle of conservation of bond order. [Part I: Olovsson et al. (2001). Acta Cryst. B57, 311-316; Part II: Olovsson et al. (2002). Acta Cryst. B58, 627-631.].

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

    PubMed

    Alkorta, Ibon; Blanco, Fernando; Solimannejad, Mohammad; Elguero, Jose

    2008-10-30

    A theoretical study of the complexes formed by hypohalous acids (HOX, X = F, Cl, Br, I, and At) with three nitrogenated bases (NH 3, N 2, and NCH) has been carried out by means of ab initio methods, up to MP2/aug-cc-pVTZ computational method. In general, two minima complexes are found, one with an OH...N hydrogen bond and the other one with a X...N halogen bond. While the first one is more stable for the smallest halogen derivatives, the two complexes present similar stabilities for the iodine case and the halogen-bonded structure is the most stable one for the hypoastatous acid complexes. PMID:18837495

  19. Strong, low-barrier hydrogen bonds may be available to enzymes.

    PubMed

    Graham, Jacob D; Buytendyk, Allyson M; Wang, Di; Bowen, Kit H; Collins, Kim D

    2014-01-21

    The debate over the possible role of strong, low-barrier hydrogen bonds in stabilizing reaction intermediates at enzyme active sites has taken place in the absence of an awareness of the upper limits to the strengths of low-barrier hydrogen bonds involving amino acid side chains. Hydrogen bonds exhibit their maximal strengths in isolation, i.e., in the gas phase. In this work, we measured the ionic hydrogen bond strengths of three enzymatically relevant model systems in the gas phase using anion photoelectron spectroscopy; we calibrated these against the hydrogen bond strength of HF2(-), measured using the same technique, and we compared our results with other gas-phase experimental data. The model systems studied here, the formate-formic acid, acetate-acetic acid, and imidazolide-imidazole anionic complexes, all exhibit very strong hydrogen bonds, whose strengths compare favorably with that of the hydrogen bifluoride anion, the strongest known hydrogen bond. The hydrogen bond strengths of these gas-phase complexes are stronger than those typically estimated as being required to stabilize enzymatic intermediates. If there were to be enzyme active site environments that can facilitate the retention of a significant fraction of the strengths of these isolated (gas-phase), hydrogen bonded couples, then low-barrier hydrogen bonding interactions might well play important roles in enzymatic catalysis.

  20. A study of hydrogen-bond dynamics in carboxylic acids by NMR T1 measurements: isotope effects and hydrogen-bond length dependence

    NASA Astrophysics Data System (ADS)

    Agaki, T.; Imashiro, F.; Terao, T.; Hirota, N.; Hayashi, S.

    1987-08-01

    Proton (deuteron) transfer of hydrogen bonds in benzoic, glutaric and p-formylbenzoic acids was studied by proton (deuteron) T1 measurements. Deuteration of carboxylic protons was found to increase the barriers to classical proton jumping as well as quantum-mechanical tunneling. The former barriers increase as the hydrogen-bond distance increases.

  1. Topological hydrogen-bond definition to characterize the structure and dynamics of liquid water.

    PubMed

    Henchman, Richard H; Irudayam, Sheeba Jem

    2010-12-23

    A definition that equates a hydrogen bond topologically with a local energy well in the potential energy surface is used to study the structure and dynamics of liquid water. We demonstrate the robustness of this hydrogen-bond definition versus the many other definitions which use fixed, arbitrary parameters, do not account for variable molecular environments, and cannot effectively resolve transition states. Our topology definition unambiguously shows that most water molecules are double acceptors but sizable proportions are single or triple acceptors. Almost all hydrogens are found to take part in hydrogen bonds. Broken hydrogen bonds only form when two molecules try to form two hydrogen bonds between them. The double acceptors have tetrahedral geometry, lower potential energy, entropy, and density, and slower dynamics. The single and triple acceptors have trigonal and trigonal bipyramidal geometry and when considered together have higher density, potential energy, and entropy, faster dynamics, and a tendency to cluster. These calculations use an extended theory for the entropy of liquid water that takes into account the variable number of hydrogen bonds. Hydrogen-bond switching is shown to depend explicitly on the variable number of hydrogen bonds accepted and the presence of interstitial water molecules. Transition state theory indicates that the switching of hydrogen bonds is a mildly activated process, requiring only a moderate distortion of hydrogen bonds. Three main types of switching events are observed depending on whether the donor and acceptor are already sharing a hydrogen bond. The switch may proceed with no intermediate or via a bifurcated-oxygen or cyclic dimer, both of which have a broken hydrogen bond and symmetric and asymmetric forms. Switching is found to be strongly coupled to whole-molecule vibration, particularly for the more mobile single and triple acceptors. Our analysis suggests that even though water is heterogeneous in terms of the

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

    NASA Astrophysics Data System (ADS)

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

    2000-11-01

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

  3. 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.

  4. Intramolecular hydrogen bonds in sulfur-containing aminophenols

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

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

  5. Bonding changes in hot fluid hydrogen at megabar pressures

    PubMed Central

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

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaojie; He, Junhui

    2015-03-01

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

  7. Chemical bonding of hydrogen molecules to transition metal complexes

    SciTech Connect

    Kubas, G.J.

    1990-01-01

    The complex W(CO){sub 3}(PR{sub 3}){sub 2}(H{sub 2}) (CO = carbonyl; PR{sub 3} = organophosphine) was prepared and was found to be a stable crystalline solid under ambient conditions from which the hydrogen can be reversibly removed in vacuum or under an inert atmosphere. The weakly bonded H{sub 2} exchanges easily with D{sub 2}. This complex represents the first stable compound containing intermolecular interaction of a sigma-bond (H-H) with a metal. The primary interaction is reported to be donation of electron density from the H{sub 2} bonding electron pair to a vacant metal d-orbital. A series of complexes of molybdenum of the type Mo(CO)(H{sub 2})(R{sub 2}PCH{sub 2}CH{sub 2}PR{sub 2}){sub 2} were prepared by varying the organophosphine substitutent to demonstrate that it is possible to bond either dihydrogen or dihydride by adjusting the electron-donating properties of the co-ligands. Results of infrared and NMR spectroscopic studies are reported. 20 refs., 5 fig.

  8. Enzymatic Functionalization of Carbon-Hydrogen Bonds1

    PubMed Central

    Lewis, Jared C.; Coelho, Pedro S.

    2010-01-01

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

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

    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

  10. Polarized vibrational spectroscopy of fiber polymers: hydrogen bonding in cellulose II.

    PubMed

    Sturcová, Adriana; His, Isabelle; Wess, Tim J; Cameron, Graeme; Jarvis, Michael C

    2003-01-01

    Vibrational spectroscopy using polarized incident radiation can be used to determine the orientation of X-H bonds with respect to coordinates such as crystallographic axes. The adaptation of this approach to polymer fibers is described here. It requires spectral intensity to be quantified around a 180 degrees range of polarization angles and not just recorded transversely and longitudinally as is normal in fiber spectroscopy. Mercerized cellulose II is used as an example. The unit cell of the cellulose II lattice contains six distinct hydroxyl groups engaged in a complex network of hydrogen bonds that hold the cellulose chains laterally together. A formalism is described to relate the variation in intensity of each O-H stretching mode to the angle between its transition moment and the chain axis as the polarization axis is rotated with respect to the fiber axis. It was necessary to include the effect of dispersion in chain orientation around the mean and the averaging of all rotational positions of the chains round their axis. The two crystallographically distinct O(2)-H groups, which are each hydrogen-bonded to only one acceptor oxygen, show a close match in orientation between the transition moments of their stretching bands and the O-H bond axis. The two O(3)-H groups each have a three-centered hydrogen bond to O-5 and O-6 of the next residue in the same chain. The transition moments of their stretching modes lay between the acceptor oxygens. Hydrogen bonding from the O(6)-H groups is still more complex but again the transition moment of each O-H bond lay within the cone of orientations described by the acceptor oxygens, provided that one additional acceptor oxygen excluded from the published crystal structure was considered. The transition moments for the O-H stretching modes were approximately aligned with the O-H bond axes, but the alignment was not necessarily exact. This approach is not restricted to hydroxyl groups, but it is particularly useful for the

  11. A QTAIM exploration of the competition between hydrogen and halogen bonding in halogenated 1-methyluracil: Water systems

    NASA Astrophysics Data System (ADS)

    Huan, Guo; Xu, Tianlv; Momen, Roya; Wang, Lingling; Ping, Yang; Kirk, Steven R.; Jenkins, Samantha; van Mourik, Tanja

    2016-10-01

    Using QTAIM we show that the hydrogen bonding complexes of 5-halogenated-1-methyluracil (XmU; X = F, Cl, Br, I or At) with a water molecule were always stronger than the corresponding halogen bonds. The strength of the hydrogen bond decreased with increasing halogen size. The hydrogen bonds displayed an admixture of covalent character but all the halogen bonds were purely electrostatic in nature. An F---O halogen bond was found and was facilitated by an intermediate F---H bonding interaction. The metallicity ξ(rb) of the C = O bonds neighboring the hydrogen bonds and of the C-X bonds contiguous with the halogen bonds was explored.

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

    PubMed Central

    Netzel, Jeanette; van Smaalen, Sander

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-06-01

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

  14. Hydrogen bonding and the phase behavior of polymer blends

    SciTech Connect

    Painter, P.C.; Coleman, M.M.

    1995-12-31

    We have developed a model that describes the phase behavior of blends where there are hydrogen bonds between the components. The parameters used in this model are determined by infrared spectroscopic studies. Recently, we have found interesting differences between parameters determined for low molecular weight model systems, blends and random copolymers of units containing identical functional groups. This can be interpreted in terms of the relative proportions of intra and inter-chain contacts and this, in turn, has a number of ramifications concerning models used to describe phase behavior.

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

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

    Molecular dynamics at the glass transition of three lactose/oil glassy systems have been investigated according to the cooperativity and fragility approaches. From Donth's approach, the cooperativity length is estimated by modulated temperature calorimetric measurements. Results reveal that modification of the disaccharide by oil leads to increase the disorder degree in the lactose, the size of the cooperative domains and the fragility index. These particular hydrogen-bonded organic glasses follow the general tendency observed on organic and inorganic polymers: the higher the cooperativity length, the higher the value of the fragility index at Tg.

  16. Electrons and Hydrogen-Bond Connectivity in Liquid Water

    SciTech Connect

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

    2006-01-13

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

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

    NASA Astrophysics Data System (ADS)

    Feldman, Kathleen E.

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

  18. 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.

  19. Modelling OH⋯O hydrogen bonds in carbohydrates

    NASA Astrophysics Data System (ADS)

    Jeffrey, G. A.

    1990-09-01

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

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

    PubMed

    Angelina, Emilio L; Peruchena, Nélida M

    2011-05-12

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

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

    PubMed

    Angelina, Emilio L; Peruchena, Nélida M

    2011-05-12

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

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

    PubMed

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

    2014-07-01

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

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

    PubMed

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

    2014-07-01

    Methanol is a versatile chemical feedstock, fuel source, and energy storage material. Many reactions involving methanol are catalyzed by transition metal surfaces, on which hydrogen-bonded methanol overlayers form. As with water, the structure of these overlayers is expected to depend on a delicate balance of hydrogen bonding and adsorbate-substrate bonding. In contrast to water, however, relatively little is known about the structures methanol overlayers form and how these vary from one substrate to another. To address this issue, herein we analyze the hydrogen bonded networks that methanol forms as a function of coverage on three catalytically important surfaces, Au(111), Cu(111), and Pt(111), using a combination of scanning tunneling microscopy and density functional theory. We investigate the effect of intermolecular interactions, surface coverage, and adsorption energies on molecular assembly and compare the results to more widely studied water networks on the same surfaces. Two main factors are shown to direct the structure of methanol on the surfaces studied: the surface coverage and the competition between the methanol-methanol and methanol-surface interactions. Additionally, we report a new chiral form of buckled hexamer formed by surface bound methanol that maximizes the interactions between methanol monomers by sacrificing interactions with the surface. These results serve as a direct comparison of interaction strength, assembly, and chirality of methanol networks on Au(111), Cu(111), and Pt(111) which are catalytically relevant for methanol oxidation, steam reforming, and direct methanol fuel cells. PMID:25005297

  5. 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. PMID:23632995

  6. Infrared Spectroscopy of Hydrogen Bonds in Benzoic Acid Derivatives

    NASA Astrophysics Data System (ADS)

    Tolstorozhev, G. B.; Bel‧kov, M. V.; Skornyakov, I. V.; Bazyl, O. K.; Artyukhov, V. Ya.; Mayer, G. V.; Shadyro, O. I.; Kuzovkov, P. V.; Brinkevich, S. D.; Samovich, S. N.

    2014-03-01

    We have measured the Fourier transform IR spectra of CCl4 solutions of benzoic acid and its biologically active derivatives. We investigated the proton-acceptor properties of the studied molecules theoretically by the molecular electrostatic potential method. The calculations are compared with experimental results. Based on an estimate of the proton-acceptor properties, we give an interpretation of the specific features of the IR spectra of benzoic acid and its derivatives in the region of the O-H and C = O vibrations. The mechanisms for interactions of the molecules are determined by the nature of substituents which are added to the benzene ring in positions para and meta to the carboxyl group. We identify the conditions for appearance of intermolecular hydrogen bonds of O-H · · · O = C, O-H · · · O-H types with formation of cyclic and linear dimers. We show that intramolecular hydrogen bonds of the type O-H · · · O-CH3 prevent the hydroxyl groups from participating in intermolecular interactions.

  7. Hydrogen bonding and multiphonon structure in copper pyrazine coordination polymers.

    PubMed

    Brown, S; Cao, J; Musfeldt, J L; Conner, M M; McConnell, A C; Southerland, H I; Manson, J L; Schlueter, J A; Phillips, M D; Turnbull, M M; Landee, C P

    2007-10-15

    We report a systematic investigation of the temperature-dependent infrared vibrational spectra of a family of chemically related coordination polymer magnets based upon bridging bifluoride (HF(2)-) and terminal fluoride (F-) ligands in copper pyrazine complexes including Cu(HF(2))(pyz)(2)BF(4), Cu(HF(2))(pyz)(2)ClO(4), and CuF(2)(H(2)O)(2)(pyz). We compare our results with several one- and two-dimensional prototype materials including Cu(pyz)(NO(3))(2) and Cu(pyz)(2)(ClO(4))(2). Unusual low-temperature hydrogen bonding, local structural transitions associated with stronger low-temperature hydrogen bonding, and striking multiphonon effects that derive from coupling of an infrared-active fundamental with strong Raman-active modes of the pyrazine building-block molecule are observed. On the basis of the spectroscopic evidence, these interactions are ubiquitous to this family of coordination polymers and may work to stabilize long-range magnetic ordering at low temperature. Similar interactions are likely to be present in other molecule-based magnets.

  8. Dissociation Energies of Sulfur-Centered Hydrogen-Bonded Complexes.

    PubMed

    Ghosh, Sanat; Bhattacharyya, Surjendu; Wategaonkar, Sanjay

    2015-11-01

    In this work we have determined dissociation energies of O-H···S hydrogen bond in the H2S complexes of various phenol derivatives using 2-color-2-photon photofragmentation spectroscopy in combination with zero kinetic energy photoelectron (ZEKE-PE) spectroscopy. This is the first report of direct determination of dissociation energy of O-H···S hydrogen bond. The ZEKE-PE spectra of the complexes revealed a long progression in the intermolecular stretching mode with significant anharmonicity. Using the anharmonicity information and experimentally determined dissociation energy, we also validated Birge-Sponer (B-S) extrapolation method, which is an approximate method to estimate dissociation energy. Experimentally determined dissociation energies were compared with a variety of ab initio calculations. One of the important findings is that ωB97X-D functional, which is a dispersion corrected DFT functional, was able to predict the dissociation energies in both the cationic as well as the ground electronic state very well for almost every case.

  9. 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.

  10. 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.

  11. Hierarchical Biomolecular Dynamics: Picosecond Hydrogen Bonding Regulates Microsecond Conformational Transitions.

    PubMed

    Buchenberg, Sebastian; Schaudinnus, Norbert; Stock, Gerhard

    2015-03-10

    Biomolecules exhibit structural dynamics on a number of time scales, including picosecond (ps) motions of a few atoms, nanosecond (ns) local conformational transitions, and microsecond (μs) global conformational rearrangements. Despite this substantial separation of time scales, fast and slow degrees of freedom appear to be coupled in a nonlinear manner; for example, there is theoretical and experimental evidence that fast structural fluctuations are required for slow functional motion to happen. To elucidate a microscopic mechanism of this multiscale behavior, Aib peptide is adopted as a simple model system. Combining extensive molecular dynamics simulations with principal component analysis techniques, a hierarchy of (at least) three tiers of the molecule's free energy landscape is discovered. They correspond to chiral left- to right-handed transitions of the entire peptide that happen on a μs time scale, conformational transitions of individual residues that take about 1 ns, and the opening and closing of structure-stabilizing hydrogen bonds that occur within tens of ps and are triggered by sub-ps structural fluctuations. Providing a simple mechanism of hierarchical dynamics, fast hydrogen bond dynamics is found to be a prerequisite for the ns local conformational transitions, which in turn are a prerequisite for the slow global conformational rearrangement of the peptide. As a consequence of the hierarchical coupling, the various processes exhibit a similar temperature behavior which may be interpreted as a dynamic transition. PMID:26579778

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

    PubMed

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

    2016-08-10

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

  13. 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.

  14. 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.

  15. 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.

  16. Detection of a transient intramolecular hydrogen bond using (1)JNH scalar couplings.

    PubMed

    Xiang, ShengQi; Zweckstetter, Markus

    2014-06-01

    Hydrogen bonds are essential for the structure, stability and folding of proteins. The identification of intramolecular hydrogen bonds, however, is challenging, in particular in transiently folded states. Here we studied the presence of intramolecular hydrogen bonds in the folding nucleus of the coiled-coil structure of the GCN4 leucine zipper. Using one-bond (1)JNH spin-spin coupling constants and hydrogen/deuterium exchange, we demonstrate that a transient intramolecular hydrogen bond is present in the partially helical folding nucleus of GCN(16-31). The data demonstrate that (1)JNH couplings are a sensitive tool for the detection of transient intramolecular hydrogen bonds in challenging systems where the effective/useable protein concentration is low. This includes peptides at natural abundance but also uniformly labeled biomolecules that are limited to low concentrations because of precipitation or aggregation.

  17. 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.

  18. Thwarting Crystallization through Hydrogen Bonding in Triazine Molecular Glasses

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  19. Hydrogen bonding as a modulator of aromaticity and electronic structure of selected ortho-hydroxybenzaldehyde derivatives.

    PubMed

    Jezierska-Mazzarello, Aneta; Panek, Jarosław J; Szatyłowicz, Halina; Krygowski, Tadeusz Marek

    2012-01-12

    Properties of hydrogen bonds can induce changes in geometric or electronic structure parameters in the vicinity of the bridge. Here, we focused primarily on the influence of intramolecular H-bonding on the molecular properties in selected ortho-hydroxybenzaldehydes, with additional restricted insight into substituent effects. Static models were obtained in the framework of density functional theory at B3LYP/6-311+G(d,p) level. The electronic structure parameters evolution was analyzed on the basis of Atoms In Molecules (AIM) and Natural Bond Orbitals methods. The aromaticity changes related to the variable proton position and presence of substituents were studied using Harmonic Oscillator Model of Aromaticity (HOMA), Nucleus-Independent Chemical Shift (NICS) and AIM-based parameter of Matta and Hernández-Trujillo. Finally, Car-Parrinello molecular dynamics was applied to study variability of the hydrogen bridge dynamics. The interplay between effects of the substitution and variable position of the bridged proton was discussed. It was found that the hydrogen bond energies are ca. 9-10 kcal/mol, and the bridged proton exhibits some degree of penetration into the acceptor region. The covalent character of the studied hydrogen bond was most observable when the bridged proton reached the middle position between the donor and acceptor regions. The aromaticity indexes showed that the aromaticity of the central phenyl ring is strongly dependent on the bridged proton position. Correlations between these parameters were found and discussed. In the applied time-scale, the analysis of time evolution of geometric parameters showed that the resonance strengthening does not play a crucial role in the studied compounds. PMID:22129217

  20. 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.

  1. 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.

  2. The gas-phase hydrogen-bonded complex between ozone and hydroperoxyl radical. A theoretical study.

    PubMed

    Mansergas, Alex; Anglada, Josep M

    2007-02-01

    We report a theoretical study on the gas-phase hydrogen-bonded complexes formed between ozone and hydroperoxyl radical, which are of interest in atmospheric chemistry. We have employed CASSCF, CASPT2, QCISD, and CCSD(T) theoretical approaches employing 6-311+G(2df,2p) and aug-cc-pVTZ basis sets, and we have found three complexes whose stabilities are computed to be 2.02, 1.19, and 1.34 kcal/mol, respectively, at 0 K. In addition, we have also found three transition states connecting these complexes that lie below the energy of the separate reactants. To help for possible experimental identification of these hydrogen-bonded complexes, we report also the computed harmonic vibrational frequencies along with the frequency shifts of the complexes, relative to the monomers, and the computed rotational constants. PMID:17266240

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

    PubMed

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

    2016-03-21

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

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

    PubMed

    Kacar, Gokhan; de With, Gijsbertus

    2016-04-14

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

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

    PubMed

    Bekö, Sándor L; Alig, Edith; Schmidt, Martin U; van de Streek, Jacco

    2014-01-01

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

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

    PubMed Central

    Bekö, Sándor L.; Alig, Edith; Schmidt, Martin U.; van de Streek, Jacco

    2014-01-01

    Inositol, 1,2,3,4,5,6-hexahydroxycyclohexane, exists in nine stereoisomers with different crystal structures and melting points. In a previous paper on the relationship between the melting points of the inositols and the hydrogen-bonding patterns in their crystal structures [Simperler et al. (2006 ▶). CrystEngComm 8, 589], it was noted that although all inositol crystal structures known at that time contained 12 hydrogen bonds per molecule, their melting points span a large range of about 170 °C. Our preliminary investigations suggested that the highest melting point must be corrected for the effect of molecular symmetry, and that the three lowest melting points may need to be revised. This prompted a full investigation, with additional experiments on six of the nine inositols. Thirteen new phases were discovered; for all of these their crystal structures were examined. The crystal structures of eight ordered phases could be determined, of which seven were obtained from laboratory X-ray powder diffraction data. Five additional phases turned out to be rotator phases and only their unit cells could be determined. Two previously unknown melting points were measured, as well as most enthalpies of melting. Several previously reported melting points were shown to be solid-to-solid phase transitions or decomposition points. Our experiments have revealed a complex picture of phases, rotator phases and phase transitions, in which a simple correlation between melting points and hydrogen-bonding patterns is not feasible. PMID:25075320

  7. Strength of hydrogen bond network takes crucial roles in the dissociation process of inhibitors from the HIV-1 protease binding pocket.

    PubMed

    Li, Dechang; Ji, Baohua; Hwang, Keh-Chih; Huang, Yonggang

    2011-01-01

    To understand the underlying mechanisms of significant differences in dissociation rate constant among different inhibitors for HIV-1 protease, we performed steered molecular dynamics (SMD) simulations to analyze the entire dissociation processes of inhibitors from the binding pocket of protease at atomistic details. We found that the strength of hydrogen bond network between inhibitor and the protease takes crucial roles in the dissociation process. We showed that the hydrogen bond network in the cyclic urea inhibitors AHA001/XK263 is less stable than that of the approved inhibitor ABT538 because of their large differences in the structures of the networks. In the cyclic urea inhibitor bound complex, the hydrogen bonds often distribute at the flap tips and the active site. In contrast, there are additional accessorial hydrogen bonds formed at the lateral sides of the flaps and the active site in the ABT538 bound complex, which take crucial roles in stabilizing the hydrogen bond network. In addition, the water molecule W301 also plays important roles in stabilizing the hydrogen bond network through its flexible movement by acting as a collision buffer and helping the rebinding of hydrogen bonds at the flap tips. Because of its high stability, the hydrogen bond network of ABT538 complex can work together with the hydrophobic clusters to resist the dissociation, resulting in much lower dissociation rate constant than those of cyclic urea inhibitor complexes. This study may provide useful guidelines for design of novel potent inhibitors with optimized interactions.

