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

    Science.gov (United States)

    Amtul, Zareen; Rahman, Atta-Ur

    2016-02-01

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

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

    Directory of Open Access Journals (Sweden)

    Marimuthu Mohana

    2016-04-01

    Full Text Available The asymmetric unit of the title compound, 4C4H4FN3O·C3H6N6, comprises of two independent 5-fluorocytosine (5FC molecules (A and B and one half-molecule of melamine (M. The other half of the melamine molecule is generated by a twofold axis. 5FC molecules A and B are linked through two different homosynthons [R22(8 ring motif]; one is formed via a pair of N—H...O hydrogen bonds and the second via a pair of N—H...N hydrogen bonds. In addition to this pairing, the O atoms of 5FC molecules A and B interact with the N2 amino group on both sides of the melamine molecule, forming a DDAA array of quadruple hydrogen bonds and generating a supramolecular pattern. The 5FC (molecules A and B and two melamine molecules interact via N—H...O, N—H...N and N—H...O, N—H...N, C—H...F hydrogen bonds forming R66(24 and R44(15 ring motifs. The crystal structure is further strengthened by C—H...F, C—F...π and π–π stacking interactions.

  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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-11-07

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

  6. Crystal structure and hydrogen-bonding patterns in 5-fluorocytosinium picrate

    Directory of Open Access Journals (Sweden)

    Marimuthu Mohana

    2017-03-01

    Full Text Available In the crystal structure of the title compound, 5-fluorocytosinium picrate, C4H5FN3O+·C6H2N3O7−, one N heteroatom of the 5-fluorocytosine (5FC ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11° with the ring of the picrate (PA− anion. In the crystal, the 5FC+ cation interacts with the PA− anion through three-centre N—H...O hydrogen bonds, forming two conjoined rings having R21(6 and R12(6 motifs, and is extended by N—H...O hydrogen bonds and C—H...O interactions into a two-dimensional sheet structure lying parallel to (001. Also present in the crystal structure are weak C—F...π interactions.

  7. 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).

  8. The 1:2 Complex of Piperazine with Some Phenols:Hydrogen Bonding Pattern Involved in Transition States in Solution

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A novel model for the 1: 2 complex of piperazine with some phenols in solution is established and verified. In CDCl3 solution, one piperazine molecule is tied to two phenol molecules by hydrogen bonds of O-H---N and N-H---O. And the protons of >NH and -OH groups exchange quickly and simultaneously between the atoms of phenol oxygen and piperazine nitrogen.

  9. 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.

  10. Supramolecular hydrogen-bonding patterns in 1:1 cocrystals of 5-fluorouracil with 4-methylbenzoic acid and 3-nitrobenzoic acid.

    Science.gov (United States)

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

    2017-03-01

    The design of a pharmaceutical cocrystal is based on the identification of specific hydrogen-bond donor and acceptor groups in active pharmaceutical ingredients (APIs) in order to choose a `complementary interacting' molecule that can act as an efficient coformer. 5-Fluorouracil (5FU) is a pyrimidine derivative with two N-H donors and C=O acceptors and shows a diversity of hydrogen-bonding motifs. Two 1:1 cocrystals of 5-fluorouracil (5FU), namely 5-fluorouracil-4-methylbenzoic acid (5FU-MBA), C4H3FN2O2·C8H8O2, (I), and 5-fluorouracil-3-nitrobenzoic acid (5FU-NBA), C4H3FN2O2·C7H5NO4, (II), have been prepared and characterized by single-crystal X-ray diffraction. In (I), the MBA molecules form carboxylic acid dimers [R2(2)(8) homosynthon]. Similarly, the 5FU molecules form two types of base pair via a pair of N-H...O hydrogen bonds [R2(2)(8) homosynthon]. In (II), 5FU interacts with the carboxylic acid group of NBA via N-H...O and O-H...O hydrogen bonds, generating an R2(2)(8) ring motif (heterosynthon). Furthermore, the 5FU molecules form base pairs [R2(2)(8) homosynthon] via N-H...O hydrogen bonds. Both of the crystal structures are stabilized by C-H...F interactions.

  11. Hydrogen bonding in tight environments

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  12. 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.

  13. Why are Hydrogen Bonds Directional?

    Indian Academy of Sciences (India)

    ABHISHEK SHAHI; ELANGANNAN ARUNAN

    2016-10-01

    The recent IUPAC recommendation on the definition of hydrogen bonding points out that directionality is a defining characteristic of a hydrogen bond and the angle ∠X-H-Y is generally linear or 180◦. It also suggests that the X-H· · ·Y angle be greater than 110◦ for an interaction to be characterized as a hydrogenbond but does not provide any rationale for the same. This article reports a rationale for limiting the angle, based on the electron density topology using the quantum theory of atoms in molecules. Electron density topology for common hydrogen bond donors HF, HCl, HBr, HNC, HCN and HCCH are reported in this work. These calculations lead to an interesting observation that the atomic basins of H atom in all these donor molecules are limited justifying the restriction of hydrogen bond angle. Moreover, similar analysis on some hydrogen bonded complexes confirms that beyond this angle the acceptor atom Y starts interacting with the atomic basin on X. However, conclusions based on bond lengths and angles have to be treated with care and as the IUPAC recommendation points out that independent ‘evidence for bond formation’ in every case is important.

  14. AAA-DDD triple hydrogen bond complexes.

    Science.gov (United States)

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

    2009-10-01

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

  15. 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.

  16. Imaging Hydrogen Bond in Real Space

    CERN Document Server

    Chen, Xiu; Liu, Lacheng; Liu, Xiaoqing; Cai, Yingxing; Liu, Nianhua; Wang, Li

    2013-01-01

    Hydrogen bond is often assumed to be a purely electrostatic interaction between a electron-deficient hydrogen atom and a region of high electron density. Here, for the first time, we directly image hydrogen bond in real space by room-temperature scanning tunneling microscopy (STM) with the assistance of resonant tunneling effect in double barrier mode. STM observations demonstrate that the C=O:HO hydrogen bonds lifted several angstrom meters above metal surfaces appear shuttle-like features with a significant contrast along the direction connected the oxygen and hydrogen atoms of a single hydrogen bond. The off-center location of the summit and the variance of the appearance height for the hydrogen bond with scanning bias reveal that there are certain hybridizations between the electron orbitals of the involved oxygen and hydrogen atoms in the C=O:HO hydrogen bond.

  17. Hydrogen bond dynamics in bulk alcohols

    Energy Technology Data Exchange (ETDEWEB)

    Shinokita, Keisuke; Cunha, Ana V.; Jansen, Thomas L. C.; Pshenichnikov, Maxim S., E-mail: Maxim.Pchenitchnikov@RuG.nl [Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen (Netherlands)

    2015-06-07

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

  18. Hydrogen Bonds in Excited State Proton Transfer

    Science.gov (United States)

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

    2016-10-01

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

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

    Science.gov (United States)

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

    2014-05-12

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

  20. 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...

  1. 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...

  2. Hydrogen bond dynamics in bulk alcohols

    NARCIS (Netherlands)

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

    2015-01-01

    Hydrogen-bonded liquids play a significant role in numerous chemical and biological phenomena. In the past decade, impressive developments in multidimensional vibrational spectroscopy and combined molecular dynamics-quantum mechanical simulation have established many intriguing features of hydrogen

  3. 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.

  4. Hydrogen bonds and van der Waals forces as tools for the construction of a herringbone pattern in the crystal structure of hexane-1,6-diaminium hexane-1,6-diyl bis-(hydrogen phospho-nate).

    Science.gov (United States)

    Reiss, Guido J; van Megen, Martin; Frank, Walter

    2017-01-01

    The asymmetric unit of the title salt, [H3N(CH2)6NH3][(HO)O2P(CH2)6PO2(OH)], consists of one half of a hexane-1,6-diaminium dication and one half of a hexane-1,6-diyl bis-(hydrogen phospho-nate) dianion. Both are located around different centres of inversion (Wyckoff sites: 2a and 2d) of the space group P21/c. The shape of the hexane-1,6-diaminium cation is best described as a double hook. Both aminium groups as well as the two attached CH2 groups are turned out from the plane of the central four C atoms. In contrast, all six C atoms of the dianion are almost in a plane. The hydrogen phospho-nate (-PO3H) groups of the anions and the aminium groups of the cations form two-dimensional O-H⋯ and O-H⋯N hydrogen-bonded networks parallel to the ac plane, built up from ten-membered and twelve-membered ring motifs with graph-set descriptors R3(3)(10) and R5(4)(12), respectively. These networks are linked by the alkyl-ene chains of the anions and cations. The resulting three-dimensional network shows a herringbone pattern, which resembles the parent structures 1,6-di-amino-hexane and hexane-1,6-di-phospho-nic acid.

  5. Water, Hydrogen Bonding and the Microwave Background

    Directory of Open Access Journals (Sweden)

    Robitaille P.-M.

    2009-04-01

    Full Text Available n this work, the properties of the water are briefly revisited. Though liquid water has a fleeting structure, it displays an astonishingly stable network of hydrogen bonds. Thus, even as a liquid, water possesses a local lattice with short range order. The presence of hydroxyl (O-H and hydrogen (H....OH2 bonds within water, indicate that it can simultaneously maintain two separate energy systems. These can be viewed as two very different temperatures. The analysis presented uses results from vibrational spec- troscopy, extracting the force constant for the hydrogen bonded dimer. By idealizing this species as a simple diatomic structure, it is shown that hydrogen bonds within wa- ter should be able to produce thermal spectra in the far infrared and microwave regions of the electromagnetic spectrum. This simple analysis reveals that the oceans have a physical mechanism at their disposal, which is capable of generating the microwave background.

  6. Distinct molecular structures and hydrogen bond patterns of α,α-diethyl-substituted cyclic imide, lactam, and acetamide derivatives in the crystalline phase

    Science.gov (United States)

    Krivoshein, Arcadius V.; Ordonez, Carlos; Khrustalev, Victor N.; Timofeeva, Tatiana V.

    2016-10-01

    α,α-Dialkyl- and α-alkyl-α-aryl-substituted cyclic imides, lactams, and acetamides show promising anticonvulsant, anxiolytic, and anesthetic activities. While a number of crystal structures of various α-substituted cyclic imides, lactams, and acetamides were reported, no in-depth comparison of crystal structures and solid-state properties of structurally matched compounds have been carried out so far. In this paper, we report molecular structure and intermolecular interactions of three α,α-diethyl-substituted compounds - 3,3-diethylpyrrolidine-2,5-dione, 3,3-diethylpyrrolidin-2-one, and 2,2-diethylacetamide - in the crystalline phase, as studied using single-crystal X-ray diffraction and IR spectroscopy. We found considerable differences in the patterns of H-bonding and packing of the molecules in crystals. These differences correlate with the compounds' melting points and are of significance to physical pharmacy and formulation development of neuroactive drugs.

  7. 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. The distribution of bond lengths was examined using infrared spectroscopy (ATR-FTIR) both prior to treatments and after. The results show that the absorbance bands of the spectra related to the hydroxyl and carboxyl stretching vibrations were changed by the treatments. Apparently, the first...

  8. 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 1H NMR, 13C NMR, IR and X-ray single-crystal diffraction. The carboxylic acid group forms classic Osbnd H ⋯ O hydrogen bonded dimers in a centrosymmetric R22(8) ring motifs for BAA-Br and BAA-Cl. However, no carboxylic acid group forms classic Osbnd H ⋯ O hydrogen bonded dimers in BAA-OCH3 and BAA-CH3. The asymmetric unit consists of two crystallographically independent molecules in BAA-OCH3. DFT computations show that the interaction energies between monomer and dimer are in the range of 0.5-3.8 kcal/mol with the B3LYP/6-31 + G*, B3LYP/6-31 ++G*, B3LYP/6-31 ++G**, and B3LYP/AUG-cc-pVDZ levels of theory. The presence of different hydrogen bond patterns is also governed by the substrate. For monomeric compounds studied herein, theoretical calculations lead to two low-energy conformers; trans (a) and cis (b). Former one is more stable than latter by about 4 kcal/mol.

  9. 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.

  10. On the nature of blueshifting hydrogen bonds.

    Science.gov (United States)

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

    2014-07-01

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

  11. Intramolecular hydrogen bonding in medicinal chemistry.

    Science.gov (United States)

    Kuhn, Bernd; Mohr, Peter; Stahl, Martin

    2010-03-25

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

  12. Hydrogen bonds and van der Waals forces as tools for the construction of a herringbone pattern in the crystal structure of hexane-1,6-diaminium hexane-1,6-diyl bis­(hydrogen phospho­nate)

    Science.gov (United States)

    Reiss, Guido J.; van Megen, Martin; Frank, Walter

    2017-01-01

    The asymmetric unit of the title salt, [H3N(CH2)6NH3][(HO)O2P(CH2)6PO2(OH)], consists of one half of a hexane-1,6-diaminium dication and one half of a hexane-1,6-diyl bis­(hydrogen phospho­nate) dianion. Both are located around different centres of inversion (Wyckoff sites: 2a and 2d) of the space group P21/c. The shape of the hexane-1,6-diaminium cation is best described as a double hook. Both aminium groups as well as the two attached CH2 groups are turned out from the plane of the central four C atoms. In contrast, all six C atoms of the dianion are almost in a plane. The hydrogen phospho­nate (–PO3H) groups of the anions and the aminium groups of the cations form two-dimensional O—H⋯ and O—H⋯N hydrogen-bonded networks parallel to the ac plane, built up from ten-membered and twelve-membered ring motifs with graph-set descriptors R 3 3(10) and R 5 4(12), respectively. These networks are linked by the alkyl­ene chains of the anions and cations. The resulting three-dimensional network shows a herringbone pattern, which resembles the parent structures 1,6-di­amino­hexane and hexane-1,6-di­phospho­nic acid. PMID:28083141

  13. 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.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2017-02-01

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

  16. 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’.

  17. Chiral benzimidazoles as hydrogen bonding organocatalysts

    OpenAIRE

    Nájera Domingo, Carmen; Yus Astiz, Miguel

    2015-01-01

    Several bifunctional organocatalysts bearing the benzimidazole unit have been designed in order to act as bifunctional systems by hydrogen bonding. Chiral 2-aminobenzimidazoles are conformational rigid guanidines able to catalyze enantioselectively Michael reaction, direct SN1 of alcohols, and aldol reactions. Some of these organocatalysts can be easily recovered by simple isolation methods and reused without loss of catalytic activity. Related (2-aminoalkyl)benzimidazoles have been used as c...

  18. Hydrogen bonds in PC61BM solids

    Science.gov (United States)

    Sheng, Chun-Qi; Li, Wen-Jie; Du, Ying-Ying; Chen, Guang-Hua; Chen, Zheng; Li, Hai-Yang; Li, Hong-Nian

    2015-09-01

    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.

  19. Studies on Hydrogen Bonding Network Structures of Konjac Glucomannan

    Institute of Scientific and Technical Information of China (English)

    PANG Jie; SUN Yu-Jing; YANG You-Hui; CHEN Yuan-Yuan; CHEN Yi-Qing; SUN Yuan-Ming

    2008-01-01

    In this paper, the hydrogen bonding network models of konjac glucomannan (KGM) are predicted in the approach of molecular dynamics (MD). These models have been proved by experiments whose results are consistent with those from simulation.The results show that the hydrogen bonding network structures of KGM are stable and the key linking points of hydrogen bonding network are at the O(6) and O(2) positions on KGM ring. Moreover, acety1 has significant influence on hydrogen bonding network and hydrogen bonding network structures are more stable after deacetylation.

  20. Intramolecular hydrogen bonding in myricetin and myricitrin

    DEFF Research Database (Denmark)

    Vojta, Danijela; Dominkovic, Katarina; Miljanic, Snezana;

    2016-01-01

    The molecular structures of myricetin (3,3’,4’,5,5’,7-hexahydroxyflavone; MCE) and myricitrin (myricetin 3-O-rhamnoside; MCI) are investigated by quantum chemical calculations (B3LYP/6-311G**). Two preferred molecular rotamers of MCI are predicted, corresponding to different conformations of the O......-rhamnoside subunit. The rotamers are characterized by different hydrogen bonded cross-links between the hydroxy groups of the rhamnoside substituent and the parent MCE moiety. The predicted OH stretching frequencies are compared with vibrational spectra of MCE and MCI recorded for the sake of this investigation (IR...

  1. Intramolecular hydrogen bonding in myricetin and myricitrin

    DEFF Research Database (Denmark)

    Vojta, Danijela; Dominkovic, Katarina; Miljanic, Snezana;

    2017-01-01

    The molecular structures of myricetin (3,3’,4’,5,5’,7-hexahydroxyflavone; MCE) and myricitrin (myricetin 3-O-rhamnoside; MCI) are investigated by quantum chemical calculations (B3LYP/6-311G**). Two preferred molecular rotamers of MCI are predicted, corresponding to different conformations of the O......-rhamnoside subunit. The rotamers are characterized by different hydrogen bonded cross-links between the hydroxy groups of the rhamnoside substituent and the parent MCE moiety. The predicted OH stretching frequencies are compared with vibrational spectra of MCE and MCI recorded for the sake of this investigation (IR...

  2. 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.

  3. 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.

  4. 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)

    WU RongLiang; JI Qing; KONG Bin; YANG XiaoZhen

    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 func-tions 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 concentra-tion 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 con-tacts 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%.

  5. 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%.

  6. Hydrogen bonding in asphaltenes and coal

    Energy Technology Data Exchange (ETDEWEB)

    Li, N.C.; Tewari, K.C.

    1978-04-01

    The objective of this program is to investigate and to determine the nature of hydrogen bonding and other molecular interactions that occur in asphaltene and coal liquids, and to seek possible correlations between the interactions and the viscosity. The asphaltene components of samples of centrifuged liquid product, CLP, and solvent-refined coal, SRC, supplied by the Pittsburgh Energy Research Center, are isolated by solvent fractionation. The compositions of the asphaltenes are obtained by elemental analysis and the molecular weights by vapor pressure osmometry. The acid/neutral and base components of the asphaltenes are separated and again elemental analysis and molecular weights are obtained. The magnetic resonance, infrared and calorimetric methods are used to determine the strength of hydrogen-bond and other molecular interactions in the fractions isolated. Investigations on the toluene-insoluble and heavy-oil fractions are also carried out. In addition, extensive proton magnetic resonance, near infrared and calorimetric studies are carried out for o-phenylphenol and quinoline, which serve as model compounds for the aromatic phenols and the heteronuclear aromatic base nitrogens, respectively, found in coal liquefaction products. This is the final report, giving a summary of activities under the Contract for the entire period.

  7. 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.

  8. EPR spin Hamiltonian parameters of encapsulated spin-labels: impact of the hydrogen bonding topology.

    Science.gov (United States)

    Frecus, Bogdan; Rinkevicius, Zilvinas; Murugan, N Arul; Vahtras, Olav; Kongsted, Jacob; Ågren, Hans

    2013-02-21

    Encapsulation of spin-labels into "host" compounds, like cucurbit[n]urils or cyclodextrins, in solutions has profound effects on the EPR spin Hamiltonian parameters of the spin-labels. In this work we study the microscopic origin of the EPR spin Hamiltonian parameters of spin-labels enclosed in hydrophobic cavities. We focus on the dependence of the EPR properties of encapsulated spin-labels on the hydrogen bonding topologies that occur upon encapsulation, and quantize various contributions to these parameters according to specific hydrogen bonding patterns. The obtained results provide refined insight into the role of the hydrogen bonding induced encapsulation shifts of EPR spin Hamiltonian parameters in solvated "spin-label@host compound" complexes.

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

    Science.gov (United States)

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

    2016-03-18

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

  10. A Statistical Theory for Hydrogen Bonding Networks: One Component Case

    Institute of Scientific and Technical Information of China (English)

    WANG Hai-Jun; BA Xin-Wu; ZHAO Min; LI Ze-Sheng

    2000-01-01

    The theory of reversible gelation is shown to be applicable to the hydrogen bonding system by analyzing their similarities in statistical viewpoint. The size distribution of hydrogen bonding clusters, the gelation condition and the generalized scaling law can be obtained directly. These results show that such a system can undergo phase transition process. Furthermore, a relationship between Gibbs free energy of forming hydrogen bond and conversions of groups is given. As an example, the chemical shift of OH groups is considered.

  11. The role of hydrogen bonding in tethered polymer layers

    OpenAIRE

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

    2008-01-01

    A molecular theory to study the properties of end tethered polymer layers, in which the polymers have the ability to form hydrogen bonds with water is presented. The approach combines the ideas of the single-chain mean-field theory to treat tethered layers with the approach of Dormidontova (Macromolecules, 2002 35,987) to include hydrogen bonds. The generalization includes the consideration of position dependent polymer-water and water-water hydrogen bonds. The theory is applied to model poly...

  12. Hydrogen-bonded sheets in benzylmethylammonium hydrogen maleate.

    Science.gov (United States)

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

    2007-10-01

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

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

    Science.gov (United States)

    Bertrand, Arthur; Lortie, Frédéric; Bernard, Julien

    2012-12-21

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

  14. Hydrogen bonds in concreto and in computro

    Science.gov (United States)

    Stouten, Pieter F. W.; Kroon, Jan

    1988-07-01

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

  15. 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.

  16. Porous Hydrogen-Bonded Organic Frameworks

    Directory of Open Access Journals (Sweden)

    Yi-Fei Han

    2017-02-01

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

  17. Hydrogen Bonding in Thermoplastic Polyurethane Elastomers: IR Thermal Analysis

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The hydrogen bond percentage and its temperature dependence of the three TPU samples synthesized from polytetrahydrofuran, 4,4-diphenylmethane diisocyanate, N-methyl diethanol amine or 1,4-butane diol were studied by means of IR thermal analysis. The enthalpy and the entropy of the hydrogen bond dissociation were determined by the Vant Hoff plot.

  18. Predictions of Glass Transition Temperature for Hydrogen Bonding Biomaterials

    NARCIS (Netherlands)

    Sman, van der R.G.M.

    2013-01-01

    We show that the glass transition of a multitude of mixtures containing hydrogen bonding materials correlates strongly with the effective number of hydroxyl groups per molecule, which are available for intermolecular hydrogen bonding. This correlation is in compliance with the topological constraint

  19. 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.

  20. Gold Nanoparticle Assemblies through Hydrogen-Bonded Supramolecular Mediators

    NARCIS (Netherlands)

    Kinge, Sachin S.; Crego-Calama, Mercedes; Reinhoudt, David N.

    2007-01-01

    The synthesis of spherical gold nanoparticle assemblies with multicomponent double rosette molecular boxes as mediators is presented. These nine-component hydrogen-bonded supramolecular structures held together by 36 hydrogen bonds induce gold nanoparticle assembly. The morphologies of the nanoparti

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

    Science.gov (United States)

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

    2016-09-06

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

  2. 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.

  3. Hydrogen-Bonded Liquid Crystal Nanocomposites.

    Science.gov (United States)

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

    2016-08-23

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

  4. The influence of hydrogen bonding on partition coefficients

    Science.gov (United States)

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

    2017-02-01

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

  5. The influence of hydrogen bonding on partition coefficients

    Science.gov (United States)

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

    2017-01-01

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

  6. 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

  7. 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.

  8. Specific Heat Properties of Proton Transfer in Hydrogen Bonded Systems

    Institute of Scientific and Technical Information of China (English)

    庞小峰; 封原平

    2003-01-01

    The thermodynamic properties of proton transport along hydrogen-bonded systems at finite temperatures have been studied by our model. We first derive the dynamic equations of the proton transport and find the solutions and the free energy of the systems. Finally, we obtain the specific heats of the hydrogen bonded systems, resulting from the motion of the soliton, by using transfer integral way. The theoretical value is basically consistent with the experimental data.

  9. 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.

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

    OpenAIRE

    1996-01-01

    Differences in the energetics of amide-amide and amide-hydroxyl hydrogen bonds in proteins have been explored from the effect of hydroxyl groups on the structure and dissolution energetics of a series of crystalline cyclic dipeptides. The calorimetrically determined energetics are interpreted in light of the crystal structures of the studied compounds. Our results indicate that the amide-amide and amide-hydroxyl hydrogen bonds both provide considerable enthalpic stability, but that the amide-...

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

    Science.gov (United States)

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

    2011-06-01

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

  12. 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

    2015-02-01

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

  13. Time-dependent density functional theory study on the electronic excited-state geometric structure, infrared spectra, and hydrogen bonding of a doubly hydrogen-bonded complex.

    Science.gov (United States)

    Liu, Yufang; Ding, Junxia; Liu, Ruiqiong; Shi, Deheng; Sun, Jinfeng

    2009-12-01

    The geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen-bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time-dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S(1) state of this doubly hydrogen-bonded FN-2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen-bonded FN-2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm(-1) observed in the IR spectra should be assigned as the doubly hydrogen-bonded FN-2MeOH complex from our calculated results. The electronic excited-state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S(1) state of the doubly hydrogen-bonded FN-2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen-bonded FN-MeOH complex and play important role on the photophysics of fluorenone in solutions.

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

    Science.gov (United States)

    Biswal, Himansu S; Wategaonkar, Sanjay

    2009-11-19

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    Inositol, 1,2,3,4,5,6-hexahydroxycyclohexane, exists in nine stereoisomers with different crystal structures and melting points. In a previous paper on the relationship between the melting points of the inositols and the hydrogen-bonding patterns in their crystal structures [Simperler et al. (2006...... ▶). CrystEngComm 8, 589], it was noted that although all inositol crystal structures known at that time contained 12 hydrogen bonds per molecule, their melting points span a large range of about 170 °C. Our preliminary investigations suggested that the highest melting point must be corrected for the effect...... 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...

  16. How universal are hydrogen bond correlations? A density functional study of intramolecular hydrogen bonding in low-energy conformers of α-amino acids

    Science.gov (United States)

    Ramaniah, Lavanya M.; Kamal, C.; Kshirsagar, Rohidas J.; Chakrabarti, Aparna; Banerjee, Arup

    2013-10-01

    Hydrogen bonding is one of the most important and ubiquitous interactions present in Nature. Several studies have attempted to characterise and understand the nature of this very basic interaction. These include both experimental and theoretical investigations of different types of chemical compounds, as well as systems subjected to high pressure. The O-H..O bond is of course the best studied hydrogen bond, and most studies have concentrated on intermolecular hydrogen bonding in solids and liquids. In this paper, we analyse and characterise normal hydrogen bonding of the general type, D-H...A, in intramolecular hydrogen bonding interactions. Using a first-principles density functional theory approach, we investigate low energy conformers of the twenty α-amino acids. Within these conformers, several different types of intramolecular hydrogen bonds are identified. The hydrogen bond within a given conformer occurs between two molecular groups, either both within the backbone itself, or one in the backbone and one in the side chain. In a few conformers, more than one (type of) hydrogen bond is seen to occur. Interestingly, the strength of the hydrogen bonds in the amino acids spans quite a large range, from weak to strong. The signature of hydrogen bonding in these molecules, as reflected in their theoretical vibrational spectra, is analysed. With the new first-principles data from 51 hydrogen bonds, various parameters relating to the hydrogen bond, such as hydrogen bond length, hydrogen bond angle, bond length and vibrational frequencies are studied. Interestingly, the correlation between these parameters in these bonds is found to be in consonance with those obtained in earlier experimental studies of normal hydrogen bonds on vastly different systems. Our study provides some of the most detailed first-principles support, and the first involving vibrational frequencies, for the universality of hydrogen bond correlations in materials.

  17. 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.

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

    Science.gov (United States)

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

    2014-05-01

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

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

    Science.gov (United States)

    Moriarty, Philip

    2014-03-01

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

  20. 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.

  1. 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...

  2. Infrared Spectra and Hydrogen Bonds of Biologically Active Benzaldehydes

    Science.gov (United States)

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

    2013-09-01

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

  3. 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.

  4. On some hydrogen bond correlations at high pressures

    Science.gov (United States)

    Sikka, S. K.

    2007-09-01

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

  5. Nature of hydrogen bonding in coal-derived asphaltenes

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, S.R.; Li, N.C.

    1978-02-01

    Reports are presented on near-infrared and proton magneti resonance studies of hydrogen bonding between the hydroxyl group of o-phenylphenol (OPP) and two coal derived asphaltenes, and their acid and base components. The asphaltenes were prepared from bituminous coal under the same conditions except that one was prepared using a CoMo catalyst. The results of the studies show that the use of the CoMo catalyst leads to a base asphaltene component of lower molecular weight and higher hydrogen-bond acceptor strength.

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

    Directory of Open Access Journals (Sweden)

    I Made Suarta

    2016-01-01

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

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

    Science.gov (United States)

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

    2014-03-07

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

  8. 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...

  9. Templation in Noncovalent Synthesis of Hydrogen-Bonded Rosettes

    NARCIS (Netherlands)

    Crego-Calama, Mercedes; Reinhoudt, David N.; Cate, ten Matthijs G.J.; Schalley, Christoph A.; Vögtle, Fritz; Dötz, Karl Heinz

    2005-01-01

    In this chapter, hydrogen-bonded assemblies based on the rosette motif are used to describe some examples of templation in noncovalent synthesis. After a brief description of the synthesis and characterization of these assemblies, the guest-templated selection and amplification of the strongest bind

  10. 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.

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

    Science.gov (United States)

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

    2014-09-01

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

  12. Watson-Crick hydrogen bonding of unlocked nucleic acids

    DEFF Research Database (Denmark)

    Langkjær, Niels; Wengel, Jesper; Pasternak, Anna

    2015-01-01

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

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

    NARCIS (Netherlands)

    Mateos-Timoneda, Miguel A.; Crego-Calama, Mercedes; Reinhoudt, David N.

    2005-01-01

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

  14. Alkyl Radicals as Hydrogen Bond Acceptors: Computational Evidence

    DEFF Research Database (Denmark)

    Hammerum, Steen

    2009-01-01

    , 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...

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

    NARCIS (Netherlands)

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

    2010-01-01

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

  16. 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.

    2015-01-01

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

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

    Science.gov (United States)

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

    1991-02-01

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

  18. Hydrogen bond and halogen bond inside the carbon nanotube

    Science.gov (United States)

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

    2011-02-01

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

  19. On the evolutionary conservation of hydrogen bonds made by buried polar amino acids: the hidden joists, braces and trusses of protein architecture

    Directory of Open Access Journals (Sweden)

    Worth Catherine L

    2010-05-01

    Full Text Available Abstract Background The hydrogen bond patterns between mainchain atoms in protein structures not only give rise to regular secondary structures but also satisfy mainchain hydrogen bond potential. However, not all mainchain atoms can be satisfied through hydrogen bond interactions that arise in regular secondary structures; in some locations sidechain-to-mainchain hydrogen bonds are required to provide polar group satisfaction. Buried polar residues that are hydrogen-bonded to mainchain amide atoms tend to be highly conserved within protein families, confirming that mainchain architecture is a critical restraint on the evolution of proteins. We have investigated the stabilizing roles of buried polar sidechains on the backbones of protein structures by performing an analysis of solvent inaccessible residues that are entirely conserved within protein families and superfamilies and hydrogen bonded to an equivalent mainchain atom in each family member. Results We show that polar and sometimes charged sidechains form hydrogen bonds to mainchain atoms in the cores of proteins in a manner that has been conserved in evolution. Although particular motifs have previously been identified where buried polar residues have conserved roles in stabilizing protein structure, for example in helix capping, we demonstrate that such interactions occur in a range of architectures and highlight those polar amino acid types that fulfil these roles. We show that these buried polar residues often span elements of secondary structure and provide stabilizing interactions of the overall protein architecture. Conclusions Conservation of buried polar residues and the hydrogen-bond interactions that they form implies an important role for maintaining protein structure, contributing strong restraints on amino acid substitutions during divergent protein evolution. Our analysis sheds light on the important stabilizing roles of these residues in protein architecture and provides

  20. 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

    not always yield consistent predictions, as illustrated by the hydrogen bonds formed by the E and Z OH groups of protonated carboxylic acids. The delta-PA and the stabilization of a series of hydrogen bonded adducts indicate that the E OH group forms the stronger hydrogen bonds, whereas the bond length...... carboxylic acids are different. The OH bond length and IR redshift afford the better measure of hydrogen bond strength....

