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Sample records for pseudolayers providing hydrogen-bonding

  1. Polarization charge densities provide a predictive quantification of hydrogen bond energies.

    Science.gov (United States)

    Klamt, Andreas; Reinisch, Jens; Eckert, Frank; Hellweg, Arnim; Diedenhofen, Michael

    2012-01-14

    A systematic density functional theory based study of hydrogen bond energies of 2465 single hydrogen bonds has been performed. In order to be closer to liquid phase conditions, different from the usual reference state of individual donor and acceptor molecules in vacuum, the reference state of donors and acceptors embedded in a perfect conductor as simulated by the COSMO solvation model has been used for the calculation of the hydrogen bond energies. The relationship between vacuum and conductor reference hydrogen bond energies is investigated and interpreted in the light of different physical contributions, such as electrostatic energy and dispersion. A very good correlation of the DFT/COSMO hydrogen bond energies with conductor polarization charge densities of separated donor and acceptor atoms was found. This provides a method to predict hydrogen bond strength in solution with a root mean square error of 0.36 kcal mol(-1) relative to the quantum chemical dimer calculations. The observed correlation is broadly applicable and allows for a predictive quantification of hydrogen bonding, which can be of great value in many areas of computational, medicinal and physical chemistry.

  2. Why are Hydrogen Bonds Directional?

    Indian Academy of Sciences (India)

    for an interaction to be characterized as a hydro- gen bond 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 topol- ogy for common hydrogen bond donors HF, HCl, ...

  3. Water's Hydrogen Bond Strength

    CERN Document Server

    Chaplin, Martin

    2007-01-01

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

  4. Hydrogen bonded supramolecular materials

    CERN Document Server

    Li, Zhan-Ting

    2015-01-01

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

  5. Hydrogen Bonding in the Active Site of Ketosteroid Isomerase: Electronic Inductive Effects and Hydrogen Bond Coupling

    Science.gov (United States)

    Hanoian, Philip; Sigala, Paul A.; Herschlag, Daniel; Hammes-Schiffer, Sharon

    2010-01-01

    Computational studies are performed to analyze the physical properties of hydrogen bonds donated by Tyr16 and Asp103 to a series of substituted phenolate inhibitors bound in the active site of ketosteroid isomerase (KSI). As the solution pKa of the phenolate increases, these hydrogen bond distances decrease, the associated NMR chemical shifts increase, and the fraction of protonated inhibitor increases, in agreement with prior experiments. The quantum mechanical/molecular mechanical calculations provide insight into the electronic inductive effects along the hydrogen-bonding network that includes Tyr16, Tyr57, and Tyr32, as well as insight into hydrogen bond coupling in the active site. The calculations predict that the most-downfield NMR chemical shift observed experimentally corresponds to the Tyr16-phenolate hydrogen bond and that Tyr16 is the proton donor when a bound naphtholate inhibitor is observed to be protonated in electronic absorption experiments. According to these calculations, the electronic inductive effects along the hydrogen-bonding network of tyrosines cause the Tyr16 hydroxyl to be more acidic than the Asp103 carboxylic acid moiety, which is immersed in a relatively nonpolar environment. When one of the distal tyrosine residues in the network is mutated to phenylalanine, thereby diminishing this inductive effect, the Tyr16-phenolate hydrogen bond lengthens, and the Asp103-phenolate hydrogen bond shortens, as observed in NMR experiments. Furthermore, the calculations suggest that the differences in the experimental NMR data and electronic absorption spectra for pKSI and tKSI, two homologous bacterial forms of the enzyme, are due predominantly to the third tyrosine that is present in the hydrogen-bonding network of pKSI but not tKSI. These studies also provide experimentally testable predictions about the impact of mutating the distal tyrosine residues in this hydrogen-bonding network on the NMR chemical shifts and electronic absorption spectra

  6. Hydrogen Bonds and Life in the Universe.

    Science.gov (United States)

    Vladilo, Giovanni; Hassanali, Ali

    2018-01-03

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

  7. Hydrogen Bond Basicity Prediction for Medicinal Chemistry Design.

    Science.gov (United States)

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

    2016-05-12

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

  8. Distance criterion for hydrogen bond

    Indian Academy of Sciences (India)

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

  9. Analysis of Hydrogen Bonds in Crystals

    Directory of Open Access Journals (Sweden)

    Sławomir J. Grabowski

    2016-05-01

    Full Text Available The determination of crystal structures provides important information on the geometry of species constituting crystals and on the symmetry relations between them. Additionally, the analysis of crystal structures is so conclusive that it allows us to understand the nature of various interactions. The hydrogen bond interaction plays a crucial role in crystal engineering and, in general, its important role in numerous chemical, physical and bio-chemical processes was the subject of various studies. That is why numerous important findings on the nature of hydrogen bonds concern crystal structures. This special issue presents studies on hydrogen bonds in crystals, and specific compounds and specific H-bonded patterns existing in crystals are analyzed. However, the characteristics of the H-bond interactions are not only analyzed theoretically; this interaction is compared with other ones that steer the arrangement of molecules in crystals, for example halogen, tetrel or pnicogen bonds. More general findings concerning the influence of the hydrogen bond on the physicochemical properties of matter are also presented.

  10. 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...

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

    OpenAIRE

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

    2006-01-01

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

  12. dimensional architectures via hydrogen bonds

    Indian Academy of Sciences (India)

    Administrator

    dimensional architectures via hydrogen bonds. LALIT RAJPUT, MADHUSHREE SARKAR and KUMAR BIRADHA*. Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302 e-mail: kbiradha@chem.iitkgp.ernet.in. Abstract. The reactions of bis(pyridylcarboxamido)alkanes (amides) and bis(3-pyridyl) ...

  13. Noncovalent synthesis using hydrogen bonding

    NARCIS (Netherlands)

    Prins, L.J.; Reinhoudt, David; Timmerman, P.

    2001-01-01

    Hydrogen bonds are like human beings in the sense that they exhibit typical grouplike behavior. As an individual they are feeble, easy to break, and sometimes hard to detect. However, when acting together they become much stronger and lean on each other. This phenomenon, which in scientific terms is

  14. 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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    OpenAIRE

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

    1996-01-01

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

  16. Hydrogen bonding in ionic liquids.

    Science.gov (United States)

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

    2015-03-07

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

  17. 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......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...... 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....

  18. Extremely strong contiguous hydrogen bonding arrays

    OpenAIRE

    Thomson, Patrick

    2013-01-01

    When multiple hydrogen bonds lie in-plane and parallel to each other in close proximity, they experience additional positive or negative secondary electrostatic interactions. When a pair of molecules are arranged such that every hydrogen bond acceptor is on one molecule and every hydrogen bond donor is on another, the positive secondary electrostatic interactions are maximised, and thus the association constant of the complex is enhanced. This thesis will present the develop...

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

    DEFF Research Database (Denmark)

    Mackeprang, Kasper; Hänninen, Vesa; Halonen, Lauri

    2015-01-01

    We have developed a model to calculate accurately the intensity of the hydrogen bonded XH-stretching vibrational transition in hydrogen bonded complexes. In the Local Mode Perturbation Theory (LMPT) model, the unperturbed system is described by a local mode (LM) model, which is perturbed...... by the intermolecular modes of the hydrogen bonded system that couple with the intramolecular vibrations of the donor unit through the potential energy surface. We have applied the model to three complexes containing water as the donor unit and different acceptor units, providing a series of increasing complex binding...... of the fundamental hydrogen bonded OH-stretching transition relative to the simpler LM model....

  20. HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis.

    Science.gov (United States)

    Durrant, Jacob D; McCammon, J Andrew

    2011-11-01

    In the current work, we present a hydrogen-bond analysis of 2673 ligand-receptor complexes that suggests the total number of hydrogen bonds formed between a ligand and its receptor is a poor predictor of ligand potency; furthermore, even that poor prediction does not suggest a statistically significant correlation between hydrogen-bond formation and potency. While we are not the first to suggest that hydrogen bonds on average do not generally contribute to ligand binding affinities, this additional evidence is nevertheless interesting. The primary role of hydrogen bonds may instead be to ensure specificity, to correctly position the ligand within the active site, and to hold the protein active site in a ligand-friendly conformation. We also present a new computer program called HBonanza (hydrogen-bond analyzer) that aids the analysis and visualization of hydrogen-bond networks. HBonanza, which can be used to analyze single structures or the many structures of a molecular dynamics trajectory, is open source and python implemented, making it easily editable, customizable, and platform independent. Unlike many other freely available hydrogen-bond analysis tools, HBonanza provides not only a text-based table describing the hydrogen-bond network, but also a Tcl script to facilitate visualization in VMD, a popular molecular visualization program. Visualization in other programs is also possible. A copy of HBonanza can be obtained free of charge from http://www.nbcr.net/hbonanza. Copyright © 2011 Elsevier Inc. All rights reserved.

  1. Hydrogen bond dynamics in bulk alcohols.

    Science.gov (United States)

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

    2015-06-07

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

  2. Revisiting Hydrogen Bond Thermodynamics in Molecular Simulations.

    Science.gov (United States)

    Sapir, Liel; Harries, Daniel

    2017-06-13

    In processes involving aqueous solutions and in almost every biomolecular interaction, hydrogen bonds play important roles. Though weak compared to the covalent bond, hydrogen bonds modify the stability and conformation of numerous small and large molecules and modulate their intermolecular interactions. We propose a simple methodology for extracting hydrogen bond strength from atomistic level simulations. The free energy associated with hydrogen bond formation is conveniently calculated as the reversible work required to reshape a completely random pair probability distribution reference state into the one found in simulations where hydrogen bonds are formed. Requiring only the probability density distribution of donor-acceptor pairs in the first solvation shell of an electronegative atom, the method uniquely defines the free energy, entropy, and enthalpy of the hydrogen bond. The method can be easily extended to molecules other than water and to multiple component mixtures. We demonstrate and apply this methodology to hydrogen bonds that form in molecular dynamics simulations between water molecules in pure water, as well as to bonds formed between different molecules in a binary mixture of a sugar (trehalose) and water. Finally, we comment on how the method should be useful in assessing the role of hydrogen bonds in different molecular mechanisms.

  3. HYDROGEN BONDING IN THE METHANOL DIMER

    Science.gov (United States)

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

  4. 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.

  5. Hydrogen bond dynamics in bulk alcohols

    Science.gov (United States)

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

    2015-06-01

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

  6. Hydrogen Bonding to Alkanes: Computational Evidence

    DEFF Research Database (Denmark)

    Hammerum, Steen; Olesen, Solveig Gaarn

    2009-01-01

    The structural, vibrational, and energetic properties of adducts of alkanes and strong cationic proton donors were studied with composite ab initio calculations. Hydrogen bonding in [D-H+ H-alkyl] adducts contributes to a significant degree to the interactions between the two components, which...... is substantiated by NBO and AIM results. The hydrogen bonds manifest themselves in the same manner as conventional hydrogen bonds, D-H bond elongation, D-H vibrational stretching frequency red shift and intensity increase, and adduct stabilization. The alkane adducts also exhibit elongation of the C-H bonds...... involved and a concurrent red shift, which is rationalized in terms of charge-transfer interactions that cause simultaneous weakening of both the O-H and C-H bonds. Like other dihydrogen-bonded adducts, the adducts possess a bent structure and asymmetric bifurcated hydrogen bonds. The hydrogen bonds...

  7. 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.

  8. Hydrogen bonding penalty upon ligand binding.

    Directory of Open Access Journals (Sweden)

    Hongtao Zhao

    Full Text Available Ligand binding involves breakage of hydrogen bonds with water molecules and formation of new hydrogen bonds between protein and ligand. In this work, the change of hydrogen bonding energy in the binding process, namely hydrogen bonding penalty, is evaluated with a new method. The hydrogen bonding penalty can not only be used to filter unrealistic poses in docking, but also improve the accuracy of binding energy calculation. A new model integrated with hydrogen bonding penalty for free energy calculation gives a root mean square error of 0.7 kcal/mol on 74 inhibitors in the training set and of 1.1 kcal/mol on 64 inhibitors in the test set. Moreover, an application of hydrogen bonding penalty into a high throughput docking campaign for EphB4 inhibitors is presented, and remarkably, three novel scaffolds are discovered out of seven tested. The binding affinity and ligand efficiency of the most potent compound is about 300 nM and 0.35 kcal/mol per non-hydrogen atom, respectively.

  9. The hydrogen bond in the solid state.

    Science.gov (United States)

    Steiner, Thomas

    2002-01-04

    The hydrogen bond is the most important of all directional intermolecular interactions. It is operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological. Research into hydrogen bonds experienced a stagnant period in the 1980s, but re-opened around 1990, and has been in rapid development since then. In terms of modern concepts, the hydrogen bond is understood as a very broad phenomenon, and it is accepted that there are open borders to other effects. There are dozens of different types of X-H.A hydrogen bonds that occur commonly in the condensed phases, and in addition there are innumerable less common ones. Dissociation energies span more than two orders of magnitude (about 0.2-40 kcal mol(-1)). Within this range, the nature of the interaction is not constant, but its electrostatic, covalent, and dispersion contributions vary in their relative weights. The hydrogen bond has broad transition regions that merge continuously with the covalent bond, the van der Waals interaction, the ionic interaction, and also the cation-pi interaction. All hydrogen bonds can be considered as incipient proton transfer reactions, and for strong hydrogen bonds, this reaction can be in a very advanced state. In this review, a coherent survey is given on all these matters.

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

    Science.gov (United States)

    Penner, Robert C.; Andersen, Ebbe S.; Jensen, Jens L.; Kantcheva, Adriana K.; Bublitz, Maike; Nissen, Poul; Rasmussen, Anton M. H.; Svane, Katrine L.; Hammer, Bjørk; Rezazadegan, Reza; Nielsen, Niels Chr.; Nielsen, Jakob T.; Andersen, Jørgen E.

    2014-12-01

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

  11. Gold setting the "gold standard" among transition metals as a hydrogen bond acceptor - a theoretical investigation.

    Science.gov (United States)

    Groenewald, Ferdinand; Raubenheimer, Helgard G; Dillen, Jan; Esterhuysen, Catharine

    2017-04-11

    The Au(i) atom of dimethylaurate (DMA) is shown to behave as a hydrogen-bond acceptor, providing theoretical evidence that it can act as a Lewis base. Calculations at the MP2/aug-cc-pVTZ-pp level of theory confirm that DMA forms hydrogen bonds decreasing in strength from -16.2 kcal mol-1 to -2.4 kcal mol-1 in the order HCN ≈ HF > H2O > HCCH > NH3 > CH4, i.e. following the trend of decreasing proton acidity of the hydrogen-bond donor. The geometrical and Atoms in Molecules (AIM) parameters of the hydrogen-bonded adducts compare well to those obtained with the auride anion, a known hydrogen-bond acceptor. Relativistic effects are shown to play a dominant role in the formation of the hydrogen bonds with DMA: omission of these effects (confirmed using two different approaches) results in the loss of the hydrogen bond. Instead, the hydrogen-bond donor interacts with the carbon atom on one of the methyl ligands, yielding an adduct that is closely comparable to those found with the Cu and Ag analogues of DMA.

  12. 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

  13. An alternative near-neighbor definition of hydrogen bonding in water.

    Science.gov (United States)

    Hammerich, A D; Buch, V

    2008-03-21

    A definition of hydrogen bonding in water is proposed in which an H...O pair forms a hydrogen bond if (a) an oxygen atom is the nearest nonchemically bonded neighbor of a hydrogen atom; and (b) the hydrogen is the first or the second intermolecular near-neighbor of the oxygen. Unlike the commonly employed hydrogen-bond definitions, this definition does not depend on the choice of geometric or energetic cutoffs applied to continuous distributions of properties. With the present definition, the distribution of O...H bond lengths decays smoothly to zero in a physically reasonable range. After correction for the presence of intermittent hydrogen bonds, this definition appears to provide a more stable description of hydrogen bonds and coordination shells than the more conventional cutoff-based definition. "Partial" H bonds satisfying only one of the two bonding requirements serve as transition states in the H-bond network evolution.

  14. Overtone Spectroscopy of Peroxyacetic Acid and Peroxyformic Acid : Influence of Intramolecular Hydrogen Bonding

    Science.gov (United States)

    Hazra, Montu K.; Kuang, Michelle; Sinha, Amitabha

    2010-06-01

    The absorption of solar radiation by hydrogen-bonded (H-bonded) complex, particularly those containing water, is important in atmospheric chemistry. However, because of their low concentration, intermolecular hydrogen bonded complexes of atmospheric interest are difficult to study in the gas phase. Consequently, our initial efforts have been directed towards investigating the spectroscopy of molecules with internal hydrogen bonds. In this talk, we present the vapor phase vibrational overtone spectra of peroxyacetic acid (PAA) and peroxyformic acid (PFA), two molecules of atmospheric importance, and discuss the effect of intramolecular hydrogen-bonding on their OH stretching overtone transition strength and band positions. A comparison of the results of PAA and PFA with those of other intramolecular H-bonded and non-H-bonded molecules provides a useful gauge of the extent of hydrogen bonding in these peroxyacids.

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

    Science.gov (United States)

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

    2015-07-15

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

  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 BOND DYNAMICS IN MEMBRANE PROTEIN FUNCTION

    OpenAIRE

    Bondar, Ana-Nicoleta; White, Stephen H.

    2011-01-01

    Changes in inter-helical hydrogen bonding are associated with the conformational dynamics of membrane proteins. The function of the protein depends on the surrounding lipid membrane. Here we review through specific examples how dynamical hydrogen bonds can ensure an elegant and efficient mechanism of long-distance intra-protein and protein-lipid coupling, contributing to the stability of discrete protein conformational substates and to rapid propagation of structural perturbations.

  18. An energetic scale for equilibrium H/D fractionation factors illuminates hydrogen bond free energies in proteins.

    Science.gov (United States)

    Cao, Zheng; Bowie, James U

    2014-05-01

    Equilibrium H/D fractionation factors have been extensively employed to qualitatively assess hydrogen bond strengths in protein structure, enzyme active sites, and DNA. It remains unclear how fractionation factors correlate with hydrogen bond free energies, however. Here we develop an empirical relationship between fractionation factors and free energy, allowing for the simple and quantitative measurement of hydrogen bond free energies. Applying our empirical relationship to prior fractionation factor studies in proteins, we find: [1] Within the folded state, backbone hydrogen bonds are only marginally stronger on average in α-helices compared to β-sheets by ∼0.2 kcal/mol. [2] Charge-stabilized hydrogen bonds are stronger than neutral hydrogen bonds by ∼2 kcal/mol on average, and can be as strong as -7 kcal/mol. [3] Changes in a few hydrogen bonds during an enzyme catalytic cycle can stabilize an intermediate state by -4.2 kcal/mol. [4] Backbone hydrogen bonds can make a large overall contribution to the energetics of conformational changes, possibly playing an important role in directing conformational changes. [5] Backbone hydrogen bonding becomes more uniform overall upon ligand binding, which may facilitate participation of the entire protein structure in events at the active site. Our energetic scale provides a simple method for further exploration of hydrogen bond free energies. © 2014 The Protein Society.

  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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. 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

    2016-09-23

    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.

  1. Subangstrom crystallography reveals that short ionic hydrogen bonds, and not a His-Asp low-barrier hydrogen bond, stabilize the transition state in serine protease catalysis.

    Science.gov (United States)

    Fuhrmann, Cynthia N; Daugherty, Matthew D; Agard, David A

    2006-07-19

    To address questions regarding the mechanism of serine protease catalysis, we have solved two X-ray crystal structures of alpha-lytic protease (alphaLP) that mimic aspects of the transition states: alphaLP at pH 5 (0.82 A resolution) and alphaLP bound to the peptidyl boronic acid inhibitor, MeOSuc-Ala-Ala-Pro-boroVal (0.90 A resolution). Based on these structures, there is no evidence of, or requirement for, histidine-flipping during the acylation step of the reaction. Rather, our data suggests that upon protonation of His57, Ser195 undergoes a conformational change that destabilizes the His57-Ser195 hydrogen bond, preventing the back-reaction. In both structures the His57-Asp102 hydrogen bond in the catalytic triad is a normal ionic hydrogen bond, and not a low-barrier hydrogen bond (LBHB) as previously hypothesized. We propose that the enzyme has evolved a network of relatively short hydrogen bonds that collectively stabilize the transition states. In particular, a short ionic hydrogen bond (SIHB) between His57 Nepsilon2 and the substrate's leaving group may promote forward progression of the TI1-to-acylenzyme reaction. We provide experimental evidence that refutes use of either a short donor-acceptor distance or a downfield 1H chemical shift as sole indicators of a LBHB.

  2. 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.

  3. Optimising hydrogen bonding in solid wood

    DEFF Research Database (Denmark)

    Engelund, Emil Tang

    2009-01-01

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

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

    Science.gov (United States)

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

    2015-05-06

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

  5. 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.

  6. Structural, intramolecular hydrogen bonding and vibrational studies ...

    Indian Academy of Sciences (India)

    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 ...

  7. Intramolecular hydrogen bonding in myricetin and myricitrin

    DEFF Research Database (Denmark)

    Vojta, Danijela; Dominkovic, Katarina; Miljanic, Snezana

    2017-01-01

    -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...

  8. Structural, intramolecular hydrogen bonding and vibrational studies ...

    Indian Academy of Sciences (India)

    Matta C F, Hernandez-Trujillo J, Tang T-H and Bader. R F W 2003 Hydrogen- Hydrogen Bonding: A Stabiliz- ing Interaction in Molecules and Crystals Chem. Eur. J. 9 1940. 37. Johnson E R, Keinan S, Mori-Sánchez P, Contreras-. García J, Cohen A J and Yang W 2010 Revealing noncovalent interactions J. Am. Chem. Soc.

  9. Water hydrogen bond dynamics in aqueous solutions of amphiphiles.

    Science.gov (United States)

    Stirnemann, Guillaume; Hynes, James T; Laage, Damien

    2010-03-04

    The hydrogen bond dynamics of water in a series of amphiphilic solute solutions are investigated through simulations and analytic modeling with an emphasis on the interpretation of experimentally accessible two-dimensional infrared (2D IR) photon echo spectra. We evidence that for most solutes the major effect in the hydration dynamics comes from the hydrophilic groups. These groups can retard the water dynamics much more significantly than can hydrophobic groups by forming strong hydrogen bonds with water. By contrast, hydrophobic groups are shown to have a very moderate effect on water hydrogen bond breaking kinetics. We also present the first calculation of the 2D IR spectra for these solutions. While 2D IR spectroscopy is a powerful technique to probe water hydrogen bond network fluctuations, interpretations of aqueous solution spectra remain ambiguous. We show that a complementary approach through simulations and calculation of the spectra lifts the ambiguity and provides a clear connection between the simulated molecular picture and the experimental spectroscopy data. For amphiphilic solute solutions, we show that, in contrast with techniques such as NMR or ultrafast anisotropy, 2D IR spectroscopy can discriminate between waters next to the solutes hydrophobic and hydrophilic groups. We also evidence that the water dynamics slowdown due to the hydrophilic groups is dramatically enhanced in the 2D IR spectral relaxation, because these groups can induce a slow chemical exchange with the bulk, even when recognized exchange signatures are absent. Implications for the understanding of water around chemically heterogeneous systems such as protein surfaces and for the interpretation of 2D IR spectra in these cases are discussed.

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

    Science.gov (United States)

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

    2016-04-07

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

  11. Gold nanoparticle assemblies through Hydrogen-bonded supramolecular mediators

    NARCIS (Netherlands)

    Kinge, S.S.; Crego Calama, Mercedes; Reinhoudt, David

    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

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

    National Research Council Canada - National Science Library

    Nicholson, Jesse

    2001-01-01

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

  13. Cosolvent Effects on Solute-Solvent Hydrogen-Bond Dynamics: Ultrafast 2D IR Investigations.

    Science.gov (United States)

    Kashid, Somnath M; Jin, Geun Young; Bagchi, Sayan; Kim, Yung Sam

    2015-12-10

    Cosolvents strongly influence the solute-solvent interactions of biomolecules in aqueous environments and have profound effects on the stability and activity of several proteins and enzymes. Experimental studies have previously reported on the hydrogen-bond dynamics of water molecules in the presence of a cosolvent, but understanding the effects from a solute's perspective could provide greater insight into protein stability. Because carbonyl groups are abundant in biomolecules, the current study used 2D IR spectroscopy and molecular dynamics simulations to compare the hydrogen-bond dynamics of the solute's carbonyl group in aqueous solution, with and without the presence of DMSO as a cosolvent. 2D IR spectroscopy was used to quantitatively estimate the time scales of the hydrogen-bond dynamics of the carbonyl group in neat water and 1:1 DMSO/water solution. The 2D IR results show spectral signatures of a chemical exchange process: The presence of the cosolvent was found to lower the hydrogen-bond exchange rate by a factor of 5. The measured exchange rates were 7.50 × 10(11) and 1.48 × 10(11) s(-1) in neat water and 1:1 DMSO/water, respectively. Molecular dynamics simulations predict a significantly shorter carbonyl hydrogen-bond lifetime in neat water than in 1:1 DMSO/water and provide molecular insights into the exchange mechanism. The binding of the cosolvent to the solute was found to be accompanied by the release of hydrogen-bonded water molecules to the bulk. The widely different hydrogen-bond lifetimes and exchange rates with and without DMSO indicate a significant change in the ultrafast hydrogen-bond dynamics in the presence of a cosolvent, which, in turn, might play an important role in the stability and activity of biomolecules.

  14. Solution and solid-state models of peptide CH...O hydrogen bonds.

    Science.gov (United States)

    Baures, Paul W; Beatty, Alicia M; Dhanasekaran, Muthu; Helfrich, Brian A; Pérez-Segarra, Waleska; Desper, John

    2002-09-25

    Fumaramide derivatives were analyzed in solution by (1)H NMR spectroscopy and in the solid state by X-ray crystallography in order to characterize the formation of CH...O interactions under each condition and to thereby serve as models for these interactions in peptide and protein structure. Solutions of fumaramides at 10 mM in CDCl(3) were titrated with DMSO-d(6), resulting in chemical shifts that moved downfield for the CH groups thought to participate in CH...O=S(CD(3))(2) hydrogen bonds concurrent with NH...O=S(CD(3))(2) hydrogen bonding. In this model, nonparticipating CH groups under the same conditions showed no significant change in chemical shifts between 0.0 and 1.0 M DMSO-d(6) and then moved upfield at higher DMSO-d(6) concentrations. At concentrations above 1.0 M DMSO-d(6), the directed CH...O=S(CD(3))(2) hydrogen bonds provide protection from random DMSO-d(6) contact and prevent the chemical shifts for participating CH groups from moving upfield beyond the original value observed in CDCl(3). X-ray crystal structures identified CH...O=C hydrogen bonds alongside intermolecular NH...O=C hydrogen bonding, a result that supports the solution (1)H NMR spectroscopy results. The solution and solid-state data therefore both provide evidence for the presence of CH...O hydrogen bonds formed concurrent with NH...O hydrogen bonding in these structures. The CH...O=C hydrogen bonds in the X-ray crystal structures are similar to those described for antiparallel beta-sheet structure observed in protein X-ray crystal structures.

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

    Indian Academy of Sciences (India)

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

  16. Hydrogen bonding in oxalic acid and its complexes: A database ...

    Indian Academy of Sciences (India)

    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, ...

  17. Oxidative coupling of sp 2 and sp 3 carbon-hydrogen bonds to construct dihydrobenzofurans.

    Science.gov (United States)

    Shi, Jiang-Ling; Wang, Ding; Zhang, Xi-Sha; Li, Xiao-Lei; Chen, Yu-Qin; Li, Yu-Xue; Shi, Zhang-Jie

    2017-08-10

    Metal-catalyzed cross-couplings provide powerful, concise, and accurate methods to construct carbon-carbon bonds from organohalides and organometallic reagents. Recent developments extended cross-couplings to reactions where one of the two partners connects with an aryl or alkyl carbon-hydrogen bond. From an economic and environmental point of view, oxidative couplings between two carbon-hydrogen bonds would be ideal. Oxidative coupling between phenyl and "inert" alkyl carbon-hydrogen bonds still awaits realization. It is very difficult to develop successful strategies for oxidative coupling of two carbon-hydrogen bonds owning different chemical properties. This article provides a solution to this challenge in a convenient preparation of dihydrobenzofurans from substituted phenyl alkyl ethers. For the phenyl carbon-hydrogen bond activation, our choice falls on the carboxylic acid fragment to form the palladacycle as a key intermediate. Through careful manipulation of an additional ligand, the second "inert" alkyl carbon-hydrogen bond activation takes place to facilitate the formation of structurally diversified dihydrobenzofurans.Cross-dehydrogenative coupling is finding increasing application in synthesis, but coupling two chemically distinct sites remains a challenge. Here, the authors report an oxidative coupling between sp 2 and sp 3 carbons by sequentially activating the more active aryl site followed by the alkyl position.

  18. NMR Spectroscopic Characterization of Charge Assisted Strong Hydrogen Bonds in Brønsted Acid Catalysis

    Science.gov (United States)

    2016-01-01

    Hydrogen bonding plays a crucial role in Brønsted acid catalysis. However, the hydrogen bond properties responsible for the activation of the substrate are still under debate. Here, we report an in depth study of the properties and geometries of the hydrogen bonds in (R)-TRIP imine complexes (TRIP: 3,3′-Bis(2,4,6-triisopropylphenyl)-1,1′-binaphthyl-2,2′-diylhydrogen phosphate). From NMR spectroscopic investigations 1H and 15N chemical shifts, a Steiner–Limbach correlation, a deuterium isotope effect as well as quantitative values of 1JNH,2hJPH and 3hJPN were used to determine atomic distances (rOH, rNH, rNO) and geometry information. Calculations at SCS-MP2/CBS//TPSS-D3/def2-SVP-level of theory provided potential surfaces, atomic distances and angles. In addition, scalar coupling constants were computed at TPSS-D3/IGLO-III. The combined experimental and theoretical data reveal mainly ion pair complexes providing strong hydrogen bonds with an asymmetric single well potential. The geometries of the hydrogen bonds are not affected by varying the steric or electronic properties of the aromatic imines. Hence, the strong hydrogen bond reduces the degree of freedom of the substrate and acts as a structural anchor in the (R)-TRIP imine complex. PMID:27936674

  19. 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'.

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

    NARCIS (Netherlands)

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

    2014-01-01

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

  1. Femtosecond dynamics in hydrogen-bonded solvents

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-09-01

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

  2. Intramolecular Energy Transfer, Charge Transfer & Hydrogen Bond

    Indian Academy of Sciences (India)

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

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

    Science.gov (United States)

    Nishio, M.

    2012-06-01

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

  4. Strengthening of hydrogen bonding with the push-pull effect

    Science.gov (United States)

    Tao, Yunwen; Zou, Wenli; Kraka, Elfi

    2017-10-01

    Theoretical studies of hydrogen-bonding based on cluster models tend to overlook the peripheral monomers which are influential. By revisiting thirteen hydrogen-bonded complexes of H2O, HF and NH3, the "push-pull" effect is identified as a general mechanism that strengthens a hydrogen bond. Enhanced Lp (X) →σ∗ (X‧ - H) charge transfer is proved to be the core of the "push-pull" effect. The charge transfer can convert an electrostatic hydrogen bond into a covalent hydrogen bond.

  5. Effect of Water Hydrogen Bonding on the Solvent-Mediated "Oscillatory" Repulsion of C60 Fullerenes in Water.

    Science.gov (United States)

    Djikaev, Yuri S; Ruckenstein, Eli

    2015-05-07

    The solvent-mediated interaction of C60 fullerenes in liquid water is examined by using the combination of the probabilistic hydrogen bond model with the density functional theory. This combination allows one to take into account the effect of hydrogen bonding between water molecules on their interaction with fullerenes and to construct an approximation for the distribution of water molecules in the system, which provides an efficient foundation for studying hydrophobic phenomena. Our numerical evaluations predict the solvent-induced interaction of two C60 fullerenes in water at 293 K to have an oscillatory-repulsive character (previously observed in molecular dynamics simulations) only when the vicinal water-water hydrogen bonds are slightly weaker than bulk ones. Besides indicating the direction of the energetic alteration of water-water hydrogen bonds near C60 fullerenes, our model also suggests that the hydrogen bonding ability of water plays a defining role in the solvent-mediated C60-C60 repulsion.

  6. 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

    2009-10-07

    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.

