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Sample records for alteredintramolecular hydrogen-bonding pattern

  1. Binding of the Respiratory Chain Inhibitor Antimycin to theMitochondrial bc1 Complex: A New Crystal Structure Reveals an AlteredIntramolecular Hydrogen-Bonding Pattern

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Li-shar; Cobessi, David; Tung, Eric Y.; Berry, Edward A.

    2005-05-10

    Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex.Structure-activity-relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding specificity, and suggested that a low pKa for the phenolic OH group and an intramolecular H-bond between that OH and the carbonyl O of the salicylamide linkage are important. Two previous X-ray structures of antimycin bound to vertebrate bc1 complex gave conflicting results. A new structure reported here of the bovine mitochondrial bc1 complex at 2.28Angstrom resolution with antimycin bound, allows us for the first time to reliably describe the binding of antimycin and shows that the intramolecular hydrogen bond described in solution and in the small-molecule structure is replaced by one involving the NH rather than carbonyl O of the amide linkage, with rotation of the amide group relative to the aromatic ring. The phenolic OH and formylamino N form H-bonds with conserved Asp228 of cyt b, and the formylamino O H-bonds via a water molecule to Lys227. A strong density the right size and shape for a diatomic molecule is found between the other side of the dilactone ring and the alpha-A helix.

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

    International Nuclear Information System (INIS)

    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. Hydrogen bonded supramolecular structures

    CERN Document Server

    Li, Zhanting

    2015-01-01

    This book covers the advances in the studies of hydrogen-bonding-driven supramolecular systems  made over the past decade. It is divided into four parts, with the first introducing the basics of hydrogen bonding and important hydrogen bonding patterns in solution as well as in the solid state. The second part covers molecular recognition and supramolecular structures driven by hydrogen bonding. The third part introduces the formation of hollow and giant macrocycles directed by hydrogen bonding, while the last part summarizes hydrogen bonded supramolecular polymers. This book is designed to b

  4. Recognizing molecular patterns by machine learning: an agnostic structural definition of the hydrogen bond

    CERN Document Server

    Gasparotto, Piero

    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 ...

  5. 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.

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

    International Nuclear Information System (INIS)

    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

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

    Directory of Open Access Journals (Sweden)

    Rychlewska Urszula

    2006-04-01

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

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

    International Nuclear Information System (INIS)

    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

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

    Science.gov (United States)

    Auvil, Tyler Jay

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

  10. Hydrogen bonding in polyanilines

    Energy Technology Data Exchange (ETDEWEB)

    Bahceci, S. (Department of Chemistry, Middle East Technical University, Ankara 06531 (Turkey)); Toppare, L. (Department of Chemistry, Middle East Technical University, Ankara 06531 (Turkey)); Yurtsever, E. (Department of Chemistry, Middle East Technical University, Ankara 06531 (Turkey))

    1994-11-29

    Hydrogen bonding between poly(bisphenol A carbonate) (PC) and polyaniline (PAn) is analyzed using semi-empirical quantum methodology. Fully optimized AM1 molecular orbital calculations are reported for various aniline structures (monomer, dimer and trimer), the monomer of the PC and the hydrogen-bonded model of PAn-PC oligomer. ((orig.))

  11. Hydrogen bonding and anaesthesia

    Science.gov (United States)

    Sándorfy, C.

    2004-12-01

    General anaesthetics act by perturbing intermolecular associations without breaking or forming covalent bonds. These associations might be due to a variety of van der Waals interactions or hydrogen bonding. Neurotransmitters all contain OH or NH groups, which are prone to form hydrogen bonds with those of the neurotransmitter receptors. These could be perturbed by anaesthetics. Aromatic rings in amino acids can act as weak hydrogen bond acceptors. On the other hand the acidic hydrogen in halothane type anaesthetics are weak proton donors. These two facts together lead to a probable mechanism of action for all general anaesthetics.

  12. Water's Hydrogen Bond Strength

    CERN Document Server

    Chaplin, Martin

    2007-01-01

    Water is necessary both for the evolution of life and its continuance. It possesses particular properties that cannot be found in other materials and that are required for life-giving processes. These properties are brought about by the hydrogen bonded environment particularly evident in liquid water. Each liquid water molecule is involved in about four hydrogen bonds with strengths considerably less than covalent bonds but considerably greater than the natural thermal energy. These hydrogen bonds are roughly tetrahedrally arranged such that when strongly formed the local clustering expands, decreasing the density. Such low density structuring naturally occurs at low and supercooled temperatures and gives rise to many physical and chemical properties that evidence the particular uniqueness of liquid water. If aqueous hydrogen bonds were actually somewhat stronger then water would behave similar to a glass, whereas if they were weaker then water would be a gas and only exist as a liquid at sub-zero temperature...

  13. Hydrogen bonded networks in formamide [HCONH2] ( = 1 − 10) clusters: A computational exploration of preferred aggregation patterns

    Indian Academy of Sciences (India)

    A Subha Mahadevi; Y Indra Neela; G Narahari Sastry

    2012-01-01

    Application of quantum chemical calculations is vital in understanding hydrogen bonding observed in formamide clusters, a prototype model for motifs found in protein secondary structure. DFT calculations have been performed on four arrangements of formamide clusters [HCONH2], ( = 1 − 10) linear, circular, helical and stacked forms. These studies reveal the maximum cooperativity in the stacked arrangement followed by the circular, helical and linear arrangements and is based on interaction energy per monomer. In all these arrangements as we increase cluster size, an increasing trend in cooperativity of hydrogen bonding is observed. Atoms-in-molecule analysis establishes the nature of bonding between the formamide monomers on the basis of electron density values obtained at the bond critical point (BCP).

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

    OpenAIRE

    Rychlewska Urszula; Francis Savarimuthu; Muthiah Packianathan; Warżajtis Beata

    2006-01-01

    Abstract Background Trimethoprim [2,4-diamino-5-(3',4',5'-trimethoxybenzyl)pyrimidine] is an antifolate drug. It selectively inhibits the bacterial dihydrofolate reductase (DHFR) enzyme. Results In the crystal structures of trimethoprim (TMP)-hydrogen phthalate (1) and trimethoprim-hydrogen adipate (2), one of the N atoms of the pyrimidine ring is protonated and it interacts with the deprotonated carboxylate oxygens through a pair of nearly parallel N-H...O hydrogen bonds to form a fork-like ...

  15. Supramolecular hydrogen-bonding patterns of co-crystals containing the active pharmaceutical ingredient (API) phloroglucinol and N-heterocycles.

    Science.gov (United States)

    Cvetkovski, Aleksandar; Bertolasi, Valerio; Ferretti, Valeria

    2016-06-01

    The active pharmaceutical ingredient phloroglucinol (PHL) has been taken as an illustrative molecule to explore the intermolecular interactions which can be established with other molecular entities to build PHL pharmaceutical co-crystals. The crystal structures of five newly synthesized co-crystals are reported, where PHL is crystallized with N-heterocycles, namely 2-hydroxy-6-methylpyridine (1), 2,4-dimethyl-6-hydroxypyrimidine (2), 4-phenylpyridine (3), 2-hydroxypyridine (4) and 2,3,5,6-tetramethylpyrazine (5). The structural characteristics of these co-crystals, as far as the hydrogen-bonding networks and the crystalline architectures are concerned, are strongly dependent on the chemical features of the coformer molecules, as well as on their size and shape. A detailed analysis of the intermolecular interactions established in all the PHL co-crystals of known structures has allowed the recognition of some regularities in the packing modes that can be useful in the design of new supramolecular adducts forming predictable structural motifs. PMID:27240764

  16. Hydrogen Bonds Involving Metal Centers

    OpenAIRE

    Pavlović, G.; N. Raos

    2006-01-01

    Hydrogen bonds involving metal center as a hydrogen donor or hydrogen acceptor are only a specific type of metal-hydrogen interactions; it is therefore not easy to differentiate hydrogen bond from other metal-hydrogen interactions, especially agostic ones. The first part of the review is therefore devoted to the results of structural chemistry and molecular spectroscopy (NMR, IR), as a tool for differentiating hydrogen bondings from other hydrogen interactions. The classical examples of Pt···...

  17. Photoinduced hydrogen-bonding dynamics.

    Science.gov (United States)

    Chu, Tian-Shu; Xu, Jinmei

    2016-09-01

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

  18. Quantum Confinement in Hydrogen Bond

    CERN Document Server

    Santos, Carlos da Silva dos; Ricotta, Regina Maria

    2015-01-01

    In this work, the quantum confinement effect is proposed as the cause of the displacement of the vibrational spectrum of molecular groups that involve hydrogen bonds. In this approach the hydrogen bond imposes a space barrier to hydrogen and constrains its oscillatory motion. We studied the vibrational transitions through the Morse potential, for the NH and OH molecular groups inside macromolecules in situation of confinement (when hydrogen bonding is formed) and non-confinement (when there is no hydrogen bonding). The energies were obtained through the variational method with the trial wave functions obtained from Supersymmetric Quantum Mechanics (SQM) formalism. The results indicate that it is possible to distinguish the emission peaks related to the existence of the hydrogen bonds. These analytical results were satisfactorily compared with experimental results obtained from infrared spectroscopy.

  19. Interpretation of hydrogen bonding in the weak and strong regions using conceptual DFT descriptors

    OpenAIRE

    Özen, Alimet Sema; Ozen, Alimet Sema; De Proft, Frank; Aviyente , Viktorya; Geerlings, Paul

    2006-01-01

    Hydrogen bonding is among the most fundamental interactions in biology and chemistry, providing an extra stabilization of 1-40 kcal/mol to the molecular systems involved. This wide range of stabilization energy underlines the need for a general and comprehensive theory that will explain the formation of hydrogen bonds. While a simple electrostatic model is adequate to describe the bonding patterns in the weak and moderate hydrogen bond regimes, strong hydrogen bonds, on the other hand, requir...

  20. Molecular structure, hydrogen-bonding patterns and topological analysis (QTAIM and NCI) of 5-methoxy-2-nitroaniline and 5-methoxy-2-nitroaniline with 2-amino-5-nitropyridine (1:1) co-crystal

    Science.gov (United States)

    Hernández-Paredes, Javier; Carrillo-Torres, Roberto C.; López-Zavala, Alonso A.; Sotelo-Mundo, Rogerio R.; Hernández-Negrete, Ofelia; Ramírez, José Zeferino; Alvarez-Ramos, Mario E.

    2016-09-01

    In this work, we report an analysis of the molecular structure and the hydrogen-bonding patterns in the crystal structures of 5-methoxy-2-nitroaniline (1) and 5-methoxy-2-nitroaniline with 2-amino-5-nitropyridine (1:1) co-crystal (2). X-ray single crystal diffraction experiments were carried out to analyse the intermolecular forces in terms of geometrical criteria. These intermolecular interactions were also investigated through topological analysis of the electron density (ρ) employing QTAIM and NCI methods. Additionally, Raman spectroscopy was employed to analyse the vibrational characteristics of the entitled materials. The supramolecular structure of (1) is produced by crosslinked chains, which are primarily dominated by N-H···O hydrogen bonds. However, C-H···O interactions reinforce this connectivity. Furthermore, the molecules in (1) are connected through two-centre instead of the three-centre hydrogen-bonding interactions between the -NH2 and -NO2 groups commonly observed in nitroanilines. The asymmetric unit of (2) contains two symmetry-independent molecules of 5-methoxy-2-nitroaniline (5M2NA) and two symmetry-independent molecules of 2-amino-5-nitropyridine (2A5NP). The supramolecular structure of (2) is developed not only for N-H···O but also N-H···N and supportive C-H···O hydrogen bonds. The two symmetry-independent 2A5NP molecules bound to each other through two-centre hydrogen bonds between the -NH2 and -NO2 groups forming C22(16) chains. 5M2NA molecules bound to these chains forming R22 9 and R22(8) synthons. Experimental and theoretical results obtained in this work suggest that C-H···O interactions play an important role in the stabilization of these supramolecular structures.

  1. Hydrogen Bonds in Polymer Folding

    OpenAIRE

    Borg, J; Jensen, M. H.; K. Sneppen; Tiana, G.

    2000-01-01

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

  2. Special Issue: Intramolecular Hydrogen Bonding

    Directory of Open Access Journals (Sweden)

    Ronald K. Castellano

    2014-09-01

    Full Text Available Intramolecular hydrogen bonds play critical structure- and function-serving roles in biological and synthetic molecular systems. This special issue, through eight contributions, showcases the prominence of these non-covalent interactions within several scientific disciplines, and in various structural contexts and environments. Reported, for example, are the consequences of intramolecular hydrogen bonds on the structures of molecules that show biological activity, for biological mechanisms, and for the conformational switching of functional synthetic molecules. Also showcased in the contributions are the state-of-the-art experimental and theoretical methods available for the characterization of intramolecular hydrogen bonds, which critically report on their strengths, geometries, and spectroscopic signatures in the gas, solid, and solution phases.

  3. Rethinking hydrogen-bond kinetics

    CERN Document Server

    Prada-Gracia, Diego

    2013-01-01

    At the fundamental level, our understanding of water hydrogen-bond dynamics has been largely built on the detailed analysis of classical molecular simulations. The latter served to develop a plethora of hydrogen bond definitions based on different properties, including geometrical distances, topology and energetics. Notwithstanding, no real consensus emerged from these approaches, making the development of a consistent and reliable definition elusive. In this contribution, a framework to study hydrogen bonds in liquid water based purely on kinetics is presented. This approach makes use of the analysis of commitment probabilities without relying on arbitrarily chosen order parameters and cutoffs. Our results provide evidence for a self-consistent description, resulting in a clear multi-exponential behavior of the kinetics.

  4. Hydrogen-bonding patterns in bis[2,4,6-triazaniumylcyclohexane-1,3,5-tris(olate)-κ(3)O,O',O'']germanium(IV) tetrachloride hexahydrate.

    Science.gov (United States)

    Neis, Christian; Morgenstern, Bernd; Hegetschweiler, Kaspar

    2016-01-01

    A first preliminary report on the crystal structure of a hydrated salt formulated as [Ge(taci)2]Cl4·13H2O (taci is 1,3,5-triamino-1,3,5-trideoxy-cis-inositol) appeared more than 20 years ago [Ghisletta (1994). PhD thesis, ETH Zürich. Switzerland]. At that time it was not possible to discriminate unambiguously between the positions of some of the chloride ions and water O atoms, and disorder was thus postulated. In a new determination, a conclusive scheme of hydrogen bonding proves to be a particularly appealing aspect of the structure. Single crystals of the title compound, C12H30GeN6O6(4+)·4Cl(-)·6H2O or [Ge(taci)2]2Cl8·12H2O, were grown from an aqueous solution by slow evaporation of the solvent. The two [Ge(taci)2](4+) cations exhibit a double-adamantane-type structure with exclusive O-atom coordination and approximate D3d symmetry. The taci ligands adopt a zwitterionic form with deprotonated hydroxy groups and protonated amino groups. Both cations are hydrogen bonded to six water molecules. The structure of the hydration shell of the two cations is, however, slightly different. The {[Ge(taci)2]·6H2O}(4+) aggregates are interlinked in all three dimensions by further hydrogen bonds of the types N-H...Cl...H-N, N-H...O(H)2...H-N, (Ge)O...H-O(H)...H-N, N-H...O(H)-H...Cl...H-N, (Ge)O...H-O-H...Cl...H-N, N-H...O(H)-H...Cl...H-(H)O...H-N, (Ge)O...H-O-H...Cl...H-(H)O...H-N and Ge(O)...H-O-H...Cl...H-O-H...O(Ge). PMID:26742824

  5. Main Chain Noncentrosymmetric Hydrogen Bonded Macromolecules Incorporating Aniline, Alkanol, and Alkanoic Acid Hydrogen Bond Donors

    OpenAIRE

    Jeremy R. Wolf

    2014-01-01

    The syntheses and characterization of three noncentrosymmetric main chain hydrogen bonded macromolecules which incorporate aniline, alkanoic acid, and alkanol hydrogen bond donor units are reported. These macromolecules participate in weak intermolecular hydrogen bonding as demonstrated using attenuated total reflectance (ATR) FTIR. The phase transitions of these macromolecules depend on the identity of the hydrogen bond donor.

  6. Neutron structure of human carbonic anhydrase II in complex with methazolamide: mapping the solvent and hydrogen-bonding patterns of an effective clinical drug

    Directory of Open Access Journals (Sweden)

    Mayank Aggarwal

    2016-09-01

    Full Text Available Carbonic anhydrases (CAs; EC 4.2.1.1 catalyze the interconversion of CO2 and HCO3−, and their inhibitors have long been used as diuretics and as a therapeutic treatment for many disorders such as glaucoma and epilepsy. Acetazolamide (AZM and methazolamide (MZM, a methyl derivative of AZM are two of the classical CA inhibitory drugs that have been used clinically for decades. The jointly refined X-ray/neutron structure of MZM in complex with human CA isoform II (hCA II has been determined to a resolution of 2.2 Å with an Rcryst of ∼16.0%. Presented in this article, along with only the second neutron structure of a clinical drug-bound hCA, is an in-depth structural comparison and analyses of differences in hydrogen-bonding network, water-molecule orientation and solvent displacement that take place upon the binding of AZM and MZM in the active site of hCA II. Even though MZM is slightly more hydrophobic and displaces more waters than AZM, the overall binding affinity (Ki for both of the drugs against hCA II is similar (∼10 nM. The plausible reasons behind this finding have also been discussed using molecular dynamics and X-ray crystal structures of hCA II–MZM determined at cryotemperature and room temperature. This study not only allows a direct comparison of the hydrogen bonding, protonation states and solvent orientation/displacement of AZM and MZM, but also shows the significant effect that the methyl derivative has on the solvent organization in the hCA II active site.

  7. Contribution of Hydrogen Bonds to Protein Stability

    Science.gov (United States)

    Pace, Nick

    2014-03-01

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

  8. Intramolecular and intermolecular hydrogen bonds in aminophenols

    International Nuclear Information System (INIS)

    IR-Fourier spectroscopy methods are adopted to study intramolecular and intermolecular hydrogen bonds that form in CCl4 solutions of aminophenol derivatives and in a solid phase of these compounds pressed in KBr. If a hydroxyl group is present in the molecule in the ortho-position to an amino group, then intramolecular interactions between OH and NH groups will take place in aminophenol solutions. Intramolecular O-HO=S=O and N-H...O=S=O hydrogen bonds are found in solutions of compounds containing a sulfonamide fragment. Additional acylation of the amino group causes an intramolecular O-H...O=C hydrogen bond to form in solutions. Functional groups OH, NH, SO2, and C=O interact with one another in various ways in the solid phase to form intermolecular hydrogen bonds in aminophenols. (authors) Keywords aminophenol - IR spectrum - intramolecular hydrogen bond - intermolecular hydrogen bond

  9. Intramolecular versus intermolecular hydrogen bonding in solution

    OpenAIRE

    Vliegenthart, J. F. G.; Kroon, Jan; Kroon-Batenburg, L.M.J.; Leeflang, B.R.

    1994-01-01

    The balance between intra- and intermolecular hydrogen bonding is studied for a solution of methyl beta-cellobioside in water and dimethylsulfoxide by 1H NMR and molecular dynamics simulations. In water O(3) predominantly interacts with water molecules, whereas in dimethylsulfoxide it is intramolecularly hydrogen bonded to O(5Œ). The temperature coefficient of the chemical shift of the hydroxy groups appears to be a reliable indicator of intermolecular hydrogen-bond formation, whereas the ex...

  10. Tetraalkylammonium Salts as Hydrogen-Bonding Catalysts.

    Science.gov (United States)

    Shirakawa, Seiji; Liu, Shiyao; Kaneko, Shiho; Kumatabara, Yusuke; Fukuda, Airi; Omagari, Yumi; Maruoka, Keiji

    2015-12-21

    Although the hydrogen-bonding ability of the α hydrogen atoms on tetraalkylammonium salts is often discussed with respect to phase-transfer catalysts, catalysis that utilizes the hydrogen-bond-donor properties of tetraalkylammonium salts remains unknown. Herein, we demonstrate hydrogen-bonding catalysis with newly designed tetraalkylammonium salt catalysts in Mannich-type reactions. The structure and the hydrogen-bonding ability of the new ammonium salts were investigated by X-ray diffraction analysis and NMR titration studies. PMID:26564098

  11. HYDROGEN BONDING IN THE METHANOL DIMER

    Science.gov (United States)

    In this work, two methanol molecules are placed in different arrangements to study hydrogen bonding in carbohydrate materials such as cellulose. Energy was calculated as a function of both hydrogen bond length and angle over wide ranges, using quantum mechanics (QM). The QM wavefunctions are analyze...

  12. 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...... substantiated by NBO and AIM results. The hydrogen bonds manifest themselves in the same manner as conventional hydrogen bonds, D-H bond elongation, D-H vibrational stretching frequency red shift and intensity increase, and adduct stabilization. The alkane adducts also exhibit elongation of the C-H bonds...... involved and a concurrent red shift, which is rationalized in terms of charge-transfer interactions that cause simultaneous weakening of both the O-H and C-H bonds. Like other dihydrogen-bonded adducts, the adducts possess a bent structure and asymmetric bifurcated hydrogen bonds. The hydrogen bonds are...

  13. A cooperative hydrogen bonding system with a Csbnd H⋯O hydrogen bond in ofloxacin

    Science.gov (United States)

    Gao, Xiuxiang; Liu, Yufeng; Li, Huizhen; Bian, Jiang; Zhao, Ying; Cao, Ye; Mao, Yuezhi; Li, Xin; Xu, Yizhuang; Ozaki, Yukihiro; Wu, Jinguang

    2013-05-01

    We have investigated a cooperative hydrogen bonding system with a Csbnd H⋯O hydrogen bond in ofloxacin by using NMR, UV-Vis spectra together with quantum chemistry calculation. Both pH-dependent NMR experiments and DFT calculation indicate that the intra-molecular Csbnd H⋯O hydrogen bond between an aromatic proton and an oxygen atom from the carboxyl group is formed. Notably, the Csbnd H⋯O hydrogen bond forms a cooperative hydrogen bonding system with a neighboring Osbnd H⋯O hydrogen bond between the carboxyl group and the keto oxygen. The cooperative hydrogen bonding system makes the formation and disruption of the Osbnd H⋯O and Csbnd H⋯O hydrogen bonds in a synergistic manner. Comparison on the pKa value of the carboxylic group in different fluoroquinolones compounds indicates that the Csbnd H⋯O hydrogen bond plays a significant role in stabilizing the Osbnd H⋯O hydrogen bond. In addition, the formation and disruption of the cooperative hydrogen bonding system could regulate the conformation of the carboxyl group, which affects the size of the conjugated system and spectral behavior of π-π transition of ofloxacin.

  14. Physical Nature of Hydrogen Bond

    CERN Document Server

    Zhyganiuk, I V

    2015-01-01

    The physical nature and the correct definition of hydrogen bond (H-bond) are considered.\\,\\,The influence of H-bonds on the thermodynamic, kinetic, and spectroscopic properties of water is analyzed.\\,\\,The conventional model of H-bonds as sharply directed and saturated bridges between water molecules is incompatible with the behavior of the specific volume, evaporation heat, and self-diffusion and kinematic shear viscosity coefficients of water. On the other hand, it is shown that the variation of the dipole moment of a water molecule and the frequency shift of valence vibrations of a hydroxyl group can be totally explained in the framework of the electrostatic model of H-bond.\\,\\,At the same time, the temperature dependences of the heat capacity of water in the liquid and vapor states clearly testify to the existence of weak H-bonds.\\,\\,The analysis of a water dimer shows that the contribution of weak H-bonds to its ground state energy is approximately 4--5 times lower in comparison with the energy of electr...

  15. HYDROGEN BONDING IN POLYMERIC ADSORBENTS BASED ADSORPTION AND SEPARATION

    Institute of Scientific and Technical Information of China (English)

    XUMancai; SHIZuoqing; 等

    2000-01-01

    After a concise introduction of hydrogen bonding effects in solute-solute and solute-solvent bonding,the design of polymeric adsorbents based on hydrogen bonding ,selectivity in adsorption through hydrogen bonding,and characterization of hydrogen bonding in adsorption and separation were reviewed with 28 references.

  16. 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 or...... 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...

  17. Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid water

    Science.gov (United States)

    Houriez, Céline; Masella, Michel; Ferré, Nicolas

    2010-09-01

    In this study, we investigated the hydrogen-bond network patterns involving the NO moieties of five small nitroxides in liquid water by analyzing nanosecond scale molecular dynamics trajectories. To this end, we implemented two types of hydrogen-bond definitions, based on electronic structure, using Bader's atoms-in-molecules analysis and based on geometric criteria. In each definition framework, the nitroxide/water hydrogen-bond networks appear very variable from a nitroxide to another. Moreover, each definition clearly leads to a different picture of nitroxide hydration. For instance, the electronic structure-based definition predicts a number of hydrogen bonds around the nitroxide NO moiety usually larger than geometric structure-based ones. One particularly interesting result is that the strength of a nitroxide/water hydrogen bond does not depend on its linearity, leading us to question the relevance of geometric definition based on angular cutoffs to study this type of hydrogen bond. Moreover, none of the hydrogen-bond definitions we consider in the present study is able to quantitatively correlate the strength of nitroxide/water hydrogen-bond networks with the aqueous nitroxide spin properties. This clearly exhibits that the hydrogen-bonding concept is not reliable enough to draw quantitative conclusions concerning such properties.

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

    Science.gov (United States)

    Sen, Ibrahim; Kara, Hulya; Azizoglu, Akın

    2016-10-01

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

  19. Intramolecular hydrogen bonding and calixarene-like structures in p-cresol/formaldehyde resins

    Science.gov (United States)

    Opaprakasit, P.; Scaroni, A.; Painter, P.

    2001-08-01

    The nature of the strong hydrogen bonds found in p-cresol/formaldehyde (PCF) resins, compared to ordinary phenolic compounds, is studied. The evidence from FTIR spectroscopy indicates that this strong interaction is due to intramolecular hydrogen bonding from "calixarene-like" structures. The formation of this structure in PCF is enabled by its "linear" (all- ortho-linkage) structure, which is not present in branched resins. Additionally, a transition is observed at around 175 to 200°C where the intramolecular hydrogen bonded structure is lost. This structure cannot be recovered upon cooling or annealing due to restrictions on conformational rotations that are coupled to a new pattern of intermolecular hydrogen bonding. However, the structure is reformed by dissolving the resin in solution and casting new films.

  20. Hydrogen bonds in methane-water clusters.

    Science.gov (United States)

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

    2016-08-24

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

  1. Recodable surfaces based on switchable hydrogen bonds.

    Science.gov (United States)

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

    2016-07-01

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

  2. 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

  3. 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

  4. Modeling the Hydrogen Bond within Molecular Dynamics

    Science.gov (United States)

    Lykos, Peter

    2004-01-01

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

  5. Statistical theory for hydrogen bonding fluid system of AaDd type (Ⅱ): Properties of hydrogen bonding networks

    Institute of Scientific and Technical Information of China (English)

    WANG HaiJun; HONG XiaoZhong; GU Fang; BA XinWu

    2007-01-01

    Making use of the invariant property of the equilibrium size distribution of the hydrogen bonding clusters formed in hydrogen bonding system of AaDd type, the analytical expressions of the free energy in pregel and postgel regimes are obtained. Then the gel free energy and the scaling behavior of the number of hydrogen bonds in gel phase near the critical point are investigated to give the corresponding scaling exponents and scaling law. Meanwhile, some properties of intermolecular and intramolecular hydrogen bonds in the system, sol and gel phases are discussed. As a result, the explicit relationship between the number of intramolecular hydrogen bonds and hydrogen bonding degree is obtained.

  6. Supramolecular hydrogen-bonding patterns in the organic-inorganic hybrid compound bis(4-amino-5-chloro-2,6-dimethylpyrimidinium) tetrathiocyanatozinc(II)-4-amino-5-chloro-2,6-dimethylpyrimidine-water (1/2/2).

    Science.gov (United States)

    Karthikeyan, Ammasai; Zeller, Matthias; Thomas Muthiah, Packianathan

    2016-04-01

    Zinc thiocyanate complexes have been found to be biologically active compounds. Zinc is also an essential element for the normal function of most organisms and is the main constituent in a number of metalloenzyme proteins. Pyrimidine and aminopyrimidine derivatives are biologically very important as they are components of nucleic acids. Thiocyanate ions can bridge metal ions by employing both their N and S atoms for coordination. They can play an important role in assembling different coordination structures and yield an interesting variety of one-, two- and three-dimensional polymeric metal-thiocyanate supramolecular frameworks. The structure of a new zinc thiocyanate-aminopyrimidine organic-inorganic compound, (C6H9ClN3)2[Zn(NCS)4]·2C6H8ClN3·2H2O, is reported. The asymmetric unit consist of half a tetrathiocyanatozinc(II) dianion, an uncoordinated 4-amino-5-chloro-2,6-dimethylpyrimidinium cation, a 4-amino-5-chloro-2,6-dimethylpyrimidine molecule and a water molecule. The Zn(II) atom adopts a distorted tetrahedral coordination geometry and is coordinated by four N atoms from the thiocyanate anions. The Zn(II) atom is located on a special position (twofold axis of symmetry). The pyrimidinium cation and the pyrimidine molecule are not coordinated to the Zn(II) atom, but are hydrogen bonded to the uncoordinated water molecules and the metal-coordinated thiocyanate ligands. The pyrimidine molecules and pyrimidinium cations also form base-pair-like structures with an R2(2)(8) ring motif via N-H...N hydrogen bonds. The crystal structure is further stabilized by intermolecular N-H...O, O-H...S, N-H...S and O-H...N hydrogen bonds, by intramolecular N-H...Cl and C-H...Cl hydrogen bonds, and also by π-π stacking interactions. PMID:27045184

  7. Water lubricates hydrogen-bonded molecular machines.

    Science.gov (United States)

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

    2013-11-01

    The mechanical behaviour of molecular machines differs greatly from that of their macroscopic counterparts. This applies particularly when considering concepts such as friction and lubrication, which are key to optimizing the operation of macroscopic machinery. Here, using time-resolved vibrational spectroscopy and NMR-lineshape analysis, we show that for molecular machinery consisting of hydrogen-bonded components the relative motion of the components is accelerated strongly by adding small amounts of water. The translation of a macrocycle along a thread and the rotation of a molecular wheel around an axle both accelerate significantly on the addition of water, whereas other protic liquids have much weaker or opposite effects. We tentatively assign the superior accelerating effect of water to its ability to form a three-dimensional hydrogen-bond network between the moving parts of the molecular machine. These results may indicate a more general phenomenon that helps explain the function of water as the 'lubricant of life'. PMID:24153370

  8. Water lubricates hydrogen-bonded molecular machines

    Science.gov (United States)

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

    2013-11-01

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

  9. Conjugation in hydrogen-bonded systems

    CERN Document Server

    Novakovskaya, Yulia V

    2012-01-01

    Analysis of the electron density distribution in clusters composed of hydrogen fluoride, water, and ammonia molecules, especially within the hydrogen-bond domains, reveals the existence of both \\sigma- and \\pi-binding between molecules. The \\sigma-kind density distribution determines the mutual orientation of molecules. A \\pi-system may be delocalized conjugated, which provides additional stabilization of molecular clusters. In those clusters where the sequence of hydrogen bonds is not planar, a peculiar kind of \\pi-conjugation exists. HF anion and H5O2 cation are characterized by quasi-triple bonds between the electronegative atoms. The most long-lived species stabilized by delocalized \\pi-binding are rings and open or closed hoops composed of fused rings. It is conjugated \\pi-system that determines cooperativity phenomenon.

  10. Pyrrolidine nucleotides conformationally constrained via hydrogen bonding

    Czech Academy of Sciences Publication Activity Database

    Pohl, Radek; Poštová Slavětínská, Lenka; Rejman, Dominik

    Praha : Institute of Organic Chemistry and Biochemistry AS CR, v. v. i, 2014 - (Hocek, M.), s. 352-353 ISBN 978-80-86241-50-0. - (Collection Symposium Series. 14). [Symposium on Chemistry of Nucleic Acid Components /16./. Český Krumlov (CZ), 08.06.2014-13.06.2014] R&D Projects: GA ČR GA13-24880S Institutional support: RVO:61388963 Keywords : pyrrolidine nucleotides * PMEA * hydrogen bond Subject RIV: CC - Organic Chemistry

  11. Anesthesia cutoff phenomenon: Interfacial hydrogen bonding

    International Nuclear Information System (INIS)

    Anesthesia cutoff refers to the phenomenon of loss of anesthetic potency in a homologous series of alkanes and their derivatives when their sizes become too large. In this study, hydrogen bonding of 1-alkanol series (ethanol to eicosanol) to dipalmitoyl-L-alpha-phosphatidylcholine (DPPC) was studied by Fourier transform infrared spectroscopy (FTIR) in DPPC-D2O-in-CCl4 reversed micelles. The alkanols formed hydrogen bonds with the phosphate moiety of DPPC and released the DPPC-bound deuterated water, evidenced by increases in the bound O-H stretching signal of the alkanol-DPPC complex and also in the free O-D stretching band of unbound D2O. These effects increased according to the elongation of the carbon chain of 1-alkanols from ethanol (C2) to 1-decanol (C10), but suddenly almost disappeared at 1-tetradecanol (C14). Anesthetic potencies of these alkanols, estimated by the activity of brine shrimps, were linearly related to hydrogen bond-breaking activities below C10 and agreed with the FTIR data in the cutoff at C10

  12. Photochromic supramolecular azopolyimides based on hydrogen bonds

    Science.gov (United States)

    Schab-Balcerzak, Ewa; Flakus, Henryk; Jarczyk-Jedryka, Anna; Konieczkowska, Jolanta; Siwy, Mariola; Bijak, Katarzyna; Sobolewska, Anna; Stumpe, Joachim

    2015-09-01

    The approach of deriving new photoresponsive active supramolecular azopolymers based on the hydrogen bonds is described. Polymers with imide rings, i.e., poly(esterimide)s and poly(etherimide)s, with phenolic hydroxyl or carboxylic groups were applied as matrixes for the polymer-dye supramolecular systems. Supramolecular films were built on the basis of the hydrogen bonds between the functional groups of the polymers and various azochromophores, that is, 4-phenylazophenol, 4-[4-(6-hydroxyhexyloxy)phenylazo]benzene, 4-[4-(6-hexadecaneoxy)phenylazo]pyridine and 4-(4-hydroxyphenylazo)pyridine. The hydrogen bonding interaction in azo-systems were studied by Fourier transform infrared spectroscopy and for selected assembles by 1H NMR technique. The obtained polyimide azo-assembles were characterized by X-ray diffraction and DSC measurements. H-bonds allow attaching a chromophore to each repeating unit of the polymer, thereby suppressing the macroscopic phase separation except for the systems based on 4-[4-(6-hydroxyhexyloxy)phenylazo]benzene. H-bonds systems were amorphous and revealed glass transition temperatures lower than for the polyimide matrixes (170-260 °C). The photoresponsive behavior of the azo-assemblies was tasted in holographic recording experiment.

  13. Hydrogen bonds in PC61BM solids

    Directory of Open Access Journals (Sweden)

    Chun-Qi Sheng

    2015-09-01

    Full Text Available We have studied the hydrogen bonds in PC61BM solids. Inter-molecular interaction is analyzed theoretically for the well-defined monoclinic (P21/n structure. The results indicate that PC61BM combines into C–H⋯Od bonded molecular chains, where Od denotes the doubly-bonded O atom of PC61BM. The molecular chains are linked together by C–H⋯Os bonds, where Os denotes the singly-bonded O atom of PC61BM. To reveal the consequences of hydrogen bond formation on the structural properties of PC61BM solids (not limited to the monoclinic structure, we design and perform some experiments for annealed samples with the monoclinic (P21/n PC61BM as starting material. The experiments include differential scanning calorimetry, X-ray diffraction and infrared absorption measurements. Structural phase transitions are observed below the melting point. The C–H⋯Od bonds seem persisting in the altered structures. The inter-molecular hydrogen bonds can help to understand the phase separation in polymer/PC61BM blends and may be responsible for the existence of liquid PC61BM.

  14. Hydrogen bonds in PC61BM solids

    International Nuclear Information System (INIS)

    We have studied the hydrogen bonds in PC61BM solids. Inter-molecular interaction is analyzed theoretically for the well-defined monoclinic (P21/n) structure. The results indicate that PC61BM combines into C–H⋯Od bonded molecular chains, where Od denotes the doubly-bonded O atom of PC61BM. The molecular chains are linked together by C–H⋯Os bonds, where Os denotes the singly-bonded O atom of PC61BM. To reveal the consequences of hydrogen bond formation on the structural properties of PC61BM solids (not limited to the monoclinic structure), we design and perform some experiments for annealed samples with the monoclinic (P21/n) PC61BM as starting material. The experiments include differential scanning calorimetry, X-ray diffraction and infrared absorption measurements. Structural phase transitions are observed below the melting point. The C–H⋯Od bonds seem persisting in the altered structures. The inter-molecular hydrogen bonds can help to understand the phase separation in polymer/PC61BM blends and may be responsible for the existence of liquid PC61BM

  15. 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.

  16. Herringbone array of hydrogen-bonded ribbons in 2-ethoxybenzamide from high-resolution X-ray powder diffraction.

    Science.gov (United States)

    Pagola, Silvina; Stephens, Peter W

    2009-11-01

    In 2-ethoxybenzamide, C(9)H(11)NO(2), the amide substituents are linked into centrosymmetric head-to-head hydrogen-bonded dimers. Additional hydrogen bonds between adjacent dimers give rise to ribbon-like packing motifs, which extend along the c axis and possess a third dimension caused by twisting of the 2-ethoxyphenyl substituent with respect to the hydrogen-bonded amide groups. The ribbons are arranged in a T-shaped herringbone pattern and cohesion between them is achieved by van der Waals forces. PMID:19893241

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

    Energy Technology Data Exchange (ETDEWEB)

    Pagola, S.; Stephens, P

    2009-01-01

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

  18. Constructing supramolecular nanostructure by hydrogen-bonding

    Institute of Scientific and Technical Information of China (English)

    LI YiBao; ZENG QingDao; WANG ZhiHui; QI GuiCun; GUAN Li; FAN XiaoLin; WANG Chen

    2008-01-01

    The diquinoxalino (2.3-2'.3'-a.c) phenazine (DQP), containing 6 nitrogen atoms, was synthesized, and its adsorption and self-assembling behavior on highly oriented pyrolytic graphite (HOPG) was studied by scanning tunneling microscopy (STM) under ambient conditions. With 1,14-tetradecanedioic acid as a bridge, uniform two-dimensional arrays of 1,14-tetradecanedioic acid/DQP nanostrueture were suc-cessfully fabricated. The result illustrates that it is possible to construct and control supramolecular nanostructure by intermolecular hydrogen-bonding.

  19. Effect of density of hydrogen-bonding donor on hydrogen-bonded multilayer buildup

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hongyu; MA Ning; WANG Zhiqiang

    2005-01-01

    The effect of density of hydrogen-bonding donor (HBD) on the formation of layer-by-layer assemblies of poly(4-vinylpyridine) and poly(4-vinylphenol) was investigated. For this purpose, a series of ethyl-substituted poly(4-vinylphenol) (EsPVPhf) with variable ethyl substitute percentage was synthesized by grafting the phenol moiety along the poly(4-vinylphenol) backbone with 1-bromoethane. UV-vis spectroscopy revealed a uniform deposition process of the hydrogen-bonded multilayer consisting of poly(4- vinylpyridine) (PVPy) and EsPVPhf with variable density of HBD. Notably, it was found that increasing the HBD density of EsPVPhf resulted in a marked decrease of both amount of polymers adsorbed and film thickness, which should be related to the EsPVPhf conformation change from coiled state to extended conformation in ethanol solution. Compared with the effect of charge density in polyelectrolyte multilayer, however, there does not exist a critical density of HBD in our case of hydrogen-bonded multilayer assembly. In addition, surface structures of PVPy/EsPVPhf multilayer films also can be tailored controllably by adjusting HBD density of EsPVPhf. As a result, a new method for tuning the structure of hydrogen-bonding-directed multilayer films was developed.

  20. 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.

  1. Electron collisions with hydrogen-bonded complexes

    International Nuclear Information System (INIS)

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

  2. Molecular dynamics simulations of the hydration of poly(vinyl methyl ether):Hydrogen bonds and quasi-hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Atomistic detailed hydration structures of poly(vinyl methyl ether)(PVME) have been investigated by molecular dynamics simulations under 300 K at various concentrations. Both radial distribution functions and the distance distributions between donors and acceptors in hydrogen bonds show that the hydrogen bonds between the polymer and water are shorter by 0.005 nm than those between water molecules. The Quasi-hydrogen bonds take only 7.2% of the van der Waals interaction pairs. It was found the hydrogen bonds are not evenly distributed along the polymer chain,and there still exists a significant amount(10%) of ether oxygen atoms that are not hydrogen bonded to water at a concentration as low as 3.3%. This shows that in polymer solutions close contacts occur not only between polymer chains but also between chain segments within the polymer,which leads to inefficient contacts between ether oxygen atoms and water molecules. Variation of the quasi-hydrogen bonds with the concentration is similar to that of hydrogen bonds,but the ratio of the repeat units forming quasi-hydrogen bonds to those forming hydrogen bonds approaches 0.2. A transition was found in the demixing enthalpy at around 30% measured by dynamic testing differential scanning calorimetry(DTDSC) for aqueous solutions of a mono-dispersed low molecular weight PVME,which can be related to the transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ~27%. The transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ~27% can be used to explain the demixing enthalpy transition at 30% at a molecular scale. In addition,at the concentration of 86%,each ether oxygen atom bonded with water is assigned 1.56 water molecules on average,and ’free’ water molecules emerge at the concentration of around 54%.

  3. Effect of Hydrogen-Bonding Junctions on Microphase Separation in Block Copolymers

    Science.gov (United States)

    Stone, Greg; Hedrick, Jim; Nederberg, Fredrik; Balsara, Nitash

    2008-03-01

    The morphology of poly(styrene-block- trimethylene carbonate) (PS-PTMC) copolymers with and without thiourea groups at the junction between the blocks was studied by a combination of small angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). The thiourea groups are known to exhibit inter-molecular hydrogen bonding. We demonstrate that the presence of thiourea groups results in increased segregation between PS and PTMC blocks. We focus on symmetric systems with total molecular weights in the 5 kg/mol range. In conventional block copolymers without hydrogen bonding groups it is difficult to obtain strong segregation in low molecular weight systems because the product chi*N controls segregation (chi is the Flory-Huggins interaction parameter and N is the number of monomers per chain). The incorporation of hydrogen bonding groups may provide a route for the generation of patterns with small, sharply defined features using block copolymers.

  4. Negligible Isotopic Effect on Dissociation of Hydrogen Bonds.

    Science.gov (United States)

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

    2016-03-31

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

  5. 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. PMID:26872049

  6. VIBRATIONAL RELAXATION ON HYDROGEN BONDING IN DINUCLEOSIDE PHOSPHATE

    OpenAIRE

    Yoshii, Giichi

    1983-01-01

    The specific interactions between bases, which depend on the dinucleoside phosphate conformations, were studied in terms of the vibrational dynamics of hydrogen-bonding. The hydrogen-bond stretching vibrations of the nucleotide complexes and dinucleoside phosphates were observed in the polycrystalline state by the Raman spectroscopy. The vibrational dynamics were investigated by measuring the line broadenings of hydrogen-bonding vibration observed in near 100cm^. The half band-widths of vibra...

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

    Science.gov (United States)

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

    2004-10-01

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

  8. 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.