  1. Hydrogen-bond and solvent dynamics in transition metal complexes: a combined simulation and NMR-investigation.

    Science.gov (United States)

    Huang, Jing; Häussinger, Daniel; Gellrich, Urs; Seiche, Wolfgang; Breit, Bernhard; Meuwly, Markus

    2012-12-13

    Self-assembling ligands through complementary hydrogen-bonding in the coordination sphere of a transition metal provides catalysts with unique properties for carbon-carbon and carbon-heteroatom formation. Their most distinguishing chemical bonding pattern is a double-hydrogen-bonded motif, which determines much of the chemical functionality. Here, we discuss the possibility of double proton transfer (DPT) along this motif using computational and experimental methods. The infrared and NMR spectral signatures for the double-hydrogen-bonded motif are analyzed. Atomistic simulations and experiments suggest that the dynamics of the catalyst is surprisingly complex and displays at least three different dynamical regimes which can be distinguished with NMR spectroscopy and analyzed from computation. The two hydrogen bonds are kept intact and in rapid tautomeric exchange down to 125 K, which provides an estimate of 5 kcal/mol for the barrier for DPT. This is confirmed by the simulations which predict 5.8 kcal/mol for double proton transfer. A mechanistic interpretation is provided and the distribution of the solvent shell surrounding the catalyst is characterized from extensive simulations.

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

    DEFF Research Database (Denmark)

    Luo, Jiangshui

    2016-01-01

    there is evidence of bond formation [6]. Hydrogen bonds in the solid state fall into the classification of strong, moderate, and weak hydrogen bonds [7]. In molecular systems like H2O (vs. H2S) or NH3 (vs. PH3), strong hydrogen bonds lead to higher melting points. However, in organic salts, the situation may...

  3. 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.

  4. 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.

  5. 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.

  6. Contribution of Hydrogen Bonds to Paper Strength Properties.

    Directory of Open Access Journals (Sweden)

    Piotr Przybysz

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

  7. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Nitin [ORNL; Neogi, Sanghamitra [Pennsylvania State University; Kent, Paul R [ORNL; Bandura, Andrei V. [St. Petersburg State University, St. Petersburg, Russia; Wesolowski, David J [ORNL; Cole, David R [ORNL; Sofo, Jorge O. [Pennsylvania State University

    2009-01-01

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

  9. Experimental and Theoretical Studies in Hydrogen-Bonding Organocatalysis

    Directory of Open Access Journals (Sweden)

    Matej Žabka

    2015-08-01

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

  10. 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…

  11. 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 in...

  12. 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...

  13. 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.

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

    Science.gov (United States)

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

    2014-12-14

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

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

    Science.gov (United States)

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

    2012-07-07

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

  16. 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.

  17. Protonic transport through solitons in hydrogen-bonded systems

    Science.gov (United States)

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

    2011-09-01

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

  18. Hirshfeld atom refinement for modelling strong hydrogen bonds.

    Science.gov (United States)

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

    2014-09-01

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

  19. The hydrogen-bond collective dynamics in liquid methanol

    Science.gov (United States)

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

    2016-12-01

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

  20. 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.

  1. 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.

  2. Stabilization of quinapril by incorporating hydrogen bonding interactions

    Directory of Open Access Journals (Sweden)

    Roy B

    2009-01-01

    Full Text Available In the present study stability of various known solvates of quinapril hydrochloride has been compared with nitromethane solvate. Nitromethane solvate was found to be more stable compared to other known solvates. Single crystal X-ray diffraction analysis of quinapril nitromethane solvate shows intermolecular hydrogen bonding between quinapril molecule and nitromethane. Stabilization of quinapril by forming strong hydrogen bonding network as in case of co-crystals was further studied by forming co-crystal with tris(hydroxymethylamino methane. Quinapril free base forms a stable salt with tris(hydroxymethylamino methane not reported earlier. Quinapril tris(hydroxymethylamino methane salt found to be stable even at 80° for 72 h i.e. hardly any formation of diketopiperazine and diacid impurity. As expected single crystal X-ray diffraction analysis reveals tris(hydroxymethylamino methane salt of quinapril shows complex hydrogen bonding network between the two entities along with ionic bond. The properties of this stable salt - stable in solid as well as solution phase, might lead to an alternate highly stable formulation.

  3. Hydrogen-bonding-induced polymorphous phase transitions in 2D organic nanostructures.

    Science.gov (United States)

    Xu, Li; Miao, Xinrui; Zha, Bao; Deng, Wenli

    2013-05-01

    The 2D self-assembly of various 2-hydroxy-7-alkoxy-9-fluorenone (HAF) molecules has been investigated by scanning tunneling microscopy (STM) at the liquid/solid interface. A systematic study revealed that HAF molecules with different numbers of carbon atoms in their alkoxy chains could form two or three different kinds of nanostructures, that is, less-ordered, flower-like, and zig-zag patterns, owing to the formation of different types of intermolecular hydrogen bonds. The observed structural transition was found to be driven by molecular thermodynamics, surface diffusion, and the voltage pulse that was applied to the STM tip. The zig-zag pattern was the most stable of these configurations. An odd-even effect on the flower-like structure, as induced by the odd and even number of carbon atoms in the side chain, was observed by STM. The influence of the odd-even effect on the melting point has a close relationship with the molecular self-assembled pattern. Our results are significant for understanding the influence of hydrogen-bonding interactions on the dominant adsorption behavior on the surface and provide a new visual approach for observing the influence of the odd-even effect on the phase transition.

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

    Science.gov (United States)

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

    1987-08-01

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

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

    Science.gov (United States)

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

    2014-01-21

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

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

    Science.gov (United States)

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

    2014-09-14

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

  7. 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.

  8. Positively charged phosphorus as a hydrogen bond acceptor

    DEFF Research Database (Denmark)

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

    2014-01-01

    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......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...

  9. Indirect Interactions Between Proton Donors Separated by Several Hydrogen Bonds

    CERN Document Server

    Ogawa, Takaya; Tamaki, Takanori; Yamaguchi, Takeo

    2016-01-01

    We expand the definition of our recently proposed proton conduction mechanism, the packed-acid mechanism, which occurs under conditions of concentrated proton donors. The original definition stated that acid-acid interactions, which help overcome the barrier of the rate-determining step, occur only when a hydrogen bond is formed directly between proton donors. Here, it is shown that proton donors can interact with each other even when the donors are separated via several H-bonds. The effect of these interactions on proton diffusivity is confirmed by ab initio calculations.

  10. 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}.

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

    Science.gov (United States)

    Slavíček, Petr; Fárník, Michal

    2011-07-14

    In this perspective article, we focus on the photochemistry of five-membered nitrogen containing heterocycles (pyrrole, imidazole and pyrazole) in clusters. These heterocycles represent paradigmatic structures for larger biologically active heterocyclic molecules and complexes. The dimers of the three molecules are also archetypes of different bonding patterns: N-H···π interaction, N-H···N hydrogen bond and double hydrogen bond. We briefly review available data on photochemistry of the title molecules in the gas phase, but primarily we focus on the new reaction channels opened upon the complexation with other heterocycles or solvent molecules. Based on ab initio calculations we discuss various possible reactions in the excited states of the clusters: (1) hydrogen dissociation, (2) hydrogen transfer between the heterocyclic units, (3) molecular ring distortion, and (4) coupled electron-proton transfer. The increasing photostability with complexity of the system can be inferred from experiments with photodissociation in these clusters. A unified view on photoinduced processes in five-membered N-heterocycles is provided. We show that even though different deactivation channels are energetically possible for the complexed heterocycles, in most cases the major result is a fast reconstruction of the ground state. The complexed or solvated heterocycles are thus inherently photostable although the stability can in principle be achieved via different reaction routes.

  12. 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.

  13. Infrared Spectroscopy of Hydrogen Bonds in Benzoic Acid Derivatives

    Science.gov (United States)

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

    2014-03-01

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

  14. Formaldoxime hydrogen bonded complexes with ammonia and hydrogen chloride

    Science.gov (United States)

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

    2015-02-01

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

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

    Science.gov (United States)

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

    2014-11-01

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

  16. 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...

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

    Science.gov (United States)

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

    2007-10-15

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

  18. Effect of quantum nuclear motion on hydrogen bonding

    Energy Technology Data Exchange (ETDEWEB)

    McKenzie, Ross H., E-mail: r.mckenzie@uq.edu.au; Bekker, Christiaan [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)

    2014-05-07

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

  19. Effect of quantum nuclear motion on hydrogen bonding

    Science.gov (United States)

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

    2014-05-01

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

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

    Science.gov (United States)

    Ghosh, Sanat; Bhattacharyya, Surjendu; Wategaonkar, Sanjay

    2015-11-01

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

  1. 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.

  2. 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.

  3. 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.

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  5. 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.

  6. 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...

  7. 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.

  8. 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.

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

    Institute of Scientific and Technical Information of China (English)

    SUN ChangLiang; ZHANG Yan; JIANG XiaoNan; WANG ChangSheng; YANG ZhongZhi

    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.

  10. 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.

  11. 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.

  12. Solvation and hydrogen bonding in alanine- and glycine-containing dipeptides probed using solution- and solid-state NMR spectroscopy.

    Science.gov (United States)

    Bhate, Manasi P; Woodard, Jaie C; Mehta, Manish A

    2009-07-15

    The NMR chemical shift is a sensitive reporter of peptide secondary structure and its solvation environment, and it is potentially rich with information about both backbone dihedral angles and hydrogen bonding. We report results from solution- and solid-state (13)C and (15)N NMR studies of four zwitterionic model dipeptides, L-alanyl-L-alanine, L-alanyl-glycine, glycyl-L-alanine, and glycyl-glycine, in which we attempt to isolate structural and environmental contributions to the chemical shift. We have mapped hydrogen-bonding patterns in the crystalline states of these dipeptides using the published crystal structures and correlated them with (13)C and (15)N magic angle spinning chemical shift data. To aid in the interpretation of the solvated chemical shifts, we performed ab initio quantum chemical calculations to determine the low-energy conformers and their chemical shifts. Assuming low energy barriers to interconversion between thermally accessible conformers, we compare the Boltzmann-averaged chemical shifts with the experimentally determined solvated-state shifts. The results allow us to correlate the observed differences in chemical shifts between the crystalline and solvated states to changes in conformation and hydrogen bonding that occur upon solvation.

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

    Science.gov (United States)

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

    2017-04-01

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

  14. 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

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

    Science.gov (United States)

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

    2001-01-01

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

  16. Characterisation of hydrogen bonding networks in RNAs via magic angle spinning solid state NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Riedel, Kerstin; Leppert, Joerg; Ohlenschlaeger, Oliver; Goerlach, Matthias; Ramachandran, Ramadurai [Institut fuer Molekulare Biotechnologie, Abteilung Molekulare Biophysik/NMR-Spektroskopie (Germany)], E-mail: raman@imb-jena.de

    2005-04-15

    It is demonstrated that the spatial proximity of {sup 1}H nuclei in hydrogen bonded base-pairs in RNAs can be conveniently mapped via magic angle spinning solid state NMR experiments involving proton spin diffusion driven chemical shift correlation of low gamma nuclei such as the imino and amino nitrogens of nucleic acid bases. As different canonical and non-canonical base-pairing schemes encountered in nucleic acids are characterised by topologically different networks of proton dipolar couplings, different base-pairing schemes lead to characteristic cross-peak intensity patterns in such correlation spectra. The method was employed in a study of a 100 kDa RNA composed of 97 CUG repeats, or (CUG){sub 97} that has been implicated in the neuromuscular disease myotonic dystrophy. {sup 15}N-{sup 15}N chemical shift correlation studies confirm the presence of Watson-Crick GC base pairs in (CUG){sub 97}.

  17. Enthalpies of hydrogen bonding of quinoline with o-phenylphenol and of hydrogen-bonding reactions involving the acid and base components of a coal-derived asphaltene

    Energy Technology Data Exchange (ETDEWEB)

    Dietz, A.G.; Blaha, C.; Li, N.C.

    1977-01-01

    Calorimetric studies are reported of hydrogen bonding between quinoline (Qu) and o-phenylphenol (OPP). The enthalpies of hydrogen-bonding of the acid and base components of a coal-derived asphaltene with OPP and Qu are also reported. The results provide strong evidence that the acid and base components of asphaltene function substantially as hydrogen donor and acceptor, respectively. 1 figure, 1 table.

  18. Hydrogen bond dynamics in alcohols studied by 2D IR spectroscopy

    NARCIS (Netherlands)

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

    2015-01-01

    Ultrafast hydrogen-bond dynamics in alcohols are studied by 2D IR spectroscopy and combined molecular dynamics—quantum mechanical simulations on the OH stretching mode. Fast memory loss in *100 fs are attributed to intact hydrogen-bond fluctuations. Stable (at the experimental timescale) hydrogen bo

  19. Temperature breaking of hydrogen bonds in ammonia studied by π --meson capture in hydrogen

    Science.gov (United States)

    Horváth, D.; Bannikov, A. V.; Kachalkin, A. K.; Lévay, B.; Petrukhin, V. I.; Vasilyev, V. A.; Yutlandov, I. A.; Strakovsky, I. I.

    1982-04-01

    The capture probability of stopped π - mesons by hydrogen atoms of ammonia increases with temperature in the liquid phase but in the supercritical phase it is temperature-independent. This can be attributed to the temperature breaking of hydrogen bonds. Rough estimates are given for the fraction of broken hydrogen bonds at various temperatures.

  20. 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…

  1. Reordering hydrogen bonds using Hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems

    NARCIS (Netherlands)

    Vreede, J.; Wolf, M.G.; de Leeuw, S.W.; Bolhuis, P.G.

    2009-01-01

    Hydrogen bonds play an important role in stabilizing (meta-)stable states in protein folding. Hence, they can potentially be used as a way to bias these states in molecular simulation methods. Previously, Wolf et al. showed that applying repulsive and attractive hydrogen bond biasing potentials in a

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

    Science.gov (United States)

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

    2013-04-01

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

  3. 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.

  4. 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.

  5. 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.

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

    Science.gov (United States)

    Schmiedekamp, Ann; Nanda, Vikas

    2009-07-01

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

  7. 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

    to 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....

  8. Reaction dynamics and statistical theory for the growth of hydrogen bonding clusters

    Institute of Scientific and Technical Information of China (English)

    WANG; Haijun; BA; Xinwu(巴信武); ZHAO; Min(赵敏)

    2002-01-01

    The similarities between the formation of hydrogen bonds and polycondensation reactions are stated from the statistical viewpoint, and then taking the hydrogen bonding system of AaDd type as an example, the growing process of hydrogen bonding clusters is investigated in terms of the theory of reaction dynamics and statistical theory for polymeric reactions. The two methods lead to the same conclusions, stating that the statistical theory for polymerization is applicable to the hydrogen bonding systems. Based on this consideration, the explicit relationship between the conversions of proton-donors and proton-acceptors and the Gibbs free energy of the system under study is given. Furthermore, the sol-gel phase transition is predicted to take place in some hydrogen bonding systems, and the corresponding generalized scaling laws describing this kind of phase transition are obtained.

  9. 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.

  10. 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.

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

    Science.gov (United States)

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

    2016-03-01

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

  12. 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.

  13. Thermotropic organization of hydrogen-bond-bridged bolaform amphiphiles.

    Science.gov (United States)

    Zhang, Jing; Zhou, Mingjun; Wang, Shan; Carr, Jessica; Li, Wen; Wu, Lixin

    2011-04-05

    A series of quaternary ammonium amphiphiles (A-n) bearing carboxylic acid groups were designed and synthesized. The branched bolaform structures can be constructed by dimerizations of carboxylic acid groups through intermolecular hydrogen bonding, as demonstrated by the Fourier transform infrared (FT-IR) spectra and the temperature-dependent FT-IR spectra. The thermotropic organizations of branched bolaform ammonium dimer complexes were characterized by differential scanning calorimetry, polarized optical microscopy, and X-ray diffraction. We investigated the influence of the spacer between the cationic group and the benzene ring on the thermotropic organization. A-6 with short lateral alkyl chains formed a simple layered structure at room temperature and exhibited smectic A mesophase above 145 °C, whereas A-8 with intermediate lateral chain length organized into smectic A phase over a wide temperature range. A further increase of the length (n = 10, 12) of the lateral chains resulted in the formation of lamellar structure with in-plane layered periodicity, which is rare in the organization of ionic compounds. A packing model of the quasi-2D lamellar was proposed on the basis of the experimental data of X-ray diffraction results. Notably, the quasi-2D lamellar structure could evolve into a simple layer with the increase of temperature. The present results showed a direct relationship in which the branched architecture can be applied to tune the self-assembly behavior of ionic amphiphiles and is allowed to construct new layered superstructure.

  14. 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...

  15. 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....

  16. 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...

  17. NMR properties of hydrogen-bonded glycine cluster in gas phase

    Science.gov (United States)

    Carvalho, Jorge R.; da Silva, Arnaldo Machado; Ghosh, Angsula; Chaudhuri, Puspitapallab

    2016-11-01

    Density Functional Theory (DFT) calculations have been performed to study the effect of the hydrogen bond formation on the Nuclear Magnetic Resonance (NMR) parameters of hydrogen-bonded clusters of glycine molecules in gas-phase. DFT predicted isotropic chemical shifts of H, C, N and O of the isolated glycine with respect to standard reference materials are in reasonable agreement with available experimental data. The variations of isotropic and anisotropic chemical shifts for all atoms constituting these clusters containing up to four glycine molecules have been investigated systematically employing gradient corrected hybrid B3LYP functional with three different types of extended basis sets. The clusters are mainly stabilized by a network of strong hydrogen bonds among the carboxylic (COOH) groups of glycine monomers. The formation of hydrogen bond influences the molecular structure of the clusters significantly which, on the other hand, gets reflected in the variations of NMR properties. The carbon (C) atom of the sbnd COOH group, the bridging hydrogen (H) and the proton-donor oxygen (O) atom of the Osbnd H bond suffer downfield shift due to the formation of hydrogen bond. The hydrogen bond lengths and the structural complexity of the clusters are found to vary with the number of participating monomers. A direct correlation between the hydrogen bond length and isotropic chemical shift of the bridging hydrogen is observed in all cases. The individual variations of the principal axis elements in chemical shift tensor provide additional insight about the different nature of the monomers within the cluster.

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

    Science.gov (United States)

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

    2016-05-20

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

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Science.gov (United States)

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

    2014-12-15

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

  1. The role of hydrogen bonding in excited state intramolecular charge transfer.

    Science.gov (United States)

    Chipem, Francis A S; Mishra, Anasuya; Krishnamoorthy, G

    2012-07-07

    Intramolecular charge transfer (ICT) that occurs upon photoexcitation of molecules is a vital process in nature and it has ample applications in chemistry and biology. The ICT process of the excited molecules is affected by several environmental factors including polarity, viscosity and hydrogen bonding. The effect of polarity and viscosity on the ICT processes is well understood. But, despite the fact that hydrogen bonding significantly influences the ICT process, the specific role of hydrogen bonding in the formation and stabilization of the ICT state is not unambiguously established. Some literature reports predicted that the hydrogen bonding of the solvent with a donor promotes the formation of a twisted intramolecular charge transfer (TICT) state. Some other reports stated that it inhibits the formation of the TICT state. Alternatively, it was proposed that the hydrogen bonding of the solvent with an acceptor favors the TICT state. It is also observed that a dynamic equilibrium is established between the free and the hydrogen bonded ICT states. This perspective focuses on the specific role played by hydrogen bonding of the solvent with the donor and the acceptor, and by proton transfer in the ICT process. The utility of such influence in molecular recognition and anion sensing is discussed with a few recent literature examples in the end.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2013-07-25

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

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

    Science.gov (United States)

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

    2016-04-01

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

  5. 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.

  6. 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.

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

    Science.gov (United States)

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

    2014-08-19

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

  8. Hydrogen bonding versus hyperconjugation in condensed-phase carbocations.

    Science.gov (United States)

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

    2013-06-21

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-03-31

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

  10. Intramolecular Hydrogen Bond in Biologically Active o-Carbonyl Hydroquinones

    Directory of Open Access Journals (Sweden)

    Maximiliano Martínez-Cifuentes

    2014-07-01

    Full Text Available Intramolecular hydrogen bonds (IHBs play a central role in the molecular structure, chemical reactivity and interactions of biologically active molecules. Here, we study the IHBs of seven related o-carbonyl hydroquinones and one structurally-related aromatic lactone, some of which have shown anticancer and antioxidant activity. Experimental NMR data were correlated with theoretical calculations at the DFT and ab initio levels. Natural bond orbital (NBO and molecular electrostatic potential (MEP calculations were used to study the electronic characteristics of these IHB. As expected, our results show that NBO calculations are better than MEP to describe the strength of the IHBs. NBO energies (∆Eij(2 show that the main contributions to energy stabilization correspond to LPàσ* interactions for IHBs, O1…O2-H2 and the delocalization LPàπ* for O2-C2 = Cα(β. For the O1…O2-H2 interaction, the values of ∆Eij(2 can be attributed to the difference in the overlap ability between orbitals i and j (Fij, instead of the energy difference between them. The large energy for the LP O2àπ* C2 = Cα(β interaction in the compounds 9-Hydroxy-5-oxo-4,8, 8-trimethyl-l,9(8H-anthracenecarbolactone (VIII and 9,10-dihydroxy-4,4-dimethylanthracen-1(4H-one (VII (55.49 and 60.70 kcal/mol, respectively when compared with the remaining molecules (all less than 50 kcal/mol, suggests that the IHBs in VIII and VII are strongly resonance assisted.

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

    Science.gov (United States)

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

    1998-07-01

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

  12. 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.

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

    Science.gov (United States)

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

    2016-06-01

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

  14. 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.

  15. Perturbation calculations on the variation of hydrogen---bond energies with intermolecular distance

    NARCIS (Netherlands)

    Duijneveldt-van de Rijdt, J.G.C.M. van; Duijneveldt, F.B. van

    1968-01-01

    In previous perturbation calculations on the hydrogen bond [6] the short-range repulsion was seriously underestimated. It is shown that this can be remedied by choosing a more realistic model system and using exact 3-centre integrals.

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

    CERN Document Server

    Zentel, Tobias

    2016-01-01

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

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

    Science.gov (United States)

    Zentel, Tobias; Kühn, Oliver

    2016-12-01

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

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

    Science.gov (United States)

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

    2016-10-01

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

  19. 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.

  20. Hydrogen bonding in transient bifunctional hypervalent radicals by neutralization-reionization mass spectrometry.

    Science.gov (United States)

    Shaffer, S A; Tureček, F

    1995-11-01

    Neutralization-reionization mass spectrometry is used to generate hypervalent 9-N-4 (ammonium) and 9-O-3 (oxonium) radicals derived from protonated α,ω-bis-(dimethylamino)alkanes and α,ω-dimethoxyalkanes, which exist as cyclic hydrogen-bonded structures in the gas phase. Collisional neutralization with dimethyl disulfide, trimethylamine, and xenon of the hydrogen-bonded onium cations followed by reionization with oxygen results in complete dissociation. Bond cleavages at the hypervalent nitrogen atoms are found to follow the order CH2-N>CH3-N>N-H, which differs from that in the monofunctional hydrogen-n-heptyldimethylammonium radical, which gives CH2-N>N-H>CH3-N. No overall stabilization through hydrogen bonding of the bifunctional hypervalent ammonium and oxonium radicals is observed. Subtle effects of ring size are found that tend to stabilize large ring structures and are attributed to intramolecular hydrogen bonding.

  1. 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

    2016-06-01

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

  2. 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.

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

    Science.gov (United States)

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

    2016-10-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  5. Fine Structure of Hydrogen Bond in Cholic Acid Revealed by 2DIR Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Based on cryogenic FT-IR spectroscopic studies of hydrogen bonds in cholic acid, two-dimensional FT-IR spectroscopy was applied to enhance our understanding of the hydrogen bonds of cholic acid. Fine spectral structures were revealed by asynchronous 2D FT-IR spectra. The co-relationship among various bands was discussed according to the synchronous 2D FT-IR spectrum.

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

    Science.gov (United States)

    Wójcik, Marek J.

    1981-11-01

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

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

    Science.gov (United States)

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

    2014-10-15

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

  8. 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.

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

    Science.gov (United States)

    Bushey, Mark Lawrence

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

  10. Hydrogen-bonded Supramolecular Rosette Ribbon Constructed from Melamine with Isophthalic Acid

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xiu-Lian

    2008-01-01

    The new complex of melamine (MA) with isophthalie acid (H2IA), [(HMA+)-(HIA-)]·2H2O, has been prepared and its structure was characterized by X-ray crystallography.The crystal is of triclinic, space group P1 with a = 7.0228(6), b = 9.1706(8), c = 12.170(1) A, α =95.337(2), β = 105.247(2), γ = 97.813(2)°, V= 742.3(1) A3, Mr= 328.30, Z= 2,Dc = 1.469 g/cm3,λ = 0.71073 A, μ(MoKa) = 0.121 mm-1 and F(000) = 344. The structure was refined to R =0.0389 and wR = 0.1093 for 2513 observed reflections with Ⅰ 2σ(Ⅰ). Melamine dimer and isophthalic acid anion are interlinked by N-H…N and N-H…O hydrogen bonds, resulting in a 1D rosette ribbon in which water molecules and amino groups are self-assembled into quasi-hexagonal patterns.

  11. 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.

  12. 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.

  13. 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.

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

    Science.gov (United States)

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

    2017-02-01

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

  15. 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.

  16. 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.

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

    Science.gov (United States)

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

    2014-03-01

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

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

    Science.gov (United States)

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

    2010-09-02

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

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

    Science.gov (United States)

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

    2016-01-01

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

  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)

    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. Structural and theoretical investigations of short hydrogen bonds: neutron diffraction and plane-wave DFT calculations of urea phosphoric acid

    Science.gov (United States)

    Wilson, Chick C.; Morrison, Carole A.

    2002-08-01

    Low temperature neutron diffraction and high level computational methods have been applied to investigate the short hydrogen bond in urea-phosphoric acid. It is found that isolated molecule calculations predict a `normal' O-H⋯O hydrogen bond, in strong disagreement with the very short, 3 c-4 e hydrogen bond found from the neutron diffraction. Extending these calculations into a periodic environment using plane-wave DFT methods give much improved agreement with experiment, with a much shorter, stronger hydrogen bond, and significant elongation of the O-H `covalent' bond.

  3. Energy decomposition analysis of cation-π, metal ion-lone pair, hydrogen bonded, charge-assisted hydrogen bonded, and π-π interactions.

    Science.gov (United States)

    Sharma, Bhaskar; Srivastava, Hemant Kumar; Gayatri, Gaddamanugu; Sastry, Garikapati Narahari

    2015-03-30

    This study probes the nature of noncovalent interactions, such as cation-π, metal ion-lone pair (M-LP), hydrogen bonding (HB), charge-assisted hydrogen bonding (CAHB), and π-π interactions, using energy decomposition schemes-density functional theory (DFT)-symmetry-adapted perturbation theory and reduced variational space. Among cation-π complexes, the polarization and electrostatic components are the major contributors to the interaction energy (IE) for metal ion-π complexes, while for onium ion-π complexes (NH4+, PH4+, OH3+, and SH3+) the dispersion component is prominent. For M-LP complexes, the electrostatic component contributes more to the IE except the dicationic metal ion complexes with H2 S and PH3 where the polarization component dominates. Although electrostatic component dominates for the HB and CAHB complexes, dispersion is predominant in π-π complexes.

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

    Science.gov (United States)

    Titantah, John Tatini; Karttunen, Mikko

    2013-10-21

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

  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. Investigation of Highly Designable Dented Structures in HP Model with Hydrogen Bond Energy

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei; HUANG Shengyou; YU Tao; ZOU Xianwu

    2007-01-01

    Some highly designable protein structures have dented on the surface of their native structures, and are not full compactly folded. According to hydrophobic-polar (HP) model the most designable structures are full compactly folded. To investigate the designability of the dented structures, we introduce the hydrogen bond energy in the secondary structures by using the secondary-structure-favored HP model proposed by Ou-yang etc. The result shows that the average designability increases with the strength of the hydrogen bond. The designabilities of the structures with same dented shape increase exponentially with the number of secondary structure sites. The dented structures can have the highest designabilities for a certain value of hydrogen bond energy density.

  7. Theoretical Study on Measure of Hydrogen Bonding Strength: R-C≡N…pyrrole Complexes

    Institute of Scientific and Technical Information of China (English)

    史福强; 安静仪; 俞稼镛

    2005-01-01

    The R-C≡N…pyrrole (R=H, CH3, CH2F, CHF2, CF3, NH2, BH2, OH, F, CH2Cl, CHCl2, CCl3, Li, Na) complexes were considered as the simple sample for measure of hydrogen bonding strength. Density functional theory B3LYP/6-311 + + G** level was applied to the optimization of geometries of complexes and monomers. Measure of hydrogen bonding strength based on geometrical and topological parameters, which were derived from the AIM theory, was analyzed. Additionally, natural bond orbital (NBO) analysis and frequency calculations were performed.From the computation results it was found that the electronic density at N-H bond critical points was also strictly correlated with the hydrogen bonding strength.

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

    Science.gov (United States)

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

    2006-11-01

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

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

    Science.gov (United States)

    Wang, Weizhou; Zhang, Yu; Huang, Kaixun

    2005-10-20

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

  10. Inversion of the balance between hydrophobic and hydrogen bonding interactions in protein folding and aggregation.

    Directory of Open Access Journals (Sweden)

    Anthony W Fitzpatrick

    2011-10-01

    Full Text Available Identifying the forces that drive proteins to misfold and aggregate, rather than to fold into their functional states, is fundamental to our understanding of living systems and to our ability to combat protein deposition disorders such as Alzheimer's disease and the spongiform encephalopathies. We report here the finding that the balance between hydrophobic and hydrogen bonding interactions is different for proteins in the processes of folding to their native states and misfolding to the alternative amyloid structures. We find that the minima of the protein free energy landscape for folding and misfolding tend to be respectively dominated by hydrophobic and by hydrogen bonding interactions. These results characterise the nature of the interactions that determine the competition between folding and misfolding of proteins by revealing that the stability of native proteins is primarily determined by hydrophobic interactions between side-chains, while the stability of amyloid fibrils depends more on backbone intermolecular hydrogen bonding interactions.

