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Sample records for hydrogen-bond switching observed

  1. IR-UV double resonance spectroscopic investigation of phenylacetylene-alcohol complexes. Alkyl group induced hydrogen bond switching.

    Science.gov (United States)

    Singh, Prashant Chandra; Patwari, G Naresh

    2008-06-12

    The electronic transitions of phenylacetylene complexes with water and trifluoroethanol are shifted to the blue, while the corresponding transitions for methanol and ethanol complexes are shifted to the red relative to the phenylacetylene monomer. Fluorescence dip infrared (FDIR) spectra in the O-H stretching region indicate that, in all the cases, phenylacetylene is acting as a hydrogen bond acceptor to the alcohols. The FDIR spectrum in the acetylenic C-H stretching region shows Fermi resonance bands for the bare phenylacetylene, which act as a sensitive tool to probe the intermolecular structures. The FDIR spectra reveal that water and trifluoroethanol interact with the pi electron density of the acetylene C-C triple bond, while methanol and ethanol interact with the pi electron density of the benzene ring. It can be inferred that the hydrogen bonding acceptor site on phenylacetylene switches from the acetylene pi to the benzene pi with lowering in the partial charge on the hydrogen atom of the OH group. The most significant finding is that the intermolecular structures of water and methanol complexes are notably distinct, which, to the best of our knowledge, this is first such observation in the case of complexes of substituted benzenes.

  2. NMR scalar couplings across Watson–Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy

    Science.gov (United States)

    Pervushin, Konstantin; Ono, Akira; Fernández, César; Szyperski, Thomas; Kainosho, Masatsune; Wüthrich, Kurt

    1998-01-01

    This paper describes the NMR observation of 15N—15N and 1H—15N scalar couplings across the hydrogen bonds in Watson–Crick base pairs in a DNA duplex, hJNN and hJHN. These couplings represent new parameters of interest for both structural studies of DNA and theoretical investigations into the nature of the hydrogen bonds. Two dimensional [15N,1H]-transverse relaxation-optimized spectroscopy (TROSY) with a 15N-labeled 14-mer DNA duplex was used to measure hJNN, which is in the range 6–7 Hz, and the two-dimensional hJNN-correlation-[15N,1H]-TROSY experiment was used to correlate the chemical shifts of pairs of hydrogen bond-related 15N spins and to observe, for the first time, hJHN scalar couplings, with values in the range 2–3.6 Hz. TROSY-based studies of scalar couplings across hydrogen bonds should be applicable for large molecular sizes, including protein-bound nucleic acids. PMID:9826668

  3. Hydrogen bonding as the origin of the switching behavior in dithiolated phenylene-vinylene oligomers

    KAUST Repository

    Obodo, Tobechukwu Joshua; Gkionis, Konstantinos; Rungger, Ivan; Sanvito, Stefano; Schwingenschlö gl, Udo

    2013-01-01

    We investigate theoretically the switching behavior of a dithiolated phenylene-vinylene oligomer sandwiched between Au(111) electrodes using self-interaction corrected density-functional theory combined with the nonequilibrium Green

  4. Interstellar hydrogen bonding

    Science.gov (United States)

    Etim, Emmanuel E.; Gorai, Prasanta; Das, Ankan; Chakrabarti, Sandip K.; Arunan, Elangannan

    2018-06-01

    This paper reports the first extensive study of the existence and effects of interstellar hydrogen bonding. The reactions that occur on the surface of the interstellar dust grains are the dominant processes by which interstellar molecules are formed. Water molecules constitute about 70% of the interstellar ice. These water molecules serve as the platform for hydrogen bonding. High level quantum chemical simulations for the hydrogen bond interaction between 20 interstellar molecules (known and possible) and water are carried out using different ab-intio methods. It is evident that if the formation of these species is mainly governed by the ice phase reactions, there is a direct correlation between the binding energies of these complexes and the gas phase abundances of these interstellar molecules. Interstellar hydrogen bonding may cause lower gas abundance of the complex organic molecules (COMs) at the low temperature. From these results, ketenes whose less stable isomers that are more strongly bonded to the surface of the interstellar dust grains have been observed are proposed as suitable candidates for astronomical observations.

  5. Hydrogen bonding as the origin of the switching behavior in dithiolated phenylene-vinylene oligomers

    KAUST Repository

    Obodo, Tobechukwu Joshua

    2013-08-29

    We investigate theoretically the switching behavior of a dithiolated phenylene-vinylene oligomer sandwiched between Au(111) electrodes using self-interaction corrected density-functional theory combined with the nonequilibrium Green\\'s-function method for quantum transport. The molecule presents a configurational bistability, which can be exploited in constructing molecular memories, switches, and sensors. We find that protonation of the terminating thiol groups is at the origin of the change in conductance. H bonding at the thiol group weakens the S-Au bond and reduces by about one order of magnitude the transmission coefficient at the Fermi level, and thus the linear response conductance. Furthermore, protonation downshifts in energy the position of the highest occupied molecular orbital, so that the current of the protonated species is lower than that of the unprotonated one along the entire bias range investigated, from −1.5 to 1.5 V. A second protonation at the opposite thiol group has only minor effects and no further drastic reduction in transmission takes place. Our results allow us to re-interpret the experimental data originally attributing the conductance reduction to H dissociation.

  6. Observation of internucleotide NH...N hydrogen bonds in the absence of directly detectable protons

    International Nuclear Information System (INIS)

    Majumdar, Ananya; Kettani, Abdelali; Skripkin, Eugene; Patel, Dinshaw J.

    1999-01-01

    Several structural motifs found in nucleic acids involve N-H ... N hydrogen bonds in which the donor hydrogens are broadened to extinction due to chemical or conformational exchange. In such situations, it is impossible to use the well-established HNN-COSY or soft HNN-COSY experiments, which report the presence of the hydrogen bond directly on the donor proton(s). We present a pulse sequence, H(CN)N(H), for alleviating this problem in hydrogen bonds of the type N d H ... N a -CH, in which the donor N d nitrogen is correlated with the corresponding non-exchangeable C-H proton associated with the acceptor N a nitrogen. In this way, missing N d H ... N a correlations in an HNN-COSY spectrum may be recovered from CH-N d correlations in the H(CN)N(H) spectrum. By correlating a different set of nuclei relative to the HNN-COSY class of experiments, the H(CN)N(H) experiment also serves to remove ambiguities associated with degeneracies in HNN-COSY spectra. The technique is demonstrated on d(GGAGGAG) 4 ,a quadruplex containing a novel A . (G . G . G . G) . A hexad and on d(GGGCAGGT) 4 , containing a G . C . G . C tetrad, in which missing NH 2 ... N7 correlations are retrieved via H8-(N2,N6) correlations in the H(CN)N(H) spectrum

  7. Observation of paramorphic phenomenon and non-tilted orthogonal smectic phases in hydrogen bonded ferroelectric liquid crystals for photonic applications

    Science.gov (United States)

    Subhasri, P.; Venugopal, D.; Jayaprakasam, R.; Chitravel, T.; Vijayakumar, V. N.

    2018-06-01

    A new class of hydrogen bonded ferroelectric liquid crystals (HBFLC) have been designed and synthesized by intermolecular hydrogen bonds between mesogenic 4-decyloxybenzoic acid (10OBA) and non-mesogenic (R)-(+)-Methylsuccinic acid (MSA) which have been confirmed through experimental and theoretical studies. Further, Mulliken population analysis clearly reveals that the existence of hydrogen bonds, strength and dynamic properties. Textural observation and its corresponding enthalpy values are analyzed by polarizing optical microscope (POM) and differential scanning calorimetry (DSC) respectively. Paramorphic changes in Sm C* phase due to the change of refractive index, which clearly reveal that the complex could be used for filtering action in photonic devices. The transition from lone pair to π* with large stabilization energy evidently exposes the chiral phases in the present HBFLC complex. Intermolecular interaction is analyzed by using natural bond orbital (NBO) studies. The highest energy in the HOMO-LUMO shows the stable phase in the HBFLC complex. Molecular structure of the HBFLC complex possesses the monoclinic which has been evinced through x-ray analysis. The randomly oriented bunch of homogeneous molecules in Sm A* phase of the HBFLC complex is reported.

  8. Towards a Molecular Movie: Real Time Observation of Hydrogen Bond Breaking by Transient 2D-IR Spectroscopy in a Cyclic Peptide

    Science.gov (United States)

    Kolano, Christoph; Helbing, Jan; Sander, Wolfram; Hamm, Peter

    Transient two-dimensional infrared spectroscopy (T2D-IR) has been used to observe in real time the non-equilibrium structural dynamics of intramolecular hydrogen bond breaking in a small cyclic disulfide-bridged peptide.

  9. Triplet excited electronic state switching induced by hydrogen bonding: A transient absorption spectroscopy and time-dependent DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Ravi Kumar, Venkatraman; Ariese, Freek; Umapathy, Siva, E-mail: umapathy@ipc.iisc.ernet.in [Inorganic and Physical Chemistry Department, Indian Institute of Science, Bangalore 560012 (India)

    2016-03-21

    The solvent plays a decisive role in the photochemistry and photophysics of aromatic ketones. Xanthone (XT) is one such aromatic ketone and its triplet-triplet (T-T) absorption spectra show intriguing solvatochromic behavior. Also, the reactivity of XT towards H-atom abstraction shows an unprecedented decrease in protic solvents relative to aprotic solvents. Therefore, a comprehensive solvatochromic analysis of the triplet-triplet absorption spectra of XT was carried out in conjunction with time dependent density functional theory using the ad hoc explicit solvent model approach. A detailed solvatochromic analysis of the T-T absorption bands of XT suggests that the hydrogen bonding interactions are different in the corresponding triplet excited states. Furthermore, the contributions of non-specific and hydrogen bonding interactions towards differential solvation of the triplet states in protic solvents were found to be of equal magnitude. The frontier molecular orbital and electron density difference analysis of the T{sub 1} and T{sub 2} states of XT indicates that the charge redistribution in these states leads to intermolecular hydrogen bond strengthening and weakening, respectively, relative to the S{sub 0} state. This is further supported by the vertical excitation energy calculations of the XT-methanol supra-molecular complex. The intermolecular hydrogen bonding potential energy curves obtained for this complex in the S{sub 0}, T{sub 1}, and T{sub 2} states support the model. In summary, we propose that the different hydrogen bonding mechanisms exhibited by the two lowest triplet excited states of XT result in a decreasing role of the nπ{sup ∗} triplet state, and are thus responsible for its reduced reactivity towards H-atom abstraction in protic solvents.

  10. Hydrophobic fluorine mediated switching of the hydrogen bonding site as well as orientation of water molecules in the aqueous mixture of monofluoroethanol: IR, molecular dynamics and quantum chemical studies.

    Science.gov (United States)

    Mondal, Saptarsi; Biswas, Biswajit; Nandy, Tonima; Singh, Prashant Chandra

    2017-09-20

    The local structures between water-water, alcohol-water and alcohol-alcohol have been investigated for aqueous mixtures of ethanol (ETH) and monofluoroethanol (MFE) by the deconvolution of IR bands in the OH stretching region, molecular dynamics simulation and quantum chemical calculations. It has been found that the addition of a small amount of ETH into the aqueous medium increases the strength of the hydrogen bonds between water molecules. In an aqueous mixture of MFE, the substitution of a single fluorine induces a change in the orientation as well as the hydrogen bonding site of water molecules from the oxygen to the fluorine terminal of MFE. The switching of the hydrogen bonding site of water in the aqueous mixture of MFE results in comparatively strong hydrogen bonds between MFE and water molecules as well as less clustering of water molecules, unlike the case of the aqueous mixture of ETH. These findings about the modification of a hydrogen bond network by the hydrophobic fluorine group probably make fluorinated molecules useful for pharmaceutical as well as biological applications.

  11. Hydrogen bonded supramolecular materials

    CERN Document Server

    Li, Zhan-Ting

    2015-01-01

    This book is an up-to-date text covering topics in utilizing hydrogen bonding for constructing functional architectures and supramolecular materials. The first chapter addresses the control of photo-induced electron and energy transfer. The second chapter summarizes the formation of nano-porous materials. The following two chapters introduce self-assembled gels, many of which exhibit unique functions. Other chapters cover the advances in supramolecular liquid crystals and the versatility of hydrogen bonding in tuning/improving the properties and performance of materials. This book is designed

  12. Hydrogen Bonds and Life in the Universe

    Directory of Open Access Journals (Sweden)

    Giovanni Vladilo

    2018-01-01

    Full Text Available The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of life. With this aim in mind, we have explored which chemical and physical properties should be expected for life possibly different from the terrestrial one, but similarly sustained by genetic and catalytic molecules. We show that functional molecules performing genetic and catalytic tasks must feature a hierarchy of chemical interactions operating in distinct energy bands. Of all known chemical bonds and forces, only hydrogen bonds are able to mediate the directional interactions of lower energy that are needed for the operation of genetic and catalytic tasks. For this reason and because of the unique quantum properties of hydrogen bonding, the functional molecules involved in life processes are predicted to have extensive hydrogen-bonding capabilities. A molecular medium generating a hydrogen-bond network is probably essential to support the activity of the functional molecules. These hydrogen-bond requirements constrain the viability of hypothetical biochemistries alternative to the terrestrial one, provide thermal limits to life molecular processes, and offer a conceptual framework to define a transition from a “covalent-bond stage” to a “hydrogen-bond stage” in prebiotic chemistry.

  13. Hydrogen Bonds and Life in the Universe

    Science.gov (United States)

    2018-01-01

    The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of life. With this aim in mind, we have explored which chemical and physical properties should be expected for life possibly different from the terrestrial one, but similarly sustained by genetic and catalytic molecules. We show that functional molecules performing genetic and catalytic tasks must feature a hierarchy of chemical interactions operating in distinct energy bands. Of all known chemical bonds and forces, only hydrogen bonds are able to mediate the directional interactions of lower energy that are needed for the operation of genetic and catalytic tasks. For this reason and because of the unique quantum properties of hydrogen bonding, the functional molecules involved in life processes are predicted to have extensive hydrogen-bonding capabilities. A molecular medium generating a hydrogen-bond network is probably essential to support the activity of the functional molecules. These hydrogen-bond requirements constrain the viability of hypothetical biochemistries alternative to the terrestrial one, provide thermal limits to life molecular processes, and offer a conceptual framework to define a transition from a “covalent-bond stage” to a “hydrogen-bond stage” in prebiotic chemistry. PMID:29301382

  14. Hydrogen Bonds and Life in the Universe.

    Science.gov (United States)

    Vladilo, Giovanni; Hassanali, Ali

    2018-01-03

    The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of life. With this aim in mind, we have explored which chemical and physical properties should be expected for life possibly different from the terrestrial one, but similarly sustained by genetic and catalytic molecules. We show that functional molecules performing genetic and catalytic tasks must feature a hierarchy of chemical interactions operating in distinct energy bands. Of all known chemical bonds and forces, only hydrogen bonds are able to mediate the directional interactions of lower energy that are needed for the operation of genetic and catalytic tasks. For this reason and because of the unique quantum properties of hydrogen bonding, the functional molecules involved in life processes are predicted to have extensive hydrogen-bonding capabilities. A molecular medium generating a hydrogen-bond network is probably essential to support the activity of the functional molecules. These hydrogen-bond requirements constrain the viability of hypothetical biochemistries alternative to the terrestrial one, provide thermal limits to life molecular processes, and offer a conceptual framework to define a transition from a "covalent-bond stage" to a "hydrogen-bond stage" in prebiotic chemistry.

  15. O hydrogen bonds in alkaloids

    Indian Academy of Sciences (India)

    An overview of general classification scheme, medicinal importance and crystal structure analysis with emphasis on the role of hydrogen bonding in some alkaloids is presented in this paper. The article is based on a general kind of survey while crystallographic analysis and role of hydrogen bonding are limited to only ...

  16. Distance criterion for hydrogen bond

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Distance criterion for hydrogen bond. In a D-H ...A contact, the D...A distance must be less than the sum of van der Waals Radii of the D and A atoms, for it to be a hydrogen bond.

  17. Vibrational polarizabilities of hydrogen-bonded water

    International Nuclear Information System (INIS)

    Torii, Hajime

    2013-01-01

    Highlights: ► Vibrational polarizabilities of hydrogen-bonded water are analyzed theoretically. ► Total vibrational polarizability is (at least) comparable to the electronic one. ► Molecular translations contribute to the vibrational polarizability below 300 cm −1 . ► Intermolecular charge fluxes along H bonds are induced by molecular translations. ► The results are discussed in relation to the observed dielectric properties. - Abstract: The vibrational polarizabilities and the related molecular properties of hydrogen-bonded water are analyzed theoretically, taking the case of (water) 30 clusters as an example case. It is shown that some off-diagonal dipole derivatives are large for the translations of incompletely hydrogen-bonded molecules, and this is reasonably explained by the scheme of intermolecular charge fluxes induced along hydrogen bonds. In total, because of these intermolecular charge fluxes, molecular translations give rise to the vibrational polarizability of 2.8–3.3 a 0 3 per molecule, which is as large as about 40% of the electronic polarizability, mainly in the frequency region below 300 cm −1 . Adding the contributions of the molecular rotations (librations) and the translation–rotation cross term, the total polarizability (electronic + vibrational) at ∼100 cm −1 is slightly larger than the double of that at >4000 cm −1 . The relation of these results to some observed time- and frequency-dependent dielectric properties of liquid water is briefly discussed

  18. Why are Hydrogen Bonds Directional?

    Indian Academy of Sciences (India)

    century and most chemists appear to think of 'chemi- cal bond' as ..... These complexes, in their global min- ima, have ... taneously act as hydrogen bond donor and acceptor displaying ... also has a local minimum, which is linear and similar to.

  19. dimensional architectures via hydrogen bonds

    Indian Academy of Sciences (India)

    Administrator

    organization and has potential applications in the field of magnetism ... The concepts of crystal engineering ... 4. However, the utilization of hydrogen bond supramolecular syn- ... sembling the coordination networks by designing the ligands ...

  20. Hydrogen bonding in tight environments

    DEFF Research Database (Denmark)

    Pirrotta, Alessandro; Solomon, Gemma C.; Franco, Ignacio

    2016-01-01

    The single-molecule force spectroscopy of a prototypical class of hydrogen-bonded complexes is computationally investigated. The complexes consist of derivatives of a barbituric acid and a Hamilton receptor that can form up to six simultaneous hydrogen bonds. The force-extension (F-L) isotherms...... of the host-guest complexes are simulated using classical molecular dynamics and the MM3 force field, for which a refined set of hydrogen bond parameters was developed from MP2 ab initio computations. The F-L curves exhibit peaks that signal conformational changes during elongation, the most prominent...... of which is in the 60-180 pN range and corresponds to the force required to break the hydrogen bonds. These peaks in the F-L curves are shown to be sensitive to relatively small changes in the chemical structure of the host molecule. Thermodynamic insights into the supramolecular assembly were obtained...

  1. What is a hydrogen bond?

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. What is a hydrogen bond? Precise definition of a hydrogen bond is still elusive!1. Several criteria are listed usually for X-H•••Y, X and Y initially thought to be F, O and N only1. Structural: The X-Y bond length is less than the sum of their van der Waals radii. X-H•••Y is ...

  2. Sensitivity enhanced NMR spectroscopy by quenching scalar coupling mediated relaxation: Application to the direct observation of hydrogen bonds in 13C/15N-labeled proteins

    Energy Technology Data Exchange (ETDEWEB)

    Liu Aizhuo; Hu Weidong; Qamar, Seema; Majumdar, Ananya [Memorial Sloan-Kettering Cancer Center, Cellular Biochemistry and Biophysics Program (United States)

    2000-05-15

    In this paper, we demonstrate that the sensitivity of triple-resonance NMR experiments can be enhanced significantly through quenching scalar coupling mediated relaxation by using composite-pulse decoupling (CPD) or an adiabatic decoupling sequence on aliphatic, in particular alpha-carbons in {sup 13}C/{sup 15}N-labeled proteins. The CPD-HNCO experiment renders 50% sensitivity enhancement over the conventional CT-HNCO experiment performed on a 12 kDa FK506 binding protein, when a total of 266 ms of amide nitrogen-carbonyl carbon defocusing and refocusing periods is employed. This is a typical time period for the direct detection of hydrogen bonds in proteins via trans-hydrogen bond {sup 3h}J{sub NC'} couplings. The experimental data fit theoretical analysis well. The significant enhancement in sensitivity makes the experiment more applicable to larger-sized proteins without resorting to perdeuteration.

  3. Simple inorganic complexes but intricate hydrogen bonding ...

    Indian Academy of Sciences (India)

    Administrator

    We are interested in obtaining single crystals of metal-opda complexes because their crystal structures would show complex hydrogen bonding network due to the presence of. –NH2 groups in the opda ligand (hydrogen bonding donor sites) and inorganic anions having mostly oxo groups (hydrogen bonding acceptor sites) ...

  4. Computational study of the signature of hydrogen-bond strength on the infrared spectra of a hydrogen-bonded complex dissolved in a polar liquid

    International Nuclear Information System (INIS)

    Hanna, Gabriel; Geva, Eitan

    2010-01-01

    The signature of hydrogen-bond strength on the one- and two-dimensional infrared spectra of the hydrogen-stretch in a hydrogen-bonded complex dissolved in a polar liquid was investigated via mixed quantum-classical molecular dynamics simulations. Non-Condon effects were found to intensify with increasing hydrogen-bond strength and to shift oscillator strength from the stable configurations that correspond to the ionic and covalent tautomers into unstable configurations that correspond to the transition-state between them. The transition-state peak is observed to blue shift and increase in intensity with increasing hydrogen-bond strength, and to dominate the spectra in the case of a strong hydrogen-bond. It is argued that the application of multidimensional infrared spectroscopy in the region of the transition-state peak can provide a uniquely direct probe of the molecular events underlying breaking and forming of hydrogen-bonds in the condensed phase.

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

    Science.gov (United States)

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

    2013-01-01

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

  6. Tetrahedrality and hydrogen bonds in water

    Science.gov (United States)

    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. Cooperativity in Surface Bonding and Hydrogen Bonding of Water and Hydroxyl at Metal Surfaces

    DEFF Research Database (Denmark)

    Schiros, T.; Ogasawara, H.; Naslund, L. A.

    2010-01-01

    of the mixed phase at metal surfaces. The surface bonding can be considered to be similar to accepting a hydrogen bond, and we can thereby apply general cooperativity rules developed for hydrogen-bonded systems. This provides a simple understanding of why water molecules become more strongly bonded...... to the surface upon hydrogen bonding to OH and why the OH surface bonding is instead weakened through hydrogen bonding to water. We extend the application of this simple model to other observed cooperativity effects for pure water adsorption systems and H3O+ on metal surfaces.......We examine the balance of surface bonding and hydrogen bonding in the mixed OH + H2O overlayer on Pt(111), Cu(111), and Cu(110) via density functional theory calculations. We find that there is a cooperativity effect between surface bonding and hydrogen bonding that underlies the stability...

  8. Effects of hydrogen bonds on solid state TATB, RDX, and DATB under high pressures

    International Nuclear Information System (INIS)

    Guo Feng; Hu Hai-Quan; Zhang Hong; Cheng Xin-Lu

    2014-01-01

    To probe the behavior of hydrogen bonds in solid energetic materials, we conduct ReaxFF and SCC–DFTB molecular dynamics simulations of crystalline TATB, RDX, and DATB. By comparing the intra- and inter-molecular hydrogen bonding rates, we find that the crystal structures are stabilized by inter-molecular hydrogen bond networks. Under high-pressure, the inter- and intra-molecular hydrogen bonds in solid TATB and DATB are nearly equivalent. The hydrogen bonds in solid TATB and DATB are much shorter than in solid RDX, which suggests strong hydrogen bond interactions existing in these energetic materials. Stretching of the C–H bond is observed in solid RDX, which may lead to further decomposition and even detonation. (condensed matter: structural, mechanical, and thermal properties)

  9. Examining student heuristic usage in a hydrogen bonding assessment.

    Science.gov (United States)

    Miller, Kathryn; Kim, Thomas

    2017-09-01

    This study investigates the role of representational competence in student responses to an assessment of hydrogen bonding. The assessment couples the use of a multiple-select item ("Choose all that apply") with an open-ended item to allow for an examination of students' cognitive processes as they relate to the assignment of hydrogen bonding within a structural representation. Response patterns from the multiple-select item implicate heuristic usage as a contributing factor to students' incorrect responses. The use of heuristics is further supported by the students' corresponding responses to the open-ended assessment item. Taken together, these data suggest that poor representational competence may contribute to students' previously observed inability to correctly navigate the concept of hydrogen bonding. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):411-416, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  10. Hydrogen bond dynamics in bulk alcohols

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  11. Theoretical Characterization of Hydrogen Bonding Interactions ...

    Indian Academy of Sciences (India)

    The highest stabilization results in case of (H2N)CHO as hydrogen bond acceptor. The variation of the substituents at –OH functional group also influences the strength of hydrogen bond; nearly all the substituents increase the stabilization energy relative to HOH. The analysis of geometrical parameters; proton affinities, ...

  12. Hydrogen bond dynamics in bulk alcohols.

    Science.gov (United States)

    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.

  13. Hydrogen bonds in concreto and in computro

    Science.gov (United States)

    Stouten, Pieter F. W.; Kroon, Jan

    1988-07-01

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

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

    International Nuclear Information System (INIS)

    Henchman, Richard H

    2016-01-01

    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. (paper)

  15. Functional chiral hydrogen-bonded assemblies

    NARCIS (Netherlands)

    Mateos timoneda, Miguel

    2005-01-01

    In this thesis different aspects of functional hydrogen-bonded (double and tetrarosette) assemblies are described. The functions were inspired by naturally occurring mechanisms such as molecular recognition, supramolecular chirality and its origin, and biostrategies for the correct folding of

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2016-03-03

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

  18. Hydrogen bonding in ionic liquids.

    Science.gov (United States)

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

    2015-03-07

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

  19. Optimising hydrogen bonding in solid wood

    DEFF Research Database (Denmark)

    Engelund, Emil Tang

    2009-01-01

    The chemical bonds of wood are both covalent bonds within the wood polymers and hydrogen bonds within and between the polymers. Both types of bonds are responsible for the coherence, strength and stiffness of the material. The hydrogen bonds are more easily modified by changes in load, moisture...... and temperature distorting the internal bonding state. A problem arises when studying hydrogen bonding in wood since matched wood specimens of the same species will have very different internal bonding states. Thus, possible changes in the bonding state due to some applied treatment such as conditioning...... maintaining 100 % moisture content of the wood. The hypothesis was that this would enable a fast stress relaxation as a result of reorganization of bonds, since moisture plasticizes the material and temperature promotes faster kinetics. Hereby, all past bond distortions caused by various moisture, temperature...

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

    Science.gov (United States)

    Takahashi, Masae; Ishikawa, Yoichi

    2013-06-01

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

  1. Electrostatics determine vibrational frequency shifts in hydrogen bonded complexes.

    Science.gov (United States)

    Dey, Arghya; Mondal, Sohidul Islam; Sen, Saumik; Ghosh, Debashree; Patwari, G Naresh

    2014-12-14

    The red-shifts in the acetylenic C-H stretching vibration of C-H∙∙∙X (X = O, N) hydrogen-bonded complexes increase with an increase in the basicity of the Lewis base. Analysis of various components of stabilization energy suggests that the observed red-shifts are correlated with the electrostatic component of the stabilization energy, while the dispersion modulates the stabilization energy.

  2. H/D Isotope Effects in Hydrogen Bonded Systems

    Directory of Open Access Journals (Sweden)

    Aleksander Filarowski

    2013-04-01

    Full Text Available An extremely strong H/D isotope effect observed in hydrogen bonded A-H…B systems is connected with a reach diversity of the potential shape for the proton/deuteron motion. It is connected with the anharmonicity of the proton/deuteron vibrations and of the tunneling effect, particularly in cases of short bridges with low barrier for protonic and deuteronic jumping. Six extreme shapes of the proton motion are presented starting from the state without possibility of the proton transfer up to the state with a full ionization. The manifestations of the H/D isotope effect are best reflected in the infra-red absorption spectra. A most characteristic is the run of the relationship between the isotopic ratio nH/nD and position of the absorption band shown by using the example of NHN hydrogen bonds. One can distinguish a critical range of correlation when the isotopic ratio reaches the value of ca. 1 and then increases up to unusual values higher than . The critical range of the isotope effect is also visible in NQR and NMR spectra. In the critical region one observes a stepwise change of the NQR frequency reaching 1.1 MHz. In the case of NMR, the maximal isotope effect is reflected on the curve presenting the dependence of Δd (1H,2H on d (1H. This effect corresponds to the range of maximum on the correlation curve between dH and ΔpKa that is observed in various systems. There is a lack in the literature of quantitative information about the influence of isotopic substitution on the dielectric properties of hydrogen bond except the isotope effect on the ferroelectric phase transition in some hydrogen bonded crystals.

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

    Science.gov (United States)

    O'Neal, Kristi L; Weber, Stephen G

    2009-01-08

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

  4. Hydrogen bonding in cytosinium dihydrogen phosphite

    OpenAIRE

    Nourredine Benali-Cherif; Amel Messai; Erwann Jeanneau; Dominique Luneau

    2009-01-01

    In the title compound, C4H8N3O4P+·H2PO3−, the cytosine molecule is monoprotonated and the phosphoric acid is in the monoionized state. Strong hydrogen bonds, dominated by N—H...O interactions, are responsible for cohesion between the organic and inorganic layers and maintain the stability of this structure.

  5. Hydrogen bonding in cytosinium dihydrogen phosphite

    Directory of Open Access Journals (Sweden)

    Nourredine Benali-Cherif

    2009-05-01

    Full Text Available In the title compound, C4H8N3O4P+·H2PO3−, the cytosine molecule is monoprotonated and the phosphoric acid is in the monoionized state. Strong hydrogen bonds, dominated by N—H...O interactions, are responsible for cohesion between the organic and inorganic layers and maintain the stability of this structure.

  6. Characterization of Hydrogen Bonds by IR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Vojta, D.

    2012-05-01

    Full Text Available In the identification and quantification of hydrogen bond, as one of the most abundant non-covalent interactions in phenomena like self-assembly and molecular recognition, IR spectrosopy has been employed as the most sensitive method. The performance of the high dilution method enables determination of the stability constant of hydrogen-bonded complex as one of the most important thermodynamic quantities used in their characterization. However, the alleged experimental simplicity of the mentioned method is loaded with errors originating not only from researcher intervention but also independent from it. The second source of error is particularly emphasized and elaborated in this paper, which is designed as the recipe for the successful characterization of hydrogen bonds. Besides the enumeration of all steps in the determination of hydrogen-bonded stability constants, the reader can be acquainted with the most important ex perimental conditions that should be fulfilled in order to minimize the naturally occurring errors in this type of investigation. In the spectral analysis, the application of both uni- and multivariate approach has been discussed. Some computer packages, considering the latter, are mentioned, described, and recommended. KUI -10/2012Received August 1, 2011Accepted October 24, 2011

  7. Hydrogen Bonding to Alkanes: Computational Evidence

    DEFF Research Database (Denmark)

    Hammerum, Steen; Olesen, Solveig Gaarn

    2009-01-01

    The structural, vibrational, and energetic properties of adducts of alkanes and strong cationic proton donors were studied with composite ab initio calculations. Hydrogen bonding in [D-H+ H-alkyl] adducts contributes to a significant degree to the interactions between the two components, which is...

  8. Improper, Blue-Shifting Hydrogen Bond

    Czech Academy of Sciences Publication Activity Database

    Hobza, Pavel; Havlas, Zdeněk

    2002-01-01

    Roč. 108, - (2002), s. 325-334 ISSN 1432-881X R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4055905; CEZ:AV0Z4040901 Keywords : improper, blue-shifting hydrogen bond * properties * nature Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.421, year: 2002

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

    Science.gov (United States)

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

    2016-08-05

    A piperidine-derived tetraalkylammonium salt with a non-coordinating counteranion worked as an effective hydrogen-bonding catalyst in an aza-Diels-Alder reaction of imines and a Danishefsky diene. The hydrogen-bonding interaction between the ammonium salt and an imine was observed as part of a (1) H NMR titration study. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Hydrogen bond dynamical properties of adsorbed liquid water monolayers with various TiO2 interfaces

    Science.gov (United States)

    English, Niall J.; Kavathekar, Ritwik S.; MacElroy, J. M. D.

    2012-12-01

    Equilibrium classical molecular dynamics (MD) simulations have been performed to investigate the hydrogen-bonding kinetics of water in contact with rutile-(110), rutile-(101), rutile-(100), and anatase-(101) surfaces at room temperature (300 K). It was observed that anatase-(101) exhibits the longest-lived hydrogen bonds in terms of overall persistence, followed closely by rutile-(110). The relaxation times, defined as the integral of the autocorrelation of the hydrogen bond persistence function, were also longer for these two cases, while decay of the autocorrelation function was slower. The increased number and overall persistence of hydrogen bonds in the adsorbed water monolayers at these surfaces, particularly for anatase-(101), may serve to promote possible water photolysis activity thereon.

  11. Intramolecularly Hydrogen-Bonded Polypyrroles as Electro-Optical Sensors

    National Research Council Canada - National Science Library

    Nicholson, Jesse

    2001-01-01

    We have developed a new class of polypyrroles bearing both hydrogen-bond acceptor and hydrogen-donor groups such that the intramolecular hydrogen bonding holds the system planar enhancing conjugation...

  12. Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

    Indian Academy of Sciences (India)

    Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

  13. Structures and the Hydrogen Bonding Abilities of Estrogens Studied by Supersonic Jet/laser Spectroscopy

    Science.gov (United States)

    Morishima, Fumiya; Inokuchi, Yoshiya; Ebata, Takayuki

    2013-06-01

    Estrone, estradiol, estriol are known as endogenous estrogen which have the same steroidal frame with different substituent, leading to difference of physiological activity upon the formation of hydrogen bond with estrogen receptor. In the present study, structures of estrogens and their hydrated clusters in a supersonic jet have been studied by various laser spectroscopic techniques and density functional theory calculation to study how the difference of substituents affects their hydrogen bonding ability. Infrared spectra in the OH stretching region indicate a formation of intramolecular hydrogen-bond in estriol, which may lead to weaker physiological activity among the three estrogens. We also measured electronic and infrared spectra of 1:1 hydrated clusters of estrogen. The results show a switch of stable hydration site from the phenolic OH group to the five member ring by substituting one more OH group.

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

    International Nuclear Information System (INIS)

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

    2016-01-01

    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.

  15. Hydrogen bonds and heat diffusion in α-helices: a computational study.

    Science.gov (United States)

    Miño, German; Barriga, Raul; Gutierrez, Gonzalo

    2014-08-28

    Recent evidence has shown a correlation between the heat diffusion pathways and the known allosteric communication pathways in proteins. Allosteric communication in proteins is a central, yet unsolved, problem in biochemistry, and the study and characterization of the structural determinants that mediate energy transfer among different parts of proteins is of major importance. In this work, we characterized the role of hydrogen bonds in diffusivity of thermal energy for two sets of α-helices with different abilities to form hydrogen bonds. These hydrogen bonds can be a constitutive part of the α-helices or can arise from the lateral chains. In our in vacuo simulations, it was observed that α-helices with a higher possibility of forming hydrogen bonds also had higher rates of thermalization. Our simulations also revealed that heat readily flowed through atoms involved in hydrogen bonds. As a general conclusion, according to our simulations, hydrogen bonds fulfilled an important role in heat diffusion in structural patters of proteins.

  16. Intramolecular Energy Transfer, Charge Transfer & Hydrogen Bond

    Indian Academy of Sciences (India)

    Ultrafast Dynamics of Chemical Reactions in Condensed Phase: Intramolecular Energy Transfer, Charge Transfer & Hydrogen Bond · PowerPoint Presentation · Slide 3 · Slide 4 · Slide 5 · Slide 6 · Slide 7 · Slide 8 · Slide 9 · Slide 10 · Slide 11 · Slide 12 · Slide 13 · Slide 14 · Slide 15 · Slide 16 · Slide 17 · Slide 18 · Slide 19.

  17. Hydrogen bond donor–acceptor–donor organocatalysis for conjugate addition of benzylidene barbiturates via complementary DAD– ADA hydrogen bonding

    NARCIS (Netherlands)

    Leung, King-Chi; Cui, Jian-Fang; Hui, Tsz-Wai; Zhou, Zhong-Yuan; Wong, Man-Kin

    2014-01-01

    A new class of hydrogen bond donor-acceptor-donor (HB-DAD) organocatalysts has been developed for conjugate addition of benzylidene barbiturates. HB-DAD organocatalyst 1a (featuring para-chloro-pyrimidine as the hydrogen bond acceptor (HBA), N-H as the hydrogen bond donor (HBD) and a trifluoroacetyl

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2001-08-01

    Students completing a year-long organic chemistry sequence were interviewed to assess how they understood, explained, and applied knowledge of hydrogen bonding to the physical behavior of molecules. Students were asked to define hydrogen bonding and explain situations in which hydrogen bonding could occur. They were asked to predict and explain how hydrogen bonding influences boiling point, the solubility of molecules, and NMR and IR spectra. Results suggest that although students may be able to give appropriate definitions of hydrogen bonding and may recognize when this phenomenon can occur, significant numbers cannot apply their knowledge of hydrogen bonding to physical properties of molecules or to the interpretation of spectral data. Some possess misconceptions concerning boiling points and the ability of molecules to induce hydrogen bonding. Instructional strategies must be adjusted to address these issues.

  20. Anharmonicity and hydrogen bonding in electrooptic sucrose crystal

    Science.gov (United States)

    Szostak, M. M.; Giermańska, J.

    1990-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Delpouve, N., E-mail: delpouve.nicolas@gmail.com [AMME-LECAP EA 4528 International Laboratory, University of Rouen, Avenue de l' Universite BP 12, 76801 Saint Etienne du Rouvray (France); Vuillequez, A.; Saiter, A.; Youssef, B.; Saiter, J.M. [AMME-LECAP EA 4528 International Laboratory, University of Rouen, Avenue de l' Universite BP 12, 76801 Saint Etienne du Rouvray (France)

    2012-09-01

    Molecular dynamics at the glass transition of three lactose/oil glassy systems have been investigated according to the cooperativity and fragility approaches. From Donth's approach, the cooperativity length is estimated by modulated temperature calorimetric measurements. Results reveal that modification of the disaccharide by oil leads to increase the disorder degree in the lactose, the size of the cooperative domains and the fragility index. These particular hydrogen-bonded organic glasses follow the general tendency observed on organic and inorganic polymers: the higher the cooperativity length, the higher the value of the fragility index at T{sub g}.

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

    International Nuclear Information System (INIS)

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

    2012-01-01

    Molecular dynamics at the glass transition of three lactose/oil glassy systems have been investigated according to the cooperativity and fragility approaches. From Donth's approach, the cooperativity length is estimated by modulated temperature calorimetric measurements. Results reveal that modification of the disaccharide by oil leads to increase the disorder degree in the lactose, the size of the cooperative domains and the fragility index. These particular hydrogen-bonded organic glasses follow the general tendency observed on organic and inorganic polymers: the higher the cooperativity length, the higher the value of the fragility index at T g .

  3. Hydrogen Bond Basicity Prediction for Medicinal Chemistry Design.

    Science.gov (United States)

    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.

  4. Strong and weak hydrogen bonds in drug–DNA complexes

    Indian Academy of Sciences (India)

    The dataset was extracted from the protein data bank (PDB). The analysis was performed with an in-house software, hydrogen bond analysis tool (HBAT). In addition to strong hydrogen bonds such as O−H···O and N−H···O, the ubiquitous presence of weak hydrogen bonds such as C−H···O is implicated in molecular ...

  5. A tensegrity model for hydrogen bond networks in proteins

    OpenAIRE

    Bywater, Robert P.

    2017-01-01

    Hydrogen-bonding networks in proteins considered as structural tensile elements are in balance separately from any other stabilising interactions that may be in operation. The hydrogen bond arrangement in the network is reminiscent of tensegrity structures in architecture and sculpture. Tensegrity has been discussed before in cells and tissues and in proteins. In contrast to previous work only hydrogen bonds are studied here. The other interactions within proteins are either much stronger − c...

  6. Hydrogen bonding between hydrides of the upper-right part of the periodic table

    Science.gov (United States)

    Simončič, Matjaž; Urbic, Tomaz

    2018-05-01

    One of the most important electrostatic interactions between molecules is most definitely the hydrogen bond. Understanding the basis of this interaction may offer us the insight needed to understand its effect on the macroscopic scale. Hydrogen bonding is for example the reason for anomalous properties in compounds like water and naturally life as we know it. The strength of the bond depends on numerous factors, among them the electronegativity of participating atoms. In this work we calculated the strength of hydrogen bonds between hydrides of the upper-right part of the periodic table (C, N, O, F, P, S, Cl, As, Se, Br) using quantum-chemical methods. The aim was to determine what influences the strength of strong and weak hydrogen bonds in simple hydrides. Various relationships were checked. A relation between the strength of the bond and the electronegativity of the participating atoms was found. We also observed a correlation between the strength of hydrogen bonds and the inter-atomic distances, along with the dependence on the charge transfer on the atom of the donor. We also report characteristic geometries of different dimers.

  7. Infrared intensities and charge mobility in hydrogen bonded complexes

    Energy Technology Data Exchange (ETDEWEB)

    Galimberti, Daria; Milani, Alberto; Castiglioni, Chiara [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta,” Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy)

    2013-08-21

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

  8. NMR and IR Investigations of Strong Intramolecular Hydrogen Bonds

    Directory of Open Access Journals (Sweden)

    Poul Erik Hansen

    2017-03-01

    Full Text Available For the purpose of this review, strong hydrogen bonds have been defined on the basis of experimental data, such as OH stretching wavenumbers, νOH, and OH chemical shifts, δOH (in the latter case, after correction for ring current effects. Limits for O–H···Y systems are taken as 2800 > νOH > 1800 cm−1, and 19 ppm > δOH > 15 ppm. Recent results as well as an account of theoretical advances are presented for a series of important classes of compounds such as β-diketone enols, β-thioxoketone enols, Mannich bases, proton sponges, quinoline N-oxides and diacid anions. The O···O distance has long been used as a parameter for hydrogen bond strength in O–H···O systems. On a broad scale, a correlation between OH stretching wavenumbers and O···O distances is observed, as demonstrated experimentally as well as theoretically, but for substituted β-diketone enols this correlation is relatively weak.

  9. Hydrogen-Bonding Interactions Trigger a Spin-Flip in Iron(III) Porphyrin Complexes**

    Science.gov (United States)

    Sahoo, Dipankar; Quesne, Matthew G; de Visser, Sam P; Rath, Sankar Prasad

    2015-01-01

    A key step in cytochrome P450 catalysis includes the spin-state crossing from low spin to high spin upon substrate binding and subsequent reduction of the heme. Clearly, a weak perturbation in P450 enzymes triggers a spin-state crossing. However, the origin of the process whereby enzymes reorganize their active site through external perturbations, such as hydrogen bonding, is still poorly understood. We have thus studied the impact of hydrogen-bonding interactions on the electronic structure of a five-coordinate iron(III) octaethyltetraarylporphyrin chloride. The spin state of the metal was found to switch reversibly between high (S=5/2) and intermediate spin (S=3/2) with hydrogen bonding. Our study highlights the possible effects and importance of hydrogen-bonding interactions in heme proteins. This is the first example of a synthetic iron(III) complex that can reversibly change its spin state between a high and an intermediate state through weak external perturbations. PMID:26109743

  10. Porous Hydrogen-Bonded Organic Frameworks

    Directory of Open Access Journals (Sweden)

    Yi-Fei Han

    2017-02-01

    Full Text Available Ordered porous solid-state architectures constructed via non-covalent supramolecular self-assembly have attracted increasing interest due to their unique advantages and potential applications. Porous metal-coordination organic frameworks (MOFs are generated by the assembly of metal coordination centers and organic linkers. Compared to MOFs, porous hydrogen-bonded organic frameworks (HOFs are readily purified and recovered via simple recrystallization. However, due to lacking of sufficiently ability to orientate self-aggregation of building motifs in predictable manners, rational design and preparation of porous HOFs are still challenging. Herein, we summarize recent developments about porous HOFs and attempt to gain deeper insights into the design strategies of basic building motifs.

  11. Proton tunnelling in intermolecular hydrogen bonds

    Energy Technology Data Exchange (ETDEWEB)

    Horsewill, A J [Nottingham Univ. (United Kingdom); Johnson, M R [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France); Trommsdorff, H P [Grenoble-1 Univ., 38 (France)

    1997-04-01

    The wavefunctions of particles extend beyond the classically accessible regions of potential energy-surfaces (PES). A manifestation of this partial delocalization is the quantum-mechanical tunneling effect which enables a particle to escape from a metastable potential-well. Tunnelling is most important for the lightest atoms, so that the determination of its contribution to proton transfer, one of the most fundamental chemical reactions, is an important issue. QENS and NMR techniques have been employed to study the motion of protons in the hydrogen bond of benzoic-acid crystals, a system which has emerged as a particularly suitable model since proton transfer occurs in a near symmetric double-well potential. The influence of quantum tunnelling was revealed and investigated in these experiments. This work provides an experimental benchmark for theoretical descriptions of translational proton-tunnelling. (author). 7 refs.

  12. Conformation and hydrogen bonding in 4-Aminobutanol

    Science.gov (United States)

    Khalil, Andrew S.; Duguay, Taylor M.; Lavrich, Richard J.

    2017-06-01

    Rotational spectra of the most abundant and four 13C isotopomers of 4-aminobutanol have been recorded in natural abundance using a Fourier-transform microwave spectrometer. For the most abundant isotopomer, 56 hyperfine components from the fifteen a- and b-type transitions measured were fit to the quadupole coupling constants, χaa = -3.843(3) MHz, χbb = 1.971(3) MHz. Rotational and centrifugal distortion constants determined from fits of the resulting unsplit line centers to the Watson A-reduction Hamiltonian are A = 4484.893(3) MHz, B = 2830.721(1) MHz, C = 1942.9710(3) MHz, ΔJ = 0.98(3) kHz, ΔJK = 1.4(1) kHz, ΔK = - 2.6(5) kHz, δJ = 0.27(1) kHz, and δK = 1.7(1) kHz. Between nine and eleven rotational transitions were measured for the 13C isotopes and rotational constants were determined by fixing the distortion constants to the values found for the normal isotope. The five sets of moments of inertia were used to determine the 4-aminobutanol substitution structure as well to perform a least-squares fit of the lowest energy ab initio structure. The heavy atom coordinates determined from these two methods are in excellent agreement. The conformation of 4-aminobutanol is stabilized by an intramolecular hydrogen bond from the alcohol proton to amino nitrogen with a resulting hydrogen bond distance of 1.891 Å. The experimental structure is consistent with the lowest energy ab initio [MP2/6-311++G(d,p)] structure.

  13. Similar strength of the NH⋯O and NH⋯S hydrogen bonds in binary complexes

    DEFF Research Database (Denmark)

    Andersen, Cecilie Lindholm; Jensen, Christine S.; Mackeprang, Kasper

    2014-01-01

    to be extremely small with only 5 and 19 cm-1 for DMA-DME and DMA-DMS, respectively. The experimentally determined integrated absorbance has been combined with a calculated oscillator strength to determine an equilibrium constant of 2 × 10-3 and 4 × 10-3 for the DMA-DME and DMA-DMS complexes, respectively....... The topological analyses reveal that several hydrogen bond interactions are present in the complexes. The calculated binding energies, geometric parameters, observed redshifts, and topological analyses suggest that oxygen and sulfur are hydrogen bond acceptors of similar strength. (Graph Presented)....

  14. Intermolecular hydrogen bonds: From temperature-driven proton ...

    Indian Academy of Sciences (India)

    Abstract. We have combined neutron scattering and a range of numerical simulations to study hydrogen bonds in condensed matter. Two examples from a recent thesis will be presented. The first concerns proton transfer with increasing temperature in short inter- molecular hydrogen bonds [1,2]. These bonds have unique ...

  15. Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol

    Directory of Open Access Journals (Sweden)

    Hailiang Zhao

    2016-12-01

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

  16. Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol.

    Science.gov (United States)

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

    2016-12-30

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

  17. Predictions of glass transition temperature for hydrogen bonding biomaterials.

    Science.gov (United States)

    van der Sman, R G M

    2013-12-19

    We show that the glass transition of a multitude of mixtures containing hydrogen bonding materials correlates strongly with the effective number of hydroxyl groups per molecule, which are available for intermolecular hydrogen bonding. This correlation is in compliance with the topological constraint theory, wherein the intermolecular hydrogen bonds constrain the mobility of the hydrogen bonded network. The finding that the glass transition relates to hydrogen bonding rather than free volume agrees with our recent finding that there is little difference in free volume among carbohydrates and polysaccharides. For binary and ternary mixtures of sugars, polyols, or biopolymers with water, our correlation states that the glass transition temperature is linear with the inverse of the number of effective hydroxyl groups per molecule. Only for dry biopolymer/sugar or sugar/polyol mixtures do we find deviations due to nonideal mixing, imposed by microheterogeneity.

  18. Hydrogen Bonding With a Hydrogen Bond: The CH4•••H2O Dimer ...

    Indian Academy of Sciences (India)

    X-H•••C hydrogen bonds in n-alkane-HX (X = F, OH) complexes are stronger than C-H•••X hydrogen bonds. R Parajuli* and E Arunan**. *Department of Physics, Amrit Campus, Tribhuvan University, Kathmandu, Nepal. **Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru 560012, India.

  19. A Computational and Theoretical Study of Conductance in Hydrogen-bonded Molecular Junctions

    Science.gov (United States)

    Wimmer, Michael

    This thesis is devoted to the theoretical and computational study of electron transport in molecular junctions where one or more hydrogen bonds are involved in the process. While electron transport through covalent bonds has been extensively studied, in recent work the focus has been shifted towards hydrogen-bonded systems due to their ubiquitous presence in biological systems and their potential in forming nano-junctions between molecular electronic devices and biological systems. This analysis allows us to significantly expand our comprehension of the experimentally observed result that the inclusion of hydrogen bonding in a molecular junction significantly impacts its transport properties, a fact that has important implications for our understanding of transport through DNA, and nano-biological interfaces in general. In part of this work I have explored the implications of quasiresonant transport in short chains of weakly-bonded molecular junctions involving hydrogen bonds. I used theoretical and computational analysis to interpret recent experiments and explain the role of Fano resonances in the transmission properties of the junction. In a different direction, I have undertaken the study of the transversal conduction through nucleotide chains that involve a variable number of different hydrogen bonds, e.g. NH˙˙˙O, OH˙˙˙O, and NH˙˙˙N, which are the three most prevalent hydrogen bonds in biological systems and organic electronics. My effort here has focused on the analysis of electronic descriptors that allow a simplified conceptual and computational understanding of transport properties. Specifically, I have expanded our previous work where the molecular polarizability was used as a conductance descriptor to include the possibility of atomic and bond partitions of the molecular polarizability. This is important because it affords an alternative molecular description of conductance that is not based on the conventional view of molecular orbitals as

  20. Study of optical shuttering action in supramolecular hydrogen bonded nematogens

    Science.gov (United States)

    Kavitha, C.; Pongali Sathya Prabu, N.; Madhu Mohan, M. L. N.

    2012-11-01

    Supramolecular hydrogen bonded mesogens are formed between p-n-undecyloxy benzoic acid (11BAO) and p-n-alkyl benzoic acids (nBA, where n = 2-8). The isolated mesogens are characterized by distinct techniques in order to appreciate the optical, thermal, electrical, and dielectric properties. The optical tilt angle measurement is studied for all the members of this homologous series and is found to concur with the mean field theory predicted value. An interesting factor to notice is the observation of optical shuttering action in nematic phase of the entire series which privilege these materials to be used as light modulators. Dielectric measurements were carried out and the dispersion curves were discussed in terms of relaxation frequency and activation energies.

  1. NMR and IR investigations of strong intramolecular hydrogen bonds

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Spanget-Larsen, Jens

    2017-01-01

    been used as a parameter for hydrogen bond strength in O–H···O systems. On a broad scale, a correlation between OH stretching wavenumbers and O···O distances is observed, as demonstrated experimentally as well as theoretically, but for substituted beta-diketone enols this correlation is relatively weak.......–1, and 19 >  dOH > 15 ppm. Recent results as well as an account of theoretical advances are presented for a series of important classes of compounds such as beta-diketone enols, beta-thioxoketone enols, Mannich bases, proton sponges, quinoline N-oxides and diacid anions. The O···O distance has long...

  2. Hydrogen bonded networks in formamide [HCONH2]n (n = 1 − 10 ...

    Indian Academy of Sciences (India)

    clusters: A computational exploration of preferred aggregation patterns. #. A SUBHA ... Application of quantum chemical calculations is vital in understanding hydrogen bonding observed in formamide ... up approach of building large assemblies from con- ..... representation of AIM analysis of all clusters is pro- vided in the ...

  3. Influence of hydrogen bonding on the generation and stabilization

    Indian Academy of Sciences (India)

    Induction and stabilization of liquid crystallinity through hydrogen bonding (HB) are now well-established. Interesting observations made on the influence of HB on LC behaviour of amido diol-based poly(esteramide)s, poly(esteramide)s containing nitro groups and azobenzene mesogen-based polyacrylates will be ...

  4. The influence of hydrogen bonding on partition coefficients

    Science.gov (United States)

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

    2017-02-01

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

  5. Hydrogen-Bonding Surfaces for Ice Mitigation

    Science.gov (United States)

    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. Thermodynamic functions of hydrogen bonding of amines in methanol derived from solution calorimetry data and headspace analysis

    International Nuclear Information System (INIS)

    Zaitseva, Ksenia V.; Varfolomeev, Mikhail A.; Solomonov, Boris N.

    2012-01-01

    Highlights: ► Solution enthalpies and activity coefficients of amines in methanol were measured. ► Thermodynamic functions of H-bonding of amines with methanol were determined. ► Specific interaction entropy of amines in methanol can be about zero or positive. ► Cooperativity of H-bonds in methanol media is smaller than in water solutions. ► A new view on analysis of specific interaction of solute with methanol is presented. - Abstract: Reactivity and equilibrium properties of organic molecules in self-associated liquids greatly depend on the hydrogen bonding with solvent. This work contains comprehensive thermodynamic analysis of hydrogen bonding of aliphatic and aromatic amines in self-associated solvent methanol. Enthalpies of solution at infinite dilution and limiting activity coefficients for the studied systems were measured experimentally. Enthalpies and Gibbs energies of hydrogen bonding of amines with neat methanol were determined. These values were found to be decreased compared with hydrogen bond energy in equimolar complexes “methanol–amine” determined in inert solvent or base media. A linear dependence between enthalpies and Gibbs energies of hydrogen bonding of amines with neat methanol was observed. It was firstly revealed that the entropy of specific interactions of amines with neat methanol can be about zero or positive. Disruption of solvent–solvent hydrogen bonds can be regarded as the most important step during dissolution of amine in methanol. It was found that the cooperative effect influences on the Gibbs energies of hydrogen bonding of amines in methanol, but in a lesser extent than in aqueous solutions. The new results show that the hydrogen bonding process in the self-associated solvents differs significantly from equimolar complexation in aprotic media.