  7. Case study of hydrogen bonding in a hydrophobic cavity.

    Science.gov (United States)

    Chen, Yi-Chen; Cheng, Chao-Sheng; Tjong, Siu-Cin; Yin, Hsien-Sheng; Sue, Shih-Che

    2014-12-18

    Protein internal hydrogen bonds and hydrophobicity determine protein folding and structure stabilization, and the introduction of a hydrogen bond has been believed to represent a better interaction for consolidating protein structure. We observed an alternative example for chicken IL-1β. The native IL-1β contains a hydrogen bond between the Y157 side-chain OηH and I133 backbone CO, whereby the substitution from Tyr to Phe abolishes the connection and the mutant without the hydrogen bond is more stable. An attempt to explain the energetic view of the presence of the hydrogen bond fails when only considering the nearly identical X-ray structures. Here, we resolve the mechanism by monitoring the protein backbone dynamics and interior hydrogen bond network. IL-1β contains a hydrophobic cavity in the protein interior, and Y157 is one of the surrounding residues. The Y157 OηH group introduces an unfavorable energy in the hydrophobic cavity, therefore sequestering itself by forming a hydrogen bond with the proximate residue I133. The hydrogen bonding confines Y157 orientation but exerts a force to disrupt the hydrogen bond network surrounding the cavity. The effect propagates over the entire protein and reduces the stability, as reflected in the protein backbone dynamics observed by an NMR hydrogen-deuterium (H/D) exchange experiment. We describe the particular case in which a hydrogen bond does not necessarily confer enhanced protein stability while the disruption of hydrophobicity must be integrally considered.

  8. Characteristics of hydrogen bond revealed from water clusters

    Science.gov (United States)

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

    2014-09-01

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

  9. The ribbon of hydrogen bonds in globular proteins. IV. The example of the papain family.

    Science.gov (United States)

    Peters, David; Peters, Jane

    2004-02-05

    A study of the role of the hydrogen-bonding side chains in the ribbon of hydrogen bonds in globular proteins, using the papain family as an example, suggests that these side chains may be divided into three categories depending on their position in the molecule. In the first category, they form part of the local ribbon, in the second they form part of the ribbon at a site remote along the main chain, and in the third they play no role in the formation of the ribbon. The second case is particularly interesting because it provides a natural mechanism for the formation of the tertiary structure of the globular proteins. The results suggest that the robustness of the globular proteins towards mutations arises from the fact that many mutations that involve hydrogen-bonding side chains either leave the hydrogen bonding of the ribbon essentially unchanged or their hydrogen bonding plays no part in the formation of the ribbon in the first place. The results show that it is possible to obtain the ribbon of hydrogen bonds for a family of proteins whose data set's are of intermediate quality by studying the ribbons of several members of such a family and then taking an average over the different partial ribbons to create a standard ribbon of hydrogen bonds for the family as a whole. This method is used here to derive the standard ribbon for the papain family with papain itself, actinidin, and human liver cathepsin B as the representatives of the family. All three members of the family fit the standard ribbon with an accuracy of 85-91%. This result opens up the use of this technique for the study of a large number of globular proteins whose recorded data sets are of intermediate quality. Copyright 2003 Wiley Periodicals, Inc.

  10. Hydrogen bond dynamics at the water/hydrocarbon interface.

    Science.gov (United States)

    Chowdhary, Janamejaya; Ladanyi, Branka M

    2009-04-02

    The dynamics of hydrogen bond formation and breakage for water in the vicinity of water/hydrocarbon liquid interfaces is studied using molecular dynamics simulations. Several liquid alkanes are considered as the hydrocarbon phase in order to determine the effects of their chain length and extent of branching on the properties of the adjacent water phase. In addition to defining the interface location in terms of the laboratory-frame density profiles, the effects of interfacial fluctuations are considered by locating the interface in terms of the proximity of the molecules of the other phase. We find that the hydrogen bond dynamics of interfacial water is weakly influenced by the identity of the hydrocarbon phase and by capillary waves. In addition to calculating hydrogen bond time correlations, we examine how the hydrogen bond dynamics depend on local coordination and determine the extent of cooperativity in the population relaxation of the hydrogen bonds that a given molecule participates in. The contributions of translational diffusion and reorientation of molecular O-H bonds to the mechanism of hydrogen bond breakage and reformation are investigated. In previous work, we have shown that rotation of the principal axes of water is anisotropic at the interface and depends on the initial orientation of the molecule relative to the interface. Here, we extend this analysis to the reorientation of the O-H vector and to hydrogen bond time correlation. We find that hydrogen bond dynamics are also sensitive to the initial orientation of the molecules participating in the hydrogen bond.

  11. 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.

  12. 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.

  13. 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...

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

    Science.gov (United States)

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

    2017-02-15

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

  15. Ultrafast Dynamics of Hydrogen Bond Breaking and Making in the Excited State of Fluoren-9-one: Time-Resolved Visible Pump-IR Probe Spectroscopic Study.

    Science.gov (United States)

    Ghosh, Rajib; Mora, Aruna K; Nath, Sukhendu; Palit, Dipak K

    2017-02-09

    The fluoren-9-one (FL) molecule, with a single hydrogen bond-accepting site (C═O group), has been used as a probe for investigation of the dynamics of a hydrogen bond in its lowest excited singlet (S1) state using the subpicosecond time-resolved visible pump-IR probe spectroscopic technique. In 1,1,1,3,3,3-hexafluoroisopropanol (HFIP), a strong hydrogen bond-donating solvent, the formation of an FL-alcohol hydrogen-bonded complex in the ground electronic (S0) state is nearly complete, with a negligible concentration of the FL molecule remaining free in solution. In addition to the presence of a band due to the hydrogen-bonded complex in the transient IR spectrum recorded immediately after photoexcitation of FL in HFIP solution, appearance of the absorption band due to a free C═O stretch provides confirmatory evidence of ultrafast photodissociation of hydrogen bonds in some of the complexes formed in the S0 state. The peak-shift dynamics of the C═O stretch bands reveal two major relaxation pathways, namely, vibrational relaxation in the S1 state of the free FL molecules and the solvent reorganization process in the hydrogen-bonded complex. The latter process follows bimodal exponential dynamics involving hydrogen bond-making and hydrogen bond-reorganization processes. The similar lifetimes of the S1 states of the FL molecules, both free and hydrogen-bonded, suggest establishment of a dynamic equilibrium between these two species in the excited state. However, investigations in two other weaker hydrogen bond-donating solvents, namely, trifluoroethanol (TFE) and perdeuterated methanol (CD3OD), reveal different features of peak-shift dynamics because of the prominence of the vibrational relaxation process over the hydrogen bond-reorganization process during the early time.

  16. Hydrogen-bond interactions in morpholinium bromide

    Directory of Open Access Journals (Sweden)

    Alvaro S. de Sousa

    2011-10-01

    Full Text Available In the title compound, C4H10NO+·Br−, which was synthesized by dehydration of diethanolamine with HBr, morpholinium and bromide ions are linked into chains by N—H...Br hydrogen bonds describing a C21(4 graph-set motif. Weaker bifurcated N—H...Br interactions join centrosymmetrically related chains through alternating binary graph-set R42(8 and R22(4 motifs, to form ladders along [100]. In addition, C—H...O interactions between centrosymmetric morpholinium cations link ladders, via R^2_2(8 motifs, to yield sheets parallel to (101, which in turn are crosslinked by weak C—H...O interactions, related across a glide plane, to form a three-dimensional network.

  17. 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.

  18. 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.

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

    Science.gov (United States)

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

    2015-09-15

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

  20. Hydrogen-Bonding-Induced Fluorescence: Water-Soluble and Polarity-Independent Solvatochromic Fluorophores.

    Science.gov (United States)

    Okada, Yohei; Sugai, Masae; Chiba, Kazuhiro

    2016-11-18

    Fluorophores with emission wavelengths that shift depending on their hydrogen-bonding microenvironment in water would be fascinating tools for the study of biological events. Herein we describe the design and synthesis of a series of water-soluble solvatochromic fluorophores, 2,5-bis(oligoethylene glycol)oxybenzaldehydes (8-11) and 2,5-bis(oligoethylene glycol)oxy-1,4-dibenzaldehydes (14-17), based on a push-pull strategy. Unlike typical examples in this class of fluorophores, the fluorescence properties of these compounds are independent of solvent polarity and become fluorescent upon intermolecular hydrogen-bonding, exhibiting high quantum yields (up to ϕ = 0.55) and large Stokes shifts (up to 134 nm). Furthermore, their emission wavelengths change depending on their hydrogen-bonding environment. The described fluorophores provide a starting point for unprecedented applications in the fields of chemical biology and medicinal chemistry.

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    to inform about molecular recognition events at the single-molecule limit. For this, we consider the force-conductance characteristics of a prototypical class of hydrogen bonded bimolecular complexes sandwiched between gold electrodes. The complexes consist of derivatives of a barbituric acid and a Hamilton...... 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...

  2. Backbone Hydrogen Bond Strengths Can Vary Widely in Transmembrane Helices.

    Science.gov (United States)

    Cao, Zheng; Hutchison, James M; Sanders, Charles R; Bowie, James U

    2017-08-09

    Although backbone hydrogen bonds in transmembrane (TM) helices have the potential to be very strong due to the low dielectric and low water environment of the membrane, their strength has never been assessed experimentally. Moreover, variations in hydrogen bond strength might be necessary to facilitate the TM helix breaking and bending that is often needed to satisfy functional imperatives. Here we employed equilibrium hydrogen/deuterium fractionation factors to measure backbone hydrogen bond strengths in the TM helix of the amyloid precursor protein (APP). We find an enormous range of hydrogen bond free energies, with some weaker than water-water hydrogen bonds and some over 6 kcal/mol stronger than water-water hydrogen bonds. We find that weak hydrogen bonds are at or near preferred γ-secretase cleavage sites, suggesting that the sequence of APP and possibly other cleaved TM helices may be designed, in part, to make their backbones accessible for cleavage. The finding that hydrogen bond strengths in a TM helix can vary widely has implications for membrane protein function, dynamics, evolution, and design.

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

    Science.gov (United States)

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

    2001-01-01

    Examines how students completing a two-semester organic sequence understand, explain, and apply hydrogen bonding to determine the physical attributes of molecules. Suggests that some students completing what is typically their second year of college-level chemistry still possess misconceptions about hydrogen bonds. (Contains 21 references.) (ASK)

  4. Noncovalent synthesis of nanostructures: combining coordination chemistry and hydrogen bonding

    NARCIS (Netherlands)

    Huck, W.T.S.; Huck, Wilhelm T.S.; Hulst, A.J.R.L.; Timmerman, P.; van Veggel, F.C.J.M.; Reinhoudt, David

    1997-01-01

    Rosettes that are held together by hydrogen bonds (see sketch on the right) were synthesized from metallodendrimers constructed by coordination chemistry. Two orthogonal, noncovalent interactions (metal-ligand and hydrogen bonding) were employed to build these nanosized dendrimers (M 7-28 kDa).

  5. Phase transition in triglycine family of hydrogen bonded ferroelectrics

    Indian Academy of Sciences (India)

    Hydrogen bonded ferroelectric crystals form a subclass of ferroelectrics in which hydrogen bonds play an important role in determining the properties. Triglycine family is one such class which includes triglycine sulphate (TGS), triglycine selenate. (TGSe), triglycine fluoroberyllate (TGFBe), mixed crystals like ...

  6. Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol

    Directory of Open Access Journals (Sweden)

    Hailiang Zhao

    2016-12-01

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

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

    Indian Academy of Sciences (India)

    Molecular dynamics simulations of dilute and concentrated aqueous NaCl solutions are carried out to investigate the changes of the hydrogen bonded structures in the vicinity of ions for different ion concentrations. An analysis of the hydrogen bond population in the first and second solvation shells of the ions and in the bulk ...

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

    Science.gov (United States)

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

    2016-12-30

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

  9. Hydrogen bond and lifetime dynamics in diluted alcohols

    NARCIS (Netherlands)

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

    2017-01-01

    Hydrogen-bonding plays a crucial role in many chemical and biochemical reactions. Alcohols, with their hydrophilic and hydrophobic groups, constitute an important class of hydrogen-bonding molecules with functional tuning possibilities through changes in the hydrophobic tails. Recent studies

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

    Indian Academy of Sciences (India)

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

  11. 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

    We describe the vibrational transitions of the donor unit in water dimer with an approach that is based on a three-dimensional local mode model. We perform a perturbative treatment of the intermolecular vibrational modes to improve the transition wavenumber of the hydrogen bonded OH......-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...

  12. Hydrogen Bond Nanoscale Networks Showing Switchable Transport Performance

    Science.gov (United States)

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

    2012-08-01

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

  13. Water-anion hydrogen bonding dynamics: Ultrafast IR experiments and simulations

    Science.gov (United States)

    Yamada, Steven A.; Thompson, Ward H.; Fayer, Michael D.

    2017-06-01

    Many of water's remarkable properties arise from its tendency to form an intricate and robust hydrogen bond network. Understanding the dynamics that govern this network is fundamental to elucidating the behavior of pure water and water in biological and physical systems. In ultrafast nonlinear infrared experiments, the accessible time scales are limited by water's rapid vibrational relaxation (1.8 ps for dilute HOD in H2O), precluding interrogation of slow hydrogen bond evolution in non-bulk systems. Here, hydrogen bonding dynamics in bulk D2O were studied from the perspective of the much longer lived (36.2 ps) CN stretch mode of selenocyanate (SeCN-) using polarization selective pump-probe (PSPP) experiments, two-dimensional infrared (2D IR) vibrational echo spectroscopy, and molecular dynamics simulations. The simulations make use of the empirical frequency mapping approach, applied to SeCN- for the first time. The PSPP experiments and simulations show that the orientational correlation function decays via fast (2.0 ps) restricted angular diffusion (wobbling-in-a-cone) and complete orientational diffusive randomization (4.5 ps). Spectral diffusion, quantified in terms of the frequency-frequency correlation function, occurs on two time scales. The initial 0.6 ps time scale is attributed to small length and angle fluctuations of the hydrogen bonds between water and SeCN-. The second 1.4 ps measured time scale, identical to that for HOD in bulk D2O, reports on the collective reorganization of the water hydrogen bond network around the anion. The experiments and simulations provide details of the anion-water hydrogen bonding and demonstrate that SeCN- is a reliable vibrational probe of the ultrafast spectroscopy of water.

  14. Nanostructure, hydrogen bonding and rheology in choline chloride deep eutectic solvents as a function of the hydrogen bond donor.

    Science.gov (United States)

    Stefanovic, Ryan; Ludwig, Michael; Webber, Grant B; Atkin, Rob; Page, Alister J

    2017-01-25

    Deep eutectic solvents (DESs) are a mixture of a salt and a molecular hydrogen bond donor, which form a eutectic liquid with a depressed melting point. Quantum mechanical molecular dynamics (QM/MD) simulations have been used to probe the 1 : 2 choline chloride-urea (ChCl : U), choline chloride-ethylene glycol (ChCl : EG) and choline chloride-glycerol (ChCl : Gly) DESs. DES nanostructure and interactions between the ions is used to rationalise differences in DES eutectic point temperatures and viscosity. Simulations show that the structure of the bulk hydrogen bond donor is largely preserved for hydroxyl based hydrogen bond donors (ChCl:Gly and ChCl:EG), resulting in a smaller melting point depression. By contrast, ChCl:U exhibits a well-established hydrogen bond network between the salt and hydrogen bond donor, leading to a larger melting point depression. This extensive hydrogen bond network in ChCl:U also leads to substantially higher viscosity, compared to ChCl:EG and ChCl:Gly. Of the two hydroxyl based DESs, ChCl:Gly also exhibits a higher viscosity than ChCl:EG. This is attributed to the over-saturation of hydrogen bond donor groups in the ChCl:Gly bulk, which leads to more extensive hydrogen bond donor self-interaction and hence higher cohesive forces within the bulk liquid.

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

    Indian Academy of Sciences (India)

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

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

    KAUST Repository

    El-Mellouhi, Fedwa

    2016-09-08

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

  17. Hydrogen Bonding and Vibrational Spectroscopy: A Theoretical Study

    Science.gov (United States)

    Chaban, Galina M.

    2005-01-01

    Effects of hydrogen bonding on vibrational spectra are studied for several hydrogen-bonded complexes, in which hydrogen bonding ranges from weak (25 kcal/mol). The systems studied include complexes of inorganic acids and salts with water and ammonia, as well as complexes of several organic molecules (nitriles and amino acids) with water. Since anharmonic effects are very strong in hydrogen-bonded systems, anharmonic vibrational frequencies and infrared intensities are computed using the correlation-corrected vibrational self-consistent field (CC-VSCF) method with ab initio potential surfaces at the MP2 and CCSD(T) levels. The most common spectral effects induced by hydrogen bonding are red shifts of stretching vibrational frequencies ranging from approx.200/cm to over 2000/cm and significant increases of infrared intensities for those bonds that participate in hydrogen bonding. However, some systems (e.g. nitrile-water complexes) exhibit shifts in the opposite direction (to the blue) upon formation of hydrogen bonds.

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

    Science.gov (United States)

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

    2011-01-01

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

  19. 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.

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

    Science.gov (United States)

    Bywater, Robert P

    2017-05-01

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

  1. A tensegrity model for hydrogen bond networks in proteins

    Directory of Open Access Journals (Sweden)

    Robert P. Bywater

    2017-05-01

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

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

    Science.gov (United States)

    Milenkovic, Stefan; Bondar, Ana-Nicoleta

    2016-02-01

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

  3. 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

  4. Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

    Science.gov (United States)

    Sigala, Paul A.; Fafarman, Aaron T.; Schwans, Jason P.; Fried, Stephen D.; Fenn, Timothy D.; Caaveiro, Jose M. M.; Pybus, Brandon; Ringe, Dagmar; Petsko, Gregory A.; Boxer, Steven G.; Herschlag, Daniel

    2013-01-01

    Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated site-specific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol–Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations. PMID:23798390

  5. The loss of a hydrogen bond: Thermodynamic contributions of a non-standard nucleotide.

    Science.gov (United States)

    Jolley, Elizabeth A; Znosko, Brent M

    2017-02-17

    Non-standard nucleotides are ubiquitous in RNA. Thermodynamic studies with RNA duplexes containing non-standard nucleotides, whether incorporated naturally or chemically, can provide insight into the stability of Watson–Crick pairs and the role of specific functional groups in stabilizing a Watson–Crick pair. For example, an A-U, inosine•U and pseudouridine•A pair each form two hydrogen bonds. However, an RNA duplex containing a central I•U pair or central Ψ•A pair is 2.4 kcal/mol less stable or 1.7 kcal/mol more stable, respectively, than the corresponding duplex containing an A-U pair. In the non-standard nucleotide purine, hydrogen replaces the exocyclic amino group of A. This replacement results in a P•U pair containing only one hydrogen bond. Optical melting studies were performed with RNA duplexes containing P•U pairs adjacent to different nearest neighbors. The resulting thermodynamic parameters were compared to RNA duplexes containing A-U pairs in order to determine the contribution of the hydrogen bond involving the exocyclic amino group. Results indicate a loss of 1.78 kcal/mol, on average, when an internal P•U replaces A-U in an RNA duplex. This value is compared to the thermodynamics of a hydrogen bond determined by similar methods. Nearest neighbor parameters were derived for use in free energy and secondary structure prediction software.

  6. Extended scale for the hydrogen-bond basicity of ionic liquids.

    Science.gov (United States)

    Cláudio, Ana Filipa M; Swift, Lorna; Hallett, Jason P; Welton, Tom; Coutinho, João A P; Freire, Mara G

    2014-04-14

    In the past decade, ionic liquids (ILs) have been the focus of intensive research regarding their use as potential and alternative solvents in many chemical applications. Targeting their effectiveness, recent investigations have attempted to establish polarity scales capable of ranking ILs according to their chemical behaviours. However, some major drawbacks have been found since polarity scales only report relative ranks because they depend on the set of probe dyes used, and they are sensitive to measurement conditions, such as purity levels of the ILs and procedures employed. Due to all these difficulties it is of crucial importance to find alternative and/or predictive methods and to evaluate them as a priori approaches capable of providing the chemical properties of ILs. Furthermore, the large number of ILs available makes their experimental characterization, usually achieved by a trial and error methodology, burdensome. In this context, we firstly evaluated COSMO-RS, COnductor-like Screening MOdel for Real Solvents, as an alternative tool to estimate the hydrogen-bond basicity of ILs. After demonstrating a straight-line correlation between the experimental hydrogen-bond basicity values and the COSMO-RS hydrogen-bonding energies in equimolar cation-anion pairs, an extended scale for the hydrogen-bond accepting ability of IL anions is proposed here. This new ranking of the ILs' chemical properties opens the possibility to pre-screen appropriate ILs (even those not yet synthesized) for a given task or application.

  7. Effect of hydrogen bond anharmonicity on supersonic discrete Davydov soliton propagation.

    Science.gov (United States)

    Cisneros-Ake, Luis A; Minzoni, A A

    2012-02-01

    We consider the propagation of energy along a protein chain in the Davydov approximation. We study the fully discrete Davydov equations including the anharmonic corrections in the hydrogen bond potential and find approximate variational solutions. We show analytically that for the harmonic interaction of the hydrogen bonds of the Davydov model the waves travel with velocities less than half the sound velocity for the relevant biological parameters. We find, for weak nonlinearity of the hydrogen bonds, two branches of soliton solutions. The first one gives a new type of strongly stable cusped discrete supersonic soliton. The second branch captures the main component of a more complicated breather solution compared to the one studied by Gaididei et al. and reproduces the Davydov soliton of the continuum limit. These results show the possibility of coherent protein chain deformation due to the anharmonicity of the hydrogen bond interactions. These supersonic waves are shown to provide a viable mechanism for energy transport in spite of the temperature influence in the soliton lifetime. © 2012 American Physical Society

  8. Improvement of Structure-Based Potentials for Protein Folding by Native and Nonnative Hydrogen Bonds

    Science.gov (United States)

    Enciso, Marta; Rey, Antonio

    2011-01-01

    Pure Gō models (where every native interaction equally stabilizes the folded state) have widely proved their convenience in the computational investigation of protein folding. However, a chemistry-based description of the real interactions also provides a desirable tune in the analysis of the folding process, and thus some hybrid Gō potentials that combine both aspects have been proposed. Among all the noncovalent interactions that contribute to protein folding, hydrogen bonds are the only ones with a partial covalent character. This feature makes them directional and, thus, more difficult to model as part of the coarse-grained descriptions that are typically employed in Gō models. Thanks to a simplified but rigorous representation of backbone hydrogen bonds that we have recently proposed, we present in this article a combined potential (Gō + backbone hydrogen bond) to study the thermodynamics of protein folding in the frame of very simple simulation models. We show that the explicit inclusion of hydrogen bonds leads to a systematic improvement in the description of protein folding. We discuss a representative set of examples (from two-state folders to downhill proteins, with different types of native structures) that reveal a relevant agreement with experimental data. PMID:21943429

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

    Science.gov (United States)

    Beck, John Frederick; Mo, Yirong

    2007-01-15

    Block-localized wave function (BLW) method, which is a variant of the ab initio valence bond (VB) theory, was employed to explore the nature of resonance-assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between pi delocalization and hydrogen-bonding interactions. We examined the dimers of formic acid, formamide, 4-pyrimidinone, 2-pyridinone, 2-hydroxpyridine, and 2-hydroxycyclopenta-2,4-dien-1-one. In addition, we studied the interactions in beta-diketone enols with a simplified model, namely the hydrogen bonds of 3-hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of pi resonance, were decomposed into the Hitler-London energy (DeltaEHL), polarization energy (DeltaEpol), charge transfer energy (DeltaECT), and electron correlation energy (DeltaEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of pi conjugation on hydrogen bonding interactions. Although it has been proposed that resonance-assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole-dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term "resonance-assisted binding (RAB)" instead of "resonance-assisted hydrogen bonding (RHAB)" to highlight the electrostatic, which is a long-range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs. Copyright (c) 2006 Wiley Periodicals, Inc.

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

    Science.gov (United States)

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

    2011-03-01

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

  11. Hydrogen bond and lifetime dynamics in diluted alcohols.

    Science.gov (United States)

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

    2017-10-25

    Hydrogen-bonding plays a crucial role in many chemical and biochemical reactions. Alcohols, with their hydrophilic and hydrophobic groups, constitute an important class of hydrogen-bonding molecules with functional tuning possibilities through changes in the hydrophobic tails. Recent studies demonstrated that for solutions of alcohols changes in the hydrophobic tail significantly affect a broad range of dynamics properties of the liquid. Still, the understanding is lacking on the origin of such differences in terms of a solvent- versus a solute-dominated effect. Here we reveal this origin by studying hydrogen-bond dynamics in a number of alcohol molecules - from methanol to butanol - diluted in a hydrogen-bond accepting environment, acetonitrile. The dynamics were investigated by pump-probe and 2D infrared spectroscopy combined with molecular dynamics-spectral simulations, using the OH stretching mode as a reporter. For all the considered alcohols, the vibrational lifetime of the OH stretching mode was found to be ∼3 ps. The hydrogen-bond dynamics exhibit similar behavior with a fast (∼200 fs) initial relaxation dominated by librational motion and a slow (∼4 ps) relaxation due to hydrogen-bond exchange dynamics. The similar dynamics over such a broad range of alcohols led us to conclude that the previously observed differences in dynamics in bulk alcohols originate from the dependence of the solvent properties on the hydrophobic tail, while the solute properties as found herein are essentially independent of the hydrophobic tail.

  12. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    Directory of Open Access Journals (Sweden)

    Peter I. Nagy

    2014-10-01

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

  13. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    Science.gov (United States)

    Nagy, Peter I.

    2014-01-01

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

  14. 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.

  15. AKT as Locus of Hydrogen Bond Network in Cancer.

    Science.gov (United States)

    Radisavljevic, Ziv

    2018-01-01

    Generation and maintenance of a cancer complexity and robustness are impossible without hydrogen element. It is essential element for the cancer signaling through the AKT locus. Hyperactivated AKT locus by a positive feedback loops from the cancer hypoxic microenvironment generates a hydrogen bond network. Such network initiates protein-protein interaction at the AKT active site and at the same time stabilizes signal propagation. A hydrogen bond network conforms an entropy/enthalpy energetic process used for the interconversion of the AKT protein in metastasis formation and maintenance. Targeting the AKT locus by the redox balance change or hydrogen balance change or proton beam radiation disrupts a hydrogen bond network leading to the disappearance of a cancer complexity and robustness causing failure of the complex energy system in solid cancers and hematological malignancy. J. Cell. Biochem. 119: 130-133, 2018. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  16. Positively charged phosphorus as a hydrogen bond acceptor

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    Science.gov (United States)

    Miller, Kathryn; Kim, Thomas

    2017-09-01

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

  18. Alkyl Radicals as Hydrogen Bond Acceptors: Computational Evidence

    DEFF Research Database (Denmark)

    Hammerum, Steen

    2009-01-01

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

  19. Observation of the slow, Debye-like relaxation in hydrogen-bonded liquids by dynamic light scattering.

    Science.gov (United States)

    Wang, Yangyang; Griffin, Philip J; Holt, Adam; Fan, Fei; Sokolov, Alexei P

    2014-03-14

    The slow, Debye-like relaxation in hydrogen-bonded liquids has largely remained a dielectric phenomenon and has thus far eluded observation by other experimental techniques. Here we report the first observation of a slow, Debye-like relaxation by both depolarized dynamic light scattering (DLS) and dielectric spectroscopy in a model hydrogen-bonded liquid, 2-ethyl-4-methylimidazole (2E4MIm). The relaxation times obtained by these two techniques are in good agreement and can be well explained by the Debye model of rotational diffusion. On the one hand, 2E4MIm is analogous to the widely studied monohydroxy alcohols in which transient chain-like supramolecular structure can be formed by hydrogen bonding. On the other hand, the hydrogen-bonded backbone of 2E4MIm is much more optically polarizable, making it possible to apply light scattering to study the dynamics of the supramolecular structure. These findings provide the missing evidence of the slow, Debye-like relaxation in DLS and open the venue for the application of dynamic light scattering to the study of supramolecular structures in hydrogen-bonded liquids.

  20. Ionization properties of mixed lipid membranes: a Gouy-Chapman model of the electrostatic-hydrogen bond switch.

    Science.gov (United States)

    Mengistu, Demmelash H; Kooijman, Edgar E; May, Sylvio

    2011-08-01

    The dissociation state of phosphatidic acid (PA) in a lipid bilayer is governed by the competition of proton binding and formation of a hydrogen bond through a mechanism termed the electrostatic-hydrogen bond switch. This mechanism has been suggested to provide the basis for the specific recognition of PA by proteins. Even in bare lipid bilayers the electrostatic-hydrogen bond switch is present if the membrane contains lipids like phosphatidylethanolamine that act as hydrogen bond donors. In this case, the dissociation state (pK(a)) of PA depends strongly on membrane composition. In the present work we incorporate the electrostatic-hydrogen bond switch mechanism into the Gouy-Chapman model for a membrane that is composed of PA and a hydrogen bond-donating zwitterionic lipid. To this end, our model integrates into the Gouy-Chapman approach a recently suggested electrostatic model for zwitterionic lipids. Hydrogen bond formation is incorporated phenomenologically as an additional non-electrostatic interaction between the phosphomonoester headgroup of PA and the zwitterionic lipid headgroup. We express the energetics of the composite membrane in terms of a free energy functional whose minimization leads to a modified non-linear Poisson-Boltzmann equation that we have solved numerically. Our calculations focus on the influence of the membrane environment on the dissociation state of PA. This influence can be expressed as a shift of the second pK(a) of PA, which we calculate as function of membrane composition, following experimental observation. The shift is large and negative if PA is the minor component in the membrane, and it changes over four pH units as function of the mole fraction of PA in the membrane. In contrast, the shift of the second pK(a) of PA remains small and is always positive if the zwitterionic lipid is unable to act as hydrogen bond donor. Hence, we find that the electrostatic-hydrogen bond switch mechanism regulates the dissociation state of PA

  1. Hydrogen bond docking site competition in methyl esters.

    Science.gov (United States)

    Zhao, Hailiang; Tang, Shanshan; Du, Lin

    2017-06-15

    The OH⋯O hydrogen bonds in the 2,2,2-trifluoroethanol (TFE)-methyl ester complexes in the gas phase have been investigated by FTIR spectroscopy and DFT calculations. Methyl formate (MF), methyl acetate (MA), and methyl trifluoroacetate (MTFA) were chosen as the hydrogen bond acceptors. A dominant inter-molecular hydrogen bond was formed between the OH group of TFE and different docking sites in the methyl esters (carbonyl oxygen or ester oxygen). The competition of the two docking sites decides the structure and spectral properties of the complexes. On the basis of the observed red shifts of the OH-stretching transition with respect to the TFE monomer, the order of the hydrogen bond strength can be sorted as TFE-MA (119cm-1)>TFE-MF (93cm-1)>TFE-MTFA (44cm-1). Combining the experimental infrared spectra with the DFT calculations, the Gibbs free energies of formation were determined to be 1.5, 4.5 and 8.6kJmol-1 for TFE-MA, TFE-MF and TFE-MTFA, respectively. The hydrogen bonding in the MTFA complex is much weaker than those of the TFE-MA and TFE-MF complexes due to the effect of the CF3 substitution on MTFA, while the replacement of an H atom with a CH3 group in methyl ester only slightly increases the hydrogen bond strength. Topological analysis and localized molecular orbital energy decomposition analysis was also applied to compare the interactions in the complexes. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Hydrogen bond docking site competition in methyl esters

    Science.gov (United States)

    Zhao, Hailiang; Tang, Shanshan; Du, Lin

    2017-06-01

    The Osbnd H ⋯ O hydrogen bonds in the 2,2,2-trifluoroethanol (TFE)-methyl ester complexes in the gas phase have been investigated by FTIR spectroscopy and DFT calculations. Methyl formate (MF), methyl acetate (MA), and methyl trifluoroacetate (MTFA) were chosen as the hydrogen bond acceptors. A dominant inter-molecular hydrogen bond was formed between the OH group of TFE and different docking sites in the methyl esters (carbonyl oxygen or ester oxygen). The competition of the two docking sites decides the structure and spectral properties of the complexes. On the basis of the observed red shifts of the OH-stretching transition with respect to the TFE monomer, the order of the hydrogen bond strength can be sorted as TFE-MA (119 cm- 1) > TFE-MF (93 cm- 1) > TFE-MTFA (44 cm- 1). Combining the experimental infrared spectra with the DFT calculations, the Gibbs free energies of formation were determined to be 1.5, 4.5 and 8.6 kJ mol- 1 for TFE-MA, TFE-MF and TFE-MTFA, respectively. The hydrogen bonding in the MTFA complex is much weaker than those of the TFE-MA and TFE-MF complexes due to the effect of the CF3 substitution on MTFA, while the replacement of an H atom with a CH3 group in methyl ester only slightly increases the hydrogen bond strength. Topological analysis and localized molecular orbital energy decomposition analysis was also applied to compare the interactions in the complexes.