  11. 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.

  12. 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.

  13. 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.

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

    Science.gov (United States)

    Hemp, Sean T; Long, Timothy E

    2012-01-01

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

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

    DEFF Research Database (Denmark)

    Kuznetsov, A.M.; Ulstrup, Jens

    2004-01-01

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

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

    Science.gov (United States)

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

    2017-01-02

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

  17. 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.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    Two equations of state (simplified PC-SAFT and CPA) are used to predict the monomer fraction of 1-alkanols in binary mixtures with n-alkanes. It is found that the choice of parameters and association schemes significantly affects the ability of a model to predict hydrogen bonding in mixtures, even...... studies, which is clarified in the present work. New hydrogen bonding data based on infrared spectroscopy are reported for seven binary mixtures of alcohols and alkanes. (C) 2007 Elsevier B.V. All rights reserved....

  19. Hydrogen bonding in asphaltenes and coal. Comprehensive progress report, December 1975--Februray 1977. [13 references

    Energy Technology Data Exchange (ETDEWEB)

    Li, N.C.

    1977-01-01

    Proton magnetic resonance (PMR) studies are reported of hydrogen bonding between the OH proton of o-phenylphenol (OPP) and the nitrogen electron donor of quinoline (Qu). Data are also reported on the hydrogen bonding of a coal-derived asphaltene and its acid and base components with OPP. Determination was made of the equilibrium constants of the 1:1 complex between OPP and Qu at 39, 32, 1, and -18/sup 0/C from the PMR studies. Qualitative results are reported for the interaction between the base fraction of asphaltene and OPP at 32, 1, and -26/sup 0/C.

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

    Science.gov (United States)

    Zhou, Pan-Pan; Qiu, Wen-Yuan

    2009-08-01

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

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

    DEFF Research Database (Denmark)

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

    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...

  2. Shear induced weakening of the hydrogen bonding lattice of the energetic material 5,5‧-Hydrazinebistetrazole at high-pressure

    Science.gov (United States)

    Ciezak-Jenkins, Jennifer A.; Jenkins, Timothy A.

    2017-02-01

    5,5‧-Hydrazinebistetrazole (HBTA) has been studied by in-situ x-ray diffraction and vibrational spectroscopy to pressures near 25 GPa at room temperature. Analysis of the x-ray diffraction pattern of HBTA collected at ambient pressure and temperature revealed a monoclinic structure consistent with that previously reported. Under compression, the x-ray diffraction reveals little evidence of a phase transition over the pressure range studied. Slight anisotropy in response to compression was noted and the β angle decreased moderately, suggesting geometry modifications occur in the hydrogen bonding lattice and between neighboring HBTA molecules as a result of compression along the c axis. Blue shifts in the Infrared active Nsbnd H stretching modes were observed, implying a weakening of the hydrogen bond with compression. The weakening of the hydrogen bonding lattice with pressure may lead to an increase in the bending angle of the Csbnd Ndbnd Nsbnd C bridge between the tetrazole rings and an increased overlap between the π-bonding orbitals. The Raman spectra showed a number of modes associated with Hsbnd Ndbnd Nsbnd H motions of the bridge become more prominent in the spectra under compression. Additionally, the possibility that the increased bend in the angle of the Csbnd Ndbnd Nsbnd C bridge results from a shearing deformation is discussed.

  3. 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.

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

    NARCIS (Netherlands)

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

    1999-01-01

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

  5. Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations

    Directory of Open Access Journals (Sweden)

    Sandeep Kumar Mishra

    2017-03-01

    Full Text Available The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.

  6. 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…

  7. Phonon driven proton transfer in crystals with short strong hydrogen bonds

    NARCIS (Netherlands)

    Fontaine-Vive, F.; Johnson, M.R.; Kearley, G.J.; Cowan, J.A.; Howard, J.A.K.; Parker, S.F.

    2006-01-01

    Recent work on understanding why protons migrate with increasing temperature in short, strong hydrogen bonds is extended here to three more organic, crystalline systems. Inelastic neutron scattering and density functional theory based simulations are used to investigate structure, vibrations, and dy

  8. Hydrogen-bond dynamics in water explored by heterodyne-detected photon echo

    NARCIS (Netherlands)

    Yeremenko, S; Pshenichnikov, MS; Wiersma, DA; Pshenichnikov, Maxim S.

    2003-01-01

    Results of heterodyne-detected photon echo experiments on the OH stretching mode of water are reported and discussed. Two vibrational dynamical processes with time constants of 130 and 900 fs were identified. The former is attributed to bond breaking dynamics of a single hydrogen bond, the latter to

  9. Observed and predicted hydrogen bond motifs in crystal structures of hydantoins, dihydrouracils and uracils

    NARCIS (Netherlands)

    Cruz-Cabeza, A.J.; Schwalbe, C.H.

    2012-01-01

    A survey of crystal structures containing hydantoin, dihydrouracil and uracil derivatives in the Cambridge Structural Database revealed four main types of hydrogen bond motifs when derivatives with extra substituents able to interfere with the main motif are excluded. All these molecules contain two

  10. Hydrogen bond fluctuations of the hydration shell of the bromide anion

    NARCIS (Netherlands)

    Timmer, R.L.A.; Bakker, H.J.

    2009-01-01

    We study the hydrogen bond dynamics of solutions of LiBr and NaBr in isotopically diluted water (2% HDO:D2O) with femtosecond spectral hole-burning spectroscopy. We study the frequency fluctuations of the O-H stretch vibrations of the HDO molecules and observe spectral dynamics with time constants o

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

    Institute of Scientific and Technical Information of China (English)

    赵新军; 高志福

    2016-01-01

    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 hydro-gen 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 se-ries: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 de-scribing 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 im-portant for understanding the shift of the lower critical solution temperature of PNIPAM brushes following the Hofmeister series.

  12. Conductivity properties of proton transfer and influence of temperature on it in hydrogen-bonded systems

    Institute of Scientific and Technical Information of China (English)

    PANGXiao-feng; YUJia-feng

    2004-01-01

    We study and calculate the mobility and oonductivity of proton transfer and influence of temperature on it by pang's dynamic model in hydrogen bonded systems, which ooincide with experiments. We further study the mechanism of magnetization of ciguid water in the basis of this model.

  13. Strong Screening Effect of Polyhedral Oligomeric Silsesquioxanes (POSS Nanoparticles on Hydrogen Bonded Polymer Blends

    Directory of Open Access Journals (Sweden)

    Chin-Wei Chiou

    2014-03-01

    Full Text Available In this study we used anionic living polymerization to prepare two different homopolymers: a poly(methyl methacrylate (PMMA and a PMMA derivative presenting polyhedral oligomeric silsesquioxane (PMA-POSS units as its side chains. We then employed differential scanning calorimetry (DSC, Fourier transform infrared (FTIR spectroscopy, and wide-angle X-ray diffraction (WAXD to investigate the miscibility and specific interactions of PMMA and PMA-POSS with three hydrogen bonding donor compounds: poly(vinyl phenol (PVPh, phenolic resin, and bisphenol A (BPA. DSC revealed that all of the PVPh/PMMA, phenolic/PMMA, and BPA/PMMA blends exhibited a single glass transition temperature, characteristic of miscible systems; FTIR spectroscopic analyses revealed that such miscibility resulted from hydrogen bonding interactions between the C=O groups of PMMA and the OH groups of these three hydrogen bonding donor compounds. In contrast, all of the PVPh/PMA-POSS, phenolic/PMA-POSS, and BPA/PMA-POSS blends were immiscible: DSC revealed two glass transition temperatures arising from strong screening effects (FTIR spectroscopy and high degrees of aggregation (WAXD of the POSS nanoparticles. We propose that the value of the intramolecular screening effect (γ should be very close to 1 for all PMA-POSS blend systems when POSS nanoparticles appear as the side chains of PMMA, such that the OH groups of the hydrogen bonding donor compounds cannot interact with the C=O groups of PMA-POSS.

  14. Conductivity properties of proton transfer and influence of temperature on it in hydrogen-bonded systems

    Institute of Scientific and Technical Information of China (English)

    PANG Xiao-feng; YU Jia-feng

    2004-01-01

    We study and calculate the mobility and conductivity of proton transfer and influence of temperature on it by pang's dynamic model in hydrogen bonded systems, which coincide with experiments. We further study the mechanism of magnetization of ciguid water in the basis of this model.

  15. 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” ...

  16. New Hydrogen Bonded Supramolecular Hydrogels Formed through Gelating Two Isomeric Building Units Simultaneously

    Institute of Scientific and Technical Information of China (English)

    Ji Wei WU; Li Ming TANG; Kai CHEN; Liang YAN; Yu Jiang WANG

    2006-01-01

    New hydrogen bonded supramolecular hydrogels were formed through simultaneously gelating two isomeric building units, 4-oxo-4-(2-pyridinylamino)butanoic acid (G1) and 4-oxo-4-(3-pyridinylamino)butanoic acid (G2) at various molar ratios in water.

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

    Science.gov (United States)

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

    2016-05-01

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

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

    Science.gov (United States)

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

    2013-07-19

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

  19. 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.

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

    Science.gov (United States)

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

    2012-11-21

    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, the response of a vibrational mode to electric field, can provide an experimental method for parsing such interactions into their electrostatic and nonelectrostatic components. In a previous study we showed that, in the case of relatively weak O-H···π hydrogen bonds, the O-H bond displays a linear response to an electric field, and we exploited this response to demonstrate that the interactions are dominated by electrostatics (Saggu, M.; Levinson, N. M.; Boxer, S. G. J. Am. Chem. Soc.2011, 133, 17414-17419). Here we extend this work to other X-H···π interactions. We find that the response of the X-H vibrational probe to electric field appears to become increasingly nonlinear in the order O-H electrostatic binding energies of the interactions, which are found to agree closely with the results of energy calculations. Taken together, these results highlight that with careful calibration vibrational probes can provide direct measurements of the electrostatic components of hydrogen bonds.

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

    DEFF Research Database (Denmark)

    Schrøder, Sidsel Dahl

    and 1,4-diaminobutane). Experimentally, the hydrogen bonds have been studied with vibrational spectroscopy in the infrared and near-infrared regions. The focus is primarily on spectra recorded in the near-infrared regions, which in these studies are dominated by O-H and N-H stretching overtones...

  2. 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...

  3. 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

    2015-11-07

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

  4. 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...

  5. Ladderlike oligomers; intramolecular hydrogen bonding, push-pull character, and electron affinity.

    Science.gov (United States)

    Pieterse, K; Vekemans, J A; Kooijman, H; Spek, A L; Meijer, E W

    2000-12-15

    Symmetrical 2,5-bis(2-aminophenyl)pyrazines have been synthesized by application of the Stille coupling strategy. These cotrimers feature three important properties, namely strong intramolecular hydrogen bonding, push-pull character, and high electron affinity. The presence of intramolecular hydrogen bonds has been confirmed by 1H NMR, IR spectroscopy, and single-crystal X-ray diffraction. The hydrogen bond strength can be increased by substituting the amino groups with stronger electron-withdrawing functionalities. Despite the anticipated enhanced pi-conjugation through planarization, a hypsochromic shift was observed in the UV/Vis spectra, explained by a decrease in push-pull character. The electron affinity of the cotrimers was deduced from the first reduction potentials measured by cyclic voltammetry and is related to the electron-withdrawing character of the amino substituents. The results obtained have been compared with those of the corresponding 4-aminophenyl analogues and show that intramolecular hydrogen bonds can be used to design polymers with enhanced pi conjugation as well as a high electron affinity.

  6. 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.

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    We have observed the NH···P hydrogen bond in a gas phase complex. The bond is identified in the dimethylamine-trimethylphosphine complex by a red shift of the fundamental NH-stretching frequency observed using Fourier transform infrared spectroscopy (FT-IR). On the basis of the measured NH...

  8. 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.

  9. Hydrogen-bonded Lamellar Network of Pyromellitic Acid Pillared by 8-Hydroxyquinoline

    Institute of Scientific and Technical Information of China (English)

    WANG, Lei; ZHANG, Hong; ZHANG, Jing-Ping; GAO, Fei-Xue; HUA, Rui-Mao; ZHOU, Guang-Yuan

    2006-01-01

    8-Hydroxyquinoline (8-q) salt of pyromellitic acid (benzene-1,2,4,5-tetracarboxylic acid, H4bta) forms robust lamellar structure where [H2bta]2- anions build up sheets through strong hydrogen bonds in two dimensions and[H-8-q]+ cations act as pillars to afford an extended three dimensional network.

  10. Efficient Energy Transfer in Supramolecular, Hydrogen-Bonded Polypyridylruthenium-Osmium Complexes

    NARCIS (Netherlands)

    Rau, Sven; Schäfer, Bernhard; Schebesta, Sebastian; Grüßing, André; Poppitz, Wolfgang; Walther, Dirk; Duati, Marco; Browne, Wesley R.; Vos, Johannes G.

    2003-01-01

    Hydrogen bond association between ruthenium bibenzimidazole and carboxylated polypyridylosmium complexes results in stable supramolecular aggregates. The determined stability constant of logK approximate to 6 +/- 0.3 allows efficient energy transfer from the ruthenium to the osmium moiety. (C) Wiley

  11. The electron density distribution in the hydrogen bond. A quantum chemical and crystallographic study

    NARCIS (Netherlands)

    Feil, Dirk

    1990-01-01

    With the help of Hartree—Fock—Slater calculations in which very large basis sets are employed, the polarisation of the water molecule by an electric field is explored. The various features in the electron density distribution are encountered again in the long hydrogen bond in the water dimer, showin

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

    Science.gov (United States)

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

    2010-08-01

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

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

    Science.gov (United States)

    1987-07-03

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

  14. The effect of large amplitude motions on the transition frequency redshift in hydrogen bonded complexes

    DEFF Research Database (Denmark)

    Mackeprang, Kasper; Kjærgaard, Henrik Grum; Salmi, Teemu

    2014-01-01

    -stretching transition. The model accurately predicts the transition wavenumbers of the vibrations in water dimer compared to experimental values and provides a physical picture that explains the redshift of the hydrogen bonded OH-oscillator. We find that it is unnecessary to include all six intermolecular modes...

  15. 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.

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

    DEFF Research Database (Denmark)

    Carlsen, Lars; Duus, Fritz

    1980-01-01

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

  17. Hydrogen-bonding study of photoexcited 4-nitro-1,8-naphthalimide in hydrogen-donating solvents

    Directory of Open Access Journals (Sweden)

    Cao Jianfang

    2016-01-01

    Full Text Available The solute–solvent interactions of 4-nitro-1,8-naphthalimide (4NNI as a hydrogen bond acceptor in hydrogen donating methanol (MeOH solvent in electronic excited states were investigated by means of the time-dependent density functional theory(TDDFT. We calculated the S0 state geometry optimizations, electronic transition energies and corresponding oscillation strengths of the low-lying electronically excited states for the isolated 4NNi and hydrogen-bonded 4NNi-(MeOH1,4 complexes using the density functional theory (DFT and TDDFT methods. The electronic excitation energies of the hydrogen-bonded complexes are correspondingly decreased compared to that of the isolated 4NNi, which revealed that the intermolecular hydrogen bond C=O···H–O and N=O···H–O in the hydrogen-bonded 4NNi-(MeOH1,4 are strengthened in the electronically excited state. The calculated results are consistent with the mechanism that hydrogen bond strengthening will induce a redshift of the corresponding electronic spectra, while hydrogen bond weakening will cause a blueshift. Furthermore, we believe that the deduction we used to depict the trend of the hydrogen bond changes in excited states exists in many other fuorescent dyes in solution.

  18. Multiple hydrogen bonding in excited states of aminopyrazine in methanol solution: time-dependent density functional theory study.

    Science.gov (United States)

    Chai, Shuo; Yu, Jie; Han, Yong-Chang; Cong, Shu-Lin

    2013-11-01

    Aminopyrazine (AP) and AP-methanol complexes have been theoretically studied by using density functional theory (DFT) and time-dependent density functional theory (TDDFT). The excited-state hydrogen bonds are discussed in detail. In the ground state the intermolecular multiple hydrogen bonds can be formed between AP molecule and protic solvents. The AP monomer and hydrogen-bonded complex of AP with one methanol are photoexcited initially to the S2 state, and then transferred to the S1 state via internal conversion. However the complex of AP with two methanol molecules is directly excited to the S1 state. From the calculated electronic excited energies and simulated absorption spectra, we find that the intermolecular hydrogen bonds are strengthened in the electronic excited states. The strengthening is confirmed by the optimized excited-state geometries. The photochemical processes in the electronic excited states are significantly influenced by the excited-state hydrogen bond strengthening.

  19. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.

    Science.gov (United States)

    Yesselman, Joseph D; Horowitz, Scott; Brooks, Charles L; Trievel, Raymond C

    2015-03-01

    The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding.

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

    Directory of Open Access Journals (Sweden)

    Malose Jack Mphahlele

    2017-01-01

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

  1. Reordering hydrogen bonds using hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems.

    Science.gov (United States)

    Vreede, Jocelyne; Wolf, Maarten G; de Leeuw, Simon W; Bolhuis, Peter G

    2009-05-07

    Hydrogen bonds play an important role in stabilizing (meta-)stable states in protein folding. Hence, they can potentially be used as a way to bias these states in molecular simulation methods. Previously, Wolf et al. showed that applying repulsive and attractive hydrogen bond biasing potentials in an alternating way significantly accelerates the folding process (Wolf, M. G.; de Leeuw, S. W. Biophys. J. 2008, 94, 3742). As the biasing potentials are only active during a fixed time interval, this alternating scheme does not represent a thermodynamic equilibrium. In this work, we present a Hamiltonian replica exchange molecular dynamics (REMD) scheme that aims to shuffle and reorder hydrogen bonds in the protein backbone. We therefore apply adapted hydrogen bond potentials in a Hamiltonian REMD scheme, which we call hydrogen bond switching (HS). To compare the performance of the HS to a standard REMD method, we performed HS and temperature REMD simulations of a beta-heptapeptide in methanol. Both methods sample the conformational space to a similar extent. As the HS simulation required only five replicas, while the REMD simulation required 20 replicas, the HS method is significantly more efficient. We tested the HS method also on a larger system, 16-residue polyalanine in water. Both of the simulations starting from a completely unfolded and a folded conformation resulted in an ensemble with, apart from the starting structure, similar conformational minima. We can conclude that the HS method provides an efficient way to sample the conformational space of a protein, without requiring knowledge of the folded states beforehand. In addition, these simulations revealed that convergence was hampered by replicas having a preference for specific biasing potentials. As this sorting effect is inherent to any Hamiltonian REMD method, finding a solution will result in an additional increase in the efficiency of Hamiltonian REMD methods in general.

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

    Science.gov (United States)

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

    2012-12-07

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

  3. 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.

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    Fangjun Yao

    2017-03-01

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

  6. 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.

  7. Theoretical Studies on the Hydrogen Bond Transfer and Proton Transfer between Anamorphoses of the Dihydrated Glycine Complex

    Institute of Scientific and Technical Information of China (English)

    WANG Ke-Cheng; MENG Xiang-Jun; SHI Jin; LI Bing-Huan

    2007-01-01

    The conversion between anamorphoses of the dihydrated glycine complex was studied by means of B3LYP/6-31++G**. It was found that proton transfer was accompanied by hydrogen bond transfer in the process of conversion between different kinds of anamorphoses. With proton transfer, the electrostatic action was notably increased and the hydrogen-bonding action was evidently strengthened when the dihydrated neutral glycine complex converts into dihydrated zwitterionic glycine complex. The activation energy required for hydrogen bond transfer between dihydrated neutral glycine complexes is very low (6.32 kJ·mol-1); however, the hydrogen bond transfer between dihydrated zwitterionic glycine complexes is rather difficult with the required activation energy of 13.52 kJ·mol-1 due to the relatively strong electrostatic action. The activation energy required by proton transfer is at least 27.33 kJ·mol-1, higher than that needed for hydrogen bond transfer. The activation energy for either hydrogen bond transfer or proton transfer is in the bond-energy scope of medium-strong hydrogen bond, so the four kinds of anamorphoses of the dihydrated glycine complex could convert mutually.

  8. 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 ℃.

  9. 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...... the complexity of the examined systems....

  10. 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

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

  11. 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.

  12. Study on UV, IR and NMR Spectra of Double Hydrogen-bonded Complexes

    Institute of Scientific and Technical Information of China (English)

    ZHU Liang-Liang; TENG Qi-Wen; WU Shi

    2006-01-01

    AM1, PM3 and DFT methods were used to study on the hydrogen-bonded dimer of melamine and [1,3] dioxane-2,4,6-trione. The electronic spectra, IR and NMR spectra of some complexes were calculated with INDO/SCI, AM1 and B3LYP/6-31G(d) methods, respectively. It is demonstrated that the negative stability energy is responsible for the formation of the complexes. Stabilization energies of these complexes were altered among the variations of electric property and steric effects of the monomers. HOMO-LUMO energy gaps were shrunk and the blue-shift of absorptions in the electronic spectra occurred. The vibrations of N-H bonds and chemical shifts of the protons changed with the formation of hydrogen bonds.

  13. 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.

  14. Density Functional Theory Study of Hydrogen Bonds of Bipyridine with 1,3,5-Benzenetricarboxylic Acid

    Institute of Scientific and Technical Information of China (English)

    LI Quan; ZHAO Keqing

    2009-01-01

    The hydrogen-bonded dimer and trimer formed between 1,3,5-benzenetricarboxylic acid and bipyridine have been investigated using a density functional theory(DFT)method and 6-31++G** basis set.The interaction enerstretching modes in the dimer and trimer red-shifted relative to those of the 1,3,5-benzenetricarhoxylic acid monomer.The natural bond orbit analysis shows that the inter-molecular charge transfers are 0.60475e and 1.20225e for the dimer and trimer,respectively.Thermodynamic analysis indicates that the formation of trimer is an exothermic H-O intermolecular hydrogen bonds between bipyridine and 1,3,5-benzenetricarboxylic acid,which is in good agreement with the experimental results.

  15. A quasi-diamondoid hydrogen-bonded framework in anhydrous sulfanilic acid.

    Science.gov (United States)

    Low, John N; Glidewell, Christopher

    2002-04-01

    The title compound (C(6)H(7)NO(3)S) exists as a zwitterion (4-ammoniobenzenesulfonate), +H(3)NC(6)H(4)SO(3)-, and these units are linked into a three-dimensional framework by two distinct two-centre N-H* * *O hydrogen bonds [H* * *O 1.84 and 1.87 A; N* * *O 2.767 (2) and 2.746 (2) A; N-H* * *O 166 and 172 degrees ] and a planar three-centre N-H* * *(O)(2) hydrogen bond [H* * *O 2.03 and 2.37 A; N* * *O 2.816 (2) and 2.877 (2) A; N-H* * *O 162 and 111 degrees; O* * *H* * *O 86 degrees ].

  16. Solid-phase synthesis of short α-helices stabilized by the hydrogen bond surrogate approach.

    Science.gov (United States)

    Patgiri, Anupam; Menzenski, Monica Z; Mahon, Andrew B; Arora, Paramjit S

    2010-11-01

    Stabilized α-helices and nonpeptidic helix mimetics have emerged as powerful molecular scaffolds for the discovery of protein-protein interaction inhibitors. Protein-protein interactions often involve large contact areas, which are often difficult for small molecules to target with high specificity. The hypothesis behind the design of stabilized helices and helix mimetics is that these medium-sized molecules may pursue their targets with higher specificity because of a larger number of contacts. This protocol describes an optimized synthetic strategy for the preparation of stabilized α-helices that feature a carbon-carbon linkage in place of the characteristic N-terminal main-chain hydrogen bond of canonical helices. Formation of the carbon-carbon bond is enabled by a microwave-assisted ring-closing metathesis reaction between two terminal olefins on the peptide chain. The outlined strategy allows the synthesis and purification of a hydrogen bond surrogate (HBS) α-helix in ∼ 1 week.

  17. IR study on hydrogen bonding in epoxy resin-silica nanocomposites

    Institute of Scientific and Technical Information of China (English)

    Wei Zhang; Abbas A. Dehghani-Sanij; Richard S. Blackburn

    2008-01-01

    The chemical and physical interactions between ingredients in composites play an important role in the improvement of service prop-sity loss of isocyanate absorption band in conjunction with the intensity growth of carboxyl absorption band indicates the progress of reaction. FT-IR spectroscopy was also adopted to examine the intermolecular hydrogen bonding of epoxy resin with silica as well as intramolecular one within polymer matrix. The vibration frequency of carboxyl group (-C=O) and hydroxyl group (-OH) shifts from 1736 to 1728 cm-1and 3420 to 3414 cm-1, respectively, indicating the occurrence of hydrogen bonding between -C=O and -OH. The vibration frequency of Si-OH moves from 3435 to 3414 cm -1, suggesting the involvement of silica. Whereas the vibration frequency of pending -OH in polymer chain moves from 3435 to 3420 cm-1 or 3414 cm-1, proposing that this kind of interaction can also happen within polymer matrix.

  18. A first-principles investigation into the hydrogen bond interaction in β-HMX

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A theoretical study of structural and electronic properties of β-HMX crystal is performed using density-functional theory(DFT). The total density of states(TDOS) is presented. The atomic orbit projected density of state(PDOS) from the p-type orbit of C,N,O and the s-type orbit of H is discussed. The study by analyzing the PDOS shows that the structure of β-HMX crystal possesses C-H···O intra- and inter-molecular hydrogen-bonding. There exists a hydrogen bonding between H5 -1s and O12 -2p orbits,between H19 -1s and O28 -2p orbits of intra molecules,and between H19 -1s and O24 -2p orbits of inter molecules. The Mulliken population analysis is also made.

  19. A study on polymorphism of hydrogen-bonded thermotropic liquid crystals

    Science.gov (United States)

    Rajanandkumar, R.; Pongali Sathya Prabu, N.; Murugadass, K.; Madhu Mohan, M. L. N.

    2016-09-01

    A novel mesogenic homologous series comprising of eight hydrogen-bonded liquid crystalline complexes are isolated and analyzed by forming a hydrogen bond between p-n alkyloxy benzoic acids (where n represent alkyloxy carbon number which varies from 5 to 12) and mesaconic acid, respectively. Eight synthesized complexes are subjected to Fourier transform infra-red spectroscopy, polarizing optical microscopy and differential scanning calorimetry studies to meet the basic characterization. The variation of optical tilt angle with respect to temperature in various conventional and smectic X phases are investigated and analyzed. A phase diagram is constructed to elucidate the mesogenic behavior of novel liquid crystalline series. The Cox ratio that reveals the order of various mesophases and the stability factor, to invoke the thermal stability of mesophases, is studied under the results of DSC thermogram.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction en...... 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...

  1. 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

    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 bondinteraction evidenced by a significantly blue......-shift of the low-frequency in-plane donor OH librational band origin. The strong correlation between the low-frequency in-plane donor OH librational motion and the secondary intermolecular O⋯HC hydrogen bond is demonstrated by electronic structure calculations. The experimental findings are further supported...

  2. Proton tunnelling and deuteration-induced phase transitions in hydrogen-bonded crystals

    Energy Technology Data Exchange (ETDEWEB)

    Matsuo, Takasuke [Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka (Japan). E-mail: matsuo@chem.sci.osaka-u.ac.jp; Inaba, Akira; Yamamuro, Osamu; Onoda-Yamamuro, Noriko [Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka (Japan)

    2000-10-09

    Experimental facts about appearance of new crystalline phases at low temperature related to deuterium substitution are collected and mechanisms of the isotope effect discussed. Compounds considered are (i) tri-alkali hydrogen selenates and sulphates, (ii) ammonium hexachlorometallates, (iii) bromo- and iodo-hydroxyphenalenone and (iv) chromium hydrogen dioxide. In (i), (iii) and (iv), linear O-H-O hydrogen bonds are involved. Proton tunnelling is the likely mechanism of the peculiar phase behaviour of (i). Definitely the tunnelling plays an essential role in (iii) but not in the extreme situation in (iv). In (ii), rotational tunnelling of an ammonium ion is the likely ingredient of the deuteration-induced phase transitions. The term proton cloud is introduced to describe the quantum mechanical distribution of the nucleus in the hydrogen bond and in the multi-valley rotational potential for an ammonium ion. (author)

  3. Influences of Temperature on Proton Conductivity in the Hydrogen-Bond Molecular Systems with Damping

    Institute of Scientific and Technical Information of China (English)

    PANG Xiao-Feng; YU Jia-Feng

    2007-01-01

    Influences of temperature of medium on proton conductivity in hydrogen-bonded systems exposed in an electric-field are numerically studied by the fourth-order Runge-Kutta method with our model. The results obtained show that the proton soliton is very robust against thermal perturbation and damping of medium, and is thermally stable in the temperature range T ≤273 K. From the simulation we find out that the mobility (or velocity) of proton conduction in ice crystal is a nonmonotonic function of temperature in the temperature range 170-273 K: i.e., it increases initially, reaches a maximum at about 191 K, subsequently decreases to a minimum at about 211 K, and then increases again. This changed rule of mobility is qualitatively consistent with its experimental data in ice in the same temperature range. This result provides an evidence for existence of solitons in the hydrogen-bonded systems.

  4. 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.

  5. 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.

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

    Science.gov (United States)

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

    2004-03-01

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

  7. Variation of persistence length with concentration in a hydrogen bonding polymer solution

    Science.gov (United States)

    Sukumaran, S.; Beaucage, G.

    2000-03-01

    Miscibility of some polymers in water is usually attributed to the ability of the polymer to hydrogen bond with water. Hydrogen bonding contributes a strong interaction component to the free energy that enhances mixing between the polymer and water. It is widely known that certain conformations of the polymer have significantly higher dipole moment and consequently higher affinity for water. If the solvent alters the bond rotation energetics of the polymer it is natural to expect the average local structure of the chain to be affected leading to a change in the persistence length. Small angle neutron scattering experiments were performed on aqueous (D2O) solutions of a polymer (PEO or PVME) at different concentrations to investigate the microscopic structure of these solutions. The persistence length was strongly dependent on concentration. A simple physical explanation for this phenomenon will be provided. Possible ramifications of such a phenomenon in understanding phase behavior will be indicated.

  8. Slow dielectric response of Debye-type in water and other hydrogen bonded liquids

    Science.gov (United States)

    Jansson, Helén; Bergman, Rikard; Swenson, Jan

    2010-05-01

    The slow dynamics of some hydrogen bonded glass-forming liquids has been investigated by broadband dielectric spectroscopy. We show that the polyalcohols glycerol, xylitol, and sorbitol, and mixtures of glycerol and water, and in fact, even pure water exhibit a process of Debye character at longer time-scales than the glass transition and viscosity related α-relaxation. Even if it is less pronounced, this process displays many similarities to the well-studied Debye-like process in monoalcohols. It can be observed in both the negative derivative of the real part of the permittivity or in the imaginary part of the permittivity, if the conductivity contribution is reduced. In the present study the conductivity contribution has been suppressed by use of a thin Teflon film placed between the sample and one of the electrodes. The new findings might have important implications for the structure and dynamics of hydrogen bonded liquids in general, and for water in particular.