  7. Thermodynamic functions of hydrogen bonding of amines in methanol derived from solution calorimetry data and headspace analysis

    Energy Technology Data Exchange (ETDEWEB)

    Zaitseva, Ksenia V., E-mail: zaitseva.ksenia@gmail.com [Chemical Institute, Kazan (Volga Region) Federal University, Kremlevskaya 18, Kazan 420008 (Russian Federation); Varfolomeev, Mikhail A., E-mail: vma.ksu@gmail.com [Chemical Institute, Kazan (Volga Region) Federal University, Kremlevskaya 18, Kazan 420008 (Russian Federation); Solomonov, Boris N., E-mail: boris.solomonov@ksu.ru [Chemical Institute, Kazan (Volga Region) Federal University, Kremlevskaya 18, Kazan 420008 (Russian Federation)

    2012-05-10

    Highlights: Black-Right-Pointing-Pointer Solution enthalpies and activity coefficients of amines in methanol were measured. Black-Right-Pointing-Pointer Thermodynamic functions of H-bonding of amines with methanol were determined. Black-Right-Pointing-Pointer Specific interaction entropy of amines in methanol can be about zero or positive. Black-Right-Pointing-Pointer Cooperativity of H-bonds in methanol media is smaller than in water solutions. Black-Right-Pointing-Pointer A new view on analysis of specific interaction of solute with methanol is presented. - Abstract: Reactivity and equilibrium properties of organic molecules in self-associated liquids greatly depend on the hydrogen bonding with solvent. This work contains comprehensive thermodynamic analysis of hydrogen bonding of aliphatic and aromatic amines in self-associated solvent methanol. Enthalpies of solution at infinite dilution and limiting activity coefficients for the studied systems were measured experimentally. Enthalpies and Gibbs energies of hydrogen bonding of amines with neat methanol were determined. These values were found to be decreased compared with hydrogen bond energy in equimolar complexes 'methanol-amine' determined in inert solvent or base media. A linear dependence between enthalpies and Gibbs energies of hydrogen bonding of amines with neat methanol was observed. It was firstly revealed that the entropy of specific interactions of amines with neat methanol can be about zero or positive. Disruption of solvent-solvent hydrogen bonds can be regarded as the most important step during dissolution of amine in methanol. It was found that the cooperative effect influences on the Gibbs energies of hydrogen bonding of amines in methanol, but in a lesser extent than in aqueous solutions. The new results show that the hydrogen bonding process in the self-associated solvents differs significantly from equimolar complexation in aprotic media.

  8. A tensegrity model for hydrogen bond networks in proteins

    Directory of Open Access Journals (Sweden)

    Robert P. Bywater

    2017-05-01

    Full Text Available Hydrogen-bonding networks in proteins considered as structural tensile elements are in balance separately from any other stabilising interactions that may be in operation. The hydrogen bond arrangement in the network is reminiscent of tensegrity structures in architecture and sculpture. Tensegrity has been discussed before in cells and tissues and in proteins. In contrast to previous work only hydrogen bonds are studied here. The other interactions within proteins are either much stronger − covalent bonds connecting the atoms in the molecular skeleton or weaker forces like the so-called hydrophobic interactions. It has been demonstrated that the latter operate independently from hydrogen bonds. Each category of interaction must, if the protein is to have a stable structure, balance out. The hypothesis here is that the entire hydrogen bond network is in balance without any compensating contributions from other types of interaction. For sidechain-sidechain, sidechain-backbone and backbone-backbone hydrogen bonds in proteins, tensegrity balance (“closure” is required over the entire length of the polypeptide chain that defines individually folding units in globular proteins (“domains” as well as within the repeating elements in fibrous proteins that consist of extended chain structures. There is no closure to be found in extended structures that do not have repeating elements. This suggests an explanation as to why globular domains, as well as the repeat units in fibrous proteins, have to have a defined number of residues. Apart from networks of sidechain-sidechain hydrogen bonds there are certain key points at which this closure is achieved in the sidechain-backbone hydrogen bonds and these are associated with demarcation points at the start or end of stretches of secondary structure. Together, these three categories of hydrogen bond achieve the closure that is necessary for the stability of globular protein domains as well as repeating

  9. A tensegrity model for hydrogen bond networks in proteins.

    Science.gov (United States)

    Bywater, Robert P

    2017-05-01

    Hydrogen-bonding networks in proteins considered as structural tensile elements are in balance separately from any other stabilising interactions that may be in operation. The hydrogen bond arrangement in the network is reminiscent of tensegrity structures in architecture and sculpture. Tensegrity has been discussed before in cells and tissues and in proteins. In contrast to previous work only hydrogen bonds are studied here. The other interactions within proteins are either much stronger - covalent bonds connecting the atoms in the molecular skeleton or weaker forces like the so-called hydrophobic interactions. It has been demonstrated that the latter operate independently from hydrogen bonds. Each category of interaction must, if the protein is to have a stable structure, balance out. The hypothesis here is that the entire hydrogen bond network is in balance without any compensating contributions from other types of interaction. For sidechain-sidechain, sidechain-backbone and backbone-backbone hydrogen bonds in proteins, tensegrity balance ("closure") is required over the entire length of the polypeptide chain that defines individually folding units in globular proteins ("domains") as well as within the repeating elements in fibrous proteins that consist of extended chain structures. There is no closure to be found in extended structures that do not have repeating elements. This suggests an explanation as to why globular domains, as well as the repeat units in fibrous proteins, have to have a defined number of residues. Apart from networks of sidechain-sidechain hydrogen bonds there are certain key points at which this closure is achieved in the sidechain-backbone hydrogen bonds and these are associated with demarcation points at the start or end of stretches of secondary structure. Together, these three categories of hydrogen bond achieve the closure that is necessary for the stability of globular protein domains as well as repeating elements in fibrous proteins.

  10. Conserved water-mediated hydrogen bond network between TM-I, -II, -VI, and -VII in 7TM receptor activation

    DEFF Research Database (Denmark)

    Nygaard, Rie; Hansen, Louise Valentin; Mokrosinski, Jacek

    2010-01-01

    Five highly conserved polar residues connected by a number of structural water molecules together with two rotamer micro-switches, TrpVI:13 and TyrVII:20, constitute an extended hydrogen bond network between the intracellular segments of TM-I, -II, -VI, and -VII of 7TM receptors. Molecular dynamics...... to apparently function as a catching trap for water molecules. Mutational analysis of the beta2-adrenergic receptor demonstrated that the highly conserved polar residues of the hydrogen bond network were all important for receptor signaling but served different functions, some dampening constitutive activity...... (AsnI:18, AspII:10, and AsnVII:13), whereas others (AsnVII:12 and AsnVII:16) located one helical turn apart and sharing a water molecule were shown to be essential for agonist-induced signaling. It is concluded that the conserved water hydrogen bond network of 7TM receptors constitutes an extended...

  11. Direct {sup 13}C-detected NMR experiments for mapping and characterization of hydrogen bonds in RNA

    Energy Technology Data Exchange (ETDEWEB)

    Fürtig, Boris, E-mail: fuertig@nmr.uni-frankfurt.de; Schnieders, Robbin; Richter, Christian; Zetzsche, Heidi; Keyhani, Sara; Helmling, Christina [Johann Wolfgang Goethe Universität Frankfurt, Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology (Germany); Kovacs, Helena [Bruker BioSpin (Switzerland); Schwalbe, Harald, E-mail: schwalbe@nmr.uni-frankfurt.de [Johann Wolfgang Goethe Universität Frankfurt, Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology (Germany)

    2016-03-15

    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 {sup 1}H detection. Here, we develop {sup 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 {sup 13}C direct detection allows correlations of donor–acceptor pairs and the localization of hydrogen-bond acceptor nucleotides. The proposed {sup 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.

  12. Mechanism of conformational coupling in SecA: Key role of hydrogen-bonding networks and water interactions.

    Science.gov (United States)

    Milenkovic, Stefan; Bondar, Ana-Nicoleta

    2016-02-01

    SecA uses the energy yielded by the binding and hydrolysis of adenosine triphosphate (ATP) to push secretory pre-proteins across the plasma membrane in bacteria. Hydrolysis of ATP occurs at the nucleotide-binding site, which contains the conserved carboxylate groups of the DEAD-box helicases. Although crystal structures provide valuable snapshots of SecA along its reaction cycle, the mechanism that ensures conformational coupling between the nucleotide-binding site and the other domains of SecA remains unclear. The observation that SecA contains numerous hydrogen-bonding groups raises important questions about the role of hydrogen-bonding networks and hydrogen-bond dynamics in long-distance conformational couplings. To address these questions, we explored the molecular dynamics of SecA from three different organisms, with and without bound nucleotide, in water. By computing two-dimensional hydrogen-bonding maps we identify networks of hydrogen bonds that connect the nucleotide-binding site to remote regions of the protein, and sites in the protein that respond to specific perturbations. We find that the nucleotide-binding site of ADP-bound SecA has a preferred geometry whereby the first two carboxylates of the DEAD motif bridge via hydrogen-bonding water. Simulations of a mutant with perturbed ATP hydrolysis highlight the water-bridged geometry as a key structural element of the reaction path. Copyright © 2015. Published by Elsevier B.V.

  13. Local electronic and geometrical structures of hydrogen-bonded complexes studied by soft X-ray spectroscopy

    International Nuclear Information System (INIS)

    Luo, Y.

    2004-01-01

    Full text: The hydrogen bond is one of the most important forms of intermolecular interactions. It occurs in all-important components of life. However, the electronic structures of hydrogen-bonded complexes in liquid phases have long been difficult to determine due to the lack of proper experimental techniques. In this talk, a recent joint theoretical and experimental effort to understand hydrogen bonding in liquid water and alcohol/water mixtures using synchrotron radiation based soft-X-ray spectroscopy will be presented. The complexity of the liquid systems has made it impossible to interpret the spectra with physical intuition alone. Theoretical simulations have thus played an essential role in understanding the spectra and providing valuable insights on the local geometrical and electronic structures of these liquids. Our study sheds light on a 40-year controversy over what kinds of molecular structures are formed in pure liquid methanol. It also suggests an explanation for the well-known puzzle of why alcohol and water do not mix completely: the system must balance nature's tendency toward greater disorder (entropy) with the molecules' tendency to form hydrogen bonds. The observation of electron sharing and broken hydrogen bonding local structures in liquid water will be presented. The possible use of X-ray spectroscopy to determinate the local arrangements of hydrogen-bonded nanostructures will also been discussed

  14. Optical modulation in nematic phase of halogen substituted hydrogen bonded liquid crystals

    Science.gov (United States)

    Vijayakumar, V. N.; Madhu Mohan, M. L. N.

    2012-01-01

    A series of halogen-substituted hydrogen-bonded liquid crystalline complexes have been designed and synthesised. A successful attempt has been made to form complementary hydrogen bonding between the dodecyloxy benzoic acid (12BAO) and halogen-substituted benzoic acids and the physical properties exhibited by the individual complexes are studied. The complexes obtained are analysed by polarising optical microscope (POM), differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FTIR) and dielectric studies. The formation of complementary hydrogen bond is confirmed through FTIR spectra. An interesting feature of this series is the observation of a field-induced transition (FiT) in nematic phase. Another interesting phenomenon is the observation of a new smectic X phase (worm-like texture) in all the synthesised complexes. Dielectric relaxation studies in the smectic C phase of these hydrogen bonded complexes along with the Arrhenius and the Cole-Cole plots are discussed. Optical tilt angle in smectic C phase and the corresponding fitted data analysis concur with the Mean field theory prediction.

  15. The Nature of the Hydrogen Bond Outline of a Comprehensive Hydrogen Bond Theory

    CERN Document Server

    Gilli, Gastone

    2009-01-01

    Hydrogen bond (H-bond) effects are known: it makes sea water liquid, joins cellulose microfibrils in trees, shapes DNA into genes and polypeptide chains into wool, hair, muscles or enzymes. Its true nature is less known and we may still wonder why O-H...O bond energies range from less than 1 to more than 30 kcal/mol without apparent reason. This H-bond puzzle is re-examined here from its very beginning and presented as an inclusive compilation of experimental H-bond energies andgeometries.New concepts emerge from this analysis: new classes of systematically strong H-bonds (CAHBs and RAHBs: cha

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

    Energy Technology Data Exchange (ETDEWEB)

    Lam, Royce K.; Smith, Jacob W.; Saykally, Richard J., E-mail: saykally@berkeley.edu [Department of Chemistry, University of California, Berkeley, California 94720, USA and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    2016-05-21

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

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

    Science.gov (United States)

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

    2016-05-01

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

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

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

    Science.gov (United States)

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

    2017-01-04

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

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

    Directory of Open Access Journals (Sweden)

    Malose Jack Mphahlele

    2017-01-01

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

  1. Effects of dimethyl sulfoxide on the hydrogen bonding structure and ...

    Indian Academy of Sciences (India)

    School of Basic Sciences, Indian Institute of Technology, Bhubaneswar 751 013, India e-mail: .... molecules are modeled by the 4-site P2 model of Luzar and Chandler9 which ..... lifetime of hydrogen bond acceptance by carbonyl oxy-.

  2. Probing hydrogen bonding interactions and proton transfer in proteins

    Science.gov (United States)

    Nie, Beining

    Scope and method of study. Hydrogen bonding is a fundamental element in protein structure and function. Breaking a single hydrogen bond may impair the stability of a protein. It is therefore important to probe dynamic changes in hydrogen bonding interactions during protein folding and function. Time-resolved Fourier transform infrared spectroscopy is highly sensitive to hydrogen bonding interactions. However, it lacks quantitative correlation between the vibrational frequencies and the number, type, and strength of hydrogen bonding interactions of ionizable and polar residues. We employ quantum physics theory based ab initio calculations to study the effects of hydrogen bonding interactions on vibrational frequencies of Asp, Glu, and Tyr residues and to develop vibrational spectral markers for probing hydrogen bonding interactions using infrared spectroscopy. In addition, proton transfer process plays a crucial role in a wide range of energy transduction, signal transduction, and enzymatic reactions. We study the structural basis for proton transfer using photoactive yellow protein as an excellent model system. Molecular dynamics simulation is employed to investigate the structures of early intermediate states. Quantum theory based ab initio calculations are used to study the impact of hydrogen bond interactions on proton affinity and proton transfer. Findings and conclusions. Our extensive density function theory based calculations provide rich structural, spectral, and energetic information on hydrogen bonding properties of protonated side chain groups of Asp/Glu and Tyr. We developed vibrational spectral markers and 2D FTIR spectroscopy for structural characterization on the number and the type of hydrogen bonding interactions of the COOH group of Asp/Glu and neutral phenolic group of Tyr. These developments greatly enhance the power of time-resolved FTIR spectroscopy as a major experimental tool for structural characterization of functionally important

  3. Amide proton temperature coefficients as hydrogen bond indicators in proteins

    International Nuclear Information System (INIS)

    Cierpicki, Tomasz; Otlewski, Jacek

    2001-01-01

    Correlations between amide proton temperature coefficients (Δσ HN /ΔT) and hydrogen bonds were investigated for a data set of 793 amides derived from 14 proteins. For amide protons showing temperature gradients more positive than -4.6 ppb/K there is a hydrogen bond predictivity value exceeding 85%. It increases to over 93% for amides within the range between -4 and -1 ppb/K. Detailed analysis shows an inverse proportionality between amide proton temperature coefficients and hydrogen bond lengths. Furthermore, for hydrogen bonds of similar bond lengths, values of temperature gradients in α-helices are on average 1 ppb/K more negative than in β-sheets. In consequence, a number of amide protons in α-helices involved in hydrogen bonds shorter than 2 A show Δσ HN /ΔT 10 helices and 98% in β-turns have temperature coefficients more positive than -4.6ppb/K. Ring current effect also significantly influences temperature coefficients of amide protons. In seven out of eight cases non-hydrogen bonded amides strongly deshielded by neighboring aromatic rings show temperature coefficients more positive than -2 ppb/K. In general, amide proton temperature gradients do not change with pH unless they correspond to conformational changes. Three examples of pH dependent equilibrium showing hydrogen bond formation at higher pH were found. In conclusion, amide proton temperature coefficients offer an attractive and simple way to confirm existence of hydrogen bonds in NMR determined structures

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

    OpenAIRE

    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-...

  5. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    Directory of Open Access Journals (Sweden)

    Peter I. Nagy

    2014-10-01

    Full Text Available 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.

  6. Hydrogen bonded nonlinear optical γ-glycine: Crystal growth and characterization

    Science.gov (United States)

    Narayana Moolya, B.; Jayarama, A.; Sureshkumar, M. R.; Dharmaprakash, S. M.

    2005-07-01

    Single crystals of γ-glycine(GG) were grown by solvent evaporation technique from a mixture of aqueous solutions of glycine and ammonium nitrate at ambient temperature. X-ray diffraction, thermogravimetric/differential thermal analysis, Fourier transform infrared spectral techniques were employed to characterize the crystal. The lattice parameters were calculated and they agree well with the reported values. GG exists as dipolar ions in which the carboxyl group is present as a carboxylate ion and the amino group as an ammonium ion. Due to this dipolar nature, glycine has a high decomposition temperature. The UV cutoff of GG is below 300 nm and has a wide transparency window, which is suitable for second harmonic generation of laser in the blue region. Nonlinear optical characteristics of GG were studied using Q switched Nd:YAG laser ( λ=1064 nm). The second harmonic generation conversion efficiency of GG is 1.5 times that of potassium dihydrogen phosphate . The X-ray diffraction and Fourier transform infrared spectral studies show the presence of strong hydrogen bonds which create and stabilize the crystal structure in GG. The main contributions to the nonlinear optical properties in GG results from the presence of the hydrogen bond and from the vibrational part due to very intense infrared bands of the hydrogen bond vibrations. GG is thermally stable up to 441 K.

  7. Discrete kink dynamics in hydrogen-bonded chains: The two-component model

    DEFF Research Database (Denmark)

    Karpan, V.M.; Zolotaryuk, Yaroslav; Christiansen, Peter Leth

    2004-01-01

    We study discrete topological solitary waves (kinks and antikinks) in two nonlinear diatomic chain models that describe the collective dynamics of proton transfers in one-dimensional hydrogen-bonded networks. The essential ingredients of the models are (i) a realistic (anharmonic) ion-proton inte......We study discrete topological solitary waves (kinks and antikinks) in two nonlinear diatomic chain models that describe the collective dynamics of proton transfers in one-dimensional hydrogen-bonded networks. The essential ingredients of the models are (i) a realistic (anharmonic) ion...... chain subject to a substrate with two optical bands), both providing a bistability of the hydrogen-bonded proton. Exact two-component (kink and antikink) discrete solutions for these models are found numerically. We compare the soliton solutions and their properties in both the one- (when the heavy ions...... principal differences, like a significant difference in the stability switchings behavior for the kinks and the antikinks. Water-filled carbon nanotubes are briefly discussed as possible realistic systems, where topological discrete (anti)kink states might exist....

  8. FTIR study of hydrogen bonding interaction between fluorinated alcohol and unsaturated esters

    Science.gov (United States)

    Sheng, Xia; Jiang, Xiaotong; Zhao, Hailiang; Wan, Dongjin; Liu, Yongde; Ngwenya, Cleopatra Ashley; Du, Lin

    2018-06-01

    The 1:1 complexes of two unsaturated esters with 2,2,2-trifluoroethanol (TFE) were investigated experimentally and computationally. The experimental observations of the spectral shifts of the OH-stretching vibrational transitions were obtained at 113 cm-1 for TFE-methyl acrylate (MA) and 92 cm-1 for TFE-vinyl acetate (VA). There are three docking sites in the two unsaturated esters for the incoming TFE. The predicted red shifts of the OH-stretching vibrational transitions were found to be larger for the Osbnd H⋯Odbnd C hydrogen bonded conformer than those for the Osbnd H⋯π and Osbnd H⋯O ones. The binding energies further prove that the Osbnd H⋯Odbnd C hydrogen bonded conformers are the most stable ones. On the basis of the DFT calculations as well as previous works, the carbonyl group is the best docking site for TFE. Furthermore, the thermodynamic equilibrium constants of TFE-MA and TFE-VA were obtained at 0.28 and 0.15 by combining the experimental spectra data and the DFT calculations. Consequently, the Gibbs free energies of formation were determined to be 3.2 and 4.8 kJ mol-1 for TFE-MA and TFE-VA, respectively. The quantum theory of atoms in molecules (AIM) and generalized Kohn-Sham energy decomposition analysis (GKS-EDA) were carried out for further characterization of the hydrogen bonding interactions. GKS-EDA shows an "electrostatic" dominated hydrogen bonding character for the Osbnd H⋯Odbnd C hydrogen bonds.

  9. Phosphatidic acid: an electrostatic/hydrogen-bond switch?

    NARCIS (Netherlands)

    Kooijman, E.E.; Testerink, C.; Munnik, T.

    2010-01-01

    Phosphatidic acid (PA) has been shown to be an important bioactive lipid that is specifically recognized by various proteins. As such, it plays a crucial role in cellular signaling in all eukaryotes. An important determinant for PA’s role in its diverse functions is its anionic headgroup that

  10. Ultrafast dynamics of hydrogen bond exchange in aqueous ionic solutions.

    Science.gov (United States)

    Park, Sungnam; Odelius, Michael; Gaffney, Kelly J

    2009-06-04

    The structural and dynamical properties of aqueous ionic solutions influence a wide range of natural and biological processes. In these solutions, water has the opportunity to form hydrogen bonds with other water molecules and anions. Knowing the time scale with which these configurations interconvert represents a key factor to understanding the influence of molecular scale heterogeneity on chemical events in aqueous ionic solutions. We have used ultrafast IR spectroscopy and Car-Parrinello molecular dynamics (CPMD) simulations to investigate the hydrogen bond (H-bond) structural dynamics in aqueous 6 M sodium perchlorate (NaClO4) solution. We have measured the H-bond exchange dynamics between spectrally distinct water-water and water-anion H-bond configurations with 2DIR spectroscopy and the orientational relaxation dynamics of water molecules in different H-bond configurations with polarization-selective IR pump-probe experiments. The experimental H-bond exchange time correlates strongly with the experimental orientational relaxation time of water molecules. This agrees with prior observations in water and aqueous halide solutions, and has been interpreted within the context of an orientational jump model for the H-bond exchange. The CPMD simulations performed on aqueous 6 M NaClO4 solution clearly demonstrate that water molecules organize into two radially and angularly distinct structural subshells within the first solvation shell of the perchlorate anion, with one subshell possessing the majority of the water molecules that donate H-bonds to perchlorate anions and the other subshell possessing predominantly water molecules that donate two H-bonds to other water molecules. Due to the high ionic concentration used in the simulations, essentially all water molecules reside in the first ionic solvation shells. The CPMD simulations also demonstrate that the molecular exchange between these two structurally distinct subshells proceeds more slowly than the H

  11. Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design.

    Science.gov (United States)

    Maguire, Jack B; Boyken, Scott E; Baker, David; Kuhlman, Brian

    2018-05-08

    Hydrogen bond networks play a critical role in determining the stability and specificity of biomolecular complexes, and the ability to design such networks is important for engineering novel structures, interactions, and enzymes. One key feature of hydrogen bond networks that makes them difficult to rationally engineer is that they are highly cooperative and are not energetically favorable until the hydrogen bonding potential has been satisfied for all buried polar groups in the network. Existing computational methods for protein design are ill-equipped for creating these highly cooperative networks because they rely on energy functions and sampling strategies that are focused on pairwise interactions. To enable the design of complex hydrogen bond networks, we have developed a new sampling protocol in the molecular modeling program Rosetta that explicitly searches for sets of amino acid mutations that can form self-contained hydrogen bond networks. For a given set of designable residues, the protocol often identifies many alternative sets of mutations/networks, and we show that it can readily be applied to large sets of residues at protein-protein interfaces or in the interior of proteins. The protocol builds on a recently developed method in Rosetta for designing hydrogen bond networks that has been experimentally validated for small symmetric systems but was not extensible to many larger protein structures and complexes. The sampling protocol we describe here not only recapitulates previously validated designs with performance improvements but also yields viable hydrogen bond networks for cases where the previous method fails, such as the design of large, asymmetric interfaces relevant to engineering protein-based therapeutics.

  12. Short hydrogen bonds in the catalytic mechanism of serine proteases

    Directory of Open Access Journals (Sweden)

    VLADIMIR LESKOVAC

    2008-04-01

    Full Text Available The survey of crystallographic data from the Protein Data Bank for 37 structures of trypsin and other serine proteases at a resolution of 0.78–1.28 Å revealed the presence of hydrogen bonds in the active site of the enzymes, which are formed between the catalytic histidine and aspartate residues and are on average 2.7 Å long. This is the typical bond length for normal hydrogen bonds. The geometric properties of the hydrogen bonds in the active site indicate that the H atom is not centered between the heteroatoms of the catalytic histidine and aspartate residues in the active site. Taken together, these findings exclude the possibility that short “low-barrier” hydrogen bonds are formed in the ground state structure of the active sites examined in this work. Some time ago, it was suggested by Cleland that the “low-barrier hydrogen bond” hypothesis is operative in the catalytic mechanism of serine proteases, and requires the presence of short hydrogen bonds around 2.4 Å long in the active site, with the H atom centered between the catalytic heteroatoms. The conclusions drawn from this work do not exclude the validity of the “low-barrier hydrogen bond” hypothesis at all, but they merely do not support it in this particular case, with this particular class of enzymes.

  13. Hydrogen bonding characterization in water and small molecules

    Science.gov (United States)

    Silvestrelli, Pier Luigi

    2017-06-01

    The prototypical hydrogen bond in water dimer and hydrogen bonds in the protonated water dimer, in other small molecules, in water cyclic clusters, and in ice, covering a wide range of bond strengths, are theoretically investigated by first-principles calculations based on density functional theory, considering not only a standard generalized gradient approximation functional but also, for the water dimer, hybrid and van der Waals corrected functionals. We compute structural, energetic, and electrostatic (induced molecular dipole moments) properties. In particular, hydrogen bonds are characterized in terms of differential electron density distributions and profiles, and of the shifts of the centres of maximally localized Wannier functions. The information from the latter quantities can be conveyed to a single geometric bonding parameter that appears to be correlated with the Mayer bond order parameter and can be taken as an estimate of the covalent contribution to the hydrogen bond. By considering the water trimer, the cyclic water hexamer, and the hexagonal phase of ice, we also elucidate the importance of cooperative/anticooperative effects in hydrogen-bonding formation.

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

    Science.gov (United States)

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

    2014-05-01

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

  15. Vibrational signatures of cation-anion hydrogen bonding in ionic liquids: a periodic density functional theory and molecular dynamics study.

    Science.gov (United States)

    Mondal, Anirban; Balasubramanian, Sundaram

    2015-02-05

    Hydrogen bonding in alkylammonium based protic ionic liquids was studied using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. Normal-mode analysis within the harmonic approximation and power spectra of velocity autocorrelation functions were used as tools to obtain the vibrational spectra in both the gas phase and the crystalline phases of these protic ionic liquids. The hydrogen bond vibrational modes were identified in the 150-240 cm(-1) region of the far-infrared (far-IR) spectra. A blue shift in the far-IR mode was observed with an increasing number of hydrogen-bonding sites on the cation; the exact peak position is modulated by the cation-anion hydrogen bond strength. Sub-100 cm(-1) bands in the far-IR spectrum are assigned to the rattling motion of the anions. Calculated NMR chemical shifts of the acidic protons in the crystalline phase of these salts also exhibit the signature of cation-anion hydrogen bonding.

  16. Cocrystals of 6-propyl-2-thiouracil: N-H···O versus N-H···S hydrogen bonds.

    Science.gov (United States)

    Tutughamiarso, Maya; Egert, Ernst

    2011-11-01

    In order to investigate the relative stability of N-H···O and N-H···S hydrogen bonds, we cocrystallized the antithyroid drug 6-propyl-2-thiouracil with two complementary heterocycles. In the cocrystal pyrimidin-2-amine-6-propyl-2-thiouracil (1/2), C(4)H(5)N(3)·2C(7)H(10)N(2)OS, (I), the `base pair' is connected by one N-H···S and one N-H···N hydrogen bond. Homodimers of 6-propyl-2-thiouracil linked by two N-H···S hydrogen bonds are observed in the cocrystal N-(6-acetamidopyridin-2-yl)acetamide-6-propyl-2-thiouracil (1/2), C(9)H(11)N(3)O(2)·2C(7)H(10)N(2)OS, (II). The crystal structure of 6-propyl-2-thiouracil itself, C(7)H(10)N(2)OS, (III), is stabilized by pairwise N-H···O and N-H···S hydrogen bonds. In all three structures, N-H···S hydrogen bonds occur only within R(2)(2)(8) patterns, whereas N-H···O hydrogen bonds tend to connect the homo- and heterodimers into extended networks. In agreement with related structures, the hydrogen-bonding capability of C=O and C=S groups seems to be comparable.

  17. Reassigning hydrogen-bond centering in dense ice

    International Nuclear Information System (INIS)

    Benoit, Magali; Romero, Aldo H.; Marx, Dominik

    2002-01-01

    Hydrogen bonds in H 2 O ice change dramatically upon compression. Thereby a hydrogen-bonded molecular crystal, ice VII, is transformed to an atomic crystal, ice X. Car-Parrinello simulations reproduce the features of the x-ray diffraction spectra up to about 170 GPa but allow for analysis in real space. Starting from molecular ice VII with static orientational disorder, dynamical translational disordering occurs first via creation of ionic defects, which results in a systematic violation of the ice rules. As a second step, the transformation to an atomic solid and thus hydrogen-bond centering occurs around 110 GPa at 300 K and no novel phase is found up to at least 170 GPa

  18. Trimeric Hydrogen Bond in Geometrically Frustrated Hydroxyl Cobalt Halogenides

    International Nuclear Information System (INIS)

    Xiao-Dong, Liu; Masato, Hagihala; Xu-Guang, Zheng; Dong-Dong, Meng; Wan-Jun, Tao; Sen-Lin, Zhang; Qi-Xin, Guo

    2011-01-01

    The mid-infrared absorption spectra of geometrically frustrated hydroxyl cobalt halogenides Co 2 (OH) 3 Cl and Co 2 (OH) 3 Br are measured by FTIR spectrometers, and the stretching vibrational modes of hydroxyl groups are found to be 3549cm −1 and 3524cm −1 respectively. Through finding their true terminal O-H group stretching vibration frequencies, we obtain 107cm −1 and 99cm −1 red shift caused by the corresponding O-H···Cl and O-H···Br hydrogen bonds. Rarely reported trimeric hydrogen bonds (Co 3 ≡O-H) 3 ···Cl/Br are pointed out to demonstrate the relative weakness of this kind of hydrogen bond which may have a critical effect on the lattice symmetry and magnetic structures. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  19. Alkyl Radicals as Hydrogen Bond Acceptors: Computational Evidence

    DEFF Research Database (Denmark)

    Hammerum, Steen

    2009-01-01

    Spectroscopic, energetic and structural information obtained by DFT and G3-type computational studies demonstrates that charged proton donors can form moderately strong hydrogen bonds to simple alkyl radicals. The presence of these bonds stabilizes the adducts and modifies their structure......, and gives rise to pronounced shifts of IR stretching frequencies and to increased absorption intensities. The hydrogen bond acceptor properties of alkyl radicals equal those of many conventional acceptors, e.g., the bond length changes and IR red-shifts suggest that tert-butyl radicals are slightly better...... acceptors than formaldehyde molecules, while propyl radicals are as good as H2O. The hydrogen bond strength appears to depend on the proton affinity of the proton donor and on the ionization energy of the acceptor alkyl radical, not on the donor-acceptor proton affinity difference, reflecting...

  20. Positively charged phosphorus as a hydrogen bond acceptor

    DEFF Research Database (Denmark)

    Hansen, Anne Schou; Du, Lin; Kjærgaard, Henrik Grum

    2014-01-01

    Phosphorus (P) is an element that is essential to the life of all organisms, and the atmospheric detection of phosphine suggests the existence of a volatile biogeochemical P cycle. Here, we investigate the ability of P to participate in the formation of OH···P hydrogen bonds. Three bimolecular......-stretching frequency red shifts and quantum chemical calculations, we find that P is an acceptor atom similar in strength to O and S and that all three P, O, and S atoms are weaker acceptors than N. The quantum chemical calculations show that both H and P in the OH···P hydrogen bond have partial positive charges......, as expected from their electronegativities. However, the electrostatic potentials show a negative potential area on the electron density surface around P that facilitates formation of hydrogen bonds....

  1. [Cleavage time for a hydrogen bond under a load].

    Science.gov (United States)

    Bespalov, S V; Tolpygo, K B

    1993-01-01

    Statistics of the hydrogen bond formation and break in a bundle of actin and myosin filaments realizing the attractive force in the sarcomere of a muscle is studied. Purely mechanical problem of the attractive-force formation and motion of myosin heads and action globules under their action is supplemented by accounting for the irreversible processes: 1. Thermal de-excitation of the latter in the chain of hydrogen bond during the elementary act of the ATP energy use resulting in fixing the extended actin filament. 2. Break of the hydrogen bonds, realizing this fixing, due to thermal fluctuations for the time tau. The average life-time turns out to be the order of time necessary for the movement of z-membrane sarcomere for the value of action filament extension delta 1, which is necessary for the process of muscle contraction to be continued.

  2. Evidence of quantum correlations in the H/D-transfer dynamics in the hydrogen bonds in partially deuterated benzoic acid crystals

    Science.gov (United States)

    Takeda, Sadamu; Tsuzumitani, Akihiko; Chatzidimitriou-Dreismann, C. A.

    1992-10-01

    A precise investigation of spin—lattice relaxation rates for protons and deuterons of partially deuterated benzoic acid crystals showed a remarkable quenching of the transfer rate of an HD pair in hydrogen-bonded dimeric units of carboxyl groups with increasing concentration of D in the surrounding hydrogen bonds. A similar effect was also observed for partially deuterated crystals of acetylenedicarboxylic acid. This finding supports recent theoretical predictions of thermally activated protonic quantum correlation in condensed matter and proposes a new mechanism for the proton transfer in hydrogen bonds in condensed matter.

  3. Role of hydrogen bonds in the reaction mechanism of chalcone isomerase.

    Science.gov (United States)

    Jez, Joseph M; Bowman, Marianne E; Noel, Joseph P

    2002-04-23

    In flavonoid, isoflavonoid, and anthocyanin biosynthesis, chalcone isomerase (CHI) catalyzes the intramolecular cyclization of chalcones into (S)-flavanones with a second-order rate constant that approaches the diffusion-controlled limit. The three-dimensional structures of alfalfa CHI complexed with different flavanones indicate that two sets of hydrogen bonds may possess critical roles in catalysis. The first set of interactions includes two conserved amino acids (Thr48 and Tyr106) that mediate a hydrogen bond network with two active site water molecules. The second set of hydrogen bonds occurs between the flavanone 7-hydroxyl group and two active site residues (Asn113 and Thr190). Comparison of the steady-state kinetic parameters of wild-type and mutant CHIs demonstrates that efficient cyclization of various chalcones into their respective flavanones requires both sets of contacts. For example, the T48A, T48S, Y106F, N113A, and T190A mutants exhibit 1550-, 3-, 30-, 7-, and 6-fold reductions in k(cat) and 2-3-fold changes in K(m) with 4,2',4'-trihydroxychalcone as a substrate. Kinetic comparisons of the pH-dependence of the reactions catalyzed by wild-type and mutant enzymes indicate that the active site hydrogen bonds contributed by these four residues do not significantly alter the pK(a) of the intramolecular cyclization reaction. Determinations of solvent kinetic isotope and solvent viscosity effects for wild-type and mutant enzymes reveal a change from a diffusion-controlled reaction to one limited by chemistry in the T48A and Y106F mutants. The X-ray crystal structures of the T48A and Y106F mutants support the assertion that the observed kinetic effects result from the loss of key hydrogen bonds at the CHI active site. Our results are consistent with a reaction mechanism for CHI in which Thr48 polarizes the ketone of the substrate and Tyr106 stabilizes a key catalytic water molecule. Hydrogen bonds contributed by Asn113 and Thr190 provide additional

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

    Science.gov (United States)

    Koenig, S; Müller, L; Smith, D K

    2001-03-02

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

  5. Ultrafast Hydrogen-Bonding Dynamics in Amyloid Fibrils.

    Science.gov (United States)

    Pazos, Ileana M; Ma, Jianqiang; Mukherjee, Debopreeti; Gai, Feng

    2018-06-08

    While there are many studies on the subject of hydrogen bonding dynamics in biological systems, few, if any, have investigated this fundamental process in amyloid fibrils. Herein, we seek to add insight into this topic by assessing the dynamics of a hydrogen bond buried in the dry interface of amyloid fibrils. To prepare a suitable model peptide system for this purpose, we introduce two mutations into the amyloid-forming Aβ(16-22) peptide. The first one is a lysine analog at position 19, which is used to help form structurally homogeneous fibrils, and the second one is an aspartic acid derivative (DM) at position 17, which is intended (1) to be used as a site-specific infrared probe and (2) to serve as a hydrogen-bond acceptor to lysine so that an inter-β-sheet hydrogen bond can be formed in the fibrils. Using both infrared spectroscopy and atomic force microscopy, we show that (1) this mutant peptide indeed forms well defined fibrils, (2) when bulk solvent is removed, there is no detectable water present in the fibrils, (3) infrared results obtained with the DM probe are consistent with a protofibril structure that is composed of two antiparallel β-sheets stacked in a parallel fashion, leading to formation of the expected hydrogen bond. Using two-dimensional infrared spectroscopy, we further show that the dynamics of this hydrogen bond occur on a timescale of ~2.3 ps, which is attributed to the rapid rotation of the -NH3+ group of lysine around its Cε-Nζ bond. Taken together, these results suggest that (1) DM is a useful infrared marker in facilitating structure determination of amyloid fibrils and (2) even in the tightly packed core of amyloid fibrils certain amino acid sidechains can undergo ultrafast motions, hence contributing to the thermodynamic stability of the system.

  6. Infrared matrix isolation study of hydrogen bonds involving C-H bonds: Substituent effects

    International Nuclear Information System (INIS)

    Jeng, M.L.H.; Ault, B.S.

    1989-01-01

    The matrix isolation technique combined with infrared spectroscopy has been employed to isolate and characterize hydrogen-bonded complexes between a series of substituted alkynes and several oxygen and nitrogen bases. Distinct evidence for hydrogen bond formation was observed in each case, with a characteristic red shift of the hydrogen stretching motion ν r . Shifts between 100 and 300 cm -1 were observed, the largest being for the complex of CF 3 CCH with (CH 3 ) 3 N. The perturbed carbon-carbon triple bond stretching vibration was observed for most complexes, as was the alkynic hydrogen bending motion. Attempts were made to correlate the magnitude of the red shift of ν s with substituent constants for the different substituted alkynes; a roughly linear correlation was found with the Hammett σ parameter. Lack of correlation Δν s with either σ 1 or σ R alone suggests that both inductive and resonance contributions to the strength of the hydrogen-bonding interaction are important

  7. Hydrogen bonding in protic ionic liquids: structural correlations, vibrational spectroscopy, and rotational dynamics of liquid ethylammonium nitrate

    Science.gov (United States)

    Zentel, Tobias; Overbeck, Viviane; Michalik, Dirk; Kühn, Oliver; Ludwig, Ralf

    2018-02-01

    The properties of the hydrogen bonds in ethylammonium nitrate (EAN) are analyzed by using molecular dynamics simulations and infrared as well as nuclear magnetic resonance experiments. EAN features a flexible three-dimensional network of hydrogen bonds with moderate strengths, which makes it distinct from related triethylammonium-based ionic liquids. First, the network’s flexibility is manifested in a not very pronounced correlation of the hydrogen bond geometries, which is caused by rapid interchanges of bonding partners. The large flexibility of the network also leads to a substantial broadening of the mid-IR absorption band, with the contributions due to N-H stretching motions ranging from 2800 to 3250 cm-1. Finally, the different dynamics are also seen in the rotational correlation of the N-H bond vector, where a correlation time as short as 16.1 ps is observed.

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

    Science.gov (United States)

    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.

  9. Supramolecular materials based on hydrogen-bonded polymers

    NARCIS (Netherlands)

    ten Brinke, Gerrit; Ruokolainen, Janne; Ikkala, Olli; Binder, W

    2007-01-01

    Combining supramolecular principles with block copolymer self-assembly offers unique possibilities to create materials with responsive and/or tunable properties. The present chapter focuses on supramolecular materials based on hydrogen bonding and (block co-) polymers. Several cases will be

  10. Watson-Crick hydrogen bonding of unlocked nucleic acids

    DEFF Research Database (Denmark)

    Langkjær, Niels; Wengel, Jesper; Pasternak, Anna

    2015-01-01

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

  11. Binding of reactive organophosphate by oximes via hydrogen bond

    Indian Academy of Sciences (India)

    In this contribution, the ability of simple oximes to bind a well-known nerve agent simulant (dimethylmethylphosphonate, DMMP) via hydrogen bond is reported. UV/Vis measurements indicate the formation of 1:1 complexes. 1H-, 31P-NMR titrations and T-ROESY experiments confirm that oximes bind the organophosphate ...

  12. Formation of a hydrogen-bonded barbiturate [2]-rotaxane.

    Science.gov (United States)

    Tron, Arnaud; Thornton, Peter J; Rocher, Mathias; Jacquot de Rouville, Henri-Pierre; Desvergne, Jean-Pierre; Kauffmann, Brice; Buffeteau, Thierry; Cavagnat, Dominique; Tucker, James H R; McClenaghan, Nathan D

    2014-03-07

    Interlocked structures containing the classic Hamilton barbiturate binding motif comprising two 2,6-diamidopyridine units are reported for the first time. Stable [2]-rotaxanes can be accessed either through hydrogen-bonded preorganization by a barbiturate thread followed by a Cu(+)-catalyzed "click" stoppering reaction or by a Cu(2+)-mediated Glaser homocoupling reaction.

  13. thermodynamic stability of hydrogen-bonded nanostructures: a calorimetric study

    NARCIS (Netherlands)

    ten Cate, M.G.J.; Huskens, Jurriaan; Crego Calama, Mercedes; Reinhoudt, David

    2004-01-01

    The self-assembly of hydrogen-bonded aggregates (rosettes) in solvent mixtures of different polarity has been studied by calorimetry. The C50 parameter, the concentration when 50 % of the components are incorporated in the assembly, is used to compare assemblies with different stoichiometry. C50 for

  14. Controlling the amplification of chirality in hydrogen-bonded assemblies

    NARCIS (Netherlands)

    Mateos timoneda, Miguel; Crego Calama, Mercedes; Reinhoudt, David

    2005-01-01

    The amplification of chirality (a high enantiomeric or diastereomeric excess induced by a small initial amount of chiral bias) on hydrogen-bonded assemblies has been studied using “sergeants-and-soldiers” experiments under thermodynamically controlled conditions. Here it is shown that different

  15. Amplification of Chirality in Hydrogen-Bonded Tetrarosette Helices

    NARCIS (Netherlands)

    Mateos timoneda, Miguel; Crego Calama, Mercedes; Reinhoudt, David

    2006-01-01

    The amplification of chirality in hydrogen-bonded tetrarosette assemblies under thermodynamic equilibrium is described. The extent of the chiral amplification obtained by means of “sergeants-and-soldiers” experiments depends only on the structure of the assembly and it is independent of the

  16. Hydrogen Bonding in Phosphine Oxide/Phosphate-Phenol Complexes

    NARCIS (Netherlands)

    Cuypers, R.; Sudhölter, E.J.R.; Zuilhof, H.

    2010-01-01

    To develop a new solvent-impregnated resin (SIR) system for the removal of phenols and thiophenols from water, complex formation by hydrogen bonding of phosphine oxides and phosphates is studied using isothermal titration calorimetry (ITC) and quantum chemical modeling. Six different computational

  17. Effects of ion concentration on the hydrogen bonded structure of ...

    Indian Academy of Sciences (India)

    WINTEC

    Effects of ion concentration on the hydrogen bonded structure of water in the vicinity of ions in aqueous NaCl solutions. A NAG. 1. , D CHAKRABORTY and A CHANDRA*. Department of Chemistry, Indian Institute of Technology, Kanpur 208 016. 1. Present address: Department of Chemistry and Chemical Engineering,.

  18. OH stretching frequencies in systems with intramolecular hydrogen bonds

    DEFF Research Database (Denmark)

    Spanget-Larsen, Jens; Hansen, Bjarke Knud Vilster; Hansen, Poul Erik

    2011-01-01

    OH stretching wavenumbers were investigated for 30 species with intramolecularly hydrogen bonded hydroxyl groups, covering the range from 3600 to ca. 1900 cm-1. Theoretical wavenumbers were predicted with B3LYP/6-31G(d) density functional theory using the standard harmonic approximation, as well...

  19. Polarization-induced sigma-holes and hydrogen bonding

    Czech Academy of Sciences Publication Activity Database

    Hennemann, M.; Murray, J. S.; Politzer, P.; Riley, Kevin Eugene; Clark, T.

    2012-01-01

    Roč. 18, č. 6 (2012), s. 2461-2469 ISSN 1610-2940 Institutional research plan: CEZ:AV0Z40550506 Keywords : hydrogen bond * sigma-hole * polarization * field effect * ab initio calculation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.984, year: 2012

  20. Defining the hydrogen bond: An account (IUPAC Technical Report)

    Czech Academy of Sciences Publication Activity Database

    Arunan, E.; Desiraju, G. R.; Klein, R. A.; Sadlej, J.; Scheiner, S.; Alkorta, I.; Clary, D. C.; Crabtree, R. H.; Dannenberg, J. J.; Hobza, Pavel; Kjaergaard, H. G.; Legon, A. C.; Mennucci, B.; Nesbitt, D. J.

    2011-01-01

    Roč. 83, č. 8 (2011), s. 1619-1636 ISSN 0033-4545 Institutional research plan: CEZ:AV0Z40550506 Keywords : bonding * electrostatic interactions * hydrogen bonding * molecular interactions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.789, year: 2011

  1. Polyamides : hydrogen bonding, the Brill transition, and superheated water

    NARCIS (Netherlands)

    Dijkstra - Vinken, E.

    2008-01-01

    Aliphatic polyamide, commonly known as nylon, was the world’s first synthetic fiber and has found its largest application range in tires, carpets, stockings, upholstery, and adhesives. All polyamides have a recurring amide group (–CONH–) present in the molecular structure with hydrogen bonds between

  2. Hydrogen bonding of formamide, urea, urea monoxide and their thio

    Indian Academy of Sciences (India)

    Ab initio and DFT methods have been employed to study the hydrogen bonding ability of formamide, urea, urea monoxide, thioformamide, thiourea and thiourea monoxide with one water molecule and the homodimers of the selected molecules. The stabilization energies associated with themonohydrated adducts and ...

  3. A novel hydrogen-bonded cyclic dibromide in an organic ...

    Indian Academy of Sciences (India)

    Unknown

    2Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstraße 40, D-24098 ... H2O molecules are linked to bromide anions via O–H⋅⋅⋅Br hydrogen bonding ..... Weiss R, Reichel S, Handlke M and Hampel F 1998.

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

    Science.gov (United States)

    Mountain, Raymond D

    2010-12-16

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

  5. Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

    International Nuclear Information System (INIS)

    Gasparotto, Piero; Ceriotti, Michele

    2014-01-01

    The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding – a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound

  6. The Role of Molecule Clustering by Hydrogen Bond in Hydrous Ethanol on Laminar Burning Velocity

    Directory of Open Access Journals (Sweden)

    I Made Suarta

    2016-01-01

    Full Text Available The role of hydrogen bond molecule clustering in laminar burning velocities was observed. The water in hydrous ethanol can change the interaction between water-ethanol molecules. A certain amount of water can become oxygenated which increases the burning velocity. The hydrogen bond interaction pattern of ethanol and water molecules was modeled. Based on the molecular model, azeotropic behavior emerges from ethanol-water hydrogen bond, which is at a 95.1%v composition. The interaction with water molecule causes the ethanol molecule to be clustered with centered oxygenated compound. So, it supplies extra oxygen and provides intermolecular empty spaces that are easily infiltrated by the air. In the azeotropic composition, the molecular bond chain is the shortest, so hypothetically the burning velocity is anticipated to increase. The laminar burning velocity of ethanol fuel was tested in a cylindrical explosion bomb in lean, stoichiometric, and rich mixtures. The experimental result showed that the maximum burning velocity occurred at hydrous ethanol of 95.5%v composition. This discrepancy is the result of the addition of energy from 7.7% free ethanol molecules that are not clustered. At the rich mixture, the burning velocity of this composition is higher than that of anhydrous ethanol.

  7. Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

    Energy Technology Data Exchange (ETDEWEB)

    Gasparotto, Piero; Ceriotti, Michele, E-mail: michele.ceriotti@epfl.ch [Laboratory of Computational Science and Modeling, and National Center for Computational Design and Discovery of Novel Materials MARVEL, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland)

    2014-11-07

    The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding – a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

  8. Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond

    Science.gov (United States)

    Gasparotto, Piero; Ceriotti, Michele

    2014-11-01

    The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding - a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

  9. Probing the Watson-Crick, wobble, and sugar-edge hydrogen bond sites of uracil and thymine.

    Science.gov (United States)

    Müller, Andreas; Frey, Jann A; Leutwyler, Samuel

    2005-06-16

    The nucleobases uracil (U) and thymine (T) offer three hydrogen-bonding sites for double H-bond formation via neighboring N-H and C=O groups, giving rise to the Watson-Crick, wobble and sugar-edge hydrogen bond isomers. We probe the hydrogen bond properties of all three sites by forming hydrogen bonded dimers of U, 1-methyluracil (1MU), 3-methyluracil (3MU), and T with 2-pyridone (2PY). The mass- and isomer-specific S1 origins exhibit large spectral blue shifts relative to the 2PY monomer. Ab initio CIS calculations of the spectral shifts of the different hydrogen-bonded dimers show a linear correlation with experiment. This correlation allows us to identify the R2PI spectra of the weakly populated Watson-Crick and wobble isomers of both 2PY.U and 2PY.T. (3) PW91 density functional calculation of the ground-state binding and dissociation energies De and D0 are in agreement with the assignment of the dominant hydrogen bond isomers of 2PY.U, 2PY.3MU and 2PY.T as the sugar-edge form. For 2PY.U, 2PY.T and 2PY.1MU the measured wobble:Watson-Crick:sugar-edge isomer ratios are in good agreement with the calculated ratios, based on the ab initio dissociation energies and gas-phase statistical mechanics. The Watson-Crick and wobble isomers are thereby determined to be several kcal/mol less strongly bound than the sugar-edge isomers. The 36 observed intermolecular frequencies of the nine different H-bonded isomers give detailed insight into the intermolecular force field.

  10. Deuteriation of an asymmetric short hydrogen bond. X-ray crystal structure of KF.(CH2CO2D)2

    International Nuclear Information System (INIS)

    Emsley, J.; Jones, D.J.; Kuroda, R.

    1981-01-01

    Deuteriation of the strong hydrogen bonds of KF.(CH 2 CO 2 H) 2 shows no isotope effect on the bond lengths. The only significant change is in the bond angle at the fluoride ion which widens to 128.5 from 116 0 . The i.r. spectrum shows very little change. Since the O-H ... F - hydrogen bonds are highly asymmetric, these observations challenge previous predictions about the effects of deuteriation on such bonds. (author)

  11. Raman Spectra and Intermolecular Hydrogen Bonds of Quinoline in Solutions

    International Nuclear Information System (INIS)

    Tukhvatullin, F.H.; Jumabayev, A.; Hushvaktov, H.; Absanov, A.; Hudoyberdiev, B.

    2012-01-01

    The half-widths of the 1014- and 1033-cm -1 bands of the Raman spectrum of quinoline at its dilution in neutral solvents (benzene, CCl 4 ) are narrowed by 1.3-1.5 times at high dilutions. This effect is associated with the increased time of the vibrational relaxation. For the 520-cm -1 band in pure liquid quinoline, the parallel polarized component at 20 o C is asymmetric in the high-frequency region. The shape of the perpendicular polarized component is complicated. A non-coincidence of the peak frequencies of the parallel and perpendicular polarized components is observed (∼ 2 cm -1 ). Quantum-chemical calculations showed that, in the region of 520 cm -1 for a monomer molecule, we should really have two near located lines with the wavenumbers 530 and 527 cm -1 (scaling factor 0.97), and with the depolarization ratios 0.61 and 0.26. In the solutions with propan-2-ol, the 1033.8-cm -1 band becomes of a doublet character. The resolution of the doublet becomes better by the dilution of a binary quinoline-alcohol solution with a large amount of a neutral solvent (benzene). The wavenumbers of bands in the triple mixture are 1033 cm -1 and 1039 cm -1 . The doublet nature of the band in the binary and triple mixtures is associated with the presence of monomer molecules and quinoline-propan-2-ol aggregates (the high-frequency line) in the liquid mixture. Quantum-chemical calculations showed that the hydrogen bonds with a length of 1.958 A and an energy gain of 22.0 kJ/mole can be formed between molecules of quinoline and alcohol. The formation of aggregates can be also detected in the 820-cm -1 band of propan-2-ol. A similar picture is observed for the 667-cm -1 band of chloroform in its solution with quinoline.

  12. A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor.

    Directory of Open Access Journals (Sweden)

    Jarosław Poznański

    Full Text Available Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors.

  13. A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor.

    Science.gov (United States)

    Poznański, Jarosław; Poznańska, Anna; Shugar, David

    2014-01-01

    Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors.

  14. Hydrogen bonding analysis of hydroxyl groups in glucose aqueous solutions by a molecular dynamics simulation study

    International Nuclear Information System (INIS)

    Chen, Cong; Li, Wei Zhong; Song, Yong Chen; Weng, Lin Dong; Zhang, Ning

    2012-01-01

    Molecular dynamics simulations have been performed to investigate hydrogen bonding characteristics of hydroxyl groups in glucose aqueous solutions with different concentrations. The hydrogen bonding abilities and strength of different O and H atom types have been calculated and compared. The acceptor/donor efficiencies have been predicted and it has been found that: (1) O2-HO2 and O3-HO3 are more efficient intramolecular hydrogen bonding acceptors than donors; (2) O1-HO1, O4-HO4 and O6-HO6 are more efficient intramolecular hydrogen bonding donors than acceptors; (5) O1-HO1 and O6-HO6 are more efficient intermolecular hydrogen bonding acceptors than donors while hydroxyl groups O2-HO2 and O4-HO4 are more efficient intermolecular hydrogen bonding donors than acceptors. The hydrogen bonding abilities of hydroxyl groups revealed that: (1) the hydrogen bonding ability of OH2-H w is larger than that of hydroxyl groups in glucose; (2) among the hydroxyl groups in glucose, the hydrogen bonding ability of O6-HO6 is the largest and the hydrogen bonding ability of O4-HO4 is the smallest; (3) the intermolecular hydrogen bonding ability of O6-HO6 is the largest; (4) the order for intramolecular hydrogen bonding abilities (from large to small) is O2-HO2, O1-HO1, O3-HO3, O6-HO6 and O4-HO4

  15. Nuclear quantum effects and hydrogen bond fluctuations in water

    Science.gov (United States)

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

    2013-01-01

    The hydrogen bond (HB) is central to our understanding of the properties of water. However, despite intense theoretical and experimental study, it continues to hold some surprises. Here, we show from an analysis of ab initio simulations that take proper account of nuclear quantum effects that the hydrogen-bonded protons in liquid water experience significant excursions in the direction of the acceptor oxygen atoms. This generates a small but nonnegligible fraction of transient autoprotolysis events that are not seen in simulations with classical nuclei. These events are associated with major rearrangements of the electronic density, as revealed by an analysis of the computed Wannier centers and 1H chemical shifts. We also show that the quantum fluctuations exhibit significant correlations across neighboring HBs, consistent with an ephemeral shuttling of protons along water wires. We end by suggesting possible implications for our understanding of how perturbations (solvated ions, interfaces, and confinement) might affect the HB network in water. PMID:24014589

  16. Experimental and Theoretical Studies in Hydrogen-Bonding Organocatalysis

    Directory of Open Access Journals (Sweden)

    Matej Žabka

    2015-08-01

    Full Text Available Chiral thioureas and squaramides are among the most prominent hydrogen-bond bifunctional organocatalysts now extensively used for various transformations, including aldol, Michael, Mannich and Diels-Alder reactions. More importantly, the experimental and computational study of the mode of activation has begun to attract considerable attention. Various experimental, spectroscopic and calculation methods are now frequently used, often as an integrated approach, to establish the reaction mechanism, the mode of activation or explain the stereochemical outcome of the reaction. This article comprises several case studies, sorted according to the method used in their study. The aim of this review is to give the investigators an overview of the methods currently utilized for mechanistic investigations in hydrogen-bonding organocatalysis.

  17. Structure and weak hydrogen bonds in liquid acetaldehyde

    Directory of Open Access Journals (Sweden)

    Cordeiro Maria A. M.

    2004-01-01

    Full Text Available Monte Carlo simulations have been performed to investigate the structure and hydrogen bonds formation in liquid acetaldehyde. An all atom model for the acetaldehyde have been optimized in the present work. Theoretical values obtained for heat of vaporisation and density of the liquid are in good agreement with experimental data. Graphics of radial distribution function indicate a well structured liquid compared to other similar dipolar organic liquids. Molecular mechanics minimization in gas phase leads to a trimer of very stable structure. The geometry of this complex is in very good agreement with the rdf. The shortest site-site correlation is between oxygen and the carbonyl hydrogen, suggesting that this correlation play a important role in the liquid structure and properties. The OxxxH average distance and the C-HxxxO angle obtained are characteristic of weak hydrogen bonds.