  9. 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...... hydrogen-bonded donor-acceptor complexes. In contrast to the above model [1], the short hydrogen bond between the donor and acceptor moieties, however, completely erodes the barrier along the proton transfer mode. This introduces some physical pattern differences from proton transfer reactions in truly...

  10. Binding of reactive organophosphate by oximes via hydrogen bond

    Indian Academy of Sciences (India)

    Andrea Pappalardo; Maria E Amato; Francesco P Ballistreri; Valentina La Paglia Fragola; Gaetano A Tomaselli; Rosa Maria Toscano; Giuseppe Trusso Sfrazzetto

    2013-07-01

    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 via hydrogen bond.

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

    Science.gov (United States)

    Joy, Stephen T; Arora, Paramjit S

    2016-04-14

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

  12. Microphase separation in hydrogen bonding polymer/surfactant melts

    NARCIS (Netherlands)

    Dormidontova, Elena; Brinke, Gerrit ten

    1999-01-01

    Phase behavior of solvent free mixtures of homopolymers and amphiphiles capable of hydrogen bonding is analyzed in weak segregation limit applying a theoretical model describing the main features of the system as a function of composition, temperature and strength of hydrogen bonding. Phase diagrams

  13. Effect of hydrogen bonds on protein stability

    CERN Document Server

    Bianco, Valentino; Franzese, Giancarlo

    2010-01-01

    The mechanism of cold- and pressure-denaturation are matter of debate. Some models propose that when denaturation occurs more hydrogen bonds between the molecules of hydration water are formed. Other models identify the cause in the density fluctuations of surface water, or the destabilization of hydrophobic contacts because of the displacement of water molecules inside the protein, as proposed for high pressures. However, it is clear that water plays a fundamental role in the process. Here, we review some models that have been proposed to give insight into this problem. Next we describe a coarse-grained model of a water monolayer that successfully reproduces the complex thermodynamics of water and compares well with experiments on proteins at low hydration level. We introduce its extension for a homopolymer in contact with the water monolayer and study it by Monte Carlo simulations. Our goal is to perform a step in the direction of understanding how the interplay of cooperativity of water and interfacial hyd...

  14. 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.

  15. Tunneling readout of hydrogen-bonding based recognition

    OpenAIRE

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

    2009-01-01

    Hydrogen bonding has a ubiquitous role in electron transport1,2 and in molecular recognition, with DNA base-pairing being the best known example.3 Scanning tunneling microscope (STM) images4 and measurements of the decay of tunnel-current as a molecular junction is pulled apart by the STM tip, 5 are sensitive to hydrogen-bonded interactions. Here we show that these tunnel-decay signals can be used to measure the strength of hydrogen bonding in DNA basepairs. Junctions that are held together b...

  16. Hydrogen bonded supramolecular elastomers : correlating hydrogen bonding strength with morphology and rheology

    OpenAIRE

    Woodward, Philip; Hermida-Merino, Daniel; Greenland, Barnaby William; Hamley, Ian William; Light, Zoe; Slark, Andrew; Hayes, Wayne

    2010-01-01

    A series of six low molecular weight elastomers with hydrogen bonding end-groups have been designed, synthesised and studied. The poly(urethane) based elastomers all contained essentially the same hard block content (ca. 11%) and differ only in the nature of their end-groups. Solution state 1H NMR spectroscopic analysis of model compounds featuring the end-groups demonstrate that they all exhibit very low binding constants, in the range 1.4 to 45.0 M-1 in CDCl3, yet the corresponding elastome...

  17. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-10-23

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

  19. Modelling of spreading process: effect from hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    Li Xin; Hu Yuan-Zhong; Jiang Lan

    2008-01-01

    Lubricant spreading on solid substrates has drawn considerable attention not only for the microscopic wetting theory but also for the dramatic application in head-disk interface of magnetic storage drive systems. Molecular dynamic simulation based on a coarse-grained bead-spring model has been used to study such a spreading process.The spreading profiles indicate that the hydrogen bonds among lubricant molecules and the hydrogen bonds between lubricant molecules and polar atoms of solid substrates will complicate the spreading process in a tremendous degree.The hydrogen bonds among lubricant molecules will strengthen the lubricant combination intensity, which may hinder most molecules from flowing down to the substrates and diffusing along the substrates. And the hydrogen bonds between lubricant molecules and polar atoms of solid substrates will confine the lubricant molecules around polar atoms, which may hinder the molecules from diffusing along the substrates and cause precursor film to vanish.

  20. Modelling of spreading process: effect from hydrogen bonds

    International Nuclear Information System (INIS)

    Lubricant spreading on solid substrates has drawn considerable attention not only for the microscopic wetting theory but also for the dramatic application in head-disk interface of magnetic storage drive systems. Molecular dynamic simulation based on a coarse-grained bead-spring model has been used to study such a spreading process. The spreading profiles indicate that the hydrogen bonds among lubricant molecules and the hydrogen bonds between lubricant molecules and polar atoms of solid substrates will complicate the spreading process in a tremendous degree. The hydrogen bonds among lubricant molecules will strengthen the lubricant combination intensity, which may hinder most molecules from flowing down to the substrates and diffusing along the substrates. And the hydrogen bonds between lubricant molecules and polar atoms of solid substrates will confine the lubricant molecules around polar atoms, which may hinder the molecules from diffusing along the substrates and cause precursor film to vanish. (condensed matter: structure, mechanical and thermal properties)

  1. Hydrogen-Bond Dynamics of Water in Ionic Solutions

    Science.gov (United States)

    Bakker, H. J.; Kropman, M. F.; Omta, A. W.; Woutersen, S.

    We study the effects of ions on the structure and dynamics of the hydrogen bonds in liquid water. As a technique we use femtosecond two-color mid-infrared spectroscopy, since this technique allows a clear distinction of the dynamics of the first solvation (hydration) shell of water molecules from the dynamics of bulk water. We find that water molecules in the first hydration shell of the halogenic anions Cl, and I show much slower hydrogen-bond dynamics than water molecules in the pure liquid. We also observe that the first hydration shell shows very slow collective orientational dynamics, and forms a rigid, long-living structure. Finally, we find that ions have surprisingly little effect on the hydrogen-bond dynamics of water molecules outside the first hydration shell, which implies that ions do not enhance or weaken the hydrogen-bond network of liquid water.

  2. Molecular orbital analysis of the hydrogen bonded water dimer

    OpenAIRE

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

    2016-01-01

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

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

    OpenAIRE

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

    2014-01-01

    Cellulose is the most familiar and most abundant strong biopolymer, but the reasons for its outstanding mechanical performance are not well understood. Each glucose unit in a cellulose chain is joined to the next by a covalent C–O–C linkage flanked by two hydrogen bonds. This geometry suggests some form of cooperativity between covalent and hydrogen bonding. Using infrared spectroscopy and X-ray diffraction, we show that mechanical tension straightens out the zigzag conformation of the cellul...

  4. Hydrogen Bonded Nanostructures on Surfaces: STM, XPS and Electrospray Deposition

    OpenAIRE

    Swarbrick, Janine Cathy

    2006-01-01

    Molecules adsorbed on surfaces can show fascinating characteristics and properties. In particular the assembly of molecules into ordered arrays on surfaces is of great interest, whether one considers possible commercial applications or fundamental physical interactions. Specifically, the mediation of ordered molecular arrangements via hydrogen bonding yields many interesting structures. This thesis focusses primarily on the importance of hydrogen bonding between molecules on surfaces in u...

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

    Science.gov (United States)

    Beck, John Frederick; Mo, Yirong

    2007-01-15

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

  6. Statistical Parameters for Hydrogen Bonding Networks: One Component Case

    Institute of Scientific and Technical Information of China (English)

    王海军; 洪晓钟; 赵敏; 巴信武

    2001-01-01

    Based on the analysis of network structures formed by hydrogen bonds as the sol-gel phase transition takesplace in a single component hydrogen bonding system, the theory of reversible gelation is applied to calculatesome statistical parameters that determine many physical and chemical properties of the networks. Then, thentunerical simulation of the number of active chains and dangling chains, the number of effective cross-linkages,the number of active and dangling mers and the modulus as a function of conversion are undertaken.

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

    Science.gov (United States)

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

    2009-05-01

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

  8. 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

    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......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...... 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...

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

    Science.gov (United States)

    Vojta, Danijela; Kovačević, Goran; Vazdar, Mario

    2014-11-01

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

  10. Rotational Spectra of Hydrogen Bonded Networks of Amino Alcohols

    Science.gov (United States)

    Zhang, Di; Zwier, Timothy S.

    2014-06-01

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

  11. 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.

  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. Positively charged phosphorus as a hydrogen bond acceptor

    DEFF Research Database (Denmark)

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

    2014-01-01

    -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......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...... 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....

  14. 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 that the...

  15. Are hydrogen bonds responsible for glycine conformational preferences?

    International Nuclear Information System (INIS)

    Highlights: → Glycine conformational preferences in the isolated state were fully investigated. → The lowest energy conformation is not stabilized by hydrogen bonding. → Steric and hyperconjugative effects were analyzed for all conformers. → Several theoretical methods were used to explain the conformational preferences. - Abstract: Glycine conformational preferences have mostly been explained as due to the formation of intramolecular hydrogen bonding, despite other possible relevant intramolecular interactions that may be present in this molecular system. This paper, within the framework of the quantum theory of atoms in molecules and natural bond orbital analysis, at the B3LYP/aug-cc-pVDZ level, shows that hydrogen bonding formally stabilizes just one of the glycine conformers. Indeed, these theoretical calculations suggest that both steric hindrance and hyperconjugative effects rule conformational preferences of this model compound and may not be ignored in discussions of amino acid conformational analyses.

  16. Hydrophobic interactions and hydrogen bonds in \\beta-sheet formation

    CERN Document Server

    Narayanan, Chitra

    2013-01-01

    In this study, we investigate interactions of extended conformations of homodimeric peptides made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains using all-atom molecular dynamics simulations to decipher driving forces for \\beta-sheet formation. We make use of a periodic boundary condition setup in which individual peptides are infinitely long and stretched. Dimers adopt \\beta-sheet conformations at short interpeptide distances (\\xi ~ 0.5 nm) and at intermediate distances (~ 0.8 nm), valine and leucine homodimers assume cross-\\beta-like conformations with side chains interpenetrating each other. These two states are identified as minima in the Potential of Mean Force (PMF). While the number of interpeptide hydrogen bonds increases with decreasing interpeptide distance, the total hydrogen bond number in the system does not change significantly, suggesting that formation of \\beta-sheet structures from extended conformations is not driven by hydrogen bonds. This is supported by...

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

    Science.gov (United States)

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

    2016-09-01

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

  18. Dissecting Proton Delocalization in an Enzyme's Hydrogen Bond Network with Unnatural Amino Acids.

    Science.gov (United States)

    Wu, Yufan; Fried, Stephen D; Boxer, Steven G

    2015-12-01

    Extended hydrogen bond networks are a common structural motif of enzymes. A recent analysis proposed quantum delocalization of protons as a feature present in the hydrogen bond network spanning a triad of tyrosines (Y(16), Y(32), and Y(57)) in the active site of ketosteroid isomerase (KSI), contributing to its unusual acidity and large isotope shift. In this study, we utilized amber suppression to substitute each tyrosine residue with 3-chlorotyrosine to test the delocalization model and the proton affinity balance in the triad. X-ray crystal structures of each variant demonstrated that the structure, notably the O-O distances within the triad, was unaffected by 3-chlorotyrosine substitutions. The changes in the cluster's acidity and the acidity's isotope dependence in these variants were assessed via UV-vis spectroscopy and the proton sharing pattern among individual residues with (13)C nuclear magnetic resonance. Our data show pKa detuning at each triad residue alters the proton delocalization behavior in the H-bond network. The extra stabilization energy necessary for the unusual acidity mainly comes from the strong interactions between Y(57) and Y(16). This is further enabled by Y(32), which maintains the right geometry and matched proton affinity in the triad. This study provides a rich picture of the energetics of the hydrogen bond network in enzymes for further model refinement. PMID:26571340

  19. 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.

  20. Solvent effects on hydrogen bonding between primary alcohols and esters

    Institute of Scientific and Technical Information of China (English)

    DHARMALINGAM K.; RAMACHANDRAN K.; SIVAGURUNATHAN P.

    2006-01-01

    The interaction by hydrogen bond formation of some primary alcohols (1-heptanol, 1-octanol and 1-decanol) with esters (methyl methacrylate, ethyl methacrylate and butyl methacrylate) was investigated in non-polar solvents viz., n-heptane,CCh and benzene by means of FTIR spectroscopy. Formation constants and free energy changes of complex formation were determined. The dependence of the equilibrium constants and free energy changes of complex formation on the alkyl chain length of both the alcohols and esters are discussed. The solvent effect on the hydrogen bond formation is discussed in terms of specific interaction between the solute and solvent.

  1. Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence.

    Science.gov (United States)

    Liu, Chengyu; Ponder, Jay W; Marshall, Garland R

    2014-11-01

    Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of α- and β-amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by β-amino acids are experimentally more stable than those formed by α-amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead to entropic destabilization. In this study, molecular dynamics simulations using the second-generation force field, AMOEBA (Ponder, J.W., et al., Current status of the AMOEBA polarizable force field. J Phys Chem B, 2010. 114(8): p. 2549-64.) explored the stability and hydrogen-bonding patterns of capped oligo-β-alanine, oligoalanine, and oligoglycine dodecamers in water. The MD simulations showed that oligo-β-alanine has strong acceptor+2 hydrogen bonds, but surprisingly did not contain a large content of 3(12) -helical structures, possibly due to the sparse distribution of the 3(12) -helical structure and other structures with acceptor+2 hydrogen bonds. On the other hand, despite its backbone flexibility, the β-alanine dodecamer had more stable and persistent <3.0 Å hydrogen bonds. Its structure was dominated more by multicentered hydrogen bonds than either oligoglycine or oligoalanine helices. The 3(1) (PII) helical structure, prevalent in oligoglycine and oligoalanine, does not appear to be stable in oligo-β-alanine indicating its competition with other structures (stacking structure as indicated by MD analyses). These differences are among the factors that shape helical structural preferences and the relative stabilities of these three oligopeptides. PMID:25116421

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

    Science.gov (United States)

    Chen, Yinshan; Zhang, Wei; Yu, Lian

    2016-08-18

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

  3. 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

  4. 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

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

    Science.gov (United States)

    Henley, Alice; Bound, Michelle; Besley, Elena

    2016-05-26

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

  6. Nuclear delocalisation of hydrogen atoms in strong hydrogen bonds

    Czech Academy of Sciences Publication Activity Database

    Dračínský, Martin; Procházková, Eliška; Čechová, Lucie; Janeba, Zlatko

    Brno: Stuare, 2015 - (Novotný, J.). C30 ISBN 978-80-86441-46-7. [NMR Valtice. Central European NMR Meeting /30./. 19.04.2015-22.04.2015, Valtice] R&D Projects: GA ČR GA15-11223S Institutional support: RVO:61388963 Keywords : NMR spectroscopy * hydrogen bonds * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry

  7. Substituent effects on intramolecular hydrogen bonds in 5-nitrosopyrimidine derivates

    Czech Academy of Sciences Publication Activity Database

    Procházková, Eliška; Čechová, Lucie; Janeba, Zlatko; Dračínský, Martin

    Praha : -, 2013. s. 149-149. [ESOR 2013. European Symposium on Organic Reactivity /14./. 01.09.2013-06.09.2013, Praha] R&D Projects: GA ČR GA13-24880S Institutional support: RVO:61388963 Keywords : NMR spectroscopy * intramolecular hydrogen bonds * 5-nitrosopyrimidine derivates * DFT calculations * UV/ VIS spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry

  8. Seeking hydrogen bonds- with and without neutron diffraction

    International Nuclear Information System (INIS)

    The hydrogen-bond interaction can be studied using a variety of spectroscopic and crystallographic techniques, as well as theoretical studies based on quantum chemical principles, semi-empirical procedures, and statistical interpretations. A degree of specificity, along with flexibility, provides H-bonded systems with a variety of unusual and interesting physical, chemical and biological properties. Neutron diffraction is the method of choice for obtaining high-precision data on hydrogen-atom positions and hydrogen-bond stereo-chemistry in crystals. Neutron inelastic scattering can provide information on the dynamics of H-bonded systems. High-precision neutron diffraction studies on a variety of crystal hydrates, amino acids and small peptides, development of semi-empirical potential functions for bent-hydrogen bonds, and statistical analysis of H-bond populations associated with various donor and acceptor groups are some of the investigations on hydrogen bonding, carried out at Trombay during the past three decades. (author). 39 refs., 7 figs., 3 tabs

  9. Adhesion between silica surfaces due to hydrogen bonding

    Science.gov (United States)

    Bowen, James; Rossetto, Hebert L.; Kendall, Kevin

    2016-09-01

    The adhesion between surfaces can be enhanced significantly by the presence of hydrogen bonding. Confined water at the nanoscale can display behaviour remarkably different to bulk water due to the formation of hydrogen bonds between two surfaces. In this work we investigate the role of confined water on the interaction between hydrophilic surfaces, specifically the effect of organic contaminants in the aqueous phase, by measuring the peak adhesive force and the work of adhesion. Atomic force microscope cantilevers presenting hemispherical silica tips were interacted with planar single crystals of silica in the presence of dimethylformamide, ethanol, and formamide; solution compositions in the range 0–100 mol% water were investigated for each molecule. Each molecule was chosen for its ability to hydrogen bond with water molecules, with increasing concentrations likely to disrupt the structure of surface-bound water layers. With the exception of aqueous solutions containing low concentrations of ethanol, all molecules decreased the ability of confined water to enhance the adhesion between the silica surfaces in excess of the predicted theoretical adhesion due to van der Waals forces. The conclusion was that adhesion depends strongly on the formation of a hydrogen-bonding network within the water layers confined between the silica surfaces.

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

    Science.gov (United States)

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

    2015-07-15

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

  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

    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. Statistical theory for hydrogen bonding fluid system of A_aD_d type(II):Properties of hydrogen bonding networks

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Making use of the invariant property of the equilibrium size distribution of the hydrogen bonding clus- ters formed in hydrogen bonding system of AaDd type,the analytical expressions of the free energy in pregel and postgel regimes are obtained.Then the gel free energy and the scaling behavior of the number of hydrogen bonds in gel phase near the critical point are investigated to give the corre- sponding scaling exponents and scaling law.Meanwhile,some properties of intermolecular and in- tramolecular hydrogen bonds in the system,sol and gel phases are discussed.As a result,the explicit relationship between the number of intramolecular hydrogen bonds and hydrogen bonding degree is obtained.

  13. Rheology of miscible polymer blends with hydrogen bonding

    Science.gov (United States)

    Yang, Zhiyi

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

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

    Science.gov (United States)

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

    2016-07-01

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

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

    Science.gov (United States)

    Ortiz de Urbina, Jordi; Sesé, Gemma

    2016-07-01

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

  16. Liquid state of hydrogen bond network in ice

    Science.gov (United States)

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

    2016-08-01

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

  17. Infrared intensities and charge mobility in hydrogen bonded complexes

    Science.gov (United States)

    Galimberti, Daria; Milani, Alberto; Castiglioni, Chiara

    2013-08-01

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

  18. Liquid state of hydrogen bond network in ice

    CERN Document Server

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

    2016-01-01

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

  19. Influence of hydrogen bonds and temperature on dielectric properties

    Science.gov (United States)

    Ortiz de Urbina, Jordi; Sesé, Gemma

    2016-07-01

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

  20. Quantum Confinement in Hydrogen Bond of DNA and RNA

    CERN Document Server

    Santos, da Silva dos; Ricotta, Regina Maria

    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.

  1. pH-sensitive nanoparticles formed by interchain hydrogen bonding

    Czech Academy of Sciences Publication Activity Database

    Koňák, Čestmír; Sedlák, M.

    Salerno : Polymer Technology Group, 2008, 721_1-721_3. ISBN 88-7897-025-5. [Annual Meeting of Polymer Processing Society /24./. Salerno (IT), 15.06.2008-19.06.2008] R&D Projects: GA AV ČR IAA100500501; GA AV ČR IAA4050403; GA ČR GESON/06/E005 Institutional research plan: CEZ:AV0Z40500505 Keywords : association * dynamic light scattering * hydrogen bonding Subject RIV: CD - Macromolecular Chemistry

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

    Science.gov (United States)

    O'Neal, Kristi L; Weber, Stephen G

    2009-01-01

    There are only a few studies of noncovalent association in fluorous solvents and even fewer that are quantitative. A full understanding, particularly of stoichiometry and binding strength of noncovalent interactions in fluorous solvents could be very useful in improved molecular-receptor-based extractions, advancements in sensor technologies, crystal engineering, and supramolecular chemistry. This work investigates hydrogen bonding between heterocyclic bases and a perfluoropolyether with a terminal carboxylic acid group (Krytox 157FSH (1)), chiefly in FC-72 (a mixture of perfluorohexanes). In particular, we were interested in whether or not proton transfer occurs, and if so, under what conditions in H-bonded complexes. Continuous variations experiments show that in FC-72 weaker bases (pyrazine, pyrimidine, and quinazoline) form 1:1 complexes with 1, whereas stronger bases (quinoline, pyridine, and isoquinoline) form 1:3 complexes. Ultraviolet and infrared spectral signatures reveal that the 1:1 complexes are molecular (B.HA) whereas the 1:3 complexes are ionic (BH+.A-HAHA). Infrared spectra of 1:3 ionic complexes are discussed in detail. Literature and experimental data on complexes between N-heterocyclic bases and carboxylic acids in a range of solvents are compiled to compare solvent effects on proton transfer. Polar solvents support ionic hydrogen bonds at a 1:1 mol ratio. In nonpolar organic solvents, ionic hydrogen bonds are only observed in complexes with 1:2 (base/acid) stoichiometries. In fluorous solvents, a larger excess of acid, 1:3, is necessary to facilitate proton transfer in hydrogen bonds between carboxylic acids and the bases studied. PMID:19195102

  3. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    OpenAIRE

    Nagy, Peter I.

    2014-01-01

    A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with int...

  4. Hydrogen Bond in Liquid Water as a Brownian Oscillator

    Science.gov (United States)

    Woutersen, Sander; Bakker, Huib J.

    1999-09-01

    We present the first experimental observation of a vibrational dynamic Stokes shift. This dynamic Stokes shift is observed in a femtosecond pump-probe study on the OH-stretch vibration of HDO dissolved in D2O. We find that the Stokes shift has a value of approximately 70 cm-1 and occurs with a time constant of approximately 500 femtoseconds. The measurements can be accurately described by modeling the hydrogen bond in liquid water as a Brownian oscillator.

  5. Ion Pairs or Neutral Molecule Adducts? Cooperativity in Hydrogen Bonding

    Science.gov (United States)

    DeKock, Roger L.; Schipper, Laura A.; Dykhouse, Stephanie C.; Heeringa, Lee P.; Brandsen, Benjamin M.

    2009-01-01

    We performed theoretical studies on the systems NH[subscript 3] times HF times mH[subscript 2]O, NH[subscript 3] times HCl times mH[subscript 2]O, with m = 0, 1, 2, and 6. The molecules with m = 0 form hydrogen-bonded adducts with little tendency to form an ion-pair structure. The molecule NH[subscript 3] times HCl times H[subscript 2]O cannot be…

  6. 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.

  7. Probing the Hydrogen Bond Strength at Single Bond Limit

    Science.gov (United States)

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

    2015-03-01

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

  8. Terahertz Vibrations and Hydrogen-Bonded Networks in Crystals

    Directory of Open Access Journals (Sweden)

    Masae Takahashi

    2014-03-01

    Full Text Available The development of terahertz technology in the last few decades has made it possible to obtain a clear terahertz (THz spectrum. THz vibrations clearly show the formation of weak bonds in crystals. The simultaneous progress in the code of first-principles calculations treating noncovalent interactions has established the position of THz spectroscopy as a powerful tool for detecting the weak bonding in crystals. In this review, we are going to introduce, briefly, the contribution of weak bonds in the construction of molecular crystals first, and then, we will review THz spectroscopy as a powerful tool for detecting the formation of weak bonds and will show the significant contribution of advanced computational codes in treating noncovalent interactions. From the second section, following the Introduction, to the seventh section, before the conclusions, we describe: (1 the crystal packing forces, the hydrogen-bonded networks and their contribution to the construction of organic crystals; (2 the THz vibrations observed in hydrogen-bonded molecules; (3 the computational methods for analyzing the THz vibrations of hydrogen-bonded molecules; (4 the dispersion correction and anharmonicity incorporated into the first-principles calculations and their effect on the peak assignment of the THz spectrum (5 the temperature dependence; and (6 the polarization dependence of the THz spectrum.

  9. Positively Charged Phosphorus as a Hydrogen Bond Acceptor.

    Science.gov (United States)

    Hansen, Anne S; Du, Lin; Kjaergaard, Henrik G

    2014-12-01

    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 alcohol-trimethylphosphine complexes have been detected. Initially, the complexes were detected using matrix isolation spectroscopy, which favors complex formation. Subsequently, the fundamental OH-stretching vibration was observed in room-temperature gas-phase spectra. On the basis of our measured OH-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. PMID:26278958

  10. Hydrogen bonds in PC{sub 61}BM solids

    Energy Technology Data Exchange (ETDEWEB)

    Sheng, Chun-Qi [Department of Physics, Zhejiang University, Hangzhou 310027 (China); Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou 311121 (China); Li, Wen-Jie; Du, Ying-Ying; Chen, Guang-Hua; Chen, Zheng; Li, Hai-Yang; Li, Hong-Nian, E-mail: phylihn@mail.zju.edu.cn [Department of Physics, Zhejiang University, Hangzhou 310027 (China)

    2015-09-15

    We have studied the hydrogen bonds in PC{sub 61}BM solids. Inter-molecular interaction is analyzed theoretically for the well-defined monoclinic (P2{sub 1}/n) structure. The results indicate that PC{sub 61}BM combines into C–H⋯O{sub d} bonded molecular chains, where O{sub d} denotes the doubly-bonded O atom of PC{sub 61}BM. The molecular chains are linked together by C–H⋯O{sub s} bonds, where O{sub s} denotes the singly-bonded O atom of PC{sub 61}BM. To reveal the consequences of hydrogen bond formation on the structural properties of PC{sub 61}BM solids (not limited to the monoclinic structure), we design and perform some experiments for annealed samples with the monoclinic (P2{sub 1}/n) PC{sub 61}BM as starting material. The experiments include differential scanning calorimetry, X-ray diffraction and infrared absorption measurements. Structural phase transitions are observed below the melting point. The C–H⋯O{sub d} bonds seem persisting in the altered structures. The inter-molecular hydrogen bonds can help to understand the phase separation in polymer/PC{sub 61}BM blends and may be responsible for the existence of liquid PC{sub 61}BM.

  11. Matrix effects on hydrogen-bonded complexes trapped in low-temperature matrices

    Science.gov (United States)

    Barnes, Austin J.; Mielke, Zofia

    2012-09-01

    There are several different possible matrix effects on hydrogen-bonded complexes trapped in low-temperature matrices: hydrogen-bonded complexes may be stabilised (compared with the gas phase) as a result of being trapped in a low-temperature matrix; metastable hydrogen-bonded complexes may be trapped in matrices; the matrix may influence the extent of proton transfer in a hydrogen-bonded complex; the matrix may influence the structure of a hydrogen-bonded complex. Each of these possible effects is examined in turn using selected examples from the literature as well as our own work.

  12. Proton irradiation effect on hydrogen bond in material and biological systems

    International Nuclear Information System (INIS)

    After proton beam irradiation, we found the magnetic structure change in graphite. This work has been published as 'Electron Spin Resonance of Proton-Irradiated Graphite' (PHYSICAL REVIEW LETTERS, 97, 137206). And this work has been selected as 'the most prominent 10 science news 2006 in Korea'. When the proton beam was irradiated on KDP single crystal with fluence of 1015 ions/cm3, and the range of irradiation energy: 300 kev ∼ 2.0 MeV, the dielectric constant and the capacitance has increased as irradiation energy was increased. This means the distance of the separation of equilibrium in hydrogen bond has enlarged by proton beam irradiation. Using X-Ray diffraction pattern measurement, we found that the lattice constant was decreased after the irradiation and the activation energy has decreased from 0.42 eV to 0.28 eV by 1H NMR spin-lattice relaxation time measurement. This means that after proton beam irradiation, the hydrogen ions in KDP are more activated. We also found similar change in hydrogen bond after proton beam irradiation by dielectric constant measurement. These results have been published as 'Structural and proton-dynamical effects in a proton-irradiated KH2PO4 single crystal' ( PRB 73, 134114. (2006) ). In order to perform finer analysis for hydrogen bonds in KDP single crystal, we focused on the domain freezing effect near the phase transition temperature of KDP. Finally we set up Debye relaxation for domain wall motion, Cole-Cole and Cole-Davison models. We also developed proton beam resist materials for lithography using proton beam irradiation and nano proton-beam writing based technology

  13. Two new hydrogen bond-supported supramolecular compounds assembly from polyoxovanadate and organoamines

    International Nuclear Information System (INIS)

    Two novel organic-inorganic hybrid compounds based on organoamines and polyoxovanadates formulated as (H2dien)4[H10V18O42(PO4)](PO4).2H2O (1) (dien=diethylenetriamine) and (Him)8[HV18O42(PO4)] (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: C16H74N12O52V18P2, 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) A3, Z=4; for compound 2, C24H41N16O46V18P, Tetragonal, space group I4/mmm, a=13.5154(8) A, b=13.5154(8) A, c=19.1136 A, β=90o, V=3491.4(3) A3, Z=2. Compound 1 consists of protonated diens together with polyoxovanadates [H10V18O42(PO4)]5-. Compound 2 is composed of protonated ims and polyoxovanadates [HV18O42(PO4)]8-. There are hydrogen-bonding interactions between polyoxovanadates and different organoamines in 1 and 2. Polyoxovanadates are linked through H2dien 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 [V18O42(PO4)] building blocks have been hydrothermally synthesized. 1 is the first 3-D supramolecular network structure consisting of [V18O42(PO4)] unit, while 2 possesses 2-D layered supramolecular structure

  14. Halogen Bonding versus Hydrogen Bonding: A Molecular Orbital Perspective

    OpenAIRE

    Wolters, Lando P.; Bickelhaupt, F. Matthias

    2012-01-01

    We have carried out extensive computational analyses of the structure and bonding mechanism in trihalides DX⋅⋅⋅A− and the analogous hydrogen-bonded complexes DH⋅⋅⋅A− (D, X, A=F, Cl, Br, I) using relativistic density functional theory (DFT) at zeroth-order regular approximation ZORA-BP86/TZ2P. One purpose was to obtain a set of consistent data from which reliable trends in structure and stability can be inferred over a large range of systems. The main objective was to achieve a detailed unders...

  15. 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 as....... This is significant in view of the fact that the full anharmonic PT2 analysis requires orders-of-magnitude more computing time than the harmonic analysis. νOH also correlates with OH chemical shifts....

  16. 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}.

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

    International Nuclear Information System (INIS)

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

  18. 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.

  19. Charge density analysis of two proton transfer complexes: Understanding hydrogen bonding and determination of in-crystal dipole moments

    Indian Academy of Sciences (India)

    Reji Thomas; Shrinwantu Pal; Ayan Datta; Mariusz K Marchewka; Henryk Ratajczak; Swapan K Pati; G U Kulkarni

    2008-11-01

    An experimental charge density study has been carried out on proton-transfer complexes exhibiting nonlinear optical (NLO) properties-melaminium tartrate monohydrate and L-asparaginium picrate employing high-resolution X-ray diffraction at 100 K. Both the complexes crystallize in non-centric space group P21 and the structures exhibit interesting patterns of N-H…O and O-H…O hydrogen bonding. Experimental determination of the dipole moment () for the asymmetric unit reveals that for both the crystals, there is a large cooperative enhancement in the crystalline arising essentially due to hydrogen bond mediated charge transfer between the melaminium ion and the L-tartrate in one case, between the Lasparaginium ion and the picrate in the other complex. We have additionally performed theoretical calculations at the density functional theory (DFT) level to understand the origin of enhancement of the dipole moments in the two systems.

  20. A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

    Energy Technology Data Exchange (ETDEWEB)

    Hamdani, Hazrina Yusof, E-mail: hazrina@mfrlab.org [School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi (Malaysia); Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas (Malaysia); Artymiuk, Peter J., E-mail: p.artymiuk@sheffield.ac.uk [Dept. of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 T2N Sheffield (United Kingdom); Firdaus-Raih, Mohd, E-mail: firdaus@mfrlab.org [School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi (Malaysia)

    2015-09-25

    A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods.

  1. A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

    Science.gov (United States)

    Hamdani, Hazrina Yusof; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2015-09-01

    A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods.

  2. A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

    International Nuclear Information System (INIS)

    A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods

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

    Science.gov (United States)

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

    2012-03-01

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

  4. Anomalies of water and hydrogen bond dynamics in hydrophobic nanoconfinement

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Pradeep [Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, New York, NY 10021 (United States); Han, Sungho; Stanley, H Eugene [Center for Polymer Studies and Department of Physics, Boston University, Boston, MA 02215 (United States)

    2009-12-16

    Using molecular dynamic (MD) simulations of the TIP5P model of water, we investigate the effect of hydrophobic confinement on the anomalies of liquid water. For confinement length Lz = 1.1 nm, such that there are 2-3 molecular layers of water, we find the presence of the bulk-like density and diffusion anomaly in the lateral directions. However, the lines of these anomalies in the P-T plane are shifted to lower temperatures (DELTATapprox40 K) and pressures compared to bulk water. Furthermore, we introduce a method to calculate the effective diffusion constant along the confinement direction and find that the diffusion anomaly is absent. Moreover, we investigate the hydrogen bond dynamics of confined water and find that the hydrogen bond dynamics preserves the characteristics of HB dynamics in bulk water, such as a non-exponential behavior followed by an exponential tail of HB lifetime probability distributions and an Arrhenius temperature dependence of the average HB lifetime. The average number and lifetime of HBs decrease in confined water compared to bulk water at the same temperature. This reduction may be the origin of the reasons for the different physical properties of confined water from bulk water, such as the 40 K temperature shift.

  5. Organization of the interior of molecular capsules by hydrogen bonding.

    Science.gov (United States)

    Atwood, Jerry L; Barbour, Leonard J; Jerga, Agoston

    2002-04-16

    The enclosure of functional entities within a protective boundary is an essential feature of biological systems. On a molecular scale, free-standing capsules with an internal volume sufficiently large to house molecular species have been synthesized and studied for more than a decade. These capsules have been prepared by either covalent synthesis or self-assembly, and the internal volumes have ranged from 200 to 1,500 A(3). Although biological systems possess a remarkable degree of order within the protective boundaries, to date only steric constraints have been used to order the guests within molecular capsules. In this article we describe the synthesis and characterization of hexameric molecular capsules held together by hydrogen bonding. These capsules possess internal order of the guests brought about by hydrogen bond donors within, but not used by, the framework of the capsule. The basic building blocks of the hexameric capsules are tetrameric macrocycles related to resorcin[4]arenes and pyrogallol[4]arenes. The former contain four 1,3-dihydroxybenzene rings bridged together by -CHR- units, whereas the latter contain four 1,2,3-trihydroxybenzene rings bridged together. We now report the synthesis of related mixed macrocycles, and the main focus is on the macrocycle composed of three 1,2,3-trihydroxybenzene rings and one 1,3-dihydroxybenzene ring bridged together. The mixed macrocycles self-assemble from a mixture of closely related compounds to form the hexameric capsule with internally ordered guests. PMID:11943875

  6. Friction and Hydration Repulsion Between Hydrogen-Bonding Surfaces

    Science.gov (United States)

    Netz, Roland

    2012-02-01

    The dynamics and statics of polar surfaces are governed by the hydrogen-bonding network and the interfacial water layer properties. Insight can be gained from all-atomistic simulations with explicit water that reach the experimentally relevant length and time scales. Two connected lines of work will be discussed: 1) On surfaces, the friction coefficient of bound peptides is very low on hydrophobic substrates, which is traced back to the presence of a depletion layer between substrate and water that forms a lubrication layer. Conversely, friction forces on hydrophilic substrates are large. A general friction law is presented and describes the dynamics of hydrogen-bonded matter in the viscous limit. 2) The so-called hydration repulsion between polar surfaces in water is studied using a novel simulation technique that allows to efficiently determine the interaction pressure at constant water chemical potential. The hydration repulsion is shown to be caused by a mixture of water polarization effects and the desorption of interfacial water.

  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. Intramolecular hydrogen-bonding studies by NMR spectroscopy

    CERN Document Server

    Cantalapiedra, N A

    2000-01-01

    o-methoxybenzamide and N-methyl-o-methylbenzamide, using the pseudo-contact shifts calculated from the sup 1 H and sup 1 sup 3 C NMR spectra. The main conformation present in solution for o-fluorobenzamide was the one held by an intramolecular N-H...F hydrogen bond. Ab-initio calculations (at the RHF/6-31G* level) have provided additional data for the geometry of the individual molecules. A conformational equilibrium study of some nipecotic acid derivatives (3-substituted piperidines: CO sub 2 H, CO sub 2 Et, CONH sub 2 , CONHMe, CONEt sub 2) and cis-1,3-disubstituted cyclohexane derivatives (NHCOMe/CO sub 2 Me, NHCOMe/CONHMe, NH sub 2 /CO sub 2 H) has been undertaken in a variety of solvents, in order to predict the intramolecular hydrogen-bonding energies involved in the systems. The conformer populations were obtained by direct integration of proton peaks corresponding to the equatorial and axial conformations at low temperature (-80 deg), and by geometrically dependent coupling constants ( sup 3 J sub H s...

  9. Hydrogen bonded complexes of cyanuric acid with pyridine and guanidinium carbonate

    Indian Academy of Sciences (India)

    K Sivashankar

    2000-12-01

    Hydrogen bonded complexes of cyanuric acid (CA) with pyridine, [C3N3H3O3:C5H5N], 1, and guanidinium carbonate [C3H2N3][C(NH2)3], 2, have been prepared at room temperature and characterized by single-crystal X-ray diffraction. Structure of 1 shows pyridine molecules substituting the inter-tape hydrogen bond in CA by N-H…N and C-H…O hydrogen bonds. The structure reveals CA-pyridine hydrogen-bonded single helices held together by dimeric N-H…O hydrogen bonding between CA molecules. In 2, the CA tapes, resembling a sine wave interact with the guanidinium cations through N-H…O and N-H…N hydrogen bonds forming guanidinium cyanurate sheets.

  10. Hydrogen bonding in oxalic acid and its complexes: A database study of neutron structures

    Indian Academy of Sciences (India)

    R Chitra; Amit Das; R R Choudhury; M Ramanadham; R Chidambaram

    2004-08-01

    The basic result of carboxylic group that the oxygen atom of the –OH never seems to be a hydrogen bond acceptor is violated in the cases, namely urea oxalic acid and bis urea oxalic acid complexes, where the hydroxyl oxygen atom is an acceptor of a weak N–H... O hydrogen bond. The parameters of this hydrogen bond, respectively in these structures are: hydrogen acceptor distance 2.110 Å and 2.127 Å and the bending angle at hydrogen, 165.6° and 165.8°. The bond strength around the hydroxyl oxygen is close to 1.91 valence units, indicating that it has hardly any strength left to form hydrogen bonds. These two structures being highly planar, force the formation of this hydrogen bond. As oxalic acid is the common moiety, the structures of the two polymorphs, -oxalic acid and -oxalic acid, also were looked into in terms of hydrogen bonding and packing.

  11. 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.

  12. Covalent features in the hydrogen bond of a water dimer: molecular orbital analysis

    OpenAIRE

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

    2015-01-01

    The covalent-like characteristics of hydrogen bonds offer a new perspective on intermolecular interactions. Here, using density functional theory and post-Hartree-Fock methods, we reveal that there are two bonding molecular orbitals (MOs) crossing the O and H atoms of the hydrogen-bond in water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. These results illustrate the covalent-like character of the hydrogen bond between water molecules, w...

  13. Enhanced photoinduced birefringence in polymer-dye complexes: Hydrogen bonding makes a difference

    OpenAIRE

    Priimagi, Arri; Kaivola, Matti; Rodriguez, Francisco J.; Kauranen, Martti

    2007-01-01

    The authors demonstrate that photoinduced birefringence in azo-dye-doped polymers is strongly enhanced by hydrogen bonding between the guest molecules and the polymer host. The primary mechanism behind the enhancement is the possibility to use high dye doping levels compared to conventional guest-host systems because dye aggregation is restrained by hydrogen bonding. Moreover, hydrogen bonding reduces the mobility of the guest molecules in the polymer host leading to a larger fraction of the ...

  14. An improved hydrogen bond potential: Impact on medium resolution protein structures

    OpenAIRE

    Fabiola, Felcy; Bertram, Richard; Korostelev, Andrei; Chapman, Michael S.

    2002-01-01

    A new semi-empirical force field has been developed to describe hydrogen-bonding interactions with a directional component. The hydrogen bond potential supports two alternative target angles, motivated by the observation that carbonyl hydrogen bond acceptor angles have a bimodal distribution. It has been implemented as a module for a macromolecular refinement package to be combined with other force field terms in the stereochemically restrained refinement of macromolecules. The parameters for...

  15. Evidence of Hydrogen Bonding in Chloroform and Polyacrylates from NMR Measurements

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The presence of hydrogen bonding in chloroform and polyacrylate mixtures was demonstrated by observation of 1H- and 13C-NMR chemical shifts. Comparison of the nuclear magnetic resonance (NMR) chemical shift in polymer solutions with their low molecular mass analogues showed the effect of steric hindrance on hydrogen bonding. This initial investigation is helpful for understanding the intermolecular interaction in relatively weak hydrogen bonding polymer solutions.

  16. Hydrogen-Bonding Liquids at Mineral Surfaces: From Fundamentals to Applications

    OpenAIRE

    Phan, A. T. V.

    2016-01-01

    Molecular-level understanding of properties of hydrogen-bonding liquids and their mixtures at solid-liquid interfaces plays a significant role in several applications including membrane-based separations, shale gas production, etc. Liquid water and ethanol are common hydrogen-bonding fluids. All-atom equilibrium molecular dynamics simulations were employed to gain insights regarding the structure and dynamics of these hydrogen-bonding liquids on various free-standing solid surfaces. Models fo...

  17. Weak C–H…O hydrogen bonds in alkaloids: An overview

    Indian Academy of Sciences (India)

    Rajnikant; Dinesh; Kamni

    2005-06-01

    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 those alkaloids whose three-dimensional structure has been reported by us. The C–H…O hydrogen bonding in the solid state in alkaloids has been found to be predominant and this observation makes the role of hydrogen bonding in organic molecular assemblies very important.

  18. A new method for quick predicting the strength of intermolecular hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    A new method is proposed to quick predict the strength of intermolecular hydrogen bonds.The method is employed to produce the hydrogen-bonding potential energy curves of twenty-nine hydro-gen-bonded dimers.The calculation results show that the hydrogen-bonding potential energy curves obtained from this method are in good agreement with those obtained from MP2/6-31+G calculations by including the BSSE correction,which demonstrate that the method proposed in this work can be used to calculate the hydrogen-bonding interactions in peptides.

  19. Estimation of Intramolecular Hydrogen-bonding Energy via the Substitution Method

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The intramolecular hydrogen-bonding energies for eighteen molecules were calculated based on the substitution method, and compared with those predicted by the cis-trans method.The energy values obtained from two methods are close to each other with a correlation coefficient of 0.96.Furthermore, the hydrogen-bonding energies based on the substitution method are consistent with the geometrical features of intramolecular hydrogen bonds.Both of them demonstrate that the substitution method is capable of providing a good estimation of intramolecular hydrogen-bonding energy.