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

    Science.gov (United States)

    Koenig, S; Müller, L; Smith, D K

    2001-03-02

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

  4. Probing the nature of hydrogen bonds in DNA base pairs.

    Science.gov (United States)

    Mo, Yirong

    2006-07-01

    Energy decomposition analyses based on the block-localized wave-function (BLW-ED) method are conducted to explore the nature of the hydrogen bonds in DNA base pairs in terms of deformation, Heitler-London, polarization, electron-transfer and dispersion-energy terms, where the Heitler-London energy term is composed of electrostatic and Pauli-exchange interactions. A modest electron-transfer effect is found in the Watson-Crick adenine-thymine (AT), guanine-cytosine (GC) and Hoogsteen adenine-thymine (H-AT) pairs, confirming the weak covalence in the hydrogen bonds. The electrostatic attraction and polarization effects account for most of the binding energies, particularly in the GC pair. Both theoretical and experimental data show that the GC pair has a binding energy (-25.4 kcal mol(-1) at the MP2/6-31G** level) twice that of the AT (-12.4 kcal mol(-1)) and H-AT (-12.8 kcal mol(-1)) pairs, compared with three conventional N-H...O(N) hydrogen bonds in the GC pair and two in the AT or H-AT pair. Although the remarkably strong binding between the guanine and cytosine bases benefits from the opposite orientations of the dipole moments in these two bases assisted by the pi-electron delocalization from the amine groups to the carbonyl groups, model calculations demonstrate that pi-resonance has very limited influence on the covalence of the hydrogen bonds. Thus, the often adopted terminology "resonance-assisted hydrogen bonding (RHAB)" may be replaced with "resonance-assisted binding" which highlights the electrostatic rather than electron-transfer nature of the enhanced stabilization, as hydrogen bonds are usually regarded as weak covalent bonds.

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

    Directory of Open Access Journals (Sweden)

    Esko Oksanen

    2017-04-01

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

  6. An insight into the influence of hydrogen bond acceptors on cellulose/1-allyl-3-methyl imidazolium chloride solution.

    Science.gov (United States)

    Jiang, Jiahao; Xiao, Yafei; Huang, Wenjuan; Gong, Peixin; Peng, Shuhua; He, Jianping; Fan, Minmin; Wang, Ke

    2017-12-15

    Although ionic liquids have been well established as effective solvents for the dissolution and processing of natural cellulose fibers, the detailed dissolution mechanism at the molecular level still remains unclear. Herein, the turbidimetric measurement showed that the solubility of cellulose in 1-allyl-3-methyl imidazolium chloride (AmimCl) decreased with increasing temperature. The temperature dependence of the OH stretching vibration band of cellulose in AmimCl was investigated by infrared spectroscopy. The interaction between AmimCl and different hydrogen bond acceptors were investigated by turbidimetry and NMR spectroscopy, which indicated that the excellent compatibility of the hydrogen bond acceptors with AmimCl provides more interaction sites for the hydroxyl groups of the cellulose. In addition, ionic liquids with a similar anionic structure of hydrogen bond acceptors have been synthesized. This study provides a green and safe guide for the preparation of ionic liquids with excellent solubility of cellulose. Copyright © 2017. Published by Elsevier Ltd.

  7. Versatile and Resilient Hydrogen-Bonded Host Frameworks.

    Science.gov (United States)

    Adachi, Takuji; Ward, Michael D

    2016-12-20

    Low-density molecular host frameworks, whether equipped with persistent molecular-scale pores or virtual pores that are sustainable only when occupied by guest molecules, have emerged as a promising class of materials owing to the ability to tailor the size, geometry, and chemical character of their free space through the versatility of organic synthesis. As such, molecular frameworks are promising candidates for storage, separations of commodity and fine chemicals, heterogeneous catalysis, and optical and electronic materials. Frameworks assembled through hydrogen bonds, though generally not stable toward collapse in the absence of guests, promise significant chemical and structural diversity, with pores that can be tailored for a wide range of guest molecules. The utility of these frameworks, however, depends on the resilience of n-dimensional hydrogen-bonded motifs that serve as reliable building blocks so that the molecular constituents can be manipulated without disruption of the anticipated global solid-state architecture. Though many hydrogen-bonded frameworks have been reported, few exist that are amenable to systematic modification, thus limiting the design of functional materials. This Account reviews discoveries in our laboratory during the past decade related to a series of host frameworks based on guanidinium cations and interchangeable organosulfonate anions, in which the 3-fold symmetry and hydrogen-bonding complementarity of these ions prompt the formation of a two-dimensional (2-D) quasi-hexagonal hydrogen-bonding network that has proven to be remarkably resilient toward the introduction of a wide range of organic pendant groups attached to the sulfonate. Since an earlier report in this journal that focused primarily on organodisulfonate host frameworks with lamellar architectures, this unusually persistent network has afforded an unparalleled range of framework architectures and hundreds of new crystalline materials with predictable solid

  8. A model of hydrogen bond formation in phosphatidylethanolamine bilayers.

    Science.gov (United States)

    Pink, D A; McNeil, S; Quinn, B; Zuckermann, M J

    1998-01-19

    We have modelled hydrogen bond formation in phospholipid bilayers formed, in excess water, from lipids with phosphatidylethanolamine (PE) headgroups. The hydrogen bonds are formed between the NH3+ group and either of the PO2- or the (sn2 chain) C=O groups. We used a model that represented the conformational states accessible to a PE headgroup by 17 states and modelled lipid dipole-dipole interactions using a non-local electrostatics theory to include the effects of hydrogen bonding in the aqueous medium. We used Monte-Carlo simulation to calculate equilibrium thermodynamic properties of bilayers in the fluid (T = 340 K) or gel (T = 300 K) phases of the bilayer. We defined Eh to be the difference in free energy between a hydrogen bond formed between a pair of lipid groups, and the energy of hydrogen bonds formed between water and those two groups, and we required its average value, [Eh], to be approximately -0.3kcal/mol (approximately -0.2 X 10(-13) erg) as reported by T.-B. Shin, R. Leventis, J.R. Silvius, Biochemistry 30 (1991) 7491. We found: (i) Eh = -0.9 X 10(-13) erg gave [Eh] = -0.21 X 10(-13) erg (gel phase) and [Eh] = -0.19 X 10(-13) erg (fluid phase). (ii) The relative number of C=O groups on the sn2 chain calculated to take part in interlipid hydrogen bonding in the fluid phase compared to the gel is 1.06 which compares well with the experimental ratio of approximately 1.25 (R.N.A.H. Lewis, R.N. McElhaney, Biophys. J. 64 (1993) 1081). The ratio of such groups taking part in interlipid hydrogen bonding compared to water hydrogen bonding in each phase was calculated to lie between 0.16 and 0.17. (iii) We calculated the distribution of positions of the headgroup moieties, P, O, CH2(alpha), CH2(beta) and N, and found that, in both phases, the O lay furthest from the hydrocarbon chain layer (average approximately 5.3A) with the PO2 and NH3 groups lying at approximately 5A. This results in the P-N dipole lying nearly parallel to the bilayer plane in both phases

  9. On the physical origin of the cation-anion intermediate bond in ionic liquids Part I. Placing a (weak) hydrogen bond between two charges.

    Science.gov (United States)

    Lehmann, Sebastian B C; Roatsch, Martin; Schöppke, Matthias; Kirchner, Barbara

    2010-07-21

    the counterions in imidazolium-based ionic liquids. While geometry and charge analysis provides attributes of weak (blue-shifted) hydrogen bonds, large bond elongations accompanied by red-shifts are obtained for the ion pairs investigated. This can be understood by the simple fact that these imidazolium-based ionic liquid ion pairs constitute weak hydrogen bonds placed between two delocalized charges.

  10. Accurate ab initio calculations of O-HO and O-H(-)O proton chemical shifts: towards elucidation of the nature of the hydrogen bond and prediction of hydrogen bond distances.

    Science.gov (United States)

    Siskos, Michael G; Tzakos, Andreas G; Gerothanassis, Ioannis P

    2015-09-07

    The inability to determine precisely the location of labile protons in X-ray molecular structures has been a key barrier to progress in many areas of molecular sciences. We report an approach for predicting hydrogen bond distances beyond the limits of X-ray crystallography based on accurate ab initio calculations of O-HO proton chemical shifts, using a combination of DFT and contactor-like polarizable continuum model (PCM). Very good linear correlation between experimental and computed (at the GIAO/B3LYP/6-311++G(2d,p) level of theory) chemical shifts were obtained with a large set of 43 compounds in CHCl3 exhibiting intramolecular O-HO and intermolecular and intramolecular ionic O-H(-)O hydrogen bonds. The calculated OH chemical shifts exhibit a strong linear dependence on the computed (O)HO hydrogen bond length, in the region of 1.24 to 1.85 Å, of -19.8 ppm Å(-1) and -20.49 ppm Å(-1) with optimization of the structures at the M06-2X/6-31+G(d) and B3LYP/6-31+G(d) level of theory, respectively. A Natural Bond Orbitals (NBO) analysis demonstrates a very good linear correlation between the calculated (1)H chemical shifts and (i) the second-order perturbation stabilization energies, corresponding to charge transfer between the oxygen lone pairs and σ antibonding orbital and (ii) Wiberg bond order of the O-HO and O-H(-)O hydrogen bond. Accurate ab initio calculations of O-HO and O-H(-)O (1)H chemical shifts can provide improved structural and electronic description of hydrogen bonding and a highly accurate measure of distances of short and strong hydrogen bonds.

  11. Phase transition in triglycine family of hydrogen bonded ...

    Indian Academy of Sciences (India)

    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.

  12. Synthesis, crystal structures, hydrogen bonding graph-sets and ...

    African Journals Online (AJOL)

    The complex consists of discrete cations (+II) and one perchlorate anion, the cations existing in a slightly distorted octahedral complex with bonding through the heterocyclic and oxime nitrogen atoms. The structure is held together through N-H…O, O-H…O and C-H...O hydrogen bonds occurring between the coordinated ...

  13. Rectangular grids formed by hydrogen-bonding interactions ...

    Indian Academy of Sciences (India)

    Administrator

    Rectangular grids formed by hydrogen-bonding interactions between successive chains of linear polymers. [Co(II)-4,4¢-bpy-Co(II)]n and their inclusion properties: Synthesis and single crystal investigations. E SURESH 1 and MOHAN M BHADBHADE 2. 1Silicates and Catalysis Division, Central Salt & Marine Chemicals ...

  14. Versatile Hydrogen-Hydrogen Bond with a Difference

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 1; Issue 6. Versatile Hydrogen-Hydrogen Bond with a Difference. A G Samuelson. Research News Volume 1 Issue 6 June 1996 pp 87-89. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/001/06/0087-0089 ...

  15. Theoretical study of intramolecular hydrogen bonding in the halo ...

    Indian Academy of Sciences (India)

    Intramolecular hydrogen bonding (IHB) of 1-amino-3-imino-prop-1-ene (AIP), as the simplest resonance-assisted ... correlations between IHB energies based on Espinosa's equation and −G(r)/V(r) values, total electronic den- sity, Laplacian of total ... bonyl oxygen atom.15–17 Finally, electron-withdrawing groups that are ...

  16. Intramolecular hydrogen bonding and tautomerism in Schiff bases ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 121; Issue 6. Intramolecular hydrogen bonding and tautomerism in Schiff bases: Part VI. Syntheses and structural investigation of salicylaldimine and naphthaldimine derivatives. Selen Bi̇lge Zeynel Kiliç Zeli̇ha Hayvali Tuncer Hökelek Serap Safran. Volume 121 ...

  17. Binding of reactive organophosphate by oximes via hydrogen bond

    Indian Academy of Sciences (India)

    J. Chem. Sci. Vol. 125, No. 4, July 2013, pp. 869–873. c Indian Academy of Sciences. Binding of reactive organophosphate by oximes via hydrogen bond. ANDREA PAPPALARDO, MARIA E AMATO, FRANCESCO P BALLISTRERI,. VALENTINA LA PAGLIA FRAGOLA, GAETANO A TOMASELLI, ROSA MARIA TOSCANO.

  18. Examining Student Heuristic Usage in a Hydrogen Bonding Assessment

    Science.gov (United States)

    Miller, Kathryn; Kim, Thomas

    2017-01-01

    This study investigates the role of representational competence in student responses to an assessment of hydrogen bonding. The assessment couples the use of a multiple-select item ("Choose all that apply") with an open-ended item to allow for an examination of students' cognitive processes as they relate to the assignment of hydrogen…

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

    Indian Academy of Sciences (India)

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

  20. Hydrogen bonded networks in formamide [HCONH 2] (= 1− 10 ...

    Indian Academy of Sciences (India)

    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 ... Molecular Modeling Group, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India ...

  1. π Hydrogen bonded complexes of Acetic acid and Trifluoroacetic ...

    Indian Academy of Sciences (India)

    Matrix isolation infrared spectra of O-H···π Hydrogen bonded complexes of Acetic acid and Trifluoroacetic acid with Benzene. PUJARINI BANERJEE, INDRANI BHATTACHARYA and TAPAS CHAKRABORTY. ∗. Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata 700 032, India.

  2. Influence of hydrogen bonding on the generation and stabilization of ...

    Indian Academy of Sciences (India)

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

  3. Dielectric relaxation and hydrogen bonding studies of 1,3 ...

    Indian Academy of Sciences (India)

    Dielectric relaxation and hydrogen bonding studies of 1,3-propanediol–dioxane mixtures using time domain reflectometry technique. MADHUKAR N SHINDE, RAVINDRA B TALWARE, PRAVIN G HUDGE,. YOGESH S JOSHI and ASHOK C KUMBHARKHANE. ∗. School of Physical Sciences, Swami Ramanand Teerth ...

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

    Indian Academy of Sciences (India)

    Abstract. Effects of dimethyl-sulfoxide (DMSO) on the hydrogen bonding structure and dynamics in aque- ous N-methylacetamide (NMA) solution are investigated by classical molecular dynamics simulations. The modifications of structure and interaction between water and NMA in presence of DMSO molecules are cal-.

  5. Intramolecular hydrogen bonding and tautomerism in Schiff bases ...

    Indian Academy of Sciences (India)

    Administrator

    2-Hydroxy Schiff bases; hydrogen bonding and tautomerism; crystal structure; heteronu- clear correlation techniques. 1. Introduction. 2-Hydroxy Schiff bases formed by condensation reactions of salicylaldehyde and 2-hydroxy-1- naphthaldehyde with various amines have been extensively studied. 1–7. This originated from ...

  6. A COMPUTATIONAL STUDY ON THE HYDROGEN-BONDED ...

    African Journals Online (AJOL)

    ABSTRACT. A theoretical study on hydrogen-bonded complex 1 formed by anthyridone (monomer. A) and 2,6-diaminopyridine-3,5-dialdehyde (monomer B) was performed using the AM1 method to obtain its binding energy. A series of complexes 2 to 9 were designed by changing the R-groups on monomer A in complex 1 ...

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

    Indian Academy of Sciences (India)

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

  8. Binding of reactive organophosphate by oximes via hydrogen bond

    Indian Academy of Sciences (India)

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

  9. Hydrogen Bonding Patterns in a Series of 3-Spirocyclic Oxindoles

    African Journals Online (AJOL)

    NICO

    Hydrogen Bonding Patterns in a Series of. 3-Spirocyclic Oxindoles. Andreas Lemmerer* and Joseph P. Michael. Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, P.O. WITS 2050, South Africa. Received 24 May 2010, revised 5 October 2010, accepted 29 October 2010.

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

    Indian Academy of Sciences (India)

    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 ...

  11. Hydrogen bond dynamics and vibrational spectral diffusion in ...

    Indian Academy of Sciences (India)

    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 ...

  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. Crystalline hydrogen-bonded nanocolumns of cyclic thiourea octamers

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-01-01

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

  14. Crystal engineering with urea and thiourea hydrogen-bonding groups

    Energy Technology Data Exchange (ETDEWEB)

    Custelcean, Radu [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division

    2007-09-11

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

  15. Hydrogen-bonding directed crystal engineering of some molecular solids

    Science.gov (United States)

    Xue, Feng

    2000-10-01

    The design of crystalline clathrates and microporous solids is a contemporary goal in crystal engineering, in which hydrogen bonds play a central role because of their strength, directionality and flexibility. We have constructed various layer- and channel-type host structures by using hydrogen-bonding interactions. A novel hydrogen-bonded supramolecular rosette structure is generated from guanidinium and hydrogen carbonate ions in (1) and ( 2). The rosettes are fused into linear ribbons, which are cross-linked by terephthalate or 4-nitrobenzoate ions functioning as hydrogen-bond acceptors, resulting in anionic host layers with tetra-n-butylammonium guest species sandwiched between them. In (3) ˜ (6), new crystalline adducts of tetraalkylammonium terephthalate/trimesate with urea and water molecules result from hydrogen-bond directed assembly of complementary acceptors and donors that generate anionic channel- and layer-type host lattices for the accommodation of bulky hydrophobic cations. Some 4,4'-disubstituted biphenyls manifest their robustness and flexibility as supramolecular building blocks to construct host structures. 4,4'-biphenyl dicarboxylate ion has a strong tendency in generating ladder-type structure in (7) ˜ (10) due to its rigidity and effectiveness as a bifunctional hydrogen-bond acceptor. In (11) ˜ (15), 4,4 '-dicyanobiphenyl, 4,4'-bipyridine-N,N '-dioxide and 4,4'-dinitrobiphenyl exhibit a constructive interplay of strong and weak hydrogen bond functionalities that generate robust synthons. 4-Tritylbenzoic acid crystallizes via the carboxyl dimer supramolecular synthon to produce a wheel-and-axle host lattice that includes different aromatic solvents in its microporous framework in (16) ˜ (25 ), in which the host architecture is robust and yet adaptive. Based on the trigonal symmetry of 2,4,6-tris-4-(halo-phenoxy)-1,3,5-triazines (halo = chloro, bromo) and the Br3 or Cl3 supramolecular synthon, a new hexagonal host lattice has been designed

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

    Science.gov (United States)

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

    1991-02-01

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

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

    Science.gov (United States)

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

    2015-12-08

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

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

    Science.gov (United States)

    Gasparotto, Piero; Ceriotti, Michele

    2014-11-01

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

  19. 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.

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

    Science.gov (United States)

    Gasparotto, Piero; Ceriotti, Michele

    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.

  1. 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.

  2. 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.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    . The topological analyses reveal that several hydrogen bond interactions are present in the complexes. The calculated binding energies, geometric parameters, observed redshifts, and topological analyses suggest that oxygen and sulfur are hydrogen bond acceptors of similar strength. (Graph Presented)....

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

    Science.gov (United States)

    Worth, Catherine L; Blundell, Tom L

    2010-05-31

    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. 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. 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 further insight into factors influencing the evolution of

  5. 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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    The far-infrared absorption spectra have been recorded for hydrogen-bonded complexes of water with methanol and t-butanol embedded in cryogenic neon matrices at 2.8 K. The partial isotopic substitution of individual subunits enabled by a dual inlet deposition procedure provides for the first time...

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

    Science.gov (United States)

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

    2016-05-17

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

  8. Explicit treatment of hydrogen bonds in the universal force field: Validation and application for metal-organic frameworks, hydrates, and host-guest complexes

    Science.gov (United States)

    Coupry, Damien E.; Addicoat, Matthew A.; Heine, Thomas

    2017-10-01

    A straightforward means to include explicit hydrogen bonds within the Universal Force Field (UFF) is presented. Instead of treating hydrogen bonds as non-bonded interaction subjected to electrostatic and Lennard-Jones potentials, we introduce an explicit bond with a negligible bond order, thus maintaining the structural integrity of the H-bonded complexes and avoiding the necessity to assign arbitrary charges to the system. The explicit hydrogen bond changes the coordination number of the acceptor site and the approach is thus most suitable for systems with under-coordinated atoms, such as many metal-organic frameworks; however, it also shows an excellent performance for other systems involving a hydrogen-bonded framework. In particular, it is an excellent means for creating starting structures for molecular dynamics and for investigations employing more sophisticated methods. The approach is validated for the hydrogen bonded complexes in the S22 dataset and then employed for a set of metal-organic frameworks from the Computation-Ready Experimental database and several hydrogen bonded crystals including water ice and clathrates. We show that the direct inclusion of hydrogen bonds reduces the maximum error in predicted cell parameters from 66% to only 14%, and the mean unsigned error is similarly reduced from 14% to only 4%. We posit that with the inclusion of hydrogen bonding, the solvent-mediated breathing of frameworks such as MIL-53 is now accessible to rapid UFF calculations, which will further the aim of rapid computational scanning of metal-organic frameworks while providing better starting points for electronic structure calculations.

  9. The role of hydrogen bonding in the fluorescence quenching of 2,6-bis((E)-2-(benzoxazol-2-yl)vinyl)naphthalene (BBVN) in methanol

    Science.gov (United States)

    Hammam, Essam; Basahi, Jalal; Ismail, Iqbal; Hassan, Ibrahim; Almeelbi, Talal

    2017-02-01

    The excited state hydrogen bonding dynamics of BBVN in hydrogen donating methanol solvent was explored at the TD-BMK/cc-pVDZ level of theory with accounting for the bulk environment effects at the polarizable continuum model (PCM). The heteroatoms of the BBVN laser dye form hydrogen bonds with four methanol molecules. In the formed BBVN-(MeOH)4 complex, the A-type hydrogen bond (N…HO), of an average strength of 25 kJ mol- 1, is twofold stronger than the B-type (O…HO) one. Upon photon absorption, the total HB binding energy increases from 78.5 kJ mol- 1 in the ground state to 82.6 kJ mol- 1 in the first singlet (S1) excited state. In consequence of the hydrogen bonding interaction, the absorption band maximum of the BBVN-(MeOH)4 complex, which was anticipated at 398 nm (exp. 397), is redshifted by 5 nm relative to that of the free dye in methanol. The spectral shift of the stretching vibrational mode for the hydrogen bonded hydroxyl groups (with a maximum shift of 285 cm- 1) from that of the free methanol indicated the elevated strengthening of hydrogen bonds in the excited state. The vibrational modes associated with hydrogen bonding provide effective accepting modes for the dissipation of the excitation energy, thus, decreasing the fluorescence quantum yield of BBVN in alcohols as compared to that in the polar aprotic solvents. Since there is no sign of photochemistry or phosphorescence, it seems reasonable in view of the outcomes of this study to assign the major decay process of the excited singlet (S1) of BBVN in alcohols to vibronically induced internal conversion (IC) facilitated by hydrogen bonding.

  10. Explicit treatment of hydrogen bonds in the universal force field: Validation and application for metal-organic frameworks, hydrates, and host-guest complexes.

    Science.gov (United States)

    Coupry, Damien E; Addicoat, Matthew A; Heine, Thomas

    2017-10-28

    A straightforward means to include explicit hydrogen bonds within the Universal Force Field (UFF) is presented. Instead of treating hydrogen bonds as non-bonded interaction subjected to electrostatic and Lennard-Jones potentials, we introduce an explicit bond with a negligible bond order, thus maintaining the structural integrity of the H-bonded complexes and avoiding the necessity to assign arbitrary charges to the system. The explicit hydrogen bond changes the coordination number of the acceptor site and the approach is thus most suitable for systems with under-coordinated atoms, such as many metal-organic frameworks; however, it also shows an excellent performance for other systems involving a hydrogen-bonded framework. In particular, it is an excellent means for creating starting structures for molecular dynamics and for investigations employing more sophisticated methods. The approach is validated for the hydrogen bonded complexes in the S22 dataset and then employed for a set of metal-organic frameworks from the Computation-Ready Experimental database and several hydrogen bonded crystals including water ice and clathrates. We show that the direct inclusion of hydrogen bonds reduces the maximum error in predicted cell parameters from 66% to only 14%, and the mean unsigned error is similarly reduced from 14% to only 4%. We posit that with the inclusion of hydrogen bonding, the solvent-mediated breathing of frameworks such as MIL-53 is now accessible to rapid UFF calculations, which will further the aim of rapid computational scanning of metal-organic frameworks while providing better starting points for electronic structure calculations.

  11. Hydrogen-bonded encapsulation complexes in protic solvents.

    Science.gov (United States)

    Amaya, Toru; Rebek, Julius

    2004-11-03

    We describe here the behavior of the hydrogen-bonded capsule 1.1 and its complexes in protic solvents. The kinetics and thermodynamics of the encapsulation process were determined through conventional (1)H NMR methods. The enthalpies and entropies of encapsulation are both positive, indicating a process that liberates solvent molecules. The rates of dissociation-association of the capsule were comparable to the rates for the in-out exchange of large guests, which suggests that guest exchange occurs by complete dissociation of the capsule in protic solvents. The stability of the hydrogen-bonded capsule 1.1 toward protic solvents depends strongly on the guests, with the best guest being dimethylstilbene 8. The results establish guidelines for the properties of capsules that could be accessed in water.

  12. Structure and weak hydrogen bonds in liquid acetaldehyde

    Directory of Open Access Journals (Sweden)

    Cordeiro Maria A. M.

    2004-01-01

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

  13. 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.

  14. Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing

    Science.gov (United States)

    Alexandrov, B. S.; Stanev, V. G.; Bishop, A. R.; Rasmussen, K. Ø.

    2012-12-01

    We study the effects of the anharmonic strand-separation dynamics of double-stranded DNA on the infrared spectra of the intramolecular base-pairing hydrogen bonds. Using the extended Peyrard-Bishop-Dauxois model for the DNA breathing dynamics coupled with the Lippincott-Schroeder potential for N-H⋯N and N-H⋯O hydrogen bonding, we identify a high-frequency (˜96 THz) feature in the infrared spectra. We show that this sharp peak arises as a result of the anharmonic base-pair breathing dynamics of DNA. In addition, we study the effects of friction on the infrared spectra. For higher temperatures (˜300 K), where the anharmonicity of DNA dynamics is pronounced, the high-frequency peak is always present irrespective of the friction strength.

  15. NMR and IR investigations of strong intramolecular hydrogen bonds

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Spanget-Larsen, Jens

    2017-01-01

    For the purpose of this review, strong hydrogen bonds have been defined on the basis of experimental data, such as OH stretching wavenumbers, vOH, and OH chemical shifts, dOH (in the latter case after correction for ring current effects). Limits for O–H···Y systems are taken as 2800 > vOH > 1800 cm...... been used as a parameter for hydrogen bond strength in O–H···O systems. On a broad scale, a correlation between OH stretching wavenumbers and O···O distances is observed, as demonstrated experimentally as well as theoretically, but for substituted beta-diketone enols this correlation is relatively weak....

  16. Experimental and Theoretical Studies in Hydrogen-Bonding Organocatalysis

    Directory of Open Access Journals (Sweden)

    Matej Žabka

    2015-08-01

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

  17. 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…

  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. Watson-Crick hydrogen bonding of unlocked nucleic acids.

    Science.gov (United States)

    Langkjær, Niels; Wengel, Jesper; Pasternak, Anna

    2015-11-15

    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 unmodified oligonucleotides and the resulting thermodynamic data support that the hydrogen bonding face of UNA is Watson-Crick like. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    O'Neal, Kristi L; Weber, Stephen G

    2009-01-08

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

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

    Science.gov (United States)

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

    2014-12-14

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

  2. H/D Isotope Effects in Hydrogen Bonded Systems

    Directory of Open Access Journals (Sweden)

    Aleksander Filarowski

    2013-04-01

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

  3. H/D isotope effects in hydrogen bonded systems.

    Science.gov (United States)

    Sobczyk, Lucjan; Obrzud, Monika; Filarowski, Aleksander

    2013-04-16

    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.

  4. The Role of Hydrogen Bond in Designing Molecular Optical Materials

    Directory of Open Access Journals (Sweden)

    Leonardo H. R. Dos Santos

    2016-04-01

    Full Text Available In this perspective article, we revise some of the empirical and semi-empirical strategies for predicting how hydrogen bonding affects molecular and atomic polarizabilities in aggregates. We use p-nitroaniline and hydrated oxalic acid as working examples to illustrate the enhancement of donor and acceptor functional-group polarizabilities and their anisotropy. This is significant for the evaluation of electrical susceptibilities in crystals; and the properties derived from them like the refractive indices.

  5. Protonic transport through solitons in hydrogen-bonded systems

    Energy Technology Data Exchange (ETDEWEB)

    Kavitha, L; Jayanthi, S; Muniyappan, A [Department of Physics, Periyar University, Salem-636 011 (India); Gopi, D, E-mail: louiskavitha@yahoo.co.in [Centre for Nanoscience and Nanotechnology, Periyar University, Salem-636 011 (India)

    2011-09-15

    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.

  6. A Study about Regioisomeric Hydroquinones with Multiple Intramolecular Hydrogen Bonding

    Directory of Open Access Journals (Sweden)

    Maximiliano Martínez-Cifuentes

    2017-04-01

    Full Text Available A theoretical exploration about hydrogen bonding in a series of synthetic regioisomeric antitumor tricyclic hydroquinones is presented. The stabilization energy for the intramolecular hydrogen bond (IHB formation in four structurally different situations were evaluated: (a IHB between the proton of a phenolic hydroxyl group and an ortho-carbonyl group (forming a six-membered ring; (b between the oxygen atom of a phenolic hydroxyl group and the proton of an hydroxyalkyl group (seven membered ring; (c between the proton of a phenolic hydroxyl group with the oxygen atom of the hydroxyl group of a hydroxyalkyl moiety (seven-membered ring; and (d between the proton of a phenolic hydroxyl group and an oxygen atom directly bonded to the aromatic ring in ortho position (five-membered ring. A conformational analysis for the rotation around the hydroxyalkyl substituent is also performed. It is observed that there is a correspondence between the conformational energies and the IHB. The strongest intramolecular hydrogen bonds are those involving a phenolic proton and a carbonyl oxygen atom, forming a six-membered ring, and the weakest are those involving a phenolic proton with the oxygen atom of the chromenone, forming five-membered rings. Additionally, the synthesis and structural assignment of two pairs of regioisomeric hydroquinones, by 2D-NMR experiments, are reported. These results can be useful in the design of biologically-active molecules.

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

    Science.gov (United States)

    Qu, Peng; Tian, Dongxu

    2014-01-01

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

  8. Terahertz Vibrations and Hydrogen-Bonded Networks in Crystals

    Directory of Open Access Journals (Sweden)

    Masae Takahashi

    2014-03-01

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

  9. Strong Ionic Hydrogen Bonding Causes a Spectral Isotope Effect in Photoactive Yellow Protein

    Science.gov (United States)

    Kaledhonkar, Sandip; Hara, Miwa; Stalcup, T. Page; Xie, Aihua; Hoff, Wouter D.

    2013-01-01

    Standard hydrogen bonds are of great importance for protein structure and function. Ionic hydrogen bonds often are significantly stronger than standard hydrogen bonds and exhibit unique properties, but their role in proteins is not well understood. We report that hydrogen/deuterium exchange causes a redshift in the visible absorbance spectrum of photoactive yellow protein (PYP). We expand the range of interpretable isotope effects by assigning this spectral isotope effect (SIE) to a functionally important hydrogen bond at the active site of PYP. The inverted sign and extent of this SIE is explained by the ionic nature and strength of this hydrogen bond. These results show the relevance of ionic hydrogen bonding for protein active sites, and reveal that the inverted SIE is a novel, to our knowledge, tool to probe ionic hydrogen bonds. Our results support a classification of hydrogen bonds that distinguishes the properties of ionic hydrogen bonds from those of both standard and low barrier hydrogen bonds, and show how this classification helps resolve a recent debate regarding active site hydrogen bonding in PYP. PMID:24314088

  10. A novel tubular hydrogen-bond pattern in a new diazaphosphole oxide: a combination of X-ray crystallography and theoretical study of hydrogen bonds.

    Science.gov (United States)

    Sabbaghi, Fahimeh; Pourayoubi, Mehrdad; Farhadipour, Abolghasem; Ghorbanian, Nazila; Andreev, Pavel V

    2017-07-01

    In the structure of 2-(4-chloroanilino)-1,3,2λ 4 -diazaphosphol-2-one, C 12 H 11 ClN 3 OP, each molecule is connected with four neighbouring molecules through (N-H) 2 ...O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R 3 3 (12) and R 4 3 (14) hydrogen-bond ring motifs, combined with a C(4) chain motif. The hole constructed in the tubular architecture includes a 12-atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other. One of the N-H groups of the diazaphosphole ring, not co-operating in classical hydrogen bonding, takes part in an N-H...π interaction. This interaction occurs within the tubular array and does not change the dimension of the hydrogen-bond pattern. The energies of the N-H...O and N-H...π hydrogen bonds were studied by NBO (natural bond orbital) analysis, using the experimental hydrogen-bonded cluster of molecules as the input file for the chemical calculations. In the 1 H NMR experiment, the nitrogen-bound proton of the diazaphosphole ring has a high value of 17.2 Hz for the 2 J H-P coupling constant.