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

    Science.gov (United States)

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

    2015-08-01

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

  19. Quantum confinement in hydrogen bond of DNA and RNA

    International Nuclear Information System (INIS)

    Dos Santos, C S; Filho, E Drigo; Ricotta, R M

    2015-01-01

    The hydrogen bond is a fundamental ingredient to stabilize the DNA and RNA macromolecules. The main contribution of this work is to describe quantitatively this interaction as a consequence of the quantum confinement of the hydrogen. The results for the free and confined system are compared with experimental data. The formalism to compute the energy gap of the vibration motion used to identify the spectrum lines is the Variational Method allied to Supersymmetric Quantum Mechanics. (papert)

  20. Finite size effects on hydrogen bonds in confined water

    International Nuclear Information System (INIS)

    Musat, R.; Renault, J.P.; Le Caer, S.; Pommeret, S.; Candelaresi, M.; Palmer, D.J.; Righini, R.

    2008-01-01

    Femtosecond IR spectroscopy was used to study water confined in 1-50 nm pores. The results show that even large pores induce significant changes (for example excited-state lifetimes) to the hydrogen-bond network, which are independent of pore diameter between 1 and 50 nm. Thus, the changes are not surface-induced but rather finite size effects, and suggest a confinement-induced enhancement of the acidic character of water. (authors)

  1. Hirshfeld atom refinement for modelling strong hydrogen bonds.

    Science.gov (United States)

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

    2014-09-01

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

  2. TDDFT study on intramolecular hydrogen bond of photoexcited methyl salicylate.

    Science.gov (United States)

    Qu, Peng; Tian, Dongxu

    2014-01-01

    The equilibrium geometries, IR-spectra and transition mechanism of intramolecular hydrogen-bonded methyl salicylate in excited state were studied using DFT and TDDFT with 6-31++G (d, p) basis set. The length of hydrogen bond OH⋯OC is decreased from 1.73 Å in the ground state to 1.41 and 1.69 Å in the excited S1 and S3 states. The increase of bond length for HO and CO group also indicates that in excited state the hydrogen bond OH⋯OC is strengthened. IR spectra show HO and CO stretching bands are strongly redshifted by 1387 and 67 cm(-1) in the excited S1 and S3 states comparing to the ground state. The excitation energy and the absorption spectrum show the S3 state is the main excited state of the low-lying excited states. By analyzing the frontier molecular orbitals, the transition from the ground state to the excited S1 and S3 states was predicted to be the π→π∗ mode. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Human DNA primase uses Watson-Crick hydrogen bonds to distinguish between correct and incorrect nucleoside triphosphates.

    Science.gov (United States)

    Moore, Chad L; Zivkovic, Aleksandra; Engels, Joachim W; Kuchta, Robert D

    2004-09-28

    Human DNA primase synthesizes short RNA primers that DNA polymerase alpha further elongates. Primase readily misincorporates the natural NTPs and will generate a wide variety of mismatches. In contrast, primase exhibited a remarkable resistance to polymerizing NTPs containing unnatural bases. This included bases whose shape was almost identical to the natural bases (4-aminobenzimidazole and 4,6-difluorobenzimidazole), bases shaped very differently than a natural base [e.g., 5- and 6-(trifluoromethyl)benzimidazole], bases much more hydrophobic than a natural base [e.g., 4- and 7-(trifluoromethyl)benzimidazole], bases of similar hydrophobicity as a natural base but with the Watson-Crick hydrogen-bonding groups in unusual positions (7-beta-D-guanine), and bases capable of forming only one Watson-Crick hydrogen bond with the template base (purine and 4-aminobenzimidazole). Primase only polymerized NTP analogues containing bases capable of forming hydrogen bonds between the equivalent of both N-1 and the exocyclic group at C-6 of a purine NTP (2-fluoroadenine, 2-chloroadenine, 3-deazaadenine, and hypoxanthine) and N-3 and the exocyclic group at C-4 of a pyrimidine. These data indicate that human primase requires the formation of Watson-Crick hydrogen bonds in order to polymerize a NTP, a situation very different than what is observed with some DNA polymerases. The implications of these results with respect to current theories of how polymerases discriminate between right and wrong (d)NTPs are discussed.

  4. Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes

    Science.gov (United States)

    Pirrotta, Alessandro; De Vico, Luca; Solomon, Gemma C.; Franco, Ignacio

    2017-03-01

    The emerging ability to study physical properties at the single-molecule limit highlights the disparity between what is observable in an ensemble of molecules and the heterogeneous contributions of its constituent parts. A particularly convenient platform for single-molecule studies are molecular junctions where forces and voltages can be applied to individual molecules, giving access to a series of electromechanical observables that can form the basis of highly discriminating multidimensional single-molecule spectroscopies. Here, we computationally examine the ability of force and conductance to inform about molecular recognition events at the single-molecule limit. For this, we consider the force-conductance characteristics of a prototypical class of hydrogen bonded bimolecular complexes sandwiched between gold electrodes. The complexes consist of derivatives of a barbituric acid and a Hamilton receptor that can form up to six simultaneous hydrogen bonds. The simulations combine classical molecular dynamics of the mechanical deformation of the junction with non-equilibrium Green's function computations of the electronic transport. As shown, in these complexes hydrogen bonds mediate transport either by directly participating as a possible transport pathway or by stabilizing molecular conformations with enhanced conductance properties. Further, we observe that force-conductance correlations can be very sensitive to small changes in the chemical structure of the complexes and provide detailed information about the behavior of single molecules that cannot be gleaned from either measurement alone. In fact, there are regions during the elongation that are only mechanically active, others that are only conductance active, and regions where both force and conductance changes as the complex is mechanically manipulated. The implication is that force and conductance provide complementary information about the evolution of molecules in junctions that can be used to

  5. Tunable GLUT-Hexose Binding and Transport via Modulation of Hexose C-3 Hydrogen-Bonding Capabilities.

    Science.gov (United States)

    Kumar Kondapi, Venkata Pavan; Soueidan, Olivier-Mohamad; Cheeseman, Christopher I; West, Frederick G

    2017-06-12

    The importance of the hydrogen bonding interactions in the GLUT-hexose binding process (GLUT=hexose transporter) has been demonstrated by studying the binding of structurally modified d-fructose analogues to GLUTs, and in one case its transport into cells. The presence of a hydrogen bond donor at the C-3 position of 2,5-anhydro-d-mannitol derivatives is essential for effective binding to GLUT5 and transport into tumor cells. Surprisingly, installation of a group that can function only as a hydrogen bond acceptor at C-3 resulted in selective recognition by GLUT1 rather than GLUT5. A fluorescently labelled analogue clearly showed GLUT-mediated transport and low efflux properties of the probe. This study reveals that a single positional modification of a 2,5-anhydro-d-mannitol derivative is sufficient to switch its binding preference from GLUT5 to GLUT1, and uncovers general scaffolds that are suitable for the potential selective delivery of molecular payloads into tumor cells via GLUT transport machinery. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Theoretical study of hydrogen bond interactions of fluvastatin with ι-carrageenan and λ-carrageenan.

    Science.gov (United States)

    Papadopoulos, Anastasios G; Sigalas, Michael P

    2011-07-01

    The binding of the reductase inhibitor drug fluvastatin, hydroxy-3-methylglutaryl coenzyme A, with the hydrophilic ι- or λ-carrageenan polymers, serving as potential controllers of the drug's release rate, have been studied at the density functional level of theory with the B3LYP exchange correlation functional. Three low energy conformers of fluvastatin have been calculated. The vibrational spectroscopic properties calculated for the most stable conformer were in satisfactory agreement with the experimental data. A series of hydrogen bonded complexes of the most stable conformer of fluvastatin anion with low molecular weight models of the polymers have been fully optimized. In almost all, intermolecular H-bonds are formed between the sulfate groups of ι- or λ-carrageenan and fluvastatin's hydroxyls, resulting in a red shift of the fluvastatin's O - H stretching vibrations. Cooperative intramolecular H-bonds within fluvastatin or ι-, λ-carrageenan are also present. The BSSE and ZPE corrected interaction energies were estimated in the range 281-318 kJ mol⁻¹ for ι-carrageenan - fluvastatin and 145-200 kJ mol⁻¹ for λ-carrageenan - fluvastatin complexes. The electron density (ρ (bcp)) and Laplacian (∇²ρ (bcp)) properties at critical points of the intermolecular hydrogen bonds, estimated by AIM (atoms in molecules) calculations, have a low and positive character (∇²ρ(bcp) > 0), consistent with the electrostatic character of the hydrogen bonds. The structural and energetic data observed, as well as the extent of the red shift of the fluvastatin's O - H stretching vibrations upon complex formation and the properties of electron density show a stronger binding of fluvastatin to ι- than to λ-carrageenan.

  7. Intramolecular hydrogen bonding in malonaldehyde and its radical analogues.

    Science.gov (United States)

    Lin, Chen; Kumar, Manoj; Finney, Brian A; Francisco, Joseph S

    2017-09-28

    High level Brueckner doubles with triples correction method-based ab initio calculations have been used to investigate the nature of intramolecular hydrogen bonding and intramolecular hydrogen atom transfer in cis-malonaldehyde (MA) and its radical analogues. The radicals considered here are the ones that correspond to the homolytic cleavage of C-H bonds in cis-MA. The results suggest that cis-MA and its radical analogues, cis-MA RS , and cis-MA RA , both exist in planar geometry. The calculated intramolecular O-H⋯O=C bond in cis-MA is shorter than that in the radical analogues. The intramolecular hydrogen bond in cis-MA is stronger than in its radicals by at least 3.0 kcal/mol. The stability of a cis-malonaldehyde radical correlates with the extent of electron spin delocalization; cis-MA RA , in which the radical spin is more delocalized, is the most stable MA radical, whereas cis-MA RS , in which the radical spin is strongly localized, is the least stable radical. The natural bond orbital analysis indicates that the intramolecular hydrogen bonding (O⋯H⋯O) in cis-malonaldehyde radicals is stabilized by the interaction between the lone pair orbitals of donor oxygen and the σ * orbital of acceptor O-H bond (n → σ * OH ). The calculated barriers indicate that the intramolecular proton transfer in cis-MA involves 2.2 kcal/mol lower barrier than that in cis-MA RS .

  8. Laser spectroscopic visualization of hydrogen bond motions in liquid water

    Science.gov (United States)

    Bratos, S.; Leicknam, J.-Cl.; Pommeret, S.; Gallot, G.

    2004-12-01

    Ultrafast pump-probe experiments are described permitting a visualization of molecular motions in diluted HDO/D 2O solutions. The experiments were realized in the mid-infrared spectral region with a time resolution of 150 fs. They were interpreted by a careful theoretical analysis, based on the correlation function approach of statistical mechanics. Combining experiment and theory, stretching motions of the OH⋯O bonds as well as HDO rotations were 'filmed' in real time. It was found that molecular rotations are the principal agent of hydrogen bond breaking and making in water. Recent literatures covering the subject, including molecular dynamics simulations, are reviewed in detail.

  9. A combined experimental and theoretical approach to the study of hydrogen bond interaction in the binary mixture of N-methylimidazole with water

    International Nuclear Information System (INIS)

    Huang, Rongyi; Du, Rongbin; Liu, Guangxiang; Zhao, Xiuqin; Ye, Shiyong; Wu, Genhua

    2012-01-01

    Highlights: ► Densities of N-methylimidazole with water binary mixture were measured. ► Excess molar volumes were fitted to Redlich–Kister polynomial equation. ► Excess molar volumes are negative in the whole mole fraction range. ► 1:1 Hydrogen complex formation between the unlike components was observed. ► Formation of hydrogen bonds in the binary mixture was confirmed by DFT//B3LYP. - Abstract: The intermolecular hydrogen bond interactions in the N-methylimidazole (MeIm) with water binary mixture have been studied by a combined experimental and theoretical approach. The densities of the binary mixture have been measured at T = (288.15 to 323.15) K and at atmospheric pressure. From the experimental data, excess molar volumes were determined as a function of composition at each temperature. The results reveal the formation of 1:1 hydrogen bond complex between MeIm with water at the maximal excess molar volume. Meanwhile, the formation of hydrogen bonds in the binary mixture was further confirmed by high level theoretical calculation. The structures, interactional energies and bond characteristics of the hydrogen bond complexes were calculated in the gas phase using density functional theory (DFT) at the B3LYP/6-311++G(d, p) theory levels. The changes of thermodynamic properties from the monomers to hydrogen bond complexes with the temperature ranging from (288.15 to 323.15) K were obtained using the statistical thermodynamic method. Thermodynamic analyses have been interpreted in terms of intermolecular interactions and excess molar volume changes in the binary mixture. It was also found that the formation reaction of the hydrogen bond complex of MeIm with water was an exothermic, entropy reduced and spontaneous thermodynamic process at all the temperature studied.

  10. Hydrogen-bonded structure in highly concentrated aqueous LiBr solutions

    International Nuclear Information System (INIS)

    Imano, Masahiro; Kameda, Yasuo; Usuki, Takeshi; Uemura, Osamu

    2001-01-01

    Neutron diffraction measurements were carried out for H/D isotopically substituted aqueous 10, 25 and 33 mol% LiBr solutions in order to obtain structural information on the intermolecular hydrogen bonds among water molecules in highly concentrated aqueous solutions. Observed scattering cross sections for D 2 O (99.9 % D), 0 H 2 O(35.9 % D) and 0-2 H 2 O(68.0 % D) solutions were combined to deduce partial structure factors, a HH (Q), a XH (Q) and a XX (Q) (X: O, Br and Li). The least squares fitting analysis was applied to the observed partial structure factors to determine the nearest neighbor interatomic distance, root-mean-square amplitude and coordination number. Intermolecular distances, r OH =1.91(1) A, r HH =2.38(1) A and r OO =3.02(1) A, between the nearest neighbor water molecules, were obtained for the 10 mol% LiBr solution. On the other hand, the intermolecular O···H interaction was found to almost disappear in concentrated 25 and 33 mol% LiBr solutions. The result implies that the hydrogen-bonded network is completely broken in highly concentrated aqueous LiBr solutions. (author)

  11. Double hydrogen bonded ferroelectric liquid crystals: A study of field induced transition (FiT)

    Science.gov (United States)

    Vijayakumar, V. N.; Madhu Mohan, M. L. N.

    2009-12-01

    A novel series of chiral hydrogen bonded liquid crystals have been isolated. Hydrogen bond was formed between chiral nonmesogen ingredient levo tartaric acid and mesogenic p-n-alkoxybenzoic acids. Phase diagram was constructed from the transition temperatures obtained by DSC and polarizing optical microscopic (POM) studies. Thermal and electrical properties exhibited by three complexes namely LTA+8BA, LTA+7BA and LTA+5BA were discussed. Salient feature of the present work was the observation of a reentrant smectic ordering in LTA+8BA complex designated as C r∗ phase. This reentrant phenomenon was confirmed by DSC thermograms, optical textures of POM and temperature variation of capacitance and dielectric loss studies. Tilt angle was measured in smectic C ∗ and reentrant smectic C r∗ phases. Another interesting feature of the present investigation was the observation of a field induced transition (FiT) in the LTA+ nBA homologous series. Three threshold field values were noticed which give rise to two new phases (E 1 and E 2) induced by electric field and on further enhancement of the applied field the mesogen behaves like an optical shutter. FiT is reversible in the sense that when applied field is removed the original texture was restored.

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

    Science.gov (United States)

    Wang, Yuhao; Sukhishvili, Svetlana

    2015-03-01

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

  13. Effect of quantum nuclear motion on hydrogen bonding

    Science.gov (United States)

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

    2014-05-01

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

  14. Effect of quantum nuclear motion on hydrogen bonding

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  15. Measurement and Theory of Hydrogen Bonding Contribution to Isosteric DNA Base Pairs

    OpenAIRE

    Khakshoor, Omid; Wheeler, Steven E.; Houk, K. N.; Kool, Eric T.

    2012-01-01

    We address the recent debate surrounding the ability of 2,4-difluorotoluene (F), a low-polarity mimic of thymine (T), to form a hydrogen-bonded complex with adenine in DNA. The hydrogen bonding ability of F has been characterized as small to zero in various experimental studies, and moderate to small in computational studies. However, recent X-ray crystallographic studies of difluorotoluene in DNA/RNA have indicated, based on interatomic distances, possible hydrogen bonding interactions betwe...

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

    DEFF Research Database (Denmark)

    Du, Lin; Tang, Shanshan; Hansen, Anne Schou

    2017-01-01

    complexes are more stable and form stronger hydrogen bonds compared to complexes with MeOH and EtOH, which are comparable, and only for the stronger hydrogen bond donor (TFE) are the small differences in acceptor molecules highlighted. The equilibrium constant for complex formation was determined from......The Osingle bondH⋯O and Osingle bondH⋯S hydrogen bonds were investigated by gas phase FTIR spectroscopy of alcohol–dimethylether and alcohol–dimethylsulfide complexes, with alcohols of increasing hydrogen bond donor strength; methanol (MeOH), ethanol (EtOH) and 2,2,2-trifluoroethanol (TFE). The TFE...

  17. The Relative Hydrogen Bonding Strength of Oxygen and Nitrogen Atoms as a Proton Acceptor

    International Nuclear Information System (INIS)

    Hyun, Jong Cheol; Lee, Ho Jin; Kim, Nak Kyoon; Choi, Young Sang; Park, Jeung Hee; Yoon, Chang Ju

    1999-01-01

    The thermodynamic parameters for the formation of the hydrogen bonding were widely used to understand the protein- ligand interaction. We have been interested in the hydrogen bonding strength of various proton acceptors toward the amide in a nonpolar solvent, This work is in the line of our interest. In drug design, the functional group is often replaced in order to enhance or reduce the binding affinity, which is usually determined by hydrogen bonding strength. Therefore, to understand this biochemical process the knowledge of relative hydrogen bonding strength is of importance.

  18. Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications.

    Science.gov (United States)

    Galek, Peter T A; Chisholm, James A; Pidcock, Elna; Wood, Peter A

    2014-02-01

    Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.

  19. Side-by-Side Comparison of Hydroperoxide and Corresponding Alcohol as Hydrogen-Bond Donors

    DEFF Research Database (Denmark)

    Møller, Kristian Holten; Tram, Camilla Mia; Kjærgaard, Henrik Grum

    2017-01-01

    tert-butanol (t-BuOH), with dimethyl ether (DME) as the hydrogen-bond acceptor. Using a combination of Fourier-transform infrared spectroscopy and quantum chemical calculations, we compare the strength of the OH-O hydrogen bond and the total strength of complexation. We find that, both in terms...... results, we find that the hydroperoxide complex is stabilized by ∼4 kJ/mol (Gibbs free energy) more than the alcohol complex. Measured red shifts show the same trend in hydrogen-bond strength with trimethylamine (N acceptor atom) and dimethyl sulfide (S acceptor atom) as the hydrogen-bond acceptors....

  20. Quantum mechanics models of the methanol dimer: OH⋯O hydrogen bonds of β-d-glucose moieties from crystallographic data.

    Science.gov (United States)

    Cintrón, Michael Santiago; Johnson, Glenn P; French, Alfred D

    2017-04-18

    The interaction of two methanol molecules, simplified models of carbohydrates and cellulose, was examined using a variety of quantum mechanics (QM) levels of theory. Energy plots for hydrogen bonding distance (H⋯O) and angle (OH⋯O) were constructed. All but two experimental structures were located in stabilized areas on the vacuum phase energy plots. Each of the 399 models was analyzed with Bader's atoms-in-molecules (AIM) theory, which showed a widespread ability by the dimer models to form OH⋯O hydrogen bonds that have bond paths and Bond Critical Points. Continuum solvation calculations suggest that a portion of the energy-stabilized structures could occur in the presence of water. A survey of the Cambridge Structural Database (CSD) for all donor-acceptor interactions in β-D-glucose moieties examined the similarities and differences among the hydroxyl groups and acetal oxygen atoms that participate in hydrogen bonds. Comparable behavior was observed for the O2H, O3H, O4H, and O6H hydroxyls, acting either as acceptors or donors. Ring O atoms showed distinct hydrogen bonding behavior that favored mid-length hydrogen bonds. Published by Elsevier Ltd.

  1. Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide

    Science.gov (United States)

    Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

    2013-09-01

    In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm-1) and μ-Raman spectra (100-4000 cm-1) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

  2. Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil

    Science.gov (United States)

    Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

    2014-06-01

    In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400 cm-1) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

  3. Communication: A hydrogen-bonded difluorocarbene complex: Ab initio and matrix isolation study

    Science.gov (United States)

    Sosulin, Ilya S.; Shiryaeva, Ekaterina S.; Tyurin, Daniil A.; Feldman, Vladimir I.

    2017-10-01

    Structure and spectroscopic features of the CF2⋯HF complexes were studied by ab initio calculations at the CCSD(T) level and matrix isolation FTIR spectroscopy. The calculations predict three stable structures. The most energetically favorable structure corresponds to hydrogen bonding of HF to the lone pair of the C atom (the interaction energy of 3.58 kcal/mol), whereas two less stable structures are the H⋯F bonded complexes (the interaction energies of 0.30 and 0.24 kcal/mol). The former species was unambiguously characterized by the absorptions in the FTIR spectra observed after X-ray irradiation of fluoroform in a xenon matrix at 5 K. The corresponding features appear at 3471 (H-F stretching), 1270 (C-F symmetric stretching, shoulder), 1175 (antisymmetric C-F stretching), and 630 (libration) cm-1, in agreement with the computational predictions. To our knowledge, it is the first hydrogen-bonded complex of dihalocarbene. Possible weaker manifestations of the H⋯F bonded complexes were also found in the C-F stretching region; however, their assignment is tentative. The H⋯C bonded complex is protected from reaction yielding a fluoroform molecule by a remarkably high energy barrier (23.85 kcal/mol), so it may be involved in various chemical reactions.

  4. Intramolecular hydrogen bonding in N-salicylideneaniline: FT-IR spectrum and quantum chemical calculations

    Science.gov (United States)

    Moosavi-Tekyeh, Zainab; Dastani, Najmeh

    2015-12-01

    FT-IR and FT-Raman spectra of N-salicylideneaniline (SAn) and its deuterated analogue (D-SAn) are recorded, and the theoretical calculations are performed on their molecular structures and vibrational frequencies. The same calculations are performed for SAn in different solutions using the polarizable conductor continuum model (CPCM) method. Comparisons between the spectra obtained and the corresponding theoretical calculations are used to assign the vibrational frequencies for these compounds. The spectral behavior of SAn upon deuteration is also used to distinguish the positions of OH vibrational frequencies. The hydrogen bond strength of SAn is investigated by applying the atoms-in-molecules (AIM) theory, natural bond orbital (NBO) analysis, and geometry calculations. The harmonic vibrational frequencies of SAn are calculated at B3LYP and X3LYP levels of theory using 6-31G*, 6-311G**, and 6-311++G** basis sets. The AIM results support a medium hydrogen bonding in SAn. The observed νOH/νOD and γOH/γOD for SAn appear at 2940/2122 and 830/589 cm-1, respectively.

  5. High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

    Science.gov (United States)

    Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

    2015-01-01

    Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from

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

    Science.gov (United States)

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

    2017-04-01

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

  7. Methyl group dynamics in paracetamol and acetanilide: probing the static properties of intermolecular hydrogen bonds formed by peptide groups

    Science.gov (United States)

    Johnson, M. R.; Prager, M.; Grimm, H.; Neumann, M. A.; Kearley, G. J.; Wilson, C. C.

    1999-06-01

    Measurements of tunnelling and librational excitations for the methyl group in paracetamol and tunnelling excitations for the methyl group in acetanilide are reported. In both cases, results are compared with molecular mechanics calculations, based on the measured low temperature crystal structures, which follow an established recipe. Agreement between calculated and measured methyl group observables is not as good as expected and this is attributed to the presence of comprehensive hydrogen bond networks formed by the peptide groups. Good agreement is obtained with a periodic quantum chemistry calculation which uses density functional methods, these calculations confirming the validity of the one-dimensional rotational model used and the crystal structures. A correction to the Coulomb contribution to the rotational potential in the established recipe using semi-emipircal quantum chemistry methods, which accommodates the modified charge distribution due to the hydrogen bonds, is investigated.

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

    Science.gov (United States)

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

    2014-05-01

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

  9. n-Electrons of heteroatoms in hydrogen bond and luminescence

    International Nuclear Information System (INIS)

    Karyakin, A.V.

    1985-01-01

    Hydrogen bond energy in the process of interaction between water molecules, water molecules and heteroatoms of organic solvents, water molecules and inorganic compounds, is determined, its mechanism being studied. On the basis of X-ray structure and IR-spectroscopic data water state in easily hydrolized compounds of zirconium and hafnium, including sulfates, nitrates, oxychlorides etc. is analyzed. Water state in uranyl nitrate hydrates, the structure of the compounds and their behaviour when they are extracted by TBP, are considered. The reasons for stability of uranyl nitrate hydrates are discussed. The effect of n-electrons of heteroatoms of simple aromatic compound on structural spectra of luminescence in aliphatic and inorganic matrices is investigated

  10. Excited hydrogen bonds in the molecular mechanism of muscle contraction.

    Science.gov (United States)

    Bespalova, S V; Tolpygo, K B

    1991-11-21

    The mechanism of muscle contraction is considered. The hydrolysis of an ATP molecule is assumed to produce the excitation of hydrogen bonds A--H...B between electronegative atoms A and B, which are contained in the myosin head and actin filament. This excitation energy epsilon f depends on the interatomic distance AB = R and generates the tractive force f = -delta epsilon f/delta R, that makes atoms AB approach each other. The swing of the myosin head results in macroscopic mutual displacement of actin and myosin polymers. The motion of the actin filament under the action of this force is studied. The conditions under which a considerable portion of the excitation energy converts into the potential tension energy of the actin filament are analysed, and the probability of higher muscle efficiency existence is discussed.

  11. Hydrogen Bonding and Stability of Hybrid Organic-Inorganic Perovskites

    KAUST Repository

    El-Mellouhi, Fedwa

    2016-09-08

    In the past few years, the efficiency of solar cells based on hybrid organic–inorganic perovskites has exceeded the level needed for commercialization. However, existing perovskites solar cells (PSCs) suffer from several intrinsic instabilities, which prevent them from reaching industrial maturity, and stabilizing PSCs has become a critically important problem. Here we propose to stabilize PSCs chemically by strengthening the interactions between the organic cation and inorganic anion of the perovskite framework. In particular, we show that replacing the methylammonium cation with alternative protonated cations allows an increase in the stability of the perovskite by forming strong hydrogen bonds with the halide anions. This interaction also provides opportunities for tuning the electronic states near the bandgap. These mechanisms should have a universal character in different hybrid organic–inorganic framework materials that are widely used.

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

    Science.gov (United States)

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

    2010-07-01

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

  13. Hydrogen Bonding and Stability of Hybrid Organic-Inorganic Perovskites

    KAUST Repository

    El-Mellouhi, Fedwa; Marzouk, Asma; Bentria, El Tayeb; Rashkeev, Sergey N.; Kais, Sabre; Alharbi, Fahhad H.

    2016-01-01

    In the past few years, the efficiency of solar cells based on hybrid organic–inorganic perovskites has exceeded the level needed for commercialization. However, existing perovskites solar cells (PSCs) suffer from several intrinsic instabilities, which prevent them from reaching industrial maturity, and stabilizing PSCs has become a critically important problem. Here we propose to stabilize PSCs chemically by strengthening the interactions between the organic cation and inorganic anion of the perovskite framework. In particular, we show that replacing the methylammonium cation with alternative protonated cations allows an increase in the stability of the perovskite by forming strong hydrogen bonds with the halide anions. This interaction also provides opportunities for tuning the electronic states near the bandgap. These mechanisms should have a universal character in different hybrid organic–inorganic framework materials that are widely used.

  14. On the physical origin of blue-shifted hydrogen bonds.

    Science.gov (United States)

    Li, Xiaosong; Liu, Lei; Schlegel, H Bernhard

    2002-08-14

    For blue-shifted hydrogen-bonded systems, the hydrogen stretching frequency increases rather than decreases on complexation. In computations at various levels of theory, the blue-shift in the archetypical system, F(3)C-H.FH, is reproduced at the Hartree-Fock level, indicating that electron correlation is not the primary cause. Calculations also demonstrate that a blue-shift does not require either a carbon center or the absence of a lone pair on the proton donor, because F(3)Si-H.OH(2), F(2)NH.FH, F(2)PH.NH(3), and F(2)PH.OH(2) have substantial blue-shifts. Orbital interactions are shown to lengthen the X-H bond and lower its vibrational frequency, and thus cannot be the source of the blue-shift. In the F(3)CH.FH system, the charge redistribution in F(3)CH can be reproduced very well by replacing the FH with a simple dipole, which suggests that the interactions are predominantly electrostatic. When modeled with a point charge for the proton acceptor, attractive electrostatic interactions elongate the F(3)C-H, while repulsive interactions shorten it. At the equilibrium geometry of a hydrogen-bonded complex, the electrostatic attraction between the dipole moments of the proton donor and proton acceptor must be balanced by the Pauli repulsion between the two fragments. In the absence of orbital interactions that cause bond elongation, this repulsive interaction leads to compression of the X-H bond and a blue-shift in its vibrational frequency.

  15. Nitroxide stable radicals interacting as Lewis bases in hydrogen bonds: A search in the Cambridge structural data base for intermolecular contacts

    Science.gov (United States)

    Alkorta, Ibon; Elguero, José; Elguero, Eric

    2017-11-01

    1125 X-ray structures of nitroxide free radicals presenting intermolecular hydrogen bonds have been reported in the Cambridge Structural Database. We will report in this paper a qualitative and quantitative analysis of these bonds. The observation in some plots of an excluded region was statistically analyzed using convex hull and kernel smooting methodologies. A theoretical study at the MP2 level with different basis has been carried out indicating that the nitronyl nitroxide radicals (five electrons) lie just in between nitroso compounds (four electrons) and amine N-oxides (six electrons) as far as hydrogen-bond basicity is concerned.

  16. Self-assembly of a [2 x 2] hydrogen bonded grid

    NARCIS (Netherlands)

    Lipkowski, P.R.; Bielejewska, A.G.; Kooijman, Huub; Spek, Anthony L.; Timmerman, P.; Reinhoudt, David

    1999-01-01

    Formation of 24 cooperative hydrogen bonds drives the spontaneous assembly of a rigid bifunctional trimelamine and bis(barbituric acid) to give selectively the [2 × 2] hydrogen-bonded grid, in preference to the corresponding [1 × 1] or polymeric assemblies.

  17. Watson-Crick hydrogen bonds : Nature and role in DNA replication

    NARCIS (Netherlands)

    Guerra, Célia Fonseca; Bickelhaupt, F. Matthias

    2006-01-01

    The hydrogen bonds in DNA Watson–Crick base pairs have long been considered predominantly electrostatic phenomena. In this chapter, we show with state-of-the-art calculations that this is not true and that electrostatic interactions and covalent contributions in these hydrogen bonds are in fact of

  18. Substituent Effects on Hydrogen Bonds in DNA : A Kohn-Sham DFT Approach

    NARCIS (Netherlands)

    Guerra, Célia Fonseca; Bickelhaupt, F. Matthias

    2006-01-01

    In this Chapter, we discuss how the hydrogen bonds in Watson-Crick base pairs can be tuned both structurally and in terms of bond strength by exposing the DNA bases to different kinds of substitutions: (1) substitution in the X-H Y hydrogen bonding moiety, (2) remote substitution, i.e., introducing

  19. The role of hydrogen bonds in the melting points of sulfonate-based protic organic salts

    DEFF Research Database (Denmark)

    Luo, Jiangshui

    2016-01-01

    There are three main types of interactions inside organic salts - electrostatic interaction, hydrogen bonding and van der Waals force [1-4]. While van der Waals force is relatively weak, it is hydrogen bonding and particularly electrostatic interaction that determine the lattice energies of ionic...

  20. Kinetic stabilities of double, tetra- and hexarosette hydrogen-bonded assemblies

    NARCIS (Netherlands)

    Prins, L.J.; Neuteboom, Edda E.; Paraschiv, V.; Crego Calama, Mercedes; Timmerman, P.; Reinhoudt, David

    2002-01-01

    A study of the kinetic stabilities of hydrogen-bonded double, tetra-, and hexarosette assemblies, comprising 36, 72, and 108 hydrogen bonds, respectively, is described. The kinetic stabilities are measured using both chiral amplification and racemization experiments. The chiral amplification studies

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

    Science.gov (United States)

    Fedor, Anna M.; Toda, Megan J.

    2014-01-01

    The hydrogen bonding of phenol can be used as an introductory model for biological systems because of its structural similarities to tyrosine, a para-substituted phenol that is an amino acid essential to the synthesis of proteins. Phenol is able to form hydrogen bonds readily in solution, which makes it a suitable model for biological…

  2. Performance of various density functionals for the hydrogen bonds in DNA base pairs

    NARCIS (Netherlands)

    van der Wijst, T.; Fonseca Guerra, C.; Swart, M.; Bickelhaupt, F.M.

    2006-01-01

    We have investigated the performance of seven popular density functionals (B3LYP, BLYP, BP86, mPW, OPBE, PBE, PW91) for describing the geometry and stability of the hydrogen bonds in DNA base pairs. For the gas-phase situation, the hydrogen-bond lengths and strengths in the DNA pairs have been

  3. Hydrogen-Bonding Capability of a Templating Difluorotoluene Nucleotide Residue in an RB69 DNA Polymerase Ternary Complex

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Shuangluo; Konigsberg, William H.; Wang, Jimin (Yale)

    2011-08-29

    Results obtained using 2,4-difluorotoluene nucleobase (dF) as a nonpolar thymine isostere by Kool and colleagues challenged the Watson-Crick dogma that hydrogen bonds between complementary bases are an absolute requirement for accurate DNA replication. Here, we report crystal structure of an RB69 DNA polymerase L561A/S565G/Y567A triple mutant ternary complex with a templating dF opposite dTTP at 1.8 {angstrom}-resolution. In this structure, direct hydrogen bonds were observed between: (i) dF and the incoming dTTP, (ii) dF and residue G568 of the polymerase, and (iii) dF and ordered water molecules surrounding the nascent base pair. Therefore, this structure provides evidence that a templating dF can form novel hydrogen bonds with the incoming dTTP and with the enzyme that differ from those formed with a templating dT.

  4. Chirality Transfer and Modulation in LB Films Derived From the Diacetylene/Melamine Hydrogen-Bonded Complex.

    Science.gov (United States)

    Zhu, Yu; Xu, Yangyang; Zou, Gang; Zhang, Qijin

    2015-08-01

    Introduction of hydrogen-bonding interaction into π-conjugated systems is a promising strategy, since the highly selective and directional hydrogen-bonding can increase the binding strength, provide enhanced stability to the assemblies, and position the π-conjugated molecules in a desired arrangement. The helical packing of the rigid melamine cores seems to play a dominating role in the subsequent formation of the peripheral helical PDA backbone. The polymerized Langmuir-Blodgett (LB) films exhibited reversible colorimetric and chiroptical changes during repeated heating-cooling cycles, which should be ascribed to the strong hydrogen-bonding interaction between the carboxylic acid and the melamine core. Further, the closely helical packing of the melamine cores could be destroyed upon exposure to HCl or NH(3) gas, whereas the peripheral helical polyaniline and polydiacetylene (PDA) backbone exhibited excellent stability. Although similar absorption changes could be observed for the films upon exposure to HCl or NH(3) gas, their distinct circular dichroism (CD) responses enabled us to distinguish the above two stimuli. © 2015 Wiley Periodicals, Inc.

  5. A quantum-chemical validation about the formation of hydrogen bonds and secondary interactions in intermolecular heterocyclic systems

    Directory of Open Access Journals (Sweden)

    Boaz Galdino Oliveira

    2009-08-01

    Full Text Available We have performed a detailed theoretical study in order to understand the charge density topology of the C2H4O···C2H2 and C2H4S···C2H2 heterocyclic hydrogen-bonded complexes. Through the calculations derived from Quantum Theory of Atoms in Molecules (QTAIM, it was observed the formation of hydrogen bonds and secondary interactions. Such analysis was performed through the determination of optimized geometries at B3LYP/6-31G(d,p level of theory, by which is that QTAIM topological operators were computed, such as the electronic density ρ(r, Laplacian Ñ2ρ(r, and ellipticity ε. The examination of the hydrogen bonds has been performed through the measurement of ρ(r, Ñ2ρ(r and ε between (O···H—C and (S···H—C, whereas the secondary interaction between axial hydrogen atoms Hα and carbon of acetylene. In this insight, it was verified the existence of secondary interaction only in C2H4S···C2H2 complex because its structure is propitious to form multiple interactions.

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

    Science.gov (United States)

    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.

  7. Hydrogen-Bonding Network and OH Stretch Vibration of Cellulose: Comparison of Computational Modeling with Polarized IR and SFG Spectra.

    Science.gov (United States)

    Lee, Christopher M; Kubicki, James D; Fan, Bingxin; Zhong, Linghao; Jarvis, Michael C; Kim, Seong H

    2015-12-10

    Hydrogen bonds play critical roles in noncovalent directional interactions determining the crystal structure of cellulose. Although diffraction studies accurately determined the coordinates of carbon and oxygen atoms in crystalline cellulose, the structural information on hydrogen atoms involved in hydrogen-bonding is still elusive. This could be complemented by vibrational spectroscopy; but the assignment of the OH stretch peaks has been controversial. In this study, we performed calculations using density functional theory with dispersion corrections (DFT-D2) for the cellulose Iβ crystal lattices with the experimentally determined carbon and oxygen coordinates. DFT-D2 calculations revealed that the OH stretch vibrations of cellulose are highly coupled and delocalized through intra- and interchain hydrogen bonds involving all OH groups in the crystal. Additionally, molecular dynamics (MD) simulations of a single cellulose microfibril showed that the conformations of OH groups exposed at the microfibril surface are not well-defined. Comparison of the computation results with the experimentally determined IR dichroism of uniaxially aligned cellulose microfibrils and the peak positions of various cellulose crystals allowed unambiguous identification of OH stretch modes observed in the vibrational spectra of cellulose.

  8. The Origin of the Non-Additivity in Resonance-Assisted Hydrogen Bond Systems.

    Science.gov (United States)

    Lin, Xuhui; Zhang, Huaiyu; Jiang, Xiaoyu; Wu, Wei; Mo, Yirong

    2017-11-09

    The concept of resonance-assisted hydrogen bond (RAHB) has been widely accepted, and its impact on structures and energetics can be best studied computationally using the block-localized wave function (BLW) method, which is a variant of ab initio valence bond (VB) theory and able to derive strictly electron-localized structures self-consistently. In this work, we use the BLW method to examine a few molecules that result from the merging of two malonaldehyde molecules. As each of these molecules contains two hydrogen bonds, these intramolecular hydrogen bonds may be cooperative or anticooperative, depended on their relative orientations, and compared with the hydrogen bond in malonaldehyde. Apart from quantitatively confirming the concept of RAHB, the comparison of the computations with and without π resonance shows that both σ-framework and π-resonance contribute to the nonadditivity in these RAHB systems with multiple hydrogen bonds.

  9. Neutron diffraction of α, β and γ cyclodextrins: hydrogen bonding patterns

    International Nuclear Information System (INIS)

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

    1983-01-01

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

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

    Science.gov (United States)

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

    2014-09-04

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

  11. Redshift or adduct stabilization -- a computational study of hydrogen bonding in adducts of protonated carboxylic acids

    DEFF Research Database (Denmark)

    Olesen, Solveig Gaarn; Hammerum, Steen

    2009-01-01

    It is generally expected that the hydrogen bond strength in a D-H-A adduct is predicted by the difference between the proton affinities of D and A, measured by the adduct stabilization, and demonstrated by the IR redshift of the D-H bond stretching vibrational frequency. These criteria do...... not always yield consistent predictions, as illustrated by the hydrogen bonds formed by the E and Z OH groups of protonated carboxylic acids. The delta-PA and the stabilization of a series of hydrogen bonded adducts indicate that the E OH group forms the stronger hydrogen bonds, whereas the bond length...... carboxylic acids are different. The OH bond length and IR redshift afford the better measure of hydrogen bond strength....

  12. Rotational and translational dynamics and their relation to hydrogen bond lifetimes in an ionic liquid by means of NMR relaxation time experiments and molecular dynamics simulation

    Science.gov (United States)

    Strate, Anne; Neumann, Jan; Overbeck, Viviane; Bonsa, Anne-Marie; Michalik, Dirk; Paschek, Dietmar; Ludwig, Ralf

    2018-05-01

    We report a concerted theoretical and experimental effort to determine the reorientational dynamics as well as hydrogen bond lifetimes for the doubly ionic hydrogen bond +OH⋯O- in the ionic liquid (2-hydroxyethyl)trimethylammonium bis(trifluoromethylsulfonyl)imide [Ch][NTf2] by using a combination of NMR relaxation time experiments, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. Due to fast proton exchange, the determination of rotational correlation times is challenging. For molecular liquids, 17O-enhanced proton relaxation time experiments have been used to determine the rotational correlation times for the OH vectors in water or alcohols. As an alternative to those expensive isotopic substitution experiments, we employed a recently introduced approach which is providing access to the rotational dynamics from a single NMR deuteron quadrupolar relaxation time experiment. Here, the deuteron quadrupole coupling constants (DQCCs) are obtained from a relation between the DQCC and the δ1H proton chemical shifts determined from a set of DFT calculated clusters in combination with experimentally determined proton chemical shifts. The NMR-obtained rotational correlation times were compared to those obtained from MD simulations and then related to viscosities for testing the applicability of popular hydrodynamic models. In addition, hydrogen bond lifetimes were derived, using hydrogen bond population correlation functions computed from MD simulations. Here, two different time domains were observed: The short-time contributions to the hydrogen lifetimes and the reorientational correlation times have roughly the same size and are located in the picosecond range, whereas the long-time contributions decay with relaxation times in the nanosecond regime and are related to rather slow diffusion processes. The computed average hydrogen bond lifetime is dominated by the long-time process, highlighting the importance and longevity of

  13. Competition between weak OH···π and CH··O hydrogen bonds: THz spectroscopy of the C2H2—H2O and C2H4—H2O complexes

    DEFF Research Database (Denmark)

    Andersen, Jonas; Heimdal, Jimmy; Nelander, B.

    2017-01-01

    an intermolecular CH⋯O hydrogen-bonded configuration of C2v symmetry with the H2O subunit acting as the hydrogen bond acceptor. The observation and assignment of two large-amplitude donor OH librational modes of the C2H4—H2O complex at 255.0 and 187.5 cm−1, respectively, confirms an intermolecular OH⋯π hydrogen...

  14. Hydrogen bonding discotic liquid crystals: Synthesis, self-assembly, and molecular recognition

    Science.gov (United States)

    Bushey, Mark Lawrence

    The triamides shown below form discotic liquid crystalline phases with intermolecular hydrogen bonding stabilizing the columnar structure, A and B. The mesomorphic orientations of the columns are dependent on the amide side chain. Three mesophasic orientations are described: columns aligned perpendicular to the surface, columns aligned parallel to the surface in a radial pattern, and columns aligned parallel to the surface in a parallel or aligned pattern. The aggregation of the tridodecyloxy-triamides show N-H shifting in the IR at elevated temperatures, an indication that hydrogen bonding is important in the association of liquid crystalline mesophases. Powder X-ray diffraction studies indicate packing of the columns into a hexagonal lattice.* Studies on triamides with chiral side chains result in molecules stacking into columns displaying a helical pitch. In concentrated solutions of dodecane, molecules with chiral side chains display behavior consistent with chiral nematic liquid crystals; a super helical packing of the chiral columns. These superhelical packed systems show temperature dependent selective reflection of visible light and fingerprint textures. Atomic force microscopy (AFM) confirms in sub-monolayer films, that molecules preferring an edge-on orientation form long columns on highly ordered pyrolytic graphite (HOPG), those that prefer a face-on orientation form large amorphous domains. Electrostatic force microscopy (EFM) images of the domains of molecules in the edge-on orientation provides no discernible polarity, imaging of the domains of molecules in the face-on orientation indicates a negative polar orientation. Scanning probe measurements (SPM) of the tridodecynyl-triamide have shown similar edge-on orientations of other tridodecyloxy-triamides. Powder X-ray diffraction of these liquid crystalline phases shows a hexagonal packing of the columnar assembly. Electro-optic switching studies indicate a piezoelectric switching mechanism, possibly

  15. Hydration dynamics of a lipid membrane: Hydrogen bond networks and lipid-lipid associations

    Science.gov (United States)

    Srivastava, Abhinav; Debnath, Ananya

    2018-03-01

    Dynamics of hydration layers of a dimyristoylphosphatidylcholine (DMPC) bilayer are investigated using an all atom molecular dynamics simulation. Based upon the geometric criteria, continuously residing interface water molecules which form hydrogen bonds solely among themselves and then concertedly hydrogen bonded to carbonyl, phosphate, and glycerol head groups of DMPC are identified. The interface water hydrogen bonded to lipids shows slower relaxation rates for translational and rotational dynamics compared to that of the bulk water and is found to follow sub-diffusive and non-diffusive behaviors, respectively. The mean square displacements and the reorientational auto-correlation functions are slowest for the interfacial waters hydrogen bonded to the carbonyl oxygen since these are buried deep in the hydrophobic core among all interfacial water studied. The intermittent hydrogen bond auto-correlation functions are calculated, which allows breaking and reformations of the hydrogen bonds. The auto-correlation functions for interfacial hydrogen bonded networks develop humps during a transition from cage-like motion to eventual power law behavior of t-3/2. The asymptotic t-3/2 behavior indicates translational diffusion dictated dynamics during hydrogen bond breaking and formation irrespective of the nature of the chemical confinement. Employing reactive flux correlation analysis, the forward rate constant of hydrogen bond breaking and formation is calculated which is used to obtain Gibbs energy of activation of the hydrogen bond breaking. The relaxation rates of the networks buried in the hydrophobic core are slower than the networks near the lipid-water interface which is again slower than bulk due to the higher Gibbs energy of activation. Since hydrogen bond breakage follows a translational diffusion dictated mechanism, chemically confined hydrogen bond networks need an activation energy to diffuse through water depleted hydrophobic environments. Our calculations

  16. Role of Monomer Sequence, Hydrogen Bonding and Mesoscale Architecture in Marine Antifouling Coatings

    Science.gov (United States)

    Segalman, Rachel

    Polypeptoids are non-natural, sequence specific polymers that offer the opportunity to probe the effect of monomer sequence, chirality, and chain shape on self-assembly and surface properties. Additionally, polypeptoid synthesis is more scaleable than traditional polypeptides suggesting their utility in large area applications. We have designed efficient marine anti-fouling coatings by using triblock copolymer scaffolds to which polypeptoids are tethered in order to tune both the modulus and surface energies with great precision. Surprisingly, when short sequences are tethered to a polymer backbone, polypeptoids consistently outperform analogous polypeptides in antifouling properties. We hypothesize that the hydrogen bonding inherent to the polypeptide backbone drives the observed differences in performance. We also find that the polymer scaffold housing the polypeptoids also plays a crucial role in directing surface presentation and therefore the overall coating properties.

  17. Economical and accurate protocol for calculating hydrogen-bond-acceptor strengths.

    Science.gov (United States)

    El Kerdawy, Ahmed; Tautermann, Christofer S; Clark, Timothy; Fox, Thomas

    2013-12-23

    A series of density functional/basis set combinations and second-order Møller-Plesset calculations have been used to test their ability to reproduce the trends observed experimentally for the strengths of hydrogen-bond acceptors in order to identify computationally efficient techniques for routine use in the computational drug-design process. The effects of functionals, basis sets, counterpoise corrections, and constraints on the optimized geometries were tested and analyzed, and recommendations (M06-2X/cc-pVDZ and X3LYP/cc-pVDZ with single-point counterpoise corrections or X3LYP/aug-cc-pVDZ without counterpoise) were made for suitable moderately high-throughput techniques.

  18. The Role of Hydrogen Bonds Of The Azeotropic Hydrous Ethanol Fuel Composition To The Exhaust Emissions

    Science.gov (United States)

    Made Suarta, I.; Nyoman Gede Baliarta, I.; Sopan Rahtika, I. P. G.; Wijaya Sunu, Putu

    2018-01-01

    In this study observed the role of hydrogen bonding to the composition of exhaust emissions which is produced hydrous ethanol fuel (95.5% v). Testing is done by using single cylinder four stroke motor engine. The composition of exhaust gas emissions is tested using exhaust gas analyzer on lean and stoichiometry mixer. The exhaust emissions produced by anhydrous ethanol were also tested. The composition of emissions produced by that two fuels is compared. The results showed CO emissions levels produced by hydrous ethanol are slightly higher than anhydrous ethanol in stoichiometric mixtures. But the composition of CO hydrous ethanol emissions is lower in the lean mix. If lean the mixer the different in the composition of emissions is increasing. On hydrous ethanol emission CO2 content little bit lower on the stoichiometric mixer and higher on the lean mixture. Exhaust emissions of ethanol fuel also produce O2. O2 hydrous ethanol emissions is higher than anhydrous ethanol fuel.

  19. Relative stabilities and the spectral signatures of stacked and hydrogen-bonded dimers of serotonin

    Science.gov (United States)

    Dev, S.; Giri, K.; Majumder, M.; Sathyamurthy, N.

    2015-10-01

    The O-HṡṡṡN hydrogen-bonded dimer of serotonin is shown to be more stable than the stacked dimer in its ground electronic state, by using the Møller-Plesset second-order perturbation theory (MP2) and the 6-31g** basis set. The vertical excitation energy for the lowest π → π* transition for the monomer as well as the dimer is predicted by time-dependent density functional theory. The experimentally observed red shift of excitation wavelength on oligomerisation is explained in terms of the change in the HOMO-LUMO energy gap due to complex formation. The impact of dimer formation on the proton magnetic resonance spectrum of serotonin monomer is also examined.

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

    Science.gov (United States)

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

    2016-05-20

    Sodium alginate/Antarctic krill protein composite material (SA/AKP) was successfully obtained by blending method. The hydrogen bonds of SA/AKP composite material were analyzed by Fourier transform infrared spectroscopy (FT-IR) and Nuclear magnetic resonance hydrogen spectrum (HNMR). Experiment manifested the existence of intermolecular and intramolecular hydrogen bonds in SA/AKP system; strength of intermolecular hydrogen bond enhanced with the increase of AKP in the composite material and the interaction strength of hydrogen bonding followed the order: OH…Ether O>OH…π>OH…N. The percentage of intermolecular hydrogen bond decreased with increase of pH. At the same time, the effect of hydrogen bonds on properties of the composite material was discussed. The increase of intermolecular hydrogen bonding led to the decrease of crystallinity, increase of apparent viscosity and surface tension, as well as obvious decrease of heat resistance of SA/AKP composite material. SA/AKP fiber SEM images and energy spectrum showed that crystallized salt was separated from the fiber, which possibly led to the fibrillation of the composite fibers. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2014-12-15

    For a complementary hydrogen-bonded complex, when every hydrogen-bond acceptor is on one side and every hydrogen-bond donor is on the other, all secondary interactions are attractive and the complex is highly stable. AAA-DDD (A=acceptor, D=donor) is considered to be the most stable among triply hydrogen-bonded sequences. The easily synthesized and further derivatized AAA-DDD system is very desirable for hydrogen-bonded functional materials. In this case, AAA and DDD, starting from 4-methoxybenzaldehyde, were synthesized with the Hantzsch pyridine synthesis and Friedländer annulation reaction. The association constant determined by fluorescence titration in chloroform at room temperature is 2.09×10(7)  M(-1) . The AAA and DDD components are not coplanar, but form a V shape in the solid state. Supramolecular polymers based on AAA-DDD triply hydrogen bonded have also been developed. This work may make AAA-DDD triply hydrogen-bonded sequences easily accessible for stimuli-responsive materials. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Soliton patterns and breakup thresholds in hydrogen-bonded chains

    International Nuclear Information System (INIS)

    Tchakoutio Nguetcho, A.S.; Kofane, T.C.

    2006-12-01

    We study the dynamics of protons in hydrogen-bonded quasi one-dimensional networks in terms of a diatomic lattice model of protons and heavy ions, with a phi-four on-site substrate potential. We show that the model with linear and nonlinear coupling between lattice sites of the quartic type for the protons admits a richer dynamics that cannot be found with linear coupling. Depending on the two types of physical boundary conditions namely, the drop and condensate types of boundary conditions, and on conditions that require the presence of linear and nonlinear dispersion terms, soliton patterns that are represented by soliton with compact support, peak, drop, bell, cusp, shock, kink, bubble and loop solitons, are derived within a continuum approximation. The phase trajectories, as well as an analytical analysis, provide information on an disintegration of soliton patterns upon reaching some critical values of the lattice parameters. The total energies of soliton patterns are exactly calculated in the displacive limit. We also show that when the phonon anharmonism is taken into account, the width and the energy of soliton patterns are in qualitative agreement with experimental data. (author)

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

    Directory of Open Access Journals (Sweden)

    Esko Oksanen

    2017-04-01

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

  4. Hydrogen bond strengths in phosphorylated and sulfated amino acid residues.

    Directory of Open Access Journals (Sweden)

    Chaya Rapp

    Full Text Available Post-translational modification by the addition of an oxoanion functional group, usually a phosphate group and less commonly a sulfate group, leads to diverse structural and functional consequences in protein systems. Building upon previous studies of the phosphoserine residue (pSer, we address the distinct nature of hydrogen bonding interactions in phosphotyrosine (pTyr and sulfotyrosine (sTyr residues. We derive partial charges for these modified residues and then study them in the context of molecular dynamics simulation of model tripeptides and sulfated protein complexes, potentials of mean force for interacting residue pairs, and a survey of the interactions of modified residues among experimental protein structures. Overall, our findings show that for pTyr, bidentate interactions with Arg are particularly dominant, as has been previously demonstrated for pSer. sTyr interactions with Arg are significantly weaker, even as compared to the same interactions made by the Glu residue. Our work sheds light on the distinct nature of these modified tyrosine residues, and provides a physical-chemical foundation for future studies with the goal of understanding their roles in systems of biological interest.

  5. Sulfate Recognition by Persistent Crystalline Capsules with Rigidified Hydrogen Bonding Cavities

    International Nuclear Information System (INIS)

    Custelcean, Radu; Remy, Priscilla; Jiang, Deen; Bonnesen, Peter V; Moyer, Bruce A

    2008-01-01

    electivity is a fundamental property of pervasive importance in chemistry and biology as reflected in phenomena as diverse as membrane transport, catalysis, sensing, adsorption, complexation, and crystallization. Although the key principles of complementarity and preorganization governing the binding interactions underlying such phenomena were delineated long ago, truly profound selectivity has proven elusive by design in part because synthetic molecular architectures are neither maximally complementary for binding target species nor sufficiently rigid. Even if a host molecule possesses a high degree of complementarity for a guest species, it all too often can distort its structure or even rearrange its conformation altogether to accommodate competing guests. One approach taken by researchers to overcome this challenge has been to devise extremely rigid molecules that bind species within complementary cavities. Although examples have been reported to demonstrate the principle, such cases are not generally of practical utility, because of inefficient synthesis and often poor kinetics. Alternatively, flexible building blocks can be employed, but then the challenge becomes one of locking them in place. Taking a cue from natural binding agents that derive their rigidity from a network of molecular interactions, especially hydrogen bonding, we present herein an example of a crystalline, self-assembled capsule that binds sulfate by a highly complementary array of rigidified hydrogen bonds (H-bonds). Although covalent or self-assembled capsules have been previously employed as anion hosts, they typically lack the strict combination of complementarity and rigidity required for high selectivity. Furthermore, the available structural data for these systems is either restricted to a limited number of anions of similar size and shape, or varies significantly from one anion to another, which hampers the rationalization of the observed selectivity. We have been employing

  6. On the observer design problem for continuous-time switched linear systems with unknown switchings

    Czech Academy of Sciences Publication Activity Database

    Gómez–Gutiérrez, D.; Čelikovský, Sergej; Ramírez–Trevino, A.; Castillo-Toledo, B.

