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Sample records for hydrogen bond donors

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

    PubMed

    Nanda, Vikas; Schmiedekamp, Ann

    2008-02-01

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

  2. Enhancement in Organic Photovoltaic Efficiency through the Synergistic Interplay of Molecular Donor Hydrogen Bonding and -Stacking

    DOE PAGESBeta

    Shewmon, Nathan; Watkins, Davita; Galindo, Johan; Zerdan, Raghida; Chen, Jihua; Keum, Jong Kahk; Roitberg, Adrian; Xue, Jiangeng; Castellano, Ronald

    2015-07-20

    For organic photovoltaic (OPV) cells based on the bulk heterojunction (BHJ) structure, it remains challenging to rationally control the degree of phase separation and percolation within blends of donors and acceptors to secure optimal charge separation and transport. Reported is a bottom-up, supramolecular approach to BHJ OPVs wherein tailored hydrogen bonding (H-bonding) interactions between π-conjugated electron donor molecules encourage formation of vertically aligned donor π-stacks while simultaneously suppressing lateral aggregation; the programmed arrangement facilitates fine mixing with fullerene acceptors and efficient charge transport. The approach is illustrated using conventional linear or branched quaterthiophene donor chromophores outfitted with terminal functional groupsmore » that are either capable or incapable of self-complementary H-bonding. When applied to OPVs, the H-bond capable donors yield a twofold enhancement in power conversion efficiency relative to the comparator systems, with a maximum external quantum efficiency of 64%. H-bond promoted assembly results in redshifted absorption (in neat films and donor:C 60 blends) and enhanced charge collection efficiency despite disparate donor chromophore structure. Both features positively impact photocurrent and fill factor in OPV devices. Film structural characterization by atomic force microscopy, transmission electron microscopy, and grazing incidence wide angle X-ray scattering reveals a synergistic interplay of lateral H-bonding interactions and vertical π-stacking for directing the favorable morphology of the BHJ.« less

  3. Enhancement in Organic Photovoltaic Efficiency through the Synergistic Interplay of Molecular Donor Hydrogen Bonding and -Stacking

    SciTech Connect

    Shewmon, Nathan; Watkins, Davita; Galindo, Johan; Zerdan, Raghida; Chen, Jihua; Keum, Jong Kahk; Roitberg, Adrian; Xue, Jiangeng; Castellano, Ronald

    2015-07-20

    For organic photovoltaic (OPV) cells based on the bulk heterojunction (BHJ) structure, it remains challenging to rationally control the degree of phase separation and percolation within blends of donors and acceptors to secure optimal charge separation and transport. Reported is a bottom-up, supramolecular approach to BHJ OPVs wherein tailored hydrogen bonding (H-bonding) interactions between π-conjugated electron donor molecules encourage formation of vertically aligned donor π-stacks while simultaneously suppressing lateral aggregation; the programmed arrangement facilitates fine mixing with fullerene acceptors and efficient charge transport. The approach is illustrated using conventional linear or branched quaterthiophene donor chromophores outfitted with terminal functional groups that are either capable or incapable of self-complementary H-bonding. When applied to OPVs, the H-bond capable donors yield a twofold enhancement in power conversion efficiency relative to the comparator systems, with a maximum external quantum efficiency of 64%. H-bond promoted assembly results in redshifted absorption (in neat films and donor:C 60 blends) and enhanced charge collection efficiency despite disparate donor chromophore structure. Both features positively impact photocurrent and fill factor in OPV devices. Film structural characterization by atomic force microscopy, transmission electron microscopy, and grazing incidence wide angle X-ray scattering reveals a synergistic interplay of lateral H-bonding interactions and vertical π-stacking for directing the favorable morphology of the BHJ.

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

    PubMed

    Samet, Masoud; Kass, Steven R

    2015-08-01

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

  5. Dinuclear zinc(II) complexes with hydrogen bond donors as structural and functional phosphatase models.

    PubMed

    Bosch, Simone; Comba, Peter; Gahan, Lawrence R; Schenk, Gerhard

    2014-09-01

    It is becoming increasingly apparent that the secondary coordination sphere can have a crucial role in determining the functional properties of biomimetic metal complexes. We have therefore designed and prepared a variety of ligands as metallo-hydrolase mimics, where hydrogen bonding in the second coordination sphere is able to influence the structure of the primary coordination sphere and the substrate binding. The assessment of a structure-function relationship is based on derivates of 2,6-bis{[bis(pyridin-2-ylmethyl)amino]methyl}-4-methylphenol (HBPMP = HL(1)) and 2-{[bis(pyridin-2-ylmethyl)amino]methyl}-6-{[(2-hydroxybenzyl)(pyridin-2-ylmethyl)amino]methyl}-4-methylphenol (H2BPBPMP = H2L(5)), well-known phenolate-based ligands for metallo-hydrolase mimics. The model systems provide similar primary coordination spheres but site-specific modifications in the secondary coordination sphere. Pivaloylamide and amine moieties were chosen to mimic the secondary coordination sphere of the phosphatase models, and the four new ligands H3L(2), H3L(3), HL(4), and H4L(6) vary in the type and geometric position of the H-bond donors and acceptors, responsible for the positioning of the substrate and release of the product molecules. Five dinuclear Zn(II) complexes were prepared and structurally characterized in the solid, and four also in solution. The investigation of the phosphatase activity of four model complexes illustrates the impact of the H-bonding network: the Michaelis-Menten constants (catalyst-substrate binding) for all complexes that support hydrogen bonding are smaller than for the reference complex, and this generally leads to higher catalytic efficiency and higher turnover numbers. PMID:25119813

  6. Unique Reactivity Patterns Catalyzed by Internal Lewis Acid Assisted Hydrogen Bond Donors

    NASA Astrophysics Data System (ADS)

    Auvil, Tyler Jay

    The advancement of hydrogen bond donor (HBD) organocatalysis has been inhibited by a number of challenges. Conventional HBDs suffer from high catalyst loadings and operate in only limited types of reactions, typically the activation of 1,2- and 1,4-acceptors for nucleophilic attack. One strategy to address the shortcomings of HBD catalysis is to design innovative catalysts with improved reactivity. To this end, boronate ureas have been developed as a new family of enhanced HBD catalysts that enable useful new reactivity patterns. Boronate ureas are easily-accessible, small organic molecules that benefit from improved catalytic abilities plausibly due to internal coordination of the urea carbonyl to a strategically placed Lewis acid. Optimization of the boronate urea scaffold has revealed their enhanced catalytic activity, enabling new directions in HBD catalysis. The discovery of boronate ureas has allowed for the unveiling of new HBD activation modes, providing unique reactivity patterns that are inaccessible with conventional HBD catalysts. Among these reactivity patterns is the activation of strained nitrocyclopropane carboxylates for nucleophilic ring-opening reactions, which affords a swift route to access gamma-amino-alpha-nitroester building blocks. The ring-opening method was highlighted by its utilization in the total synthesis of a CB-1 receptor inverse agonist, which was recently patented by Eli Lilly. Additionally, boronate ureas can elicit carbene-like reactivity from alpha-diazocarbonyl compounds, allowing for organocatalytic heteroatom-hydrogen insertions reactions, the first of their kind. The boronate urea activation of alpha-nitrodiazoesters has permitted the development of an unsymmetric double alpha-arylation process, affording a synthetically challenging motif in a single flask. The alpha-arylation reaction proceeds through a conceptually novel organocatalytic transient N--H insertion process, employing anilines as carbene activators. The use

  7. Two different hydrogen bond donor ligands together: a selectivity improvement in organometallic {Re(CO)3} anion hosts.

    PubMed

    Ion, Laura; Nieto, Sonia; Pérez, Julio; Riera, Lucía; Riera, Víctor; Díaz, Jesús; López, Ramón; Anderson, Kirsty M; Steed, Jonathan W

    2011-09-01

    Rhenium(I) compounds [Re(CO)(3)(Hdmpz)(2)(ampy)]BAr'(4) and [Re(CO)(3)(N-MeIm)(2)(ampy)]BAr'(4) (Hdmpz = 3,5-dimethylpyrazole, N-MeIm = N-methylimidazole, ampy = 2-aminopyridine or 3-aminopyridine) have been prepared stepwise as the sole reaction products in good yields. The cationic complexes feature two different types of hydrogen bond donor ligands, and their anion binding behavior has been studied both in solution and in the solid state. Compounds with 2-ampy ligands are labile in the presence of nearly all of the anions tested. The X-ray structure of the complex [Re(CO)(3)(Hdmpz)(2)(ampy)](+) (2) shows that the 2-ampy ligand is metal-coordinated through the amino group, a fact that can be responsible for its labile character. The 3-ampy derivatives (coordinated through the pyridinic nitrogen atom) are stable toward the addition of several anions and are more selective anion hosts than their tris(pyrazole) or tris(imidazole) counterparts. This selectivity is higher for compound [Re(CO)(3)(N-MeIm)(2)(MeNA)]BAr'(4) (5·BAr'(4), MeNA = N-methylnicotinamide) that features an amido moiety, which is a better hydrogen bond donor than the amino group. Some of the receptor-anion adducts have been characterized in the solid state by X-ray diffraction, showing that both types of hydrogen bond donor ligands of the cationic receptor participate in the interaction with the anion hosts. DFT calculations suggest that coordination of the ampy ligands is more favorable through the amino group only for the cationic complex 2, as a consequence of the existence of a strong intramolecular hydrogen bond. In all other cases, the pyridinic coordination is clearly favored. PMID:21834508

  8. Enantio- and periselective nitroalkene Diels-Alder reactions catalyzed by helical-chiral hydrogen bond donor catalysts.

    PubMed

    Peng, Zhili; Narcis, Maurice J; Takenaka, Norito

    2013-01-01

    Helical-chiral double hydrogen bond donor catalysts promote the nitroalkene Diels-Alder reaction in an enantio- and periselective manner. This represents the first asymmetric catalytic nitroalkene Diels-Alder reaction via LUMO-lowering catalysis. To gain an insight into this new process, the substrate scope of our catalyst was investigated by exploiting readily available 5-substituted pentamethylcyclopentadienes. The catalyst was found to tolerate dienes with different steric demands as well as dienes substituted with heteroatoms. The synthetic utility of 5-substituted pentamethylcyclopentadienes is rather limited, and thus we have developed a three-step route to 1,4,5,5-tetrasubstituted cyclopentadienes from commercially available ketones. PMID:23966083

  9. B4H4 and B4(CH3)4 as Unique Electron Donors in Hydrogen-Bonded and Halogen-Bonded Complexes.

    PubMed

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

    2016-07-21

    Ab initio MP2/aug'-cc-pVTZ calculations have been carried out on B4H4 and B4(CH3)4 to investigate the base properties of these molecules with Td symmetry. Each face of the tetrahedral structure of B4H4 and B4(CH3)4 is stabilized by a two-electron, three-center B-B-B bond. The face uses these two electrons to act uniquely as an electron-pair donor for the formation of stable hydrogen-bonded and halogen-bonded complexes with C3v symmetry. The hydrogen-bonded complexes are B4H4:HY and B4(CH3)4:HY, with HY = HNC, HF, HCl, HCN, and HCCH; the halogen-bonded complexes are B4H4:ClY and B4(CH3)4:ClY, with ClY = ClF, ClCl, ClNC, ClCN, ClCCH, and ClH. The absolute values of the binding energies of the hydrogen-bonded complexes B4(CH3)4:HY and of the halogen-bonded complexes B4(CH3)4:ClY are significantly greater than the binding energies of the corresponding complexes with B4H4. The binding energies of each series correlate with the distance from the hydrogen-bonded H atom or halogen-bonded Cl atom to the centroid of the interacting face. Charge transfer stabilizes all complexes and occurs from the B2-B3-B4 orbital of the face to the antibonding H-X orbital of HY in hydrogen-bonded complexes and to the antibonding Cl-X orbital of ClY in halogen-bonded complexes, with X being the atom of Y that is directly bonded to either H or Cl. For fixed HY, EOM-CCSD spin-spin coupling constants J(X-B1) are greater than J(X-Bn) for complexes B4H4:HY, even though the X-B1 distances are longer. B1 and Bn are the atoms at the apex and in the interacting face, respectively. Similarly, for complexes B4H4:ClY, J(Cl-B1) is greater than J(Cl-Bn). In the halogen-bonded complexes, both coupling constants correlate with the corresponding distances. PMID:27399838

  10. Adaptation of a Small-Molecule Hydrogen-Bond Donor Catalyst to an Enantioselective Hetero-Diels–Alder Reaction Hypothesized for Brevianamide Biosynthesis

    PubMed Central

    2015-01-01

    Chiral diamine-derived hydrogen-bond donors were evaluated for their ability to effect stereocontrol in an intramolecular hetero-Diels–Alder (HDA) reaction hypothesized in the biosynthesis of brevianamides A and B. Collectively, these results provide proof of principle that small-molecule hydrogen-bond catalysis, if even based on a hypothetical biosynthesis construct, holds significant potential within enantioselective natural product synthesis. PMID:25697748

  11. Microwave and Quantum Chemical Study of the Hydrazino Group as Proton Donor in Intramolecular Hydrogen Bonding of (2-Fluoroethyl)hydrazine (FCH2CH2NHNH2).

    PubMed

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

    2015-09-01

    The microwave spectrum of (2-fluoroethyl)hydrazine (FCH2CH2NHNH2) was studied in the 11-123 GHz spectral region to investigate the ability of the hydrazino group to form intramolecular hydrogen bonds acting as a proton donor. This group can participate both in five-member and in six-member internal hydrogen bonds with the fluorine atom. The spectra of four conformers were assigned, and the rotational and centrifugal distortion constants of these rotameric forms were determined. Two of these conformers have five-member intramolecular hydrogen bonds, while the two other forms are without this interaction. The internal hydrogen bonds in the two hydrogen-bonded forms are assumed to be mainly electrostatic in origin because the N-H and C-F bonds are nearly parallel and the associated bond moments are antiparallel. This is the first example of a gas-phase study of a hydrazine where the hydrazino functional group acts as a proton donor in weak intramolecular hydrogen bonds. Extensive quantum chemical calculations at the B3LYP/cc-pVTZ, MP2/cc-pVTZ, and CCSD/cc-pVQZ levels of theory accompanied and guided the experimental work. These calculations predict the existence of no less than 18 conformers, spanning a CCSD internal energy range of 15.4 kJ/mol. Intramolecular hydrogen bonds are predicted to be present in seven of these conformers. Three of these forms have six-member hydrogen bonds, while four have five-member hydrogen bonds. The three lowest-energy conformers have five-member internal hydrogen bonds. The spectrum of the conformer with the lowest energy was not assigned because it has a very small dipole moment. The CCSD relative energies of the two hydrogen-bonded rotamers whose spectra were assigned are 1.04 and 1.62 kJ/mol, respectively, whereas the relative energies of the two conformers with assigned spectra and no hydrogen bonds have relative energies of 6.46 and 4.89 kJ/mol. PMID:26258892

  12. Molecular dynamics study of the encapsulation capability of a PCL-PEO based block copolymer for hydrophobic drugs with different spatial distributions of hydrogen bond donors and acceptors.