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

    PubMed

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

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

    2016-04-01

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

  12. Investigation of structure and hydrogen bonding of superhydrous phase B (HT) under pressure using first-principles density functional calculations

    NASA Astrophysics Data System (ADS)

    Poswal, H. K.; Sharma, Surinder M.; Sikka, S. K.

    2010-03-01

    High-pressure behaviour of superhydrous phase B (high temperature; HT) of Mg10Si3O14(OH)4 (Shy B) is investigated with the help of density functional theory-based first-principles calculations. In addition to the lattice parameters and equation of state, we use these calculations to determine the positional parameters of atoms as a function of pressure. Our results show that the compression induced structural changes involve cooperative distortions in the full geometry of the hydrogen bonds. The bond-bending mechanism proposed by Hofmeister et al. (Vibrational spectra of dense hydrous magnesium silicates at high pressure: Importance of the hydrogen bond angle, Am. Miner. 84 (1999), pp. 454-464) for hydrogen bonds to relieve the heightened repulsion due to short H- - -H contacts is not found to be effective in Shy B. The calculated O-H bond contraction is consistent with the observed blue shift in the stretching frequency of the hydrogen bond. These results establish that one can use first-principles calculations to obtain reliable insights into the pressure-induced bonding changes of complex minerals.

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

    PubMed

    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

    2014-12-17

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

  14. Doubly Cavitand-Capped Porphyrin Capsule by Hydrogen Bonds.

    PubMed

    Kishimoto, Kazuki; Nakamura, Munechika; Kobayashi, Kenji

    2016-02-18

    The components of a 1:2 mixture of meso-tetrakis(4-dodecyl-3,5-dihydroxyphenyl)porphyrin (1) and a bowl-shaped tetrakis(4-pyridylethynyl)cavitand (2) in CDCl3 or C6 D6 self-assemble quantitatively into the doubly cavitand-capped porphyrin capsule 2⋅1⋅2 through eight ArOH⋅⋅⋅Npy hydrogen bonds. Capsule 2⋅1⋅2 possesses two cavities divided by the porphyrin ring and encapsulates two molecules of 1-acetoxy-3,5-dimethoxybenzene (G) as a guest to form G/G@(2⋅1⋅2). Remarkable solvent effect was observed, in which the apparent association constant of 2⋅1⋅2 with G in C6 D6 was much greater than that in CDCl3. PMID:26728330

  15. 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.

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

    PubMed

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

    2011-02-24

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

  17. 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.

  18. Polar distortions in hydrogen-bonded organic ferroelectrics

    NASA Astrophysics Data System (ADS)

    Stroppa, Alessandro; di Sante, Domenico; Horiuchi, Sachio; Tokura, Yoshinori; Vanderbilt, David; Picozzi, Silvia

    2011-07-01

    Although ferroelectric compounds containing hydrogen bonds were among the first to be discovered, organic ferroelectrics are relatively rare. The discovery of high polarization at room temperature in croconic acid [Horiuchi , Nature (London) NATUAS0028-083610.1038/nature08731463, 789 (2010)] has led to a renewed interest in organic ferroelectrics. We present an ab initio study of two ferroelectric organic molecular crystals, 1-cyclobutene-1,2-dicarboxylic acid (CBDC) and 2-phenylmalondialdehyde (PhMDA). By using a distortion-mode analysis we shed light on the microscopic mechanisms contributing to the polarization, which we find to be as large as 14.3 and 7.0 μC/cm2 for CBDC and PhMDA, respectively. These results suggest that it may be fruitful to search among known but poorly characterized organic compounds for organic ferroelectrics with enhanced polar properties suitable for device applications.

  19. Effect of salts addition on hydrogen production by C. acetobutylicum.

    PubMed

    Alshiyab, H; Kalil, M S; Hamid, A A; Wan Yusoff, W M

    2008-09-15

    The objective of this study is to investigate the effect of salts addition to fermentation medium on hydrogen production, under anaerobic batch culture system. In this study, batch experiments were conducted to investigate the inhibitory effect of both NaCl and sodium acetate on hydrogen production. The optimum pH and temperature for hydrogen production were at initial pH of 7.0 and 30 degrees C. Enhanced production of hydrogen, using glucose as substrate was achieved. In the absence of Sodium Chloride and Sodium Acetate enhanced hydrogen yield (Y(P/S)) from 350 mL g(-1) glucose utilized to 391 mL g(-1) glucose utilized with maximum hydrogen productivity of 77.5 ml/L/h. Results also show that sodium chloride and sodium acetate in the medium adversely affect growth. Hydrogen yield per biomass (Y(P/X)) of 254 ml/L/g, biomass per substrate utilized (Y(X/S)) of 0.268 and (Y(H2/S) of 0.0349. The results suggested that Sodium at any concentration resulted to inhibit the bacterial productivity of hydrogen.

  20. 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.

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

    PubMed

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

    2016-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1997-11-01

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

  3. Comparative study of weak interactions in molecular crystals: H-H bonds vs hydrogen bonds.

    PubMed

    Wolstenholme, David J; Cameron, T Stanley

    2006-07-20

    The crystal structures of tetraphenylphosphonium squarate, bianthrone, and bis(benzophenone)azine are shown to contain a variety of C-H(delta+)...(delta+)H-C interactions, as well as a variety of C-H...O and C-H...C(pi) interactions. Each of these molecules possesses interactions that can possibly be characterized as either H-H bonds or weak hydrogen bonds based on the first four criteria proposed by Koch and Popelier. These interactions have been completely characterized topologically after the multipole refinement of the structures. It appears that weak interactions of the form C-H(delta+)...(delta+)H-C possess certain correlations between the various properties of the electron density at the bond critical points. The coexistence of the three types of interactions makes it possible to establish similarities and differences in the correlations of these weak interactions. This all leads to a better understanding of H-H interactions and how they fit into the hierarchy of weak interactions.

  4. The Effect of Intermolecular Modes on the Xh-Stretching Vibrations in Hydrogen Bonded Complexes

    NASA Astrophysics Data System (ADS)

    Mackeprang, Kasper; Kjaergaard, Henrik G.

    2016-06-01

    Vibrational spectra of hydrogen bonded bimolecular complexes (XH\\cdotsY, where X is the hydrogen bond donor atom, and Y is the acceptor atom) have long been a theoretical challenge. Specifically, the XH-stretching motion is difficult to describe due to the effect of the large amplitude intermolecular modes inherent to complexes. We have developed a vibrational model, the Local Mode Perturbation Theory (LMPT) model, to accurately determine the transition wavenumber and oscillator strength of the XH-stretching transition in hydrogen bonded bimolecular complexes. The model is based on a local mode (LM) model of the XH-stretching transition and the effect of the intermolecular modes is included via Rayleigh-Schrödinger perturbation theory. Our model has significantly improved results obtained using the LM model (see Figure). Additionally, our LMPT model does not require a full-dimensional anharmonic calculation, which enables application to large systems and the usage of higher level ab initio theory for the required potential energy surfaces. This work was inspired by our recent efforts to accurately determine equilibrium constants of complex formation, which rely on an accurate determination of the oscillator strength of the XH-stretching transition.

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

    NASA Astrophysics Data System (ADS)

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

    2005-09-01

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

  6. A comparative study of the chalcogen bond, halogen bond and hydrogen bond S⋯O/Cl/H formed between SHX and HOCl.

    PubMed

    Fang, Yi; Li, An Yong; Ma, Fei Yan

    2015-03-01

    Ab initio quantum chemistry methods were used to analyze the noncovalent interactions between HOCl and SHX (X = F, CN, NC, Cl, Br, NO2, CCH, CH3, H). Three energetic minimal configurations were characterized for each case, where the S center acts as a Lewis acid interacting with O to form a chalcogen bond, as well as a Lewis base interacting with Cl or H of HOCl to form halogen bond and hydrogen bond, respectively. An electronegative substituent such as F, CN, NC and NO2 tends to form a stronger chalcogen bond, while an electropositive substituent such as CCH, CH3 and H is inclined to form a more stable H-bonded complex. The chalcogen-bonded, halogen-bonded and H-bonded complexes are stabilized by charge transfers from Lp(O) to σ*(SX), from Lp(S) to σ*(ClO), and from Lp(S) to σ*(HO), respectively. As a result, the SHX unit becomes positively charged in halogen-bonded and hydrogen-bonded complexes but negatively charged in chalcogen-bonded complexes. Theory of atoms in molecules, natural bond orbital analysis, molecular electrostatic potential and localized molecular orbital energy decomposition analysis were applied to investigate these noncovalent bonds.

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

    PubMed

    Jang, Do Soo; Choi, Gildon; Cha, Hyung Jin; Shin, Sejeong; Hong, Bee Hak; Lee, Hyeong Ju; Lee, Hee Cheon; Choi, Kwan Yong

    2015-05-01

    Low-barrier hydrogen bonds (LBHBs) have been proposed to have important influences on the enormous reaction rate increases achieved by many enzymes. Δ(5)-3-ketosteroid isomerase (KSI) catalyzes the allylic isomerization of Δ(5)-3-ketosteroid to its conjugated Δ(4)-isomers at a rate that approaches the diffusion limit. Tyr14, a catalytic residue of KSI, has been hypothesized to form an LBHB with the oxyanion of a dienolate steroid intermediate generated during the catalysis. The unusual chemical shift of a proton at 16.8 ppm in the nuclear magnetic resonance spectrum has been attributed to an LBHB between Tyr14 Oη and C3-O of equilenin, an intermediate analogue, in the active site of D38N KSI. This shift in the spectrum was not observed in Y30F/Y55F/D38N and Y30F/Y55F/Y115F/D38N mutant KSIs when each mutant was complexed with equilenin, suggesting that Tyr14 could not form LBHB with the intermediate analogue in these mutant KSIs. The crystal structure of Y30F/Y55F/Y115F/D38N-equilenin complex revealed that the distance between Tyr14 Oη and C3-O of the bound steroid was within a direct hydrogen bond. The conversion of LBHB to an ordinary hydrogen bond in the mutant KSI reduced the binding affinity for the steroid inhibitors by a factor of 8.1-11. In addition, the absence of LBHB reduced the catalytic activity by only a factor of 1.7-2. These results suggest that the amount of stabilization energy of the reaction intermediate provided by LBHB is small compared with that provided by an ordinary hydrogen bond in KSI. PMID:25947291

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

    NASA Astrophysics Data System (ADS)

    Zhang, Lin; Chen, Teli; Ban, Heng; Liu, Ling

    2014-06-01

    Using atomistic simulations, we demonstrate that β-sheet, an essential component of spider silk protein, has a thermal conductivity 1-2 orders of magnitude higher than that of some other protein structures reported in the literature. In contrast to several other nanostructured materials of similar bundled/layered structures (e.g. few-layer graphene and bundled carbon nanotubes), the β-sheet is found to uniquely feature enhanced thermal conductivity with an increased number of constituting units, i.e. β-strands. Phonon analysis identifies inter-β-strand hydrogen bonding as the main contributor to the intriguing phenomenon, which prominently influences the state of phonons in both low- and high-frequency regimes. A thermal resistance model further verifies the critical role of hydrogen bonding in thermal conduction through β-sheet structures.Using atomistic simulations, we demonstrate that β-sheet, an essential component of spider silk protein, has a thermal conductivity 1-2 orders of magnitude higher than that of some other protein structures reported in the literature. In contrast to several other nanostructured materials of similar bundled/layered structures (e.g. few-layer graphene and bundled carbon nanotubes), the β-sheet is found to uniquely feature enhanced thermal conductivity with an increased number of constituting units, i.e. β-strands. Phonon analysis identifies inter-β-strand hydrogen bonding as the main contributor to the intriguing phenomenon, which prominently influences the state of phonons in both low- and high-frequency regimes. A thermal resistance model further verifies the critical role of hydrogen bonding in thermal conduction through β-sheet structures. Electronic supplementary information (ESI) available: Structure of the β-sheets, computational model, determination of area and temperature gradient, and additional phonon DOS results. See DOI: 10.1039/c4nr01195c

  9. The role of hydrogen bond networks in the barrierless thermal denaturation of a native protein.

    PubMed

    Djikaev, Y S; Ruckenstein, Eli

    2009-07-28

    Using the mean first passage time analysis, we have recently developed a kinetic model for the thermal unfolding of a native protein in a barrierless way. A protein was considered as a random heteropolymer consisting of hydrophobic and hydrophilic beads with all the bonds and bond angles equal and constant. As a crucial idea of the model the overall potential around a folded part (cluster) of the protein in which a protein residue performs a chaotic motion was considered to be a combination of three potentials: effective pairwise, average dihedral, and confining. However, the hydrogen bonding of water molecules was not taken into account explicitly. In this paper we improve that model by combining it with a probabilistic approach to water hydrogen bonding. Thus, an additional contribution due to the disruption of hydrogen bond networks around the interacting particles (a cluster of native residues and a residue in the protein unfolded part) appears in the overall potential field around a cluster. The overall potential as a function of the distance from the cluster center has a double well shape. This allows one to determine the rates with which the cluster emits and absorbs residues by using the mean first passage time analysis. Due to a sufficiently large temperature increase or decrease, the emission rate becomes larger than the absorption rate in the whole range of cluster sizes. This leads to the unfolding of the protein in a barrierless way reminiscent of spinodal decomposition. Knowing the cluster emission and absorption rates as functions of temperature and cluster size, one can find the threshold temperatures of cold and hot barrierless denaturation as well as the corresponding unfolding times. The extended model is then applied to the unfolding of bovine pancreatic ribonuclease, consisting of 124 residues whereof 43 are hydrophobic (neutral beads are considered to be hydrophobic as well) and 81 hydrophilic.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2016-08-01

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

  12. 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.

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

    PubMed

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

    2016-02-01

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

  14. 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

  15. 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.

  16. Chiral shift reagent for amino acids based on resonance-assisted hydrogen bonding.

    PubMed

    Chin, Jik; Kim, Dong Chan; Kim, Hae-Jo; Panosyan, Francis B; Kim, Kwan Mook

    2004-07-22

    [structure: see text] A chiral aldehyde that forms resonance-assisted hydrogen bonded imines with amino acids has been developed. This hydrogen bond not only increases the equilibrium constant for imine formation but also provides a highly downfield-shifted NMR singlet for evaluating enantiomeric excess and absolute stereochemistry of amino acids. PMID:15255698

  17. 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…

  18. Calorimetric Investigation of Hydrogen Bonding of Formamide and Its Methyl Derivatives in Organic Solvents and Water

    NASA Astrophysics Data System (ADS)

    Varfolomeev, Mikhail A.; Rakipov, Ilnaz T.; Solomonov, Boris N.

    2013-04-01

    Formamide and its derivatives have a large number of practical applications; also they are structural fragments of many biomolecules. Hydrogen bonds strongly affect their physicochemical properties. In the present work a calorimetric study of formamide and its methyl derivatives was carried out. Enthalpies of solution at infinite dilution of formamide, N-methylformamide, and N, N-dimethylformamide in organic solvents at 298.15 K were measured. The relationships between the obtained enthalpies of solvation and the structure of the studied compounds were observed. Hydrogen-bond enthalpies of amides with chlorinated alkanes, ethers, ketones, esters, nitriles, amines, alcohols, and water were determined. The strength of hydrogen bonds of formamide, N-methylformamide, and N, N-dimethylformamide with proton donor solvents is practically equal. Enthalpies of hydrogen bonds of formamide with the proton acceptor solvents are two times larger in magnitude than the enthalpies of N-methylformamide. The process of hydrogen bonding of amides in aliphatic alcohols and water is complicated. The obtained enthalpies of hydrogen bonding in aliphatic alcohols vary considerably from the amide structure due to the competition between solute-solvent and solvent-solvent hydrogen bonds. Fourier transform infrared spectroscopic measurements were carried out to explain the calorimetric data. Hydration enthalpies of methyl derivatives of formamides contain a contribution of the hydrophobic effect. New thermochemical data on the hydrogen bonding of formamides may be useful for predicting the properties of biomacromolecules.

  19. Strong intermolecular vibrational coupling through cyclic hydrogen-bonded structures revealed by ultrafast continuum mid-IR spectroscopy.

    PubMed

    Stingel, Ashley M; Calabrese, Carmella; Petersen, Poul B

    2013-12-12

    Cyclic hydrogen-bonded structures are common motifs in biological systems, providing structural stability and mediating proton transfer for redox reactions. The mechanism of proton transfer across hydrogen-bonded interfaces depends on the strength of the intermolecular coupling between bridging OH/NH vibrational modes. Here we present a novel ultrafast continuum mid-IR spectroscopy experiment to study the vibrational dynamics of the 7-azaindole-acetic acid (7AI-Ac) heterodimer as a model system for asymmetric cyclic hydrogen-bonded structures. In addition to spreading of the excitation across the whole OH band within the time resolution of the experiment, excitation of a 300 cm(-1) region of the ∼1000 cm(-1) broad OH stretching mode of the acetic acid monomer leads to a frequency shift in the NH stretching mode of the 7AI monomer. This indicates that the NH and OH stretching modes located on the two monomers are strongly coupled despite being separated by 750 cm(-1). The strong coupling further causes the OH and NH bands to decay with a common decay time of ∼2.5 ps. This intermolecular coupling is mediated through the hydrogen-bonded structure of the 7AI-Ac heterodimer and is likely a general property of cyclic hydrogen-bonded structures. Characterizing the vibrational dynamics of and the coupling between the high-frequency OH/NH modes will be important for understanding proton transfer across such molecular interfaces.

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

    PubMed

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

    2015-10-14

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

  1. Role of Bulk Water Environment in Regulation of Functional Hydrogen-Bond Network in Photoactive Yellow Protein.

    PubMed

    Tamura, Koichi; Hayashi, Shigehiko

    2015-12-24

    Photoactive yellow protein is a soluble photoreceptor protein involved in signal transduction for phototaxis. A hydrogen-bond between the chromophore, p-coumaric acid (pCA), and a nearby carboxyl group of Glu46 at the active site is known to play a crucial role in the formation of the signaling state in the photoactivation. Since the hydrogen-bond at the active site as well as the extensive conformational changes of the protein in the formation of the signaling state are considered to be controlled by water molecules, we theoretically examined influence of bulk water environment on the functionally important hydrogen-bond by means of molecular simulations. Theoretical analysis of potential energy profiles of the proton transfer between pCA and Glu46 with quantum mechanical/molecular mechanical (QM/MM) calculations revealed critical effect of electrostatic screening of bulk water on the electronic character of the hydrogen-bond. Moreover, QM/MM free energy geometry optimizations identified the water-penetrating state where Glu46 forming a putative low-barrier hydrogen-bond with pCA is hydrated by water molecules penetrating from bulk environment in addition to the water-excluded state which corresponds to X-ray crystallographic structures. The present results suggest that the water-penetrating state is a precursory conformational substate that leads to efficient formation of the signaling state.

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

    PubMed

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

    2015-09-16

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

  3. 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.

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

    PubMed

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

    2014-12-01

    The definition of a hydrogen bond (H-bond) is intimately related to the topological and dynamic properties of the hydrogen bond network within liquid water. The development of a universal H-bond definition for water is an active area of research as it would remove many ambiguities in the network properties that derive from the fixed definition employed to assign whether a water dimer is hydrogen bonded. This work investigates the impact that an electronic-structure based definition, an energetic, and a geometric definition of the H-bond has upon both topological and dynamic network behavior of simulated water. In each definition, the use of a cutoff (either geometric or energetic) to assign the presence of a H-bond leads to the formation of transiently bonded or broken dimers, which have been quantified within the simulation data. The relative concentration of transient species, and their duration, results in two of the three definitions sharing similarities in either topological or dynamic features (H-bond distribution, H-bond lifetime, etc.), however no two definitions exhibit similar behavior for both classes of network properties. In fact, two networks with similar local network topology (as indicated by similar average H-bonds) can have dramatically different global network topology (as indicated by the defect state distributions) and altered H-bond lifetimes. A dynamics based correction scheme is then used to remove artificially transient H-bonds and to repair artificially broken bonds within the network such that the corrected network exhibits the same structural and dynamic properties for two H-bond definitions (the properties of the third definition being significantly improved). The algorithm described represents a significant step forward in the development of a unified hydrogen bond network whose properties are independent of the original hydrogen bond definition that is employed.

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

    NASA Astrophysics Data System (ADS)

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

    2006-06-01

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

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

    PubMed

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

    2016-03-14

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

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

    PubMed

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

    2016-03-14

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

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

    PubMed Central

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

    2013-01-01

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

  9. Metal-activated histidine carbon donor hydrogen bonds contribute to metalloprotein folding and function.

    PubMed

    Schmiedekamp, Ann; Nanda, Vikas

    2009-07-01

    Carbon donor hydrogen bonds are typically weak interactions that contribute less than 2 kcal/mol, and provide only modest stabilization in proteins. One exception is the class of hydrogen bonds donated by heterocyclic side chain carbons. Histidine is capable of particularly strong interactions through the Cepsilon(1) and Cdelta(2) carbons when the imidazole is protonated or bound to metal. Given the frequent occurrence of metal-bound histidines in metalloproteins, we characterized the energies of these interactions through DFT calculations on model compounds. Imidazole-water hydrogen bonding could vary from -11.0 to -17.0 kcal/mol, depending on the metal identity and oxidation state. A geometric search of metalloprotein structures in the PDB identified a number of candidate His C-H...O hydrogen bonds which may be important for folding or function. DFT calculations on model complexes of superoxide reductase show a carbon donor hydrogen bond positioning a water molecule above the active site.

  10. The strength of side chain hydrogen bonds in the plasma membrane

    NASA Astrophysics Data System (ADS)

    Hristova, Kalina; Sarabipour, Sarvenaz

    2013-03-01

    There are no direct quantitative measurements of hydrogen bond strengths in membrane proteins residing in their native cellular environment. To address this knowledge gap, here we use fluorescence resonance energy transfer (FRET) to measure the impact of hydrogen bonds on the stability of a membrane protein dimer in vesicles derived from eukaryotic plasma membranes, and we compare these results to previous measurements of hydrogen bond strengths in model lipid bilayers. We demonstrate that FRET measurements of membrane protein interactions in plasma membrane vesicles have the requisite sensitivity to quantify the strength of hydrogen bonds. We find that the hydrogen bond-mediated stabilization in the plasma membrane is small, only -0.7 kcal/mole. It is the same as in model lipid bilayers, despite the different nature and dielectric properties of the two environments.

  11. Infrared spectroscopic study of molecular hydrogen bonding in chiral smectic liquid crystals

    PubMed

    Jang; Park; Kim; Glaser; Clark

    2000-10-01

    We report the use of Fourier-transform infrared (IR) spectroscopy to probe intermolecular and intramolecular hydrogen bonding in thermotropic liquid-crystal phases. Infrared spectra of aligned smectic liquid crystal materials vs temperature, and of isotropic liquid-crystal mixtures vs concentration were measured in homologs both with and without hydrogen bonding. Hydrogen bonding significantly changes the direction and magnitude of the vibrational dipole transition moments, causing marked changes in the IR dichroic absorbance profiles of hydrogen-bonded molecular subfragments. A GAUSSIAN94 computation of the directions, magnitudes, and frequencies of the vibrational dipole moments of molecular subfragments shows good agreement with the experimental data. The results show that IR dichroism can be an effective probe of hydrogen bonding in liquid-crystal phases.