    2015-01-01

    Roč. 352, č. 4 (2015), s. 1595-1612 ISSN 0016-0032 R&D Projects: GA ČR GA13-20433S Institutional support: RVO:67985556 Keywords : observer design * switched systems Subject RIV: BC - Control Systems Theory Impact factor: 2.327, year: 2015 http://library.utia.cas.cz/separaty/2015/TR/celikovsky-0442959.pdf

  7. Gas phase detection of the NH-P hydrogen bond and importance of secondary interactions

    DEFF Research Database (Denmark)

    Møller, Kristian Holten; Hansen, Anne Schou; Kjærgaard, Henrik Grum

    2015-01-01

    bond compared to secondary interactions. We find that B3LYP favors the hydrogen bond and M06-2X favors the secondary interactions leading to under- and overestimation, respectively, of the hydrogen bond angle relative to a DF-LCCSD(T)-F12a calculated angle. The remaining functionals tested, B3LYP-D3, B......3LYP-D3BJ, CAM-B3LYP, and ωB97X-D, as well as MP2, show comparable contributions from the hydrogen bond and the secondary interactions and are close to DF-LCCSD(T)-F12a results....

  8. Switched-Observer-Based Adaptive Neural Control of MIMO Switched Nonlinear Systems With Unknown Control Gains.

    Science.gov (United States)

    Long, Lijun; Zhao, Jun

    2017-07-01

    In this paper, the problem of adaptive neural output-feedback control is addressed for a class of multi-input multioutput (MIMO) switched uncertain nonlinear systems with unknown control gains. Neural networks (NNs) are used to approximate unknown nonlinear functions. In order to avoid the conservativeness caused by adoption of a common observer for all subsystems, an MIMO NN switched observer is designed to estimate unmeasurable states. A new switched observer-based adaptive neural control technique for the problem studied is then provided by exploiting the classical average dwell time (ADT) method and the backstepping method and the Nussbaum gain technique. It effectively handles the obstacle about the coexistence of multiple Nussbaum-type function terms, and improves the classical ADT method, since the exponential decline property of Lyapunov functions for individual subsystems is no longer satisfied. It is shown that the technique proposed is able to guarantee semiglobal uniformly ultimately boundedness of all the signals in the closed-loop system under a class of switching signals with ADT, and the tracking errors converge to a small neighborhood of the origin. The effectiveness of the approach proposed is illustrated by its application to a two inverted pendulum system.

  9. Computational and Empirical Trans-hydrogen Bond Deuterium Isotope Shifts Suggest that N1-N3 A:U Hydrogen Bonds of RNA are Shorter than those of A:T Hydrogen Bonds of DNA

    International Nuclear Information System (INIS)

    Kim, Yong-Ick; Manalo, Marlon N.; Perez, Lisa M.; LiWang, Andy

    2006-01-01

    Density functional theory calculations of isolated Watson-Crick A:U and A:T base pairs predict that adenine 13 C2 trans-hydrogen bond deuterium isotope shifts due to isotopic substitution at the pyrimidine H3, 2h Δ 13 C2, are sensitive to the hydrogen-bond distance between the N1 of adenine and the N3 of uracil or thymine, which supports the notion that 2h Δ 13 C2 is sensitive to hydrogen-bond strength. Calculated 2h Δ 13 C2 values at a given N1-N3 distance are the same for isolated A:U and A:T base pairs. Replacing uridine residues in RNA with 5-methyl uridine and substituting deoxythymidines in DNA with deoxyuridines do not statistically shift empirical 2h Δ 13 C2 values. Thus, we show experimentally and computationally that the C7 methyl group of thymine has no measurable affect on 2h Δ 13 C2 values. Furthermore, 2h Δ 13 C2 values of modified and unmodified RNA are more negative than those of modified and unmodified DNA, which supports our hypothesis that RNA hydrogen bonds are stronger than those of DNA. It is also shown here that 2h Δ 13 C2 is context dependent and that this dependence is similar for RNA and DNA

  10. Thermal decay of rhodopsin: role of hydrogen bonds in thermal isomerization of 11-cis retinal in the binding site and hydrolysis of protonated Schiff base.

    Science.gov (United States)

    Liu, Jian; Liu, Monica Yun; Nguyen, Jennifer B; Bhagat, Aditi; Mooney, Victoria; Yan, Elsa C Y

    2009-07-01

    Although thermal stability of the G protein-coupled receptor rhodopsin is directly related to its extremely low dark noise level and has recently generated considerable interest, the chemistry behind the thermal decay process of rhodopsin has remained unclear. Using UV-vis spectroscopy and HPLC analysis, we have demonstrated that the thermal decay of rhodopsin involves both hydrolysis of the protonated Schiff base and thermal isomerization of 11-cis to all-trans retinal. Examining the unfolding of rhodopsin by circular dichroism spectroscopy and measuring the rate of thermal isomerization of 11-cis retinal in solution, we conclude that the observed thermal isomerization of 11-cis to all-trans retinal happens when 11-cis retinal is in the binding pocket of rhodopsin. Furthermore, we demonstrate that solvent deuterium isotope effects are involved in the thermal decay process by decreasing the rates of thermal isomerization and hydrolysis, suggesting that the rate-determining step of these processes involves breaking hydrogen bonds. These results provide insight into understanding the critical role of an extensive hydrogen-bonding network on stabilizing the inactive state of rhodopsin and contribute to our current understanding of the low dark noise level of rhodopsin, which enables this specialized protein to function as an extremely sensitive biological light detector. Because similar hydrogen-bonding networks have also been suggested by structural analysis of two other GPCRs, beta1 and beta2 adrenergic receptors, our results could reveal a general role of hydrogen bonds in facilitating GPCR function.

  11. Hydrogen bonds in the vicinity of the special pair of the bacterial reaction center probed by hydrostatic high-pressure absorption spectroscopy.

    Science.gov (United States)

    Kangur, Liina; Jones, Michael R; Freiberg, Arvi

    2017-12-01

    Using the native bacteriochlorophyll a pigment cofactors as local probes, we investigated the response to external hydrostatic high pressure of reaction center membrane protein complexes from the photosynthetic bacterium Rhodobacter sphaeroides. Wild-type and engineered complexes were used with a varied number (0, 1 or 2) of hydrogen bonds that bind the reaction center primary donor bacteriochlorophyll cofactors to the surrounding protein scaffold. A pressure-induced breakage of hydrogen bonds was established for both detergent-purified and membrane-embedded reaction centers, but at rather different pressures: between 0.2 and 0.3GPa and at about 0.55GPa, respectively. The free energy change associated with the rupture of the single hydrogen bond present in wild-type reaction centers was estimated to be equal to 13-14kJ/mol. In the mutant with two symmetrical hydrogen bonds (FM197H) a single cooperative rupture of the two bonds was observed corresponding to an about twice stronger bond, rather than a sequential rupture of two individual bonds. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Adaptive polymeric nanomaterials utilizing reversible covalent and hydrogen bonding

    Science.gov (United States)

    Neikirk, Colin

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

  13. Observer-Based Robust Control of Uncertain Switched Fuzzy Systems with Combined Switching Controller

    Directory of Open Access Journals (Sweden)

    Hong Yang

    2013-01-01

    Full Text Available The observer-based robust control for a class of switched fuzzy (SF time-delay systems involving uncertainties and external disturbances is investigated in this paper. A switched fuzzy system, which differs from existing ones, is firstly employed to describe a nonlinear system. Next, a combined switching controller is proposed. The designed controller based on the observer instead of the state information integrates the advantages of both the switching controllers and the supplementary controllers but eliminates their disadvantages. The proposed controller provides good performance during the transient period, and the chattering effect is removed when the system state approaches the origin. Sufficient condition for the solvability of the robust control problem is given for the case that the state of system is not available. Since convex combination techniques are used to derive the delay-independent criteria, some subsystems are allowed to be unstable. Finally, various comparisons of the elaborated examples are conducted to demonstrate the effectiveness of the proposed control design approach.

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

    Energy Technology Data Exchange (ETDEWEB)

    Fifield, Leonard S.; Grate, Jay W.

    2010-06-01

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

  15. Hydrogen peroxide coordination to cobalt(II) facilitated by second-sphere hydrogen bonding

    Czech Academy of Sciences Publication Activity Database

    Wallen, C.M.; Palatinus, Lukáš; Bacsa, J.; Scarborough, C.C.

    2016-01-01

    Roč. 55, č. 39 (2016), s. 11902-11906 ISSN 0044-8249 Institutional support: RVO:68378271 Keywords : cobalt * hydrogen bonds * peroxides * peroxido ligands * second-sphere interactions Subject RIV: CC - Organic Chemistry

  16. Observability of Automata Networks: Fixed and Switching Cases.

    Science.gov (United States)

    Li, Rui; Hong, Yiguang; Wang, Xingyuan

    2018-04-01

    Automata networks are a class of fully discrete dynamical systems, which have received considerable interest in various different areas. This brief addresses the observability of automata networks and switched automata networks in a unified framework, and proposes simple necessary and sufficient conditions for observability. The results are achieved by employing methods from symbolic computation, and are suited for implementation using computer algebra systems. Several examples are presented to demonstrate the application of the results.

  17. Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase

    International Nuclear Information System (INIS)

    Langkilde, Annette; Kristensen, Søren M.; Lo Leggio, Leila; Mølgaard, Anne; Jensen, Jan H.; Houk, Andrew R.; Navarro Poulsen, Jens-Christian; Kauppinen, Sakari; Larsen, Sine

    2008-01-01

    The short hydrogen bonds in rhamnogalacturonan acetylesterase have been investigated by structure determination of an active-site mutant, 1 H NMR spectra and computational methods. Comparisons are made to database statistics. A very short carboxylic acid carboxylate hydrogen bond, buried in the protein, could explain the low-field (18 p.p.m.) 1 H NMR signal. An extremely low-field signal (at approximately 18 p.p.m.) in the 1 H NMR spectrum of rhamnogalacturonan acetylesterase (RGAE) shows the presence of a short strong hydrogen bond in the structure. This signal was also present in the mutant RGAE D192N, in which Asp192, which is part of the catalytic triad, has been replaced with Asn. A careful analysis of wild-type RGAE and RGAE D192N was conducted with the purpose of identifying possible candidates for the short hydrogen bond with the 18 p.p.m. deshielded proton. Theoretical calculations of chemical shift values were used in the interpretation of the experimental 1 H NMR spectra. The crystal structure of RGAE D192N was determined to 1.33 Å resolution and refined to an R value of 11.6% for all data. The structure is virtually identical to the high-resolution (1.12 Å) structure of the wild-type enzyme except for the interactions involving the mutation and a disordered loop. Searches of the Cambridge Structural Database were conducted to obtain information on the donor–acceptor distances of different types of hydrogen bonds. The short hydrogen-bond interactions found in RGAE have equivalents in small-molecule structures. An examination of the short hydrogen bonds in RGAE, the calculated pK a values and solvent-accessibilities identified a buried carboxylic acid carboxylate hydrogen bond between Asp75 and Asp87 as the likely origin of the 18 p.p.m. signal. Similar hydrogen-bond interactions between two Asp or Glu carboxy groups were found in 16% of a homology-reduced set of high-quality structures extracted from the PDB. The shortest hydrogen bonds in RGAE are

  18. Chemometric characterization of the hydrogen bonding complexes of secondary amides and aromatic hydrocarbons

    OpenAIRE

    Jović, Branislav; Nikolić, Aleksandar; Petrović, Slobodan

    2012-01-01

    The paper reports the results of the study of hydrogen bonding complexes between secondary amides and various aromatic hydrocarbons. The possibility of using chemometric methods was investigated in order to characterize N-H•••π hydrogen bonded complexes. Hierarchical clustering and Principal Component Analysis (PCA) have been applied on infrared spectroscopic and Taft parameters of 43 N-substituted amide complexes with different aromatic hydrocarbons. Results obtained in this report are...

  19. Hydrogen bonds of DsrD protein revealed by neutron crystallography

    International Nuclear Information System (INIS)

    Chatake, Toshiyuki; Higuchi, Yoshiki; Mizuno, Nobuhiro; Tanaka, Ichiro; Niimura, Nobuo; Morimoto, Yukio

    2008-01-01

    Hydrogen bonds of DNA-binding protein DsrD have been determined by neutron diffraction. In terms of proton donors and acceptors, DsrD protein shows striking differences from other proteins. The features of hydrogen bonds in DsrD protein from sulfate-reducing bacteria have been investigated by neutron protein crystallography. The function of DsrD has not yet been elucidated clearly, but its X-ray crystal structure revealed that it comprises a winged-helix motif and shows the highest structural homology to the DNA-binding proteins. Since any neutron structure of a DNA recognition protein has not yet been obtained, here detailed information on the hydrogen bonds in the winged-helix-motif protein is given and the following features found. (i) The number of hydrogen bonds per amino acid of DsrD is relatively fewer than for other proteins for which neutron structures were determined previously. (ii) Hydrogen bonds are localized between main-chain and main-chain atoms; there are few hydrogen bonds between main-chain and side-chain atoms and between side-chain and side-chain atoms. (iii) Hydrogen bonds inducted by protonation of specific amino acid residues (Glu50) seem to play an essential role in the dimerization of DsrD. The former two points are related to the function of the DNA-binding protein; the three-dimensional structure was mainly constructed by hydrogen bonds in main chains, while the side chains appeared to be used for another role. The latter point would be expected to contribute to the crystal growth of DsrD

  20. Hydrogen-Bonding Interactions Trigger a Spin-Flip in Iron(III) Porphyrin Complexes**

    OpenAIRE

    Sahoo, Dipankar; Quesne, Matthew G; de?Visser, Sam P; Rath, Sankar Prasad

    2015-01-01

    A key step in cytochrome?P450 catalysis includes the spin-state crossing from low spin to high spin upon substrate binding and subsequent reduction of the heme. Clearly, a weak perturbation in P450 enzymes triggers a spin-state crossing. However, the origin of the process whereby enzymes reorganize their active site through external perturbations, such as hydrogen bonding, is still poorly understood. We have thus studied the impact of hydrogen-bonding interactions on the electronic structure ...

  1. Hydrogen-Bonding Interactions Trigger a Spin-Flip in Iron(III) Porphyrin Complexes**

    OpenAIRE

    Sahoo, Dipankar; Quesne, Matthew G; de Visser, Sam P; Rath, Sankar Prasad

    2015-01-01

    A key step in cytochrome P450 catalysis includes the spin-state crossing from low spin to high spin upon substrate binding and subsequent reduction of the heme. Clearly, a weak perturbation in P450 enzymes triggers a spin-state crossing. However, the origin of the process whereby enzymes reorganize their active site through external perturbations, such as hydrogen bonding, is still poorly understood. We have thus studied the impact of hydrogen-bonding interactions on the electronic structure ...

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

    Science.gov (United States)

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

    2016-07-28

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Hermann, Andreas, E-mail: a.hermann@ed.ac.uk; Nelmes, Richard J.; Loveday, John S. [Centre for Science at Extreme Conditions and SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom); Guthrie, Malcolm [Centre for Science at Extreme Conditions and SUPA, School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom); European Spallation Source AB, P.O. Box 176, SE-22100 Lund (Sweden)

    2015-12-28

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

  4. Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

    Science.gov (United States)

    Mondal, Abhisek; Datta, Saumen

    2017-06-01

    Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  5. A theoretical perspective of the nature of hydrogen-bond types - the atoms in molecules approach

    Science.gov (United States)

    Vijaya Pandiyan, B.; Kolandaivel, P.; Deepa, P.

    2014-06-01

    Hydrogen bonds and their strength were analysed based on their X-H proton-donor bond properties and the parameters of the H-Y distance (Y proton acceptor). Strong, moderate and weak interactions in hydrogen-bond types were verified through the proton affinities of bases (PA), deprotanation enthalpies of acids (DPE) and the chemical shift (σ). The aromaticity and anti-aromaticity were analysed by means of the NICS (0) (nucleus-independent chemical shift), NICS (1) and ΔNICS (0), ΔNICS (1) of hydrogen-bonded molecules. The strength of a hydrogen bond depends on the capacity of hydrogen atom engrossing into the electronegative acceptor atom. The correlation between the above parameters and their relations were discussed through curve fitting. Bader's theory of atoms in molecules has been applied to estimate the occurrence of hydrogen bonds through eight criteria reported by Popelier et al. The lengths and potential energy shifts have been found to have a strong negative linear correlation, whereas the lengths and Laplacian shifts have a strong positive linear correlation. This study illustrates the common factors responsible for strong, moderate and weak interactions in hydrogen-bond types.

  6. Effect of pressure on the solution structure and hydrogen bond properties of aqueous N-methylacetamide

    International Nuclear Information System (INIS)

    Sarma, Rahul; Paul, Sandip

    2012-01-01

    Highlights: ► NMA molecules are associated mostly through their hydrophobic methyl groups. ► High pressure reduces association propensity causing dispersion of these moieties. ► Orientational polarization of vicinal water molecules near O and H atoms of NMA. ► NMA prefers to be a H-bond acceptor rather than a donor in interaction with water. ► Energy of these hydrogen bonds reduces slightly at high pressure. -- Abstract: Effects of high pressure on hydrophobic and hydrogen bonding interactions are investigated by employing molecular dynamics (MD) simulations of aqueous N-methylacetamide (NMA) solutions. Such systems are of interest mainly because high pressure causes protein denaturation and NMA is a computationally effective model to understand the atomic-level picture of pressure-induced structural transitions of protein. Simulations are performed for five different pressure values ranging from 1 atm to 8000 atm. We find that NMA molecules are associated mostly through their hydrophobic methyl groups and high pressure reduces this association propensity, causing dispersion of these moieties. At high pressure, structural void decreases and the packing efficiency of water molecules around NMA molecules increases. Hydrogen bond properties calculations show favorable NMA–NMA hydrogen bonds as compared to those of NMA–water hydrogen bonds and preference of NMA to be a hydrogen bond acceptor rather than a donor in interaction with water.

  7. Heterogeneous Amyloid β-Sheet Polymorphs Identified on Hydrogen Bond Promoting Surfaces Using 2D SFG Spectroscopy.

    Science.gov (United States)

    Ho, Jia-Jung; Ghosh, Ayanjeet; Zhang, Tianqi O; Zanni, Martin T

    2018-02-08

    Two-dimensional sum-frequency generation spectroscopy (2D SFG) is used to study the structures of the pentapeptide FGAIL on hydrogen bond promoting surfaces. FGAIL is the most amyloidogenic portion of the human islet amyloid polypeptide (hIAPP or amylin). In the presence of a pure gold surface, FGAIL does not form ordered structures. When the gold is coated with a self-assembled monolayer of mercaptobenzoic acid (MBA), 2D SFG spectra reveal features associated with β-sheets. Also observed are cross peaks between the FGAIL peptides and the carboxylic acid groups of the MBA monolayer, indicating that the peptides are in close contact with the surface headgroups. In the second set of samples, FGAIL peptides chemically ligated to the MBA monolayer also exhibited β-sheet features but with a much simpler spectrum. From simulations of the experiments, we conclude that the hydrogen bond promoting surface catalyzes the formation of both parallel and antiparallel β-sheet structures with several different orientations. When ligated, parallel sheets with only a single orientation are the primary structure. Thus, this hydrogen bond promoting surface creates a heterogeneous distribution of polymorph structures, consistent with a concentration effect that allows nucleation of many different amyloid seeding structures. A single well-defined seed favors one polymorph over the others, showing that the concentrating influence of a membrane can be counterbalanced by factors that favor directed fiber growth. These experiments lay the foundation for the measurement and interpretation of β-sheet structures with heterodyne-detected 2D SFG spectroscopy. The results of this model system suggest that a heterogeneous distribution of polymorphs found in nature are an indication of nonselective amyloid aggregation whereas a narrow distribution of polymorph structures is consistent with a specific protein or lipid interaction that directs fiber growth.

  8. Activation and thermodynamic parameter study of the heteronuclear C=O···H-N hydrogen bonding of diphenylurethane isomeric structures by FT-IR spectroscopy using the regularized inversion of an eigenvalue problem.

    Science.gov (United States)

    Spegazzini, Nicolas; Siesler, Heinz W; Ozaki, Yukihiro

    2012-08-02

    The doublet of the ν(C=O) carbonyl band in isomeric urethane systems has been extensively discussed in qualitative terms on the basis of FT-IR spectroscopy of the macromolecular structures. Recently, a reaction extent model was proposed as an inverse kinetic problem for the synthesis of diphenylurethane for which hydrogen-bonded and non-hydrogen-bonded C=O functionalities were identified. In this article, the heteronuclear C=O···H-N hydrogen bonding in the isomeric structure of diphenylurethane synthesized from phenylisocyanate and phenol was investigated via FT-IR spectroscopy, using a methodology of regularization for the inverse reaction extent model through an eigenvalue problem. The kinetic and thermodynamic parameters of this system were derived directly from the spectroscopic data. The activation and thermodynamic parameters of the isomeric structures of diphenylurethane linked through a hydrogen bonding equilibrium were studied. The study determined the enthalpy (ΔH = 15.25 kJ/mol), entropy (TΔS = 14.61 kJ/mol), and free energy (ΔG = 0.6 kJ/mol) of heteronuclear C=O···H-N hydrogen bonding by FT-IR spectroscopy through direct calculation from the differences in the kinetic parameters (δΔ(‡)H, -TδΔ(‡)S, and δΔ(‡)G) at equilibrium in the chemical reaction system. The parameters obtained in this study may contribute toward a better understanding of the properties of, and interactions in, supramolecular systems, such as the switching behavior of hydrogen bonding.

  9. DNA polymerase catalysis in the absence of Watson-Crick hydrogen bonds

    Science.gov (United States)

    Potapova, Olga; Chan, Chikio; DeLucia, Angela M.; Helquist, Sandra A.; Kool, Eric T.; Grindley, Nigel D. F.; Joyce, Catherine M.

    2008-01-01

    We report the first pre-steady-state kinetic studies of DNA replication in the absence of hydrogen bonds. We have used nonpolar nucleotide analogues that mimic the shape of a Watson-Crick base pair in order to investigate the kinetic consequences of a lack of hydrogen bonds in the polymerase reaction catalyzed by the Klenow fragment of DNA Polymerase I from Escherichia coli. With a thymine isostere lacking hydrogen bonding ability in the nascent pair, the efficiency (kpol/Kd) of the polymerase reaction is decreased by 30-fold, affecting ground state (Kd) and transition state (kpol) approximately equally. When both thymine and adenine analogues in the nascent pair lack hydrogen bonding ability, the efficiency of the polymerase reaction is decreased by about 1000-fold, with most the decrease attributable to the transition state. Reactions using nonpolar analogues at the primer terminal base pair demonstrated the requirement for a hydrogen bond between the polymerase and the minor groove of the primer-terminal base. The R668A mutation of Klenow fragment abolished this requirement, identifying R668 as the probable hydrogen bond donor. Detailed examination of the kinetic data suggested that Klenow fragment has an extremely low tolerance of even minor deviations of the analogue base pairs from ideal Watson-Crick geometry. Consistent with this idea, some analogue pairings were better tolerated by Klenow fragment mutants having more spacious active sites. By contrast, the Y-family polymerase Dbh was much less sensitive to changes in base pair dimensions, and more dependent on hydrogen bonding between base-paired partners. PMID:16411765

  10. Microwave measurements of the tropolone–formic acid doubly hydrogen bonded dimer

    Energy Technology Data Exchange (ETDEWEB)

    Pejlovas, Aaron M.; Kukolich, Stephen G. [Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 (United States); Serrato, Agapito; Lin, Wei [Department of Chemistry, University of Texas Rio Grande Valley, Brownsville, Texas 78520 (United States)

    2016-01-28

    The microwave spectrum was measured for the doubly hydrogen bonded dimer formed between tropolone and formic acid. The predicted symmetry of this dimer was C{sub 2v}(M), and it was expected that the concerted proton tunneling motion would be observed. After measuring 25 a- and b-type rotational transitions, no splittings which could be associated with a concerted double proton tunneling motion were observed. The calculated barrier to the proton tunneling motion is near 15 000 cm{sup −1}, which would likely make the tunneling frequencies too small to observe in the microwave spectra. The rotational and centrifugal distortion constants determined from the measured transitions were A = 2180.7186(98) MHz, B = 470.873 90(25) MHz, C = 387.689 84(22) MHz, D{sub J} = 0.0100(14) kHz, D{sub JK} = 0.102(28) kHz, and D{sub K} = 13.2(81) kHz. The B3LYP/aug-cc-pVTZ calculated rotational constants were within 1% of the experimentally determined values.

  11. Dual hydrogen-bonding motifs in complexes formed between tropolone and formic acid

    Science.gov (United States)

    Nemchick, Deacon J.; Cohen, Michael K.; Vaccaro, Patrick H.

    2016-11-01

    The near-ultraviolet π*←π absorption system of weakly bound complexes formed between tropolone (TrOH) and formic acid (FA) under cryogenic free-jet expansion conditions has been interrogated by exploiting a variety of fluorescence-based laser-spectroscopic probes, with synergistic quantum-chemical calculations built upon diverse model chemistries being enlisted to unravel the structural and dynamical properties of the pertinent ground [X˜ 1A'] and excited [A˜ 1A'(" separators="π*π )] electronic states. For binary TrOH ṡ FA adducts, the presence of dual hydrogen-bond linkages gives rise to three low-lying isomers designated (in relative energy order) as INT, EXT1, and EXT2 depending on whether docking of the FA ligand to the TrOH substrate takes place internal or external to the five-membered reaction cleft of tropolone. While the symmetric double-minimum topography predicted for the INT potential surface mediates an intermolecular double proton-transfer event, the EXT1 and EXT2 structures are interconverted by an asymmetric single proton-transfer process that is TrOH-centric in nature. The A ˜ -X ˜ origin of TrOH ṡ FA at ν˜ 00=27 484 .45 cm-1 is displaced by δ ν˜ 00=+466 .76 cm-1 with respect to the analogous feature for bare tropolone and displays a hybrid type - a/b rotational contour that reflects the configuration of binding. A comprehensive analysis of vibrational landscapes supported by the optically connected X˜ 1A' and A˜ 1A'(" separators="π*π ) manifolds, including the characteristic isotopic shifts incurred by partial deuteration of the labile TrOH and FA protons, has been performed leading to the uniform assignment of numerous intermolecular (viz., modulating hydrogen-bond linkages) and intramolecular (viz., localized on monomer subunits) degrees of freedom. The holistic interpretation of all experimental and computational findings affords compelling evidence that an external-binding motif (attributed to EXT1), rather than the

  12. Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family

    Directory of Open Access Journals (Sweden)

    Dallakyan Sargis

    2008-08-01

    Full Text Available Abstract Background Gram-negative bacteria use periplasmic-binding proteins (bPBP to transport nutrients through the periplasm. Despite immense diversity within the recognized substrates, all members of the family share a common fold that includes two domains that are separated by a conserved hinge. The hinge allows the protein to cycle between open (apo and closed (ligated conformations. Conformational changes within the proteins depend on a complex interplay of mechanical and thermodynamic response, which is manifested as an increase in thermal stability and decrease of flexibility upon ligand binding. Results We use a distance constraint model (DCM to quantify the give and take between thermodynamic stability and mechanical flexibility across the bPBP family. Quantitative stability/flexibility relationships (QSFR are readily evaluated because the DCM links mechanical and thermodynamic properties. We have previously demonstrated that QSFR is moderately conserved across a mesophilic/thermophilic RNase H pair, whereas the observed variance indicated that different enthalpy-entropy mechanisms allow similar mechanical response at their respective melting temperatures. Our predictions of heat capacity and free energy show marked diversity across the bPBP family. While backbone flexibility metrics are mostly conserved, cooperativity correlation (long-range couplings also demonstrate considerable amount of variation. Upon ligand removal, heat capacity, melting point, and mechanical rigidity are, as expected, lowered. Nevertheless, significant differences are found in molecular cooperativity correlations that can be explained by the detailed nature of the hydrogen bond network. Conclusion Non-trivial mechanical and thermodynamic variation across the family is explained by differences within the underlying H-bond networks. The mechanism is simple; variation within the H-bond networks result in altered mechanical linkage properties that directly affect

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

    Science.gov (United States)

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

    2016-06-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Hardeep Saluja

    2016-06-01

    Full Text Available 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.

  15. Intramolecular Hydrogen Bonding and Conformational Preferences of Arzanol—An Antioxidant Acylphloroglucinol

    Directory of Open Access Journals (Sweden)

    Liliana Mammino

    2017-08-01

    Full Text Available Arzanol is a naturally-occurring prenylated acylphloroglucinol isolated from Helichrysum italicum and exhibiting anti-oxidant, antibiotic and antiviral activities. The molecule contains an α-pyrone moiety attached to the phloroglucinol moiety through a methylene bridge. The presence of several hydrogen bond donor or acceptor sites makes intramolecular hydrogen bonding patterns the dominant stabilising factor. Conformers with all the possible different hydrogen bonding patterns were calculated at the HF/6-31G(d,p and DFT/B3LYP/6-31+G(d,p levels with fully relaxed geometry in vacuo and in three solvents—chloroform, acetonitrile and water (these levels being chosen to enable comparisons with previous studies on acylphloroglucinols. Calculations in solution were performed with the Polarisable Continuum Model. The results show that the lowest energy conformers have the highest number of stronger intramolecular hydrogen bonds. The influence of intramolecular hydrogen bonding patterns on the other molecular properties is also analysed.

  16. NMR Study on the Interaction of Trehalose with Lactose and Its Effect on the Hydrogen Bond Interaction in Lactose

    Directory of Open Access Journals (Sweden)

    Eric Morssing Vilén

    2013-08-01

    Full Text Available Trehalose, a well-known stress-protector of biomolecules, has been investigated for its effect on the mobility, hydration and hydrogen bond interaction of lactose using diffusion-ordered NMR spectroscopy and NMR of hydroxy protons. In ternary mixtures of trehalose, lactose and water, the two sugars have the same rate of diffusion. The chemical shifts, temperature coefficients, vicinal coupling constants and ROE of the hydroxy protons in trehalose, lactose and sucrose were measured for the disaccharides alone in water/acetone-d6 solutions as well as in mixtures. The data indicated that addition of trehalose did not change significantly the strength of the hydrogen bond interaction between GlcOH3 and GalO5' in lactose. Small upfield shifts were however measured for all hydroxy protons when the sugar concentration was increased. The chemical shift of the GlcOH3 signal in lactose showed less change, attributed to the spatial proximity to GalO5'. Chemical exchange between hydroxy protons of lactose and trehalose was observed in the ROESY NMR spectra. Similar effects were observed with sucrose indicating no specific effect of trehalose at the concentrations investigated (73 to 763 mg/mL and suggesting that it is the concentration of hydroxy groups more than the type of sugars which is guiding intermolecular interactions.

  17. Change of hydrogen bonding structure in ionic liquid mixtures by anion type

    Science.gov (United States)

    Cha, Seoncheol; Kim, Doseok

    2018-05-01

    Ionic liquid mixtures have gained attention as a way of tuning material properties continuously with composition changes. For some mixture systems, physicochemical properties such as excess molar volume have been found to be significantly different from the value expected by linear interpolation, but the origin of this deviation is not well understood yet. The microstructure of the mixture, which can range from an ideal mixture of two initial consisting ionic liquids to a different structure from those of pure materials, has been suggested as the origin of the observed deviation. The structures of several different ionic liquid mixtures are studied by IR spectroscopy to confirm this suggestion, as a particular IR absorption band (νC(2)-D) for the moiety participating in the hydrogen bonding changes sensitively with the change of the anion in the ionic liquid. The absorbance of νC(2)-D changes proportionally with the composition, and a relatively small excess molar volume is observed for the mixtures containing an electronegative halide anion. By contrast, the absorbance changes nonlinearly, and the excess molar volumes are larger for the mixtures of which one of the anions has multiple interaction sites.

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

    Science.gov (United States)

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

    2015-05-06

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

  19. Non-Classical C–H···X Hydrogen Bonding and Its Role in Asymmetric Organocatalysis

    KAUST Repository

    Ajitha, Manjaly John; Huang, Kuo-Wei

    2016-01-01

    Non-classical hydrogen bonds (NCHBs) have attracted significant interest in the past decade particularly because of their important role in asymmetric catalytic systems. These weak interactions (< 4 kcal/mol) offer much flexibility1 Introduction2 Hydrogen Bonds (HBs) and Non-Classical Hydrogen Bonds (NCHBs)3 Early Developments in NCHBs4 Selected Examples of NCHBs in Organic Transformations5 Recent Examples of NCHBs in Enantioselective Reactions6 Conclusions and Outlook

  20. Synthesis and Crystal Structure of a Three—dimensionla Manganese(Ⅱ)Complex COnstructed via Covalent and Hydrogen Bonds

    Institute of Scientific and Technical Information of China (English)

    WANGRui-Hu; ChenLi-Hua; 等

    2003-01-01

    The assembly of 1,4-benzenedicarboxylic acid (H2bdc),4,4′-bipyridine (4,4′-bipy),trimethyltin chloride and MnBr2.4H2O in hydrothermal conditions gave rise to a hydrogen-bonded three-dimensional complex {Mn(4,4′-bipy).4H2O](bdc}nwhich has been characterized by single-crystal X-ray diffraction.The complex crystallizes in the monoclinic system,space group,P2/n with a=7.0001(2),b=11.5540(3),c=11.4192(1)°↑A,β=101.754(2)°,V=904.21(4)°↑A3,Z=2,C18H20MnN2O8,Mr=447.30,Dc=1.643 g/cm3,F(000)=462 and μ(Mokα)=0.783mm1,The final R and wR are 0.0499 and 0.1301,respectively for 1335 observed reflctions with I≥2σ(I).The Mn(Ⅱ)is six-coordinated in a distorted octahedral geometry,4,4′-Bipyridine in a μ-bridge mode links [Mn(H2O)4]2+ into a linear cation chain.bdc acts as a counter anion and links the linear chains into a three-dimensional structure through hydrogen bonds.

  1. Supramolecular Assembly of Gold Nanoparticles in PS-b-P2VP Diblock Copolymers via Hydrogen Bonding

    Science.gov (United States)

    Jang, Se Gyu; Hawker, Craig J.; Kramer, Edward J.

    2011-03-01

    We report a simple route to control the spatial distribution of Au nanoparticles (Au-NPs) in PS- b -P2VP diblock copolymers using hydrogen bonding between P2VP and the hydroxyl-containing (PI-OH) units in PS- b -PIOH thiol-terminated ligands on Au-NP. End-functional thiol ligands of poly(styrene- b -1,2&3,4-isoprene-SH) are synthesized by anionic polymerization. After synthesis of Au-NPs, the inner PI block is hydroxylated by hydroboration and the resulting micelle-like Au-NPs consist of a hydrophobic PS outer brush and a hydrophilic inner PI-OH block. The influence of the hydroxyl groups is significant with strong segregation being observed to the PS/P2VP interface and then to the P2VP domain of lamellar-forming PS-b-P2VP diblock copolymers as the length of the PI-OH block is increased. The strong hydrogen bonding between nanoparticle block copolymer ligands and the P2VP block allows the Au-NPs to be incorporated within the P2VP domain to high Au--NP volume fractions ϕp without macrophase separation, driving transitions from lamellar to bicontinuous morphologies as ϕp increases.

  2. Theoretical research on effects of substituents and the solvent on quadruple hydrogen bonded complexes

    Directory of Open Access Journals (Sweden)

    Lingjia Xu

    2007-04-01

    Full Text Available Semiempirical AM1 and INDO/CIS methods were used to study the structures and spectroscopy of hydrogen bonded complexes formed by the oligophenyleneethynylene (monomer A with isophthalic acid (monomer B. The binding energies of the complexes are lowered by increasing electron-donating abilities of the substituents near the hydrogen bonds on monomer A. The first absorptions in the electronic spectra and the vibration frequencies of the N-H bonds in the IR spectra for the complexes are both red-shifted compared with those of the monomers. The presence of dimethylsulfoxide (DMSO can reduce the binding energy of the complex through hydrogen bonding. This results in a blue-shift for the first absorption in the electronic spectrum and red-shift for the vibration frequencies of the N-H bonds in the IR spectrum of the complex.

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

    Science.gov (United States)

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

    2017-02-15

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

  4. Mechanical tunability via hydrogen bonding in metal-organic frameworks with the perovskite architecture.

    Science.gov (United States)

    Li, Wei; Thirumurugan, A; Barton, Phillip T; Lin, Zheshuai; Henke, Sebastian; Yeung, Hamish H-M; Wharmby, Michael T; Bithell, Erica G; Howard, Christopher J; Cheetham, Anthony K

    2014-06-04

    Two analogous metal-organic frameworks (MOFs) with the perovskite architecture, [C(NH2)3][Mn(HCOO)3] (1) and [(CH2)3NH2][Mn(HCOO)3] (2), exhibit significantly different mechanical properties. The marked difference is attributed to their distinct modes of hydrogen bonding between the A-site amine cation and the anionic framework. The stronger cross-linking hydrogen bonding in 1 gives rise to Young's moduli and hardnesses that are up to twice those in 2, while the thermal expansion is substantially smaller. This study presents clear evidence that the mechanical properties of MOF materials can be substantially tuned via hydrogen-bonding interactions.

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

    International Nuclear Information System (INIS)

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

    2005-01-01

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

  6. Hydrogen-bond memory and water-skin supersolidity resolving the Mpemba paradox.

    Science.gov (United States)

    Zhang, Xi; Huang, Yongli; Ma, Zengsheng; Zhou, Yichun; Zhou, Ji; Zheng, Weitao; Jiang, Qing; Sun, Chang Q

    2014-11-14

    The Mpemba paradox, that is, hotter water freezes faster than colder water, has baffled thinkers like Francis Bacon, René Descartes, and Aristotle since B.C. 350. However, a commonly accepted understanding or theoretical reproduction of this effect remains challenging. Numerical reproduction of observations, shown herewith, confirms that water skin supersolidity [Zhang et al., Phys. Chem. Chem. Phys., DOI: ] enhances the local thermal diffusivity favoring heat flowing outwardly in the liquid path. Analysis of experimental database reveals that the hydrogen bond (O:H-O) possesses memory to emit energy at a rate depending on its initial storage. Unlike other usual materials that lengthen and soften all bonds when they absorb thermal energy, water performs abnormally under heating to lengthen the O:H nonbond and shorten the H-O covalent bond through inter-oxygen Coulomb coupling [Sun et al., J. Phys. Chem. Lett., 2013, 4, 3238]. Cooling does the opposite to release energy, like releasing a coupled pair of bungees, at a rate of history dependence. Being sensitive to the source volume, skin radiation, and the drain temperature, the Mpemba effect proceeds only in the strictly non-adiabatic 'source-path-drain' cycling system for the heat "emission-conduction-dissipation" dynamics with a relaxation time that drops exponentially with the rise of the initial temperature of the liquid source.

  7. Miscibility and Hydrogen Bonding in Blends of Poly(4-vinylphenol/Poly(vinyl methyl ketone

    Directory of Open Access Journals (Sweden)

    Hana Bourara

    2014-10-01

    Full Text Available The miscibility and phase behavior of poly(4-vinylphenol (PVPh with poly(vinyl methyl ketone (PVMK was investigated by differential scanning calorimetry (DSC, Fourier transform infrared spectroscopy (FTIR and scanning electron microscopy (SEM. It was shown that all blends of PVPh/PVMK are totally miscible. A DSC study showed the apparition of a single glass transition (Tg over their entire composition range. When the amount of PVPh exceeds 50% in blends, the obtained Tgs are found to be significantly higher than those observed for each individual component of the mixture, indicating that these blends are capable of forming interpolymer complexes. FTIR analysis revealed the existence of preferential specific interactions via hydrogen bonding between the hydroxyl and carbonyl groups, which intensified when the amount of PVPh was increased in blends. Furthermore, the quantitative FTIR study carried out for PVPh/PVMK blends was also performed for the vinylphenol (VPh and vinyl methyl ketone (VMK functional groups. These results were also established by scanning electron microscopy study (SEM.

  8. Toward accurate prediction of potential energy surfaces and the spectral density of hydrogen bonded systems

    International Nuclear Information System (INIS)

    Rekik, Najeh

    2014-01-01

    Despite the considerable progress made in quantum theory and computational methods, detailed descriptions of the potential energy surfaces of hydrogen-bonded systems have not yet been achieved. In addition, the hydrogen bond (H-bond) itself is still so poorly understood at the fundamental level that it remains unclear exactly what geometry constitutes a “real” H-bond. Therefore, in order to investigate features essential for hydrogen bonded complexes, a simple, efficient, and general method for calculating matrix elements of vibrational operators capable of describing the stretching modes and the H-bond bridges of hydrogen-bonded systems is proposed. The derived matrix elements are simple and computationally easy to evaluate, which makes the method suitable for vibrational studies of multiple-well potentials. The method is illustrated by obtaining potential energy surfaces for a number of two-dimensional systems with repulsive potentials chosen to be in Gaussian form for the stretching mode and of the Morse-type for the H-bond bridge dynamics. The forms of potential energy surfaces of weak and strong hydrogen bonds are analyzed by varying the asymmetry of the Gaussian potential. Moreover, the choice and applicability of the selected potential for the stretching mode and comparison with other potentials used in the area of hydrogen bond research are discussed. The approach for the determination of spectral density has been constructed in the framework of the linear response theory for which spectral density is obtained by Fourier transform of the autocorrelation function of the dipole moment operator of the fast mode. The approach involves anharmonic coupling between the high frequency stretching vibration (double well potential) and low-frequency donor-acceptor stretching mode (Morse potential) as well as the electrical anharmonicity of the dipole moment operator of the fast mode. A direct relaxation mechanism is incorporated through a time decaying exponential

  9. An S-N2-model for proton transfer in hydrogen-bonded systems

    DEFF Research Database (Denmark)

    Kuznetsov, A.M.; Ulstrup, Jens

    2004-01-01

    A new mechanism of proton transfer in donor-acceptor complexes with long hydrogen bonds is suggested. The transition is regarded as totally adiabatic. Two closest water molecules that move synchronously by hindered translation to and from the reaction complex are crucial. The water molecules induce...... a shift of the proton from the donor to the acceptor with simultaneous breaking/formation of hydrogen bonds between these molecules and the proton donor and acceptor. Expressions for the activation barrier and kinetic hydrogen isotope effect are derived. The general scheme is illustrated with the use...... of model molecular potentials, and with reference to the excess proton conductivity in aqueous solution....

  10. Chemometric characterization of the hydrogen bonding complexes of secondary amides and aromatic hydrocarbons

    Directory of Open Access Journals (Sweden)

    Jović Branislav

    2012-01-01

    Full Text Available The paper reports the results of the study of hydrogen bonding complexes between secondary amides and various aromatic hydrocarbons. The possibility of using chemometric methods was investigated in order to characterize N-H•••π hydrogen bonded complexes. Hierarchical clustering and Principal Component Analysis (PCA have been applied on infrared spectroscopic and Taft parameters of 43 N-substituted amide complexes with different aromatic hydrocarbons. Results obtained in this report are in good agreement with conclusions of other spectroscopic and thermodynamic analysis.

  11. Hydrogen bonding-mediated dehydrogenation in the ammonia borane combined graphene oxide systems

    Science.gov (United States)

    Kuang, Anlong; Liu, Taijuan; Kuang, Minquan; Yang, Ruifeng; Huang, Rui; Wang, Guangzhao; Yuan, Hongkuan; Chen, Hong; Yang, Xiaolan

    2018-03-01

    The dehydrogenation of ammonia borane (AB) adsorbed on three different graphene oxide (GO) sheets is investigated within the ab initio density functional theory. The energy barriers to direct combination the hydrogens of hydroxyl groups and the hydridic hydrogens of AB to release H2 are relatively high, indicating that the process is energetically unfavorable. Our theoretical study demonstrates that the dehydrogenation mechanism of the AB-GO systems has undergone two critical steps, first, there is the formation of the hydrogen bond (O-H-O) between two hydroxyl groups, and then, the hydrogen bond further react with the hydridic hydrogens of AB to release H2 with low reaction barriers.

  12. DNA-inspired hierarchical polymer design: electrostatics and hydrogen bonding in concert.

    Science.gov (United States)

    Hemp, Sean T; Long, Timothy E

    2012-01-01

    Nucleic acids and proteins, two of nature's biopolymers, assemble into complex structures to achieve desired biological functions and inspire the design of synthetic macromolecules containing a wide variety of noncovalent interactions including electrostatics and hydrogen bonding. Researchers have incorporated DNA nucleobases into a wide variety of synthetic monomers/polymers achieving stimuli-responsive materials, supramolecular assemblies, and well-controlled macromolecules. Recently, scientists utilized both electrostatics and complementary hydrogen bonding to orthogonally functionalize a polymer backbone through supramolecular assembly. Diverse macromolecules with noncovalent interactions will create materials with properties necessary for biomedical applications. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Long range order and hydrogen bonding in liquid methanol: A Monte Carlo simulation

    Energy Technology Data Exchange (ETDEWEB)

    Shilov, I.Y.; Rode, B.M. [Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck (Austria); Durov, V.A. [Department of Physical Chemistry, Faculty of Chemistry, Lomonosov Moscow State University, Moscow (Russian Federation)

    1999-02-01

    A Monte Carlo simulation of liquid methanol was performed in NVT ensemble at 298 K using a cubic simulation box containing 500 molecules. Long-range correlations in the liquid are discussed on the basis of site-site radial distribution functions. Hydrogen bonding and topological structure of the methanol aggregates were evaluated in detail, namely the number of linked molecules, formation of branches and cyclic structures. The necessity of larger simulation boxes for a full structural description and thermodynamic characterization of hydrogen-bonded liquids is clearly established by the results. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)

  14. Mannobiose Binding Induces Changes in Hydrogen Bonding and Protonation States of Acidic Residues in Concanavalin A As Revealed by Neutron Crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Gerlits, Oksana O. [UT/ORNL; Coates, Leighton [Biology; Woods, Robert J. [Complex; Kovalevsky, Andrey [Biology

    2017-08-30

    Plant lectins are carbohydrate-binding proteins with various biomedical applications. Concanavalin A (Con A) holds promise in treating cancerous tumors. To better understand the Con A carbohydrate binding specificity, we obtained a room-temperature neutron structure of this legume lectin in complex with a disaccharide Manα1–2Man, mannobiose. The neutron structure afforded direct visualization of the hydrogen bonding between the protein and ligand, showing that the ligand is able to alter both protonation states and interactions for residues located close to and distant from the binding site. An unprecedented low-barrier hydrogen bond was observed forming between the carboxylic side chains of Asp28 and Glu8, with the D atom positioned equidistant from the oxygen atoms having an O···D···O angle of 101.5°.

  15. Patterns of hydrogen bonding involving thiourea in the series of thioureaṡtrans-1,2-bispyridyl ethylene cocrystals - A comparative study

    Science.gov (United States)

    Kole, Goutam Kumar; Kumar, Mukesh

    2018-07-01

    Thiourea is known to act as a template to preorganise a series of trans-1,2-bispyridyl ethylenes (bpe), where the thiourea molecules present in an infinite zigzag chain with R22(8) graph set (the β-tape) which offers three different types of hydrogen bonding [J. Am. Chem. Soc. 132 (2010) 13434]. This article reports a new cocrystal of thiourea with 3,4‧-bpe and acts as a 'missing link' in the series. In this cocrystal, thiourea present in an infinite corrugated chain with R21(6) graph set, a rarely observed thiourea synthon i.e. α-tape. A comparative study has been discussed which demonstrates various types of hydrogen bonding that exist in the series and their impact on the parallel stacking of the pyridyl based olefins.

  16. Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme

    Energy Technology Data Exchange (ETDEWEB)

    Kanematsu, Yusuke; Tachikawa, Masanori [Quantum Chemistry Division, Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027 (Japan)

    2014-11-14

    Multicomponent quantum mechanical (MC-QM) calculation has been extended with ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) scheme [ONIOM(MC-QM:MM)] to take account of both the nuclear quantum effect and the surrounding environment effect. The authors have demonstrated the first implementation and application of ONIOM(MC-QM:MM) method for the analysis of the geometry and the isotope shift in hydrogen-bonding center of photoactive yellow protein. ONIOM(MC-QM:MM) calculation for a model with deprotonated Arg52 reproduced the elongation of O–H bond of Glu46 observed by neutron diffraction crystallography. Among the unique isotope shifts in different conditions, the model with protonated Arg52 with solvent effect reasonably provided the best agreement with the corresponding experimental values from liquid NMR measurement. Our results implied the availability of ONIOM(MC-QM:MM) to distinguish the local environment around hydrogen bonds in a biomolecule.

  17. Induced Smectic X Phase Through Intermolecular Hydrogen-Bonded Liquid Crystals Formed Between Citric Acid and p- n-(Octyloxy)Benzoic Acid

    Science.gov (United States)

    Sundaram, S.; Subhasri, P.; Rajasekaran, T. R.; Jayaprakasam, R.; Senthil, T. S.; Vijayakumar, V. N.

    2017-08-01

    Hydrogen-bonded liquid crystal (HBLC) is synthesized from citric acid (CA) and 4-(octyloxy)benzoic acid (8OBA) with different mole ratios. Fourier transform infrared spectroscopy (FT-IR) confirms the presence of hydrogen bond between CA and 8OBA. Nuclear magnetic resonance (NMR) spectroscopic studies validate the intermolecular complementary, cyclic type of hydrogen bond, and molecular environment in the designed HBLC complex. Powder X-ray diffraction analysis reveals the monoclinic nature of liquid crystal complex in solid phase. Liquid crystal parameters such as phase transition temperature and enthalpy values for the corresponding mesogenic phases are investigated using a polarizing optical microscope (POM) and differential scanning calorimetry (DSC). It is observed that the change in chain length and steric hindrance while increasing the mole ratio in HBLC complex induces a new smectic X (Sm X) along with higher-order smectic G (Sm G) phases by quenching of smectic C (Sm C). From the experimental observations, induced Sm X phase has been identified as a finger print texture. Also, Sm G is a multi-colored mosaic texture in 1:1, 1:2, and 1:3 mol ratios. The optical tilt angle, thermal stability factor, and enhanced thermal span width of CA + 8OBA complex are discussed.

  18. Encapsulation of Protonated Diamines in a Water-Soluble Chiral, Supramolecular Assembly Allows for Measurement of Hydrogen-Bond Breaking Followed by Nitrogen Inversion/Rotation (NIR)

    Energy Technology Data Exchange (ETDEWEB)

    Meux, Susan C.; Pluth, Michael D.; Bergman, Robert G.; Raymond, Kenneth N.

    2007-09-19

    Amine nitrogen inversion, difficult to observe in aqueous solution, is followed in a chiral, supramolecular host molecule with purely-rotational T-symmetry that reduces the local symmetry of encapsulated monoprotonated diamines and enables the observation and quantification of {Delta}G{double_dagger} for the combined hydrogen-bond breaking and nitrogen inversion rotation (NIR) process. Free energies of activation for the combined hydrogen-bond breaking and NIR process inside of the chiral assembly were determined by the NMR coalescence method. Activation parameters for ejection of the protonated amines from the assembly confirm that the NIR process responsible for the coalescence behavior occurs inside of the assembly rather than by a guest ejection/NIR/re-encapsulation mechanism. For one of the diamines, N,N,N{prime},N{prime}-tetramethylethylenediamine (TMEDA), the relative energy barriers for the hydrogen-bond breaking and NIR process were calculated at the G3(MP2)//B3LYP/6-31++G(d,p) level of theory, and these agreed well with the experimental data.

  19. On Hydrogen Bonding in the Intramolecularly Chelated Taitomers of Enolic Malondialdehyde and its Mono- and Dithio-Analogues

    DEFF Research Database (Denmark)

    Carlsen, Lars; Duus, Fritz

    1980-01-01

    The intramolecular hydrogen bondings in enolic malondialdehyde and it mono- and dithio-analogues have been evaluated by a semiempricial SCF–MO–CNDO method. The calculations predict that the hydrogen bonds play an important part in the stabilities of malondialdehyde and monothiomalondialdehyde...

  20. Ultrafast OH-stretching frequency shifts of hydrogen- bonded 2-naphthol photoacid-base complexes in solution

    Directory of Open Access Journals (Sweden)

    Batista VictorS.

    2013-03-01

    Full Text Available We characterize the transient solvent-dependent OH-stretching frequency shifts of photoacid 2-naphthol hydrogen-bonded with CH3CN in the S0- and S1-states using a combined experimental and theoretical approach, and disentangle specific hydrogen-bonding contributions from nonspecific dielectric response.

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

    DEFF Research Database (Denmark)

    Andersen, Jonas; Heimdal, J.; Larsen, René Wugt

    2015-01-01

    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 OH...O hydrogen bond formation. The experimental findings are supported by complementary...

  2. Hydrogen bond nature of ferroelectric material studied by X-ray and neutron diffraction. Electric dipole moment and proton tunneling

    International Nuclear Information System (INIS)

    Noda, Yukio; Kiyanagi, Ryoji; Mochida, Tomoyuki; Sugawara, Tadashi

    2006-01-01

    Hydrogen bond nature of MeHPLN and BrHPLN is studied using x-ray and neutron diffraction technique. We found that electric dipole moment of hydrogen atom plays an important role for the phase transition, and proton tunneling model is confirmed on this isolated hydrogen bond system. (author)

  3. Vibrational transitions in hydrogen bonded bimolecular complexes – A local mode perturbation theory approach to transition frequencies and intensities

    DEFF Research Database (Denmark)

    Mackeprang, Kasper; Kjærgaard, Henrik Grum

    2017-01-01

    The local mode perturbation theory (LMPT) model was developed to improve the description of hydrogen bonded XH-stretching transitions, where X is typically O or N. We present a modified version of the LMPT model to extend its application from hydrated bimolecular complexes to hydrogen bonded...

  4. Control of structural isomerism in noncovalent hydrogen-bonded assemblies using peripheral chiral information

    NARCIS (Netherlands)

    Prins, L.J.; Jolliffe, K.A.; Hulst, A.J.R.L.; Timmerman, P.; Reinhoudt, David

    2000-01-01

    The results of a systematic study of the structural isomerism in more than 30 noncovalent hydrogen-bonded assemblies are described. These dynamic assemblies, composed of three calix[4]arene dimelamines and six barbiturates/cyanurates, can be present in three isomeric forms with either D3, C3h, or Cs

  5. Noncovalent assembly of a fifteen-component hydrogen-bonded nanostructure

    NARCIS (Netherlands)

    Jolliffe, K.A.; Timmerman, P.; Reinhoudt, David

    1999-01-01

    A total of 72 hydrogen bonds are formed in the spontaneous association of calix[4]arene tetramelamine and barbituric acid derivatives to give nanosized assemblies of the type represented in the picture. These consist of 15 components that assemble in a completely diastereoselective sense: of the

  6. Watson-Crick base pairs with thiocarbonyl groups: How sulfur changes the hydrogen bonds in DNA

    NARCIS (Netherlands)

    Fonseca Guerra, C.; Baerends, E.J.; Bickelhaupt, F.M.

    2008-01-01

    We have theoretically analyzed mimics of Watson-Crick AT and GC base pairs in which N-H•••O hydrogen bonds are replaced by N-H•••S, using the generalized gradient approximation (GGA) of density functional theory at BP86/TZ2P level. The general effect of the above substitutions is an elongation and a

  7. Solvent effects on hydrogen bonds in Watson-Crick, mismatched, and modified DNA base pairs

    NARCIS (Netherlands)

    Poater, Jordi; Swart, Marcel; Guerra, Celia Fonseca; Bickelhaupt, F. Matthias

    2012-01-01

    We have theoretically analyzed a complete series of Watson–Crick and mismatched DNA base pairs, both in gas phase and in solution. Solvation causes a weakening and lengthening of the hydrogen bonds between the DNA bases because of the stabilization of the lone pairs involved in these bonds. We have

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

    Science.gov (United States)

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

    2015-01-01

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

  9. Hydrogen bonding properties and intermediate structure of N-(2-carboxyphenyl)salicylidenimine

    NARCIS (Netherlands)

    Ligtenbarg, Alette G.J.; Hage, Ronald; Meetsma, Auke; Feringa, Ben L.