  11. Hydrogen bonds in the blends of polybenzoxazines and N,N‧-(pyridine-2,6-diyl)diacetamide: Inter- or intra-molecular hydrogen bonds?

    Science.gov (United States)

    Bai, Yun; Yang, Po; Wang, Tao; Gu, Yi

    2017-11-01

    This work aims at probing the formation of hydrogen bonds in the blends of polybenzoxazines and additional hydrogen-bond donor moieties-containing compounds. Based on experimental study and computer simulations, we found that the dominant hydrogen bonds of p-cresol-aniline-based dimer (pC-a-D) and polybenzoxazines (PpC-a) were sbnd OH⋯N while N,N‧-(pyridine-2,6-diyl)diacetamide (DAA) was sbnd NH⋯Odbnd Csbnd hydrogen bond. After blending pC-a-D or PpC-a with DAA, additional hydrogen bonds formed, i.e., sbnd OH⋯Odbnd Csbnd and sbnd OH⋯sbnd NH. Moreover, the total quantity of hydrogen bonds of the blends increased. These results suggested that hydrogen bonds formed between polybenzoxazines and the additional hydrogen-bond donor moieties-containing polymers or compounds, and furthermore would be desirable to foster the promoted performance. This novel insight about polybenzoxazine blends is anticipated to help researchers explore more blends of polybenzoxazines with excellent properties.

  12. Experimental measurement and theory of substituent effects in π-hydrogen bonding: complexes of substituted phenols with benzene.

    Science.gov (United States)

    Nikolova, Valia; Ilieva, Sonia; Galabov, Boris; Schaefer, Henry F

    2014-08-01

    IR spectroscopic experiments and theoretical DFT computations reveal the effects of aromatic substituents on π-hydrogen bonding between monosubstituted phenol derivatives and benzene. Simultaneous formation of two π-hydrogen bonds (red-shifting O-H···π and blue-shifting ortho-C-H···π) contribute to the stability of these complexes. The interaction of the acidic phenol O-H proton-donating group with the benzene π-system dominates the complex formation. The experimental shifts of O-H stretching frequencies for the different phenol complexes vary in the range 45-74 cm(-1). Strong effects on hydrogen-bonding energies and frequency shifts of electron-withdrawing aromatic substituents and very weak influence of electron-donating groups have been established. Experimental quantities and theoretical parameters are employed in rationalizing the properties of these complexes. The acidities of the proton-donating phenols describe quantitatively the hydrogen-bonding process. The results obtained provide clear evidence that, when the structural variations are in the proton-donating species, the substituent effects on π-hydrogen bonding follow classic mechanisms, comprising both resonance and direct through-space influences. The performance of three alternative DFT functionals (B3LYP, B97-D, and PBE0 combined with the 6-311++G(2df,2p) basis set) in predicting the O-H frequency shifts upon complexation is examined. For comparison, O-H frequency shifts for several complexes were also determined at MP2/6-31++G(d,p).

  13. The loss of a hydrogen bond: Thermodynamic contributions of a non-standard nucleotide

    OpenAIRE

    Jolley, Elizabeth A.; Znosko, Brent M.

    2016-01-01

    Abstract Non-standard nucleotides are ubiquitous in RNA. Thermodynamic studies with RNA duplexes containing non-standard nucleotides, whether incorporated naturally or chemically, can provide insight into the stability of Watson?Crick pairs and the role of specific functional groups in stabilizing a Watson?Crick pair. For example, an A-U, inosine?U and pseudouridine?A pair each form two hydrogen bonds. However, an RNA duplex containing a central I?U pair or central ??A pair is 2.4 kcal/mol le...

  14. Mediation of hydrogen-bond coupling interactions by programmable heating and salting

    OpenAIRE

    Zhang, Xi; Huang, Yongli; Ma, Zengsheng; Zhou, Yichun; Sun, Chang Q.

    2013-01-01

    We show that programmable heating and salting share the same effect on the frequency shift of the O:H and the H-O stretching phonons of the O:H-O hydrogen bond, which revealed that both heating and salting lengthens and softens the O:H bond and shortens and stiffens the H-O bond due to the weakening of the Coulomb repulsion between electron pairs of adjacent oxygen atoms. Understanding provides possible mechanism for the Hofmeister series and the detergent effect on cloth cleaning.

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

    Science.gov (United States)

    Henchman, Richard H; Irudayam, Sheeba Jem

    2010-12-23

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

  16. Vapor pressure and intramolecular hydrogen bonding in fluorotelomer alcohols.

    Science.gov (United States)

    Krusic, Paul J; Marchione, Alexander A; Davidson, Fredric; Kaiser, Mary A; Kao, Chien-Ping C; Richardson, Raymond E; Botelho, Miguel; Waterland, Robert L; Buck, Robert C

    2005-07-21

    Vapor pressure and aqueous solubility are important parameters used to estimate the potential for transport of chemical substances in the atmosphere. For fluorotelomer alcohols (FTOHs), currently under scrutiny by environmental scientists as potential precursors of persistent perfluorocarboxylates (PFCAs), vapor pressure is the more significant property since these compounds are only very sparingly soluble in water. We have measured the vapor pressures of a homologous series of fluorotelomer alcohols, F(CF2CF2)nCH2CH2OH (n = 2-5), in the temperature range 21-250 degrees C by three independent methods: (a) a method suitable for very low vapor pressures at ambient temperatures (gas-saturation method), (b) an improved boiling point method at controlled pressures (Scott method), and (c) a novel method, requiring milligram quantities of substance, based on gas-phase NMR, a technique largely unfamiliar to chemists and holding promise for studies of relevance to environmental chemistry. The concordant values obtained indicate that recently published vapor pressure data overestimate the vapor pressure at ambient temperature, and therefore the volatility, of this series of fluorinated compounds. It was suggested that substantial intramolecular -O-H...F- hydrogen bonding between the hydroxylic proton and the two fluorines next to the ethanol moiety was responsible for their putative high volatility. Therefore, we have used gas-phase NMR, gas-phase FTIR, 2D NMR heteronuclear Overhauser effect measurements, and high-level ab initio computations to investigate the intramolecular hydrogen bonding in fluorotelomer alcohols. Our studies unequivocally show that hydrogen bonding of this type is not significant and cannot contribute to and cause unusual volatility. The substantially lower vapor pressure at ambient temperatures than previously reported resulting from our work is important in developing a valid understanding of the environmental transport behavior of this class of

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

  18. Discrimination of hydrogen-bonded complexes with axial chirality

    Science.gov (United States)

    Alkorta, Ibon; Elguero, José

    2002-10-01

    The chiral self-discrimination of twelve molecules showing axial chirality has been studied. They included peroxides, hydrazines, carboxylic acids, amides, and allenes. The homo and heterochiral dimers of the selected compounds, that present two hydrogen bonds, have been studied by means of density functional theory (B3LYP/6-31+G**) and ab initio (MP2/6-31+G** and MP2/6-311++G**) methods. The energetic differences found for the complexes of each compound have been rationalized based on their electron density maps and the natural bond orbital analysis. In some cases, intermolecular oxygen-oxygen interactions have been found and interpreted as additional stabilizing contacts.

  19. 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}.

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

    Science.gov (United States)

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

    2011-12-08

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

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

    Science.gov (United States)

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

    2015-12-17

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

  2. Can QTAIM topological parameters be a measure of hydrogen bonding strength?

    Science.gov (United States)

    Mo, Yirong

    2012-05-31

    The block-localized wave function (BLW) method, which is the simplest variant of ab initio valence bond (VB) theory, together with the quantum theory of atoms in molecules (QTAIM) approach, have been used to probe the intramolecular hydrogen bonding interactions in a series of representative systems of resonance-assisted hydrogen bonds (RAHBs). RAHB is characteristic of the cooperativity between the π-electron delocalization and hydrogen bonding interactions and is identified in many biological systems. While the deactivation of the π resonance in these RAHB systems by the use of the BLW method is expected to considerably weaken the hydrogen bonding strength, little change on the topological properties of electron densities at hydrogen bond critical points (HBCPs) is observed. This raises a question of whether the QTAIM topological parameters can be an effective measure of hydrogen bond strength.

  3. Common Hydrogen Bond Interactions in Diverse Phosphoryl Transfer Active Sites

    Science.gov (United States)

    Summerton, Jean C.; Martin, Gregory M.; Evanseck, Jeffrey D.; Chapman, Michael S.

    2014-01-01

    Phosphoryl transfer reactions figure prominently in energy metabolism, signaling, transport and motility. Prior detailed studies of selected systems have highlighted mechanistic features that distinguish different phosphoryl transfer enzymes. Here, a top-down approach is developed for comparing statistically the active site configurations between populations of diverse structures in the Protein Data Bank, and it reveals patterns of hydrogen bonding that transcend enzyme families. Through analysis of large samples of structures, insights are drawn at a level of detail exceeding the experimental precision of an individual structure. In phosphagen kinases, for example, hydrogen bonds with the O3β of the nucleotide substrate are revealed as analogous to those in unrelated G proteins. In G proteins and other enzymes, interactions with O3β have been understood in terms of electrostatic favoring of the transition state. Ground state quantum mechanical calculations on model compounds show that the active site interactions highlighted in our database analysis can affect substrate phosphate charge and bond length, in ways that are consistent with prior experimental observations, by modulating hyperconjugative orbital interactions that weaken the scissile bond. Testing experimentally the inference about the importance of O3β interactions in phosphagen kinases, mutation of arginine kinase Arg280 decreases kcat, as predicted, with little impact upon KM. PMID:25238155

  4. 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.

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

    Science.gov (United States)

    Wang, Yuhao; Sukhishvili, Svetlana

    2015-03-01

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

  6. Direct observation of intermolecular interactions mediated by hydrogen bonding

    Energy Technology Data Exchange (ETDEWEB)

    De Marco, Luigi; Reppert, Mike [Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139 (United States); Department of Chemistry, James Frank Institute and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637 (United States); Thämer, Martin; Tokmakoff, Andrei, E-mail: tokmakoff@uchicago.edu [Department of Chemistry, James Frank Institute and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637 (United States)

    2014-07-21

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

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

    Science.gov (United States)

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

    2002-04-16

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

  8. THE HYBRID COUMPOUNDS AND THE INFLUENCE OF HYDROGEN BONDING

    Directory of Open Access Journals (Sweden)

    F ALLOUCHE

    2014-12-01

    Full Text Available Organic–inorganic hybrid materials have received increasing attention in recent research particularly because of their ability to combine the specific properties of inorganic frameworks and the features of organic molecules, including the formation of weak interactions. These materials have recently attracted further interest due to their attractive potential for application as insulators in the electronics industry. They offer promising opportunities for the development of efficient conductors, ferroelectrics, and semiconductors in a wide range of electronic applications [1,2]. The hybrid compounds are rich in H-bonds and they could be used to this effect because of their potential importance in constructing sophisticated assemblies from discrete ionic or molecular building blocks due to its strength and directionality. In order to enrich the varieties in such kinds of hybrid materials and to investigate the influence of hydrogen bonds on the on the structural features, they have synthesized a new compound, This kind of hydrogen bonding appears in the active sites of several biological systems and is observed in similar previously studied hybrid compounds.

  9. NMR and IR Investigations of Strong Intramolecular Hydrogen Bonds

    Directory of Open Access Journals (Sweden)

    Poul Erik Hansen

    2017-03-01

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

  10. The Influence of Small Monovalent Cations on Neighbouring Hydrogen Bonds of Aquo-Protein Complexes

    Science.gov (United States)

    Sagarik, Kritsana P.; Rode, Bernd M.

    1981-12-01

    The influence of small monovalent metal ions on hydrogen bonds of aquo-protein complexes is studied on Li+/HCONH2-OH2 as an example. Using results obtained from ab initio calculations with minimal GLO basis sets, the remarkable changes in the hydrogen bond energy and charge distribution, due to metal ion complex formation, are discussed. The metal ion seems to enhance strongly the donor-acceptor interaction of the O ... H-N-C=0 hydrogen-bonded system.

  11. Hydrogen Bond Network of Water around Protein Investigated with Terahertz and Infrared Spectroscopy.

    Science.gov (United States)

    Shiraga, Keiichiro; Ogawa, Yuichi; Kondo, Naoshi

    2016-12-20

    The dynamical and structural properties of water at protein interfaces were characterized on the basis of the broadband complex dielectric constant (0.25 to 400 THz) of albumin aqueous solutions. Our analysis of the dielectric responses between 0.25 and 12 THz first revealed hydration water with retarded reorientational dynamics extending ∼8.5 Å (corresponding to three to four layers) out from the albumin surface. Second, the number of nonhydrogen-bonded water was decreased in the presence of the albumin solute, indicating protein inhibits the fragmentation of the water hydrogen-bond network. Finally, water molecules at the albumin interface were found to form a distorted hydrogen-bond structure due to topological and energetic disorder of the protein surface. In addition, the intramolecular O-H stretching vibration of water (∼100 THz), which is sensitive to hydrogen-bond environment, pointed to a trend that hydration water has a larger population of strongly hydrogen-bonded water molecules compared with that of bulk water. From these experimental results, we concluded that the "strengthened" water hydrogen bonds at the protein interface dynamically slow down the reorientational motion of water and form the less-defective hydrogen-bond network by inhibiting the fragmentation of water-water hydrogen bonds. Nevertheless, such a strengthened water hydrogen-bond network is composed of heterogeneous hydrogen-bond distances and angles, and thus characterized as structurally "distorted." Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  12. Effects of ion atmosphere on hydrogen-bond dynamics in aqueous electrolyte solutions

    Science.gov (United States)

    Chandra

    2000-07-24

    We have performed a series of molecular dynamics simulations of aqueous NaCl and KCl solutions at different concentrations to investigate the effects of ion atmosphere on the dynamics of water-water hydrogen bonds at room temperature. The average number of hydrogen bonds per water molecule decreases with increase of ion concentration. The dynamics of hydrogen-bond breaking is found to accelerate somewhat and that of hydrogen-bond structural relaxation, which occurs at a longer time scale, is found to slow down with increasing ion concentration for both NaCl and KCl solutions.

  13. Fluorescence detection of cytosine/guanine transversion based on a hydrogen bond forming ligand.

    Science.gov (United States)

    Nishizawa, Seiichi; Yoshimoto, Keitaro; Seino, Takehiro; Xu, Chun-Yan; Minagawa, Masakazu; Satake, Hiroyuki; Tong, Aijun; Teramae, Norio

    2004-05-10

    In combination with abasic site (AP site)-containing oligodeoxynucleotides (ODNs), we demonstrate potential use of a hydrogen bond forming ligand, 2-amino-7-methyl-1,8-naphthyridine (AMND), for the fluorescence detection of the cytosine (C)/guanine (G) mutation sequence of the cancer repression gene p53. Our method is based on construction of the AP site in ODN duplexes, which allows small synthetic ligands to bind to target nucleobases accompanied by fluorescence signaling: an AP site-containing ODN is hybridized with a target ODN so as to place the AP site toward a target nucleobase, by which hydrophobic microenvironments are provided for ligands to recognize target nucleobases through hydrogen-bonding. In 10mM sodium cacodylate buffer solutions (pH, 7.0) containing 100mM NaCl and 1.0mM EDTA, AMND is found to strongly bind to C (K(d)=1.5x10(-6)M) in the target ODN while the binding affinity for G is relatively moderate (K(d)=50x10(-6)M). Significant fluorescence quenching of AMND is observed only when binding to C, making it possible to judge the C/G transversion with the naked eye.

  14. Mechanism of concerted hydrogen bond reorientation in clathrates of Dianin's compound and hydroquinone.

    Science.gov (United States)

    Nemkevich, Alexandra; Spackman, Mark A; Corry, Ben

    2011-11-23

    Molecular dynamics provides a means to examine the mechanism of reorientation of hydrogen bond networks that are present in a range of biological and crystalline materials. Simulations of hydroxyl reorientation in the six-membered hydrogen bonded rings in crystalline clathrates of Dianin's compound (DC) and hydroquinone (HQ) reveal that in the clathrate of Dianin's compound with ethanol (DC:ethanol), hydroxyl groups perform single independent flips, and occasionally all six hydroxyls in a ring reorient following a sequential mechanism with participation of the guest ethanol molecule. The free energy estimated for this process agrees well with experimental results. The simulations suggest that hydroxyl reorientation occurs in the empty DC lattice as well, but at a higher energy cost, from which we conclude that it is the participation of ethanol that lowers the barrier of reorientation. Single independent flips of hydroxyl groups are observed to be more frequent in the hydroquinone clathrate with methanol (HQ:methanol) than in DC:ethanol, but reorientation of all six hydroxyls does not occur. This is attributed to the larger difference in energy between the original and reoriented positions of hydroxyl hydrogen atoms in HQ:methanol compared to DC:ethanol.

  15. 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.

  16. 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 3.613 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 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole

  17. 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

  18. Mechanisms of hydrogen bond formation between ionic liquids and cellulose and the influence of water content.

    Science.gov (United States)

    Rabideau, Brooks D; Ismail, Ahmed E

    2015-02-28

    We study the dynamics of the formation of multiple hydrogen bonds between ionic liquid anions and cellulose using molecular dynamics simulations. We examine fifteen different ionic liquids composed of 1-alkyl-3-methylimidazolium cations ([Cnmim], n = 1, 2, 3, 4, 5) paired with either chloride, acetate or dimethylphosphate. We map the transitions of anions hydrogen bonded to cellulose into different bonding states. We find that increased tail length in the ionic liquids has only a very minor effect on these transitions, tending to slow the dynamics of the transitions and increasing the hydrogen bond lifetimes. Each anion can form up to four hydrogen bonds with cellulose. We find that this hydrogen bond "redundancy" leads to multiply bonded anions having lifetimes three to four times that of singly bound anions. Such redundant hydrogen bonds account for roughly half of all anion-cellulose hydrogen bonds. Additional simulations for [C2mim]Cl, [C2mim]Ac and [C2mim]DMP were performed at different water concentrations between 70 mol% and 90 mol%. It was found that water crowds the hydrogen bond-accepting sites of the anions, preventing interactions with cellulose. The more water that is present in the system, the more crowded these sites become. Thus, if a hydrogen bond between an anion and cellulose breaks, the likelihood that it will be replaced by a nearby water molecule increases as well. We show that the formation of these "redundant" hydrogen bonding states is greatly affected by the presence of water, leading to steep drops in hydrogen bonding between the anions and cellulose.

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

    Science.gov (United States)

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

    1997-11-01

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

  20. 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.

  1. Hydrogen-Bonding Modification in Biuret Under Pressure.

    Science.gov (United States)

    Borstad, Gustav M; Ciezak-Jenkins, Jennifer A

    2017-02-02

    Biuret (C2H5N3O2) has been studied to 30 GPa by Raman spectroscopy and 50 GPa by X-ray diffraction. Raman peaks exhibit shoulders and splitting that suggests that the molecules undergo reorientation in response to compression. These are observed in three pressure ranges: the first from 3-5 GPa, the second from 8-12 GPa, and finally from 16-20 GPa. The particular modes in the sample that are observed to change in the Raman are strongly linked to the molecular vibrations involving the N-H and the C═O bond, which are most strongly coupled to the hydrogen-bonded lattice structure. The X-ray diffraction suggests that the crystal maintains a monoclinic structure to the highest pressures studied. Although there was a considerable degree of hysteresis observed in some X-ray runs, all the changes observed under pressure are reversible.

  2. Hydrogen bond-assisted macrocyclic oligocholate transporters in lipid membranes.

    Science.gov (United States)

    Widanapathirana, Lakmini; Li, Xueshu; Zhao, Yan

    2012-07-14

    Three macrocyclic oligocholates containing a carboxyl group, a guanidinium ion, and a Cbz-protected amine, respectively, were studied as membrane transporters for hydrophilic molecules. To permeate glucose across lipid bilayers, the macrocycles stacked over one another to form a transmembrane nanopore, driven by a strong tendency of the water molecules in the internal cavities of the amphiphilic macrocycles to aggregate in a nonpolar environment. To transport larger guests such as carboxyfluorescein (CF), the macrocycles acted as carriers to shuttle the guest across the membrane. Hydrogen-bonds between the side chains of the macrocycles strongly affected the transport properties. Surprisingly, the carboxyl group turned out to be far more effective at assisting the aggregation of the oligocholate macrocycles in the membrane than the much stronger carboxylate-guanidinium salt bridge, likely due to competition from the phosphate groups of the lipids for the guanidinium.

  3. Extent of hydrogen-bond protection in folded proteins: a constraint on packing architectures.

    OpenAIRE

    Fernández, Ariel; Berry, R. Stephen

    2002-01-01

    Progressive structuring and ultimately exclusion of water by hydrophobes surrounding backbone hydrogen bonds turn the latter into guiding factors of protein folding. Here we demonstrate that an arrangement of five hydrophobes yields an optimal hydrogen-bond stabilization. This motif is shown to be nearly ubiquitous in native folds.

  4. 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.

  5. 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

  6. 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…

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    results, we find that the hydroperoxide complex is stabilized by ∼4 kJ/mol (Gibbs free energy) more than the alcohol complex. Measured red shifts show the same trend in hydrogen-bond strength with trimethylamine (N acceptor atom) and dimethyl sulfide (S acceptor atom) as the hydrogen-bond acceptors....

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

    DEFF Research Database (Denmark)

    Luo, Jiangshui

    2016-01-01

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

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

    DEFF Research Database (Denmark)

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

    2004-01-01

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

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    complexes are more stable and form stronger hydrogen bonds compared to complexes with MeOH and EtOH, which are comparable, and only for the stronger hydrogen bond donor (TFE) are the small differences in acceptor molecules highlighted. The equilibrium constant for complex formation was determined from...

  11. Substituent effects on hydrogen bonds in DNA : A kohn-sham DFT approach

    NARCIS (Netherlands)

    Guerra, Célia Fonseca; Bickelhaupt, F. Matthias

    2006-01-01

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

  12. The elusive ≡C-H···O complex in the hydrogen bonded systems of ...

    Indian Academy of Sciences (India)

    Abstract. Hydrogen-bonded complexes of phenylacetylene (PhAc) with methanol (MeOH) and diethylether. (DEE) were studied using matrix isolation infrared spectroscopy. This study specifically searched for the ≡C-. H···O hydrogen bonded complex in these systems, which manifest a n-σ* interaction and which is a local.

  13. Nanostructures via noncovalent synthesis: 144 hydrogen bonds bring together 27 components

    NARCIS (Netherlands)

    Paraschiv, V.; Crego Calama, Mercedes; Fokkens, R.H.; Padberg, Clemens J.; Timmerman, P.; Reinhoudt, David

    2001-01-01

    This paper describes the spontaneous and reversible assembly of 20 kDa synthetic hydrogen-bonded assemblies via the formation of 144 cooperative hydrogen bonds. These nanostructures (3.0 × 5.5 nm), consisting of 27 different components, have been carefully characterized using a combination of 1H NMR

  14. The elusive≡ CH··· O complex in the hydrogen bonded systems of ...

    Indian Academy of Sciences (India)

    Hydrogen-bonded complexes of phenylacetylene (PhAc) with methanol (MeOH) and diethylether (DEE) were studied using matrix isolation infrared spectroscopy. This study specifically searched for the ≡CH · · ·O hydrogen bonded complex in these systems, which manifest a n-σ* interaction and which is a local minimum ...

  15. 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

  16. Hydrogen bonding and vibrational energy relaxation in water-acetonitrile mixtures

    NARCIS (Netherlands)

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

    2004-01-01

    We present a study of the effect of hydrogen bonding on vibrational energy relaxation of the OH-stretching mode in pure water and in water-acetonitrile mixtures. The extent of hydrogen bonding is controlled by dissolving water at various concentrations in acetonitrile. Infrared frequency-resolved

  17. Effect of protonation and hydrogen bonding on 2, 4, 6-substituted pyrimidine and its salt complex-experimental and theoretical evidence.

    Science.gov (United States)

    Pillai, Chithra Neelakanda; Chellapan, James

    2014-03-01

    Quantum molecular simulations of chemical systems can provide detailed information that is often inaccessible to direct experimental measurement. Pyrimidine is an interesting π-electron heterocyclic aromatic system which acts as the building block of many nucleic acid bases. The hydrogen bonds associated with the 2, 4, and 6-substituted pyrimidine and its hydrogen sulfate anion are considered for this current work. The experimental and computational evidence for the strength of these intra and intermolecular hydrogen are determined using vibrational spectra and quantum chemical calculations. Thus the effect of hydrogen bonding on the title compound is studied using its geometrical parameters, interaction energies, and vibrational spectra. Aromaticity and charge transfer studies have been performed to ascertain the aromatic behavior of the molecule. The PES scan studies have been done by varying the bond length to ascertain the protonation process of the compound. The IR spectral red shift (∼100 cm⁻¹), blue shift (∼97 cm⁻¹) and broadening of the polar stretching peaks shows the inter and intramolecular hydrogen bonding strength. Bond length alternation of proton donors along with the enormous interaction energies (∼0.5-150 kJ mol⁻¹) between the lone pair and proton donors provides clear evidence for this hydrogen bonding. The charge transfer due to the methyl substitutions which enhances the possibility of hydrogen bonding has been discussed. The main scope of this work is to study the protonation and hydrogen bonding associated with charge transfer which has great effect on the 2-amino-4, 6-dimethyl pyrimidinium hydrogen sulfate (ADHS) molecule.

  18. Hydrogen-bonding layer-by-layer-assembled biodegradable polymeric micelles as drug delivery vehicles from surfaces.

    Science.gov (United States)

    Kim, Byeong-Su; Park, Sang Wook; Hammond, Paula T

    2008-02-01

    We present the integration of amphiphilic block copolymer micelles as nanometer-sized vehicles for hydrophobic drugs within layer-by-layer (LbL) films using alternating hydrogen bond interactions as the driving force for assembly for the first time, thus enabling the incorporation of drugs and pH-sensitive release. The film was constructed based on the hydrogen bonding between poly(acrylic acid) (PAA) as an H-bond donor and biodegradable poly(ethylene oxide)-block-poly(epsilon-caprolactone) (PEO-b-PCL) micelles as the H-bond acceptor when assembled under acidic conditions. By taking advantage of the weak interactions of the hydrogen-bonded film on hydrophobic surfaces, it is possible to generate flexible free-standing films of these materials. A free-standing micelle LbL film of (PEO-b-PCL/PAA)60 with a thickness of 3.1 microm was isolated, allowing further characterization of the bulk film properties, including morphology and phase transitions, using transmission electron microscopy and differential scanning calorimetry. Because of the sensitive nature of the hydrogen bonding employed to build the multilayers, the film can be rapidly deconstructed to release micelles upon exposure to physiological conditions. However, we could also successfully control the rate of film deconstruction by cross-linking carboxylic acid groups in PAA through thermally induced anhydride linkages, which retard the drug release to the surrounding medium to enable sustained release over multiple days. To demonstrate efficacy in delivering active therapeutics, in vitro Kirby-Bauer assays against Staphylococcus aureus were used to illustrate that the drug-loaded micelle LbL film can release significant amounts of an active antibacterial drug, triclosan, to inhibit the growth of bacteria. Because the micellar encapsulation of hydrophobic therapeutics does not require specific chemical interactions, we believe this noncovalent approach provides a new route to integrating active small

  19. Polyelectrolyte conformational transition in aqueous solvent mixture influenced by hydrophobic interactions and hydrogen bonding effects: PAA-water-ethanol.

    Science.gov (United States)

    Sappidi, Praveenkumar; Natarajan, Upendra

    2016-03-01

    Molecular dynamics simulations of poly(acrylic acid) PAA chain in water-ethanol mixture were performed for un-ionized and ionized cases at different degree-of-ionization 0%, 80% and 100% of PAA chain by Na(+) counter-ions and co-solvent (ethanol) concentration in the range 0-90vol% ethanol. Aspects of structure and dynamics were investigated via atom pair correlation functions, number and relaxation of hydrogen bonds, nearest-neighbor coordination numbers, and dihedral angle distribution function for back-bone and side-groups of the chain. With increase in ethanol concentration, chain swelling is observed for un-ionized chain (f=0) and on the contrary chain shrinkage is observed for partially and fully ionized cases (i.e., f=0.8 and 1). For un-ionized PAA, with increase in ethanol fraction ϕeth the number of PAA-ethanol hydrogen bonds increases while PAA-water decreases. Increase in ϕeth leads to PAA chain expansion for un-ionized case and chain shrinkage for ionized case, in agreement with experimental observations on this system. For ionized-PAA case, chain shrinkage is found to be influenced by intermolecular hydrogen bonding with water as well as ethanol. The localization of ethanol molecules near the un-ionized PAA backbone at higher levels of ethanol is facilitated by a displacement of water molecules indicating presence of specific ethanol hydration shell, as confirmed by results of the RDF curves and coordination number calculations. This behavior, controlled by hydrogen bonding provides a significant contribution to such a conformational transition behavior of the polyelectrolyte chain. The interactions between counter-ions and charges on the PAA chain also influence chain collapse. The underlying origins of polyelectrolyte chain collapse in water-alcohol mixtures are brought out for the first time via explicit MD simulations by this study. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Xiang, ShengQi; Zweckstetter, Markus

    2014-06-01

    Hydrogen bonds are essential for the structure, stability and folding of proteins. The identification of intramolecular hydrogen bonds, however, is challenging, in particular in transiently folded states. Here we studied the presence of intramolecular hydrogen bonds in the folding nucleus of the coiled-coil structure of the GCN4 leucine zipper. Using one-bond (1)JNH spin-spin coupling constants and hydrogen/deuterium exchange, we demonstrate that a transient intramolecular hydrogen bond is present in the partially helical folding nucleus of GCN(16-31). The data demonstrate that (1)JNH couplings are a sensitive tool for the detection of transient intramolecular hydrogen bonds in challenging systems where the effective/useable protein concentration is low. This includes peptides at natural abundance but also uniformly labeled biomolecules that are limited to low concentrations because of precipitation or aggregation. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. The solvation of NaCl in model water with different hydrogen bond strength.

    Science.gov (United States)

    Gu, B; Zhang, F S; Wang, Z P; Zhou, H Y

    2008-11-14

    Based on hybrid water models, we design a series of solvent environments with different hydrogen bond strength and study the solvation of NaCl in them. The microstructures and dynamical behaviors of solvents and ion solutes are presented in detail to trace the correlations between the hydrogen bond strength of water and the solvation mechanism of the ions. In the process of the solvation of NaCl, the balance of the competition between breaking original solvent structures and formation of hydration shells around ions is sensitive to the hydrogen bonding ability of water. The results indicate that NaCl is most ideally dissolved in natural water with the strongest hydration effects around both cations and anions. In solvents with both reduced and enhanced hydrogen bond strength, the ions are more inclined to be in contact or aggregate into clusters of different sizes. These phenomena show that appropriate hydrogen bond strength is crucial for water's natural dissolving capacity.

  2. 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

    changes and the redshift favor the Z OH group, matching the results of NBO and AIM calculations. This reflects that the thermochemistry of adduct formation is not a good measure of the hydrogen bond strength in charged adducts, and that the ionic interactions in the E and Z adducts of protonated......It is generally expected that the hydrogen bond strength in a D-H-A adduct is predicted by the difference between the proton affinities of D and A, measured by the adduct stabilization, and demonstrated by the IR redshift of the D-H bond stretching vibrational frequency. These criteria do...... not always yield consistent predictions, as illustrated by the hydrogen bonds formed by the E and Z OH groups of protonated carboxylic acids. The delta-PA and the stabilization of a series of hydrogen bonded adducts indicate that the E OH group forms the stronger hydrogen bonds, whereas the bond length...

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

    Science.gov (United States)

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

    2017-11-09

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

  4. 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....