  12. 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.

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

    PubMed

    Grayson, Matthew N; Houk, K N

    2016-07-27

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

  14. Comparison of the proton-transfer paths in hydrogen bonds from theoretical potential-energy surfaces and the concept of conservation of bond order III. O-H-O hydrogen bonds.

    PubMed

    Majerz, Irena; Olovsson, Ivar

    2010-01-01

    The quantum-mechanically derived reaction coordinates (QMRC) for the proton transfer in O-H-O hydrogen bonds have been derived from ab initio calculations of potential-energy surfaces. A comparison is made between the QMRC and the corresponding bond-order reaction coordinates (BORC) derived by applying the Pauling bond order concept together with the principle of conservation of bond order. In agreement with earlier results for N-H-N(+) hydrogen bonds there is virtually perfect agreement between the QMRC and BORC curves for intermolecular O-H-O hydrogen bonds. For intramolecular O-H-O hydrogen bonds, the donor and acceptor parts of the molecule impose strong constraints on the O···O distance and the QMRC does not follow the BORC relation in the whole range. The neutron-determined proton positions are located close to the theoretically calculated potential-energy minima, and where the QMRC and the BORC curves coincide with each other. The results confirm the universal character of intermolecular hydrogen bonds: BORC is identical with QMRC and the proton can be moved from donor to acceptor keeping its valency equal to 1. The shape of PES for intramolecular hydrogen bonds is more complex as it is sensitive to the geometry of the molecule as well as of the hydrogen bridge.

  15. Vibrational spectral diffusion and hydrogen bond dynamics in heavy water from first principles.

    PubMed

    Mallik, Bhabani S; Semparithi, A; Chandra, Amalendu

    2008-06-12

    We present a first-principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in heavy water without using any empirical model potentials. The calculations are based on ab initio molecular dynamics simulations for trajectory generation and a time series analysis using the wavelet method for frequency calculations. It is found that, in deuterated water, although a one-to-one relation does not exist between the instantaneous frequency of an OD bond and the distance of its associated hydrogen bond, such a relation does hold on average. The dynamics of spectral diffusion is investigated by means of frequency-time correlation and spectral hole dynamics calculations. Both of these functions are found to have a short-time decay with a time scale of approximately 100 fs corresponding to dynamics of intact hydrogen bonds and a slower long-time decay with a time constant of approximately 2 ps corresponding to lifetimes of hydrogen bonds. The connection of the slower time scale to the dynamics of local structural relaxation is also discussed. The dynamics of hydrogen bond making is shown to have a rather fast time scale of approximately 100 fs; hence, it can also contribute to the short-time dynamics of spectral diffusion. A damped oscillation is also found at around 150-200 fs, which is shown to have come from underdamped intermolecular vibrations of a hydrogen-bonded water pair. Such assignments are confirmed by independent calculations of power spectra of intermolecular motion and hydrogen bond kinetics using the population correlation function formalism. The details of the time constants of frequency correlations and spectral shifts are found to depend on the frequencies of chosen OD bonds and are analyzed in terms of the dynamics of hydrogen bonds of varying strengths and also of free non-hydrogen-bonded OD groups.

  16. Molecular chirality and chiral capsule-type dimer formation of cyclic triamides via hydrogen-bonding interactions.

    PubMed

    Fujimoto, Noriko; Matsumura, Mio; Azumaya, Isao; Nishiyama, Shizuka; Masu, Hyuma; Kagechika, Hiroyuki; Tanatani, Aya

    2012-05-18

    Chiral properties of bowl-shaped cyclic triamides bearing functional groups with hydrogen-bonding ability were examined. Chiral induction of cyclic triamide 3a was observed by addition of chiral amine in solution, and chiral separation was achieved by simple crystallization to afford chiral capsule-type dimer structure of 4a.

  17. Temperature effects on the hydrophobic interaction of parallel plates in the framework of the probabilistic approach to hydrogen bonding.

    PubMed

    Djikaev, Y S; Ruckenstein, Eli

    2010-03-15

    Recently, we have proposed a probabilistic approach to examine the effect of water-water hydrogen bond networks around two foreign hydrophobic particles (immersed in water) on their interaction. Because of the proximity to a particle, a water molecule in the first hydration shell around it forms a smaller number of hydrogen bonds compared to a bulk molecule. The probabilistic approach allows one to analytically evaluate the former number if the latter is known (which is usually the case). On the other hand, the former bonds may be slightly (energetically) enhanced compared to the latter if at least one of the two bonded molecules lie in the first hydration shell and does not form a bond with a nearest neighbor site on the particle surface. When two hydrophobic particles are sufficiently close to each other, the overlap of boundary water-water hydrogen bond networks gives rise to an additional attractive force between them. In this paper we use the probabilistic approach to examine the effect of solvent temperature on the solvent-mediated interaction of two hydrophobic particles. Their hydrophobic attraction is affected by the solvent (water) temperature because the density of the solvent, strength of a hydrogen bonds, and number of hydrogen bonds per molecule are sensitive thereto (the pressure effects are not considered here). The probabilistic approach predicts that the solvent-mediated attraction of hydrophobic solutes is driven by the favorable entropic component ("-temperature x entropy") of the potential of mean force that dominates the unfavorable energetic component. This attraction decreases as the temperature increases.

  18. Structural Implications of Hydrogen-Bond Energetics in Membrane Proteins Revealed by High-Pressure Spectroscopy

    PubMed Central

    Freiberg, Arvi; Kangur, Liina; Olsen, John D.; Hunter, C. Neil

    2012-01-01

    The light-harvesting 1 (LH1) integral membrane complex of Rhodobacter sphaeroides provides a convenient model system in which to examine the poorly understood role of hydrogen bonds (H-bonds) as stabilizing factors in membrane protein complexes. We used noncovalently bound arrays of bacteriochlorophyll chromophores within native and genetically modified variants of LH1 complexes to monitor local changes in the chromophore binding sites induced by externally applied hydrostatic pressure. Whereas membrane-bound complexes demonstrated very high resilience to pressures reaching 2.1 GPa, characteristic discontinuous shifts and broadenings of the absorption spectra were observed around 1 GPa for detergent-solubilized proteins, in similarity to those observed when specific (α or β) H-bonds between the chromophores and the surrounding protein were selectively removed by mutagenesis. These pressure effects, which were reversible upon decompression, allowed us to estimate the rupture energies of H-bonds to the chromophores in LH1 complexes. A quasi-independent, additive role of H-bonds in the α- and β-sublattices in reinforcing the wild-type LH1 complex was established. A comparison of a reaction-center-deficient LH1 complex with complexes containing reaction centers also demonstrated a stabilizing effect of the reaction center. This study thus provides important insights into the design principles of natural photosynthetic complexes. PMID:23283234

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  20. Absolute rate calculations: atom and proton transfers in hydrogen-bonded systems.

    PubMed

    Barroso, Mónica; Arnaut, Luis G; Formosinho, Sebastião J

    2005-02-01

    We calculate energy barriers of atom- and proton-transfer reactions in hydrogen-bonded complexes in the gas phase. Our calculations do not involve adjustable parameters and are based on bond-dissociation energies, ionization potentials, electron affinities, bond lengths, and vibration frequencies of the reactive bonds. The calculated barriers are in agreement with experimental data and high-level ab initio calculations. We relate the height of the barrier with the molecular properties of the reactants and complexes. The structure of complexes with strong hydrogen bonds approaches that of the transition state, and substantially reduces the barrier height. We calculate the hydrogen-abstraction rates in H-bonded systems using the transition-state theory with the semiclassical correction for tunneling, and show that they are in excellent agreement with the experimental data. H-bonding leads to an increase in tunneling corrections at room temperature. PMID:15751360

  1. NMR study of the FH⋯F hydrogen bond. Relation between hydrogen atom position and FH⋯F bond length

    NASA Astrophysics Data System (ADS)

    Panich, A. M.

    1995-07-01

    1H and 19F NMR study of (NH 4) 3BiBr 6NH 4Br·2NH 4HF 2 shows the bifluoride ion in this compound to be asymmetric with distances r( HF) = 1.042 ± 0.002 and R( FF) = 2.373 ± 0.008 Å. Existing NMR and neutron diffraction data for the FH⋯F hydrogen bond in solids have been studied to find a relation between the position of the hydrogen atom and FH⋯F bond length. Such a relation has been established and explained in the framework of the two-dimensional dynamic model of the hydrogen bond. The dependencies of r(AH) on R(AB) for the OH⋯O and FH⋯F bonds are shown to be similar.

  2. 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

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

    PubMed

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

    2016-05-20

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

  4. Hydrogen addition reactions of aliphatic hydrocarbons in comets

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

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

    PubMed

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

    2016-06-01

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

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

    PubMed

    Zhou, Pan-Pan; Qiu, Wen-Yuan

    2009-08-01

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

  7. On the Intramolecular Hydrogen Bond in Solution: Car-Parrinello and Path Integral Molecular Dynamics Perspective.

    PubMed

    Dopieralski, Przemyslaw; Perrin, Charles L; Latajka, Zdzislaw

    2011-11-01

    The issue of the symmetry of short, low-barrier hydrogen bonds in solution is addressed here with advanced ab initio simulations of a hydrogen maleate anion in different environments, starting with the isolated anion, going through two crystal structures (sodium and potassium salts), then to an aqueous solution, and finally in the presence of counterions. By Car-Parrinello and path integral molecular dynamics simulations, it is demonstrated that the position of the proton in the intramolecular hydrogen bond of an aqueous hydrogen maleate anion is entirely related to the solvation pattern around the oxygen atoms of the intramolecular hydrogen bond. In particular, this anion has an asymmetric hydrogen bond, with the proton always located on the oxygen atom that is less solvated, owing to the instantaneous solvation environment. Simulations of water solutions of hydrogen maleate ion with two different counterions, K(+) and Na(+), surprisingly show that the intramolecular hydrogen-bond potential in the case of the Na(+) salt is always asymmetric, regardless of the hydrogen bonds to water, whereas for the K(+) salt, the potential for H motion depends on the location of the K(+). It is proposed that repulsion by the larger and more hydrated K(+) is weaker than that by Na(+) and competitive with solvation by water. PMID:26598249

  8. A theoretical forecast of the hydrogen bond changes in the electronic excited state for BN and its derivatives

    NASA Astrophysics Data System (ADS)

    Wang, Dandan; Hao, Ce; Wang, Se; Dong, Hong; Qiu, Jieshan

    2012-02-01

    The relationship between electronic spectral shifts and hydrogen-bonding dynamics in electronically excited states of the hydrogen-bonded complex is put forward. Hydrogen bond strengthening will induce a redshift of the corresponding electronic spectra, while hydrogen bond weakening will cause a blueshift. Time-dependent density function theory (TDDFT) was used to study the excitation energies in both singlet and triplet electronically excited states of Benzonitrile (BN), 4-aminobenzonitrile (ABN), and 4-dimethylaminobenzonitrile (DMABN) in methanol solvents. Only the intermolecular hydrogen bond C≡N...H-O was involved in our system. A fairly accurate forecast of the hydrogen bond changes in lowlying electronically excited states were presented in light of a very thorough consideration of their related electronic spectra. The deduction we used to depict the trend of the hydrogen bond changes in excited states could help others understand hydrogen-bonding dynamics more effectively.

  9. Enhanced silencing and stabilization of siRNA polyplexes by histidine-mediated hydrogen bonds

    PubMed Central

    Chou, Szu-Ting; Hom, Kellie; Zhang, Daoning; Leng, Qixin; Tricoli, Lucas J.; Hustedt, Jason M.; Lee, Amy; Shapiro, Michael J.; Seog, Joonil; Kahn, Jason D.; Mixson, A. James

    2013-01-01

    Branched peptides containing histidines and lysines (HK) have been shown to be effective carriers for DNA and siRNA. We anticipate that elucidation of the binding mechanism of HK with siRNA will provide greater insight into the self-assembly and delivery of the HK:siRNA polyplex. Non-covalent bonds between histidine residues and nucleic acids may enhance the stability of siRNA polyplexes. We first compared the polyplex biophysical properties of a branched HK with those of branched asparagines-lysine peptide (NK). Consistent with siRNA silencing experiments, gel electrophoresis demonstrated that the HK siRNA polyplex maintained its integrity with prolonged incubation in serum, whereas siRNA in complex with NK was degraded in a time-dependent manner. Isothermal titration calorimetry of various peptides binding to siRNA at pH 7.3 showed that branched polylysine, interacted with siRNA was initially endothermic, whereas branched HK exhibited an exothermic reaction at initial binding. The exothermic interaction indicates formation of non-ionic bonds between histidines and siRNA; purely electrostatic interaction is entropy-driven and endothermic. To investigate the type of non-ionic bond, we studied the protonation state of imidazole rings of a selectively 15N labeled branched HK by heteronuclear single quantum coherence NMR. The peak of Nδ1-H tautomers of imidazole shifted downfield (in the direction of deprotonation) by 0.5 to 1.0 ppm with addition of siRNA, providing direct evidence that histidines formed hydrogen bonds with siRNA at physiological pH. These results establish that histidine-rich peptides form hydrogen bonds with siRNA, thereby enhancing the stability and biological activity of the polyplex in vitro and in vivo. PMID:24161165

  10. Tuning of Thioredoxin Redox Properties by Intramolecular Hydrogen Bonds

    PubMed Central

    Røhr, Åsmund Kjendseth; Hammerstad, Marta; Andersson, K. Kristoffer

    2013-01-01

    Thioredoxin-like proteins contain a characteristic C-x-x-C active site motif and are involved in a large number of biological processes ranging from electron transfer, cellular redox level maintenance, and regulation of cellular processes. The mechanism for deprotonation of the buried C-terminal active site cysteine in thioredoxin, necessary for dissociation of the mixed-disulfide intermediate that occurs under thiol/disulfide mediated electron transfer, is not well understood for all thioredoxin superfamily members. Here we have characterized a 8.7 kD thioredoxin (BC3987) from Bacillus cereus that unlike the typical thioredoxin appears to use the conserved Thr8 side chain near the unusual C-P-P-C active site to increase enzymatic activity by forming a hydrogen bond to the buried cysteine. Our hypothesis is based on biochemical assays and thiolate pKa titrations where the wild type and T8A mutant are compared, phylogenetic analysis of related thioredoxins, and QM/MM calculations with the BC3987 crystal structure as a precursor for modeling of reduced active sites. We suggest that our model applies to other thioredoxin subclasses with similar active site arrangements. PMID:23936007

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

    PubMed

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

    2016-09-01

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

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

    PubMed

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

    2016-09-01

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

  13. 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

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

    NASA Astrophysics Data System (ADS)

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

    2007-06-01

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

  15. Entrapment and release difference resulting from hydrogen bonding interactions in niosome.

    PubMed

    Hao, Yong-Mei; Li, Ke'an

    2011-01-17

    In this study the influence of hydrogen bonding interaction between niosomal membrane and solutes on the drug loading and release was investigated. Salicylic acid (SA) and p-hydroxyl benzoic acid (p-BA) were selected as models. Niosomes were prepared with 1:1 molar ratios of various surfactants and cholesterol by film hydration technique, and the corresponding formulation variables were optimized to achieve the maximum entrapment efficiencies (EE%). The EE% of different formulations followed the trend Span 60>Span 40>Span 20>Span 80. Additionally, it was also found that the EE% of p-BA was much higher than that of SA. This difference may be due to the formation of hydrogen bond between p-BA and niosomal membrane, and the corresponding interaction diagram has been proposed and confirmed indirectly by UV spectroscopy method. The quantitative analysis of hydrogen binding interaction between solutes and niosome has been finished firstly, and the corresponding entrapment equilibrium constant K has been calculated as well. Moreover, in vitro the release of both drugs from niosomes was examined in simulated gastric fluid (SGF) and simulated intestinal fluid (SIF), respectively. The results indicated that the release of p-BA in SIF was much slower than that in SGF, and the release rate of SA in SGF is apparently slower than that in SIF. The possible mechanism was given as well.

  16. 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.

  17. Strikingly different effects of hydrogen bonding on the photodynamics of individual nucleobases in DNA: comparison of guanine and cytosine.

    PubMed

    Zelený, Tomáš; Ruckenbauer, Matthias; Aquino, Adelia J A; Müller, Thomas; Lankaš, Filip; Dršata, Tomáš; Hase, William L; Nachtigallova, Dana; Lischka, Hans

    2012-08-22

    Ab initio surface hopping dynamics calculations were performed to study the photophysical behavior of cytosine and guanine embedded in DNA using a quantum mechanical/molecular mechanics (QM/MM) approach. It was found that the decay rates of photo excited cytosine and guanine were affected in a completely different way by the hydrogen bonding to the DNA environment. In case of cytosine, the geometrical restrictions exerted by the hydrogen bonds did not influence the relaxation time of cytosine significantly due to the generally small cytosine ring puckering required to access the crossing region between excited and ground state. On the contrary, the presence of hydrogen bonds significantly altered the photodynamics of guanine. The analysis of the dynamics indicates that the major contribution to the lifetime changes comes from the interstrand hydrogen bonds. These bonds considerably restricted the out-of-plane motions of the NH(2) group of guanine which are necessary for the ultrafast decay to the ground state. As a result, only a negligible amount of trajectories decayed into the ground state for guanine embedded in DNA within the simulation time of 0.5 ps, while for comparison, the isolated guanine relaxed to the ground state with a lifetime of about 0.22 ps. These examples show that, in addition to phenomena related to electronic interactions between nucleobases, there also exist relatively simple mechanisms in DNA by which the lifetime of a nucleobase is significantly enhanced as compared to the gas phase. PMID:22845192

  18. 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.

  19. Hydrogen-Bonding Toughened Hydrogels and Emerging CO2-Responsive Shape Memory Effect.

    PubMed

    Xu, Bing; Zhang, Yinyu; Liu, Wenguang

    2015-09-01

    A double hydrogen bonding (DHB) hydrogel is constructed by copolymerization of 2-vinyl-4,6-diamino-1,3,5-triazine (hydrophobic hydrogen bonding monomer) and N,N-dimethylacrylamide (hydrophilic hydrogen bonding monomer) with polyethylene glycol diacrylates. The DHB hydrogels demonstrate tunable robust mechanical properties by varying the ratio of hydrogen bonding monomer or crosslinker. Importantly, because of synergistic energy dissipating mechanism of strong diaminotriazine (DAT) hydrogen bonding and weak amide hydrogen bonding, the DHB hydrogels exhibit high toughness (up to 2.32 kJ m(-2)), meanwhile maintaining 0.7 MPa tensile strength, 130% elongation at break, and 8.3 MPa compressive strength. Moreover, rehydration can help to recover the mechanical properties of the cyclic loaded-unloaded gels. Attractively, the DHB hydrogels are responsive to CO2 in water, and demonstrate unprecedented CO2-triggered shape memory behavior owing to the reversible destruction and reconstruction of DAT hydrogen bonding upon passing and degassing CO2 without introducing external acid. The CO2 triggering mechanism may point out a new approach to fabricate shape memory hydrogels.

  20. An AAA-DDD triply hydrogen-bonded complex easily accessible for supramolecular polymers.

    PubMed

    Han, Yi-Fei; Chen, Wen-Qiang; Wang, Hong-Bo; Yuan, Ying-Xue; Wu, Na-Na; Song, Xiang-Zhi; Yang, Lan

    2014-12-15

    For a complementary hydrogen-bonded complex, when every hydrogen-bond acceptor is on one side and every hydrogen-bond donor is on the other, all secondary interactions are attractive and the complex is highly stable. AAA-DDD (A=acceptor, D=donor) is considered to be the most stable among triply hydrogen-bonded sequences. The easily synthesized and further derivatized AAA-DDD system is very desirable for hydrogen-bonded functional materials. In this case, AAA and DDD, starting from 4-methoxybenzaldehyde, were synthesized with the Hantzsch pyridine synthesis and Friedländer annulation reaction. The association constant determined by fluorescence titration in chloroform at room temperature is 2.09×10(7)  M(-1) . The AAA and DDD components are not coplanar, but form a V shape in the solid state. Supramolecular polymers based on AAA-DDD triply hydrogen bonded have also been developed. This work may make AAA-DDD triply hydrogen-bonded sequences easily accessible for stimuli-responsive materials.

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

    PubMed

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

    2016-06-20

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

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

    PubMed

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

    2016-06-20

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

  3. Parameter-Free Hydrogen-Bond Definition to Classify Protein Secondary Structure.

    PubMed

    Haghighi, Hasti; Higham, Jonathan; Henchman, Richard H

    2016-08-25

    DSSP is the most commonly used method to assign protein secondary structure. It is based on a hydrogen-bond definition with an energy cutoff. To assess whether hydrogen bonds defined in a parameter-free way may give more generality while preserving accuracy, we examine a series of hydrogen-bond definitions to assign secondary structure for a series of proteins. Assignment by the strongest-acceptor bifurcated definition with provision for unassigned donor hydrogens, termed the SABLE method, is found to match DSSP with 95% agreement. The small disagreement mainly occurs for helices, turns, and bends. While there is no absolute way to assign protein secondary structure, avoiding molecule-specific cutoff parameters should be advantageous in generalizing structure-assignment methods to any hydrogen-bonded system. PMID:27067825

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

    PubMed

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

    2015-09-15

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

  5. 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…

  6. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

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

    PubMed

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

    2016-06-22

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

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

    PubMed

    Davis, Alexander C; Francisco, Joseph S

    2014-11-20

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  12. 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.

  13. 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

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

    NASA Astrophysics Data System (ADS)

    Takahashi, Masae; Ishikawa, Yoichi

    2013-06-01

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

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

    PubMed

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

    2014-01-15

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

  16. Reorientation of Isomeric Butanols: The Multiple Effects of Steric Bulk Arrangement on Hydrogen-Bond Dynamics.

    PubMed

    Mesele, Oluwaseun O; Vartia, Anthony A; Laage, Damien; Thompson, Ward H

    2016-03-01

    Molecular dynamics simulations are used to investigate OH reorientation in the four isomeric butanols in their bulk liquid state to examine the influence of the arrangement of the steric bulk on the alcohol reorientational and hydrogen-bond (H-bond) dynamics. The results are interpreted within the extended jump model in which the OH reorientation is decomposed into contributions due to "jumps" between H-bond partners and "frame" reorientation of the intact H-bonded pair. Reorientation is fastest in iso-butanol and slowest in tert-butanol, while sec- and n-butanol have similar reorientation times. This latter result is a fortuitous cancellation between the jump and frame reorientation in the two alcohols. The extended jump model is shown to provide a quantitative description of the OH reorientation times. A detailed analysis of the jump times shows that a combination of entropic, enthalpic, and dynamical factors, including transition state recrossing effects, all play a role. A simple model based on the liquid structure is proposed to estimate the energetic and entropic contributions to the jump time. This represents the groundwork for a predictive model of OH reorientation in alcohols, but additional studies are required to better understand the frame reorientation and transition state recrossing effects.

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

    SciTech Connect

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

    2013-06-26

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

  18. Quantification of hyperconjugative effect on the proton donor X-H bond length changes in the red- and blueshifted hydrogen-bonded complexes

    NASA Astrophysics Data System (ADS)

    Zhou, Pan-Pan; Qiu, Wen-Yuan; Jin, Neng-Zhi

    2012-08-01

    A whole dataset containing 55 hydrogen bonds were studied at the MP2/aug-cc-pVTZ level of theory. The changes of geometries and stretching vibrational frequencies show that there are 31 redshifted and 24 blueshifted hydrogen-bonded complexes. Natural bond orbital analysis was carried out at the B3LYP/aug-cc-pVTZ level of theory to obtain the electron densities in the bonding and antibonding orbitals of the proton donor X-H bond, which are closely associated with its bond length. Based on their relationship, a generally applicable method considering both the electron densities in the bonding and antibonding orbitals of the proton donor X-H bond has been developed to quantitatively describe the hyperconjugative effect on the X-H bond length changes in these hydrogen-bonded complexes.