    1999-01-01

    The hydrogen bonding properties, the nature of the tautomeric structure and dimerization of N-(2-carboxyphenyl)salicylidenimine 1 has been studied. The crystal and molecular structure of 1 has been determined by single-crystal X-ray diffraction analysis. This compound forms a dimer in the solid

  10. A theoretical perspective of the nature of hydrogen-bond types - the atoms in molecules approach

    Czech Academy of Sciences Publication Activity Database

    Pandiyan, B. V.; Kolandaivel, P.; Deepa, Palanisamy

    2014-01-01

    Roč. 112, č. 12 (2014), s. 1609-1623 ISSN 0026-8976 Institutional support: RVO:61388963 Keywords : hydrogen bond * proton affinity * deprotanation enthalpy * atoms in molecules * chemical shift Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.720, year: 2014

  11. Hydrogen Bonding in DNA Base Pairs: Reconciliation of Theory and Experiment

    NARCIS (Netherlands)

    Fonseca Guerra, C.; Bickelhaupt, F.M.; Snijders, J.G.; Baerends, E.J.

    2000-01-01

    Up till now, there has been a significant disagreement between theory and experiment regarding hydrogen bond lengths in Watson - Crick base pairs. To investigate the possible sources of this discrepancy, we have studied numerous model systems for adenine - thymine (AT) and guanine - cytosine (GC)

  12. What Is a Hydrogen Bond? Resonance Covalency in the Supramolecular Domain

    Science.gov (United States)

    Weinhold, Frank; Klein, Roger A.

    2014-01-01

    We address the broader conceptual and pedagogical implications of recent recommendations of the International Union of Pure and Applied Chemistry (IUPAC) concerning the re-definition of hydrogen bonding, drawing upon the recommended IUPAC statistical methodology of mutually correlated experimental and theoretical descriptors to operationally…

  13. On prediction of OH stretching frequencies in intramolecularly hydrogen bonded systems

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Spanget-Larsen, Jens

    2012-01-01

    OH stretching frequencies are investigated for a series of non-tautomerizing systems with intramolecular hydrogen bonds. Effective OH stretching wavenumbers are predicted by the application of empirical correlation procedures based on the results of B3LYP/6-31G(d) theoretical calculations...

  14. Solution and solid-phase halogen and C-H hydrogen bonding to perrhenate.

    Science.gov (United States)

    Massena, Casey J; Riel, Asia Marie S; Neuhaus, George F; Decato, Daniel A; Berryman, Orion B

    2015-01-28

    (1)H NMR spectroscopic and X-ray crystallographic investigations of a 1,3-bis(4-ethynyl-3-iodopyridinium)benzene scaffold with perrhenate reveal strong halogen bonding in solution, and bidentate association in the solid state. A nearly isostructural host molecule demonstrates significant C-H hydrogen bonding to perrhenate in the same phases.

  15. Restructuring the crystalline cellulose hydrogen bond network enhances its depolymerization rate

    Science.gov (United States)

    Shishir P.S. Chundawat; Giovanni Bellesia; Nirmal Uppugundla; Leonardo da Costa Sousa; Dahai Gao; Albert M. Cheh; Umesh P. Agarwal; Christopher M. Bianchetti; George N. Phillips; Paul Langan; Venkatesh Balan; S. Gnanakaran; Bruce E. Dale

    2011-01-01

    Conversion of lignocellulose to biofuels is partly inefficient due to the deleterious impact of cellulose crystallinity on enzymatic saccharification. We demonstrate how the synergistic activity of cellulases was enhanced by altering the hydrogen bond network within crystalline cellulose fibrils. We provide a molecular-scale explanation of these phenomena through...

  16. Neural Plasticity and Memory: Is Memory Encoded in Hydrogen Bonding Patterns?

    Science.gov (United States)

    Amtul, Zareen; Rahman, Atta-Ur

    2016-02-01

    Current models of memory storage recognize posttranslational modification vital for short-term and mRNA translation for long-lasting information storage. However, at the molecular level things are quite vague. A comprehensive review of the molecular basis of short and long-lasting synaptic plasticity literature leads us to propose that the hydrogen bonding pattern at the molecular level may be a permissive, vital step of memory storage. Therefore, we propose that the pattern of hydrogen bonding network of biomolecules (glycoproteins and/or DNA template, for instance) at the synapse is the critical edifying mechanism essential for short- and long-term memories. A novel aspect of this model is that nonrandom impulsive (or unplanned) synaptic activity functions as a synchronized positive-feedback rehearsal mechanism by revising the configurations of the hydrogen bonding network by tweaking the earlier tailored hydrogen bonds. This process may also maintain the elasticity of the related synapses involved in memory storage, a characteristic needed for such networks to alter intricacy and revise endlessly. The primary purpose of this review is to stimulate the efforts to elaborate the mechanism of neuronal connectivity both at molecular and chemical levels. © The Author(s) 2014.

  17. Flip-flop motion of circular hydrogen bond array in thiacalix[4]arene

    Czech Academy of Sciences Publication Activity Database

    Lang, J.; Vágnerová, K.; Czernek, Jiří; Lhoták, P.

    2006-01-01

    Roč. 18, č. 4 (2006), s. 371-381 ISSN 1061-0278 R&D Projects: GA AV ČR KJB4050311 Institutional research plan: CEZ:AV0Z40500505 Keywords : flip-flop motion * hydrogen bond * enthalpy Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.861, year: 2006

  18. Diels-Alder reactions in water : Enforced hydrophobic interaction and hydrogen bonding

    NARCIS (Netherlands)

    Engberts, Jan B.F.N.

    1995-01-01

    Second-order rate constants have been measured for the Diels-Alder (DA) reactions of cyclopentadiene with dienophiles of varying hydrophobicity and hydrogen-bond acceptor capacity in water, in a series of organic solvents and in alcohol-water mixtures. The intramolecular DA reaction of

  19. DIELS-ALDER REACTIONS IN WATER - ENFORCED HYDROPHOBIC INTERACTION AND HYDROGEN-BONDING

    NARCIS (Netherlands)

    Engberts, J.B.F.N.

    Second-order rate constants have been measured for the Diels-Alder (DA) reactions of cyclopentadiene with dienophiles of varying hydrophobicity and hydrogen-bond acceptor capacity in water, in a series of organic solvents and in alcohol-water mixtures. The intramolecular DA reaction of

  20. Photoswitchable Intramolecular Hydrogen Bonds in 5-Phenylazopyrimidines Revealed By In Situ Irradiation NMR Spectroscopy

    Czech Academy of Sciences Publication Activity Database

    Procházková, Eliška; Čechová, Lucie; Kind, J.; Janeba, Zlatko; Thiele, C. M.; Dračínský, Martin

    2018-01-01

    Roč. 24, č. 2 (2018), s. 492-498 ISSN 0947-6539 R&D Projects: GA ČR GA15-11223S Institutional support: RVO:61388963 Keywords : azopyrimidines * heterocycles * hydrogen bonds * NMR spectroscopy * UV/Vis in situ irradiation Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 5.317, year: 2016

  1. Intrinsic self-healing thermoset through covalent and hydrogen bonding interactions

    NARCIS (Netherlands)

    Araya-Hermosilla, R.; Lima, G. M. R.; Raffa, P.; Fortunato, G.; Pucci, A.; Flores, Mario E.; Moreno-Villoslada, I.; Broekhuis, A. A.; Picchioni, F.

    The intrinsic self-healing ability of polyketone (PK) chemically modified into furan and/or OH groups containing derivatives is presented. Polymers bearing different ratios of both functional groups were cross-linked via furan/bis-maleimide (Diels-Alder adducts) and hydrogen bonding interactions

  2. High Charge Mobility of a Perylene Bisimide Dye with Hydrogen-bond Formation Group

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A perylene bisimide dye covalently bonded with a hydrogen-bond formation group of 1,3, 5-triazine-2, 4-diamine has been synthesized. Its casting films show a charge carrier mobility over 10-3 cm2/Vs, which is in the range of the highest values found for other promising charge transport materials suitable for solution processable technique.

  3. A spiral-like chain from a hydrogen-bonded cyclic dichloride contain ...

    Indian Academy of Sciences (India)

    TECS

    in the form of small hydrogen bonded clusters. The results of a ... cules,4 have been recently published.5,6 Studies on water clusters are of current research interest7 as evidenced by the .... bromide dihydrate.38 The IR spectrum of the hydra-.

  4. The nature of hydrogen bonding in R-2(2)(8) crystal motifs - a computational exploration

    Czech Academy of Sciences Publication Activity Database

    Deepa, Palanisamy; Solomon, R. V.; Vedha, S. A.; Kolandaivel, P.; Venuvanalingam, P.

    2014-01-01

    Roč. 112, č. 24 (2014), s. 3195-3205 ISSN 0026-8976 Institutional support: RVO:61388963 Keywords : NCI plot * hydrogen bonds * R-2(2)(8) motif * organic crystals * NBO * QTAIM analysis Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.720, year: 2014

  5. Preparation of supramolecular polymers by copolymerization of monomers containing quadruple hydrogen bonding units with regular monomers

    NARCIS (Netherlands)

    2004-01-01

    The invention relates to the synthesis of polymers containing self-complementary quadruple hydrogen groups by copolymerizing monomers containing a quadruple hydrogen bonding group with one or more monomers of choice. The resulting polymers show unique new characteristics due to the presence of

  6. Excited state hydrogen bonding fluorescent probe: Role of structure and environment

    Energy Technology Data Exchange (ETDEWEB)

    Dey, Debarati, E-mail: debaratidey07@gmail.com [Department of Chemistry, Vidyasagar College, 39 Sankar Ghosh Lane, Kolkata 700006 (India); Sarangi, Manas Kumar [Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064 (India); Ray, Angana; Bhattacharyya, Dhananjay [Computational Science Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064 (India); Maity, Dilip Kumar [Department of Chemistry, University College of Science and Technology, 92 A.P.C. Road, Kolkata 700009 (India)

    2016-05-15

    An environment sensitive fluorescent probe, 11-benzoyl-dibenzo[a,c]phenazine (BDBPZ), has been synthesized and characterized that acts via excited state hydrogen bonding (ESHB). On interaction with hydrogen bond donating solvents the fluorescence intensity of BDBPZ increases abruptly with a concomitant bathochromic shift. The extent of fluorescence increment and the red-shift of λ{sub max} depend on hydrogen bond donating ability of the solvent associated. ESHB restricts the free rotation of the benzoyl group and hence blocks the non-radiative deactivation pathway. BDBPZ forms an exciplex with organic amine in nonpolar medium that readily disappears on increasing the polarity of the solvent. In polar environment the fluorescence of both the free molecule and excited state hydrogen bonded species are quenched on addition of amine unlike its parent dibenzo[a,c]phenazine (DBPZ), that remains very much inaccessible towards the solvent as well as quencher molecules due to its structure. This newly synthesized derivative BDBPZ is much more interactive due to the benzoyl group that is flanked outside the skeletal aromatic rings of DBPZ, which helps to sense the environment properly and thus shows better ESHB capacity than DBPZ.

  7. Photoinduced Intramolecular Bifurcate Hydrogen Bond: Unusual Mutual Influence of the Components.

    Science.gov (United States)

    Sigalov, Mark V; Shainyan, Bagrat A; Sterkhova, Irina V

    2017-09-01

    A series of 7-hydroxy-2-methylidene-2,3-dihydro-1H-inden-1-ones with 2-pyrrolyl (3), 4-dimethylaminophenyl (4), 4-nitrophenyl (5), and carboxyl group (6) as substituents at the exocyclic double bond was synthesized in the form of the E-isomers (4-6) or predominantly as the Z-isomer (3) which in solution is converted to the E-isomer. The synthesized compounds and their model analogues were studied by NMR spectroscopy, X-ray analysis, and MP2 theoretical calculations. The E-isomers having intramolecular O-H···O═C hydrogen bond are converted by UV irradiation to the Z-isomers having bifurcated O-H···O···H-X hydrogen bond. Unexpected shortening (and, thus, strengthening) of the O-H···O═C component of the bifurcated hydrogen bond upon the formation of the C═O···H-X hydrogen bond was found experimentally, proved theoretically (MP2), and explained by a roundabout interaction of the H-donor (HX) and H-acceptor (C═O) via the system of conjugated bonds.

  8. Novel indole-based inhibitors of IMPDH: introduction of hydrogen bond acceptors at indole C-3.

    Science.gov (United States)

    Watterson, Scott H; Dhar, T G Murali; Ballentine, Shelley K; Shen, Zhongqi; Barrish, Joel C; Cheney, Daniel; Fleener, Catherine A; Rouleau, Katherine A; Townsend, Robert; Hollenbaugh, Diane L; Iwanowicz, Edwin J

    2003-04-07

    The development of a series of novel indole-based inhibitors of 5'-inosine monophosphate dehydrogenase (IMPDH) is described. Various hydrogen bond acceptors at C-3 of the indole were explored. The synthesis and the structure-activity relationships (SARs) derived from in vitro studies are outlined.

  9. Effect of intramolecular hydrogen bonding and electron donation on substituted anthrasemiquinone characteristics

    International Nuclear Information System (INIS)

    Pal, H.; Mukherjee, T.

    1994-01-01

    The acid-base and redox characteristics of the semiquinones of a number of hydroxy and amino-substituted anthraquinones have been investigated. Results are explained on the basis of electron-donating properties and intramolecular hydrogen bond forming capabilities of the substituents. (author). 4 refs., 1 tab., 1 fig

  10. Indirect measurement of the cooperative hydrogen bonding of polymers using NMR quadrupole relaxation and PFG methods

    Czech Academy of Sciences Publication Activity Database

    Kříž, Jaroslav; Dybal, Jiří

    2008-01-01

    Roč. 265, č. 1 (2008), s. 225-232 ISSN 1022-1360. [European Symposium on Polymer Spectroscopy /17./. Seggauberg Leibnitz, 09.9.2007-12.09.2007] R&D Projects: GA AV ČR IAA400500604 Institutional research plan: CEZ:AV0Z40500505 Keywords : cooperative bonding * hydrogen bond * NMR * poly(4-vinylphenol) Subject RIV: CD - Macromolecular Chemistry

  11. How far can a single hydrogen bond tune the spectral properties of the GFP chromophore?

    DEFF Research Database (Denmark)

    Kiefer, Hjalte; Lattouf, Elie; Persen, Natascha Wardinghus

    2015-01-01

    Photoabsorption of the hydrogen-bonded complex of a neutral and an anionic Green Fluorescent Protein chromophore has been studied using a new dual-detection approach to action-absorption spectroscopy. Following absorption of one photon, dissociation through a single channel ensures that the full ...

  12. Unambiguous Determination of Intermolecular Hydrogen Bond of NMR Structure by Molecular Dynamics Refinement Using All-Atom Force Field and Implicit Solvent Model

    International Nuclear Information System (INIS)

    Jee, Jun Goo

    2010-01-01

    It has been shown that AMD refinement is very useful for defining an intermolecular hydrogen bond in NMR structure calculation. The refined structure also provides a clue for explaining the pH dependence in Ub and UIM complexes. As reported by Choi et al., serine-mediated hydrogen bonds are the third most populated hydrogen bonds found in protein-protein intermolecular interactions, after the backbone-backbone and backbone-aspartate ones. The abundance imposes the requirement of an method to determine the interface of protein-protein complexes. The precise geometry is particularly important in the complex structures between Ub and UBDs. Ub recognizes various targets with the same surface, where both hydrophobic and hydrophobic interactions are involved. Hence, the details of the hydrophilic interactions are necessary to find the common binding modes. The structure determination of a biomolecule by NMR depends heavily on the distance restraints derived by the NOE cross peaks that are observed between two protons within 6 A through space. Therefore, the existence of the NOE peaks and their correct assignments to two corresponding protons are essential for an accurate and precise structure determination. Recent developments of NOE assignment and calculation algorithms have enabled the determination of protein 3D structures without any manual interpretation, provided chemical shifts are assigned in most atoms and sufficient NOE peaks exist. Along with these advances, the necessity of determining complicated structures such as complexes is increasing

  13. Energy of Intramolecular Hydrogen Bonding in ortho-Hydroxybenzaldehydes, Phenones and Quinones. Transfer of Aromaticity from ipso-Benzene Ring to the Enol System(s

    Directory of Open Access Journals (Sweden)

    Danuta Rusinska-Roszak

    2017-03-01

    Full Text Available Intramolecular hydrogen bonding (HB is one of the most studied noncovalent interactions of molecules. Many physical, spectral, and topological properties of compounds are under the influence of HB, and there are many parameters used to notice and to describe these changes. Hitherto, no general method of measurement of the energy of intramolecular hydrogen bond (EHB has been put into effect. We propose the molecular tailoring approach (MTA for EHB calculation, modified to apply it to Ar-O-H∙∙∙O=C systems. The method, based on quantum calculations, was checked earlier for hydroxycarbonyl-saturated compounds, and for structures with resonance-assisted hydrogen bonding (RAHB. For phenolic compounds, the accuracy, repeatability, and applicability of the method is now confirmed for nearly 140 structures. For each structure its aromaticity HOMA indices were calculated for the central (ipso ring and for the quasiaromatic rings given by intramolecular HB. The comparison of calculated HB energies and values of estimated aromaticity indices allowed us to observe, in some substituted phenols and quinones, the phenomenon of transfer of aromaticity from the ipso-ring to the H-bonded ring via the effect of electron delocalization.

  14. Development of simulation approach for two-dimensional chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface

    Science.gov (United States)

    Qin, Yuan; Yao, Man; Hao, Ce; Wan, Lijun; Wang, Yunhe; Chen, Ting; Wang, Dong; Wang, Xudong; Chen, Yonggang

    2017-09-01

    Two-dimensional (2D) chiral self-assembly system of 5-(benzyloxy)-isophthalic acid derivative/(S)-(+)-2-octanol/highly oriented pyrolytic graphite was studied. A combined density functional theory/molecular mechanics/molecular dynamics (DFT/MM/MD) approach for system of 2D chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface was thus proposed. Structural models of the chiral assembly were built on the basis of scanning tunneling microscopy (STM) images and simplified for DFT geometry optimization. Merck Molecular Force Field (MMFF) was singled out as the suitable force field by comparing the optimized configurations of MM and DFT. MM and MD simulations for hexagonal unit model which better represented the 2D assemble network were then preformed with MMFF. The adhesion energy, evolution of self-assembly process and characteristic parameters of hydrogen bond were obtained and analyzed. According to the above simulation, the stabilities of the clockwise and counterclockwise enantiomorphous networks were evaluated. The calculational results were supported by STM observations and the feasibility of the simulation method was confirmed by two other systems in the presence of chiral co-absorbers (R)-(-)-2-octanol and achiral co-absorbers 1-octanol. This theoretical simulation method assesses the stability trend of 2D enantiomorphous assemblies with atomic scale and can be applied to the similar hydrogen bond driven 2D chirality of molecular self-assembly system.

  15. Spectroscopic studies of the intramolecular hydrogen bonding in o-hydroxy Schiff bases, derived from diaminomaleonitrile, and their deprotonation reaction products

    Science.gov (United States)

    Szady-Chełmieniecka, Anna; Kołodziej, Beata; Morawiak, Maja; Kamieński, Bohdan; Schilf, Wojciech

    2018-01-01

    The structural study of five Schiff bases derived from diaminomaleonitrile (DAMN) and 2-hydroxy carbonyl compounds was performed using 1H, 13C and 15N NMR methods in solution and in the solid state as well. ATR-FTIR and X-Ray spectroscopies were used for confirmation of the results obtained by NMR method. The imine obtained from DAMN and benzaldehyde was synthesized as a model compound which lacks intramolecular hydrogen bond. Deprotonation of all synthesized compounds was done by treating with tetramethylguanidine (TMG). NMR data revealed that salicylidene Schiff bases in DMSO solution exist as OH forms without intramolecular hydrogen bonds and independent on the substituents in aromatic ring. In the case of 2-hydroxy naphthyl derivative, the OH proton is engaged into weak intramolecular hydrogen bond. Two of imines (salDAMN and 5-BrsalDAMN) exist in DMSO solution as equilibrium mixtures of two isomers (A and B). The structures of equilibrium mixture in the solid state have been studied by NMR, ATR-FTIR and X-Ray methods. The deprotonation of three studied compounds (salDAMN, 5-BrsalDAMN, and 5-CH3salDAMN) proceeded in two different ways: deprotonation of oxygen atom (X form) or of nitrogen atom of free primary amine group of DAMN moiety (Y form). For 5-NO2salDAMN and naphDAMN only one form (X) was observed.

  16. Multicomponent hydrogen-bonding organic solids constructed from 6-hydroxy-2-naphthoic acid and N-heterocycles: Synthesis, structural characterization and synthon discussion

    Science.gov (United States)

    Zong, Yingxia; Shao, Hui; Pang, Yanyan; Wang, Debao; Liu, Kang; Wang, Lei

    2016-07-01

    Seven novel multicomponent crystals involving various substituted organic amine molecules and 6-hydroxy-2-naphthoic acid were prepared and characterized by using single crystal X-ray diffraction, infrared and thermogravimetric analyses (TGA). Crystal structures with 1,4-bis(imidazol) butane (L1) 1, 1,4-bis(imidazol-1-ylmethyl)benzene (L2) 2, 1-phenyl piperazine 3, 2-amino-4-hydroxy-6-methyl pyrimidine 4, 4,4'-bipyridine 5, 5,5'-dimethyl-2,2'-dipyridine 6, 2-amino-4,6-dimethyl pyrimidine 7 were determined. Among the seven molecular complexes, total proton transfer from 6-hydroxy-2-naphthoic acid to coformer has occurred in crystals 1-4, while the remaining were cocrystals. X-ray single-crystal structures of these complexes reveal that strong hydrogen bonding O-H···O/N-H···O/O-H···N and weak C-H···O/C-H···π/π···π intermolecular interactions direct the packing modes of molecular crystals together. The analysis of supramolecular synthons in the present structures shows that some classical supramolecular synthons like pyridine-carboxylic acid heterosynthon R22 (7) and aminopyridine-carboxylic acid heterosynthon R22 (8), are again observed in constructing the hydrogen-bonding networks in this paper. Besides, we noticed that water molecules act as a significant hydrogen-bonding connector in constructing supramolecular architectures of 3, 4, 6, and 7.

  17. Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations

    DEFF Research Database (Denmark)

    Eildal, Jonas N N; Hultqvist, Greta; Balle, Thomas

    2013-01-01

    -protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as β-strands to form an extended antiparallel β-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains...... of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding...... to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ΔΔG = 1.3 to >3.8 kcal mol(-1...

  18. Hydrogen-bonded clusters of 1, 1'-ferrocenedicarboxylic acid on Au(111) are initially formed in solution

    Science.gov (United States)

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

    2015-03-01

    Low-temperature scanning tunneling microscopy is used to observe self-assembled structures of ferrocenedicarboxylic acid (Fc(COOH)2) on the Au(111) surface. The surface is prepared by pulse-deposition of Fc(COOH)2 dissolved in methanol, and the solvent is evaporated before imaging. While the rows of hydrogen-bonded dimers that are common for carboxylic acid species are observed, the majority of adsorbed Fc(COOH)2 is instead found in six-molecule clusters with a well-defined and chiral geometry. The coverage and distribution of these clusters are consistent with a random sequential adsorption model, showing that solution-phase species are determinative of adsorbate distribution for this system under these reaction conditions.

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

    Science.gov (United States)

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Layered vanadyl (IV) nitroprusside: Magnetic interaction through a network of hydrogen bonds

    Energy Technology Data Exchange (ETDEWEB)

    Gil, D.M. [Instituto de Química Física, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Lorenzo 456, T4000CAN San Miguel de Tucumán (Argentina); Osiry, H. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México (Mexico); Pomiro, F.; Varetti, E.L. [CEQUINOR (CONICET-UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 47 and 115, 1900, La Plata (Argentina); Carbonio, R.E. [INFIQC – CONICET, Departamento de Físico Química, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre esq, Medina Allende, Ciudad Universitaria, X5000HUA Córdoba (Argentina); Alejandro, R.R. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México (Mexico); Ben Altabef, A. [INQUINOA-UNT-CONICET, Instituto de Química Física, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Lorenzo 456, T4000CAN San Miguel de Tucumán (Argentina); and others

    2016-07-15

    The hydrogen bond and π-π stacking are two non-covalent interactions able to support cooperative magnetic ordering between paramagnetic centers. This contribution reports the crystal structure and related magnetic properties for VO[Fe(CN){sub 5}NO]·2H{sub 2}O, which has a layered structure. This solid crystallizes with an orthorhombic unit cell, in the Pna2{sub 1} space group, with cell parameters a=14.1804(2), b=10.4935(1), c=7.1722(8) Å and four molecules per unit cell (Z=4). Its crystal structure was solved and refined from powder X-ray diffraction data. Neighboring layers remain linked through a network of hydrogen bonds involving a water molecule coordinated to the axial position for the V atom and the unbridged axial NO and CN ligands. An uncoordinated water molecule is found forming a triple bridge between these last two ligands and the coordinated water molecule. The magnetic measurements, recorded down to 2 K, shows a ferromagnetic interaction between V atoms located at neighboring layers, with a Curie-Weiss constant of 3.14 K. Such ferromagnetic behavior was interpreted as resulting from a superexchange interaction through the network of strong OH····O{sub H2O}, OH····N{sub CN}, and OH····O{sub NO} hydrogen bonds that connects neighboring layers. The interaction within the layer must be of antiferromagnetic nature and it was detected close to 2 K. - Graphical abstract: Coordination environment for the metals in vanadyl (II) nitroprusside dihydrate. Display Omitted - Highlights: • Crystal structure of vanadyl nitroprusside dehydrate. • Network of hydrogen bonds. • Magnetic interactions through a network of hydrogen bonds. • Layered transition metal nitroprussides.

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  2. Entanglement and co-tunneling of two equivalent protons in hydrogen bond pairs

    Science.gov (United States)

    Smedarchina, Zorka; Siebrand, Willem; Fernández-Ramos, Antonio

    2018-03-01

    A theoretical study is reported of a system of two identical symmetric hydrogen bonds, weakly coupled such that the two mobile protons can move either separately (stepwise) or together (concerted). It is modeled by two equivalent quartic potentials interacting through dipolar and quadrupolar coupling terms. The tunneling Hamiltonian has two imaginary modes (reaction coordinates) and a potential with a single maximum that may turn into a saddle-point of second order and two sets of (inequivalent) minima. Diagonalization is achieved via a modified Jacobi-Davidson algorithm. From this Hamiltonian the mechanism of proton transfer is derived. To find out whether the two protons move stepwise or concerted, a new tool is introduced, based on the distribution of the probability flux in the dividing plane of the transfer mode. While stepwise transfer dominates for very weak coupling, it is found that concerted transfer (co-tunneling) always occurs, even when the coupling vanishes since the symmetry of the Hamiltonian imposes permanent entanglement on the motions of the two protons. We quantify this entanglement and show that, for a wide range of parameters of interest, the lowest pair of states of the Hamiltonian represents a perfect example of highly entangled quantum states in continuous variables. The method is applied to the molecule porphycene for which the observed tunneling splitting is calculated in satisfactory agreement with experiment, and the mechanism of double-proton tunneling is found to be predominantly concerted. We show that, under normal conditions, when they are in the ground state, the two porphycene protons are highly entangled, which may have interesting applications. The treatment also identifies the conditions under which such a system can be handled by conventional one-instanton techniques.

  3. Oligomers Based on a Weak Hydrogen Bond Network: the Rotational Spectrum of the Tetramer of Difluoromethane

    Science.gov (United States)

    Feng, Gang; Evangelisti, Luca; Caminati, Walther; Cacelli, Ivo; Carbonaro, Laura; Prampolini, Giacomo

    2013-06-01

    Following the investigation of the rotational spectra of three conformers (so-called ``book'', ``prism'' and ``cage'') of the water hexamer, and of some other water oligomers, we report here the rotational spectrum of the tetramer of a freon molecule. The pulse jet Fourier transform microwave (pj-FTMW) spectrum of an isomer of the difluoromethane tetramer has been assigned. This molecular system is made of units of a relatively heavy asymmetric rotor, held together by a network of weak hydrogen bonds. The search of the rotational spectrum has been based on a high-level reference method, the CCSD(T)/CBS protocol. It is interesting to outline that the rotational spectrum of the water tetramer was not observed, probably because the minimum energy structures of this oligomer is effectively nonpolar in its ground states, or because of high energy tunnelling splittings. The rotational spectra of the monomer, dimer, trimer and tetramer of difluoromethane have been assigned in 1952, 1999, 2007, and 2013 (present work), with a decreasing time spacing between the various steps, looking then promising for a continuous and rapid extension of the size limits of molecular systems accessible to MW spectroscopy. C. Pérez, M. T. Muckle, D. P. Zaleski, N. A. Seifert, B. Temelso, G. C. Shields, Z. Kisiel, B. H. Pate, Science {336} (2012) 897. D. R. Lide, Jr., J. Am. Chem. Soc. {74} (1952) 3548. W. Caminati, S. Melandri, P. Moreschini, P. G. Favero, Angew. Chem. Int. Ed. {38} (1999) 2924. S. Blanco, S. Melandri, P. Ottaviani, W. Caminati, J. Am. Chem. Soc. {129} (2007) 2700.

  4. Polarized IR spectra of resonance assisted hydrogen bond (RAHB) in 2-hydroxyazobenzenes

    International Nuclear Information System (INIS)

    Rospenk, Maria; Majewska, Paulina; Czarnik-Matusewicz, Boguslawa; Sobczyk, Lucjan

    2006-01-01

    The polarized IR spectra in the region 4000-400 cm -1 over the temperature range 298-370 K of liquid crystalline (LC) 4-chloro-2'-hydroxy-4'-pentyloxyazobenzene (CHPAB) containing strong O-H...N RAHBs were studied. It has been established that molecules of this compound undergoes a spontaneous ordering in thin layers (10-20 μm) between the KRS-5 plates. The order degree expressed by the S parameter exceeds 0.6 for the Smectic A and crystalline phases. The best indicator of orientation is the mode at 1084 cm -1 as its transition dipole moment is oriented parallel to the long axis of the molecule. A good marker is also the γ(OH) band with the transition dipole moment nearly perpendicular to the long axis. The intramolecular O-H...N hydrogen bonding shows features characteristic of RAHB. The transition dipole moment of the ν(OH) vibrations forms with the long axis of the molecule the angle equal to 43 ± 3 deg. (the OH bond is oriented to this axis at the angle of 9 deg.) that convincingly speaks in favour of a coupling between the proton and π-electron motions. Similar behaviour is manifested by a broad absorption in the finger print region that can be interpreted in terms of the modification of the potential energy shape due to the plane-to-plane intermolecular interaction and appearance of the second minimum. A marked ordering of molecules in the isotropic phase is also observed evidencing some alignment of molecules extended far beyond the monomolecular layers on the surfaces of the KRS-5 windows

  5. Hydrogen-bonding behavior of various conformations of the HNO3…(CH3OH)2 ternary system.

    Science.gov (United States)

    Özsoy, Hasan; Uras-Aytemiz, Nevin; Balcı, F Mine

    2017-12-21

    Nine minima were found on the intermolecular potential energy surface for the ternary system HNO 3 (CH 3 OH) 2 at the MP2/aug-cc-pVDZ level of theory. The cooperative effect, which is a measure of the hydrogen-bonding strength, was probed in these nine conformations of HNO 3 …(CH 3 OH) 2 . The results are discussed here in terms of structures, energetics, infrared vibrational frequencies, and topological parameters. The cooperative effect was observed to be an important contributor to the total interaction energies of the cyclic conformers of HNO 3 …(CH 3 OH) 2 , meaning that it cannot be neglected in simulations in which the pair-additive potential is applied. Graphical abstract The H-bonding behavior of various conformations of the HNO 3 (CH 3 OH) 2 trimer was investigated.

  6. Enhanced dispersion stability and mobility of carboxyl-functionalized carbon nanotubes in aqueous solutions through strong hydrogen bonds

    International Nuclear Information System (INIS)

    Bahk, Yeon Kyoung; He, Xu; Gitsis, Emmanouil; Kuo, Yu-Ying; Kim, Nayoung; Wang, Jing

    2015-01-01

    Dispersion of carbon nanotubes has been heavily studied due to its importance for their technical applications, toxic effects, and environmental impacts. Common electrolytes, such as sodium chloride and potassium chloride, promote agglomeration of nanoparticles in aqueous solutions. On the contrary, we discovered that acetic electrolytes enhanced the dispersion of multi-walled carbon nanotubes (MWCNTs) with carboxyl functional group through the strong hydrogen bond, which was confirmed by UV–Vis spectrometry, dispersion observations and aerosolization-quantification method. When concentrations of acetate electrolytes such as ammonium acetate (CH 3 CO 2 NH 4 ) and sodium acetate (CH 3 CO 2 Na) were lower than 0.03 mol per liter, MWCNT suspensions showed better dispersion and had higher mobility in porous media. The effects by the acetic environment are also applicable to other nanoparticles with the carboxyl functional group, which was demonstrated with polystyrene latex particles as an example

  7. Enhanced dispersion stability and mobility of carboxyl-functionalized carbon nanotubes in aqueous solutions through strong hydrogen bonds

    Energy Technology Data Exchange (ETDEWEB)

    Bahk, Yeon Kyoung; He, Xu; Gitsis, Emmanouil; Kuo, Yu-Ying [ETH Zurich, Institute of Environmental Engineering (Switzerland); Kim, Nayoung [EMPA, Building Energy Materials and Components (Switzerland); Wang, Jing, E-mail: jing.wang@ifu.baug.ethz.ch [ETH Zurich, Institute of Environmental Engineering (Switzerland)

    2015-10-15

    Dispersion of carbon nanotubes has been heavily studied due to its importance for their technical applications, toxic effects, and environmental impacts. Common electrolytes, such as sodium chloride and potassium chloride, promote agglomeration of nanoparticles in aqueous solutions. On the contrary, we discovered that acetic electrolytes enhanced the dispersion of multi-walled carbon nanotubes (MWCNTs) with carboxyl functional group through the strong hydrogen bond, which was confirmed by UV–Vis spectrometry, dispersion observations and aerosolization-quantification method. When concentrations of acetate electrolytes such as ammonium acetate (CH{sub 3}CO{sub 2}NH{sub 4}) and sodium acetate (CH{sub 3}CO{sub 2}Na) were lower than 0.03 mol per liter, MWCNT suspensions showed better dispersion and had higher mobility in porous media. The effects by the acetic environment are also applicable to other nanoparticles with the carboxyl functional group, which was demonstrated with polystyrene latex particles as an example.

  8. The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain.

    Directory of Open Access Journals (Sweden)

    Søren W. Pedersen

    Full Text Available Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds and destabilizes hydrogen bonds formed by the carbonyl oxygen. The overall stability of the PDZ domain generally decreased for all amide-to-ester mutants due to an increase in the unfolding rate constant. For this particular region of the PDZ domain, it is therefore clear that native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding. Moreover, three of the five amide-to-ester mutants displayed an increase in the folding rate constant suggesting that the hydrogen bonds are involved in non-native interactions in the transition state for folding.

  9. The nature of hydrogen-bonding interactions in nonsteroidal anti-inflammatory drugs revealed by polarized IR spectroscopy

    Science.gov (United States)

    Hachuła, Barbara

    2018-01-01

    The influence of hydrogen-bonding interactions in the solid phase on the IR spectroscopic pattern of the νOsbnd H band of nonsteroidal anti-inflammatory drugs (NSAIDs) was studied experimentally by IR spectroscopy with the use of polarized light at two temperatures (293 K and 77 K) and in isotopic dilution. The neat and deuterated crystals of (S)-naproxen ((S)-NPX), (R)-flurbiprofen ((R)-FBP), (RS)-flurbiprofen ((RS)-FBP) and (RS)-ketoprofen ((RS)-KTP) were obtained by melt crystallization between the two squeezed CaF2 plates. The vibrational spectra of selected α-aryl propionic acid derivatives (2APAs) reflected the characteristics of their hydrogen-bond networks, i.e., 2APAs were characterized by the chain ((S)-NPX, (R)-FBP) and by dimeric ((RS)-FBP, (RS)-KTP) arrangement of hydrogen bonds in the crystal lattice. Spectroscopic results showed that the interchain (through-space) exciton coupling, between two laterally-spaced hydrogen bonds, dominates in the crystals of four NSAIDs. The same exciton coupled hydrogen bonds were also responsible for the H/D isotopic recognition mechanism in the crystalline spectra of deuterated 2APAs. The presented spectral results may help to predict the hydrogen bond motifs in the crystalline NSAIDs, which structures are not yet known, based on their IR spectra of hydrogen bond in the crystals.

  10. Simulation of the effect of hydrogen bonds on water activity of glucose and dextran using the Veytsman model.

    Science.gov (United States)

    De Vito, Francesca; Veytsman, Boris; Painter, Paul; Kokini, Jozef L

    2015-03-06

    Carbohydrates exhibit either van der Waals and ionic interactions or strong hydrogen bonding interactions. The prominence and large number of hydrogen bonds results in major contributions to phase behavior. A thermodynamic framework that accounts for hydrogen bonding interactions is therefore necessary. We have developed an extension of the thermodynamic model based on the Veytsman association theory to predict the contribution of hydrogen bonds to the behavior of glucose-water and dextran-water systems and we have calculated the free energy of mixing and its derivative leading to chemical potential and water activity. We compared our calculations with experimental data of water activity for glucose and dextran and found excellent agreement far superior to the Flory-Huggins theory. The validation of our calculations using experimental data demonstrated the validity of the Veytsman model in properly accounting for the hydrogen bonding interactions and successfully predicting water activity of glucose and dextran. Our calculations of the concentration of hydrogen bonds using the Veytsman model were instrumental in our ability to explain the difference between glucose and dextran and the role that hydrogen bonds play in contributing to these differences. The miscibility predictions showed that the Veytsman model is also able to correctly describe the phase behavior of glucose and dextran. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. RAFT Polymerization of Styrene and Maleimide in the Presence of Fluoroalcohol: Hydrogen Bonding Effects with Classical Alternating Copolymerization as Reference

    Directory of Open Access Journals (Sweden)

    Fangjun Yao

    2017-03-01

    Full Text Available The impacts of hydrogen bonding on polymerization behavior has been of interest for a long time; however, universality and in-depth understanding are still lacking. For the first time, the effect of hydrogen bonding on the classical alternating-type copolymerization of styrene and maleimide was explored. N-phenylmaleimide (N-PMI/styrene was chosen as a model monomer pair in the presence of hydrogen bonding donor solvent 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP, which interacted with N-PMI via hydrogen bonding. Reversible addition-fragmentation chain transfer polymerization (RAFT technique was used to guarantee the “living” polymerization and thus the homogeneity of chain compositions. In comparison with the polymerization in nonhydrogen bonding donor solvent (toluene, the copolymerization in HFIP exhibited a high rate and a slight deviation from alternating copolymerization tendency. The reactivity ratios of N-PMI and St were revealed to be 0.078 and 0.068, respectively, while the reactivity ratios in toluene were 0.026 and 0.050. These interesting results were reasonably explained by using computer simulations, wherein the steric repulsion and electron induction by the hydrogen bonding between HFIP and NPMI were revealed. This work first elucidated the hydrogen bonding interaction in the classical alternating-type copolymerization, which will enrich the research on hydrogen bonding-induced polymerizations.

  12. Hydrogen-Bonded Complexes of Phenylacetylene with Water, Methanol, Ammonia, and Methylamine. The Origin of Methyl Group-Induced Hydrogen Bond Switching

    Czech Academy of Sciences Publication Activity Database

    Sedlák, Robert; Hobza, Pavel; Patwari, G. N.

    2009-01-01

    Roč. 113, č. 24 (2009), s. 6620-6625 ISSN 1089-5639 R&D Projects: GA MŠk LC512 Grant - others:DST(IN) SR/S1/PC/23/2008 Institutional research plan: CEZ:AV0Z40550506 Keywords : infrared spectra * ab initio CCSD(T) calculations * phenylacetylene Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.899, year: 2009

  13. Experimental evidence for the blue-shifted hydrogen-bonded complexes of CHF3 with π-electron donors.

    Science.gov (United States)

    Gopi, R; Ramanathan, N; Sundararajan, K

    2017-06-15

    Blue-shifted hydrogen-bonded complexes of fluoroform (CHF 3 ) with benzene (C 6 H 6 ) and acetylene (C 2 H 2 ) have been investigated using matrix isolation infrared spectroscopy and ab initio computations. For CHF 3 -C 6 H 6 complex, calculations performed at the B3LYP and MP2 levels of theory using 6-311++G (d,p) and aug-cc-pVDZ basis sets discerned two minima corresponding to a 1:1 hydrogen-bonded complex. The global minimum correlated to a structure, where the interaction is between the hydrogen of CHF 3 and the π-electrons of C 6 H 6 and a weak local minimum was stabilized through H…F interaction. For the CHF 3 -C 2 H 2 complex, computation performed at MP2/aug-cc-pVDZ level of theory yielded two minima, corresponding to the cyclic C-H…π complex A (global) and a linear C-H…F (n-σ) complex B (local). Experimentally a blue-shift of 32.3cm -1 and 7.7cm -1 was observed in the ν 1 C-H stretching mode of CHF 3 sub-molecule in Ar matrix for the 1:1 C-H…π complexes of CHF 3 with C 6 H 6 and C 2 H 2 respectively. Natural bond orbital (NBO), Atoms-in-molecule (AIM) and energy decomposition (EDA) analyses were carried out to explain the blue-shifting and the nature of the interaction in these complexes. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Similarities between intra- and intermolecular hydrogen bonds in RNA kissing complexes found by means of cross-correlated relaxation

    International Nuclear Information System (INIS)

    Dittmer, Jens; Kim, Chul-Hyun; Bodenhausen, Geoffrey

    2003-01-01

    The bond lengths and dynamics of intra- and intermolecular hydrogen bonds in an RNA kissing complex have been characterized by determining the NMR relaxation rates of various double- and triple-quantum coherences that involve an imino proton and two neighboring nitrogen-15 nuclei belonging to opposite bases. New experiments allow one to determine the chemical shift anisotropy of the imino protons. The bond lengths derived from dipolar relaxation and the lack of modulations of the nitrogen chemical shifts indicate that the intermolecular hydrogen bonds which hold the kissing complex together are very similar to the intramolecular hydrogen bonds in the double-stranded stem of the RNA

  15. Novel alternating polymer adsorption/surface activation self-assembled film based on hydrogen bond

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Yongjun; Yang Shuguang; Guan Ying; Miao Xiaopeng; Cao Weixiao; Xu Jian

    2003-08-01

    By combining hydrogen bonding layer-by-layer self-assembly and the stepwise chemisorption method, a new alternating polymer adsorption/surface activation self-assembly method was developed. First a layer of diphenylamine-4-diazonium-formaldehyde resin (diazo resin or DR) is deposited on a substrate. In the following surface activation step, the diazonium groups on the surface couple with resorcin in the outside solution. The deposition of another layer of DR is feasible due to the formation of hydrogen bond between the diazonium group of DR and the hydroxy group of the resorcin moieties. The resulting film is photosensitive. After UV irradiation, the film becomes very stable towards polar organic solvents.

  16. Competing hydrogen bonding in methoxyphenols: The rotational spectrum of o-vanillin

    Science.gov (United States)

    Cocinero, Emilio J.; Lesarri, Alberto; Écija, Patricia; Basterretxea, Francisco; Fernández, José A.; Castaño, Fernando

    2011-05-01

    The conformational preferences of o-vanillin have been investigated in a supersonic jet expansion using Fourier transform microwave (FT-MW) spectroscopy. Three molecular conformations were derived from the rotational spectrum. The two most stable structures are characterized by a moderate O sbnd H···O dbnd C hydrogen bond between the aldehyde and the hydroxyl groups, with the methoxy side chain either in plane (global minimum a- cis-trans) or out of plane (a- cis-gauche) with respect to the aromatic ring. In the third conformer the aldehyde group is rotated by ca. 180°, forming a O sbnd H···O hydrogen bond between the methoxy and hydroxyl groups (s- trans-trans). Rotational parameters and relative populations are provided for the three conformations, which are compared with the results of ab initio (MP2) and density-functional (B3LYP, M05-2X) theoretical predictions.

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

    DEFF Research Database (Denmark)

    Bekö, Sándor L; Alig, Edith; Schmidt, Martin U

    2014-01-01

    Inositol, 1,2,3,4,5,6-hexahydroxycyclohexane, exists in nine stereoisomers with different crystal structures and melting points. In a previous paper on the relationship between the melting points of the inositols and the hydrogen-bonding patterns in their crystal structures [Simperler et al. (2006...... ▶). CrystEngComm 8, 589], it was noted that although all inositol crystal structures known at that time contained 12 hydrogen bonds per molecule, their melting points span a large range of about 170 °C. Our preliminary investigations suggested that the highest melting point must be corrected for the effect...... ordered phases could be determined, of which seven were obtained from laboratory X-ray powder diffraction data. Five additional phases turned out to be rotator phases and only their unit cells could be determined. Two previously unknown melting points were measured, as well as most enthalpies of melting...

  18. Measurement and modelling of hydrogen bonding in 1-alkanol plus n-alkane binary mixtures

    DEFF Research Database (Denmark)

    von Solms, Nicolas; Jensen, Lars; Kofod, Jonas L.

    2007-01-01

    Two equations of state (simplified PC-SAFT and CPA) are used to predict the monomer fraction of 1-alkanols in binary mixtures with n-alkanes. It is found that the choice of parameters and association schemes significantly affects the ability of a model to predict hydrogen bonding in mixtures, eve...... studies, which is clarified in the present work. New hydrogen bonding data based on infrared spectroscopy are reported for seven binary mixtures of alcohols and alkanes. (C) 2007 Elsevier B.V. All rights reserved....... though pure-component liquid densities and vapour pressures are predicted equally accurately for the associating compound. As was the case in the study of pure components, there exists some confusion in the literature about the correct interpretation and comparison of experimental data and theoretical...

  19. Does the Intramolecular Hydrogen Bond Affect the Spectroscopic Properties of Bicyclic Diazole Heterocycles?

    Directory of Open Access Journals (Sweden)

    Paweł Misiak

    2018-01-01

    Full Text Available The formation of an intramolecular hydrogen bond in pyrrolo[1,2-a]pyrazin-1(2H-one bicyclic diazoles was analyzed, and the influence of N-substitution on HB formation is discussed in this study. B3LYP/aug-cc-pVDZ calculations were performed for the diazole, and the quantum theory of atoms in molecules (QTAIM approach as well as the natural bond orbital (NBO method was applied to analyze the strength of this interaction. It was found that the intramolecular hydrogen bond that closes an extra ring between the C=O proton acceptor group and the CH proton donor, that is, C=O⋯H–C, influences the spectroscopic properties of pyrrolopyrazine bicyclic diazoles, particularly the carbonyl frequencies. The influence of N-substitution on the aromaticity of heterocyclic rings is also discussed in this report.

  20. A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method

    DEFF Research Database (Denmark)

    Kromann, Jimmy Charnley; Christensen, Anders Steen; Svendsen, Casper Steinmann

    2014-01-01

    We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction...... in GAMESS, while the corresponding numbers for PM6-DH+ implemented in MOPAC are 54, 17, 15, and 2. The PM6-D3H+ method as implemented in GAMESS offers an attractive alternative to PM6-DH+ in MOPAC in cases where the LBFGS optimizer must be used and a vibrational analysis is needed, e.g., when computing...... vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent, compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible....

  1. Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds

    International Nuclear Information System (INIS)

    Feng Yexin; Chen Ji; Wang Enge; Li Xin-Zheng

    2016-01-01

    The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice. (topical review)

  2. Distribution of short block copolymer chains in Binary Blends of Block Copolymers Having Hydrogen Bonding

    Science.gov (United States)

    Kwak, Jongheon; Han, Sunghyun; Kim, Jin Kon

    2014-03-01

    A binary mixture of two block copolymers whose blocks are capable of forming the hydrogen bonding allows one to obtain various microdomains that could not be expected for neat block copolymer. For instance, the binary blend of symmetric polystyrene-block-poly(2-vinylpyridine) copolymer (PS-b-P2VP) and polystyrene-block-polyhydroxystyrene copolymer (PS-b-PHS) blends where the hydrogen bonding occurred between P2VP and PHS showed hexagonally packed (HEX) cylindrical and body centered cubic (BCC) spherical microdomains. To know the exact location of short block copolymer chains at the interface, we synthesized deuterated polystyrene-block-polyhydroxystyrene copolymer (dPS-b-PHS) and prepared a binary mixture with PS-b-P2VP. We investigate, via small angle X-ray scattering (SAXS) and neutron reflectivity (NR), the exact location of shorter dPS block chain near the interface of the microdomains.

  3. Biasing hydrogen bond donating host systems towards chemical warfare agent recognition.

    Science.gov (United States)

    Hiscock, Jennifer R; Wells, Neil J; Ede, Jayne A; Gale, Philip A; Sambrook, Mark R

    2016-10-12

    A series of neutral ditopic and negatively charged, monotopic host molecules have been evaluated for their ability to bind chloride and dihydrogen phosphate anions, and neutral organophosphorus species dimethyl methylphosphonate (DMMP), pinacolyl methylphosphonate (PMP) and the chemical warfare agent (CWA) pinacolyl methylphosphonofluoridate (GD, soman) in organic solvent via hydrogen bonding. Urea, thiourea and boronic acid groups are shown to bind anions and neutral guests through the formation of hydrogen bonds, with the urea and thiourea groups typically exhibiting higher affinity interactions. The introduction of a negative charge on the host structure is shown to decrease anion affinity, whilst still allowing for high stability host-GD complex formation. Importantly, the affinity of the host for the neutral CWA GD is greater than for anionic guests, thus demonstrating the potential for selectivity reversal based on charge repulsion.

  4. Studies of Hydrogen Bonding Between N, N-Dimethylacetamide and Primary Alcohols

    Directory of Open Access Journals (Sweden)

    M. S. Manjunath

    2009-01-01

    Full Text Available Hydrogen bonding between N, N-dimethylacetamide (DMA and alcohols has been studied in carbon tetrachloride solution by an X-band Microwave bench at 936GHz. The dielectric relaxation time (τ of the binary system are obtained by both Higasi's method and Gopalakrishna method. The most likely association complex between alcohol and DMA is 1:1 stoichiometric complex through the hydroxyl group of the alcohol and the carbonyl group of amide. The results show that the interaction between alcohols and amides is 1:1 complex through the free hydroxyl group of the alcohol and the carbonyl group of amide and the alkyl chain-length of both the alcohols and amide plays an important role in the determination of the strength of hydrogen bond (O-H: C=O formed and suggests that the proton donating ability of alcohols is in the order: 1-propanol < 1-butanol < 1-pentanol and the accepting ability of DMA.

  5. Water's Interfacial Hydrogen Bonding Structure Reveals the Effective Strength of Surface-Water Interactions.

    Science.gov (United States)

    Shin, Sucheol; Willard, Adam P

    2018-06-05

    We combine all-atom molecular dynamics simulations with a mean field model of interfacial hydrogen bonding to analyze the effect of surface-water interactions on the structural and energetic properties of the liquid water interface. We show that the molecular structure of water at a weakly interacting ( i.e., hydrophobic) surface is resistant to change unless the strength of surface-water interactions are above a certain threshold. We find that below this threshold water's interfacial structure is homogeneous and insensitive to the details of the disordered surface, however, above this threshold water's interfacial structure is heterogeneous. Despite this heterogeneity, we demonstrate that the equilibrium distribution of molecular orientations can be used to quantify the energetic component of the surface-water interactions that contribute specifically to modifying the interfacial hydrogen bonding network. We identify this specific energetic component as a new measure of hydrophilicity, which we refer to as the intrinsic hydropathy.

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

    DEFF Research Database (Denmark)

    Andersen, Jonas; Heimdal, J.; Larsen, René Wugt

    2015-01-01

    ⋯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 bondinteraction 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 conformationalenergy differences together with second-order vibrational perturbation theory calculations of the large-amplitude donor OH librational band origins....

  7. Single-crystal neutron diffraction studies of hydrogen-bonded systems: Two recent examples from IPNS

    Energy Technology Data Exchange (ETDEWEB)

    Koetzle, Thomas F. [IPNS Division, Argonne National Laboratory, Argonne, IL 60439 (United States)], E-mail: tkoetzle@anl.gov; Piccoli, Paula M.B.; Schultz, Arthur J. [IPNS Division, Argonne National Laboratory, Argonne, IL 60439 (United States)

    2009-02-21

    Beginning with work in the 1950s at the first generation of research reactors, studies of hydrogen-bonded systems have been a prime application for single-crystal neutron diffraction. The range of systems studied was extended in the 1960s and 1970s, with the advent of high flux reactor sources, and beginning around 1980 studies at pulsed neutron sources have made increasingly important contributions. Recently at the Argonne Intense Pulsed Neutron Source (IPNS), working with collaborators, we completed two studies of hydrogen-bonded systems that will serve to illustrate topics of current interest. In the first study, on andrographolide, an active diterpenoid natural product, our neutron diffraction results definitively characterize the hydrogen-bonding interactions. The second IPNS study is on tetraacetylethane (TAE), a {beta}-diketone enol system with a very short, strong intramolecular O-H...O hydrogen bond. At IPNS, we have determined the neutron crystal structure of TAE at five temperatures between 20 and 298 K to investigate changes in the structure with temperature and to probe for disorder. Despite the successes illustrated by the two examples presented here and by many other studies, at present applications of single-crystal neutron diffraction continue to be extremely flux limited and constrained by the requirement for mm-size crystals for many problems. These limitations are being addressed through the realization of powerful instruments at a new generation of pulsed neutron sources, including in the USA the TOPAZ and MaNDi single-crystal diffractometers that are under development at the Spallation Neutron Source (SNS)

  8. Single-crystal neutron diffraction studies of hydrogen-bonded systems: Two recent examples from IPNS

    Science.gov (United States)

    Koetzle, Thomas F.; Piccoli, Paula M. B.; Schultz, Arthur J.

    2009-02-01

    Beginning with work in the 1950s at the first generation of research reactors, studies of hydrogen-bonded systems have been a prime application for single-crystal neutron diffraction. The range of systems studied was extended in the 1960s and 1970s, with the advent of high flux reactor sources, and beginning around 1980 studies at pulsed neutron sources have made increasingly important contributions. Recently at the Argonne Intense Pulsed Neutron Source (IPNS), working with collaborators, we completed two studies of hydrogen-bonded systems that will serve to illustrate topics of current interest. In the first study, on andrographolide, an active diterpenoid natural product, our neutron diffraction results definitively characterize the hydrogen-bonding interactions. The second IPNS study is on tetraacetylethane (TAE), a β-diketone enol system with a very short, strong intramolecular O-H⋯O hydrogen bond. At IPNS, we have determined the neutron crystal structure of TAE at five temperatures between 20 and 298 K to investigate changes in the structure with temperature and to probe for disorder. Despite the successes illustrated by the two examples presented here and by many other studies, at present applications of single-crystal neutron diffraction continue to be extremely flux limited and constrained by the requirement for mm-size crystals for many problems. These limitations are being addressed through the realization of powerful instruments at a new generation of pulsed neutron sources, including in the USA the TOPAZ and MaNDi single-crystal diffractometers that are under development at the Spallation Neutron Source (SNS).

  9. Single-crystal neutron diffraction studies of hydrogen-bonded systems: Two recent examples from IPNS

    International Nuclear Information System (INIS)

    Koetzle, Thomas F.; Piccoli, Paula M.B.; Schultz, Arthur J.

    2009-01-01

    Beginning with work in the 1950s at the first generation of research reactors, studies of hydrogen-bonded systems have been a prime application for single-crystal neutron diffraction. The range of systems studied was extended in the 1960s and 1970s, with the advent of high flux reactor sources, and beginning around 1980 studies at pulsed neutron sources have made increasingly important contributions. Recently at the Argonne Intense Pulsed Neutron Source (IPNS), working with collaborators, we completed two studies of hydrogen-bonded systems that will serve to illustrate topics of current interest. In the first study, on andrographolide, an active diterpenoid natural product, our neutron diffraction results definitively characterize the hydrogen-bonding interactions. The second IPNS study is on tetraacetylethane (TAE), a β-diketone enol system with a very short, strong intramolecular O-H...O hydrogen bond. At IPNS, we have determined the neutron crystal structure of TAE at five temperatures between 20 and 298 K to investigate changes in the structure with temperature and to probe for disorder. Despite the successes illustrated by the two examples presented here and by many other studies, at present applications of single-crystal neutron diffraction continue to be extremely flux limited and constrained by the requirement for mm-size crystals for many problems. These limitations are being addressed through the realization of powerful instruments at a new generation of pulsed neutron sources, including in the USA the TOPAZ and MaNDi single-crystal diffractometers that are under development at the Spallation Neutron Source (SNS).