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

    International Nuclear Information System (INIS)

    Density functional calculations with Becke's three parameter hybrid method using the correlation functional of Lee, Yang and Parr (B3LYP) were carried out for 3,3'-benzylidenebis(4-hydroxycoumarin) (phenyldicoumarol, PhDC), 3,3'-methylenebis(4-hydroxycoumarin) (dicoumarol, DC) and the parent compound, 4-hydroxycoumarin (4-HC). Different basis sets were tested in the course of the calculations: 6-31G*, 6-31+G** and 6-311G*. In full agreement with available X-ray data, B3LYP/6-31G* calculations of the lowest-energy conformer, PhDC showed two O-H···O asymmetrical intramolecular hydrogen bonds with O···O distances 2.638 and 2.696 A. The HB energies in PhDC were estimated of -55.46 and -52.32 kJ/mol, respectively. The values obtained correlated with the calculated and experimental O···O distances and predicted difference in the hydrogen bonding strengths in PhDC. The total HB energy in PhDC was calculated of -107.73 kJ/mol. At the same level of theory, both O···O intramolecular distances in DC were calculated identical (2.696 A) and thus two symmetrical hydrogen bondings were obtained. The single HB strength was estimated of -50.89 kJ/mol and the total one of -101.79 kJ/mol. The electron density (ρb) and Laplacian (∇2ρb) properties, estimated by AIM calculations, showed that both O···H bonds have low ρb and positive ∇2ρb values (consistent with electrostatic character of the HBs), whereas both O-H bonds have covalent character (∇2ρb-1) in comparison with that obtained for the second O-H which forms the weaker HB in PhDC (-559 cm-1)

  1. Hydrogen bonds of anti-HIV active aminophenols

    Science.gov (United States)

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

    2011-05-01

    Analysis of IR-Fourier spectra from solutions and crystals of antiviral sulfo-containing aminophenols has shown that various types of intramolecular and intermolecular interactions can occur in molecules of these compounds. Three types of intramolecular hydrogen bonds (O-HṡṡṡN, O-HṡṡṡO=S=O, and N-HṡṡṡO=S=O) are formed in CCl4 solutions of the sulfo-containing aminophenols. The formation of intermolecular H-bonds involving the NH- and OH-groups and the preservation of the intramolecular O-HṡṡṡO=S=O H-bond are characteristic of the anti-HIV active aminophenol crystals. Spectral attributes are determined in order to distinguish between the anti-HIV active and inactive sulfo-containing aminophenols.

  2. Intramolecular hydrogen bonds in sulfur-containing aminophenols

    Science.gov (United States)

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

    2010-07-01

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

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

    Science.gov (United States)

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

    2016-04-01

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

  4. Proton irradiation effect on hydrogen bond material and biological systems

    International Nuclear Information System (INIS)

    When the proton beam was irradiated on partially deuterated KH2PO4 single crystal with fluence of 1015ions/cm3, and irradiation energy of 1.0 MeV, the ferroelectric phase transition temperature was significantly raised by 5 K. Increase of the phase transition temperature can be closely related to the structural modification involving the hydrogen-bond geometry, demonstrating that proton irradiation can be adopted as a powerful means of atomic-scale modification of the microscopic structures in hydrogen-bonded ferroelectrics. These results have been published as 'Significant increase of the ferroelectric phase transition temperature in partially deuterated KH2PO-4 by proton irradiation'. We have studied the microscopic structure and dynamics in a proton-irradiated KH2PO4 single crystal. Our 1H and 31P nuclear magnetic resonance measurements indicate that proton irradiation gives rise to a decrease in the local dipolar order of the rigid lattice protons and an increase in interstitial protons as well as structural distortion of the PO4 tetrahedra. While the luminescence was severely weakened by the low-energy irradiation with a high dosage, it was affected only weakly by the high-energy irradiation with a low dosage. The electroluminescence was affected by the irradiation more severely than the photoluminescence was, preserving the external quantum efficiency. While the luminescence spectrum of the severely damaged polymer was broadened with a blue-shift, a weak damage resulted only in a decrease in the luminescence intensity apparently preserving the spectral shape. The change in the luminescence spectra may be explained by chain conformational disorders as well as chain scission induced by the irradiation.

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

    Science.gov (United States)

    Kondo, Makoto; Kasahara, Yasutoshi; Ishikawa, Haruki

    2015-06-01

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

  6. The quantum dynamics of proton transfer in the hydrogen bond

    International Nuclear Information System (INIS)

    The wavefunctions of particles extend beyond the classically accessible regions of potential energy surfaces. A manifestation of this partial delocalisation is the quantum mechanical tunnelling 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. NMR techniques have been employed to study the motion of hydrogen atoms in the hydrogen bond of benzoic acid, a system which has emerged as particularly suitable since proton transfer occurs in a near symmetric double minimum potential (DMP). The influence of proton tunnelling has been investigated by making direct measurements of the spectral density function from the dispersion of the spin-lattice relaxation time using field-cycling. The incoherent tunnelling rate is measured directly from the half-width of the spectral density function at low temperature and the proton transfer rate has been determined over the full range of temperature. This reveals the smooth transition between quantum and classical behaviour. The dynamics have been modelled as the behaviour of a particle in a DMP which is coupled to a bath of quantum oscillators (phonons). At high temperature an Arrhenius rate law applies whereas at low temperatures the dynamics are described by incoherent quantum tunnelling. Models that include only ground state tunnelling fail to fit the observed behaviour in the interfacial region. When tunnelling via excited states of the DMP is included then near perfect agreement with experiment is obtained. This represents the first quantitative study of the role of the excited states in the dynamics of the hydrogen bond. Additional measurements will be presented which investigate the isotope effects of the heavier atoms in the skeletal framework and the effects of hydrostatic pressure. The benefits of using single

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

    DEFF Research Database (Denmark)

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

    2004-01-01

    -proton interaction in the hydrogen bond. (ii) a harmonic coupling between the protons in adjacent hydrogen bonds, and (iii) a harmonic coupling between the nearest-neighbor heavy ions (an isolated diatomic chain with the lowest acoustic band) or instead a harmonic on-site potential for the heavy ions (a diatomic...

  8. 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…

  9. Fluorescence and picosecond laser photolysis studies on the deactivation processes of excited hydrogen bonding systems

    Science.gov (United States)

    Ikeda, Noriaka; Okada, Tadashi; Mataga, Noboru

    1980-01-01

    The fluorescence quenching reaction of 2-naphthylamine and 1-pyrenol due to hydrogen bonding interaction with pyndine has been investigated Absorption spectra due to the state formed by charge transfer from excited naphthylamine to hydrogen bonded pyridine have been observed by means of picosecond laser photolysis.

  10. Evaluation of the individual hydrogen bonding energies in N-methylacetamide chains

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The individual hydrogen bonding energies in N-methylacetamide chains were evaluated at the MP2/6-31+G** level including BSSE correction and at the B3LYP/6-311++G(3df,2pd) level including BSSE and van der Waals correction.The calculation results indicate that compared with MP2 results,B3LYP calculations without van der Waals correction underestimate the individual hydrogen bonding energies about 5.4 kJ m ol-1 for both the terminal and central hydrogen bonds,whereas B3LYP calculations with van der Waals correction produce almost the same individual hydrogen bonding energies as MP2 does for those terminal hydrogen bonds,but still underestimate the individual hydrogen bonding energies about 2.5 kJ mol-1 for the hydrogen bonds near the center.Our calculation results show that the individual hydrogen bonding energy becomes more negative (more attractive) as the chain becomes longer and that the hydrogen bonds close to the interior of the chain are stronger than those near the ends.The weakest individual hydrogen bonding energy is about-29.0 kJ m ol-1 found in the dimer,whereas with the growth of the N-methylacetamide chain the individual hydrogen bonding energy was estimated to be as large as-62.5 kJ mol-1 found in the N-methylacetamide decamer,showing that there is a significant hydrogen bond cooperative effect in N-methylacetamide chains.The natural bond orbital analysis indicates that a stronger hydrogen bond corresponds to a larger positive charge for the H atom and a larger negative charge for the O atom in the N-H···O=C bond,corresponds to a stronger second-order stabilization energy between the oxygen lone pair and the N-H antibonding orbital,and corresponds to more charge transfer between the hydrogen bonded donor and acceptor molecules.

  11. Effects of hydrogen-bond environment on single particle and pair dynamics in liquid water

    Indian Academy of Sciences (India)

    Amalendu Chandra; Snehasis Chowdhuri

    2001-10-01

    We have performed molecular dynamics simulations of liquid water at 298 and 258 K to investigate the effects of hydrogen-bond environment on various single-particle and pair dynamical properties of water molecules at ambient and supercooled conditions. The water molecules are modelled by the extended simple point charge (SPC/E) model. We first calculate the distribution of hydrogen-bond environment in liquid water at both temperatures and then investigate how the selfdiffusion and orientational relaxation of a single water molecule and also the relative diffusion and relaxation of the hydrogen-bond of a water pair depend on the nature of the hydrogen-bond environment of the tagged molecules. We find that the various dynamical quantities depend significantly on the hydrogen-bond environment, especially at the supercooled temperature. The present study provides a molecular-level insight into the dynamics of liquid water under ambient and supercooled conditions.

  12. Pyrrolic Amide: A New Hydrogen Bond Building Block for Self-assembly

    Institute of Scientific and Technical Information of China (English)

    YIN Zhen-Ming; LI Jian-Feng; HE Jia-Qi; ZHU Xiao-Qing; CHENG Jin-Pei

    2003-01-01

    @@ Molecular self-assembly has emerged as a powerful technology for the synthesis of nanostructured materials. In design of various molecular assemblies, hydrogen bonding is a preferably selected intra- or inter-molecular weak interaction in recent research by virtue of the directionality and specificity. The research for novel hydrogen bond building blocks that self-assembly into well defined structures is great important not only for gaining an understanding of the concepts of self-assembly but also for the design of new molecular materials. Pyrrolic amide moiety has one hydrogen bond acceptor (C =O) and two hydrogen bond donors (pyrrole NH and amide NH). By deliberately design, pyrrolic amide compounds would be new kinds hydrogen bond building blocks. So, pyrrolic amide compounds 1 ~ 6, which bear one, two or three pyrrolic amide moieties respectively, were designed and synthesized.

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

    Science.gov (United States)

    Hristova, Kalina; Sarabipour, Sarvenaz

    2013-03-01

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

  14. Effect of Hydrogen Bonding on Linear and Nonlinear Rheology of Entangled Polymer Melts

    DEFF Research Database (Denmark)

    Shabbir, Aamir; Goldansaz, Hadi; Hassager, Ole;

    2015-01-01

    AA along the backbone. Assuming superposition holds and subtracting out the linear chain rheology from LVE, the hydrogen bonding contribution to LVE is exposed. Hydrogen bonding affects linear viscoelasticity at frequencies below the inverse reptation time. More specifically, the presence of hydrogen...... bonds causes G′ and G″ as a function of frequency to shift to a power law scaling of 0.5. Furthermore, the magnitude of G′ and G″ scales linearly with the number of hydrogen-bonding groups. The nonlinear extensional rheology shows extreme strain hardening. The magnitude of extensional stress has a...... strongly nonlinear dependence on the number of hydrogenbonding groups. These results are aimed at uncovering the molecular influence of hydrogen bonding on linear and nonlinear rheology to aid future molecular synthesis and model development....

  15. A femtosecond midinfrared pump-probe study of hydrogen-bonding in ethanol

    Science.gov (United States)

    Woutersen, S.; Emmerichs, U.; Bakker, H. J.

    1997-08-01

    We present a femtosecond midinfrared pump-probe study of hydrogen bonding. It is shown that upon excitation of the OH-stretching vibration of hydrogen-bonded ethanol dissolved in CCl4, the hydrogen bonds are predissociated on a femtosecond time scale. The measured predissociation time constant depends strongly on the excitation frequency, and ranged from ˜250 fs at 3330 cm-1 to ˜900 fs at 3450 cm-1. The time constant of the subsequent reassociation of the hydrogen bonds was found to be 15 ps, in accordance with previous picosecond studies. Furthermore, polarization-resolved measurements show that orientational relaxation takes place on a time scale much shorter than the pulse length of ˜200 fs. This rapid orientational relaxation can be explained from the fast delocalization of the O-H stretching excitation over the hydrogen-bonded ethanol oligomers. The orientational anisotropy R reaches a value of 0.15 instantaneously, and remains constant for all delays.

  16. Molecular assembly of highly symmetric molecules under a hydrogen bond framework controlled by alkyl building blocks: a simple approach to fine-tune nanoscale structures.

    Science.gov (United States)

    Tanphibal, Pimsai; Tashiro, Kohji; Chirachanchai, Suwabun

    2016-01-14

    To date, molecular assemblies under the contribution of hydrogen bond in combination with weak interactions and their consequent morphologies have been variously reported; however, how the systematic variation of the structure can fine-tune the morphologies has not yet been answered. The present work finds an answer through highly symmetric molecules, i.e. diamine-based benzoxazine dimers. This type of molecule develops unique molecular assemblies with their networks formed by hydrogen bonds at the terminal, while, at the same time, their hydrogen bonded frameworks are further controlled by the hydrophobic segment at the center of the molecule. When this happens, slight differences in hydrophobic alkyl chain lengths (, , and ) bring a significant change to the molecular assemblies, thus resulting in tunable morphologies, i.e. spheres, needles and dendrites. The superimposition between the crystal lattice obtained from X-ray single crystal analysis and the electron diffraction pattern obtained from transmission electron microscopy allows us to identify the molecular alignment from single molecules to self-assembly until the morphologies developed. The present work, for the first time, shows the case of symmetric molecules, where the hydrophobic building block controls the hydrogen bond patterns, leading to the variation of molecular assemblies with tunable morphologies. PMID:26482133

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

    Science.gov (United States)

    Smedley, Sarah Black

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

  18. Strong and weak hydrogen bonds in drug–DNA complexes: A statistical analysis

    Indian Academy of Sciences (India)

    Sunil K Panigrahi; Gautam R Desiraju

    2007-06-01

    A statistical analysis of strong and weak hydrogen bonds in the minor groove of DNA was carried out for a set of 70 drug–DNA complexes. The terms `strong’ and `weak’ pertain to the inherent strengths and weakness of the donor and acceptor fragments rather than to any energy considerations. 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 recognition. On an average, there are 1.4 weak hydrogen bonds for every strong hydrogen bond. For both categories of interaction, the N(3) of purine and the O(2) of pyrimidine are favoured acceptors. Donor multifurcation is common with the donors generally present in the drug molecules, and shared by hydrogen bond acceptors in the minor groove. Bifurcation and trifurcation are most commonly observed. The metrics for strong hydrogen bonds are consistent with established trends. The geometries are variable for weak hydrogen bonds. A database of recognition geometries for 26 literature amidinium-based inhibitors of Human African Trypanosomes (HAT) was generated with a docking study using seven inhibitors which occur in published crystal structures included in the list of 70 complexes mentioned above, and 19 inhibitors for which the drug–DNA complex crystal structures are unknown. The virtual geometries so generated correlate well with published activities for these 26 inhibitors, justifying our assumption that strong and weak hydrogen bonds are optimized in the active site.

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

    Science.gov (United States)

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

    2011-04-01

    We have investigated the dynamics of the hydrogen bonds that connect the components of a [2]rotaxane in solution. In this rotaxane, the amide groups in the benzylic-amide macrocycle and the succinamide thread are connected by four equivalent N-H⋅⋅⋅O=C hydrogen bonds. The fluctuations of these hydrogen bonds are mirrored by the frequency fluctuations of the NH-stretch modes, which are probed by means of three-pulse photon-echo peak shift spectroscopy. The hydrogen-bond fluctuations occur on three different time scales, with time constants of 0.1, 0.6, and ≥200 ps. Comparing these three time scales to the ones found in liquid formamide, which contains the same hydrogen-bonded amide motif but without mechanical constraints, we find that the faster two components, which are associated with small-amplitude fluctuations in the strength of the N-H⋅⋅⋅O=C hydrogen bonds, are very similar in the liquid and the rotaxane. However, the third component, which is associated with the breaking and subsequent reformation of hydrogen bonds, is found to be much slower in the rotaxane than in the liquid. It can be concluded that the mechanical bonding in a rotaxane does not influence the amplitude and time scale of the small-amplitude fluctuations of the hydrogen bonds, but strongly slows down the complete dissociation of these hydrogen bonds. This is probably because in a rotaxane breaking of the macrocycle-axle contacts is severely hindered by the mechanical constraints. The hydrogen-bond dynamics in rotaxane-based molecular machines can therefore be regarded as liquidlike on a time scale 1 ps and less, but structurally frozen on longer (up to at least 200 ps) time scales. PMID:21476761

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

    Science.gov (United States)

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

    2011-04-01

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

  1. Statistical theory for hydrogen bonding fluid system of AaDd type (Ⅲ): Equation of state and fluctuations

    Institute of Scientific and Technical Information of China (English)

    WANG HaiJun; GU Fang; HONG XiaoZhong; BA XinWu

    2007-01-01

    The equation of the state of the hydrogen bonding fluid system of AaDd type is studied by the principle of statistical mechanics. The influences of hydrogen bonds on the equation of state of the system are obtained based on the change in volume due to hydrogen bonds. Moreover, the number density fluctuations of both molecules and hydrogen bonds as well as their spatial correlation property are investigated. Furthermore, an equation describing relation between the number density correlation function of "molecules-hydrogen bonds" and that of molecules and hydrogen bonds is derived. As application,taking the van der Waals hydrogen bonding fluid as an example, we considered the effect of hydrogen bonds on its relevant statistical properties.

  2. Effect of quantum nuclear motion on hydrogen bonding

    CERN Document Server

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

    2014-01-01

    This work considers how the properties of hydrogen bonded complexes, D-H....A, 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 (D) and acceptor (A) 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 A, i.e., from strong to weak bonds. The position of the proton and its longitudinal vibrational frequency, along with the isotope effects in both are discussed. An analysis of the secondary geometric isotope effects, 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 the b...

  3. Do cooperative cycles of hydrogen bonding exist in proteins?

    CERN Document Server

    Sharley, John N

    2016-01-01

    The closure of cooperative chains of Hydrogen Bonding, HB, to form cycles can enhance cooperativity. Cycles of charge transfer can balance charge into and out of every site, eliminating the charge build-up that limits the cooperativity of open unidirectional chains of cooperativity. If cycles of cooperative HB exist in proteins, these could be expected to be significant in protein structure and function in ways described below. We investigate whether cooperative HB cycles not traversing solvent, ligand or modified residues occur in protein by means including search of Nuclear Magnetic Resonance spectroscopy entries of the Protein Data Bank. We find no mention of an example of this kind of cycle in the literature. For amide-amide HB, for direct inter-amide interactions, when the energy associated with Natural Bond Orbital, NBO, steric exchange is deducted from that of NBO donor-acceptor interactions, the result is close to zero, so that HB is not primarily due to the sum of direct inter-amide NBO interactions....

  4. Effect of hydrogen bonding on infrared absorption intensity

    CERN Document Server

    Athokpam, Bijyalaxmi; McKenzie, Ross H

    2016-01-01

    We consider how the infrared intensity of an O-H stretch in a hydrogen bonded complex varies as the strength of the H-bond varies from weak to strong. We obtain trends for the fundamental and overtone transitions as a function of donor-acceptor distance R, which is a common measure of H-bond strength. Our calculations use a simple two-diabatic state model that permits symmetric and asymmetric bonds, i.e. where the proton affinity of the donor and acceptor are equal and unequal, respectively. The dipole moment function uses a Mecke form for the free OH dipole moment, associated with the diabatic states. The transition dipole moment is calculated using one-dimensional vibrational eigenstates associated with the H-atom transfer coordinate on the ground state adiabatic surface of our model. Over 20-fold intensity enhancements for the fundamental are found for strong H-bonds, where there are significant non-Condon effects. The isotope effect on the intensity yields a non-monotonic H/D intensity ratio as a function...

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

    Science.gov (United States)

    Baranović, Goran; Biliškov, Nikola; Vojta, Danijela

    2012-08-16

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

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

    Science.gov (United States)

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

    2016-05-01

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

  7. Two-dimensional interlocked pentagonal bilayer ice: how do water molecules form a hydrogen bonding network?

    Science.gov (United States)

    Zhu, Weiduo; Zhao, Wen-Hui; Wang, Lu; Yin, Di; Jia, Min; Yang, Jinlong; Zeng, Xiao Cheng; Yuan, Lan-Feng

    2016-06-01

    The plethora of ice structures observed both in bulk and under nanoscale confinement reflects the extraordinary ability of water molecules to form diverse forms of hydrogen bonding networks. An ideal hydrogen bonding network of water should satisfy three requirements: (1) four hydrogen bonds connected with every water molecule, (2) nearly linear hydrogen bonds, and (3) tetrahedral configuration for the four hydrogen bonds around an O atom. However, under nanoscale confinement, some of the three requirements have to be unmet, and the selection of the specific requirement(s) leads to different types of hydrogen bonding structures. According to molecular dynamics (MD) simulations for water confined between two smooth hydrophobic walls, we obtain a phase diagram of three two-dimensional (2D) crystalline structures and a bilayer liquid. A new 2D bilayer ice is found and named the interlocked pentagonal bilayer ice (IPBI), because its side view comprises interlocked pentagonal channels. The basic motif in the top view of IPBI is a large hexagon composed of four small pentagons, resembling the top view of a previously reported "coffin" bilayer ice [Johnston, et al., J. Chem. Phys., 2010, 133, 154516]. First-principles optimizations suggest that both bilayer ices are stable. However, there are fundamental differences between the two bilayer structures due to the difference in the selection among the three requirements. The IPBI sacrifices the linearity of hydrogen bonds to retain locally tetrahedral configurations of the hydrogen bonds, whereas the coffin structure does the opposite. The tradeoff between the conditions of an ideal hydrogen bonding network can serve as a generic guidance to understand the rich phase behaviors of nanoconfined water. PMID:27063210

  8. 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.

  9. Covalent features in the hydrogen bond of a water dimer: molecular orbital analysis

    CERN Document Server

    Wang, Bo; Dai, Xing; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin

    2015-01-01

    The covalent-like characteristics of hydrogen bonds offer a new perspective on intermolecular interactions. Here, using density functional theory and post-Hartree-Fock methods, we reveal that there are two bonding molecular orbitals (MOs) crossing the O and H atoms of the hydrogen-bond in water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. These results illustrate the covalent-like character of the hydrogen bond between water molecules, which contributes to the essential understanding of ice, liquid water, related materials, and life sciences.

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

    Science.gov (United States)

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

    2016-04-21

    Dicarboxylic acids represent an important class of water-soluble organic compounds found in the atmosphere. In this work we are studying properties of dicarboxylic acid homodimer complexes (HO2C(CH2)nCO2(-)[HO2C(CH2)nCO2H], n = 0-12), as potentially important intermediates in aerosol formation processes. Our approach is based on experimental data from negative ion photoelectron spectra of the dimer complexes combined with updated measurements of the corresponding monomer species. These results are analyzed with quantum-mechanical calculations, which provide further information about equilibrium structures, thermochemical parameters associated with the complex formation, and evaporation rates. We find that upon formation of the dimer complexes the electron binding energies increase by 1.3-1.7 eV (30.0-39.2 kcal/mol), indicating increased stability of the dimerized complexes. Calculations indicate that these dimer complexes are characterized by the presence of strong intermolecular hydrogen bonds with high binding energies and are thermodynamically favorable to form with low evaporation rates. Comparison with the previously studied HSO4(-)[HO2C(CH2)2CO2H] complex (J. Phys. Chem. Lett. 2013, 4, 779-785) shows that HO2C(CH2)2CO2(-)[HO2C(CH2)2CO2H] has very similar thermochemical properties. These results imply that dicarboxylic acids not only can contribute to the heterogeneous complexes formation involving sulfuric acid and dicarboxylic acids but also can promote the formation of homogeneous complexes by involving dicarboxylic acids themselves. PMID:27032015

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

    Science.gov (United States)

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

    2014-12-01

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

  12. Hydrogen bond networks: Structure and dynamics via first-principles spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Schiffmann, Christoph; Sebastiani, Daniel [Department of Physics, Dahlem Center for Complex Quantum Systems, Free University Berlin (Germany)

    2012-02-15

    Different hydrogen bonding networks, same principle: hydrogen bonds are the most common fundamental structural driving forces, which determine structural and dynamical properties of numerous functional materials. First-principles calculations of spectroscopic parameters can help to understand local geometric motifs, but also more complex processes such as hydrogen bond lifetimes and ion transport processes in condensed phases. In this feature article, we review the relevance of structure-spectroscopy-relationships, we discuss recent ab initio calculations eludicating the structure of supramolecular assemblies, and highlight the importance of incorporating atomic and molecular mobility by means of molecular dynamics (MD) simulations. Complex hydrogen bonding networks: vinyl-phosphonic acid polymers (left) and aqueous hydrochloric acid (right). (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  13. A DFT Study on Intramolecular Hydrogen Bond in Substituted Catechols and Their Radicals

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Density functional theory (DFT) at B3LYP/6-31G(d,p) level was employed to calculate intramolecular hydrogen bond enthalpies (HIHB), O-H charge differences, O-H bond lengths and bond orders for various substituted catechols and their radicals generated after H-abstraction. It was found that although the charge difference between hydrogen-bonded H and O played a role in determining HIHB, HIHB was mainly governed by the hydrogen bond length. As the oxygen-centered radical has great tendency to form a chemical bond with the H atom, hydrogen bond lengths in catecholic radicals are systematically shorter than those in catechols. Hence, the HIHB for the former are higher than those for the latter.

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

    DEFF Research Database (Denmark)

    Hansen, Poul Erik

    2015-01-01

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

  15. Theoretical Chemistry Study of the Hydrogen-bonded Interaction between Acylamine and Chloromethane Compounds

    Institute of Scientific and Technical Information of China (English)

    GE Qing-Yu; WANG Hai-Jun; CHEN Jian-Hua

    2005-01-01

    The hydrogen-bonded interaction between acylamine and chloromethane was studied using theoretical calculation methods. Looking the interaction system as a hydrogen-bonded complex, the geometric optimization of the interaction system was performed with HF and B3LYP methods at 6-311++G** level. Stable structures of these complexes were obtained. Binding energies and some other physical chemistry parameters of them were computed and compared. According to the calculation results, it can be identified that DMA (DMF or DEF) can form stable complex with chloromethane by the hydrogen-bonded interaction between them. The stable orders of these hydrogen-bonded complexes were obtained and described as: DMF-CHCl3>DMF-CH2Cl2>DMF-CH3Cl, DEF-CHCl3>DEF-CH2Cl2>DEF-CH3Cl, DMA-CHCl3>DMA-CH2Cl2>DMA-CH3Cl, respectively.

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

    Science.gov (United States)

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

    2016-01-01

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

  17. Nuclear quantum effects of hydrogen bonds probed by tip-enhanced inelastic electron tunneling.

    Science.gov (United States)

    Guo, Jing; Lü, Jing-Tao; Feng, Yexin; Chen, Ji; Peng, Jinbo; Lin, Zeren; Meng, Xiangzhi; Wang, Zhichang; Li, Xin-Zheng; Wang, En-Ge; Jiang, Ying

    2016-04-15

    We report the quantitative assessment of nuclear quantum effects on the strength of a single hydrogen bond formed at a water-salt interface, using tip-enhanced inelastic electron tunneling spectroscopy based on a scanning tunneling microscope. The inelastic scattering cross section was resonantly enhanced by "gating" the frontier orbitals of water via a chlorine-terminated tip, so the hydrogen-bonding strength can be determined with high accuracy from the red shift in the oxygen-hydrogen stretching frequency of water. Isotopic substitution experiments combined with quantum simulations reveal that the anharmonic quantum fluctuations of hydrogen nuclei weaken the weak hydrogen bonds and strengthen the relatively strong ones. However, this trend can be completely reversed when a hydrogen bond is strongly coupled to the polar atomic sites of the surface. PMID:27081066

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

    Science.gov (United States)

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

    2014-09-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-05-01

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

  20. Reorientational motion and hydrogen-bond stretching dynamics in liquid water

    Science.gov (United States)

    Bakker, H. J.; Woutersen, S.; Nienhuys, H.-K.

    2000-08-01

    The reorientational motion of the molecules in liquid water is investigated by measuring the anisotropy decay of the O-H stretching mode of HDO dissolved in D 2O using femtosecond mid-infrared pump-probe spectroscopy. We observe that the anisotropy shows a non-exponential decay with an initial fast component of which the amplitude increases with increasing lengths of the O-H⋯O hydrogen bond. The experimental results can be accurately described with a model in which the dependence of the reorientation rate on the hydrogen-bond length and the stochastic modulation of this length are accounted for. It is found that the O-H group of a water molecule can only reorient after the O-H⋯O hydrogen bond has sufficiently lengthened. As a result, the effective rate of reorientation of the molecules in liquid water is determined by the rate at which the length of the hydrogen bonds is modulated.

  1. Quantum delocalization of protons in the hydrogen bond network of an enzyme active site

    CERN Document Server

    Wang, Lu; Boxer, Steven G; Markland, Thomas E

    2015-01-01

    Enzymes utilize protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.

  2. A database study of intermolecular NH...O hydrogen bonds for carboxylates, sulfonates and monohydrogen phosphonates

    International Nuclear Information System (INIS)

    A search of the Cambridge Structural Database (CSD, version 5.05, 1993) was performed in order to compare the geometrical features of the hydrogen bonds involving on the one hand amino groups and on the other hand carboxylates, sulfonates or monohydrogen phosponates. Phosphonates were not considered because only four entries containing amino and phosphonate moieities were located in the CSD. The hydroxylic group of monohydrogen phosphonates primarily acts as a hydrogen-bond donor. The three moieties under study show NH..O hydrogen bonds with similar geometrical features. This statistical analysis has focused on the hydrogen-bond distances and angles and on the distributions of the H atoms around the acceptor O atoms of carboxylates, sulfonates or monohydrogen phosphonates. (orig.)

  3. 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.

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

    International Nuclear Information System (INIS)

    The short hydrogen bonds in rhamnogalacturonan acetylesterase have been investigated by structure determination of an active-site mutant, 1H 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.) 1H NMR signal. An extremely low-field signal (at approximately 18 p.p.m.) in the 1H 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 1H 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 pKa 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 all

  5. Cocrystals of the antibiotic trimethoprim with glutarimide and 3,3-dimethylglutarimide held together by three hydrogen bonds.

    Science.gov (United States)

    Ton, Quoc Cuong; Egert, Ernst

    2015-01-01

    The antibiotic trimethoprim [5-(3,4,5-trimethoxybenzyl)pyrimidine-2,4-diamine] was cocrystallized with glutarimide (piperidine-2,6-dione) and its 3,3-dimethyl derivative (4,4-dimethylpiperidine-2,6-dione). The cocrystals, viz. trimethoprim-glutarimide (1/1), C14H18N4O3·C5H7NO2, (I), and trimethoprim-3,3-dimethylglutarimide (1/1), C14H18N4O3·C7H11NO2, (II), are held together by three neighbouring hydrogen bonds (one central N-H...N and two N-H...O) between the pyrimidine ring of trimethoprim and the imide group of glutarimide, with an ADA/DAD pattern (A = acceptor and D = donor). These heterodimers resemble two known cocrystals of trimethoprim with barbituric acid and its 5,5-diethyl derivative. Trimethoprim shows a conformation in which the planes of the pyrimidine and benzene rings are approximately perpendicular to one another. In its glutarimide coformer, five of the six ring atoms lie in a common plane; the C atom opposite the N atom deviates by about 0.6 Å. The crystal packing of each of the two cocrystals is characterized by an extended network of hydrogen bonds and contains centrosymmetrically related trimethoprim homodimers formed by a pair of N-H...N hydrogen bonds. This structural motif occurs in five of the nine published crystal structures in which neutral trimethoprim is present. PMID:25567580

  6. Statistical theory for hydrogen bonding fluid system of AaDd type (I): The geometrical phase transition

    Institute of Scientific and Technical Information of China (English)

    WANG Haijun; HONG Xiaozhong; GU Fang; BA Xinwu

    2006-01-01

    The influence of hydrogen bonds on the physical and chemical properties of hydrogen bonding fluid system of AaDd type is investigated from two viewpoints by the principle of statistical mechanics. In detail, we proposed two new ways that can be used to obtain the equilibrium size distribution of the hydrogen bonding clusters, and derived the analytical expression of a relationship between the hydrogen bonding free energy and hydrogen bonding degree. For the nonlinear hydrogen bonding systems, it is shown that the sol-gel phase transition can take place under proper conditions, which is further proven to be a kind of geometrical phase transition rather than a thermodynamic one. Moreover, several problems associated with the geometrical phase transition and liquid-solid phase transition in nonlinear hydrogen bonding systems are discussed.

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

    OpenAIRE

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

    2008-01-01

    Hydrogen bonds stabilize and direct chemistry performed by metalloenzymes. With inspiration from enzymes, we will utilize an approach that incorporates intramolecular hydrogen bond donors to determine their effects on the stability and reactivity of metal complexes. Our premise is that control of secondary coordination sphere interactions will promote new function in synthetic metal complexes. Multidentate ligands have been developed that create rigid organic structures around metal ions. The...

  8. Vibrational Energies of the Hydrogen Bonds of H_3O_2^- and H_5O_2^+

    OpenAIRE

    Gamble, Stephanie Nicole

    2016-01-01

    We approximate the vibrational energies of the symmetric and asymmetric stretches of the hydrogen bonds of the molecules H_3O_2^- and H_5O_2^+ by applying an improvement to the standard time-independent Born-Oppenheimer approximation. These two molecules are symmetric around a central hydrogen which participates in hydrogen bonding. Unlike the standard Born-Oppenheimer approximation, this approximation appropriately scales the hydrogen nuclei differently than the heavier oxygen nuclei. This r...

  9. Isolation of Cellulose Nanofibers: Effect of Biotreatment on Hydrogen Bonding Network in Wood Fibers

    OpenAIRE

    Sreekumar Janardhnan; Mohini Sain

    2011-01-01

    The use of cellulose nanofibres as high-strength reinforcement in nano-biocomposites is very enthusiastically being explored due to their biodegradability, renewability, and high specific strength properties. Cellulose, through a regular network of inter- and intramolecular hydrogen bonds, is organized into perfect stereoregular configuration called microfibrils which further aggregate to different levels to form the fibre. Intermolecular hydrogen bonding at various levels, especially at the ...

  10. Effects of hydrogen bonding on supercooled liquid dynamics and the implications for supercooled water

    OpenAIRE

    Mattsson, Johan; Bergman, Rikard; Jacobsson, Per; Börjesson, Lars

    2008-01-01

    The supercooled state of bulk water is largely hidden by unavoidable crystallization, which creates an experimentally inaccessible temperature regime - a 'no man's land'. We address this and circumvent the crystallization problem by systematically studying the supercooled dynamics of hydrogen bonded oligomeric liquids (glycols), where water corresponds to the chain-ends alone. This novel approach permits a 'dilution of water' by altering the hydrogen bond concentration via variations in chain...

  11. Effect of temperature and glycerol on the hydrogen-bond dynamics of water

    OpenAIRE

    GhattyVenkataKrishna, Pavan K.; Uberbacher, Edward C.

    2015-01-01

    The effect of glycerol, water and glycerol-water binary mixtures on the structure and dynamics of biomolecules has been well studied. However, a lot remains to be learned about the effect of varying glycerol concentration and temperature on the dynamics of water. We have studied the effect of concentration and temperature on the hydrogen bonded network formed by water molecules. A strong correlation between the relaxation time of the network and average number of hydrogen bonds per water mole...

  12. Hydrogen bonds of DsrD protein revealed by neutron crystallography

    International Nuclear Information System (INIS)

    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

  13. Computational studies on supramolecular hydrogen-bonded structures: from nanocapsules to proteins

    OpenAIRE

    Santos Garcia, Eva

    2008-01-01

    of the thesis entitled: Computational studies on supramolecular hydrogen-bonded structures: from nanocapsules to proteins.In this thesis different methods were used to study several systems in which the hydrogen bond has a key role. The validity of the theoretical methods applied was always contrasted with the experimental evidences available from the group of Prof. Javier de Mendoza in the context of an intense collaboration in the Institute of Chemical Research of Catalonia (ICIQ). In certa...

  14. Experimental quantification of electrostatics in X-H···π hydrogen bonds

    OpenAIRE

    Saggu, Miguel; Levinson, Nicholas M.; Boxer, Steven G.

    2012-01-01

    Hydrogen bonds are ubiquitous in chemistry and biology. The physical forces that govern hydrogen bonding interactions have been heavily debated, with much of the discussion focused on the relative contributions of electrostatic vs. quantum mechanical effects. In principle, the vibrational Stark effect (VSE), the response of a vibrational mode to electric field, can provide an experimental method for parsing such interactions into their electrostatic and non-electrostatic components. In a prev...

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

    International Nuclear Information System (INIS)

    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)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

  16. 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.

  17. Hydrogen bonding at C=Se acceptors in selenoureas, selenoamides and selones.

    Science.gov (United States)

    Bibelayi, Dikima; Lundemba, Albert S; Allen, Frank H; Galek, Peter T A; Pradon, Juliette; Reilly, Anthony M; Groom, Colin R; Yav, Zéphyrin G

    2016-06-01

    In recent years there has been considerable interest in chalcogen and hydrogen bonding involving Se atoms, but a general understanding of their nature and behaviour has yet to emerge. In the present work, the hydrogen-bonding ability and nature of Se atoms in selenourea derivatives, selenoamides and selones has been explored using analysis of the Cambridge Structural Database and ab initio calculations. In the CSD there are 70 C=Se structures forming hydrogen bonds, all of them selenourea derivatives or selenoamides. Analysis of intramolecular geometries and ab initio partial charges show that this bonding stems from resonance-induced C(δ+)=Se(δ-) dipoles, much like hydrogen bonding to C=S acceptors. C=Se acceptors are in many respects similar to C=S acceptors, with similar vdW-normalized hydrogen-bond lengths and calculated interaction strengths. The similarity between the C=S and C=Se acceptors for hydrogen bonding should inform and guide the use of C=Se in crystal engineering. PMID:27240763

  18. Theory of tunneling across hydrogen-bonded base pairs for DNA recognition and sequencing

    Science.gov (United States)

    Lee, Myeong H.; Sankey, Otto F.

    2009-05-01

    We present the results of first-principles calculations for the electron tunnel current through hydrogen-bonded DNA base pairs and for (deoxy)nucleoside-nucleobase pairs. Electron current signals either through a base pair or through a deoxynucleoside-nucleobase pair are a potential mechanism for recognition or identification of the DNA base on a single-stranded DNA polymer. Four hydrogen-bonded complexes are considered: guanine-cytosine, diaminoadenine-thymine, adenine-thymine, and guanine-thymine. First, the electron tunneling properties are examined through their complex band structure (CBS) and the metal contact’s Fermi-level alignment. For gold contacts, the metal Fermi level lies near the highest occupied molecular orbital for all DNA base pairs. The decay constant determined by the complex band structure at the gold Fermi level shows that tunnel current decays more slowly for base pairs with three hydrogen bonds (guanine-cytosine and diaminoadenine-thymine) than for base pairs with two hydrogen bonds (adenine-thymine and guanine-thymine). The decay length and its dependence on hydrogen-bond length are examined. Second, the conductance is computed using density functional theory Green’s-function scattering methods and these results agree with estimates made from the tunneling decay constant obtained from the CBS. Changing from a base pair to a deoxynucleoside-nucleobase complex shows a significant decrease in conductance. It also becomes difficult to distinguish the current signal by only the number of hydrogen bonds.

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

    Energy Technology Data Exchange (ETDEWEB)

    Sarma, Rahul [Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati 781 039, Assam (India); Paul, Sandip, E-mail: sandipp@iitg.ernet.in [Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati 781 039, Assam (India)

    2012-10-15

    Highlights: Black-Right-Pointing-Pointer NMA molecules are associated mostly through their hydrophobic methyl groups. Black-Right-Pointing-Pointer High pressure reduces association propensity causing dispersion of these moieties. Black-Right-Pointing-Pointer Orientational polarization of vicinal water molecules near O and H atoms of NMA. Black-Right-Pointing-Pointer NMA prefers to be a H-bond acceptor rather than a donor in interaction with water. Black-Right-Pointing-Pointer 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.

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

    Science.gov (United States)

    Dagade, Dilip H; Barge, Seema S

    2016-03-16

    A near-IR spectral study on pure water and aqueous salt solutions is used to investigate stoichiometric concentrations of different types of hydrogen-bonded water species in liquid water and in water comprising the hydration shell of salts. Analysis of the thermodynamics of hydrogen-bond formation signifies that hydrogen-bond making and breaking processes are dominated by enthalpy with non-negligible heat capacity effects, as revealed by the temperature dependence of standard molar enthalpies of hydrogen-bond formation and from analysis of the linear enthalpy-entropy compensation effects. A generalized method is proposed for the simultaneous calculation of the spectrum of water in the hydration shell and hydration number of solutes. Resolved spectra of water in the hydration shell of different salts clearly differentiate hydrogen bonding of water in the hydration shell around cations and anions. A comparison of resolved liquid water spectra and resolved hydration-shell spectra of ions highlights that the ordering of absorption frequencies of different kinds of hydrogen-bonded water species is also preserved in the bound state with significant changes in band position, band width, and band intensity because of the polarization of water molecules in the vicinity of ions. PMID:26749515

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

    International Nuclear Information System (INIS)

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

  2. Short, strong hydrogen bonds on enzymes: NMR and mechanistic studies

    Science.gov (United States)

    Mildvan, A. S.; Massiah, M. A.; Harris, T. K.; Marks, G. T.; Harrison, D. H. T.; Viragh, C.; Reddy, P. M.; Kovach, I. M.

    2002-09-01

    The lengths of short, strong hydrogen bonds (SSHBs) on enzymes have been determined with high precision (±0.05 Å) from the chemical shifts ( δ), and independently from the D/ H fractionation factors ( φ) of the highly deshielded protons involved. These H-bond lengths agree well with each other and with those found by protein X-ray crystallography, within the larger errors of the latter method (±0.2 to±0.8 Å) [Proteins 35 (1999) 275]. A model dihydroxynaphthalene compound shows a SSHB of 2.54±0.04 Å based on δ=17.7 ppm and φ=0.56±0.04, in agreement with the high resolution X-ray distance of 2.55±0.06 Å. On ketosteroid isomerase, a SSHB is found (2.50±0.02 Å), based on δ=18.2 ppm and φ=0.34, from Tyr-14 to the 3-O - of estradiol, an analog of the enolate intermediate. Its strength is ˜7 kcal/mol. On triosephosphate isomerase, SSHBs are found from Glu-165 to the 1-NOH of phosphoglycolohydroxamic acid (PGH), an analog of the enolic intermediate (2.55±0.05 Å), and from His-95 to the enolic-O - of PGH (2.62±0.02 Å). In the methylglyoxal synthase-PGH complex, a SSHB (2.51±0.02 Å) forms between Asp-71 and the NOH of PGH with a strength of ≥4.7 kcal/mol. When serine proteases bind mechanism-based inhibitors which form tetrahedral Ser-adducts analogous to the tetrahedral intermediates in catalysis, the Asp⋯His H-bond of the catalytic triad becomes a SSHB [Proc. Natl Acad. Sci. USA 95 (1998) 14664], 2.49-2.63 Å in length. Similarly, on the serine-esterase, butyrylcholinesterase complexed with the mechanism-based inhibitor m-( N, N, N-trimethylammonio)-2,2,2-trifluoroacetophenone, a SSHB forms between Glu-327 and His-438 of the catalytic triad, 2.61±0.04 Å in length, based on δ=18.1 ppm and φ=0.65±0.10. Very similar results are obtained with (human) acetylcholinesterase. The strength of this SSHB is at least 4.9 kcal/mol.