  19. Quantification of hyperconjugative effect on the proton donor X-H bond length changes in the red- and blueshifted hydrogen-bonded complexes.

    PubMed

    Zhou, Pan-Pan; Qiu, Wen-Yuan; Jin, Neng-Zhi

    2012-08-28

    A whole dataset containing 55 hydrogen bonds were studied at the MP2/aug-cc-pVTZ level of theory. The changes of geometries and stretching vibrational frequencies show that there are 31 redshifted and 24 blueshifted hydrogen-bonded complexes. Natural bond orbital analysis was carried out at the B3LYP/aug-cc-pVTZ level of theory to obtain the electron densities in the bonding and antibonding orbitals of the proton donor X-H bond, which are closely associated with its bond length. Based on their relationship, a generally applicable method considering both the electron densities in the bonding and antibonding orbitals of the proton donor X-H bond has been developed to quantitatively describe the hyperconjugative effect on the X-H bond length changes in these hydrogen-bonded complexes.

  20. Novel method for concentrating and drying polymeric nanoparticles: hydrogen bonding coacervate precipitation.

    PubMed

    D'Addio, Suzanne M; Kafka, Concepcion; Akbulut, Mustafa; Beattie, Patrick; Saad, Walid; Herrera, Margarita; Kennedy, Michael T; Prud'homme, Robert K

    2010-04-01

    Nanoparticles have significant potential in therapeutic applications to improve the bioavailability and efficacy of active drug compounds. However, the retention of nanometer sizes during concentrating or drying steps presents a significant problem. We report on a new concentrating and drying process for poly(ethylene glycol) (PEG) stabilized nanoparticles, which relies upon the unique pH sensitive hydrogen bonding interaction between PEG and polyacid species. In the hydrogen bonding coacervate precipitation (HBCP) process, PEG protected nanoparticles rapidly aggregate into an easily filterable precipitate upon the addition various polyacids. When the resulting solid is neutralized, the ionization of the acid groups eliminates the hydrogen bonded structure and the approximately 100 nm particles redisperse back to within 10% of their original size when poly(acrylic acid) and citric acid are used and 45% when poly(aspartic acid) is used. While polyacid concentrations of 1-5 wt % were used to form the precipitates, the incorporation of the acid into the PEG layer is approximately 1:1 (acid residue):(ethylene oxide unit) in the final dried precipitate. The redispersion of dried beta-carotene nanoparticles protected with PEG-b-poly(lactide-co-glycolide) polymers dried by HBCP was compared with the redispersion of particles dried by freeze-drying with sucrose as a cryprotectant, spray freeze-drying, and normal drying. Freeze-drying with 0, 2, and 12 wt % sucrose solutions resulted in size increases of 350%, 50%, and 6%, respectively. Spray freeze-drying resulted in particles with increased sizes of 50%, but no cryoprotectant and only moderate redispersion energy was required. Conventional drying resulted in solids that could not be redispersed back to nanometer size. The new HBCP process offers a promising and efficient way to concentrate or convert nanoparticle dispersions into a stable dry powder form.

  1. Cooperativity in ordinary ice and breaking of hydrogen bonds.

    PubMed

    Ruckenstein, Eli; Shulgin, Ivan L; Shulgin, Leonid I

    2007-06-28

    The total interaction energy between two H-bonded water molecules in a condensed phase is composed of a binding energy between them and an energy due to a cooperative effect. An approximate simple expression is suggested for the dependence of the interaction energy between two H-bonded water molecules on the number of neighboring water molecules with which they are H-bonded. Using this expression, the probabilities of breaking a H bond with various numbers of H-bonded neighbors are estimated. These probabilities are used in computer simulations of the breaking of specified fractions of H bonds in an ordinary (hexagonal) ice. A large "piece" of hexagonal ice (up to 8 millions molecules) is built up, and various percentages of H bonds are considered broken. It is shown that 62-63% of H bonds must be broken in order to disintegrate the "piece" of ice into disconnected clusters. This value is only a little larger than the percolation threshold (61%) predicted both by the percolation theory for tetrahedral ice and by simulations in which all H bonds were considered equally probable to be broken. When the percentage of broken bonds is smaller than 62-63%, there is a network of H-bonded molecules which contains the overwhelming majority of water molecules. This result contradicts some models of water which consider that water consists of a mixture of water clusters of various sizes. The distribution of water molecules with unequal probabilities for breaking is compared with the simulation involving equal probabilities for breaking. It was found that in the former case, there is an enhanced number of water monomers without H bonds, that the numbers of 2- and 3-bonded molecules are smaller, and the number of 4-bonded molecules is larger than in the latter case.

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

    NASA Astrophysics Data System (ADS)

    Xin-Jun, Zhao; Zhi-Fu, Gao

    2016-07-01

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

  3. 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

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

    PubMed

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

    2000-12-01

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

  5. Telomere structure and stability: covalency in hydrogen bonds, not resonance assistance, causes cooperativity in guanine quartets.

    PubMed

    Fonseca Guerra, Célia; Zijlstra, Hester; Paragi, Gábor; Bickelhaupt, F Matthias

    2011-11-01

    We show that the cooperative reinforcement between hydrogen bonds in guanine quartets is not caused by resonance-assisted hydrogen bonding (RAHB). This follows from extensive computational analyses of guanine quartets (G(4)) and xanthine quartets (X(4)) based on dispersion-corrected density functional theory (DFT-D). Our investigations cover the situation of quartets in the gas phase, in aqueous solution as well as in telomere-like stacks. A new mechanism for cooperativity between hydrogen bonds in guanine quartets emerges from our quantitative Kohn-Sham molecular orbital (MO) and corresponding energy decomposition analyses (EDA). Our analyses reveal that the intriguing cooperativity originates from the charge separation that goes with donor-acceptor orbital interactions in the σ-electron system, and not from the strengthening caused by resonance in the π-electron system. The cooperativity mechanism proposed here is argued to apply, beyond the present model systems, also to other hydrogen bonds that show cooperativity effects.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

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

    SciTech Connect

    Fifield, Leonard S.; Grate, Jay W.

    2010-06-01

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

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

    PubMed

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

    2016-09-19

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

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

    NASA Astrophysics Data System (ADS)

    Isaev, A. N.

    2016-03-01

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

  11. Water dynamics: relation between hydrogen bond bifurcations, molecular jumps, local density & hydrophobicity.

    PubMed

    Titantah, John Tatini; Karttunen, Mikko

    2013-10-21

    Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. We employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total simulation time was ≈ 2 ns. Both bulk water and water in the presence of a small hydrophobic molecule were simulated. We show that large-angle jumps and bond bifurcations are fundamental properties of water dynamics and that they are intimately coupled to both local density and hydrogen bond strength oscillations in scales from about 60 to a few hundred femtoseconds: Local density differences are the driving force for bond bifurcations and the consequent large-angle jumps. The jumps are intimately connected to the recently predicted hydrogen bond energy asymmetry. Our analysis also appears to confirm the existence of the so-called negativity track provided by the lone pairs of electrons on the oxygen atom to enable water rotation.

  12. Sequence-specific association in aqueous media by integrating hydrogen bonding and dynamic covalent interactions.

    PubMed

    Li, Minfeng; Yamato, Kazuhiro; Ferguson, Joseph S; Gong, Bing

    2006-10-01

    Oligoamide strands that associate in a sequence-specific fashion into hydrogen-bonded duplexes in nonpolar solvents were converted into disulfide cross-linked duplexes in aqueous media. Thus, by incorporating trityl-protected thiol groups, which allows the reversible formation of disulfide bonds, into the oligoamide strands, only duplexes consisting of complementary hydrogen-bonding sequences were formed in aqueous solution as well as in methanol. The sequence-specific cross-linking of oligoamide strands was confirmed by MALDI-TOF, reverse-phase HPLC, and by isolating a cross-linked duplex. This study demonstrates that the sequence-specificity characteristic of multiply hydrogen-bonded systems can be extended into competitive media through the interplay of H-bonding and reversible covalent interactions, based on which a new class of molecular associating and ligating units that are compatible with both polar and nonpolar environments can be conveniently obtained.

  13. Hydrogen-bonding interactions between a nitrile-based functional ionic liquid and DMSO

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

    Task-specific ionic liquids (TSILs) have been introduced by incorporating additional functional groups in the cation or anion to impart specific properties or reactivates. In this work, the hydrogen-bonding interactions between a nitrile-functional TSIL 1-propylnitrile-3-methylimidazolium tetrafluoroborate ([PCNMIM][BF4]) and dimethyl sulphoxide (DMSO) were investigated in detail by attenuated total reflection infrared spectroscopy (ATR-IR), combined with hydrogen nuclear magnetic resonance (1H NMR) and density functional theory calculations (DFT). It was found that, first, introducing a nitrile group into the alkyl chain does not change the main interaction site in the cation. It is still the C2 hydrogen. So the v(C2-H) is more sensitive to the environmental change and can be used as an indicator of the environments change of IL. Second, the wavenumber shift changes of v(C2-H) have two turning points (xDMSO ≈ 0.6 and 0.9), dividing the dilution process into three stages. Combined with the calculation results, the dilution process is identified as: From larger ion clusters to smaller ion clusters (xDMSO < 0.6), then to ion pairs (0.6 0.9). Introducing a nitrile group into the alkyl chain does not influence the dilution process of IL dissolving in DMSO. Third, the Ctbnd N in [PCNMIM][BF4] can work as an electron donor in forming hydrogen-bonds with the methyl group of [PCNMIM]+ and DMSO, but its strength is weaker than that formed by the imidazolium ring C-Hs. The dual roles of the cation to work as both electron acceptor and donor expand the wide applications of this nitrile-functional ionic liquid.

  14. Coherent Two-Dimensional Infrared Spectroscopy of Vibrational Excitons in Hydrogen-Bonded Liquids

    NASA Astrophysics Data System (ADS)

    Paarmann, Alexander

    The structure and structural dynamics of hydrogen bonded liquids were studied experimentally and theoretically with coherent two-dimensional infrared (2DIR) spectroscopy. The resonant intermolecular interactions within the fully resonant hydrogen bond networks give access to spatial correlations in the dynamics of the liquid structures. New experimental and theoretical tools were developed that significantly reduced the technical challenges of these studies. A nanofluidic flow device was designed and manufactured providing sub-micron thin, actively stabilized liquid sample layers between similarly thin windows. A simulation protocol for nonlinear vibrational response calculations of disordered fluctuating vibrational excitons was developed that allowed for the first treatment of resonant intermolecular interactions in the 2DIR response of liquid water. The 2DIR spectrum of the O-H stretching vibration of pure liquid water was studied experimentally at different temperatures. At ambient conditions the loss of frequency correlations is extremely fast, and is attributed to very efficient modulations of the two-dimensional O-H stretching vibrational potential through librational motions in the hydrogen bond network. At temperatures near freezing, the librational motions are significantly reduced leading to a pronounced slowing down of spectral diffusion dynamics. Comparison with energy transfer time scales revealed the first direct proof of delocalization of the vibrational excitations. This work establishes a fundamentally new view of vibrations in liquid water by providing a spatial length scale of correlated hydrogen-bond motions. The linear and 2DIR response of the amide I mode in neat liquid formamide was found to be dominated by excitonic effects due to largely delocalized vibrational excitations. The spectral response and dynamics are very sensitive to the excitonic mode structure and infrared activity distributions, leading to a pronounced asymmetry of linear

  15. Hydrogen bonding mediated by key orbital interactions determines hydration enthalpy differences of phosphate water clusters.

    PubMed

    Ruben, Eliza A; Chapman, Michael S; Evanseck, Jeffrey D

    2007-10-25

    Electronic structure calculations have been carried out to provide a molecular interpretation for dihydrogen phosphate stability in water relative to that of metaphosphate. Specifically, hydration enthalpies of biologically important metaphosphate and dihydrogen phosphate with one to three waters have been computed with second-order Møller-Plesset perturbation and density functional theory (B3LYP) with up to the aug-cc-pvtz basis set and compared to experiment. The inclusion of basis set superposition error corrections and supplemental diffuse functions are necessary to predict hydration enthalpies within experimental uncertainty. Natural bond orbital analysis is used to rationalize underlying hydrogen bond configurations and key orbital interactions responsible for the experimentally reported difference in hydration enthalpies between metaphosphate and dihydrogen phosphate. In general, dihydrogen phosphate forms stronger hydrogen bonds compared to metaphosphate due to a greater charge transfer or enhanced orbital overlap between the phosphoryl oxygen lone pairs, n(O), and the antibonding O-H bond of water. Intramolecular distal lone pair repulsion with the donor n(O) orbital of dihydrogen phosphate distorts symmetric conformations, which improves n(O) and sigma*(O-H) overlap and ultimately the hydrogen bond strength. Unlike metaphosphate, water complexed to dihydrogen phosphate can serve as both a hydrogen bond donor and a hydrogen bond acceptor, which results in cooperative charge transfer and a reduction of the energy gap between n(O) and sigma*(O-H), leading to stronger hydrogen bonds. This study offers insight into how orbital interactions mediate hydrogen bond strengths with potential implications on the understanding of the kinetics and mechanism in enzymatic phosphoryl transfer reactions.

  16. Quantum Calculations on Hydrogen Bonds in Certain Water Clusters Show Cooperative Effects

    SciTech Connect

    Znamenskiy, Vasiliy S.; Green, Michael E.

    2007-01-09

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

  17. Quantum Calculations on Hydrogen Bonds in Certain Water Clusters Show Cooperative Effects.

    SciTech Connect

    Znamenskiy, Vasiliy S.; Green, Michael E.

    2006-12-08

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

  18. Normal coordinate analysis of bilirubin vibrational spectra: Effects of intramolecular hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Yang, Bijun; Taylor, Robert C.; Morris, Michael D.; Wang, Xiu-Zhen; Wu, Jin-guang; Yu, Bao-Zhu; Xu, Guang-xian; Soloway, Roger D.

    1993-11-01

    Normal coordinate analyses are presented for half-bilirubin molecules. Calculations for the AB pyrromethenone include intramolecular hydrogen bonds, while those for the CD chromophore exclude intramolecular hydrogen bonds. Valence force-field parameters have been optimized to correlate closely with the IR and Raman spectra of the target molecules. The results of the calculations are compared with the spectra of bilirubin IXa and various model compounds in the solid state and solution.

  19. How Alcohol Chain-Length and Concentration Modulate Hydrogen Bond Formation in a Lipid Bilayer

    PubMed Central

    Dickey, Allison N.; Faller, Roland

    2007-01-01

    Molecular dynamics simulations are used to measure the change in properties of a hydrated dipalmitoylphosphatidylcholine bilayer when solvated with ethanol, propanol, and butanol solutions. There are eight oxygen atoms in dipalmitoylphosphatidylcholine that serve as hydrogen bond acceptors, and two of the oxygen atoms participate in hydrogen bonds that exist for significantly longer time spans than the hydrogen bonds at the other six oxygen atoms for the ethanol and propanol simulations. We conclude that this is caused by the lipid head group conformation, where the two favored hydrogen-bonding sites are partially protected between the head group choline and the sn-2 carbonyl oxygen. We find that the concentration of the alcohol in the ethanol and propanol simulations does not have a significant influence on the locations of the alcohol/lipid hydrogen bonds, whereas the concentration does impact the locations of the butanol/lipid hydrogen bonds. The concentration is important for all three alcohol types when the lipid chain order is examined, where, with the exception of the high-concentration butanol simulation, the alcohol molecules having the longest hydrogen-bonding relaxation times at the favored carbonyl oxygen acceptor sites also have the largest order in the upper chain region. The lipid behavior in the high-concentration butanol simulation differs significantly from that of the other alcohol concentrations in the order parameter, head group rotational relaxation time, and alcohol/lipid hydrogen-bonding location and relaxation time. This appears to be the result of the system being very near to a phase transition, and one occurrence of lipid flip-flop is seen at this concentration. PMID:17218462

  20. 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

  1. Alignment of paired molecules of C60 within a hexagonal platform networked through hydrogen-bonds.

    PubMed

    Hisaki, Ichiro; Nakagawa, Shoichi; Sato, Hiroyasu; Tohnai, Norimitsu

    2016-07-28

    We demonstrate, for the first time, that a hydrogen-bonded low-density organic framework can be applied as a platform to achieve periodic alignment of paired molecules of C60, which is the smallest example of a finite-numbered cluster of C60. The framework is a layered assembly of a hydrogen-bonded 2D hexagonal network (LA-H-HexNet) composed of dodecadehydrotribenzo[18]annulene derivatives. PMID:27417325

  2. 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

  3. Thermal-sensitive viscosity transition of elongated micelles induced by breaking intermolecular hydrogen bonding of amide groups.

    PubMed

    Morita, Clara; Imura, Yoshiro; Ogawa, Tetsuya; Kurata, Hiroki; Kawai, Takeshi

    2013-05-01

    A heat-induced viscosity transition of novel worm-like micelles of a long alkyl-chain amidoamine derivative (C18AA) bearing intermolecular hydrogen-bonding group was investigated by cryo-TEM, FT-IR, and rheological measurements. At lower temperature, C18AA forms straight elongated micelles with a length on the order of micrometers due to strong intermolecular hydrogen-bonded packing of the amide groups, although the micelles rarely entangle and have low value of zero-shear viscosity. The straight elongated micelles likely became flexible and underwent a morphological transition from straight structure to worm-like structure at a certain temperature, which caused a drastic increase in viscosity due to entanglement of the micelles. This morphological transition was caused by a defect of intermolecular hydrogen bonding between the amide groups on heating. Furthermore, addition of LiCl, which acts as hydrogen-bond breaker, also promoted the viscosity transition, leading to a lowering of the transition temperature.

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

    PubMed Central

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

    2016-01-01

    The asymmetric unit of the title compound, 4C4H4FN3O·C3H6N6, comprises of two independent 5-fluoro­cytosine (5FC) mol­ecules (A and B) and one half-mol­ecule of melamine (M). The other half of the melamine mol­ecule is generated by a twofold axis. 5FC mol­ecules A and B are linked through two different homosynthons [R 2 2(8) ring motif]; one is formed via a pair of N—H⋯O hydrogen bonds and the second via a pair of N—H⋯N hydrogen bonds. In addition to this pairing, the O atoms of 5FC mol­ecules A and B inter­act with the N2 amino group on both sides of the melamine mol­ecule, forming a DDAA array of quadruple hydrogen bonds and generating a supra­molecular pattern. The 5FC (mol­ecules A and B) and two melamine mol­ecules inter­act via N—H⋯O, N—H⋯N and N—H⋯O, N—H⋯N, C—H⋯F hydrogen bonds forming R 6 6(24) and R 4 4(15) ring motifs. The crystal structure is further strengthened by C—H⋯F, C—F⋯π and π–π stacking inter­actions. PMID:27375887

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

    ERIC Educational Resources Information Center

    Weiss, Hilton M.

    2010-01-01

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

  6. Unconventional hydrogen bonding to organic ions in the gas phase: stepwise association of hydrogen cyanide with the pyridine and pyrimidine radical cations and protonated pyridine.

    PubMed

    Hamid, Ahmed M; El-Shall, M Samy; Hilal, Rifaat; Elroby, Shaaban; Aziz, Saadullah G

    2014-08-01

    Equilibrium thermochemical measurements using the ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes for the stepwise association of HCN molecules with the pyridine and pyrimidine radical cations forming the C5H5N(+·)(HCN)n and C4H4N2 (+·)(HCN)n clusters, respectively, with n = 1-4. For comparison, the binding of 1-4 HCN molecules to the protonated pyridine C5H5NH(+)(HCN)n has also been investigated. The binding energies of HCN to the pyridine and pyrimidine radical cations are nearly equal (11.4 and 12.0 kcal/mol, respectively) but weaker than the HCN binding to the protonated pyridine (14.0 kcal/mol). The pyridine and pyrimidine radical cations form unconventional carbon-based ionic hydrogen bonds with HCN (CH(δ+)⋯NCH). Protonated pyridine forms a stronger ionic hydrogen bond with HCN (NH(+)⋯NCH) which can be extended to a linear chain with the clustering of additional HCN molecules (NH(+)⋯NCH··NCH⋯NCH) leading to a rapid decrease in the bond strength as the length of the chain increases. The lowest energy structures of the pyridine and pyrimidine radical cation clusters containing 3-4 HCN molecules show a strong tendency for the internal solvation of the radical cation by the HCN molecules where bifurcated structures involving multiple hydrogen bonding sites with the ring hydrogen atoms are formed. The unconventional H-bonds (CH(δ+)⋯NCH) formed between the pyridine or the pyrimidine radical cations and HCN molecules (11-12 kcal/mol) are stronger than the similar (CH(δ+)⋯NCH) bonds formed between the benzene radical cation and HCN molecules (9 kcal/mol) indicating that the CH(δ+) centers in the pyridine and pyrimidine radical cations have more effective charges than in the benzene radical cation.

  7. 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.

  8. 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.

  9. Hydrogen Bonding in Liquid Water and in the Hydration Shell of Salts.

    PubMed

    Dagade, Dilip H; Barge, Seema S

    2016-03-16

    A near-IR spectral study on pure water and aqueous salt solutions is used to investigate stoichiometric concentrations of different types of hydrogen-bonded water species in liquid water and in water comprising the hydration shell of salts. Analysis of the thermodynamics of hydrogen-bond formation signifies that hydrogen-bond making and breaking processes are dominated by enthalpy with non-negligible heat capacity effects, as revealed by the temperature dependence of standard molar enthalpies of hydrogen-bond formation and from analysis of the linear enthalpy-entropy compensation effects. A generalized method is proposed for the simultaneous calculation of the spectrum of water in the hydration shell and hydration number of solutes. Resolved spectra of water in the hydration shell of different salts clearly differentiate hydrogen bonding of water in the hydration shell around cations and anions. A comparison of resolved liquid water spectra and resolved hydration-shell spectra of ions highlights that the ordering of absorption frequencies of different kinds of hydrogen-bonded water species is also preserved in the bound state with significant changes in band position, band width, and band intensity because of the polarization of water molecules in the vicinity of ions.

  10. Knowledge-based model of hydrogen-bonding propensity in organic crystals.

    PubMed

    Galek, Peter T A; Fábián, László; Motherwell, W D Samuel; Allen, Frank H; Feeder, Neil

    2007-10-01

    A new method is presented to predict which donors and acceptors form hydrogen bonds in a crystal structure, based on the statistical analysis of hydrogen bonds in the Cambridge Structural Database (CSD). The method is named the logit hydrogen-bonding propensity (LHP) model. The approach has a potential application in identifying both likely and unusual hydrogen bonding, which can help to rationalize stable and metastable crystalline forms, of relevance to drug development in the pharmaceutical industry. Whilst polymorph prediction techniques are widely used, the LHP model is knowledge-based and is not restricted by the computational issues of polymorph prediction, and as such may form a valuable precursor to polymorph screening. Model construction applies logistic regression, using training data obtained with a new survey method based on the CSD system. The survey categorizes the hydrogen bonds and extracts model parameter values using descriptive structural and chemical properties from three-dimensional organic crystal structures. LHP predictions from a fitted model are made using two-dimensional observables alone. In the initial cases analysed, the model is highly accurate, achieving approximately 90% correct classification of both observed hydrogen bonds and non-interacting donor-acceptor pairs. Extensive statistical validation shows the LHP model to be robust across a range of small-molecule organic crystal structures. PMID:17873446

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  12. 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.