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

    Science.gov (United States)

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

    2014-06-01

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

  11. Termodynamic Stability of Hydrogen-Bonded Systems in Polar and Nonpolar Environments

    Czech Academy of Sciences Publication Activity Database

    Pašalič, H.; Aquino, A. J. A.; Tunega, D.; Haberhauer, G.; Gerzabek, M. H.; Georg, H. C.; Moraes, T. F.; Coutinho, K.; Canuto, S.; Lischka, Hans

    2010-01-01

    Roč. 31, č. 10 (2010), s. 2046-2055 ISSN 0192-8651 R&D Projects: GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : hydrogen- bond ed systems * complexation in solution * thermodynamic properties * explicit and implicit solvation models * molecular dynamics and Monte Carlo simulations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.050, year: 2010

  12. Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes

    DEFF Research Database (Denmark)

    Pirrotta, Alessandro; De Vico, Luca; Solomon, Gemma C.

    2017-01-01

    to inform about molecular recognition events at the single-molecule limit. For this, we consider the force-conductance characteristics of a prototypical class of hydrogen bonded bimolecular complexes sandwiched between gold electrodes. The complexes consist of derivatives of a barbituric acid and a Hamilton...... is mechanically manipulated. The implication is that force and conductance provide complementary information about the evolution of molecules in junctions that can be used to interrogate basic structure-transport relations at the single-molecule limit....

  13. Theoretical investigations into the blue-shifting hydrogen bond in benzene complexes

    Czech Academy of Sciences Publication Activity Database

    Špirko, Vladimír; Hobza, Pavel

    2006-01-01

    Roč. 7, č. 3 (2006), s. 640-643 ISSN 1439-4235 R&D Projects: GA ČR(CZ) GA203/05/0009; GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : blue-shifting hydrogen bond * benzene complexes * London dispersion Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.449, year: 2006

  14. Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

    Science.gov (United States)

    Prisk, T. R.; Hoffmann, C.; Kolesnikov, A. I.; Mamontov, E.; Podlesnyak, A. A.; Wang, X.; Kent, P. R. C.; Anovitz, L. M.

    2018-05-01

    Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factor reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10-100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.

  15. Solute's perspective on how trimethylamine oxide, urea, and guanidine hydrochloride affect water's hydrogen bonding ability.

    Science.gov (United States)

    Pazos, Ileana M; Gai, Feng

    2012-10-18

    While the thermodynamic effects of trimethylamine oxide (TMAO), urea, and guanidine hydrochloride (GdnHCl) on protein stability are well understood, the underlying mechanisms of action are less well characterized and, in some cases, even under debate. Herein, we employ the stretching vibration of two infrared (IR) reporters, i.e., nitrile (C≡N) and carbonyl (C═O), to directly probe how these cosolvents mediate the ability of water to form hydrogen bonds with the solute of interest, e.g., a peptide. Our results show that these three agents, despite having different effects on protein stability, all act to decrease the strength of the hydrogen bonds formed between water and the infrared probe. While the behavior of TMAO appears to be consistent with its protein-protecting ability, those of urea and GdnHCl are inconsistent with their role as protein denaturants. The latter is of particular interest as it provides strong evidence indicating that although urea and GdnHCl can perturb the hydrogen-bonding property of water their protein-denaturing ability does not arise from a simple indirect mechanism.

  16. The Strength of Hydrogen Bonds between Fluoro-Organics and Alcohols, a Theoretical Study.

    Science.gov (United States)

    Rosenberg, Robert E

    2018-05-10

    Fluorinated organic compounds are ubiquitous in the pharmaceutical and agricultural industries. To better discern the mode of action of these compounds, it is critical to understand the strengths of hydrogen bonds involving fluorine. There are only a few published examples of the strengths of these bonds. This study provides a high level ab initio study of inter- and intramolecular hydrogen bonds between RF and R'OH, where R and R' are aryl, vinyl, alkyl, and cycloalkyl. Intermolecular binding energies average near 5 kcal/mol, while intramolecular binding energies average about 3 kcal/mol. Inclusion of zero-point energies and applying a counterpoise correction lessen the difference. In both series, modest increases in binding energies are seen with increased acidity of R'OH and increased electron donation of R in RF. In the intramolecular compounds, binding energy increases with the rigidity of the F-(C) n -OH ring. Inclusion of free energy corrections at 298 K results in exoergic binding energies for the intramolecular compounds and endoergic binding energies for the intermolecular compounds. Parameters such as bond lengths, vibrational frequencies, and atomic populations are consistent with formation of a hydrogen bond and with slightly stronger binding in the intermolecular cases over the intramolecular cases. However, these parameters correlated poorly with binding energies.

  17. Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry.

    Science.gov (United States)

    Morrison, Lindsay J; Chai, Wenrui; Rosenberg, Jake A; Henkelman, Graeme; Brodbelt, Jennifer S

    2017-08-02

    Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.

  18. Weak hydrogen bonding interactions influence slip system activity and compaction behavior of pharmaceutical powders.

    Science.gov (United States)

    Khomane, Kailas S; Bansal, Arvind K

    2013-12-01

    Markedly different mechanical behavior of powders of polymorphs, cocrystals, hydrate/anhydrate pairs, or structurally similar molecules has been attributed to the presence of active slip planes system in their crystal structures. Presence of slip planes in the crystal lattice allows easier slip under the applied compaction pressure. This allows greater plastic deformation of the powder and results into increased interparticulate bonding area and greater tensile strength of the compacts. Thus, based on this crystallographic feature, tableting performance of the active pharmaceutical ingredients can be predicted. Recently, we encountered a case where larger numbers of CH···O type interactions across the proposed slip planes hinder the slip and thus resist plastic deformation of the powder under the applied compaction pressure. Hence, attention must be given to these types of interactions while identifying slip planes by visualization method. Generally, slip planes are visualized as flat layers often strengthened by a two-dimensional hydrogen-bonding network within the layers or planes. No hydrogen bonding should exist between these layers to consider them as slip planes. Moreover, one should also check the presence of CH···O type interactions across these planes. Mercury software provides an option for visualization of these weak hydrogen bonding interactions. Hence, caution must be exercised while selecting appropriate solid form based on this crystallographic feature. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association.

  19. Hydrogen bonding interactions between ethylene glycol and water: density, excess molar volume, and spectral study

    Institute of Scientific and Technical Information of China (English)

    ZHANG JianBin; ZHANG PengYan; MA Kai; HAN Fang; CHEN GuoHua; WEI XiongHui

    2008-01-01

    Studies of the density and the excess molar volume of ethylene glycol (EG)-water mixtures were carried out to illustrate the hydrogen bonding interactions of EG with water at different temperatures, The re-sults suggest that a likely complex of 3 ethylene glycol molecules bonding with 4 water molecules in an ethylene glycol-water mixture (EGW) is formed at the maximal excess molar volume, which displays stronger absorption capabilities for SO2 when the concentration of SO2 reaches 400×106 (volume ratio) in the gas phase. Meanwhile, FTIR and UV spectra of EGWs were recorded at various EG concentra-tions to display the hydrogen bonding interactions of EG with water. The FTIR spectra show that the stretching vibrational band of hydroxyl in the EGWs shifts to a lower frequency and the bending vibra-tional band of water shifts to a higher frequency with increasing the EG concentration, respectively. Furthermore, the UV spectra show that the electron transferring band of the hydroxyl oxygen in EG shows red shift with increasing the EG concentration. The frequency shifts in FTIR spectra and the shifts of absorption bands in UV absorption spectra of EGWs are interpreted as the strong hydrogen bonding interactions of the hydrogen atoms in water with the hydroxyl oxygen atoms of EG.

  20. Hydrogen-bond network and pH sensitivity in human transthyretin

    Energy Technology Data Exchange (ETDEWEB)

    Yokoyama, Takeshi, E-mail: tyokoya3@pha.u-toyama.ac.jp; Mizuguchi, Mineyuki; Nabeshima, Yuko [University of Toyama, 2630 Sugitani, Toyama 930-0914 (Japan); Kusaka, Katsuhiro; Yamada, Taro [Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan); Hosoya, Takaaki [Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan); Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511 (Japan); Ohhara, Takashi [Comprehensive Research Organization for Science and Society, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan); Kurihara, Kazuo [Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195 (Japan); Tanaka, Ichiro [Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan); Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511 (Japan); Niimura, Nobuo [Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan)

    2013-11-01

    The neutron crystal structure of human transthyretin is presented. Transthyretin (TTR) is a tetrameric protein. TTR misfolding and aggregation are associated with human amyloid diseases. Dissociation of the TTR tetramer is believed to be the rate-limiting step in the amyloid fibril formation cascade. Low pH is known to promote dissociation into monomer and the formation of amyloid fibrils. In order to reveal the molecular mechanisms underlying pH sensitivity and structural stabilities of TTR, neutron diffraction studies were conducted using the IBARAKI Biological Crystal Diffractometer with the time-of-flight method. Crystals for the neutron diffraction experiments were grown up to 2.5 mm{sup 3} for four months. The neutron crystal structure solved at 2.0 Å revealed the protonation states of His88 and the detailed hydrogen-bond network depending on the protonation states of His88. This hydrogen-bond network is involved in monomer–monomer and dimer–dimer interactions, suggesting that the double protonation of His88 by acidification breaks the hydrogen-bond network and causes the destabilization of the TTR tetramer. Structural comparison with the X-ray crystal structure at acidic pH identified the three amino acid residues responsible for the pH sensitivity of TTR. Our neutron model provides insights into the molecular stability related to amyloidosis.

  1. Performance of Several Density Functional Theory Methods on Describing Hydrogen-Bond Interactions.

    Science.gov (United States)

    Rao, Li; Ke, Hongwei; Fu, Gang; Xu, Xin; Yan, Yijing

    2009-01-13

    We have investigated eleven density functionals, including LDA, PBE, mPWPW91, TPSS, B3LYP, X3LYP, PBE0, O3LYP, B97-1, MPW1K, and TPSSh, for their performances on describing hydrogen bond (HB) interactions. The emphasis has been laid not only on their abilities to calculate the intermolecular hydrogen bonding energies but also on their performances in predicting the relative energies of intermolecular H-bonded complexes and the conformer stabilities due to intramolecular hydrogen bondings. As compared to the best theoretical values, we found that although PBE and PBE0 gave the best estimation of HB strengths, they might fail to predict the correct order of relative HB energies, which might lead to a wrong prediction of the global minimum for different conformers. TPSS and TPSSh did not always improve over PBE and PBE0. B3LYP was found to underestimate the intermolecular HB strengths but was among the best performers in calculating the relative HB energies. We showed here that X3LYP and B97-1 were able to give good values for both absolute HB strengths and relative HB energies, making these functionals good candidates for HB description.

  2. The contribution of the hydrogen bond acidity on the lipophilicity of drugs estimated from chromatographic measurements.

    Science.gov (United States)

    Pallicer, Juan M; Pascual, Rosalia; Port, Adriana; Rosés, Martí; Ràfols, Clara; Bosch, Elisabeth

    2013-02-14

    The influence of the hydrogen bond acidity when the 1-octanol/water partition coefficient (log P(o/w)) of drugs is determined from chromatographic measurements was studied in this work. This influence was firstly evaluated by means of the comparison between the Abraham solvation parameter model when it is applied to express the 1-octanol/water partitioning and the chromatographic retention, expressed as the solute polarity p. Then, several hydrogen bond acidity descriptors were compared in order to determine properly the log P(o/w) of drugs. These descriptors were obtained from different software and comprise two-dimensional parameters such as the calculated Abraham hydrogen bond acidity A and three-dimensional descriptors like HDCA-2 from CODESSA program or WO1 and DRDODO descriptors calculated from Volsurf+software. The additional HOMO-LUMO polarizability descriptor should be added when the three-dimensional descriptors are used to complement the chromatographic retention. The models generated using these descriptors were compared studying the correlations between the determined log P(o/w) values and the reference ones. The comparison showed that there was no significant difference between the tested models and any of them was able to determine the log P(o/w) of drugs from a single chromatographic measurement and the correspondent molecular descriptors terms. However, the model that involved the calculated A descriptor was simpler and it is thus recommended for practical uses. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. Vibrational Spectroscopy of Intramolecular Hydrogen Bonds in the Infrared and Near-Infrared Regions

    DEFF Research Database (Denmark)

    Schrøder, Sidsel Dahl

    and 1,4-diaminobutane). Experimentally, the hydrogen bonds have been studied with vibrational spectroscopy in the infrared and near-infrared regions. The focus is primarily on spectra recorded in the near-infrared regions, which in these studies are dominated by O-H and N-H stretching overtones....... Overtone spectra have been recorded with intracavity laser photoacoustic laser spectroscopy and conventional long path absorption spectroscopy. Theoretically, a combination of electronic structure calculations and local mode models have been employed to guide the assignment of bands in the vibrational......,4-diaminobutane, no sign of intramolecular N-H···N hydrogen bonds were identified in the overtone spectra. However, theoretical analyzes indicate that intramolecular N-H···N hydrogen bonds are present in all three diamines if two hydrogen atoms on one of the methylene groups are substituted with triuoromethyl...

  4. Measuring the relative hydrogen-bonding strengths of alcohols in aprotic organic solvents.

    Science.gov (United States)

    Tessensohn, Malcolm E; Lee, Melvyn; Hirao, Hajime; Webster, Richard D

    2015-01-12

    Voltammetric experiments with 9,10-anthraquinone and 1,4-benzoquinone performed under controlled moisture conditions indicate that the hydrogen-bond strengths of alcohols in aprotic organic solvents can be differentiated by the electrochemical parameter ΔEp (red) =|Ep (red(1)) -Ep (red(2)) |, which is the potential separation between the two one-electron reduction processes. This electrochemical parameter is inversely related to the strength of the interactions and can be used to differentiate between primary, secondary, tertiary alcohols, and even diols, as it is sensitive to both their steric and electronic properties. The results are highly reproducible across two solvents with substantially different hydrogen-bonding properties (CH3 CN and CH2 Cl2 ) and are supported by density functional theory calculations. This indicates that the numerous solvent-alcohol interactions are less significant than the quinone-alcohol hydrogen-bonding interactions. The utility of ΔEp (red) was illustrated by comparisons between 1) 3,3,3-trifluoro-n-propanol and 1,3-difluoroisopropanol and 2) ethylene glycol and 2,2,2-trifluoroethanol. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Directory of Open Access Journals (Sweden)

    Sándor L. Bekö

    2014-01-01

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

  6. Overnight switching from oxcarbazepine to eslicarbazepine acetate: an observational study.

    Science.gov (United States)

    Schmid, E; Kuchukhidze, G; Kirschner, M; Leitinger, M; Höfler, J; Rohracher, A; Kalss, G; Wendling, A-S; Steinhoff, B J; Trinka, E

    2017-04-01

    There are clinical situations where it might be appropriate to switch patients from immediate-release oxcarbazepine (OXC) to eslicarbazepine acetate (ESL). We investigated the effects of transitioning patients overnight from OXC to ESL. A retrospective, single-center study was conducted in which patients with drug-resistant focal epilepsy on a stable dose of immediate-release OXC for at least 4 weeks were switched overnight to ESL. Patients were switched because they experienced persistent seizures with OXC but were unable to tolerate increased OXC dosing due to adverse events. Tolerability was assessed using the Adverse Events Profile (AEP), quality of life was assessed using the Quality of Life in Epilepsy Inventory 10 (QOLIE-10), and alertness was assessed as reaction time using a subtest of the Test Battery for Attention Performance version 2.3. Assessments were performed immediately prior to and 5 days after switching from OXC to ESL (days 0 and 5, respectively). The analysis included 21 patients (12 women, 9 men; mean age 36 years). After switching from OXC to ESL, there were significant improvements in mean scores for AEP (Peffects, quality of life, and alertness. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  7. Sorption of CO 2 in a hydrogen-bonded diamondoid network of sulfonylcalix[4]arene

    Energy Technology Data Exchange (ETDEWEB)

    Sinnwell, Michael A. [Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, WA, USA; Atwood, Jerry L. [Department of Chemistry, University of Missouri-Columbia, Columbia, MO, USA; Thallapally, Praveen K. [Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, WA, USA

    2018-02-08

    An organic material, p-tert-butyltetrasulfonylcalix[4]arene, self-assembles via hydrogen bonding to form a diamondoid supramolecular network. Possessing discrete, zero-dimensional (0D) microcavities, the thiacalixarene derivative adsorbs CO2 at high pressures

  8. Isotope dependent, temperature regulated, energy repartitioning in a low-barrier, short-strong hydrogen bonded cluster

    NARCIS (Netherlands)

    Li, X. H.; Oomens, J.; Eyler, J. R.; Moore, D. T.; Iyengar, S. S.

    2010-01-01

    We investigate and analyze the vibrational properties, including hydrogen/deuterium isotope effects, in a fundamental organic hydrogen bonded system using multiple experimental (infrared multiple photon dissociation and argon-tagged action spectroscopy) and computational techniques. We note a

  9. Tyrosine B10 triggers a heme propionate hydrogen bonding network loop with glutamine E7 moiety

    International Nuclear Information System (INIS)

    Ramos-Santana, Brenda J.; López-Garriga, Juan

    2012-01-01

    Highlights: ► H-bonding network loop by PheB10Tyr mutation is proposed. ► The propionate group H-bonding network restricted the flexibility of the heme. ► The hydrogen bonding interaction modulates the electron density of the iron. ► Propionate H-bonding network loop explains the heme-ligand stabilization. -- Abstract: Propionates, as peripheral groups of the heme active center in hemeproteins have been described to contribute in the modulation of heme reactivity and ligand selection. These electronic characteristics prompted the question of whether the presence of hydrogen bonding networks between propionates and distal amino acids present in the heme ligand moiety can modulate physiological relevant events, like ligand binding association and dissociation activities. Here, the role of these networks was evaluated by NMR spectroscopy using the hemoglobin I PheB10Tyr mutant from Lucina pectinata as model for TyrB10 and GlnE7 hemeproteins. 1 H-NMR results for the rHbICN PheB10Tyr derivative showed chemical shifts of TyrB10 OHη at 31.00 ppm, GlnE7 N ε1 H/N ε2 H at 10.66 ppm/−3.27 ppm, and PheE11 C δ H at 11.75 ppm, indicating the presence of a crowded, collapsed, and constrained distal pocket. Strong dipolar contacts and inter-residues crosspeaks between GlnE7/6-propionate group, GlnE7/TyrB10 and TyrB10/CN suggest that this hydrogen bonding network loop between GlnE7, TyrB10, 6-propionate group, and the heme ligand contribute significantly to the modulation of the heme iron electron density as well as the ligand stabilization mechanism. Therefore, the network loop presented here support the fact that the electron withdrawing character of the hydrogen bonding is controlled by the interaction of the propionates and the nearby electronic environments contributing to the modulation of the heme electron density state. Thus, we hypothesize that in hemeproteins with similar electrostatic environment the flexibility of the heme-6-propionate promotes a hydrogen

  10. Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs.

    Science.gov (United States)

    Takezawa, Yusuke; Shionoya, Mitsuhiko

    2012-12-18

    With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely based on highly specific molecular recognition between nucleobases through the specific hydrogen bonds in the Watson-Crick base pairing system. While the native base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative base pairing systems in recent decades. Most of these new systems were designed based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA base pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme in biological systems, metal-coordination bonding. In this Account, we provide an overview of the chemistry of metal-mediated base pairing including basic concepts, molecular design, characteristic structures and properties, and possible applications of DNA-based molecular systems. We describe several examples of artificial metal-mediated base pairs, such as Cu(2+)-mediated hydroxypyridone base pair, H-Cu(2+)-H (where H denotes a hydroxypyridone-bearing nucleoside), developed by us and other researchers. To design the metallo-base pairs we carefully chose appropriate combinations of ligand-bearing nucleosides and metal ions. As expected from their stronger bonding through metal coordination, DNA duplexes possessing metallo-base pairs exhibited higher thermal stability than natural hydrogen-bonded DNAs. Furthermore, we could also use metal-mediated base pairs to construct or induce other high-order structures. These features could lead to metal-responsive functional

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

    Science.gov (United States)

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

    2015-01-01

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

  12. NMR experiments for the rapid identification of P=O···H-X type hydrogen bonds in nucleic acids.

    Science.gov (United States)

    Duchardt-Ferner, Elke; Wöhnert, Jens

    2017-10-01

    Hydrogen bonds involving the backbone phosphate groups occur with high frequency in functional RNA molecules. They are often found in well-characterized tertiary structural motifs presenting powerful probes for the rapid identification of these motifs for structure elucidation purposes. We have shown recently that stable hydrogen bonds to the phosphate backbone can in principle be detected by relatively simple NMR-experiments, providing the identity of both the donor hydrogen and the acceptor phosphorous within the same experiment (Duchardt-Ferner et al., Angew Chem Int Ed Engl 50:7927-7930, 2011). However, for imino and hydroxyl hydrogen bond donor groups rapidly exchanging with the solvent as well as amino groups broadened by conformational exchange experimental sensitivity is severely hampered by extensive line broadening. Here, we present improved methods for the rapid identification of hydrogen bonds to phosphate groups in nucleic acids by NMR. The introduction of the SOFAST technique into 1 H, 31 P-correlation experiments as well as a BEST-HNP experiment exploiting 3h J N,P rather than 2h J H,P coupling constants enables the rapid and sensitive identification of these hydrogen bonds in RNA. The experiments are applicable for larger RNAs (up to ~ 100-nt), for donor groups influenced by conformational exchange processes such as amino groups and for hydrogen bonds with rather labile hydrogens such as 2'-OH groups as well as for moderate sample concentrations. Interestingly, the size of the through-hydrogen bond scalar coupling constants depends not only on the type of the donor group but also on the structural context. The largest coupling constants were measured for hydrogen bonds involving the imino groups of protonated cytosine nucleotides as donors.

  13. Predictors of switching from mania to depression in a large observational study across Europe (EMBLEM)

    DEFF Research Database (Denmark)

    Vieta, Eduard; Angst, Jules; Reed, Catherine

    2009-01-01

    BACKGROUND: The risk of switching from mania to depression in bipolar disorder has been poorly studied. Large observational studies may be useful in identifying variables that predict switch to depression after mania and provide data on medication use and outcomes in "real world" patients. METHOD...... Depression Rating Scale. Switching was defined using CGI-BP mania and depression such that patients changed from manic and not depressed to depressed but not manic over two consecutive observations within the first 12 weeks of follow-up. Cox proportional hazards models identified baseline variables...... independently associated with switch to depression. RESULTS: Of 2390 patients who participated in the maintenance phase (i.e. up to 24 months), 120 (5.0%) switched to depression within the first 12 weeks. Factors associated with greater switching to depression include previous depressive episodes, substance...

  14. Molecular Dynamics Investigation of the Effects of Concentration on Hydrogen Bonding in Aqueous Solutions of Methanol, Ethylene Glycol and Glycerol

    International Nuclear Information System (INIS)

    Zhang, Ning; Li, Weizhong; Chen, Cong; Zuo, Jianguo; Weng, Lindong

    2013-01-01

    Hydrogen bonding interaction between alcohols and water molecules is an important characteristic in the aqueous solutions of alcohols. In this paper, a series of molecular dynamics simulations have been performed to investigate the aqueous solutions of low molecular weight alcohols (methanol, ethylene glycol and glycerol) at the concentrations covering a broad range from 1 to 90 mol %. The work focuses on studying the effect of the alcohols molecules on the hydrogen bonding of water molecules in binary mixtures. By analyzing the hydrogen bonding ability of the hydroxyl (-OH) groups for the three alcohols, it is found that the hydroxyl group of methanol prefers to form more hydrogen bonds than that of ethylene glycol and glycerol due to the intra-and intermolecular effects. It is also shown that concentration has significant effect on the ability of alcohol molecule to hydrogen bond water molecules. Understanding the hydrogen bonding characteristics of the aqueous solutions is helpful to reveal the cryoprotective mechanisms of methanol, ethylene glycol and glycerol in aqueous solutions

  15. The origin of enantioselectivity in the l-threonine-derived phosphine-sulfonamide catalyzed aza-Morita-Baylis-Hillman reaction: Effects of the intramolecular hydrogen bonding

    KAUST Repository

    Lee, Richmond

    2013-01-01

    l-Threonine-derived phosphine-sulfonamide 4 was identified as the most efficient catalyst to promote enantioselective aza-Morita-Baylis-Hillman (MBH) reactions, affording the desired aza-MBH adducts with excellent enantioselectivities. Density functional theory (DFT) studies were carried out to elucidate the origin of the observed enantioselectivity. The importance of the intramolecular N-H⋯O hydrogen-bonding interaction between the sulfonamide and enolate groups was identified to be crucial in inducing a high degree of stereochemical control in both the enolate addition to imine and the subsequent proton transfer step, affording aza-MBH reactions with excellent enantioselectivity. © 2013 The Royal Society of Chemistry.

  16. EPR-spin probe studies of model polymers: separation of covalent cross-linking effects from hydrogen bonding effects in swelled Argonne Premium Coal samples

    Energy Technology Data Exchange (ETDEWEB)

    Spears, D.R.; Sady, W.; Tucker, D.; Kispert, L.D. (University of Alabama, Tuscaloosa, AL (United States). Chemistry Dept.)

    The swelling behaviour of 2-12% cross-linked polystyrene-divinylbenzene (PSDVB) copolymers was examined by an EPR-spin probe technique. It was observed that the mechanism of spin probe inclusion was the intercalation into the matrix rather than diffusion into the pores. The disruption of van der Waals forces between adjacent aromatic rings appeared to be the primary mechanism for pyridine swelling of PSDVB. By comparing the data to results from coal swelling studies it was also inferred that the extent of hydrogen bonding in coal will have a much greater impact on its swelling properties than its covalently cross-linked character. 24 refs., 6 figs.

  17. Predictors of switching from mania to depression in a large observational study across Europe (EMBLEM).

    Science.gov (United States)

    Vieta, Eduard; Angst, Jules; Reed, Catherine; Bertsch, Jordan; Haro, Josep Maria

    2009-11-01

    The risk of switching from mania to depression in bipolar disorder has been poorly studied. Large observational studies may be useful in identifying variables that predict switch to depression after mania and provide data on medication use and outcomes in "real world" patients. EMBLEM (European Mania in Bipolar Longitudinal Evaluation of Medication) is a 2-year, prospective, observational study of patients with a manic/mixed episode. Symptom severity measures included Clinical Global Impression-Bipolar Disorder scale (CGI-BP), Young Mania Rating Scale (YMRS) and 5-item Hamilton Depression Rating Scale. Switching was defined using CGI-BP mania and depression such that patients changed from manic and not depressed to depressed but not manic over two consecutive observations within the first 12 weeks of follow-up. Cox proportional hazards models identified baseline variables independently associated with switch to depression. Of 2390 patients who participated in the maintenance phase (i.e. up to 24 months), 120 (5.0%) switched to depression within the first 12 weeks. Factors associated with greater switching to depression include previous depressive episodes, substance abuse, greater CGI-BP overall severity and benzodiazepine use. Factors associated with lower switching rates were greater CGI-BP depression, lower YMRS severity and atypical antipsychotic use. The definition of switching biased against patients with mixed episodes being likely to switch. Strictly defined, switch to depression from mania occurs in a small proportion of bipolar patients. Clinical history, illness severity, co-morbidities and treatment patterns are associated with switching to depression. Atypical antipsychotics may protect against switch to depression.

  18. Predictors of switching from mania to depression in a large observational study across Europe (EMBLEM)

    NARCIS (Netherlands)

    Vieta, Eduard; Angst, Jules; Reed, Catherine; Bertsch, Jordan; Maria Haro, Josep

    Background: The risk of switching from mania to depression in bipolar disorder has been poorly studied. Large observational studies may be useful in identifying variables that predict switch to depression after mania and provide data on medication use and outcomes in "real world" patients. Method:

  19. Predictors of switching from mania to depression in a large observational study across Europe (EMBLEM)

    NARCIS (Netherlands)

    Vieta, Eduard; Angst, Jules; Reed, Catherine; Bertsch, Jordan; Maria Haro, Josep

    2009-01-01

    Background: The risk of switching from mania to depression in bipolar disorder has been poorly studied. Large observational studies may be useful in identifying variables that predict switch to depression after mania and provide data on medication use and outcomes in "real world" patients. Method:

  20. Polymer Soft-Landing Isolation of Acetylene on Polystyrene and Poly(vinylpyridine): A Novel Approach to Probing Hydrogen Bonding in Polymers.

    Science.gov (United States)

    Li, Yike; Samet, Cindy

    2015-09-17

    Hydrogen-bonded complexes of acetylene (Ac) with the polymers polystyrene (PS), poly(4-vinylpyridine) (P4VP), and poly(2-vinylpyridine) (P2VP) have been characterized for the first time at 16 K in a "polymer soft-landing isolation" experiment which is being pioneered in our research laboratory. In particular, changes in vibrational modes of Ac provide ample evidence for hydrogen-bonded complexes between Ac and the phenyl groups of PS or the pyridyl groups of P4VP and P2VP. With PS, the proton on the top Ac molecule of the classic T-shaped Ac dimer interacts with the π cloud of the benzene (Bz) ring to form a C-H---π interaction, while the π cloud of the lower Ac forms a second C-H---π interaction with a proton on the Bz ring. An analogous (ring)1-(Ac)2 double interaction occurs between an Ac dimer and the pyridine (Pyr) rings on both P2VP and P4VP, yielding a C-H---N and C-H---π interaction. With P4VP and P2VP a second bridged (ring)2-(Ac)2 product is formed, with the Ac dimer forming nearly collinear C-H---N hydrogen bonds to adjacent Pyr rings. On P2VP this bridged product is the only one after extensive annealing. These complexes in which Ac acts as both proton donor and acceptor have not previously been observed in conventional matrix isolation experiments. This study is the second from our laboratory employing this method, which represents a slight modification of the traditional matrix isolation technique.

  1. Multiple Hydrogen Bond Tethers for Grazing Formic Acid in Its Complexes with Phenylacetylene.

    Science.gov (United States)

    Karir, Ginny; Kumar, Gaurav; Kar, Bishnu Prasad; Viswanathan, K S

    2018-03-01

    Complexes of phenylacetylene (PhAc) and formic acid (FA) present an interesting picture, where the two submolecules are tethered, sometimes multiply, by hydrogen bonds. The multiple tentacles adopted by PhAc-FA complexes stem from the fact that both submolecules can, in the same complex, serve as proton acceptors and/or proton donors. The acetylenic and phenyl π systems of PhAc can serve as proton acceptors, while the ≡C-H or -C-H of the phenyl ring can act as a proton donor. Likewise, FA also is amphiprotic. Hence, more than 10 hydrogen-bonded structures, involving O-H···π, C-H···π, and C-H···O contacts, were indicated by our computations, some with multiple tentacles. Interestingly, despite the multiple contacts in the complexes, the barrier between some of the structures is small, and hence, FA grazes around PhAc, even while being tethered to it, with hydrogen bonds. We used matrix isolation infrared spectroscopy to experimentally study the PhAc-FA complexes, with which we located global and a few local minima, involving primarily an O-H···π interaction. Experiments were corroborated by ab initio computations, which were performed using MP2 and M06-2X methods, with 6-311++G (d,p) and aug-cc-pVDZ basis sets. Single-point energy calculations were also done at MP2/CBS and CCSD(T)/CBS levels. The nature, strength, and origin of these noncovalent interactions were studied using AIM, NBO, and LMO-EDA analysis.

  2. Computational insights into the photocyclization of diclofenac in solution: effects of halogen and hydrogen bonding.

    Science.gov (United States)

    Bani-Yaseen, Abdulilah Dawoud

    2016-08-21

    The effects of noncovalent interactions, namely halogen and hydrogen bonding, on the photochemical conversion of the photosensitizing drug diclofenac (DCF) in solution were investigated computationally. Both explicit and implicit solvent effects were qualitatively and quantitatively assessed employing the DFT/6-31+G(d) and SQM(PM7) levels of theory. Full geometry optimizations were performed in solution for the reactant DCF, hypothesized radical-based intermediates, and the main product at both levels of theories. Notably, in good agreement with previous experimental results concerning the intermolecular halogen bonding of DCF, the SQM(PM7) method revealed different values for d(ClO, Å) and ∠(C-ClO, °) for the two chlorine-substituents of DCF, with values of 2.63 Å/162° and 3.13 Å/142° for the trans and cis orientations, respectively. Employing the DFT/6-31+G(d) method with implicit solvent effects was not conclusive; however, explicit solvent effects confirmed the key contribution of hydrogen and halogen bonding in stabilizing/destabilizing the reactant and hypothesized intermediates. Interestingly, the obtained results revealed that a protic solvent such as water can increase the rate of photocyclization of DCF not only through hydrogen bonding effects, but also through halogen bonding. Furthermore, the atomic charges of atoms majorly involved in the photocyclization of DCF were calculated using different methods, namely Mulliken, Hirshfeld, and natural bond orbital (NBO). The obtained results revealed that in all cases there is a notable nonequivalency in the noncovalent intermolecular interactions of the two chlorine substituents of DCF and the radical intermediates with the solvent, which in turn may account for the discrepancy of their reactivity in different media. These computational results provide insight into the importance of halogen and hydrogen bonding throughout the progression of the photochemical conversion of DCF in solution.

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

    Science.gov (United States)

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

    2010-04-05

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

  4. Two new hydrogen bond-supported supramolecular compounds assembly from polyoxovanadate and organoamines

    International Nuclear Information System (INIS)

    Duan Weijie; Cui Xiaobing; Xu Yan; Xu Jiqing; Yu Haihui; Yi Zhihui; Cui Jiwen; Wang Tiegang

    2007-01-01

    Two novel organic-inorganic hybrid compounds based on organoamines and polyoxovanadates formulated as (H 2 dien) 4 [H 10 V 18 O 42 (PO 4 )](PO 4 ).2H 2 O (1) (dien=diethylenetriamine) and (Him) 8 [HV 18 O 42 (PO 4 )] (2) (im=imidazole) have been prepared under hydrothermal conditions by using different starting materials, and characterized by elemental analyses, IR, ESR, XPS, TGA and single-crystal X-ray diffraction analyses. Crystal data for compound 1: C 16 H 74 N 12 O 52 V 18 P 2 , Monoclinic, space group C2/c, a=23.9593(4) A, b=13.0098(2) A, c=20.1703(4) A, β=105.566(3) o , V=6056.6(19) A 3 , Z=4; for compound 2, C 24 H 41 N 16 O 46 V 18 P, Tetragonal, space group I4/mmm, a=13.5154(8) A, b=13.5154(8) A, c=19.1136 A, β=90 o , V=3491.4(3) A 3 , Z=2. Compound 1 consists of protonated diens together with polyoxovanadates [H 10 V 18 O 42 (PO 4 )] 5- . Compound 2 is composed of protonated ims and polyoxovanadates [HV 18 O 42 (PO 4 )] 8- . There are hydrogen-bonding interactions between polyoxovanadates and different organoamines in 1 and 2. Polyoxovanadates are linked through H 2 dien into a three-dimensional network via hydrogen bonds in 1, while polyoxovanadates are linked by Him into a two-dimensional layer network via hydrogen bonds in 2. The crystal packing patterns of the two compounds reveal various supramolecular frameworks. - Graphical abstract: Two new organic-inorganic hybrid compounds based on [V 18 O 42 (PO 4 )] building blocks have been hydrothermally synthesized. 1 is the first 3-D supramolecular network structure consisting of [V 18 O 42 (PO 4 )] unit, while 2 possesses 2-D layered supramolecular structure

  5. Thermal generation and mobility of charge carriers in collective proton transport in hydrogen-bonded chains

    International Nuclear Information System (INIS)

    Peyrard, M.; Boesch, R.; Kourakis, I.

    1991-01-01

    The transport of protons in hydrogen-bonded systems is a long standing problem which has not yet obtained a satisfactorily theoretical description. Although this problem was examined first for ice, it is relevant in many systems and in particular in biology for the transport along proteins or for proton conductance across membranes, an essential process in cell life. The broad relevance makes the study of proton conduction very appealing. Since the original work of Bernal and Fowler on ice, the idea that the transport occurs through chains of hydrogen bonds has been well accepted. Such ''proton wires'' were invoked by Nagle and Morowitz for proton transport across membranes proteins and more recently across lipid bilayers. In this report, we assume the existence of such an hydrogen-bonded chain and discuss its consequences on the dynamics of the charge carriers. We show that this assumption leads naturally to the idea of soliton transport and we put a special emphasis on the role of the coupling between the protons and heavy ions motions. The model is presented. We show how the coupling affects strongly the dynamics of the charge carriers and we discuss the role it plays in the thermal generation of carriers. The work presented has been performed in 1986 and 87 with St. Pnevmatikos and N. Flyzanis and was then completed in collaboration with D. Hochstrasser and H. Buettner. Therefore the results presented in this part are not new but we think that they are appropriate in the context of this multidisciplinary workshop because they provide a rather complete example of the soliton picture for proton conduction. This paper discusses the thermal generation of the charge carriers when the coupling between the protons and heavy ions dynamics is taken into account. The results presented in this part are very recent and will deserve further analysis but they already show that the coupling can assist for the formation of the charge carriers

  6. Hydrogen bonding donation of N-methylformamide with dimethylsulfoxide and water

    Science.gov (United States)

    Borges, Alexandre; Cordeiro, João M. M.

    2013-04-01

    20% N-methylformamide (NMF) mixtures with water and with dimethylsulfoxide (DMSO) have been studied. A comparison between the hydrogen bonding (H-bond) donation of N-methylformamide with both solvents in the mixtures is presented. Results of radial distribution functions, pair distribution energies, molecular dipole moment correlation, and geometry of the H-bonded species in each case are shown. The results indicate that the NMF - solvent H-bond is significantly stronger with DMSO than with water. The solvation shell is best organized in the DMSO mixture than in the aqueous one.

  7. A new empirical potential function and its application to hydrogen bonding

    International Nuclear Information System (INIS)

    Kang, Y.K.; Jhon, M.S.

    1981-01-01

    A new potential function based on spectroscopic results for diatomic molecules is presented and applied to the hydrogen bonding systems. The potential energy of interaction is supposed to have electrostatic, polarization, dispersion, repulsion and effective charge-transfer contributions. Estimates of the effective charge-transfer quantity have been made based on the average charge of the proton donor and the acceptor atoms. For dimers such as water, methanol, acetic acid and formic acid, the vibrational stretching frequencies and dimerization energies are calculated and discussed in connection with Badger-Bauer rule. (author)

  8. Influence of intramolecular hydrogen bonds on the binding potential of methylated β-cyclodextrin derivatives

    Directory of Open Access Journals (Sweden)

    Gerhard Wenz

    2012-11-01

    Full Text Available Various heptasubstituted derivatives of β-cyclodextrin (β-CD bearing 1, 2 and 3 methyl substituents per glucose unit were synthesized by regioselective methods. Binding free energies and binding enthalpies of these hosts towards 4-tert-butylbenzoate and adamantane-1-carboxylate were determined by isothermal titration microcalorimetry (ITC. It was found that methyl substituents at the secondary positions of β-CD lead to a tremendous reduction of the binding potential, while methylation at the primary positions significantly improved binding. Stabilizing intramolecular hydrogen bonds between the glucose units were made responsible for the high binding potentials of those β-CD derivatives that possess secondary hydroxy groups.

  9. Two-dimensional gold nanostructures with high activity for selective oxidation of carbon–hydrogen bonds

    KAUST Repository

    Wang, Liang

    2015-04-22

    Efficient synthesis of stable two-dimensional (2D) noble metal catalysts is a challenging topic. Here we report the facile synthesis of 2D gold nanosheets via a wet chemistry method, by using layered double hydroxide as the template. Detailed characterization with electron microscopy and X-ray photoelectron spectroscopy demonstrates that the nanosheets are negatively charged and [001] oriented with thicknesses varying from single to a few atomic layers. X-ray absorption spectroscopy reveals unusually low gold–gold coordination numbers. These gold nanosheets exhibit high catalytic activity and stability in the solvent-free selective oxidation of carbon–hydrogen bonds with molecular oxygen.

  10. Smart supramolecular sensing with cucurbit[n]urils: probing hydrogen bonding with SERS.

    Science.gov (United States)

    de Nijs, Bart; Kamp, Marlous; Szabó, Istvan; Barrow, Steven J; Benz, Felix; Wu, Guanglu; Carnegie, Cloudy; Chikkaraddy, Rohit; Wang, Wenting; Deacon, William M; Rosta, Edina; Baumberg, Jeremy J; Scherman, Oren A

    2017-12-04

    Rigid gap nano-aggregates of Au nanoparticles formed using cucurbit[n]uril (CB[n]) molecules are used to investigate the competitive binding of ethanol and methanol in an aqueous environment. We show it is possible to detect as little as 0.1% methanol in water and a ten times higher affinity to methanol over ethanol, making this a useful technology for quality control in alcohol production. We demonstrate strong interaction effects in the SERS peaks, which we demonstrate are likely from the hydrogen bonding of water complexes in the vicinity of the CB[n]s.

  11. Two-dimensional gold nanostructures with high activity for selective oxidation of carbon-hydrogen bonds

    Science.gov (United States)

    Wang, Liang; Zhu, Yihan; Wang, Jian-Qiang; Liu, Fudong; Huang, Jianfeng; Meng, Xiangju; Basset, Jean-Marie; Han, Yu; Xiao, Feng-Shou

    2015-04-01

    Efficient synthesis of stable two-dimensional (2D) noble metal catalysts is a challenging topic. Here we report the facile synthesis of 2D gold nanosheets via a wet chemistry method, by using layered double hydroxide as the template. Detailed characterization with electron microscopy and X-ray photoelectron spectroscopy demonstrates that the nanosheets are negatively charged and [001] oriented with thicknesses varying from single to a few atomic layers. X-ray absorption spectroscopy reveals unusually low gold-gold coordination numbers. These gold nanosheets exhibit high catalytic activity and stability in the solvent-free selective oxidation of carbon-hydrogen bonds with molecular oxygen.

  12. Analysis of polarization in hydrogen bonded complexes: An asymptotic projection approach

    Science.gov (United States)

    Drici, Nedjoua

    2018-03-01

    The asymptotic projection technique is used to investigate the polarization effect that arises from the interaction between the relaxed, and frozen monomeric charge densities of a set of neutral and charged hydrogen bonded complexes. The AP technique based on the resolution of the original Kohn-Sham equations can give an acceptable qualitative description of the polarization effect in neutral complexes. The significant overlap of the electron densities, in charged and π-conjugated complexes, impose further development of a new functional, describing the coupling between constrained and non-constrained electron densities within the AP technique to provide an accurate representation of the polarization effect.

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

    Science.gov (United States)

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

    2008-10-30

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

  14. Deuterium isotope effects on 13C and 15N chemical shifts of intramolecularly hydrogen-bonded enaminocarbonyl derivatives of Meldrum’s and Tetronic acid

    Science.gov (United States)

    Ullah, Saif; Zhang, Wei; Hansen, Poul Erik

    2010-07-01

    Secondary deuterium isotope effects on 13C and 15N nuclear shieldings in a series of cyclic enamino-diesters and enamino-esters and acyclic enaminones and enamino-esters have been examined and analysed using NMR and DFT (B3LYP/6-31G(d,p)) methods. One-dimensional and two-dimensional NMR spectra of enaminocarbonyl and their deuterated analogues were recorded in CDCl 3 and CD 2Cl 2 at variable temperatures and assigned. 1JNH coupling constants for the derivatives of Meldrum's and tetronic acids reveal that they exist at the NH-form. It was demonstrated that deuterium isotope effects, for the hydrogen bonded compounds, due to the deuterium substitution at the nitrogen nucleus lead to large one-bond isotope effects at nitrogen, 1Δ 15N(D), and two-bond isotope effects on carbon nuclei, 2ΔC(ND), respectively. A linear correlations exist between 2ΔC(ND) and 1Δ 15N(D) whereas the correlation with δNH is divided into two. A good agreement between the experimentally observed 2ΔC(ND) and calculated dσ 13C/dR NH was obtained. A very good correlation between calculated NH bond lengths and observed NH chemical shifts is found. The observed isotope effects are shown to depend strongly on Resonance Assisted Hydrogen bonding.

  15. A Raman spectroscopy study on the effects of intermolecular hydrogen bonding on water molecules absorbed by borosilicate glass surface

    Science.gov (United States)

    Li, Fabing; Li, Zhanlong; Wang, Ying; Wang, Shenghan; Wang, Xiaojun; Sun, Chenglin; Men, Zhiwei

    2018-05-01

    The structural forms of water/deuterated water molecules located on the surface of borosilicate capillaries have been first investigated in this study on the basis of the Raman spectral data obtained at different temperatures and under atmospheric pressure for molecules in bulk and also for molecules absorbed by borosilicate glass surface. The strongest two fundamental bands locating at 3063 cm-1 (2438 cm-1) in the recorded Raman spectra are assigned here to the Osbnd H (Osbnd D) bond stretching vibrations and they are compared with the corresponding bands observed at 3124 cm-1 (2325 cm-1) in the Raman spectrum of ice Ih. Our spectroscopic observations have indicated that the structure of water and deuterated water molecules on borosilicate surface is similar to that of ice Ih (hexagonal phase of ice). These observations have also indicated that water molecules locate on the borosilicate surface so as to construct a bilayer structure and that strong and weak intermolecular hydrogen bonds are formed between water/deuterated molecules and silanol groups on borosilicate surface. In accordance with these findings, water and deuterated water molecules at the interface of capillary have a higher melting temperature.

  16. Drug-protein hydrogen bonds govern the inhibition of the ATP hydrolysis of the multidrug transporter P-glycoprotein.

    Science.gov (United States)

    Chufan, Eduardo E; Kapoor, Khyati; Ambudkar, Suresh V

    2016-02-01

    P-glycoprotein (P-gp) is a member of the ATP-binding cassette transporter superfamily. This multidrug transporter utilizes energy from ATP hydrolysis for the efflux of a variety of hydrophobic and amphipathic compounds including anticancer drugs. Most of the substrates and modulators of P-gp stimulate its basal ATPase activity, although some inhibit it. The molecular mechanisms that are in play in either case are unknown. In this report, mutagenesis and molecular modeling studies of P-gp led to the identification of a pair of phenylalanine-tyrosine structural motifs in the transmembrane region that mediate the inhibition of ATP hydrolysis by certain drugs (zosuquidar, elacridar and tariquidar), with high affinity (IC50's ranging from 10 to 30nM). Upon mutation of any of these residues, drugs that inhibit the ATPase activity of P-gp switch to stimulation of the activity. Molecular modeling revealed that the phenylalanine residues F978 and F728 interact with tyrosine residues Y953 and Y310, respectively, in an edge-to-face conformation, which orients the tyrosines in such a way that they establish hydrogen-bond contacts with the inhibitor. Biochemical investigations along with transport studies in intact cells showed that the inhibitors bind at a high affinity site to produce inhibition of ATP hydrolysis and transport function. Upon mutation, they bind at lower affinity sites, stimulating ATP hydrolysis and only poorly inhibiting transport. These results also reveal that screening chemical compounds for their ability to inhibit the basal ATP hydrolysis can be a reliable tool to identify modulators with high affinity for P-gp. Published by Elsevier Inc.

  17. Template Synthesis, Crystal Structure, and Magnetic Properties of a Dinuclear Copper(II) Complex with Cooperative Hydrogen Bonding

    International Nuclear Information System (INIS)

    Kang, Shin Geol; Nam, Kwang Hee; Min, Kil Sik; Lee, Uk

    2011-01-01

    The dinuclear complex with cooperative hydrogen bonds can be prepared by the metal-directed reaction of Eq. This work shows that the coordinated hydroxyl group trans to the secondary amino group is deprotonated more readily than that trans to the tertiary amino group and acts as the hydrogen-bond accepter. The lattice water molecules in act as bridges between the two mononuclear units through hydrogen bonds. The complex is quite stable as the dimeric form even in various polar solvents. The complex exhibits a weak antiferromagnetic interaction between the metal ions in spite of relatively long Cu···Cu distance. This strongly supports the suggestion that the antiferromagnetic behavior is closely related to the cooperative hydrogen bonds. The design and synthesis of polynuclear transition metal complexes have received much attention because of their potential applications in various fields, such as catalysis, supramolecular chemistry, and materials chemistry. Until now, various types of dinuclear copper(II) complexes have been prepared and investigated. Some dinuclear copper(II) complexes resulting from cooperative hydrogen bonding, such as containing two N_2O_2 donor sets, are also reported

  18. Bane of Hydrogen-Bond Formation on the Photoinduced Charge-Transfer Process in Donor–Acceptor Systems

    KAUST Repository

    Alsam, Amani Abdu

    2017-03-14

    Controlling the ultrafast dynamical process of photoinduced charge transfer at donor acceptor interfaces remains a major challenge for physical chemistry and solar cell communities. The process is complicated by the involvement of other complex dynamical processes, including hydrogen bond formation, energy transfer, and solvation dynamics occurring on similar time scales. In this study, we explore the remarkable impact of hydrogen-bond formation on the interfacial charge transfer between a negatively charged electron donating anionic porphyrin and a positively charged electron accepting pi-conjugated polymer, as a model system in solvents with different polarities and capabilities for hydiogen bonding using femtosecond transient absorption spectroscopy. Unlike the conventional understanding of the key role of hydrogen bonding in promoting the charge-transfer process, our steadystate and time-resolved results reveal that the intervening hydrogen-bonding environment and, consequently, the probable longer spacing between the donor and acceptor molecules significantly hinders the charge-transfer process between them. These results show that site-specific hydrogen bonding and geometric considerations between donor and acceptor can be exploited to control both the charge-transfer dynamics and its efficiency not only at donor acceptor interfaces but also in complex biological systems.

  19. COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures.

    Science.gov (United States)

    Firdaus-Raih, Mohd; Hamdani, Hazrina Yusof; Nadzirin, Nurul; Ramlan, Effirul Ikhwan; Willett, Peter; Artymiuk, Peter J

    2014-07-01

    Hydrogen bonds are crucial factors that stabilize a complex ribonucleic acid (RNA) molecule's three-dimensional (3D) structure. Minute conformational changes can result in variations in the hydrogen bond interactions in a particular structure. Furthermore, networks of hydrogen bonds, especially those found in tight clusters, may be important elements in structure stabilization or function and can therefore be regarded as potential tertiary motifs. In this paper, we describe a graph theoretical algorithm implemented as a web server that is able to search for unbroken networks of hydrogen-bonded base interactions and thus provide an accounting of such interactions in RNA 3D structures. This server, COGNAC (COnnection tables Graphs for Nucleic ACids), is also able to compare the hydrogen bond networks between two structures and from such annotations enable the mapping of atomic level differences that may have resulted from conformational changes due to mutations or binding events. The COGNAC server can be accessed at http://mfrlab.org/grafss/cognac. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Statics and dynamics of free and hydrogen-bonded OH groups at the air/water interface.

    Science.gov (United States)

    Vila Verde, Ana; Bolhuis, Peter G; Campen, R Kramer

    2012-08-09

    We use classical atomistic molecular dynamics simulations of two water models (SPC/E and TIP4P/2005) to investigate the orientation and reorientation dynamics of two subpopulations of OH groups belonging to water molecules at the air/water interface at 300 K: those OH groups that donate a hydrogen bond (called "bonded") and those that do not (called "free"). Free interfacial OH groups reorient in two distinct regimes: a fast regime from 0 to 1 ps and a slow regime thereafter. Qualitatively similar behavior was reported by others for free OH groups near extended hydrophobic surfaces. In contrast, the net reorientation of bonded OH groups occurs at a rate similar to that of bulk water. This similarity in reorientation rate results from compensation of two effects: decreasing frequency of hydrogen-bond breaking/formation (i.e., hydrogen-bond exchange) and faster rotation of intact hydrogen bonds. Both changes result from the decrease in density at the air/water interface relative to the bulk. Interestingly, because of the presence of capillary waves, the slowdown of hydrogen-bond exchange is significantly smaller than that reported for water near extended hydrophobic surfaces, but it is almost identical to that reported for water near small hydrophobic solutes. In this sense water at the air/water interface has characteristics of water of hydration of both small and extended hydrophobic solutes.

  1. Hydrogen bond based smart polymer for highly selective and tunable capture of multiply phosphorylated peptides.

    Science.gov (United States)

    Qing, Guangyan; Lu, Qi; Li, Xiuling; Liu, Jing; Ye, Mingliang; Liang, Xinmiao; Sun, Taolei

    2017-09-06

    Multisite phosphorylation is an important and common mechanism for finely regulating protein functions and subsequent cellular responses. However, this study is largely restricted by the difficulty to capture low-abundance multiply phosphorylated peptides (MPPs) from complex biosamples owing to the limitation of enrichment materials and their interactions with phosphates. Here we show that smart polymer can serve as an ideal platform to resolve this challenge. Driven by specific but tunable hydrogen bonding interactions, the smart polymer displays differential complexation with MPPs, singly phosphorylated and non-modified peptides. Importantly, MPP binding can be modulated conveniently and precisely by solution conditions, resulting in highly controllable MPP adsorption on material surface. This facilitates excellent performance in MPP enrichment and separation from model proteins and real biosamples. High enrichment selectivity and coverage, extraordinary adsorption capacities and recovery towards MPPs, as well as high discovery rates of unique phosphorylation sites, suggest its great potential in phosphoproteomics studies.Capture of low-abundance multiply phosphorylated peptides (MPPs) is difficult due to limitation of enrichment materials and their interactions with phosphates. Here the authors show, a smart polymer driven by specific but tunable hydrogen bonding interactions can differentially complex with MPPs, singly phosphorylated and non-modified peptides.

  2. On the mean kinetic energy of the proton in strong hydrogen bonded systems

    Energy Technology Data Exchange (ETDEWEB)

    Finkelstein, Y. [Nuclear Research Center–Negev, Beer-Sheva 84190 (Israel); Moreh, R. [Physics Department, Ben-Gurion University of the Negev, Beer-Sheva 84105 (Israel); Shang, S. L.; Wang, Y.; Liu, Z. K. [Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Shchur, Ya. [Institute for Condensed Matter Physics, 1 Svientsitskii str., L’viv 79011 (Ukraine)

    2016-02-07

    The mean atomic kinetic energies of the proton, Ke(H), and of the deuteron, Ke(D), were calculated in moderate and strongly hydrogen bonded (HB) systems, such as the ferro-electric crystals of the KDP type (XH{sub 2}PO{sub 4}, X = K, Cs, Rb, Tl), the DKDP (XD{sub 2}PO{sub 4}, X = K, Cs, Rb) type, and the X{sub 3}H(SO{sub 4}){sub 2} superprotonic conductors (X = K, Rb). All calculations utilized the simulated partial phonon density of states, deduced from density functional theory based first-principle calculations and from empirical lattice dynamics simulations in which the Coulomb, short range, covalent, and van der Waals interactions were accounted for. The presently calculated Ke(H) values for the two systems were found to be in excellent agreement with published values obtained by deep inelastic neutron scattering measurements carried out using the VESUVIO instrument of the Rutherford Laboratory, UK. The Ke(H) values of the M{sub 3}H(SO{sub 4}){sub 2} compounds, in which the hydrogen bonds are centro-symmetric, are much lower than those of the KDP type crystals, in direct consistency with the oxygen-oxygen distance R{sub OO}, being a measure of the HB strength.

  3. Origins of IR Intensity in Overtones and Combination Bands in Hydrogen Bonded Systems

    Science.gov (United States)

    Horvath, Samantha; McCoy, Anne B.

    2010-06-01

    As the infrared spectra of an increasing number of hydrogen bonded and ion/water complexes have been investigated experimentally, we find that they often contain bands with significant intensity that cannot be attributed to fundamental transitions. In this talk, we explore several sources of the intensity of these overtone and combination bands. A common source of intensity is mode-mode coupling, as is often seen between the proton transfer coordinate and the associated heavy atom vibration. A second important mechanism involves large changes in the dipole moment due the loss of a hydrogen bond. This results in intense overtone transitions involving non-totally symmetric vibrations as well as the introduction of intense combination bands involving intramolecular bending coupled to hindered rotations. These effects will be discussed in the context of several systems, including the spectra of complexes of argon atoms with {H}_3{O}^+, F^-\\cdotH_2O, Cl^-\\cdotH_2O, protonated water clusters,^a and HOONO. T. Guasco, S. Olesen and M. A. Johnson, private communication S. Horvath, A. B. McCoy, J. R. Roscioli and M. A. Johnson, J. Phys. Chem. A, 112, 12337-44 (2008) S. Horvath, A. B. McCoy, B. M. Eliot, G. H. Weddle, J. R. Roscioli and M. A. Johnson, J. Phys. Chem. A, 115, 1556-68 (2010). A. B. McCoy, M. K. Sprague and M. Okumura, J. Phys. Chem. A, 115, 1324-33 (2010)

  4. Hydrogen bonding in (substituted benzene)·(water)n clusters with n≤4

    International Nuclear Information System (INIS)

    Barth, H.-D.; Buchhold, K.; Djafari, S.; Reimann, B.; Lommatzsch, U.; Brutschy, B.