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

    Indian Academy of Sciences (India)

    Bikshandarkoil R srinivasan; Sunder N Dhuri; Jyoti V Sawant; Christian Näther; Wolfgang Bensch

    2006-03-01

    The organic diammonium salt N,N'-dibenzyl-N,N,N',N'-tetramethylethylenediammonium dibromide dihydrate, (dbtmen)Br2.2H2O (1), was prepared by the reaction of N,N,N',N'-tetramethylethylenediamine (tmen) with benzyl bromide. 1 crystallizes in the triclinic space group 1 with the following unit cell dimensions for C20H34Br2N2O2 (M = 494.31): = 8.6672(6) Å, = 11.7046(8) Å, = 11.7731(8) Å, = 76.988(8)°, = 88.978(8)°, = 76.198(8)° R, = 1129.26(13) Å3, = 2. Three components, namely the (dbtmen)2+ dication, two bromide anions and two crystal water molecules constitute the structural arrangement of 1. H2O molecules are linked to bromide anions via O-H$\\cdots$Br hydrogen bonding interactions resulting in the formation of a four-membered {O2Br2} cyclic dibromide. The {O2Br2} units and the dications are arranged as alternating layers extending in the crystallographic plane. The arrangement of anions and cations may be viewed as a typical lamellar structure. The crystal water molecules can be removed by heating 1 at 140°C and the anhydrous dibromide thus formed can be fully rehydrated as evidenced by IR spectra and X-ray powder patterns.

  4. Controlled release and enhanced antibacterial activity of salicylic acid by hydrogen bonding with chitosan☆

    Institute of Scientific and Technical Information of China (English)

    Zujin Yang; Yanxiong Fang; Hongbing Ji

    2016-01-01

    Microcapsules of salicylic acid (SA) with chitosan were prepared by spray drying method. Various analytical methods were used to characterize the nature of microcapsules. Fourier-transform infrared spectroscopy (FTIR) confirmed the presence of intermolecular interactions between chitosan and SA. Particle size analysis showed that the average size of microcapsules ranged from 2 to 20μm. Scanning electron microscopy (SEM) studies indicated that the microspheres were spherical and had a relatively smooth surface. Microbiological assay of antibacterial activity for SA and its microcapsules was measured using different bacterial strains. It was found that the antibacterial activity of SA was improved after the formation of microcapsules. The in vitro release profile showed that the microcapsules could control SA release from 1 h to 4 h. Kinetic studies revealed that the release pattern follows Korsmeyer–Peppas mechanism. Enhanced antibacterial activity of the SA micro-capsules was attributed to the synergistic effects of intermolecular hydrogen-bonding interactions N–H⋯O and O–H⋯O_C between SA and chitosan. It was also confirmed by quantum chemical calculation.

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

    Science.gov (United States)

    Isaev, A. N.

    2016-03-01

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

  6. Evaluation of the nonrandom hydrogen bonding (NRHB) theory and the simplified perturbed-chain-statistical associating fluid theory (sPC-SAFT). 2. Liquid-liquid equilibria and prediction of monomer fraction in hydrogen bonding systems

    DEFF Research Database (Denmark)

    Tsivintzelis, Ioannis; Grenner, Andreas; Economou, Ioannis;

    2008-01-01

    Two statistical thermodynamic models, the nonrandom hydrogen bonding (NRHB) theory, which is a compressible lattice model, and the simplified perturbed-chain-statistical associating fluid theory (sPC-SAFT), which is based on Wertheim's perturbation theory, were used to model liquid-liquid equilib...... treatment of hydrogen bonding, yielded similar predictions for the fraction of non-hydrogen bonded molecules (monomer fraction) in pure 1-alkanols and in 1-alkanol-n-hexane mixtures....

  7. Intramolecular electron density redistribution upon hydrogen bond formation in the anion methyl orange at the water/1,2-dichloroethane interface probed by phase interference second harmonic generation

    Science.gov (United States)

    Rinuy; Piron; Brevet; Blanchard-Desce; Girault

    2000-09-15

    Surface second harmonic generation (SSHG) studies of the azobenzene derivative p-dimethylaminoazobenzene sulfonate, often referred as Methyl Orange (MO), at the neat water/1,2-dichloroethane (DCE) interface is reported. The two forms of the anionic MO dye, which are usually observed in bulk solution, with one form being hydrogen bonded to a water molecule through the azo nitrogens (MO/H2O) and the other form not being hydrogen bonded (MO) have also been observed at the water/DCE interface. Their equilibrium constant has been compared with the corresponding bulk solution and found to be identical. The adsorption equilibrium of the two forms has been determined and the Gibbs energy of adsorption measured to be -30 kJmol(-1) for both forms. From a light polarisation analysis of the SH signal, the angle of orientation of the MO transition dipole moment was found to be 34 +/- 2 degrees for MO and 43 +/- 2 degrees for MO/H2O under the assumption of a Dirac delta function for the angle distribution, a difference explained by the different solvation properties of the two forms. Furthermore, the wavelength dependence analysis of these data revealed an interference pattern resulting from the electronic density redistribution within the hydrated anionic form occurring upon the formation of the hydrogen bond with a water molecule. This interference pattern was clearly evidenced with the use of another dye at the interface in order to define a phase reference to both forms of Methyl Orange. PMID:11039537

  8. Short Hydrogen Bonds and Proton Delocalization in Green Fluorescent Protein (GFP).

    Science.gov (United States)

    Oltrogge, Luke M; Boxer, Steven G

    2015-06-24

    Short hydrogen bonds and specifically low-barrier hydrogen bonds (LBHBs) have been the focus of much attention and controversy for their possible role in enzymatic catalysis. The green fluorescent protein (GFP) mutant S65T, H148D has been found to form a very short hydrogen bond between Asp148 and the chromophore resulting in significant spectral perturbations. Leveraging the unique autocatalytically formed chromophore and its sensitivity to this interaction we explore the consequences of proton affinity matching across this putative LBHB. Through the use of noncanonical amino acids introduced through nonsense suppression or global incorporation, we systematically modify the acidity of the GFP chromophore with halogen substituents. X-ray crystal structures indicated that the length of the interaction with Asp148 is unchanged at ∼2.45 Å while the absorbance spectra demonstrate an unprecedented degree of color tuning with increasing acidity. We utilized spectral isotope effects, isotope fractionation factors, and a simple 1D model of the hydrogen bond coordinate in order to gain insight into the potential energy surface and particularly the role that proton delocalization may play in this putative short hydrogen bond. The data and model suggest that even with the short donor-acceptor distance (∼2.45 Å) and near perfect affinity matching there is not a LBHB, that is, the barrier to proton transfer exceeds the H zero-point energy. PMID:27162964

  9. Isolation of Cellulose Nanofibers: Effect of Biotreatment on Hydrogen Bonding Network in Wood Fibers

    Directory of Open Access Journals (Sweden)

    Sreekumar Janardhnan

    2011-01-01

    Full Text Available The use of cellulose nanofibres as high-strength reinforcement in nano-biocomposites is very enthusiastically being explored due to their biodegradability, renewability, and high specific strength properties. Cellulose, through a regular network of inter- and intramolecular hydrogen bonds, is organized into perfect stereoregular configuration called microfibrils which further aggregate to different levels to form the fibre. Intermolecular hydrogen bonding at various levels, especially at the elementary level, is the major binding force that one need to overcome to reverse engineer these fibres into their microfibrillar level. This paper briefly describes a novel enzymatic fibre pretreatment developed to facilitate the isolation of cellulose microfibrils and explores effectiveness of biotreatment on the intermolecular and intramolecular hydrogen bonding in the fiber. Bleached Kraft Softwood Pulp was treated with a fungus (OS1 isolated from elm tree infected with Dutch elm disease. Cellulose microfibrils were isolated from these treated fibers by high-shear refining. The % yield of nanofibres and their diameter distribution (<50 nm isolated from the bio-treated fibers indicated a substantial increase compared to those isolated from untreated fibers. FT-IR spectral analysis indicated a reduction in the density of intermolecular and intramolecular hydrogen bonding within the fiber. X-ray spectrometry indicated a reduction in the crystallinity. Hydrogen bond-specific enzyme and its application in the isolation of new generation cellulose nano-fibers can be a huge leap forward in the field of nano-biocomposites.

  10. 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.

  11. Monitoring Backbone Hydrogen-Bond Formation in β-Barrel Membrane Protein Folding.

    Science.gov (United States)

    Raschle, Thomas; Rios Flores, Perla; Opitz, Christian; Müller, Daniel J; Hiller, Sebastian

    2016-05-10

    β-barrel membrane proteins are key components of the outer membrane of bacteria, mitochondria and chloroplasts. Their three-dimensional structure is defined by a network of backbone hydrogen bonds between adjacent β-strands. Here, we employ hydrogen-deuterium (H/D) exchange in combination with NMR spectroscopy and mass spectrometry to monitor backbone hydrogen bond formation during folding of the outer membrane protein X (OmpX) from E. coli in detergent micelles. Residue-specific kinetics of interstrand hydrogen-bond formation were found to be uniform in the entire β-barrel and synchronized to formation of the tertiary structure. OmpX folding thus propagates via a long-lived conformational ensemble state in which all backbone amide protons exchange with the solvent and engage in hydrogen bonds only transiently. Stable formation of the entire OmpX hydrogen bond network occurs downhill of the rate-limiting transition state and thus appears cooperative on the overall folding time scale. PMID:27062600

  12. Hydrogen bonding and solution state structure of salicylaldehyde-4-phenylthiosemicarbazone: A combined experimental and theoretical study

    Science.gov (United States)

    Novak, Predrag; Pičuljan, Katarina; Hrenar, Tomica; Biljan, Tomislav; Meić, Zlatko

    2009-02-01

    Hydrogen bonding in salicylaldehyde-4-phenylthiosemicarbazone ( 1) has been studied by using experimental (NMR, Raman and UV spectroscopies) and quantum chemical (DFT) methods. It has been demonstrated that 1 adopted the hydroxy-thione tautomeric form in solution as found also in the solid state and previously indicated by secondary deuterium isotope effects. Apart from the intra-molecular hydrogen bonds new interactions between 1 and solvent molecules were formed as well. Changes in NMR chemical shifts and calculations have pointed towards a formation of inter-molecular three-centered hydrogen bonds in each of the studied complexes involving OH and NH groups of 1 and associated solvent molecules. Stabilization energies of intra-molecular hydrogen bonds were found to decrease with the increase of the solvent polarity. Two-dimensional NOESY spectra indicated conformational changes in solution with respect to the structure observed in the solid state. These were accounted for by a relatively low barrier of the rotation of the N sbnd N single bond thus enabling a molecule to posses a higher conformational flexibility in solution with portions of skewed conformations. The results presented here can help in a better understanding of the role hydrogen bonds can play in bioactivity of related thiosemicarbazone derivatives and their metal complexes.

  13. A theoretical study of solvent effects on the characteristics of the intramolecular hydrogen bond in Droxidopa

    Indian Academy of Sciences (India)

    Mehdi Yoosefian; Hassan Karimi-Maleh; Afsaneh L Sanati

    2015-06-01

    The molecular structures and intramolecular hydrogen bond of Droxidopa have been investigated with density functional theory. It is found that strong hydrogen bonds (O–H…N and O…H–O) exist in the title compound. These hydrogen bonds play essential roles in determining conformational preferences and energy, which would have important effects in biological activity mechanisms that will strongly influence its characteristics in solution. A computational study of a representative number of actual and model structures was carried out in five solvents with different polarities and different types of interactions with solute molecules: water, ethanol, carbon tetrachloride, dimethyl sulfoxide, and tetrahydrofuran, utilizing the polarizable continuum model (PCM) model. The calculations were performed at the B3LYP/6-311++G(d,p) level of theory. In addition, the topological properties of the electron density distributions for O–H…N(O) intramolecular hydrogen bond were analyzed in terms of the Bader’s theory of atoms in molecules. Furthermore, the analyses of different hydrogen bonds in this molecule by quantum theory of natural bond orbital (NBO) methods support the density functional theory (DFT) results.

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

    Energy Technology Data Exchange (ETDEWEB)

    Horowitz, Scott; Dirk, Lynnette M.A.; Yesselman, Joseph D.; Nimtz, Jennifer S.; Adhikari, Upendra; Mehl, Ryan A.; Scheiner, Steve; Houtz, Robert L.; Al-Hashimi, Hashim M.; Trievel, Raymond C. [Oregon State U.; (Michigan); (Utah SU); (HHMI); (Kentucky)

    2013-09-06

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

  15. Variation of geometries and electron properties along proton transfer in strong hydrogen-bond complexes

    Science.gov (United States)

    Pacios, L. F.; Gálvez, O.; Gómez, P. C.

    2005-06-01

    Proton transfer in hydrogen-bond systems formed by 4-methylimidazole in both neutral and protonated cationic forms and by acetate anion are studied by means of MP2/6-311++G(d,p) ab initio calculations. These two complexes model the histidine (neutral and protonated)-aspartate diad present in the active sites of enzymes the catalytic mechanism of which involves the formation of strong hydrogen bonds. We investigate the evolution of geometries, natural bond orbital populations of bonds and electron lone pairs, topological descriptors of the electron density, and spatial distributions of the electron localization function along the process N-H ⋯O→N⋯H⋯O→N⋯H-O, which represents the stages of the H-transfer. Except for a sudden change in the population of electron lone pairs in N and O at the middle N...H...O stage, all the properties analyzed show a smooth continuous behavior along the covalent → hydrogen bond transit inherent to the transfer, without any discontinuity that could identify a formation or breaking of the hydrogen bond. This way, the distinction between covalent or hydrogen-bonding features is associated to subtle electron rearrangement at the intermolecular space.

  16. Simultaneous photon absorption as a probe of molecular interaction and hydrogen-bond cooperativity in liquids.

    Science.gov (United States)

    Woutersen, Sander

    2007-10-21

    We have investigated the simultaneous absorption of near-infrared photons by pairs of neighboring molecules in liquid methanol. Simultaneous absorption by two OH-stretching modes is found to occur at an energy higher than the sum of the two absorbing modes. This frequency shift arises from interaction between the modes, and its value has been used to determine the average coupling between neighboring methanol molecules. We find a rms coupling strength of 46+/-1 cm(-1), larger than can be explained from a transition-dipole coupling mechanism, suggesting that hydrogen-bond mediated interactions also contribute to the coupling. The most important aspect of simultaneous vibrational absorption is that it allows for a quantitative investigation of hydrogen-bond cooperativity. We derive the extent to which the hydrogen-bond strengths of neighboring molecules are correlated by comparing the line shape of the absorption band caused by simultaneous absorption with that of the fundamental transition. Surprisingly, neighboring hydrogen bonds in methanol are found to be strongly correlated, and from the data we obtain an estimate for the hydrogen-bond correlation coefficient of 0.69+/-0.12. PMID:17949183

  17. Simultaneous photon absorption as a probe of molecular interaction and hydrogen-bond cooperativity in liquids

    Science.gov (United States)

    Woutersen, Sander

    2007-10-01

    We have investigated the simultaneous absorption of near-infrared photons by pairs of neighboring molecules in liquid methanol. Simultaneous absorption by two OH-stretching modes is found to occur at an energy higher than the sum of the two absorbing modes. This frequency shift arises from interaction between the modes, and its value has been used to determine the average coupling between neighboring methanol molecules. We find a rms coupling strength of 46±1cm-1, larger than can be explained from a transition-dipole coupling mechanism, suggesting that hydrogen-bond mediated interactions also contribute to the coupling. The most important aspect of simultaneous vibrational absorption is that it allows for a quantitative investigation of hydrogen-bond cooperativity. We derive the extent to which the hydrogen-bond strengths of neighboring molecules are correlated by comparing the line shape of the absorption band caused by simultaneous absorption with that of the fundamental transition. Surprisingly, neighboring hydrogen bonds in methanol are found to be strongly correlated, and from the data we obtain an estimate for the hydrogen-bond correlation coefficient of 0.69±0.12.

  18. Nano breathers and molecular dynamics simulations in hydrogen-bonded chains.

    Science.gov (United States)

    Kavitha, L; Muniyappan, A; Prabhu, A; Zdravković, S; Jayanthi, S; Gopi, D

    2013-01-01

    Non-linear localization phenomena in biological lattices have attracted a steadily growing interest and their existence has been predicted in a wide range of physical settings. We investigate the non-linear proton dynamics of a hydrogen-bonded chain in a semi-classical limit using the coherent state method combined with a Holstein-Primakoff bosonic representation. We demonstrate that even a weak inherent discreteness in the hydrogen-bonded (HB) chain may drastically modify the dynamics of the non-linear system, leading to instabilities that have no analog in the continuum limit. We suggest a possible localization mechanism of polarization oscillations of protons in a hydrogen-bonded chain through modulational instability analysis. This mechanism arises due to the neighboring proton-proton interaction and coherent tunneling of protons along hydrogen bonds and/or around heavy atoms. We present a detailed analysis of modulational instability, and highlight the role of the interaction strength of neighboring protons in the process of bioenergy localization. We perform molecular dynamics simulations and demonstrate the existence of nanoscale discrete breather (DB) modes in the hydrogen-bonded chain. These highly localized and long-lived non-linear breather modes may play a functional role in targeted energy transfer in biological systems. PMID:23860832

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

    Science.gov (United States)

    McQueen-Mason, S; Cosgrove, D J

    1994-07-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-05-06

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

  1. Complexation of two non-fully hydrogen bonded aromatic hydrazide heptamers toward n-octyl-α-L-glucopyranoside in chloroform

    Institute of Scientific and Technical Information of China (English)

    DU Ping; XU YunXiang; JIANG XiKui; LI ZhanTing

    2009-01-01

    Two aromatic hydrazide haptamers have been prepared, with both consisting of two hydrogen bonded folded segments. Compared to their fully hydrogen bonded analogues, the flexibility of their backbones increases due to lack of one or two intramolecular hydrogen bonds at the middle aromatic unit. (2D) 1H NMR, circular dichroism and fluorescent studies revealed that both oligomers moderately complex n-octyl-α-L-glucopyranoside in chloroform.

  2. Investigation of polarized infrared spectra of the hydrogen bond in molecular crystals. New spectral effects in the vibrational spectroscopy of hydrogen bonded systems

    International Nuclear Information System (INIS)

    A review of the experimental as well as of the theoretical studies, performed on the area of the infrared spectroscopy of hydrogen bonded molecular crystals, is given. Discussion of some physical phenomena is presented, responsible for basic spectral effects registered in the infrared spectra, as breaking of vibrational dipole selection rules in the IR spectra, linear dichroic as well as temperature effects, observed in the frequency range of the proton stretching vibrations. Also some newly recognized H/D isotopic effects for hydrogen bonded systems are presented, deduced from a quantitative analysis of the polarized spectra in the IR, namely the so called 'self-organization' effects and the 'long-range' H/D isotope effects. (author)

  3. A direct experimental evidence for an aromatic C-H⋯O hydrogen bond by fluorescence-detected infrared spectroscopy

    Science.gov (United States)

    Venkatesan, V.; Fujii, A.; Ebata, T.; Mikami, N.

    2004-08-01

    Formation of a weak aromatic C-H⋯O hydrogen bond has been discerned both experimentally and computationally in the 1,2,4,5-tetrafluorobenzene (TFB)-water system. The intermolecular structure of the isolated TFB-water cluster in a supersonic jet was characterized using fluorescence-detected infrared spectroscopy. The formation of a weak hydrogen bond in the cluster was directly evidenced by a low-frequency shift and intensity enhancement of the hydrogen-bonded aromatic C-H stretch in the TFB moiety. This is the first direct observation of an aromatic C-H⋯O hydrogen bond in isolated gas phase clusters.

  4. Anomalous temperature effect on the hydrogen bond strength and phase transition in 2,4,6-trimethylpyridinium pentachlorophenolate.

    Science.gov (United States)

    Majerz, Irena; Jakubas, Ryszard

    2004-06-01

    The phase transition in 2,4,6-trimethylpyridinium pentachlorophenolate has been studied by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and dielectric method as well as theoretical calculations. The crystal undergoes a first order phase transition of order-disorder type at 376 K. The transition to the high temperature phase causes anomalous hydrogen-bond shortening. Experimental and theoretical results show that the change in the mutual orientation of the phenol and pyridine rings is connected with the change of the hydrogen bond. Such an effect, which appears in the present simple hydrogen-bond complex, may be common also for the other hydrogen-bond complexes.

  5. Probing defects and correlations in the hydrogen-bond network of ab initio water

    CERN Document Server

    Gasparotto, Piero; Ceriotti, Michele

    2016-01-01

    The hydrogen-bond network of water is characterized by the presence of coordination defects relative to the ideal tetrahedral network of ice, whose fluctuations determine the static and time-dependent properties of the liquid. Because of topological constraints, such defects do not come alone, but are highly correlated coming in a plethora of different pairs. Here we discuss in detail such correlations in the case of ab initio water models and show that they have interesting similarities to regular and defective solid phases of water. Although defect correlations involve deviations from idealized tetrahedrality, they can still be regarded as weaker hydrogen bonds that retain a high degree of directionality. We also investigate how the structure and population of coordination defects is affected by approximations to the inter-atomic potential, finding that in most cases, the qualitative features of the hydrogen bond network are remarkably robust.

  6. The effect of large amplitude motions on the vibrational intensities in hydrogen bonded complexes

    DEFF Research Database (Denmark)

    Mackeprang, Kasper; Hänninen, Vesa; Halonen, Lauri;

    2015-01-01

    We have developed a model to calculate accurately the intensity of the hydrogen bonded XH-stretching vibrational transition in hydrogen bonded complexes. In the Local Mode Perturbation Theory (LMPT) model, the unperturbed system is described by a local mode (LM) model, which is perturbed by the...... intermolecular modes of the hydrogen bonded system that couple with the intramolecular vibrations of the donor unit through the potential energy surface. We have applied the model to three complexes containing water as the donor unit and different acceptor units, providing a series of increasing complex binding...... energy: H2O⋯N2, H2O⋯H2O, and H2O⋯NH3. Results obtained by the LMPT model are presented and compared with calculated results obtained by other vibrational models and with previous results from gas-phase and helium-droplet experiments. We find that the LMPT model reduces the oscillator strengths of the...

  7. Hydrogen Bonding between Metal-Ion Complexes and Noncoordinated Water: Electrostatic Potentials and Interaction Energies.

    Science.gov (United States)

    Andrić, Jelena M; Misini-Ignjatović, Majda Z; Murray, Jane S; Politzer, Peter; Zarić, Snežana D

    2016-07-01

    The hydrogen bonding of noncoordinated water molecules to each other and to water molecules that are coordinated to metal-ion complexes has been investigated by means of a search of the Cambridge Structural Database (CSD) and through quantum chemical calculations. Tetrahedral and octahedral complexes that were both charged and neutral were studied. A general conclusion is that hydrogen bonds between noncoordinated water and coordinated water are much stronger than those between noncoordinated waters, whereas hydrogen bonds of water molecule in tetrahedral complexes are stronger than in octahedral complexes. We examined the possibility of correlating the computed interaction energies with the most positive electrostatic potentials on the interacting hydrogen atoms prior to interaction and obtained very good correlation. This study illustrates the fact that electrostatic potentials computed for ground-state molecules, prior to interaction, can provide considerable insight into the interactions. PMID:26989883

  8. Hydrogen bonding of formamide, urea, urea monoxide and their thio-analogs with water and homodimers

    Indian Academy of Sciences (India)

    Damanjit Kaur; Shweta Khanna

    2014-11-01

    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 homodimers’ formation were evaluated at B3LYP/6-311++G** and MP2/6-311++G∗∗ levels. The energies were corrected for zero-point vibrational energies and basis set superposition error using counterpoise method. Atoms in molecules study has been carried out in order to characterize the hydrogen bonds through the changes in electron density and laplacian of electron density. A natural energy decomposition and natural bond orbital analysis was performed to understand the nature of hydrogen bonding.

  9. Hydrogen Bond Fluctuations Control Photochromism in a Reversibly Photo-Switchable Fluorescent Protein.

    Science.gov (United States)

    Morozov, Dmitry; Groenhof, Gerrit

    2016-01-11

    Reversibly switchable fluorescent proteins (RSFPs) are essential for high-resolution microscopy of biological samples, but the reason why these proteins are photochromic is still poorly understood. To address this problem, we performed molecular dynamics simulations of the fast switching Met159Thr mutant of the RSFP Dronpa. Our simulations revealed a ground state structural heterogeneity in the chromophore pocket that consists of three populations with one, two, or three hydrogen bonds to the phenolate moiety of the chromophore. By means of non-adiabatic quantum mechanics/molecular dynamics simulations, we demonstrated that the subpopulation with a single hydrogen bond is responsible for off-switching through photo-isomerization of the chromophore, whereas two or more hydrogen bonds inhibit the isomerization and promote fluorescence instead. While rational design of new RSFPs has so far focused on structure alone, our results suggest that structural heterogeneity must be considered as well. PMID:26612709

  10. Monitoring the pH Triggered Collapse of Liposomes in the Far IR Hydrogen Bonding Continuum.

    Science.gov (United States)

    Srour, Batoul; Erhard, Birgit; Süss, Regine; Hellwig, Petra

    2016-05-01

    Far infrared spectra of complex molecular structures like lipid membranes or proteins show large and broad continuum modes that include contributions of the internal hydrogen bonding of the assembled structures. Here we corroborate the pH triggered structural rearrangement in pH-sensitive liposomes with a clear shift of the far-infrared mode from 170 to 159 cm(-1). This spectral change was accompanied by the broadening of the hydrogen bonding signature by about 25 cm(-1) and correlates with the well-known hydrogen bonding dependent shifts of the ν(PO2(-))(as) vibration of the lipid headgroup in the mid infrared and with further shifts of functional group vibrations. Far infrared spectroscopy is thus a useful tool for the investigation of conformational changes in large molecular structures. PMID:27092567

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

    Science.gov (United States)

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

    2013-06-01

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

  12. Electrostatic interaction of pi-acidic amides with hydrogen-bond acceptors.

    Science.gov (United States)

    Li, Yi; Snyder, Lawrence B; Langley, David R

    2003-10-01

    Interactions between N-methylacetamide (NMA) and N-methylated derivatives of uracil, isocyanurate and barbituric acid have been studied using ab initio methods at the local MP2/6-31G** level of theory. The results were compared to similar interactions between the oxygen atom of NMA and the pi-clouds of perfluorobenzene, quinone and trimethyltriazine. The pi-acidic amides of isocyanurate and barbituric acid were found to interact with a hydrogen bond acceptor primarily through electrostatic attractions. These groups may be used as alternatives of a hydrogen bond donor to complement a hydrogen bond acceptor or an anion in molecular recognition and drug design. Examples of such interactions were identified through a search of the CSD database. PMID:12951105

  13. Tunable capsule space: self-assembly of hemispherical cavitands with hydrogen-bonding linkers.

    Science.gov (United States)

    Yamanaka, Masamichi; Ishii, Kei; Yamada, Yoshifumi; Kobayashi, Kenji

    2006-11-10

    Fine and/or drastic tuning of capsule space has been attained by alteration of the hydrogen-bonding linker and/or hemispherical cavitand, respectively. Two molecules of tetracarboxyl-cavitand 1 or tetrakis(4-carboxyphenyl)-cavitand 2 as a hemisphere and four molecules of 2-aminopyrimidine (2-AP) or tetrahydro-2-pyrimidinone (THP) as an equatorial hydrogen-bonding linker self-assemble into a capsule [(1)2.(2-AP)4] (3), [(1)2.(THP)4] (4), [(2)2.(2-AP)4] (5), or [(2)2.(THP)4] (6), respectively, via 16 hydrogen bonds. These capsules provide isolated nanospace and can encapsulate one guest molecule (7-13) in solution. Each capsule has a different cavity size and shows particular guest selectivity on the competitive encapsulation experiments. PMID:17081009

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

    Science.gov (United States)

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

    2015-09-01

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

  15. 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.

  16. Hydrogen Bonding in Ionic Liquids Probed by Linear and Nonlinear Vibrational Spectroscopy

    CERN Document Server

    Roth, C; Kerlé, D; Friedriszik, F; Lütgens, M; Lochbrunner, S; Kühn, O; Ludwig, R

    2012-01-01

    Three imidazolium-based ionic liquids of the type [Cnmim][NTf2] with varying alkyl chain lengths (n = 1, 2 and 8) at the 1 position of the imidazolium ring were studied applying IR, linear Raman, and multiplex CARS spectroscopy. The focus has been on the CH-stretching region of the imidazolium ring, which is supposed to carry information about a possible hydrogen bonding network in the ionic liquid. The measurements are compared to calculations of the corresponding anharmonic vibrational spectra for a cluster of [C2mim][NTf2] consisting of four ion pairs. The results support the hypothesis of moderate hydrogen bonding involving the C(4)-H and C(5)-H groups and somewhat stronger hydrogen bonds of the C(2)-H groups.

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

    International Nuclear Information System (INIS)

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

  18. Toxin-induced pore formation is hindered by intermolecular hydrogen bonding in sphingomyelin bilayers.

    Science.gov (United States)

    García-Linares, Sara; Palacios-Ortega, Juan; Yasuda, Tomokazu; Åstrand, Mia; Gavilanes, José G; Martínez-Del-Pozo, Álvaro; Slotte, J Peter

    2016-06-01

    Sticholysin I and II (StnI and StnII) are pore-forming toxins that use sphingomyelin (SM) for membrane binding. We examined how hydrogen bonding among membrane SMs affected the StnI- and StnII-induced pore formation process, resulting in bilayer permeabilization. We compared toxin-induced permeabilization in bilayers containing either SM or dihydro-SM (lacking the trans Δ(4) double bond of the long-chain base), since their hydrogen-bonding properties are known to differ greatly. We observed that whereas both StnI and StnII formed pores in unilamellar vesicles containing palmitoyl-SM or oleoyl-SM, the toxins failed to similarly form pores in vesicles prepared from dihydro-PSM or dihydro-OSM. In supported bilayers containing OSM, StnII bound efficiently, as determined by surface plasmon resonance. However, StnII binding to supported bilayers prepared from dihydro-OSM was very low under similar experimental conditions. The association of the positively charged StnII (at pH7.0) with unilamellar vesicles prepared from OSM led to a concentration-dependent increase in vesicle charge, as determined from zeta-potential measurements. With dihydro-OSM vesicles, a similar response was not observed. Benzyl alcohol, which is a small hydrogen-bonding compound with affinity to lipid bilayer interfaces, strongly facilitated StnII-induced pore formation in dihydro-OSM bilayers, suggesting that hydrogen bonding in the interfacial region originally prevented StnII from membrane binding and pore formation. We conclude that interfacial hydrogen bonding was able to affect the membrane association of StnI- and StnII, and hence their pore forming capacity. Our results suggest that other types of protein interactions in bilayers may also be affected by hydrogen-bonding origination from SMs. PMID:26975250

  19. Effects of hydrogen bonds in association with flavin and substrate in flavoenzyme d-amino acid oxidase. The catalytic and structural roles of Gly313 and Thr317.

    Science.gov (United States)

    Setoyama, Chiaki; Nishina, Yasuzo; Tamaoki, Haruhiko; Mizutani, Hisashi; Miyahara, Ikuko; Hirotsu, Ken; Shiga, Kiyoshi; Miura, Retsu

    2002-01-01

    According to the three-dimensional structure of a porcine kidney D-amino acid oxidase-substrate (D-leucine) complex model, the G313 backbone carbonyl recognizes the substrate amino group by hydrogen bonding and the side-chain hydroxyl of T317 forms a hydrogen bond with C(2)=O of the flavin moiety of FAD [Miura et al. (1997) J. Biochem. 122, 825-833]. We have designed and expressed the G313A and T317A mutants and compared their enzymatic and spectroscopic properties with those of the wild type. The G313A mutant shows decreased activities to various D-amino acids, but the pattern of substrate specificity is different from that of the wild type. The results imply that the hydrogen bond between the G313 backbone carbonyl and the substrate amino group plays important roles in substrate recognition and in defining the substrate specificity of D-amino acid oxidase. The T317A mutant shows a decreased affinity for FAD. The steady-state kinetic measurements indicate diminished activities of T317A to substrate D-amino acids. The transient kinetic parameters measured by stopped-flow spectroscopy revealed that T317 plays key roles in stabilizing the purple intermediate, a requisite intermediate in the oxidative half-reaction, and in enhancing the release of the product from the active site, thereby optimizing the overall catalytic process of D-amino acid oxidase. PMID:11754736

  20. On the relation between hydrogen bonds, tetrahedral order and molecular mobility in model water

    CERN Document Server

    Pereyra, R G; Malaspina, D C; Carignano, M A

    2013-01-01

    We studied by molecular dynamics simulations the relation existing between the lifetime of hydrogen bonds, the tetrahedral order and the diffusion coefficient of model water. We tested four different models: SPC/E, TIP4P-Ew, TIP5P-Ew and Six-site, these last two having sites explicitly resembling the water lone pairs. While all the models perform reasonably well at ambient conditions, their behavior is significantly different for temperatures below 270 K. The models with explicit lone-pairs have a longer hydrogen bond lifetime, a better tetrahedral order and a smaller diffusion coefficient than the models without them.

  1. Isotopic effects in hydrogen-bonded crystals with order-disorder phase transition

    International Nuclear Information System (INIS)

    The influence of geometric isotopic effects on the Curie temperature for hydrogen-containing crystals is considered. The experimental pressure dependence of the Curie temperature for iodate crystals, obtained by us, and the known concentration dependences of the Curie temperature for some KDP-kind crystal are explained in the frame of pseudo spin Ising's model, by taking into account the geometry changes of hydrogen bonds under pressure and due to the isotopic exchange. For the first time, the analytic equations for the dependence of the Curie temperature on the length of a hydrogen bond is obtained

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

    International Nuclear Information System (INIS)

    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.)

  3. Hydrogen-bonded multilayers of micelles of a dually responsive dicationic block copolymer

    OpenAIRE

    Erel, İrem; Karahan, H. Enis; Demirel, A. Levent; Tuncer, Cansel; Bütün, Vural

    2012-01-01

    We report the fabrication of hydrogen-bonded multilayers of micelles of a dually responsive, dicationic block copolymer, poly[2-(N-morpholino)ethyl methacrylate-block-2-(diisopropylamino)ethyl methacrylate] (PMEMA-b-PDPA). By taking advantage of the difference in the hydrophilicity of PMEMA and PDPA blocks, micelles with a PMEMA-corona and a PDPA-core were obtained above pH 6.5 and were assembled layer-by-layer at the surface with tannic acid (TA) at pH 7.4 through hydrogen bonding interactio...

  4. 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...

  5. Hydrogen bonding in barbituric and 2-thiobarbituric acids: a theoretical and FT-IR study

    Science.gov (United States)

    Ramondo, Fabio; Pieretti, Andrea; Gontrani, Lorenzo; Bencivenni, Luigi

    2001-09-01

    The effects of intermolecular hydrogen bonding on the molecular properties of barbituric acid (BA) and thiobarbituric acid are discussed on the basis of density functional theory calculations. B3LYP methods were applied to monomers and cyclic dimers. Trimer and hexamer of BA were studied as examples where several CO and NH groups are involved in hydrogen bonding. The theoretical IR spectra of monomers and all oligomers here considered are compared with the FT-IR spectra measured in Ar and nitrogen matrices at different concentrations.

  6. QUANTUM-MECHANICAL PROPERTIES OF PROTON TRANSPORT IN THE HYDROGEN-BONDED MOLECULAR SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    PANG XIAO-FENG; LI PING

    2000-01-01

    The dynamic equations of the proton transport along the hydrogen bonded molecular systems have been obtainedby using completely quantum-mechanical method to be based on new Hamiltonian and model we proposed. Somequantum-mechanical features of the proton-solitons have also been given in such a case. The alternate motion of twodefects resulting from proton transfer occurred in the systems can be explained by the results. The results obtainedshow that the proton-soliton has corpuscle feature and obey classical equations of motion, while the free soliton movesin uniform velocity along the hydrogen bonded chains.

  7. Negligible effect of ions on the hydrogen-bond structure in liquid water.

    Science.gov (United States)

    Omta, Anne Willem; Kropman, Michel F; Woutersen, Sander; Bakker, Huib J

    2003-07-18

    The effects of ions on bulk properties of liquid water, such as viscosity, have suggested that ions alter water's hydrogen-bonding network. We measured the orientational correlation time of water molecules in Mg(ClO4)2, NaClO4, and Na2SO4 solutions by means of femtosecond pump-probe spectroscopy. The addition of ions had no influence on the rotational dynamics of water molecules outside the first solvation shells of the ions. This result shows that the presence of ions does not lead to an enhancement or a breakdown of the hydrogen-bond network in liquid water. PMID:12869755

  8. Negligible Effect of Ions on the Hydrogen-Bond Structure in Liquid Water

    Science.gov (United States)

    Omta, Anne Willem; Kropman, Michel F.; Woutersen, Sander; Bakker, Huib J.

    2003-07-01

    The effects of ions on bulk properties of liquid water, such as viscosity, have suggested that ions alter water's hydrogen-bonding network. We measured the orientational correlation time of water molecules in Mg(ClO4)2, NaClO4, and Na2SO4 solutions by means of femtosecond pump-probe spectroscopy. The addition of ions had no influence on the rotational dynamics of water molecules outside the first solvation shells of the ions. This result shows that the presence of ions does not lead to an enhancement or a breakdown of the hydrogen-bond network in liquid water.

  9. 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

    The far-infrared absorption spectra have been recorded for hydrogen-bonded complexes of water with ethanol embedded in cryogenic neon matrices at 2.8 K. The partial isotopic H/D-substitution of the ethanol subunit enabled by a dual inlet deposition procedure enables the observation and unambiguous......⋯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...

  10. A HYDROGEN BONDING ASSISTED CATALYST SCREENED OUT VIA COMBINATORIAL CHEMISTRY STRATEGY

    Institute of Scientific and Technical Information of China (English)

    XUMancai; OUZhize; 等

    2000-01-01

    Possibilities for enhancement of catalytic reaction rate by combining phase transfer catalysis and hydrogen bonding of the catalyst with the substrate and reagent were studied.A phase transfer catalyst library with sixty polystyrene-supported quaternary ammonium salt catalysts was synthesized.The reduction of acetophenone by NaBH4 was used as the probing reaction to select out the ost active catalyst in the library by using iterative method.which was the gel-type triethanolamine aminsating strongly asic anion exchange resin with the crosslinking degeree of 2% A hydrogen bonding assisted catalytic mechanism was proposed to explain the high catalytic activity of the catalyst.

  11. A temperature dependent infrared absorption study of strong hydrogen bonds in bis(glycinium)oxalate

    Science.gov (United States)

    Bhatt, Himal; Deo, M. N.; Murli, C.; Vishwakarma, S. R.; Chitra, R.; Sharma, Surinder M.

    2016-05-01

    We report infrared absorption studies on Bis(glycinium)oxalate, an organic complex of the simplest amino acid Glycine, under varying temperatures in the range 77 - 350 K. The measurements have been carried out in the spectral range 400 - 4000 cm-1 and the strongest O-H---O hydrogen bond, which plays a vital role in the structural stabilization, has been studied. Subtle changes in widths of modes and temperature dependent frequency variations have been observed near 250 K. The hydrogen bonding network remains stable in the entire temperature range. This is in contrast to its reported high pressure behavior.

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

    CERN Document Server

    McKenzie, Ross H

    2014-01-01

    Four diabatic states are used to construct a simple model for double proton transfer in hydrogen bonded complexes. Key parameters in the model are the proton donor-acceptor separation R and the ratio, D_1/D_2, between the proton affinity of a donor with one and two protons. Depending on the values of these two parameters the model describes four qualitatively different ground state potential energy surfaces, having zero, one, two, or four saddle points. In the limit D_2=D_1 the model reduces to two decoupled hydrogen bonds. As R decreases a transition can occur from a concerted to a sequential mechanism for double proton transfer.

  13. Dynamics of hydrogen bonds in water and consequences for the unusual behaviour of supercooled water

    Indian Academy of Sciences (India)

    José Teixeira

    2008-10-01

    The dynamics of liquid water is evaluated by the coherent quasi-elastic scattering at two different momentum transfers, in order to discriminate hydrogen bond life-time from molecular dynamics. The results indicate a possible issue for the puzzle of the behaviour of supercooled water.

  14. Anion–arene adducts: C–H hydrogen bonding, anion– interaction, and carbon bonding motifs

    OpenAIRE

    Hay, Benjamin P.; Bryantsev, Vyacheslav S.

    2008-01-01

    This article summarizes experimental and theoretical evidence for the existence of four distinct binding modes for complexes of anions with charge-neutral arenes. These include C–H hydrogen bonding and three motifs involving the arene– system—the noncovalent anion– interaction, weakly covalent interaction, and strongly covalent interaction.

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

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, J.; Wugt Larsen, R., E-mail: rewl@kemi.dtu.dk [Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kongens Lyngby (Denmark); Heimdal, J. [MAX-IV Laboratory, Lund University, P.O. Box 118, 22100 Lund (Sweden)

    2015-12-14

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

  16. IR spectroscopy of monohydrated tryptamine cation: Rearrangement of the intermolecular hydrogen bond induced by photoionization

    Science.gov (United States)

    Sakota, Kenji; Kouno, Yuuki; Harada, Satoshi; Miyazaki, Mitsuhiko; Fujii, Masaaki; Sekiya, Hiroshi

    2012-12-01

    Rearrangement of intermolecular hydrogen bond in a monohydrated tryptamine cation, [TRA(H2O)1]+, has been investigated in the gas phase by IR spectroscopy and quantum chemical calculations. In the S0 state of TRA(H2O)1, a water molecule is hydrogen-bonded to the N atom of the amino group of a flexible ethylamine side chain [T. S. Zwier, J. Phys. Chem. A 105, 8827 (2001), 10.1021/jp011659+]. A remarkable change in the hydrogen-bonding motif of [TRA(H2O)]+ occurs upon photoionization. In the D0 state of [TRA(H2O)1]+, the water molecule is hydrogen-bonded to the NH group of the indole ring of TRA+, indicating that the water molecule transfers from the amino group to NH group. Quantum chemical calculations are performed to investigate the pathway of the water transfer. Two potential energy barriers emerge in [TRA(H2O)1]+ along the intrinsic reaction coordinate of the water transfer. The water transfer event observed in [TRA(H2O)1]+ is not an elementary but a complex process.

  17. Crystal structures and hydrogen bonding in the morpholinium salts of four phenoxyacetic acid analogues

    Directory of Open Access Journals (Sweden)

    Graham Smith

    2015-11-01

    Full Text Available The anhydrous salts morpholinium (tetrahydro-2-H-1,4-oxazin-4-ium phenoxyacetate, C4H10NO+·C8H7O3−, (I, morpholinium (4-fluorophenoxyacetate, C4H10NO+·C8H6 FO3−, (II, and isomeric morpholinium (3,5-dichlorophenoxyacetate (3,5-D, (III, and morpholinium (2,4-dichlorophenoxyacetic acid (2,4-D, C4H10NO+·C8H5Cl2O3−, (IV, have been determined and their hydrogen-bonded structures are described. In the crystals of (I, (III and (IV, one of the the aminium H atoms is involved in a three-centre asymmetric cation–anion N—H...O,O′ R12(4 hydrogen-bonding interaction with the two carboxyl O-atom acceptors of the anion. With the structure of (II, the primary N—H...O interaction is linear. In the structures of (I, (II and (III, the second N—H...Ocarboxyl hydrogen bond generates one-dimensional chain structures extending in all cases along [100]. With (IV, the ion pairs are linked though inversion-related N—H...O hydrogen bonds [graph set R42(8], giving a cyclic heterotetrameric structure.