  5. Hydrogen-Bond Symmetrization Breakdown and Dehydrogenation Mechanism of FeO2H at High Pressure.

    Science.gov (United States)

    Zhu, Sheng-Cai; Hu, Qingyang; Mao, Wendy L; Mao, Ho-Kwang; Sheng, Hongwei

    2017-09-06

    The cycling of hydrogen plays an important role in the geochemical evolution of our planet. Under high-pressure conditions, asymmetric hydroxyl bonds tend to form a symmetric O-H-O configuration in which H is positioned at the center of two O atoms. The symmetrization of O-H bonds improves their thermal stability and as such, water-bearing minerals can be present deeper in the Earth's lower mantle. However, how exactly H is recycled from the deep mantle remains unclear. Here, we employ first-principles free-energy landscape sampling methods together with high pressure-high temperature experiments to reveal the dehydrogenation mechanism of a water-bearing mineral, FeO2H, at deep mantle conditions. Experimentally, we show that ∼50% H is released from symmetrically hydrogen-bonded ε-FeO2H upon transforming to a pyrite-type phase (Py-phase). By resolving the lowest-energy transition pathway from ε-FeO2H to the Py-phase, we demonstrate that half of the O-H bonds in the mineral rupture during the structural transition, leading toward the breakdown of symmetrized hydrogen bonds and eventual dehydrogenation. Our study sheds new light on the stability of symmetric hydrogen bonds during structural transitions and provides a dehydrogenation mechanism for hydrous minerals existing in the deep mantle.

  6. A single-molecule perspective on the role of solvent hydrogen bonds in protein folding and chemical reactions.

    Science.gov (United States)

    Dougan, Lorna; Koti, Ainavarapu Sri Rama; Genchev, Georgi; Lu, Hui; Fernandez, Julio M

    2008-12-22

    We present an array of force spectroscopy experiments that aim to identify the role of solvent hydrogen bonds in protein folding and chemical reactions at the single-molecule level. In our experiments we control the strength of hydrogen bonds in the solvent environment by substituting water (H(2)O) with deuterium oxide (D(2)O). Using a combination of force protocols, we demonstrate that protein unfolding, protein collapse, protein folding and a chemical reaction are affected in different ways by substituting H(2)O with D(2)O. We find that D(2)O molecules form an integral part of the unfolding transition structure of the immunoglobulin module of human cardiac titin, I27. Strikingly, we find that D(2)O is a worse solvent than H(2)O for the protein I27, in direct contrast with the behaviour of simple hydrocarbons. We measure the effect of substituting H(2)O with D(2)O on the force dependent rate of reduction of a disulphide bond engineered within a single protein. Altogether, these experiments provide new information on the nature of the underlying interactions in protein folding and chemical reactions and demonstrate the power of single-molecule techniques to identify the changes induced by a small change in hydrogen bond strength.

  7. Insights into the spontaneity of hydrogen bond formation between formic acid and phthalimide derivatives.

    Science.gov (United States)

    Júnior, Rogério V A; Moura, Gustavo L C; Lima, Nathalia B D

    2016-11-01

    We evaluated a group of phthalimide derivatives, which comprise a convenient test set for the study of the multiple factors involved in the energetics of hydrogen bond formation. Accordingly, we carried out quantum chemical calculations on the hydrogen bonded complexes formed between a sample of phthalimide derivatives with formic acid with the intent of identifying the most important electronic and structural factors related to how their strength and spontaneity vary across the series. The geometries of all species considered were fully optimized at DFT B3LYP/6-31++G(d,p), RM1, RM1-DH2, and RM1-D3H4 level, followed by frequency calculations to determine their Gibbs free energies of hydrogen bond formation using Gaussian 2009 and MOPAC 2012. Our results indicate that the phthalimide derivatives that form hydrogen bond complexes most favorably, have in their structures only one C=O group and at least one NH group. On the other hand, the phthalimide derivatives predicted to form hydrogen bonds least favorably, possess in their structures two carbonyl groups, C=O, and no NH group. The ability to donate electrons and simultaneously receive one acidic hydrogen is the most important property related to the spontaneity of hydrogen bond formation. We further chose two cyclic compounds, phthalimide and isoindolin-1-one, in which to study the main changes in molecular, structural and spectroscopic properties as related to the formation of hydrogen bonds. Thus, the greatest ability of the isoindolin-1-one compound in forming hydrogen bonds is evidenced by the larger effect on the structural, vibrational, and chemical shifts properties associated with the O-H group. In summary, the electron-donating ability of the hydrogen bond acceptor emerged as the most important property differentiating the spontaneity of hydrogen bond formation in this group of complexes.

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

    Science.gov (United States)

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

    2016-03-03

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

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

    Science.gov (United States)

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

    2011-04-07

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

  10. Supramolecular heterostructures formed by sequential epitaxial deposition of two-dimensional hydrogen-bonded arrays

    Science.gov (United States)

    Korolkov, Vladimir V.; Baldoni, Matteo; Watanabe, Kenji; Taniguchi, Takashi; Besley, Elena; Beton, Peter H.

    2017-12-01

    Two-dimensional (2D) supramolecular arrays provide a route to the spatial control of the chemical functionality of a surface, but their deposition is in almost all cases limited to a monolayer termination. Here we investigated the sequential deposition of one 2D array on another to form a supramolecular heterostructure and realize the growth—normal to the underlying substrate—of distinct ordered layers, each of which is stabilized by in-plane hydrogen bonding. For heterostructures formed by depositing terephthalic acid or trimesic acid on cyanuric acid/melamine, we have determined, using atomic force microscopy under ambient conditions, a clear epitaxial arrangement despite the intrinsically distinct symmetries and/or lattice constants of each layer. Structures calculated using classical molecular dynamics are in excellent agreement with the orientation, registry and dimensions of the epitaxial layers. Calculations confirm that van der Waals interactions provide the dominant contribution to the adsorption energy and registry of the layers.

  11. Indirect use of deuterium in solution NMR studies of protein structure and hydrogen bonding.

    Science.gov (United States)

    Tugarinov, Vitali

    2014-02-01

    A description of the utility of deuteration in protein NMR is provided with an emphasis on quantitative evaluation of the effects of deuteration on a number of NMR parameters of proteins: (1) chemical shifts, (2) scalar coupling constants, (3) relaxation properties (R1 and R2 rates) of nuclei directly attached to one or more deuterons as well as protons of methyl groups in a highly deuterated environment, (4) scalar relaxation of 15N and 13C nuclei in 15N-D and 13C-D spin systems as a measure of hydrogen bonding strength, and (5) NOE-based applications of deuteration in NMR studies of protein structure. The discussion is restricted to the 'indirect' use of deuterium in the sense that the description of NMR parameters and properties of the nuclei affected by nearby deuterons (15N, 13C, 1H) is provided rather than those of deuterium itself. Copyright © 2013 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Abdullah M. A. Al Majid

    2014-01-01

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

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

    Science.gov (United States)

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

    2009-06-04

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

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

    OpenAIRE

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

    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 ...

  15. Polarized infrared microspectroscopy of single spruce fibers: hydrogen bonding in wood polymers.

    Science.gov (United States)

    Schmidt, Martin; Gierlinger, Notburga; Schade, Ulrich; Rogge, Tilmann; Grunze, Michael

    2006-12-05

    We studied wood polymers in their native composite structure using mechanically isolated single spruce (Picea abies [L.] Karst.) fibers. Dichroic infrared spectra of fibers placed in a custom-built microfluidic cuvette were acquired in air, in liquid (heavy) water, and in liquid dimethylacetamide using a novel combination of synchrotron-based Fourier transform infrared microspectroscopy with polarization modulation. Differences were observed in the O-H stretching frequency region of the spruce spectra upon changing the ambient conditions. Analysis of these spectral variations provides information on hydrogen bonding, orientation, and accessibility of structural units of the wood polymers in the spruce cell walls. Our in situ approach contributes to a further understanding of the structural details of wood polymers in their native setting. (c) 2006 Wiley Periodicals, Inc.

  16. Sodium-ion electrolytes based on ionic liquids: a role of cation-anion hydrogen bonding.

    Science.gov (United States)

    Chaban, Vitaly V; Andreeva, Nadezhda A

    2016-08-01

    Recent success of the sodium-ion batteries fosters an academic interest for their investigation. Room-temperature ionic liquids (RTILs) constitute universal solvents providing non-volatility and non-flammability to electrolytes. In the present work, we consider four families of RTILs as prospective solvents for NaBF4 and NaNO3 with an inorganic salt concentration of 25 and 50 mol%. We propose a methodology to rate RTILs according to their solvation capability using parameters of the computed radial distribution functions. Hydrogen bonds between the cations and the anions of RTILs were found to indirectly favor sodium solvation, irrespective of the particular RTIL and its concentration. The best performance was recorded in the case of cholinium nitrate. The reported observations and correlations of ionic structures and properties offer important assistance to an emerging field of sodium-ion batteries. Graphical Abstract Sodium-ion electrolytes.

  17. Unveiled electric profiles within hydrogen bonds suggest DNA base pairs with similar bond strengths.

    Directory of Open Access Journals (Sweden)

    Y B Ruiz-Blanco

    Full Text Available Electrical forces are the background of all the interactions occurring in biochemical systems. From here and by using a combination of ab-initio and ad-hoc models, we introduce the first description of electric field profiles with intrabond resolution to support a characterization of single bond forces attending to its electrical origin. This fundamental issue has eluded a physical description so far. Our method is applied to describe hydrogen bonds (HB in DNA base pairs. Numerical results reveal that base pairs in DNA could be equivalent considering HB strength contributions, which challenges previous interpretations of thermodynamic properties of DNA based on the assumption that Adenine/Thymine pairs are weaker than Guanine/Cytosine pairs due to the sole difference in the number of HB. Thus, our methodology provides solid foundations to support the development of extended models intended to go deeper into the molecular mechanisms of DNA functioning.

  18. 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…

  19. Double hydrogen bond interaction in 7-azaindole complexes with protic solvents.

    Science.gov (United States)

    Fakhraee, Sara; Souri, Maryam

    2016-11-01

    The double hydrogen bond interaction between 7-azaindole (7AI) and protic solvents including methanol (MeOH), formamide (FM), formic acid (FA), pyridone (PY) and 7AI has been investigated as a proper model of mutations generated by tautomeric shifts in hydrogen-bonded bases of DNA. The results confirm electrostatic nature for all considered hydrogen bonds except for NH hydrogen bond in 7AI-FA. The largest interaction and polarization energies are obtained for 7AI-FA by means of energy decomposition analyses (EDA). The EDA results show an inverse competitive correlation between polarization and electrostatic components of attraction energy to determine the nature of hydrogen bond. The red-shifted hydrogen bonds are identified for all complexes as a result of hyperconjugation, except for 7AI-MeOH, which its blue-shift effect is attributed to the rehybridization dominating of CH bond. Investigation of aromaticity indices for 7AI complexes represents an increase in aromaticity of pentagonal ring and a decrease in hexagonal ring. Finally, the double hydrogen bond between 7AI and FA is identified as dominant interaction to achieve the tautomerization of 7AI in all applied approaches. Copyright © 2016 Elsevier Inc. All rights reserved.

  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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. [The Effect of Hydrogen Bonding on the Spectrum of HPAM in Various Systems].

    Science.gov (United States)

    Zhai, Zheng

    2015-11-01

    IR and UV-Vis was employed to analyzed the spectrum effect of hydrogen bonding on the partially hydrolyzed polyacrylamide polymer(HPAM). The study reveals that, the characteristic absorption peak of free amino group moves to the low frequency due to the formation of intramolecular hydrogen bonding between amide group and carboxyl group. In the water solution, intramolecular hydrogen bonding is the main factor that shifted maximal absorption towards long wavelength. Intramolecular hydrogen bonding and intermolecular hydrogen bonds exist at the same time in the water solution contains intermediate sodium and calcium ions. While in the high concentration solution, the main form between amide group and carboxyl group is intermolecular hydrogen bonding. The effect of hydrogen bonding on the spectrum of HPAM demonstrates different extent in various systems. In the water solution, the maximum absorption wavelength red shifts 8 nm. In the system contains sodium ions, this shift is 4 nm. And this shift is only 2 nm in the solution contains both sodium ions and calcium ions.

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

    Science.gov (United States)

    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 [⟨dO-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. Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons

    Science.gov (United States)

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

    2018-01-01

    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 homolog 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 Asp23 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 E. coli homolog YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with an LBHB. A PDB-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short (=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. PMID:27989121

  4. 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.

  5. Network analysis and percolation transition in hydrogen bonded clusters: nitric acid and water extracted by tributyl phosphate.

    Science.gov (United States)

    Servis, Michael J; Wu, David T; Braley, Jenifer C

    2017-05-10

    Extraction of polar molecules by amphiphilic species results in a complex variety of clusters whose topologies and energetics control phase behavior and efficiency of liquid-liquid separations. A computational approach including quantum mechanical vibrational frequency calculations and molecular dynamics simulation with intermolecular network theory is used to provide a robust assessment of extractant and polar solute association through hydrogen bonding in the tributyl phosphate (TBP)/HNO3/H2O/dodecane system for the first time. The distribution of local topologies of the TBP/HNO3/H2O hydrogen bonded clusters is shown to be consistent with an equilibrium binding model. Mixed TBP/HNO3/H2O clusters are predicted that have not been previously observable in experiment due to limitations in scattering and spectroscopic resolution. Vibrational frequency calculations are compared with experimental data to validate the experimentally observed TBP-HNO3-HNO3 Chain structure. At high nitric acid and water loading, large hydrogen-bonded clusters of 20 to 80 polar solutes formed. The cluster sizes were found to be exponentially distributed, consistent with a constant average solute association free energy in that size range. Due to the deficit of hydrogen bond donors in the predominantly TBP/HNO3 organic phase, increased water concentrations lower the association free energy and enable growth of larger cluster sizes. For sufficiently high water concentrations, changes in the cluster size distribution are found to be consistent with the formation of a percolating cluster rather than reverse micelles, as has been commonly assumed for the occurrence of an extractant-rich third phase in metal-free solvent extraction systems. Moreover, the compositions of the large clusters leading to percolation agrees with the 1 : 3 TBP : HNO3 ratio reported in the experimental literature for TBP/HNO3/H2O third phases. More generally, the network analysis of cluster formation from atomic

  6. Influence of hydrogen bond accepting ability of anions on the adsorption performance of ionic liquid surface molecularly imprinted polymers.

    Science.gov (United States)

    Zhu, Guifen; Gao, Xia; Wang, Xiaolong; Wang, Jianji; Fan, Jing

    2018-01-12

    To illuminate the influence mechanism of anionic structure of ionic liquids (ILs) on the adsorption performance of surface molecularly imprinted polymers (MIPs), in this work, six newly designed MIPs were prepared on the surface of amino-poly(styrene-divinylbenzene) particles by using imidazolium ILs with the same cation [C 4 mim] + but different anions (Cl, CH 3 SO 3 , PF 6 , BF 4 , C 4 F 7 O 2 , C 4 F 9 SO 3 ) as template molecules, methacrylic acid as functional monomer, and ethylene dimethacrylate as cross-linker. The resulting MIP materials were characterized by IR and SEM, and the influence of hydrogen bond accepting ability of anions on the adsorption performance of the MIPs for the ILs was investigated in acetonitrile. It was found that adsorption capacity of the MIPs towards the ILs decreased in the order MIP [C4mim][Cl]  > MIP [C4mim][C4F7O2]  ≥ MIP [C4mim][BF4] and MIP [C4mim][CH3SO3]  > MIP [C4mim][C4F9SO3]  > MIP [C4mim][PF6] , which is in good agreement with the ability of anions of the ILs to form hydrogen bonds. Ultraviolet, 1 H-NMR and 35 Cl-NMR spectroscopy was then used to study the interactions of anions of the ILs with the functional monomer. It was found that the hydrogen bond interaction between anions of the ILs and acidic proton of the functional monomer was the main driving force for the high adsorption selectivity of the imprinted polymers, and the stronger hydrogen bond interaction indicates higher binding capacity and higher selectivity of the polymers towards the ILs. It was also verified that the ILs with stronger hydrogen bond accepting ability of anions could be selectively extracted by the corresponding IL-MIPs. These results may provide new insight into the recognition mechanism of MIPs for ILs, and are also useful for the rational design of this new class of imprinting materials. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. 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...

  8. Spectroscopic Evidences for Strong Hydrogen Bonds with Selenomethionine in Proteins.

    Science.gov (United States)

    Mundlapati, V Rao; Sahoo, Dipak Kumar; Ghosh, Sanat; Purame, Umesh Kumar; Pandey, Shubhant; Acharya, Rudresh; Pal, Nitish; Tiwari, Prince; Biswal, Himansu S

    2017-02-16

    Careful protein structure analysis unravels many unknown and unappreciated noncovalent interactions that control protein structure; one such unrecognized interaction in protein is selenium centered hydrogen bonds (SeCHBs). We report, for the first time, SeCHBs involving the amide proton and selenium of selenomethionine (Mse), i.e., amide-N-H···Se H-bonds discerned in proteins. Using mass selective and conformer specific high resolution vibrational spectroscopy, gold standard quantum chemical calculations at CCSD(T), and in-depth protein structure analysis, we establish that amide-N-H···Se and amide-N-H···Te H-bonds are as strong as conventional amide-NH···O and amide-NH···O═C H-bonds despite smaller electronegativity of selenium and tellurium than oxygen. It is in fact, electronegativity, atomic charge, and polarizability of the H-bond acceptor atoms are at play in deciding the strength of H-bonds. The amide-N-H···Se and amide-N-H···Te H-bonds presented here are not only new additions to the ever expanding world of noncovalent interactions, but also are of central importance to design new force-fields for better biomolecular structure simulations.

  9. Self-discrimination of enantiomers in hydrogen-bonded dimers.

    Science.gov (United States)

    Alkorta, Ibon; Elguero, Jose

    2002-02-20

    The homochiral and heterochiral hydrogen-bonded (HB) dimers of a set of small model molecules (alpha-amino alcohols) have been studied by means of ab initio methods. The gas-phase calculations have been carried out with the hybrid HF/DFT B3LYP method and the 6-311++G** basis set. The electron density of the complexes has been analyzed using the atoms in molecules (AIM) methodology, which allows characterization of the HB interactions and additional intermolecular contacts. To take into account the water solvation effect, the polarized continuum model (PCM) method has been used to evaluate the Delta G(solv). The gas-phase results show that the heterochiral dimers are the most stable ones for each case studied, while in solution for several cases, the relative stability is reversed and the homochiral dimers become more stable. The AIM analysis shows the typical bond critical points characteristic of the HB and additional bond critical points denoting, in this case, destabilization of intermolecular interaction as CF(3)...F(3)C and CH(3)...H(3)C contacts.

  10. Rotational Spectra of Hydrogen Bonded Networks of Amino Alcohols

    Science.gov (United States)

    Zhang, Di; Zwier, Timothy S.

    2014-06-01

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

  11. Importance of hydrogen bonds to stabilities of copper water complexes

    Science.gov (United States)

    Sukrat, Kanjarat; Parasuk, Vudhichai

    2007-10-01

    An investigation of structures and stabilization energies of copper-water complexes is presented. Possible cluster geometries of [Cu(H 2O) n] 2+ for n = 1-8 were optimized using HF/6-31G(d,p), and energies were determined at the MP2/6-31G(d,p) and B3LYP/6-31G(d,p) levels of theory. In addition, for n = 6, 7, and 8 geometry optimizations at MP2/6-311g(d,p) have been carried out. The basis set effect on stabilization energies was also considered by performing MP2 with 6-31++G(d,p), 6-311G(d,p) and 6-311G(2df,p) single point energy calculations. Only five- and six-fold coordination complexes were obtained with square pyramid (spy) and octahedral (oct) copper coordination as their most stable structures. The hydrogen bonds which form between water molecules in the first and second solvation shell play an important role for the stabilities of the complexes.

  12. Quantum effects in a simple ring with hydrogen bonds.

    Science.gov (United States)

    Kariev, Alisher M; Green, Michael E

    2015-05-14

    Complexes containing multiple arginines are common in proteins. The arginines are typically salt-bridged or hydrogen-bonded, so that their charges do not repel. Here we present a quantum calculation of a ring in which the components of a salt bridge composed of a guanidinium, the arginine side chain, and a carboxylic acid are separated by water molecules. When one water molecule is displaced from the ring, atomic charges of the other water molecule, as well as other properties, are significantly affected. The exchange and correlation energy differences between optimized and displaced rings are larger than thermal energy at room temperature, and larger than the sum of other energy differences. This suggests that calculations on proteins and other systems where such a ring may occur must take quantum effects into account; charges on certain atoms shift as substituents are added to the system: another water molecule, an -OH, or -CN bonded to either moiety. Also, charge shifts accompany proton shifts from the acid to guanidinium to ionize the salt bridge. The consequences of moving one water out of the ring give evidence for electron delocalization. Bond order and atomic charges are determined using natural bond orbital calculations. The geometry of the complex changes with ionization as well as the -OH and -CN additions but not in a simple manner. These results help in understanding the role of groups of arginines in salt-bridged clusters in proteins.

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

    Science.gov (United States)

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

    2016-05-05

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

  14. Deactivation of 6-Aminocoumarin Intramolecular Charge Transfer Excited State through Hydrogen Bonding

    Science.gov (United States)

    Krystkowiak, Ewa; Dobek, Krzysztof; Maciejewski, Andrzej

    2014-01-01

    This paper presents results of the spectral (absorption and emission) and photophysical study of 6-aminocoumarin (6AC) in various aprotic hydrogen-bond forming solvents. It was established that solvent polarity as well as hydrogen-bonding ability influence solute properties. The hydrogen-bonding interactions between S1-electronic excited solute and solvent molecules were found to facilitate the nonradiative deactivation processes. The energy-gap dependence on radiationless deactivation in aprotic solvents was found to be similar to that in protic solvents. PMID:25244014

  15. 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.

  16. FT-IR and NIR spectroscopic investigation of hydrogen bonding in indole-ether systems

    Science.gov (United States)

    Kordić, B.; Kovačević, M.; Sloboda, T.; Vidović, A.; Jović, B.

    2017-09-01

    This paper reports FTIR and NIR spectroscopic study of hydrogen bonding between indole and different ethers in carbon tetrachloride. With increase in ether concentration increase in intensity of red-shifted band, and decrease of intensity of monomer band has been observed. The FTIR and NIR spectroscopic characteristics for N-H⋯O hydrogen bonded complexes and also the equilibrium constants for 1:1 complex formation are given. Influence of structural differences of ethers on hydrogen bonding was investigated using Taft equation. Good correlation has been obtained.

  17. The change in hydrogen bond strength accompanying charge rearrangement: Implications for enzymatic catalysis

    OpenAIRE

    Shan, Shu-ou; Herschlag, Daniel

    1996-01-01

    The equilibrium for formation of the intramolecular hydrogen bond (KHB) in a series of substituted salicylate monoanions was investigated as a function of ΔpKa, the difference between the pKa values of the hydrogen bond donor and acceptor, in both water and dimethyl sulfoxide. The dependence of log KHB upon ΔpKa is linear in both solvents, but is steeper in dimethyl sulfoxide (slope = 0.73) than in water (slope = 0.05). Thus, hydrogen bond strength can undergo ...

  18. 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

    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......-alpha-H...O=C hydrogen bonds. The former is thoroughly investigated, whereas the structure of the latter still is the subject of much discussion. We show that the hydrogen bonds between peptide chains are considerably weaker than what is found in studies of smaller models, e.g., the N-methylacetamide molecule...

  19. Hydrogen bonds in ethylene glycol, monoethanolamine, and ethylenediamine complexes with water

    Science.gov (United States)

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

    2017-02-01

    The structures of ethylene glycol, aminoethanol, and ethylenediamine complexes with water and the formation of hydrogen bonds of different types are optimized using the B3LYP hybrid functional and the aug-CC-pVTZ basis. The parameters of the hydrogen bonds, their energies of interaction, and their oscillation frequencies are calculated, and NBO and QTAIM analyses are performed. The order of hydrogen bonds according to strength is obtained: O-HW···N > O-HW···O > O-H···OW.

  20. 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

    2013-12-02

    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. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Intermolecular and intramolecular hydrogen bonds involving fluorine atoms: implications for recognition, selectivity, and chemical properties.

    Science.gov (United States)

    Dalvit, Claudio; Vulpetti, Anna

    2012-02-06

    A correlation between 19F NMR isotropic chemical shift and close intermolecular F⋅⋅⋅H-X contacts (with X=N or O) has been identified upon analysis of the X-ray crystal structures of fluorinated molecules listed in the Cambridge Structural Database (CSD). An optimal F⋅⋅⋅X distance involving primary and shielded secondary fluorine atoms in hydrogen-bond formation along with a correlation between F⋅⋅⋅H distance and F⋅⋅⋅H-X angle were also derived from the analysis. The hydrogen bonds involving fluorine are relevant, not only for the recognition mechanism and stabilization of a preferred conformation, but also for improvement in the permeability of the molecules, as shown with examples taken from a proprietary database. Results of an analysis of the small number of fluorine-containing natural products listed in the Protein Data Bank (PDB) appear to strengthen the derived correlation between 19F NMR isotropic chemical shift and interactions involving fluorine (also known as the "rule of shielding") and provides a hypothesis for the recognition mechanism and catalytic activity of specific enzymes. Novel chemical scaffolds, based on the rule of shielding, have been designed for recognizing distinct structural motifs present in proteins. It is envisaged that this approach could find useful applications in drug design for the efficient optimization of chemical fragments or promising compounds by increasing potency and selectivity against the desired biomolecular target. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Directory of Open Access Journals (Sweden)

    Antonino Natalello

    2011-04-01

    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.

  3. 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

  4. Three substituted (E)-3-aryl-2-(thienyl)acrylonitriles: isolated molecules, simple hydrogen-bonded chains and hydrogen-bonded sheets.

    Science.gov (United States)

    Cobo, Debora; Quiroga, Jairo; de la Torre, José M; Cobo, Justo; Low, John N; Glidewell, Christopher

    2006-09-01

    The structure of (E)-2-(2-thienyl)-3-(3,4,5-trimethoxyphenyl)acrylonitrile, C16H15NO3S, contains no direction-specific intermolecular interactions. The molecules of (E)-3-(4-bromophenyl)-2-(2-thienyl)acrylonitrile, C13H8BrNS, exhibit orientational disorder of the thienyl fragment, and the molecules are linked into simple C(5) chains by a single C-H...N hydrogen bond. In (E)-3-phenyl-2-(3-thienyl)acrylonitrile, C13H9NS, the molecules are linked into sheets by a combination of one C-H...N hydrogen bond and one C-H...pi(arene) hydrogen bond.

  5. Measuring the micro-polarity and hydrogen-bond donor/acceptor ability of thermoresponsive N-isopropylacrylamide/N-tert-butylacrylamide copolymer films using solvatochromic indicators.

    Science.gov (United States)

    Szczupak, Boguslaw; Ryder, Alan G; Togashi, Denisio M; Rochev, Yuri A; Gorelov, Alexander V; Glynn, Thomas J

    2009-04-01

    Thin polymer films are important in many areas of biomaterials research, biomedical devices, and biological sensors. The accurate in situ measurement of multiple physicochemical properties of thin polymer films is critical in understanding biocompatibility, polymer function, and performance. In this work we demonstrate a facile spectroscopic methodology for accurately measuring the micro-polarity and hydrogen-bond donor/acceptor ability for a series of relatively hydrophilic thermoresponsive copolymers. The micro-polarity of the N-isopropylacrylamide (NIPAM) and N-tert-butylacrylamide (NtBA) co-polymers was evaluated by means of the E(T)(30), alpha, beta, and pi empirical solvatochromic polarity parameters. The data shows that increasing the NtBA fraction in the dry copolymer film reduces polarity and hydrogen-bonding ability. Within the Kamlet-Taft polarity framework, the NIPAM/NtBA copolymer films are strong hydrogen-bond acceptors, strongly dipolar/polarizable, and rather moderate hydrogen-bond donors. This characterization provides a more comprehensive physicochemical description of polymers, which aids the interpretation of film performance. Comparison of the measured E(T)(30) values with literature data for other water-soluble polymers show that dry NIPAM/NtBA copolymers are slightly more polar than poly(ethylene oxide), less polar than polyvinylalcohol, and approximately the same polarity as poly(N-vinyl-2-pyrrolidone). These findings indicate that this spectroscopic method is a facile, rapid, and nondestructive methodology for measuring polymer properties in situ, suitable for most biomaterials research laboratories.

  6. Dynamics and mechanism of structural diffusion in linear hydrogen bond.

    Science.gov (United States)

    Chaiwongwattana, Sermsiri; Phonyiem, Mayuree; Vchirawongkwin, Viwat; Prueksaaroon, Supakit; Sagarik, Kritsana

    2012-01-15

    Dynamics and mechanism of proton transfer in a protonated hydrogen bond (H-bond) chain were studied, using the CH(3)OH(2)(+)(CH(3)OH)(n) complexes, n = 1-4, as model systems. The present investigations used B3LYP/TZVP calculations and Born-Oppenheimer MD (BOMD) simulations at 350 K to obtain characteristic H-bond structures, energetic and IR spectra of the transferring protons in the gas phase and continuum liquid. The static and dynamic results were compared with the H(3)O(+)(H(2)O)(n) and CH(3)OH(2)(+)(H(2)O)(n) complexes, n = 1-4. It was found that the H-bond chains with n = 1 and 3 represent the most active intermediate states and the CH(3)OH(2)(+)(CH(3)OH)(n) complexes possess the lowest threshold frequency of proton transfer. The IR spectra obtained from BOMD simulations revealed that the thermal energy fluctuation and dynamics help promote proton transfer in the shared-proton structure with n = 3 by lowering the vibrational energy for the interconversion between the oscillatory shuttling and structural diffusion motions, leading to a higher population of the structural diffusion motion than in the shared-proton structure with n = 1. Additional explanation on the previously proposed mechanisms was introduced, with the emphases on the energetic of the transferring proton, the fluctuation of the number of the CH(3)OH molecules in the H-bond chain, and the quasi-dynamic equilibriums between the shared-proton structure (n = 3) and the close-contact structures (n ≥ 4). The latter prohibits proton transfer reaction in the H-bond chain from being concerted, since the rate of the structural diffusion depends upon the lifetime of the shared-proton intermediate state. Copyright © 2011 Wiley Periodicals, Inc.

  7. 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.

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

    National Research Council Canada - National Science Library

    Chin-Wei Chiou; Yung-Chih Lin; Lei Wang; Chiharu Hirano; Yoshinori Suzuki; Teruaki Hayakawa; Shiao-Wei Kuo

    2014-01-01

    ...) 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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-05-01

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

  10. De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity

    Science.gov (United States)

    Boyken, Scott E.; Chen, Zibo; Groves, Benjamin; Langan, Robert A.; Oberdorfer, Gustav; Ford, Alex; Gilmore, Jason; Xu, Chunfu; DiMaio, Frank; Pereira, Jose Henrique; Sankaran, Banumathi; Seelig, Georg; Zwart, Peter H.; Baker, David

    2017-01-01

    In nature, structural specificity in DNA and proteins is encoded quite differently: in DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen bond networks with atomic accuracy is a milestone for protein design and enables the programming of protein interaction specificity for a broad range of synthetic biology applications. PMID:27151862

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

    Science.gov (United States)

    Zentel, Tobias; Kühn, Oliver

    2016-12-21

    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.

  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. 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.

  14. [Intermolecular hydrogen bond between protein and flavonoid and its contribution to the stability of the flavonoids].

    Science.gov (United States)

    Fang, Ru; Leng, Xiao-jing; Wu, Xia; Li, Qi; Hao, Rui-fang; Ren, Fa-zheng; Jing, Hao

    2012-01-01

    The interactions between three proteins (BSA, lysozyme and myoglobin) and three flavonoids (quercetin, kaempferol and rutin) were analyzed, using three-dimensional fluorescence spectrometry in combination with UV-Vis spectrometry and Fourier transform infrared (FTIR) spectroscopy. The stabilities of unbound flavonoids and protein-bound flavonoids were compared. The correlation between the interaction and stability was analyzed. The results showed that the hydrophobic interaction was the main binding code in all proteins and flavonoids systems. However, the hydrogen bond has been involved merely in the BSA system. The stability of all three flavonoids (quercetin, kaempferol and rutin) was improved by BSA. There was a great correlation between the hydrogen bonding and the stability of the flavonoids in the presence of BSA. It suggested that the protection of BSA on the flavonoids was due to the intermolecular hydrogen bonding between BSA and flavonoid, and the stronger hydrogen bonding resulted in more protection.