    1998-01-01

    Infrared ion-depletion spectroscopy, a double resonance method combining vibrational predissociation with resonant two-photon ionization (R2PI) spectroscopy, has been applied to study mixed clusters of the type (substituted benzene)·(H 2 O) n with n≤4. The UV chromophores were p-difluorobenzene, fluorobenzene, benzene, toluene, p-xylene and anisole. From the IR depletion spectra in the region of the OH stretching vibrations it could be shown that the water molecules are attached as subclusters to the chromophores. Size and configuration of the subclusters could be deduced from the IR depletion spectra. In the anisole·(H 2 O) 1 a nd 2 complexes the water clusters form an ordinary hydrogen bond to the oxygen atom of the methoxy group. In all other mixed complexes a π-hydrogen bond is formed between one of the free OH groups of a water subcluster and the π-system of the chromophore. According to the strength of this interaction the frequency of the respective absorption band exhibits a characteristic red-shift which could be related to the total atomic charges in the aromatic ring. (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

  5. Hydrogen-Bonded Polymer-Small Molecule Complexes with Tunable Mechanical Properties.

    Science.gov (United States)

    Liu, Tianqi; Peng, Xin; Chen, Ya-Nan; Bai, Qing-Wen; Shang, Cong; Zhang, Lin; Wang, Huiliang

    2018-03-13

    A novel type of polymeric material with tunable mechanical properties is fabricated from polymers and small molecules that can form hydrogen-bonded intermolecular complexes (IMCs). In this work, poly(vinyl alcohol) (PVA)-glycerol hydrogels are first prepared, and then they are dried to form IMCs. The tensile strengths and moduli of IMCs decrease dramatically with increasing glycerol content, while the elongations increase gradually. The mechanical properties are comparable with or even superior to those of common engineering plastics and rubbers. The IMCs with high glycerol content also show excellent flexibility and cold-resistance at subzero temperatures. Cyclic tensile and stress relaxation tests prove that there is an effective energy dissipation mechanism in IMCs and dynamic mechanical analysis confirms their physical crosslinking nature. FTIR and NMR characterizations prove the existence of hydrogen bonding between glycerol and PVA chains, which suppresses the crystallization of PVA from X-ray diffraction measurement. These PVA-glycerol IMCs may find potential applications in barrier films, biomedical packaging, etc., in the future. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Hydrogen Bond Induces Hierarchical Self-Assembly in Liquid-Crystalline Block Copolymers.

    Science.gov (United States)

    Huang, Shuai; Pang, Linlin; Chen, Yuxuan; Zhou, Liming; Fang, Shaoming; Yu, Haifeng

    2018-03-01

    Microphase-separated structures of block copolymers (BCs) with a size of sub-10 nm are usually obtained by hydrogen-bond-induced self-assembly of BCs through doping with small molecules as functional additives. Here, fabrication of hierarchically self-assembled sub-10 nm structures upon microphase separation of amphiphilic liquid-crystalline BCs (LCBCs) at the existence of hydrogen bonds but without any dopants is reported. The newly introduced urethane groups in the side chain of the hydrophobic block of LCBCs interact with the ether groups of the hydrophilic poly(ethylene oxide) (PEO) block, leading to imperfect crystallization of the PEO blocks. Both crystalline and amorphous domains coexist in the separated PEO phase, enabling a lamellar structure to appear inside the PEO nanocylinders. This provides an elegant method to fabricate controllable sub-10 nm microstructures in well-defined polymer systems without the introduction of any dopants. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. On the mean kinetic energy of the proton in strong hydrogen bonded systems

    International Nuclear Information System (INIS)

    Finkelstein, Y.; Moreh, R.; Shang, S. L.; Wang, Y.; Liu, Z. K.; Shchur, Ya.

    2016-01-01

    The mean atomic kinetic energies of the proton, Ke(H), and of the deuteron, Ke(D), were calculated in moderate and strongly hydrogen bonded (HB) systems, such as the ferro-electric crystals of the KDP type (XH 2 PO 4 , X = K, Cs, Rb, Tl), the DKDP (XD 2 PO 4 , X = K, Cs, Rb) type, and the X 3 H(SO 4 ) 2 superprotonic conductors (X = K, Rb). All calculations utilized the simulated partial phonon density of states, deduced from density functional theory based first-principle calculations and from empirical lattice dynamics simulations in which the Coulomb, short range, covalent, and van der Waals interactions were accounted for. The presently calculated Ke(H) values for the two systems were found to be in excellent agreement with published values obtained by deep inelastic neutron scattering measurements carried out using the VESUVIO instrument of the Rutherford Laboratory, UK. The Ke(H) values of the M 3 H(SO 4 ) 2 compounds, in which the hydrogen bonds are centro-symmetric, are much lower than those of the KDP type crystals, in direct consistency with the oxygen-oxygen distance R OO , being a measure of the HB strength

  8. Dynamic study of excited state hydrogen-bonded complexes of harmane in cyclohexane-toluene mixtures.

    Science.gov (United States)

    Carmona, Carmen; Balón, Manuel; Galán, Manuel; Guardado, Pilar; Muñoz, María A

    2002-09-01

    Photoinduced proton transfer reactions of harmane or 1-methyl-9H-pyrido[3,4-b]indole (HN) in the presence of the proton donor hexafluoroisopropanol (HFIP) in cyclohexane-toluene mixtures (CY-TL; 10% vol/vol of TL) have been studied. Three excited state species have been identified: a 1:2 hydrogen-bonded proton transfer complex (PTC), between the pyridinic nitrogen of the substrate and the proton donor, a hydrogen-bonded cation-like exciplex (CL*) with a stoichiometry of at least 1:3 and a zwitterionic exciplex (Z*). Time-resolved fluorescence measurements evidence that upon excitation of ground state PTC, an excited state equilibrium is established between PTC* and the cationlike exciplex, CL*, lambdaem approximately/= 390 nm. This excited state reaction is assisted by another proton donor molecule. Further reaction of CL* with an additional HFIP molecule produces the zwitterionic species, Z*, lambda(em) approximately/= 500 nm. From the analysis of the multiexponential decays, measured at different emission wavelengths and as a function of HFIP concentration, the mechanism of these excited state reactions has been established. Thus, three rate constants and three reciprocal lifetimes have been determined. The simultaneous study of 1,9-dimethyl-9H-pyrido[3,4-b]indole (MHN) under the same experimental conditions has helped to understand the excited state kinetics of these processes.

  9. Azobenzene dye-coupled quadruply hydrogen-bonding modules as colorimetric indicators for supramolecular interactions

    Directory of Open Access Journals (Sweden)

    Yagang Zhang

    2012-04-01

    Full Text Available The facile coupling of azobenzene dyes to the quadruply hydrogen-bonding modules 2,7-diamido-1,8-naphthyridine (DAN and 7-deazaguanine urea (DeUG is described. The coupling of azobenzene dye 2 to mono-amido DAN units 4, 7, and 9 was effected by classic 4-(dimethylaminopyridine (DMAP-catalyzed peptide synthesis with N-(3-dimethylaminopropyl-N’-ethyl carbodiimide hydrochloride (EDC as activating agent, affording the respective amide products 5, 8, and 10 in 60–71% yield. The amide linkage was formed through either the aliphatic or aromatic ester group of 2, allowing both the flexibility and absorption maximum to be tuned. Azobenzene dye 1 was coupled to the DeUG unit 11 by Steglich esterification to afford the product amide 12 in 35% yield. Alternatively, azobenzene dye 16 underwent a room-temperature copper-catalyzed azide–alkyne Huisgen cycloaddition with DeUG alkyne 17 to give triazole 18 in 71% yield. Azobenzene coupled DAN modules 5, 8, and 10 are bright orange–red in color, and azobenzene coupled DeUG modules 12 and 18 are orange–yellow in color. Azobenzene coupled DAN and DeUG modules were successfully used as colorimetric indicators for specific DAN–DeUG and DAN–UPy (2-ureido-4(1H-pyrimidone quadruply hydrogen-bonding interactions.

  10. High strength films from oriented, hydrogen-bonded "graphamid" 2D polymer molecular ensembles.

    Science.gov (United States)

    Sandoz-Rosado, Emil; Beaudet, Todd D; Andzelm, Jan W; Wetzel, Eric D

    2018-02-27

    The linear polymer poly(p-phenylene terephthalamide), better known by its tradename Kevlar, is an icon of modern materials science due to its remarkable strength, stiffness, and environmental resistance. Here, we propose a new two-dimensional (2D) polymer, "graphamid", that closely resembles Kevlar in chemical structure, but is mechanically advantaged by virtue of its 2D structure. Using atomistic calculations, we show that graphamid comprises covalently-bonded sheets bridged by a high population of strong intermolecular hydrogen bonds. Molecular and micromechanical calculations predict that these strong intermolecular interactions allow stiff, high strength (6-8 GPa), and tough films from ensembles of finite graphamid molecules. In contrast, traditional 2D materials like graphene have weak intermolecular interactions, leading to ensembles of low strength (0.1-0.5 GPa) and brittle fracture behavior. These results suggest that hydrogen-bonded 2D polymers like graphamid would be transformative in enabling scalable, lightweight, high performance polymer films of unprecedented mechanical performance.

  11. HR-EELS study of hydrogen bonding configuration, chemical and thermal stability of detonation nanodiamond films

    Energy Technology Data Exchange (ETDEWEB)

    Michaelson, Sh.; Akhvlediani, R. [Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000 (Israel); Petit, T.; Girard, H.A.; Arnault, J.C. [CEA, LIST, Diamond Sensors Laboratory, F-91191 Gif sur Yvette (France); Hoffman, A., E-mail: choffman@tx.technion.ac.il [Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000 (Israel)

    2014-06-01

    Nano-diamond films composed of 3–10 nm grains prepared by the detonation method and deposited onto silicon substrates by drop-casting were examined by high resolution electron energy loss spectroscopy (HR-EELS), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and secondary ion mass spectroscopy (SIMS). The impact of (i) ex-situ ambient annealing at 400 °C and (ii) ex-situ hydrogenation on hydrogen bonding and its thermal stability were examined. In order to clarify the changes in hydrogen bonding configuration detected on the different surfaces as a function of thermal annealing, in-situ hydrogenation by thermally activated atomic hydrogen was performed and examined. This study provides direct evidence that the exposure to ambient conditions and medium temperature ambient annealing have a pronounced effect on the hydrogen-carbon bonding configuration onto the nano-diamond surfaces. In-situ 1000 °C annealing results in irreversible changes of the film surface and partial nano-diamond silicidation.

  12. New insights into the dual fluorescence of methyl salicylate: effects of intermolecular hydrogen bonding and solvation.

    Science.gov (United States)

    Zhou, Panwang; Hoffmann, Mark R; Han, Keli; He, Guozhong

    2015-02-12

    In this paper, we propose a new and complete mechanism for dual fluorescence of methyl salicylate (MS) under different conditions using a combined experimental (i.e., steady-state absorption and emission spectra and time-resolved fluorescence spectra) and theoretical (i.e., time-dependent density function theory) study. First, our theoretical study indicates that the barrier height for excited state intramolecular proton transfer (ESIPT) reaction of ketoB depends on the solvent polarity. In nonpolar solvents, the ESIPT reaction of ketoB is barrierless; the barrier height will increase with increasing solvent polarity. Second, we found that, in alcoholic solvents, intermolecular hydrogen bonding plays a more important role. The ketoB form of MS can form two hydrogen bonds with alcoholic solvents; one will facilitate ESIPT and produce the emission band in the blue region; the other one precludes ESIPT and produces the emission band in the near-UV region. Our proposed new mechanism can well explain previous results as well as our new experimental results.

  13. Microscopic dynamics of the hydrogen bonded systems studied by quasi-elastic slow neutron scattering

    International Nuclear Information System (INIS)

    Padureanu, I.; Aranghel, D.; Radulescu, A.; Ion, M.; Lechner, R. E.; Desmedt, A.; Pieper, J.

    2002-01-01

    The detailed understanding of the dynamical properties in highly viscous liquids such as glycerol, as well the supercooled and glassy state has attracted a great deal of attention. Glycerol is a hydrogen bonded forming system considered as intermediate between fragile and strong glasses with a glass transition temperature T g ∼ 185 K, melting temperature T m 290 K and a sound velocity V S ∼ 3330 m/s. Incoherent neutron scattering experiments from glasses generally show a broad feature with a maximum around 2 to 10 meV. This large contribution of such unusual low frequency excitations obeying the Bose-Einstein statistics to the density of states is referred to as 'boson peak' (BP) with a maximum near a frequency of 1 THz. A very much-debated question is the dramatic changes in the properties as well as the nature of the boson peak and the acoustic modes occurring in the neighborhood of this frequency. So far the experiments were not able to give a definite answer concerning the excitations giving rise to the boson peak. The inelastic X-ray scattering across the liquid glass transition in glycerol revealed propagating collective excitations in the whole liquid-glass transition temperature range. This conclusion challenges the present understanding of glasses and supercooled liquids particularly with their thermal properties. New experiments at lower temperatures than those investigated so far where the phonon scattering processes are less hard have been proposed. The relationship between the low frequency features, the microscopic structure, the nature of the forces and the atomic motions taking place at low frequencies is still an open question. According to the mode coupling theory (MCT) the glass transition is interpreted as a two-step process where the glass structure is softened by fast local motions (β - process) until some temperature T c >T g , where the structure breaks down leading to diffusion (α-process). It is an open question, whether MCT can

  14. FT-IR spectroelectrochemical study of the reduction of 1,4-dinitrobenzene on Au electrode: Hydrogen bonding and protonation in proton donor mixed media

    International Nuclear Information System (INIS)

    Tian Dexiang; Jin Baokang

    2011-01-01

    Highlights: → 1,4-Dinitrobenzene electrochemical reduction on the Au electrode is explored. → Radical anion (PNB· - ) is found both in aprotic media and in proton donors mixed media. → The H-bonding forming between PNB· - , PNB 2- and proton donors in low donors concentration. → The protonation of PNB 2- occurs in high concentration proton donor mixed media. - Abstract: The electrochemical behavior of 1,4-dinitrobenzene (1,4-PNB) on the Au electrode was investigated by cyclic voltammetry (CV), in situ FT-IR spectroelectrochemistry, cyclic voltabsorptometry (CVA) and derivative cyclic voltabsorptometry (DCVA) techniques. In aprotic media, 1,4-dinitrobenzene is reversibly reduced in two-step one-electron transfer. A series of IR absorption bands at 1056, 1210, 1341, 1356, 1464 and 1549 cm -1 , tracing to PNB; PNB· - and PNB 2- are observed. In the presence of proton donors mixed media, with increasing concentrations of proton donors, hydrogen-bonding and protonation process are found successively. The values of combining proton donors with per PNB 2- to form hydrogen-bonding are estimated by using electrochemical parameters. The result of forming aromatic nitroso compound is supported by tracing the change of IR absorption bands at 1149 and 1587 cm -1 at high concentration of proton donors. Based on CVA and DCVA techniques, it is clearly distinguished that the mechanisms of electrochemical reduction of PNB are elaborated in different systems.

  15. {sup 2}H NMR study of phase transition and hydrogen dynamics in hydrogen bonded organic antiferroelectric 55DMBP-H{sub 2}ca

    Energy Technology Data Exchange (ETDEWEB)

    Asaji, Tetsuo, E-mail: asaji@chs.nihon-u.ac.jp; Hara, Masamichi; Fujimori, Hiroki [Nihon University, Department of Chemistry, College of Humanities and Sciences (Japan); Hagiwara, Shoko [Nihon University, Department of Chemistry, Graduate School of Integrated Basic Sciences (Japan)

    2016-12-15

    Hydrogen dynamics in one-dimensional hydrogen bonded organic antiferroelectric, co-crystal of 5,5’-dimethyl-2,2’-bipyridine (55DMBP) and chloranilic acid (H{sub 2}ca), was investigated by use of {sup 2}H high resolution solid-state NMR. The two types of hydrogen bonds O-H …N and N{sup +}-H …O{sup −} in the antiferroelectric phase were clearly observed as the splitting of the side band of the {sup 2}H MAS NMR spectra of the acid-proton deuterated compound 55DMBP-D {sub 2}ca. The temperature dependence of the spin-lattice relaxation time was measured of the N{sup +}-H and O-H deuterons, respectively. It was suggested that the motion of the O-H deuteron is already in the antiferroelectric phase in the fast-motion regime in the NMR time scale, while that of the N{sup +}-H deuteron is a slow motion. In the high-temperature paraelectric phase, the both deuterons become equivalent and the fast motion of the deuterons in the NMR time scale is taking place with the activation energy of 7.9 kJ mol{sup −1}.

  16. In situ ultra-small-angle X-ray scattering study under uniaxial stretching of colloidal crystals prepared by silica nanoparticles bearing hydrogen-bonding polymer grafts

    Directory of Open Access Journals (Sweden)

    Ryohei Ishige

    2016-05-01

    Full Text Available A molded film of single-component polymer-grafted nanoparticles (SPNP, consisting of a spherical silica core and densely grafted polymer chains bearing hydrogen-bonding side groups capable of physical crosslinking, was investigated by in situ ultra-small-angle X-ray scattering (USAXS measurement during a uniaxial stretching process. Static USAXS revealed that the molded SPNP formed a highly oriented twinned face-centered cubic (f.c.c. lattice structure with the [11−1] plane aligned nearly parallel to the film surface in the initial state. Structural analysis of in situ USAXS using a model of uniaxial deformation induced by rearrangement of the nanoparticles revealed that the f.c.c. lattice was distorted in the stretching direction in proportion to the macroscopic strain until the strain reached 35%, and subsequently changed into other f.c.c. lattices with different orientations. The lattice distortion and structural transition behavior corresponded well to the elastic and plastic deformation regimes, respectively, observed in the stress–strain curve. The attractive interaction of the hydrogen bond is considered to form only at the top surface of the shell and then plays an effective role in cross-linking between nanoparticles. The rearrangement mechanism of the nanoparticles is well accounted for by a strong repulsive interaction between the densely grafted polymer shells of neighboring particles.

  17. Microscopic mechanism of electron transfer through the hydrogen bonds between carboxylated alkanethiol molecules connected to gold electrodes

    KAUST Repository

    Li, Yang; Tu, Xingchen; Wang, Minglang; Wang, Hao; Sanvito, Stefano; Hou, Shimin

    2014-01-01

    © 2014 AIP Publishing LLC. The atomic structure and the electron transfer properties of hydrogen bonds formed between two carboxylated alkanethiol molecules connected to gold electrodes are investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. Three types of molecular junctions are constructed, in which one carboxyl alkanethiol molecule contains two methylene, -CH2, groups and the other one is composed of one, two, or three -CH2 groups. Our calculations show that, similarly to the cases of isolated carboxylic acid dimers, in these molecular junctions the two carboxyl, -COOH, groups form two H-bonds resulting in a cyclic structure. When self-interaction corrections are explicitly considered, the calculated transmission coefficients of these three H-bonded molecular junctions at the Fermi level are in good agreement with the experimental values. The analysis of the projected density of states confirms that the covalent Au-S bonds localized at the molecule-electrode interfaces and the electronic coupling between -COOH and S dominate the low-bias junction conductance. Following the increase of the number of the -CH2 groups, the coupling between -COOH and S decreases deeply. As a result, the junction conductance decays rapidly as the length of the H-bonded molecules increases. These findings not only provide an explanation to the observed distance dependence of the electron transfer properties of H-bonds, but also help the design of molecular devices constructed through H-bonds.

  18. Microscopic mechanism of electron transfer through the hydrogen bonds between carboxylated alkanethiol molecules connected to gold electrodes

    KAUST Repository

    Li, Yang

    2014-11-07

    © 2014 AIP Publishing LLC. The atomic structure and the electron transfer properties of hydrogen bonds formed between two carboxylated alkanethiol molecules connected to gold electrodes are investigated by employing the non-equilibrium Green\\'s function formalism combined with density functional theory. Three types of molecular junctions are constructed, in which one carboxyl alkanethiol molecule contains two methylene, -CH2, groups and the other one is composed of one, two, or three -CH2 groups. Our calculations show that, similarly to the cases of isolated carboxylic acid dimers, in these molecular junctions the two carboxyl, -COOH, groups form two H-bonds resulting in a cyclic structure. When self-interaction corrections are explicitly considered, the calculated transmission coefficients of these three H-bonded molecular junctions at the Fermi level are in good agreement with the experimental values. The analysis of the projected density of states confirms that the covalent Au-S bonds localized at the molecule-electrode interfaces and the electronic coupling between -COOH and S dominate the low-bias junction conductance. Following the increase of the number of the -CH2 groups, the coupling between -COOH and S decreases deeply. As a result, the junction conductance decays rapidly as the length of the H-bonded molecules increases. These findings not only provide an explanation to the observed distance dependence of the electron transfer properties of H-bonds, but also help the design of molecular devices constructed through H-bonds.

  19. Modeling evolution of hydrogen bonding and stabilization of transition states in the process of cocaine hydrolysis catalyzed by human butyrylcholinesterase.

    Science.gov (United States)

    Gao, Daquan; Zhan, Chang-Guo

    2006-01-01

    Molecular dynamics (MD) simulations and quantum mechanical/molecular mechanical (QM/MM) calculations were performed on the prereactive enzyme-substrate complex, transition states, intermediates, and product involved in the process of human butyrylcholinesterase (BChE)-catalyzed hydrolysis of (-)-cocaine. The computational results consistently reveal a unique role of the oxyanion hole (consisting of G116, G117, and A199) in BChE-catalyzed hydrolysis of cocaine, compared to acetylcholinesterase (AChE)-catalyzed hydrolysis of acetylcholine. During BChE-catalyzed hydrolysis of cocaine, only G117 has a hydrogen bond with the carbonyl oxygen (O31) of the cocaine benzoyl ester in the prereactive BChE-cocaine complex, and the NH groups of G117 and A199 are hydrogen-bonded with O31 of cocaine in all of the transition states and intermediates. Surprisingly, the NH hydrogen of G116 forms an unexpected hydrogen bond with the carboxyl group of E197 side chain and, therefore, is not available to form a hydrogen bond with O31 of cocaine in the acylation. The NH hydrogen of G116 is only partially available to form a weak hydrogen bond with O31 of cocaine in some structures involved in the deacylation. The change of the estimated hydrogen-bonding energy between the oxyanion hole and O31 of cocaine during the reaction process demonstrates how the protein environment can affect the energy barrier for each step of the BChE-catalyzed hydrolysis of cocaine. These insights concerning the effects of the oxyanion hole on the energy barriers provide valuable clues on how to rationally design BChE mutants with a higher catalytic activity for the hydrolysis of (-)-cocaine. 2005 Wiley-Liss, Inc.

  20. Measurement and theory of hydrogen bonding contribution to isosteric DNA base pairs.

    Science.gov (United States)

    Khakshoor, Omid; Wheeler, Steven E; Houk, K N; Kool, Eric T

    2012-02-15

    We address the recent debate surrounding the ability of 2,4-difluorotoluene (F), a low-polarity mimic of thymine (T), to form a hydrogen-bonded complex with adenine in DNA. The hydrogen bonding ability of F has been characterized as small to zero in various experimental studies, and moderate to small in computational studies. However, recent X-ray crystallographic studies of difluorotoluene in DNA/RNA have indicated, based on interatomic distances, possible hydrogen bonding interactions between F and natural bases in nucleic acid duplexes and in a DNA polymerase active site. Since F is widely used to measure electrostatic contributions to pairing and replication, it is important to quantify the impact of this isostere on DNA stability. Here, we studied the pairing stability and selectivity of this compound and a closely related variant, dichlorotoluene deoxyriboside (L), in DNA, using both experimental and computational approaches. We measured the thermodynamics of duplex formation in three sequence contexts and with all possible pairing partners by thermal melting studies using the van't Hoff approach, and for selected cases by isothermal titration calorimetry (ITC). Experimental results showed that internal F-A pairing in DNA is destabilizing by 3.8 kcal/mol (van't Hoff, 37 °C) as compared with T-A pairing. At the end of a duplex, base-base interactions are considerably smaller; however, the net F-A interaction remains repulsive while T-A pairing is attractive. As for selectivity, F is found to be slightly selective for adenine over C, G, T by 0.5 kcal mol, as compared with thymine's selectivity of 2.4 kcal/mol. Interestingly, dichlorotoluene in DNA is slightly less destabilizing and slightly more selective than F, despite the lack of strongly electronegative fluorine atoms. Experimental data were complemented by computational results, evaluated at the M06-2X/6-31+G(d) and MP2/cc-pVTZ levels of theory. These computations suggest that the pairing energy of F to A

  1. Hydrogen bonded 1D-3D supramolecular structures from Benzylamine and organic acidic components

    Science.gov (United States)

    Gao, Xingjun; Li, XiaoLiang; Jin, Shouwen; Hu, Kaikai; Guo, Jianzhong; Guo, Ming; Xu, Weiqiang; Wang, Daqi

    2018-03-01

    Cocrystallization of the commonly available organic amine, benzylamine, with a series of organic acids afforded a total of seven organic salts with the compositions: (benzylamine)2: (p-nitrophenol)2: (H2O) (1) [(HL)2+⋯(npl-)2⋯(H2O), npl- = p-nitrophenolate], (benzylamine): (4-tert-butylbenzoic acid) (2) [(HL+)⋯(tba-), tba- = 4-tert-butylbenzoate], (benzylamine): (3,4-dichlorobenzoic acid) (3) [(HL+)⋯dcba-), dcba- = 3,4-dichlorobenzoate], (benzylamine): (2,5-dihydroxybenzoic acid) (4) [(HL+)⋯(dhba-), dhba- = 2,5-dihydroxybenzoate], (benzylamine): (2-bromo-but-2-enedioic acid) (5) [(HL+)⋯(Hbba-), Hbba- = 2-bromo-hydrogenbut-2-enedioate], (benzylamine): (2,6-pyridinedicarboxylic acid) (6) [(HL+)⋯(Hpdc-), Hpdc- = 2,6-pyridine hydrogendicarboxylate], and (benzylamine)2: (3-nitrophthalic acid): 2(H2O) (7) [(HL+)2⋯(npa2-)⋯(H2O)2, npa2- = 3-nitrophthalate]. The seven salts have been characterised by X-ray diffraction analysis, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The results reveal that among the seven investigated crystals the NH2 in the benzylamine are protonated when the organic acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted Nsbnd H⋯O hydrogen bond between the NH3+ and deprotonated acidic groups. Except the Nsbnd H⋯O hydrogen bond, the Osbnd H⋯O hydrogen bonds (charge assisted or neutral) were also found at the salts 1, 4, 5, 6, and 7. Further analysis of the crystal packing of the salts indicated that a different family of additional CHsbnd O/CH2sbnd O, CH-π/CH2-π, Cπ-Cπ, Osbnd O, O-Cπ, O-π, and Cl-π associations also contribute to the stabilization and expansion of the total high-dimensional framework structures. For the coexistence of the various weak nonbonding interactions, these structures adopted a variety of

  2. Structure of the DNA duplex d(ATTAAT2 with Hoogsteen hydrogen bonds.

    Directory of Open Access Journals (Sweden)

    Francisco J Acosta-Reyes

    Full Text Available The traditional Watson-Crick base pairs in DNA may occasionally adopt a Hoogsteen conformation, with a different organization of hydrogen bonds. Previous crystal structures have shown that the Hoogsteen conformation is favored in alternating AT sequences of DNA. Here we present new data for a different sequence, d(ATTAAT2, which is also found in the Hoogsteen conformation. Thus we demonstrate that other all-AT sequences of DNA with a different sequence may be found in the Hoogsteen conformation. We conclude that any all-AT sequence might acquire this conformation under appropriate conditions. We also compare the detailed features of DNA in either the Hoogsteen or Watson-Crick conformations.

  3. Functional organic materials based on polymerized liquid-crystal monomers: supramolecular hydrogen-bonded systems.

    Science.gov (United States)

    Broer, Dirk J; Bastiaansen, Cees M W; Debije, Michael G; Schenning, Albertus P H J

    2012-07-16

    Functional organic materials are of great interest for a variety of applications. To obtain precise functional properties, well-defined hierarchically ordered supramolecular materials are crucial. The self-assembly of liquid crystals has proven to be an extremely useful tool in the development of well-defined nanostructured materials. We have chosen the illustrative example of photopolymerizable hydrogen-bonding mesogens to show that a wide variety of functional materials can be made from a relatively simple set of building blocks. Upon mixing these compounds with other reactive mesogens, nematic, chiral nematic, and smectic or columnar liquid-crystalline phases can be formed that can be applied as actuators, sensors and responsive reflectors, and nanoporous membranes, respectively. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. From Coordination Cages to a Stable Crystalline Porous Hydrogen-Bonded Framework

    Energy Technology Data Exchange (ETDEWEB)

    Ju, Zhanfeng [State Key Lab of Structure Chemistry, Fujian Institute of Research on the Structure of Matter, CAS, Fuzhou 350002 P. R. China; Liu, Guoliang [State Key Lab of Structure Chemistry, Fujian Institute of Research on the Structure of Matter, CAS, Fuzhou 350002 P. R. China; Chen, Yu-Sheng [ChemMatCARS, Center for Advanced Radiation Sources, The University of Chicago, Argonne Illinois 60439 USA; Yuan, Daqiang [State Key Lab of Structure Chemistry, Fujian Institute of Research on the Structure of Matter, CAS, Fuzhou 350002 P. R. China; Chen, Banglin [Department of Chemistry, University of Texas at San Antonio, San Antonio Texas 78249-0698 USA

    2017-03-20

    A stable framework has been constructed through multiple charge-assisted H-bonds between cationic coordination cages and chloride ions. The framework maintained its original structure upon desolvation, which has been established by single-crystal structure analysis. This is the first fully characterized stable porous framework based on coordination cages after desolvation, with a moderately high Brunauer–Emmett–Teller (BET) surface area of 1201 m2 g-1. This work will not only give a light to construct stable porous frameworks based on coordination cages and thus broaden their applications, but will also provide a new avenue to the assembly of other porous materials such as porous organic cages and hydrogen-bonded organic frameworks (HOFs) through non covalent bonds.

  5. Hydrogen-bonding interactions in thiosemicarbazones of carboxylic acids: Structure of 2-ketobutyric acid thiosemicarbazone hemihydrate

    International Nuclear Information System (INIS)

    Sonawane, P.; Chikate, R.; Kumbhar, A.; Padhye, S.; Doedens, R.J.

    1991-01-01

    2-Thiosemicarbazonobutanoic acid hemihydrate, C 5 H 9 N 3 O 2 S.0.5H 2 O, M r =184.22, triclinic, Panti 1, a=8.163(2), b=8.868(2), c=12.438(2) A, α=72.99(2), β=79.47(2), γ=84.06(2)deg, V=845.3(3) A 3 , Z=4, D x =1.447 Mg m -3 , λ(Mo Kα)=0.71073 A, μ=0.332 mm -1 , F(000)=392, T=296 K, R=0.038 for 3830 independent reflections with I>3σ(I). Three hydrogen bonds link the two crystallographically independent molecules in a pairwise fashion. The two molecules both have E configurations about each C-N and N-N bond, but differ by nearly 180deg in the orientation of the -COOH group. (orig.)

  6. Hydrogen bonding controlled catalysis of a porous organic framework containing benzimidazole moieties

    KAUST Repository

    Liu, Bing

    2014-01-01

    A microporous organic framework (JUC-Z12) was synthesized quantitatively from tetra(4-formylphenyl)methane and 3,3′-diaminobenzidine. JUC-Z12 shows high thermal stability (>400 °C), a large surface area (SBET = 750 m2 g-1), a well-defined uniform micropore distribution (1.09 nm) and high Qst for H2 (-8.1 kJ mol-1), CO2 (-29.5 kJ mol-1), and CH 4 (-22.2 kJ mol-1). It also exhibits selective catalytic activities in the Knoevenagel reaction, which is supposed to be controlled by hydrogen bonding between substrates and JUC-Z12. The JUC-Z12 catalyst can be easily isolated from the reaction mixture by simple filtration and reused with high activity. This journal is © the Partner Organisations 2014.

  7. Intra- und intermolecular hydrogen bonds. Spectroscopic, quantum chemical and molecular dynamics studies

    International Nuclear Information System (INIS)

    Simperler, A.

    1999-03-01

    Intra- and intermolecular H-bonds have been investigated with spectroscopic, quantum chemical, and molecular dynamics methods. The work is divided into the following three parts: 1. Intramolecular interactions in ortho-substituted phenols. Theoretical and experimental data that characterizes the intramolecular hydrogen bonds in 48 different o-substituted phenols are discussed. The study covers various kinds of O-H ... Y -type interactions (Y= N, O, S, F, Cl, Br, I, C=C, C=-C, and C-=N). The bond strength sequences for several series of systematically related compounds as obtained from IR spectroscopy data (i.e., v(OH) stretching frequencies) are discussed and reproduced with several theoretical methods (B3LYP/6-31G(d,p), B3LYP/6-311G(d,p), B3LYP/6-31++G(d,p), B3LYP/DZVP, MP2/6-31G(d,p), and MP2/6-31++G(d,p) levels of theory). The experimentally determined sequences are interpreted in terms of the intrinsic properties of the molecules: hydrogen bond distances, Mulliken partial charges, van der Waals radii, and electron densities of the Y-proton acceptors. 2. Competitive hydrogen bonds and conformational equilibria in 2,6-disubstituted phenols containing two different carbonyl substituents. The rotational isomers of ten unsymmetrical 2,6-disubstituted phenols as obtained by combinations of five different carbonyl substituents (COOH, COOCH 3 , CHO, COCH 3 , and CONH 2 ) have been theoretically investigated at the B3LYP/6-31G(d,p) level of theory. The relative stability of four to five conformers of each compound were determined by full geometry optimization for free molecules as well as for molecules in reaction fields with dielectric constants up to ε=37.5. A comparison with IR spectroscopic data of available compounds revealed excellent agreement with the theoretically predicted stability sequences and conformational equilibria. The stability of a conformer could be interpreted to be governed by the following two contributions: (i) an attractive hydrogen bond

  8. Electron detachment of the hydrogen-bonded amino acid side-chain guanine complexes

    Science.gov (United States)

    Wang, Jing; Gu, Jiande; Leszczynski, Jerzy

    2007-07-01

    The photoelectron spectra of the hydrogen-bonded amino acid side-chain-guanine complexes has been studied at the partial third order (P3) self-energy approximation of the electron propagator theory. The correlation between the vertical electron detachment energy and the charge distributions on the guanine moiety reveals that the vertical electron detachment energy (VDE) increases as the positive charge distribution on the guanine increases. The low VDE values determined for the negatively charged complexes of the guanine-side-chain-group of Asp/Glu suggest that the influence of the H-bonded anionic groups on the VDE of guanine could be more important than that of the anionic backbone structure. The even lower vertical electron detachment energy for guanine is thus can be expected in the H-bonded protein-DNA systems.

  9. The role of hydrogen bonding on kinetics of rearrangement of heterocyclic aldoximes in perchloric acide

    International Nuclear Information System (INIS)

    Azzouz, A.S.; Abdullah, K.A.; Al-Niemi, I.

    1995-01-01

    Four paris of syn and anti aromatic heterocyclic aldoximes as 2-thiophenealdoxime, 2- furfuraladoxime, 2-pyridinealdoxime and 2-pyrrolealdoxime are prepared. The strcutures of these geometrical isomers are confirmed by the meaasurements of their U.V. I, R and melting points. Experiments show the existence of these aldoximers in an intramolecular hy-drogen bonding with variable strength depending on the hetero ztoms in the aldoximes. The first order rate constants of the rearrangement of syn aldoximes follow the order of hetero S>O>N, while the anti aldoximes show irregular order, Factors governing the aniti constants of the rearrangement of syn and anti aldoximes are analysed. Activation parameters are estimated and discussed on the basis of isokinetic relation-ship. The differences in physical and spectroscpic behavior of aldoximes lead to an important suggestion regarding the configuration of oxime. (author). 27 refs., 2 figs., 2 tabs

  10. Phase transition and intramolecular hydrogen bonding in nitro derivatives of ortho-hydroxy acetophenones

    Science.gov (United States)

    Filarowski, A.; Kochel, A.; Koll, A.; Bator, G.; Mukherjee, S.

    2006-03-01

    The crystal structures of two ortho-hydroxy aryl ketones (5-chloro-3-nitro-2-hydroxyacetophenone, 5-methyl-3-nitro-2-hydroxyacetophenone and the complex 5-chloro-3-nitro-2-hydroxyacetophenone with 2-aminobenzoic acid (anthranilic acid)) were determined by X-ray diffraction. The existence of an intramolecular hydrogen bond of enol character between the hydroxyl and acetyl groups was found by the X-ray method. The enol character was also confirmed by DFT (B3LYP/6-31+G(d,p)) calculations. A phase transition was found at 138 K in 5-chloro-3-nitro-2-hydroxyacetophenone. This phase transition was investigated by differential scanning calorimetry (DSC), dilatometry, and the dielectric method. A study of the nitro-group dynamics in the ortho-hydroxy acetophenones was carried out with DFT (B3LYP/6-31+G(d,p)) calculations.

  11. Hydrogen-bonded co-crystal structure of benzoic acid and zwitterionic l-proline

    Directory of Open Access Journals (Sweden)

    Aaron M. Chesna

    2017-03-01

    Full Text Available The title compound [systematic name: benzoic acid–pyrrolidin-1-ium-2-carboxylate (1/1], C7H6O2·C5H9NO2, is an example of the application of non-centrosymmetric co-crystallization for the growth of a crystal containing a typically centrosymmetric component in a chiral space group. It co-crystallizes in the space group P212121 and contains benzoic acid and l-proline in equal proportions. The crystal structure exhibits chains of l-proline zwitterions capped by benzoic acid molecules which form a C(5[R33(11] hydrogen-bonded network along [100]. The crystal structure is examined and compared to that of a similar co-crystal containing l-proline zwitterions and 4-aminobenzoic acid.

  12. Substituent Effects on the Hydrogen Bonding Between Phenolate and HF, H2O and NH3

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    B3LYP/6-31+g(d) calculations were performed on the hydrogen bonded complexes between substituted phenolates and HF, H2O as well as NH3. It was found that some properties of the non-covalent complexes, including the interaction energies, donor-acceptor (host-guest) distances, bond lengths, and vibration frequencies, could show well-defined substituent effects. Thus, from the substituent studies we can not only understand the mechanism of a particular non-covalent interaction better, but also easily predict the interaction energies and structures of a particular non-covalent complex, which might otherwise be very hard or resource-consuming to be known. This means that substituent effect is indeed a useful tool to be used in supramolecular chemistry and therefore, many valuable studies remain to be carried out.

  13. The hydrogen-bond network of water supports propagating optical phonon-like modes.

    Science.gov (United States)

    Elton, Daniel C; Fernández-Serra, Marivi

    2016-01-04

    The local structure of liquid water as a function of temperature is a source of intense research. This structure is intimately linked to the dynamics of water molecules, which can be measured using Raman and infrared spectroscopies. The assignment of spectral peaks depends on whether they are collective modes or single-molecule motions. Vibrational modes in liquids are usually considered to be associated to the motions of single molecules or small clusters. Using molecular dynamics simulations, here we find dispersive optical phonon-like modes in the librational and OH-stretching bands. We argue that on subpicosecond time scales these modes propagate through water's hydrogen-bond network over distances of up to 2 nm. In the long wavelength limit these optical modes exhibit longitudinal-transverse splitting, indicating the presence of coherent long-range dipole-dipole interactions, as in ice. Our results indicate the dynamics of liquid water have more similarities to ice than previously thought.

  14. A low-barrier hydrogen bond mediates antibiotic resistance in a noncanonical catalytic triad

    Science.gov (United States)

    2018-01-01

    One group of enzymes that confer resistance to aminoglycoside antibiotics through covalent modification belongs to the GCN5-related N-acetyltransferase (GNAT) superfamily. We show how a unique GNAT subfamily member uses a previously unidentified noncanonical catalytic triad, consisting of a glutamic acid, a histidine, and the antibiotic substrate itself, which acts as a nucleophile and attacks the acetyl donor molecule. Neutron diffraction studies allow for unambiguous identification of a low-barrier hydrogen bond, predicted in canonical catalytic triads to increase basicity of the histidine. This work highlights the role of this unique catalytic triad in mediating antibiotic resistance while providing new insights into the design of the next generation of aminoglycosides. PMID:29632894

  15. Rotational Isomers, Intramolecular Hydrogen Bond, and IR Spectra of o-Vinylphenol Homologs

    Science.gov (United States)

    Glazunov, V. P.; Berdyshev, D. V.; Balaneva, N. N.; Radchenko, O. S.; Novikov, V. L.

    2018-03-01

    The ν(OH) stretching-mode bands in solution IR spectra of five o-vinylphenol (o-VPh) homologs in the slightly polar solvents CCl4 and n-hexane were studied. Several rotamers with free OH groups were found in solutions of o-VPh and its methyl-substituted derivatives in n-hexane. The proportion of rotamers in o-VPh homologs with intramolecular hydrogen bonds (IHBs) O-H...π varied from 22 to 97% in the gas and cyclohexane according to B3LYP/cc-pVTZ calculations. The theoretically estimated effective enthalpies -ΔH of their IHBs varied in the range 0.20-2.24 kcal/mol.

  16. Dimeric Self-assembling via Hydrogen Bonding and Emissive Behavior of a New Copper (I Complex

    Directory of Open Access Journals (Sweden)

    Juciely M. dos Reis

    2017-04-01

    Full Text Available This work describes the synthesis, structural characterization and emissive behavior of a new copper (I complex based on 1-thiocarbamoyl-5-(4-methoxiphenyl-3-phenyl-4,5-dihydro-1H-pyrazole ligand. A dimeric self-assembling via hydrogen bonding was determined by analyzing the short contacts present in the solid-state structure by means of X-ray crystallography. The spectroscopic properties were determined using UV-Vis and fluorescence experiments and an interesting behavior as bluish luminescence was assigned mainly to the mixed (MLCT + IL electronic transitions of the Cu(Id10 ® (S=C–Nligand type. The complete characterization of the new copper (I complex also included elemental analyses and IR spectroscopy. DOI: http://dx.doi.org/10.17807/orbital.v9i1.952

  17. Fluorescence Correlation Spectroscopy to Study Diffusion of Polymer Chains within Layered Hydrogen-Bonded Polymer Films

    Science.gov (United States)

    Pristinski, Denis; Kharlampieva, Evguenia; Sukhishvili, Svetlana

    2002-03-01

    Fluorescence Correlation Spectroscopy (FCS) has been used to probe molecular motions within polymer multilayers formed by hydrogen-bonding sequential self-assembly. Polyethylene glycol (PEG) molecules were end-labeled with the fluorescent tags, and self-assembled with polymethacrylic acid (PMAA) using layer-by-layer deposition. We have found that molecules included in the top adsorbed layer have significant mobility at the millisecond time scale, probably due to translational diffusion. However, their dynamics deviate from classical Brownian motion with a single diffusion time. Possible reasons for the deviation are discussed. We found that motions were significantly slowed with increasing depth within the PEG/PMAA multilayer. This phenomena occured in a narrow pH range around 4.0 in which intermolecular interactions were relatively weak.

  18. Proton conductivity in quasi-one dimensional hydrogen-bonded systems: A nonlinear approach

    International Nuclear Information System (INIS)

    Tsironis, G.; Phevmatikos, S.

    1988-01-01

    Defect formation and transport in a hydrogen-bonded system is studied via a two-sublattice soliton-bearing one-dimensional model. Ionic and orientational defects are associated with distinct nonlinear topological excitations in the present model. The dynamics of these excitations is studied both analytically and with the use of numerical simulations. It is shown that the two types of defects are soliton solutions of a double Sine--Gordon equation which describes the motion of the protons in the long-wavelength limit. With each defect there is an associated deformation in the ionic lattice that, for small speeds, follows the defect dynamically albeit resisting its motion. Free propagation as well as collision properties of the proton solitons are presented. 33 refs., 10 figs

  19. Hydrogen bond indices and tertiary structure of yeast tRNA sup(Phe)

    International Nuclear Information System (INIS)

    Giambiagi, M.S. de; Giambiagi, M.; Esquivel, D.M.S.

    1982-01-01

    The rigidity and stability of the tertiary structure of yeast tRNA sup(Phe) is related to a bond index employed in an IEHT calculation. The index permits a quantitative estimate of the electronic cloud along the hydrogen bond, having thus an appealing physical meaning. The results indicate that Hoogsteen-type bonds have, as expected, greater electronic population than Watson-Crick type ones. Other non-Watson-Crick pairings, the wobble pair and G 15 -C 48 , exhibit high values of the index for the NH...O bond. In the triples, the electronic density of the hydrogen bridges does not weaken, comparing it with the one of the pairs involved. Contour density maps are shown and dipolar moments of pairs and triples are qualitatively discussed. (Author) [pt

  20. Aggregation control of quantum dots through ion-mediated hydrogen bonding shielding.

    Science.gov (United States)

    Liu, Jianbo; Yang, Xiaohai; Wang, Kemin; He, Xiaoxiao; Wang, Qing; Huang, Jin; Liu, Yan

    2012-06-26

    Nanoparticle stabilization against detrimental aggregation is a critical parameter that needs to be well controlled. Herein, we present a facile and rapid ion-mediated dispersing technique that leads to hydrophilic aggregate-free quantum dots (QDs). Because of the shielding of the hydrogen bonds between cysteamine-capped QDs, the presence of F(-) ions disassembled the aggregates of QDs and afforded their high colloidal stability. The F(-) ions also greatly eliminated the nonspecific adsorption of the QDs on glass slides and cells. Unlike the conventional colloidal stabilized method that requires the use of any organic ligand and/or polymer for the passivation of the nanoparticle surface, the proposed approach adopts the small size and large diffusion coefficient of inorganic ions as dispersant, which offers the disaggregation a fast reaction dynamics and negligible influence on their intrinsic surface functional properties. Therefore, the ion-mediated dispersing strategy showed great potential in chemosensing and biomedical applications.

  1. Short Carboxylic Acid–Carboxylate Hydrogen Bonds Can Have Fully Localized Protons

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Jiusheng; Pozharski, Edwin; Wilson, Mark A.

    2017-01-17

    Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15–0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor–acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [O–O> = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O–O distance with increasing H-bond donor pKa. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid–carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.

  2. Crystal structure, vibrational spectra and DFT studies of hydrogen bonded 1,2,4-triazolium hydrogenselenate

    Science.gov (United States)

    Arjunan, V.; Thirunarayanan, S.; Marchewka, M. K.; Mohan, S.

    2017-10-01

    The new hydrogen bonded molecular complex 1,2,4-triazolium hydrogenselenate (THS) is prepared by the reaction of 1H-1,2,4-triazole and selenic acid. This complex is stabilised by N-H⋯O and C-H⋯O hydrogen bonding and electrostatic attractive forces between 1H and 1,2,4-triazolium cations and hydrogen selenate anions. The XRD studies revealed that intermolecular proton transfer occur from selenic acid to 1H-1,2,4-triazole molecule, results in the formation of 1,2,4-triazolium hydrogenselenate which contains 1,2,4-triazolium cations and hydrogenselenate anions. The molecular structure of THS crystal has also been optimised by using Density Functional Theory (DFT) using B3LYP/cc-pVTZ and B3LYP/6-311++G** methods in order to find the whole characteristics of the molecular complex. The theoretical structural parameters such as bond length, bond angle and dihedral angle determined by DFT methods are well agreed with the XRD parameters. The atomic charges and thermodynamic properties are also calculated and analysed. The energies of frontier molecular orbitals HOMO, LUMO, HOMO-1, LUMO+1 and LUMO-HUMO energy gap are calculated to understand the kinetic stability and chemical reactivity of the molecular complex. The natural bond orbital analysis (NBO) has been performed in order to study the intramolecular bonding interactions and delocalisation of electrons. These intra molecular charge transfer may induce biological activities such as antimicrobials, antiinflammatory, antifungal etc. The complete vibrational assignments of THS have been performed by using FT-IR and FT-Raman spectra.

  3. Hydrogen-bonding effects on film structure and photoelectrochemical properties of porphyrin and fullerene composites on nanostructured TiO 2 electrodes

    NARCIS (Netherlands)

    Kira, Aiko; Tanaka, Masanobu; Umeyama, Tomokazu; Matano, Yoshihiro; Yoshimoto, Naoki; Zhang, Yi; Ye, Shen; Lehtivuori, Heli; Tkachenko, Nikolai V.; Lemmetyinen, Helge; Imahori, Hiroshi

    2007-01-01

    Hydrogen-bonding effects on film structures and photophysical, photoelectrochemical, and photovoltaic properties have been examined in mixed films of porphyrin and fullerene composites with and without hydrogen bonding on nanostructured TiO2 electrodes. The nanostructured TiO2 electrodes modified

  4. A long symmetric N· · ·H· · ·N hydrogen bond inbis(4-aminopyridinium)(1+) azide(1−): redetermination from the original data

    Czech Academy of Sciences Publication Activity Database

    Fábry, Jan

    2017-01-01

    Roč. 73, č. 9 (2017), s. 1344-1347 ISSN 2056-9890 R&D Projects: GA ČR(CZ) GA15-12653S Institutional support: RVO:68378271 Keywords : hydrogen bonding * symmetric hydrogen bonds * primary amine group Subject RIV: CC - Organic Chemistry OBOR OECD: Organic chemistry

  5. Hydrogen-bonding versus .pi.-.pi. stacking in the design of organic semiconductors: from dyes to oligomers

    Czech Academy of Sciences Publication Activity Database

    Gospodinova, Natalia; Tomšík, Elena

    2015-01-01

    Roč. 43, April (2015), s. 33-47 ISSN 0079-6700 R&D Projects: GA ČR(CZ) GA13-00270S; GA ČR GPP108/11/P763 Institutional support: RVO:61389013 Keywords : organic semiconductors * hydrogen bonds * nematic liquid crystals Subject RIV: CD - Macromolecular Chemistry Impact factor: 27.184, year: 2015

  6. Near-infrared analysis of hydrogen-bonding in glass- and rubber-state amorphous saccharide solids.

    Science.gov (United States)

    Izutsu, Ken-ichi; Hiyama, Yukio; Yomota, Chikako; Kawanishi, Toru

    2009-01-01

    Near-infrared (NIR) spectroscopic analysis of noncrystalline polyols and saccharides (e.g., glycerol, sorbitol, maltitol, glucose, sucrose, maltose) was performed at different temperatures (30-80 degrees C) to elucidate the effect of glass transition on molecular interaction. Transmission NIR spectra (4,000-12,000 cm(-1)) of the liquids and cooled-melt amorphous solids showed broad absorption bands that indicate random configuration of molecules. Heating of the samples decreased an intermolecular hydrogen-bonding OH vibration band intensity (6,200-6,500 cm(-1)) with a concomitant increase in a free and intramolecular hydrogen-bonding OH group band (6,600-7,100 cm(-1)). Large reduction of the intermolecular hydrogen-bonding band intensity at temperatures above the glass transition (T(g)) of the individual solids should explain the higher molecular mobility and lower viscosity in the rubber state. Mixing of the polyols with a high T(g) saccharide (maltose) or an inorganic salt (sodium tetraborate) shifted both the glass transition and the inflection point of the hydrogen-bonding band intensity to higher temperatures. The implications of these results for pharmaceutical formulation design and process monitoring (PAT) are discussed.

  7. Orbital interactions and charge redistribution in weak hydrogen bonds: The Watson-Crick AT mimic adenine-2,4-difluorotoluene

    NARCIS (Netherlands)

    Fonseca Guerra, C.; Bickelhaupt, F.M.

    2003-01-01

    An overview is given of results that reestablish hydrogen bonding as an essential factor in DNA replication involving natural bases as well as less polar mimics and they also confirm the importance of steric factors, in line with Kool's experimental work. In addition they show that knowledge of the

  8. Are the hydrogen bonds of RNA (.U) stronger than those of DNA (A.T)? A quantum mechanics study

    Czech Academy of Sciences Publication Activity Database

    Pérez, A.; Šponer, Jiří; Jurečka, Petr; Hobza, Pavel; Luque, Javier F.; Orozco, Modesto

    2005-01-01

    Roč. 11, č. 17 (2005), s. 5062-5066 ISSN 0947-6539 R&D Projects: GA ČR(CZ) GA203/05/0009 Institutional research plan: CEZ:AV0Z50040507 Keywords : density functional calculations * DNA * hydrogen bonds Subject RIV: BO - Biophysics Impact factor: 4.907, year: 2005

  9. Hydrogen–Hydrogen Bonding in Planar Biphenyl, Predicted by Atoms-In-Molecules Theory, Does Not Exist

    NARCIS (Netherlands)

    Poater, J; Sola, M.; Bickelhaupt, F.M.

    2006-01-01

    Based on an Atoms-in-Molecules (AIM) analysis, Matta et al. (Chem. Eur. J.2003, 9, 1940) recently claimed evidence for the existence of hydrogen–hydrogen bonding between ortho-hydrogen atoms, pointing towards each other from adjacent phenyl groups in planar biphenyl. This AIM result is opposed to

  10. [Two-dimensional model of a double-well potential: proton transfer when a hydrogen bond is deformed].

    Science.gov (United States)

    Krasilnikov, P M

    2014-01-01

    The potential energy cross-section profile along a hydrogen bond may contain two minima in certain conditions; it is so-called a double well potential. The H-bond double well potential is essential for proton transfer along this hydrogen bond. We have considered the two-dimensional model of such double well potential in harmonic approximation, and we have also investigated the proton tunneling in it. In real environments thermal motion of atoms or conformational changes may cause reorientation and relative shift of molecule fragment forming the hydrogen bond and, as a result, the hydrogen bond isdeformed. This deformation is liable to change the double well potential form and, hence, the probability of the proton tunneling is changed too. As it is shown the characteristic time of proton tunneling is essentially increased by even small relative shift of heavy atoms forming the H-bond and also rotational displacement of covalent bond generated by one of heavy atoms and the proton (hydrogen atom). However, it is also shown, at the certain geometry of the H-bond deformation the opposite effect occurred, i.e., the characteristic time is not increased and even decreased. Notice that such its behavior arises from two-dimensionality of potential wells; this and other properties of our model are discussed in detail.

  11. Expanding the peptide beta-turn in alphagamma hybrid sequences: 12 atom hydrogen bonded helical and hairpin turns.

    Science.gov (United States)

    Chatterjee, Sunanda; Vasudev, Prema G; Raghothama, Srinivasarao; Ramakrishnan, Chandrasekharan; Shamala, Narayanaswamy; Balaram, Padmanabhan

    2009-04-29

    Hybrid peptide segments containing contiguous alpha and gamma amino acid residues can form C(12) hydrogen bonded turns which may be considered as backbone expanded analogues of C(10) (beta-turns) found in alphaalpha segments. Exploration of the regular hydrogen bonded conformations accessible for hybrid alphagamma sequences is facilitated by the use of a stereochemically constrained gamma amino acid residue gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn), in which the two torsion angles about C(gamma)-C(beta) (theta(1)) and C(beta)-C(alpha) (theta(2)) are predominantly restricted to gauche conformations. The crystal structures of the octapeptides Boc-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-OMe (1) and Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe (2) reveal two distinct conformations for the Aib-Gpn segment. Peptide 1 forms a continuous helix over the Aib(2)-Aib(6) segment, while the peptide 2 forms a beta-hairpin structure stabilized by four cross-strand hydrogen bonds with the Aib-Gpn segment forming a nonhelical C(12) turn. The robustness of the helix in peptide 1 in solution is demonstrated by NMR methods. Peptide 2 is conformationally fragile in solution with evidence of beta-hairpin conformations being obtained in methanol. Theoretical calculations permit delineation of the various C(12) hydrogen bonded structures which are energetically feasible in alphagamma and gammaalpha sequences.