  18. Phase transition in triglycine family of hydrogen bonded ferroelectrics: An interpretation based on structural studies

    Indian Academy of Sciences (India)

    R R Choudhury; R Chitra; P U Sastry; Amit Das; M Ramanadham

    2004-07-01

    Using the crystal structure, a comprehensive interpretation of the origin of ferroelectricity in the hydrogen bonded triglycine family of crystals is given. Our detailed analysis showed that the instability of nitrogen double well potential plays a driving role in the mechanism of the ferroelectric transitions in these crystals.

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

    International Nuclear Information System (INIS)

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

  20. 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

    2016-05-21

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

  1. Alternating deposition multilayer films of dendrimers/poly(4-vinylpyridine) based on hydrogen bonding

    Institute of Scientific and Technical Information of China (English)

    SUN Jing; WANG Liyan; GAO Jian; YU Xi; ZHANG Xi

    2005-01-01

    @@ Layer-by-layer (LbL) assembly technique has been an important method for constructing layered nanostructural materials[1-4]. Although the electrostatic interaction is the primary driving force for building LbL multilayers, our group[5] and other group[6] have reported early that hydrogen bonding interaction can be also used as the driving force.

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

    Science.gov (United States)

    Green, Thomas K.; Lane, Charles A.

    2006-01-01

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

  3. 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…

  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. 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 indu...

  6. Hydrogen-bond network breakage as a first step to isopropanol crystallization

    International Nuclear Information System (INIS)

    Here we present an experimental study of isopropanol crystallization in real time by means of a novel setup combining simultaneously structural measurements with dynamical techniques. By coupling time resolved neutron diffraction and dielectric spectroscopy experiments we demonstrate that a breakage of the hydrogen-bond network is a precursor step for the crystallization of isopropanol

  7. 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

  8. 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.

  9. Vibrational relaxation and coupling of two OH-stretch oscillators with an intramolecular hydrogen bond.

    Science.gov (United States)

    Lock, A J; Gilijamse, J J; Woutersen, S; Bakker, H J

    2004-02-01

    We studied the vibrational dynamics of the OH-stretch oscillators of an alcohol with two vicinal OH groups using femtosecond midinfrared pump-probe spectroscopy. The absorption spectrum of pinacol (2,3-dimethyl-2,3-butanediol) in CDCl3 shows two OH-stretch peaks belonging to hydrogen bonded and free OH groups. The anharmonicities of the hydrogen-bonded and free OH-stretch vibrations are 180 and 160 cm(-1), respectively. The lifetime T1 of the OH-stretch vibration is found to be 3.5 +/- 0.4 ps for the hydrogen bonded and 7.4 +/- 0.5 ps for the free OH group. We observed sidebands in the transient spectra after excitation of the bonded OH group, which we attribute to a progression in a low-frequency hydrogen-bond mode. The sideband is redshifted 60 cm(-1) with respect to the 0 --> 1 transition. Due to the coupling between the two OH groups and the presence of the sidebands, simultaneous excitation of both OH-stretch vibrations leads to oscillations on the pump-probe signal with frequencies of 40 and 60 cm(-1). PMID:15268374

  10. Vibrational relaxation and coupling of two OH-stretch oscillators with an intramolecular hydrogen bond

    Science.gov (United States)

    Lock, A. J.; Gilijamse, J. J.; Woutersen, S.; Bakker, H. J.

    2004-02-01

    We studied the vibrational dynamics of the OH-stretch oscillators of an alcohol with two vicinal OH groups using femtosecond midinfrared pump-probe spectroscopy. The absorption spectrum of pinacol (2,3-dimethyl-2,3-butanediol) in CDCl3 shows two OH-stretch peaks belonging to hydrogen bonded and free OH groups. The anharmonicities of the hydrogen-bonded and free OH-stretch vibrations are 180 and 160 cm-1, respectively. The lifetime T1 of the OH-stretch vibration is found to be 3.5±0.4 ps for the hydrogen bonded and 7.4±0.5 ps for the free OH group. We observed sidebands in the transient spectra after excitation of the bonded OH group, which we attribute to a progression in a low-frequency hydrogen-bond mode. The sideband is redshifted 60 cm-1 with respect to the 0→1 transition. Due to the coupling between the two OH groups and the presence of the sidebands, simultaneous excitation of both OH-stretch vibrations leads to oscillations on the pump-probe signal with frequencies of 40 and 60 cm-1.

  11. Oscillatory Shear Flow-Induced Alignment of Lamellar Melts of Hydrogen-Bonded Comb Copolymer Supramolecules

    NARCIS (Netherlands)

    Moel, Karin de; Mäki-Ontto, Riikka; Stamm, Manfred; Ikkala, Olli; Brinke, Gerrit ten; M„ki-Ontto, R.; Maki-Ontto, R

    2001-01-01

    In this work we present the orientational behavior of comb copolymer-like supramolecules P4VP(PDP)1.0, obtained by hydrogen bonding between poly(4-vinylpyridine) and pentadecylphenol, during large-amplitude oscillatory shear flow experiments over a broad range of frequencies (0.001-10 Hz). The align

  12. 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.

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

    International Nuclear Information System (INIS)

    The stabilization of aminophenol derivatives and their radicals due to internal hydrogen bonding has been analyzed by means of density functional theory and by topological electron density analysis. The calculations have been carried out at the B3LYP level of theory, using several basis sets, and by means of the CBS-4M composite approach. A strong O-H...NH2 hydrogen bond is found to stabilize the aminophenol with the lone-pair of the nitrogen atom co-planar with the aromatic ring, contrasting with the optimized structure found for aniline. The effect of electron donors and electron acceptors on the strength of the internal hydrogen bond is also analyzed. For one of the species studied, 2,6-diaminophenol, the computed O-H bond dissociation enthalpy is only 300 kJ/mol, the lowest value found so far for phenol and other compounds containing the O-H bond, almost 25 kJ/mol lower than those found experimentally for pyrogallol and for vitamin E. The explanation for such a small value comes from the enhanced stabilization of the corresponding radical species by internal hydrogen bonding, combined with a decrease of the steric effects caused by rotation of the amino groups

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

    Science.gov (United States)

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

    2006-05-01

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

  15. 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.; Michelsen, Michael Locht; Kontogeorgis, Georgios

    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...

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

    Science.gov (United States)

    Xin-Jun, Zhao; Zhi-Fu, Gao

    2016-07-01

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

  17. Hydrogen bonding versus stacking stabilization by modified nucleobases incorporated in PNA. DNA duplexes

    DEFF Research Database (Denmark)

    Sen, Anjana; Nielsen, Peter E

    2009-01-01

    The effects of incorporation of the modified nucleobases, 2,6-diaminopurine (D) (substituting for adenine) and 7-chloro-1,8-naphthyridin-2-(1H)-one (bicyclic thymine, bT) (substituting for thymine), that stabilize PNA.DNA duplex formation by increasing hydrogen bonding and/or base pair stacking...

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

    Science.gov (United States)

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

    2015-11-01

    Deep eutectic solvents (DESs) have emerged as promising alternative candidates for CO2 capture in recent years. In this work, several novel DESs were firstly prepared to enhance CO2 absorption. Structural and physical properties of DESs were investigated, as well as their absorption performance of CO2. A distinct depression in the melting point up to 80 K of DESs was observed compared with that of BMIMCl. The observed red shifts of the C2H group in an imidazolium ring and its chemical shifts downfield in NMR spectra are indicative of a hydrogen bond interaction between BMIMCl and MEA. In particular, CO2 uptake in MEA : ILs (4 : 1) at room temperature and atmospheric pressure is up to 21.4 wt%, which is higher than that of 30 wt% MEA (13%). A hydrogen bond related mechanism was proposed in which ILs act as a medium to improve CO2 uptake through hydrogen bonds. Finally, the firstly reported overall heat of CO2 absorption is slightly higher than that of 30 wt% MEA, implying that the hydrogen bonds of DESs contribute to the overall heat of CO2 absorption. This study reveals that the heat of CO2 absorption can be tailored by the proper molar ratio of MEA and ILs. PMID:26435384

  19. Hydrogen-bonded Intramolecular Charge Transfer Excited State of Dimethylaminobenzophenone using Time Dependent Density Functional Theory

    Institute of Scientific and Technical Information of China (English)

    Yu-ling Chu; Zhong Yang; Zhe-feng Pan; Jing Liu; Yue-yi Han; Yong Ding; Peng Song

    2012-01-01

    Density functional theory and time-dependent density-functional theory have been used to investigate the photophysical properties and relaxation dynamics of dimethylaminobenzophenone (DMABP) and its hydrogen-bonded DMABP-MeOH dimer.It is found that,in nonpolar aprotic solvent,the transitions from S0 to S1 and S2 states of DMABP have both n→π* and π→π* characters,with the locally excited feature mainly located on the C=O group and the partial CT one characterized by electron transfer mainly from the dimethylaminophenyl group to the C=O group.But when the intermolecular hydrogen bond C=O…H-O is formed,the highly polar intramolecular charge transfer character switches over to the first excited state of DMABP-MeOH dimer and the energy difference between the two lowlying electronically excited states increases.To gain insight into the relaxation dynamics of DMABP and DMABP-MeOH dimer in the excited state,the potential energy curves for conformational relaxation are calculated.The formation of twisted intramolecular charge transfer state via diffusive twisting motion of the dimethylamino/dimethylaminophenyl groups is found to be the major relaxation process.In addition,the decay of the S1 state of DMABP-MeOH dimer to the ground state,through nonradiative intermolecular hydrogen bond stretching vibrations,is facilitated by the formation of the hydrogen bond between DMABP and alcohols.

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

    Science.gov (United States)

    Kaiser, Alexander; Ismailova, Oksana; Koskela, Antti; Huber, Stefan E.; Ritter, Marcel; Cosenza, Biagio; Benger, Werner; Nazmutdinov, Renat; Probst, Michael

    2014-01-01

    Molecular dynamics simulations of liquid ethylene glycol described by the OPLS-AA force field were performed to gain insight into its hydrogen-bond structure. We use the population correlation function as a statistical measure for the hydrogen-bond lifetime. In an attempt to understand the complicated hydrogen-bonding, we developed new molecular visualization tools within the Vish Visualization shell and used it to visualize the life of each individual hydrogen-bond. With this tool hydrogen-bond formation and breaking as well as clustering and chain formation in hydrogen-bonded liquids can be observed directly. Liquid ethylene glycol at room temperature does not show significant clustering or chain building. The hydrogen-bonds break often due to the rotational and vibrational motions of the molecules leading to an H-bond half-life time of approximately 1.5 ps. However, most of the H-bonds are reformed again so that after 50 ps only 40% of these H-bonds are irreversibly broken due to diffusional motion. This hydrogen-bond half-life time due to diffusional motion is 80.3 ps. The work was preceded by a careful check of various OPLS-based force fields used in the literature. It was found that they lead to quite different angular and H-bond distributions. PMID:24748697

  1. Geometrical Preferences of the Hydrogen Bonds on Protein-Ligand Binding Interface Derived from Statistical Surveys and Quantum Mechanics Calculations.

    Science.gov (United States)

    Liu, Zhiguo; Wang, Guitao; Li, Zhanting; Wang, Renxiao

    2008-11-11

    We have conducted potential of mean force (PMF) analyses to derive the geometrical parameters of various types of hydrogen bonds on protein-ligand binding interface. Our PMF analyses are based on a set of 4535 high-quality protein-ligand complex structures, which are compiled through a systematic mining of the entire Protein Data Bank. Hydrogen bond donor and acceptor atoms are classified into several basic types. Both distance- and angle-dependent statistical potentials are derived for each donor-acceptor pair, from which distance and angle cutoffs are obtained in an objective, unambiguous manner. These donor-acceptor pairs are also studied by quantum mechanics (QM) calculations at the MP2/6-311++G** level on model molecules. Comparison of the outcomes of PMF analyses and QM calculations suggests that QM calculation may serve as an alternative approach for characterizing hydrogen bond geometry. Both of our PMF analyses and QM calculations indicate that C-H···O hydrogen bonds are relatively weak as compared to common hydrogen bonds formed between nitrogen and oxygen atoms. A survey on the protein-ligand complex structures in our data set has revealed that Cα-H···O hydrogen bonds observed in protein-ligand binding are frequently accompanied by bifurcate N-H···O hydrogen bonds. Thus, the Cα-H···O hydrogen bonds in such cases would better be interpreted as secondary interactions. PMID:26620338

  2. 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

    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, wh......, whereas dithiomalondialdehyde hardly exists as a hydrogen-chelated tautomeric form....

  3. 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.

  4. Hydrogen bonding to carbonyl oxygen of nitrogen-pyramidalized amide - detection of pyramidalization direction preference by vibrational circular dichroism spectroscopy.

    Science.gov (United States)

    Wang, Siyuan; Taniguchi, Tohru; Monde, Kenji; Kawahata, Masatoshi; Yamaguchi, Kentaro; Otani, Yuko; Ohwada, Tomohiko

    2016-03-01

    Nitrogen-pyramidalization of amide increases electron density on nitrogen and decreases that on carbonyl oxygen. We identified hydrogen-bonding to carbonyl of nitrogen-pyramidalized bicyclic β-proline derivatives by crystallography, and by NMR and vibrational circular dichroism (VCD) spectroscopy in solution. Such hydrogen-bonding can switch the preferred nitrogen-pyramidalization direction, as detected by VCD spectroscopy. PMID:26889607

  5. Enthalpy of cooperative hydrogen bonding in complexes of tertiary amines with aliphatic alcohols: Calorimetric study

    International Nuclear Information System (INIS)

    Research highlights: → Solution enthalpies of aliphatic alcohols in tertiary amines and vice versa were measured. → The enthalpies of specific interaction of amines in aliphatic alcohols are lower than the enthalpies of hydrogen bonding in 1:1 complexes amine-alcohol determined in base media. → Hydrogen bond cooperativity factors in multi-particle complexes of alcohols with aromatic amines are approximately equal for all alcohols. → Hydrogen bond cooperativity factors in multi-particle complexes of alcohols with trialkylamines decrease with increasing of alkyl radical length in alcohol and amine molecules. - Abstract: The work is devoted to the investigation of thermodynamics of specific interaction of the tertiary aliphatic and aromatic amines with associated solvents as which aliphatic alcohols were taken. Solution enthalpies of aliphatic alcohols in amines (tri-n-propylamine, 2-methylpyridine, 3-methylpyridine, N-methylimidazole) as well as amines in alcohols were measured at infinite dilution. The enthalpies of specific interaction (H-bonding) in systems studied were determined based on experimental data. The enthalpies of specific interaction of amines in aliphatic alcohols significantly lower than the enthalpies of hydrogen bonding in complexes amine-alcohol of 1:1 composition determined in base media due to the reorganization of aliphatic alcohols as solvents. The determination of solvent reorganization contribution makes possible to define the hydrogen bonding enthalpies of amines with clusters of alcohols. Obtained enthalpies of hydrogen bonding in multi-particle complexes are sensitive to the influence of cooperative effect. It was shown, that hydrogen bond cooperativity factors in multi-particle complexes of alcohols with amines are approximately equal for all alcohols when pyridines and N-methylimidazole as solutes are used. At the same time, H-bonding cooperativity factors in complexes of trialkylamines with associative species of alcohols

  6. Hydrogen-bond lifetime measured by time-resolved 2D-IR spectroscopy: N-methylacetamide in methanol

    Science.gov (United States)

    Woutersen, S.; Mu, Y.; Stock, G.; Hamm, P.

    2001-05-01

    2D vibrational spectroscopy is applied to investigate the equilibrium dynamics of hydrogen bonding of N-methylacetamide (NMA) dissolved in methanol- d4. For this particular solute-solvent system, roughly equal populations are found for two conformers of the solute-solvent complex, one of which forms a hydrogen bond from the CO group of NMA to the surrounding solvent, and one of which does not. Using time-resolved 2D-IR spectroscopy on the amide I band of NMA, the exchange between both conformers is resolved. Equilibration of each conformer is completed after 4.5 ps, while the formation and breaking of the hydrogen bond occurs on a slower, 10-15 ps time scale. This interpretation is supported by classical molecular-dynamics simulations of NMA in methanol. The calculations predict a 64% population of the hydrogen-bonded conformer and an average hydrogen-bond lifetime of ≈12 ps.

  7. Enzyme:substrate hydrogen bond shortening during the acylation phase of serine protease catalysis.

    Science.gov (United States)

    Fodor, Krisztián; Harmat, Veronika; Neutze, Richard; Szilágyi, László; Gráf, László; Katona, Gergely

    2006-02-21

    Atomic resolution (hydrogen bonds between the enzyme and the substrate changed during catalysis. The well-conserved hydrogen bonds of antiparallel beta-sheet between the enzyme and the substrate become significantly shorter in the transition from a Michaelis complex analogue (Pontastacus leptodactylus (narrow-fingered crayfish) trypsin (CFT) in complex with Schistocerca gregaria (desert locust) trypsin inhibitor (SGTI) at 1.2 A resolution) to an acyl-enzyme intermediate (N-acetyl-Asn-Pro-Ile acyl-enzyme intermediate of porcine pancreatic elastase at 0.95 A resolution) presumably synchronously with the nucleophilic attack on the carbonyl carbon atom of the scissile peptide bond. This is interpreted as an active mechanism that utilizes the energy released from the stronger hydrogen bonds to overcome the energetic barrier of the nucleophilic attack by the hydroxyl group of the catalytic serine. In the CFT:SGTI complex this hydrogen bond shortening may be hindered by the 27I-32I disulfide bridge and Asn-15I of SGTI. The position of the catalytic histidine changes slightly as it adapts to the different nucleophilic attacker during the transition from the Michaelis complex to the acyl-enzyme state, and simultaneously its interaction with Asp-102 and Ser-214 becomes stronger. The oxyanion hole hydrogen bonds provide additional stabilization for acyl-ester bond in the acyl-enzyme than for scissile peptide bond of the Michaelis complex. Significant deviation from planarity is not observed in the reactive bonds of either the Michaelis complex or the acyl-enzyme. In the Michaelis complex the electron distribution of the carbonyl bond is distorted toward the oxygen atom compared to other peptide bonds in the structure, which indicates the polarization effect of the oxyanion hole. PMID:16475800

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

    International Nuclear Information System (INIS)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Mackenzie, Rebecca B.; Dewberry, Christopher T.; Leopold, Kenneth R., E-mail: A.C.Legon@bristol.ac.uk, E-mail: david.tew@bristol.ac.uk, E-mail: kleopold@umn.edu [Department of Chemistry, University of Minnesota, 207 Pleasant St., SE, Minneapolis, Minnesota 55455 (United States); Coulston, Emma; Cole, George C. [Department of Chemistry, University of Exeter, Stocker Road, Exeter EX4 4QD (United Kingdom); Legon, Anthony C., E-mail: A.C.Legon@bristol.ac.uk, E-mail: david.tew@bristol.ac.uk, E-mail: kleopold@umn.edu; Tew, David P., E-mail: A.C.Legon@bristol.ac.uk, E-mail: david.tew@bristol.ac.uk, E-mail: kleopold@umn.edu [Department of Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS (United Kingdom)

    2015-09-14

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

  10. Statistical theory for hydrogen bonding fluid system of A_aD_d type(Ⅲ):Equation of state and fluctuations

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The equation of the state of the hydrogen bonding fluid system of AaDd type is studied by the principle of statistical mechanics. The influences of hydrogen bonds on the equation of state of the system are obtained based on the change in volume due to hydrogen bonds. Moreover,the number density fluc-tuations of both molecules and hydrogen bonds as well as their spatial correlation property are inves-tigated. Furthermore,an equation describing relation between the number density correlation function of "molecules-hydrogen bonds" and that of molecules and hydrogen bonds is derived. As application,taking the van der Waals hydrogen bonding fluid as an example,we considered the effect of hydrogen bonds on its relevant statistical properties.

  11. Hydrogen Bonds in Coal——The Influence of Coal Rank and the Recognition of a New Hydrogen Bond in Coal

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    By means of in-situ diffuse reflectance FTIR, the IR spectra of 6 coals with different ranks were obtained from room temperature to 230 ℃. A new curve fitting method was used to recognize the different hydrogen bonds in the coals, and the influence of coal ranks on the distribution of hydrogen bonds(HBs) in the coals and their thermal stability were discussed. The results show that there is another new HB(around 2514 cm-1) between the -SH in mercaptans or thiophenols and the nitrogen in the pyridine-like compounds in the coals, and the evidence for that was provided. The controversial band of the HB between hydroxyl and the nitrogen of the pyridine-like compounds was determined in the range of 3028-2984 cm-1, and the result is consistent with but more specific than that of Painter et al.. It was found that the stability of different HBs in the coals is influenced by both coal rank and temperature. For some HBs, the higher the coal rank, the higher the stability of them. Within the temperature range of our research, the stability of the HB between the hydroxyl and the π bond increases to some extent for some coals at temperatures higher than 110 or 140 ℃.

  12. 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.

  13. Control over the Hydrogen-Bond Docking Site in Anisole by Ring Methylation.

    Science.gov (United States)

    Gottschalk, Hannes C; Altnöder, Jonas; Heger, Matthias; Suhm, Martin A

    2016-01-26

    The supramolecular docking of methanol to anisole may occur via an OH⋅⋅⋅O hydrogen bond or via an OH⋅⋅⋅π contact. The subtle balance between these two structures can be varied in supersonic jets by one order of magnitude through single to triple methylation of the aromatic ring and introduction of a single tert-butyl substituent, as evidenced by infrared spectroscopy. This steep variation makes it possible to assess the accuracy of relative quantum-chemical energy predictions on a kJ mol(-1) level, promising insights into inductive, mesomeric, and dispersive effects. The zero-point-corrected B3LYP-D3/aVTZ level is shown to provide an accurate relative description of the two very different hydrogen bonds, similar to a wavefunction-based protocol including CCSD(T) corrections applied to the same structures. M06-2X alone systematically overestimates the stability of π coordination. PMID:26695475

  14. 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 en...... 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....... energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and 3 or more imaginary frequencies using PM6-D3H+ implemented...

  15. Hydrogen bonding in cubic (H2O)8 and OH·(H2O)7 clusters

    International Nuclear Information System (INIS)

    A systematic study is presented for OH·(H2O)7 clusters derived from the cubic (H2O)8 octamer by replacing one water with a hydroxyl radical. The system is a prototype for atmospheric water clusters containing the environmentally important OH species, and for OH adsorbed at the surface of ice. The full set of 39 symmetry-distinct cubic OH·(H2O)7 clusters is enumerated, and the structures are determined using ab initio quantum chemical methods. Graph invariants are employed to obtain a unified analysis of the stability and structure of cubic (H2O)8 and OH·(H2O)7, relating these physical properties to the various hydrogen-bond topologies present in these clusters. To accomplish this the graph invariant formalism is extended to treat a hydrogen bonding impurity within a pure water network

  16. Influence of hydrogen bonding on the geometry of the adenine fragment

    Science.gov (United States)

    Słowikowska, Joanna Maria; Woźniak, Krzysztof

    1996-01-01

    The crystal structures of two adenine derivatives, N(6),9-dimethyl-8-butyladenine (I) and its hydrate (1 : 1) (II), have been determined by single-crystal X-ray diffraction. The geometrical features of both structures are discussed. The influence of protonation, substitution and hydrogen bond formation on the geometry of the adenine fragment was studied, based on data retrieved from the Cambridge Structural Database. Total correlation analysis showed mutual correlation between the structural parameters in the adenine ring system; partial correlation calculations for the adenine nucleoside fragments suggest intercorrelation between the parameters of the hydrogen bonding involved in base pairing and the N(adenine)-C(sugar) bond through the adenine fragment; few such correlations were found for fragments without the sugar substituent.

  17. Structure and property of the hydrogen bonding complex between triazines and water

    Institute of Scientific and Technical Information of China (English)

    LI Quan

    2006-01-01

    Density functional theory B3LYP is employed to obtain the optimized geometries of the ground state and interaction energy for triazines and water complexes. The results show that the 1,2,3-triazine-water, 1,2,4-triazine-water and 1,3,5-triazine-water complex on the ground state have Cs, Cs and C1 symmetry, and strong hydrogen bonding interaction with -17.83, -17.38 and -13.55 kJ/mol after basis set superposition error and zero-point vibration energy correction, respectively, and bond in the triazines complex. The first singlet (n, π*) vertical excitation energy of the monomer and the hydrogen bonding complexes between triazines and water is investigated by time-dependent density functional theory.

  18. A multiscale approach to model hydrogen bonding: The case of polyamide

    Energy Technology Data Exchange (ETDEWEB)

    Gowers, Richard J., E-mail: richard.gowers@manchester.ac.uk; Carbone, Paola, E-mail: paola.carbone@manchester.ac.uk [School of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL (United Kingdom)

    2015-06-14

    We present a simple multiscale model for polymer chains in which it is possible to selectively remove degrees of freedom. The model integrates all-atom and coarse-grained potentials in a simple and systematic way and allows a fast sampling of the complex conformational energy surface typical of polymers whilst maintaining a realistic description of selected atomistic interactions. In particular, we show that it is possible to simultaneously reproduce the structure of highly directional non-bonded interactions such as hydrogen bonds and efficiently explore the large number of conformations accessible to the polymer chain. We apply the method to a melt of polyamide removing from the model only the degrees of freedom associated to the aliphatic segments and keeping at atomistic resolution the amide groups involved in the formation of the hydrogen bonds. The results show that the multiscale model produces structural properties that are comparable with the fully atomistic model despite being five times faster to simulate.

  19. 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.

  20. Hydrogen-Bonded Organic Frameworks (HOFs): A New Class of Porous Crystalline Proton-Conducting Materials.

    Science.gov (United States)

    Karmakar, Avishek; Illathvalappil, Rajith; Anothumakkool, Bihag; Sen, Arunabha; Samanta, Partha; Desai, Aamod V; Kurungot, Sreekumar; Ghosh, Sujit K

    2016-08-26

    Two porous hydrogen-bonded organic frameworks (HOFs) based on arene sulfonates and guanidinium ions are reported. As a result of the presence of ionic backbones appended with protonic source, the compounds exhibit ultra-high proton conduction values (σ) 0.75× 10(-2)  S cm(-1) and 1.8×10(-2)  S cm(-1) under humidified conditions. Also, they have very low activation energy values and the highest proton conductivity at ambient conditions (low humidity and at moderate temperature) among porous crystalline materials, such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs). These values are not only comparable to the conventionally used proton exchange membranes, such as Nafion used in fuel cell technologies, but is also the highest value reported in organic-based porous architectures. Notably, this report inaugurates the usage of crystalline hydrogen-bonded porous organic frameworks as solid-state proton conducting materials. PMID:27464784

  1. Uncovering Intramolecular π-Type Hydrogen Bonds in Solution by NMR Spectroscopy and DFT Calculations.

    Science.gov (United States)

    Mastrorilli, Piero; Gallo, Vito; Todisco, Stefano; Latronico, Mario; Saielli, Giacomo

    2016-06-01

    Reaction between the phosphinito bridged diplatinum species [(PHCy2 )Pt(μ-PCy2 ){κ(2) P,O-μ-P(O)Cy2 }Pt(PHCy2 )](Pt-Pt) (1), and (trimethylsilyl)acetylene at 273 K affords the σ-acetylide complex [(PHCy2 )(η(1) -Me3 SiC≡C)Pt(μ-PCy2 )Pt(PHCy2 ){κP-P(OH)Cy2 }](Pt-Pt) (2) featuring an intramolecular π-type hydrogen bond. Scalar and dipolar couplings involving the POH proton were detected by 2D NMR experiments. Relativistic DFT calculations of the geometry, relative energy, and NMR properties of model systems of 2 confirmed the structural assignment and allowed the energy of the π-type hydrogen bond to be estimated (ca. 22 kJ mol(-1) ). PMID:27097847

  2. Performance of a Nonempirical Density Functional on Molecules and Hydrogen-Bonded Complexes

    CERN Document Server

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

    2016-01-01

    Recently, Tao and Mo (TM) derived a new meta-generalized gradient approximation based on a model exchange hole. In this work, the performance of this functional is assessed on standard test sets, using the 6-311++G(3df,3pd) basis set. These test sets include 223 G3/99 enthalpies of formation, 58 electron affinities, 8 proton affinities, 96 bond lengths, 82 harmonic vibrational frequencies, and 10 hydrogen-bonded molecular complexes. Our calculations show that the TM functional can achieve remarkable accuracy for most molecular properties, improving upon non-empirical density functionals considered here. In particular, it delivers the best accuracy for proton affinities, harmonic vibrational frequencies, and hydrogen-bonded dissociation energies and bond lengths, compared to other semilocal density-functional approximations considered in this work.

  3. An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases.

    Science.gov (United States)

    Cooper, Valentino R; Thonhauser, T; Langreth, David C

    2008-05-28

    We apply the van der Waals density functional (vdW-DF) to study hydrogen bonding and stacking interactions between nucleobases. The excellent agreement of our results with high level quantum chemical calculations highlights the value of the vdW-DF for first-principles investigations of biologically important molecules. Our results suggest that, in the case of hydrogen-bonded nucleobase pairs, dispersion interactions reduce the cost of propeller twists while having a negligible effect on buckling. Furthermore, the efficient scaling of DFT methods allowed for the easy optimization of separation distance between nucleobase stacks, indicating enhancements in the interaction energy of up to 3 kcalmol over previous fixed distance calculations. We anticipate that these results are significant for extending the vdW-DF method to model larger vdW complexes and biological molecules. PMID:18513005

  4. DFT study of the intramolecular hydrogen bonds in the amino and nitro-derivatives of malonaldehyde

    International Nuclear Information System (INIS)

    The keto and enol conformations of 2-NH2-, 3-NH2-, 4-NH2-, 3-NO2-malonaldehyde, malonamide and nitromalonamide were studied at ab initio B3LYP/6-31G** level in order to determine the conformational equilibrium and the substituent effects on the strength of the various intramolecular hydrogen bonds, paying particular attention to the O-H?O bridge. The π-electron delocalization and the related resonance parameter were calculated following the procedure suggested by Grabowski, and compared with the Gilli λ-parameter. The obtained results show that the hydrogen bond strength (EHB) is mainly governed by the resonance variations inside the chelate ring induced by the substituent groups. In the nitromalonamide, where the conjugated system is enlarged by the presence of the nitro group and two additional (H)N-H?O bridges, the resonance contribution reaches 63%, but it is strongly dependent on the molecular geometry of the open conformation

  5. ADSORPTION OF CAFFEINE BY HYDROGEN DONATING ADSORBENTS BASED ON HYDROGEN BONDING

    Institute of Scientific and Technical Information of China (English)

    XUMancai; SHIZuoqing; 等

    2000-01-01

    The adsorption isotherms of caffeine from aqueous solution onto three hydrogen donating adsorbents-hydroxypolystyrene,polystryene-azo-pyrogallol,and D72 resin-were measured.The adsorption enthalpies calculated from the isotherms according to the Clausisu-Clapeyron equation were -24-36kJ/mol,-32-37kJ/mol,and -19-24kJ/mol respectively.These values implied that the adsorption processes were based on hydrogen bonding.Furthermore.the mechanism of the adsorption of caffeine onto D72 resin was studied by IR spectra and the small molecular model experiments,and the results showed that the adsorption of caffeine onto hydrogen donating adsorbents was based on hydrogen bonding.

  6. Repulsive tip tilting as the dominant mechanism for hydrogen bond-like features in atomic force microscopy imaging

    Science.gov (United States)

    Lee, Alex J.; Sakai, Yuki; Kim, Minjung; Chelikowsky, James R.

    2016-05-01

    Experimental atomic force microscopy (AFM) studies have reported distinct features in regions with little electron density for various organic systems. These unexpected features have been proposed to be a direct visualization of intermolecular hydrogen bonding. Here, we apply a computational method using ab initio real-space pseudopotentials along with a scheme to account for tip tilting to simulate AFM images of the 8-hydroxyquinoline dimer and related systems to develop an understanding of the imaging mechanism for hydrogen bonds. We find that contrast for the observed "hydrogen bond" feature comes not from the electrostatic character of the bonds themselves but rather from repulsive tip tilting induced by neighboring electron-rich atoms.

  7. Modeling the vapor-liquid equilibria of polymer-solvent mixtures: Systems with complex hydrogen bonding behavior

    DEFF Research Database (Denmark)

    Tsivintzelis, Ioannis; Kontogeorgis, Georgios

    2009-01-01

    The vapor–liquid equilibria of binary polymer–solvent systems was modeled using the Non-Random Hydrogen Bonding (NRHB) model. Mixtures of poly(ethylene glycol), poly(propylene glycol), poly(vinyl alcohol) and poly(vinyl acetate) with various solvents were investigated, while emphasis was put on...... hydrogen bonding systems, in which functional groups of the polymer chain can self-associate or cross-associate with the solvent molecules. Effort has been made to explicitly account for all hydrogen bonding interactions. The results reveal that the NRHB model offers a flexible approach to account for...

  8. Experimental and theoretical study on the hydrogen bonding between dopamine hydrochloride and N,N-dimethyl formamide

    Science.gov (United States)

    Zhai, Cuiping; Li, Dan; Li, Lina; Sun, Fang; Ma, Huiting; Liu, Xuejun

    2015-06-01

    The hydrogen bonding between dopamine hydrochloride (DH) and N,N-dimethyl formamide (DMF) were investigated by UV-visible spectra (UV-Vis), cyclic voltammetry (CV) and density functional theory (DFT). It was found that the position of UV-Vis absorption band and the anodic/cathodic peak potentials of DH were all affected by the concentrations of DH in DMF. It was suggested that hydrogen bonding were formed between DH and DMF, which was confirmed by the DFT results. AIM analyses were performed to elucidate the nature of the hydrogen bonding in the mixtures.

  9. Self-assembly of chiral hydrogen-bonded grid layers from terephthalic Siamese twins

    Czech Academy of Sciences Publication Activity Database

    Holý, Petr; Sehnal, Petr; Tichý, Miloš; Závada, Jiří; Císařová, I.

    2003-01-01

    Roč. 14, č. 2 (2003), s. 245-253. ISSN 0957-4166 R&D Projects: GA ČR GA203/00/0138; GA ČR GA203/99/M037 Institutional research plan: CEZ:AV0Z4055905 Keywords : biphenyls * hydrogen-bonded * X-ray crystallographic structures Subject RIV: CC - Organic Chemistry Impact factor: 2.178, year: 2003

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

    OpenAIRE

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

    2015-01-01

    Nature uses orthogonal interactions over different length scales to construct structures with hierarchical levels of order and provides an important source of inspiration for the creation of synthetic functional materials. Here, we report the programmed assembly of monodisperse cylindrical block comicelle building blocks with crystalline cores to create supermicelles using spatially confined hydrogen-bonding interactions. We also demonstrate that it is possible to further program the self-ass...

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

    Science.gov (United States)

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

    2016-04-01

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

  12. Sphalerite is a geochemical catalyst for carbon−hydrogen bond activation

    OpenAIRE

    Shipp, Jessie A.; Gould, Ian R.; Shock, Everett L.; Williams, Lynda B.; Hartnett, Hilairy E.

    2014-01-01

    Organic compound transformations in the Earth commonly take place in the presence of minerals and aqueous solutions, but a mechanistic understanding of how minerals influence hydrothermal organic reactivity is virtually nonexistent. We present the first description of mineral catalysis of a fundamental organic reaction—carbon−hydrogen bond activation. The discovery that a common mineral, sphalerite (ZnS), can readily accomplish this reaction will interest not only geochemists but also the org...

  13. SYNTHESIS OF 8-HYDROXYQUINOLINE CHALCONES: TRANS CONFIGURATION, INTRAMOLECULAR HYDROGEN BONDS, BROMINATION, AND ANTIFUNGAL ACTIVITY

    OpenAIRE

    ALONSO J MARRUGO-GONZÁLEZ; VALERIE D ORLOV; ROBERTO FERNANDEZ-MAESTRE

    2012-01-01

    Nine (8-Hydroxyquinolin-5-yl)-arylpropenones were synthesized and their structures demonstrated by IR and NMRspectroscopy. These molecules showed transconfiguration and strong intramolecular hydrogen bonding; in the IR spectra of 5-formyl-8-hydroxyquinoline, 5-acetyl-8-hydroxyquinoline, 1-(8-hydroxyquinolin-5-yl)-3-phenylprop-2-en-1-one and 3-(8-hydroxyquinolin-5-yl)-1-phenylprop-2-en-1-one in CHCl3, besides the known intermolecular hydrogen band (~3180 cm-1), we identified the intramolecular...

  14. Ion-Specific Long-Range Correlations on Interfacial Water Driven by Hydrogen Bond Fluctuations

    OpenAIRE

    Enami, Shinichi; Colussi, Agustín J.

    2014-01-01

    Some of the most important processes in nature involve interfacial water. It has long been conjectured that specific ion effects therein are associated with the unique properties of interfacial water. Here we reveal the mechanism of such association by showing that the strength of ion-specific long-range correlations tracks the amplification of fluctuations on the surface of water-alcohol mixtures at the percolation thresholds of their hydrogen-bonded water networks. We used in situ online el...

  15. Studies on Electronic Charge of the Hydrogen Bond Proton in Model Molecular Systems

    OpenAIRE

    Henryk Chojnacki

    2003-01-01

    Abstract: The population analysis of the hydrogen bond atoms was analyzed within the different basis sets for model molecular systems for the ground and low-lying excited electronic states. The Mulliken, Lőwdin and Hirshfeld methods were used in our investigations. It has been shown that normally the proton is transferred, however, in some excited electronic states the hydrogen atom displacement might be responsible for the tautomeric interconversion.

  16. Competition between halogen, dihalogen and hydrogen bonds in bromo- and iodomethanol dimers

    Czech Academy of Sciences Publication Activity Database

    Riley, K. E.; Řezáč, Jan; Hobza, Pavel

    2013-01-01

    Roč. 19, č. 7 (2013), s. 2879-2883. ISSN 1610-2940 R&D Projects: GA ČR GBP208/12/G016 Grant ostatní: Operational Program Research and Development for Innovations(XE) CZ 1.05/2.1.00/03/0058 Institutional support: RVO:61388963 Keywords : dihalogen bond * halogen bond * hydrogen bond * noncovalent interactions Subject RIV: CE - Biochemistry Impact factor: 1.867, year: 2013

  17. 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. PMID:22810913

  18. Importance of Indole N-H Hydrogen Bonding in the Organization and Dynamics of Gramicidin Channels

    OpenAIRE

    Chaudhuri, Arunima; Haldar, Sourav; Sun, Haiyan; Koeppe, Roger E.; Chattopadhyay, Amitabha

    2013-01-01

    The linear ion channel peptide gramicidin represents an excellent model for exploring the principles underlying membrane protein structure and function, especially with respect to tryptophan residues. The tryptophan residues in gramicidin channels are crucial for the structure and function of the channel. In order to test the importance of indole hydrogen bonding for the biophysical properties of gramicidin channels, we monitored the effect of N-methylation of gramicidin tryptophans, using a ...

  19. Dynamic Properties of Proton Transfer in the Anharmonic-Interaction Hydrogen Bond Systems

    Institute of Scientific and Technical Information of China (English)

    YAN Xun-Ling; DONG Rui-Xin; PANG Xiao-Feng

    2001-01-01

    We analyze the properties of the excited solitary-wave model in the case of anharmonic-interaction of heavy ionic lattice in hydrogen bond systems.In this case,some new phenomena appear.We find different types of solutions for the proton displacement and influences on the kinks and pulse solitary waves by numerical calculation.For each of them we have presented a direct relation with the effective potential of the system.

  20. 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-bonded 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

  1. Influence of ions on the hydrogen-bond structure in liquid water

    Science.gov (United States)

    Omta, Anne Willem; Kropman, Michel F.; Woutersen, Sander; Bakker, Huib J.

    2003-12-01

    The orientational-correlation time of water molecules in ionic solutions has been measured with femtosecond pump-probe spectroscopy. It is found that the addition of ions has no influence on the rotational dynamics of water molecules outside the first solvation shells of the ions. This shows that the presence of ions does not lead to an enhancement or a breakdown of the hydrogen-bond network in liquid water.

  2. Hydrogen Bond, Tautomerism, and Structure of 2-Nitroresorcinol: A Microwave Spectroscopy Study

    Science.gov (United States)

    Caminati, W.; Velino, B.; Danieli, R.

    1993-09-01

    The microwave spectra of 2-nitroresorcinol and of its O-D mono- and dideuterated species have been investigated in the frequency range 28-40 GHz. The assigned spectra belong to a planar tautomer with C2v symmetry and two internal hydrogen bonds between the two hydroxyl groups and the two nitro group oxygens. The rotational spectra of four vibrational satellites of two low energy vibrations have also been assigned for the normal isotopomer.

  3. Photochemistry of hydrogen bonded heterocycles probed by photodissociation experiments and ab initio methods

    Czech Academy of Sciences Publication Activity Database

    Slavíček, Petr; Fárník, Michal

    2011-01-01

    Roč. 13, č. 26 (2011), s. 12123-12137. ISSN 1463-9076 R&D Projects: GA ČR GA203/09/0422; GA ČR GAP208/11/0161 Institutional research plan: CEZ:AV0Z40400503 Keywords : photochemistry * hydrogen bonded heterocycles * ab initio methods Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.573, year: 2011

  4. Understanding the role of hydrogen bonds in water dynamics and protein stability

    OpenAIRE

    Bianco, Valentino; Iskrov, Svilen; Franzese, Giancarlo

    2011-01-01

    The mechanisms of cold and pressure denaturation of proteins are a matter of debate, but it is commonly accepted that water plays a fundamental role in the process. It has been proposed that the denaturation process is related to an increase of hydrogen bonds among hydration water molecules. Other theories suggest that the causes of denaturation are the density fluctuations of surface water, or the destabilization of hydrophobic contacts as a consequence of water molecule inclusions inside th...

  5. 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)

  6. Single-crystal neutron diffraction studies of hydrogen-bonded systems: Two recent examples from IPNS

    International Nuclear Information System (INIS)

    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).

  7. 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).

  8. Synthesis of 2,6-diaminopyridine substituted -oxoketene ,-acetals: Crystal structure and hydrogen bonding interactions

    Indian Academy of Sciences (India)

    Okram Mukherjee Singh; Laishram Ronibala Devi; Neeladri Das

    2013-09-01

    Polyaza -oxoketene ,-acetals can exist as either enamino or imino tautomeric forms. Based on the spectroscopic data and structural analysis of one of the ,-acetals, the stereochemistry was unambiguously assigned as an all--configuration. The crystal structure confirms the enamino structure and shows extensive use of C-H…X (X = N, O, and S) weak hydrogen bonding interactions, thereby generating a 3-dimensional network in solid state.

  9. Mass spectrometry of hydrogen bonded clusters of heterocyclic molecules: Electron ionization vs. photoionization

    Czech Academy of Sciences Publication Activity Database

    Poterya, Viktoriya; Tkáč, Ondřej; Fedor, Juraj; Fárník, Michal; Slavíček, P.; Buck, U.

    2010-01-01

    Roč. 290, 2-3 (2010), s. 85-93. ISSN 1387-3806 R&D Projects: GA AV ČR KAN400400651; GA AV ČR KJB400400902; GA ČR GA203/09/0422 Institutional research plan: CEZ:AV0Z40400503 Keywords : cluster photochemistry * hydrogen bonded clusters * heterocyclic molecule Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.009, year: 2010

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

    Science.gov (United States)

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

    2015-05-01

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

  11. 2D-IR spectroscopy of hydrogen-bond-mediated vibrational excitation transfer.