  9. 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.

  10. Ammonia as a case study for the spontaneous ionization of a simple hydrogen-bonded compound.

    Science.gov (United States)

    Palasyuk, Taras; Troyan, Ivan; Eremets, Mikhail; Drozd, Vadym; Medvedev, Sergey; Zaleski-Ejgierd, Patryk; Magos-Palasyuk, Ewelina; Wang, Hongbo; Bonev, Stanimir A; Dudenko, Dmytro; Naumov, Pavel

    2014-03-24

    Modern ab initio calculations predict ionic and superionic states in highly compressed water and ammonia. The prediction apparently contradicts state-of-the-art experimentally established phase diagrams overwhelmingly dominated by molecular phases. Here we present experimental evidence that the threshold pressure of ~120 GPa induces in molecular ammonia the process of autoionization to yet experimentally unknown ionic compound--ammonium amide. Our supplementary theoretical simulations provide valuable insight into the mechanism of autoionization showing no hydrogen bond symmetrization along the transformation path, a remarkably small energy barrier between competing phases and the impact of structural rearrangement contribution on the overall conversion rate. This discovery is bridging theory and experiment thus opening new possibilities for studying molecular interactions in hydrogen-bonded systems. Experimental knowledge on this novel ionic phase of ammonia also provides strong motivation for reconsideration of the theory of molecular ice layers formation and dynamics in giant gas planets.

  11. Substituent effects in double-helical hydrogen-bonded AAA-DDD complexes.

    Science.gov (United States)

    Wang, Hong-Bo; Mudraboyina, Bhanu P; Wisner, James A

    2012-01-27

    Two series of DDD and AAA hydrogen-bond arrays were synthesized that form triply-hydrogen-bonded double-helical complexes when combined in CDCl(3) solution. Derivatization of the DDD arrays with electron-withdrawing groups increases the complex association constants by up to a factor of 30 in those arrays examined. Derivatization of the AAA arrays with electron donating substituents reveals a similar magnitude effect on the complex stabilities. The effect of substitution on both types of arrays are modeled quite satisfactorily (R(2) > 0.96 in all cases) as free energy relationships with respect to the sums of their Hammett substituent constants. In all, the complex stabilities can be manipulated over more than three orders of magnitude (>20 kJ mol(-1)) using this type of modification.

  12. Aliphatic C-H---Anion Hydrogen Bonds: Weak Contacts or Strong Interactions?

    Energy Technology Data Exchange (ETDEWEB)

    Hay, Benjamin [ORNL; Pedzisa, Lee [ORNL

    2009-01-01

    Electronic structure calculations, MP2/aug-cc-pVDZ, are used to determine C H---Cl hydrogen bond energies for a series of XCH3 donor groups in which the electron-withdrawing ability of X is varied over a wide range of values. When attached to polarizing substituents, aliphatic CH groups are moderate to strong hydrogen bond donors, exhibiting interaction energies comparable to those obtained with O H and N H groups. The results explain why aliphatic C H donors are observed to function as competitive binding sites in solution and suggest that such C H---anion contacts should be considered as possible contributors when evaluating the denticity of an anion receptor.

  13. Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole.

    Directory of Open Access Journals (Sweden)

    Daniel A Kraut

    2006-04-01

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

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

    Science.gov (United States)

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

    2015-10-05

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

  15. A molecular dynamics study of guest-host hydrogen bonding in alcohol clathrate hydrates.

    Science.gov (United States)

    Hiratsuka, Masaki; Ohmura, Ryo; Sum, Amadeu K; Alavi, Saman; Yasuoka, Kenji

    2015-05-21

    Clathrate hydrates are typically stabilized by suitably sized hydrophobic guest molecules. However, it has been experimentally reported that isomers of amyl-alcohol C5H11OH can be enclosed into the 5(12)6(4) cages in structure II (sII) clathrate hydrates, even though the effective radii of the molecules are larger than the van der Waals radii of the cages. To reveal the mechanism of the anomalous enclathration of hydrophilic molecules, we performed ab initio and classical molecular dynamics simulations (MD) and analyzed the structure and dynamics of a guest-host hydrogen bond for sII 3-methyl-1-butanol and structure H (sH) 2-methyl-2-butanol clathrate hydrates. The simulations clearly showed the formation of guest-host hydrogen bonds and the incorporation of the O-H group of 3-methyl-1-butanol guest molecules into the framework of the sII 5(12)6(4) cages, with the remaining hydrophobic part of the amyl-alcohol molecule well accommodated into the cages. The calculated vibrational spectra of alcohol O-H bonds showed large frequency shifts due to the strong guest-host hydrogen bonding. The 2-methyl-2-butanol guests form strong hydrogen bonds with the cage water molecules in the sH clathrate, but are not incorporated into the water framework. By comparing the structures of the alcohols in the hydrate phases, the effect of the location of O-H groups in the butyl chain of the guest molecules on the crystalline structure of the clathrate hydrates is indicated.

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

    Science.gov (United States)

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

    2014-06-01

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

  17. Neutron diffraction study of hydrogen-bond symmetrization in δ-AlOOD

    Science.gov (United States)

    Sano-Furukawa, A.; Hattori, T.; Kuribayashi, T.

    2013-12-01

    δ-AlOOH, a high-pressure polymorph of diaspore, is an important hydrous mineral in the deep earth that has the ability to transport hydrogen into the lower mantle. Theoretical studies have pointed out that hydrogen would locate at the center between two oxygen atoms at high pressure, which is so called hydrogen-bond symmetrization [1]. It was also suggested that the symmetrization would trigger the increase of bulk modulus, which is one of the important parameters of minerals at high pressure. The transition of δ-AlOOH(D) at high pressure has been suggested by X-ray and neutron diffraction [2, 3]. X-ray diffraction study found that the axes a and b where the hydrogen bond is oriented become less compressible above 12 GPa in δ-AlOOD. Neutron diffraction study on δ-AlOOD up to 9.2 GPa showed the increase of O-D bond distance, that is considered as a precousor phenomena of the symmetrization. However, the pressure was insufficient to observe the symmetrization. To investigate the symmetrization of hydrogen bond directly, we conducted neutron diffraction experiments to 16.7 GPa at PLANET, MLF in J-PARC. Powder sample of δ-AlOOD was loaded in Paris-Edinburgh press with double-toroid sintered diamond anvils with methanol-ethanol mixture of pressure medium. In the experiments, the disappearance of 120 refrection was observed at 12.1 GPa, indicating the transition from P21nm to Pnnm, which can be attributed to the disorder of hydrogen bond or the symmtrization. Results of Rietveld refienment will be shown in the presentation. [1] Tsuchiya et al., Geophys. Res. Lett., 29, 1909, 2002. [2] Sano-Furukawa et al., Am. Mineral., 93, 1558-1567, 2008. [3] Sano-Furukawa et al., Am. Mineral., 94, 1255-1261, 2009.

  18. Chiral Hydrogen Bond Environment Providing Unidirectional Rotation in Photoactive Molecular Motors.

    Science.gov (United States)

    García-Iriepa, Cristina; Marazzi, Marco; Zapata, Felipe; Valentini, Alessio; Sampedro, Diego; Frutos, Luis Manuel

    2013-05-02

    Generation of a chiral hydrogen bond environment in efficient molecular photoswitches is proposed as a novel strategy for the design of photoactive molecular motors. Here, the following strategy is used to design a retinal-based motor presenting singular properties: (i) a single excitation wavelength is needed to complete the unidirectional rotation process (360°); (ii) the absence of any thermal step permits the process to take place at low temperatures; and (iii) the ultrafast process permits high rotational frequencies.

  19. Hydrogen-bonded proton transfer in the protonated guanine-cytosine (GC+H)+ base pair.

    Science.gov (United States)

    Lin, Yuexia; Wang, Hongyan; Gao, Simin; Schaefer, Henry F

    2011-10-13

    The single proton transfer at the different sites of the Watson-Crick (WC) guanine-cytosine (GC) DNA base pair are studied here using density functional methods. The conventional protonated structures, transition state (TS) and proton-transferred product (PT) structures of every relevant species are optimized. Each transition state and proton-transferred product structure has been compared with the corresponding conventional protonated structure to demonstrate the process of proton transfer and the change of geometrical structures. The relative energies of the protonated tautomers and the proton-transfer energy profiles in gas and solvent are analyzed. The proton-transferred product structure G(+H(+))-H(+)C(N3)(-H(+))(PT) has the lowest relative energy for which only two hydrogen bonds exist. Almost all 14 isomers of the protonated GC base pair involve hydrogen-bonded proton transfer following the three pathways, with the exception of structure G-H(+)C(O2). When the positive charge is primarily "located" on the guanine moiety (H(+)G-C, G-H(+)C(C4), and G-H(+)C(C6)), the H(1) proton transfers from the N(1) site of guanine to the N(3) site of cytosine. The structures G-H(+)C(C5) and G-H(+)C(C4) involve H(4a) proton transfer from the N(4) of cytosine to the O(6) site of guanine. H(2a) proton transfer from the N(2) site of guanine to the O(2) site of cytosine is found only for the structure G-H(+)C(C4). The structures to which a proton is added on the six-centered sites adjoining the hydrogen bonds are more prone to proton transfer in the gas phase, whereas a proton added on the minor groove and the sites adjoining the hydrogen bonds is favorable to the proton transfer in energy in the aqueous phase.

  20. 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.

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

    Science.gov (United States)

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

    2013-05-18

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

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

    Science.gov (United States)

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

    2013-09-28

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

  3. Molecularly Defined Nanostructures Based on a Novel AAA-DDD Triple Hydrogen-Bonding Motif.

    Science.gov (United States)

    Papmeyer, Marcus; Vuilleumier, Clément A; Pavan, Giovanni M; Zhurov, Konstantin O; Severin, Kay

    2016-01-26

    A facile and flexible method for the synthesis of a new AAA-DDD triple hydrogen-bonding motif is described. Polytopic supramolecular building blocks with precisely oriented AAA and DDD groups are thus accessible in few steps. These building blocks were used for the assembly of large macrocycles featuring four AAA-DDD interactions and a macrobicyclic complex with a total of six AAA-DDD interactions.

  4. 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...

  5. 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.

  6. 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.

  7. Density Functional Theory Study of Red-shifted Hydrogen Bonds of 4-Pyridinemethanol with Water

    Institute of Scientific and Technical Information of China (English)

    LI Quan; CAI Jing; CHEN Jun-Rong; ZHAO Ke-Qing

    2008-01-01

    The hydrogen bonds of 1∶1 and 1∶2 complexes formed between 4-pyridinemethanol and water have been investigated using a density functional theory (DFT) method and 6-311++G** basis set, and three and eight stable geometries have been obtained for 1∶1 and 1∶2 complexes, respectively.The interaction energy is -20.536 and -44.256 kJ/mol for the most stable 1∶1 and 1∶2 complexes, respectively, after the basis set superposition error and zero-point corrections.The formation of O-H…N(O) hydrogen bonds makes O-H symmetric stretching modes in the complexes red-shifted relative to those of the monomer.The natural bond orbit analysis indicates that the intermolecular charge transfer between 4-pyridinemethanol and water is 0.02642 e and 0.03813 e for the most stable 1∶1 and 1∶2 complexes, respectively.In addition, TD-B3LYP/6-311++G** calculations show that formation of water-OH…N and water-OH…OH hydrogen bonds makes maximum absorbance wavelength λmax blue-shifted 8-16 nm and red-shifted 4-11 nm compared to that of 4-pyridinemethanol monomer molecule, respectively.

  8. Hydrogen bonding interactions between ethylene glycol and water: density, excess molar volume, and spectral study

    Institute of Scientific and Technical Information of China (English)

    ZHANG JianBin; ZHANG PengYan; MA Kai; HAN Fang; CHEN GuoHua; WEI XiongHui

    2008-01-01

    Studies of the density and the excess molar volume of ethylene glycol (EG)-water mixtures were carried out to illustrate the hydrogen bonding interactions of EG with water at different temperatures, The re-sults suggest that a likely complex of 3 ethylene glycol molecules bonding with 4 water molecules in an ethylene glycol-water mixture (EGW) is formed at the maximal excess molar volume, which displays stronger absorption capabilities for SO2 when the concentration of SO2 reaches 400×106 (volume ratio) in the gas phase. Meanwhile, FTIR and UV spectra of EGWs were recorded at various EG concentra-tions to display the hydrogen bonding interactions of EG with water. The FTIR spectra show that the stretching vibrational band of hydroxyl in the EGWs shifts to a lower frequency and the bending vibra-tional band of water shifts to a higher frequency with increasing the EG concentration, respectively. Furthermore, the UV spectra show that the electron transferring band of the hydroxyl oxygen in EG shows red shift with increasing the EG concentration. The frequency shifts in FTIR spectra and the shifts of absorption bands in UV absorption spectra of EGWs are interpreted as the strong hydrogen bonding interactions of the hydrogen atoms in water with the hydroxyl oxygen atoms of EG.

  9. Theoretical Studies on the Stabilities and Hydrogen Bond Actions of (H2O)n Clusters

    Institute of Scientific and Technical Information of China (English)

    MENG Xiang-Jun; WANG Ke-Cheng; WU Wen-Sheng; LI Bing-Huan; WANG De-Jin

    2006-01-01

    The stable configurations and hydrogen bond nature of (H2O)n clusters (n = 3~6) have been investigated by the B3LYP method at the 6-31++g** level. Upon calculation, four conclusions have been drawn: (1) In the (H2O)3~5 clusters, cyclic configurations were confirmed to be the most stable. But in the (H2O)3~4 ones, only cyclic configurations could be observed. From n= 5 ((H2O)5 clusters), three-dimensional configuration could be found; (2) In the (H2O)6 clusters, all configurations are inclined to be three-dimensional except the most stable configuration which is cyclic; (3) The stable order of (H2O)6 clusters indicates that it is the arrangement of hydrogen bond that plays a decisive role in the cluster stabilities, the zero-point energy is also important, and cluster stabilities are independent on the number of hydrogen bonds; (4) There exist strong cooperativity and superadditivity in the (H2O)n clusters.

  10. Discrete kink dynamics in hydrogen-bonded chains: the one-component model.

    Science.gov (United States)

    Karpan, V M; Zolotaryuk, Y; Christiansen, P L; Zolotaryuk, A V

    2002-12-01

    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 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 the Morse potential and the cooperativity of the hydrogen bond (the coupling constant of the interaction between nearest-neighbor protons).

  11. Investigation on Thermal and Optical Properties of Hydrogen-Bonded Binary Liquid Crystals

    Science.gov (United States)

    Ranjeeth kumar, T.; Sundaram, S.; Vasanthi, T.; Subhasri, P.; Chitravel, T.; Senthil, T. S.; Jayaprakasam, R.; Vijayakumar, V. N.

    2016-12-01

    A homologous series of hydrogen-bonded liquid crystals (HBLCs) are synthesized and characterized. Intermolecular hydrogen bonding occurs between 4-methoxycinnamic acid (4MCA) and p-n-alkyloxy benzoic acids (nOBA, where n = 3, 7 to 12). These binary complexes have been obtained by following well-designed synthesis route. The subsequent binary complexes have been characterized by polarizing optical thermal microscopy (POM), differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR). The present work explains the details of the association between the mesogenic phase behavior and H-bonding in the homologous series of 4MCA + nOBA. Nematic phase is interrelated with the closed dimers between acid molecules through the formation of strong hydrogen bonds. But, high concentrations are linked to the manifestation of smectic phases that disturb the local order of the nematic phase. As a result, the higher-order mesophases are observed in the present binary complex series. The inclusion of nematic LC (4MCA) in the nOBA alters the melting temperature and the clearing temperature as lower than those of the individual. Also, the wide mesophase regions of the present series are identified compared to those of the constituent mesogens. The optical tilt angle of binary mixtures for smectic C phase and thermal stability factors of the mesogenic phases have been discussed.

  12. 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.

  13. Three closely related dibenzazepine carboxylic acids: hydrogen-bonded aggregation in one, two and three dimensions.

    Science.gov (United States)

    Sanabría, Carlos M; Palma, Alirio; Cobo, Justo; Glidewell, Christopher

    2014-03-01

    In the structure of (6R*,11R*)-5-acetyl-11-ethyl-6,11-dihydro-5H-dibenzo[b,e]azepine-6-carboxylic acid, C19H19NO3, (I), the molecules are linked into sheets by a combination of O-H...O and C-H...O hydrogen bonds; in the structure of the monomethyl analogue (6RS,11SR)-5-acetyl-11-ethyl-2-methyl-6,11-dihydro-5H-dibenzo[b,e]azepine-6-carboxylic acid, C20H21NO3, (II), the molecules are linked into simple C(7) chains by O-H...O hydrogen bonds; and in the structure of the dimethyl analogue (6RS,11SR)-5-acetyl-11-ethyl-1,3-dimethyl-6,11-dihydro-5H-dibenzo[b,e]azepine-6-carboxylic acid, C21H23NO3, (III), a combination of O-H...O, C-H...O and C-H...π(arene) hydrogen bonds links the molecules into a three-dimensional framework structure. None of these structures exhibits the R2(2)(8) dimer motif characteristic of simple carboxylic acids.

  14. Tunneling and delocalization effects in hydrogen bonded systems: a study in position and momentum space.

    Science.gov (United States)

    Morrone, Joseph A; Lin, Lin; Car, Roberto

    2009-05-28

    Novel experimental and computational studies have uncovered the proton momentum distribution in hydrogen bonded systems. In this work, we utilize recently developed open path integral Car-Parrinello molecular dynamics methodology in order to study the momentum distribution in phases of high pressure ice. Some of these phases exhibit symmetric hydrogen bonds and quantum tunneling. We find that the symmetric hydrogen bonded phase possesses a narrowed momentum distribution as compared with a covalently bonded phase, in agreement with recent experimental findings. The signatures of tunneling that we observe are a narrowed distribution in the low-to-intermediate momentum region, with a tail that extends to match the result of the covalently bonded state. The transition to tunneling behavior shows similarity to features observed in recent experiments performed on confined water. We corroborate our ice simulations with a study of a particle in a model one-dimensional double well potential that mimics some of the effects observed in bulk simulations. The temperature dependence of the momentum distribution in the one-dimensional model allows for the differentiation between ground state and mixed state tunneling effects.

  15. Theoretical Study of Intramolecular Interactions in Peri-Substituted Naphthalenes: Chalcogen and Hydrogen Bonds

    Directory of Open Access Journals (Sweden)

    Goar Sánchez–Sanz

    2017-02-01

    Full Text Available A theoretical study of the peri interactions, both intramolecular hydrogen (HB and chalcogen bonds (YB, in 1-hydroxy-8YH-naphthalene, 1,4-dihydroxy-5,8-di-YH-naphthalene, and 1,5-dihydroxy-4,8-di-YH-naphthalene, with Y = O, S, and Se was carried out. The systems with a OH:Y hydrogen bond are the most stable ones followed by those with a chalcogen O:Y interaction, those with a YH:O hydrogen bond (Y = S and Se being the least stable ones. The electron density values at the hydrogen bond critical points indicate that they have partial covalent character. Natural Bond Orbital (NBO analysis shows stabilization due to the charge transfer between lone pair orbitals towards empty Y-H that correlate with the interatomic distances. The electron density shift maps and non-covalent indexes in the different systems are consistent with the relative strength of the interactions. The structures found on the CSD were used to compare the experimental and calculated results.

  16. Hydrogen bond-promoted metallic state in a purely organic single-component conductor under pressure.

    Science.gov (United States)

    Isono, Takayuki; Kamo, Hiromichi; Ueda, Akira; Takahashi, Kazuyuki; Nakao, Akiko; Kumai, Reiji; Nakao, Hironori; Kobayashi, Kensuke; Murakami, Youichi; Mori, Hatsumi

    2013-01-01

    Purely organic materials are generally insulating. Some charge-carrier generation, however, can provide them with electrical conductivity. In multi-component organic systems, carrier generation by intermolecular charge transfer has given many molecular metals. By contrast, in purely organic single-component systems, metallic states have rarely been realized although some neutral-radical semiconductors have been reported. Here we uncover a new type of purely organic single-component molecular conductor by utilizing strong hydrogen-bonding interactions between tetrathiafulvalene-based electron-donor molecules. These conductors are composed of highly symmetric molecular units constructed by the strong intra-unit hydrogen bond. Moreover, we demonstrate that, in this system, charge carriers are produced by the partial oxidation of the donor molecules and delocalized through the formation of the symmetric intra-unit hydrogen bonds. As a result, our conductors show the highest room-temperature electrical conductivity and the metallic state under the lowest physical pressure among the purely organic single-component systems, to our knowledge.

  17. 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.

  18. Molecular structure of hydrazoic acid with hydrogen-bonded tetramers in nearly planar layers.

    Science.gov (United States)

    Evers, Jürgen; Göbel, Michael; Krumm, Burkhard; Martin, Franz; Medvedyev, Sergey; Oehlinger, Gilbert; Steemann, Franz Xaver; Troyan, Ivan; Klapötke, Thomas M; Eremets, Mikhail I

    2011-08-10

    Hydrazoic acid (HN(3))--potentially explosive, highly toxic, and very hygroscopic--is the simplest covalent azide and contains 97.7 wt % nitrogen. Although its molecular structure was established decades ago, its crystal structure has now been solved by X-ray diffraction for the first time. Molecules of HN(3) are connected to each other by hydrogen bonds in nearly planar layers parallel to (001) with stacking sequence A, B, ... The layer distance, at 2.950(1) Å, is shorter than that in 2H-graphite [3.355(2) Å]. The hydrogen bonds N-H···N are of great interest, since the azido group consists of three homonuclear atoms with identical electronegativity, but different formal charges. These hydrogen bonds are bifurcated into moderate ones with ≈2.0 Å and into weak ones with ≈2.6 Å. The moderate ones build up tetramers (HN(3))(4) in a nearly planar net of eight-membered rings. To the best of our knowledge, such a network of tetramers of a simple molecule is unique.

  19. 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.

  20. Desolvation penalty for burying hydrogen-bonded peptide groups in protein folding.

    Science.gov (United States)

    Baldwin, Robert L

    2010-12-16

    A novel analysis of the enthalpy of protein unfolding is proposed and used to test for a desolvation penalty when hydrogen-bonded peptide groups are desolvated via folding. The unfolding enthalpy has three components, (1) the change when peptide hydrogen bonds are broken and the exposed -CO and -NH groups are solvated, (2) the change when protein-protein van der Waals interactions are broken and replaced by protein-water van der Waals interactions, and (3) the change produced by the hydrophobic interaction when nonpolar groups in the protein interior (represented as a liquid hydrocarbon) are transferred to water. A key feature of the analysis is that the enthalpy change from the hydrophobic interaction goes through 0 at 22 °C according to the liquid hydrocarbon model. Protein unfolding enthalpies are smaller at 22 °C than the enthalpy change for unfolding an alanine peptide helix. Data in the literature indicate that the van der Waals contribution to the unfolding enthalpy is considerably larger than the unfolding enthalpy itself at 22 °C, and therefore, a sizable desolvation penalty is predicted. Such a desolvation penalty was predicted earlier from electrostatic calculations of a stabilizing interaction between water and the hydrogen-bonded peptide group.

  1. 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.

  2. O-H···S hydrogen bonds conform to the acid-base formalism.

    Science.gov (United States)

    Bhattacharyya, Surjendu; Bhattacherjee, Aditi; Shirhatti, Pranav R; Wategaonkar, Sanjay

    2013-08-29

    Hydrogen bonding interaction between the ROH hydrogen bond donor and sulfur atom as an acceptor has not been as well characterized as the O-H···O interaction. The strength of O-H···O interactions for a given donor has been well documented to scale linearly with the proton affinity (PA) of the H-bond acceptor. In this regard, O-H···O interactions conform to the acid-base formalism. The importance of such correlation is to be able to estimate molecular property of the complex from the known thermodynamic data of its constituents. In this work, we investigate the properties of O-H···S interaction in the complexes of the H-bond donor and sulfur containing acceptors of varying proton affinity. The hydrogen bonded complexes of p-Fluorophenol (FP) with four different sulfur containing acceptors and their oxygen analogues, namely H2O/H2S, MeOH/MeSH, Me2O/Me2S and tetrahydrofuran (THF)/tetrahydrothiophene (THT) were characterized in regard to its S1-S0 excitation spectra and the IR spectra. Two-color resonantly enhanced multiphoton ionization (2c-R2PI), resonant ion-dip infrared (RIDIR) spectroscopy, and IR-UV hole burning spectroscopic techniques were used to probe the hydrogen bonds in the aforementioned complexes. The spectroscopic data along with the ab initio calculations were used to deduce the strength of the O-H···S hydrogen bonding interactions in these system relative to that in the O-H···O interactions. It was found that, despite being dominated by the dispersion interaction, the O-H···S interactions conform to the acid-base formalism as in the case of more conventional O-H···O interactions. The dissociation energies and the red shifts in the O-H stretching frequencies correlated very well with the proton affinity of the acceptors. However, the O-H···S interaction did not follow the same correlation as that in the O-H···O H-bond. The energy decomposition analysis showed that the dissociation energies and the red shifts in the O

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

    Science.gov (United States)

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

    2013-06-24

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

  4. Structural, intramolecular hydrogen bonding and vibrational studies on 3-amino-4-methoxy benzamide using density functional theory

    Indian Academy of Sciences (India)

    G SUBHAPRIYA; S KALYANARAMAN; S GANDHIMATHI; N SURUMBARKUZHALI; V KRISHNAKUMAR

    2017-02-01

    An extensive theoretical study on the molecular structure and vibrational analysis of 3-amino-4- methoxy benzamide (3A4MBA) was undertaken using density functional theoretical (DFT) method. The possibility of formation of intramolecular hydrogen bonding was identified from structural parameter analysis and confirmed with the natural bond orbital (NBO), molecular electrostatic potential (MEP) and natural charge analysis. The harmonic oscillator model of aromaticity (HOMA) index elucidated the impact of hydrogen bonding in the ring. Intramolecular hydrogen bonding energy has been calculated from topological study. The lowwavenumber vibrational modes obtained from experimental FT-Raman spectrum also supported the presence of hydrogen bonding. Bands are assigned for vibrational frequencies using DFT/B3LYP/6-311++G** level of theory.

  5. Using Raman Spectroscopy and ab initio Calculations to Investigate lntermolecular Hydrogen Bonds in Binary Mixture (Tetrahydrofuran+Water)

    Institute of Scientific and Technical Information of China (English)

    WU Nan-nan; OUYANG Shun-li; LI Zuo-wei; LIU Jing-yao; GAO Shu-qin

    2011-01-01

    We analyzed the properties and structures of the hydrogen-bonded complexes of tetrahydrofuran(THF)and water by means of experimental Raman spectra and ab initio calculations.The optimized geometries and vibrational frequencies of the neat THF molecule and its hydrogen-bonded complexes with water(THF/H2O) were calculated at the MP2/6-31 l+G(d,p) level of theory.We found that the intermolecular hydrogen bonds which are formed from the binary mixtures of the neat THF and water with different molar ratios could explain the changes in wavenumber position and linewidth very well.The combination of ab initio calculations and experimental Raman spectral data provides an insight into the hydrogen bonds leading to the concentration dependent changes in the spectral features.

  6. 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.

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

    Science.gov (United States)

    Mackeprang, Kasper; Kjaergaard, Henrik G.

    2017-04-01

    The local mode perturbation theory (LMPT) model was developed to improve the description of hydrogen bonded XH-stretching transitions, where X is typically O or N. We present a modified version of the LMPT model to extend its application from hydrated bimolecular complexes to hydrogen bonded bimolecular complexes with donors such as alcohols, amines and acids. We have applied the modified model to a series of complexes of different hydrogen bond type and complex energy. We found that the differences between local mode (LM) and LMPT calculated fundamental XH-stretching transition wavenumbers and oscillator strengths were correlated with the strength of the hydrogen bond. Overall, we have found that the LMPT model in most cases predicts transition wavenumbers within 20 cm-1 of the experimental values.

  8. 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.

  9. 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...

  10. Slow magnetic relaxation in a hydrogen-bonded 2D array of mononuclear dysprosium(III) oxamates.

    Science.gov (United States)

    Fortea-Pérez, Francisco R; Vallejo, Julia; Julve, Miguel; Lloret, Francesc; De Munno, Giovanni; Armentano, Donatella; Pardo, Emilio

    2013-05-01

    The reaction of N-(2,6-dimethylphenyl)oxamic acid with dysprosium(III) ions in a controlled basic media afforded the first example of a mononuclear lanthanide oxamate complex exhibiting a field-induced slow magnetic relaxation behavior typical of single-ion magnets (SIMs). The hydrogen-bond-mediated self-assembly of this new bifunctional dysprosium(III) SIM in the solid state provides a unique example of 2D hydrogen-bonded polymer with a herringbone net topology.

  11. 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.

  12. 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.

  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. AIScore chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes.

    Science.gov (United States)

    Raub, Stephan; Steffen, Andreas; Kämper, Andreas; Marian, Christel M

    2008-07-01

    In this work we report on a novel scoring function that is based on the LUDI model and focuses on the prediction of binding affinities. AIScore extends the original FlexX scoring function using a chemically diverse set of hydrogen-bonded interactions derived from extensive quantum chemical ab initio calculations. Furthermore, we introduce an algorithmic extension for the treatment of multifurcated hydrogen bonds (XFurcate). Charged and resonance-assisted hydrogen bond energies and hydrophobic interactions as well as a scaling factor for implicit solvation were fitted to experimental data. To this end, we assembled a set of 101 protein-ligand complexes with known experimental binding affinities. Tightly bound water molecules in the active site were considered to be an integral part of the binding pocket. Compared to the original FlexX scoring function, AIScore significantly improves the prediction of the binding free energies of the complexes in their native crystal structures. In combination with XFurcate, AIScore yields a Pearson correlation coefficient of R P = 0.87 on the training set. In a validation run on the PDBbind test set we achieved an R P value of 0.46 for 799 attractively scored complexes, compared to a value of R P = 0.17 and 739 bound complexes obtained with the FlexX original scoring function. The redocking capability of AIScore, on the other hand, does not fully reach the good performance of the original FlexX scoring function. This finding suggests that AIScore should rather be used for postscoring in combination with the standard FlexX incremental ligand construction scheme.

  15. 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.

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

    Science.gov (United States)

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

    2017-03-01

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

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

    Science.gov (United States)

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

    2010-04-01

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

  18. Probing hydrogen bond interactions in a shear thickening polysaccharide using nonlinear shear and extensional rheology.