  15. 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

  16. Quantifying Hydrogen-Bond Populations in Dimethyl Sulfoxide/Water Mixtures.

    Science.gov (United States)

    Oh, Kwang-Im; Rajesh, Kavya; Stanton, John F; Baiz, Carlos R

    2017-09-11

    Dimethyl sulfoxide (DMSO) disrupts the hydrogen-bond networks in water. The widespread use of DMSO as a cosolvent, along with its unusual attributes, have inspired numerous studies. Herein, infrared absorption spectroscopy of the S=O stretching mode combined with molecular dynamics and quantum chemistry models were used to directly quantify DMSO/water hydrogen-bond populations in binary mixtures. Singly H-bonded species are dominant at 10 mol %, due to strong DMSO-water interactions. We found an unexpected increase in non-hydrogen-bonded DMSO near the eutectic point (ca. 35 mol %) which also correlates with several abnormalities in the bulk solution properties. We find evidence for three distinct regimes: 1) strong DMSO-water interactions (90 mol %). We propose a "step in" mechanism, which involves hydrogen bonding between water and the DMSO aggregate species. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

    Hansen, Poul Erik

    2015-01-30

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

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

    DEFF Research Database (Denmark)

    Hansen, Poul Erik

    2015-01-01

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

  19. Diferrocenyl tosyl hydrazone with an ultrastrong NHFe hydrogen bond as double click switch.

    Science.gov (United States)

    Förster, Christoph; Veit, Philipp; Ksenofontov, Vadim; Heinze, Katja

    2015-01-28

    The ultrastrong and short intramolecular NHFe hydrogen bond in diferrocenyl hydrazone raises the barrier for intramolecular electron transfer in its mixed-valent cation and is only disrupted by double oxidation to .

  20. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Langkilde, Annette; Kristensen, Søren M.; Lo Leggio, Leila; Mølgaard, Anne [Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen (Denmark); Jensen, Jan H. [Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen (Denmark); Department of Chemistry, University of Iowa, IA 52242 (United States); Houk, Andrew R. [Department of Chemistry, University of Iowa, IA 52242 (United States); Navarro Poulsen, Jens-Christian [Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen (Denmark); Kauppinen, Sakari [Novozymes, Novo Allé, DK-2880 Bagsvaerd (Denmark); Larsen, Sine, E-mail: slarsen@esrf.fr [Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen (Denmark); European Synchrotron Radiation Facility (ESRF), BP 220, F-38043 Grenoble CEDEX (France)

    2008-08-01

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

  2. Hydrogen bond docking preference in furans: OH⋯π vs. OH⋯O.

    Science.gov (United States)

    Jiang, Xiaotong; Tsona, Narcisse T; Tang, Shanshan; Du, Lin

    2018-02-15

    The docking sites of hydrogen bonds in complexes formed between 2,2,2-trifluoroethanol (TFE), furan (Fu), and 2-methyl furan (MF) have been investigated. Using density functional theory (DFT) calculations, gas phase and matrix isolation FTIR spectroscopies, the strengths of OH⋯O and OH⋯π hydrogen bonds in the complexes were compared to find the docking preference. Calculations suggest that the hydrogen bond donor, TFE, is more likely to dock onto the oxygen atom of the aromatic furans ring, and consequently, the OH⋯O type hydrogen bond is relatively stronger than the OH⋯π type. The FTIR spectrum in the OH-stretching fundamental range obtained at room temperatures has been compared with that obtained at extremely low temperatures in the matrix. The fundamental and the red shifts of OH-stretching vibrations were observed in both FTIR spectra, confirming the formation of hydrogen bonded complexes. By assessing the ability of furan and MF to participate in the formation of OH⋯O hydrogen bond, the effect of ring methylation has been highlighted. From the calculated geometric and thermodynamic parameters as well as the frequency shift of the OH-stretching vibrations in complexes, TFE-MF is found to be more stable than TFE-Fu, which suggests that the strength of the OH⋯O hydrogen bond in TFE-MF originates from the high activity of the furan molecule caused by the methylation of the aromatic ring. The present study furthers the knowledge of docking preference in heteroaromatic molecules and is helpful to understand the nature of intermolecular interactions between hydrogen bond donors and acceptors, including both electron-deficient atoms and π cloud. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Enhancing the hydrogen bond between the bridged hydrogen atom of diborane and ammonia.

    Science.gov (United States)

    Gao, Lei; Zhang, Xueying; Meng, Lingpeng; Zeng, Yanli

    2015-09-01

    The character of the bridged hydrogen atom (Hb) of B2H6 has become a hot issue in recent years. In this work, the complexes B2H6 · · · NH3, B2H2X4 · · · nNH3 (n = 1, 2) and 2HF · · · B2H2X4 · · · 2NH3 (X = Cl, Br, I) were constructed and studied based on the M06-2X calculations to investigate how to enhance the Hb · · · N hydrogen-bonded interaction. When the terminal hydrogen atoms (Ht) of B2H6 were replaced by X (X = Cl, Br, I) atoms, the Hb · · · N hydrogen bond were strengthened. According to the electrostatic potentials in B2H2X4, two HF molecules were added to the interspace of the B-H-B-H four-membered ring of the B2H2X4 · · · 2NH3 complexes, and H · · · X hydrogen bond formed, resulting in further enhancing effect of Hb · · · N hydrogen bond. As a result, the positive cooperative effect of Hb · · · N hydrogen bond and H · · · X hydrogen bond do enhance the interactions of each other. The two measures not only enhance the strength of Hb · · · N hydrogen bond, but also achieve the goal to make the Hb · · · N hydrogen bond perpendicular to B · · · B direction.

  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. A second order thermodynamic perturbation theory for hydrogen bond cooperativity in water

    OpenAIRE

    Marshall, Bennett D.

    2017-01-01

    It has been extensively demonstrated through first principles quantum mechanics calculations that water exhibits strong hydrogen bond cooperativity. Classical molecular simulation and statistical mechanics methods typically assume pairwise additivity, meaning they cannot account for these 3-body and higher cooperative effects. In this document, we extend second order thermodynamic perturbation theory to correct for hydrogen bond cooperativity in 4 site water. We show that the association theo...

  6. Hydrogen bond docking preference in furans: Osbnd H ⋯ π vs. Osbnd H ⋯ O

    Science.gov (United States)

    Jiang, Xiaotong; Tsona, Narcisse T.; Tang, Shanshan; Du, Lin

    2018-02-01

    The docking sites of hydrogen bonds in complexes formed between 2,2,2-trifluoroethanol (TFE), furan (Fu), and 2-methyl furan (MF) have been investigated. Using density functional theory (DFT) calculations, gas phase and matrix isolation FTIR spectroscopies, the strengths of Osbnd H ⋯ O and Osbnd H ⋯ π hydrogen bonds in the complexes were compared to find the docking preference. Calculations suggest that the hydrogen bond donor, TFE, is more likely to dock onto the oxygen atom of the aromatic furans ring, and consequently, the Osbnd H ⋯ O type hydrogen bond is relatively stronger than the Osbnd H ⋯ π type. The FTIR spectrum in the OH-stretching fundamental range obtained at room temperatures has been compared with that obtained at extremely low temperatures in the matrix. The fundamental and the red shifts of OH-stretching vibrations were observed in both FTIR spectra, confirming the formation of hydrogen bonded complexes. By assessing the ability of furan and MF to participate in the formation of Osbnd H ⋯ O hydrogen bond, the effect of ring methylation has been highlighted. From the calculated geometric and thermodynamic parameters as well as the frequency shift of the OH-stretching vibrations in complexes, TFE-MF is found to be more stable than TFE-Fu, which suggests that the strength of the Osbnd H ⋯ O hydrogen bond in TFE-MF originates from the high activity of the furan molecule caused by the methylation of the aromatic ring. The present study furthers the knowledge of docking preference in heteroaromatic molecules and is helpful to understand the nature of intermolecular interactions between hydrogen bond donors and acceptors, including both electron-deficient atoms and π cloud.

  7. Urea, but not guanidinium, destabilizes proteins by forming hydrogen bonds to the peptide group

    OpenAIRE

    Lim, Woon Ki; Rösgen, Jörg; Englander, S. Walter

    2009-01-01

    The mechanism by which urea and guanidinium destabilize protein structure is controversial. We tested the possibility that these denaturants form hydrogen bonds with peptide groups by measuring their ability to block acid- and base-catalyzed peptide hydrogen exchange. The peptide hydrogen bonding found appears sufficient to explain the thermodynamic denaturing effect of urea. Results for guanidinium, however, are contrary to the expectation that it might H-bond. Evidently, urea and guanidiniu...

  8. Charge Transfer Interaction and Hydrogen Bonding between Vitamine K1 and Dihydrovitamine K1

    Science.gov (United States)

    Nagahira, Yukio; Matsuki, Kazunori; Fukutome, Hideo

    1981-01-01

    We studied visible and infrared spectra, in particular their temperature dependence, of Vitamine K1 oil dissolving dihydrovitamine K1. Vitamine K1 and dihydrovitamine K1 were found to form charge transfer complexes and hydrogen bonds in the mixture. A co-crystal of Dihydrovitamine K1 and Vitamine K1 with charge transfer interaction and hydrogen bonding was shown to grow in a narrow temperature range near -20°C.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-10-15

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

  10. Quantification of Hydrogen Bond Strength Based on Interaction Coordinates: A New Approach.

    Science.gov (United States)

    Pandey, Sarvesh Kumar; Manogaran, Dhivya; Manogaran, Sadasivam; Schaefer, Henry F

    2017-08-17

    A new approach to quantify hydrogen bond strengths based on interaction coordinates (HBSBIC) is proposed and is very promising. In this research, it is assumed that the projected force field of the fictitious three atoms fragment (DHA) where D is the proton donor and A is the proton acceptor from the full molecular force field of the H-bonded complex characterizes the hydrogen bond. The "interaction coordinate (IC)" derived from the internal compliance matrix elements of this three-atom fragment measures how the DH covalent bond (its electron density) responds to constrained optimization when the HA hydrogen bond is stretched by a known amount (its electron density is perturbed by a specified amount). This response of the DH bond, based on how the IC depends on the electron density along the HA bond, is a measure of the hydrogen bond strength. The inter- and intramolecular hydrogen bond strengths for a variety of chemical and biological systems are reported. When defined and evaluated using the IC approach, the HBSBIC index leads to satisfactory results. Because this involves only a three-atom fragment for each hydrogen bond, the approach should open up new directions in the study of "appropriate small fragments" in large biomolecules.

  11. Solvatomagnetic Comparison Method: A Proper Quantification of Solvent Hydrogen-Bond Basicity.

    Science.gov (United States)

    Laurence, Christian; Legros, Julien; Nicolet, Pierre; Vuluga, Daniela; Chantzis, Agisilaos; Jacquemin, Denis

    2014-07-10

    The hydrogen-bond-acceptor basicity of an important class of solvents, the amphiprotic solvents (water, alcohols, primary and secondary amides, and carboxylic acids), has not yet been properly parametrized. In this work, the first scale of solvent hydrogen-bond basicity applicable to amphiprotic solvents is established by means of a new method that compares the 19 F NMR chemical shifts of 4-fluorophenol and 4-fluoroanisole in hydrogen-bond-acceptor solvents. This so-called solvatomagnetic comparison method is free of the shortcomings of the solvatochromic comparison method used so far and is easier to carry out than the pure base calorimetric method. The validity of the new scale is assessed by good linear correlations with spectroscopic, thermodynamic, and kinetic solute properties depending on the solvent hydrogen-bond basicity. In such correlation analysis of solvent effects on physicochemical properties, solvent and solute hydrogen-bond basicity scales must not be mixed, since it is shown here that solute and solvent scales are not equivalent. A comprehensive collection of parameters quantifying the hydrogen-bond basicity is presented for 168 solvents.

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

    Science.gov (United States)

    Mondal, Abhisek; Datta, Saumen

    2017-06-01

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

  13. The influence of elongational flow on hydrogen bond formation and stability of the homogeneous phase of binary hydrogen- bonded polymer blends

    NARCIS (Netherlands)

    Dormidontova, Elena E.; Brinke, Gerrit ten

    2000-01-01

    Macrophase separation tendency induced by flow in binary blends of polymers capable of single hydrogen bonding between one of the chain ends is studied analytically. To describe the conformational and orientational properties of a polymer chain a simple dumbbell model is applied. It is demonstrated

  14. Hydrogen-bond-mediated asymmetric cascade reaction of stable sulfur ylides with nitroolefins: scope, application and mechanism.

    Science.gov (United States)

    Lu, Liang-Qiu; Li, Fang; An, Jing; Cheng, Ying; Chen, Jia-Rong; Xiao, Wen-Jing

    2012-03-26

    A hydrogen-bond-mediated asymmetric [4+1] annulation/rearrangement cascade of stable sulfur ylides and nitroolefins was developed. This reaction provides a facile route to enantioenriched 4,5-substituted oxazolidinones in moderate to excellent isolated yields (65-96 %) with excellent stereocontrol (up to more than 95:5 d.r. and 97:3 e.r.). This methodology was successfully applied to the concise synthesis of two bioactive molecules. The stereocontrolled modes and mechanism have been proposed to explain the origin of this stereochemistry. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Hydrogen bond symmetrization and equation of state of phase D

    Science.gov (United States)

    Hushur, A.; Manghnani, M. H.; Lonappan, D.; Smyth, J. R.; Ye, Y.; Dera, P. K.; Frost, D. J.; Hellebrand, E.

    2010-12-01

    We have synthesized phase D at 24 GPa and temperatures of 1250 to 1100°C under conditions of high silica activity. Electron microprobe analysis yielded a crystal composition of Mg1.0Si1.7H3.0O6, and showed phase D coexisting with MgSiO3-perovskite, stishovite, and superhydrous phase B in the P-T quenched end product in the platinum capsule. Phase D sample was identified by Raman spectroscopy and extracted from the capsule for this study. The compressibility of this high-silica-activity phase D has been measured up to 60 GPa at ambient temperature by powder XRD in a diamond anvil cell, using Ne gas as pressure medium. In addition to phase D, diffraction peaks from stishovite and neon are also observed in the XRD patterns. The V decreases smoothly with increasing pressure up to 40 GPa, consistent with the results reported in earlier studies. However, a kink is observed in the trend of V versus pressure above ~40 GPa, which reflects a change in the compression behavior. If we use neon pressure scale by Fei et al (2007), the data to 30 GPa fit well to a third-order Birch-Murnaghan EoS, yielding Vo = 85.09 ± 0.15 Å3; Ko = 167.9 ± 8.6 GPa and Ko' = 4.3 ± 0.5, similar to results for Fe-Al free phase D (Vo = 85.66 ± 0.01 Å3; Ko = 166 ± 3 GPa and Ko' = 4.1 ± 0.3) reported by Frost and Fei [1999]. However, these parameters are larger than those reported for Fe-Al bearing Phase D [Litasov et al. 2007, 2008] and for Fe-Al free Phase D [Shinmei et al. 2008]. The abnormal volume change in this study is attributed to the reported hydrogen bond symetrization in phase D [Tsuchiya et al. 2005]. A least-squares fit using a third-order Birch-Murnaghan EoS to the data of below 30 GPa yields a bulk modulus Ko = 173 (2) GPa for hydrogen off-centered (HOC) phase and Ko = 212 (15) GPa for the data above 40 GPa, hydrogen centered (HC) phase, assuming Ko' is 4. The calculated bulk modulus Ko of HC phase (212 GPa) is 18% larger than the bulk modulus Ko of HOC phase (173 GPa).

  16. Studying the Effect of Site-Specific Hydrophobicity and Polarization on Hydrogen Bond Energy of Protein Using a Polarizable Method.

    Science.gov (United States)

    Ji, Chang G; Xiao, Xudong; Zhang, John Z H

    2012-06-12

    Quantification of backbone hydrogen bond energies in protein folding has remained elusive despite extensive theoretical and experimental investigations over the past 70 years. This is due to difficulties in experimental mutagenesis study as well as the lack of quantitatively reliable methods in theoretical calculation. Recent advance in experiment has enabled accurate measurement of site-specific backbone hydrogen bond energy in protein. In the present work, we developed an accurate and practical polarizable method to study site-specific hydrogen bond energies in the PIN WW domain. Excellent quantitative agreement between our calculated hydrogen bonding energy and recent experimental measurement is obtained. The direct comparison between theory and experiment helps uncover the microscopic mechanism of experimentally observed context dependent hydrogen bond contribution to protein stability in beta-sheet. In particular, our study reveals two effects that act in a cooperative manner to impact the strength of a hydrogen bond. One is the dynamic stability of the hydrogen bond determined by nearby solvent molecules, and the other is the polarization state of the hydrogen bond influenced by local electrostatic environment. The polar character of the hydrogen bond results in strong coupling between hydrophobic and polarization interactions in a cooperative manner. This nonadditive character in hydrogen bonding should help us better understand the microscopic mechanism in protein folding. Our study also investigated the possible structural effect of backbone amide to ester mutation which should be helpful to experimentalists using this technique in mutagenesis study.

  17. Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps

    Science.gov (United States)

    2014-01-01

    Background Sequence determines the three-dimensional structure of RNAs, and thereby plays an important role in carrying out various biological functions. RNA duplexes containing Watson-Crick (WC) basepairs, interspersed with non-Watson-Crick basepairs, are the dominant structural unit and form the scaffold for the 3-dimensional structure of RNA. It is therefore crucial to understand the geometric variation in the dinucleotide steps that form the helices. We have carried out a detailed analysis of the dinucleotide steps formed by AU and GC Watson-Crick basepairs in RNA structures (both free and protein bound) and compared the results to that seen in DNA. Further, the effect of protein binding on these steps was examined by comparing steps in free RNA structures with protein bound RNA structures. Results Characteristic sequence dependent geometries are observed for the RR, RY and YR type of dinucleotide steps in RNA. Their geometric parameters show correlated variations that are different from those observed in B-DNA helices. Subtle, but statistically significant differences are seen in roll, slide and average propeller-twist values, between the dinucleotide steps of free RNA and protein bound RNA structures. Many non-canonical cross-strand and intra-strand hydrogen bonds were identified that can stabilise the RNA dinucleotide steps, among which YR steps show presence of many new unreported interactions. Conclusions Our work provides for the first time a detailed analysis of the conformational preferences exhibited by Watson-Crick basepair containing steps in RNA double helices. Overall, the WC dinucleotide steps show considerable conformational variability. Furthermore, we have identified hydrogen bond interactions in several of the dinucleotide steps that could play a role in determining the preferred geometry, in addition to the intra-basepair hydrogen bonds and stacking interactions. Protein binding affects the conformation of the steps that are in direct contact

  18. Polymerization Effect of Electrolytes on Hydrogen-Bonding Cryoprotectants: Ion–Dipole Interactions between Metal Ions and Glycerol

    Science.gov (United States)

    2015-01-01

    Protectants which are cell membrane permeable, such as glycerol, have been used effectively in the cryopreservation field for a number of decades, for both slow cooling and vitrification applications. In the latter case, the glass transition temperature (Tg) of the vitrification composition is key to its application, dictating the ultimate storage conditions. It has been observed that the addition of some electrolytes to glycerol, such as MgCl2, could elevate the Tg of the mixture, thus potentially providing more storage condition flexibility. The microscopic mechanisms that give rise to the Tg-enhancing behavior of these electrolytes are not yet well understood. The current study focuses on molecular dynamics simulation of glycerol mixed with a variety of metal chlorides (i.e., NaCl, KCl, MgCl2, and CaCl2), covering a temperature range that spans both the liquid and glassy states. The characteristics of the ion–dipole interactions between metal cations and hydroxyl groups of glycerol were analyzed. The interruption of the original hydrogen-bonding network among glycerol molecules by the addition of ions was also investigated in the context of hydrogen-bonding quantity and lifetime. Divalent metal cations were found to significantly increase the Tg by strengthening the interacting network in the electrolyte/glycerol mixture via strong cation–dipole attractions. In contrast, monovalent cations increased the Tg insignificantly, as the cation–dipole attraction was only slightly stronger than the original hydrogen-bonding network among glycerol molecules. The precursor of crystallization of NaCl and KCl was also observed in these compositions, potentially contributing to weak Tg-enhancing ability. The Tg-enhancing mechanisms elucidated in this study suggest a structure-enhancing role for divalent ions that could be of benefit in the design of protective formulations for biopreservation purposes. PMID:25405831

  19. Polymerization effect of electrolytes on hydrogen-bonding cryoprotectants: ion-dipole interactions between metal ions and glycerol.

    Science.gov (United States)

    Weng, Lindong; Elliott, Gloria D

    2014-12-11

    Protectants which are cell membrane permeable, such as glycerol, have been used effectively in the cryopreservation field for a number of decades, for both slow cooling and vitrification applications. In the latter case, the glass transition temperature (Tg) of the vitrification composition is key to its application, dictating the ultimate storage conditions. It has been observed that the addition of some electrolytes to glycerol, such as MgCl2, could elevate the Tg of the mixture, thus potentially providing more storage condition flexibility. The microscopic mechanisms that give rise to the Tg-enhancing behavior of these electrolytes are not yet well understood. The current study focuses on molecular dynamics simulation of glycerol mixed with a variety of metal chlorides (i.e., NaCl, KCl, MgCl2, and CaCl2), covering a temperature range that spans both the liquid and glassy states. The characteristics of the ion-dipole interactions between metal cations and hydroxyl groups of glycerol were analyzed. The interruption of the original hydrogen-bonding network among glycerol molecules by the addition of ions was also investigated in the context of hydrogen-bonding quantity and lifetime. Divalent metal cations were found to significantly increase the Tg by strengthening the interacting network in the electrolyte/glycerol mixture via strong cation-dipole attractions. In contrast, monovalent cations increased the Tg insignificantly, as the cation-dipole attraction was only slightly stronger than the original hydrogen-bonding network among glycerol molecules. The precursor of crystallization of NaCl and KCl was also observed in these compositions, potentially contributing to weak Tg-enhancing ability. The Tg-enhancing mechanisms elucidated in this study suggest a structure-enhancing role for divalent ions that could be of benefit in the design of protective formulations for biopreservation purposes.

  20. Gas Phase Detection of the NH-P Hydrogen Bond and Importance of Secondary Interactions.

    Science.gov (United States)

    Møller, Kristian H; Hansen, Anne S; Kjaergaard, Henrik G

    2015-11-05

    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-stretching frequency red shifts, we find that P is a hydrogen bond acceptor atom similar in strength to S. Both are stronger acceptors than O and significantly weaker acceptors than N. The hydrogen bond angle, ∠NHP, is found to be very sensitive to the functional employed in density functional theory (DFT) optimizations of the complex and is a possible parameter to assess the quality of DFT functionals. Natural bonding orbital (NBO) energies and results from the topological methods atoms in molecules (AIM) and noncovalent interactions (NCI) indicate that the sensitivity is caused by the weakness of the hydrogen bond compared to secondary interactions. We find that B3LYP favors the hydrogen bond and M06-2X favors the secondary interactions leading to under- and overestimation, respectively, of the hydrogen bond angle relative to a DF-LCCSD(T)-F12a calculated angle. The remaining functionals tested, B3LYP-D3, B3LYP-D3BJ, CAM-B3LYP, and ωB97X-D, as well as MP2, show comparable contributions from the hydrogen bond and the secondary interactions and are close to DF-LCCSD(T)-F12a results.

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

    DEFF Research Database (Denmark)

    Tsivintzelis, Ioannis; Grenner, Andreas; Economou, Ioannis

    2008-01-01

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

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

    Science.gov (United States)

    Møller, Kristian H; Tram, Camilla Mia; Kjaergaard, Henrik G

    2017-04-20

    Hydroperoxides are formed in significant amounts in the atmosphere by oxidation of volatile organic compounds and are key in aerosol formation. In a room-temperature experiment, we detected the formation of bimolecular complexes of tert-butyl hydroperoxide (t-BuOOH) and the corresponding alcohol tert-butanol (t-BuOH), with dimethyl ether (DME) as the hydrogen-bond acceptor. Using a combination of Fourier-transform infrared spectroscopy and quantum chemical calculations, we compare the strength of the OH-O hydrogen bond and the total strength of complexation. We find that, both in terms of observed red shifts and determined equilibrium constants, t-BuOOH is a significantly better hydrogen-bond donor than t-BuOH, a result that is backed by a number of calculated parameters and can be explained by a weaker OH bond in the hydroperoxide. On the basis of combined experimental and theoretical results, we find that the hydroperoxide complex is stabilized by ∼4 kJ/mol (Gibbs free energy) more than the alcohol complex. Measured red shifts show the same trend in hydrogen-bond strength with trimethylamine (N acceptor atom) and dimethyl sulfide (S acceptor atom) as the hydrogen-bond acceptors.

  3. Hydrogen bond cooperativity and the three-dimensional structures of water nonamers and decamers.

    Science.gov (United States)

    Pérez, Cristóbal; Zaleski, Daniel P; Seifert, Nathan A; Temelso, Berhane; Shields, George C; Kisiel, Zbigniew; Pate, Brooks H

    2014-12-22

    Broadband rotational spectroscopy of water clusters produced in a pulsed molecular jet expansion has been used to determine the oxygen atom geometry in three isomers of the nonamer and two isomers of the decamer. The isomers for each cluster size have the same nominal geometry but differ in the arrangement of their hydrogen bond networks. The nearest neighbor OO distances show a characteristic pattern for each hydrogen bond network isomer that is caused by three-body effects that produce cooperative hydrogen bonding. The observed structures are the lowest energy cluster geometries identified by quantum chemistry and the experimental and theoretical OO distances are in good agreement. The cooperativity effects revealed by the hydrogen bond OO distance variations are shown to be consistent with a simple model for hydrogen bonding in water that takes into account the cooperative and anticooperative bonding effects of nearby water molecules. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

    Woutersen, Sander

    2007-10-21

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

  5. How short is the strongest hydrogen bond in the proton-bound homodimers of pyridine derivatives?

    Science.gov (United States)

    Gurinov, Andrey A; Lesnichin, Stepan B; Limbach, Hans-Heinrich; Shenderovich, Ilya G

    2014-11-13

    Hydrogen bond geometries in the proton-bound homodimers of ortho-unsubstituted and ortho-methylsubstituted pyridine derivatives in aprotic polar solution were estimated using experimental NMR data. Within the series of homodimers studied the hydrogen bond lengths depend on the proton affinity of pyridines and--at least for the ortho-methylsubstituted pyridines--on the pKa of the conjugate acids in an approximately quadratic manner. The shortest possible hydrogen bond in the homodimers of ortho-unsubstituted pyridines is characterized by the N···N distance of 2.613 Å. Steric repulsion between the methyl groups of the ortho-methylsubstituted pyridines becomes operative at an N···N distance of ∼2.7 Å and limits the closest approach to 2.665 Å.

  6. Molecular tuning of the closed shell C-H···F-C hydrogen bond.

    Science.gov (United States)

    Lu, Norman; Ley, Rebecca M; Cotton, Charles E; Chung, Wei-Cheng; Francisco, Joseph S; Negishi, Ei-ichi

    2013-08-29

    The existence of the rare six-membered and intramolecular C-H···F-C hydrogen-bond has been experimentally proven in the gas phase and in the solid state recently. However, the effect of the substituents on this C-H···F-C hydrogen-bond system has never been reported. In view of the importance of this type of C-H···F-C H-bonding whose weak interaction has been found critical in nanotechnology and biological systems, the nine functional groups composed of electron donating and electron withdrawing groups are inserted into this C-H···F-C interaction to study the group effect on the hydrogen bonding. Group effects on this C-H···F-C H-bonding system have been found, and their effects on the H-bonding system have been found to be tunable.

  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......-stretching frequency red shifts, we find that P is a hydrogen bond acceptor atom similar in strength to S. Both are stronger acceptors than O and significantly weaker acceptors than N. The hydrogen bond angle, ∠NHP, is found to be very sensitive to the functional employed in density functional theory (DFT......) optimizations of the complex and is a possible parameter to assess the quality of DFT functionals. Natural bonding orbital (NBO) energies and results from the topological methods atoms in molecules (AIM) and noncovalent interactions (NCI) indicate that the sensitivity is caused by the weakness of the hydrogen...

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  9. Adsorption of bisphenol A based on synergy between hydrogen bonding and hydrophobic interaction.

    Science.gov (United States)

    Zhou, Xiangyu; Wei, Junfu; Liu, Kai; Liu, Nana; Zhou, Bin

    2014-11-25

    The study mainly investigated the synergetic adsorption of hydrogen bonding and hydrophobic interaction. To simplify the adsorption driving forces and binding sites, the hydrophilic and hydrophobic microdomain was introduced onto polypropylene (PP) nonwoven. The amphiphilic structure was constructed for the adsorption of bisphenol A (BPA). A solvent shielding experiment was conducted to calculate the contributions of diverse interactions. Also, a specific structure without hydrophilic microdomain was constructed as comparison to determine the adsorption rate and quantify the diffusion behaviors. On the basis of double-exponential model, the adsorption process can be distinctly divided into three stages, namely film diffusion stage, intralayer diffusion stage, and dynamic equilibrium stage. The adsorption rate was dramatically improved due to the influence of hydrophilic microdomain and participation of hydrogen bonding adsorption. Discussions on adsorption priority were also proposed. The results of surface energy heterogeneity revealed that the hydrophilic microdomain or the hydrogen bonding site was occupied preferentially.

  10. Bio-inspired carbon nanotube-polymer composite yarns with hydrogen bond-mediated lateral interactions.

    Science.gov (United States)

    Beese, Allison M; Sarkar, Sourangsu; Nair, Arun; Naraghi, Mohammad; An, Zhi; Moravsky, Alexander; Loutfy, Raouf O; Buehler, Markus J; Nguyen, SonBinh T; Espinosa, Horacio D

    2013-04-23

    Polymer composite yarns containing a high loading of double-walled carbon nanotubes (DWNTs) have been developed in which the inherent acrylate-based organic coating on the surface of the DWNT bundles interacts strongly with poly(vinyl alcohol) (PVA) through an extensive hydrogen-bond network. This design takes advantage of a toughening mechanism seen in spider silk and collagen, which contain an abundance of hydrogen bonds that can break and reform, allowing for large deformation while maintaining structural stability. Similar to that observed in natural materials, unfolding of the polymeric matrix at large deformations increases ductility without sacrificing stiffness. As the PVA content in the composite increases, the stiffness and energy to failure of the composite also increases up to an optimal point, beyond which mechanical performance in tension decreases. Molecular dynamics (MD) simulations confirm this trend, showing the dominance of nonproductive hydrogen bonding between PVA molecules at high PVA contents, which lubricates the interface between DWNTs.

  11. A combined deuterium NMR and quantum chemical investigation of inequivalent hydrogen bonds in organic solids.

    Science.gov (United States)

    Webber, Renee; Penner, Glenn H

    2012-01-01

    Deuterium magic angle spinning (MAS) NMR spectroscopy and quantum chemical calculations are used to investigate organic solids in which inequivalent hydrogen bonds are present. The use of (2)H MAS allows one to measure the chemical shift, δ, quadrupolar coupling constant, C(Q), and asymmetry in the quadrupolar interaction, η(Q), for each type of hydrogen bond present in the system. Quantum chemical calculations of the magnetic shielding (σ, which can be related to δ) and the electric field gradient (EFG, which can be related to C(Q)) are compared to the experimental results and are discussed with respect to the relative strengths of the hydrogen bonds within each system. Copyright © 2012 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2014-06-04

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

  13. Selective C70 encapsulation by a robust octameric nanospheroid held together by 48 cooperative hydrogen bonds

    Science.gov (United States)

    Markiewicz, Grzegorz; Jenczak, Anna; Kołodziejski, Michał; Holstein, Julian J.; Sanders, Jeremy K. M.; Stefankiewicz, Artur R.

    2017-05-01

    Self-assembly of multiple building blocks via hydrogen bonds into well-defined nanoconstructs with selective binding function remains one of the foremost challenges in supramolecular chemistry. Here, we report the discovery of a enantiopure nanocapsule that is formed through the self-assembly of eight amino acid functionalised molecules in nonpolar solvents through 48 hydrogen bonds. The nanocapsule is remarkably robust, being stable at low and high temperatures, and in the presence of base, presumably due to the co-operative geometry of the hydrogen bonding motif. Thanks to small pore sizes, large internal cavity and sufficient dynamicity, the nanocapsule is able to recognize and encapsulate large aromatic guests such as fullerenes C60 and C70. The structural and electronic complementary between the host and C70 leads to its preferential and selective binding from a mixture of C60 and C70.

  14. 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....... 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...

  15. Role of hydrogen bonding in ligand interaction with the N-methyl-D-aspartate receptor ion channel

    Energy Technology Data Exchange (ETDEWEB)

    Leeson, P.D.; Carling, R.W.; James, K.; Smith, J.D.; Moore, K.W.; Wong, E.H.; Baker, R. (Merck Sharp Laboratory, Harlow, Essex (England))

    1990-05-01

    Displacement of (3H)MK-801 (dizocilpine, 1) binding to rat brain membranes has been used to evaluate the affinities of novel dibenzocycloalkenimines related to 1 for the ion channel binding site (also known as the phencyclidine or PCP receptor) on the N-methyl-D-aspartate (NMDA) subtype of excitory amino acid receptor. In common with many other agents having actions in the central nervous system, these compounds contain a hydrophobic aromatic moiety and a basic nitrogen atom. The conformational rigidity of these ligands provides a unique opportunity to evaluate the importance of specific geometrical properties that influence active-site recognition, in particular the role of the nitrogen atom in hydrogen-bonding interactions. The relative affinities (IC50s) of hydrocarbon-substituted analogues of 1 and ring homologated cyclooctenimines illustrate the importance of size-limited hydrophobic binding of both aryl rings and of the quaternary C-5 methyl group. Analysis of the binding of a series of the 10 available structurally rigid dibenzoazabicyclo(x.y.z)alkanes, by using molecular modeling techniques, uncovered a highly significant correlation between affinity and a proposed ligand-active site hydrogen bonding vector (r = 0.950, p less than 0.001). These results are used to generate a pharmacophore of the MK-801 recognition site/PCP receptor, which accounts for the binding of all of the known ligands.