  13. A C alpha-H...O hydrogen bond in a membrane protein is not stabilizing.

    PubMed

    Yohannan, Sarah; Faham, Salem; Yang, Duan; Grosfeld, David; Chamberlain, Aaron K; Bowie, James U

    2004-03-01

    Hydrogen bonds involving a carbon donor are very common in protein structures, and energy calculations suggest that Calpha-H...O hydrogen bonds could be about one-half the strength of traditional hydrogen bonds. It has therefore been proposed that these nontraditional hydrogen bonds could be a significant factor in stabilizing proteins, particularly membrane proteins as there is a low dielectric and no competition from water in the bilayer core. Nevertheless, this proposition has never been tested experimentally. Here, we report an experimental test of the significance of Calpha-H...O bonds for protein stability. Thr24 in bacteriorhodopsin, which makes an interhelical Calpha-H...O hydrogen bond to the Calpha of Ala51, was changed to Ala, Val, and Ser, and the thermodynamic stability of the mutants was measured. None of the mutants had significantly reduced stability. In fact, T24A was more stable than the wild-type protein by 0.6 kcal/mol. Crystal structures were determined for each of the mutants, and, while some structural changes were seen for T24S and T24V, T24A showed essentially no apparent structural alteration that could account for the increased stability. Thus, Thr24 appears to destabilize the protein rather than stabilize. Our results suggest that Calpha-H...O bonds are not a major contributor to protein stability.

  14. Hydrogen bond cooperativity in water hexamers: atomic energy perspective of local stabilities.

    PubMed

    Albrecht, Laura; Chowdhury, Saptarshi; Boyd, Russell J

    2013-10-17

    Atomic energies are used to describe local stability in eight low-lying water hexamers: prism, cage, boat 1, boat 2, bag, chair, book 1, and book 2. The energies are evaluated using the quantum theory of atoms in molecules (QTAIM) at MP2/aug-cc-pVTZ geometries. It is found that the simple, stabilizing cooperativity observed in linear hydrogen-bonded water systems is diminished as clusters move from nearly planar to three-dimensional structures. The prism, cage, and bag clusters can have local water stabilities differing up to 5 kcal mol(-1) as a result of mixed cooperative and anticooperative interactions. At the atomic level, in many cases a water may have a largely stabilized oxygen atom but the net water stability will be diminished due to strong destabilization of the water's hydrogen atoms. Analysis of bond critical point (BCP) electron densities shows that the reduced cooperativity results in a decrease in hydrogen bond strength and an increase in covalent bond strength, most evident in the prism. The chair, with the greatest cooperativity, has the largest average electron density at the BCP per hydrogen bond, whereas the cage has the largest total value for BCP density at all hydrogen bonds. The cage also has the second largest value (after the prism) for covalent bond critical point densities and an oxygen-oxygen BCP which may factor into the experimentally observed stability of the structure.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    Control of tritium retention and its removal from the first wall of future fusion devices are one of the most crucial issues for safety and effective use for fuel. Nitrogen addition into remote edge plasmas has been considered and tested as an effective method for suppression of carbon film deposition and reduction of hydrogen isotope absorption in the deposited films. In this paper we have investigated the scavenger effects of nitrogen injected into low temperature D2/CH4 plasmas on hydrogenated carbon film growth using a small helical device. The result of the deposition shows that the key reactive particles with CN and ND(H) bonds to suppression of hydrogenated carbon film growth and hydrogen isotope absorption are much slowly generated compared with hydrocarbon particles such as CD(H)x and C2D(H)x. This may be due to the slow atomic nitrogen diffusion into hydrogenated carbon layer and the chemical equilibrium between nitrogen absorption.

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

    PubMed

    Saluja, Hardeep; Mehanna, Ahmed; Panicucci, Riccardo; Atef, Eman

    2016-01-01

    The purpose of this study is to confirm the impact of polar functional groups on inter and intra-molecular hydrogen bonding in haloperidol (HP) and droperidol (DP) and, hence, their effects on dissolution using a new approach. To confirm our theory, a new molecule: deshydroxy-haloperidol (DHP) was designed and its synthesis was requested from a contract laboratory. The molecule was then studied and compared to DP and HP. Unlike DHP, both the HP and DP molecules have hydrogen donor groups, therefore, DHP was used to confirm the relative effects of the hydrogen donor group on solubility and crystal packing. The solid dispersions of the three structurally related molecules: HP, DP, and DHP were prepared using PVPK30, and characterized using XRPD and IR. A comparative dissolution study was carried out in aqueous medium. The absence of a hydrogen bonding donor group in DHP resulted in an unexpected increase in its aqueous solubility and dissolution rate from solid dispersion, which is attributed to weaker crystal pack. The increased dissolution rate of HP and DP from solid dispersions is attributed to drug-polymer hydrogen bonding that interferes with the drug-drug intermolecular hydrogen bonding and provides thermodynamic stability of the dispersed drug molecules. The drug-drug intermolecular hydrogen bond is the driving force for precipitation and crystal packing. PMID:27258248

  17. Complementary halogen and hydrogen bonding: sulfur...iodine interactions and thioamide ribbons.

    PubMed

    Arman, Hadi D; Gieseking, Rebecca L; Hanks, Timothy W; Pennington, William T

    2010-03-21

    Complementary halogen bonding and hydrogen bonding coexist in co-crystals of organoiodines with molecules containing the thioamide functionality. Thiourea.organoiodine co-crystals are shown to exhibit a remarkably reliable synthon with complementary N-H...S ribbons and S...I interactions.

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

    PubMed

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

    2015-09-14

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

  19. 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.

  20. Hydrogen Bonding Based Layer-by-Layer Assembly of Poly(vinyl alcohol) with Weak Polyacids

    NASA Astrophysics Data System (ADS)

    Lee, Hyomin; Mensire, Remy; Cohen, Robert; Rubner, Michael

    2012-02-01

    Multilayer thin films that consist of poly(vinyl alcohol) (PVA) and weak polyacids such as poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA) were prepared by hydrogen bonding interactions. Both the degree of hydrolysis and molecular weight of PVA were investigated in terms of their influence on growth behavior and pH stability. Multilayer films containing PVA and PAA could be assembled successfully only by using partially hydrolyzed PVA and low pH solutions. By comparing films containing PAA with those containing a more strongly interacting partner, PMAA, it was shown that the extent of PVA hydrolysis becomes significant only when weak hydrogen bonding pairs such as PVA and PAA were used. pH-triggered dissolution experiments demonstrated that the degree of hydrolysis can be used as an additional parameter by which to tune the pH stability of the film. Also, the presence of an abundance of free hydroxyl and carboxylic acid groups in the multilayer allowed enhanced pH stability to be obtained by thermal and chemical methods as well as numerous opportunities for post-assembly functionalization.

  1. Hydrogen bonding and orientation effects on the accommodation of methylamine at the air-water interface

    NASA Astrophysics Data System (ADS)

    Hoehn, Ross D.; Carignano, Marcelo A.; Kais, Sabre; Zhu, Chongjing; Zhong, Jie; Zeng, Xiao C.; Francisco, Joseph S.; Gladich, Ivan

    2016-06-01

    Methylamine is an abundant amine compound detected in the atmosphere which can affect the nature of atmospheric aerosol surfaces, changing their chemical and optical properties. Molecular dynamics simulation results show that methylamine accommodation on water is close to unity with the hydrophilic head group solvated in the interfacial environment and the methyl group pointing into the air phase. A detailed analysis of the hydrogen bond network indicates stronger hydrogen bonds between water and the primary amine group at the interface, suggesting that atmospheric trace gases will likely react with the methyl group instead of the solvated amine site. These findings suggest new chemical pathways for methylamine acting on atmospheric aerosols in which the methyl group is the site of orientation specific chemistry involving its conversion into a carbonyl site providing hydrophilic groups for uptake of additional water. This conversion may explain the tendency of aged organic aerosols to form cloud condensation nuclei. At the same time, formation of NH2 radical and formaldehyde is suggested to be a new source for NH2 radicals at aerosol surfaces, other than by reaction of absorbed NH3. The results have general implications for the chemistry of other amphiphilic organics, amines in particular, at the surface of atmospherically relevant aerosols.

  2. Metal-free oxidation of aromatic carbon-hydrogen bonds through a reverse-rebound mechanism.

    PubMed

    Yuan, Changxia; Liang, Yong; Hernandez, Taylor; Berriochoa, Adrian; Houk, Kendall N; Siegel, Dionicio

    2013-07-11

    Methods for carbon-hydrogen (C-H) bond oxidation have a fundamental role in synthetic organic chemistry, providing functionality that is required in the final target molecule or facilitating subsequent chemical transformations. Several approaches to oxidizing aliphatic C-H bonds have been described, drastically simplifying the synthesis of complex molecules. However, the selective oxidation of aromatic C-H bonds under mild conditions, especially in the context of substituted arenes with diverse functional groups, remains a challenge. The direct hydroxylation of arenes was initially achieved through the use of strong Brønsted or Lewis acids to mediate electrophilic aromatic substitution reactions with super-stoichiometric equivalents of oxidants, significantly limiting the scope of the reaction. Because the products of these reactions are more reactive than the starting materials, over-oxidation is frequently a competitive process. Transition-metal-catalysed C-H oxidation of arenes with or without directing groups has been developed, improving on the acid-mediated process; however, precious metals are required. Here we demonstrate that phthaloyl peroxide functions as a selective oxidant for the transformation of arenes to phenols under mild conditions. Although the reaction proceeds through a radical mechanism, aromatic C-H bonds are selectively oxidized in preference to activated Csp3-H bonds. Notably, a wide array of functional groups are compatible with this reaction, and this method is therefore well suited for late-stage transformations of advanced synthetic intermediates. Quantum mechanical calculations indicate that this transformation proceeds through a novel addition-abstraction mechanism, a kind of 'reverse-rebound' mechanism as distinct from the common oxygen-rebound mechanism observed for metal-oxo oxidants. These calculations also identify the origins of the experimentally observed aryl selectivity.

  3. Mechanical properties of a metal-organic framework containing hydrogen-bonded bifluoride linkers.

    PubMed

    Li, Wei; Kiran, M S R N; Manson, Jamie L; Schlueter, John A; Thirumurugan, A; Ramamurty, U; Cheetham, Anthony K

    2013-05-18

    We report the mechanical properties of a framework structure, [Cu2F(HF)(HF2)(pyz)4][(SbF6)2]n (pyz = pyrazine), in which [Cu(pyz)2](2+) layers are pillared by HF2(-) anions containing the exceptionally strong F-H···F hydrogen bonds. Nanoindentation studies on single-crystals clearly demonstrate that such bonds are extremely robust and mechanically comparable with coordination bonds in this system.

  4. Selective Breaking of Hydrogen Bonds of Layered Carbon Nitride for Visible Light Photocatalysis.

    PubMed

    Kang, Yuyang; Yang, Yongqiang; Yin, Li-Chang; Kang, Xiangdong; Wang, Lianzhou; Liu, Gang; Cheng, Hui-Ming

    2016-08-01

    Selective breaking of the hydrogen bonds of graphitic carbon nitride can introduce favorable features, including increased band tails close to the band edges and the creation of abundant pores. These features can simultaneously improve the three basic processes of photocatalysis. As a consequence, the photocatalytic hydrogen-generation activity of carbon nitride under visible light is drastically increased by tens of times.

  5. The role of drug-polymer hydrogen bonding interactions on the molecular mobility and physical stability of nifedipine solid dispersions.

    PubMed

    Kothari, Khushboo; Ragoonanan, Vishard; Suryanarayanan, Raj

    2015-01-01

    We investigated the influence of drug-polymer hydrogen bonding interactions on molecular mobility and the physical stability in solid dispersions of nifedipine with each of the polymers polyvinylpyrrolidone (PVP), hydroxypropylmethyl cellulose (HPMCAS), and poly(acrylic acid) (PAA). The drug-polymer interactions were monitored by FT-IR spectroscopy, the molecular mobility was characterized using broadband dielectric spectroscopy, and the crystallization kinetics was evaluated by powder X-ray diffractometry. The strength of drug-polymer hydrogen bonding, the structural relaxation time, and the crystallization kinetics were rank ordered as PVP > HPMCAS > PAA. At a fixed polymer concentration, the fraction of the drug bonded to the polymer was the highest with PVP. Addition of 20% w/w polymer resulted in ∼65-fold increase in the relaxation time in the PVP dispersion and only ∼5-fold increase in HPMCAS dispersion. In the PAA dispersions, there was no evidence of drug-polymer interactions and the polymer addition did not influence the relaxation time. Thus, the strongest drug-polymer hydrogen bonding interactions in PVP solid dispersions translated to the longest structural relaxation times and the highest resistance to drug crystallization.

  6. Electronic absorption spectra of cryogenic systems with hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Meister, T. G.; Zelikina, G. Ya.; Artamonova, O. M.

    1989-05-01

    The thermodynamic equilibrium ? has been studied by recording the 1Lb band of benzene and toluene (YR 2) dissolved in liquid Kr and CF 4 (toluene was also dissolved in liquid Ar), with addition of CHF 3(R 1XH) in a broad temperature range for each of the systems. The narrowness of the vibronic components (VC) of the 1Lb band in cryogenic solvents, i.e. liquified gases, made it possible to work with the separate vibronic components 6 10( A00) for benzene and 0-0 for toluene. The values of the equilibrium constant K were obtained by measuring the integrated intensities of the VCs of the 1Lb band of the complex and of the monomer. The enthalpy Wg  |Δ Hg| of the unexcited complex R 1XH⋯YR 2 formation was obtained from the temperature dependence of the K values; the enthalpy change Δ W due to the electronic excitation in YR 2 was obtained from the spectral shift due to the H-bond formation; therefore the enthalpy We  |Δ He| of formation of the excited complex R 1XH⋯(YE) 2* was calculated: We = Wg - Δ W. For both complexes in all the solvents used the following enthalpy values were obtained: Wg = 2.4±0.4 kcal mol -1; We = 1.6±0.5 kcal mol -1.

  7. Metal-and hydrogen-bonding competition during water absorption on Pd(111) and Ru(0001)

    SciTech Connect

    Tatarkhanov, Mouslim; Ogletree, D. Frank; Rose, Franck; Mitsui, Toshiyuki; Fomin, Evgeny; Rose, Mark; Cerda, Jorge I.; Salmeron, Miquel

    2009-09-03

    The initial stages of water adsorption on the Pd(111) and Ru(0001) surfaces have been investigated experimentally by Scanning Tunneling Microscopy in the temperature range between 40 K and 130 K, and theoretically with Density Functional Theory (DFT) total energy calculations and STM image simulations. Below 125 K water dissociation does not occur at any appreciable rate and only molecular films are formed. Film growth starts by the formation of flat hexamer clusters where the molecules bind to the metal substrate through the O-lone pair while making H-bonds with neighboring molecules. As coverage increases, larger networks of linked hexagons are formed with a honeycomb structure, which requires a fraction of the water molecules to have their molecular plane perpendicular to the metal surface with reduced water-metal interaction. Energy minimization favors the growth of networks with limited width. As additional water molecules adsorb on the surface they attach to the periphery of existing islands, where they interact only weakly with the metal substrate. These molecules hop along the periphery of the clusters at intermediate temperatures. At higher temperatures they bind to the metal to continue the honeycomb growth. The water-Ru interaction is significantly stronger than the water-Pd interaction, which is consistent with the greater degree of hydrogen-bonded network formation and reduced water-metal bonding observed on Pd relative to Ru.

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

    PubMed

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

    2014-07-01

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

  9. Delicate balance of hydrogen bonding forces in D-threoninol.

    PubMed

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

    2014-09-01

    The seven most stable conformers of D-threoninol (2(S)-amino-1,3(S)-butanediol), a template used for the synthesis of artificial nucleic acids, have been identified and characterized from their pure rotational transitions in the gas phase using chirped-pulse Fourier transform microwave spectroscopy. D-Threoninol is a close analogue of glycerol, differing by substitution of an NH2 group for OH on the C(β) carbon and by the presence of a terminal CH3 group that breaks the symmetry of the carbon framework. Of the seven observed structures, two are H-bonded cycles containing three H-bonds that differ in the direction of the H-bonds in the cycle. The other five are H-bonded chains containing OH···NH···OH H-bonds with different directions along the carbon framework and different dihedral angles along the chain. The two structural types (cycles and chains of H-bonds) are in surprisingly close energetic proximity. Comparison of the rotational constants with the calculated structures at the MP2/6-311++G(d,p) level of theory reveals systematic changes in the H-bond distances that reflect NH2 as a better H-bond acceptor and poorer donor, shrinking the H-bond distances by ∼0.2 Å in the former case and lengthening them by a corresponding amount in the latter. Thus revealed is the subtle effect of asymmetric substitution on the energy landscape of a simple molecule, likely to be important in living systems.

  10. Alkoxyboration: Ring-Closing Addition of B–O σ Bonds across Alkynes

    PubMed Central

    2015-01-01

    For nearly 70 years, the addition of boron–X σ bonds to carbon–carbon multiple bonds has been employed in the preparation of organoboron reagents. However, the significantly higher strength of boron–oxygen bonds has thus far precluded their activation for addition, preventing a direct route to access a potentially valuable class of oxygen-containing organoboron reagents for divergent synthesis. We herein report the realization of an alkoxyboration reaction, the addition of boron–oxygen σ bonds to alkynes. Functionalized O-heterocyclic boronic acid derivatives are produced using this transformation, which is mild and exhibits broad functional group compatibility. Our results demonstrate activation of this boron–O σ bond using a gold catalysis strategy that is fundamentally different from that used previously for other boron addition reactions. PMID:24588331

  11. Neutral redox-active hydrogen- and halogen-bonding [2]rotaxanes for the electrochemical sensing of chloride.

    PubMed

    Lim, Jason Y C; Cunningham, Matthew J; Davis, Jason J; Beer, Paul D

    2014-12-14

    The first examples of redox-active ferrocene-functionalised neutral [2]rotaxanes have been synthesised via chloride anion templation. (1)H NMR spectroscopic titrations reveal that these [2]rotaxane host systems recognize chloride selectively over other halides and oxoanions in highly-competitive aqueous media. By replacing the hydrogen bonding prototriazole units of the rotaxane axle component with iodotriazole halogen bond-donor groups, the degree of chloride selectivity of the [2]rotaxanes is modulated. Electrochemical voltammetric experiments demonstrate that the rotaxanes can sense chloride via cathodic perturbations of the respective rotaxanes' ferrocene-ferrocenium redox-couple upon anion addition.

  12. Insights on hydrogen-bond lifetimes in liquid and supercooled water.

    PubMed

    Martiniano, H F M C; Galamba, N

    2013-12-19

    We study the temperature dependence of the lifetime of geometric and geometric/energetic water hydrogen-bonds (H-bonds), down to supercooled water, through molecular dynamics. The probability and lifetime of H-bonds that break either by translational or librational motions and those of energetic broken H-bonds, along with the effects of transient broken H-bonds and transient H-bonds, are considered. We show that the fraction of transiently broken energetic H-bonds increases at low temperatures and that this energetic breakdown is caused by oxygen-oxygen electrostatic repulsions upon too small amplitude librations to disrupt geometric H-bonds. Hence, differences between geometric and energetic continuous H-bond lifetimes are associated with large H-bond energy fluctuations, in opposition to moderate geometric fluctuations, within common energetic and geometric H-bond definition thresholds. Exclusion of transient broken H-bonds and transient H-bonds leads to H-bond definition-independent mean lifetimes and activation energies, ~11 kJ/mol, consistent with the reactive flux method and experimental scattering results. Further, we show that power law decay of specific temporal H-bond lifetime probability distributions is associated with librational and translational motions that occur on the time scale (~0.1 ps) of H-bond breaking /re-forming dynamics. While our analysis is diffusion-free, the effect of diffusion on H-bond probability distributions where H-bonds are allowed to break and re-form, switching acceptors in between, is shown to result in neither exponential nor power law decay, similar to the reactive flux correlation function.

  13. Hydrogen-bonded glycine-HCN complexes in gas phase: structure, energetics, electric properties and cooperativity

    NASA Astrophysics Data System (ADS)

    Machado da Silva, Arnaldo; Chakrabarty, Sumana; Chaudhuri, Puspitapallab

    2015-03-01

    Twelve hydrogen-bonded complexes of glycine and hydrogen cyanide have been studied using high-level quantum-chemical calculations in gas phase. In particular, six 1:1 glycine-HCN dimers and six 1:2 glycine-HCN trimers have been considered. Besides the characteristics of the hydrogen bonds and their effect on molecular structure and energetics, several molecular electric properties have been calculated utilising two different models: MP2/6-31++G(d,p) and DFT-B3LYP/6-31++G(d,p). Although the structural parameters calculated by the two models are similar, equilibrium electronic energies of the clusters show model dependence. The lowest energy dimer is same in both the models which is ca. 3.0 kcal/mol more stable than the highest energy dimer. However, the lowest energy trimer is different in two methods. The energetic difference of stability between the highest and lowest trimer is 4.2 kcal/mol (4.4 kcal/mol) at an MP2 (B3LYP) level of calculation. The bond angles of glycine, in particular, are quite sensitive to the hydrogen-bond formation. Four out of six trimers are found to be strongly cooperative in both the models. Significant changes of dipole moments and polarisabilities of isolated glycine and hydrogen cyanide are observed due to the formation of hydrogen bonding. The Rayleigh scattering intensities of all clusters are much larger than those of their constituent monomers.

  14. Nature of the asymmetry in the hydrogen-bond networks of hexagonal ice and liquid water.

    PubMed

    Kühne, Thomas D; Khaliullin, Rustam Z

    2014-03-01

    The interpretation of the X-ray spectra of water as evidence for its asymmetric structure has challenged the traditional nearly tetrahedral model and initiated an intense debate about the order and symmetry of the hydrogen-bond network in water. Here, we present new insights into the nature of local interactions in ice and liquid water obtained using a first-principle energy decomposition method. A comparative analysis shows that the majority of molecules in liquid water in our simulation exhibit hydrogen-bonding energy patterns similar to those in ice and retain the four-fold coordination with only moderately distorted tetrahedral configurations. Although this result indicates that the traditional description of liquid water is fundamentally correct, our study also demonstrates that for a significant fraction of molecules the hydrogen-bonding environments are highly asymmetric with extremely weak and distorted bonds.

  15. α-Halogenoacetanilides as hydrogen-bonding organocatalysts that activate carbonyl bonds: fluorine versus chlorine and bromine.

    PubMed

    Koeller, Sylvain; Thomas, Coralie; Peruch, Fréderic; Deffieux, Alain; Massip, Stéphane; Léger, Jean-Michel; Desvergne, Jean-Pierre; Milet, Anne; Bibal, Brigitte

    2014-03-01

    α-Halogenoacetanilides (X=F, Cl, Br) were examined as H-bonding organocatalysts designed for the double activation of CO bonds through NH and CH donor groups. Depending on the halide substituents, the double H-bond involved a nonconventional CH⋅⋅⋅O interaction with either a HCXn (n=1-2, X=Cl, Br) or a HCAr bond (X=F), as shown in the solid-state crystal structures and by molecular modeling. In addition, the catalytic properties of α-halogenoacetanilides were evaluated in the ring-opening polymerization of lactide, in the presence of a tertiary amine as cocatalyst. The α-dichloro- and α-dibromoacetanilides containing electron-deficient aromatic groups afforded the most attractive double H-bonding properties towards CO bonds, with a NH⋅⋅⋅O⋅⋅⋅HCX2 interaction.

  16. The hydrogen bond in ice probed by soft x-ray spectroscopy and density functional theory

    SciTech Connect

    Nilsson, A.; Ogasawara, H.; Cavalleri, M.; Nordlund, D.; Nyberg, M.; Wernet, Ph.; Pettersson, L.G.M.