    Science.gov (United States)

    Chuntonov, Lev

    2016-05-18

    Vibrational excitation transfer along the hydrogen-bond-mediated pathways in the complex of methyl acetate (MA) and 4-cyanophenol (4CP) was studied by dual-frequency femtosecond two-dimensional infrared spectroscopy. We excited the energy-donating ester carbonyl stretching vibrational mode and followed the transfer to the energy-accepting benzene ring and cyano stretching vibrations. The complexes with no, one, and two hydrogen-bonded 4CP molecules were studied. Vibrational relaxation of the carbonyl mode is more efficient in both hydrogen-bonded complexes as compared with free MA molecules. The inter-molecular transport in a hydrogen-bonded complex involving a single 4CP molecule is slower than that in a complex with two 4CP molecules. In the former, vibrational relaxation leads to local heating, as shown by the spectroscopy of the carbonyl mode, whereas the local heating is suppressed in the latter because the excitation redistribution is more efficient. At early times, the transfer to the benzene ring is governed by its direct coupling with the energy-donating carbonyl mode, whereas at later times intermediate states are involved. The transfer to a more distant site of the cyano group in 4CP involves intermediate states at all times, since no direct coupling between the energy-donating and accepting modes was observed. We anticipate that our findings will be of importance for spectroscopic studies of bio-molecular structures and dynamics, and inter- and intra-molecular signaling pathways, and for developing molecular networking applications. PMID:27145861

  12. Structure and Hydrogen Bonding of Water in Polyacrylate Gels: Effects of Polymer Hydrophilicity and Water Concentration.

    Science.gov (United States)

    Mani, Sriramvignesh; Khabaz, Fardin; Godbole, Rutvik V; Hedden, Ronald C; Khare, Rajesh

    2015-12-10

    The ability to tune the hydrophilicity of polyacrylate copolymers by altering their composition makes these materials attractive candidates for membranes used to separate alcohol-water mixtures. The separation behavior of these polyacrylate membranes is governed by a complex interplay of factors such as water and alcohol concentrations, water structure in the membrane, polymer hydrophilicity, and temperature. We use molecular dynamics simulations to investigate the effect of polymer hydrophilicity and water concentration on the structure and dynamics of water molecules in the polymer matrix. Samples of poly(n-butyl acrylate) (PBA), poly(2-hydroxyethyl acrylate) (PHEA), and a 50/50 copolymer of BA and HEA were synthesized in laboratory, and their properties were measured. Model structures of these systems were validated by comparing the simulated values of their volumetric properties with the experimental values. Molecular simulations of polyacrylate gels swollen in water and ethanol mixtures showed that water exhibits very different affinities toward the different (carbonyl, alkoxy, and hydroxyl) functional groups of the polymers. Water molecules are well dispersed in the system at low concentrations and predominantly form hydrogen bonds with the polymer. However, water forms large clusters at high concentrations along with the predominant formation of water-water hydrogen bonds and the acceleration of hydrogen bond dynamics. PMID:26514915

  13. Discrete kink dynamics in hydrogen-bonded chains: The one-component model

    DEFF Research Database (Denmark)

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

    2002-01-01

    We study topological solitary waves (kinks and antikinks) in a nonlinear one-dimensional Klein-Gordon chain with the on-site potential of a double-Morse type. This chain is used to describe the collective proton dynamics in quasi-one-dimensional networks of hydrogen bonds, where the on-site poten......We study topological solitary waves (kinks and antikinks) in a nonlinear one-dimensional Klein-Gordon chain with the on-site potential of a double-Morse type. This chain is used to describe the collective proton dynamics in quasi-one-dimensional networks of hydrogen bonds, where the on......-site potential plays the role of the proton potential in the hydrogen bond. The system supports a rich variety of stationary kink solutions with different symmetry properties. We study the stability and bifurcation structure of all these stationary kink states. An exactly solvable model with a piecewise...... "parabola-constant" approximation of the double-Morse potential is suggested and studied analytically. The dependence of the Peierls-Nabarro potential on the system parameters is studied. Discrete traveling-wave solutions of a narrow permanent profile are shown to exist, depending on the anharmonicity of...

  14. From ab initio quantum chemistry to molecular dynamics: The delicate case of hydrogen bonding in ammonia

    CERN Document Server

    Boese, A D; Martin, J M L; Marx, D; Chandra, Amalendu; Martin, Jan M.L.; Marx, Dominik

    2003-01-01

    The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liq...

  15. Effect of hydrogen bonding and complexation with metal ions on the fluorescence of luotonin A.

    Science.gov (United States)

    Miskolczy, Zsombor; Biczók, László

    2013-05-01

    Fluorescence characteristics of a biologically active natural alkaloid, luotonin A (LuA), were studied by steady-state and time-resolved spectroscopic methods. The rate constant of the radiationless deactivation from the singlet-excited state diminished by more than one order of magnitude when the solvent polarity was changed from toluene to water. Dual emission was found in polyfluorinated alcohols of large hydrogen bond donating ability due to photoinitiated proton displacement along the hydrogen bond. In CH2Cl2, LuA produced both 1 : 1 and 1 : 2 hydrogen-bonded complexes with hexafluoro-2-propanol (HFIP) in the ground state. Photoexcitation of the 1 : 2 complex led to protonated LuA, whose fluorescence appeared at a long wavelength. LuA served as a bidentate ligand forming 1 : 1 complexes with metal ions in acetonitrile. The stability of the complexes diminished in the series of Cd(2+) > Zn(2+) > Ag(+), and upon competitive binding of water to the metal cations. The effect of chelate formation on the fluorescent properties was revealed. PMID:23487318

  16. Hydrogen bonding induced polymorphism in the scandium(III) complex with ε-caprolactam

    International Nuclear Information System (INIS)

    Two polymorphs of [Sc(cpl)6][Cr(NCS)6] (cpl=ε- C6H11NO), trigonal and monoclinic, form purple elongated narrow plates and brownish-purple prisms and are formed concomitantly irrespectively of the crystallization conditions. In the trigonal polymorph both cation and anion possess C3i site symmetry while in the monoclinic form cation and anion lie on inversion centre and 2-fold axis respectively. The nature of the polymorphism traces back to a redistribution of inter- and intramolecular hydrogen bonds that causes different conformation of the complex cations, different hydrogen bonding and different molecular packings. The [Sc(cpl)6]3+ cations in the structure of the trigonal polymorph form intermolecular N(H)..S, and in the monoclinic form both N(H)..S inter- and N(H)..O intramolecular hydrogen bonds with NCS groups of [Cr(NCS)6]3- and cpl ligands. This aggregation leads to chains, where the cations and the anions alternate, in the trigonal modification and to layers, in which each ion is surrounded by four counterions, in the monoclinic form. Both polymorphs possess thermochromic properties, and a reversible color change from light purple to dark green takes place at 470-475 K.

  17. High Pressure Raman Spectroscopy of Hydrogen Bonded, Layered Crystal of Squaric Acid

    Science.gov (United States)

    Dreger, Zbigniew; Zhou, Juefei; Tao, Yuchuan; Gupta, Yogendra

    2013-06-01

    High pressure Raman spectroscopy experiments were carried out on squaric acid (H2C4O4) to understand the role of hydrogen bonding on the structural and chemical stability of layered molecular crystals. Measurements in a diamond anvil cell up to 70 GPa revealed several instances of structural changes: (1) disappearance of some lattice modes at 0.6-0.9 GPa, indicating a change in the crystal structure symmetry from monoclinic to tetragonal, (2) disappearance of some intramolecular modes at 3 GPa, indicating possible symmetrization of hydrogen bonding in crystal layers, and (3) appearance of new intramolecular modes at 13-14 GPa. The latter changes were accompanied by a gradual increase in the Raman intensity and changes in the widths of lattice and intramolecular modes. No chemical changes were observed over the pressure range examined. These results suggest that hydrogen bonding network in layers is preserved to the highest applied pressures. However, the layers could be distorted with respect to each other above 13 GPa. Work supported by DOE/NNSA and ONR/MURI.

  18. 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.

  19. Hydrophobic, Polar and Hydrogen Bonding Based Drug-Receptor Interaction of Tetrahydroimidazobenzodiazepinones

    Directory of Open Access Journals (Sweden)

    V. K. Sahu

    2008-01-01

    Full Text Available Anti-HIV drug discovery has been increasingly focusing on HIV-1-RT (reverse transcriptase as a potential therapeutic target. Tetrahydroimidazobenzodiazepinone (TIBO belongs to non-nucleoside group of reverse transcriptase inhibitors (NNRTIs. A computational chemistry study has been performed on a series of tetrahydroimidazo-benzodiazepinones as HIV-1-NNRT inhibitors. Problem statement: In order to search out new drug of desired activity from the lead compounds, there was need to know the interaction of drugs with their receptor i.e., type of force(s that have predominant role. Approach: Log P and SASA have been used for measurement of hydrophobic interaction, energy of protonation for measurement of most favorable hydrogen bond acceptor site, bond length and bond strain for measurement of strength of hydrogen bond formed between drug and receptor, atomic charges, ionization potential, electronegativity, E‡n and E‡m and their difference ΔE‡nm for measurement of polar interaction. The 3D modeling and geometry optimization of the compounds and receptor amino acids have been done by semiempirical method with MOPAC2002 associated with CAChe software. Results: The study has shown that hydrophobic interaction is predominant and made major contribution, while hydrogen bonding and polar interactions help in proper orientation of the compound (or its functional groups to make maximam interaction. Conclusion: In this study theoretical technique has been discussed by which new hypothetical HIV-1-NNRT inhibitors can be developed prior to their synthesis only by introducing effective hydrophobic substituents at specific sites.

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

    Science.gov (United States)

    Chipman, Daniel M

    2006-01-28

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

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

    Science.gov (United States)

    Kacar, Gokhan; de With, Gijsbertus

    2016-04-14

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

  2. Merocyanine dyes containing imide functional groups: synthesis and studies on hydrogen bonding to melamine receptors.

    Science.gov (United States)

    Würthner, Frank; Yao, Sheng

    2003-11-14

    The condensation of the CH acidic heterocycles 4-alkyl-2,6-dioxo-1,2,5,6-tetrahydropyridine-3-carbonitrile (5a and b) and barbituric acid (15) with electron-rich thiophene aldehydes and benzaldehyde derivatives affords the respective monomethine dyes 10-13 and 17-19. The formylation of 5a,b and 15 with N,N'-diphenylformamidine or dibutylformamide in acetic anhydride and further reaction with 4-picolinium salts 9a,b provide the dimethine dyes 14 and 20a,b. Triple hydrogen bonding of the imide groups of merocyanine dyes 10-14 has been investigated by NMR titration experiments with melamine 21. Despite rather pronounced variations of the charge-transfer properties within the given series of dyes, minor changes of their binding constants have been observed. These results could be rationalized by semiempirical calculations that reveal small changes in the charge density at the oxygen functionalities involved in hydrogen bonding upon variation of the electron-donating carbocyclic or heterocyclic groups at the terminal double bond. Although the binding constants for triple hydrogen bonding between imides and melamines are rather weak in chloroform, they proved to be strong enough to facilitate dissolution of some of these dyes in aliphatic solvents by coordination to amphiphilic melamines and dipolar aggregation. UV-vis spectral changes observed in methylcyclohexane vs chloroform suggest the formation of colloidal assemblies through noncovalent polymerization. PMID:14604366

  3. Dipole and hydrogen-bonding interactions in polyaniline: a mechanism for conductivity enhancement

    Energy Technology Data Exchange (ETDEWEB)

    Shacklette, L.W. (Allied Signal, Inc., Research and Technology, Morristown, NJ 07962-1021 (United States))

    1994-08-01

    Experimental and theoretical evidence indicate that polyaniline and its oligomers interact strongly with polar and/or hydrogen-bonding molecules. Empirical studies of the solubility properties of doped and undoped polyaniline indicate strong components to the cohesive energy density arising from polar and hydrogen-bonding interactions. Calculations on model oligomer compounds by semi-empirical and force field methods indicate that such interactions with inserted solvent molecules cause a redistribution of charge on the backbone in the direction of the equilibrium distribution characteristic of the bare radical cation (polaron) in the absence of a counterion. By lessening the polarization effects of the counterion, polar and/or hydrogen-bonding solvents, such as water or m-cresol, can contribute to a reduced scattering cross section for defects created by the polarization effects of the dopant anion. Such an effect can account for the reversible enhancement of the conductivity of polyaniline that is brought about by complexation with polar molecules such as water. ((orig.))

  4. Stabilities and Spectroscopy of Hydrogen Bonding Complexes Formed by 2,4-Bis(acrylamido)pyrimidines

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ye; LI Ting; TENG Qi-Wen

    2008-01-01

    Hydrogen bonds play important roles to living organisms containing pyrimidine-based derivatives.The electronic structures of the hydrogen bonding complexes formed by 2,4-bis(acrylamido)pyrimidine (2,4-BAAP) derivatives with 1-substituted uracil were studied using Austin Model 1 (AMl) and density function theory (DFT) methods.The UV and NMR spectra of the complexes were calculated with the INDO/CIS (configuration interaction for singlet in intermediate neglect of differential overlap) and B3LYP/6-31G(d)methods.It was shown that the complexes could be formed via the triple hydrogen bonding between two monomers owing to the negative binding energies.The binding energies of the complexes were weakened in the presence of substituents,but this weakening effect depended on the simultaneous influence of the electronic and steric effects.The binding energies of the complexes were also decreased owing to the formation of the isomeric complexes in the presence of piperidyl on 2,4-BAAP.The energy gaps of the complexes were lessened in the presence of electron-donating groups.Holes and electrons were easily injected to the complexes due to the extension of the conjugation chain.The first UV absorptions of the complexes relative to those of the parent compound were red-shifted because of the narrow energy gaps.The chemical shifts of the carbon atoms on the C=O bonds in the complexes were changed downfield.

  5. Wetting Camphor: Multi-Isotopic Substitution Identifies the Complementary Roles of Hydrogen Bonding and Dispersive Forces.

    Science.gov (United States)

    Pérez, Cristóbal; Krin, Anna; Steber, Amanda L; López, Juan C; Kisiel, Zbigniew; Schnell, Melanie

    2016-01-01

    Using broadband rotational spectroscopy, we report here on the delicate interplay between hydrogen bonds and dispersive forces when an unprecedentedly large organic molecule (camphor, C10H16O) is microsolvated with up to three molecules of water. Unambiguous assignment was achieved by performing multi H2(18)O isotopic substitution of clustered water molecules. The observation of all possible mono- and multi-H2(18)O insertions in the cluster structure yielded accurate structural information that is not otherwise achievable with single-substitution experiments. The observed clusters exhibit water chains starting with a strong hydrogen bond to the C═O group and terminated by a mainly van der Waals (dispersive) contact to one of the available sites at the monomer moiety. The effect of hydrogen bond cooperativity is noticeable, and the O···O distances between the clustered water subunits decrease with the number of attached water molecules. The results reported here will further contribute to reveal the hydrophobic and hydrophilic interactions in systems of increasing size. PMID:26689110

  6. Intermolecular hydrogen bonds: From temperature-driven proton transfer in molecular crystals to denaturation of DNA

    Indian Academy of Sciences (India)

    Mark Johnson

    2008-11-01

    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 physical and chemical properties and are thought to play a fundamental role in processes like enzymatic catalysis. By combining elastic and inelastic neutron scattering results with ab initio, lattice dynamics and molecular dynamics simulations, low frequency lattice modes are identified which modulate the potential energy surface of the hydrogen bond proton and drive proton transfer. The second example concerns base-pair opening in DNA which is the fundamental physical process underlying biological processes like denaturation and transcription. We have used an emprical force field and a large scale, all-atom phonon calculation to gain insight into the base-pair opening modes and the apparent `energy gap' between the accepted frequencies for these modes (∼ 100 cm-1 or ∼ 140 K) and the temperature of the biological processes (room temperature to 100° C) [3]. Inelastic neutron scattering spectra on aligned, highly crystalline DNA samples, produced at the ILL, provide the reference data for evaluating the precision of these simulation results.

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

    Science.gov (United States)

    Gil, D. M.; Osiry, H.; Pomiro, F.; Varetti, E. L.; Carbonio, R. E.; Alejandro, R. R.; Ben Altabef, A.; Reguera, E.

    2016-07-01

    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)5NO]·2H2O, which has a layered structure. This solid crystallizes with an orthorhombic unit cell, in the Pna21 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····OH2O, OH····NCN, and OH····ONO hydrogen bonds that connects neighboring layers. The interaction within the layer must be of antiferromagnetic nature and it was detected close to 2 K.

  8. Hydrogen bonding induced polymorphism in the scandium(III) complex with ε-caprolactam

    Energy Technology Data Exchange (ETDEWEB)

    Virovets, Alexander V.; Peresypkina, Eugenia V. [Institute of Inorganic Chemistry SB RAS, Novosibirsk (Russian Federation); Novosibirsk State Univ. (Russian Federation); Cherkasova, Elizaveta V.; Cherkasova, Tatjana G. [Kuzbass State Technical Univ., Kemerovo (Russian Federation)

    2015-11-01

    Two polymorphs of [Sc(cpl){sub 6}][Cr(NCS){sub 6}] (cpl=ε- C{sub 6}H{sub 11}NO), trigonal and monoclinic, form purple elongated narrow plates and brownish-purple prisms and are formed concomitantly irrespectively of the crystallization conditions. In the trigonal polymorph both cation and anion possess C{sub 3i} site symmetry while in the monoclinic form cation and anion lie on inversion centre and 2-fold axis respectively. The nature of the polymorphism traces back to a redistribution of inter- and intramolecular hydrogen bonds that causes different conformation of the complex cations, different hydrogen bonding and different molecular packings. The [Sc(cpl){sub 6}]{sup 3+} cations in the structure of the trigonal polymorph form intermolecular N(H)..S, and in the monoclinic form both N(H)..S inter- and N(H)..O intramolecular hydrogen bonds with NCS groups of [Cr(NCS){sub 6}]{sup 3-} and cpl ligands. This aggregation leads to chains, where the cations and the anions alternate, in the trigonal modification and to layers, in which each ion is surrounded by four counterions, in the monoclinic form. Both polymorphs possess thermochromic properties, and a reversible color change from light purple to dark green takes place at 470-475 K.

  9. Theoretical Study on the Structures and Properties of Hydrogen Bonding Complexes between Diazines and Water

    Institute of Scientific and Technical Information of China (English)

    LI, Quan; HUANG, Fang-Qian; HU, Jing-Dan; ZHAO, Ke-Qing

    2006-01-01

    Density functional theory B3LYP method and second-order Moller-Plesset perturbation theory MP2 method were employed to obtain the optimized geometries of the ground state and interaction energy for diazines and water complexes. The results show that the ground state complexes have strong hydrogen bonding interaction with -20.99,- 16.73 and - 15.31 kJ/mol after basis set superposition error and zero-point vibration energy correction for pyridazine-water, pyrimidine-water and pyrazine-water, respectively, and large red-shift for the symmetric H-O stretching vibration frequencies due to the formation of N…H-O hydrogen bond in the diazine-water complexes.The NBO analysis indicates that intermolecular charge transfer are 0.0316, 0.0255 and 0.0265 e respectively. In addition, the first singlet (n,π*) vertical excitation energy of the monomer and the hydrogen bonding complexes between diazines and water was investigated by time-dependent density functional theory.

  10. Vibrational Spectroscopy of Intramolecular Hydrogen Bonds in the Infrared and Near-Infrared Regions

    DEFF Research Database (Denmark)

    Schrøder, Sidsel Dahl

    This PhD thesis describes the gas phase studies of four intramolecular hydrogen bonds: O-H···O (in methyl lactate), O-H···π (in methallyl carbinol and allyl carbinol), O-H···N (in methylated and triuoromethylated 2-aminoethanol) and N-H···N (in the diamines 1,2-diaminoethane, 1,3-diaminopropane 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...... spectra. The experimental characterization of hydrogen bonds have been complemented by theoretical analyzes. These analyzes are based on the electron density topology, natural bond orbital theory and visualization of the distribution of electrostatic potential energy in the molecules. In these studies...

  11. Hydrogen-bond network and pH sensitivity in human transthyretin

    International Nuclear Information System (INIS)

    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 mm3 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

  12. Nature, Strength, and Cooperativity of the Hydrogen-Bonding Network in α-Chitin.

    Science.gov (United States)

    Deringer, Volker L; Englert, Ulli; Dronskowski, Richard

    2016-03-14

    Chitin is an abundant biopolymer that stabilizes the exoskeleton of insects and gives structure to plants. Its macroscopic properties go back to an intricate network of hydrogen bonds that connect the polymer strands, and these intermolecular links have been under ongoing study. Here, we use atomistic simulations to explore hydrogen bonding in the most abundant form, α-chitin. The crystal structure exhibits disorder, and so discrete models are systematically derived as suitable approximants to the macroscopic material. These models then allow us to perform dispersion-corrected density-functional theory (DFT-D) simulations on the three-dimensional crystal network and on lower-dimensional fragments. Thereby, we rationalize the nature of hydrogen bonding and the role of crystallographic disorder for the stability of α-chitin, and complement previous, larger-scale molecular-dynamics (MD) simulations as well as recent fiber-diffraction experiments. Our results provide new, atomic-level insight into one of Nature's most abundant building materials, and the techniques and concepts are likely transferable to other biopolymers. PMID:26828306

  13. Structural role of hydrogen bond networks in amino acid-acid systems. (I) The network with highly polarizable OHO hydrogen bonds in sarcosine-methanesulfonic acid (2:1) crystal

    International Nuclear Information System (INIS)

    The sarcosine-methanesulfonic acid (2:1) crystal was selected for examination of two problems: relations between different components of the amino acid-acid hydrogen bond network and a role of very strong and highly polarizable OHO hydrogen bond in the main structural units of the crystal: sarcosinium-sarcosine dimers (complexes). Our observations are based on phase transitions of the crystal monitored by DSC, X-ray diffraction and temperature evolutions of selected bands of IR spectra. Our experimental and DFT results provide information on the potential energy profile of the OHO proton and its evolution with temperature. The O...O distance of the primary hydrogen bond remains almost unchanged and its proton is strongly delocalized and sensitive on neighbour NHO hydrogen bond. We propose a possible mechanism of the phase transitions and coupling between νC=O vibrations of the carboxyl group and moving of the proton in neighbour OHO hydrogen bridge

  14. Structural role of hydrogen bond networks in amino acid-acid systems. (II) The network with weakly polarizable OHO hydrogen bonds in sarcosine-p-toluenesulfonic acid (1:1) crystal

    International Nuclear Information System (INIS)

    The sarcosine-p-toluenesulfonic acid (1:1) crystal crystallizes as monoclinic system and belongs to the: (i) P21/c at 293 and 200 K; (ii) P21/n at 100 K space groups. It was selected for examination of two problems: relations between different components of the amino acid-acid hydrogen bond network and a role of medium strong and weakly polarizable OHO hydrogen bond in the main structural units of the crystal: sarcosinium-p-toluenesulfonate complexes. Our observations are based on phase transitions of the crystal monitored by DSC, X-ray diffraction and temperature evolutions of selected modes of IR spectra. The O...O distance of the primary hydrogen bond as well as conformations of sarcosinium and p-toluenesulfonate are very sensitive on state of NHO secondary hydrogen bonds

  15. Tyrosine B10 triggers a heme propionate hydrogen bonding network loop with glutamine E7 moiety

    Energy Technology Data Exchange (ETDEWEB)

    Ramos-Santana, Brenda J., E-mail: brenda.ramos@upr.edu [Department of Chemistry, University of Puerto Rico, Mayagueez Campus, P.O. Box 9019, Mayagueez 00681-9019 (Puerto Rico); Lopez-Garriga, Juan, E-mail: juan.lopez16@upr.edu [Department of Chemistry, University of Puerto Rico, Mayagueez Campus, P.O. Box 9019, Mayagueez 00681-9019 (Puerto Rico)

    2012-08-10

    Highlights: Black-Right-Pointing-Pointer H-bonding network loop by PheB10Tyr mutation is proposed. Black-Right-Pointing-Pointer The propionate group H-bonding network restricted the flexibility of the heme. Black-Right-Pointing-Pointer The hydrogen bonding interaction modulates the electron density of the iron. Black-Right-Pointing-Pointer Propionate H-bonding network loop explains the heme-ligand stabilization. -- Abstract: Propionates, as peripheral groups of the heme active center in hemeproteins have been described to contribute in the modulation of heme reactivity and ligand selection. These electronic characteristics prompted the question of whether the presence of hydrogen bonding networks between propionates and distal amino acids present in the heme ligand moiety can modulate physiological relevant events, like ligand binding association and dissociation activities. Here, the role of these networks was evaluated by NMR spectroscopy using the hemoglobin I PheB10Tyr mutant from Lucina pectinata as model for TyrB10 and GlnE7 hemeproteins. {sup 1}H-NMR results for the rHbICN PheB10Tyr derivative showed chemical shifts of TyrB10 OH{eta} at 31.00 ppm, GlnE7 N{sub {epsilon}1}H/N{sub {epsilon}2}H at 10.66 ppm/-3.27 ppm, and PheE11 C{sub {delta}}H at 11.75 ppm, indicating the presence of a crowded, collapsed, and constrained distal pocket. Strong dipolar contacts and inter-residues crosspeaks between GlnE7/6-propionate group, GlnE7/TyrB10 and TyrB10/CN suggest that this hydrogen bonding network loop between GlnE7, TyrB10, 6-propionate group, and the heme ligand contribute significantly to the modulation of the heme iron electron density as well as the ligand stabilization mechanism. Therefore, the network loop presented here support the fact that the electron withdrawing character of the hydrogen bonding is controlled by the interaction of the propionates and the nearby electronic environments contributing to the modulation of the heme electron density state. Thus

  16. Tyrosine B10 triggers a heme propionate hydrogen bonding network loop with glutamine E7 moiety

    International Nuclear Information System (INIS)

    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. 1H-NMR results for the rHbICN PheB10Tyr derivative showed chemical shifts of TyrB10 OHη at 31.00 ppm, GlnE7 Nε1H/Nε2H at 10.66 ppm/−3.27 ppm, and PheE11 CδH 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 bonding

  17. Hydrogen bonded supramolecular architectures of copper (II) complexes of amidino Ο alkylurea derivatives

    International Nuclear Information System (INIS)

    Forty-four copper(ll) complexes of bi- tri- and tetra-dentate amidino-O-alkylurea derivative ligands have been prepared by methanolysis or ethanolysis of the corresponding cyanoguanidine derivative in the presence of CuX2 (X = Cl, Br, NO3 or BF4). Preliminary characterisation was based on elemental and spectroscopic (IR, MS, UV/Vis and EPR) analysis. Whenever possible single crystal X-ray diffraction experiments have been undertaken to confirm the identification, and to investigate the architectures of the hydrogen-bonded supramolecular constructions, of the complexes. When using copper(ll) sulfate, esterification of the sulfate anion to form methylsulfate and ethylsulfate occurred. When recrystallising a tetrafluoroborate-containing product from methanol, alcoholysis of tetrafluoroborate to form difluorodimethoxyborate occurred. These esterification and methanolysis reactions are attributed to the ability of alkylsulfate and difluorodimethoxyborate to act as hydrogen-bond acceptors in the supramolecular synthons, which generate the extended structure. The preparation of manganese(ll), cobalt(ll), nickel(ll) and cadmium(ll) chloride complexes was attempted by replacement of the copper(ll) centre. The synthetic route involved formation of the free ligand by addition of hydrogen sulfide under acidic conditions to the appropriate copper(ll) complex followed by addition to the required metal(ll) chloride. Structural analysis of the single crystals grown from the products of these reactions showed that hydrolysis of the imino groups of the free ligand to form carbonyl groups had occurred. DNA-base binding to copper(ll) complexes of amidino-O-alkylurea derivatives was investigated to assess the ability of the base (i) to replace co-ordinated anion and (ii) to form complementary DDA:AAD triple hydrogen bonds with the co-ordinated amidino-O-alkylurea ligand. Crystallographic analysis revealed that the anion replacement by base readily occurs but not the formation of

  18. Quantum Mechanical Study on the Blue-Shifting Hydrogen-Bond between 3-Aminophenol and CHX3 (X F, Cl)

    International Nuclear Information System (INIS)

    Intermolecular bonding between 3-aminophenol and two halomethanes, namely fluoroform and chloroform, was quantum mechanically investigated. Several low-energy structures are found, and all geometries within 1 kcal/mol show π-hydrogen bonds between the aromatic ring and the hydrogen atom of the halomethane. The C H stretching frequency of halomethane involved in the π-hydrogen bond is blue-shifted, and the amount of blue shift is the largest with the most stable isomer and decreases with decreasing stability. Binding energy, infrared intensity, and dipole moment as a function of relative stability are also reported. This study forms another example of a blue-shifting hydrogen bond, or an anti-hydrogen bond

  19. Hydrogen bond dynamics and vibrational spectral diffusion in aqueous solution of acetone: A first principles molecular dynamics study

    Indian Academy of Sciences (India)

    Bhabani S Mallik; Amalendu Chandra

    2012-01-01

    We present an ab initio molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous solution of acetone at room temperature. It is found that the frequencies of OD bonds in the acetone hydration shell have a higher stretch frequency than those in the bulk water. Also, on average, the frequencies of hydration shell OD modes are found to increase with increase in the acetone-water hydrogen bond distance. The vibrational spectral diffusion of the hydration shell water molecules reveals three time scales: A short-time relaxation (∼80 fs) corresponding to the dynamics of intact acetone-water hydrogen bonds, a slower relaxation (∼1.3 ps) corresponding to the lifetime of acetone-water hydrogen bonds and another longer time constant (∼12 ps) corresponding to the escape dynamics of water from the solute hydration shell. The present first principles results are compared with those of available experiments and classical simulations.

  20. Novel hot-melting hyperbranched poly(ester-amine) bearing self-complementary quadruple hydrogen bonding units

    Institute of Scientific and Technical Information of China (English)

    Yi Peng Qiu; Li Ming Tang; Yu Wang; Shi You Guan

    2008-01-01

    Hyperbranched poly(amine-ester)s bearing serf-complementary quadruple hydrogen bonding units display excellent mechanical and temperature-dependent melt rheological properties,which make them suitable as novel hot-melting materials.

  1. Quantum molecular dynamics and molecular interactions studied by NMR and INS Nuclear magnetic resonance; Proton tunnelling; Hydrogen bond

    CERN Document Server

    Jones, N

    2002-01-01

    The wavefunction of a particle extends into the classically forbidden barrier region of the potential energy surface. The consequence of this partial delocalisation is the phenomenon of quantum tunnelling, an effect which enables a particle to penetrate a potential barrier of magnitude greater than the energy of the particle. The tunnelling probability is an exponential function of the particle mass. The effect is therefore an important contribution to the behaviour of light atoms, in particular the proton. The hydrogen bond has long been appreciated to be an essential component of many biological and chemical systems, and the proton transfer reaction in the hydrogen bond is fundamental to many of these processes. The proton behaviour in the hydrogen bonds of benzoic acid, acetylacetone and calix-4-arene has been studied. A variety of techniques, both experimental and computational, were adopted for the study of the three hydrogen bonded systems. The complementary spectroscopic techniques of inelastic neutron...

  2. High-Resolution Rotational Spectroscopy Study of the Smallest Sugar Dimer: Interplay of Hydrogen Bonds in the Glycolaldehyde Dimer.

    Science.gov (United States)

    Zinn, Sabrina; Medcraft, Chris; Betz, Thomas; Schnell, Melanie

    2016-05-10

    Molecular recognition of carbohydrates plays an important role in nature. The aggregation of the smallest sugar, glycolaldehyde, was studied in a conformer-selective manner using high-resolution rotational spectroscopy. Two different dimer structures were observed. The most stable conformer reveals C2 -symmetry by forming two intermolecular hydrogen bonds, giving up the strong intramolecular hydrogen bonds of the monomers and thus showing high hydrogen bond selectivity. By analyzing the spectra of the (13) C and (18) O isotopologues of the dimer in natural abundance, we could precisely determine the heavy backbone structure of the dimer. Comparison to the monomer structure and the complex with water provides insight into intermolecular interactions. Despite hydrogen bonding being the dominant interaction, precise predictions from quantum-chemical calculations highly rely on the consideration of dispersion. PMID:27060475

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

    Science.gov (United States)

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

    2006-06-01

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

  4. Surface-Mediated Hydrogen Bonding of Proteinogenic α-Amino Acids on Silicon.

    Science.gov (United States)

    Rahsepar, Fatemeh R; Moghimi, Nafiseh; Leung, K T

    2016-05-17

    Understanding the adsorption, film growth mechanisms, and hydrogen bonding interactions of biological molecules on semiconductor surfaces has attracted much recent attention because of their applications in biosensors, biocompatible materials, and biomolecule-based electronic devices. One of the most challenging questions when studying the behavior of biomolecules on a metal or semiconductor surface is "What are the driving forces and film growth mechanisms for biomolecular adsorption on these surfaces?" Despite a large volume of work on self-assembly of amino acids on single-crystal metal surfaces, semiconductor surfaces offer more direct surface-mediated interactions and processes with biomolecules. This is due to their directional surface dangling bonds that could significantly perturb hydrogen bonding arrangements. For all the proteinogenic biomolecules studied to date, our group has observed that they generally follow a "universal" three-stage growth process on Si(111)7×7 surface. This is supported by corroborating data obtained from a three-pronged approach of combining chemical-state information provided by X-ray photoelectron spectroscopy (XPS) and the site-specific local density-of-state images obtained by scanning tunneling microscopy (STM) with large-scale quantum mechanical modeling based on the density functional theory with van der Waals corrections (DFT-D2). Indeed, this three-stage growth process on the 7×7 surface has been observed for small benchmark biomolecules, including glycine (the simplest nonchiral amino acid), alanine (the simplest chiral amino acid), cysteine (the smallest amino acid with a thiol group), and glycylglycine (the smallest (di)peptide of glycine). Its universality is further validated here for the other sulfur-containing proteinogenic amino acid, methionine. We use methionine as an example of prototypical proteinogenic amino acids to illustrate this surface-mediated process. This type of growth begins with the formation of

  5. High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

    OpenAIRE

    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 tor...

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

    International Nuclear Information System (INIS)

    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

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

    Science.gov (United States)

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

    2014-06-01

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

  8. Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome

    Directory of Open Access Journals (Sweden)

    Ghosh Sujit K

    2009-07-01

    Full Text Available Abstract Background Conformational flexibility in structured RNA frequently is critical to function. The 30S ribosomal subunit exists in different conformations in different functional states due to changes in the central part of the 16S rRNA. We are interested in evaluating the factors that might be responsible for restricting flexibility to specific parts of the 16S rRNA using biochemical data obtained from the 30S subunit in solution. This problem was approached taking advantage of the observation that there must be a high degree of conformational flexibility at sites where UV photocrosslinking occurs and a lack of flexibility inhibits photoreactivity at many other sites that are otherwise suitable for reaction. Results We used 30S x-ray structures to quantify the properties of the nucleotide pairs at UV- and UVA-s4U-induced photocrosslinking sites in 16S rRNA and compared these to the properties of many hundreds of additional sites that have suitable geometry but do not undergo photocrosslinking. Five factors that might affect RNA flexibility were investigated – RNA interactions with ribosomal proteins, interactions with Mg2+ ions, the presence of long-range A minor motif interactions, hydrogen bonding and the count of neighboring heavy atoms around the center of each nucleobase to estimate the neighbor packing density. The two factors that are very different in the unreactive inflexible pairs compared to the reactive ones are the average number of hydrogen bonds and the average value for the number of neighboring atoms. In both cases, these factors are greater for the unreactive nucleotide pairs at a statistically very significant level. Conclusion The greater extent of hydrogen bonding and neighbor atom density in the unreactive nucleotide pairs is consistent with reduced flexibility at a majority of the unreactive sites. The reactive photocrosslinking sites are clustered in the 30S subunit and this indicates nonuniform patterns of

  9. Alcohol adducts of alkoxides: Intramolecular hydrogen bonding as a general structural feature

    International Nuclear Information System (INIS)

    Characterization of Zr2(OiPr)8(iPrOH)2 by 1H and 13C NMR spectroscopy, ir spectroscopy, and single-crystal x-ray diffraction (-100 degree C) is reported. The unit cell contains four half-dimers in the asymmetric unit, all of which differ only in the rotational conformation about Zr-O and O-C bonds. In each dimer, the edge-shared bioctahedron has two μ-OiPr groups. On opposite sides of this Zr2(μ-OR)2 plane, each dimer forms two hydrogen bonds, one each between a coordinated alcohol and a terminal alkoxide. The NMR spectra at 25 degree C are so simple as to be structurally uninformative, a result of rapid fluxionality which includes, as one component, proton migration among all OiPr units. At -80 degree C in toluene, the NMR spectra are now too complex to be accounted for by a single edge-shared bioctahedral structure. The hafnium analogue is isomorphous with the zirconium compound. Although Ce2(OiPr)8(iPrOH)2 is not isomorphous, it exhibits an analogous hydrogen-bonded structure in which the O hor-ellipsis O distance is as short as it is in the Zr analogue, in spite of a metal-metal separation which is longer by 0.28 angstrom. The generality of hydrogen bonding between M-OR and M-O(H)R groups when they are aligned parallel in a metal cluster is reviewed. 44 refs., 2 figs., 4 tabs

  10. OH stretching frequencies in systems with intramolecular hydrogen bonds: Harmonic and anharmonic analyses

    International Nuclear Information System (INIS)

    Graphical abstract: Stretching wavenumbers for intramolecularly hydrogen-bonded OH groups computed with second order perturbation theoretical anharmonic procedures were found to be essentially linearly related to those obtained within the much faster harmonic analysis. Moreover, the observed OH stretching wavenumbers were found to correlate linearly with predicted harmonic wavenumbers, thereby providing an approximate empirical relationship for the prediction of OH stretching bands. Highlights: ► Stretching wavenumbers for intramolecularly hydrogen-bonded OH groups. ► Harmonic and second order perturbation theory anharmonic approximations. ► Computed harmonic and anharmonic wavenumbers linearly related. ► Linear correlations between observed and computed wavenumbers. ► Linear correlation with OH proton NMR chemical shifts. - Abstract: 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 as the second-order perturbation theoretical (PT2) anharmonic approximations available with the Gaussian software package. The wavenumbers computed with the anharmonic procedures were found to be essentially linearly related to those obtained within the harmonic analysis. The theoretical wavenumbers were compared with experimental values taken from the literature, supplemented with values estimated from infrared (IR) absorption spectra recorded for the purpose of this study. An approximately linear relationship was established between the observed wavenumbers νOH and the results of the harmonic analysis. This is significant in view of the fact that the full anharmonic PT2 analysis requires orders-of-magnitude more computing time than the harmonic analysis. νOH also correlates with OH chemical shifts.

  11. DFT Study of Hydrogen-Bonded 1,3,5-Triazine-Water Complexes

    Institute of Scientific and Technical Information of China (English)

    LI,Quan; HU,Jing-Dan; ZHAO,Ke-Qing

    2007-01-01

    The 1,3,5-triazine-water hydrogen bonding interactions have been investigated using the density functional theory B3LYP method and 6-31 + + G** basis, obtaining one, two and seven energy minima of the ground states for the 1,3,5-triazine-water, 1,3,5-triazine-(water)2 and 1,3,5-triazine-(water)3 complexes respectively. The fully optimized geometries and binding energies were reported for the various stationary points. The global minima of 1,3,5-triazine-(water)2 and 1,3,5-triazine-(water)3 complexes have a hydrogen bond N…H-O and a chain of water molecules, terminated by a hydrogen bond O…H-C. The binding energies are 13.38, 39.52 and 67.79 kJ/mol for the most stable 1,3,5-triazine-water, 1,3,5-triazine-(water)2 and 1,3,5-triazine-(water)3 complexes respectively, after the basis set superposition error and zero point energy corrections. The H-O symmetric stretching modes of water in the complexes are red-shifted relative to those of the monomer water. In addition, the NBO analysis indicates that inter-molecule charge transfer is 0.02145 e, 0.02501 e and 0.02777 e for the most stable 1∶1, 1∶2 and 1∶3 complexes between 1,3,5-triazine and water, respectively.

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

    Science.gov (United States)

    Angelina, Emilio L; Peruchena, Nélida M

    2011-05-12

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

  13. Hydrogen bonding in thiobenzamide synthon and its Cadmium complex: Crystal structure and Hirshfeld analysis

    Indian Academy of Sciences (India)

    INES RIGANE; SIWAR WALHA; ABDELHAMID BEN SALAH

    2016-09-01

    The thiobenzamid TBA and its Cd(II) complex, dichlorothiobenzamidecadmium(II) [Cd(TBA)Cl₂] complex has been synthesized and characterized by FT-IR, FT-Raman and UV–Vis spectroscopy. The crystal and molecular structure of TBA and [Cd(TBA)Cl₂] were determined by single crystal X-ray diffraction analysis. The molecular arrangement in the crystal structure of TBA can be described on the basis of supramolecular dimeric synthons built up by four independent TBA molecules stacked via N-H. . .S hydrogen bonds. The 3D Hirshfeld surfaces and the associated 2D fingerprint plots were investigated for intermolecular interactions. The N-H. . .S hydrogen bond percentages were estimated to be 23.1%, 22.9%, 30.6% and 27.3% of Hirshfeld surfaces area respectively for each TBA molecule. Synthons are associated through C–H. . . π interactions at percentage of 33.8%, 38.2%, 24.3% and 19.4% to result in 3D network. The dichlorothiobenzamide cadmium(II) complex bonded by sulfur atom of thiobenzamide shows a double chain of distorted octahedra around the cadmium atoms running along the a axis and the packing is stabilized by intra- and inter-chain hydrogen bonding interactions of the type N–H. . .Cl and aromatic π. . .π stacking interactions between ring centroids at 21.8% and 7.6% of the Hirshfeld surface area, respectively. The decomposition of the complex to cadmium sulfide has been investigated by thermogravimetric analysis (TGA).

  14. Hydrogen Bonds, Hydrophobicity Forces and the Character of the Collapse Transition

    OpenAIRE

    Irbäck, A.; Sjunnesson, F.; S. Wallin

    2001-01-01

    We study the thermodynamic behavior of a model protein with 54 amino acids that is designed to form a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid, and has the Ramachandran torsion angles as its only degrees of freedom. The force field is based on hydrogen bonds and effective hydrophobicity forces. We study how the character of the collapse transition depends on the strengths of these forces. For a suitable choice o...

  15. Performance of a Nonempirical Density Functional on Molecules and Hydrogen-Bonded Complexes

    OpenAIRE

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

    2016-01-01

    Recently, Tao and Mo (TM) derived a new meta-generalized gradient approximation based on a model exchange hole. In this work, the performance of this functional is assessed on standard test sets, using the 6-311++G(3df,3pd) basis set. These test sets include 223 G3/99 enthalpies of formation, 58 electron affinities, 8 proton affinities, 96 bond lengths, 82 harmonic vibrational frequencies, and 10 hydrogen-bonded molecular complexes. Our calculations show that the TM functional can achieve rem...

  16. Hydrogen bond and protonation in carbonyl nitrosyl complexes of transition metals

    International Nuclear Information System (INIS)

    Infrared spectroscopy was used to study interaction of CoM(CO)2(NO) π-complexes, where M=Cr, Mo, Cp=η5-C5H5, with perfluorotert butanol (PFTB) and HCl in liquid Xe solutions at low temperatures. It is shown that mentioned complexes can form earlier unknown type of hydrogen bond with PFTB and HCl by oxygen atom of nitrosyl group of transition metal atom. Protonation of complexes dissolved in liquid Xe by transition metal atom during their interaction with HCl was reveald

  17. 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.