  16. Probing the hydrogen-bond network of water via time-resolved soft x-ray spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Huse, Nils; Wen, Haidan; Nordlund, Dennis; Szilagyi, Erzsi; Daranciang, Dan; Miller, Timothy A.; Nilsson, Anders; Schoenlein, Robert W.; Lindenberg, Aaron M.

    2009-04-24

    We report time-resolved studies of hydrogen bonding in liquid H2O, in response to direct excitation of the O-H stretch mode at 3 mu m, probed via soft x-ray absorption spectroscopy at the oxygen K-edge. This approach employs a newly developed nanofluidic cell for transient soft x-ray spectroscopy in liquid phase. Distinct changes in the near-edge spectral region (XANES) are observed, and are indicative of a transient temperature rise of 10K following transient laser excitation and rapid thermalization of vibrational energy. The rapid heating occurs at constant volume and the associated increase in internal pressure, estimated to be 8MPa, is manifest by distinct spectral changes that differ from those induced by temperature alone. We conclude that the near-edge spectral shape of the oxygen K-edge is a sensitive probe of internal pressure, opening new possibilities for testing the validity of water models and providing new insight into the nature of hydrogen bonding in water.

  17. Quantitative evaluation on activated property-tunable bulk liquid water with reduced hydrogen bonds using deconvoluted Raman spectroscopy.

    Science.gov (United States)

    Chen, Hsiao-Chien; Mai, Fu-Der; Yang, Kuang-Hsuan; Chen, Liang-Yih; Yang, Chih-Ping; Liu, Yu-Chuan

    2015-01-06

    Interesting properties of water with distinguishable hydrogen-bonding structure on interfacial phase or in confined environment have drawn wide attentions. However, these unique properties of water are only found within the interfacial phase and confined environment, thus, their applications are limited. In addition, quantitative evaluation on these unique properties associating with the enhancement of water's physical and chemical activities represents a notable challenge. Here we report a practicable production of free-standing liquid water at room temperature with weak hydrogen-bonded structure naming Au nanoparticles (NPs)-treated (AuNT) water via treating by plasmon-induced hot electron transfer occurred on resonantly illuminated gold NPs (AuNPs). Compared to well-known untreated bulk water (deionized water), the prepared AuNT water exhibits many distinct activities in generally physical and chemical reactions, such as high solubilities to NaCl and O2. Also, reducing interaction energy within water molecules provides lower overpotential and higher efficiency in electrolytic hydrogen production. In addition, these enhanced catalytic activities of AuNT water are tunable by mixing with deionized water. Also, most of these tunable activities are linearly proportional to its degree of nonhydrogen-bonded structure (DNHBS), which is derived from the O-H stretching in deconvoluted Raman spectrum.

  18. Van der Waals versus hydrogen-bonding forces in a crystalline analog of cellotetraose: cyclohexyl 4'-O-cyclohexyl beta-D-cellobioside cyclohexane solvate.

    Science.gov (United States)

    Yoneda, Yuko; Mereiter, Kurt; Jaeger, Christian; Brecker, Lothar; Kosma, Paul; Rosenau, Thomas; French, Alfred

    2008-12-10

    Hydrogen bonding is important in cellulosic and other carbohydrate structures, but the role of interactions between nonpolar groups is less understood. Therefore, we synthesized cyclohexyl 4'-O cyclohexyl beta-D-cellobioside (8), a molecule that has two glucose rings and two nonpolar cyclohexyl rings. Key to attaching the 4'-Ocyclohexyl group was making the 4'-O,6'-O-cyclohexylidene ketal. After peracetylation, the cyclohexylidene ketal ring was opened regioselectively, providing 65% of 8 after final deacetylation. Comparison of the crystal structure of 8, as the cyclohexane solvate, with those of cellulose and its fragments, especially cellotetraose with four glucose rings, revealed extensive effects from the cyclohexyl groups. Three conformationally unique molecules (A, B, and C) are in the triclinic unit cell of 8, along with two solvent cyclohexanes. When viewed down the crystal's a-axis, the array of C, A, and B looks like the letter N, with A inclined so that its cyclohexyl groups can stack with those of the reducing ends of the B and C molecules. The lower left and upper right points of the N are stacks of cyclohexyl rings on the nonreducing ends of B and C, interspersed with solvent cyclohexanes. Whereas cellotetraose has antiparallel (up-down) packing, A and B in 8 are oriented "down" in the unit cell while C is "up". "Down-down-up" (or, alternatively, "up-up-down") packing is rare for carbohydrates. Other unusual details include 06 in all three staggered orientations: one is tg, two are gg, and three are gt, confirmed with CP/MAS 13C NMR. The tg O6 donates a proton to an intramolecular hydrogen bond to O2', opposite to the major schemes in native cellulose I. A similar but novel O6B-H...O2'B hydrogen bond is based on a slightly distorted gg orientation. The hydrogen bonds between parallel molecules are unique, with linkages between O2'A and O2'B, O3'A and O3'B, and O6A and O6B. Other details, such as the bifurcated O3...O5' and ...O6' hydrogen bonds are

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

    Science.gov (United States)

    Arunan, Elangannan; Mani, Devendra

    2015-01-01

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

  20. Inter-hydrogen bond coupling in crystals of 3-phenylpyrazole polymorphs investigated by polarized IR spectroscopy.

    Science.gov (United States)

    Hachuła, Barbara; Flakus, Henryk T; Garbacz, Aleksandra; Stolarczyk, Agnieszka

    2014-04-05

    The remarkably strong differences in the fine structure patterns of the νN-H and νN-D bands, temperature and H/D isotopic effects in crystals of two 3-phenylpyrazole (3PhPz) polymorphs, with tetrameric and hexameric hydrogen bond aggregates, were examined by polarized IR spectroscopy, aided by the calculations utilizing the "strong-coupling" model. Experimental and theoretical approaches have suggested that the anti-co-operativity of hydrogen bonds is the main factor responsible for the differences in the spectral properties of both polymorphs. This interaction affects hydrogen-bond geometry of the associates constituting the lattices and in consequence decides about the relative contribution of two different exciton coupling mechanism, "through-space" (SS) and "tail-to-head" (TH), in the spectra generation. The relative contribution of each individual exciton coupling mechanism in the spectra generation is temperature-dependent. In tetramers the TH coupling mechanism dominates at low temperatures, whereas the role of the SS mechanism increases at higher temperatures. For the hexamers the SS mechanism dominates in the wide temperature range. The two types of 3PhPz associates exhibit two different ways of occurring of the H/D isotopic recognition in the crystal hydrogen bonds. In the tetrameric polymorph identical hydrogen isotope atoms exist in entire hydrogen-bonded cycle of 3PhPz. In the case of 3PhPz hexamers, the H/D isotopic recognition mechanism involves pairs of the closely-spaced hydrogen bonds in a cycle. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. Strong and weak hydrogen bonds in protein-ligand complexes of kinases: a comparative study.

    Science.gov (United States)

    Panigrahi, Sunil K

    2008-05-01

    Strong and weak hydrogen bonds between protein and ligand are analyzed in a group of 233 X-ray crystal structures of the kinase family. These kinases are from both eukaryotic and prokaryotic organisms. The dataset comprises of 44 sub-families, out of which 35 are of human origin and the rest belong to other organisms. Interaction analysis was carried out in the active sites, defined here as a sphere of 10 A radius around the ligand. A majority of the interactions are observed between the main chain of the protein and the ligand atoms. As a donor, the ligand frequently interacts with amino acid residues like Leu, Glu and His. As an acceptor, the ligand interacts often with Gly, and Leu. Strong hydrogen bonds N-H...O, O-H...O, N-H...N and weak bonds C-H...O, C-H...N are common between the protein and ligand. The hydrogen bond donor capacity of Gly in N-H...O and C-H...O interactions is noteworthy. Similarly, the acceptor capacity of main chain Glu is ubiquitous in several kinase sub-families. Hydrogen bonds between protein and ligand form characteristic hydrogen bond patterns (supramolecular synthons). These synthon patterns are unique to each sub-family. The synthon locations are conserved across sub-families due to a higher percentage of conserved sequences in the active sites. The nature of active site water molecules was studied through a novel classification scheme, based on the extent of exposure of water molecules. Water which is least exposed usually participates in hydrogen bond formation with the ligand. These findings will help structural biologists, crystallographers and medicinal chemists to design better kinase inhibitors.

  2. H2O and CO coadsorption on Co (0001): The effect of intermolecular hydrogen bond

    Science.gov (United States)

    Jiawei, Wu; Chen, Jun; Guo, Qing; Su, Hai-Yan; Dai, Dongxu; Yang, Xueming

    2017-09-01

    The co-adsorption of CO and H2O on a Co(0001) surface at 100 K has been systematically studied using temperature programmed desorption (TPD) and density functional theory (DFT) calculations. While the TPD spectra of CO is almost not affected by the presence of H2O, the stabilization of H2O by co-adsorbed CO is found for the first time in a large coverage range (0.15 ML interaction between H2O molecules and the attractive interaction between H2O and CO molecules, respectively. With increasing the coverage of predosed CO, not only the position of the high temperature peak shifts toward higher temperature (by about 15 K), but the intensity is greatly strengthened until a maximum is achieved when θCO = 0.36 ML. DFT calculations suggest that the attractive interaction between H2O and CO on Co(0001) originates from the formation of intermolecular hydrogen bonds. This work not only provides insights into water gas shift reactions with H2O and CO as reactants, but opens new avenues for a volume of catalytic process of technological importance.

  3. Reorganization of hydrogen bond network makes strong polyelectrolyte brushes pH-responsive.

    Science.gov (United States)

    Wu, Bo; Wang, Xiaowen; Yang, Jun; Hua, Zan; Tian, Kangzhen; Kou, Ran; Zhang, Jian; Ye, Shuji; Luo, Yi; Craig, Vincent S J; Zhang, Guangzhao; Liu, Guangming

    2016-08-01

    Weak polyelectrolytes have found extensive practical applications owing to their rich pH-responsive properties. In contrast, strong polyelectrolytes have long been regarded as pH-insensitive based on the well-established fact that the average degree of charging of strong polyelectrolyte chains is independent of pH. The possible applications of strong polyelectrolytes in smart materials have, thus, been severely limited. However, we demonstrate that almost all important properties of strong polyelectrolyte brushes (SPBs), such as chain conformation, hydration, stiffness, surface wettability, lubricity, adhesion, and protein adsorption are sensitive to pH. The pH response originates from the reorganization of the interchain hydrogen bond network between the grafted chains, triggered by the pH-mediated adsorption-desorption equilibrium of hydronium or hydroxide with the brushes. The reorganization process is firmly identified by advanced sum-frequency generation vibrational spectroscopy. Our findings not only provide a new understanding of the fundamental properties of SPBs but also uncover an extensive family of building blocks for constructing pH-responsive materials.

  4. Lipin 2 binds phosphatidic acid by the electrostatic hydrogen bond switch mechanism independent of phosphorylation.

    Science.gov (United States)

    Eaton, James M; Takkellapati, Sankeerth; Lawrence, Robert T; McQueeney, Kelley E; Boroda, Salome; Mullins, Garrett R; Sherwood, Samantha G; Finck, Brian N; Villén, Judit; Harris, Thurl E

    2014-06-27

    Lipin 2 is a phosphatidic acid phosphatase (PAP) responsible for the penultimate step of triglyceride synthesis and dephosphorylation of phosphatidic acid (PA) to generate diacylglycerol. The lipin family of PA phosphatases is composed of lipins 1-3, which are members of the conserved haloacid dehalogenase superfamily. Although genetic alteration of LPIN2 in humans is known to cause Majeed syndrome, little is known about the biochemical regulation of its PAP activity. Here, in an attempt to gain a better general understanding of the biochemical nature of lipin 2, we have performed kinetic and phosphorylation analyses. We provide evidence that lipin 2, like lipin 1, binds PA via the electrostatic hydrogen bond switch mechanism but has a lower rate of catalysis. Like lipin 1, lipin 2 is highly phosphorylated, and we identified 15 phosphosites. However, unlike lipin 1, the phosphorylation of lipin 2 is not induced by insulin signaling nor is it sensitive to inhibition of the mammalian target of rapamycin. Importantly, phosphorylation of lipin 2 does not negatively regulate either membrane binding or PAP activity. This suggests that lipin 2 functions as a constitutively active PA phosphatase in stark contrast to the high degree of phosphorylation-mediated regulation of lipin 1. This knowledge of lipin 2 regulation is important for a deeper understanding of how the lipin family functions with respect to lipid synthesis and, more generally, as an example of how the membrane environment around PA can influence its effector proteins. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. 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.

  6. Can quantum-mechanical calculations yield reasonable estimates of hydrogen-bonding acceptor strength? The case of hydrogen-bonded complexes of methanol.

    Science.gov (United States)

    Koné, Mawa; Illien, Bertrand; Laurence, Christian; Graton, Jérôme

    2011-12-01

    The thermodynamics and some vibrational properties of hydrogen-bonded complexes of methanol with 23 hydrogen-bond acceptors (HBAs) have been determined in CCl(4) by FTIR spectrometry. The experimental sample contains carbon, nitrogen, oxygen, sulfur, fluorine, and chlorine organic bases and covers an energetic range of 13 kJ mol(-1) in the basicity scale (-ΔG), 22 kJ mol(-1) in the affinity scale (-ΔH), and 400 cm(-1) in the spectroscopic scale (Δν((OH))) (from benzene to trimethylphosphane oxide and amines). The experimental results in CCl(4) are compared to those computed in the gas phase at various levels of theory. Ninety five percent of the variance of the red shift and 89% of the variance of the intensification of the OH stretching upon hydrogen bonding are explained by gas-phase B3LYP/6-31+G(d,p) calculations. However, this level does not satisfactorily explain the thermodynamic properties. Only 68% of the variance of the methanol affinity (-ΔH) is taken into account. MP2/aug-cc-pVTZ//B3LYP/6-31+G(d,p) affinity calculations raise the explanation to 77% for all HBAs and to 93% when three outliers (Me(2)SO, Me(3)PO, and tetrahydrothiophene) are excluded. Discrepancies are analyzed in terms of experimental errors, calculation approximations, and solvation. © 2011 American Chemical Society

  7. TD-DFT study on electron transfer mobility and intramolecular hydrogen bond of substituted indigo derivatives

    Science.gov (United States)

    Ma, Chi; Li, Hui; Yang, Yonggang; Li, Donglin; Liu, Yufang

    2015-10-01

    The density functional theory (DFT) and time-dependent density functional theory (TDDFT) method were carried out to investigate the ground and excited states of indigo and its derivative molecules. The results demonstrate that the intramolecular hydrogen bond I is weakened and the intramolecular hydrogen bond II is strengthened upon photo-excitation to the S1 state. In the absorption spectra, the substitution at R4R4, of indigo causes a significant redshift. In addition, the halogen substitution obviously increases the electron transfer mobility of indigo. It is proved that the halogen substitution may be a new method to design high performance organic semiconductors.

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

    Directory of Open Access Journals (Sweden)

    Jović Branislav

    2012-01-01

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

  9. 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....

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

    Science.gov (United States)

    Hemp, Sean T; Long, Timothy E

    2012-01-01

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

  11. 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...

  12. Hydrogen bonds and van der waals forces in ice at ambient and high pressures.

    Science.gov (United States)

    Santra, Biswajit; Klimeš, Jiří; Alfè, Dario; Tkatchenko, Alexandre; Slater, Ben; Michaelides, Angelos; Car, Roberto; Scheffler, Matthias

    2011-10-28

    The first principles methods, density-functional theory and quantum Monte Carlo, have been used to examine the balance between van der Waals (vdW) forces and hydrogen bonding in ambient and high-pressure phases of ice. At higher pressure, the contribution to the lattice energy from vdW increases and that from hydrogen bonding decreases, leading vdW to have a substantial effect on the transition pressures between the crystalline ice phases. An important consequence, likely to be of relevance to molecular crystals in general, is that transition pressures obtained from density-functional theory exchange-correlation functionals which neglect vdW forces are greatly overestimated.

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

    Science.gov (United States)

    Wimmer, Michael

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

  14. Raman Spectroscopy of Dense H2O and the Transition to Symmetric Hydrogen Bonds

    Science.gov (United States)

    Goncharov, Alexander F.; Struzhkin, Viktor V.; Mao, Ho-Kwang; Hemley, Russell J.

    1999-09-01

    High-pressure Raman measurements of H2O ice using synthetic diamond anvils reveal major changes associated with the transition to the nonmolecular, symmetric hydrogen-bonded state. At 60 GPa the strongly pressure-dependent O-H symmetric stretching mode disappears, and the translational modes exhibit frequency and damping anomalies. With further increase in pressure, a single peak appears and becomes the dominant feature in the spectrum in the megabar range. The band is assigned to the predicted Raman-active O-O mode of the nonmolecular phase, consistent with the formation of cuprite-type ice X with static, symmetric hydrogen bonds.

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

    Science.gov (United States)

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

    2018-03-01

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

  16. Proof for the concerted inversion mechanism in the trans-->cis isomerization of azobenzene using hydrogen bonding to induce isomer locking.

    Science.gov (United States)

    Bandara, H M Dhammika; Friss, Tracey R; Enriquez, Miriam M; Isley, William; Incarvito, Christopher; Frank, Harry A; Gascon, Jose; Burdette, Shawn C

    2010-07-16

    Azobenzene undergoes reversible cistrans photoisomerization upon irradiation. Substituents often change the isomerization behavior of azobenzene, but not always in a predictive manner. The synthesis and properties of three azobenzene derivatives, AzoAMP-1, -2, and -3, are reported. AzoAMP-1 (2,2'-bis[N-(2-pyridyl)methyl]diaminoazobenzene), which possesses two aminomethylpyridine groups ortho to the azo group, exhibits minimal trans-->cis photoisomerization and extremely rapid cis-->trans thermal recovery. AzoAMP-1 adopts a planar conformation in the solid state and is much more emissive (Phi(fl) = 0.003) than azobenzene when frozen in a matrix of 1:1 diethylether/ethanol at 77 K. Two strong intramolecular hydrogen bonds between anilino protons and pyridyl and azo nitrogen atoms are responsible for these unusual properties. Computational data predict AzoAMP-1 should not isomerize following S(2)azobenzene. Confirmation that the AzoAMP-1 and -2 retain excited state photochemistry analogous to azobenzene was provided by ultrafast transient absorption spectroscopy of both compounds in the visible spectral region. The isomerization of azobenzene occurs via a concerted inversion mechanism where both aryl rings must adopt a collinear arrangement prior to inversion. The hydrogen bonding in AzoAMP-1 prevents both aryl rings from adopting this conformation. To further probe the mechanism of isomerization, AzoAMP-3, which has only one anilinomethylpyridine substituent for hydrogen bonding, was prepared and characterized. AzoAMP-3 does not isomerize and exhibits emission (Phi(fl) = 0.0008) at 77 K. The hydrogen bonding motif in AzoAMP-1 and AzoAMP-3 provides the first example where inhibiting the concerted inversion pathway in an azobenzene prevents isomerization. These molecules provide important supporting evidence for the spectroscopic and computational studies aimed at elucidating the isomerization mechanism in azobenzene.

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

    Science.gov (United States)

    Kanematsu, Yusuke; Tachikawa, Masanori

    2014-11-14

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

  18. Investigation of the structure of ethanol-water mixtures by molecular dynamics simulation I: analyses concerning the hydrogen-bonded pairs.

    Science.gov (United States)

    Gereben, Orsolya; Pusztai, László

    2015-02-19

    Series of molecular dynamics simulations for ethanol-water mixtures with 20-80 mol % ethanol content, pure ethanol, and water were performed. In each mixture, for ethanol the OPLS force field was used, combined with three different water force fields, the SPC/E, the TIP4P-2005, and the SWM4-DP. Water potential models were distinguished on the basis of deviations between calculated and measured total scattering X-ray structure factors aided by ethanol-water pair binding energy comparison. No single water force field could provide the best agreement with experimental data at all concentrations: at the ethanol content of 80% the SWM-DP, for 60 mol % the SWM4-DP and the TIP4P-2005, whereas for the 40 and 20 mol % mixtures TIP4P-2005 water force field provided the closest match. Coordination numbers and hydrogen bonds/molecule values were calculated, revealing that the oxygen-oxygen first coordination numbers strongly overestimate the average number of hydrogen bonds/molecule. The center-of-molecule distributions indicate that the ethanol-ethanol first coordination sphere expands with increasing water concentration while the size of the first water-water coordination sphere does not change. Various two and three-dimensional distributions were calculated that reveal the differences between simulations with different water force fields. Detailed conformational analyses of the hydrogen-bonded pairs were performed; drawings of the characteristic molecular arrangements are provided.

  19. The Relation Between Lipase Thermostability and Dynamics of Hydrogen Bond and Hydrogen Bond Network Based on Long Time Molecular Dynamics Simulation.

    Science.gov (United States)

    Zhang, Leiyu; Ding, Yanrui

    2017-01-01

    Compared with the wild type of lipase (WTL), mutant lipase 6B has twelve mutations (A15S, F17S, A20E, N89Y, G111D, L114P, A132D, M134E, M137P, I157M, S163P, N166Y). The melting temperature of 6B (78.2°C) is much higher than that of WTL (56°C). Hydrogen bond (HB) play an important role in stabilizing the protein. It is important to analyze how mutations affect hydrogen bond and hydrogen bond network and explain how hydrogen bond and hydrogen bond network affect lipase thermostability by the change of the intensity of HB and HB networks with temperature changing. Study the dynamics of HB and HB networks to find that how HBs and HB networks change over time and over temperature in WTL and 6B. Long time MD simulations of WTL and 6B are carried out to analyze how mutations affect hydrogen bond and hydrogen bond network. All proteins were simulated at 300K, 325K, 350K, 375K, 400K for 300ns respectively. The definition of HB is that the distance between acceptor and donor is smaller than a cutoff 3.0 Å and the angle between Donor-H and H-Acceptor is larger than 120o. If two or more HBs connect together, they formed HB network. In the network, residues that formed HB represent nodes, the HB interactions between residues represent edges. The persistence value of HB is computed by . The persistence values of HBs formed by mutations A15S, A20E, G111D, M137P, N166Y are significantly different from that of WTL. HB Glu20-Ser24, Asp111-Asp144, Leu160-Tyr166 and Lys170-Tyr166 are important to stabilize 6B. In addition, the HB networks dynamics show that there are three HB networks are more stable in mutants than that in WTL. The first HB network makes β3, β5, loop and 310-helix closely connect with each other at mutants. The second HB network increases the rigidity of the loop, αC, β3 and β5. The third HB network enhances the interaction between loops, αB and αC. The higher HB persistence value generally means that the HB is more stable. These mutations directly improve

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

    Science.gov (United States)

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

    2000-11-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

  2. 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.

  3. Single Molecule Force Spectroscopy of self complementary hydrogen-bonded supramolecular systems: dimers, polymers and solvent effects

    NARCIS (Netherlands)

    Embrechts, A.

    2011-01-01

    The work described in this Thesis aimed at a better understanding of the structure-property relationships of supramolecular assemblies with a specific focus on hydrogen-bond dimers and polymers. The hydrogen-bond strength of (supra)molecular complexes in different solvents is usually determined by

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

  5. Cooperative Effect of a Metal Ion and Hydrogen Bonds on Phosphodiester Cleavage in Acetonitrile

    National Research Council Canada - National Science Library

    Kondo, Shin-ichi; Sakuno, Yuichi; Yokoyama, Takashi; Yano, Yumihiko

    2001-01-01

    Cleavage of an activated phosphodiester by Zn(NO3)2·6H2O was accelerated (9 × 103-fold) by cooperative effect of a metal ion and hydrogen bonds in the presence of a bismelamine derivative bearing a 2,2...

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

    Science.gov (United States)

    Green, Thomas K.; Lane, Charles A.

    2006-01-01

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

  8. Engineering Hydrogen Bonding Interaction and Charge Separation in Bio-Polymers for Green Lubrication.

    Science.gov (United States)

    Mu, Liwen; Shi, Yijun; Hua, Jing; Zhuang, Wei; Zhu, Jiahua

    2017-06-08

    Synthetic additives are widely used in lubricants nowadays to upgrade lubrication properties. The potential of integrating sustainable components in modern lubricants has rarely been studied yet. In this work, two sustainable resources lignin and gelatin have been synergistically incorporated into ethylene glycol (EG), and their tribological properties were systematically investigated. The abundant hydrogen bonding sites in lignin and gelatin as well as their interchain interaction via hydrogen bonding play the dominating roles in tuning the physicochemical properties of the mixture and improving lubricating properties. Moreover, the synergistic combination of lignin and gelatin induces charge separation of gelatin that enables its preferable adsorption on the friction surface through electrostatic force and forms a robust lubrication layer. This layer will be strengthened by lignin through the interpolymer chain hydrogen bonding. At an optimized lignin:gelatin mass ratio of 1:1 and 19 wt % loading of each in EG, the friction coefficient can be greatly stabilized and the wear loss was reduced by 89% compared to pure EG. This work presents a unique synergistic phenomenon between gelatin and lignin, where hydrogen bonding and change separation are revealed as the key factor that bridges the individual components and improves overall lubricating properties.

  9. Minor groove hydrogen bonds and the replication of unnatural base pairs.

    Science.gov (United States)

    Matsuda, Shigeo; Leconte, Aaron M; Romesberg, Floyd E

    2007-05-02

    As part of an effort to expand the genetic alphabet, we examined the synthesis of DNA with six different unnatural nucleotides bearing methoxy-derivatized nucleobase analogues. Different nucleobase substitution patterns were used to systematically alter the nucleobase electronics, sterics, and hydrogen-bonding potential. We determined the ability of the Klenow fragment of E. coli DNA polymerase I to synthesize and extend the different unnatural base pairs and mispairs under steady-state conditions. Unlike other hydrogen-bond acceptors examined in the past, the methoxy groups do not facilitate mispairing, implying that they are not recognized by any of the hydrogen-bond donors of the natural nucleobases; however, they do facilitate replication. The more efficient replication results largely from an increase in the rate of extension of primers terminating at the unnatural base pair and, interestingly, requires that the methoxy group be at the ortho position where it is positioned in the developing minor groove and can form a functionally important hydrogen bond with the polymerase. Thus, ortho methoxy groups should be generally useful for the effort to expand the genetic alphabet.

  10. Hexagonal wheel formation through the hydrogen-bonded assembly of cobalt Pacman complexes.

    Science.gov (United States)

    Leeland, James W; White, Fraser J; Love, Jason B

    2011-04-14

    A cobalt aquo-hydroxo complex of a ditopic Schiff-base pyrrole-crown ether macrocycle has been prepared and forms a rigid Pacman-clefted structure that assembles through hydrogen-bonding into a hexagonal wheel motif in the solid state.

  11. Influence of second sphere hydrogen bonding interaction on a manganese(II)-aquo complex.

    Science.gov (United States)

    El Ghachtouli, Sanae; Guillot, Régis; Dorlet, Pierre; Anxolabéhère-Mallart, Elodie; Aukauloo, Ally

    2012-02-14

    We have developed a pentadentate N(4)O ligand scaffold with a benzimidazole group placed in a rigid fashion to develop hydrogen bonding interaction with the ligand in the sixth position. The mononuclear Mn(II) complex with a water molecule was isolated and characterized. We discuss the role of the outer sphere ligand in stabilising a Mn(II)-aquo complex.

  12. 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...

  13. 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

  14. 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.

  15. 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...

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

    Science.gov (United States)

    Amtul, Zareen; Rahman, Atta-Ur

    2016-02-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

  18. 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.

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

    Science.gov (United States)

    Weinhold, Frank; Klein, Roger A.

    2014-01-01

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

  20. 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.

  1. Strong and weak hydrogen bonds in drug–DNA complexes: A ...

    Indian Academy of Sciences (India)

    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 ...

  2. Strong and weak hydrogen bonds in drug–DNA complexes: A ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    The analysis was performed with an in-house software, hydrogen bond analysis tool (HBAT). In addition to strong ..... drug design. However, the purpose of using docking in the present context is different. Molecular docking was carried out to estimate the best drug–DNA geometries in cases where the crystal structures of ...

  3. 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.

    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)

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

    Indian Academy of Sciences (India)

    TECS

    A spiral-like chain from a hydrogen-bonded cyclic dichloride contain- ing a water dimer in a quaternary diammonium dichloride trihydrate. #. BIKSHANDARKOIL R SRINIVASAN,1,* RATHAN G MHALSIKAR,1 KOYAR S RANE,1. CHRISTIAN NÄTHER2 and WOLFGANG BENSCH2. 1Department of Chemistry, Goa University ...

  5. Fine tuning of mixed ionic and hydrogen bond interactions for plasmid delivery using lipoplexes.

    Science.gov (United States)

    Seguin, Johanne; Dhotel, Hélène; Kai-Luen, René; Bessodes, Michel; Mignet, Nathalie

    2015-02-01

    Non viral gene transfection has been mostly reached via cationic polymer and lipid, required for DNA complexation and cell internalisation. However, cationic charges often induce cytotoxicity and limit the efficacy of the lipoplexes in vivo due to their fast elimination from the blood stream. Few years ago, we had developed noncationic lipid interacting with DNA via hydrogen bond interactions. To take advantage of both the internalisation efficacy of cationic complexes and the higher DNA release efficacy of non cationic lipids, we chose to mix both ionic and hydrogen bond interactions within one lipoplex. The idea behind this strategy would be to reduce the overall charge while maintaining a high level of transfection. Four mixed formulations of cationic lipid and thiourea lipid were prepared. We found that decreasing ionic interactions and increasing hydrogen bond interactions improved cationic lipoplexes properties. Indeed, we showed that replacement of net positive charges by hydrogen bond interactions with DNA phosphates led to efficient lipoplexes for in vitro DNA transfection at lower cationic charge content, which consequently reduced lipoplex cytotoxicity. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2011-02-10

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

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

    NARCIS (Netherlands)

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

    1999-01-01

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

  8. Insights into hydrogen bond donor promoted fixation of carbon dioxide with epoxides catalyzed by ionic liquids.

    Science.gov (United States)

    Liu, Mengshuai; Gao, Kunqi; Liang, Lin; Wang, Fangxiao; Shi, Lei; Sheng, Li; Sun, Jianmin

    2015-02-28

    Catalytic coupling of carbon dioxide with epoxides to obtain cyclic carbonates is an important reaction that has been receiving renewed interest. In this contribution, the cycloaddition reaction in the presence of various hydrogen bond donors (HBDs) catalyzed by hydroxyl/carboxyl task-specific ionic liquids (ILs) is studied in detail. It was found that the activity of ILs could be significantly enhanced in the presence of ethylene glycol (EG), and EG/HEBimBr were the most efficient catalysts for the CO2 cycloaddition to propylene oxide. Moreover, the binary catalysts were also efficiently versatile for the CO2 cycloaddition to less active epoxides such as styrene oxide and cyclohexene oxide. Besides, the minimum energy paths for this hydrogen bond-promoted catalytic reaction were calculated using the density functional theory (DFT) method. The DFT results suggested that the ring-closing reaction was the rate-determining step in the HEBimBr-catalyzed cycloaddition reaction but the EG addition could remarkably reduce its energy barrier as the formation of a hydrogen bond between EG and the oxygen atom of epoxides led this process along the standard SN2 mechanism. As a result, the ring-opening reaction became the rate-determining step in the EG/HEBimBr-catalyzed cycloaddition reaction. The work reported herein helped the understanding and design of catalysts for efficient fixation of CO2 to epoxides via hydrogen bond activation.

  9. Characterization of hydrogen-bonded supramolecular assemblies by MALDI-TOF mass spectrometry after Ag+ labeling

    NARCIS (Netherlands)

    Jolliffe, K.A.; Crego Calama, Mercedes; Fokkens, R.H.; Nibbering, N.M.M.; Timmerman, P.; Reinhoudt, David

    1998-01-01

    The high affinity of Ag+ ions for aromatic pi donors and cyano groups is exploited in a novel MALDI-TOF mass spectrometric method for the identification of hydrogen-bonded assemblies. The interaction with the Ag+ ions - which, for example, can be complexed by two phenyl groups in a sandwich-type

  10. 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

  11. Hydrogen bond dynamics is believed to be the key factor in changing

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Hydrogen bond dynamics is believed to be the key factor in changing. ~ . Time scale of HB dynamics ~ 0.5 ps. Lawrence and Skinner J. Chem. Phys., 118, 264 (2003). has two time scales: 40 fs (for HB stretch) and 465 fs ...