    PubMed

    Patel, Sarthak K; Lavasanifar, Afsaneh; Choi, Phillip

    2010-03-01

    Molecular dynamics simulation was used to study the potential of using a block copolymer containing three poly(epsilon-caprolactone) (PCL) blocks of equal length connected to one end of a poly(ethylene oxide) (PEO) block, designated as PEO-b-3PCL, to encapsulate two classes of hydrophobic drugs with distinctively different molecular structures. In particular, the first class of drugs consisted of two cucurbitacin drugs (CuB and CuI) that contain multiple hydrogen bond donors and acceptors evenly distributed on their molecules while the other class of drugs (fenofibrate and nimodipine) contain essentially only clustered hydrogen bond acceptors. In the case of cucurbitacin drugs, the results showed that PEO-b-3PCL lowered the Flory-Huggins interaction parameters (chi) considerably (i.e., increased the drug solubility) compared to the linear di-block copolymer PEO-b-PCL with the same PCL/PEO (w/w) ratio of 1.0. However, the opposite effect was observed for fenofibrate and nimodipine. Analysis of the intermolecular interactions indicates that the number of hydrogen bonds formed between the three PCL blocks and cucurbitacin drugs is significantly higher than that of the linear di-block copolymer. On the other hand, owing to the absence of hydrogen bond donors and the clustering of the hydrogen bond acceptors on the fenofibrate and nimodipine molecules, this significantly reduces the number of hydrogen bonds formed in the multi-PCL block environment, leading to unfavourable chi values. The findings of the present work suggest that multi-hydrophobic block architecture could potentially increase the drug loading for hydrophobic drugs with structures containing evenly distributed multiple hydrogen bond donors and acceptors. PMID:19962756

  13. The donor OH stretching-libration dynamics of hydrogen-bonded methanol dimers in cryogenic matrices.

    PubMed

    Heger, M; Andersen, J; Suhm, M A; Wugt Larsen, R

    2016-02-01

    FTIR spectra of the methanol dimer trapped in neon matrices are presented. The fundamental, overtone and combination bands involving the donor OH libration and stretching motions were observed in order to extract relevant anharmonicity constants. We find a stretching-libration coupling constant of +43(5) cm(-1) and a diagonal librational anharmonicity constant of -71(5) cm(-1). The spectra are compared to a number of VPT2 calculations and a torsionally localized monomer model in order to enhance previous explanations of the observable OH stretching red-shift upon dimerization. PMID:26763101

  14. Thermal cracking with hydrogen donor diluent

    SciTech Connect

    Derbyshire, F.; Varghese, P.; Whitehurst, D.D.

    1983-07-26

    An improved hydrogen donor for hydrogen donor diluent cracking is provided by extraction with naphtha from the cracked product and hydrogenation by hydrogen transfer from a lower boiling hydrogen donor such as tetralin.

  15. 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

  16. Organocatalytic asymmetric Henry reaction of 1H-pyrrole-2,3-diones with bifunctional amine-thiourea catalysts bearing multiple hydrogen-bond donors

    PubMed Central

    Zhang, Ming-Liang; Yue, Deng-Feng; Wang, Zhen-Hua; Luo, Yuan; Zhang, Xiao-Mei

    2016-01-01

    Summary For the first time, a catalytic asymmetric Henry reaction of 1H-pyrrole-2,3-diones was achieved with a chiral bifunctional amine-thiourea as a catalyst possessing multiple hydrogen-bond donors. With this developed method, a range of 3-hydroxy-3-nitromethyl-1H-pyrrol-2(3H)-ones bearing quaternary stereocenters were obtained in acceptable yield (up to 75%) and enantioselectivity (up to 73% ee). PMID:26977188

  17. Organocatalytic asymmetric Henry reaction of 1H-pyrrole-2,3-diones with bifunctional amine-thiourea catalysts bearing multiple hydrogen-bond donors.

    PubMed

    Zhang, Ming-Liang; Yue, Deng-Feng; Wang, Zhen-Hua; Luo, Yuan; Xu, Xiao-Ying; Zhang, Xiao-Mei; Yuan, Wei-Cheng

    2016-01-01

    For the first time, a catalytic asymmetric Henry reaction of 1H-pyrrole-2,3-diones was achieved with a chiral bifunctional amine-thiourea as a catalyst possessing multiple hydrogen-bond donors. With this developed method, a range of 3-hydroxy-3-nitromethyl-1H-pyrrol-2(3H)-ones bearing quaternary stereocenters were obtained in acceptable yield (up to 75%) and enantioselectivity (up to 73% ee). PMID:26977188

  18. NAD(P)H-Independent Asymmetric C=C Bond Reduction Catalyzed by Ene Reductases by Using Artificial Co-substrates as the Hydrogen Donor

    PubMed Central

    Winkler, Christoph K; Clay, Dorina; Entner, Marcello; Plank, Markus; Faber, Kurt

    2014-01-01

    To develop a nicotinamide-independent single flavoenzyme system for the asymmetric bioreduction of C=C bonds, four types of hydrogen donor, encompassing more than 50 candidates, were investigated. Six highly potent, cheap, and commercially available co-substrates were identified that (under the optimized conditions) resulted in conversions and enantioselectivities comparable with, or even superior to, those obtained with traditional two-enzyme nicotinamide adenine dinucleotide phosphate (NAD(P)H)-recycling systems. PMID:24382795

  19. A Comparative PCET Study of a Donor-Acceptor Pair Linked by Ionized and Non-ionized Asymmetric Hydrogen-Bonded Interfaces

    PubMed Central

    Young, Elizabeth R.; Rosenthal, Joel; Hodgkiss, Justin M.

    2012-01-01

    A Zn(II) porphyrin-amidinium is the excited state electron donor (D) to a naphthalene diimide acceptor (A) appended with either a carboxylate or sulfonate functionality. The two-point hydrogen bond (---[H+]---) formed between the amidinium and carboxylate or sulfonate establishes a proton-coupled electron transfer (PCET) pathway for charge transfer. The two D---[H+]---A assemblies differ only by the proton configuration within the hydrogen bonding interface. Specifically, the amidinium transfers a proton to the carboxylate to form a non-ionized amidine-carboxylic acid two-point hydrogen network whereas the amidinium maintains both protons when bound to the sulfonate functionality forming an ionized amidinium-sulfonate two-point hydrogen network. These two interface configurations within the dyads thus allow for a direct comparison of PCET kinetics for the same donor and acceptor juxtaposed by an ionized and non-ionized hydrogen-bonded interface. Analysis of PCET kinetics ascertained from transient absorption and transient emission spectroscopy reveal that the ionized interface is more strongly impacted by the local solvent environment, thus establishing that the initial static configuration of the proton interface is a critical determinant to the kinetics of PCET. PMID:19489645

  20. Reactivity studies of oxo-Mo(IV) complexes containing potential hydrogen-bond acceptor/donor phenolate ligands.

    PubMed

    Ng, Victor Wee Lin; Taylor, Michelle K; Young, Charles G

    2012-03-01

    Reactivity studies of oxo-Mo(IV) complexes, Tp(iPr)MoO{2-OC(6)H(4)C(O)R-κ(2)O,O'} (R = Me, Et, OMe, OEt, OPh, NHPh), containing chelated hydrogen-bond donor/acceptor phenolate ligands are reported. Hydrolysis/oxidation of Tp(iPr)MoO(2-OC(6)H(4)CO(2)Ph-κ(2)O,O') in the presence of methanol yields tetranuclear [Tp(iPr)MoO(μ-O)(2)MoO](2)(μ-OMe)(2) (1), while condensation of Tp(iPr)MoO{2-OC(6)H(4)C(O)Me-κ(2)O,O'} and methylamine gives the chelated iminophenolate complex, Tp(iPr)MoO{2-OC(6)H(4)C(Me)NMe-κ(2)O,N} (2), rather than the aqua complex, Tp(iPr)MoO{2-OC(6)H(4)C(Me)NMe-κO}(OH(2)). The oxo-Mo(IV) complexes are readily oxidized by dioxygen or hydrogen peroxide to the corresponding cis-dioxo-Mo(VI) complexes, Tp(iPr)MoO(2){2-OC(6)H(4)C(O)R}; in addition, suitable one-electron oxidants, e.g., [FeCp(2)]BF(4) and [N(C(6)H(4)Br)(3)][SbCl(6)], oxidize the complexes to their EPR-active (g(iso) ≈ 1.942) molybdenyl counterparts (3, 4). Molybdenyl complexes such as Tp(iPr)MoOCl{2-OC(6)H(4)C(O)R} (5) and Tp(iPr)MoOCl(2) also form when the complexes react with chlorinated solvents. The ester derivatives (R = OMe, OEt, OPh) react with propylene sulfide to form cis-oxosulfido-Mo(VI) complexes, Tp(iPr)MoOS{2-OC(6)H(4)C(O)R}, that crystallize as dimeric μ-disulfido-Mo(V) species, [Tp(iPr)MoO{2-OC(6)H(4)C(O)R}](2)(μ-S(2)) (6-8). The crystal structures of [Tp(iPr)MoO(μ-O)(2)MoO](2)(μ-OMe)(2), Tp(iPr)MoO{2-OC(6)H(4)C(Me)NMe}, Tp(iPr)MoOCl{2-OC(6)H(4)C(O)NHPh}·{2-HOC(6)H(4)C(O)NHPh}, and [Tp(iPr)MoO{2-OC(6)H(4)C(O)R}](2)(μ-S(2)) (R = OMe, OEt) are reported. PMID:22356251

  1. Controlled energy transfer between isolated donor-acceptor molecules intercalated in thermally self-ensemble two-dimensional hydrogen bonding cages

    NASA Astrophysics Data System (ADS)

    Al Attar, Hameed A.; Monkman, Andrew P.

    2012-12-01

    Thermally assembled hydrogen bonding cages which are neither size nor guest specific have been developed using a poly (vinyl alcohol) (PVA) host. A water-soluble conjugated polymer poly(2,5-bis(3-sulfonatopropoxy)-1,4-phenylene, disodium salt-alt-1,4-phenylene) (PPP-OPSO3) as a donor and tris(2,2-bipyridyl)- ruthenium(II) [Ru(bpy)32+] as an acceptor have been isolated and trapped in such a PVA matrix network. This is a unique system that shows negligible exciton diffusion and the donor and acceptor predominantly interact by a direct single step excitation transfer process (DSSET). Singlet and triplet exciton quenching have been studied. Time-resolved fluorescence lifetime measurement at different acceptor concentrations has enabled us to determine the dimensionality of the energy-transfer process within the PVA scaffold. Our results reveal that the PVA hydrogen bonding network effectively isolates the donor-acceptor molecules in a two-dimensional layer structure (lamella) leading to the condition where a precise control of the energy and charge transfer is possible.

  2. A cadmium hydroxide complex of a N3S-donor ligand containing two hydrogen bond donors: synthesis, characterization, and CO2 reactivity.

    PubMed

    Allred, Russell A; Huefner, Sara A; Rudzka, Katarzyna; Arif, Atta M; Berreau, Lisa M

    2007-01-21

    Treatment of the ebnpa (N-2-(ethylthio)ethyl-N,N-bis((6-neopentylamino-2-pyridyl)methyl)amine) ligand with a molar equivalent amount of Cd(ClO(4))(2).5H(2)O in CH(3)CN followed by the addition of [Me(4)N]OH.5H(2)O yielded the cadmium hydroxide complex [(ebnpaCd)(2)(mu-OH)(2)](ClO(4))(2) (1). Complex 1 has a binuclear cation in the solid-state with secondary hydrogen-bonding and CH/pi interactions involving the ebnpa ligand. In acetonitrile, 1 forms a binuclear/mononuclear equilibrium mixture. The formation of a mononuclear species has been confirmed by conductance measurements of 1 at low concentrations. Variable temperature studies of the binuclear/mononuclear equilibrium provided the standard enthalpy and entropy associated with the formation of the monomer as DeltaH degrees = +31(2) kJ mol(-1) and DeltaS degrees = +108(8) J mol(-1) K(-1), respectively. Enhanced secondary hydrogen-bonding interactions involving the terminal Cd-OH moiety may help to stabilize the mononuclear complex. Treatment of 1 with CO(2) in acetonitrile results in the formation of a binuclear cadmium carbonate complex, [(ebnpaCd)(2)(mu-CO(3))](ClO(4))(2) (2). PMID:17200755

  3. Electrochemical activation of a tetrathiafulvalene halogen bond donor in solution.

    PubMed

    Oliveira, R; Groni, S; Fave, C; Branca, M; Mavré, F; Lorcy, D; Fourmigué, M; Schöllhorn, B

    2016-06-21

    The halogen bond donor properties of iodo-tetrathiafulvalene (I-TTF) can be electrochemically switched and controlled via reversible oxidation in the solution phase. Interestingly the activation of only one single halogen bond yielded already a strong and selective interaction, quantified by cyclic voltammetry. The standard potentials of the redox couples I-TTF(0/1+) and I-TTF(1+/2+) were observed to shift upon the addition of halides. These anions selectively stabilize the cationic I-TTF species through halogen bonding in polar liquid electrolytes. The thermodynamic affinity constants for chloride and bromide binding to the oxidized species have been determined. Competition in halide binding between I-TTF(1+) and other halogen bond donors allowed for comparing the relative donor strength of the respective electrophilic species. Furthermore it has been shown that halogen bonding can prevail over hydrogen bonding in the investigated system. PMID:27231819

  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. Solution chemistry of a water-soluble eta2-H2 ruthenium complex: evidence for coordinated H2 acting as a hydrogen bond donor.

    PubMed

    Szymczak, Nathaniel K; Zakharov, Lev N; Tyler, David R

    2006-12-13

    The ability of an eta2-H2 ligand to participate in intermolecular hydrogen bonding in solution has long been an unresolved issue. Such species are proposed to be key intermediates in numerous important reactions such as the proton-transfer pathway of H2 production by hydrogenase enzymes. We present the synthesis of several new water-soluble ruthenium coordination complexes including an eta2-H2 complex that is surprisingly inert to substitution by water. The existence of dihydrogen hydrogen bonding (DHHB) was experimentally probed by monitoring the chemical shift of H-bonded Ru-(H2) complexes using NMR spectroscopy, by UV-visible spectroscopy, and by monitoring the rotational dynamics of a hydrogen-bonding probe molecule. The results provide strong evidence that coordinated H2 can indeed participate in intermolecular hydrogen bonding to bulk solvent and other H-bond acceptors. PMID:17147394

  6. 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.

  7. New biologically active hydrogen sulfide donors.

    PubMed

    Roger, Thomas; Raynaud, Francoise; Bouillaud, Frédéric; Ransy, Céline; Simonet, Serge; Crespo, Christine; Bourguignon, Marie-Pierre; Villeneuve, Nicole; Vilaine, Jean-Paul; Artaud, Isabelle; Galardon, Erwan

    2013-11-25

    Generous donors: The dithioperoxyanhydrides (CH3 COS)2 , (PhCOS)2 , CH3 COSSCO2 Me and PhCOSSCO2 Me act as thiol-activated hydrogen sulfide donors in aqueous buffer solution. The most efficient donor (CH3 COS)2 can induce a biological response in cells, and advantageously replace hydrogen sulfide in ex vivo vascular studies. PMID:24115650

  8. 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.

  9. 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.

  10. Hyperfine and Nuclear Quadrupole Tensors of Nitrogen Donors in the QA Site of Bacterial Reaction Centers: Correlation of the Histidine Nδ Tensors with Hydrogen Bond Strength

    PubMed Central

    2015-01-01

    X- and Q-band pulsed EPR spectroscopy was applied to study the interaction of the QA site semiquinone (SQA) with nitrogens from the local protein environment in natural abundance 14N and in 15N uniformly labeled photosynthetic reaction centers of Rhodobacter sphaeroides. The hyperfine and nuclear quadrupole tensors for His-M219 Nδ and Ala-M260 peptide nitrogen (Np) were estimated through simultaneous simulation of the Q-band 15N Davies ENDOR, X- and Q-band 14,15N HYSCORE, and X-band 14N three-pulse ESEEM spectra, with support from DFT calculations. The hyperfine coupling constants were found to be a(14N) = 2.3 MHz, T = 0.3 MHz for His-M219 Nδ and a(14N) = 2.6 MHz, T = 0.3 MHz for Ala-M260 Np. Despite that His-M219 Nδ is established as the stronger of the two H-bond donors, Ala-M260 Np is found to have the larger value of a(14N). The nuclear quadrupole coupling constants were estimated as e2Qq/4h = 0.38 MHz, η = 0.97 and e2Qq/4h = 0.74 MHz, η = 0.59 for His-M219 Nδ and Ala-M260 Np, respectively. An analysis of the available data on nuclear quadrupole tensors for imidazole nitrogens found in semiquinone-binding proteins and copper complexes reveals these systems share similar electron occupancies of the protonated nitrogen orbitals. By applying the Townes–Dailey model, developed previously for copper complexes, to the semiquinones, we find the asymmetry parameter η to be a sensitive probe of the histidine Nδ–semiquinone hydrogen bond strength. This is supported by a strong correlation observed between η and the isotropic coupling constant a(14N) and is consistent with previous computational works and our own semiquinone-histidine model calculations. The empirical relationship presented here for a(14N) and η will provide an important structural characterization tool in future studies of semiquinone-binding proteins. PMID:25026433

  11. 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

  12. Thermodynamics of the hydrogen bonding of nitrogen-containing cyclic and aromatic compounds with proton donors: The structure-property relationship

    NASA Astrophysics Data System (ADS)

    Rakipov, I. T.; Varfolomeev, M. A.; Kirgizov, A. Yu.; Solomonov, B. N.