    Science.gov (United States)

    Jaishankar, Aditya; Wee, May; Matia-Merino, Lara; Goh, Kelvin K T; McKinley, Gareth H

    2015-06-05

    Mamaku gum is a polysaccharide extracted from the fronds of the black tree fern found in New Zealand. The cooked pith has traditionally been used for various medicinal purposes and as a food source by the Maori people of New Zealand. It has potential applications as a thickener in the food industry and as a palliative for patients with dysphagia. Studies on the shear rheology of Mamaku gum have revealed that the gum exhibits shear thickening at a critical shear rate due to a transition from intra- to inter-molecular chain interactions upon shear-induced chain elongation. In this paper, we demonstrate that these interactions are primarily due to hydrogen bonding. We perform extensional rheology on mixtures of Mamaku gum and urea (a known disruptor of hydrogen bonds) to quantify the nature of these interactions. Capillary Breakup Extensional Rheometry (CaBER) performed on the pure Mamaku gum solutions yield plateau values of the Trouton ratio as high as ∼10(4), showing that the viscoelasticity of the gum in uniaxial elongation is much higher than in shear. For all Mamaku concentrations tested, the extensional viscosity decreases upon increasing urea concentration. Furthermore, the relaxation time decreases exponentially with increasing urea concentration. This exponential relationship is independent of the Mamaku concentration, and is identical to the relationships between urea concentration and characteristic timescales measured in nonlinear shear rheology. We show using the sticky reptation model for polymers with multiple sticker groups along the backbone how such a relationship is consistent with a linear decrease in the free energy for hydrogen bond dissociation. We then demonstrate that a time-concentration superposition principle can be used to collapse the viscoelastic properties of the Mamaku-gum/urea mixtures.

  19. Vibrational dephasing and frequency shifts of hydrogen-bonded pyridine-water complexes.

    Science.gov (United States)

    Kalampounias, A G; Tsilomelekis, G; Boghosian, S

    2015-01-25

    In this paper we present the picosecond vibrational dynamics and Raman shifts of hydrogen-bonded pyridine-water complexes present in aqueous solutions in a wide concentration range from dense to extreme dilute solutions. We studied the vibrational dephasing and vibrational frequency modulation by calculating time correlation functions of vibrational relaxation by fits in the frequency domain. The concentration induced variations in bandwidths, band frequencies and characteristic dephasing times have been estimated and interpreted as effects due to solute-solvent interactions. The time-correlation functions of vibrational dephasing were obtained for the ring breathing mode of both "free" and hydrogen-bonded pyridine molecules and it was found that sufficiently deviate from the Kubo model. There is a general agreement in the whole concentration range with the modeling proposed by the Rothschild approach, which applies to complex liquids. The results have shown that the reorientation of pyridine aqueous solutions is very slow and hence in both scattering geometries only vibrational dephasing is probed. It is proposed that the spectral changes depend on the perturbations induced by the dynamics of the water molecules in the first hydration cell and water in bulk, while at extreme dilution conditions, the number of bulk water molecules increases and the interchange between molecules belonging to the first hydration cell may not be the predominant modulation mechanism. The evolution of several parameters, such as the characteristic times, the percentage of Gaussian character in the peak shape and the a parameter are indicative of drastic variations at extreme dilution revealing changes in the vibrational relaxation of the pyridine complexes in the aqueous environment. The higher dilution is correlated to diffusion of water molecules into the reference pyridine system in agreement with the jump diffusion model, while at extreme dilutions, almost all pyridine molecules are

  20. Two-dimensional gold nanostructures with high activity for selective oxidation of carbon-hydrogen bonds

    Science.gov (United States)

    Wang, Liang; Zhu, Yihan; Wang, Jian-Qiang; Liu, Fudong; Huang, Jianfeng; Meng, Xiangju; Basset, Jean-Marie; Han, Yu; Xiao, Feng-Shou

    2015-04-01

    Efficient synthesis of stable two-dimensional (2D) noble metal catalysts is a challenging topic. Here we report the facile synthesis of 2D gold nanosheets via a wet chemistry method, by using layered double hydroxide as the template. Detailed characterization with electron microscopy and X-ray photoelectron spectroscopy demonstrates that the nanosheets are negatively charged and [001] oriented with thicknesses varying from single to a few atomic layers. X-ray absorption spectroscopy reveals unusually low gold-gold coordination numbers. These gold nanosheets exhibit high catalytic activity and stability in the solvent-free selective oxidation of carbon-hydrogen bonds with molecular oxygen.

  1. Dielectric spectroscopy investigation of ion-containing and intermolecular hydrogen-bonded polymer systems

    Science.gov (United States)

    Atorngitjawat, Pornpen

    Ion-containing and intermolecular hydrogen-bonded polymers are used widely in a variety of industrial and commercial applications, from food packaging to battery electrolytes to pharmaceuticals. Yet the dynamics of these polymers, which are both complex and important to the application, are poorly understood. This thesis provides the first systematic study of the dynamics of several ion-containing and intermolecular hydrogen-bonded polymers by broadband dielectric relaxation spectroscopy. The systems under consideration include sulfonated polystyrene (SPS) in acid (SPS-H) and neutralized forms, and mixtures of poly(2-vinylpyridine) (P2VPy) with lithium perchlorate (LiClO4) and low molecular weight phenolic molecules. Dynamic mechanical analysis, Fourier transform infrared spectroscopy, differential scanning calorimetry, small-angle X-ray scattering and wide-angle X-ray diffraction were employed in a complementary role. Multiple relaxations were generally observed at high temperatures. For SPS ionomers, the segmental process, Maxwell-Wagner-Sillars interfacial polarization, and electrode polarization were detected. Three relaxations were also found in spectra of SPS-H, attributed to the segmental process, hydrogen bond association/dissociation, and electrode polarization. Three dielectric relaxations above the segmental process were observed for P2VPy-LiClO4 mixtures: ion-mode relaxation, slow hindered segmental relaxation and electrode polarization. However, only electrode polarization was observed above the segmental relaxation for all P2VPy--small phenolic molecule mixtures, except P2VPy + 10 mol% 2,3,3,4,4,5-hexahydroxybenzophenone. This mixture exhibited an additional relaxation due to Maxwell-Wagner-Sillars interfacial polarization, arising from the existence of phase-separated complexes within the P2VPy matrix. Sub-Tg local relaxations were suppressed by ionic intermolecular interactions for SPS ionomers and P2VPy-LiClO4 mixtures. Intermolecular hydrogen

  2. Investigation of hydrogen bonded molecular solids by diffraction, spectroscopy, and computational chemistry

    Science.gov (United States)

    Hudson, Matthew R.

    The nature of hydrogen-bonding interactions in the solid state is examined through the investigation of molecular crystals by incoherent inelastic neutron scattering (INS) spectroscopy, Raman spectroscopy, X-ray and neutron diffraction, and computational chemistry. The molecular solids studied range from small organic molecules to larger inorganic acid salts. Hydrogen bonding is the primary mode of interaction in the solid state for each of the systems studied. INS spectra were collected at 25 K for each molecular solid and the motions of the hydrogen atoms assigned. Raman spectra were collected at 78 and 298 K to aid in the molecular mode assignments of the INS spectra and to examine possible phase changes as a function of temperature. Neutron diffraction was employed, when possible, to accurately locate the hydrogen atom positions, and X-ray diffraction was performed to obtain accurate unit cell dimensions and to obtain initial characterizations of the samples. The diffraction structures served as the basis for solid-state density functional theory (DFT) calculations. DFT simulations were used to aid in the vibrational normal mode assignments, to investigate possible solid-phase transitions, and as a test of the limits of basis sets and the available DFT theory. Of the six molecular solids studied, several important observations were made: (1) the determination of a structural phase transition in L-alanine alaninium nitrate by both spectroscopic and theoretical methods, (2) the structure of picolinic acid was elucidated at 25 K and room-temperature by the combination of INS and theory, (3) glycine lithium sulfate was found to be a useful test of DFT to accurately optimize the structure and calculate the normal modes of a complex 3D network of hydrogen-bonding interactions, (4) nicotinic acid was found to be a useful test of one dimensional hydrogen-bonding interactions with pi-stacking interactions dominating the orthogonal directions, and (5) parabanic acid

  3. (±-2-Oxocyclopentaneacetic acid: catemeric hydrogen bonding in a γ-keto acid

    Directory of Open Access Journals (Sweden)

    Georgia Efthimiopoulos

    2009-04-01

    Full Text Available The title racemate, C7H10O3, aggregates in the solid as acid-to-ketone hydrogen-bonding catemers [O...O = 2.7050 (13 Å and O—H...O = 166.1 (17°] having glide-related components. Four such heterochiral chains, paired centrosymmetrically about ({script{1over 2}}, {script{1over 2}}, {script{1over 2}} in the cell, proceed through the cell in the 010 direction, with alignment with respect to the c axis of ++−−.

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

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Spanget-Larsen, Jens

    2012-01-01

    OH stretching frequencies are investigated for a series of non-tautomerizing systems with intramolecular hydrogen bonds. Effective OH stretching wavenumbers are predicted by the application of empirical correlation procedures based on the results of B3LYP/6-31G(d) theoretical calculations......-hydroxyquinoline N-oxide. The spectrum of the former displays a broad, composite band between 3500 and 2500 cm–1 which can be assigned to overlapping monomer and dimer contributions. In the latter case, the results support a reassignment of the OH stretching band of 8-hydroxyquinoline N-oxide; the reassignment...

  5. NMR diffusion spectroscopy for the characterization of multicomponent hydrogen-bonded assemblies in solution

    NARCIS (Netherlands)

    Timmerman, Peter; Weidmann, Jean-Luc; Jolliffe, Katrina A.; Prins, Leonard J.; Reinhoudt, David N.; Shinkai, Seiji; Frish, Limor; Cohen, Yoram

    2000-01-01

    NMR diffusion measurements on 10 different multicomponent hydrogen-bonded assemblies, viz. the three single rosettes SR1–SR3 ( 13· 2a3, 13· 2b3, 13· 2c3) the double rosettes DR1–DR5 ( 3a3· 2a6, 3b3· 2b6, 3c3· 2a6, 3d3· 2a6, 3e3· 2a6), and DR6 ( 4a3· 16), and the tetrarosette TR ( 53· 2a12) are descr

  6. 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.

  7. Properties of Proton Transfer in Hydrogen-Bonded Systems at Finite Temperature

    Institute of Scientific and Technical Information of China (English)

    PANG Xiao-Feng

    2002-01-01

    The properties of proton transfer along hydrogen-bonded molecular systems are studied at finite temperature. The dynamic equations of the proton transport along the systems are obtained by using a completely quantummechanics method. From the dynamic equations and its soliton solutions we find out specific heat arising from the motionof solitons in the systems with finite temperature and the critical temperature of the soliton in the protein molecules,which is about 318 K. This shows that we can continuously study some biological phenomena in the living systems bythis model.

  8. 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.

  9. Small-molecule recognition for controlling molecular motion in hydrogen-bond-assembled rotaxanes.

    Science.gov (United States)

    Martinez-Cuezva, Alberto; Berna, Jose; Orenes, Raul-Angel; Pastor, Aurelia; Alajarin, Mateo

    2014-06-23

    Di(acylamino)pyridines successfully template the formation of hydrogen-bonded rotaxanes through five-component clipping reactions. A solid-state study showed the participation of the pyridine nitrogen atom in the stabilization of the mechanical bond between the thread and the benzylic amide macrocycle. The addition of external complementary binders to a series of interlocked bis(2,6-di(acylamino)pyridines) promoted restraint of the back and forward ring motion. The original translation can be restored through a competitive recognition event by the addition of a preorganized bis(di(acylamino)pyridine) that forms stronger ADA-DAD complexes with the external binders.

  10. 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.

  11. Short, strong hydrogen bond between an aryloxide and phenol in aprotic media

    Science.gov (United States)

    Buzzeo, Marisa C.; Zakharov, Lev N.; Rheingold, Arnold L.; Doerrer, Linda H.

    2003-09-01

    Three examples of unsupported short, strong hydrogen bonds (SSHBs) between phenolic moieties in aprotic media are reported in three salts of the biphenoxide [{3,5-OC 6(CF 3) 2H 3} 2H] - anion, analogous to bifluoride, [FHF] -. The compounds were synthesized with three different cobalticinium cations and characterized via solution NMR and UV-Vis spectroscopies, elemental analyses, and single-crystal X-ray diffraction. These SSHB protons do not exchange with the aprotic solvent in solution or in the solid state and are important contributors to the study of SSHBs in enzyme active sites that often exclude water.

  12. Flat versus twisted rotamers of 2,4-disubstituted thiazoles: the effect of intermolecular hydrogen bonds.

    Science.gov (United States)

    Bernès, Sylvain; Berros, Martha I; Rodríguez de Barbarín, Cecilia; Sánchez-Viesca, Francisco

    2002-03-01

    In the title compounds, 2-amino-4-(2-chloro-4,5-dimethoxyphenyl)-1,3-thiazole, C(11)H(11)ClN(2)O(2)S, (I), and 4-(2-chloro-4,5-dimethoxyphenyl)-2-methyl-1,3-thiazole, C(12)H(12)ClNO(2)S, (II), the dihedral angles between the thiazole moiety and the chloroaryl group are 51.61 (10) and 8.44 (14), respectively. This difference is a consequence of intermolecular hydrogen bonds forcing the stabilization of a twisted rotamer in (I). Substitution of the amino function by a methyl group precludes these contacts, giving a flat rotamer in (II).

  13. A simple and realistic model system for studying hydrogen bonds in beta-sheets

    DEFF Research Database (Denmark)

    Rossmeisl, Jan; Hinnemann, Berit; Jacobsen, Karsten Wedel

    2003-01-01

    We investigate the interaction between peptide chains at the level of state-of-the-art ab initio density functional theory. We propose an interacting periodic polypeptide model for studying the interactions in beta-sheets and apply this to glycine and alanine peptide chains in both parallel...... and antiparallel structures. The calculated structures of alanine are compared to x-ray structures of beta-sheets and the model is found to reproduce the geometry of the hydrogen bonds very well both concerning parallel and antiparallel beta-sheets. We investigate the structures of both the N-H...O=C and the C...

  14. 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.

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

    Science.gov (United States)

    Paarmann, Alexander

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

  16. (14)N NQR, (1)H NMR and DFT/QTAIM study of hydrogen bonding and polymorphism in selected solid 1,3,4-thiadiazole derivatives.

    Science.gov (United States)

    Seliger, Janez; Zagar, Veselko; Latosińska, Jolanta N

    2010-10-28

    The 1,3,4-thiadiazole derivatives (2-amino-1,3,4-thiadiazole, acetazolamide, sulfamethizole) have been studied experimentally in the solid state by (1)H-(14)N NQDR spectroscopy and theoretically by Density Functional Theory (DFT). The specific pattern of the intra and intermolecular interactions in 1,3,4-thiadiazole derivatives is described within the QTAIM (Quantum Theory of Atoms in Molecules)/DFT formalism. The results obtained in this work suggest that considerable differences in the NQR parameters permit differentiation even between specific pure association polymorphic forms and indicate that the stronger hydrogen bonds are accompanied by the larger η and smaller ν(-) and e(2)Qq/h values. The degree of π-electron delocalization within the 1,3,4-thiadiazole ring and hydrogen bonds is a result of the interplay between the substituents and can be easily observed as a change in NQR parameters at N atoms. In the absence of X-ray data NQR parameters can clarify the details of crystallographic structure revealing information on intermolecular interactions.

  17. Intramolecular and intermolecular hydrogen-bonding effects on photophysical properties of 2'-aminoacetophenone and its derivatives in solution.

    Science.gov (United States)

    Shimada, Hirofumi; Nakamura, Akihito; Yoshihara, Toshitada; Tobita, Seiji

    2005-04-01

    Effects of intra- and intermolecular hydrogen-bonds on the photophysical properties of 2'-aminoacetophenone derivatives (X-C6H4-COCH3) having a substituted amino group (X) with different hydrogen-bonding ability to the carbonyl oxygen (X: NH2(AAP), NHCH3(MAAP), N(CH3)2(DMAAP), NHCOCH3(AAAP), NHCOCF3(TFAAP)) are investigated by means of steady-state and time-resolved fluorescence spectroscopy and time-resolved thermal lensing. Based on the photophysical parameters obtained in aprotic solvents with different polarity and protic solvents with different hydrogen-bonding ability, the characteristic photophysical behavior of the 2'-aminoacetophenone derivatives is discussed in terms of hydrogen-bonding and n,pi*-pi,pi* vibronic coupling. The dominant deactivation process of AAP and MAAP in nonpolar aprotic solvents is the extremely fast internal conversion (k(ic)= 1.0 x 10(11) s(-1) for AAP and 3.9 x 10(10) s(-1) for MAAP in n-hexane). The internal conversion rates of both compounds decrease markedly with increasing solvent polarity, suggesting that vibronic interactions between close-lying S1(pi,pi*) and S2(n,pi*) states lead to the large increase in the non-radiative decay rate of the lowest excited singlet state. It is also suggested that for MAAP, which has a stronger hydrogen-bond as compared to AAP, an intramolecular hydrogen-bonding induced deactivation is involved in the dissipation of the S1 state. For DMAAP, which cannot possess an intramolecular hydrogen-bond, the primary relaxation mechanism of the S1 state in nonpolar aprotic solvents is the intersystem crossing to the triplet state, whereas in protic solvents very efficient internal conversion due to intermolecular hydrogen-bonding is induced. In contrast, the fluorescence spectra of AAAP and TFAAP, which have an amino group with a much stronger hydrogen-bonding ability, give strongly Stokes-shifted fluorescence, indicating that these compounds undergo excited-state intramolecular proton transfer reaction

  18. Synthesis and structures of two supramolecular complexes constructed via hydrogen bond linking

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Two supramolecular complexes,[Ni(rac-L)]3[CrO4]2[ClO4]2-4H2O (1) and [meso-H2L]0.5[VO3]-0.16H2O (2) (L= 5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetra-decane),have been prepared in an aqueous solu-tion,and detected by elemental analysis,IR,TG,and single crystal X-ray diffraction analyses. Com-pound 1 shows a one-dimensional hexagonal prism formed by the hydrogen bonding interactions between the secondary amines of rac-L and CrO42-anion/water molecules. Compound 2 displays a three-dimensional structure constructed by the hydrogen bond linking the helical chains of [VO3]nn-to the secondary amines of meso-L to generate 1D hexagon-shaped channels,and the channels are oc-cupied by guest water molecules.

  19. Solvent based hydrogen bonding: impact on poly(3-hexylthiophene) nanoscale morphology and charge transport characteristics.

    Science.gov (United States)

    Chang, Mincheol; Choi, Dalsu; Fu, Boyi; Reichmanis, Elsa

    2013-06-25

    We demonstrate that supramolecular assembly and subsequent enhancement of charge transport characteristics of conjugated polymers can be facilitated simply by adding small amounts of a more volatile poor solvent, which can hydrogen bond with the majority solvent. Addition of up to 2 vol % acetone to a precursor solution of poly(3-hexylthiophene) (P3HT) in chloroform leads to approximately a 4-fold increase in P3HT field-effect mobility. The improvement is associated with hydrogen bonding interactions between acetone and chloroform which decrease the evaporation rate of the mixed solvent. P3HT is less soluble in the binary solvent than in the more readily vaporized chloroform component, and this characteristic enables the supramolecular assembly of P3HT chains at the nanoscale. Two-dimensional molecular ordering of the polymer film was controlled by varying the quantity of poor solvent added to the precursor solution, and the correlation between field-effect mobility and molecular ordering was investigated. Hansen solubility parameters were used to systematically understand how the solvent mixture enhances the alignment and assembly of polymer chains and influences subsequent thin film properties. The value of the relative energy difference (RED) of the solvent with respect to P3HT increased from less than 1 to more than 1 during film formation, which indicates that the solvent characteristics are initially those of a good solvent but transform into those of a poor dissolution medium. A mechanistic illustration of the molecular ordering process during film formation is postulated.

  20. Azobenzene dye-coupled quadruply hydrogen-bonding modules as colorimetric indicators for supramolecular interactions

    Directory of Open Access Journals (Sweden)

    Yagang Zhang

    2012-04-01

    Full Text Available The facile coupling of azobenzene dyes to the quadruply hydrogen-bonding modules 2,7-diamido-1,8-naphthyridine (DAN and 7-deazaguanine urea (DeUG is described. The coupling of azobenzene dye 2 to mono-amido DAN units 4, 7, and 9 was effected by classic 4-(dimethylaminopyridine (DMAP-catalyzed peptide synthesis with N-(3-dimethylaminopropyl-N’-ethyl carbodiimide hydrochloride (EDC as activating agent, affording the respective amide products 5, 8, and 10 in 60–71% yield. The amide linkage was formed through either the aliphatic or aromatic ester group of 2, allowing both the flexibility and absorption maximum to be tuned. Azobenzene dye 1 was coupled to the DeUG unit 11 by Steglich esterification to afford the product amide 12 in 35% yield. Alternatively, azobenzene dye 16 underwent a room-temperature copper-catalyzed azide–alkyne Huisgen cycloaddition with DeUG alkyne 17 to give triazole 18 in 71% yield. Azobenzene coupled DAN modules 5, 8, and 10 are bright orange–red in color, and azobenzene coupled DeUG modules 12 and 18 are orange–yellow in color. Azobenzene coupled DAN and DeUG modules were successfully used as colorimetric indicators for specific DAN–DeUG and DAN–UPy (2-ureido-4(1H-pyrimidone quadruply hydrogen-bonding interactions.

  1. 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.

  2. 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).

  3. Self-assembly of thiophene derivatives on highly oriented pyrolytic graphite: hydrogen bond effect.

    Science.gov (United States)

    Xu, Li-Ping; Liu, Yibiao; Zhao, Jing; Wang, Shuqi; Lin, Chen-Sheng; Zhang, Rui-Qin; Wen, Yongqiang; Du, Hongwu; Zhang, Xueji

    2013-02-01

    In this paper, to elucidate the hydrogen bond effect on the assembly behavior, we studied the assembly structures of two carboxylic substituted thiophene derivatives on highly oriented pyrolytic graphite (HOPG) by scanning tunneling microscopy. Here thiophene-2-carboxylic acid (TCA) and thiophene-2,5-dicarboxylic acid (TDA) were employed. TDA molecules spontaneously adsorb on the HOPG surface and self-organize into a two-dimensional (2D) assembly with well-defined structure. Two types of domain could be observed. Each TDA molecule appears as a round circle with two small faint dots and forms hydrogen bonds with neighbours. Besides monolayer structure, a bilayer structure of TDA adlayer on HOPG was also observed in this research. Remnant TDA molecules adsorb on the monolayer of TDA and bilayer structure is formed. In contrast to TDA, no ordered structure of TCA on HOPG can be observed. TCA molecules have high propensity to form dimers through H-bond between carboxylic groups. But TCA dimer is not stable enough for either adsorption or imaging. Our result provides a new example for understanding hydrogen effect on stabilizing and controlling two-dimensional assembly structure and is helpful for surface nanofabrication and development of electric nanodevices.

  4. Engineered Hydrogen-Bonded Glycopolymer Capsules and Their Interactions with Antigen Presenting Cells.

    Science.gov (United States)

    Kempe, Kristian; Xiang, Sue D; Wilson, Paul; Rahim, Md Arifur; Ju, Yi; Whittaker, Michael R; Haddleton, David M; Plebanski, Magdalena; Caruso, Frank; Davis, Thomas P

    2017-02-22

    Hollow glycopolymer microcapsules were fabricated by hydrogen-bonded layer-by-layer (LbL) assembly, and their interactions with a set of antigen presenting cells (APCs), including dendritic cells (DCs), macrophages (MACs), and myeloid derived suppressor cells (MDSCs), were investigated. The glycopolymers were obtained by cascade postpolymerization modifications of poly(oligo(2-ethyl-2-oxazoline methacrylate)-stat-glycidyl methacrylate) involving the modification of the glycidyl groups with propargylamine and the subsequent attachment of mannose azide by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). Multilayer assembly of the hydrogen-bonding pair (glycopolymer/poly(methacrylic acid) (PMA)) onto planar and particulate supports (SiO2 particles, d = 1.16 μm) yielded stable glycopolymer films upon cross-linking by CuAAC. The silica (SiO2) particle templates were removed yielding hollow monodisperse capsules, as demonstrated by fluorescence and scanning electron microscopy. Cellular uptake studies using flow cytometry revealed the preferential uptake of the capsules by DCs when compared to MACs or MDSCs. Mannosylated capsules showed a cytokine independent cis-upregulation of CD80 specifically on DCs and a trans-downregulation of PDL-1 on MDSCs. Thus, the glycopolymer capsules may have potential as vaccine carriers, as they are able to upregulate costimulatory molecules for immune cell stimulation on DCs and at the same time downregulate immune inhibitory receptors on suppressor APC such as MDSCs.

  5. A TDDFT/EFP1 study on hydrogen bonding dynamics of coumarin 151 in water

    Science.gov (United States)

    Ramegowda, Mariyappa

    2015-02-01

    Change in energy of hydrogen bonds (HBs) upon excitation, plays an important role on the spectra of chemical and biological molecules. Effective fragment potential (EFP) method of explicit water molecules embedded in polarizable continuum medium (PCM) is used for the solvation of 7-Amino-4-(trifluoromethyl)coumarin (C151). Time dependent density functional theory (TDDFT) calculations combined with EFP/PCM had been carried out to study the electronic structure and the exited state properties of C151 with five water molecules (C151-(H2O)5 complex). S0 state and S1 state geometries were optimized using DFT/TDDFT with PBE0 functional combined with cc-pVDZ basis set, the transition energies are computed with same basis set and functional. Change in HB energy is calculated using the procedure proposed by T. Nagata et al. to calculate solute-solvent interaction energy in Nagata et al. (2011). Upon photoexcitation of C151-(H2O)5 complex, A type (N⋯Hsbnd O) HB is weakened with decrease of energy by 4.37 kJ/mol, whereas B and C type (Cdbnd O⋯Hsbnd O and Nsbnd H⋯O) HBs are strengthened with increase of 5.62 and 10.21 kJ/mol energy, respectively. This study again confirmed that the intermolecular hydrogen bonds between C151 chromophore and aqueous solvents are strengthened, not cleaved upon electronic excitation.

  6. 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.

  7. Hydrogen Bonding and Multiphonon Structure in One- and Two-Dimensional Polymeric Magnets

    Science.gov (United States)

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

    2007-03-01

    We report a systematic investigation of the temperature dependent infrared vibrational spectra of a family of chemically related coordination polymeric magnets based upon two different bridging anions, fluoride (F^-) and bifluoride (HF2^-), in copper-pyrazine complexes including Cu(HF2)(pyz)2BF4, Cu(HF2)(pyz)2ClO4, and CuF2(H2O)(pyz)). We compare our results with several one- and two-dimensional prototype materials including Cu(NO3)2(pyz) and Cu(ClO4)(pyz) 2. Unusual low temperature hydrogen bonding, local structural transitions associated with stronger low-temperature hydrogen bonding, and striking multiphonon effects that derive from coupling of an infrared-active fundamental with strong Raman-active modes of the pyrazine building-block molecule are observed. Based on the spectroscopic evidence, these interactions are common to this family of coordination polymers and work to stabilize the low temperature magnetic state. Similar interactions are likely to be present in other molecule-based magnets.

  8. Effects of glycerol on the molecular mobility and hydrogen bond network in starch matrix.

    Science.gov (United States)

    Liang, Jun; Ludescher, Richard D

    2015-01-22

    The effects of glycerol on molecular mobility and hydrogen bonding network in an amorphous glassy starch matrix were studied using phosphorescence and IR spectroscopy. Amorphous potato starch films containing varying amounts of glycerol (0, 5, 10, 20 and 30 wt.%) were formulated by rapidly dehydrating aqueous potato starch gel (5%, w/v) with a corresponding content of glycerol; X-ray diffraction data confirm that the films contained negligible content of crystalline starch. Erythrosin B (Ery B) phosphorescence was used to monitor the molecular mobility of these matrices over the temperature range from 0 to 100°C. Analysis of Ery B emission peak frequency, band width and intensity decay provided information about thermally-activated modes of molecular mobility in the matrix. Dipolar relaxation around the triplet state of Ery B was enhanced by addition of glycerol and the extent of relaxation increased at low and intermediate but decreased at higher temperature. The glycerol content-dependent onset temperature for this transition was 70°C for pure starch and decreased to 40°C for a matrix with 30% glycerol. Measurements of the rate of non-radiative decay from the Ery B triplet state indicated that glycerol plasticized the starch matrix above ∼10 wt.% while acting as an antiplastizer to increase the matrix molecular mobility at lower content. These matrix properties were related to glycerol-dependent increases in hydrogen bond strength as measured by IR.

  9. Hydrogen Bonding and Dielectric Spectra of Ethylene Glycol–Water Mixtures from Molecular Dynamics Simulations

    Science.gov (United States)

    2016-01-01

    Mixtures of ethylene glycol with water are a prominent example of media with variable viscosity. Classical molecular dynamics simulations at room temperature were performed for mixtures of ethylene glycol (EG) and water with EG mole fractions of xE = 0.0, 0.1, 0.2, 0.4, 0.6, 0.9, 1.0. The calculated dielectric loss spectra were in qualitative agreement with experiment. We found a slightly overestimated slowdown of the dynamics with increasing EG concentration compared to experimental data. Statistics of the hydrogen bond network and hydrogen bond lifetimes were derived from suitable time correlation functions and also show a slowdown in the dynamics with increasing xE. A similar picture is predicted for the time scales of EG conformer changes and for molecular reorientation. A slight blue shift was obtained for the power spectra of the molecular center of mass motion. The results were used to give a qualitative interpretation of the origin of three different relaxation times that appear in experimental complex dielectric spectra and of their change with xE. PMID:27649083

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

    Science.gov (United States)

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

    2013-12-01

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

  11. 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...

  12. 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.

  13. 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.

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

    Science.gov (United States)

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

    2009-12-21

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

  15. Cα-H···O=C hydrogen bonds contribute to the specificity of RGD cell-adhesion interactions

    Directory of Open Access Journals (Sweden)

    Humphries Martin J

    2005-02-01

    Full Text Available Abstract Background The Arg-Gly-Asp (RGD cell adhesion sequence occurs in several extracellular matrix molecules known to interact with integrin cell-surface receptors. Recently published crystal structures of the extracellular regions of two integrins in complex with peptides containing or mimicking the RGD sequence have identified the Arg and Asp residues as key specificity determinants for integrin recognition, through hydrogen bonding and metal coordination interactions. The central Gly residue also appears to be in close contact with the integrin surface in these structures. Results When hydrogen atoms are modelled on the central Gly residue with standard stereochemistry, the interaction between this residue and a carbonyl group in the integrin surface shows all the hallmarks of Cα-H···O=C hydrogen bonding, as seen in the collagen triple helix and in many crystal structures of small organic molecules. Moreover, molecular dynamic simulations of the docking of RGD-containing fragments on integrin surfaces support the occurrence of these interactions. There appears to be an array of four weak and conventional hydrogen bonds lining up the RGD residues with main chain carbonyl groups in the integrin surface. Conclusions The occurrence of weak Cα-H···O=C hydrogen bonds in the RGD-integrin interaction highlights the importance of the conserved Gly residue in the RGD motif and its contribution to integrin-ligand binding specificity. Our analysis shows how weak hydrogen bonds may also play important biological roles by contributing to the specificity of macromolecular recognition.

  16. 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.