    2005-04-15

    We combine photoelectron and x-ray absorption spectroscopy with density functional theory to derive a molecular orbital picture of the hydrogen bond in ice. We find that the hydrogen bond involves donation and back-donation of charge between the oxygen lone pair and the O-H antibonding orbitals on neighboring molecules. Together with internal s-p rehybridization this minimizes the repulsive charge overlap of the connecting oxygen and hydrogen atoms, which is essential for a strong attractive electrostatic interaction. Our joint experimental and theoretical results demonstrate that an electrostatic model based on only charge induction from the surrounding medium fails to properly describe the internal charge redistributions upon hydrogen bonding.

  17. Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network.

    PubMed

    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.

  18. 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

    2013-12-01

    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.

  19. The hydrogen bond network in I β cellulose as observed by infrared spectrometry

    NASA Astrophysics Data System (ADS)

    Maréchal, Y.; Chanzy, H.

    2000-05-01

    FT-IR spectra of I β cellulose were recorded on films made of hydrothermally treated Valonia microcrystals. Polarized spectra of these not completely disordered systems allowed to define the spectra along the cellulose c chain axis as well as along a perpendicular axis which may slightly vary from one sample to another one. Weakening and ruptures of some hydrogen bonds upon heating the samples at 115°C, as well as evaporation of D 2O molecules and H/D exchanges after immersion in a D 2O vapor were followed spectroscopically. A critical analysis of the spectra allowed to propose a detailed assignment for most of the bands at wavenumbers higher than 800 cm -1. From this analysis it appeared that the majority (more than 2/3) of C2O2H alcohols were involved in weak hydrogen bonds or perhaps even not hydrogen-bonded at all. On the other hand, the minority of C2O2H established a hydrogen bond with the O6 atom of an adjacent primary alcohol of the same chain. This particular hydrogen bond was the strongest found in these crystals. With the proposed assignment, hydroxymethyl moieties were found adopting three conformations (a dominant one and two minor) allowing the formation of different hydrogen bonds on adjacent chains. These conformations corresponded to three slightly different C4-C5-C6-O6 ( χ) dihedral angles. Most probably the primary alcohols that accept a hydrogen bond from the adjacent C2O2H alcohols were not the ones which adopt the dominant conformation.

  20. Understanding the Thermodynamics of Hydrogen Bonding in Alcohol-Containing Mixtures: Cross-Association.

    PubMed

    Fouad, Wael A; Wang, Le; Haghmoradi, Amin; Asthagiri, D; Chapman, Walter G

    2016-04-01

    The thermodynamics of hydrogen bonding in 1-alcohol + water binary mixtures is studied using molecular dynamic (MD) simulation and the polar and perturbed chain form of the statistical associating fluid theory (polar PC-SAFT). The fraction of free monomers in pure saturated liquid water is computed using both TIP4P/2005 and iAMOEBA simulation water models. Results are compared to spectroscopic data available in the literature as well as to polar PC-SAFT. Polar PC-SAFT models hydrogen bonds using single bondable association sites representing electron donors and electron acceptors. The distribution of hydrogen bonds in pure alcohols is computed using the OPLS-AA force field. Results are compared to Monte Carlo (MC) simulations available in the literature as well as to polar PC-SAFT. The analysis shows that hydrogen bonding in pure alcohols is best predicted using a two-site model within the SAFT framework. On the other hand, molecular simulations show that increasing the concentration of water in the mixture increases the average number of hydrogen bonds formed by an alcohol molecule. As a result, a transition in association scheme occurs at high water concentrations where hydrogen bonding is better captured within the SAFT framework using a three-site alcohol model. The knowledge gained in understanding hydrogen bonding is applied to model vapor-liquid equilibrium (VLE) and liquid-liquid equilibrium (LLE) of mixtures using polar PC-SAFT. Predictions are in good agreement with experimental data, establishing the predictive power of the equation of state. PMID:26979297

  1. Simulating hydrogen-bond clustering and phase behaviour of imidazole oligomers

    NASA Astrophysics Data System (ADS)

    Harvey, Jacob A.; Basak, Dipankar; Venkataraman, Dhandapani; Auerbach, Scott M.

    2012-05-01

    We have modelled structures and dynamics of hydrogen bond networks that form from imidazoles tethered to oligomeric aliphatic backbones in crystalline and glassy phases. We have studied the behaviour of oligomers containing 5 or 10 imidazole groups. These systems have been simulated over the range 100-900 K with constant-pressure molecular dynamics using the AMBER 94 forcefield, which was found to show good agreement with ab initio calculations on hydrogen bond strengths and imidazole rotational barriers. Hypothetical crystalline solids formed from packed 5-mers and 10-mers melt above 600 K, then form glassy solids upon cooling. Viewing hydrogen bond networks as clusters, we gathered statistics on cluster sizes and percolating pathways as a function of temperature, for comparison with the same quantities extracted from neat imidazole liquid. We have found that, at a given temperature, the glass composed of imidazole 5-mers shows the same hydrogen bond mean cluster size as that from the 10-mer glass, and that this size is consistently larger than that in liquid imidazole. Hydrogen bond clusters were found to percolate across the simulation cell for all glassy and crystalline solids, but not for any imidazole liquid. The apparent activation energy associated with hydrogen bond lifetimes in these glasses (9.3 kJ mol-1) is close to that for the liquid (8.7 kJ mol-1), but is substantially less than that in the crystalline solid (13.3 kJ mol-1). These results indicate that glassy oligomeric solids show a promising mixture of extended hydrogen bond clusters and liquid-like dynamics.

  2. The effect of intermolecular hydrogen bonding on the planarity of amides.

    PubMed

    Platts, James A; Maarof, Hasmerya; Harris, Kenneth D M; Lim, Gin Keat; Willock, David J

    2012-09-14

    Ab initio and density functional theory (DFT) calculations on some model systems are presented to assess the extent to which intermolecular hydrogen bonding can affect the planarity of amide groups. Formamide and urea are examined as archetypes of planar and non-planar amides, respectively. DFT optimisations suggest that appropriately disposed hydrogen-bond donor or acceptor molecules can induce non-planarity in formamide, with OCNH dihedral angles deviating by up to ca. 20° from planarity. Ab initio energy calculations demonstrate that the energy required to deform an amide molecule from the preferred geometry of the isolated molecule is more than compensated by the stabilisation due to hydrogen bonding. Similarly, the NH(2) group in urea can be made effectively planar by the presence of appropriately positioned hydrogen-bond acceptors, whereas hydrogen-bond donors increase the non-planarity of the NH(2) group. Small clusters (a dimer, two trimers and a pentamer) extracted from the crystal structure of urea indicate that the crystal field acts to force planarity of the urea molecule; however, the interaction with nearest neighbours alone is insufficient to induce the molecule to become completely planar, and longer-range effects are required. Finally, the potential for intermolecular hydrogen bonding to induce non-planarity in a model of a peptide is explored. Inter alia, the insights obtained in the present work on the extent to which the geometry of amide groups may be deformed under the influence of intermolecular hydrogen bonding provide structural guidelines that can assist the interpretation of the geometries of such groups in structure determination from powder X-ray diffraction data. PMID:22847473

  3. Density functional study of hydrogen bond formation between methanol and organic molecules containing Cl, F, NH2, OH, and COOH functional groups.

    PubMed

    Kolev, Stefan K; St Petkov, Petko; Rangelov, Miroslav A; Vayssilov, Georgi N

    2011-12-01

    Various hydrogen-bonded complexes of methanol with different proton accepting and proton donating molecules containing Cl, F, NH(2), OH, OR, and COOH functional groups have been modeled using DFT with hybrid B3LYP and M05-2X functionals. The latter functional was found to provide more accurate estimates of the structural and thermodynamic parameters of the complexes of halides, amines, and alcohols. The characteristics of these complexes are influenced not only by the principle hydrogen bond of the methanol OH with the proton acceptor heteroatom, but also by additional hydrogen bonds of a C-H moiety with methanol oxygen as a proton acceptor. The contribution of the former hydrogen bond in the total binding enthalpy increases in the order chlorides < fluorides < alcohols < amines, while the contribution of the second type of hydrogen bond increases in the reverse order. A general correlation was found between the binding enthalpy of the complex and the electrostatic potential at the hydrogen center participating in the formation of the hydrogen bond. The calculated binding enthalpies of different complexes were used to clarify which functional groups can potentially form a hydrogen bond to the 2'-OH hydroxyl group in ribose, which is strong enough to block it from participation in the intramolecular catalytic activation of the peptide bond synthesis. Such blocking could result in inhibition of the protein biosynthesis in the living cell if the corresponding group is delivered as a part of a drug molecule in the vicinity of the active site in the ribosome. According to our results, such activity can be accomplished by secondary or tertiary amines, alkoxy groups, deprotonated carboxyl groups, and aliphatic fluorides, but not by the other modeled functional groups. PMID:21992409

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

    PubMed Central

    Chakrabarti, Shaon; Hinczewski, Michael; Thirumalai, D.

    2014-01-01

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

  5. Hydrogen bonding constrains free radical reaction dynamics at serine and threonine residues in peptides.

    PubMed

    Thomas, Daniel A; Sohn, Chang Ho; Gao, Jinshan; Beauchamp, J L

    2014-09-18

    Free radical-initiated peptide sequencing (FRIPS) mass spectrometry derives advantage from the introduction of highly selective low-energy dissociation pathways in target peptides. An acetyl radical, formed at the peptide N-terminus via collisional activation and subsequent dissociation of a covalently attached radical precursor, abstracts a hydrogen atom from diverse sites on the peptide, yielding sequence information through backbone cleavage as well as side-chain loss. Unique free-radical-initiated dissociation pathways observed at serine and threonine residues lead to cleavage of the neighboring N-terminal Cα-C or N-Cα bond rather than the typical Cα-C bond cleavage observed with other amino acids. These reactions were investigated by FRIPS of model peptides of the form AARAAAXAA, where X is the amino acid of interest. In combination with density functional theory (DFT) calculations, the experiments indicate the strong influence of hydrogen bonding at serine or threonine on the observed free radical chemistry. Hydrogen bonding of the side-chain hydroxyl group with a backbone carbonyl oxygen aligns the singly occupied π orbital on the β-carbon and the N-Cα bond, leading to low-barrier β-cleavage of the N-Cα bond. Interaction with the N-terminal carbonyl favors a hydrogen-atom transfer process to yield stable c and z(•) ions, whereas C-terminal interaction leads to effective cleavage of the Cα-C bond through rapid loss of isocyanic acid. Dissociation of the Cα-C bond may also occur via water loss followed by β-cleavage from a nitrogen-centered radical. These competitive dissociation pathways from a single residue illustrate the sensitivity of gas-phase free radical chemistry to subtle factors such as hydrogen bonding that affect the potential energy surface for these low-barrier processes.

  6. Theoretical aspects of binary and ternary complexes of aziridine···ammonia ruled by hydrogen bond strength.

    PubMed

    Oliveira, Boaz G; Araújo, Regiane C M U

    2012-06-01

    B3LYP calculations, ChelpG atomic charges, and quantum theory of atoms in molecules (QTAIM) integrations were used to investigate the binary (1:1) and ternary (1:2) hydrogen-bonded complexes formed by aziridine (1) and ammonia (2). In a series of analysis, geometry data, electronic parameters, vibrational oscillators, and topological descriptors were used to evaluate hydrogen bond strength, and additionally to determine the more prominent molecular deformations upon the formation of C(2)H(5)N···NH(3) (1:1) and C(2)H(5)N···2NH(3) (1:2) systems. Taking a spectroscopic viewpoint, results obtained from analysis of the harmonic infrared spectrum were examined. From these, new vibrational modes and red- and blue-shifts related to the stretch frequencies of either donors or acceptors of protons were identified. Furthermore, the molecular topology of the electronic density modeled in accord with QTAIM was absolutely critical in defining bond critical points (BCP) and ring critical points (RCP) on the heterocyclic structures. Taking all the results together allowed us to identify and characterize all the N···H hydrogen bonds, as well as the strain ring of the aziridine and its stability.

  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. Hydrogen-Bonding Network and OH Stretch Vibration of Cellulose: Comparison of Computational Modeling with Polarized IR and SFG Spectra.

    PubMed

    Lee, Christopher M; Kubicki, James D; Fan, Bingxin; Zhong, Linghao; Jarvis, Michael C; Kim, Seong H

    2015-12-10

    Hydrogen bonds play critical roles in noncovalent directional interactions determining the crystal structure of cellulose. Although diffraction studies accurately determined the coordinates of carbon and oxygen atoms in crystalline cellulose, the structural information on hydrogen atoms involved in hydrogen-bonding is still elusive. This could be complemented by vibrational spectroscopy; but the assignment of the OH stretch peaks has been controversial. In this study, we performed calculations using density functional theory with dispersion corrections (DFT-D2) for the cellulose Iβ crystal lattices with the experimentally determined carbon and oxygen coordinates. DFT-D2 calculations revealed that the OH stretch vibrations of cellulose are highly coupled and delocalized through intra- and interchain hydrogen bonds involving all OH groups in the crystal. Additionally, molecular dynamics (MD) simulations of a single cellulose microfibril showed that the conformations of OH groups exposed at the microfibril surface are not well-defined. Comparison of the computation results with the experimentally determined IR dichroism of uniaxially aligned cellulose microfibrils and the peak positions of various cellulose crystals allowed unambiguous identification of OH stretch modes observed in the vibrational spectra of cellulose.

  9. The role of hydrogen-bonding interactions in acidic sugar reaction pathways.

    PubMed

    Qian, Xianghong; Johnson, David K; Himmel, Michael E; Nimlos, Mark R

    2010-09-01

    Previously, theoretical multiple sugar (beta-d-xylose and beta-d-glucose) reaction pathways were discovered that depended on the initial protonation site on the sugar molecules using Car-Parrinello-based molecular dynamics (CPMD) simulations [Qian, X. H.; Nimlos, M. R.; Davis, M.; Johnson, D. K.; Himmel, M. E. Carbohydr. Res.2005, 340, 2319-2327]. In addition, simulation results showed that water molecules could participate in the sugar reactions, thus altering the reaction pathways. In the present study, the temperature and water density effects on the sugar degradation pathways were investigated with CPMD. We found that changes in both temperature and water density could profoundly affect the mechanisms and pathways. We attributed these effects to both the strength of hydrogen bonding and proton affinity of water. PMID:20667524

  10. Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination.

    PubMed

    Takezawa, Yusuke; Nishiyama, Kotaro; Mashima, Tsukasa; Katahira, Masato; Shionoya, Mitsuhiko

    2015-10-12

    A novel bifacial ligand-bearing nucleobase, 5-hydroxyuracil (U(OH) ), which forms both a hydrogen-bonded base pair (U(OH) -A) and a metal-mediated base pair (U(OH) -M-U(OH) ) has been developed. The U(OH) -M-U(OH) base pairs were quantitatively formed in the presence of lanthanide ions such as Gd(III) when U(OH) -U(OH) pairs were consecutively incorporated into DNA duplexes. This result established metal-assisted duplex stabilization as well as DNA-templated assembly of lanthanide ions. Notably, a duplex possessing U(OH) -A base pairs was destabilized by addition of Gd(III) ions. This observation suggests that the hybridization behaviors of the U(OH) -containing DNA strands are altered by metal complexation. Thus, the U(OH) nucleobase with a bifacial base-pairing property holds great promise as a component for metal-responsive DNA materials.

  11. Quantum effects of hydrogen atoms on the dynamical rearrangement of hydrogen-bond networks in liquid water.

    PubMed

    Hyeon-Deuk, Kim; Ando, Koji

    2010-04-28

    Quantum effects such as zero-point energy and delocalization of wave packets (WPs) representing water hydrogen atoms are essential to understand anomalous energetics and dynamics in water. Since quantum calculations of many-body dynamics are highly complicated, no one has yet directly viewed the quantum WP dynamics of hydrogen atoms in liquid water. Our semiquantum molecular dynamics simulation made it possible to observe the hydrogen WP dynamics in liquid water. We demonstrate that the microscopic WP dynamics are closely correlated with and actually play key roles in the dynamical rearrangement in the hydrogen-bond network (HBN) of bulk water. We found the quantum effects of hydrogen atoms on liquid water dynamics such as the rearrangement of HBN and the concomitant fluctuation and relaxation. Our results provide new physical insights on HBN dynamics in water whose significance is not limited to pure liquid dynamics but also a greater understanding of chemical and biological reactions in liquid water.

  12. Interaction of multiple bonded and unsaturated heavier main group compounds with hydrogen, ammonia, olefins, and related molecules.

    PubMed

    Power, Philip P

    2011-08-16

    We showed in 2005 that a digermyne, a main group compound with a digermanium core and aromatic substituents, reacted directly with hydrogen at 25 °C and 1 atm to give well-defined hydrogen addition products. This was the first report of a reaction of main group molecules with hydrogen under ambient conditions. Our group and a number of others have since shown that several classes of main group molecules, either alone or in combination, react directly (in some cases reversibly) with hydrogen under mild conditions. Moreover, this reactivity was not limited to hydrogen but also included direct reactions with other important small molecules, including ammonia, boranes, and unactivated olefins such as ethylene. These reactions were largely unanticipated because main group species were generally considered to be too unreactive to effect such transformations. In this Account, we summarize recent developments in the reactions of the multiple bonded and other open shell derivatives of the heavier main group elements with hydrogen, ammonia, olefins, or related molecules. We focus on results generated primarily in our laboratory, which are placed in the context of parallel findings by other researchers. The close relationship between HOMO-LUMO separations, symmetry considerations, and reactivity of the open shell in main group compounds is emphasized, as is their similarity in reactivity to transition metal organometallic compounds. The unexpectedly potent reactivity of the heavier main group species arises from the large differences in bonding between the light and heavy elements. Specifically, the energy levels within the heavier element molecules are separated by much smaller gaps as a result of generally lower bond strengths. In addition, the ordering and symmetries of the energy levels are generally different for their light counterparts. Such differences lie at the heart of the new reactions. Moreover, the reactivity of the molecules can often be interpreted

  13. Carbon–carbon bond activation of cyclobutenones enabled by the addition of chiral organocatalyst to ketone

    PubMed Central

    Li, Bao-Sheng; Wang, Yuhuang; Jin, Zhichao; Zheng, Pengcheng; Ganguly, Rakesh; Chi, Yonggui Robin

    2015-01-01

    The activation of carbon–carbon (C–C) bonds is an effective strategy in building functional molecules. The C–C bond activation is typically accomplished via metal catalysis, with which high levels of enantioselectivity are difficult to achieve due to high reactivity of metal catalysts and the metal-bound intermediates. It remains largely unexplored to use organocatalysis for C–C bond activation. Here we describe an organocatalytic activation of C–C bonds through the addition of an NHC to a ketone moiety that initiates a C–C single bond cleavage as a key step to generate an NHC-bound intermediate for chemo- and stereo-selective reactions. This reaction constitutes an asymmetric functionalization of cyclobutenones using organocatalysts via a C–C bond activation process. Structurally diverse and multicyclic compounds could be obtained with high optical purities via an atom and redox economic process. PMID:25652912

  14. 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.

  15. (-)-Dioxosantadienic acid: hydrogen-bonding patterns in a bicyclic sesquiterpenoid keto acid and its monohydrate.

    PubMed

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

    2001-09-01

    The anhydrous form, (I), of the title compound, (-)-2-(1,2,3,4,4a,7-hexahydro-4a,8-dimethyl-1,7-dioxo-2-naphthyl)propionic acid, C(15)H(18)O(4), derived from a naturally occurring sesquiterpenoid, has two molecules in the asymmetric unit, (I) and (I'), differing in the conformations of the saturated ring and the carboxyl group. The compound aggregates as carboxyl-to-ketone hydrogen-bonding catemers [O.O = 2.776 (3) and 2.775 (3) A]. Two crystallographically independent sets of single-strand hydrogen-bonding helices with opposite end-to-end orientation pass through the cell in the b direction, one consisting exclusively of molecules of (I) and the other entirely of (I'). Three C-H.O=C close contacts are found in (I). The monohydrate, C(15)H(18)O(4).H(2)O, (II), with two molecules of (I) plus two water molecules in its asymmetric unit, forms a complex three-dimensional hydrogen-bonding network including acid-to-water, water-to-acid, water-to-ketone, water-to-water and acid-to-acid hydrogen bonds, plus three C-H.O=C close contacts. In both (I) and (II), only the ketone remote from the acid is involved in hydrogen bonding. PMID:11588376

  16. 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.

  17. Wetting Properties of Chemically Modified Surfaces: The role of hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Bekele, Selemon; Tsige, Mesfin

    2015-03-01

    Many industrial processing operations involve the spreading of a liquid on a solid material. Controlling the wetting of one material by another is of crucial importance in such applications as adhesion, coating and oil recovery. A strategy often employed to control the wettability of solid surfaces is a combination of surface patterning and chemical surface modification. In order to understand the effect of surface chemistry on the wetting process, we have carried out all-atom molecular dynamics (MD) simulations of a water droplet spreading on pure and oxidized polystyrene surfaces. Our previous results show that the contact angle generally decreases with increasing oxygen concentration and there is a correlation between the spreading and hydrogen bonding. In this talk, we will present results on the structure and dynamics of the hydrogen bonds in the interfacial region between water and the polystyrene substrate. We will discuss our findings on hydrogen bond lifetimes, time correlations functions and number of hydrogen bonds per water molecule for the hydrogen bonds around the water/polystyrene interface which are found to play a role in the spreading process. This work was supported by NSF Grant DMR0847580.

  18. 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.

  19. Hydrogen Bonds in Crystalline Imidazoles Studied by 15N NMR and ab initio MO Calculations

    NASA Astrophysics Data System (ADS)

    Ueda, Takahiro; Nagatomo, Shigenori; Masui, Hirotsugu; Nakamura, Nobuo; Hayashi, Shigenobu

    1999-07-01

    Intermolecular hydrogen bonds of the type N-H...N in crystals of imidazole and its 4-substituted and 4,5-disubstituted derivatives were studied by 15N CP/MAS NMR and an ab initio molecular orbital (MO) calculation. In the 15N CP/MAS NMR spectrum of each of the imidazole derivatives, two peaks due to the two different functional groups, >NH and =N-, were observed. The value of the 15N isotropic chemical shift for each nitrogen atom depends on both the length of the intermolecular hydrogen bond and the kind of the substituent or substituents. It was found that the difference between the experimen-tal chemical shifts of >NH and =N-varies predominantly with the hydrogen bond length but does not show any systematic dependence on the kind of substituent. The ab initio MO calculations suggest that the hydrogen bond formation influences the 15N isotropic chemical shift predominantly, and that the difference between the 15N isotropic chemical shift of >NH and =N-varies linearly with the hydrogen bond length.

  20. Tuning the interaction energy of hydrogen bonds: the effect of the substituent.

    PubMed

    Mata, Ignasi; Molins, Elies; Alkorta, Ibon; Espinosa, Enrique

    2011-11-17

    The effect of the substituent R in the hydrogen bonding properties of FH···FR (R = H, Al, Li, Cl and CCH) complexes has been studied by theoretical calculations. The dependency of the interaction energy with the hydrogen bond distance and R is explained in terms of the topologies of the electron density and the electrostatic potential. A simple model of the hydrogen bond interaction energy, which can be assimilated to an interaction potential, is defined in terms of a stabilizing mutual polarization of the monomers and an overall destabilizing contribution associated with the electron density reorganization when the overlap of the closed shells is large enough. This model shows an excellent agreement with the ab initio interaction energies and is common for all the analyzed complexes. The substituent effect is represented in the model by a single parameter that can be calculated from the electron distribution in the acceptor atom region. The perturbation in the hydrogen bonding interaction induced by the change of R presents a close similarity with that produced by an external electric field of the same order of magnitude than those found in crystalline solids, indicating that both perturbations should play a significant and similar role on the properties of hydrogen bonds in condensed matter.