    2014-12-01

    Enthalpies of dissolution are measured at infinite dilution of nitrogen-containing cyclic (pyrrolidine, piperidine) and aromatic compounds (aniline, N-methylaniline, N,N-dimethylaniline, N-methylimidazole, pyridine, 2-, 3-, 4-methylpyridine, pyrrole, N-methylpyrrole) in chloroform and dichloromethane, and vice versa ( T = 298.15 K). The enthalpies of hydrogen bonds in the above systems are calculated. Relationships between resulting thermochemical data and the structure of nitrogen-containing cyclic and aromatic compounds are explored.

  13. Hydrogen enhancement of silicon thermal donor formation

    NASA Astrophysics Data System (ADS)

    Lamp, C. D.; James, D. J., II

    1993-04-01

    Oxygen-related thermal donor formation in Czochralski silicon is characterized by the capacitance-voltage and deep level transient spectroscopy techniques as a function of 450 °C anneal time following hydrogenation. Increases in the formation rate and number of thermal donor (TD) defects found after hydrogenation are reported. This study finds an increase in TD+/++ concentration in the near-surface region at short anneal times, but at longer times an elevated concentration was not observed. No acceleration through the sequence of thermal donor defects was detected. This fails to support the model of hydrogen lowering the barrier to oxygen diffusion and accelerating the TDn→TDn+1 transitions. This study does, however, support a model in which the hydrogen increases the available thermal donor core sites.

  14. Hydrogen shallow donors in ZnO and rutile TiO2

    NASA Astrophysics Data System (ADS)

    Weber, Jörg; Lavrov, Edward V.; Herklotz, Frank

    2012-05-01

    A combined study of IR absorption, photoconductivity, photoluminescence and Raman measurements in ZnO samples supports the theoretical suggestions of a shallow bond-centered hydrogen donor and a shallow hydrogen donor within the oxygen vacancy. In rutile TiO2 we also identify a shallow hydrogen donor in contrast to recent theoretical predictions. A possible solution to this obvious discrepancy is proposed.

  15. 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.

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

    PubMed

    Henchman, Richard H

    2016-09-28

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

  17. Hydrogen-donor coal liquefaction process

    DOEpatents

    Wilson, Jr., Edward L.; Mitchell, Willard N.

    1980-01-01

    Improved liquid yields are obtained during the hydrogen-donor solvent liquefaction of coal and similar carbonaceous solids by maintaining a higher concentration of material having hydrogenation catalytic activity in the downstream section of the liquefaction reactor system than in the upstream section of the system.

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

    PubMed

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

    2014-09-01

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

  19. 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

  20. Cobalt(III) Werner Complexes with 1,2-Diphenylethylenediamine Ligands: Readily Available, Inexpensive, and Modular Chiral Hydrogen Bond Donor Catalysts for Enantioselective Organic Synthesis

    PubMed Central

    2015-01-01

    In the quest for new catalysts that can deliver single enantiomer pharmaceuticals and agricultural chemicals, chemists have extensively mined the “chiral pool”, with little in the way of inexpensive, readily available building blocks now remaining. It is found that Werner complexes based upon the D3 symmetric chiral trication [Co(en)3]3+ (en = 1,2-ethylenediamine), which features an earth abundant metal and cheap ligand type, and was among the first inorganic compounds resolved into enantiomers 103 years ago, catalyze a valuable carbon–carbon bond forming reaction, the Michael addition of malonate esters to nitroalkenes, in high enantioselectivities and without requiring inert atmosphere conditions. The title catalysts, [Co((S,S)-dpen)3]3+ ((S,S)-33+) 3X–, employ a commercially available chiral ligand, (S,S)-1,2-diphenylethylenediamine. The rates and ee values are functions of the configuration of the cobalt center (Λ/Δ) and the counteranions, which must be lipophilic to solubilize the trication in nonaqueous media. The highest enantioselectivities are obtained with Λ and 2Cl–BArf–, 2BF4–BArf–, or 3BF4– salts (BArf– = B(3,5-C6H3(CF3)2)4–). The substrates are not activated by metal coordination, but rather by second coordination sphere hydrogen bonding involving the ligating NH2 groups. Crystal structures and NMR data indicate enthalpically stronger interactions with the NH moieties related by the C3 symmetry axis, as opposed to those related by the C2 symmetry axes; rate trends and other observations suggest this to be the catalytically active site. Both Λ- and Δ-(S,S)-33+ 2Cl–BArf– are effective catalysts for additions of β-ketoesters to RO2CN=NCO2R species (99–86% yields, 81–76% ee), which provide carbon–nitrogen bonds and valuable precursors to α-amino acids. PMID:27162946

  1. Cobalt(III) Werner Complexes with 1,2-Diphenylethylenediamine Ligands: Readily Available, Inexpensive, and Modular Chiral Hydrogen Bond Donor Catalysts for Enantioselective Organic Synthesis.

    PubMed

    Lewis, Kyle G; Ghosh, Subrata K; Bhuvanesh, Nattamai; Gladysz, John A

    2015-03-25

    In the quest for new catalysts that can deliver single enantiomer pharmaceuticals and agricultural chemicals, chemists have extensively mined the "chiral pool", with little in the way of inexpensive, readily available building blocks now remaining. It is found that Werner complexes based upon the D3 symmetric chiral trication [Co(en)3](3+) (en = 1,2-ethylenediamine), which features an earth abundant metal and cheap ligand type, and was among the first inorganic compounds resolved into enantiomers 103 years ago, catalyze a valuable carbon-carbon bond forming reaction, the Michael addition of malonate esters to nitroalkenes, in high enantioselectivities and without requiring inert atmosphere conditions. The title catalysts, [Co((S,S)-dpen)3](3+) ((S,S)-3 (3+)) 3X(-), employ a commercially available chiral ligand, (S,S)-1,2-diphenylethylenediamine. The rates and ee values are functions of the configuration of the cobalt center (Λ/Δ) and the counteranions, which must be lipophilic to solubilize the trication in nonaqueous media. The highest enantioselectivities are obtained with Λ and 2Cl(-)BArf (-), 2BF4 (-)BArf (-), or 3BF4 (-) salts (BArf (-) = B(3,5-C6H3(CF3)2)4 (-)). The substrates are not activated by metal coordination, but rather by second coordination sphere hydrogen bonding involving the ligating NH2 groups. Crystal structures and NMR data indicate enthalpically stronger interactions with the NH moieties related by the C3 symmetry axis, as opposed to those related by the C2 symmetry axes; rate trends and other observations suggest this to be the catalytically active site. Both Λ- and Δ-(S,S)-3 (3+) 2Cl(-)BArf (-) are effective catalysts for additions of β-ketoesters to RO2CN=NCO2R species (99-86% yields, 81-76% ee), which provide carbon-nitrogen bonds and valuable precursors to α-amino acids. PMID:27162946

  2. Donor center formation in hydrogen implanted silicon

    NASA Astrophysics Data System (ADS)

    Neustroev, E. P.; Antonova, I. V.; Stas, V. F.; Popov, V. P.; Obodnikov, V. I.

    1999-10-01

    The shallow donor centers formed beyond the hydrogen projected range in temperature interval of 350-550°C have been studied in the present work. It has been shown that hydrogen implantation enhances thermal donor (TD) formation in the whole crystal (up to 360 μm). Two different mechanisms of enhancement must be distinguished. The first is a hydrogen-related increase in the TD formation rate, which provides a TD profile up to ∼150 μm described by a diffusion coefficient of 5×10 -9 cm 2/s at 450°C. The second mechanism of acceleration is connected to some mobile point defects (vacancy or interstitial type) from the implanted layer with a diffusion coefficient of about 1×10 -7 cm 2/s. The last mechanism is also manifested in the case of oxygen implantation.

  3. 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

  4. 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

  5. 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.

  6. Hydrogen Bonds in Polymer Folding

    NASA Astrophysics Data System (ADS)

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

    2001-02-01

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

  7. Characteristics of hydrogen bond revealed from water clusters

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  8. Introducing a Hydrogen-Bond Donor into a Weakly Nucleophilic Brønsted Base: Alkali Metal Hexamethyldisilazides (MHMDS, M=Li, Na, K, Rb and Cs) with Ammonia.

    PubMed

    Neufeld, Roman; Michel, Reent; Herbst-Irmer, Regine; Schöne, Ralf; Stalke, Dietmar

    2016-08-22

    Alkali metal 1,1,1,3,3,3-hexamethyldisilazide (MHMDSs) are one of the most utilised weakly nucleophilic Brønsted bases in synthetic chemistry and especially in natural product synthesis. Like lithium organics, they aggregate depending on the employed donor solvents. Thus, they show different reactivity and selectivity as a function of their aggregation and solvation state. To date, monomeric LiHMDS with monodentate donor bases was only characterised in solution. Since the first preparation of LiHMDS in 1959 by Wannagat and Niederprüm, all efforts to crystallise monomeric LiHMDS in the absence of chelating ligands failed. Herein, we present ammonia adducts of LiHMDS, NaHMDS, KHMDS, RbHMDS and CsHMDS with unprecedented aggregation motifs: 1) The hitherto missing monomeric key compound in the LiHMDS aggregation architectures. Monomeric crystal structures of trisolvated LiHMDS (1) and NaHMDS (2), showing unique intermolecular hydrogen bonds, 2) the unprecedented tetrasolvated KHMDS (3) and RbHMDS (4) dimers and 3) the disolvated CsHMDS (5) dimer with very close intermolecular Si-CH3 ⋅⋅⋅Cs s-block "agostic" interactions have been prepared and characterised by single-crystal X-ray structure analysis. PMID:27457218

  9. 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

  10. Influence of the structure of polyfluorinated alcohols on Brønsted acidity/hydrogen-bond donor ability and consequences on the promoter effect.

    PubMed

    Vuluga, Daniela; Legros, Julien; Crousse, Benoit; Slawin, Alexandra M Z; Laurence, Christian; Nicolet, Pierre; Bonnet-Delpon, Danièle

    2011-02-18

    The influence of substituents on the properties of tri- and hexafluorinated alcohols derived from 2,2,2-trifluoroethanol (TFE) and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) was examined. Measurements of specific solvent-solute interactions revealed that H-bond donation (HBD) of fluorinated alcohols is sensitive to the steric hindrance of the OH group, whereas their Brønsted acidity is dependent only on the number of fluorine atoms. For hexafluorinated alcohols (HFAs), their association with amines characterized by X-ray diffraction showed that the balance between HBD and acidity is influenced by their structure. Moreover, the ability of HFAs to donate H-bonds is exerted in synclinal (sc), synperiplanar (sp), and also antiperiplanar (ap) conformations along the C-O bond. Comparison of the effects of fluorinated alcohols as promoting solvents in three reactions is reported. The positive correlation between rate constants and H-bonding donation ability for sulfide oxidation and imino Diels-Alder reaction brings to light the role of this property, while acidity might have a minor influence. In the third reaction, epoxide opening by piperidine, none of these properties can clearly be put forward at this stage. PMID:21244078

  11. Contribution of hydrogen bonds to protein stability.

    PubMed

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

    2014-05-01

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

  12. Contribution of hydrogen bonds to protein stability

    PubMed Central

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

    2014-01-01

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

  13. Contribution of Hydrogen Bonds to Protein Stability

    NASA Astrophysics Data System (ADS)

    Pace, Nick

    2014-03-01

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

  14. Hydrogen bonded structures in organic amine oxalates

    NASA Astrophysics Data System (ADS)

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

    2002-05-01

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

  15. Mapping Buried Hydrogen-Bonding Networks.

    PubMed

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

    2016-05-24

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

  16. Challenging Dogmas: Hydrogen Bond Revisited.

    PubMed

    Tafipolsky, Maxim

    2016-07-01

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

  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. 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...

  19. 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.

  20. Hydrogen donor solvent coal liquefaction process

    DOEpatents

    Plumlee, Karl W.

    1978-01-01

    An indigenous hydrocarbon product stream boiling within a range of from about C.sub.1 -700.degree. F., preferably C.sub.1 -400.degree. F., is treated to produce an upgraded hydrocarbon fuel component and a component which can be recycled, with a suitable donor solvent, to a coal liquefaction zone to catalyze the reaction. In accordance therewith, a liquid hydrocarbon fraction with a high end boiling point range up to about 700.degree. F., preferably up to about 400.degree. F., is separated from a coal liquefaction zone effluent, the separated fraction is contacted with an alkaline medium to provide a hydrocarbon phase and an aqueous extract phase, the aqueous phase is neutralized, and contacted with a peroxygen compound to convert indigenous components of the aqueous phase of said hydrocarbon fraction into catalytic components, such that the aqueous stream is suitable for recycle to the coal liquefaction zone. Naturally occurring phenols and alkyl substituted phenols, found in the aqueous phase, are converted, by the addition of hydroxyl constituents to phenols, to dihydroxy benzenes which, as disclosed in copending Application Ser. Nos. 686,813 now U.S. Pat. No. 4,049,536; 686,814 now U.S. Pat. No. 4,049,537; 686,827 now U.S. Pat. No. 4,051,012 and 686,828, K. W. Plumlee et al, filed May 17, 1976, are suitable hydrogen transfer catalysts.

  1. 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.

  2. Cationic Multidentate Halogen-Bond Donors in Halide Abstraction Organocatalysis: Catalyst Optimization by Preorganization.

    PubMed

    Jungbauer, Stefan H; Huber, Stefan M

    2015-09-23

    In contrast to hydrogen bonding, which is firmly established in organocatalysis, there are still very few applications of halogen bonding in this field. Herein, we present the first catalytic application of cationic halogen-bond donors in a halide abstraction reaction. First, halopyridinium-, haloimidazolium-, and halo-1,2,3-triazolium-based catalysts were systematically tested. In contrast to the pyridinium compounds, both the imidazolium and the triazolium salts showed promising potency. For the haloimidazolium-based organocatalysts, we could show that the catalytic activity is based on halogen bonding using, e.g., the chlorinated derivatives as reference compounds. On the basis of these studies, halobenzimidazolium organocatalysts were then investigated. Monodentate compounds featured the same trends as the corresponding imidazolium analogues but showed a stronger catalytic activity. In order to prepare bidentate versions which are preorganized for anion binding, a new class of rigid bis(halobenzimidazolium) compounds was synthesized and structurally characterized. The corresponding syn isomer showed unprecedented catalytic potency and could be used in as low as 0.5 mol % in the benchmark reaction of 1-chloroisochroman with a silyl enol ether. Calculations confirmed that the syn isomer may bind in a bidentate fashion to chloride. The respective anti isomer is less active and binds halides in a monodentate fashion. Kinetic investigations confirmed that the syn isomer led to a 20-fold rate acceleration compared to a neutral tridentate halogen-bond donor. The strength of the preorganized halogen-bond donor seems to approach the limit under the reaction conditions, as decomposition is observed in the presence of chloride in the same solvent at higher temperatures. Calorimetric titrations of the syn isomer with bromide confirmed the strong halogen-bond donor strength of the former (K ≈ 4 × 10(6) M(-1), ΔG ≈ 38 kJ/mol). PMID:26329271

  3. Persistent hydrogen bonding in polymorphic crystal structures.

    PubMed

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

    2009-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  5. Hydrogen-bond kinetics in liquid water

    NASA Astrophysics Data System (ADS)

    Luzar, Alenka; Chandler, David

    1996-01-01

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

  6. An unconventional halogen bond with carbene as an electron donor: An ab initio study

    NASA Astrophysics Data System (ADS)

    Li, Qingzhong; Wang, Yilei; Liu, Zhenbo; Li, Wenzuo; Cheng, Jianbo; Gong, Baoan; Sun, Jiazhong

    2009-02-01

    An unconventional halogen bond has been proved to exist in H2C-BrH complex. The halogen bond energy of H2C-BrH complex is calculated at four levels of theory [MP2, MP4, CCSD, and CCSD(T)]. The result shows that the carbene is a better electron donor. The substitution effect is prominent in this interaction. For example, the interaction energy in H2C-BrCN complex is increased by more than 300% relative to H2C-BrH complex. The analyses of NBO, AIM, and energy components were used to unveil the nature of the interaction. The results show that this novel halogen bond has similar characteristics to hydrogen bonds.