  17. An insight into the photophysical properties of amide hydrogen bonded N-(benzo[d]thiazol-2-yl) acetamide crystals

    Science.gov (United States)

    Balijapalli, Umamahesh; Udayadasan, Sathiskumar; Panyam Muralidharan, Vivek; Sukumarapillai, Dileep Kumar; Shanmugam, Easwaramoorthi; Paduthapillai Gopal, Aravindan; S. Rathore, Ravindranath; Kulathu Iyer, Sathiyanarayanan

    2017-02-01

    Three distinct, hydrogen bond associated N-(benzo[d]thiazol-2-yl) acetamides were synthesized by refluxing benzothiazoles with acetic acid. The nature of the assemblies was characteristic to the substituent in the benzothiazole moiety. In N-(benzo[d]thiazol-2-yl)acetamide, water acts as a bridge for forming three hydrogen bonds, as an acceptor to amide Nsbnd H, and donors to carbonyl of amide and thiazole nitrogen assembles of three different N-(benzo[d]thiazol-2-yl)acetamide molecules. The N-(6-methylbenzo[d]thiazol-2-yl)acetamide formed a (amide) N-H…N (thiazole) bonded R22(8) molecular dimers by two homo-intermolecular hydrogen bonding interactions. N-(6-methoxybenzo[d]thiazol-2-yl)acetamide formed (amide)N-H…O (acid) & (acid)O-H…N (thiazole) interactions with the acetic acid, forming a R22(8) hydrogen-bonded ring by two hetero-intermolecular hydrogen bonding interactions.

  18. 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.

  19. Thermodynamic consequences of disrupting a water-mediated hydrogen bond network in a protein:pheromone complex.

    Science.gov (United States)

    Sharrow, Scott D; Edmonds, Katherine A; Goodman, Michael A; Novotny, Milos V; Stone, Martin J

    2005-01-01

    The mouse pheromones (+/-)-2-sec-butyl-4,5-dihydrothiazole (SBT) and 6-hydroxy-6-methyl-3-heptanone (HMH) bind into an occluded hydrophobic cavity in the mouse major urinary protein (MUP-1). Although the ligands are structurally unrelated, in both cases binding is accompanied by formation of a similar buried, water-mediated hydrogen bond network between the ligand and several backbone and side chain groups on the protein. To investigate the energetic contribution of this hydrogen bond network to ligand binding, we have applied isothermal titration calorimetry to measure the binding thermodynamics using several MUP mutants and ligand analogs. Mutation of Tyr-120 to Phe, which disrupts a hydrogen bond from the phenolic hydroxyl group of Tyr-120 to one of the bound water molecules, results in a substantial loss of favorable binding enthalpy, which is partially compensated by a favorable change in binding entropy. A similar thermodynamic effect was observed when the hydrogen bonded nitrogen atom of the heterocyclic ligand was replaced by a methyne group. Several other modifications of the protein or ligand had smaller effects on the binding thermodynamics. The data provide supporting evidence for the role of the hydrogen bond network in stabilizing the complex.

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

    Science.gov (United States)

    Dalvit, Claudio; Vulpetti, Anna

    2016-05-23

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

  1. 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.

  2. 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.

  3. Cooperative intramolecularly hydrogen-bonded motif in the structure of 2:2 complex of TBD with 4-nitrocatechol

    Science.gov (United States)

    Ng, S. W.; Naumov, P.; Chantrapromma, S.; Raj, S. S. S.; Fun, H.-K.; Ibrahim, A. R.; Wojciechowski, G.; Brzezinski, B.

    2001-07-01

    In the crystal of the 2:2 complex of 1,5,7-triazabicyclo[4.4.0]dec-5-ene with 4-nitrocatechol the proton from 1-hydroxyl group of 4-nitrocatechol moiety is transferred to TBD to form ion-pair; two adjacent ion-pairs are linked across a center of inversion. The structure exhibits a cooperative, intramolecularly hydrogen-bonded motif. The hydrogen bonds are relatively long and, and they display only minor proton polarizability. The structure of the complex is retained in chloroform solution, as shown by FT-IR and 1H NMR measurement; in acetonitrile, the compound partially dissociates. The partial dissociation is implied by the presence of free cations, and also by that of the (O⋯H⋯O) - hydrogen bonds formed between two mono-deprotonated 4-nitrocatechol molecules.

  4. C-H(ax)...Y(ax) contacts in cyclohexane derivatives revisited-identification of improper hydrogen-bonded contacts.

    Science.gov (United States)

    Kolocouris, Antonios

    2009-03-06

    The structure of 111 cyclohexane derivatives bearing the axial substitution Y(ax)-C was optimized at the B3LYP/6-31+G(d,p) level. The natural bond orbital analysis revealed the presence of overlap interactions between the axial substituent and the antibonding sigma*(C-Hax) orbitals; these calculated hyperconjugative interactions suggest the presence of improper H-bonded contacts. The addition of an appropriate bridging fragment between the axial substituent and cyclohexane carbon strengthens significantly the hydrogen-bonding component of the contact and several structures of axially substituted cyclohexane derivatives including such hydrogen-bonded C-H(ax)...Y(ax)-C contacts were retrieved from the Cambridge Crystallographic Database. Overall, the calculations predicted that the C-H(ax)...Y(ax)-C contacts in common cyclohexane derivatives that are generally thought to be steric in nature (Pauli repulsive forces) include an improper hydrogen-bonding component.

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  6. The dispersion correction and weak-hydrogen-bond network in low-frequency vibration of solid-state salicylic acid

    Science.gov (United States)

    Takahashi, Masae; Ishikawa, Yoichi; Ito, Hiromasa

    2012-04-01

    We perform the dispersion-corrected first-principles calculations of vibrational absorption and the far-infrared (terahertz) spectroscopic experiments at different temperature to examine the effect of weak-hydrogen-bond network on the low-frequency vibrations of solid-state salicylic acid. By dispersion correction, calculated frequencies improve especially in the intermonomer torsion and interdimer translational modes which are closely related to the weak hydrogen bonds. The calculated frequencies and their relative intensities reproduce the observed spectrum in the accuracy of 10 cm-1 or less. Weak-hydrogen-bond network causes a large frequency shift of out-of-plane intermonomer modes and enhances interdimer translational modes accompanied by the O⋯H stretching vibrations.

  7. Investigations into the nature of halogen- and hydrogen-bonding interactions of some heteroaromatic rings with dichlorine monoxide.

    Science.gov (United States)

    Wu, Junyong

    2014-09-01

    We have studied the structures, properties, and nature of halogen- and hydrogen-bonding interactions between some heteroaromatic rings (C(5)H(5)N, C(4)H(4)O, and C(4)H(4)S) with Cl(2)O at the MP2/aug-cc-pVTZ level. We also considered the solvent effect on the halogen bonds and hydrogen bonds in the C(5)H(5)N-Cl(2)O complexes and found that the solvent has a weakening effect on the π-type halogen bond and hydrogen bond but a prominent enhancing effect on σ-type halogen bond. The complexes have also been analyzed with symmetry adapted perturbation theory method (SAPT).

  8. 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.

  9. Orientation hydrogen-bonding effect on vibronic spectra of isoquinoline in water solvent: Franck-Condon simulation and interpretation

    Science.gov (United States)

    Liu, Yu-Hui; Wang, Shi-Ming; Wang, Chen-Wen; Zhu, Chaoyuan; Han, Ke-Li; Lin, Sheng-Hsien

    2016-10-01

    The excited-state orientation hydrogen-bonding dynamics, and vibronic spectra of isoquinoline (IQ) and its cationic form IQc in water have been investigated at the time-dependent density functional theory quantum chemistry level plus Franck-Condon simulation and interpretation. The excited-state orientation hydrogen bond strengthening has been found in IQ:H2O complex due to the charge redistribution upon excitation; this is interpreted by simulated 1:1 mixed absorption spectra of free IQ and IQ:H2O complex having best agreement with experimental results. Conversely, the orientation hydrogen bond in IQc:H2O complex would be strongly weakening in the S1 state and this is interpreted by simulated absorption spectra of free IQc having best agreement with experimental results. By performing Franck-Condon simulation, it reveals that several important vibrational normal modes with frequencies about 1250 cm-1 involving the wagging motion of the hydrogen atoms are very sensitive to the formation of the orientation hydrogen bond for the IQ/IQc:H2O complex and this is confirmed by damped Franck-Condon simulation with free IQ/IQc in water. However, the emission spectra of the IQ and IQc in water have been found differently. Upon the excitation, the simulated fluorescence of IQ in water is dominated by the IQ:H2O complex; thus hydrogen bond between IQ and H2O is much easier to form in the S1 state. While the weakened hydrogen bond in IQc:H2O complex is probably cleaved upon the laser pulse because the simulated emission spectrum of the free IQc is in better agreement with the experimental results.

  10. Hydrogen bond switching among flavin and amino acid side chains in the BLUF photoreceptor observed by ultrafast infrared spectroscopy.

    Science.gov (United States)

    Bonetti, Cosimo; Mathes, Tilo; van Stokkum, Ivo H M; Mullen, Katharine M; Groot, Marie-Louise; van Grondelle, Rienk; Hegemann, Peter; Kennis, John T M

    2008-11-15

    BLUF domains constitute a recently discovered class of photoreceptor proteins found in bacteria and eukaryotic algae. BLUF domains are blue-light sensitive through a FAD cofactor that is involved in an extensive hydrogen-bond network with nearby amino acid side chains, including a highly conserved tyrosine and glutamine. The participation of particular amino acid side chains in the ultrafast hydrogen-bond switching reaction with FAD that underlies photoactivation of BLUF domains is assessed by means of ultrafast infrared spectroscopy. Blue-light absorption by FAD results in formation of FAD(*-) and a bleach of the tyrosine ring vibrational mode on a picosecond timescale, showing that electron transfer from tyrosine to FAD constitutes the primary photochemistry. This interpretation is supported by the absence of a kinetic isotope effect on the fluorescence decay on H/D exchange. Subsequent protonation of FAD(*-) to result in FADH(*) on a picosecond timescale is evidenced by the appearance of a N-H bending mode at the FAD N5 protonation site and of a FADH(*) C=N stretch marker mode, with tyrosine as the likely proton donor. FADH(*) is reoxidized in 67 ps (180 ps in D(2)O) to result in a long-lived hydrogen-bond switched network around FAD. This hydrogen-bond switch shows infrared signatures from the C-OH stretch of tyrosine and the FAD C4=O and C=N stretches, which indicate increased hydrogen-bond strength at all these sites. The results support a previously hypothesized rotation of glutamine by approximately 180 degrees through a light-driven radical-pair mechanism as the determinant of the hydrogen-bond switch.

  11. Measurement and theory of hydrogen bonding contribution to isosteric DNA base pairs.

    Science.gov (United States)

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

    2012-02-15

    We address the recent debate surrounding the ability of 2,4-difluorotoluene (F), a low-polarity mimic of thymine (T), to form a hydrogen-bonded complex with adenine in DNA. The hydrogen bonding ability of F has been characterized as small to zero in various experimental studies, and moderate to small in computational studies. However, recent X-ray crystallographic studies of difluorotoluene in DNA/RNA have indicated, based on interatomic distances, possible hydrogen bonding interactions between F and natural bases in nucleic acid duplexes and in a DNA polymerase active site. Since F is widely used to measure electrostatic contributions to pairing and replication, it is important to quantify the impact of this isostere on DNA stability. Here, we studied the pairing stability and selectivity of this compound and a closely related variant, dichlorotoluene deoxyriboside (L), in DNA, using both experimental and computational approaches. We measured the thermodynamics of duplex formation in three sequence contexts and with all possible pairing partners by thermal melting studies using the van't Hoff approach, and for selected cases by isothermal titration calorimetry (ITC). Experimental results showed that internal F-A pairing in DNA is destabilizing by 3.8 kcal/mol (van't Hoff, 37 °C) as compared with T-A pairing. At the end of a duplex, base-base interactions are considerably smaller; however, the net F-A interaction remains repulsive while T-A pairing is attractive. As for selectivity, F is found to be slightly selective for adenine over C, G, T by 0.5 kcal mol, as compared with thymine's selectivity of 2.4 kcal/mol. Interestingly, dichlorotoluene in DNA is slightly less destabilizing and slightly more selective than F, despite the lack of strongly electronegative fluorine atoms. Experimental data were complemented by computational results, evaluated at the M06-2X/6-31+G(d) and MP2/cc-pVTZ levels of theory. These computations suggest that the pairing energy of F to A

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

    Science.gov (United States)

    Kawashima, Yukio; Tachikawa, Masanori

    2013-05-01

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

  13. 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.

  14. Emergence of hydrogen bonds from molecular dynamics simulation of substituted N-phenylthiourea-catechol oxidase complex.

    Science.gov (United States)

    Park, Kyung-Lae

    2017-01-01

    A series of N-phenylthiourea derivatives was built starting from the X-ray structure in the molecular mechanics framework and the interaction profile in the complex with the catechol oxidase was traced using molecular dynamics simulation. The results showed that the geometry and interactions between ligand and receptor were highly related to the position of the substituted side chains of phenyl moiety. At the end of molecular dynamics run, a concentrated multicenter hydrogen bond was created between the substituted ligand and receptor. The conformation of the ligand itself were also restricted in the receptor pocket. Furthermore, the simulation time of 50 ns were found to be long enough to explore the relevant conformational space and the stationary behavior of the molecular dynamic could be observed.

  15. Stability of Complex Biomolecular Structures: Vander Waals, Hydrogen Bond Cooperativity, and Nuclear Quantum Effects

    CERN Document Server

    Rossi, Mariana; Michaelides, Angelos

    2016-01-01

    Biomolecules are complex systems stabilized by a delicate balance of weak interactions, making it important to assess all energetic contributions in an accurate manner. However, it is a priori unclear which contributions make more of an impact. Here, we examine stacked polyglutamine (polyQ) strands, a peptide repeat often found in amyloid aggregates. We investigate the role of hydrogen bond (HB) cooperativity, van der Waals (vdW) dispersion interactions, and quantum contributions to free energies, including anharmonicities through density functional theory and ab initio path integral simulations. Of these various factors, we find that the largest impact on structural stabilization comes from vdW interactions. HB cooperativity is the second largest contribution as the size of the stacked chain grows. Competing nuclear quantum effects make the net quantum contribution small but very sensitive to anharmonicities, vdW, and the number of HBs. Our results suggest that a reliable treatment of these systems can only ...

  16. Seawater-Assisted Self-Healing of Catechol Polymers via Hydrogen Bonding and Coordination Interactions.

    Science.gov (United States)

    Li, Jincai; Ejima, Hirotaka; Yoshie, Naoko

    2016-07-27

    It is highly desirable to prevent crack formation in polymeric materials at an early stage and to extend their lifespan, particularly when repairs to these materials would be difficult for humans. Here, we designed and synthesized catechol-functionalized polymers that can self-heal in seawater through hydrogen bonding and coordination. These bioinspired acrylate polymers are originally viscous materials, but after coordination with environmentally safe, common metal cations in seawater, namely, Ca(2+) and Mg(2+), the mechanical properties of the polymers were greatly enhanced from viscous to tough, hard materials. Reduced swelling in seawater compared with deionized water owing to the higher osmotic pressure resulted in greater toughness (∼5 MPa) and self-healing efficiencies (∼80%).

  17. Subsurface hydrogen bonds at the polar Zn-terminated ZnO(0001) surface

    DEFF Research Database (Denmark)

    Hellström, Matti; Beinik, Igor; Broqvist, Peter;

    2016-01-01

    The role of hydrogen and other defects in the stabilization of polar oxide interfaces is a matter of significant fundamental and practical interest. Using experimental (scanning tunneling microscopy, x-ray photoelectron spectroscopy) and theoretical (density functional theory) surface science...... (hcp) and zinc-blende (fcc) lattice positions, giving a characteristic “striped” c(√12×√12)R30° surface morphology with three types of rows: wurtzite Zn, zinc-blende Zn, and Zn vacancies. Interstitial H plays a central role in such a reconstruction, as it helps to compensate the excessive Zn deficiency....... We propose a model in which hydrogen occupies positions in half of the vacancy rows to form hydroxide ions that can participate in hydrogen bonds in the O subsurface layer as a result of the mixed wurtzite/zinc-blende stacking....

  18. Ion channel stability and hydrogen bonding. Molecular modelling of channels formed by synthetic alamethicin analogues.

    Science.gov (United States)

    Breed, J; Kerr, I D; Molle, G; Duclohier, H; Sansom, M S

    1997-12-04

    Several analogues of the channel-forming peptaibol alamethicin have been demonstrated to exhibit faster switching between channel substates than does unmodified alamethicin. Molecular modelling studies are used to explore the possible molecular basis of these differences. Models of channels formed by alamethicin analogues were generated by restrained molecular dynamics in vacuo and refined by short molecular dynamics simulations with water molecules within and at either mouth of the channel. A decrease in backbone solvation was found to correlate with a decrease in open channel stability between alamethicin and an analogue in which all alpha-amino-isobutyric acid residues of alamethicin were replaced by leucine. A decrease in the extent of hydrogen-bonding at residue 7 correlates with lower open channel stabilities of analogues in which the glutamine at position 7 was replaced by smaller polar sidechains. These two observations indicate the importance of alamethicin/water H-bonds in stabilizing the open channel.

  19. Thermoresponsive synergistic hydrogen bonding switched by several guest units in a water-soluble polymer.

    Science.gov (United States)

    Hao, Zhenhua; Li, Guangxiang; Yang, Ke; Cai, Yuanli

    2013-03-12

    Thermoresponsive synergistic hydrogen bonding (H-bonding) switched by several guest units in a water-soluble polymer is reported. Adjusting the distribution of guest units can effectively change the synergistic H-bonding inside polymer chains, thus widely switch the preorganization and thermoresponsive behavior of a water-soluble polymer. The synergistic H-bonding is also evidenced by converting less polar aldehyde groups into water-soluble oxime groups, which bring about the lowering-down of cloud point and an amplified hysteresis effect. This is a general approach toward the wide tunability of thermosensitivity of a water-soluble polymer simply by adjusting the distribution of several guest H-bonding units.

  20. 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.

  1. Intramolecular hydrogen bonding in myricetin and myricitrin. Quantum chemical calculations and vibrational spectroscopy

    Science.gov (United States)

    Vojta, Danijela; Dominković, Katarina; Miljanić, Snežana; Spanget-Larsen, Jens

    2017-03-01

    The molecular structures of myricetin (3,3‧,4‧,5,5‧,7-hexahydroxyflavone; MCE) and myricitrin (myricetin 3-O-rhamnoside; MCI) are investigated by quantum chemical calculations (B3LYP/6-311G**). Two preferred molecular rotamers of MCI are predicted, corresponding to different conformations of the O-rhamnoside subunit. The rotamers are characterized by different hydrogen bonded cross-links between the hydroxy groups of the rhamnoside substituent and the parent MCE moiety. The predicted OH stretching frequencies are compared with vibrational spectra of MCE and MCI recorded for the sake of this investigation (IR and Raman). In addition, a reassignment of the Cdbnd O stretching bands is suggested.

  2. Olefin metathesis and quadruple hydrogen bonding: A powerful combination in multistep supramolecular synthesis

    Science.gov (United States)

    Scherman, Oren A.; Ligthart, G. B. W. L.; Ohkawa, Haruki; Sijbesma, Rint P.; Meijer, E. W.

    2006-08-01

    We show that combining concepts generally used in covalent organic synthesis such as retrosynthetic analysis and the use of protecting groups, and applying them to the self-assembly of polymeric building blocks in multiple steps, results in a powerful strategy for the self-assembly of dynamic materials with a high level of architectural control. We present a highly efficient synthesis of bifunctional telechelic polymers by ring-opening metathesis polymerization (ROMP) with complementary quadruple hydrogen-bonding motifs. Because the degree of functionality for the polymers is 2.0, the formation of alternating, blocky copolymers was demonstrated in both solution and the bulk leading to stable, microphase-separated copolymer morphologies. ring-opening metathesis polymerization | self-assembly | block copolymer | retrosynthesis

  3. Olefin metathesis and quadruple hydrogen bonding: A powerful combination in multistep supramolecular synthesis

    Science.gov (United States)

    Scherman, Oren A.; Ligthart, G. B. W. L.; Ohkawa, Haruki; Sijbesma, Rint P.; Meijer, E. W.

    2006-01-01

    We show that combining concepts generally used in covalent organic synthesis such as retrosynthetic analysis and the use of protecting groups, and applying them to the self-assembly of polymeric building blocks in multiple steps, results in a powerful strategy for the self-assembly of dynamic materials with a high level of architectural control. We present a highly efficient synthesis of bifunctional telechelic polymers by ring-opening metathesis polymerization (ROMP) with complementary quadruple hydrogen-bonding motifs. Because the degree of functionality for the polymers is 2.0, the formation of alternating, blocky copolymers was demonstrated in both solution and the bulk leading to stable, microphase-separated copolymer morphologies. PMID:16877543

  4. 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.

  5. Dimeric Self-assembling via Hydrogen Bonding and Emissive Behavior of a New Copper (I Complex

    Directory of Open Access Journals (Sweden)

    Juciely M. dos Reis

    2017-04-01

    Full Text Available This work describes the synthesis, structural characterization and emissive behavior of a new copper (I complex based on 1-thiocarbamoyl-5-(4-methoxiphenyl-3-phenyl-4,5-dihydro-1H-pyrazole ligand. A dimeric self-assembling via hydrogen bonding was determined by analyzing the short contacts present in the solid-state structure by means of X-ray crystallography. The spectroscopic properties were determined using UV-Vis and fluorescence experiments and an interesting behavior as bluish luminescence was assigned mainly to the mixed (MLCT + IL electronic transitions of the Cu(Id10 ® (S=C–Nligand type. The complete characterization of the new copper (I complex also included elemental analyses and IR spectroscopy. DOI: http://dx.doi.org/10.17807/orbital.v9i1.952

  6. A Novel Hydrogen-bonded Three-dimensional Network Complex Containing Nickel

    Institute of Scientific and Technical Information of China (English)

    WANG Li; LI Juan; WANG En-bo

    2004-01-01

    A novel complex, (H3O)2[Ni(2,6-pydc)2] · 2H2O was synthesized in an aqueous solution and characterized by means of single-crystal X-ray diffraction, elemental analyses and IR spectra. The X-ray structural analysis revealed that the novel compound forms three-dimensional(3D) networks by both π-π stacking and hydrogen-bonding interactions. The crystal data for the complex are a = 13. 853 (3) nm, b= 9. 6892 (19) nm,c=13.732(3) nm, α=90. 00°, β=115.52(3)°, γ=90.00°, Z=3, R1=0. 0786, wR2=0.1522.

  7. Existence of aromatic sp~2 C-H…O = C intramolecular interaction similar to hydrogen bond

    Institute of Scientific and Technical Information of China (English)

    Zeper Abliz; Hiroshi Moriyama; Junji Aoki; Toyotoshi Ueda

    1996-01-01

    A ’H NMR signal shifted drastically to down field (δ - 10.0) at the bay area and in dose proximity to C = O group for H-1 was observed through complete assignments of 1H NMR spectra for pyridino- and benzobenzanthrones. It is concluded that this phenomenon is due not only to the anisotropy effect of C=O plus aromatic ring current effect, but also to the electrostatic attraction of C-H (δ+)…O(δ-)=C interaction. The evidence for the sp2C-H…O = C intramolecular interaction similar to hydrogen bond has also been given by EI-MS and MS/MS (CID) spectroscopy and IR spectroscopy, as well as MNDO-PM3 calculations. This new kind of interaction might be called ’quasi-hydrogen bond’.

  8. Hydrogen bonding: a channel for protons to transfer through acid-base pairs.

    Science.gov (United States)

    Wu, Liang; Huang, Chuanhui; Woo, Jung-Je; Wu, Dan; Yun, Sung-Hyun; Seo, Seok-Jun; Xu, Tongwen; Moon, Seung-Hyeon

    2009-09-10

    Different from H(3)O(+) transport as in the vehicle mechanism, protons find another channel to transfer through the poorly hydrophilic interlayers in a hydrated multiphase membrane. This membrane was prepared from poly(phthalazinone ether sulfone kentone) (SPPESK) and H(+)-form perfluorosulfonic resin (FSP), and poorly hydrophilic electrostatically interacted acid-base pairs constitute the interlayer between two hydrophilic phases (FSP and SPPESK). By hydrogen bonds forming and breaking between acid-base pairs and water molecules, protons transport directly through these poorly hydrophilic zones. The multiphase membrane, due to this unique transfer mechanism, exhibits better electrochemical performances during fuel cell tests than those of pure FSP and Nafion-112 membranes: 0.09-0.12 S cm(-1) of proton conductivity at 25 degrees C and 990 mW cm(-2) of the maximum power density at a current density of 2600 mA cm(-2) and a cell voltage of 0.38 V.

  9. Theoretical study of bifurcated bent blue-shifted hydrogen bonds CH2…Y

    Institute of Scientific and Technical Information of China (English)

    LI AnYong

    2008-01-01

    Ab initio quantum chemistry methods were applied to study the bifurcated bent hydrogen bonds Y… MP2/6-311++G(2df,2p) levels. The results show that in each complex there are two equivalent natural bond orbital analysis shows that these blue-shifted H-bonds are caused by three factors: large rehybridization; small direct intermolecular hyperconjugation and larger indirect intermolecular hy-perconjugation; large decrease of intramolecular hyperconjugation. The topological analysis of elec-tron density shows that in each complex there are three intermolecular critical points: there is one bond critical point between the acceptor atom Y and each hydrogen, and there is a ring critical point inside the tetragon YHCH, so these interactions are exactly H-bonding.

  10. FTIR study of hydrogen bonding between substituted benzyl alcohols and acrylic esters

    Directory of Open Access Journals (Sweden)

    P. Sivagurunathan

    2016-11-01

    Full Text Available Hydrogen bonding between substituted benzyl alcohols (benzyl alcohol, o-aminobenzyl alcohol, o-chlorobenzyl alcohol and o-nitrobenzyl alcohol and acrylic esters (methyl methacrylate, ethyl methacrylate is studied in carbon tetrachloride by using the FTIR spectroscopic method. Utilizing the Nash method, the formation constant (K of the 1:1 complexes is calculated. Using the K value, the Gibbs free energy change (ΔG0 is also calculated. The calculated formation constant and Gibbs free energy change values vary with the substituent of benzyl alcohol and ester chain length, which suggests that the proton donating ability of substituted benzyl alcohols is in the order: o-aminobenzyl alcohol < benzyl alcohol < o-chlorobenzyl alcohol < o-nitrobenzyl alcohol, and proton accepting ability of acrylic esters is in the order: methyl methacrylate < ethyl methacrylate.

  11. The FORMAMIDE_2-H_2O Complex: Structure and Hydrogen Bond Cooperative Effects

    Science.gov (United States)

    Blanco, Susana; Pinacho, Pablo; Lopez, Juan Carlos

    2016-06-01

    The adduct formamide_2-H_20 has been detected in a supersonic expansion and its rotational spectra in the 5-13 GHz frequency region characterized by narrow-band molecular beam Fourier transform microwave spectroscopy (MB-FTMW). The spectrum shows the hyperfine structure due to the presence of two 14N-nuclei. This hyperfine structure has been analyzed and the determined quadrupole coupling constants together with the rotational constants have been a key for the identification of the adduct structure on the light of ab initio computations. The rotational parameters are consistent with the formation of a three body cycle thanks to the double proton acceptor/proton donor character of both formamide and water. The low value of the planar moment of inertia Pcc indicates that the heavy atom skeleton of the cluster is essentially planar. A detailed analysis of the results reveals the subtle effects of hydrogen bond cooperative effects in this system.

  12. 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.

  13. Hydrogen bonding in acetylacetaldehyde: Theoretical insights from the theory of atoms in molecules

    Science.gov (United States)

    Nowroozi, A.; Jalbout, A. F.; Roohi, H.; Khalilinia, E.; Sadeghi, M.; de Leon, A.; Raissi, H.

    All the possible conformations of tautomeric structures (keto and enol) of acetylacetaldehyde (AAD) were fully optimized at HF, B3LYP, and MP2 levels with 6-31G(d,p) and 6-311++G(d,p) basis sets to determine the conformational equilibrium. Theoretical results show that two chelated enol forms have extra stability with respect to the other conformers, but identification of global minimum is very difficult. The high level ab initio calculations G2(MP2) and CBS-QB3) also support the HF conclusion. It seems that the chelated enol forms have equal stability, and the energy gap between them is probably lies in the computational error range. Finally, the analysis of hydrogen bond in these molecules by quantum theory of atoms in molecules (AIM) and natural bond orbital (NBO) methods fairly support the ab initio results.

  14. 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.

  15. 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.

  16. Hydrogen bonding in asphaltenes and coal. Quarterly Report for July 1, 1978 - September 30, 1978

    Energy Technology Data Exchange (ETDEWEB)

    Li, N.C.; Tewari, K.C.

    1978-09-29

    Two coal liquid products derived from the same Kentucky hvAb coal have been separated into toluene-insoluble, asphaltene, and pentane-soluble heavy oil fractions. Viscosity and calorimetric studies are reported of the interaction between heavy oil and asphaltene(A) and its acid/neutral(AA) and base(BA) components in solvent benzene. The increase in viscosity and molar enthalpy of interaction, {Delta}H{sup 0}, in the order BA>A>AA, correlate well with the proton magnetic resonance downfield chemical shift of the OH signal of o-phenylphenol, as a function of added asphaltene (A, AA, BA) concentration in solvent CS{sub 2}· The results suggest that when asphaltene .and heavy oil are present together, hydrogen-bonding involving largely phenolic OH, is one of the mechanisms by which asphaltene-heavy oil interactions are achieved and, in part, is responsible for the viscosity increase of coal liquids.

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

    Science.gov (United States)

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

    2010-12-01

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

  18. 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.

  19. Halogen- and hydrogen-bonding catenanes for halide-anion recognition.

    Science.gov (United States)

    Gilday, Lydia C; Beer, Paul D

    2014-07-01

    Halogen-bonding (XB) interactions were exploited in the solution-phase assembly of anion-templated pseudorotaxanes between an isophthalamide-containing macrocycle and bromo- or iodo-functionalised pyridinium threading components. (1)H NMR spectroscopic titration investigations demonstrated that such XB interpenetrated assemblies are more stable than analogous hydrogen bonding (HB) pseudorotaxanes. The stability of the anion-templated halogen-bonded pseudorotaxane architectures was exploited in the preparation of new halogen-bonding interlocked catenane species through a Grubbs' ring-closing metathesis (RCM) clipping methodology. The catenanes' anion recognition properties in the competitive CDCl(3)/CD(3) OD 1:1 solvent mixture revealed selectivity for the heavier halides iodide and bromide over chloride and acetate.

  20. Catalysis of Heterocyclic Azadiene Cycloaddition Reactions by Solvent Hydrogen Bonding: Concise Total Synthesis of Methoxatin.

    Science.gov (United States)

    Glinkerman, Christopher M; Boger, Dale L

    2016-09-28

    Although it has been examined for decades, no general approach to catalysis of the inverse electron demand Diels-Alder reactions of heterocyclic azadienes has been introduced. Typically, additives such as Lewis acids lead to nonproductive consumption of the electron-rich dienophiles without productive activation of the electron-deficient heterocyclic azadienes. Herein, we report the first general method for catalysis of such cycloaddition reactions by using solvent hydrogen bonding of non-nucleophilic perfluoroalcohols, including hexafluoroisopropanol (HFIP) and trifluoroethanol (TFE), to activate the electron-deficient heterocyclic azadienes. Its use in promoting the cycloaddition of 1,2,3-triazine 4 with enamine 3 as the key step of a concise total synthesis of methoxatin is described.