  18. Digital Operation of Microelectronic Circuits Analogous to Protein Hydrogen Bonding Networks

    Directory of Open Access Journals (Sweden)

    Elitsa Gieva

    2012-12-01

    Full Text Available Two hydrogen bonding networks with water molecules and branching residues extracted from β-lactamase protein are investigated and their proton transfer characteristics are studied by creating analogous electrical circuits consisting of block-elements. The block-elements and their proton transfer are described by polynomials that are coded in Matlab and in Verilog-A for use in the Spectre simulator of Cadence IC design system. DC and digital pulse analyses are performed to demonstrate that some circuit outputs behave as repeaters while other - behave as inverters. The results also showed that the HBN circuits might behave as a D-latch and a demultiplexer.

  19. BASE-INDUCED RELEASE OF MOLECULES FROM HYDROGEN BONDING DIRECTED LAYER-BY-LAYER FILM

    Institute of Scientific and Technical Information of China (English)

    Yu Fu; Huan Chen; Shi-long Bai; Feng-wei Huo; Zhi-qiang Wang; Xi Zhang

    2003-01-01

    On the basis of hydrogen bonding directed layer-by-layer (LbL) assembly we have fabricated two multilayer systems, poly(acrylic acid) bearing spironaphthoxazine (PAA-SO)/poly(4-vinylpyridine) and carboxyl-terminated polyether dendrimer (dendrimer-COOH)/poly(4-vinylpyridine). UV-Vis spectroscopy indicates that either PAA-SO or dendrimer COOH can be released from the corresponding multilayer assemblies upon immerssion in a basic aqueous solution.Furthermore, the rate of molecule release can be controlled either by changing the pH value or by adjusting the layer structure.

  20. Phase transitions and dynamical properties of quasi-one-dimensional structures with hydrogen bonds

    Directory of Open Access Journals (Sweden)

    R.Ya. Stetsiv

    2012-03-01

    Full Text Available The frequency dependence of dynamical conductivity of the quasi-one-dimensional structures with hydrogen bonds is studies on the bases of pseudospin-electron model. It is taken into account the proton-electron interaction, external longitudinal field h, the tunneling hopping of protons, electron transfer and direct interaction between protons. The dependence of the electron concentration and mean number of protons on site on temperature and external field are obtained. The phase transition lines from uniform phase into charge ordered phase is determined. The dependence of the dynamical conductivity on temperature and field h and it changes at the phase transitions are obtained.

  1. 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.

  2. Assembling one-dimensional coordination polymers into threedimensional architectures via hydrogen bonds

    Indian Academy of Sciences (India)

    Lalit Rajput; Madhushree Sarkar; Kumar Biradha

    2010-09-01

    The reactions of bis(pyridylcarboxamido)alkanes (amides) and bis(3-pyridyl)alkanediamides (reverse amides) with copper(II) and zinc(II) in the presence of various anions resulted in onedimensional polymeric crystalline complexes with or without guest inclusion. The crystal structure analyses of these complexes reveal that the one-dimensional networks observed here are of three types: simple linear chain, chains with wavy nature and chains containing cavities. The self-complementary amide groups of the ligands assembled these coordination networks into higher dimensional architectures via N-H$\\cdots$O hydrogen bonds.

  3. Contribution of a Low-Barrier Hydrogen Bond to Catalysis Is Not Significant in Ketosteroid Isomerase

    OpenAIRE

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

    2015-01-01

    Low-barrier hydrogen bonds (LBHBs) have been proposed to have important influences on the enormous reaction rate increases achieved by many enzymes. Δ5-3-ketosteroid isomerase (KSI) catalyzes the allylic isomerization of Δ5-3-ketosteroid to its conjugated Δ4-isomers at a rate that approaches the diffusion limit. Tyr14, a catalytic residue of KSI, has been hypothesized to form an LBHB with the oxyanion of a dienolate steroid intermediate generated during the catalysis. The unusual chemical shi...

  4. Unified description of hydrogen bonding by a two-state effective Hamiltonian

    CERN Document Server

    McKenzie, Ross H

    2011-01-01

    An effective Hamiltonian is considered for hydrogen bonding between two molecules due to the quantum mechanical interaction between the orbitals of the H-atom and the donor and acceptor atoms in the molecules. The Hamiltonian acts on two diabatic states and has a simple chemically motivated form for its matrix elements. The model gives insight into the "H-bond puzzle", describes different classes of bonds, and empirical correlations between the donor-acceptor distance $R$ and binding energies, bond lengths, and the softening of vibrational frequencies. A key prediction is the UV photo-dissociation of H-bonded complexes via an excited electronic state with an exalted vibrational frequency.

  5. Rotational isomers, intramolecular hydrogen bond, and IR spectra of o-vinylphenol

    International Nuclear Information System (INIS)

    Absorption bands of OH stretching vibrations in IR spectra of o-vinylphenol (o-VP) in the weakly polar solvents CCl4 and n-hexane were studied. Several rotamers of the free OH group were observed for o-VP in n-hexane. The fraction of o-VP rotamers with an O–H…π intramolecular hydrogen bond (IHB) was less than 20% according to experimental estimates for CCl4 solutions and calculations in the gas phase and cyclohexane. The theoretical effective enthalpy of the o-VP IHB was estimated for rotamer A (–ΔH=0.20 kcal/mol). (authors)

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

    Science.gov (United States)

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

    2016-08-01

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

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

    Science.gov (United States)

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

    2015-07-01

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

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

    Science.gov (United States)

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

    2016-06-01

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

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

    Science.gov (United States)

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

    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. Project supported by the National Natural Science Foundation of China (Grant Nos. 11275008, 91021007, and 10974012) and the China Postdoctoral Science Foundation (Grant No. 2014M550005).

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

    International Nuclear Information System (INIS)

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

  11. Intramolecular hydrogen bonding in 5-nitrosalicylaldehyde: IR spectrum and quantum chemical calculations

    Science.gov (United States)

    Moosavi-Tekyeh, Zainab; Taherian, Fatemeh; Tayyari, Sayyed Faramarz

    2016-05-01

    The structural parameters, and vibrational frequencies of 5-nitrosalicylaldehyde (5NSA) were studied by the FT-IR and Raman spectra and the quantum chemical calculations carried out at the B3LYP/6-311++G(d,p) level of theory in order to investigate the intramolecular hydrogen bonding (IHB) present in its structure. The strength and nature of IHB in the optimized structure of 5NSA were studied in detail by means of the atoms in molecules (AIM) and the natural bond orbital (NBO) approaches. The results obtained were then compared with the corresponding data for its parent molecule, salicylaldehyde (SA). Comparisons made between the geometrical structures for 5NSA and SA, their OH/OD stretching and out-of-plane bending modes, their enthalpies for the hydrogen bond, and their AIM parameters demonstrated a stronger H-bonding in 5NSA compared with that in SA. The calculated binding enthalpy (ΔHbind) for 5NSA was -10.92 kcal mol-1. The observed νOH and γOH appeared at about 3120 cm-1 and 786 cm-1 respectively. The stretching frequency shift of H-bond formation was 426 cm-1 which is consistent with ΔHbind and the strength of H-bond in 5NSA. The delocalization energies and electron delocalization indices derived by the NBO and AIM approaches indicate that the resonance effects were responsible for the stronger IHB in 5NSA than in SA.

  12. HR-EELS study of hydrogen bonding configuration, chemical and thermal stability of detonation nanodiamond films

    International Nuclear Information System (INIS)

    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.

  13. Vibrational dephasing in ionic liquids as a signature of hydrogen bonding.

    Science.gov (United States)

    Chatzipapadopoulos, Susana; Zentel, Tobias; Ludwig, Ralf; Lütgens, Matthias; Lochbrunner, Stefan; Kühn, Oliver

    2015-08-24

    Understanding both structure and dynamics is crucial for producing tailor-made ionic liquids (ILs). We studied the vibrational and structural dynamics of medium versus weakly hydrogen-bonded CH groups of the imidazolium ring in ILs of the type [1-alkyl-3-methylimidazolium][bis(trifluoromethanesulfonyl)imide] ([Cn mim][NTf2 ]), with n=1, 2, and 8, by time-resolved coherent anti-Stokes Raman scattering (CARS) and quantum-classical hybrid (QCH) simulations. From the time series of the CARS spectra, dephasing times were extracted by modeling the full nonlinear response. From the QCH calculations, pure dephasing times were obtained by analyzing the distribution of transition frequencies. Experiments and calculations reveal larger dephasing rates for the vibrational stretching modes of C(2)H compared with the more weakly hydrogen-bonded C(4,5)H. This finding can be understood in terms of different H-bonding motifs and the fast interconversion between them. Differences in population relaxation rates are attributed to Fermi resonance interactions. PMID:26175228

  14. The influence of hydrogen bonding on the diffusion behaviour of diastereoisomeric tripeptide derivatives

    Science.gov (United States)

    Gröbel, Angela; Plass, Monika

    1999-05-01

    The diffusion behaviour of the diastereoisomers of Z-Ala-Phe-Val-OMe and Z-Ala-Leu-Val-OMe was studied in solutions of carbon tetrachloride and toluene. The capillary method according to Anderson was used for the diffusion experiment. The loss of the concentration of the tripeptide derivatives in the course of the time was monitored by infrared spectroscopy using their NH stretching vibrations. In general, the diffusion rate of the substances in toluene was 50-100 times larger than in carbon tetrachloride. Also the diastereoisomers differ in their diffusion properties. In carbon tetrachloride this effect is very small but still significant. It can be explained by the strong intramolecular hydrogen bonding of the peptides which leads to C 5 and C 7 rings. In toluene the different configuration of the compounds whose changes are connected with the change in their polar properties are responsible for the observed diffusion rates. The diffusion rate will be discussed in terms of equilibrium constants describing the intramolecular association behaviour and molecular descriptors of the tripeptide derivatives obtained from HPLC measurements in polar solvents. It will be shown that the diffusion rate correlates with the McGowan volume Vx and in part with the effective hydrogen bond acidity ∑ α2H.

  15. Hydrogen bonding of single acetic acid with water molecules in dilute aqueous solutions

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In separation processes,hydrogen bonding has a very significant effect on the efficiency of isolation of acetic acid (HOAc) from HOAc/H2O mixtures. This intermolecular interaction on aggregates composed of a single HOAc molecule and varying numbers of H2O molecules has been examined by using ab initio molecular dynamics simulations (AIMD) and quantum chemical calculations (QCC). Thermodynamic data in aqueous solution were obtained through the self-consistent reaction field calculations and the polarizable continuum model. The aggregation free energy of the aggregates in gas phase as well as in aqueous system shows that the 6-membered ring is the most favorable structure in both states. The relative stability of the ring structures inferred from the thermodynamic properties of the QCC is consistent with the ring distributions of the AIMD simulation. The study shows that in dilute aqueous solution of HOAc the more favorable molecular interaction is the hydrogen bonding between HOAc and H2O molecules,resulting in the separation of acetic acid from the HOAc/H2O mixtures with more difficulty than usual.

  16. On the mean kinetic energy of the proton in strong hydrogen bonded systems

    International Nuclear Information System (INIS)

    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 (XH2PO4, X = K, Cs, Rb, Tl), the DKDP (XD2PO4, X = K, Cs, Rb) type, and the X3H(SO4)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 M3H(SO4)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 ROO, being a measure of the HB strength

  17. Bifurcated hydrogen bonds stabilize fibrils of poly(L-glutamic) acid.

    Science.gov (United States)

    Fulara, Aleksandra; Dzwolak, Wojciech

    2010-06-24

    Model fibrillating homopolypeptides have been providing many insightful analogies to the clinically important phenomena of protein misfolding and amyloidogenesis. Here we show that the beta(2) structural variant of poly(l-glutamic) acid forms fibrils with an amyloid-like morphology, ability to enhance fluorescence of thioflavin T, and seeding properties. The beta(2) fibrils are formed upon heating of aqueous solutions of alpha-helical poly(l-glutamic) acid, which leads to a significant increase of pD (pH) of unbuffered samples and a concomitant precipitation of fibrils with unusual infrared traits: amide I' band being dramatically red-shifted to 1596 cm(-1), and the -COOD stretching band split into two peaks around 1730 and 1719 cm(-1). We are proposing that formation of three-center hydrogen bonds involving bifurcated peptide carbonyl acceptors (>C=O) and main chains' NH, as well as side chains' -COOH proton donors is likely to underlie the observed infrared characteristics of beta(2) fibrils. Such bonds provide additional conformational constraints in a tightly packed environment around glutamate side chains resulting in the decreased overall acidity of the polypeptide. The presence of bifurcated hydrogen bonds in amyloid fibrils may be an overlooked factor in fibrils' robustness, thermodynamic stability and the ability to propagate their own growth. PMID:20509699

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

    Science.gov (United States)

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

    2016-06-01

    Methylamine is an abundant amine compound detected in the atmosphere which can affect the nature of atmospheric aerosol surfaces, changing their chemical and optical properties. Molecular dynamics simulation results show that methylamine accommodation on water is close to unity with the hydrophilic head group solvated in the interfacial environment and the methyl group pointing into the air phase. A detailed analysis of the hydrogen bond network indicates stronger hydrogen bonds between water and the primary amine group at the interface, suggesting that atmospheric trace gases will likely react with the methyl group instead of the solvated amine site. These findings suggest new chemical pathways for methylamine acting on atmospheric aerosols in which the methyl group is the site of orientation specific chemistry involving its conversion into a carbonyl site providing hydrophilic groups for uptake of additional water. This conversion may explain the tendency of aged organic aerosols to form cloud condensation nuclei. At the same time, formation of NH2 radical and formaldehyde is suggested to be a new source for NH2 radicals at aerosol surfaces, other than by reaction of absorbed NH3. The results have general implications for the chemistry of other amphiphilic organics, amines in particular, at the surface of atmospherically relevant aerosols. PMID:27276960

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

    Energy Technology Data Exchange (ETDEWEB)

    McKenzie, Ross H., E-mail: r.mckenzie@uq.edu.au [School of Mathematics and Physics, University of Queensland, Brisbane 4072 (Australia); Athokpam, Bijyalaxmi; Ramesh, Sai G. [Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012 (India)

    2015-07-28

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

  20. 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.

  1. Water-containing hydrogen-bonding network in the active center of channelrhodopsin.

    Science.gov (United States)

    Ito, Shota; Kato, Hideaki E; Taniguchi, Reiya; Iwata, Tatsuya; Nureki, Osamu; Kandori, Hideki

    2014-03-01

    Channelrhodopsin (ChR) functions as a light-gated ion channel in Chlamydomonas reinhardtii. Passive transport of cations by ChR is fundamentally different from the active transport by light-driven ion pumps such as archaerhodopsin, bacteriorhodopsin, and halorhodopsin. These microbial rhodopsins are important tools for optogenetics, where ChR is used to activate neurons by light, while the ion pumps are used for neural silencing. Ion-transport functions by these rhodopsins strongly depend on the specific hydrogen-bonding networks containing water near the retinal chromophore. In this work, we measured protein-bound water molecules in a chimeric ChR protein of ChR1 (helices A to E) and ChR2 (helices F and G) of Chlamydomonas reinhardtii using low-temperature FTIR spectroscopy at 77 K. We found that the active center of ChR possesses more water molecules (9 water vibrations) than those of other microbial (2-6 water vibrations) and animal (6-8 water vibrations) rhodopsins. We conclude that the protonated retinal Schiff base interacts with the counterion (Glu162) directly, without the intervening water molecule found in proton-pumping microbial rhodopsins. The present FTIR results and the recent X-ray structure of ChR reveal a unique hydrogen-bonding network around the active center of this light-gated ion channel. PMID:24512107

  2. Hydrogen-bond interaction assisted branched copolymer HILIC material for separation and N-glycopeptides enrichment.

    Science.gov (United States)

    Shao, Wenya; Liu, Jianxi; Yang, Kaiguang; Liang, Yu; Weng, Yejing; Li, Senwu; Liang, Zhen; Zhang, Lihua; Zhang, Yukui

    2016-09-01

    Hydrophilic interaction chromatography (HILIC) has attracted increasing attention in recent years due to its efficient application in the separation of polar compounds and the enrichment of glycopeptides. However, HILIC materials are still of weak hydrophilicity and thereby present weak retention and selectivity. In this work, branched copolymer modified hydrophilic material Sil@Poly(THMA-co-MBAAm), with high hydrophilicity and unique "claw-like" polyhydric groups, were prepared by "grafting from" thiol-ene click reaction. Due to the abundant functional groups provided by branched copolymer, the material showed excellent retention for nucleosides, necleobases, acidic compounds, sugars and peptides. Furthermore, Sil@Poly(THMA-co-MBAAm) was also applied for the N-glycosylation sites profiling towards the digests of the mouse brain, and 1997N-glycosylated peptides were identified, corresponding to 686 glycoprotein groups. Due to the assisted hydrogen-bond interaction, the selectivity for glycopeptide enrichment in the real sample reached 94.6%, which was the highest as far as we know. All these results indicated that such hydrogen-bond interaction assisted branched copolymer HILIC material possessed great potential for the separation and large scale glycoproteomics analysis. PMID:27343616

  3. DNA-triplex conformation from normal mode and hydrogen bond stability calculations.

    Science.gov (United States)

    Chen, Y. Z.; Prohofsky, E. W.; Powell, J. W.; White, A. P.

    1996-03-01

    Triple-stranded DNAs are of potential applications in genome mapping and in the treatment of genetic disorders with little side-effect. Despite significant interests, structural information of DNA triplexes is limited and sometimes conflicting. For instance, two structural models with different conformation have been proposed for a DNA-triplex Poly(dA)\\cdot2Poly(dT). We propose that the sensitivity of normal modes and hydrogen-bond stability on conformation can be used to determine the structure of biomolecules difficult to access by other methods. The structural model representative of the true conformation should have normal modes in agreement with observations, and have most stable hydrogen bonds which melt at observed temperatures. We carried out calculations on the two models of Poly(dA)\\cdot2Poly(dT) and found that one model is consistent with observations at high humidity and thus most likely a good approximation to the true conformation in that environment. Our method has potential application in structural prediction for other biomolecules.

  4. 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)

  5. Nonadiabatic dynamics of floppy hydrogen bonded complexes: the case of the ionized ammonia dimer.

    Science.gov (United States)

    Chalabala, Jan; Slavíček, Petr

    2016-07-27

    In the case of the ammonia dimer, we address the following questions: how ultrafast ionization dynamics is controlled by hydrogen bonding and whether we can control the products via selective ionization of a specific electron. We use quantum chemical calculations and ab initio non-adiabatic molecular dynamics simulations to model the femtosecond dynamics of the ammonia dimer upon ionization. The role of nuclear quantum effects and thermal fluctuations in predicting the structure of the dimer is emphasized; it is shown that the minimum energy and vibrationally averaged structures are rather different. The ground state structure subsequently controls the ionization dynamics. We describe reaction pathways, electronic population transfers and reaction yields with respect to ionization from different molecular orbitals. The simulations showed that the ionized ammonia dimer is highly unstable and its decay rate is primarily driven by the position of the electron hole. In the case of ground state ionization (i.e. the HOMO electron is ionized), the decay is likely to be preceded by a proton transfer (PT) channel yielding NH4(+) and NH2˙ fragments. The PT is less intense and slower compared with the ionized water dimer. After ionizing deeper lying electrons, mainly NH3(+)˙ and NH3 fragments are formed. Overall, our results show that the ionization dynamics of the ammonia and water dimers differ due to the nature of the hydrogen bond in these systems. PMID:27402376

  6. Mutations in Antibody Fragments Modulate Allosteric Response Via Hydrogen-Bond Network Fluctuations.

    Science.gov (United States)

    Srivastava, Amit; Tracka, Malgorzata B; Uddin, Shahid; Casas-Finet, Jose; Livesay, Dennis R; Jacobs, Donald J

    2016-05-10

    A mechanical perturbation method that locally restricts conformational entropy along the protein backbone is used to identify putative allosteric sites in a series of antibody fragments. The method is based on a distance constraint model that integrates mechanical and thermodynamic viewpoints of protein structure wherein mechanical clamps that mimic substrate or cosolute binding are introduced. Across a set of six single chain-Fv fragments of the anti-lymphotoxin-β receptor antibody, statistically significant responses are obtained by averaging over 10 representative structures sampled from a molecular dynamics simulation. As expected, the introduced clamps locally rigidify the protein, but long-ranged increases in both rigidity and flexibility are also frequently observed. Expanding our analysis to every molecular dynamics frame demonstrates that the allosteric responses are modulated by fluctuations within the hydrogen-bond network where the native ensemble is comprised of conformations that both are, and are not, affected by the perturbation in question. Population shifts induced by the mutations alter the allosteric response by adjusting which hydrogen-bond networks are the most probable. These effects are compared using response maps that track changes across each single chain-Fv fragment, thus providing valuable insight into how sensitive allosteric mechanisms are to mutations. PMID:27166802

  7. Intermolecular interactions in cyclic complexes with hydrogen bond of bifunctional N-containing compounds in solution

    International Nuclear Information System (INIS)

    The structure of molecular and ionic hydrogen-bonded complexes formed by bifunctional N-containing molecules, which can act as proton donor and proton acceptor simultaneously, and the nature of molecular interactions in these complexes were studied in solution. The spectroscopic, steric and thermodynamic characteristics of self-associates of 3,5-dimethylpyrazole, diphenylformamidine, diphenylguanidine and diphenyltriazene and complexes of these compounds with carboxylic acids were obtained. The quantum chemical calculations of the structure of complexes and the vibrational frequencies in IR spectra were carried out in the harmonic approximation and with the anharmonic effects taken into account. It was shown that under the interaction with weak carboxylic acids (HCOOH, CH3COOH, CH2ClCOOH) the complexes have molecular structure with two H-bonds NH...O=C and OH...N, and the interaction with strong acids (CHCl2COOH, CCl3COOH, CF3COOH) results in formation of cyclic hydrogen-bonded ionic pairs with proton transfer from hydroxyl group to the N atom of the azo-compound. (authors)

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

    CERN Document Server

    McKenzie, Ross H; Ramesh, Sai

    2015-01-01

    If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor $\\Phi$ is correlated with the strength of the intramolecular hydrogen bonds. This correlation has been used to determine the length of the H-bonds (donor-acceptor separation) in a diverse range of enzymes and has been argued to support the existence of short low-barrier H-bonds. Starting with a potential energy surface based on a simple diabatic state model for H-bonds we calculate $\\Phi$ as a function of the proton donor-acceptor distance $R$. For numerical results, we use a parameterization of the model for symmetric O-H.... O bonds. We consider the relative contributions of the O-H stretch vibration, O-H bend vibrations (both in plane and out of plane), tunnelling splitting effects at...

  9. Hydrogen bonding in (substituted benzene)·(water)n clusters with n≤4

    International Nuclear Information System (INIS)

    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)·(H2O)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·(H2O)1and2 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.)

  10. ADSORPTION OF TANNIN FROM AQUEOUS SOLUTION ONTO MACROPOROUS CROSSLINKED POLY(N—VINYL—ACETAMIDE)VIA HYDROGEN BONDING

    Institute of Scientific and Technical Information of China (English)

    XUMancai; XUMingcheng; 等

    2000-01-01

    A Strongly hydrophilic hydrogen-bonding adsorbent-macroporous crosslinked Poly(Nvinyl-acetamide),which contain both hydrogen bond acceptor and donator,was synthesized.Adsorption mechanism and dynamic adsorption of tannin from aqueous solution onto the adsorbent were investigated.Most of the differntial adsorption heats for various adsorption capacities calculated from the adsorption isotherms according to Clapeyron-Clausius equation lay in the range of hydrogen bond energy(8-50J/mol).Adsorption properties of the adsorbent were studied in detail.These results revealed a hydrogen bonding mechanism of the adsorption of tannin from aqueous solution onto the adsorbent.The result of the dynamic adsorption of tanning with the initial concentration under 600mg/L showed that the adsorption rate of tannin exceeded 90% when the flow rate was 3BV/h and the effluent volume reached 100BV.Therefore,the developed hydrogen-bonding adsorbent-macroporous crosslinked poly(N-vinyl-acetamide)-is an excellent adsorbent to remove tannin from extract of natural products,and has great value in application.

  11. On the Correlation between the Blue Shift of Hydrogen Bonding and the Proton Donor-Proton Acceptor Distance

    Institute of Scientific and Technical Information of China (English)

    WANG,Jin-Ti(王金姼); FENG,Yong(封勇); LIU,Lei(刘磊); LI,Xiao-Song(李晓松); GUO,Qing-Xiang(郭庆祥)

    2004-01-01

    It is demonstrated that in all types of hydrogen bonds (X-H…Y) there is a balance between the long-range attractive orbital interactions and short-range Pauli/nucleus repulsions. When the proton acceptor approaches the proton donor from distance, the hydrogen bonding energy becomes more negative at relatively large distance, goes through a minimum, and then starts to become less negative when the short-range repulsive forces come into effect.Meanwhile, the X-H bond length increases at relatively large distances, goes through a maximum and starts to shorten when the short-range repulsive forces come into effect. Whether the hydrogen bond is red or blue shifted is dictated by the energy minimum position. If at the energy minimum position the X-H bond length is shorter than that for the free monomer, the hydrogen bond is blue shifted and vice versa. Further studies demonstrate that the recent report about the correlation of C-H bond lengths with proton donor-acceptor distance in F3C-H…OH2 and F3C-H…Cl- is not fully correct because the authors conducted an inappropriate comparison. Furthermore, it is shown for the first time that the Pauli/nucleus repulsion theory is applicable to the blue-shifted hydrogen bonds in the X-H…π complexes and the blue-shifted lithium bonds in the X-Li…Y complexes.

  12. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure.

    Science.gov (United States)

    Boobbyer, D N; Goodford, P J; McWhinnie, P M; Wade, R C

    1989-05-01

    An empirical energy function designed to calculate the interaction energy of a chemical probe group, such as a carbonyl oxygen or an amine nitrogen atom, with a target molecule has been developed. This function is used to determine the sites where ligands, such as drugs, may bind to a chosen target molecule which may be a protein, a nucleic acid, a polysaccharide, or a small organic molecule. The energy function is composed of a Lennard-Jones, an electrostatic and a hydrogen-bonding term. The latter is dependent on the length and orientation of the hydrogen bond and also on the chemical nature of the hydrogen-bonding atoms. These terms have been formulated by fitting to experimental observations of hydrogen bonds in crystal structures. In the calculations, thermal motion of the hydrogen-bonding hydrogen atoms and lone-pair electrons may be taken into account. For example, in a alcoholic hydroxyl group, the hydrogen may rotate around the C-O bond at the observed tetrahedral angle. In a histidine residue, a hydrogen atom may be bonded to either of the two imidazole nitrogens and movement of this hydrogen will cause a redistribution of charge which is dependent on the nature of the probe group and the surrounding environment. The shape of some of the energy functions is demonstrated on molecules of pharmacological interest. PMID:2709375

  13. Patterning a hydrogen-bonded molecular monolayer with a hand-controlled scanning probe microscope

    Directory of Open Access Journals (Sweden)

    Matthew F. B. Green

    2014-10-01

    Full Text Available One of the paramount goals in nanotechnology is molecular-scale functional design, which includes arranging molecules into complex structures at will. The first steps towards this goal were made through the invention of the scanning probe microscope (SPM, which put single-atom and single-molecule manipulation into practice for the first time. Extending the controlled manipulation to larger molecules is expected to multiply the potential of engineered nanostructures. Here we report an enhancement of the SPM technique that makes the manipulation of large molecular adsorbates much more effective. By using a commercial motion tracking system, we couple the movements of an operator's hand to the sub-angstrom precise positioning of an SPM tip. Literally moving the tip by hand we write a nanoscale structure in a monolayer of large molecules, thereby showing that our method allows for the successful execution of complex manipulation protocols even when the potential energy surface that governs the interaction behaviour of the manipulated nanoscale object(s is largely unknown.

  14. Hydrogen Bonds in GlcNAc(β1,3)Gal(β)OMe in DMSO Studied by NMR Spectroscopy and Molecular Dynamics Simulations

    International Nuclear Information System (INIS)

    Hydrogen bond is an important factor in the structures of carbohydrates. Because of great strength, short range, and strong angular dependence, hydrogen bonding is an important factor stabilizing the structure of carbohydrate. In this study, conformational properties and the hydrogen bonds in GlcNAc(β1,3)Gal(β)OMe in DMSO are investigated through NMR spectroscopy and molecular dynamics simulation. Lowest energy structure in the adiabatic energy map was utilized as an initial structure for the molecular dynamics simulations in DMSO. NOEs, temperature coefficients, SIMPLE NMR data, and molecular dynamics simulations proved that there is a strong intramolecular hydrogen bond between O7' and HO3' in GlcNAc(β1,3)Gal(β)OMe in DMSO. In aqueous solution, water molecule makes intermolecular hydrogen bonds with the disaccharides and there was no intramolecular hydrogen bonds in water. Since DMSO molecule is too big to be inserted deep into GlcNAc(β1,3)Gal(β)OMe, DMSO can not make strong intermolecular hydrogen bonding with carbohydrate and increases the ability of O7' in GlcNAc(β1,3)Gal(β)OMe to participate in intramolecular hydrogen bonding. Molecular dynamics simulation in conjunction with NMR experiments proves to be efficient way to investigate the intramolecular hydrogen bonding existed in carbohydrate

  15. Ab initio and AIM theoretical analysis of hydrogen-bond radius of HD (D = F, Cl, Br, CN, HO, HS and CCH) donors and some acceptors

    OpenAIRE

    Raghavendra, B; Pankaj K Mandal; Arunan, E

    2006-01-01

    Recently, we defined ‘hydrogen-bond radii’ for various hydrogen-bond donors, DH where D=F, Cl, Br, CN, HO or CCH from an empirical analysis. It was shown that the $A^{...} H$ distances in $B^{...}HD$ complexes could be written as a sum of hydrogen bond radius for DH and a constant acceptor radius for A, which is the bonding atom/centre in B. This manuscript reports the determination of the hydrogen-bond radii for these molecules and $H_2S$ from ab initio and atoms in molecules (AIM) theoreti...

  16. Replacing the hydrogen in the intermolecular hydrogen bond of the cyanuric acid-bipyridyl adduct by Ag(I)

    Indian Academy of Sciences (India)

    K Sivashankar; Anupama Ranganathan; V R Pedireddi

    2000-04-01

    A complex between cyanuric acid (CA), 4,4′-bipyridyl (BP) and Ag(I), with the composition, [Ag2(C3H2N3O3-N)2 (C10H8N2-N)] has been prepared. Crystal structure analysis shows that it has a chain structure in which the CA molecules are linked to the BP units through silver atoms by the formation of N-Ag-N bonds, wherein one of the hydrogens of CA is replaced by Ag(I), showing thereby the chains connected to one another by N-H${\\ldots}$O hydrogen bonds formed between the CA molecules. This intermolecular chain structure resembles the chain structure of the CA.BP adduct where CA-BP-CA chains formed by N-H${\\ldots}$N hydrogen bonds are linked to one another by N-H${\\ldots}$O hydrogen bonds between the CA molecules.

  17. Effects of dimethyl sulfoxide on the hydrogen bonding structure and dynamics of aqueous N-methylacetamide solution

    Indian Academy of Sciences (India)

    APRAMITA CHAND; SNEHASIS CHOWDHURI

    2016-06-01

    Effects of dimethyl-sulfoxide (DMSO) on the hydrogen bonding structure and dynamics in aqueousN-methylacetamide (NMA) solution are investigated by classical molecular dynamics simulations. Themodifications of structure and interaction between water and NMA in presence of DMSO molecules are calculatedby various site-site radial distribution functions and average interaction energies between these speciesin the solution. It is observed that the aqueous peptide hydrogen bond interaction is relatively stronger withincreasing concentration of DMSO, whereas methyl-methyl interaction between NMA and DMSO decreasessignificantly. The DMSO molecule prefers to interact with amide-hydrogen of NMA even at lower DMSO concentration.The lifetimes and structural-relaxation times of NMA-water, water-water and DMSO-water hydrogenbonds are found to increase with increasing DMSO concentration in the solution. The slower translationaland rotational dynamics of NMA is observed in concentrated DMSO solution due to formation of strongerinter-species hydrogen bonds in the solution.

  18. Hydrogen bonds in 1-indanone: Charge density analysis and simulation of the inelastic neutron scattering spectrum in solid phase

    International Nuclear Information System (INIS)

    The influence of the intermolecular interactions on the vibrational dynamics of 1-indanone has been checked by simulating the INS spectrum from molecular and DFT periodic calculations, showing that, even in the case of weak hydrogen bonds, those modes associated with lower energy transfer are affected in the solid state. The electron charge distribution of solid 1-indanone has also been studied from a DFT periodic calculation. In order to obtain some insight into the intermolecular interactions Bader's atoms in molecules theory has been used. After a careful analysis of the topological properties of the calculated electron density, bond paths, critical points and other related properties, most of the C-H...π and C-H...O weak hydrogen bonds predicted in the experimental X-ray structure are confirmed. In addition some new H?H interactions were found. Furthermore, a natural bond orbital analysis was performed describing each hydrogen bond as donor-acceptor interactions

  19. Hydrogen bonding asymmetric star-shape derivative of bile acid leads to supramolecular fibrillar aggregates that wrap into micrometer spheres.

    Science.gov (United States)

    Myllymäki, Teemu T T; Nonappa; Yang, Hongjun; Liljeström, Ville; Kostiainen, Mauri A; Malho, Jani-Markus; Zhu, X X; Ikkala, Olli

    2016-09-14

    We report that star-shaped molecules with cholic acid cores asymmetrically grafted by low molecular weight polymers with hydrogen bonding end-groups undergo aggregation to nanofibers, which subsequently wrap into micrometer spherical aggregates with low density cores. Therein the facially amphiphilic cholic acid (CA) is functionalized by four flexible allyl glycidyl ether (AGE) side chains, which are terminated with hydrogen bonding 2-ureido-4[1H]pyrimidinone (UPy) end-groups as connected by hexyl spacers, denoted as CA(AGE6-C6H12-UPy)4. This wedge-shaped molecule is expected to allow the formation of a rich variety of solvent-dependent structures due to the complex interplay of interactions, enabled by its polar/nonpolar surface-active structure, the hydrophobicity of the CA in aqueous medium, and the possibility to control hydrogen bonding between UPy molecules by solvent selection. In DMSO, the surfactant-like CA(AGE6-C6H12-UPy)4 self-assembles into nanometer scale micelles, as expected due to its nonpolar CA apexes, solubilized AGE6-C6H12-UPy chains, and suppressed mutual hydrogen bonds between the UPys. Dialysis in water leads to nanofibers with lateral dimensions of 20-50 nm. This is explained by promoted aggregation as the hydrogen bonds between UPy molecules start to become activated, the reduced solvent dispersibility of the AGE-chains, and the hydrophobicity of CA. Finally, in pure water the nanofibers wrap into micrometer spheres having low density cores. In this case, strong complementary hydrogen bonds between UPy molecules of different molecules can form, thus promoting lateral interactions between the nanofibers, as allowed by the hydrophobic hexyl spacers. The wrapping is illustrated by transmission electron microscopy tomographic 3D reconstructions. More generally, we foresee hierarchically structured matter bridging the length scales from molecular to micrometer scale by sequentially triggering supramolecular interactions. PMID:27491728

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

    International Nuclear Information System (INIS)

    The maximum-entropy charge densities of six amino acids and peptides reveal systematic dependencies of the properties at bond critical points on bond lengths. MEM densities demonstrate that low-order multipoles (lmax = 1) and isotropic atomic displacement parameters for H atoms in the multipole model are insufficient for capturing all the features of charge densities in hydrogen bonds. Charge densities have been determined by the Maximum Entropy Method (MEM) from the high-resolution, low-temperature (T ≃ 20 K) X-ray diffraction data of six different crystals of amino acids and peptides. A comparison of dynamic deformation densities of the MEM with static and dynamic deformation densities of multipole models shows that the MEM may lead to a better description of the electron density in hydrogen bonds in cases where the multipole model has been restricted to isotropic displacement parameters and low-order multipoles (lmax = 1) for the H atoms. Topological properties at bond critical points (BCPs) are found to depend systematically on the bond length, but with different functions for covalent C—C, C—N and C—O bonds, and for hydrogen bonds together with covalent C—H and N—H bonds. Similar dependencies are known for AIM properties derived from static multipole densities. The ratio of potential and kinetic energy densities |V(BCP)|/G(BCP) is successfully used for a classification of hydrogen bonds according to their distance d(H⋯O) between the H atom and the acceptor atom. The classification based on MEM densities coincides with the usual classification of hydrogen bonds as strong, intermediate and weak [Jeffrey (1997) ▶. An Introduction to Hydrogen Bonding. Oxford University Press]. MEM and procrystal densities lead to similar values of the densities at the BCPs of hydrogen bonds, but differences are shown to prevail, such that it is found that only the true charge density, represented by MEM densities, the multipole model or some other method can lead

  1. Computational evidence for intramolecular hydrogen bonding and nonbonding X···O interactions in 2'-haloflavonols

    Directory of Open Access Journals (Sweden)

    Tânia A. O. Fonseca

    2012-01-01

    Full Text Available The conformational isomerism and stereoelectronic interactions present in 2'-haloflavonols were computationally analyzed. On the basis of the quantum theory of atoms in molecules (QTAIM and natural bond orbital (NBO analysis, the conformer stabilities of 2'-haloflavonols were found to be dictated mainly by a C=O···H–O intramolecular hydrogen bond, but an unusual C–F···H–O hydrogen-bond and intramolecular C–X···O nonbonding interactions are also present in such compounds.

  2. Dynamical Binding of Hydrogen Bond Surrogate-Derived Bak Helices to Anti-apoptotic Protein Bcl-xL

    OpenAIRE

    Bao, Ju; Dong, Xiao Y.; John Z. H. Zhang; Arora, Paramjit S.

    2009-01-01

    A new peptide modification strategy was recently developed to replace the i to i+4 hydrogen bond of the main chain of an a-helix with a carbon-carbon covalent bond to afford highly stable constrained α-helices, termed Hydrogen Bond Surrogate (HBS) helices. HBS helices that mimic the Bak BH3 domains were experimentally demonstrated to target protein Bcl-xL with high affinity. In this study, molecular dynamics (MD) simulation is used to understand how the covalent modification of the natural Ba...

  3. Infrared study of the hydrogen bonding site in a poly-functional schiff base: N( sp2) or N( sp)?

    Science.gov (United States)

    Laureys, C.; Zeegers-Huyskens, Th.

    1987-05-01

    The hydrogen bond complexes between phenol derivatives and the Schiff base [(diphenylmethylene)amino]-acetonitrile have been studied by infrared spectroscopy in carbon tetrachloride solution. The thermodynamic data and the infrared spectra investigated in the ν OH, ν CN and ν CN region indicate that complex formation occurs at the nitrogen atom of the nitrile function. The hydrogen bonding site is in this case governed by the accessibility of the lone pair which is markedly higher for the N( sp) than the N( sp2) electrons.

  4. 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

    The far-infrared absorption spectra have been recorded for hydrogen-bonded complexes of water with methanol and t-butanol embedded in cryogenic neon matrices at 2.8 K. The partial isotopic substitution of individual subunits enabled by a dual inlet deposition procedure provides for the first time...... unambiguous assignments of the intermolecular high-frequency out-of-plane and low-frequency in-plane donor OH librational modes for mixed alcohol–water complexes. The vibrational assignments confirm directly that water acts as the hydrogen bond donor in the most stable mixed complexes and the tertiary alcohol...

  5. Estimation of Abraham solvation equation coefficients for hydrogen bond formation from Abraham solvation parameters for solute acidity and basicity.

    Science.gov (United States)

    van Noort, Paul

    2013-01-01

    Abraham solvation equations find widespread use in environmental chemistry and pharmaco-chemistry. The coefficients in these equations, which are solvent (system) descriptors, are usually determined by fitting experimental data. To simplify the determination of these coefficients in Abraham solvation equations, this study derives equations, based on Abraham solvation parameters for hydrogen acidity and basicity of the solvents involved, to estimate the value of the coefficients for hydrogen bond formation. These equations were applied to calculate Abraham solvation parameters for hydrogen acidity and basicity for polyoxymethylene, polyacrylate, sodium dodecylsulfate, some ionic liquids, alkanoyl phosphatidyl cholines, and lipids for which fitted values for Abraham coefficients for hydrogen bond formation were available. PMID:22892357

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

    Directory of Open Access Journals (Sweden)

    Vöhringer Peter

    2013-03-01

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

  7. Hydrogen bonds in the structure of BaC2O4xD2O

    International Nuclear Information System (INIS)

    The hydrogen bonds in the crystal structure of BaC2O4xD2O were investigated from profile refinement of neutron powder diffraction data. The structure is monoclinic, space group C2/m (No. 12) with the lattice parameters a = 10.0648(3), b = 7.9350(2), c = 6.8503(2) Aa, β = 122.35(2) deg. and Z = 4. The barium atom in the structure is coordinated with ten oxygen atoms, the oxalate ion is planar, and the OD-O hydrogen-bond length is 2.762(5) Aa. (au)

  8. Hydrogen bond dynamics in liquid water: Ab initio molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Cheolhee; Kim, Eunae [College of Pharmacy, Chosun University, Gwangju (Korea, Republic of); Yeom, Min Sun [Korea Institute of Science and Technology Information, Daejeon (Korea, Republic of)

    2016-01-15

    The effect of intermolecular interaction on the distribution of the harmonic vibrational frequencies of water molecules was investigated through ab initio molecular dynamics simulations based on the Born-Oppenheimer approach. For single water, the effect of the dynamics of the oxygen atom in single water and the simulation time step on the frequency distribution were examined. The distributions of the OH stretching and HOH bending vibrational frequencies of liquid water were compared to those of single water. The probability distributions of the change in OH bond length and the lifetime of the dangling OH bond were also obtained. The distribution of the frequencies was strongly affected by the long lifetime of the dangling OH bond, resulting in the formation of hydrogen bonds between water molecules.

  9. Nano-scale hydrogen-bond network improves the durability of greener cements.

    Science.gov (United States)

    Jacobsen, Johan; Rodrigues, Michelle Santos; Telling, Mark T F; Beraldo, Antonio Ludovico; Santos, Sérgio Francisco; Aldridge, Laurence P; Bordallo, Heloisa N

    2013-01-01

    More than ever before, the world's increasing need for new infrastructure demands the construction of efficient, sustainable and durable buildings, requiring minimal climate-changing gas-generation in their production. Maintenance-free "greener" building materials made from blended cements have advantages over ordinary Portland cements, as they are cheaper, generate less carbon dioxide and are more durable. The key for the improved performance of blends (which substitute fine amorphous silicates for cement) is related to their resistance to water penetration. The mechanism of this water resistance is of great environmental and economical impact but is not yet understood due to the complexity of the cement's hydration reactions. Using neutron spectroscopy, we studied a blend where cement was replaced by ash from sugar cane residuals originating from agricultural waste. Our findings demonstrate that the development of a distinctive hydrogen bond network at the nano-scale is the key to the performance of these greener materials. PMID:24036676

  10. Mixed Intramolecular Hydrogen Bonding in Dihydroxythiophene-based Units and Boron and Technetium Chelation

    International Nuclear Information System (INIS)

    Three novel potential metal ion chelating units have been synthesized and characterized: 5-hexylcarbamoyl- 3,4-dihydroxythiophene-2-carboxylic acid methyl ester (5), 3-benzyloxy-4-hydroxythiophene-2,5-dicarboxylic acid bis-hexylamide (6), and 3,4-dihydroxythiophene-2,5-dicarboxylic acid bis-hexylamide (7). The crystal structure of 6 was obtained and suggests the presence of three distinct intramolecular hydrogen bonds, namely [Namide-H···O] [O-H···Oamide] and [Namide-H···S]. Boron chelation with 5, 6 and 7 through the use of BF3, B(OH)3 or B(OMe)3 was probed by 1H, 11B, and 13C NMR spectroscopy. Technetium (I) chelation with 5, 6 and 7 was also studied via HPLC elutions using [99mTc(CO)3(OH2)3]+

  11. Proton conductivity in quasi-one dimensional hydrogen-bonded systems: A nonlinear approach

    International Nuclear Information System (INIS)

    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

  12. Electronic structure of planar-quasicycled organic molecules with intramolecular hydrogen bond

    Directory of Open Access Journals (Sweden)

    ALEXEI N. PANKRATOV

    2007-03-01

    Full Text Available By means of the HF/6-311G(d,p method, the electronic structure of the series of organic molecules, among which are malonaldehyde, acetylacetone, thiomalonaldehyde,’the derivatives of aniline 2-XC6H4NH2, phenol 2-XC6H4OH, benzenethiol 2-XC6H4SH (X = CHO, COOH, COO-, NO, NO2, OH, OCH3, SH, SCH3, F, Cl, Br, 8-hydroxyquinoline, 8-mercaptoquinoline, tropolone, has been studied. The intramolecular hydrogen bond (IHB has been established to lead to a local electron redistribution in quasicycle, and primarily to the electron density transfer between the direct IHB participants – from the hydrogen atom toward the proton-aceptor atom. On forming the IHB of the S–H···O type, the electron density in general decreases on the sulphohydryl hydrogen atom and increases on the sulphur atom.