  7. 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.

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

    PubMed Central

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

    2010-01-01

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

  9. 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

  10. Fano resonances in photoconductivity spectra of hydrogen donors in ZnO and rutile

    NASA Astrophysics Data System (ADS)

    Lavrov, E. V.; Herklotz, F.; Weber, J.

    2015-02-01

    The results of photoconductivity studies of hydrogen donors in ZnO and rutile TiO2 are presented. It is shown that local vibrational modes of O-H bonds comprising donors in both semiconductors can be detected in photoconductivity spectra as Fano resonances at 3611 and 3290 cm-1 in the case of ZnO and TiO2, respectively. The frequencies of these features red-shift in energy down to 2668 (ZnO) and 2445 cm-1 (TiO2) if hydrogen is substituted by deuterium. Based on the frequency of the deuterium resonance it is concluded that the ionization energy of the hydrogen donor in TiO2 is less than 300 meV, which is in variance with predictions of theory. The reasons for such a discrepancy are discussed.

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

    PubMed

    Palanivel, Umadevi; Lakshmipathi, Senthilkumar

    2016-08-01

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

  12. Hydrogen bonding nature during ADP crystallization

    NASA Astrophysics Data System (ADS)

    Sun, Congting; Xue, Dongfeng

    2014-02-01

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

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

    PubMed

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

    2016-07-20

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

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

    PubMed

    Bauzá, Antonio; Frontera, Antonio

    2016-07-27

    In this manuscript the ability of hydrogen and halogen bonding interactions, as well as metal coordination to enhance FF interactions involving fluorine substituted aromatic rings has been studied at the RI-MP2/def2-TZVPD level of theory. We have used 4-fluoropyridine, 4-fluorobenzonitrile, 3-(4-fluorophenyl)propiolonitrile and their respective meta derivatives as aromatic compounds. In addition, we have used HF and IF as hydrogen and halogen bond donors, respectively, and Ag(i) as the coordination metal. Furthermore, we have also used HF as an electron rich fluorine donor entity, thus establishing FF interactions with the above mentioned aromatic systems. Moreover, a CSD (Cambridge Structural Database) search has been carried out and some interesting examples have been found, highlighting the impact of FF interactions involving aromatic fluorine atoms in solid state chemistry. Finally, cooperativity effects between FF interactions and both hydrogen and halogen bonding interactions have been analyzed and compared. We have also used Bader's theory of "atoms in molecules" to further describe the cooperative effects. PMID:27401347

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

    PubMed

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

    2016-04-01

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

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

    PubMed

    Baranović, Goran; Biliškov, Nikola; Vojta, Danijela

    2012-08-16

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

  17. A molecular electrostatic potential analysis of hydrogen, halogen, and dihydrogen bonds.

    PubMed

    Mohan, Neetha; Suresh, Cherumuttathu H

    2014-03-01

    Hydrogen, halogen, and dihydrogen bonds in weak, medium and strong regimes (<1 to ∼ 60 kcal/mol) have been investigated for several intermolecular donor-acceptor (D-A) complexes at ab initio MP4//MP2 method coupled with atoms-in-molecules and molecular electrostatic potential (MESP) approaches. Electron density ρ at bond critical point correlates well with interaction energy (Enb) for each homogeneous sample of complexes, but its applicability to the entire set of complexes is not satisfactory. Analysis of MESP minimum (V(min)) and MESP at the nuclei (Vn) shows that in all D-A complexes, MESP of A becomes more negative and that of D becomes less negative suggesting donation of electrons from D to A leading to electron donor-acceptor (eDA) interaction between A and D. MESP based parameter ΔΔVn measures donor-acceptor strength of the eDA interactions as it shows a good linear correlation with Enb for all D-A complexes (R(2) = 0.976) except the strongly bound bridged structures. The bridged structures are classified as donor-acceptor-donor complexes. MESP provides a clear evidence for hydrogen, halogen, and dihydrogen bond formation and defines them as eDA interactions in which hydrogen acts as electron acceptor in hydrogen and dihydrogen bonds while halogen acts as electron acceptor in halogen bonds. PMID:24506527

  18. 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.

  19. Roles of molecular hydrogen and a hydrogen donor solvent in the cracking of moal model compounds with dispersed catalysts

    SciTech Connect

    Suzuki, Toshimitsu; Ikenaga, Na-oki; Sakota, Takahiro

    1994-12-31

    It is of great importance to evaluate quantitative hydrogen transfer process by using coal model compounds with a hydrogen-donor solvent. Cronauer el al. showed that in the cracking of benzyl phenyl ether the hydrogen required to stabilize free radicals comes from a donor solvent or intramolecular rearrangement and not from gaseous hydrogen in the absence of a catalyst. Korobkov et al. and Schlosberg et al. showed that the thermolysis of benzyl phenyl ether and dibenzyl ether were accomplished by intramolecular rearrangements. Yokokawa et al. reported that tetralin retarded the catalyzed hydrocracking of coal model compounds containing C-C and C-O bonds. However, few studies dealt with quantitative discussion in the hydrogen transfer process from a hydrogen-donor solvent or molecular hydrogen to free radicals derived from a model compound except a series of studies by Nicole and co-workers. On the other hand, it is well known that the amount of naphthalene produced from tetralin decreases after the liquefaction of coal in tetralin with catalyst as compared to the liquefaction in the absence of catalysts. To account for this, two mechanisms are proposed. One is that the catalyst hydrogenates naphthalene produced from tetralin, and the other is that the catalyst promotes the direct hydrogen transfer from molecular hydrogen to free radicals. The purpose of this work is to elucidate the role of catalyst and tetralin by means of the quantitative treatment of the hydrogen transfer reaction stabilizing thermally decomposed free radicals. Cracking of benzyl phenyl ether (BPE), dibenzyl ether (DBE), 1,2-diphenylethane, and 1,3-diphenylpropane was studied in tetralin in the presence of highly disposed catalyst.

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

    NASA Astrophysics Data System (ADS)

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

    1999-04-01

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

  1. 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

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

    PubMed

    Carr, P W; Dolan, J W; Dorsey, J G; Snyder, L R; Kirkland, J J

    2015-05-22

    Column selectivity in reversed-phase chromatography (RPC) can be described in terms of the hydrophobic-subtraction model, which recognizes five solute-column interactions that together determine solute retention and column selectivity: hydrophobic, steric, hydrogen bonding of an acceptor solute (i.e., a hydrogen-bond base) by a stationary-phase donor group (i.e., a silanol), hydrogen bonding of a donor solute (e.g., a carboxylic acid) by a stationary-phase acceptor group, and ionic. Of these five interactions, hydrogen bonding between donor solutes (acids) and stationary-phase acceptor groups is the least well understood; the present study aims at resolving this uncertainty, so far as possible. Previous work suggests that there are three distinct stationary-phase sites for hydrogen-bond interaction with carboxylic acids, which we will refer to as column basicity I, II, and III. All RPC columns exhibit a selective retention of carboxylic acids (column basicity I) in varying degree. This now appears to involve an interaction of the solute with a pair of vicinal silanols in the stationary phase. For some type-A columns, an additional basic site (column basicity II) is similar to that for column basicity I in primarily affecting the retention of carboxylic acids. The latter site appears to be associated with metal contamination of the silica. Finally, for embedded-polar-group (EPG) columns, the polar group can serve as a proton acceptor (column basicity III) for acids, phenols, and other donor solutes. PMID:25890437

  3. Correlation of Hydrogen-Atom Abstraction Reaction Efficiencies for Aryl Radicals with their Vertical Electron Affinities and the Vertical Ionization Energies of the Hydrogen Atom Donors

    PubMed Central

    Jing, Linhong; Nash, John J.

    2009-01-01

    The factors that control the reactivities of aryl radicals toward hydrogen-atom donors were studied by using a dual-cell Fourier-transform ion cyclotron resonance mass spectrometer (FT – ICR). Hydrogen-atom abstraction reaction efficiencies for two substrates, cyclohexane and isopropanol, were measured for twenty-three structurally different, positively-charged aryl radicals, which included dehydrobenzenes, dehydronaphthalenes, dehydropyridines, and dehydro(iso)quinolines. A logarithmic correlation was found between the hydrogen-atom abstraction reaction efficiencies and the (calculated) vertical electron affinities (EA) of the aryl radicals. Transition state energies calculated for three of the aryl radicals with isopropanol were found to correlate linearly with their (calculated) EAs. No correlation was found between the hydrogen-atom abstraction reaction efficiencies and the (calculated) enthalpy changes for the reactions. Measurement of the reaction efficiencies for the reactions of several different hydrogen-atom donors with a few selected aryl radicals revealed a logarithmic correlation between the hydrogen-atom abstraction reaction efficiencies and the vertical ionization energies (IE) of the hydrogen-atom donors, but not the lowest homolytic X – H (X = heavy atom) bond dissociation energies of the hydrogen-atom donors. Examination of the hydrogen-atom abstraction reactions of twenty-nine different aryl radicals and eighteen different hydrogen-atom donors showed that the reaction efficiency increases (logarithmically) as the difference between the IE of the hydrogen-atom donor and the EA of the aryl radical decreases. This dependence is likely to result from the increasing polarization, and concomitant stabilization, of the transition state as the energy difference between the neutral and ionic reactants decreases. Thus, the hydrogen-atom abstraction reaction efficiency for an aryl radical can be “tuned” by structural changes that influence either

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

    NASA Astrophysics Data System (ADS)

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

    1996-06-01

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

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

    PubMed

    Topić, Filip; Rissanen, Kari

    2016-05-25

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

  6. Probing the Hydrogen Bond Strength at Single Bond Limit

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  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. Alcohols as hydrogen-donor solvents for treatment of coal

    DOEpatents

    Ross, David S.; Blessing, James E.

    1981-01-01

    A method for the hydroconversion of coal by solvent treatment at elevated temperatures and pressure wherein an alcohol having an .alpha.-hydrogen atom, particularly a secondary alcohol such as isopropanol, is utilized as a hydrogen donor solvent. In a particular embodiment, a base capable of providing a catalytically effective amount of the corresponding alcoholate anion under the solvent treatment conditions is added to catalyze the alcohol-coal reaction.

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

    PubMed

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

    2015-12-14

    The far-infrared absorption spectra have been recorded for hydrogen-bonded complexes of water with ethanol embedded in cryogenic neon matrices at 2.8 K. The partial isotopic H/D-substitution of the ethanol subunit enabled by a dual inlet deposition procedure enables the observation and unambiguous assignment of the intermolecular high-frequency out-of-plane and the low-frequency in-plane donor OH librational modes for two different conformations of the mixed binary ethanol/water complex. The resolved donor OH librational bands confirm directly previous experimental evidence that ethanol acts as the O⋯HO hydrogen bond acceptor in the two most stable conformations. In the most stable conformation, the water subunit forces the ethanol molecule into its less stable gauche configuration upon dimerization owing to a cooperative secondary weak O⋯HC hydrogen bond interaction evidenced by a significantly blue-shift of the low-frequency in-plane donor OH librational band origin. The strong correlation between the low-frequency in-plane donor OH librational motion and the secondary intermolecular O⋯HC hydrogen bond is demonstrated by electronic structure calculations. The experimental findings are further supported by CCSD(T)-F12/aug-cc-pVQZ calculations of the conformational energy differences together with second-order vibrational perturbation theory calculations of the large-amplitude donor OH librational band origins. PMID:26671383

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    SciTech Connect

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

    2015-12-14

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

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

    PubMed

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

    2016-03-16

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

  13. Do Hydrogen Bonds Influence Excitonic Splittings?

    PubMed

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

    2016-01-01

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

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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.

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

    PubMed

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

    2016-03-01

    In RNA secondary structure determination, it is essential to determine whether a nucleotide is base-paired and not. Base-pairing of nucleotides is mediated by hydrogen bonds. The NMR characterization of hydrogen bonds relies on experiments correlating the NMR resonances of exchangeable protons and can be best performed for structured parts of the RNA, where labile hydrogen atoms are protected from solvent exchange. Functionally important regions in RNA, however, frequently reveal increased dynamic disorder which often leads to NMR signals of exchangeable protons that are broadened beyond (1)H detection. Here, we develop (13)C direct detected experiments to observe all nucleotides in RNA irrespective of whether they are involved in hydrogen bonds or not. Exploiting the self-decoupling of scalar couplings due to the exchange process, the hydrogen bonding behavior of the hydrogen bond donor of each individual nucleotide can be determined. Furthermore, the adaption of HNN-COSY experiments for (13)C direct detection allows correlations of donor-acceptor pairs and the localization of hydrogen-bond acceptor nucleotides. The proposed (13)C direct detected experiments therefore provide information about molecular sites not amenable by conventional proton-detected methods. Such information makes the RNA secondary structure determination by NMR more accurate and helps to validate secondary structure predictions based on bioinformatics. PMID:26852414

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

    PubMed

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Dormidontova, Elena E.

    2004-03-01

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

  4. One-step versus stepwise mechanism in protonated amino acid-promoted electron-transfer reduction of a quinone by electron donors and two-electron reduction by a dihydronicotinamide adenine dinucleotide analogue. Interplay between electron transfer and hydrogen bonding.

    PubMed

    Yuasa, Junpei; Yamada, Shunsuke; Fukuzumi, Shunichi

    2008-04-30

    Semiquinone radical anion of 1-(p-tolylsulfinyl)-2,5-benzoquinone (TolSQ(*-)) forms a strong hydrogen bond with protonated histidine (TolSQ(*-)/His x 2 H(+)), which was successfully detected by electron spin resonance. Strong hydrogen bonding between TolSQ(*-) and His x 2 H(+) results in acceleration of electron transfer (ET) from ferrocenes [R2Fc, R = C5H5, C5H4(n-Bu), C5H4Me] to TolSQ, when the one-electron reduction potential of TolSQ is largely shifted to the positive direction in the presence of His x 2 H(+). The rates of His x 2 H(+)-promoted ET from R2Fc to TolSQ exhibit deuterium kinetic isotope effects due to partial dissociation of the N-H bond in His x 2 H(+) at the transition state, when His x 2 H(+) is replaced by the deuterated compound (His x 2 D(+)-d6). The observed deuterium kinetic isotope effect (kH/kD) decreases continuously with increasing the driving force of ET to approach kH/kD = 1.0. On the other hand, His x 2 H(+) also promotes a hydride reduction of TolSQ by an NADH analogue, 9,10-dihydro-10-methylacridine (AcrH2). The hydride reduction proceeds via the one-step hydride-transfer pathway. In such a case, a large deuterium kinetic isotope effect is observed in the rate of the hydride transfer, when AcrH2 is replaced by the dideuterated compound (AcrD2). In sharp contrast to this, no deuterium kinetic isotope effect is observed, when His x 2 H(+) is replaced by His x 2 D(+)-d6. On the other hand, direct protonation of TolSQ and 9,10-phenanthrenequinone (PQ) also results in efficient reductions of TolSQH(+) and PQH(+) by AcrH2, respectively. In this case, however, the hydride-transfer reactions occur via the ET pathway, that is, ET from AcrH2 to TolSQH(+) and PQH(+) occurs in preference to direct hydride transfer from AcrH2 to TolSQH(+) and PQH(+), respectively. The AcrH2(*+) produced by the ET oxidation of AcrH2 by TolSQH(+) and PQH(+) was directly detected by using a stopped-flow technique. PMID:18386924

  5. 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

  6. 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.