  1. Microwave Spectrum of Hydrogen Bonded HEXAFLUOROISOPROPANOL•••WATER Complex

    Science.gov (United States)

    Shahi, Abhishek; Arunan, Elangannan

    2014-06-01

    Stabilizing α-helical structure of protein and dissolving a hard to dissolve polymer, polythene terphthalete, are some of the unique properties of the organic solvent Hexafluoroisopropanol (HFIP). After determining the complete microwave spectrum of HFIP monomer, we have recorded the spectrum of HFIP***H_2O complex. Ab initio calculations were used to optimize three different possible structures. The global minimum, structure 1, had HFIP as proton donor. Another promising structure, Structure 2, has been obtained from a molecular dynamic study. A total of 46 observed lines have been fitted well for obtaining the rotational and distortion constants within experimental uncertainty. The observed rotational constants are A = 1134.53898(77) MHz, B = 989.67594(44) MHz and C = 705.26602(20) MHz. Interestingly, the rotational constants of structure 1, structure 2 and experiments were very close. Experimentally observed distortion constants were close to structure 1. b-type transitions were stronger than c-type which is also consistent with the calculated dipole moment components of structure 1. Calculations predict a non-zero a-dipole moment but experimentally a-type transitions were absent. Microwave spectra of two of the deuterium isotopologues of this complex i.e. HFIP***D_2O (30 transitions) and HFIP***HOD (33 transitions) have been also observed. Search for other isotopologues are in progress. To characterize the nature of hydrogen bonding, Atoms in Molecules and Natural Bond Orbital theoretical analysis have been done. Experimental structure and these theoretical analyses indicate that the hydrogen bonding in HFIP***H_2O complex is stronger than that in water dimer. A. Shahi and E. Arunan, Talk number RK16, 68th International Symposium on Molecular Spectroscopy 2013, Ohio, USA. Yamaguchi, T.; Imura, S.; Kai, T.; Yoshida, K. Zeitschrift für Naturforsch. A 2013, 68a, 145.

  2. Short Carboxylic Acid–Carboxylate Hydrogen Bonds Can Have Fully Localized Protons

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Jiusheng; Pozharski, Edwin; Wilson, Mark A.

    2017-01-17

    Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15–0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor–acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [O–O> = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O–O distance with increasing H-bond donor pKa. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid–carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.

  3. A major role for side-chain polyglutamine hydrogen bonding in irreversible ataxin-3 aggregation.

    Directory of Open Access Journals (Sweden)

    Antonino Natalello

    Full Text Available The protein ataxin-3 consists of an N-terminal globular Josephin domain (JD and an unstructured C-terminal region containing a stretch of consecutive glutamines that triggers the neurodegenerative disorder spinocerebellar ataxia type 3, when it is expanded beyond a critical threshold. The disease results from misfolding and aggregation, although the pathway and structure of the aggregation intermediates are not fully understood. In order to provide insight into the mechanism of the process, we monitored the aggregation of a normal (AT3Q24 ataxin-3, an expanded (AT3Q55 ataxin-3, and the JD in isolation. We observed that all of them aggregated, although the latter did so at a much slower rate. Furthermore, the expanded AT3Q55 displayed a substantially different behavior with respect to the two other variants in that at the latest stages of the process it was the only one that did the following: i lost its reactivity towards an anti-oligomer antibody, ii generated SDS-insoluble aggregates, iii gave rise to bundles of elongated fibrils, and iv displayed two additional bands at 1604 and 1656 cm(-1 in FTIR spectroscopy. Although these were previously observed in other aggregated polyglutamine proteins, no one has assigned them unambiguously, yet. By H/D exchange experiments we show for the first time that they can be ascribed to glutamine side-chain hydrogen bonding, which is therefore the hallmark of irreversibly SDS-insoluble aggregated protein. FTIR spectra also showed that main-chain intermolecular hydrogen bonding preceded that of glutamine side-chains, which suggests that the former favors the latter by reorganizing backbone geometry.

  4. Doing the Limbo with a Low Barrier: Hydrogen Bonding and Proton Transfer in Hydroxyformylfulvene

    Science.gov (United States)

    Vealey, Zachary; Nemchick, Deacon; Vaccaro, Patrick

    2016-06-01

    Model compounds continue to play crucial roles for elucidating the ubiquitous phenomena of hydrogen bonding and proton transfer, often yielding invaluable insights into kindred processes taking place in substantially larger species. The symmetric double-minimum topography that characterizes the potential-energy landscape for an important subset of these systems allows unambiguous signatures of molecular dynamics (in the form of tunneling-induced bifurcations) to be extracted directly from spectral measurements. As a relatively unexplored member of this class, 6-hydroxy-2-formylfulvene (HFF) contains an intramolecular O-H···O interaction that has participating atoms from the hydroxylic (donor) and ketonic (acceptor) moieties closely spaced in a quasi-linear configuration. This unusual arrangement suggests proton transduction to occur with minimal encumbrance, possibly leading to a pronounced dislocation of the shuttling hydron commensurate with the concepts of low-barrier hydrogen bonding (which are distinguished by great strength, short distance, and vanishingly small potential barriers). A variety of spectroscopic probes built primarily upon the techniques of laser-induced fluorescence and dispersed fluorescence have been enlisted to acquire the first vibronically resolved information reported for the ground [tilde{X}1A1] and lowest-lying singlet excited [tilde{A}1B{2} (π*π)] electronic manifolds of HFF entrained in a cold supersonic free-jet expansion. These experimental findings will be discussed and compared to those obtained for related proton-transfer systems, with complimentary quantum-chemical calculations serving to unravel the unique bonding motifs and reactive pathways inherent to HFF.

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

    Science.gov (United States)

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

    2016-11-01

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

  6. A Major Role for Side-Chain Polyglutamine Hydrogen Bonding in Irreversible Ataxin-3 Aggregation

    Science.gov (United States)

    Relini, Annalisa; Apicella, Alessandra; Invernizzi, Gaetano; Casari, Carlo; Gliozzi, Alessandra; Doglia, Silvia Maria; Tortora, Paolo; Regonesi, Maria Elena

    2011-01-01

    The protein ataxin-3 consists of an N-terminal globular Josephin domain (JD) and an unstructured C-terminal region containing a stretch of consecutive glutamines that triggers the neurodegenerative disorder spinocerebellar ataxia type 3, when it is expanded beyond a critical threshold. The disease results from misfolding and aggregation, although the pathway and structure of the aggregation intermediates are not fully understood. In order to provide insight into the mechanism of the process, we monitored the aggregation of a normal (AT3Q24) ataxin-3, an expanded (AT3Q55) ataxin-3, and the JD in isolation. We observed that all of them aggregated, although the latter did so at a much slower rate. Furthermore, the expanded AT3Q55 displayed a substantially different behavior with respect to the two other variants in that at the latest stages of the process it was the only one that did the following: i) lost its reactivity towards an anti-oligomer antibody, ii) generated SDS-insoluble aggregates, iii) gave rise to bundles of elongated fibrils, and iv) displayed two additional bands at 1604 and 1656 cm−1 in FTIR spectroscopy. Although these were previously observed in other aggregated polyglutamine proteins, no one has assigned them unambiguously, yet. By H/D exchange experiments we show for the first time that they can be ascribed to glutamine side-chain hydrogen bonding, which is therefore the hallmark of irreversibly SDS-insoluble aggregated protein. FTIR spectra also showed that main-chain intermolecular hydrogen bonding preceded that of glutamine side-chains, which suggests that the former favors the latter by reorganizing backbone geometry. PMID:21533208

  7. Hydration and hydrogen bond network of water around hydrophobic surface investigated by terahertz spectroscopy.

    Science.gov (United States)

    Shiraga, K; Suzuki, T; Kondo, N; Ogawa, Y

    2014-12-21

    Water conformation around hydrophobic side chains of four amino acids (glycine, L-alanine, L-aminobutyric acid, and L-norvaline) was investigated via changes in complex dielectric constant in the terahertz (THz) region. Each of these amino acids has the same hydrophilic backbone, with successive additions of hydrophobic straight methylene groups (-CH2-) to the side chain. Changes in the degree of hydration (number of dynamically retarded water molecules relative to bulk water) and the structural conformation of the water hydrogen bond (HB) network related to the number of methylene groups were quantitatively measured. Since dielectric responses in the THz region represent water relaxations and water HB vibrations at a sub-picosecond and picosecond timescale, these measurements characterized the water relaxations and HB vibrations perturbed by the methylene apolar groups. We found each successive straight -CH2- group on the side chain restrained approximately two hydrophobic hydration water molecules. Additionally, the number of non-hydrogen-bonded (NHB) water molecules increased slightly around these hydrophobic side chains. The latter result seems to contradict the iceberg model proposed by Frank and Evans, where water molecules are said to be more ordered around apolar surfaces. Furthermore, we compared the water-hydrophilic interactions of the hydrophilic amino acid backbone with those with the water-hydrophobic interactions around the side chains. As the hydrophobicity of the side chain increased, the ordering of the surrounding water HB network was altered from that surrounding the hydrophilic amino acid backbone, thereby diminishing the fraction of NHB water and ordering the surrounding tetrahedral water HB network.

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

    Science.gov (United States)

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

    2014-07-03

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

  9. 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.

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

    Science.gov (United States)

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

    2012-05-18

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

  11. 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,

  12. Force spectroscopy of hyaluronan by atomic force microscopy: from hydrogen-bonded networks toward single-chain behavior.

    Science.gov (United States)

    Giannotti, Marina I; Rinaudo, Marguerite; Vancso, G Julius

    2007-09-01

    The conformational behavior of hyaluronan (HA) polysaccharide chains in aqueous NaCl solution was characterized directly at the single-molecule level. This communication reports on one of the first single-chain atomic force microscopy (AFM) experiments performed at variable temperatures, investigating the influence of the temperature on the stability of the HA single-chain conformation. Through AFM single-molecule force spectroscopy, the temperature destabilization of a local structure was proven. This structure involved a hydrogen-bonded network along the polymeric chain, with hydrogen bonds between the polar groups of HA and possibly water, and a change from a nonrandom coil to a random coil behavior was observed when increasing the temperature from 29 +/- 1 to 46 +/- 1 degrees C. As a result of the applied force, this superstructure was found to break progressively at room temperature. The use of a hydrogen-bonding breaker solvent demonstrated the hydrogen-bonded water-bridged nature of the network structure of HA single chains in aqueous NaCl solution.

  13. Correlations and predictions of carboxylic acid pKa values using intermolecular structure and properties of hydrogen-bonded complexes.

    Science.gov (United States)

    Tao, Li; Han, Jun; Tao, Fu-Ming

    2008-01-31

    Density functional theory calculations have been preformed on a series of hydrogen-bonded complexes of substituted aliphatic and aromatic carboxylic acids with ammonia. Molecular properties, particularly those related to hydrogen bonding, have been carefully examined for their interdependence as well as dependence on the acidity of the acid. The bond length and stretching frequency of the hydroxyl group and the hydrogen-bond length and energy of the complex are shown to be highly correlated with each other and are linearly correlated with available literature pKa values of the carboxylic acids. The linear correlations resulting from the fit to the available pKa values can be used to predict the pKa values of similar carboxylic acids. The pKa values so predicted using the different molecular properties are highly consistent and in good agreement with the literature values. This study suggests that calculated molecular properties of hydrogen-bonded complexes allow effective and systematic prediction of pKa values for a large range of organic acids using the established linear correlations. This approach is unique in its capability to determine the acidity of a particular functional group or the local acidity within a large molecular system such as a protein.

  14. Communication: The highest frequency hydrogen bond vibration and an experimental value for the dissociation energy of formic acid dimer

    DEFF Research Database (Denmark)

    Kollipost, F.; Larsen, René Wugt; Domanskaya, A.V.

    2012-01-01

    . Comparison to earlier studies at room temperature reveals the large influence of thermal excitation on the band maximum. Together with three Bu combination states involving hydrogen bond fundamentals and with recent progress for the Raman-active modes, this brings into reach an accurate statistical...

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

    Science.gov (United States)

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

    2010-03-01

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

  16. 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.

  17. Hydrogen bonding interactions in ethanol and acetonitrile binary system: A near and mid-infrared spectroscopic study

    Science.gov (United States)

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

    2014-07-01

    The hydrogen bond interactions in C2H5OHsbnd CH3CN binary system have been studied in detail by near-infrared spectroscopy (NIR), attenuated total reflection (ATR) mid-infrared spectroscopy (mid-IR), and density functional theory (DFT) calculations. The collected spectra were analyzed with excess spectroscopy and two-dimensional correlation spectroscopy (2D-COS) including moving-window 2D-COS. The main conclusions are: (1) A number of species, namely multimer, trimmer, and dimer of C2H5OH, and C2H5OH⋯CD3CN hydrogen bonding complex, have been identified in the binary system C2H5OHsbnd CH3CN experimentally. The linear relationship between the observed and calculated wavenumbers of the concerned species assisted us in doing the assignments. (2) Adding acetonitrile, the hydrogen bonds in C2H5OH are weakened and C2H5OH multimers dissociate. Meanwhile, C2H5OH dimers and C2H5OH⋯CD3CN hydrogen bonding complex form, and the former also transform to the latter. The dissociation of C2H5OH multimers slows down gradually during the dilution process and at the mole fraction 0.7 of acetonitrile, all the C2H5OH multimers have dissociated.

  18. Transient hydrogen bonding in uniformly ¹³C,¹⁵N-labeled carbohydrates in water.

    Science.gov (United States)

    Norris, Scott E; Landström, Jens; Weintraub, Andrej; Bull, Thomas E; Widmalm, Göran; Freedberg, Darón I

    2012-03-01

    We report NMR studies of transient hydrogen bonding in a polysaccharide (PS) dissolved in water without cosolvent at ambient temperature. The PS portion of the Escherichia coli O142 lipopolysaccharide is comprised of repeating pentasaccharide units of GalNAc (N-acetyl galactosamine), GlcNAc (N-acetyl glucosamine), and rhamnose in a 3:1:1 ratio, respectively. A 105-ns molecular dynamics (MD) simulation on one pentasaccharide repeat unit predicts transient inter-residue hydrogen bonds from the GalNAc NH groups in the PS. To investigate these predictions experimentally, the PS was uniformly ¹³C,¹⁵N enriched and the NH, carbonyl, C2, C4, and methyl resonances of the GalNAc and GlcNAc residues assigned using through-bond triple-resonance NMR experiments. Temperature dependence of amide NH chemical shifts and one-bond NH J couplings support that NH groups on two of the GalNAc residues are donors in transient hydrogen bonds. The remaining GalNAc and GlcNAc NHs do not appear to be donors from either temperature-dependent chemical shifts or one-bond NH J couplings. These results substantiate the presence of weak or partial hydrogen bonds in carbohydrates, and that MD simulations of repeating units in PSs provide insight into overall PS structure and dynamics.

  19. Hydrogen bonding in asphaltenes and coal. Progress report, July 1, 1976--December 31, 1976. [Between quinoline and o-phenylphenol

    Energy Technology Data Exchange (ETDEWEB)

    Li, N.C.

    1977-01-04

    Calorimetric studies of hydrogen bonding between quinoline and o-phenylphenol were carried out because they represent the nitrogenous heteronuclear aromatic bases and aromatic bases, respectively, found in the liquefaction products from coal. Further experiments are planned to try to resolve discrepancies observed between experimental and calculated values. (EJH)

  20. 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...

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

    Directory of Open Access Journals (Sweden)

    Dechang Li

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

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

    Science.gov (United States)

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

    2011-01-01

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

  3. 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.

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

    Science.gov (United States)

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

    2016-09-08

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

  5. Synthesis of metal-hydrazone complexes and vapochromic behavior of their hydrogen-bonded proton-transfer assemblies.

    Science.gov (United States)

    Kobayashi, Atsushi; Dosen, Masa-aki; Chang, Mee; Nakajima, Kiyohiko; Noro, Shin-ichiro; Kato, Masako

    2010-11-03

    We synthesized and investigated a new series of metal-hydrazone complexes, including deprotonated [MX(mtbhp)] and protonated forms [MX(Hmtbhp)](ClO(4)) (M = Pd(2+), Pt(2+); X = Cl(-), Br(-); Hmtbhp = 2-(2-(2-(methylthio)benzylidene)hydrazinyl)pyridine) and hydrogen-bonded proton-transfer (HBPT) assemblies containing [PdBr(mtbhp)] and bromanilic acid (H(2)BA). The mtbhp hydrazone ligand acts as a tridentate SNN ligand and provides a high proton affinity. UV-vis spectroscopy revealed that these metal-hydrazone complexes follow a reversible protonation-deprotonation reaction ([MX(mtbhp)] + H(+) ⇋ [MX(Hmtbhp)](+)), resulting in a remarkable color change from red to yellow. Reactions between proton acceptor [PdBr(mtbhp)] (A) and proton donor H(2)BA (D) afforded four types of HBPT assemblies with different D/A ratios: for D/A = 1:1, {[PdBr(Hmtbhp)](HBA)·Acetone} and {[PdBr(Hmtbhp)](HBA)·2(1,4-dioxane)}; for D/A = 1:2, [PdBr(Hmtbhp)](2)(BA); and for D/A = 3:2, {[PdBr(Hmtbhp)](2)(HBA)(2)(H(2)BA)·2Acetonitrile}. The proton donor gave at least one proton to the acceptor to form the hydrogen bonded A···D pair of [PdBr(Hmtbhp)](+)···HBA(-). The strength of the hydrogen bond in the pair depends on the kind of molecule bound to the free monoanionic bromanilate OH group. Low-temperature IR spectra (T < 150 K) showed that the hydrogen bond distance between [PdBr(Hmtbhp)](+) and bromanilate was short enough (ca. 2.58 Å) to induce proton migration in the [PdBr(Hmtbhp)](2)(BA) assembly in the solid state. The hydrogen bonds formed not only between [PdBr(Hmtbhp)](+) and HBA(-) but also between HBA(-) and neutral H(2)BA molecules in the {[PdBr(Hmtbhp)](2)(HBA)(2)(H(2)BA)·2Acetonitrile} assembly. The H(2)BA-based flexible hydrogen bond network and strong acidic host structure result in an interesting vapor adsorption ability and vapochromic behavior in this assembly because the vapor-induced rearrangement of the hydrogen bond network, accompanied by changes in

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

    Science.gov (United States)

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

    2014-08-27

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

  7. Halogen Bonding or Hydrogen Bonding between 2,2,6,6-Tetramethyl-piperidine-noxyl Radical and Trihalomethanes CHX3 (X=Cl, Br, I)

    Institute of Scientific and Technical Information of China (English)

    Xiao-ran Zhao; Xue Pang; Xiao-qing Yan; Wei-jun Jin

    2013-01-01

    The halogen and hydrogen bonding complexes between 2,2,6,6-tetramethylpiperidine-noxyl and trihalomethanes (CHX3,X=Cl,Br,I) are simulated by computational quantum chemistry.The molecular electrostatic potentials,geometrical parameters and interaction energy of halogen and hydrogen bonding complexes combined with natural bond orbital analysis are obtained.The results indicate that both halogen and hydrogen bonding interactions obey the order Cl<Br<I,and hydrogen bonding is stronger than the corresponding halogen bond ing.So,hydrogen bonding complexes should be dominant in trihalomethanes.However,it is possible that halogen bonding complex is competitive,even preponderant,in triiodomethane due to the similar interaction energy.This work might provide useful information on specific solvent effects as well as for understanding the mechanism of nitroxide radicals as a bioprobe to interact with the halogenated compounds in biological and biochemical fields.

  8. Theoretical study of the N-H…O red-shifted and blue-shifted hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    YANG Yong; ZHANG WeiJun; PEI ShiXin; SHAO Jie; HUANG Wei; GAO XiaoMing

    2007-01-01

    Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO…HNO, HCOOH…HNO, HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F. The geometric structures and vibrational frequencies of these six complexes at the MP2/6-31+G(d,p), MP2/6-311++G(d,p), B3LYP/6-31+G(d,p) and B3LYP/6-311++G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO…HNO and HCOOH…HNO the N-H bond is strongly contracted and N-H…O blue-shifted hydrogen bonds are observed. While in complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F, the N-H bond is elongated and N-H…O red-shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X-H bond length in the X-H…Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X-H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO…HNO and HCOOH…HNO, the shortening effects dominate which lead to the blue shift of the N-H stretching frequencies. In complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F where elongating effects are dominant, the N-H…O hydrogen bonds are red-shifted.

  9. Effect of Water Content in N-Methylmorpholine N-Oxide/Cellulose Solutions on Thermodynamics, Structure, and Hydrogen Bonding.

    Science.gov (United States)

    Rabideau, Brooks D; Ismail, Ahmed E

    2015-12-03

    Native crystalline cellulose is notoriously difficult to dissolve due to its dense hydrogen bond network between chains and weaker hydrophobic forces between cellulose sheets. N-Methylmorpholine N-oxide (NMMO), the solvent behind the Lyocell process, is one of the most successful commercial solvents for the nonderivatized dissolution of cellulose. In this process, water plays a very important role. Its presence at low concentrations allows NMMO to dissolve substantial amounts of cellulose, while at much higher concentrations it precipitates the crystalline fibers. Using all-atom molecular dynamics, we study the thermodynamic and structural properties of ternary solutions of cellulose, NMMO, and water. Using the two-phase thermodynamic method to calculate solvent entropy, we estimate the free energy of dissolution of cellulose as a function of the water concentration and find a transition of spontaneity that is in excellent agreement with experiment. In pure water, we find that cellulose dissolution is nonspontaneous, a result that is due entirely to strong decreases in water entropy. Although the combined effect of enthalpy on dissolution in water is negligible, we observe a net loss of hydrogen bonds, resulting in a change in hydrogen bond energy that opposes dissolution. At lower water concentrations, cellulose dissolution is spontaneous and largely driven by decreases in enthalpy, with solvent entropy playing only a very minor role. When searching for the root causes of this enthalpy decrease, a complex picture emerges in which not one but many different factors contribute to NMMO's good solvent behavior. The reduction in enthalpy is led by the formation of strong hydrogen bonds between cellulose and NMMO's N-oxide, intensified through van der Waals interactions between NMMO's nonpolar body and the nonpolar surfaces of cellulose and unhindered by water at low concentrations due to the formation of efficient hydrogen bonds between water and cellulose.

  10. Study of hydrogen-bonding, vibrational dynamics and structure-activity relationship of genistein using spectroscopic techniques coupled with DFT

    Science.gov (United States)

    Singh, Harshita; Singh, Swapnil; Srivastava, Anubha; Tandon, Poonam; Bharti, Purnima; Kumar, Sudhir; Dev, Kapil; Maurya, Rakesh

    2017-02-01

    The conformational and hydrogen bonding studies of genistein have been performed by combined spectroscopic and quantum chemical approach. The vibrational spectra (FT-IR and FT-Raman), UV-visible and 1H and 13C NMR absorption spectra of genistein have been recorded and examined. The vibrational wavenumbers of optimized geometry and total energy for isolated molecule and hydrogen-bonded dimers of genistein have been determined using the quantum chemical calculation (DFT/B3LYP) with extended 6-311++G (d,p) basis set. The vibrational assignments for the observed FT-IR and FT-Raman spectra of genistein are provided by calculations on monomer and hydrogen-bonded dimer. The quantum theory of atoms in molecules (QTAIM) is used for investigating the nature and strength of hydrogen-bonds. UV-visible spectrum of the genistein was recorded in methanol solvent and the electronic properties were calculated by using time-dependent density functional theory (TD-DFT). The computed HOMO and LUMO energies predicted the type of transition as π → π*. The 1H and 13C NMR signals of the genistein were computed by the Gauge including atomic orbital (GIAO) approach. Natural bond orbital (NBO) analysis predicted the stability of molecules due to charge delocalization and hyper conjugative interactions. NBO analysis shows that there is an Osbnd H⋯O inter and intramolecular hydrogen bond, and π → π* transition in the monomer and dimer, which is consistent with the conclusion obtained by the investigation of molecular structure and assignment of UV-visible spectra.

  11. Dynamics of supercritical methanol of varying density from first principles simulations: hydrogen bond fluctuations, vibrational spectral diffusion, and orientational relaxation.

    Science.gov (United States)

    Yadav, Vivek Kumar; Chandra, Amalendu

    2013-06-14

    A first principles study of the dynamics of supercritical methanol is carried out by means of ab initio molecular dynamics simulations. In particular, the fluctuation dynamics of hydroxyl stretch frequencies, hydrogen bonds, dangling hydroxyl groups, and orientation of methanol molecules are investigated for three different densities at 523 K. Apart from the dynamical properties, various equilibrium properties of supercritical methanol such as the local density distributions and structural correlations, hydrogen bonding aspects, frequency-structure correlations, and dipole distributions of methanol molecules are also investigated. In addition to the density dependence of various equilibrium and dynamical properties, their dependencies on dispersion interactions are also studied by carrying out additional simulations using a dispersion corrected density functional for all the systems. It is found that the hydrogen bonding between methanol molecules decreases significantly as we move to the supercritical state from the ambient one. The inclusion of dispersion interactions is found to increase the number of hydrogen bonds to some extent. Calculations of the frequency-structure correlation coefficient reveal that a statistical correlation between the hydroxyl stretch frequency and the nearest hydrogen-oxygen distance continues to exist even at supercritical states of methanol, although it is weakened with increase of temperature and decrease of density. In the supercritical state, the frequency time correlation function is found to decay with two time scales: One around or less than 100 fs and the other in the region of 250-700 fs. It is found that, for supercritical methanol, the times scales of vibrational spectral diffusion are determined by an interplay between the dynamics of hydrogen bonds, dangling OD groups, and inertial rotation of methanol molecules and the roles of these various components are found to vary with density of the supercritical solvent. Effects

  12. Neutron Compton Scattering as a Probe of Hydrogen Bonded (and other) Systems

    Energy Technology Data Exchange (ETDEWEB)

    Reiter, George

    2010-12-22

    One of the two major themes of the proposal was to study quantum coherence in stressed hydrogen bond networks. Our experiments on double wall carbon nanotubes and two versions of Nafion, together with earlier work on water confined in xerogel and in single wall carbon nanotubes demonstrate that water confined in dimensions on the order of 20 Angstroms is in a qualitatively different quantum ground state than bulk water. It cannot be described as a collection of molecules interacting only electrostatically. This has major implications for biology, where most of the water in the cell is confined to distances on that order, and for fuel cell development using Nafion like materials, where the conduction mechanism is expected to be strongly affected by the quantum state of the water. We have demonstrated its importance in the binding of water molecules to DNA. Protein folding experiments at several concentrations have been carried out and are presently being analyzed. Initial analysis shows strong temperature dependent effects on the proton momentum distribution. The theoretical work proposed has been completed, and complements the experiments by demonstrating that even in room temperature bulk water, the electron density overlap between donor and acceptor molecules in the hydrogen bond has a significant measurable effect on the momentum distribution of the protons. The electrons are distributed throughout the hydrogen bond network, not simply in localized molecules. We had proposed to look at low coverage experiments on MCM-41, and have done so, revealing the details of the interaction of water molecules with silanol groups. Related experiments, not proposed, on water layers on SnO2 and TiO2 powders have confirmed the strong deviations of the proton momentum distribution for water molecules adsorbed on these surfaces. These results are not yet published. Another major theme was to measure Born-Oppenheimer potentials in M3H(XO4)2 systems. We have done this for Rb3(SO4

  13. Novel one-dimensional lanthanide acrylic acid complexes: an alternative chain constructed by hydrogen bonding

    Science.gov (United States)

    Li, Hui; Hu, Chang Wen

    2004-12-01

    Novel one-dimensional (1D) chains of three lanthanide complexes La(L 1) 3(CH 3OH)]·CH 3OH (L 1=(E)-3-(2-hydroxyl-phenyl)-acrylic acid) 1, La(L 2) 3(H 2O) 2]·2.75H 2O (L 2=(E)-3-(3-hydroxyl-phenyl)-acrylic acid) 2, and La(L 3) 3(CH 3OH) 2(H 2O)]·CH 3OH (L 3=(E)-3-(4-hydroxyl-phenyl)-acrylic acid) 3 are reported. The crystal structure data are as follows for 1: C 29H 29LaO 11, monoclinic, P2 1/ n, a=15.4289(12) Å, b=7.9585(6) Å, c=23.041(2) Å, β=99.657(2)°, Z=4, R1=0.0637, w R2=0.0919; for 2: C 27H 30.50LaO 13.75, triclinic, P-1, a=8.4719(17) Å, b=13.719(3) Å, c=14.570(3) Å, α=62.19(3)°, β=99.657(2)°, γ=78.22(3)°, Z=2, R1=0.0384, w R2=0.0820; and for 3: C 30H 35LaO 13, monoclinic, P2(1)/ c, a=9.5667(6) Å, b=24.3911(15) Å, c=14.0448(9) Å, β=109.245(2)°, Z=4, R1=0.0374, w R2=0.0630. All the three structure data were collected using graphite monochromated molybdenum Kα radiation and refined using full-matrix least-squares techniques on F 2. These structures show that four kinds of the carboxylato bridge modes are included in these chains to link the La(III) ions. It is the first time that it has been found that the intra-chain hydrogen bonding can construct an alternative chain even, when the coordination bridge mode is the same along the chain (complex 2). There are 2D and 3D hydrogen bonding in the crystal lattices of complexes 1- 3.

  14. Molecular dynamics simulation of amorphous indomethacin-poly(vinylpyrrolidone) glasses: solubility and hydrogen bonding interactions.

    Science.gov (United States)

    Xiang, Tian-Xiang; Anderson, Bradley D

    2013-03-01

    Amorphous drug dispersions are frequently employed to enhance solubility and dissolution of poorly water-soluble drugs and thereby increase their oral bioavailability. Because these systems are metastable, phase separation of the amorphous components and subsequent drug crystallization may occur during storage. Computational methods to determine the likelihood of these events would be very valuable, if their reliability could be validated. This study investigates amorphous systems of indomethacin (IMC) in poly(vinylpyrrolidone) (PVP) and their molecular interactions by means of molecular dynamics (MD) simulations. IMC and PVP molecules were constructed using X-ray diffraction data, and force-field parameters were assigned by analogy with similar groups in Amber-ff03. Five assemblies varying in PVP and IMC composition were equilibrated in their molten states then cooled at a rate of 0.03 K/ps to generate amorphous glasses. Prolonged aging dynamic runs (100 ns) at 298 K and 1 bar were then carried out, from which solubility parameters, the Flory-Huggins interaction parameter, and associated hydrogen bonding properties were obtained. Calculated glass transition temperature (T(g)) values were higher than experimental results because of the faster cooling rates in MD simulations. Molecular mobility as characterized by atomic fluctuations was substantially reduced below the T(g) with IMC-PVP systems exhibiting lower mobilities than that found in amorphous IMC, consistent with the antiplasticizing effect of PVP. The number of IMC-IMC hydrogen bonds (HBs) formed per IMC molecule was substantially lower in IMC-PVP mixtures, particularly the fractions of IMC molecules involved in two or three HBs with other IMC molecules that may be potential precursors for crystal growth. The loss of HBs between IMC molecules in the presence of PVP was largely compensated for by the formation of IMC-PVP HBs. The difference (6.5 MPa(1/2)) between the solubility parameters in amorphous IMC

  15. Hydrogen-bonded porous coordination polymers: structural transformation, sorption properties, and particle size from kinetic studies.