  1. Short Hydrogen Bonds and Proton Delocalization in Green Fluorescent Protein (GFP).

    PubMed

    Oltrogge, Luke M; Boxer, Steven G

    2015-06-24

    Short hydrogen bonds and specifically low-barrier hydrogen bonds (LBHBs) have been the focus of much attention and controversy for their possible role in enzymatic catalysis. The green fluorescent protein (GFP) mutant S65T, H148D has been found to form a very short hydrogen bond between Asp148 and the chromophore resulting in significant spectral perturbations. Leveraging the unique autocatalytically formed chromophore and its sensitivity to this interaction we explore the consequences of proton affinity matching across this putative LBHB. Through the use of noncanonical amino acids introduced through nonsense suppression or global incorporation, we systematically modify the acidity of the GFP chromophore with halogen substituents. X-ray crystal structures indicated that the length of the interaction with Asp148 is unchanged at ∼2.45 Å while the absorbance spectra demonstrate an unprecedented degree of color tuning with increasing acidity. We utilized spectral isotope effects, isotope fractionation factors, and a simple 1D model of the hydrogen bond coordinate in order to gain insight into the potential energy surface and particularly the role that proton delocalization may play in this putative short hydrogen bond. The data and model suggest that even with the short donor-acceptor distance (∼2.45 Å) and near perfect affinity matching there is not a LBHB, that is, the barrier to proton transfer exceeds the H zero-point energy. PMID:27162964

  2. Empirical hydrogen-bond potential functions--an old hat reconditioned.

    PubMed

    Korth, Martin

    2011-12-01

    The accurate description of hydrogen-bond interactions is of vital importance for the computational modeling of biological systems. Standard force field (FF) as well as semiempirical quantum mechanical (SQM) methods are now known to have considerable problems with the accurate description of hydrogen bonds. It was found that the performance of SQM methods can be greatly improved with empirical hydrogen-bond correction terms. In the first part of this work we review the improvements developed during the recent revival of dedicated hydrogen-bond terms, also in the light of earlier FF-related work. The second part presents new findings connected to open questions in this field, namely, a study on the importance of angular and torsional information, a scheme how to avoid atom-type-defined target angles and a reduced version of our DH(+) model for the application to force-field methods and physically motivated protein-ligand scoring functions. Our results highlight the importance of using a complete geometric description (including angular and torsional coordinates) for the accurate treatment of hydrogen bonding. The reduced DH(+) model-applied to a modified version of the UFF force field-shows a much improved accuracy for non-covalent interactions also with FF methods, with gains in accuracy by more than one order of magnitude.

  3. Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases.

    PubMed

    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

    2013-10-16

    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.

  4. Molecular Seesaw: How Increased Hydrogen Bonding Can Hinder Excited-State Proton Transfer.

    PubMed

    Welsch, Ralph; Driscoll, Eric; Dawlaty, Jahan M; Miller, Thomas F

    2016-09-15

    A previously unexplained effect in the relative rate of excited-state intramolecular proton transfer (ESIPT) in related indole derivatives is investigated using both theory and experiment. Ultrafast spectroscopy [ J. Phys. Chem. A, 2015, 119, 5618-5625 ] found that although the diol 1,3-bis(2-pyridylimino)-4,7-dihydroxyisoindole exhibits two equivalent intramolecular hydrogen bonds, the ESIPT rate associated with tautomerization of either hydrogen bond is a factor of 2 slower than that of the single intramolecular hydrogen bond in the ethoxy-ol 1,3-bis(2-pyridylimino)-4-ethoxy-7-hydroxyisoindole. Excited-state electronic structure calculations suggest a resolution to this puzzle by revealing a seesaw effect in which the two hydrogen bonds of the diol are both longer than the single hydrogen bond in the ethoxy-ol. Semiclassical rate theory recovers the previously unexplained trends and leads to clear predictions regarding the relative H/D kinetic isotope effect (KIE) for ESIPT in the two systems. The theoretical KIE predictions are tested using ultrafast spectroscopy, confirming the seesaw effect. PMID:27556887

  5. 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.

  6. Toxin-induced pore formation is hindered by intermolecular hydrogen bonding in sphingomyelin bilayers.

    PubMed

    García-Linares, Sara; Palacios-Ortega, Juan; Yasuda, Tomokazu; Åstrand, Mia; Gavilanes, José G; Martínez-del-Pozo, Álvaro; Slotte, J Peter

    2016-06-01

    Sticholysin I and II (StnI and StnII) are pore-forming toxins that use sphingomyelin (SM) for membrane binding. We examined how hydrogen bonding among membrane SMs affected the StnI- and StnII-induced pore formation process, resulting in bilayer permeabilization. We compared toxin-induced permeabilization in bilayers containing either SM or dihydro-SM (lacking the trans Δ(4) double bond of the long-chain base), since their hydrogen-bonding properties are known to differ greatly. We observed that whereas both StnI and StnII formed pores in unilamellar vesicles containing palmitoyl-SM or oleoyl-SM, the toxins failed to similarly form pores in vesicles prepared from dihydro-PSM or dihydro-OSM. In supported bilayers containing OSM, StnII bound efficiently, as determined by surface plasmon resonance. However, StnII binding to supported bilayers prepared from dihydro-OSM was very low under similar experimental conditions. The association of the positively charged StnII (at pH7.0) with unilamellar vesicles prepared from OSM led to a concentration-dependent increase in vesicle charge, as determined from zeta-potential measurements. With dihydro-OSM vesicles, a similar response was not observed. Benzyl alcohol, which is a small hydrogen-bonding compound with affinity to lipid bilayer interfaces, strongly facilitated StnII-induced pore formation in dihydro-OSM bilayers, suggesting that hydrogen bonding in the interfacial region originally prevented StnII from membrane binding and pore formation. We conclude that interfacial hydrogen bonding was able to affect the membrane association of StnI- and StnII, and hence their pore forming capacity. Our results suggest that other types of protein interactions in bilayers may also be affected by hydrogen-bonding origination from SMs. PMID:26975250

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

    PubMed

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

    2016-03-01

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

  8. 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

  9. Hydration and hydrogen bond network of water around hydrophobic surface investigated by terahertz spectroscopy.

    PubMed

    Shiraga, K; Suzuki, T; Kondo, N; Ogawa, Y

    2014-12-21

    Water conformation around hydrophobic side chains of four amino acids (glycine, L-alanine, L-aminobutyric acid, and L-norvaline) was investigated via changes in complex dielectric constant in the terahertz (THz) region. Each of these amino acids has the same hydrophilic backbone, with successive additions of hydrophobic straight methylene groups (-CH2-) to the side chain. Changes in the degree of hydration (number of dynamically retarded water molecules relative to bulk water) and the structural conformation of the water hydrogen bond (HB) network related to the number of methylene groups were quantitatively measured. Since dielectric responses in the THz region represent water relaxations and water HB vibrations at a sub-picosecond and picosecond timescale, these measurements characterized the water relaxations and HB vibrations perturbed by the methylene apolar groups. We found each successive straight -CH2- group on the side chain restrained approximately two hydrophobic hydration water molecules. Additionally, the number of non-hydrogen-bonded (NHB) water molecules increased slightly around these hydrophobic side chains. The latter result seems to contradict the iceberg model proposed by Frank and Evans, where water molecules are said to be more ordered around apolar surfaces. Furthermore, we compared the water-hydrophilic interactions of the hydrophilic amino acid backbone with those with the water-hydrophobic interactions around the side chains. As the hydrophobicity of the side chain increased, the ordering of the surrounding water HB network was altered from that surrounding the hydrophilic amino acid backbone, thereby diminishing the fraction of NHB water and ordering the surrounding tetrahedral water HB network.

  10. Hydration and hydrogen bond network of water around hydrophobic surface investigated by terahertz spectroscopy

    NASA Astrophysics Data System (ADS)

    Shiraga, K.; Suzuki, T.; Kondo, N.; Ogawa, Y.

    2014-12-01

    Water conformation around hydrophobic side chains of four amino acids (glycine, L-alanine, L-aminobutyric acid, and L-norvaline) was investigated via changes in complex dielectric constant in the terahertz (THz) region. Each of these amino acids has the same hydrophilic backbone, with successive additions of hydrophobic straight methylene groups (-CH2-) to the side chain. Changes in the degree of hydration (number of dynamically retarded water molecules relative to bulk water) and the structural conformation of the water hydrogen bond (HB) network related to the number of methylene groups were quantitatively measured. Since dielectric responses in the THz region represent water relaxations and water HB vibrations at a sub-picosecond and picosecond timescale, these measurements characterized the water relaxations and HB vibrations perturbed by the methylene apolar groups. We found each successive straight -CH2- group on the side chain restrained approximately two hydrophobic hydration water molecules. Additionally, the number of non-hydrogen-bonded (NHB) water molecules increased slightly around these hydrophobic side chains. The latter result seems to contradict the iceberg model proposed by Frank and Evans, where water molecules are said to be more ordered around apolar surfaces. Furthermore, we compared the water-hydrophilic interactions of the hydrophilic amino acid backbone with those with the water-hydrophobic interactions around the side chains. As the hydrophobicity of the side chain increased, the ordering of the surrounding water HB network was altered from that surrounding the hydrophilic amino acid backbone, thereby diminishing the fraction of NHB water and ordering the surrounding tetrahedral water HB network.

  11. 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

  12. Theoretical studies for Lewis acid-base interactions and C-H...O weak hydrogen bonding in various CO2 complexes.

    PubMed

    Kim, Kyung Hyun; Kim, Yongho

    2008-02-21

    Comprehension of the basic concepts for the design of CO2-philic molecules is important due to the possibility for "green" chemistry in supercritical CO2 of substitute solvent systems. Lewis acid-base interactions and C-H...O weak hydrogen bonding were suggested as two key factors in the solubility of CO2-philic molecules. To isolate the stabilization energy of weak hydrogen bonding from the overall binding energy, high-level quantum mechanical calculations were performed for the van der Waals complexes of CO2 with methane, methylacetate, dimethylether, acetaldehyde, and 1,2-dimethoxyethane. Structures and energies were calculated at the MP2 level of theory using the 6-31+G(d) and aug-cc-pVDZ basis sets with basis set superposition error corrections. In addition, the single-point energies were calculated using recently developed multilevel methods. This study shows that the Lewis acid-base interaction has a significant impact on the complex stability compared to the C-H...O weak hydrogen bond. The additional stabilization energy of the cooperative weak hydrogen bond with alpha-proton of the carbonyl group was negligible on the enhancement of supercritical CO2 solubility. However, the stabilization energy was larger for the ether group, such that it may have an important role in increasing the supercritical CO2 solubility. Additional formation of cooperative weak hydrogen bonds may not further increase the solubility due to the stability reduction by steric hindrance.

  13. 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.

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

    PubMed

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

    2015-05-01

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

  15. Thermal diffusion and colored energy dissipation in hydrogen bonded liquids

    NASA Astrophysics Data System (ADS)

    Dettori, Riccardo; Melis, Claudio; Ceriotti, Michele; Donadio, Davide; Colombo, Luciano

    H-bonded liquids show a manifold energy dissipation dynamics due to: strong directionality of H-bonds and complexity of their network. This affects both thermal diffusion and energy dissipation mechanisms in pump-probe spectroscopy experiments. By nonequilibrium molecular dynamics (MD) simulations we investigate such phenomena in liquid methanol. While heat transport is studied by approach-to-equilibrium MD, energy dissipation is investigated by making use of a novel Generalized Langevin Equation (GLE) colored noise thermostat, which can generate a non-equilibrium frequency-resolved dynamics by using a correlated noise. The colored thermostat can thermally excite a narrow range of vibrational modes, typically the stretching mode of the OH involved in H-bonding, leaving the other degrees of freedom at the equilibrium temperature. The energy dissipation is then observed as a function of time, by probing the excitation decay and the energy transfer to other modes. In particular, by monitoring in time the different contributions to the potential energy of the system, we evaluate how energy is transferred from the excited mode to other modes of the nearby molecules and provide understanding on the dynamics of H-bonded liquids, as resulting from current experimental investigations

  16. Quantitative evaluation on activated property-tunable bulk liquid water with reduced hydrogen bonds using deconvoluted Raman spectroscopy.

    PubMed

    Chen, Hsiao-Chien; Mai, Fu-Der; Yang, Kuang-Hsuan; Chen, Liang-Yih; Yang, Chih-Ping; Liu, Yu-Chuan

    2015-01-01

    Interesting properties of water with distinguishable hydrogen-bonding structure on interfacial phase or in confined environment have drawn wide attentions. However, these unique properties of water are only found within the interfacial phase and confined environment, thus, their applications are limited. In addition, quantitative evaluation on these unique properties associating with the enhancement of water's physical and chemical activities represents a notable challenge. Here we report a practicable production of free-standing liquid water at room temperature with weak hydrogen-bonded structure naming Au nanoparticles (NPs)-treated (AuNT) water via treating by plasmon-induced hot electron transfer occurred on resonantly illuminated gold NPs (AuNPs). Compared to well-known untreated bulk water (deionized water), the prepared AuNT water exhibits many distinct activities in generally physical and chemical reactions, such as high solubilities to NaCl and O2. Also, reducing interaction energy within water molecules provides lower overpotential and higher efficiency in electrolytic hydrogen production. In addition, these enhanced catalytic activities of AuNT water are tunable by mixing with deionized water. Also, most of these tunable activities are linearly proportional to its degree of nonhydrogen-bonded structure (DNHBS), which is derived from the O-H stretching in deconvoluted Raman spectrum. PMID:25471522

  17. Quantitative evaluation on activated property-tunable bulk liquid water with reduced hydrogen bonds using deconvoluted Raman spectroscopy.

    PubMed

    Chen, Hsiao-Chien; Mai, Fu-Der; Yang, Kuang-Hsuan; Chen, Liang-Yih; Yang, Chih-Ping; Liu, Yu-Chuan

    2015-01-01

    Interesting properties of water with distinguishable hydrogen-bonding structure on interfacial phase or in confined environment have drawn wide attentions. However, these unique properties of water are only found within the interfacial phase and confined environment, thus, their applications are limited. In addition, quantitative evaluation on these unique properties associating with the enhancement of water's physical and chemical activities represents a notable challenge. Here we report a practicable production of free-standing liquid water at room temperature with weak hydrogen-bonded structure naming Au nanoparticles (NPs)-treated (AuNT) water via treating by plasmon-induced hot electron transfer occurred on resonantly illuminated gold NPs (AuNPs). Compared to well-known untreated bulk water (deionized water), the prepared AuNT water exhibits many distinct activities in generally physical and chemical reactions, such as high solubilities to NaCl and O2. Also, reducing interaction energy within water molecules provides lower overpotential and higher efficiency in electrolytic hydrogen production. In addition, these enhanced catalytic activities of AuNT water are tunable by mixing with deionized water. Also, most of these tunable activities are linearly proportional to its degree of nonhydrogen-bonded structure (DNHBS), which is derived from the O-H stretching in deconvoluted Raman spectrum.

  18. 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/

  19. Aromatic and aliphatic CH hydrogen bonds fight for chloride while competing alongside ion pairing within triazolophanes.

    PubMed

    Hua, Yuran; Ramabhadran, Raghunath O; Uduehi, Esther O; Karty, Jonathan A; Raghavachari, Krishnan; Flood, Amar H

    2011-01-01

    Triazolophanes are used as the venue to compete an aliphatic propylene CH hydrogen-bond donor against an aromatic phenylene one. Longer aliphatic C-H...Cl(-) hydrogen bonds were calculated from the location of the chloride within the propylene-based triazolophane. The gas-phase energetics of chloride binding (ΔG(bind) , ΔH(bind) , ΔS(bind) ) and the configurational entropy (ΔS(config) ) were computed by taking all low-energy conformations into account. Comparison between the phenylene- and propylene-based triazolophanes shows the computed gas-phase free energy of binding decreased from ΔG(bind) =-194 to -182 kJ mol(-1) , respectively, with a modest enthalpy-entropy compensation. These differences were investigated experimentally. An (1) H NMR spectroscopy study on the structure of the propylene triazolophane's 1:1 chloride complex is consistent with a weaker propylene CH hydrogen bond. To quantify the affinity differences between the two triazolophanes in dichloromethane, it was critical to obtain an accurate binding model. Four equilibria were identified. In addition to 1:1 complexation and 2:1 sandwich formation, ion pairing of the tetrabutylammonium chloride salt (TBA(+) ⋅Cl(-) ) and cation pairing of TBA(+) with the 1:1 triazolophane-chloride complex were observed and quantified. Each complex was independently verified by ESI-MS or diffusion NMR spectroscopy. With ion pairing deconvoluted from the chloride-receptor binding, equilibrium constants were determined by using (1) H NMR (500 μM) and UV/Vis (50 μM) spectroscopy titrations. The stabilities of the 1:1 complexes for the phenylene and propylene triazolophanes did not differ within experimental error, ΔG=(-38±2) and (-39±1) kJ mol(-1) , respectively, as verified by an NMR spectroscopy competition experiment. Thus, the aliphatic CH donor only revealed its weaker character when competing with aromatic CH donors within the propylene-based triazolophane.

  20. Hydrophobic, Non-Hydrogen-Bonding Bases and Base Pairs in DNA

    PubMed Central

    Schweitzer, Barbara A.; Kool, Eric T.

    2009-01-01

    We report the properties of hydrophobic isosteres of pyrimidines and purines in synthetic DNA duplexes. Phenyl nucleosides 1 and 2 are nonpolar isosteres of the natural thymidine nucleoside, and indole nucleoside 3 is an analog of the complementary purine 2-aminodeoxyadenosine. The nucleosides were incorporated into synthetic oligodeoxynucleotides and were paired against each other and against the natural bases. Thermal denaturation experiments were used to measure the stabilities of the duplexes at neutral pH. It is found that the hydrophobic base analogs are nonselective in pairing with the four natural bases but selective for pairing with each other rather than with the natural bases. For example, compound 2 selectively pairs with itself rather than with A, T, G, or C; the magnitude of this selectivity is found to be 6.5–9.3 °C in Tm or 1.5–1.8 kcal/mol in free energy (25 °C). All possible hydrophobic pairing combinations of 1, 2, and 3 were examined. Results show that the pairing affinity depends on the nature of the pairs and on position in the duplex. The highest affinity pairs are found to be the 1–1 and 2–2 self-pairs and the 1–2 heteropair. The best stabilization occurs when the pairs are placed at the ends of duplexes rather than internally; the internal pairs may be destabilized by imperfect steric mimicry which leads to non-ideal duplex structure. In some cases the hydrophobic pairs are significantly stabilizing to the DNA duplex; for example, when situated at the end of a duplex, the 1–1 pair is more stabilizing than a T–A pair. When situated internally, the affinity of the 1–1 pair is the same as, or slightly better than, the analogous T–T mismatch pair, which is known to have two hydrogen bonds. The studies raise the possibility that hydrogen bonds may not always be required for the formation of stable duplex DNA-like structure. In addition, the results point out the importance of solvation and desolvation in natural base pairing

  1. Energy decomposition analysis of cation-π, metal ion-lone pair, hydrogen bonded, charge-assisted hydrogen bonded, and π-π interactions.

    PubMed

    Sharma, Bhaskar; Srivastava, Hemant Kumar; Gayatri, Gaddamanugu; Sastry, Garikapati Narahari

    2015-03-30

    This study probes the nature of noncovalent interactions, such as cation-π, metal ion-lone pair (M-LP), hydrogen bonding (HB), charge-assisted hydrogen bonding (CAHB), and π-π interactions, using energy decomposition schemes-density functional theory (DFT)-symmetry-adapted perturbation theory and reduced variational space. Among cation-π complexes, the polarization and electrostatic components are the major contributors to the interaction energy (IE) for metal ion-π complexes, while for onium ion-π complexes (NH4+, PH4+, OH3+, and SH3+) the dispersion component is prominent. For M-LP complexes, the electrostatic component contributes more to the IE except the dicationic metal ion complexes with H2 S and PH3 where the polarization component dominates. Although electrostatic component dominates for the HB and CAHB complexes, dispersion is predominant in π-π complexes.

  2. Molecular dynamics simulations of ubiquinone; a survey over torsional potentials and hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Nilsson, J. Arvid; Lyubartsev, Alexander; Eriksson, Leif A.; Laaksonen, Aatto

    Molecular dynamics simulations, both classical and Car-Parrinello, have been carried out to investigate ubiquinone (UQ), a proton mediator in both oxidative and photo-phosphorylation. The main objectives have been to follow the dynamics of methoxy groups, conformation of the tail with respect to the ring, hydration and hydrogen bond structure around UQ. The methoxy groups are found to be able to rotate fairly freely. The tail in both UQ and UQ - is approximately perpendicular to the ring plane. Only weak hydrogen bonds are formed between the neutral form of ubiquinone and water molecules in the solvent, while the anionic form shows a distinct solute-solvent hydrogen bond structure. We also conclude that anionic UQ can be accurately modelled by molecular mechanics methods, but the conformation of the methoxy groups in neutral UQ can hardly be properly modelled using a standard force field.

  3. (+/-)-3-Oxocyclohexanecarboxylic and -acetic acids: contrasting hydrogen-bonding patterns in two homologous keto acids.

    PubMed

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

    2002-03-01

    The crystal structures for the title compounds reveal fundamentally different hydrogen-bonding patterns. (+/-)-3-Oxocyclohexanecarboxylic acid, C(7)H(10)O(3), displays acid-to-ketone catemers having a glide relationship for successive components of the hydrogen-bonding chains which advance simultaneously by two cells in a and one in c [O...O = 2.683 (3) A and O-H...O = 166]. A pair of intermolecular close contacts exists involving the acid carbonyl group. The asymmetric unit in (+/-)-3-oxocyclohexaneacetic acid, C(8)H(12)O(3), utilizes only one of two available isoenthalpic conformers and its aggregation involves mutual hydrogen bonding by centrosymmetric carboxyl dimerization [O.O = 2.648 (3) A and O-H...O = 171]. Intermolecular close contacts exist for both the ketone and the acid carbonyl group. PMID:11870311

  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. Electrostatic interaction of pi-acidic amides with hydrogen-bond acceptors.

    PubMed

    Li, Yi; Snyder, Lawrence B; Langley, David R

    2003-10-01

    Interactions between N-methylacetamide (NMA) and N-methylated derivatives of uracil, isocyanurate and barbituric acid have been studied using ab initio methods at the local MP2/6-31G** level of theory. The results were compared to similar interactions between the oxygen atom of NMA and the pi-clouds of perfluorobenzene, quinone and trimethyltriazine. The pi-acidic amides of isocyanurate and barbituric acid were found to interact with a hydrogen bond acceptor primarily through electrostatic attractions. These groups may be used as alternatives of a hydrogen bond donor to complement a hydrogen bond acceptor or an anion in molecular recognition and drug design. Examples of such interactions were identified through a search of the CSD database.