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

    PubMed

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

    2015-07-28

    If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent, it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor Φ is correlated with the strength of the intramolecular hydrogen bonds. This correlation has been used to determine the length of the H-bonds (donor-acceptor separation) in a diverse range of enzymes and has been argued to support the existence of short low-barrier H-bonds. Starting with a potential energy surface based on a simple diabatic state model for H-bonds, we calculate Φ as a function of the proton donor-acceptor distance R. For numerical results, we use a parameterization of the model for symmetric O-H⋯O bonds [R. H. McKenzie, Chem. Phys. Lett. 535, 196 (2012)]. We consider the relative contributions of the O-H stretch vibration, O-H bend vibrations (both in plane and out of plane), tunneling splitting effects at finite temperature, and the secondary geometric isotope effect. We compare our total Φ as a function of R with NMR experimental results for enzymes, and in particular with an earlier model parametrization Φ(R), used previously to determine bond lengths. PMID:26233131

  8. 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.

  9. Role of the Uranyl Oxo Group as a Hydrogen Bond Acceptor

    SciTech Connect

    Watson, Lori A; Hay, Benjamin

    2011-01-01

    Density functional theory calculations have been used to evaluate the geometries and energetics of interactions between a number of uranyl complexes and hydrogen bond donor groups. The results reveal that although traditional hydrogen bond donors are repelled by the oxo group in the [UO{sub 2}(OH{sub 2}){sub 5}]{sup 2+} species, they are attracted to the oxo groups in [UO{sub 2}(OH{sub 2}){sub 2}(NO{sub 3}){sub 2}]{sup 0}, [UO{sub 2}(NO{sub 3}){sub 3}]{sup -}, and [UO{sub 2}Cl{sub 4}]{sup 2-} species. Hydrogen bond strength depends on the equatorial ligation and can exceed 15 kcal mol{sup -1}. The results also reveal the existence of directionality at the uranyl oxo acceptor, with a weak preference for linear U=O---H angles.

  10. Femtosecond dynamics in hydrogen-bonded solvents

    SciTech Connect

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

    1993-09-01

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

  11. Donor level of interstitial hydrogen in semiconductors: Deep level transient spectroscopy

    NASA Astrophysics Data System (ADS)

    Kolkovsky, Vl.; Dobaczewski, L.; Nielsen, K. Bonde; Kolkovsky, V.; Larsen, A. Nylandsted; Weber, J.

    2009-12-01

    The behaviour of hydrogen in crystalline semiconductors has attracted considerable interest during several decades. Due to its high diffusion rate and ability to react with a wide variety of lattice imperfections such as intrinsic point defects, impurities, interfaces and surfaces, hydrogen is an impurity of fundamental importance in semiconductor materials. It has been already evidenced in previous investigations that the most fundamental hydrogen-related defects in-group IV semiconductors are interstitial hydrogen atoms occupying the bond-centre site ( BC) or the interstitial tetrahedral site ( T). Using first-principles calculations Van de Walle predicted similar properties of isolated hydrogen in other II-VI and III-V semiconductors. Another interesting prediction shown in that work was the existence of a universal alignment for the hydrogen electronic (-/+) level. Until now there is no direct experimental information regarding the individual isolated hydrogen states in compound semiconductors and most reported properties have been inferred indirectly. In the present work in-situ conventional deep level transient spectroscopy (DLTS) and high-resolution Laplace DLTS techniques are used to analyse hydrogen-related levels after low-temperature proton implantation in different II-VI and III-V semiconductors including GaAs, ZnO and CdTe. From these experimental observations the donor level of isolated hydrogen is found to keep almost a constant value in the absolute energy scale taking into account different band-offsets calculated for the whole group of semiconductors.

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Nishio, M.

    2012-06-01

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

  16. 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.

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

    PubMed

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

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

  19. Electron collisions with hydrogen-bonded complexes

    SciTech Connect

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

    2011-12-15

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

  20. Hydrogen bonding in the ethanol-water dimer.

    PubMed

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

    2015-10-01

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

  1. 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.

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

    PubMed

    Joy, Stephen T; Arora, Paramjit S

    2016-04-14

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

  3. 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

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

    NASA Astrophysics Data System (ADS)

    Chao, Chi-Yang

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

  5. A coordinatively saturated sulfate encapsulated in a metal-organic framework functionalized with urea hydrogen-bonding groups

    SciTech Connect

    Custelcean, Radu; Moyer, Bruce A.; Hay, Benjamin P.

    2005-10-14

    A functional coordination polymer decorated with urea hydrogen-bonding donor groups has been designed for optional binding of sulfate; self-assembly of a tripodal tri-urea linker with Ag2SO4 resulted in the formation of a 1D metal-organic framework that encapsulated SO42- anions via twelve complementary hydrogen bonds, which represents the highest coordination number observed for sulfate in a natural or synthetic host.

  6. Tetrahedrality and hydrogen bonds in water

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  7. Blue shifted hydrogen bond in 3-methylindole.CHX(3) complexes (X = Cl, F).

    PubMed

    Shirhatti, Pranav R; Wategaonkar, Sanjay

    2010-07-01

    Although the first experimental report on the blue shifted hydrogen bond in gas phase appeared about a decade ago, not many examples have been reported in the literature thereafter. Computational studies on systems exhibiting such blue shifted hydrogen bond however have been abundant since then. Many of these theoretical predictions remain to be verified experimentally. In this work we present an example of blue shifted hydrogen bond observed in the weakly bound complexes of 3-methylindole and CHX(3) (X = F, Cl). The complexes were prepared using the supersonic jet expansion method and studied using the laser spectroscopic methods. The key findings were that these complexes exhibit C-Hpi type hydrogen bonding interaction and the CH is bound to the phenyl part of the aromatic plane. The CH stretch was found to be blue shifted by 2 and 16 cm(-1) in the case of CHCl(3) and CHF(3), respectively. Ab initio calculations along with atoms-in-molecule analysis and natural bond orbital analysis support the experimental findings. The computed results at the DFT/MP2 level also indicated that the IR intensity of the H-bond donor CH-stretch increases by two to three orders of magnitude for the CHCl(3) complex whereas for the fluoroform complex the same decreases by an order of magnitude, which are consistent with the trend reported in the case of C-HO type of blue shifting hydrogen bonds. PMID:20407683

  8. Hydrogen Bond Basicity Prediction for Medicinal Chemistry Design.

    PubMed

    Kenny, Peter W; Montanari, Carlos A; Prokopczyk, Igor M; Ribeiro, Jean F R; Sartori, Geraldo Rodrigues

    2016-05-12

    Hydrogen bonding is discussed in the context of medicinal chemistry design. Minimized molecular electrostatic potential (Vmin) is shown to be an effective predictor of hydrogen bond basicity (pKBHX), and predictive models are presented for a number of hydrogen bond acceptor types relevant to medicinal chemistry. The problems posed by the presence of nonequivalent hydrogen bond acceptor sites in molecular structures are addressed by using nonlinear regression to fit measured pKBHX to calculated Vmin. Predictions are made for hydrogen bond basicity of fluorine in situations where relevant experimental measurements are not available. It is shown how predicted pKBHX can be used to provide insight into the nature of bioisosterism and to profile heterocycles. Examples of pKBHX prediction for molecular structures with multiple, nonequivalent hydrogen bond acceptors are presented. PMID:26872049

  9. Negligible Isotopic Effect on Dissociation of Hydrogen Bonds.

    PubMed

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

    2016-03-31

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

  10. 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.

  11. Asymmetric Transfer Hydrogenation of Imines using Alcohol: Efficiency and Selectivity are Influenced by the Hydrogen Donor.

    PubMed

    Pan, Hui-Jie; Zhang, Yao; Shan, Chunhui; Yu, Zhaoyuan; Lan, Yu; Zhao, Yu

    2016-08-01

    The influence of the alcohol, as the hydrogen donor, on the efficiency and selectivity of the asymmetric transfer hydrogenation (ATH) of imines is reported for the first time. This discovery not only leads to a highly enantioselective access to N-aryl and N-alkyl amines, but also provides new insight into the mechanism of the ATH of imines. Both experimental and computational studies provide support for the reaction pathway involving an iridium alkoxide as the reducing species. PMID:27374880

  12. 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.

  13. Interpretation of Spectroscopic Markers of Hydrogen Bonds.

    PubMed

    Scheiner, Steve

    2016-07-18

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

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

    PubMed

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

    2004-10-01

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

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

    PubMed

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

    2016-08-01

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

  16. Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions, Chemical Properties, and Ligand/Protein Fluorine NMR Screening.

    PubMed

    Dalvit, Claudio; Vulpetti, Anna

    2016-05-23

    It is known that strong hydrogen-bonding interactions play an important role in many chemical and biological systems. However, weak or very weak hydrogen bonds, which are often difficult to detect and characterize, may also be relevant in many recognition and reaction processes. Fluorine serving as a hydrogen-bond acceptor has been the subject of many controversial discussions and there are different opinions about it. It now appears that there is compelling experimental evidence for the involvement of fluorine in weak intramolecular or intermolecular hydrogen bonds. Using established NMR methods, we have previously characterized and measured the strengths of intermolecular hydrogen-bond complexes involving the fluorine moieties CH2 F, CHF2 , and CF3 , and have compared them with the well-known hydrogen-bond complex formed between acetophenone and the strong hydrogen-bond donor p-fluorophenol. We now report evidence for the formation of hydrogen bonds involving fluorine with significantly weaker donors, namely 5-fluoroindole and water. A simple NMR method is proposed for the simultaneous measurement of the strengths of hydrogen bonds between an acceptor and a donor or water. Important implications of these results for enzymatic/chemical reactions involving fluorine, for chemical and physical properties, and for ligand/protein (19) F NMR screening are analyzed through experiments and theoretical simulations. PMID:27112430

  17. 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

  18. 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

  19. Theoretical study on the intramolecular hydrogen bond in chloro-substituted N,N-dimethylaminomethylphenols. I. Structural effects*1

    NASA Astrophysics Data System (ADS)

    Koll, A.; Parasuk, V.; Parasuk, W.; Karpfen, A.; Wolschann, P.

    2004-08-01

    Ab initio and density functional calculations are applied to study the influence of an increasing number of chlorine substituents on the properties of the intramolecular hydrogen bond in substituted Mannich bases. It is shown, that not only the acidity of the proton donor, which depends on the number of chlorine atoms at the aromatic ring, but also steric interactions modify the geometry of the hydrogen bond. Specific interactions of O-Cl⋯H-O hydrogen-bonding in some derivatives are estimated by calculations on related chlorophenols.

  20. Theoretical study on the intramolecular hydrogen bond in chloro-substituted N, N-dimethylaminomethylphenols. I. Structural effects

    NASA Astrophysics Data System (ADS)

    Koll, A.; Parasuk, V.; Parasuk, W.; Karpfen, A.; Wolschann, P.

    2004-03-01

    Ab initio and density functional calculations are applied to study the influence of an increasing number of chlorine substituents on the properties of the intramolecular hydrogen bond in substituted Mannich bases. It is shown, that not only the acidity of the proton donor, which depends on the number of chlorine atoms at the aromatic ring, but also steric interactions modify the geometry of the hydrogen bond. Specific interactions of O-Cl⋯H-O hydrogen-bonding in some derivatives are estimated by calculations on related chlorophenols.

  1. 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.

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

    PubMed

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

    2014-11-01

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

  3. 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

  4. Supramolecular control of organic p/n-heterojunctions by complementary hydrogen bonding.

    PubMed

    Black, Hayden T; Lin, Huaping; Bélanger-Gariépy, Francine; Perepichka, Dmitrii F

    2014-01-01

    The supramolecular structure of organic semiconductors (OSCs) is the key parameter controlling their performance in organic electronic devices, and thus methods for controlling their self-assembly in the solid state are of the upmost importance. Recently, we have demonstrated the co-assembly of p- and n-type organic semiconductors through a three-point hydrogen-bonding interaction, utilizing an electron-rich dipyrrolopyridine (P2P) heterocycle which is complementary to naphthalenediimides (NDIs) both in its electronic structure and H bonding motif. The hydrogen-bonding-mediated co-assembly between P2P donor and NDI acceptor leads to ambipolar co-crystals and provides unique structural control over their solid-state packing characteristics. In this paper we expand our discussion on the crystal engineering aspects of H bonded donor-acceptor assemblies, reporting three new single co-crystal X-ray diffraction structures and analyzing the different packing characteristics that arise from the molecular structures employed. Particular attention is given toward understanding the formation of the two general motifs observed, segregated and mixed stacks. Co-assembly of the donor and acceptor components into a single, crystalline material, allows the creation of ambipolar semiconductors where the mutual arrangement of p- and n-conductive channels is engineered by supramolecular design based on complementary H bonding. PMID:25263229

  5. O–H hydrogen bonding promotes H-atom transfer from a C–H bonds for C-alkylation of alcohols

    PubMed Central

    Jeffrey, Jenna L.; Terrett, Jack A.; MacMillan, David W. C.

    2015-01-01

    The efficiency and selectivity of hydrogen atom transfer from organic molecules are often difficult to control in the presence of multiple potential hydrogen atom donors and acceptors. Here, we describe the mechanistic evaluation of a mode of catalytic activation that accomplishes the highly selective photoredox α-alkylation/lactonization of alcohols with methyl acrylate via a hydrogen atom transfer mechanism. Our studies indicate a particular role of tetra-n-butylammonium phosphate in enhancing the selectivity for α C–H bonds in alcohols in the presence of allylic, benzylic, α-C=O, and α-ether C–H bonds. PMID:26316601

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Ting, Melodie; Peters, Nancy J. S.

    2009-09-01

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

  8. 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

  9. A diabatic state model for double proton transfer in hydrogen bonded complexes

    SciTech Connect

    McKenzie, Ross H.

    2014-09-14

    Four diabatic states are used to construct a simple model for double proton transfer in hydrogen bonded complexes. Key parameters in the model are the proton donor-acceptor separation R and the ratio, D{sub 1}/D{sub 2}, between the proton affinity of a donor with one and two protons. Depending on the values of these two parameters the model describes four qualitatively different ground state potential energy surfaces, having zero, one, two, or four saddle points. Only for the latter are there four stable tautomers. In the limit D{sub 2} = D{sub 1} the model reduces to two decoupled hydrogen bonds. As R decreases a transition can occur from a synchronous concerted to an asynchronous concerted to a sequential mechanism for double proton transfer.

  10. Hydrogen-bonding interactions in adrenaline-water complexes: DFT and QTAIM studies of structures, properties, and topologies.

    PubMed

    Wang, Hongke; Huang, Zhengguo; Shen, Tingting; Guo, Lingfei

    2012-07-01

    ωB97XD/6-311++G(d,p) calculations were carried out to investigate the hydrogen-bonding interactions between adrenaline (Ad) and water. Six Ad-H(2)O complexes possessing various types of hydrogen bonds (H-bonds) were characterized in terms of their geometries, energies, vibrational frequencies, and electron-density topology. Natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses were performed to elucidate the nature of the hydrogen-bonding interactions in these complexes. The intramolecular H-bond between the amino and carboxyl oxygen atom of Ad was retained in most of the complexes, and cooperativity between the intra- and intermolecular H-bonds was present in some of the complexes. H-bonds in which hydroxyls of Ad/water acted as proton donors were stronger than other H-bonds. Both hydrogen-bonding interactions and structural deformation play important roles in the relative stabilities of the complexes. The intramolecular H-bond was broken during the formation of the most stable complex, which indicates that Ad tends to break the intramolecular H-bond and form two new intermolecular H-bonds with the first water molecule. PMID:22212733

  11. How Do Distance and Solvent Affect Halogen Bonding Involving Negatively Charged Donors?

    PubMed

    Chen, Zhaoqiang; Wang, Guimin; Xu, Zhijian; Wang, Jinan; Yu, Yuqi; Cai, Tingting; Shao, Qiang; Shi, Jiye; Zhu, Weiliang

    2016-09-01

    It was reported that negatively charged donors can form halogen bonding, which is stable, especially, in a polar environment. On the basis of a survey of the Protein Data Bank, we noticed that the distance between the negative charge center and the halogen atom of an organohalogen may vary greatly. Therefore, a series of model systems, composed of 4-halophenyl-conjugated polyene acids and ammonia, were designed to explore the potential effect of distance on halogen bonding in different solvents. Quantum mechanics (QM) calculations demonstrated that the longer the distance, the stronger the bonding. The energy decomposition analysis on all of the model systems demonstrated that electrostatic interaction contributes the most (44-56%) to the overall binding, followed by orbital interaction (42-36%). Natural bond orbital calculations showed that electron transfer takes place from the acceptor to the donor, whereas the halogen atom becomes more positive during the bonding, which is in agreement with the result of neutral halogen bonding. QM/molecular mechanics calculations demonstrated that the polarity of binding pockets makes all of the interactions attractive in a protein system. Hence, the strength of halogen bonding involving negatively charged donors could be adjusted by changing the distance between the negative charge center and halogen atom and the environment in which the bonding exists, which may be applied in material and drug design for tuning their function and activity. PMID:27504672

  12. 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.