  13. Stretchable gas barrier achieved with partially hydrogen-bonded multilayer nanocoating.

    Science.gov (United States)

    Holder, Kevin M; Spears, Benjamin R; Huff, Molly E; Priolo, Morgan A; Harth, Eva; Grunlan, Jaime C

    2014-05-01

    Super gas barrier nanocoatings are recently demonstrated by combining polyelectrolytes and clay nanoplatelets with layer-by-layer deposition. These nanobrick wall thin films match or exceed the gas barrier of SiOx and metallized films, but they are relatively stiff and lose barrier with significant stretching (≥ 10% strain). In an effort to impart stretchability, hydrogen-bonding polyglycidol (PGD) layers are added to an electrostatically bonded thin film assembly of polyethylenimine (PEI) and montmorillonite (MMT) clay. The oxygen transmission rate of a 125-nm thick PEI-MMT film increases more than 40x after being stretched 10%, while PGD-PEI-MMT trilayers of the same thickness maintain its gas barrier. This stretchable trilayer system has an OTR three times lower than the PEI-MMT bilayer system after stretching. This report marks the first stretchable high gas barrier thin film, which is potentially useful for applications that require pressurized elastomers. PMID:24700525

  14. New observations on hydrogen bonding in ice by density functional theory simulations

    International Nuclear Information System (INIS)

    In this paper, we report on a series of computational simulations on hydrogen bonding in two ice phases (Ih and Ic) using CASTEP with PW91 and RPBE exchange—correlation based on ab initio density functional theory. The strength of the H-bond is correlated with intramolecular O—H stretching, and the energy splitting exists for both the H-bond and covalent O—H stretching. By analyzing the dispersion relationship of ω(q), we observe the separation of the longitudinal optic (LO) mode from transverse optic (TO) mode at the gamma point, seemingly interpreting the controversial two H-bond peaks in the vibrational spectrum of ice recorded by inelastic incoherent neutron scattering experiments. The test of ambient environment on phonon density of sates (PDOS) shows that the relaxed tetrahedral structure is the most stable structural configuration for water clusters. (condensed matter: structural, mechanical, and thermal properties)

  15. Molecular modeling of hydrogen bonding fluids: Vapor-liquid coexistence and interfacial properties

    CERN Document Server

    Horsch, Martin; Merker, Thorsten; Schnabel, Thorsten; Huang, Yow-Lin; Hasse, Hans; Vrabec, Jadran

    2010-01-01

    A major challenge for molecular modeling consists in optimizing the unlike interaction potentials. In many cases, combination rules are generally suboptimal when accurate predictions of properties like the mixture vapor pressure are needed. However, the well known Lorentz-Berthelot rule performs quite well and can be used as a starting point. If more accurate results are required, it is advisable to adjust the dispersive interaction energy parameter. In the present study, mixture properties are explored for binary systems containing hydrogen bonding components. Furthermore, vapor-liquid interface cluster criteria and contact angles are discussed and remarks on computational details are given. Finally, a sterically accurate generic model for benzyl alcohol is introduced and evaluated.

  16. Assembly of oriented zeolite monolayers and thin films on polymeric surfaces via hydrogen bonding.

    Science.gov (United States)

    Zhou, Ming; Liu, Xiufeng; Zhang, Baoquan; Zhu, Huiming

    2008-10-21

    The b-oriented monolayers of microsized silicalite-1 crystals have been manually assembled on glass plate supported poly(ethylene oxide) (PEO), poly(vinyl alcohol) (PVA), chitosan, and poly(methyl methacrylate) (PMMA) thin films via hydrogen bonding with much enhanced binding strength and satisfactory degrees of coverage and close packing. The exerted pressure and rubbing time in the manual assembly do not affect the binding strength of the silicalite-1 monolayer on the glass plate supported polymeric film. This manual assembly has been further applied to fabricate zeolite monolayers on commercially available Plexiglas surfaces and b-oriented multilayered films of silicalite-1 crystals on glass plates. The assembly method established in this study provides a feasible way to produce zeolite monolayers on polymer-modified solid substrates and Plexiglas and to fabricate zeolite-polymer composite membranes by means of the layer-by-layer technique. PMID:18785711

  17. Room temperature supramolecular columnar liquid crystals formed by hydrogen bonding of isoquinoline derivatives

    Science.gov (United States)

    Hyup Lee, Jun; Lee, Seung Jun; Jho, Jae Young

    2014-07-01

    We report new self-assembled discotic liquid crystals exhibiting columnar mesophases at room temperature, which are constructed by intermolecular hydrogen bonding between the core of 1,3,5-trihydroxybenzene or 1,3,5-cyclohexanetricarboxylic acid and the peripheral molecules of isoquinoline derivatives. The mesomorphic properties of supramolecular liquid crystals were investigated by differential scanning calorimetry, polarized optical microscopy, and X-ray diffraction studies. The self-assembled liquid crystals exhibited rectangular columnar phases (Colro) with an ordered stacking structure of the mesogens in a column at room temperature, regardless of the type of the core molecule, due probably to the close-packed aromatic rings around a core molecule and the angular structure in three arms of the discotic mesogen. These room temperature columnar phases are rare examples for the discotic liquid crystals, and our findings in the present study provide a new way to prepare low melting columnar liquid crystalline materials for molecular electronics.

  18. Hydrogen-bonding interactions in thiosemicarbazones of carboxylic acids: Structure of 2-ketobutyric acid thiosemicarbazone hemihydrate

    International Nuclear Information System (INIS)

    2-Thiosemicarbazonobutanoic acid hemihydrate, C5H9N3O2S.0.5H2O, Mr=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) A3, Z=4, Dx=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.)

  19. Hydrogen Bond Formation between the Carotenoid Canthaxanthin and the Silanol Group on MCM-41 Surface.

    Science.gov (United States)

    Gao, Yunlong; Xu, Dayong; Kispert, Lowell D

    2015-08-20

    The formation of one or two hydrogen bonds (H-bonds) between canthaxanthin (CAN), a dye, and the silanol group(s) on the MCM-41 surface has been studied by density functional theory (DFT) calculations and calorimetric experiments. It was found that the formation of the H-bond(s) stabilized the CAN molecule more than its radical cation (CAN(•+)). The charge distribution, bond lengths, and the HOMO and LUMO energies of CAN are also affected. The formation of the H-bond(s) explains the lower photoinduced electron transfer efficiency of CAN imbedded in Cu-MCM-41 versus that for β-carotene (CAR) imbedded in Cu-MCM-41 where complex formation with Cu(2+) dominates. These calculations show that to achieve high electron transfer efficiency for a dye-sensitized solar cell, H-bonding between the dye and the host should be avoided. PMID:26230844

  20. 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.

  1. Hydrogen-bonded complexes of 2-aminopyrimidine-parabenzoquinone in an argon matrix

    Science.gov (United States)

    Plokhotnichenko, A. M.; Stepanian, S. G.; Karachevtsev, V. A.; Adamowicz, L.

    2006-02-01

    The H-bonded complexes of 2-aminopyrimidine (NH2Py) with parabenzoquinone (Qu) in a low-temperature argon matrix are investigated by the method of IR spectroscopy. The IR absorption spectra in the spectral range 400-3600cm-1 are obtained for different concentration ratios of these compounds at a temperature of 11K. The molar integrated absorption coefficients in the bands of the stretching modes of the free and H-bonded NH2 group are determined. Quantum-mechanical calculations of the IR spectra of the NH2Py and Qu molecules and their dimers are carried out. A comparison of the experimental and calculated results permits the conclusion that NH2Py-Qu dimers in an argon matrix have a planar structure with two weak hydrogen bonds, NH ⋯O and CH ⋯N.

  2. Large Angular Jump Mechanism Observed for Hydrogen Bond Exchange in Aqueous Perchlorate Solution

    Energy Technology Data Exchange (ETDEWEB)

    Ji, Minbiao; /SLAC, PULSE /Stanford U., Phys. Dept.; Odelius3, Michael; /Stockholm U.; Gaffney1, K.J.; /aff SLAC, PULSE

    2010-06-11

    The mechanism for hydrogen bond (H-bond) switching in solution has remained subject to debate despite extensive experimental and theoretical studies. We have applied polarization-selective multidimensional vibrational spectroscopy to investigate the H-bond exchange mechanism in aqueous NaClO{sub 4} solution. The results show that a water molecule shifts its donated H-bonds between water and perchlorate acceptors by means of large, prompt angular rotation. Using a jump-exchange kinetic model, we extract an average jump angle of 49 {+-} 4{sup o}, in qualitative agreement with the jump angle observed in molecular dynamics simulations of the same aqueous NaClO{sub 4} solution.

  3. Liquid crystal nanocomposites produced by mixtures of hydrogen bonded achiral liquid crystals and functionalized carbon nanotubes

    Science.gov (United States)

    Katranchev, B.; Petrov, M.; Keskinova, E.; Naradikian, H.; Rafailov, P. M.; Dettlaff-Weglikowska, U.; Spassov, T.

    2014-12-01

    The liquid crystalline (LC) nature of alkyloxybenzoic acids is preserved after adding of any mesogenic or non-mesogenic compound through hydrogen bonding. However, this noncovalent interaction provokes a sizable effect on the physical properties as, e. g. melting point and mesomorphic states. In the present work we investigate nanocomposites, prepared by mixture of the eighth homologue of p-n-alkyloxybenzoic acids (8OBA) with single-walled carbon nanotubes (SWCNT) with the purpose to modify the optical properties of the liquid crystal. We exercise optical control on the LC system by inserting SWCNT specially functionalized by carboxylic groups. Since the liquid crystalline state combines order and mobility at the molecular (nanoscale) level, molecular modification can lead to different macroscopical nanocomposite symmetry. The thermal properties of the functionalized nanocomposite are confirmed by DSC analyses. The mechanism of the interaction between surface-treated nanoparticles (functionalized nanotubes) and the liquid crystal 8OBA bent- dimer molecules is briefly discussed.

  4. Hydrogen bonds in the nucleobase-gold complexes: Photoelectron spectroscopy and density functional calculations

    Science.gov (United States)

    Cao, Guo-Jin; Xu, Hong-Guang; Li, Ren-Zhong; Zheng, Weijun

    2012-01-01

    The nucleobase-gold complexes were studied with anion photoelectron spectroscopy and density functional calculations. The vertical detachment energies of uracil-Au-, thymine-Au-, cytosine-Au-, adenine-Au-, and guanine-Au- were estimated to be 3.37 ± 0.08 eV, 3.40 ± 0.08 eV, 3.23 ± 0.08 eV, 3.28 ± 0.08 eV, and 3.43 ± 0.08 eV, respectively, based on their photoelectron spectra. The combination of photoelectron spectroscopy experiments and density functional calculations reveals the presence of two or more isomers for these nucleobase-gold complexes. The major isomers detected in the experiments probably are formed by Au anion with the canonical tautomers of the nucleobases. The gold anion essentially interacts with the nucleobases through N-H...Au hydrogen bonds.

  5. Strong orbital interaction in a weak CH-π hydrogen bonding system.

    Science.gov (United States)

    Li, Jianfu; Zhang, Rui-Qin

    2016-01-01

    For the first time, the intermolecular orbital interaction between benzene and methane in the benzene-methane complex, a representative of weak interaction system, has been studied by us using ab initio calculations based on different methods and basis sets. Our results demonstrate obvious intermolecular orbital interaction between benzene and methane involving orbital overlaps including both occupied and unoccupied orbitals. Similar to interatomic orbital interaction, the intermolecular interaction of orbitals forms "bonding" and "antibonding" orbitals. In the interaction between occupied orbitals, the total energy of the complex increases because of the occupation of the antibonding orbital. The existence of the CH-π hydrogen bond between benzene and methane causes a decrease in rest energy level, leading to at least -1.51 kcal/mol intermolecular interaction energy. Our finding extends the concept of orbital interaction from the intramolecular to the intermolecular regime and gives a reliable explanation of the deep orbital reformation in the benzene-methane complex. PMID:26927609

  6. Silver-catalyzed silicon-hydrogen bond functionalization by carbene insertion.

    Science.gov (United States)

    Iglesias, M José; Nicasio, M Carmen; Caballero, Ana; Pérez, Pedro J

    2013-01-28

    The catalytic functionalization of silicon-hydrogen bonds by means of the insertion of carbene units :CHCO(2)Et from ethyl diazoacetate (EDA) has been achieved using a silver-based catalyst, constituting the first example of this metal to promote this transformation. Competition experiments have revealed that the relative reactivity of substituted silanes depends on the bond dissociation energy of the Si-H bond (tertiary > secondary > primary for ethyl substituted). In the presence of bulky substituents such order reverts to secondary > primary ≈ tertiary (for phenyl substituted). Screening with other diazo compounds has shown that N(2)C(Ph)CO(2)Et displays similar reactivity to that of EDA, whereas other N(2)C(R)CO(2)Et (R = Me, CO(2)Et) gave lower conversions. PMID:23114570

  7. Molecular structure and intramolecular hydrogen bonding in 2-hydroxybenzophenones: A theoretical study

    Indian Academy of Sciences (India)

    Mansoureh Zahedi-Tabrizi; Sayyed Faramarz Tayyari; Farideh Badalkhani-Khamseh; Reihaneh Ghomi; Fatemeh Afshar-Qahremani

    2014-07-01

    The intramolecular hydrogen bonding (IHB) in a series of 3-, 4- and 5-substituted 2-hydroxybenzophenone (HBP) is studied using density functional theory calculations. All calculations are performed at the B3LYP level, using 6-311++G∗∗ basis set. To understand the substitution effects on the nature of IHB and the electronic structure of the chelated ring system, the vibrational frequencies, 1H chemical shift, topological parameters, natural bond orders and natural charges over atoms involved in the chelated ring of HBP and its derivatives were calculated. TheWiberg bond indices and the natural charges over atoms involved in the chelated ring have been computed using the natural bond orbital (NBO) analysis. The computations were further complemented with an atoms-in-molecules (AIM) topological analysis to characterize the nature of the IHB in the considered molecules. Several correlations between geometrical parameters, 1H NMR chemical shift and topological parameters with the IHB strength are obtained.

  8. On the role of interfacial hydrogen bonds in "on-water" catalysis

    CERN Document Server

    Karhan, Kristof; Kühne, Thomas D

    2014-01-01

    Numerous experiments have demonstrated that many classes of organic reactions exhibit increased reaction rates when performed in heterogeneous water emulsions. Despite enormous practical importance of the observed "on-water" catalytic effect and several mechanistic studies, its microscopic origins remains unclear. In this work, the second generation Car-Parrinello molecular dynamics method is extended to self-consistent charge density-functional based tight-binding in order to study "on-water" catalysis of the Diels-Alder reaction between dimethyl azodicarboxylate and quadricyclane. We find that the stabilization of the transition state by dangling hydrogen bonds exposed at the aqueous interfaces plays a significantly smaller role in "on-water" catalysis than has been suggested previously.

  9. Distal Hydrogen-bonding Interactions in Ligand Sensing and Signaling by Mycobacterium tuberculosis DosS.

    Science.gov (United States)

    Basudhar, Debashree; Madrona, Yarrow; Yukl, Erik T; Sivaramakrishnan, Santhosh; Nishida, Clinton R; Moënne-Loccoz, Pierre; Ortiz de Montellano, Paul R

    2016-07-29

    Mycobacterium tuberculosis DosS is critical for the induction of M. tuberculosis dormancy genes in response to nitric oxide (NO), carbon monoxide (CO), or hypoxia. These environmental stimuli, which are sensed by the DosS heme group, result in autophosphorylation of a DosS His residue, followed by phosphotransfer to an Asp residue of the response regulator DosR. To clarify the mechanism of gaseous ligand recognition and signaling, we investigated the hydrogen-bonding interactions of the iron-bound CO and NO ligands by site-directed mutagenesis of Glu-87 and His-89. Autophosphorylation assays and molecular dynamics simulations suggest that Glu-87 has an important role in ligand recognition, whereas His-89 is essential for signal transduction to the kinase domain, a process for which Arg-204 is important. Mutation of Glu-87 to Ala or Gly rendered the protein constitutively active as a kinase, but with lower autophosphorylation activity than the wild-type in the Fe(II) and the Fe(II)-CO states, whereas the E87D mutant had little kinase activity except for the Fe(II)-NO complex. The H89R mutant exhibited attenuated autophosphorylation activity, although the H89A and R204A mutants were inactive as kinases, emphasizing the importance of these residues in communication to the kinase core. Resonance Raman spectroscopy of the wild-type and H89A mutant indicates the mutation does not alter the heme coordination number, spin state, or porphyrin deformation state, but it suggests that interdomain interactions are disrupted by the mutation. Overall, these results confirm the importance of the distal hydrogen-bonding network in ligand recognition and communication to the kinase domain and reveal the sensitivity of the system to subtle differences in the binding of gaseous ligands. PMID:27235395

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

    Science.gov (United States)

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

    2016-04-01

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

  11. Electronic structure, stacking energy, partial charge, and hydrogen bonding in four periodic B-DNA models

    Science.gov (United States)

    Poudel, Lokendra; Rulis, Paul; Liang, Lei; Ching, W. Y.

    2014-08-01

    We present a theoretical study of the electronic structure of four periodic B-DNA models labeled (AT)10,(GC)10, (AT)5(GC)5, and (AT-GC)5 where A denotes adenine, T denotes thymine, G denotes guanine, and C denotes cytosine. Each model has ten base pairs with Na counterions to neutralize the negative phosphate group in the backbone. The (AT)5(GC)5 and (AT-GC)5 models contain two and five AT-GC bilayers, respectively. When compared against the average of the two pure models, we estimate the AT-GC bilayer interaction energy to be 19.015 Kcal/mol, which is comparable to the hydrogen bonding energy between base pairs obtained from the literature. Our investigation shows that the stacking of base pairs plays a vital role in the electronic structure, relative stability, bonding, and distribution of partial charges in the DNA models. All four models show a highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) gap ranging from 2.14 to 3.12 eV with HOMO states residing on the PO4 + Na functional group and LUMO states originating from the bases. Our calculation implies that the electrical conductance of a DNA molecule should increase with increased base-pair mixing. Interatomic bonding effects in these models are investigated in detail by analyzing the distributions of the calculated bond order values for every pair of atoms in the four models including hydrogen bonding. The counterions significantly affect the gap width, the conductivity, and the distribution of partial charge on the DNA backbone. We also evaluate quantitatively the surface partial charge density on each functional group of the DNA models.

  12. Electronic origin of the dependence of hydrogen bond strengths on nearest-neighbor and next-nearest-neighbor hydrogen bonds in polyhedral water clusters (H2O)n, n = 8, 20 and 24

    Energy Technology Data Exchange (ETDEWEB)

    Iwata, Suehiro; Akase, Dai; Aida, Misako; Xantheas, Sotiris S.

    2016-08-04

    The relative stability and the characteristics of the hydrogen bond networks in the cubic cages of (H2O)8, dodecahedral cages of (H2O)20,and tetrakaidodecahedral cages of (H2O)24 are studied. The charge-transfer and dispersion interaction terms of every pair of the hydrogen bonds are evaluated by using the perturbation theory based on the locally-projected molecular orbital (LPMO PT). Every water molecule and every hydrogen-bonded pair in polyhedral clusters are classified by the types of the adjacent molecules and hydrogen bonds. The relative binding energies among the polyhedral clusters are grouped by these classifications. The necessary condition for the stable conformers and the rules of the ordering of the relative stability among the isomers are derived from the analysis. The O–O distances and the pair-wise charge-transfer terms are dependent not only on the types of the hydrogen donor and acceptor waters but also on the types of the adjacent waters. This dependence is analyzed with Mulliken’s charge-transfer theory. The work is partially supported by the Grant-in-Aid for Science Research of JSPS (SI, DA, MA). SSX was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Battelle operates the Pacific Northwest National Laboratory for the US Department of Energy.

  13. Cooperativity and Site-Selectivity of Intramolecular Hydrogen Bonds on the Fluorescence Quenching of Modified GFP Chromophores.

    Science.gov (United States)

    Chang, Deng-Hsiang; Ou, Chun-Lin; Hsu, Hung-Yu; Huang, Guan-Jhih; Kao, Chen-Yi; Liu, Yi-Hung; Peng, Shie-Ming; Diau, Eric Wei-Guang; Yang, Jye-Shane

    2015-12-18

    This paper provides the first example of experimentally characterized hydrogen-bond cooperativity on fluorescence quenching with a modified green fluorescence protein (GFP) chromophore that contains a 6-membered C═N···H-O and a 7-membered C═O···H-O intramolecular H-bonds. Variable-temperature (1)H NMR and electronic absorption and emission spectroscopies were used to elucidate the preference of intra- vs intermolecular H-bonding at different concentrations (1 mM and 10 μM), and X-ray crystal structures provide clues of possible intermolecular H-bonding modes. In the ground state, the 6-membered H-bond is significant but the 7-membered one is rather weak. However, fluorescence quenching is dominated by the 7-membered H-bond, indicating a strengthening of the H-bond in the excited state. The H-bonding effect is more pronounced in more polar solvents, and no intermediates were observed from femtosecond fluorescence decays. The fluorescence quenching is attributed to the occurrence of diabatic excited-state proton transfer. Cooperativity of the two intramolecular H-bonds on spectral shifts and fluorescence quenching is evidenced by comparing with both the single H-bonded and the non-H-bonded counterparts. The H-bond cooperativity does not belong to the conventional patterns of σ- and π-cooperativity but a new type of polarization interactions, which demonstrates the significant interplay of H-bonds for multiple H-bonding systems in the electronically excited states. PMID:26583964

  14. Role of hydrogen-bonding and photoinduced electron transfer (PET) on the interaction of resorcinol based acridinedione dyes with Bovine Serum Albumin (BSA) in water

    Energy Technology Data Exchange (ETDEWEB)

    Kumaran, Rajendran, E-mail: kumaranwau@rediffmail.com [Department of Chemistry, Dwaraka Doss Goverdhan Doss, Vaishnav College (Autonomous), 833, Gokul Bagh, E.V.R. Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu (India); Vanjinathan, Mahalingam [Department of Chemistry, Dwaraka Doss Goverdhan Doss, Vaishnav College (Autonomous), 833, Gokul Bagh, E.V.R. Periyar Road, Arumbakkam, Chennai 600106, Tamil Nadu (India); Ramamurthy, Perumal [National Centre for Ultrafast Processes, University of Madras, Taramani Campus Chennai 600113, Tamil Nadu (India)

    2015-08-15

    a decrease in the alpha helical content of the protein. The shape and the pattern of CD bands after the addition of ADDR dye to BSA remain largely unaltered. - Highlights: • Steady-state absorption, emission of PET and non-PET based Acridinedione dyes with BSA. • Fluorescence enhancement with red shift. • Hydrogen-bonding interaction. • Bi-exponential fluorescence lifetime signifies free dye and dye bound to BSA.

  15. 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)

    decrease in the alpha helical content of the protein. The shape and the pattern of CD bands after the addition of ADDR dye to BSA remain largely unaltered. - Highlights: • Steady-state absorption, emission of PET and non-PET based Acridinedione dyes with BSA. • Fluorescence enhancement with red shift. • Hydrogen-bonding interaction. • Bi-exponential fluorescence lifetime signifies free dye and dye bound to BSA

  16. Thermodynamics of hydrogen bonding of weak bases in alcohol solutions: Calorimetry of solution, IR-spectroscopy and vapor pressure analysis

    Science.gov (United States)

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

    2012-06-01

    The properties of solutes and their reactivity in aliphatic alcohols significantly depend on the formation of hydrogen bonds. In this work, calorimetric, FTIR-spectroscopic and gas chromatographic vapor pressure studies of hydrogen bonds of weak bases in solution of aliphatic alcohols were carried out. Enthalpies of solutions at infinite dilution of ketones, nitriles and acetates in methanol and octan-1-ol were measured. Obtained from the calorimetric data, the enthalpies of specific interaction of weak bases in aliphatic alcohols unexpectedly found to be positive. IR spectra of solutions of ketones in aliphatic alcohols at infinite dilution were measured at different temperatures. Enthalpies of specific interaction in studied systems obtained from the spectroscopic data confirmed the endothermic process and are in good agreement with calorimetric results. Gibbs energies and entropies of specific interaction of weak bases in aliphatic alcohols were determined. Obtained results show, that the hydrogen bonding process of weak bases in aliphatic alcohols differs substantially from the formation of complexes 1:1 ROH⋯B (B - weak proton acceptor) in aprotic media. The complicated process of hydrogen bonding of weak bases in aliphatic alcohols apparently is controlled by the entropy factor, because these values are above zero.

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

    Science.gov (United States)

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

    2015-10-01

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

  18. 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

    simulations showed that, although the fewer water molecules in rhodopsin were relatively movable, the hydrogen bond network of the beta2-adrenergic receptor was fully loaded with water molecules that were surprisingly immobilized between the two rotamer switches, both apparently being in their closed...

  19. The structure and orientation of the C-H...OC hydrogen bonding in PHB studied by polarized infrared spectroscopy

    Czech Academy of Sciences Publication Activity Database

    Murakami, R.; Sato, H.; Dybal, Jiří; Iwata, T.; Zhang, J.; Tashiro, K.; Noda, I.; Ozaki, Y.

    Nishinomiya : Kwansei Gakuin University, 2005. s. 59. [International Symposium of Research Center for Environment Friendly Polymers /1./. 24.10.2005-25.10.2005, Nishinomiya] Institutional research plan: CEZ:AV0Z40500505 Keywords : poly(3-hydroxybutyrate) * polarized infrared spectra * hydrogen bonding Subject RIV: CD - Macromolecular Chemistry

  20. Through-bond photoinduced electron transfer in a porphyrin-fullerene conjugate held by a Hamilton type hydrogen bonding motif.

    Science.gov (United States)

    D'Souza, Francis; Venukadasula, Ganesh M; Yamanaka, Ken-ichi; Subbaiyan, Navaneetha K; Zandler, Melvin E; Ito, Osamu

    2009-03-21

    Control over the occurrence of through-bond electron transfer in self-assembled donor-acceptor conjugates is often difficult, since through-space electron transfer also competes due to the flexible nature of the spacer used to link the entities. In the present study, we have constructed a self-assembled donor-acceptor conjugate held solely by complementary hydrogen bonding and established through-bond electron transfer. The protocol used here is a Hamilton type hydrogen bonding motif involving self-assembly of a carboxylic acid functionalized porphyrin and 2-aminopyridine functionalized fullerene. Owing to the presence of two-point hydrogen bonds, the structure of the dyad is free from rotation with a donor-acceptor distance positioned appropriately to justify the through-bond electron transfer. Detailed spectral, computational and photochemical studies reveal efficient photoinduced charge separation and slow charge recombination in the studied conjugate, thus, bringing out the fundamental advantages of the directional hydrogen-bonding in the construction of donor-acceptor conjugates based on biomimetic principles and their functional role in governing electron transfer events. PMID:19262925

  1. Stochastic Liouville equations for hydrogen-bonding fluctuations and their signatures in two-dimensional vibrational spectroscopy of water

    NARCIS (Netherlands)

    Jansen, TL; Hayashi, T; Zhuang, W; Mukamel, S

    2005-01-01

    The effects of hydrogen-bond forming and breaking kinetics on the linear and coherent third-order infrared spectra of the OH stretch of HOD in D2O are described by Markovian, not necessarily Gaussian, fluctuations and simulated using the stochastic Liouville equations. Slow (0.5 ps) fluctuations are

  2. 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: 26.932, year: 2014

  3. The meso Helix: Symmetry and Symmetry-Breaking in Dynamic Oligourea Foldamers with Reversible Hydrogen-Bond Polarity.

    Science.gov (United States)

    Wechsel, Romina; Raftery, James; Cavagnat, Dominique; Guichard, Gilles; Clayden, Jonathan

    2016-08-01

    Oligoureas (up to n=6) of meso cyclohexane-1,2-diamine were synthesized by chain extension with an enzymatically desymmetrized monomer 2. Despite being achiral, the meso oligomers adopt chiral canonical 2.5-helical conformations, the equally populated enantiomeric screw-sense conformers of which are in slow exchange on the NMR timescale, with a barrier to screw-sense inversion of about 70 kJ mol(-1) . Screw-sense inversion in these helical foldamers is coupled with cyclohexane ring-flipping, and results in a reversal of the directionality of the hydrogen bonding in the helix. The termini of the meso oligomers are enantiotopic, and desymmetrized analogues of the oligoureas with differentially and enantioselectively protected termini display moderate screw-sense preferences. A screw-sense preference may furthermore be induced in the achiral, meso oligoureas by formation of a 1:1 hydrogen-bonded complex with the carboxylate anion of Boc-d-proline. The meso oligoureas are the first examples of hydrogen-bonded foldamers with reversible hydrogen-bond directionality. PMID:27298097

  4. Hydrogen-bonded oligothiophene rosettes with a benzodithiophene terminal unit: self-assembly and application to bulk heterojunction solar cells.

    Science.gov (United States)

    Ouchi, Hayato; Lin, Xu; Kizaki, Takahiro; Prabhu, Deepak D; Silly, Fabien; Kajitani, Takashi; Fukushima, Takanori; Nakayama, Ken-Ichi; Yagai, Shiki

    2016-06-14

    Benzodithiophene-functionalized oligothiophene with barbituric acid hydrogen-bonding unit self-assembles into nanoscopic structures via the formation of rosettes. The nanostructures show a power conversion efficiency of 3% upon mixing with PC61BM in bulk-heterojunction solar cells without thermal annealing. PMID:27251116

  5. The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes.

    Science.gov (United States)

    Berg, Lotta; Mishra, Brijesh Kumar; Andersson, C David; Ekström, Fredrik; Linusson, Anna

    2016-02-01

    Molecular recognition events in biological systems are driven by non-covalent interactions between interacting species. Here, we have studied hydrogen bonds of the CH⋅⋅⋅Y type involving electron-deficient CH donors using dispersion-corrected density functional theory (DFT) calculations applied to acetylcholinesterase-ligand complexes. The strengths of CH⋅⋅⋅Y interactions activated by a proximal cation were considerably strong; comparable to or greater than those of classical hydrogen bonds. Significant differences in the energetic components compared to classical hydrogen bonds and non-activated CH⋅⋅⋅Y interactions were observed. Comparison between DFT and molecular mechanics calculations showed that common force fields could not reproduce the interaction energy values of the studied hydrogen bonds. The presented results highlight the importance of considering CH⋅⋅⋅Y interactions when analysing protein-ligand complexes, call for a review of current force fields, and opens up possibilities for the development of improved design tools for drug discovery. PMID:26751405

  6. 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

  7. Highly Extensible Supramolecular Elastomers with Large Stress Generation Capability Originating from Multiple Hydrogen Bonds on the Long Soft Network Strands.

    Science.gov (United States)

    Hayashi, Mikihiro; Noro, Atsushi; Matsushita, Yushu

    2016-04-01

    Highly extensible supramolecular elastomers are prepared from ABA triblock-type copolymers bearing glassy end blocks and a long soft middle block with multiple hydrogen bonds. The copolymer used is polystyrene-b-[poly(butyl acrylate)-co-polyacrylamide]-b-polystyrene (S-Ba-S), which is synthesized via reversible addition-fragmentation chain transfer (RAFT) polymerization. Tensile tests reveal that the breaking elongation (εb ) increases with an increase in the middle block molecular weight (Mmiddle ). Especially, the largest S-Ba-S with Mmiddle of 3140k, which is synthesized via high-pressure RAFT polymerization, achieves εb of over 2000% with a maximum tensile stress of 3.6 MPa, while the control sample without any middle block hydrogen bonds, polystyrene-b-poly(butyl acrylate)-b-polystyrene with Mmiddle of 2780k, is merely a viscous material due to the large volume fraction of soft block. Thus, incorporation of hydrogen bonds into the large molecular weight soft middle block is found to be beneficial to prepare supramolecular elastomers attaining high extensibility and sufficiently large stress generation ability simultaneously. This outcome is probably due to concerted combination of entropic changes and internal potential energy changes originating from the dissociation of multiple hydrogen bonds by elongation. PMID:26914643

  8. Low cost prediction of relative stabilities of hydrogen bonded complexes from atomic multipole moments for overly short intermolecular distances.

    Science.gov (United States)

    Beker, Wiktor; Langner, Karol M; Dyguda-Kazimierowicz, Edyta; Feliks, Mikołaj; Sokalski, W Andrzej

    2013-08-01

    The relative stability of biologically relevant, hydrogen bonded complexes with shortened distances can be assessed at low cost by the electrostatic multipole term alone more successfully than by ab initio methods. These results imply that atomic multipole moments may help improve ligand-receptor ranking predictions, particularly in cases where accurate structural data are not available. PMID:23696072

  9. 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 translati...

  10. The relation of the number of hydrogen-bond acceptors with recoveries of immunosuppressants in DBS analysis

    NARCIS (Netherlands)

    Koster, Remco A.; Alffenaar, Jan-Willem C.; Botma, Rixt; Greijdanus, Ben; Uges, Donald R. A.; Kosterink, Jos G. W.; Touw, Daan J.

    2015-01-01

    BACKGROUND: We investigated the influence of the number of hydrogen-bond acceptors on the recovery of immunosuppressant drugs and their structural analogs. This hypothesis was tested by evaluation of the extraction recoveries of tacrolimus, ascomycin, sirolimus, everolimus and temsirolimus with 12,

  11. Analysis of the number of hydrogen bond groups of a multiwalled carbon nanotube probe tip for chemical force microscopy

    International Nuclear Information System (INIS)

    In this paper, we describe a statistical method of quantification of the number of functional groups at the contact area of a probe tip for atomic force microscopy from the result of repetitive pull-off force measurements. We have investigated laboratory-made carbon nanotube (CNT) probe tips to apply them for chemical force microscopy because limited number of functional groups at the tip-end is expected. Using a CNT tip, we conducted repetitive pull-off force measurements against a self-assembled monolayer terminated with carboxyl group and analyzed them in terms of the number of hydrogen bond groups at the CNT tip. The elementary hydrogen bond rupture force quantum in n-decane medium was estimated to be 84.2 ± 0.5 pN in the present system. Thus it was revealed that only a couple of hydrogen bond groups of the CNT tip were participating in hydrogen bonding with the sample on an average in this experimental system.

  12. 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%). PMID:26781581

  13. Density functional for van der Waals forces accounts for hydrogen bond in benchmark set of water hexamers

    DEFF Research Database (Denmark)

    Kelkkanen, Kari André; Lundqvist, Bengt; Nørskov, Jens Kehlet

    2009-01-01

    A recent extensive study has investigated how various exchange-correlation (XC) functionals treat hydrogen bonds in water hexamers and has shown traditional generalized gradient approximation and hybrid functionals used in density-functional (DF) theory to give the wrong dissociation-energy trend...

  14. The study of hydrogen bonding and π⋯π interactions in phenol⋯ethynylbenzene complex by IR spectroscopy.

    Science.gov (United States)

    Vojta, Danijela; Vazdar, Mario

    2014-11-11

    Weak hydrogen bonds between phenol and ethynylbenzene in tetrachloroethene were explored by using FTIR spectroscopy. Association constants (Kc) were determined by high dilution method at two temperatures, 20°C and 26°C, and they are, respectively, 0.54±0.09 mol(-1) dm3 and 0.36±0.08 mol(-1) dm3. The position of ethynylbenzene stretching band, when in hydrogen bonding complex with phenol (CC⋯), is proposed to be governed by the interplay of OH⋯π (CC moiety or phenyl ring of ethynylbenzene) and π⋯π (phenyl ring of phenol⋯CC moiety or phenyl ring of ethynylbenzene) interactions. This conclusion is supported by the findings on the complex between ethanol and ethynylbenzene; in the latter, CC⋯ stretching band is shifted to the higher wavenumbers, as expected when ethynylbenzene interacts with hydrogen bond donor. Geometries and energies of the presumed complexes, as well as their vibrational spectra, are predicted by using ab initio calculations. The spectroscopic and thermodynamic data obtained here offer the missing pieces in the present picture of migration of H-atom of phenol OH group between competing hydrogen bond accepting centers on ethynylbenzene. PMID:24845872

  15. Effects of Hydrogen-bonding Interaction and Polarity on Emission Spectrum of Naphthalene-Triethylamine in Mixed Solvent

    Institute of Scientific and Technical Information of China (English)

    XIE Guo-bin; Yoshimi Sueishi; Shunzo Yamamoto

    2004-01-01

    The effects of the protic and aprotic polar solvents on the emission spectrum of the naphthalene-triethylamine system in THF were studied under conditions of steady-state illumination. The fluorescence spectrum of the naphthalene-triethylamine system consists of two emission bands, the fluorescence band of naphthalene (band A, 329 nm) and the emission band of the exciplex(band B, 468 nm). The intensities of both the emission bands decrease with increasing the solvent polarity. The intensity of band B also decreases due to the hydrogen-bonding interaction between triethylamine and protic solvent, while that of band A increases. It is thus suggested that the quenching of naphthalene fluorescence by triethylamine in THF occurs through the charge transfer and electron transfer reactions. The spectral changes upon the increase of solvent polarity can be explained by the dependences of the equilibrium constant between exciplex and ion-pair and the rate constant for the electron transfer reaction from triethylamine to the excited naphthalene on the relative permittivity of solvent. It is shown that the formation of intermolecular hydrogen-bonding between triethylamine and protic solvent suppresses the quenching reaction by the decrease in free amine. Acetonitrile has only a polar effect and trichloroacetic acid only a hydrogen-bonding(or protonation) effect, while alcohols have both the effects. The effects of alcohols could be separated into the effects of solvent polarity and intermolecular hydrogen-bonding interaction quantitatively.

  16. 1,2,3-Triazole Bridge as Conformational Constrain in β-Hairpin Peptides: Analysis of Hydrogen-Bonded Positions.

    Science.gov (United States)

    Celentano, V; Diana, D; Di Salvo, C; De Rosa, L; Romanelli, A; Fattorusso, R; D'Andrea, L D

    2016-04-11

    Conformational constrained β-hairpin peptides are useful tool to modulate protein-protein interactions. A triazole bridge in hydrogen-bonded positions between two antiparallel strands induces a conformational stabilization of the β-hairpin peptide. The entity of the stability of the β-hairpin peptide depends on the length of the bridge. PMID:26938670

  17. Is there a sphingomyelin-based hydrogen bond barrier at the mammalian host-schistosome parasite interface?

    Science.gov (United States)

    Migliardo, Federica; Tallima, Hatem; El Ridi, Rashika

    2014-03-01

    Schistosomes develop, mature, copulate, lay eggs, and live for years in the mammalian host bloodstream, importing nutrients across the tegument, but entirely impervious to the surrounding elements of the immune system. We have hypothesized that sphingomyelin (SM) in the parasite apical lipid bilayer is responsible for these sieving properties via formation of a tight hydrogen bond network with the surrounding water. Here we have used quasi-elastic neutron scattering for characterizing the diffusion of larval and adult Schistosoma mansoni and adult Schistosoma haematobium in the surrounding medium, under various environmental conditions. The results documented the presence of a hydrogen bond barrier around larvae and adult schistosomes. The hydrogen bond network readily collapses if worms are subjected to hypoxic conditions, likely via activation of the parasite tegument-associated neutral sphingomyelinase, and consequent excessive SM hydrolysis. The slower dynamics of lung-stage larvae as compared to adult worms has been related to the existence of hydrogen-bonded networks of different strength and then to their differential resistance to immune attacks. PMID:23943053

  18. Electrical conductivity studies for hydrogen-bonded supramolecular polymer formed by dialkylurea in non-polar solvent

    International Nuclear Information System (INIS)

    Graphical abstract: Display Omitted -- Highlights: • The electrical conductivity of urea-based supramolecular polymers formed in non-polar medium is investigated with the use of the impedance spectroscopy. • The thermal activation energy of the direct current electrical conductivity is independent of the medium viscosity. • The correlation between the relaxation times of the charge curriers translation and the dipolar entities rotation is observed. • The presented data point out for the participation of the protons, releasing in the acts of the hydrogen bonds breaking, in the electrical conductivity of the studied supramolecular system. -- Abstract: The electrical features of the supramolecular hydrogen-bonded polymers formed by N,N′-di(2-ethylhexyl)urea (EHU) in non-polar medium were investigated with the use of the impedance spectroscopy. It was found that the thermal activation energy of the direct current electrical conductivity is independent of the medium viscosity in a large range of EHU mole fraction (0.3 < x ≤ 1), in full analogy to behavior of the activation energy of the dipolar relaxation time of the entities resulting from the thermally stimulating breaking of the hydrogen bonds chains. Besides, in that urea concentration range one observes the correlation between the relaxation times of the charge carriers translation and the dipolar entities rotation. The presented data point out for the participation of the protons, released in the acts of the hydrogen bonds breaking, in the electrical conductivity of the studied supramolecular system

  19. De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.

    Science.gov (United States)

    Boyken, Scott E; Chen, Zibo; Groves, Benjamin; Langan, Robert A; Oberdorfer, Gustav; Ford, Alex; Gilmore, Jason M; Xu, Chunfu; DiMaio, Frank; Pereira, Jose Henrique; Sankaran, Banumathi; Seelig, Georg; Zwart, Peter H; Baker, David

    2016-05-01

    In nature, structural specificity in DNA and proteins is encoded differently: In DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here, we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen-bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen-bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen-bond networks with atomic accuracy enables the programming of protein interaction specificity for a broad range of synthetic biology applications; more generally, our results demonstrate that, even with the tremendous diversity observed in nature, there are fundamentally new modes of interaction to be discovered in proteins. PMID:27151862

  20. The effect of hydrogen bonding on torsional dynamics: A combined far-infrared jet and matrix isolation study of methanol dimer

    DEFF Research Database (Denmark)

    Kollipost, F.; Andersen, Jonas; Wallin Mahler Andersen, Denise; Heimdal, J.; Heger, M.; Suhm, M. A.; Larsen, René Wugt

    2014-01-01

    The effect of strong intermolecular hydrogen bonding on torsional degrees of freedom is investigated by far-infrared absorption spectroscopy for different methanol dimer isotopologues isolated in supersonic jet expansions or embedded in inert neon matrices at low temperatures. For the vacuum-isolated......) levels in order to quantify the contribution of vibrational anharmonicity for this important class of intermolecular hydrogen bond vibrational motion....