  6. UV raman examination of alpha-helical peptide water hydrogen bonding.

    PubMed

    Pimenov, Konstantin V; Bykov, Sergei V; Mikhonin, Aleksandr V; Asher, Sanford A

    2005-03-01

    UV resonance Raman spectra (UVRS) of an alpha-helical, 21 residue, mainly Ala peptide (AP) in the dehydrated solid state were compared to those in aqueous solution at different temperatures. The UVRS amide band frequencies of a dehydrated solid alpha-helix peptide show frequency shifts compared to those in aqueous solution due to the loss of amide backbone hydrogen bonding to water; the amide II and amide III bands of the solid alpha-helix downshift, while the amide I band upshifts. The shifts are identical in direction but smaller than those that occur for alpha-helices in aqueous solution as the temperature increases; water hydrogen bonding strengths decrease as the temperature increases. The UV Raman amide band frequency shifts can be used to monitor alpha-helix hydrogen bonding. PMID:15740105

  7. Structures and the Hydrogen Bonding Abilities of Estrogens Studied by Supersonic Jet/laser Spectroscopy

    NASA Astrophysics Data System (ADS)

    Morishima, Fumiya; Inokuchi, Yoshiya; Ebata, Takayuki

    2013-06-01

    Estrone, estradiol, estriol are known as endogenous estrogen which have the same steroidal frame with different substituent, leading to difference of physiological activity upon the formation of hydrogen bond with estrogen receptor. In the present study, structures of estrogens and their hydrated clusters in a supersonic jet have been studied by various laser spectroscopic techniques and density functional theory calculation to study how the difference of substituents affects their hydrogen bonding ability. Infrared spectra in the OH stretching region indicate a formation of intramolecular hydrogen-bond in estriol, which may lead to weaker physiological activity among the three estrogens. We also measured electronic and infrared spectra of 1:1 hydrated clusters of estrogen. The results show a switch of stable hydration site from the phenolic OH group to the five member ring by substituting one more OH group.

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

    PubMed

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

    2013-04-23

    Polymer composite yarns containing a high loading of double-walled carbon nanotubes (DWNTs) have been developed in which the inherent acrylate-based organic coating on the surface of the DWNT bundles interacts strongly with poly(vinyl alcohol) (PVA) through an extensive hydrogen-bond network. This design takes advantage of a toughening mechanism seen in spider silk and collagen, which contain an abundance of hydrogen bonds that can break and reform, allowing for large deformation while maintaining structural stability. Similar to that observed in natural materials, unfolding of the polymeric matrix at large deformations increases ductility without sacrificing stiffness. As the PVA content in the composite increases, the stiffness and energy to failure of the composite also increases up to an optimal point, beyond which mechanical performance in tension decreases. Molecular dynamics (MD) simulations confirm this trend, showing the dominance of nonproductive hydrogen bonding between PVA molecules at high PVA contents, which lubricates the interface between DWNTs. PMID:23548065

  9. Hydrogen-bond cooperative effects in small cyclic water clusters as revealed by the interacting quantum atoms approach.

    PubMed

    Guevara-Vela, José Manuel; Chávez-Calvillo, Rodrigo; García-Revilla, Marco; Hernández-Trujillo, Jesús; Christiansen, Ove; Francisco, Evelio; Martín Pendás, Angel; Rocha-Rinza, Tomás

    2013-10-11

    The cooperative effects of hydrogen bonding in small water clusters (H2 O)n (n=3-6) have been studied by using the partition of the electronic energy in accordance with the interacting quantum atoms (IQA) approach. The IQA energy splitting is complemented by a topological analysis of the electron density (ρ(r)) compliant with the quantum theory of atoms-in-molecules (QTAIM) and the calculation of electrostatic interactions by using one- and two-electron integrals, thereby avoiding convergence issues inherent to a multipolar expansion. The results show that the cooperative effects of hydrogen bonding in small water clusters arise from a compromise between: 1) the deformation energy (i.e., the energy necessary to modify the electron density and the configuration of the nuclei of the isolated water molecules to those within the water clusters), and 2) the interaction energy (Eint ) of these contorted molecules in (H2 O)n . Whereas the magnitude of both deformation and interaction energies is enhanced as water molecules are added to the system, the augmentation of the latter becomes dominant when the size of the cluster is increased. In addition, the electrostatic, classic, and exchange components of Eint for a pair of water molecules in the cluster (H2 O)n-1 become more attractive when a new H2 O unit is incorporated to generate the system (H2 O)n with the last-mentioned contribution being consistently the most important part of Eint throughout the hydrogen bonds under consideration. This is opposed to the traditional view, which regards hydrogen bonding in water as an electrostatically driven interaction. Overall, the trends of the delocalization indices, δ(Ω,Ω'), the QTAIM atomic charges, the topology of ρ(r), and the IQA results altogether show how polarization, charge transfer, electrostatics, and covalency contribute to the cooperative effects of hydrogen bonding in small water clusters. It is our hope that the analysis presented in this paper could

  10. 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.

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

    PubMed

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

    2015-10-01

    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.

  12. 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.

  13. Molecular Conductance through a Quadruple-Hydrogen-Bond-Bridged Supramolecular Junction.

    PubMed

    Wang, Lin; Gong, Zhong-Liang; Li, Shu-Ying; Hong, Wenjing; Zhong, Yu-Wu; Wang, Dong; Wan, Li-Jun

    2016-09-26

    A series of self-complementary ureido pyrimidinedione (UPy) derivatives modified with different aurophilic anchoring groups were synthesized. Their electron transport properties through the quadruple hydrogen bonds in apolar solvent were probed employing the scanning tunneling microscopy break junction (STMBJ) technique. The molecule terminated with a thiol shows the optimal electron transport properties, with a statistical conductance value that approaches 10(-3)  G0 . The (1) H NMR spectra and control experiments verify the formation of quadruple hydrogen bonds, which can be effectively modulated by the polarity of the solvent environment. These findings provide a new design strategy for supramolecular circuit elements in molecular electronics. PMID:27576570

  14. Semiquantal molecular dynamics simulations of hydrogen-bond dynamics in liquid water using multi-dimensional Gaussian wave packets.

    PubMed

    Ono, Junichi; Ando, Koji

    2012-11-01

    A semiquantal (SQ) molecular dynamics (MD) simulation method based on an extended Hamiltonian formulation has been developed using multi-dimensional thawed gaussian wave packets (WPs), and applied to an analysis of hydrogen-bond (H-bond) dynamics in liquid water. A set of Hamilton's equations of motion in an extended phase space, which includes variance-covariance matrix elements as auxiliary coordinates representing anisotropic delocalization of the WPs, is derived from the time-dependent variational principle. The present theory allows us to perform real-time and real-space SQMD simulations and analyze nuclear quantum effects on dynamics in large molecular systems in terms of anisotropic fluctuations of the WPs. Introducing the Liouville operator formalism in the extended phase space, we have also developed an explicit symplectic algorithm for the numerical integration, which can provide greater stability in the long-time SQMD simulations. The application of the present theory to H-bond dynamics in liquid water is carried out under a single-particle approximation in which the variance-covariance matrix and the corresponding canonically conjugate matrix are reduced to block-diagonal structures by neglecting the interparticle correlations. As a result, it is found that the anisotropy of the WPs is indispensable for reproducing the disordered H-bond network compared to the classical counterpart with the use of the potential model providing competing quantum effects between intra- and intermolecular zero-point fluctuations. In addition, the significant WP delocalization along the out-of-plane direction of the jumping hydrogen atom associated with the concerted breaking and forming of H-bonds has been detected in the H-bond exchange mechanism. The relevance of the dynamical WP broadening to the relaxation of H-bond number fluctuations has also been discussed. The present SQ method provides the novel framework for investigating nuclear quantum dynamics in the many

  15. Additional disulfide bonds in insulin: Prediction, recombinant expression, receptor binding affinity, and stability

    PubMed Central

    Vinther, Tine N; Pettersson, Ingrid; Huus, Kasper; Schlein, Morten; Steensgaard, Dorte B; Sørensen, Anders; Jensen, Knud J; Kjeldsen, Thomas; Hubalek, František

    2015-01-01

    The structure of insulin, a glucose homeostasis-controlling hormone, is highly conserved in all vertebrates and stabilized by three disulfide bonds. Recently, we designed a novel insulin analogue containing a fourth disulfide bond located between positions A10-B4. The N-terminus of insulin's B-chain is flexible and can adapt multiple conformations. We examined how well disulfide bond predictions algorithms could identify disulfide bonds in this region of insulin. In order to identify stable insulin analogues with additional disulfide bonds, which could be expressed, the Cβ cut-off distance had to be increased in many instances and single X-ray structures as well as structures from MD simulations had to be used. The analogues that were identified by the algorithm without extensive adjustments of the prediction parameters were more thermally stable as assessed by DSC and CD and expressed in higher yields in comparison to analogues with additional disulfide bonds that were more difficult to predict. In contrast, addition of the fourth disulfide bond rendered all analogues resistant to fibrillation under stress conditions and all stable analogues bound to the insulin receptor with picomolar affinities. Thus activity and fibrillation propensity did not correlate with the results from the prediction algorithm. PMID:25627966

  16. A Major Role for Side-Chain Polyglutamine Hydrogen Bonding in Irreversible Ataxin-3 Aggregation

    PubMed Central

    Relini, Annalisa; Apicella, Alessandra; Invernizzi, Gaetano; Casari, Carlo; Gliozzi, Alessandra; Doglia, Silvia Maria; Tortora, Paolo; Regonesi, Maria Elena

    2011-01-01

    The protein ataxin-3 consists of an N-terminal globular Josephin domain (JD) and an unstructured C-terminal region containing a stretch of consecutive glutamines that triggers the neurodegenerative disorder spinocerebellar ataxia type 3, when it is expanded beyond a critical threshold. The disease results from misfolding and aggregation, although the pathway and structure of the aggregation intermediates are not fully understood. In order to provide insight into the mechanism of the process, we monitored the aggregation of a normal (AT3Q24) ataxin-3, an expanded (AT3Q55) ataxin-3, and the JD in isolation. We observed that all of them aggregated, although the latter did so at a much slower rate. Furthermore, the expanded AT3Q55 displayed a substantially different behavior with respect to the two other variants in that at the latest stages of the process it was the only one that did the following: i) lost its reactivity towards an anti-oligomer antibody, ii) generated SDS-insoluble aggregates, iii) gave rise to bundles of elongated fibrils, and iv) displayed two additional bands at 1604 and 1656 cm−1 in FTIR spectroscopy. Although these were previously observed in other aggregated polyglutamine proteins, no one has assigned them unambiguously, yet. By H/D exchange experiments we show for the first time that they can be ascribed to glutamine side-chain hydrogen bonding, which is therefore the hallmark of irreversibly SDS-insoluble aggregated protein. FTIR spectra also showed that main-chain intermolecular hydrogen bonding preceded that of glutamine side-chains, which suggests that the former favors the latter by reorganizing backbone geometry. PMID:21533208

  17. 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.

  18. Luminescent gold(I) metallo-acids and their hydrogen bonded supramolecular liquid crystalline derivatives with decyloxystilbazole as hydrogen acceptor.

    PubMed

    Coco, Silverio; Cordovilla, Carlos; Domínguez, Cristina; Espinet, Pablo

    2008-12-28

    Gold complexes of 4-isocyanobenzoic acid, [AuX(CNC(6)H(4)CO(2)H)] (X = C[triple bond]C-C(6)H(4)-C(9)H(19), C(6)F(5), C(6)F(4)OC(6)H(13), C(6)F(4)C(6)F(4)Br) and [(mu-4,4'-C(6)F(4)C(6)F(4)){Au(CNC(6)H(4)CO(2)H)}(2)], have been isolated. These metallo-acids are luminescent. The single crystal X-ray diffraction study of [Au(C(6)F(5))(CNC(6)H(4)CO(2)H)](infinity) confirms a rod-like structure of the molecule, with a linear coordination around the gold atom, which extends into a supramolecular entity supported by hydrogen bond, gold-gold, and fluorophilic (F(ortho) ... F(meta)) interactions. The carboxylic acid group of the gold isocyanide complexes acts also as a hydrogen donor towards the hydrogen acceptor decyloxystilbazole, affording some hydrogen-bonded supramolecular liquid crystals.

  19. Direct detection of N-H[...]O=C hydrogen bonds in biomolecules by NMR spectroscopy.

    PubMed

    Cordier, Florence; Nisius, Lydia; Dingley, Andrew J; Grzesiek, Stephan

    2008-01-01

    A nuclear magnetic resonance (NMR) experiment is described for the direct detection of N-H[...]O=C hydrogen bonds (H-bonds) in 15N and 13C isotope-labeled biomolecules. This quantitative 'long-range' HNCO-COSY (correlation spectroscopy) experiment detects and quantifies electron-mediated scalar couplings across the H-bond (H-bond scalar couplings), which connect the magnetically active (15)N and (13)C nuclei on both sides of the H-bond. Detectable H-bonds comprise the canonical backbone H-bonds in proteins as well as other H-bonds in proteins and nucleic acids with N-H donors and O=C (carbonylic or carboxylic) acceptors. Unlike other NMR observables, which provide only indirect evidence of the presence of H-bonds, the H-bond scalar couplings identify all partners of the H-bond, the donor, the donor proton and the acceptor, in a single experiment. The size of the scalar couplings can be related to H-bond geometries. The time required to detect the N-H[...]O=C H-bonds in small proteins (< or = approximately 10 kDa) is typically on the order of 1 d at millimolar concentrations, whereas H-bond detection for larger proteins (< or = approximately 30 kDa) may be possible within several days depending on concentration, isotope composition, magnetic field strength and molecular weight. The proteins ubiquitin (8.6 kDa), dimeric RANTES (2 x 8.5 kDa) and MAP30 (30 kDa) are used as examples to illustrate this procedure. PMID:18274525

  20. Transition metal-catalyzed process for addition of amines to carbon-carbon double bonds

    DOEpatents

    Hartwig, John F.; Kawatsura, Motoi; Loeber, Oliver

    2002-01-01

    The present invention is directed to a process for addition of amines to carbon-carbon double bonds in a substrate, comprising: reacting an amine with a compound containing at least one carbon-carbon double bond in the presence a transition metal catalyst under reaction conditions effective to form a product having a covalent bond between the amine and a carbon atom of the former carbon-carbon double bond. The transition metal catalyst comprises a Group 8 metal and a ligand containing one or more 2-electron donor atoms. The present invention is also directed to enantioselective reactions of amine compounds with compounds containing carbon-carbon double bonds, and a calorimetric assay to evaluate potential catalysts in these reactions.

  1. Pressure-induced hydrogen bonding: structure of D2S phase I'

    PubMed

    Loveday; Nelmes; Klotz; Besson; Hamel

    2000-07-31

    The full structure of the high-pressure cubic phase I' of hydrogen sulfide has been solved using neutron diffraction data. The molecules are partially rotationally disordered about the <111> axes, as in phase II at ambient pressure but with markedly greater nonuniformity of the toroidal D distribution. The changes in structure at the II-->I' transition signal the onset of significant pressure-induced hydrogen bonding.

  2. Metal-free, polyether-mediated H2-release from ammonia borane: roles of hydrogen bonding interactions in promoting dehydrogenation.

    PubMed

    Kim, Yongmin; Baek, Hyunjae; Lee, Jin Hee; Yeo, Shinyoung; Kim, Kibum; Hwang, Son-Jong; Eun, Bit; Nam, Suk Woo; Lim, Tae-Hoon; Yoon, Chang Won

    2013-12-01

    Polyetheral additives were found to be efficient promoters to enhance the rate of H2-release from ammonia borane (AB) at various temperatures. In particular, tetraethylene glycol dimethyl ether (T4EGDE, 29 wt% relative to AB + T4EGDE) exhibited significantly improved activities for AB dehydrogenation, with the material-based hydrogen storage capacity of 10.3 wt% at 125 °C within 40 min. In situ FT-IR spectroscopy indicated the formation of B-(cyclodiborazanyl)amino-borohydride (BCDB), borazine, and μ-aminodiborane as gaseous byproducts. In addition, (11)B nuclear magnetic resonance (NMR) spectroscopy further revealed that diammoniate of diborane (DADB) was initially formed to give polyaminoborane as liquid and/or solid spent-fuel, consistent with previous reports. Density Functional Theory (DFT) calculations suggested that hydrogen bonding interactions between AB and a polyetheral promoter initially played an important role in increasing the reactivity of B-H bonds of AB by transferring electron density from oxygen atoms of the promoter into B-H bonds of AB. These partially activated, hydridic B-H bonds were proposed to help promote the formation of diammoniate of diborane (DADB), which is considered as a reactive intermediate, eventually enhancing the rate of H2-release from AB. In addition, our in situ solid state (11)B magic angle spinning (MAS) NMR measurements further confirmed that the rate of DADB formation from AB with a small quantity of T4EGDE was found to be much faster than that of pristine AB even at 50 °C. This metal-free method for H2-release from AB with an added, small quantity of polyethers would be helpful to develop feasible hydrogen storage systems for long-term fuel cell applications. PMID:24068365

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  4. Hydrogen bond dynamics of superheated water and methanol by ultrafast IR-pump and EUV-photoelectron probe spectroscopy.

    PubMed

    Vöhringer-Martinez, E; Link, O; Lugovoy, E; Siefermann, K R; Wiederschein, F; Grubmüller, H; Abel, B

    2014-09-28

    Supercritical water and methanol have recently drawn much attention in the field of green chemistry. It is crucial to an understanding of supercritical solvents to know their dynamics and to what extent hydrogen (H) bonds persist in these fluids. Here, we show that with femtosecond infrared (IR) laser pulses water and methanol can be heated to temperatures near and above their critical temperature Tc and their molecular dynamics can be studied via ultrafast photoelectron spectroscopy at liquid jet interfaces with high harmonics radiation. As opposed to previous studies, the main focus here is the comparison between the hydrogen bonded systems of methanol and water and their interpretation by theory. Superheated water initially forms a dense hot phase with spectral features resembling those of monomers in gas phase water. On longer timescales, this phase was found to build hot aggregates, whose size increases as a function of time. In contrast, methanol heated to temperatures near Tc initially forms a broad distribution of aggregate sizes and some gas. These experimental features are also found and analyzed in extended molecular dynamics simulations. Additionally, the simulations enabled us to relate the origin of the different behavior of these two hydrogen-bonded liquids to the nature of the intermolecular potentials. The combined experimental and theoretical approach delivers new insights into both superheated phases and may contribute to understand their different chemical reactivities. PMID:25102451

  5. Hydrate frameworks involving the pyridazino[4,5-d]pyridazine unit as a multiple hydrogen-bond acceptor.

    PubMed

    Zhylenko, Iryna S; Solntsev, Pavlo V; Rusanov, Eduard B; Chernega, Alexander N; Domasevitch, Konstantin V

    2008-04-01

    1,4,5,8-Tetramethylpyridazino[4,5-d]pyridazine trihydrate, C(10)H(12)N(4) x 3 H(2)O, (I), and 1,2,3,6,7,8-hexahydrocinnolino[5,4,3-cde]cinnoline tetrahydrate, C(12)H(12)N(4) x 4 H(2)O, (II), exhibit exceptional functionality of the condensed N(4)-heteroaromatic frame as a symmetric acceptor of four hydrogen bonds [N...O = 2.843 (2)-2.8716 (10) A]. Thus, all the N atoms of the electron-deficient and highly pi-acidic polynitrogen heterocycles function as lone-pair donors. In (I), all the molecular components lie on or across special positions; the site symmetry is 2/m for the organic and m2m and m for the two water molecules. In (II), the organic polycycle lies across a crystallographic inversion center. Both structures involve a hydrogen-bonded centrosymmetric water-pyridazine dimer as the basic supramolecular unit, which is integrated into two-dimensional [in (I)] and three-dimensional [in (II)] hydrate frameworks by hydrogen bonding with the additional water molecules [O...O = 2.744 (2)-2.8827 (19) A]. The hydrate connectivity exists in the form of an (H(2)O)(3) trimer in (I) and as a one-dimensional zigzag (H(2)O)(n) chain in (II).

  6. Tuning the mechanical properties of graphene oxide paper and its associated polymer nanocomposites by controlling cooperative intersheet hydrogen bonding.

    PubMed

    Compton, Owen C; Cranford, Steven W; Putz, Karl W; An, Zhi; Brinson, L Catherine; Buehler, Markus J; Nguyen, SonBinh T

    2012-03-27

    The mechanical properties of pristine graphene oxide paper and paper-like films of polyvinyl alcohol (PVA)-graphene oxide nanocomposite are investigated in a joint experimental-theoretical and computational study. In combination, these studies reveal a delicate relationship between the stiffness of these papers and the water content in their lamellar structures. ReaxFF-based molecular dynamics (MD) simulations elucidate the role of water molecules in modifying the mechanical properties of both pristine and nanocomposite graphene oxide papers, as bridge-forming water molecules between adjacent layers in the paper structure enhance stress transfer by means of a cooperative hydrogen-bonding network. For graphene oxide paper at an optimal concentration of ~5 wt % water, the degree of cooperative hydrogen bonding within the network comprising adjacent nanosheets and water molecules was found to optimally enhance the modulus of the paper without saturating the gallery space. Introducing PVA chains into the gallery space further enhances the cooperativity of this hydrogen-bonding network, in a manner similar to that found in natural biomaterials, resulting in increased stiffness of the composite. No optimal water concentration could be found for the PVA-graphene oxide nanocomposite papers, as dehydration of these structures continually enhances stiffness until a final water content of ~7 wt % (additional water cannot be removed from the system even after 12 h of annealing).

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

    SciTech Connect

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

    2015-09-25

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

  8. Evidence for intramolecular OH⋯π hydrogen bonding in unsaturated alcohols from UV photoelectron spectroscopy

    NASA Astrophysics Data System (ADS)

    Kowski, Klaus; Lüttke, Wolfgang; Rademacher, Paul

    2001-06-01

    The gas phase He(I) photoelectron (PE) spectra of several unsaturated alcohols ( 1- 11) have been measured and analysed with respect to intramolecular OH⋯π hydrogen bonding. Evidence for such a hydrogen bond has been detected in the spectra of 2-allylphenol ( 1) and 2-phenylethan-1-ol ( 3). 1 exists as a conformational mixture of a hydrogen bonded form 1a and an open form 1b in a composition of roughly 2:1. A strong ionization band (IP v=10.01 eV; where IP v is the vertical ionization potential) is assigned to the ethylenic CC double bond in the major conformer ( 1a) and a weak band (IP v=9.72 eV) to that of the minor conformer ( 1b). The latter IP coincides with the corresponding ionization of allylbenzene. In the series of ω-phenylalkan-1-ols, compound 3 exhibits an unusually low nπ(O) ionization indicating hydrogen bonding between the OH group and the π electron system of the phenyl ring. The higher homologs 4 and 5 prefer 'open' conformations without such interaction. The PE spectra of alkenols such as but-3-en-1-ol ( 7) and pent-4-en-1-ol ( 8) as well as of alkynols such as but-3-yn-1-ol ( 10) and pent-4-yn-1-ol ( 11) are consistent with OH⋯π hydrogen bonded conformers. The methanol/ethylene hetero-dimer has a T-shaped structure, as indicated by B3LYP/6-311++G(d) calculations, with a binding energy of 5.65 kJ mol -1.

  9. Experimental quantification of electrostatics in X-H···π hydrogen bonds

    PubMed Central

    Saggu, Miguel; Levinson, Nicholas M.; Boxer, Steven G.

    2012-01-01

    Hydrogen bonds are ubiquitous in chemistry and biology. The physical forces that govern hydrogen bonding interactions have been heavily debated, with much of the discussion focused on the relative contributions of electrostatic vs. quantum mechanical effects. In principle, the vibrational Stark effect (VSE), the response of a vibrational mode to electric field, can provide an experimental method for parsing such interactions into their electrostatic and non-electrostatic components. In a previous study we showed that, in the case of relatively weak O-H···π hydrogen bonds, the O-H bond displays a linear response to electric field, and we exploited this response to demonstrate that the interactions are dominated by electrostatics (Saggu, M.; Levinson, N. M.; Boxer, S. G. J. Am. Chem. Soc. 2011, 133, 17414–17419). Here we extend this work to other X-H···π interactions. We find that the response of the X-H vibrational probe to electric field appears to become increasingly nonlinear in the order O-H