  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. Molecular orbital analysis of the hydrogen bonded water dimer

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  15. 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

  16. 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.

  17. 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

  18. 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.

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

    PubMed

    Kozlowska, Mariana; Goclon, Jakub; Rodziewicz, Pawel

    2016-04-18

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

  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. Nickel-catalyzed transfer hydrogenation of ketones using ethanol as a solvent and a hydrogen donor.

    PubMed

    Castellanos-Blanco, Nahury; Arévalo, Alma; García, Juventino J

    2016-09-14

    We report a nickel(0)-catalyzed direct transfer hydrogenation (TH) of a variety of alkyl-aryl, diaryl, and aliphatic ketones with ethanol. This protocol implies a reaction in which a primary alcohol serves as a hydrogen atom source and solvent in a one-pot reaction without any added base. The catalytic activity of the nickel complex [(dcype)Ni(COD)] (e) (dcype: 1,2-bis(dicyclohexyl-phosphine)ethane, COD: 1,5-cyclooctadiene), towards transfer hydrogenation (TH) of carbonyl compounds using ethanol as the hydrogen donor was assessed using a broad scope of ketones, giving excellent results (up to 99% yield) compared to other homogeneous phosphine-nickel catalysts. Control experiments and a mercury poisoning experiment support a homogeneous catalytic system; the yield of the secondary alcohols formed in the TH reaction was monitored by gas chromatography (GC) and NMR spectroscopy. PMID:27511528

  2. Proton transfer through hydrogen bonds in two-dimensional water layers: A theoretical study based on ab initio and quantum-classical simulations

    SciTech Connect

    Bankura, Arindam; Chandra, Amalendu

    2015-01-28

    The dynamics of proton transfer (PT) through hydrogen bonds in a two-dimensional water layer confined between two graphene sheets at room temperature are investigated through ab initio and quantum-classical simulations. The excess proton is found to be mostly solvated as an Eigen cation where the hydronium ion donates three hydrogen bonds to the neighboring water molecules. In the solvation shell of the hydronium ion, the three coordinated water molecules with two donor hydrogen bonds are found to be properly presolvated to accept a proton. Although no hydrogen bond needs to be broken for transfer of a proton to such presolvated water molecules from the hydronium ion, the PT rate is still found to be not as fast as it is for one-dimensional chains. Here, the PT is slowed down as the probability of finding a water with two donor hydrogen bonds in the solvation shell of the hydronium ion is found to be only 25%-30%. The hydroxide ion is found to be solvated mainly as a complex anion where it accepts four H-bonds through its oxygen atom and the hydrogen atom of the hydroxide ion remains free all the time. Here, the presolvation of the hydroxide ion to accept a proton requires that one of its hydrogen bonds is broken and the proton comes from a neighboring water molecule with two acceptor and one donor hydrogen bonds. The coordination number reduction by breaking of a hydrogen bond is a slow process, and also the population of water molecules with two acceptor and one donor hydrogen bonds is only 20%-25% of the total number of water molecules. All these factors together tend to slow down the hydroxide ion migration rate in two-dimensional water layers compared to that in three-dimensional bulk water.

  3. Effect of pressure on methylated glycine derivatives: relative roles of hydrogen bonds and steric repulsion of methyl groups.

    PubMed

    Kapustin, Eugene A; Minkov, Vasily S; Boldyreva, Elena V

    2014-06-01

    Infinite head-to-tail chains of zwitterions present in the crystals of all amino acids are known to be preserved even after structural phase transitions. In order to understand the role of the N-H...O hydrogen bonds linking zwitterions in these chains in structural rearrangements, the crystal structures of the N-methyl derivatives of glycine (N-methylglycine, or sarcosine, with two donors for hydrogen bonding; two polymorphs of N,N-dimethylglycine, DMG-I and DMG-II, with one donor for hydrogen bond; and N,N,N-trimethylglycine, or betaine, with no hydrogen bonds) were studied at different pressures. Methylation has not only excluded the formation of selected hydrogen bonds, but also introduced bulky mobile fragments into the structure. The effects of pressure on the systems of the series were compared with respect to distorting and switching over hydrogen bonds and inducing reorientation of the methylated fragments. Phase transitions with fragmentation of the single crystals into fine powder were observed for partially methylated N-methyl- and N,N-dimethylglycine, whereas the structural changes in betaine were continuous with some peculiar features in the 1.4-2.9 GPa pressure range and accompanied by splitting of the crystals into several large fragments. Structural rearrangements in sarcosine and betaine were strongly dependent on the rate of pressure variation: the higher the rate of increasing pressure, the lower the pressure at which the phase transition occurred. PMID:24892599

  4. 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.

  5. 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.

  6. The role of hydrogen bonding in tethered polymer layers

    PubMed Central

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

    2009-01-01

    A molecular theory to study the properties of end tethered polymer layers, in which the polymers have the ability to form hydrogen bonds with water is presented. The approach combines the ideas of the single-chain mean-field theory to treat tethered layers with the approach of Dormidontova (Macromolecules, 2002 35,987) to include hydrogen bonds. The generalization includes the consideration of position dependent polymer-water and water-water hydrogen bonds. The theory is applied to model poly ethylene oxide (PEO) and the predictions are compared with equivalent polymer layers that do not form hydrogen bonds. It is found that increasing the temperature lowers the solubility of the PEO and results in a collapse of the layer at high enough temperatures. The properties of the layer and their temperature dependence are shown to be the result of the coupling between the conformational entropy of the chains, the ability of the polymer to form hydrogen bonds, and the intermolecular interactions. The structural and thermodynamic properties of the PEO layers, such as the lateral pressure-area isotherms and polymer chemical potentials, are studied as a function of temperature and type of tethering surface. The possibility of phase separation of the PEO layer at high enough temperature is predicted, due to the reduced solubility induced by breaking of polymer-water hydrogen bonds. A discussion of the advantages and limitations of the theory, together with how to apply the approach to different hydrogen bonding polymers is presented. PMID:19367906

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

    PubMed

    Taylor, L S; Zografi, G

    1998-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  9. Hydrogen 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

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

    PubMed

    Tutughamiarso, Maya; Wagner, Guido; Egert, Ernst

    2012-08-01

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

  11. 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.

  12. Three component assemblies by orthogonal H-bonding and donor-acceptor charge-transfer interaction.

    PubMed

    Kar, Haridas; Ghosh, Suhrit

    2014-02-01

    Three component supramolecular assemblies from a mixture of an aromatic donor (D), acceptor (A) and external structure directing agent (ESDA) are achieved by orthogonal noncovalent interactions involving two different types of H-bonding and alternate D-A stacking. An ESDA containing amide or urea produces a charge-transfer gel and sol, respectively, owing to their contrasting morphology. PMID:24309620

  13. 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

  14. 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

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

    PubMed

    Nagy, Peter I

    2014-01-01

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

  16. Relationship between the broad OH stretching band of methanol and hydrogen-bonding patterns in the liquid phase.

    PubMed

    Ohno, Keiichi; Shimoaka, Takafumi; Akai, Nobuyuki; Katsumoto, Yukiteru

    2008-08-14

    The OH stretching (nu(OH)) band of methanol observed in condensed phase has been analyzed in terms of hydrogen-bonding patterns. Quantum chemical calculations for methanol clusters have revealed that broadening of the nu(OH) envelope is reasonably reproduced by considering nearest and next-nearest neighbor interactions through hydrogen bonding. Because the hydrogen bond formed between donor (D) and acceptor (A) is cooperatively strengthened or weakened by a newly formed hydrogen bond at D or A, we have proposed the following notation for hydrogen-bonding patterns of monohydric alcohols: a(D)DAd(A)a(A), where a is the number of protons accepted by D (a(D)) or A (a(A)), and d(A) is the number of protons donated by A. The indicator of the hydrogen-bond strength, which is given by M(OH) = a(D) + d(A) - a(A), is correlated well with the nu(OH) wavenumber of the methanol molecule D participating in the a(D)DAd(A)a(A) pattern. The correlation between M(OH) and the hydrogen-bonding energy of the a(D)DAd(A)a(A) pattern has also been deduced from the calculation results for the clusters. The nu(OH) bands of methanol measured in the CCl4 solution and pure liquid have been successfully analyzed by the method proposed here. PMID:18636720

  17. Electrical current through individual pairs of phosphorus donor atoms and silicon dangling bonds

    PubMed Central

    Ambal, K.; Rahe, P.; Payne, A.; Slinkman, J.; Williams, C. C.; Boehme, C.

    2016-01-01

    Nuclear spins of phosphorus [P] donor atoms in crystalline silicon are among the most coherent qubits found in nature. For their utilization in scalable quantum computers, distinct donor electron wavefunctions must be controlled and probed through electrical coupling by application of either highly localized electric fields or spin-selective currents. Due to the strong modulation of the P-donor wavefunction by the silicon lattice, such electrical coupling requires atomic spatial accuracy. Here, the spatially controlled application of electrical current through individual pairs of phosphorus donor electron states in crystalline silicon and silicon dangling bond states at the crystalline silicon (100) surface is demonstrated using a high‐resolution scanning probe microscope operated under ultra‐high vacuum and at a temperature of 4.3K. The observed pairs of electron states display qualitatively reproducible current-voltage characteristics with a monotonous increase and intermediate current plateaus. PMID:26758087

  18. Hydrogen Sulfide Donor GYY4137 Protects against Myocardial Fibrosis

    PubMed Central

    Meng, Guoliang; Zhu, Jinbiao; Xiao, Yujiao; Huang, Zhengrong; Zhang, Yuqing; Tang, Xin; Xie, Liping; Chen, Yu; Shao, Yongfeng; Ferro, Albert; Wang, Rui; Moore, Philip K.; Ji, Yong

    2015-01-01

    Hydrogen sulfide (H2S) is a gasotransmitter which regulates multiple cardiovascular functions. However, the precise roles of H2S in modulating myocardial fibrosis in vivo and cardiac fibroblast proliferation in vitro remain unclear. We investigated the effect of GYY4137, a slow-releasing H2S donor, on myocardial fibrosis. Spontaneously hypertensive rats (SHR) were administrated with GYY4137 by intraperitoneal injection daily for 4 weeks. GYY4137 decreased systolic blood pressure and inhibited myocardial fibrosis in SHR as evidenced by improved cardiac collagen volume fraction (CVF) in the left ventricle (LV), ratio of perivascular collagen area (PVCA) to lumen area (LA) in perivascular regions, reduced hydroxyproline concentration, collagen I and III mRNA expression, and cross-linked collagen. GYY4137 also inhibited angiotensin II- (Ang II-) induced neonatal rat cardiac fibroblast proliferation, reduced the number of fibroblasts in S phase, decreased collagen I and III mRNA expression and protein synthesis, attenuated oxidative stress, and suppressed α-smooth muscle actin (α-SMA), transforming growth factor-β1 (TGF-β1) expression as well as Smad2 phosphorylation. These results indicate that GYY4137 improves myocardial fibrosis perhaps by a mechanism involving inhibition of oxidative stress, blockade of the TGF-β1/Smad2 signaling pathway, and decrease in α-SMA expression in cardiac fibroblasts. PMID:26078813

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

    PubMed

    Arunan, Elangannan; Mani, Devendra

    2015-01-01

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

  20. Hydrogen abstraction in the neutral molecular cluster of benzophenone and hydrogen donors formed in a supersonic free jet expansion

    SciTech Connect

    Matsushita, Yoshihisa; Kajii, Yoshizumi; Obi, Kinichi

    1992-08-06

    This paper discusses how benzophenone undergoes photoreduction to form benzophenone ketyl radical by an intracellular reaction in the benzophenone 1,4-cyclohexadiene mixed expansion in a supersonic free jet expansion. No ketyl radical fluorescence is observed when triethylamine, 2-propanol, or ethanol is the hydrogen donor; thus the normal molecular cluster activity depends on the nature of the hydrogen donor. 36 refs., 5 figs.

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

    PubMed

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

    2009-05-01

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

  2. Correlation between hydrogen bond basicity and acetylene solubility in room temperature ionic liquids.

    PubMed

    Palgunadi, Jelliarko; Hong, Sung Yun; Lee, Jin Kyu; Lee, Hyunjoo; Lee, Sang Deuk; Cheong, Minserk; Kim, Hoon Sik

    2011-02-10

    Room temperature ionic liquids (RTILs) are proposed as the alternative solvents for the acetylene separation in ethylene generated from the naphtha cracking process. The solubility behavior of acetylene in RTILs was examined using a linear solvation energy relationship based on Kamlet-Taft solvent parameters including the hydrogen-bond acidity or donor ability (α), the hydrogen-bond basicity or acceptor ability (β), and the polarity/polarizability (π*). It is found that the solubility of acetylene linearly correlates with β value and is almost independent of α or π*. The solubility of acetylene in RTILs increases with increasing hydrogen-bond acceptor (HBA) ability of the anion, but is little affected by the nature of the cation. Quantum mechanical calculations demonstrate that the acidic proton of acetylene specifically forms hydrogen bond with a basic oxygen atom on the anion of a RTIL. On the other hand, although C-H···π interaction is plausible, all optimized structures indicate that the acidic protons on the cation do not specifically associate with the π cloud of acetylene. Thermodynamic analysis agrees well with the proposed correlation: the higher the β value of a RTIL is, the more negative the enthalpy of acetylene absorption in the RTIL is. PMID:21218815

  3. Enantioselective Claisen rearrangements with a hydrogen-bond donor catalyst.

    PubMed

    Uyeda, Christopher; Jacobsen, Eric N

    2008-07-23

    N,N'-Diphenylguanidinium ion associated with the noncoordinating BArF counterion is shown to be an effective catalyst for the [3,3]-sigmatropic rearrangement of a variety of substituted allyl vinyl ethers. Highly enantioselective catalytic Claisen rearrangements of ester-substituted allyl vinyl ethers are then documented using a new C2-symmetric guanidinium ion derivative. PMID:18576616

  4. Hydrogen induced electric conduction in undoped ZnO and Ga-doped ZnO thin films: Creating native donors via reduction, hydrogen donors, and reactivating extrinsic donors

    SciTech Connect

    Akazawa, Housei

    2014-09-01

    The manner in which hydrogen atoms contribute to the electric conduction of undoped ZnO and Ga-doped ZnO (GZO) films was investigated. Hydrogen atoms were permeated into these films through annealing in an atmospheric H{sub 2} ambient. Because the creation of hydrogen donors competes with the thermal annihilation of native donors at elevated temperatures, improvements to electric conduction from the initial state can be observed when insulating ZnO films are used as samples. While the resistivity of conductive ZnO films increases when annealing them in a vacuum, the degree of increase is mitigated when they are annealed in H{sub 2}. Hydrogenation of ZnO crystals was evidenced by the appearance of OH absorption signals around a wavelength of 2700 nm in the optical transmittance spectra. The lowest resistivity that was achieved by H{sub 2} annealing was limited to 1–2 × 10{sup −2} Ω cm, which is one order of magnitude higher than that by native donors (2–3 × 10{sup −3} Ω cm). Hence, all native donors are converted to hydrogen donors. In contrast, GZO films that have resistivities yet to be improved become more conductive after annealing in H{sub 2} ambient, which is in the opposite direction of GZO films that become more resistive after vacuum annealing. Hydrogen atoms incorporated into GZO crystals should assist in reactivating Ga{sup 3+} donors.