    Science.gov (United States)

    Uemura, Kazuhiro; Saito, Kazuya; Kitagawa, Susumu; Kita, Hidetoshi

    2006-12-20

    Three new coordination polymers, [CoCl2(4-pmna)2]n (1), {[Co(NCS)2(4-pmna)2].2Me2CO}n (2 superset 2Me2CO), and {[Co(4-pmna)2(H2O)2](NO3)2.2CH3OH}n (3 superset 2H2O.2MeOH) (4-pmna = N-(pyridin-4-ylmethyl)nicotinamide), have been synthesized and characterized using single-crystal X-ray diffraction. The cobalt(II) atoms are bridged by 4-pmna ligands in all three compounds to form double-stranded one-dimensional "repeated rhomboid-type" chains with rectangular-shaped cavities. In 1, each chain slips and obstructs the neighboring cavities so that there are no guest-incorporated pores. Both 2 superset 2Me2CO and 3 superset 2H2O.2MeOH do not have such a staggered arrangement and have pores that can be filled with a guest molecule. Compound 3 superset 2H2O.2MeOH traps guest molecules with multiple hydrogen bonds and shows a reversible structural rearrangement during adsorption and desorption. The new crystalline compound, 3, is stabilized by forming hydrogen bonds with the amide moieties of the 4-pmna ligands and was characterized using infrared spectroscopy. The clathration enthalpy of the reaction 3 + 2H2O(l) + 2MeOH(l) 3 superset 2H2O.2MeOH (approximately 35 kJ/mol) was estimated from differential scanning calorimetry data by considering the vaporization enthalpies of H2O and MeOH. The desorption process of 3 superset 2H2O.2MeOH --> 3 follows a single zero-order reaction mechanism under isothermal conditions. The activation energy of ca. 100 kJ/mol was obtained by plotting the logarithm of the reaction time for the same reacted fraction versus the reciprocal of the temperature. Moreover, the distribution of the one-dimensional channels in 3 superset 2H2O.2MeOH was estimated using the observation that the reaction rate is directly proportional to the total sectional area.

  16. Using multiple hydrogen bonding cross-linkers to access reversibly responsive three dimensional graphene oxide architecture

    Science.gov (United States)

    Han, Junkai; Shen, Yongtao; Feng, Wei

    2016-07-01

    Three-dimensional (3D) graphene materials have attracted a lot of attention for efficiently utilizing inherent properties of graphene sheets. However, 3D graphene materials reported in the previous literature are constructed through covalent or weak non-covalent interactions, causing permanent structure/property changes. In this paper, a novel 3D graphene material of dynamic interactions between lamellas with 2-ureido-4[1H]-pyrimidinone as a supra-molecular motif has been synthesized. This 3D graphene material shows enhanced sheet interactions while the cross-linking takes place. With proper solvent stimulation, the integrated 3D graphene material can disassemble as isolated sheets. The driving force for the 3D structure assembly or disassembly is considered to be the forming or breaking of the multiple hydrogen bonding pairs. Furthermore, the 3D material is used as an intelligent dye adsorber to adsorb methylene blue and release it. The controllable and reversible characteristic of this 3D graphene material may open an avenue to the synthesis and application of novel intelligent materials.Three-dimensional (3D) graphene materials have attracted a lot of attention for efficiently utilizing inherent properties of graphene sheets. However, 3D graphene materials reported in the previous literature are constructed through covalent or weak non-covalent interactions, causing permanent structure/property changes. In this paper, a novel 3D graphene material of dynamic interactions between lamellas with 2-ureido-4[1H]-pyrimidinone as a supra-molecular motif has been synthesized. This 3D graphene material shows enhanced sheet interactions while the cross-linking takes place. With proper solvent stimulation, the integrated 3D graphene material can disassemble as isolated sheets. The driving force for the 3D structure assembly or disassembly is considered to be the forming or breaking of the multiple hydrogen bonding pairs. Furthermore, the 3D material is used as an

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Dallakyan Sargis

    2008-08-01

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

  19. Structural Criteria for the Rational Design of Selective Ligands: Convergent Hydrogen Bonding Sites for the Nitrate Anion

    Energy Technology Data Exchange (ETDEWEB)

    Hay, Benjamin P.; Gutowski, Maciej S.; Dixon, David A.; Garza , Jorge; Vargas, Rubicelia; Moyer, Bruce A.

    2004-06-30

    Molecular hosts for anion complexation are often constructed by combining two or more hydrogen bonding functional groups, D–H. The deliberate design of complementary host architectures requires knowledge of the optimal geometry for the hydrogen bonds formed between the host and the guest. Herein, we present a detailed study of the structural aspects of hydrogen bonding interactions with the NO3– anion. A large number of crystal structures are analyzed to determine the number of hydrogen bond contacts per anion and to further characterize the structural aspects of these interactions. Electronic structure calculations are used to determine stable geometries and interaction energies for NO3– complexes with several simple molecules possessing D–H groups, including water, methanol, N-methylformamide, and methane. Theoretical results are reported at several levels of density functional theory, including BP86/DN**, B3LYP/TZVP, and B3LYP/TZVP+, and at MP2/aug-cc-pVDZ. In addition, MP2 binding energies for these complexes were obtained at the complete basis set limit by extrapolating from single point energies obtained with larger correlation-consistent basis sets. The results establish that NO3– has an intrinsic hydrogen bonding topography in which there are six optimal sites for proton location. The structural features observed in crystal structures and in the optimized geometries of complexes are explained by a preference to locate the D–H protons in these positions. For the strongest hydrogen bonding interactions, the N–O•••H angle is bent at an angle of 115 ± 10°, and the hydrogen atom lies in the NO3– plane giving O–N–O•••H dihedral angles of 0 and 180°. In addition, the D-H vector points towards the oxygen atom, giving D–H•••O angles that are near linear, 170 ± 10°. Due to steric hindrance, simple alcohol O–H and amide N–H donors form 3:1 complexes with NO3–, with H•••O distances of 1.85 ± 0.5 Å. Thus, the

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Daniel J Kuster

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

  2. Structural and thermotropic peculiarities of hydrogen-bonded liquid crystals confined in mesoporous molecular sieves

    Science.gov (United States)

    Gnatyuk, I.; Gavrilko, T.; Yaroshchuk, O.; Holovina, N.; Shcherban, N.; Baran, J.; Drozd, M.

    2016-12-01

    The phase behaviour and structural organization of hydrogen-bonded liquid crystals were investigated under confinement to mesoporous molecular sieves. As such liquid crystalline compounds, 4-hexylbenzoic and 4-butylcyclohexanecarboxylic acids with different head group structure and alkyl chain length where selected and filled in the AlMCM-41 sieves. With FTIR spectroscopy it was found that some part of incorporated acid molecules, presumably located in the inner space of the AlMCM-41 pores, is in undissociated form of open dimers or chain associates and thus shows spectroscopic features characteristic to the bulk-like species. The other FTIR spectra components indicate strong interaction of the incorporated monomeric molecules with the pore surface. Two specific mechanisms are shown to be involved in molecular interactions at the interface: (1) deprotonation of monomeric acid molecules on the pore surface with formation of COO- carboxylate ions and (2) bonding of these ions to the pore surface by a coordinated bond R-COO-…Al+ with Lewis acid sites. Differential scanning calorimetry revealed that these near-surface processes lead to complete suppression of mesomorphic properties of the studied acids under confinement to nanopores.

  3. The role of hydrogen bonding in the phase behaviour of supramolecular liquid crystal dimers

    Science.gov (United States)

    Martínez-Felipe, Alfonso; Imrie, Corrie T.

    2015-11-01

    The phase behaviour of equimolar mixtures of 4-octyloxybenzoic acid, OOBA, and either 1-(4-butylazobenzene-4‧-oxy)-6-(4-oxypyridine)pentane, BuABO5OPyr, or 1-(4-butylazobenzene-4‧-oxy)-6-(4-oxypyridine)hexane, BuABO6OPyr, is reported. OOBA exhibits enantiotropic smectic C and nematic phases, whereas BuABO5OPyr and BuABO6OPyr are not liquid crystalline. Both the OOBA/BuABO5OPyr and OOBA/BuABO6OPyr equimolar mixtures show an enantiotropic smectic A phase identified using X-ray diffraction and polarised light microscopy. The liquid crystallinty of the mixtures is attributed, in part, to the formation of a 1:1 hydrogen-bonded complex between OOBA and either BuABO5OPyr or BuABO6OPyr. Differences in the transitional properties of the mixtures are accounted for in terms of the average shapes of these 1:1 complexes. Temperature dependent FTIR spectroscopy shows, however, that the formation of the complex is not quantitative in the mixtures but instead a complex mixture exists over the complete temperature range studied, involving the 1:1 complex, both cyclic and open acid dimers, free acid and hence, free BuABOnOPyr molecules.

  4. Theoretical study of bifurcated bent blue-shifted hydrogen bonds CH2…Y

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Ab initio quantum chemistry methods were applied to study the bifurcated bent hydrogen bonds Y… H2CZ (Z = O, S, Se) and Y…H2CZ2 (Z = F, Cl, Br) (Y = Cl-, Br-) at the MP2/6-311++G(d,p) and MP2/6-311++G(2df,2p) levels. The results show that in each complex there are two equivalent blue-shifted H-bonds Y…H—C, and that the interaction energies and blue shifts are large, the energy of each Y…H—C H-bond is 15-27 kJ/mol, and Δr(CH) = -0.1 - -0.5 pm and Δv(CH) = 30 - 80 cm-1. The natural bond orbital analysis shows that these blue-shifted H-bonds are caused by three factors: large rehybridization; small direct intermolecular hyperconjugation and larger indirect intermolecular hy- perconjugation; large decrease of intramolecular hyperconjugation. The topological analysis of elec- tron density shows that in each complex there are three intermolecular critical points: there is one bond critical point between the acceptor atom Y and each hydrogen, and there is a ring critical point inside the tetragon YHCH, so these interactions are exactly H-bonding.

  5. Hydrogen-bonding interactions between [BMIM][BF4] and acetonitrile.

    Science.gov (United States)

    Zheng, Yan-Zhen; Wang, Nan-Nan; Luo, Jun-Jie; Zhou, Yu; Yu, Zhi-Wu

    2013-11-07

    In this work, the interactions between a representative imidazolium-based ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) and acetonitrile (CH3CN) were investigated in detail using attenuated total reflection infrared spectroscopy (ATR-IR), hydrogen nuclear magnetic resonance ((1)H NMR), and density functional theory calculations. The main conclusions are: (1) a number of species in the [BMIM][BF4]-CH3CN mixtures were identified with the help of excess infrared spectroscopy and quantum chemical calculations. The dilution process of the ionic liquid by acetonitrile was found to be the transformation from ion clusters to ion pairs. (2) The solvent molecules cannot break apart the strong Coulombic interaction between [BMIM](+) and [BF4](-) but can break apart the ion cluster into an ion pair within the concentration range investigated. The strength of hydrogen bonds between the C-Hs of [BMIM](+) and the N of acetonitrile is enhanced during the dilution process. (3) The methyl group of CH3CN locates above/below the imidazolium ring in the solution. These in-depth studies on the properties of the ionic liquid-acetonitrile mixed solvents may shed light on exploring their applications as reaction media in electrochemistry and chemical synthesis.

  6. Hydrogen bonding interactions in nicotinamide Ionic Liquids: A comparative spectroscopic and DFT studies

    Science.gov (United States)

    Shukla, Madhulata

    2017-03-01

    Being biodegradable in nature nicotinamide based Ionic Liquids (ILs) are gaining much attention now a day. Nicotinamide iodide (i.e 1-methyl-3ethoxy carbonyl pyridinium iodide (mNicI)) and 1-methyl-3ethoxy carbonyl pyridinium trifilimide (mNicNTf2) new ILs has been synthesized and has been characterized using different spectroscopic techniques like NMR, UV visible and infrared spectroscopy. Theoretical studies have been performed on several nicotinamide ILs. Geometry and spectral features were further characterized by Density Functional Theory (DFT) calculation. NBO charge distribution and electrostatic potential diagram presents in depth knowledge about interactions between cation and anion. A comparative theoretical study between mNicI and its other analogues i. e 1-methyl-3 ethoxy carbonyl pyridinium chloride and bromide i. e mNicCl and mNicBr has also been performed. Csbnd H⋯X hydrogen bonding along with C⋯X interaction has been reported for the first time for the nicotinamide based ILs. C2sbnd H stretching frequency shifts to higher wavenumber with change to a lesser electronegative anion. mNicCl and mNicBr are expected to be solid in nature with the evidence from the red shift in stretching frequency as compared to mNicI. TD-DFT calculation of mNicI proved that pale yellow color of liquid is due to inherent transition from anion to cation.

  7. Influence of Fluorination on the Conformational Properties and Hydrogen-Bond Acidity of Benzyl Alcohol Derivatives

    Science.gov (United States)

    Bogdan, Elena; Compain, Guillaume; Mtashobya, Lewis; Le Questel, Jean-Yves; Besseau, François; Galland, Nicolas; Linclau, Bruno; Graton, Jérôme

    2015-01-01

    The effect of fluorination on the conformational and hydrogen-bond (HB)-donating properties of a series of benzyl alcohols has been investigated experimentally by IR spectroscopy and theoretically with quantum chemical methods (ab initio (MP2) and DFT (MPWB1K)). It was found that o-fluorination generally resulted in an increase in the HB acidity of the hydroxyl group, whereas a decrease was observed upon o,o′-difluorination. Computational analysis showed that the conformational landscapes of the title compounds are strongly influenced by the presence of o-fluorine atoms. Intramolecular interaction descriptors based on AIM, NCI and NBO analyses reveal that, in addition to an intramolecular OH⋅⋅⋅F interaction, secondary CH⋅⋅⋅F and/or CH⋅⋅⋅O interactions also occur, contributing to the stabilisation of the various conformations, and influencing the overall HB properties of the alcohol group. The benzyl alcohol HB-donating capacity trends are properly described by an electrostatic potential based descriptor calculated at the MPWB1K/6-31+G(d,p) level of theory, provided solvation effects are taken into account for these flexible HB donors. PMID:26130594

  8. Binary mixtures of hydrogen-bonded ferroelectric liquid crystals. Thermal span enhancement in smectic X* phase

    Energy Technology Data Exchange (ETDEWEB)

    Sangameswari, Gopal; Prabu, Nataraj Pongali Sathya; Madhu Mohan, Mathukumalli Lakshmi Narayana [Bannari Amman Institute of Technology, Sathyamangalam (India). Liquid Crystal Research Laboratory (LCRL)

    2015-07-01

    Thermotropic hydrogen-bonded ferroelectric binary liquid crystal mixtures comprising of N-carbamyl-l-glutamic acid (CGA) and p-n-alkyloxy benzoic acids (BAO) are investigated. Variation in the molar proportion of X and Y (where X=CGA+5BAO and Y=CGA+9BAO, CGA+10BAO, CGA+11BAO, and CGA+12BAO) comprising of four series yielded 36 binary mixtures. Optical and thermal properties of these mixtures are meticulously studied in the present article. In addition to the traditional phases, a novel smectic ordering namely smectic X* is observed in all the four series. The aim of the investigation is to obtain abundance occurrence of smectic X* with a large thermal span, and hence, the proportions of the binary mixtures are so chosen that the prelude task is accomplished. Optical tilt angle in smectic X* and smectic C* phases is experimentally determined, and a theoretical fit is performed. Phase diagrams of the four series are constructed from the data obtained from the differential scanning calorimetry and correlated with the phases recorded by the polarising optical microscope studies. Thermal stability factor and thermal equilibrium are also premeditated.

  9. Proton dynamics in the hydrogen bonds of 4-amino-3,5-dihalogenobenzoic acid

    Energy Technology Data Exchange (ETDEWEB)

    Asaji, Tetsuo, E-mail: asaji@chs.nihon-u.ac.jp [Department of Chemistry, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550 (Japan); Ueda, Kouhei; Oguni, Masaharu [Department of Chemistry, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551 (Japan)

    2015-08-18

    Highlights: • 4-Amino-3,5-dichlorobenzoic acid has a symmetric dimer structure. • The compound undergoes a phase transition at 138 K. • The symmetry breaking of the dimer was revealed by {sup 35}Cl NQR. • The proton dynamics was analyzed by coherent and incoherent tunneling models. - Abstract: On the polycrystalline sample of 4-amino-3,5-dihalogenobenzoic acid, 4-NH{sub 2}-3,5-X{sub 2}C{sub 6}H{sub 2}COOH, which has a symmetric dimer structure in the crystal, the proton tunneling in the hydrogen bonds has been investigated by NQR and NMR spin–lattice relaxation times T{sub 1} measurements. Two {sup 35}Cl NQR lines of the X = Cl derivative show the existence of two crystallographically inequivalent chlorine atoms in the high-temperature phase, in consistency with the reported crystal structure. Below 138 K, each splits into a doublet indicating the symmetry breaking of the benzoic acid dimer. The proton dynamics was analyzed by a coherent and incoherent tunneling models, for the high- and low-temperature phases, respectively. The temperature dependence of the correlation time of proton translation was estimated. As for the X = I derivative, the proton dynamics was discussed similarly by {sup 1}H NMR T{sub 1} data by assuming occurrence of a phase transition at low-temperature.

  10. A computational NQR study on the hydrogen-bonded lattice of cytosine-5-acetic acid.

    Science.gov (United States)

    Mirzaei, Mahmoud; Hadipour, Nasser L

    2008-04-15

    A computational study at the level of density functional theory (DFT) employing 6-311++G** standard basis set was carried out to evaluate nuclear quadrupole resonance (NQR) spectroscopy parameters in cytosine-5-acetic acid (C5AA). Since the electric field gradient (EFG) tensors are very sensitive to the electrostatic environment at the sites of quadruple nuclei, the most possible interacting molecules with the target one were considered in a five-molecule model system of C5AA using X-ray coordinates transforming. The hydrogen atoms positions were optimized and two model systems of original and H-optimized C5AA were considered in NQR calculations. The calculated EFG tensors at the sites of (17)O, (14)N, and (2)H nuclei were converted to their experimentally measurable parameters, quadrupole coupling constants and asymmetry parameters. The evaluated NQR parameters reveal that the nuclei in original and H-optimized systems contribute to different hydrogen bonding (HB) interaction. The comparison of calculated parameters between optimized isolated gas-phase and crystalline monomer also shows the relationship between the structural deformation and NQR parameters in C5AA. The basis set superposition error (BSSE) calculations yielded no significant errors for employed basis set in the evaluation of NQR parameters. All the calculations were performed by Gaussian 98 package of program.

  11. Subsurface hydrogen bonds at the polar Zn-terminated ZnO(0001) surface

    Science.gov (United States)

    Hellström, Matti; Beinik, Igor; Broqvist, Peter; Lauritsen, Jeppe V.; Hermansson, Kersti

    2016-12-01

    The role of hydrogen and other defects in the stabilization of polar oxide interfaces is a matter of significant fundamental and practical interest. Using experimental (scanning tunneling microscopy, x-ray photoelectron spectroscopy) and theoretical (density functional theory) surface science techniques, we find that the polar Zn-terminated ZnO(0001) surface becomes excessively Zn deficient during high-temperature annealing (780 K) in ultrahigh vacuum (UHV). The Zn vacancies align themselves into rows parallel to the [10 1 ¯0 ] direction, and the remaining surface Zn ions alternately occupy wurtzite (hcp) and zinc-blende (fcc) lattice positions, giving a characteristic "striped" c (√{12 }×√{12 })R 30 ° surface morphology with three types of rows: wurtzite Zn, zinc-blende Zn, and Zn vacancies. Interstitial H plays a central role in such a reconstruction, as it helps to compensate the excessive Zn deficiency. We propose a model in which hydrogen occupies positions in half of the vacancy rows to form hydroxide ions that can participate in hydrogen bonds in the O subsurface layer as a result of the mixed wurtzite/zinc-blende stacking.

  12. Hydrogen bonded rings, chains and lassos: the case of t-butyl alcohol clusters

    Science.gov (United States)

    Zimmermann, D.; Häber, Th.; Schaal, H.; Suhm, M. A.

    Infrared OH stretching spectra of hydrogen bonded 2-methyl-propan-2-ol (t-butyl alcohol) clusters are investigated by ragout-jet FTIR spectroscopy. A spectral difference technique is used to discriminate approximately between neighbouring cluster sizes. Dimers, trimers and cyclic tetramers can be detected along with larger clusters, which exhibit a surprisingly structured vibrational fingerprint. Comparison is made to the spectra of related alcohols and to energetic and harmonic vibrational predictions from electronic structure calculations. The experimentally observed 32% increase in OH stretching wavenumber shift from methanol dimer to t-butyl alcohol dimer is reproduced at the HF/3-21G level (+ 33%). It is also qualitatively correct at the MP2/6-31+ G* level (+ 15%), whereas it has the wrong sign at the B3LYP/6-31+ G* level (-5%) and is negligible at the HF/6-31+ G* level, disregarding anharmonic effects. The cyclic tetramer of t-butyl alcohol is found to be particularly stable due to a favourable up-down alternation of the bulky t-butyl groups. Beyond the t-butyl alcohol tetramer, lasso structures are found to be energetically competitive with simple ring structures. A many-body decomposition shows that this is due to a reduced cooperativity in the sterically hindered pentamer ring. The resulting thermodynamic and kinetic relevance of cyclic tetramers is discussed.

  13. Electronic structure contribution to hydrogen bonding interaction of a water dimer

    CERN Document Server

    Zhang, Zhiyuan; Wang, Bo; Wang, Zhigang

    2016-01-01

    Hydrogen bond (H-bond) covalency has recently been observed in ice and liquid water, while the penetrating molecular orbitals (MOs) in the H-bond region of most typical water dimer system, (H2O)2, have also been discovered. However, obtaining the quantitative contribution of these MOs to the H-bond interaction is still problematic. In this work, we introduced the orbital-resolved electron density projected integral (EDPI) along the H-bond to approach this problem. The calculations show that, surprisingly, the electronic occupied orbital (HOMO-4) of (H2O)2 accounts for about 40% of the electron density at the bond critical point. Moreover, the charge transfer analysis visualizes the electron accumulating effect of the orbital interaction within the H-bond between water molecules, supporting its covalent-like character. Our work expands the classical understanding of H-bond with specific contributions from certain MOs, and will also advance further research into such covalency and offer quantitative electronic ...

  14. Conserved hydrogen bonds and water molecules in MDR HIV-1 protease substrate complexes

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhigang [Wayne State Univ., Detroit, MI (United States); Case Western Reserve Univ., Cleveland, OH (United States); Harbor Hospital Baltimore, MD (United States); Wang, Yong [Wayne State Univ., Detroit, MI (United States); Yedidi, Ravikiran S. [Wayne State Univ., Detroit, MI (United States); National Institutes of Health, Bethesda, MD (United States); Dewdney, Tamaria G. [Wayne State Univ., Detroit, MI (United States); Reiter, Samuel J. [Wayne State Univ., Detroit, MI (United States); Brunzelle, Joseph S. [Northwestern Univ. Feinberg School of Medicine, Chicago, IL (United States); Kovari, Iulia A. [Wayne State Univ., Detroit, MI (United States); Kovari, Ladislau C. [Wayne State Univ., Detroit, MI (United States)

    2012-12-19

    Success of highly active antiretroviral therapy (HAART) in anti-HIV therapy is severely compromised by the rapidly developing drug resistance. HIV-1 protease inhibitors, part of HAART, are losing their potency and efficacy in inhibiting the target. Multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, 90) was selected for the present study to understand the binding to its natural substrates. The nine crystal structures of MDR769 HIV-1 protease substrate hepta-peptide complexes were analyzed in order to reveal the conserved structural elements for the purpose of drug design against MDR HIV-1 protease. Our structural studies demonstrated that highly conserved hydrogen bonds between the protease and substrate peptides, together with the conserved crystallographic water molecules, played a crucial role in the substrate recognition, substrate stabilization and protease stabilization. Additionally, the absence of the key flap-ligand bridging water molecule might imply a different catalytic mechanism of MDR769 HIV-1 protease compared to that of wild type (WT) HIV-1 protease.

  15. Thymine- and Adenine-Functionalized Polystyrene Form Self-Assembled Structures through Multiple Complementary Hydrogen Bonds

    Directory of Open Access Journals (Sweden)

    Yu-Shian Wu

    2014-06-01

    Full Text Available In this study, we investigated the self-assembly of two homopolymers of the same molecular weight, but containing complementary nucleobases. After employing nitroxide-mediated radical polymerization to synthesize poly(vinylbenzyl chloride, we converted the polymer into poly(vinylbenzyl azide through a reaction with NaN3 and then performed click chemistry with propargyl thymine and propargyl adenine to yield the homopolymers, poly(vinylbenzyl triazolylmethyl methylthymine (PVBT and poly(vinylbenzyl triazolylmethyl methyladenine (PVBA, respectively. This PVBT/PVBA blend system exhibited a single glass transition temperature over the entire range of compositions, indicative of a miscible phase arising from the formation of multiple strong complementary hydrogen bonds between the thymine and adenine groups of PVBT and PVBA, respectively; Fourier transform infrared and 1H nuclear magnetic resonance spectroscopy confirmed the presence of these noncovalent interactions. In addition, dynamic rheology, dynamic light scattering and transmission electron microscopy provided evidence for the formation of supramolecular network structures in these binary PVBT/PVBA blend systems.

  16. Pickering Emulsion Gels Prepared by Hydrogen-Bonded Zein/Tannic Acid Complex Colloidal Particles.

    Science.gov (United States)

    Zou, Yuan; Guo, Jian; Yin, Shou-Wei; Wang, Jin-Mei; Yang, Xiao-Quan

    2015-08-26

    Food-grade colloidal particles and complexes, which are formed via modulation of the noncovalent interactions between macromolecules and natural small molecules, can be developed as novel functional ingredients in a safe and sustainable way. For this study was prepared a novel zein/tannic acid (TA) complex colloidal particle (ZTP) based on the hydrogen-bonding interaction between zein and TA in aqueous ethanol solution by using a simple antisolvent approach. Pickering emulsion gels with high oil volume fraction (φ(oil) > 50%) were successfully fabricated via one-step homogenization. Circular dichroism (CD) and small-angle X-ray scattering (SAXS) measurements, which were used to characterize the structure of zein/TA complexes in ethanol solution, clearly showed that TA binding generated a conformational change of zein without altering their supramolecular structure at pH 5.0 and intermediate TA concentrations. Consequently, the resultant ZTP had tuned near neutral wettability (θ(ow) ∼ 86°) and enhanced interfacial reactivity, but without significantly decreased surface charge. These allowed the ZTP to stabilize the oil droplets and further triggered cross-linking to form a continuous network among and around the oil droplets and protein particles, leading to the formation of stable Pickering emulsion gels. Layer-by-layer (LbL) interfacial architecture on the oil-water surface of the droplets was observed, which implied a possibility to fabricate hierarchical interface microstructure via modulation of the noncovalent interaction between hydrophobic protein and natural polyphenol.

  17. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    Science.gov (United States)

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  18. Proton transfer in hydrogen-bonded network of phenol molecules: intracluster formation of water.

    Science.gov (United States)

    Lengyel, Jozef; Gorejová, Radka; Herman, Zdeněk; Fárník, Michal

    2013-11-07

    Electron ionization and time-of-flight mass spectrometry was used to investigate the phenol clusters (PhOH)n of different size from single molecule to large clusters: in coexpansion with He, the dimers n = 2 are mostly generated; in Ar, large species of n ≥ 10 also occur. Besides [(PhOH)n](+•) cluster ion series, hydrated phenol cluster ions [(PhOH)n·xH2O](+•) with up to x = 3 water molecules and dehydrated phenol clusters [(PhOH)n-H2O](+•) were observed. The hydrated phenol series exhibits minima and maxima that are interpreted as evidence for proton transfer between the hydrogen bonded cluster ions of cyclic structures. The proton transfer leads to a water generation within the clusters, and subsequent elimination of the diphenyl ether molecule(s) from the cluster yields the hydrated phenol cluster ions. Alternatively, a water molecule release yields a series of dehydrated phenols, among which the diphenyl ether ion [PhOPh](+•) (n = 2) constitutes the maximum.

  19. Can hydrogen bonds improve the hole-mobility in amorphous organic semiconductors? Experimental and theoretical insights

    KAUST Repository

    Mimaite, Viktorija

    2015-01-01

    © The Royal Society of Chemistry 2015. Five hole-transporting triphenylamine derivatives containing methoxy and methyl groups are synthesized and investigated. The hole-mobility increases in the presence of methyl and methoxy substituents, exceeding 10-2 cm2 V-1 s-1 in the case of methyl groups. Quantum mechanical calculations on these compounds indicate very different dipole moments and intermolecular interaction strengths, with intriguing correlations with the trend in hole-mobility. Temperature dependent hole-mobility measurements indicate disorder dominated hole transport. The values of the energetic disorder parameter (σ) decrease upon methyl and methoxy substitutions despite the increase in dipole moments. This trend is discussed as a function of the interaction energy between adjacent molecules, the dipole moment, the molecular polarizability, and the conformational degree of freedom. Our results indicate that the global decrease of σ upon methyl and methoxy substitutions is dominated by the larger decrease in the geometrical randomness component of the energetic disorder. A direct correlation is established between the decrease in geometrical randomness and the increase in intermolecular interaction energies, mainly stemming from the additional C-H⋯π, O, N hydrogen bonds induced by methyl and methoxy groups.

  20. A spectrochemometric approach to tautomerism and hydrogen-bonding in 3-acyltetronic acids

    Science.gov (United States)

    Hofmann, Jan Philipp; Duus, Fritz; Bond, Andrew D.; Hansen, Poul Erik

    2006-06-01

    3-Acyltetronic acids bearing different 3- and 5-substituents have been examined focussing on tautomerism and inter- and intramolecular hydrogen-bonding properties of these β,β'-tricarbonyl compounds in solution as well as in the solid state. Spectroscopic methods like NMR, IR, Raman-spectroscopy as well as X-ray diffractometry and MAS-NMR for the solid state have been applied. In a solution of CDCl 3, the acids exist as cis/trans pair both involving the 3-acyl group in a ratio 60/40. The pair also involving the carbonyl group at C-4 is tautomeric and the most abundant, whereas the other isomer only shows one form with an exo-cyclic double bond. NMR and IR measurements are in agreement. In the solid state, only one of the four possible tautomers is found. DFT-calculations on the B3LYP/6-31G** level helped to verify the assignment of the IR- and NMR-spectra and yielded an estimation of the relative thermodynamic stabilities of the tautomers of several 3-acyltetronic acids. Low temperature NMR experiments gave an insight into the equilibria. Deuterium isotope effects on the 13C NMR chemical shifts have been observed for 5,5-dimethyl 3-pivaloyltetronic acid at low temperature in order to examine the fast internal equilibria.