  12. Understanding the influence of low-frequency vibrations on the hydrogen bonds of acetic acid and acetamide dimers.

    Science.gov (United States)

    Copeland, Christopher; Menon, Omkaran; Majumdar, D; Roszak, Szczepan; Leszczynski, Jerzy

    2017-09-20

    Low-frequency vibrations coupled to high-frequency modes are known to influence the hydrogen bond strengths in a weakly interacting dimer. In this context, various acetic acid and acetamide dimers were analyzed using Møller-Plesset second-order perturbation (MP2) and density functional theory (DFT)-based approaches with explicit anharmonicity corrections. The computed low-frequency fundamentals as well as the high-frequency modes, which were found to be related to hydrogen bonding (OH/NH stretching modes), were analyzed and their computed intensities were correlated with their hydrogen-bond strengths/binding energies. There are similarities in the nature of eight low-frequency fundamentals of these two dimers, and the in-plane bending and stretch-bend fundamentals of the different dimers of these two species (in this low-frequency region) have specific roles in their relative stability order. The computed linear correlations were further verified against the results from coupled cluster calculations including triple excitation (CCSD(T)), Gaussian-G4 (G4), Gaussian-G2-MP2 (G2MP2) and complete basis set (CBS-QB3) methods of high accuracy energy calculations. As a consequence of such linear correlations, an additive property of local fragment energies (responsible for hydrogen bonding) was found to be a valid approximation to predict the binding energies of such dimers and the idea was found to be extendable to the other homologues of these acids/amides.

  13. Solution Phase Measurement of Both Weak Sigma and C-H---X- Hydrogen Bonding Interactions in Synthetic Anion Receptors

    Energy Technology Data Exchange (ETDEWEB)

    Berryman, Mr. Orion B. [University of Oregon; Sather, Mr. Aaron C [University of Oregon; Hay, Benjamin [ORNL; Meisner, Mr. Jeffrey S. [University of Oregon; Johnson, Prof. Darren W. [University of Oregon

    2008-01-01

    A series of tripodal receptors preorganize electron-deficient aromatic rings to bind halides in organic solvents using weak sigma anion-to-arene interactions or C-H---X- hydrogen bonds. 1H NMR spectroscopy proves to be a powerful technique for quantifying binding in solution, and determining the interaction motifs, even in cases of weak binding.

  14. INCREASING THE THERMOSTABILITY OF THE NEUTRAL PROTEINASE OF BACILLUS-STEAROTHERMOPHILUS BY IMPROVEMENT OF INTERNAL HYDROGEN-BONDING

    NARCIS (Netherlands)

    EIJSINK, VGH; VRIEND, G; VANDERZEE, [No Value; VANDENBURG, B; VENEMA, G

    1992-01-01

    In an attempt to increase the thermostability of the neutral proteinase of Bacillus stearothermophilus the buried Ala-170 was replaced by serine. Molecular-dynamics simulations showed that Ser-170 stabilizes the enzyme by formation of an internal hydrogen bond. In addition, the hydroxy group of

  15. Nonlinear effects at volume charge polarization and calculation of the structure radiation changes in the crystals with hydrogen bonds

    International Nuclear Information System (INIS)

    Tonkonogov, M.P.; Medvedev, V.Ya.

    2003-01-01

    The formulas for volume charge distribution, complex permittivity, static dielectric constant for the crystals with hydrogen bonds are proposed. With help of the formulas the structure defect concentration, relaxation energy of relaxators were calculated for important electronic and optoelectronic materials as mica, KDP and DKDP crystals, gypsum, talk

  16. Two independent hydrogen bonded complexes of bis(1-piperidiniumacetate) hydrochloride in crystal and in the PM3 optimized structure

    International Nuclear Information System (INIS)

    Dega-Szafran, Z.; Petryna, M.; Dutkiewicz, G.; Kosturkiewicz, Z.

    2003-01-01

    Bis(1-piperidiniumacetate) hydrochloride, (PAA) 2 H · Cl + , has been synthesized and its structure solved by X-ray diffraction. The crystals belong to the triclinic system with two symmetrically independent hydrogen bonded complexes, denoted A and B, at two different inversion centers. The compound crystallizes in the space group P1 with a = 8.559(1), b = 9.625(1), c = 11.441(1) A, α = 74.85(1) o , β = 68.22(1) o , γ 84.10(1) o , Z = 2, R = 0.036. Each complex consists of two 1-piperidiniumacetate moieties. Four 1-piperidiniumacetates, as zwitterions, are held together by a network of hydrogen bonds of the types O...H...O (2.462(3) and 2.463(3) A), N-H...O (2.755(2) A) and N-H...Cl (3.167(2) A). Both N-H atoms in a complex A interact with chlorine anions. A number of weak C-H...Cl contacts stabilize the three-dimensional crystal structure. In the isolated molecule of (PAA) 2 H · Cl + optimized by the PM3 method, there also are two independent hydrogen bonded complexes. In complex A the natural form of 1-piperidineacetic acid interacts with its anionic form, while in complex B the 1-piperidiniumacetic acid, as a cation, forms a hydrogen bond with its zwitterionic form. FTIR spectrum of bis(1-piperidiniumacetate) hydrochloride has been analysed and discussed. (author)

  17. Modeling the Solid-Liquid Equilibrium in Pharmaceutical-Solvent Mixtures: Systems with Complex Hydrogen Bonding Behvaior

    DEFF Research Database (Denmark)

    Tsivintzelis, Ioannis; Economou, Ioannis; Kontogeorgis, Georgios

    2009-01-01

    simpler molecules of similar chemical structure and/or are fitted to Hansen's partial solubility parameters. The methodology is applied to modeling the solubility of three pharmaceuticals, namely acetanilide, phenacetin, and paracetamol, using the nonrandom hydrogen bonding (NRHB) EoS. In all cases...

  18. Anion-assisted trans-cis isomerization of palladium(II) phosphine complexes containing acetanilide functionalities through hydrogen bonding interactions.

    Science.gov (United States)

    Lu, Xiao-Xia; Tang, Hau-San; Ko, Chi-Chiu; Wong, Jenny Ka-Yan; Zhu, Nianyong; Yam, Vivian Wing-Wah

    2005-03-28

    The anion-assisted shift of trans-cis isomerization equilibrium of a palladium(II) complex containing acetanilide functionalities brought about by allosteric hydrogen bonding interactions has been established by UV/Vis, 1H NMR, 31P NMR and ESI-MS studies.

  19. Hydrogen bonding strength of diblock copolymers affects the self-assembled structures with octa-functionalized phenol POSS nanoparticles.

    Science.gov (United States)

    Lu, Yi-Syuan; Yu, Chia-Yu; Lin, Yung-Chih; Kuo, Shiao-Wei

    2016-02-28

    In this study, the influence of the functional groups by the diblock copolymers of poly(styrene-b-4-vinylpyridine) (PS-b-P4VP), poly(styrene-b-2-vinylpyridine) (PS-b-P2VP), and poly(styrene-b-methyl methacrylate) (PS-b-PMMA) on their blends with octa-functionalized phenol polyhedral oligomeric silsesquioxane (OP-POSS) nanoparticles (NPs) was investigated. The relative hydrogen bonding strengths in these blends follow the order PS-b-P4VP/OP-POSS > PS-b-P2VP/OP-POSS > PS-b-PMMA/OP-POSS based on the Kwei equation from differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopic analyses. Small-angle X-ray scattering and transmission electron microscopic analyses show that the morphologies of the self-assembly structures are strongly dependent on the hydrogen bonding strength at relatively higher OP-POSS content. The PS-b-P4VP/OP-POSS hybrid complex system with the strongest hydrogen bonds shows the order-order transition from lamellae to cylinders and finally to body-centered cubic spheres upon increasing OP-POSS content. However, PS-b-P2VP/OP-POSS and PS-b-PMMA/OP-POSS hybrid complex systems, having relatively weaker hydrogen bonds, transformed from lamellae to cylinder structures at lower OP-POSS content (50 wt%).

  20. Dynamics of circular hydrogen bond array in calix[4]arene in a nonpolar solvent: A nuclear magnetic resonance study

    Czech Academy of Sciences Publication Activity Database

    Lang, J.; Deckerová, V.; Czernek, Jiří; Lhoták, P.

    2005-01-01

    Roč. 122, - (2005), 044506/1-044506/11 ISSN 0021-9606 R&D Projects: GA AV ČR KJB4050311 Institutional research plan: CEZ:AV0Z40500505 Keywords : hydrogen bonds * organic compounds * spin-spin relaxation Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.138, year: 2005

  1. Microscopic observation of zenithal bistable switching in nematic devices with different surface relief structures

    International Nuclear Information System (INIS)

    Uche, C; Elston, S J; Parry-Jones, L A

    2005-01-01

    Nematic liquid crystals have been shown to exhibit zenithal electro-optic bistability in devices containing sinusoidal and deformed sinusoidal gratings. Recently it has been shown that zenithal bistable states can also be supported at isolated edges of square gratings. In this paper, we present microscopic observations of bistability in cells containing sinusoidal gratings and long-pitch square gratings. We have also investigated a novel display based on square wells. High frame-rate video microscopy was used to obtain time-sequenced images when the devices were switched with monopolar pulses. These show that zenithal bistable switching can occur by two different processes: (i) domain growth (observed in cells containing sinusoidal gratings) and (ii) homogenous switching (observed in cells containing isolated edges

  2. Quantitative separation of the influence of hydrogen bonding of ethanol/water mixture on the shape recovery behavior of polyurethane shape memory polymer

    International Nuclear Information System (INIS)

    Lu, Haibao; Leng, Jinsong; Min Huang, Wei; Fu, Y Q

    2014-01-01

    A thermally responsive polyurethane shape memory polymer (SMP) can be actuated in water through a hydrogen bonding interaction between water and the SMP. In this work, we present a comprehensive approach to quantify the hydrogen bonding on the shape recovery behavior of a polyurethane SMP. The stimuli response to the hydrogen bonding of the polyurethane SMP was investigated in ethanol/water mixtures by varying the water content. It was found that depending on the water content, the SMP features a critical hydrogen bonding strength associated with its shape recovery behavior. The Hildebrand solubility parameter theory was employed to quantitatively identify and separate the hydrogen bonding effect of the ethanol/water mixture on the shape recovery ratio and the time. Furthermore, a phenomenological model was developed to predict the glass transition temperature and the shape recovery time of a polyurethane SMP and was verified by the available experimental results. (paper)

  3. The Born-Oppenheimer molecular simulations of infrared spectra of crystalline poly-(R)-3-hydroxybutyrate with analysis of weak Csbnd H⋯Odbnd C hydrogen bonds

    Science.gov (United States)

    Brela, Mateusz Z.; Boczar, Marek; Wójcik, Marek J.; Sato, Harumi; Nakajima, Takahito; Ozaki, Yukihiro

    2017-06-01

    In this letter we present results of study of weak Csbnd H⋯Odbnd C hydrogen bonds of crystalline poly-(R)-3-hydroxybutyrate (PHB) by using Born-Oppenheimer molecular dynamics. The polymeric structure and IR spectra of PHB result from the presence of the weak hydrogen bonds. We applied the post-molecular dynamics analysis to consider a Cdbnd O motion as indirectly involved in the hydrogen bonds. Quantization of the nuclear motion of the oxygens was done to perform detailed analysis of the strength and properties of the Cdbnd O bands involved in the weak hydrogen bonds. We have also shown the dynamic character of the weak hydrogen bond interactions.

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  5. Role of hydrogen-bonding and photoinduced electron transfer (PET) on the interaction of resorcinol based acridinedione dyes with Bovine Serum Albumin (BSA) in water

    International Nuclear Information System (INIS)

    Kumaran, Rajendran; Vanjinathan, Mahalingam; Ramamurthy, Perumal

    2015-01-01

    Resorcinol based acridinedione (ADDR) dyes are a class of laser dyes and have structural similarity with purine derivatives, nicotinamide adenine dinucleotide (NADH) analogs. These dyes are classified into photoinduced electron transfer (PET) and non-photoinduced electron transfer dyes, and the photophysical properties of family of these dyes exhibiting PET behavior are entirely different from that of non-PET dyes. The PET process in ADDR dyes is governed by the solvent polarity such that an ADDR dye exhibits PET process through space in an aprotic solvent like acetonitrile and does not exhibit the same in protic solvents like water and methanol. A comparison on the fluorescence emission, lifetime and nature of interaction of various ADDR dyes with a large globular protein like Bovine Serum Albumin (BSA) was carried out in aqueous solution. The interaction of PET based ADDR dyes with BSA in water is found to be largely hydrophobic, but hydrogen-bonding interaction of BSA with dye molecule influences the fluorescence emission of the dye and shifts the emission towards red region. Fluorescence spectral studies reveal that the excited state properties of PET based ADDR dyes are largely influenced by the addition of BSA. The microenvironment around the dye results in significant change in the fluorescence lifetime and emission. Fluorescence enhancement with a red shift in the emission results after the addition of BSA to ADDR dyes containing free amino hydrogen in the 10th position of basic acridinedione dye. The amino hydrogen (N–H) in the 10th position of ADDR dye is replaced by methyl group (N–CH 3 ), a significant decrease in the fluorescence intensity with no apparent shift in the emission maximum was observed after the addition of BSA. The nature of interaction between ADDR dyes with BSA is hydrogen-bonding and the dye remains unbound even at the highest concentration of BSA. Circular Dichroism (CD) studies show that the addition of dye to BSA results in a

  6. Probing hydrogen bonds in the antibody-bound HIV-1 gp120 V3 loop by solid state NMR REDOR measurements

    Energy Technology Data Exchange (ETDEWEB)

    Balbach, John J. [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Yang Jun; Weliky, David P. [Michigan State University, Department of Chemistry (United States); Steinbach, Peter J. [National Institutes of Health, Center for Molecular Modeling, Center for Information Technology (United States); Tugarinov, Vitali; Anglister, Jacob [Weizmann Institute of Science, Department of Structural Biology (Israel); Tycko, Robert [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2000-04-15

    We describe solid state NMR measurements on frozen solutions of the complex of the 24-residue HIV-1 gp120 V3 loop peptide RP135 with the Fab fragment of the anti-gp120 antibody 0.5{beta}, using rotational echo double resonance (REDOR). In order to probe possible hydrogen bonding between arginine side chains and glycine backbone carbonyls in the region of the conserved Gly-Pro-Gly-Arg (GPGR) motif of the V3 loop, RP135 samples were prepared with {sup 15}N labels at the {eta} nitrogen positions of arginine side chains and {sup 13}C labels at glycine carbonyl positions and {sup 13}C-detected {sup 13}C-{sup 15}N REDOR measurements were performed on peptide/antibody complexes of these labeled samples. Such hydrogen bonding was previously observed in a crystal structure of the V3 loop peptide/antibody complex RP142/59.1 [Ghiara et al. (1994) Science, 264, 82-85], but is shown by the REDOR measurements to be absent in the RP135/0.5{beta} complex. These results confirm the antibody-dependent conformational differences in the GPGR motif suggested by previously reported solid state NMR measurements of {phi} and {psi} backbone dihedral angles in the RP135/0.5{beta} complex. In addition, we describe REDOR measurements on the helical synthetic peptide MB(i+4)EK in frozen solution that establish our ability to detect {sup 13}C-{sup 15}N dipole-dipole couplings in the distance range appropriate to these hydrogen bonding studies. We also report the results of molecular modeling calculations on the central portion RP135, using a combination of the solid state NMR restraints of Weliky et al. [Nat. Struct. Biol., 6, 141-145, 1999] and the liquid state NMR restraints of Tugarinov et al. (Nat. Struct. Biol., 6, 331-335, 1999]. The dynamics calculations demonstrate the mutual compatibility of the two sets of experimental structural restraints and reduce ambiguities in the solid state NMR restraints that result from symmetry and signal-to-noise considerations.

  7. Probing hydrogen bonds in the antibody-bound HIV-1 gp120 V3 loop by solid state NMR REDOR measurements

    International Nuclear Information System (INIS)

    Balbach, John J.; Yang Jun; Weliky, David P.; Steinbach, Peter J.; Tugarinov, Vitali; Anglister, Jacob; Tycko, Robert

    2000-01-01

    We describe solid state NMR measurements on frozen solutions of the complex of the 24-residue HIV-1 gp120 V3 loop peptide RP135 with the Fab fragment of the anti-gp120 antibody 0.5β, using rotational echo double resonance (REDOR). In order to probe possible hydrogen bonding between arginine side chains and glycine backbone carbonyls in the region of the conserved Gly-Pro-Gly-Arg (GPGR) motif of the V3 loop, RP135 samples were prepared with 15 N labels at the η nitrogen positions of arginine side chains and 13 C labels at glycine carbonyl positions and 13 C-detected 13 C- 15 N REDOR measurements were performed on peptide/antibody complexes of these labeled samples. Such hydrogen bonding was previously observed in a crystal structure of the V3 loop peptide/antibody complex RP142/59.1 [Ghiara et al. (1994) Science, 264, 82-85], but is shown by the REDOR measurements to be absent in the RP135/0.5β complex. These results confirm the antibody-dependent conformational differences in the GPGR motif suggested by previously reported solid state NMR measurements of φ and Ψ backbone dihedral angles in the RP135/0.5β complex. In addition, we describe REDOR measurements on the helical synthetic peptide MB(i+4)EK in frozen solution that establish our ability to detect 13 C- 15 N dipole-dipole couplings in the distance range appropriate to these hydrogen bonding studies. We also report the results of molecular modeling calculations on the central portion RP135, using a combination of the solid state NMR restraints of Weliky et al. [Nat. Struct. Biol., 6, 141-145, 1999] and the liquid state NMR restraints of Tugarinov et al. (Nat. Struct. Biol., 6, 331-335, 1999]. The dynamics calculations demonstrate the mutual compatibility of the two sets of experimental structural restraints and reduce ambiguities in the solid state NMR restraints that result from symmetry and signal-to-noise considerations

  8. Nitrile Probes of Electric Field Agree with Independently Measured Fields in Green Fluorescent Protein Even in the Presence of Hydrogen Bonding.

    Science.gov (United States)

    Slocum, Joshua D; Webb, Lauren J

    2016-05-25

    There is growing interest in using the nitrile vibrational oscillation as a site-specific probe of local environment to study dynamics, folding, and electrostatics in biological molecules such as proteins. Nitrile probes have been used extensively as reporters of electric field using vibrational Stark effect spectroscopy. However, the analysis of frequencies in terms of electric fields is potentially complicated by the large ground state dipole moment of the nitrile, which may irrevocably perturb the protein under investigation, and the ability of nitriles to accept hydrogen bonds, which causes frequency shifts that are not described by the Stark effect. The consequence of this is that vibrational spectroscopy of nitriles in biomolecules could be predominately sensitive to their local hydration status, not electrostatic environment, and have the potential to be particularly destabilizing to the protein. Here, we introduce green fluorescent protein (GFP) as a model system for addressing these concerns using biosynthetically incorporated p-cyanophenylalanine (pCNF) residues in the interior of GFP and measuring absorption energies of both the intrinsic GFP fluorophore and pCNF residues in response to a series of amino acid mutations. We show that observed changes in emission energy of GFP due to the mutations strongly correlate with changes in electric field experienced by both the nitrile probes and the intrinsic fluorophore. Additionally, we show that changes in electric field measured from the intrinsic fluorophore due to amino acid mutations are unperturbed by the addition of pCNF residues inserted nearby. Finally, we show that changes in electric field experienced by the vibrational probes trend monotonically with changes in field experienced by the native fluorophore even though the nitrile probe is engaged in moderate hydrogen bonding to nearby water molecules, indicated by the temperature dependence of the nitrile's absorption energy. Together these results

  9. Hydrogen bonding interactions in PN...HX complexes: DFT and ab initio studies of structure, properties and topology.

    Science.gov (United States)

    Varadwaj, Pradeep Risikrishna

    2010-05-01

    Spin-restricted DFT (X3LYP and B3LYP) and ab initio (MP2(fc) and CCSD(fc)) calculations in conjunction with the Aug-CC-pVDZ and Aug-CC-pVTZ basis sets were performed on a series of hydrogen bonded complexes PN...HX (X = F, Cl, Br) to examine the variations of their equilibrium gas phase structures, energetic stabilities, electronic properties, and vibrational characteristics in their electronic ground states. In all cases the complexes were predicted to be stable with respect to the constituent monomers. The interaction energy (Delta E) calculated using a super-molecular model is found to be in this order: PN...HF > PN...HCl > PN...HBr in the series examined. Analysis of various physically meaningful contributions arising from the Kitaura-Morokuma (KM) and reduced variational space self-consistent-field (RVS-SCF) energy decomposition procedures shows that the electrostatic energy has significant contribution to the over-all interaction energy. Dipole moment enhancement (Delta mu) was observed in these complexes expected of predominant dipole-dipole electrostatic interaction and was found to follow the trend PN...HF > PN...HCl > PN...HBr at the CCSD level. However, the DFT (X3LYP and B3LYP) and MP2 levels less accurately determined these values (in this order HF 0, nabla(2)rho(c) > 0 and H(c) > 0 at the BCP) whilst the bonds in PN (rho(c) > 0, nabla(2)rho(c) > 0 and H(c) 0, nabla(2)rho(c) BD*(HX) delocalization.

  10. Disruption of a hydrogen bond network in human versus spider monkey cytochrome c affects heme crevice stability.

    Science.gov (United States)

    Goldes, Matthew E; Jeakins-Cooley, Margaret E; McClelland, Levi J; Mou, Tung-Chung; Bowler, Bruce E

    2016-05-01

    The hypothesis that the recent rapid evolution of primate cytochromes c, which primarily involves residues in the least stable Ω-loop (Ω-loop C, residues 40-57), stabilizes the heme crevice of cytochrome c relative to other mammals, is tested. To accomplish this goal, we have compared the properties of human and spider monkey cytochrome c and a set of four variants produced in the process of converting human cytochrome c into spider monkey cytochrome c. The global stability of all variants has been measured by guanidine hydrochloride denaturation. The stability of the heme crevice has been assessed with the alkaline conformational transition. Structural insight into the effects of the five amino acid substitutions needed to convert human cytochrome c into spider monkey cytochrome c is provided by a 1.15Å resolution structure of spider monkey cytochrome c. The global stability for all variants is near 9.0kcal/mol at 25°C and pH7, which is higher than that observed for other mammalian cytochromes c. The heme crevice stability is more sensitive to the substitutions required to produce spider monkey cytochrome c with decreases of up to 0.5 units in the apparent pKa of the alkaline conformational transition relative to human cytochrome c. The structure of spider monkey cytochrome c indicates that the Y46F substitution destabilizes the heme crevice by disrupting an extensive hydrogen bond network that connects three surface loops including Ω-loop D (residues 70-85), which contains the Met80 heme ligand. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase

    International Nuclear Information System (INIS)

    Lyubimov, Artem Y.; Chen, Lin; Sampson, Nicole S.; Vrielink, Alice

    2009-01-01

    The importance of active-site electrostatics for oxidative and reductive half-reactions in a redox flavoenzyme (cholesterol oxidase) have been investigated by a combination of biochemistry and atomic resolution crystallography. A detailed examination of active-site dynamics demonstrates that the oxidation of substrate and the re-oxidation of the flavin cofactor by molecular oxygen are linked by a single active-site asparagine. Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3β-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH⋯π interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall k cat . Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0 Å resolution) reveals significant perturbations in the active site. As predicted, Asp485 is oriented away from the flavin moiety, such that any stabilizing interaction with the reduced flavin is abolished. Met122 and Glu361 form unusual hydrogen bonds to the functional group of Asp485 and are displaced from the positions they occupy in the wild-type active site. The overall effect is to disrupt the stabilization of the reduced FAD cofactor during catalysis. Furthermore, a narrow transient channel that is shown to form when the wild-type Asn485 forms the NH⋯π interaction with FAD and that has been proposed to function as an access route of molecular oxygen, is not observed in either of the mutant structures, suggesting that the dynamics of the active site are altered

  12. Guanine is indispensable for immunoglobulin switch region RNA-DNA hybrid formation

    International Nuclear Information System (INIS)

    Mizuta, Ryushin; Mizuta, Midori; Kitamura, Daisuke

    2005-01-01

    It is suggested that the formation of the switch (S) region RNA-DNA hybrid and the subsequent generation of higher-order chromatin structures including R-loop initiate a class switch recombination of the immunoglobulin gene. The primary factor of this recombination is the S-region derived noncoding RNA. However, the biochemical character of this guanine-rich (G-rich) transcript is poorly understood. The present study was performed to analyze the structure of this G-rich RNA using atomic force microscope (AFM). The in vitro transcribed S-region RNA was spread on a mica plate, air-dried and observed by non-contact mode AFM in air. The G-rich transcripts tend to aggregate on the template DNA and to generate a higher-order RNA-DNA complex. However, the transcripts that incorporated guanine analogues as substitutes for guanine neither aggregated nor generated higher-order structures. Incorporation of guanine analogues in transcribes RNA partially disrupts hydrogen bonds related to guanine, such as Watson-Crick GC-base pair and Hoogsteen bond GG-base pair. Thus, aggregation of S-region RNA and generation of the higher-order RNA-DNA complex are attributed to hydrogen bonds of guanine. (author)

  13. Conformational Effects through Hydrogen Bonding in a Constrained γ-Peptide Template: From Intraresidue Seven-Membered Rings to a Gel-Forming Sheet Structure.

    Science.gov (United States)

    Awada, Hawraà; Grison, Claire M; Charnay-Pouget, Florence; Baltaze, Jean-Pierre; Brisset, François; Guillot, Régis; Robin, Sylvie; Hachem, Ali; Jaber, Nada; Naoufal, Daoud; Yazbeck, Ogaritte; Aitken, David J

    2017-05-05

    A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.

  14. Sensitivity of hydrogen bonds of DNA and RNA to hydration, as gauged by 1JNH measurements in ethanol-water mixtures

    International Nuclear Information System (INIS)

    Manalo, Marlon N.; Kong Xiangming; LiWang, Andy

    2007-01-01

    Hydrogen-bond lengths of nucleic acids are (1) longer in DNA than in RNA, and (2) sequence dependent. The physicochemical basis for these variations in hydrogen-bond lengths is unknown, however. Here, the notion that hydration plays a significant role in nucleic acid hydrogen-bond lengths is tested. Watson-Crick N1...N3 hydrogen-bond lengths of several DNA and RNA duplexes are gauged using imino 1 J NH measurements, and ethanol is used as a cosolvent to lower water activity. We find that 1 J NH values of DNA and RNA become less negative with added ethanol, which suggests that mild dehydration reduces hydrogen-bond lengths even as the overall thermal stabilities of these duplexes decrease. The 1 J NH of DNA are increased in 8 mol% ethanol to those of RNA in water, which suggests that the greater hydration of DNA plays a significant role in its longer hydrogen bonds. The data also suggest that ethanol-induced dehydration is greater for the more hydrated G:C base pairs and thereby results in greater hydrogen-bond shortening than for the less hydrated A:T/U base pairs of DNA and RNA

  15. A Relativity Enhanced, Medium-Strong Au(I)···H-N Hydrogen Bond in a Protonated Phenylpyridine-Gold(I) Thiolate.

    Science.gov (United States)

    Berger, Raphael J F; Schoiber, Jürgen; Monkowius, Uwe

    2017-01-17

    Gold is an electron-rich metal with a high electronegativity comparable to that of sulfur. Hence, hydrogen bonds of the Au(I)···H-E (E = electronegative element) type should be possible, but their existence is still under debate. Experimental results are scarce and often contradictory. As guidance for possible preparative work, we have theoretically investigated (ppyH)Au(SPh) (ppy = 2-phenylpyridine) bearing two monoanionic ligands which are not strongly electronegative at the same time to further increase the charge density on the gold(I) atom. The protonated pyridine nitrogen atom in ppy is geometrically ideally suited to place a proton in close proximity to the gold atom in a favorable geometry for a classical hydrogen bond arrangement. Indeed, the results of the calculations indicate that the hydrogen bonded conformation of (ppyH)Au(SPh) represents a minimum geometry with bond metrics in the expected range for medium-strong hydrogen bonds [r(N-H) = 1.043 Å, r(H···Au) = 2.060 Å, a(N-H···Au) = 141.4°]. The energy difference between the conformer containing the H···Au bond and another conformer without a hydrogen bond amounts to 7.8 kcal mol -1 , which might serve as an estimate of the hydrogen bond strength. Spectroscopic properties were calculated, yielding further characteristics of such hydrogen bonded gold species.

  16. Can hydrogen bonds improve the hole-mobility in amorphous organic semiconductors? Experimental and theoretical insights

    KAUST Repository

    Mimaite, Viktorija; Grazulevicius, Juozas Vidas; Laurinaviciute, Rasa; Volyniuk, Dmytro; Jankauskas, Vygintas; Sini, Gjergji

    2015-01-01

    © The Royal Society of Chemistry 2015. Five hole-transporting triphenylamine derivatives containing methoxy and methyl groups are synthesized and investigated. The hole-mobility increases in the presence of methyl and methoxy substituents, exceeding 10-2 cm2 V-1 s-1 in the case of methyl groups. Quantum mechanical calculations on these compounds indicate very different dipole moments and intermolecular interaction strengths, with intriguing correlations with the trend in hole-mobility. Temperature dependent hole-mobility measurements indicate disorder dominated hole transport. The values of the energetic disorder parameter (σ) decrease upon methyl and methoxy substitutions despite the increase in dipole moments. This trend is discussed as a function of the interaction energy between adjacent molecules, the dipole moment, the molecular polarizability, and the conformational degree of freedom. Our results indicate that the global decrease of σ upon methyl and methoxy substitutions is dominated by the larger decrease in the geometrical randomness component of the energetic disorder. A direct correlation is established between the decrease in geometrical randomness and the increase in intermolecular interaction energies, mainly stemming from the additional C-H⋯π, O, N hydrogen bonds induced by methyl and methoxy groups.

  17. Local vibrational modes of the formic acid dimer - the strength of the double hydrogen bond

    Science.gov (United States)

    Kalescky, R.; Kraka, E.; Cremer, D.

    2013-07-01

    The 24 normal and 24 local vibrational modes of the formic acid dimer formed by two trans formic acid monomers to a ring (TT1) are analysed utilising preferentially experimental frequencies, but also CCSD(T)/CBS and ωB97X-D harmonic vibrational frequencies. The local hydrogen bond (HB) stretching frequencies are at 676 cm-1 and by this 482 and 412 cm-1 higher compared to the measured symmetric and asymmetric HB stretching frequencies at 264 and 194 cm-1. The adiabatic connection scheme between local and normal vibrational modes reveals that the lowering is due to the topology of dimer TT1, mass coupling, and avoided crossings involving the HṡṡṡOC bending modes. The HB local mode stretching force constant is related to the strength of the HB whereas the normal mode stretching force constant and frequency lead to an erroneous underestimation of the HB strength. The HB in TT1 is stabilised by electron delocalisation in the O=C-O units fostered by forming a ring via double HBs. This implies that the CO apart from the OH local stretching frequencies reflect the strength of the HB via their red or blue shifts relative to their corresponding values in trans formic acid.

  18. A Direct Proof of the Resonance-Impaired Hydrogen Bond (RIHB) Concept.

    Science.gov (United States)

    Lin, Xuhui; Wu, Wei; Mo, Yirong

    2018-01-24

    The concept of resonance-enhanced hydrogen bond (RAHB) has been widely accepted and applied as it highlights the positive impact of π-conjugation on intramolecular H-bonds. However, electron delocalization is directional and there is a possibility that π-resonance goes from the H-bond acceptor to the H-bond donor, leading to a negative impact on H-bonds. Here we used the block-localized wavefunction (BLW) method which is a variant of ab initio valence bond (VB) theory and able to derive strictly electron-localized structures self-consistently, to quantify the interplay between H-bond and π-resonance in the terms of geometry, energetics and spectral properties. The comparison of geometrical optimizations with and without π-resonance shows that conjugation can indeed either enhance or weaken intramolecular H-bonds. We further experimented with various substituents attached to either the H-bond acceptor and/or H-bond donor side(s) to tune the H-bonding strength in both directions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Proton dynamics in the hydrogen bonds of 4-amino-3,5-dihalogenobenzoic acid

    Energy Technology Data Exchange (ETDEWEB)

    Asaji, Tetsuo, E-mail: asaji@chs.nihon-u.ac.jp [Department of Chemistry, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550 (Japan); Ueda, Kouhei; Oguni, Masaharu [Department of Chemistry, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551 (Japan)

    2015-08-18

    Highlights: • 4-Amino-3,5-dichlorobenzoic acid has a symmetric dimer structure. • The compound undergoes a phase transition at 138 K. • The symmetry breaking of the dimer was revealed by {sup 35}Cl NQR. • The proton dynamics was analyzed by coherent and incoherent tunneling models. - Abstract: On the polycrystalline sample of 4-amino-3,5-dihalogenobenzoic acid, 4-NH{sub 2}-3,5-X{sub 2}C{sub 6}H{sub 2}COOH, which has a symmetric dimer structure in the crystal, the proton tunneling in the hydrogen bonds has been investigated by NQR and NMR spin–lattice relaxation times T{sub 1} measurements. Two {sup 35}Cl NQR lines of the X = Cl derivative show the existence of two crystallographically inequivalent chlorine atoms in the high-temperature phase, in consistency with the reported crystal structure. Below 138 K, each splits into a doublet indicating the symmetry breaking of the benzoic acid dimer. The proton dynamics was analyzed by a coherent and incoherent tunneling models, for the high- and low-temperature phases, respectively. The temperature dependence of the correlation time of proton translation was estimated. As for the X = I derivative, the proton dynamics was discussed similarly by {sup 1}H NMR T{sub 1} data by assuming occurrence of a phase transition at low-temperature.

  20. Weak hydrogen bond topology in 1,1-difluoroethane dimer: A rotational study

    Science.gov (United States)

    Chen, Junhua; Zheng, Yang; Wang, Juan; Feng, Gang; Xia, Zhining; Gou, Qian

    2017-09-01

    The rotational spectrum of the 1,1-difluoroethane dimer has been investigated by pulsed-jet Fourier transform microwave spectroscopy. Two most stable isomers have been detected, which are both stabilized by a network of three C—H⋯F—C weak hydrogen bonds: in the most stable isomer, two difluoromethyl C—H groups and one methyl C—H group act as the weak proton donors whilst in the second isomer, two methyl C—H groups and one difluoromethyl C—H group act as the weak proton donors. For the global minimum, the measurements have also been extended to its four 13C isotopologues in natural abundance, allowing a precise, although partial, structural determination. Relative intensity measurements on a set of μa-type transitions allowed estimating the relative population ratio of the two isomers as NI/NII ˜ 6/1 in the pulsed jet, indicating a much larger energy gap between these two isomers than that expected from ab initio calculation, consistent with the result from pseudo-diatomic dissociation energies estimation.

  1. Conserved hydrogen bonds and water molecules in MDR HIV-1 protease substrate complexes

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhigang [Wayne State Univ., Detroit, MI (United States); Case Western Reserve Univ., Cleveland, OH (United States); Harbor Hospital Baltimore, MD (United States); Wang, Yong [Wayne State Univ., Detroit, MI (United States); Yedidi, Ravikiran S. [Wayne State Univ., Detroit, MI (United States); National Institutes of Health, Bethesda, MD (United States); Dewdney, Tamaria G. [Wayne State Univ., Detroit, MI (United States); Reiter, Samuel J. [Wayne State Univ., Detroit, MI (United States); Brunzelle, Joseph S. [Northwestern Univ. Feinberg School of Medicine, Chicago, IL (United States); Kovari, Iulia A. [Wayne State Univ., Detroit, MI (United States); Kovari, Ladislau C. [Wayne State Univ., Detroit, MI (United States)

    2012-12-19

    Success of highly active antiretroviral therapy (HAART) in anti-HIV therapy is severely compromised by the rapidly developing drug resistance. HIV-1 protease inhibitors, part of HAART, are losing their potency and efficacy in inhibiting the target. Multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, 90) was selected for the present study to understand the binding to its natural substrates. The nine crystal structures of MDR769 HIV-1 protease substrate hepta-peptide complexes were analyzed in order to reveal the conserved structural elements for the purpose of drug design against MDR HIV-1 protease. Our structural studies demonstrated that highly conserved hydrogen bonds between the protease and substrate peptides, together with the conserved crystallographic water molecules, played a crucial role in the substrate recognition, substrate stabilization and protease stabilization. Additionally, the absence of the key flap-ligand bridging water molecule might imply a different catalytic mechanism of MDR769 HIV-1 protease compared to that of wild type (WT) HIV-1 protease.

  2. Interpretation of IR and Raman spectra of dopamine neurotransmitter and effect of hydrogen bond in HCl

    Science.gov (United States)

    Yadav, T.; Mukherjee, V.

    2018-05-01

    The potential energy scanning with respect to the different dihedral angles were performed to search possible numbers of dopamine (neutral) conformers and further, fifteen conformers of dopamine were identified on the basis of energy minima. Vibrational frequencies were calculated for all the conformers of dopamine. Density functional theory was employed to carry out all the computations. The exchange correlation functional B3LYP and the basis set 6-31++G(d,p) were included in DFT calculation. The FTIR and FT-Raman spectra of dopamine hydrochloride were also recorded in the spectral region 400-4000 cm-1 and 50-4000 cm-1 respectively. The normal coordinate analysis was also performed to scale DFT calculated force constants and to calculate potential energy distributions. The detailed vibrational spectral analysis and the assignments of the bands, done on the best-fit basis comparison of the experimentally obtained and theoretically calculated IR and Raman spectra, match quite well indicating DFT calculations as very accurate source of normal mode assignments. The interaction of the most stable conformer of dopamine with HCl was also studied to know the effect of hydrogen bond on its geometry and dynamics. The stability of the dopamine in isolated and protonated forms arising from hyperconjugative interactions was also analyzed by natural bond orbital analysis.

  3. Comparison of hydrogen bonding in 1-octanol and 2-octanol as probed by spectroscopic techniques.

    Science.gov (United States)

    Palombo, Francesca; Sassi, Paola; Paolantoni, Marco; Morresi, Assunta; Cataliotti, Rosario Sergio

    2006-09-14

    Liquid 1-octanol and 2-octanol have been investigated by infrared (IR), Raman, and Brillouin experiments in the 10-90 degrees C temperature range. Self-association properties of the neat liquids are described in terms of a three-state model in which OH oscillators differently implicated in the formation of H-bonds are considered. The results are in quantitative agreement with recent computational studies for 1-octanol. The H-bond probability is obtained by Raman data, and a stochastic model of H-bonded chains gives a consistent picture of the self-association characteristics. Average values of hydrogen bond enthalpy and entropy are evaluated. The H-bond formation enthalpy is ca. -22 kJ/mol and is slightly dependent on the structural isomerism. The different degree of self-association for the two octanols is attributed to entropic factors. The more shielded 2-isomer forms larger fractions of smaller, less cooperative, and more ordered clusters, likely corresponding to cyclic structures. Signatures of a different cluster organization are also evidenced by comparing the H-bond energy dispersion (HBED) of OH stretching IR bands. A limiting cooperative H-bond enthalpy value of 27 kJ/mol is found. It is also proposed that the different H-bonding capabilities may modulate the extent of interaggregate hydrocarbon interactions, which is important in explaining the differences in molar volume, compressibility, and vaporization enthalpy for the two isomers.

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

    Directory of Open Access Journals (Sweden)

    Christer B. Aakeröy

    2015-09-01

    Full Text Available 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.

  5. Comparison of Degrees of Potential-Energy-Surface Anharmonicity for Complexes and Clusters with Hydrogen Bonds

    Science.gov (United States)

    Kozlovskaya, E. N.; Doroshenko, I. Yu.; Pogorelov, V. E.; Vaskivskyi, Ye. V.; Pitsevich, G. A.

    2018-01-01

    Previously calculated multidimensional potential-energy surfaces of the MeOH monomer and dimer, water dimer, malonaldehyde, formic acid dimer, free pyridine-N-oxide/trichloroacetic acid complex, and protonated water dimer were analyzed. The corresponding harmonic potential-energy surfaces near the global minima were constructed for series of clusters and complexes with hydrogen bonds of different strengths based on the behavior of the calculated multidimensional potential-energy surfaces. This enabled the introduction of an obvious anharmonicity parameter for the calculated potential-energy surfaces. The anharmonicity parameter was analyzed as functions of the size of the analyzed area near the energy minimum, the number of points over which energies were compared, and the dimensionality of the solved vibrational problem. Anharmonicity parameters for potential-energy surfaces in complexes with strong, medium, and weak H-bonds were calculated under identical conditions. The obtained anharmonicity parameters were compared with the corresponding diagonal anharmonicity constants for stretching vibrations of the bridging protons and the lengths of the hydrogen bridges.

  6. Characterization of the hydrogen bond in molecular systems of biological interest by neutron scattering

    International Nuclear Information System (INIS)

    Cavillon, F.

    2004-10-01

    This work presents a methodology for the analysis of the scattering spectra of neutrons on molecular liquids. This method is based on the adjustment of the molecular form factor concerning great momentum transfer. The subtraction of the intra-molecular contributions gives access to information on inter-molecular interactions such as the hydrogen bond. 3 systems with increasing levels of difficulty have been studied: the ammonia molecule, the N-methyl-formamide (NMF) and the N-methyl-acetamide (NMA). The value we get for the N-D intermolecular distance of the liquid ammonia molecule is 1.7 angstrom, this value is different from the value generally admitted (2.3 angstrom) but we have validated it by studying the isotopic substitution N 14 /N 15 . The adjustment to the NMF is obtained with a good accuracy but the characterization of the hydrogen bound is more delicate to infer. A preliminary study of the NMA molecule shows that this method can give relevant results on complex molecules

  7. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    International Nuclear Information System (INIS)

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions. We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%

  8. Increased helix and protein stability through the introduction of a new tertiary hydrogen bond.

    Science.gov (United States)

    Peterson, R W; Nicholson, E M; Thapar, R; Klevit, R E; Scholtz, J M

    1999-03-12

    In an effort to quantify the importance of hydrogen bonding and alpha-helix formation to protein stability, a capping box motif was introduced into the small phosphocarrier protein HPr. Previous studies had confirmed that Ser46, at the N-cap position of the short helix-B in HPr, serves as an N-cap in solution. Thus, only a single-site mutation was required to produce a canonical S-X-X-E capping box: Lys49 at the N3 position was substituted with a glutamic acid residue. Thermal and chemical denaturation studies on the resulting K49E HPr show that the designed variant is approximately 2 kcal mol-1 more stable than the wild-type protein. However, NMR studies indicate that the side-chain of Glu49 does not participate in the expected capping H-bond interaction, but instead forms a new tertiary H-bond that links helix-B to the four-stranded beta-sheet of HPr. Here, we demonstrate that a strategy in which new non-native H-bonds are introduced can generate proteins with increased stability. We discuss why the original capping box design failed, and compare the energetic consequences of the new tertiary side-chain to main-chain H-bond with a local (helix-capping) side-chain to main-chain H-bond on the protein's global stability. Copyright 1999 Academic Press.

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

    International Nuclear Information System (INIS)

    Bankura, Arindam; Chandra, Amalendu

    2015-01-01

    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

  10. On the characterization of dynamic supramolecular systems: a general mathematical association model for linear supramolecular copolymers and application on a complex two-component hydrogen-bonding system.

    Science.gov (United States)

    Odille, Fabrice G J; Jónsson, Stefán; Stjernqvist, Susann; Rydén, Tobias; Wärnmark, Kenneth

    2007-01-01

    A general mathematical model for the characterization of the dynamic (kinetically labile) association of supramolecular assemblies in solution is presented. It is an extension of the equal K (EK) model by the stringent use of linear algebra to allow for the simultaneous presence of an unlimited number of different units in the resulting assemblies. It allows for the analysis of highly complex dynamic equilibrium systems in solution, including both supramolecular homo- and copolymers without the recourse to extensive approximations, in a field in which other analytical methods are difficult. The derived mathematical methodology makes it possible to analyze dynamic systems such as supramolecular copolymers regarding for instance the degree of polymerization, the distribution of a given monomer in different copolymers as well as its position in an aggregate. It is to date the only general means to characterize weak supramolecular systems. The model was fitted to NMR dilution titration data by using the program Matlab, and a detailed algorithm for the optimization of the different parameters has been developed. The methodology is applied to a case study, a hydrogen-bonded supramolecular system, salen 4+porphyrin 5. The system is formally a two-component system but in reality a three-component system. This results in a complex dynamic system in which all monomers are associated to each other by hydrogen bonding with different association constants, resulting in homo- and copolymers 4n5m as well as cyclic structures 6 and 7, in addition to free 4 and 5. The system was analyzed by extensive NMR dilution titrations at variable temperatures. All chemical shifts observed at different temperatures were used in the fitting to obtain the DeltaH degrees and DeltaS degrees values producing the best global fit. From the derived general mathematical expressions, system 4+5 could be characterized with respect to above-mentioned parameters.

  11. Theoretical estimation of pnicogen bonds and hydrogen bonds in small heterocyclic complexes: Red-shifts and blue-shifts ruled by polarization effects

    International Nuclear Information System (INIS)

    Oliveira, Boaz G.

    2014-01-01

    Graphical abstract: - Highlights: • This paper definitively discusses the interaction strength. • Analyses of the red-shifts and blue-shift. • Stretch frequencies of the hydrogen bonds and pnicogen bonds in heterocyclic compounds. • Theoretical calculations derived from topological parameters of the Quantum Theory of Atoms in Molecules (QTAIM). • The analysis of the Natural Bond Orbital (NBO) in line with the Bent’s rule of the chemical bonding. - Abstract: The occurrence of pnicogen bonds (N⋯P) and hydrogen bonds (F⋯H or Cl⋯H) in heterocyclic complexes formed by C 2 H 5 N⋯PH 3 , C 2 H 5 N⋯PH 2 F and C 2 H 5 N⋯PH 2 Cl was investigated at the B3LYP/6-311++G(d,p) level of theory. Analysis of the infrared spectra revealed the appearance of both red and blue shifts for the P–H bonds. However, in the case of the P–F and P–Cl bonds only red shifts were observed. The phenomenology of these vibration modes was interpreted on the basis of the QTAIM atomic radii as well as the contributions of the s and p orbitals determined via NBO calculations. The results of this latter investigation are consistent with the rehybridization theory and the Bent rule for chemical bonding. The charge transfer between N and P was determined in order to verify whether these atoms present an acid or base profile upon the formation of the pnicogen bonds

  12. Controlled supramolecular assembly of micelle-like gold nanoparticles in PS-b-P2VP diblock copolymers via hydrogen bonding.

    Science.gov (United States)

    Jang, Se Gyu; Kramer, Edward J; Hawker, Craig J

    2011-10-26

    We report a facile strategy to synthesize amphiphilic gold (Au) nanoparticles functionalized with a multilayer, micelle-like structure consisting of a Au core, an inner hydroxylated polyisoprene (PIOH) layer, and an outer polystyrene shell (PS). Careful control of enthalpic interactions via a systematic variation of structural parameters, such as number of hydroxyl groups per ligand (N(OH)) and styrene repeating units (N(PS)) as well as areal chain density of ligands on the Au-core surface (Σ), enables precise control of the spatial distribution of these nanoparticles. This control was demonstrated in a lamellae-forming poly(styrene-b-2-vinylpyridine) (PS-b-P2VP) diblock copolymer matrix, where the favorable hydrogen-bonding interaction between hydroxyl groups in the PIOH inner shell and P2VP chains in the PS-b-P2VP diblock copolymer matrix, driving the nanoparticles to be segregated in P2VP domains, could be counter balanced by the enthalphic penalty of mixing of the PS outer brush with the P2VP domains. By varying N(OH), N(PS), and Σ, the nanoparticles could be positioned in the PS or P2VP domains or at the PS/P2VP interface. In addition, the effect of additives interfering with the hydrogen-bond formation between hydroxyl groups on Au nanoparticles and P2VP chains in a diblock copolymer matrix was investigated, and an interesting pea-pod-like segregation of Au nanoparticles in PS domains was observed.

  13. Combined effects of π-π stacking and hydrogen bonding on the (N1) acidity of uracil and hydrolysis of 2'-deoxyuridine.

    Science.gov (United States)

    Kellie, Jennifer L; Navarro-Whyte, Lex; Carvey, Matthew T; Wetmore, Stacey D

    2012-03-01

    M06-2X/6-31+G(d,p) is used to study the simultaneous effects of π-π stacking interactions with phenylalanine (modeled as benzene) and hydrogen bonding with small molecules (HF, H(2)O, and NH(3)) on the N1 acidity of uracil and the hydrolytic deglycosylation of 2'-deoxyuridine (dU) (facilitated by fully (OH(-)) or partially (HCOO(-)···H(2)O) activated water). When phenylalanine is complexed with isolated uracil, the proton affinity of all acceptor sites significantly increases (by up to 28 kJ mol(-1)), while the N1 acidity slightly decreases (by ~6 kJ mol(-1)). When small molecules are hydrogen bound to uracil, addition of the phenylalanine ring can increase or decrease the acidity of uracil depending on the number and nature (acidity) of the molecules bound. Furthermore, a strong correlation between the effects of π-π stacking on the acidity of U and the dU deglycosylation reaction energetics is found, where the hydrolysis barrier can increase or decrease depending on the nature and number of small molecules bound, the nucleophile considered (which dictates the negative charge on U in the transition state), and the polarity of the (bulk) environment. These findings emphasize that the catalytic (or anticatalytic) role of the active-site aromatic amino acid residues is highly dependent on the situation under consideration. In the case of uracil-DNA glycosylase (UNG), which catalyzes the hydrolytic excision of uracil from DNA, the type of discrete hydrogen-bonding interactions with U, the nature of the nucleophile, and the anticipated weak, nonpolar environment in the active site suggest that phenylalanine will be slightly anticatalytic in the chemical step, and therefore experimentally observed contributions to catalysis may entirely result from associated structural changes that occur prior to deglycosylation.

  14. Different Supramolecular Coordination Polymers of [N,N'-di(pyrazin-2-yl-pyridine-2,6-diamine]Ni(II with Anions and Solvent Molecules as a Result of Hydrogen Bonding

    Directory of Open Access Journals (Sweden)

    Hsin-Ta Wang

    2007-04-01

    Full Text Available Ni(II complexes of N,N'–di(pyrazin–2–ylpyridine–2,6–diamine (H2dpzpda with different anions were synthesized and their structures were determined by X-ray diffraction. Hydrogen bonds between the amino groups and anions assembled the mononuclear molecules into different architectures. The perchlorate complex had a 1-D chain structure, whereas switching the anion from perchlorate to nitrate resulted in a corresponding change of the supramolecular structure from 1-D to 3-D. When the nitrate complex packed with the co-crystallized water, a double chain structure was formed through hydrogen bonding. The magnetic studies revealed values of g = 2.14 and D = 3.11 cm-1 for [Ni(H2dpzpda2](ClO42 (1 and g = 2.18 and D = 2.19 cm-1 for [Ni(H2dpzpda2](NO32 (2, respectively.

  15. Calculation of near-edge x-ray-absorption fine structure at finite temperatures: Spectral signatures of hydrogen bond breaking in liquid water

    International Nuclear Information System (INIS)

    Hetenyi, Balazs; De Angelis, Filippo; Giannozzi, Paolo; Car, Roberto

    2004-01-01

    We calculate the near-edge x-ray-absorption fine structure of H 2 O in the gas, hexagonal ice, and liquid phases using heuristic density-functional based methods. We present a detailed comparison of our results with experiment. The differences between the ice and water spectra can be rationalized in terms of the breaking of hydrogen bonds around the absorbing molecule. In particular the increase in the pre-edge absorption feature from ice to water is shown to be due to the breaking of a donor hydrogen bond. We also find that in water approximately 19% of hydrogen bonds are broken

  16. Microscopic models for proton transfer in water and strongly hydrogen-bonded complexes with a single-well proton potential

    DEFF Research Database (Denmark)

    Kuznetsov, A.M.; Ulstrup, Jens

    2004-01-01

    A new mechanism and formalism for proton transfer in donor-acceptor complexes with long hydrogen bonds introduced recently [1], is applied to a proton transfer in liquid water. "Structural diffusion" of hydroxonium ions is regarded as totally adiabatic process, with synchronous hindered translation...... of two closest water molecules to and from the reaction complex as crucial steps. The water molecules induce a "gated" shift of the proton from the donor to the acceptor in the double-well potential with simultaneous breaking/formation of hydrogen bonds between these molecules and the proton donor...... and acceptor. The short-range and long-range proton transfer as "structural diffusion" of Zundel complexes is also considered. The theoretical formalism is illustrated with the use of Morse, exponential, and harmonic molecular potentials. This approach is extended to proton transfer in strongly hydrogen...

  17. A two-dimensional hydrogen-bonded water layer in the structure of a cobalt(III) cubane complex.

    Science.gov (United States)

    Qi, Ji; Zhai, Xiang-Sheng; Zhu, Hong-Lin; Lin, Jian-Li

    2014-02-01

    A tetranuclear Co(III) oxide complex with cubane topology, tetrakis(2,2'-bipyridine-κ(2)N,N')di-μ2-carbonato-κ(4)O:O'-tetra-μ3-oxido-tetracobalt(III) pentadecahydrate, [Co4(CO3)2O4(C10H8N2)4]·15H2O, with an unbounded hydrogen-bonded water layer, has been synthesized by reaction of CoCO3 and 2,2'-bipyridine. The solvent water molecules form a hydrogen-bonded net with tetrameric and pentameric water clusters as subunits. The Co4O4 cubane-like cores are sandwiched between the water layers, which are further stacked into a three-dimensional metallo-supramolecular network.

  18. The thermodynamic stability of hydrogen bonded and cation bridged complexes of humic acid models-A theoretical study

    International Nuclear Information System (INIS)

    Aquino, Adelia J.A.; Tunega, Daniel; Pasalic, Hasan; Haberhauer, Georg; Gerzabek, Martin H.; Lischka, Hans

    2008-01-01

    Hydrogen bonded and cation bridged complexation of poly(acrylic acid) oligomers, representing a model compound for humic acids, with acetic acid and the herbicide (4-chloro-2-methylphenoxy) acetic acid (MCPA) have been studied by means of density functional theory. Solvation effects were computed by means of a combination of microsolvation (explicit insertion of water molecules) and global solvation (polarizable continuum approach). The stability of hydrogen bonded complexes in solution is characterized by a strong competition between solute and solvent molecules. The cation bridged complexes of the negatively charged (deprotonated) ligands were found to be strongly favored explaining the capability of humic acids to fixate anionic species from soil solutions and the ability to form cross-linking structures within the humic acid macromolecules

  19. Communication: Towards the binding energy and vibrational red shift of the simplest organic hydrogen bond: Harmonic constraints for methanol dimer

    International Nuclear Information System (INIS)

    Heger, Matthias; Suhm, Martin A.; Mata, Ricardo A.

    2014-01-01

    The discrepancy between experimental and harmonically predicted shifts of the OH stretching fundamental of methanol upon hydrogen bonding to a second methanol unit is too large to be blamed mostly on diagonal and off-diagonal anharmonicity corrections. It is shown that a decisive contribution comes from post-MP2 electron correlation effects, which appear not to be captured by any of the popular density functionals. We also identify that the major deficiency is in the description of the donor OH bond. Together with estimates for the electronic and harmonically zero-point corrected dimer binding energies, this work provides essential constraints for a quantitative description of this simple hydrogen bond. The spectroscopic dissociation energy is predicted to be larger than 18 kJ/mol and the harmonic OH-stretching fundamental shifts by about −121 cm −1 upon dimerization, somewhat more than in the anharmonic experiment (−111 cm −1 )

  20. A spectroscopic study of the hydrogen bonding and pi-pi stacking interactions of harmane with quinoline.

    Science.gov (United States)

    Balón, M; Guardado, P; Muñoz, M A; Carmona, C

    1998-01-01

    A spectroscopic (UV-vis, Fourier transform IR, steady state, and time-resolved fluorescence) study of the interactions of the ground and excited singlet states of harmane (1-methyl-9H-pyrido/3,4-b/indole) with quinoline has been carried out in cyclohexane, toluene, and buffered pH=8.7 aqueous solutions. To analyze how the number of rings in the substrate influences these interactions, pyridine and phenanthridine have also been included in this study. In cyclohexane and toluene 1:1 stoichiometric hydrogen-bonded complexes are formed in both the ground and the excited singlet states. As the number of rings of the benzopyridines and the solvent polarity increase hydrogen-bonding interactions weaken and pi-pi van der Waals interactions become apparent.