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

    NASA Astrophysics Data System (ADS)

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

    1992-07-01

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

  6. The influence of large-amplitude librational motion on the hydrogen bond energy for alcohol-water complexes.

    PubMed

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

    2015-10-01

    The far-infrared absorption spectra have been recorded for hydrogen-bonded complexes of water with methanol and t-butanol embedded in cryogenic neon matrices at 2.8 K. The partial isotopic substitution of individual subunits enabled by a dual inlet deposition procedure provides for the first time unambiguous assignments of the intermolecular high-frequency out-of-plane and low-frequency in-plane donor OH librational modes for mixed alcohol-water complexes. The vibrational assignments confirm directly that water acts as the hydrogen bond donor in the most stable mixed complexes and the tertiary alcohol is a superior hydrogen bond acceptor. The class of large-amplitude donor OH librational motion is shown to account for up to 5.1 kJ mol(-1) of the destabilizing change of vibrational zero-point energy upon intermolecular OHO hydrogen bond formation. The experimental findings are supported by complementary electronic structure calculations at the CCSD(T)-F12/aug-cc-pVTZ level of theory. PMID:26304774

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

    PubMed

    Korth, Hans-Gert; Mulder, Peter

    2013-08-01

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

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

    PubMed Central

    Horowitz, Scott; Trievel, Raymond C.

    2012-01-01

    Carbon-oxygen (CH···O) hydrogen bonding represents an unusual category of molecular interactions first documented in biological structures over 4 decades ago. Although CH···O hydrogen bonding has remained generally underappreciated in the biochemical literature, studies over the last 15 years have begun to yield direct evidence of these interactions in biological systems. In this minireview, we provide a historical context of biological CH···O hydrogen bonding and summarize some major advancements from experimental studies over the past several years that have elucidated the importance, prevalence, and functions of these interactions. In particular, we examine the impact of CH···O bonds on protein and nucleic acid structure, molecular recognition, and enzyme catalysis and conclude by exploring overarching themes and unresolved questions regarding unconventional interactions in biomolecular structure. PMID:23048026

  9. Probing second-sphere hydrogen-bonding interactions in metal complexes with time-resolved photoacoustic

    NASA Astrophysics Data System (ADS)

    Borsarelli, C. D.

    2005-06-01

    Depending on the Lewis acid-base properties of the ligand moiety and the surrounding molecules, some coordination metal complexes can interact with the solvent molecules through second-sphere donor-acceptor (SSDA) interactions. In aqueous media, hydrogen bonding governs the solute-solvent interactions. In this report, the enthalpy content, δHMLCT, and the structural volume change, δVMLCT, associated with the formation and decay of the metal-to-ligand charge-transfer triplet state (^3MLCT) of ruthenium (II) bipyridine cyano complexes were determined using time-resolved photoacoustics (TRP), in water, water pools of reverse micelles, and in the presence of polyammonium macrocycle [32]ane-[N8H8]8+, for the formation of supercomplexes. The results are explained as function of the structure and properties of the hydrogen-bonding interactions between the metal complexes and the surrounding molecules.

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

    SciTech Connect

    Van Buskirk, C.S.

    1988-01-01

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

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

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

    PubMed Central

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

    2014-01-01

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

  18. Anion Binding in Metal-Organic Frameworks Functionalized with Urea Hydrogen-Bonding Groups

    SciTech Connect

    Custelcean, Radu; Moyer, Bruce A; Bryantsev, Vyacheslav S.; Hay, Benjamin P.

    2006-01-01

    A series of metal-organic frameworks (MOFs) functionalized with urea hydrogen-bonding groups has been synthesized and structurally analyzed by single-crystal X-ray diffraction to evaluate the efficacy of anion coordination by urea within the structural constraints of the MOFs. We found that urea-based functionalities may be used for anion binding within metal-organic frameworks when the tendency for urea{hor_ellipsis}urea self-association is decreased by strengthening the intramolecular CH{hor_ellipsis}O hydrogen bonding of N-phenyl substituents to the carbonyl oxygen atom. Theoretical calculations indicate that N,N'-bis(m-pyridyl)urea (BPU) and N,N'-bis(m-cyanophenyl)urea (BCPU) should have enhanced hydrogen-bonding donor abilities toward anions and decreased tendencies to self-associate into hydrogen-bonded tapes compared to other disubstituted ureas. Accordingly, BPU and BCPU were incorporated in MOFs as linkers through coordination of various Zn, Cu, and Ag transition metal salts, including Zn(ClO{sub 4}){sub 2}, ZnSO{sub 4}, Cu(NO{sub 3}){sub 2}, Cu(CF{sub 3}SO{sub 3}){sub 2}, AgNO{sub 3}, and AgSO{sub 3}CH{sub 3}. Structural analysis by single-crystal X-ray diffraction showed that these linkers are versatile anion binders, capable of chelate hydrogen bonding to all of the oxoanions explored. Anion coordination by the urea functionalities was found to successfully compete with urea self-association in all cases except for that of charge-diffuse perchlorate.

  19. Supramolecular hydrogen-bonded structures between melamine and N-heterocycles

    NASA Astrophysics Data System (ADS)

    Makowski, Sophia J.; Lacher, Monika; Lermer, Claudia; Schnick, Wolfgang

    2012-04-01

    Melamine (M) forms hydrogen bonded adducts with the N-heterocycles tris(2-pyridyl)-triazine (TPTZ) and tetrakis(4-N-methylpyridinumyl)porphyrin tetratosylate (TMPyP-Tos). The 4:3 adduct 4M·3TPTZ was obtained under solvent-free conditions and the 3:1 adduct 3M·TMPyP-Tos·9H2O in aqueous solution. In both adduct phases N-heterocycles are arranged in π-π stacks and melamine molecules are arranged perpendicular to these stacks. Whereas cohesion between the extended π-systems of N-heterocycles is mainly achieved by dispersive interactions no stacking interactions between melamine molecules occur. Melamine units are orientated in such a way to be located most suitable as donors and acceptors, respectively, for a dense hydrogen bonding network. In 4M·3TPTZ all molecules are involved in hydrogen bonding, whereas in 3M·TMPyP-Tos·9H2O hydrogen bridges are primarily formed between melamine, tosylate and water units and the macrocycle TMPyP is mainly bound by electrostatic interactions.

  20. Universality in hydrogen-bond networks

    NASA Astrophysics Data System (ADS)

    Nadler, Walter; Krausche, Thomas

    1991-12-01

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

  1. Influence of Hydrogen Bonding on the Kinetic Stability of Vapor Deposited Triazine Glasses

    NASA Astrophysics Data System (ADS)

    Laventure, Audrey; Gujral, Ankit; Lebel, Olivier; Pellerin, Christian; Ediger, Mark D.

    Physical vapor deposition (PVD) can produce glasses with enhanced kinetic stability, high density and anisotropy. However, the influence of hydrogen bonding on these properties has not been fully explored. We vapor deposit a series of triazine derivatives containing functional groups with different H-bonding capability, i.e. NHMe (H-bond donor), OMe (H-bond acceptor) and Et (none) using a wide range of substrate temperatures, from 0.60 to 1.05Tg. PVD glasses of the NHMe derivative have inferior kinetic stability compared to its OMe and Et analogues. This behavior can be rationalized by the higher average number of bonded NH per molecule found in PVD glasses of the NHMe derivative, as quantified by infrared spectroscopy (IR). Despite this difference in H-bonding, IR and wide angle X-ray scattering reveal that all three compounds show a tendency to orient parallel to the substrate at low substrate temperatures. Our results support the hypothesis that strong intermolecular interactions, such as H-bonds, can hinder mobility of the molecules at the interface and thus limit their possibility to sample the potential energy landscape to produce stable glasses.

  2. Influence of intermolecular amide hydrogen bonding on the geometry, atomic charges, and spectral modes of acetanilide: An ab initio study

    NASA Astrophysics Data System (ADS)

    Binoy, J.; Prathima, N. B.; Murali Krishna, C.; Santhosh, C.; Hubert Joe, I.; Jayakumar, V. S.

    2006-08-01

    Acetanilide, a compound of pharmaceutical importance possessing pain-relieving properties due to its blocking the pulse dissipating along the nerve fiber, is subjected to vibrational spectral investigation using NIR FT Raman, FT-IR, and SERS. The geometry, Mulliken charges, and vibrational spectrum of acetanilide have been computed using the Hartree-Fock theory and density functional theory employing the 6-31G (d) basis set. To investigate the influence of intermolecular amide hydrogen bonding, the geometry, charge distribution, and vibrational spectrum of the acetanilide dimer have been computed at the HF/6-31G (d) level. The computed geometries reveal that the acetanilide molecule is planar, while twisting of the secondary amide group with respect to the phenyl ring is found upon hydrogen bonding. The trans isomerism and “amido” form of the secondary amide, hyperconjugation of the C=O group with the adjacent C-C bond, and donor-acceptor interaction have been investigated using computed geometry. The carbonyl stretching band position is found to be influenced by the tendency of the phenyl ring to withdraw nitrogen lone pair, intermolecular hydrogen bonding, conjugation, and hyperconjugation. A decrease in the NH and C=O bond orders and increase in the C-N bond orders due to donor-acceptor interaction can be observed in the vibrational spectra. The SERS spectral analysis reveals that the flat orientation of the molecule on the adsorption plane is preferred.

  3. 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

    Hydrogen bond can be regarded as an interaction between a base and a proton covalently bound to another base. In this context the strength of hydrogen bond scales with the proton affinity of the acceptor base and the pKa of the donor, i.e., it follows the acid-base formalism. This has been amply demonstrated in conventional hydrogen bonds. Is this also true for the unconventional hydrogen bonds involving lesser electronegative elements such as sulfur atom? In our previous work, we had established that the strength of O-H···S hydrogen bonding (HB) interaction scales with the proton affinity (PA) of the acceptor. In this work, we have investigated the other counterpart, i.e., the H-bonding interaction between the photoacids with different pKa values with a common base such as the H2O and H2S. The 1:1 complexes of five para substituted phenols p-aminophenol, p-cresol, p-fluorophenol, p-chlorophenol, and p-cyanophenol with H2O and H2S were investigated experimentally and computationally. The investigations were also extended to the excited states. The experimental observations of the spectral shifts in the O-H stretching frequency and the S1-S0 band origins were correlated with the pKa of the donors. Ab initio calculations at the MP2 and various dispersion corrected density functional levels of theory were performed to compute the dissociation energy (D0) of the complexes. The quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI) method, natural bonding orbital (NBO) analysis, and natural decomposition analysis (NEDA) were carried out for further characterization of HB interaction. The O-H stretching frequency red shifts and the dissociation energies were found to be lower for the O-H···S hydrogen bonded systems compared to those for the O-H···O H-bound systems. Despite being dominated by the dispersion interaction the O-H···S interaction in the H2S complexes also conformed to the acid-base formalism, i.e., the D0 and the O-H red shift

  4. Tunneling spectroscopy measurements on hydrogen-bonded supramolecular polymers

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

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

    PubMed

    Xu, Huafeng; Dill, Ken A

    2005-12-15

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

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

    PubMed

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

    2016-09-01

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

  7. Exploring the Potential of Diarylacetylenediols as Hydrogen Bonding Catalysts

    PubMed Central

    Türkmen, Yunus E.; Rawal, Viresh H.

    2014-01-01

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

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

    PubMed Central

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

    1996-01-01

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

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

    PubMed

    Bower, John F; Krische, Michael J

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Bower, John F.; Krische, Michael J.

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

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

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

    PubMed

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

    2012-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    SciTech Connect

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

    2009-01-01

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

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

    PubMed Central

    Ross, P D; Rekharsky, M V

    1996-01-01

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

  16. 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.

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

    PubMed

    Henley, Alice; Bound, Michelle; Besley, Elena

    2016-05-26

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  1. General quantitative model for coal liquefaction kinetics: the thermal cleavage/hydrogen donor capping mechanism. [59 references

    SciTech Connect

    Gangwer, T

    1980-01-01

    A mechanism for coal liquefaction, based on the concept of thermal cleavage-hydrogen capping donor complexes, is proposed and the quantitative agreement between the derived rate laws and the kinetic data obtained from fifteen publications is presented. The mechanism provides rate laws which describe the preasphaltene, asphaltene, oil and gas time/yield curves for the coal liquefaction process. A simplistic dissolution model is presented and used to relate the proposed mechanism to the experimentally observed products. Based on the quality of the mechanistic fit to the reported coal liquefaction systems, which cover a diverse range of reaction conditions, coal types and donor solvent compositions, it is proposed that the donor solvent/thermal bond cleavage/hydrogen capping mechanism provides a good, quantitative description of the rate limiting process. Interpretation of the rate constant/temperature dependencies in terms of transition state theory indicates formation of the activated complex can involve either physically or chemically controlled steps. A uniform free energy of activation of 52 kcal was found for the diverse liquefaction systems indicating a common transition state describes the reactions. Thus the proposed mechanism unifies the diverse liquefaction kinetic data by using a set of uniform reaction sequences, which have a common transition state, to describe the conversion chemistry. The mechanism thereby creates a common base for intercomparison, interpretation and evaluation of coal conversion for the broad range of processes currently being investigated in the liquefaction field.

  2. Low-barrier hydrogen bonds and enzymatic catalysis.

    PubMed

    Cleland, W W

    2000-10-01

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

  3. Testing Electrostatic Complementarity in Enzyme Catalysis: Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole

    PubMed Central

    Kraut, Daniel A; Sigala, Paul A; Pybus, Brandon; Liu, Corey W; Ringe, Dagmar; Petsko, Gregory A

    2006-01-01

    A longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis. Experimental evaluation of this contribution, however, has been difficult. We have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. Phenolates, analogs of the transition state and reaction intermediate, bind and accept two hydrogen bonds in an active site oxyanion hole. The binding of substituted phenolates of constant molecular shape but increasing p K a models the charge accumulation in the oxyanion hole during the enzymatic reaction. As charge localization increases, the NMR chemical shifts of protons involved in oxyanion hole hydrogen bonds increase by 0.50–0.76 ppm/p K a unit, suggesting a bond shortening of ˜0.02 Å/p K a unit. Nevertheless, there is little change in binding affinity across a series of substituted phenolates (ΔΔG = −0.2 kcal/mol/p K a unit). The small effect of increased charge localization on affinity occurs despite the shortening of the hydrogen bonds and a large favorable change in binding enthalpy (ΔΔH = −2.0 kcal/mol/p K a unit). This shallow dependence of binding affinity suggests that electrostatic complementarity in the oxyanion hole makes at most a modest contribution to catalysis of ˜300-fold. We propose that geometrical complementarity between the oxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution. PMID:16602823

  4. Superprotonics—crystals with rearranging hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Makarova, I. P.

    2015-03-01

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

  5. 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.

  6. 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.

  7. Crystalline hydrogen-bonded nanocolumns of cyclic thiourea octamers

    SciTech Connect

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

    2007-01-01

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

  8. 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

  9. Inner reorganization limiting electron transfer controlled hydrogen bonding: intra- vs. intermolecular effects.

    PubMed

    Martínez-González, Eduardo; Frontana, Carlos

    2014-05-01

    In this work, experimental evidence of the influence of the electron transfer kinetics during electron transfer controlled hydrogen bonding between anion radicals of metronidazole and ornidazole, derivatives of 5-nitro-imidazole, and 1,3-diethylurea as the hydrogen bond donor, is presented. Analysis of the variations of voltammetric EpIcvs. log KB[DH], where KB is the binding constant, allowed us to determine the values of the binding constant and also the electron transfer rate k, confirmed by experiments obtained at different scan rates. Electronic structure calculations at the BHandHLYP/6-311++G(2d,2p) level for metronidazole, including the solvent effect by the Cramer/Truhlar model, suggested that the minimum energy conformer is stabilized by intramolecular hydrogen bonding. In this structure, the inner reorganization energy, λi,j, contributes significantly (0.5 eV) to the total reorganization energy of electron transfer, thus leading to a diminishment of the experimental k. PMID:24653999

  10. Structural Evidence for Inter-Residue Hydrogen Bonding Observed for Cellobiose in Aqueous Solution

    PubMed Central

    O'Dell, William B.; Baker, David C.; McLain, Sylvia E.

    2012-01-01

    The structure of the disaccharide cellulose subunit cellobiose (4-O-β-D-glucopyranosyl-D-glucose) in solution has been determined via neutron diffraction with isotopic substitution (NDIS), computer modeling and nuclear magnetic resonance (NMR) spectroscopic studies. This study shows direct evidence for an intramolecular hydrogen bond between the reducing ring HO3 hydroxyl group and the non-reducing ring oxygen (O5′) that has been previously predicted by computation and NMR analysis. Moreover, this work shows that hydrogen bonding to the non-reducing ring O5′ oxygen is shared between water and the HO3 hydroxyl group with an average of 50% occupancy by each hydrogen-bond donor. The glycosidic torsion angles φH and ψH from the neutron diffraction-based model show a fairly tight distribution of angles around approximately 22° and −40°, respectively, in solution, consistent with the NMR measurements. Similarly, the hydroxymethyl torsional angles for both reducing and non-reducing rings are broadly consistent with the NMR measurements in this study, as well as with those from previous measurements for cellobiose in solution. PMID:23056199

  11. Extraction of pyridines into fluorous solvents based on hydrogen bond complex formation with carboxylic acid receptors.

    PubMed

    O'Neal, Kristi L; Geib, Steven; Weber, Stephen G

    2007-04-15

    by a weak pyridine ring CH-O bond and is supported by two more carboxylic acid H-bond donors. We estimate that the free energy of formation of this complex from a free acid, pyridine, and a carboxylic acid dimer to be approximately -39 kJ mol-1; this is the first reported hydrogen bond strength in a fluorous environment. PMID:17375900

  12. Theoretical prediction of hydrogen-bond basicity pKBHX using quantum chemical topology descriptors.

    PubMed

    Green, Anthony J; Popelier, Paul L A

    2014-02-24

    Hydrogen bonding plays an important role in the interaction of biological molecules and their local environment. Hydrogen-bond strengths have been described in terms of basicities by several different scales. The pKBHX scale has been developed with the interests of medicinal chemists in mind. The scale uses equilibrium constants of acid···base complexes to describe basicity and is therefore linked to Gibbs free energy. Site specific data for polyfunctional bases are also available. The pKBHX scale applies to all hydrogen-bond donors (HBDs) where the HBD functional group is either OH, NH, or NH+. It has been found that pKBHX can be described in terms of a descriptor defined by quantum chemical topology, ΔE(H), which is the change in atomic energy of the hydrogen atom upon complexation. Essentially the computed energy of the HBD hydrogen atom correlates with a set of 41 HBAs for five common HBDs, water (r2=0.96), methanol (r2=0.95), 4-fluorophenol (r2=0.91), serine (r2=0.93), and methylamine (r2=0.97). The connection between experiment and computation was strengthened with the finding that there is no relationship between ΔE(H) and pKBHX when hydrogen fluoride was used as the HBD. Using the methanol model, pKBHX predictions were made for an external set of bases yielding r2=0.90. Furthermore, the basicities of polyfunctional bases correlate with ΔE(H), giving r2=0.93. This model is promising for the future of computation in fragment-based drug design. Not only has a model been established that links computation to experiment, but the model may also be extrapolated to predict external experimental pKBHX values. PMID:24460383

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  14. 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

  15. 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

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

    PubMed

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

    2015-07-15

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

  17. Hydrogen as an electron donor for dechlorination of tetrachloroethene by an anaerobic mixed culture.

    PubMed Central

    DiStefano, T D; Gossett, J M; Zinder, S H

    1992-01-01

    Hydrogen served as an electron donor in the reductive dechlorination of tetrachloroethene to vinyl chloride and ethene over periods of 14 to 40 days in anaerobic enrichment cultures; however, sustained dechlorination for more extended periods required the addition of filtered supernatant from a methanol-fed culture. This result suggests a nutritional dependency of hydrogen-utilizing dechlorinators on the metabolic products of other organisms in the more diverse, methanol-fed system. Vancomycin, an inhibitor of cell wall synthesis in eubacteria, was found to inhibit acetogenesis when added at 100 mg/liter to both methanol-fed and hydrogen-fed cultures. The effect of vancomycin on dechlorination was more complex. Methanol could not sustain dechlorination when vancomycin inhibited acetogenesis, while hydrogen could. These results are consistent with a model in which hydrogen is the electron donor directly used for dechlorination by organisms resistant to vancomycin and with the hypothesis that the role of acetogens in methanol-fed cultures is to metabolize a portion of the methanol to hydrogen. Methanol and other substrates shown to support dechlorination in pure and mixed cultures may merely serve as precursors for the formation of an intermediate hydrogen pool. This hypothesis suggests that, for bioremediation of high levels of tetrachloroethene, electron donors that cause the production of a large hydrogen pool should be selected or methods that directly use H2 should be devised. PMID:1482184

  18. Extraction of reference eastern shale with hydrogen donor and nondonor solvents

    SciTech Connect

    McKay, J.F.; Blanche, M.S.

    1985-09-01

    Oil shale from the New Albany Formation in Bullitt County, Kentucky, was treated with water together with hydrogen-donor and nondonor solvents at 400/sup 0/C and extracted with benzene-methanol. The purpose of the experiments was to measure the amount of liquid organic material recovered with hydrogen-donor and nondonor solvents. Liquid organic material amounting to approximately double that recovered by a Fischer assay experiment was recovered with tetralin, a hydrogen-donor solvent, and with naphthalene, a nondonor solvent. The shale was also treated with tetralin and water for periods of 5 minutes to 60 minutes to measure the effect of time on yield of liquid product. The results showed that yields increased with time and that treatment times of about 30 minutes were required to recover more liquid product than that produced by a Fischer assay experiment. 10 refs., 1 fig., 2 tabs.

  19. 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.

  20. Thermally activated delayed fluorescence evidence in non-bonding transition electron donor-acceptor molecules

    NASA Astrophysics Data System (ADS)

    Marghad, Ikbal; Clochard, M. C.; Ollier, N.; Wade, Travis L.; Aymes-Chodur, C.; Renaud, C.; Zissis, G.

    2015-09-01

    The exhibition of thermally activated delayed fluorescence on triazine derivative by the introduction of a nonbonding part is demonstrated. Two molecules containing triazine core as acceptor and carbazole part as donor has been synthesized and characterized. One of these molecules bears an additional nonbonding part by the means of a phenoxy group. The results indicated that the molecule bearing the nonbonding molecular part (phenoxy) exhibit thermally activated delayed fluorescence while not on molecule free of non-bonding group. The results are supported by, photoluminescence, spectral analysis time-resolved fluorescence and time-dependent density functional estimation

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

    NASA Astrophysics Data System (ADS)

    Taneri, Sencer

    2013-05-01

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

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

    SciTech Connect

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

    1996-03-05

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

  3. Predictive binding geometry of ligands to DNA minor groove: isohelicity and hydrogen-bonding pattern.

    PubMed

    Stockert, Juan C

    2014-01-01

    The interaction of drugs and dyes with nucleic acids, particularly when binding to DNA minor groove occurs, has increasing importance in biomedical sciences. This is due to the resulting biological activity and to the possibility of recognizing AT and GC base pairs. In such cases, DNA binding can be predicted if appropriate helical and hydrogen-bonding parameters are deduced from DNA models, and a simplified geometrical rule in the form of a stencil is then applied on computer-drawn molecules of interest. Relevant structure parameter values for minor groove binders are the length (4.6 < L < 5.4 Å) and angle (152 < σ < 156.5°) between three consecutive units, measured at the level of hydrogen donor or acceptor groups. Application of the stencil shows that predictive methods can aid in the design of new compounds, by checking the possible binding of isohelical sequence-specific ligands along the DNA minor groove. PMID:24162975

  4. The exploration of hydrogen bonding properties of 2,6- and 3,5-diethynylpyridine by IR spectroscopy.

    PubMed

    Vojta, Danijela; Kovačević, Goran; Vazdar, Mario

    2014-11-01

    Hydrogen bonding properties of 2,6- and 3,5-diethynylpyridine were analyzed by exploring of their interactions with trimethylphosphate, as hydrogen bond acceptor, or phenol, as hydrogen bond donor, in tetrachloroethene C2Cl4. The employment of IR spectroscopy enabled unravelling of their interaction pattern as well as the determination of their association constants (Kc) and standard reaction enthalpies (ΔrH(⦵)). The association of diethynylpyridines with trimethylphosphate in stoichiometry 1:1 is established through CH⋯O hydrogen bond, accompanied by the secondary interaction between CC moiety and CH3 group of trimethylphosphate. In the complexes with phenol, along with the expected OH⋯N interaction, CC⋯HO interaction is revealed. In contrast to 2,6-diethynylpyridine where the spatial arrangement of hydrogen bond accepting groups enables the simultaneous involvement of phenol OH group in both OH⋯N and OH⋯CC hydrogen bond, in the complex between phenol and 3,5-diethynylpyridine this is not possible. It is postulated that cooperativity effects, arisen from the certain type of resonance-assisted hydrogen bonds, contribute the stability gain of the latter. Associations of diethynylpyridines with trimethylphosphate are characterized as weak (Kc≈0.8-0.9mol(-1)dm(3); -ΔrH(⦵)≈5-8kJmol(-1)), while their complexes with phenol as medium strong (Kc≈5mol(-1)dm(3); -ΔrH(⦵)≈15-35kJmol(-1)). Experimental findings on the studied complexes are supported with the calculations conducted at B3LYP/6-311++G(d,p) level of theory in the gas phase. Two conformers of diethynylpyridine⋯trimethylphosphate dimers are formed via CH⋯O interaction, whereas dimers between phenol and diethynylpyridines are established through OH⋯N interaction. PMID:25467686

  5. The exploration of hydrogen bonding properties of 2,6- and 3,5-diethynylpyridine by IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Vojta, Danijela; Kovačević, Goran; Vazdar, Mario

    2015-02-01

    Hydrogen bonding properties of 2,6- and 3,5-diethynylpyridine were analyzed by exploring of their interactions with trimethylphosphate, as hydrogen bond acceptor, or phenol, as hydrogen bond donor, in tetrachloroethene C2Cl4. The employment of IR spectroscopy enabled unravelling of their interaction pattern as well as the determination of their association constants (Kc) and standard reaction enthalpies (ΔrH⦵). The association of diethynylpyridines with trimethylphosphate in stoichiometry 1:1 is established through tbnd Csbnd H⋯O hydrogen bond, accompanied by the secondary interaction between Ctbnd C moiety and CH3 group of trimethylphosphate. In the complexes with phenol, along with the expected OH⋯N interaction, Ctbnd C⋯HO interaction is revealed. In contrast to 2,6-diethynylpyridine where the spatial arrangement of hydrogen bond accepting groups enables the simultaneous involvement of phenol OH group in both OH⋯N and OH⋯Ctbnd C hydrogen bond, in the complex between phenol and 3,5-diethynylpyridine this is not possible. It is postulated that cooperativity effects, arisen from the certain type of resonance-assisted hydrogen bonds, contribute the stability gain of the latter. Associations of diethynylpyridines with trimethylphosphate are characterized as weak (Kc ≈ 0.8-0.9 mol-1 dm3; -ΔrH⦵ ≈ 5-8 kJ mol-1), while their complexes with phenol as medium strong (Kc ≈ 5 mol-1 dm3; -ΔrH⦵ ≈ 15-35 kJ mol-1). Experimental findings on the studied complexes are supported with the calculations conducted at B3LYP/6-311++G(d,p) level of theory in the gas phase. Two conformers of diethynylpyridine⋯trimethylphosphate dimers are formed via tbnd Csbnd H⋯O interaction, whereas dimers between phenol and diethynylpyridines are established through OH⋯N interaction.

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

    PubMed

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

    2016-04-01

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

  7. Fundamental Kinetics of Supercritical Coal Liquefaction: Effect of Catalysts and Hydrogen-Donor Solvents

    SciTech Connect

    McCoy, Ben J; Madras, Girodhar; Smith, J M; Kodera, Yoichi

    1997-04-16

    This is the quarterly report on our recent progress toward the overall objective to understand the supercritical fluid extraction of hydrocarbons from coal. Our strategy is to simulate coal as a high molecular-weight polymeric material by studying the degradation of polymers under various conditions. The hypothesis we are testing is that degradation of such macromolecules is applicable to the decomposition (depolymerization) of the coal network. Polymer degradation and coal liquefaction are influenced strongly by the solvent in the reaction. This motivated our investigation of the effect of hydrogen donor solvents on polymer degradation. In particular, we obtained new experimental data to show how a hydrogen donor, 6-hydroxy tetralin, influences the degradation rate of polystyrene. We also developed a detailed radical mechanism for hydrogen donation based on the Rice-Herzfeld chain reaction concept with the elementary steps of initiation, depropagation, hydrogen abstraction, and termination. Expressions for the degradation rate parameters were obtained by applying continuous distribution kinetics to the MWD of the reacting polymer. The theory explains the different influences of the hydrogen donor solvent on the degradation rate coefficients for different polymers. Though developed for the degradation of polymers, the mechanism and the theory are potentially applicable for chain scission and addition reactions among distributions of paraffins, olefins, and radicals of all chain lengths. The concepts can, in principle, be extended to examine the effect of hydrogen donors on coal liquefaction and on the complex mixture of liquefaction compounds. Based on this work, a research paper titled "Effect of Hydrogen Donors on Polymer Degradation", has been submitted for publication. Our research paper entitled, "Molecular weight effect on the dynamics of polystyrene degradation", has been accepted for publication by the journal, Industrial and Engineering Chemistry Research.

  8. Phenyl- and mesitylglyoxylic acids: catemeric hydrogen bonding in two alpha-keto acids

    PubMed

    Chen; Brunskill; Hall; Lalancette; Thompson

    2000-09-01

    alpha-Oxobenzeneacetic (phenylglyoxylic) acid, C(8)H(6)O(3), adopts a transoid dicarbonyl conformation in the solid state, with the carboxyl group rotated 44.4 (1) degrees from the nearly planar benzoyl moiety. The heterochiral acid-to-ketone catemers [O.O = 2. 686 (3) and H.O = 1.78 (4) A] have a second, longer, intermolecular O-H.O contact to a carboxyl sp(3) O atom [O.O = 3.274 (2) and H.O = 2.72 (4) A], with each flat ribbon-like chain lying in the bc plane and extending in the c direction. In alpha-oxo-2,4, 6-trimethylbenzeneacetic (mesitylglyoxylic) acid, C(11)H(12)O(3), the ketone is rotated 49.1 (7) degrees from planarity with the aryl ring and the carboxyl group is rotated a further 31.2 (7) degrees from the ketone plane. The solid consists of chiral conformers of a single handedness, aggregating in hydrogen-bonding chains whose units are related by a 3(1) screw axis, producing hydrogen-bonding helices that extend in the c direction. The hydrogen bonding is of the acid-to-acid type [O.O = 2.709 (6) and H.O = 1.87 (5) A] and does not formally involve the ketone; however, the ketone O atom in the acceptor molecule has a close polar contact with the same donor carboxyl group [O.O = 3.005 (6) and H.O = 2.50 (5) A]. This secondary hydrogen bond is probably a major factor in stabilizing the observed cisoid dicarbonyl conformation. Several intermolecular C-H.O close contacts were found for the latter compound. PMID:10986514

  9. 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.

  10. 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