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

    Science.gov (United States)

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

    2011-03-01

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

  13. 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.

  14. The role of the hydrogen bonding network for the shear modulus of PIPD

    NARCIS (Netherlands)

    Hageman, J.C.L.; Wijs, G.A. de; Groot, R.A. de; Klop, E.A.

    2005-01-01

    Ab initio total energy calculations at the DFT-GGA level for PIPD are reported. Both the monoclinic crystal with a bi-directional hydrogen-bond network and the triclinic crystal with a sheet-like network are studied. It is concluded that the latter is the more plausible microstructure for the fibre

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

    DEFF Research Database (Denmark)

    Schrøder, Sidsel Dahl

    , weak intramolecular hydrogen bonds in methyl lactate, allyl carbinol and methallyl carbinol have been identified and characterized. The effect of substitution of two hydrogen atoms on one of the methylene groups with either methyl groups or tri uoromethyl groups on the intramolecular......,4-diaminobutane, no sign of intramolecular N-H···N hydrogen bonds were identified in the overtone spectra. However, theoretical analyzes indicate that intramolecular N-H···N hydrogen bonds are present in all three diamines if two hydrogen atoms on one of the methylene groups are substituted with triuoromethyl......This PhD thesis describes the gas phase studies of four intramolecular hydrogen bonds: O-H···O (in methyl lactate), O-H···π (in methallyl carbinol and allyl carbinol), O-H···N (in methylated and triuoromethylated 2-aminoethanol) and N-H···N (in the diamines 1,2-diaminoethane, 1,3-diaminopropane...

  16. Diastereoselective noncovalent synthesis of hydrogen-bonded double-rosette assemblies

    NARCIS (Netherlands)

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

    2002-01-01

    Chiral centers present either in the dimelamine components of calix[4]arene 1 or in the cyanurate components CA quantitatively induce one handedness (P or M) in the corresponding hydrogen-bonded assemblies 13(CA)6 (de>98 %). The high degree of chiral induction results from the presence of six chiral

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

    NARCIS (Netherlands)

    Engberts, Jan B.F.N.

    1995-01-01

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

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

    NARCIS (Netherlands)

    Engberts, J.B.F.N.

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

  19. Adsorption properties of polyvinyl-alcohol-grafted particles toward genistein driven by hydrogen-bond interaction.

    Science.gov (United States)

    Zhang, Yanyan; Gao, Baojiao; Xu, Zeqing

    2013-05-09

    The adsorption properties of polyvinyl alcohol (PVA)-grafted silica gel particles PVA/SiO2 toward genistein are researched in this paper. The effects of the main factors on the adsorption properties are investigated, the adsorption mechanism is explored in depth, and the adsorption thermodynamics is researched. The experimental results show that the conventional hydrogen bond is formed between the hydroxyl groups with high density on the surfaces of PVA/SiO2 and the phenolic hydroxyl groups in genistein, while π-type hydrogen bond is formed between the hydroxyl groups of PVA/SiO2 and the conjugated aromatic rings. It is the two types of hydrogen bond that make the functional composite particles PVA/SiO2 produce very strong physical adsorption toward genistein. The competitive adsorption of the solvent can have severe negative impact on the adsorption capacity of genistein. Increasing temperature will weaken the hydrogen-bond interaction between PVA/SiO2 particles and genistein. The existence of electrolytes in the protic solvent will affect the adsorption negatively. The adsorption process of PVA/SiO2 particles toward genistein is exothermic and driven by enthalpy. The adsorption isotherm data matches the Langmuir model.

  20. Hydrogen- Bond- Assisted Activation of Allylic Alcohols for Palladium- Catalyzed Coupling Reactions

    NARCIS (Netherlands)

    Gumrukcu, Y.; de Bruin, B.; Reek, J.

    2014-01-01

    We report direct activation of allylic alcohols using a hydrogen-bond-assisted palladium catalyst and use this for alkylation and amination reactions. The novel catalyst comprises a palladium complex based on a functionalized monodentate phosphoramidite ligand in combination with urea additives and

  1. 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

  2. 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

  3. 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

  4. Aggregation behavior of sodium dioctylsulfosuccinate in aqueous ethylene glycol medium. A case of hydrogen bonding between surfactant and solvent and its manifestation in the surface tension isotherm.

    Science.gov (United States)

    Das, D; Dey, J; Chandra, A K; Thapa, U; Ismail, K

    2012-11-13

    The dependence of critical micelle concentration (cmc) of sodium dioctylsulfosuccinate (AOT) on the amount of ethylene glycol (EG) in water + EG medium was reported to be unusual and different from that of other surfactants to the extent that the cmc of AOT in EG is lower than in water. It is yet to be understood why AOT behaves so in water + EG medium, although AOT is known to have some special properties. Hence in the present study cmc of AOT in water + EG medium in the range from 0 to 100% (by weight) EG is measured by using surface tension and fluorescence emission methods. In contrast to what was reported, this study revealed that with respect to EG amount the cmc of AOT follows the general trend and AOT has higher cmc in EG than in water. On the other hand, it was surprisingly found that a break in the surface tension isotherm occurs in the premicellar region when the amount of EG exceeds 50% rendering a bisigmoidal shape to the surface tension isotherm. UV spectral study showed that AOT and EG undergo hydrogen bonding in the premicellar region when the EG amount is ≥50% and this hydrogen bonding becomes less on adding NaCl. The density functional theory calculations also showed formation of hydrogen bonds between EG and AOT through the sulfonate group of AOT providing thereby support to the experimental findings. The calculations predicted a highly stable AOT-EG-H(2)O trimer complex with a binding energy of -37.93 kcal mol(-1). The present system is an example, which is first of its kind, of a case where hydrogen bonding with surfactant and solvent molecules results in a surface tension break.

  5. Architecture-based multiscale computational modeling of plant cell wall mechanics to examine the hydrogen-bonding hypothesis of the cell wall network structure model.

    Science.gov (United States)

    Yi, Hojae; Puri, Virendra M

    2012-11-01

    A primary plant cell wall network was computationally modeled using the finite element approach to study the hypothesis of hemicellulose (HC) tethering with the cellulose microfibrils (CMFs) as one of the major load-bearing mechanisms of the growing cell wall. A computational primary cell wall network fragment (10 × 10 μm) comprising typical compositions and properties of CMFs and HC was modeled with well-aligned CMFs. The tethering of HC to CMFs is modeled in accordance with the strength of the hydrogen bonding by implementing a specific load-bearing connection (i.e. the joint element). The introduction of the CMF-HC interaction to the computational cell wall network model is a key to the quantitative examination of the mechanical consequences of cell wall structure models, including the tethering HC model. When the cell wall network models with and without joint elements were compared, the hydrogen bond exhibited a significant contribution to the overall stiffness of the cell wall network fragment. When the cell wall network model was stretched 1% in the transverse direction, the tethering of CMF-HC via hydrogen bonds was not strong enough to maintain its integrity. When the cell wall network model was stretched 1% in the longitudinal direction, the tethering provided comparable strength to maintain its integrity. This substantial anisotropy suggests that the HC tethering with hydrogen bonds alone does not manifest sufficient energy to maintain the integrity of the cell wall during its growth (i.e. other mechanisms are present to ensure the cell wall shape).

  6. Halogen-bond and hydrogen-bond interactions between three benzene derivatives and dimethyl sulphoxide.

    Science.gov (United States)

    Zheng, Yan-Zhen; Wang, Nan-Nan; Zhou, Yu; Yu, Zhi-Wu

    2014-04-21

    Halogen-bonds, like hydrogen-bonds, are a kind of noncovalent interaction and play an important role in diverse fields including chemistry, biology and crystal engineering. In this work, a comparative study was carried out to examine the halogen/hydrogen-bonding interactions between three fluoro-benzene derivatives and dimethyl sulphoxide (DMSO). A number of conclusions were obtained by using attenuated total reflection infrared spectroscopy (ATR-IR), nuclear magnetic resonance (NMR) and ab initio calculations. Electrostatic surface potential, geometry, energy, vibrational frequency, intensity and the natural population analysis (NPA) of the monomers and complexes are studied at the MP2 level of theory with the aug-cc-pVDZ basis set. First, the interaction strength decreases in the order C6F5H-DMSO ∼ ClC6F4H-DMSO > C6F5Cl-DMSO, implying that the hydrogen-bond is stronger than the halogen-bond in the systems and, when interacting with ClC6F4H, DMSO favors the formation of a hydrogen-bond rather than a halogen-bond. Second, attractive energy dependences on 1/r(3.3) and 1/r(3.1) were established for the hydrogen-bond and halogen-bond, respectively. Third, upon the formation of a hydrogen-bond and halogen-bond, there is charge transfer from DMSO to the hydrogen-bond and halogen-bond donor. The back-group CH3 was found to contribute positively to the stabilization of the complexes. Fourth, an isosbestic point was detected in the ν(C-Cl) absorption band in the C6F5Cl-DMSO-d6 system, indicating that there exist only two dominating forms of C6F5Cl in binary mixtures; the non-complexed and halogen-bond-complexed forms. The presence of stable complexes in C6F5H-DMSO and ClC6F4H-DMSO systems are evidenced by the appearance of new peaks with fixed positions.

  7. Cooperativity between the dihydrogen bond and the NHC hydrogen bond in LiH-(HCN)n Complexes.

    Science.gov (United States)

    Li, Qing-Zhong; Hu, Ting; An, Xiu-Lin; Gong, Bao-An; Cheng, Jian-Bo

    2008-09-15

    The cooperativity between the dihydrogen bond and the NHC hydrogen bond in LiH-(HCN)(n) (n=2 and 3) complexes is investigated at the MP2 level of theory. The bond lengths, dipole moments, and energies are analyzed. It is demonstrated that synergetic effects are present in the complexes. The cooperativity contribution of the dihydrogen bond is smaller than that of the NHC hydrogen bond. The three-body energy in systems involving different types of hydrogen bonds is larger than that in the same hydrogen-bonded systems. NBO analyses indicate that orbital interaction, charge transfer, and bond polarization are mainly responsible for the cooperativity between the two types of hydrogen bonds.

  8. 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...

  9. The Different Sensitive Behaviors of a Hydrogen-Bond Acidic Polymer-Coated SAW Sensor for Chemical Warfare Agents and Their Simulants

    Directory of Open Access Journals (Sweden)

    Yin Long

    2015-07-01

    Full Text Available A linear hydrogen-bond acidic (HBA linear functionalized polymer (PLF, was deposited onto a bare surface acoustic wave (SAW device to fabricate a chemical sensor. Real-time responses of the sensor to a series of compounds including sarin (GB, dimethyl methylphosphonate (DMMP, mustard gas (HD, chloroethyl ethyl sulphide (2-CEES, 1,5-dichloropentane (DCP and some organic solvents were studied. The results show that the sensor is highly sensitive to GB and DMMP, and has low sensitivity to HD and DCP, as expected. However, the sensor possesses an unexpected high sensitivity toward 2-CEES. This good sensing performance can’t be solely or mainly attributed to the dipole-dipole interaction since the sensor is not sensitive to some high polarity solvents. We believe the lone pair electrons around the sulphur atom of 2-CEES provide an electron-rich site, which facilitates the formation of hydrogen bonding between PLF and 2-CEES. On the contrary, the electron cloud on the sulphur atom of the HD molecule is offset or depleted by its two neighbouring strong electron-withdrawing groups, hence, hydrogen bonding can hardly be formed.

  10. Identification by nuclear magnetic resonance spectroscopy of an active-site hydrogen-bond network in human monoacylglycerol lipase (hMGL): implications for hMGL dynamics, pharmacological inhibition, and catalytic mechanism.

    Science.gov (United States)

    Karageorgos, Ioannis; Tyukhtenko, Sergiy; Zvonok, Nikolai; Janero, David R; Sallum, Christine; Makriyannis, Alexandros

    2010-08-01

    Intramolecular hydrogen bonding is an important determinant of enzyme structure, catalysis, and inhibitor action. Monoacylglycerol lipase (MGL) modulates cannabinergic signaling as the main enzyme responsible for deactivating 2-arachidonoylglycerol (2-AG), a primary endocannabinoid lipid messenger. By enhancing tissue-protective 2-AG tone, targeted MGL inhibitors hold therapeutic promise for managing pain and treating inflammatory and neurodegenerative diseases. We report study of purified, solubilized human MGL (hMGL) to explore the details of hMGL catalysis by using two known covalent hMGL inhibitors, the carbamoyl tetrazole AM6701 and N-arachidonoylmaleimide (NAM), that act through distinct mechanisms. Using proton nuclear magnetic resonance spectroscopy (NMR) with purified wild-type and mutant hMGLs, we have directly observed a strong hydrogen-bond network involving Asp239 and His269 of the catalytic triad and neighboring Leu241 and Cys242 residues. hMGL inhibition by AM6701 alters this hydrogen-bonding pattern through subtle active-site structural rearrangements without influencing hydrogen-bond occupancies. Rapid carbamoylation of hMGL Ser122 by AM6701 and elimination of the leaving group is followed by a slow hydrolysis of the carbamate group, ultimately regenerating catalytically competent hMGL. In contrast, hMGL titration with NAM, which leads to cysteine alkylation, stoichiometrically decreases the population of the active-site hydrogen bonds. NAM prevents reformation of this network, and in this manner inhibits hMGL irreversibly. These data provide detailed molecular insight into the distinctive mechanisms of two covalent hMGL inhibitors and implicate a hydrogen-bond network as a structural feature of hMGL catalytic function.

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

    Science.gov (United States)

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

    2014-12-07

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-07-15

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

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

    Science.gov (United States)

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

    2015-05-22

    Column selectivity in reversed-phase chromatography (RPC) can be described in terms of the hydrophobic-subtraction model, which recognizes five solute-column interactions that together determine solute retention and column selectivity: hydrophobic, steric, hydrogen bonding of an acceptor solute (i.e., a hydrogen-bond base) by a stationary-phase donor group (i.e., a silanol), hydrogen bonding of a donor solute (e.g., a carboxylic acid) by a stationary-phase acceptor group, and ionic. Of these five interactions, hydrogen bonding between donor solutes (acids) and stationary-phase acceptor groups is the least well understood; the present study aims at resolving this uncertainty, so far as possible. Previous work suggests that there are three distinct stationary-phase sites for hydrogen-bond interaction with carboxylic acids, which we will refer to as column basicity I, II, and III. All RPC columns exhibit a selective retention of carboxylic acids (column basicity I) in varying degree. This now appears to involve an interaction of the solute with a pair of vicinal silanols in the stationary phase. For some type-A columns, an additional basic site (column basicity II) is similar to that for column basicity I in primarily affecting the retention of carboxylic acids. The latter site appears to be associated with metal contamination of the silica. Finally, for embedded-polar-group (EPG) columns, the polar group can serve as a proton acceptor (column basicity III) for acids, phenols, and other donor solutes. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Hydrogen-bond-reversal symmetry and its violation in ice nanotubes.

    Science.gov (United States)

    Kirov, Mikhail V

    2016-05-01

    Recently, a new type of generalized symmetry of ice structures was introduced which takes into account the change of direction of all hydrogen bonds. The energy nonequivalence of pairs of configurations with opposite direction of all hydrogen bonds was established in the course of computer simulation of bilayer ice and other four-coordinated structures without `dangling' hydrogen atoms. In this article, the results of detailed investigations of the violation of the hydrogen-bond-reversal symmetry in ice nanotubes consisting of stacked n-membered rings are presented. A comprehensive classification of all possible hydrogen-bonding configurations and their division into two classes (antisymmetrical and non-antisymmetrical) are given. Attention is focused on the most stable configurations that have no longitudinally arranged water molecules. This restriction made the asymmetry very difficult to find. For example, it was established that the asymmetry (non-antisymmetrical configurations) in ice nanotubes with square, pentagonal and hexagonal cross sections appears only when the number of transverse rings in the unit cell is more than six. It is shown that this is related to the well known combinatorial problem of enumerating the symmetry-distinct necklaces of black and white beads. It was found that, among the ice nanotubes that had been considered, hydrogen-bond-reversal asymmetry is most conspicuous in wide nanotubes such as heptagonal and octagonal. In this case the asymmetry is observed for unit cells of any length. In order to verify the results of the symmetry analysis and to confirm the energy nonequivalence of some (non-antisymmetrical) configurations, approximate calculations of the binding energy have been performed using the package TINKER.

  15. 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.

  16. Interfacial Hydrogen Bonds and Their Influence Mechanism on Increasing the Thermal Stability of Nano-SiO2-Modified Meta-Aramid Fibres

    National Research Council Canada - National Science Library

    Chao Tang; Xu Li; Zhiwei Li; Jian Hao

    2017-01-01

    ... of nano-SiO2/meta-aramid fibre interfacial hydrogen bonds and the strengthening mechanism behind interfacial hydrogen bonds on the thermal stability of meta-aramid fibres using molecular dynamics...

  17. 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.

  18. Trimethoxybenzanilide-based P-glycoprotein modulators: an interesting case of lipophilicity tuning by intramolecular hydrogen bonding.

    Science.gov (United States)

    Tardia, Piero; Stefanachi, Angela; Niso, Mauro; Stolfa, Diana Antonella; Mangiatordi, Giuseppe Felice; Alberga, Domenico; Nicolotti, Orazio; Lattanzi, Gianluca; Carotti, Angelo; Leonetti, Francesco; Perrone, Roberto; Berardi, Francesco; Azzariti, Amalia; Colabufo, Nicola Antonio; Cellamare, Saverio

    2014-08-14

    One of the principal reasons for the chemotherapy failure is the overexpression of drug efflux pumps, ABCB1 (also known as MDR1 or P-gp) and ABCC1 (also known as MRP1), whose inhibition remains a priority to circumvent drug resistance. We have recently shown a clear trend between lipophilicity and P-glycoprotein inhibitory activity for a class of galloyl-based modulators targeting P-glycoprotein and MRP1. Herein we report a new series of polymethoxy benzamides, whose lipophilicity was modulated through the establishment of an intramolecular hydrogen bond (IMHB) which allows reaching of P-gp inhibitory activity at the submicromolar IC50 level. The present study provides a strong rationale for candidates in the presence of IMHB as a key element for a high P-gp inhibitory activity.

  19. 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.

  20. The investigation of the hydrogen bond saturation effect during the dipole-dipole induced azobenzene supramolecular self-assembly.

    Science.gov (United States)

    Li, Linfeng; Wu, Rongliang; Guang, Shanyi; Su, Xinyan; Xu, Hongyao

    2013-12-21

    The substituent group and hydrogen bonds play important roles in supramolecular self-assembly. To exploit the influential mechanism of hydrogen bonds during the dipole-dipole induced supramolecular self-assembly, some rigid azobenzene molecules with different electronegativity and hydrogen bonding capabilities were identified and designed. Different regular-shaped architectures were constructed via a simple solution process under mild conditions. Both experimental results and density functional theory calculations show that weak π-π stacking interactions lead to thick and short nanocylinders, strong dipole-dipole interactions and dipole induced π-π stacking lead to long and thin nanorods, appropriate hydrogen bonds consolidate the dipole-dipole interactions and dipole induced π-π stacking, forming thin nanosheets, while excessive hydrogen bonds in azobenzene would ruin the regular-shaped structures, giving irregular and stochastic aggregates. Namely there exists a certain hydrogen bond saturation effect in generating azobenzene nanostructures driven by dipole-dipole interactions. The results indicate that the morphologies of organic materials with azobenzene structures can be effectively controlled through rational molecular design by way of introducing appropriate dipole and hydrogen bonds.

  1. Dynamics of the water hydrogen bond network at ionic, nonionic, and hydrophobic interfaces in nanopores and reverse micelles.

    Science.gov (United States)

    Rosenfeld, Daniel E; Schmuttenmaer, Charles A

    2011-02-10

    The effects of water confinement on hydrogen bond dynamics and hydrogen bond exchange have been analyzed by molecular dynamics simulations for a series of different sizes of spherical nanopores of ionic, nonionic, and hydrophobic interfaces. We have calculated translational diffusion residence times, orientational decay time constants, the infrared spectra, correlation functions describing the hydrogen bond network, the hydrogen bond exchange time and rate constant, and ensemble averages of the hydrogen bond exchange reaction coordinate. We focus on the interfacial layer and bulklike interior of these small water containing nanostructures. Our results indicate a universal slowdown in rotational and hydrogen bond dynamics at the interface relative to bulk water. The interiors of nanopores with highly charged interfaces undergo qualitatively different dynamics than those in other nanopores. The rotational jump hydrogen bond exchange mechanism is shown to be robust and universal, even for this variety of interfaces. The implications of these results are discussed in terms of the role of confinement vs interface structure on water dynamics in nanopores.

  2. 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.

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

    Science.gov (United States)

    Hachuła, Barbara

    2018-01-01

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

  4. Novel flexible frameworks of porous cobalt(II) coordination polymers that show selective guest adsorption based on the switching of hydrogen-bond pairs of amide groups.

    Science.gov (United States)

    Uemura, Kazuhiro; Kitagawa, Susumu; Kondo, Mitsuru; Fukui, Kôichi; Kitaura, Ryo; Chang, Ho-Chol; Mizutani, Tadashi

    2002-08-16

    Four porous crystalline coordination polymers with two-dimensional frameworks of a double-edged axe-shaped motif, [[Co(NCS)(2)(3-pia)(2)] x 2 EtOH.11 H(2)O](n) (1 a), [[Co(NCS)(2)(3-pia)(2)] x 4 Me(2)CO](n) (3 a), [[Co(NCS)(2)(3-pia)(2)] x 4T HF](n) (3 b) and [[Co(NCS)(2)(3-pna)(2)](n)] (5), have been synthesized by the reaction of cobalt(II) thiocyanate with N-(3-pyridyl)isonicotinamide (3-pia) or N-(3-pyridyl)nicotinamide (3-pna). X-ray crystallographic characterization reveals that adjacent layers are stacked such that channels are created, except in 5. The channels form a hydrogen-bonded interior for guest molecules; in practice, 1 a contains ethanol and water molecules as guests in the channels with hydrogen bonds, whereas 3 b (3 a) contains tetrahydrofuran (acetone) molecules. In 1 a, the "double-edged axe-shaped" motifs in adjacent sheets are not located over the top of each other, while the motifs in 3 b stack so perfectly as to overlap each other in an edge-to-edge fashion. This subtle change in the three-dimensional framework is associated with the template effect of the guests. Compound 5 has no guest molecules and, therefore, the amide groups in one sheet are used for hydrogen-bonding links with adjacent sheets. Removal of the guest molecules from 1 a and 3 b (3 a) causes a structural conversion accompanied by a color change. Pink 1 a cannot retain its original framework and changes into a blue amorphous compound. On the other hand, the framework of pink 3 b (3 a) is transformed to a new crystalline framework of violet 4. Interestingly, 4 reverts to the original pink crystals of 3 b (3 a) when it is exposed to THF (or acetone) vapor. Spectroscopic measurements (visible, EPR, and IR) provide a clue to the crystal-to-crystal transformation; on removal of the guests, the amide groups are used to form the beta sheet-type hydrogen bonding between the sheets, and thus the framework withstands significant stress on removal of guest molecules. This mechanism is

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

    DEFF Research Database (Denmark)

    Mackeprang, Kasper; Kjærgaard, Henrik Grum

    2017-01-01

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

  6. Note: Charge transfer in a hydrated peptide group is determined mainly by its intrinsic hydrogen-bond energetics

    Energy Technology Data Exchange (ETDEWEB)

    Mirkin, Noemi G.; Krimm, Samuel [LSA Biophysics, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109-1055 (United States)

    2014-01-28

    Charge transfer in a hydrogen-bonded N-methylacetamide(H{sub 2}O){sub 3} system is obtained from ωB97X-D/6-31++G** and CHelpG atomic charge calculations of individual peptide-water interactions as well as that of the entire complex. In the latter, the electron transfer to water is 0.19 e, influenced primarily by the hydrogen bonds to the C=O group. The values of such charge transfer are paralleled by the corresponding intrinsic hydrogen-bond energies. These results support the desirability of incorporating charge transfer in molecular mechanics energy functions.

  7. Defective continuous hydrogen-bond networks: an alternative interpretation of IR spectroscopy.

    Science.gov (United States)

    Schmidt, Diedrich A; Miki, Kazushi

    2008-09-15

    We apply our previously developed deconvolution method and interpretation to analyze changes in the OH stretching band [nu(OH) band] of low-concentration (NaCl and KCl. We treat these simple, monovalent ions as defects in the hydrogen-bond network of pure water and quantify the changes in the spectra at low defect concentration with an "order parameter". Order-parameter analysis of difference spectra of the two solutions leads to hydration numbers of 7.0+/-1.0 and 5.9+/-0.3 for K(+) and Na(+), respectively. Additionally, we find that changes in the nu(OH) band due to low concentrations of ions result from changes in the topology of the hydrogen-bond network.

  8. The Hydrogen bonding effects in structural analysis of phenilon C-2: the quantum-chemical interpretation

    Directory of Open Access Journals (Sweden)

    Andrey V. Tokar

    2017-11-01

    Full Text Available Using ab initio methods of quantum chemistry the structure and spectral properties for molecular complexes, which were formed by monomer of phenilon С-2 chain, including some intra- and intermolecular hydrogen bonding effects as well as electrostatic interactions with evaluation of their contributions in total stabilization energy, have been investigated at natural bond orbitals theory. It is shown, that the overlapping of n1,2(O→ σ*(NН type with energies 15.4 and 9.5 kJ/mol, which correspond to the strong hydrogen bonding between amide groups, is a main direction for co-operating of some area for structural fragments of macromolecules. The proposed theoretical models are validated in reflection of spectral and energetic parameters for investigating system.

  9. Physical Stabilization of Pharmaceutical Glasses Based on Hydrogen Bond Reorganization under Sub-Tg Temperature.

    Science.gov (United States)

    Tominaka, Satoshi; Kawakami, Kohsaku; Fukushima, Mayuko; Miyazaki, Aoi

    2017-01-03

    Amorphous solid dispersions (ASDs) play a key role in the pharmaceutical industry through the use of high-energy amorphous state to improve solubility of pharmaceutical agents. Understanding the physical stability of pharmaceutical glasses is of great importance for their successful development. We focused on the anti-HIV agent, ritonavir (RTV), and investigated the influence of annealing at temperatures below the glass transition temperature (sub-Tg) on physical stability, and found that the sub-Tg annealing effectively stabilized RTV glasses. Through the atomic structure analyses using X-ray pair distribution functions and infrared spectroscopy, we ascertained that this fascinating effect of the sub-Tg annealing originated from strengthened hydrogen bonding between molecules and probably from a better local packing associated with the stronger hydrogen bonds. The sub-Tg annealing is effective as a physical stabilization strategy for some pharmaceutical molecules, which have relatively large energy barrier for nucleation.

  10. 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. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    DEFF Research Database (Denmark)

    Schrøder, Sidsel Dahl

    and 1,4-diaminobutane). Experimentally, the hydrogen bonds have been studied with vibrational spectroscopy in the infrared and near-infrared regions. The focus is primarily on spectra recorded in the near-infrared regions, which in these studies are dominated by O-H and N-H stretching overtones....... Overtone spectra have been recorded with intracavity laser photoacoustic laser spectroscopy and conventional long path absorption spectroscopy. Theoretically, a combination of electronic structure calculations and local mode models have been employed to guide the assignment of bands in the vibrational......, weak intramolecular hydrogen bonds in methyl lactate, allyl carbinol and methallyl carbinol have been identified and characterized. The effect of substitution of two hydrogen atoms on one of the methylene groups with either methyl groups or tri uoromethyl groups on the intramolecular...

  12. Flavin-Protein Complexes: Aromatic Stacking Assisted by a Hydrogen Bond.

    Science.gov (United States)

    Hamdane, Djemel; Bou-Nader, Charles; Cornu, David; Hui-Bon-Hoa, Gaston; Fontecave, Marc

    2015-07-21

    Enzyme-catalyzed reactions often rely on a noncovalently bound cofactor whose reactivity is tuned by its immediate environment. Flavin cofactors, the most versatile catalyst encountered in biology, are often maintained within the protein throughout numbers of complex ionic and aromatic interactions. Here, we have investigated the role of π-π stacking and hydrogen bond interactions between a tyrosine and the isoalloxazine moiety of the flavin adenine dinucleotide (FAD) in an FAD-dependent RNA methyltransferase. Combining several static and time-resolved spectroscopies as well as biochemical approaches, we showed that aromatic stacking is assisted by a hydrogen bond between the phenol group and the amide of an adjacent active site loop. A mechanism of recognition and binding of the redox cofactor is proposed.

  13. Hydrogen-bond promoted nucleophilic fluorination: concept, mechanism and applications in positron emission tomography.

    Science.gov (United States)

    Lee, Ji-Woong; Oliveira, Maria Teresa; Jang, Hyeong Bin; Lee, Sungyul; Chi, Dae Yoon; Kim, Dong Wook; Song, Choong Eui

    2016-08-22

    Due to the tremendous interest in carbon-fluorine bond-forming reactions, research efforts in this area have been dedicated to the development of facile processes to synthesize small fluorine-containing organic molecules. Among others, PET (Positron Emission Tomography) is one of the most important applications of fluorine chemistry. Recognizing the specific requirements of PET processes, some groups have focused on fluorination reactions using alkali metal fluorides, particularly through SN2-type reactions. However, a common "misconception" about the role of protic solvents and hydrogen bonding interactions in this class of reactions has hampered the employment of these excellent promoters. Herein, we would like to review recent discoveries in this context, showing straightforward nucleophilic fluorination reactions using alkali metal fluorides promoted by protic solvents. Simultaneous dual activation of reacting partners by intermolecular hydrogen bonding and the enhancement of the "effective fluoride nucleophilicity", which is Nature's biocatalytic approach with the fluorinase enzyme, are the key to this unprecedentedly successful nucleophilic fluorination.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-06-14

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

  15. Diketopyrrolopyrrole Columnar Liquid-Crystalline Assembly Directed by Quadruple Hydrogen Bonds.

    Science.gov (United States)

    Soberats, Bartolome; Hecht, Markus; Würthner, Frank

    2017-08-28

    A diketopyrrolopyrrole (DPP) dye self-assembles via a unique hydrogen-bonding motif into an unprecedented columnar liquid-crystalline (LC) structure. X-ray and polarized FTIR experiments reveal that the DPPs organize into a one-dimensional assembly with the chromophores oriented parallel to the columnar axis. This columnar structure is composed of two π-π-stacked DPP dimers with mirror-image configurations that stack alternately through quadruple hydrogen bonding by 90° rotation. This exotic packing is dictated by the complementarity between H-bonds and the steric demands of the wedge-shaped groups attached at the core. This novel LC supramolecular material opens a new avenue of research on DPP dye assemblies with photofunctional properties tailored by H-bonding networks. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Hydrogen-bonding networks from first-principles: exploring the guanidine crystal.

    Science.gov (United States)

    Hoepfner, Veronika; Deringer, Volker L; Dronskowski, Richard

    2012-05-10

    Hydrogen bonding is among the most important interactions in molecular crystals, and examples are abundant. As a consequence of such interactions, many molecules crystallize in complex but intriguing structures, in contrast to the relatively simple packing principles of metallic or ionic solids. In this work, we present a computational approach based on plane-wave density-functional theory (DFT) and supercell techniques, aiming to understand and quantify hydrogen-bonded networks in the solid state and in two-, one-, and zero-dimensional fragments derived from the molecular crystal. With such methodology at hand, we investigate guanidine, a fitting example of a molecular crystal and an important compound for inorganic and organic chemistry alike. On the basis of our computations, we discuss the initially proposed layered structure of guanidine and identify both stabilizing and destabilizing cooperative interactions in the three crystalline dimensions.

  17. 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.

  18. Compressed hydrogen-bond effects in the pressure-frozen chloroacetic acid.

    Science.gov (United States)

    Gajda, Roman; Katrusiak, Andrzej

    2007-12-01

    The competing effects of squeezed OH...O bonds, destabilizing the H-atom position, and of displaced hydrogen donor and acceptor groups, favouring the ordered H-atom sites, have been tuned by pressure in the pressure-frozen dichloroacetic acid. Its structure has been determined at 0.1, 0.7, 0.9 and 1.4 GPa: in this pressure range the crystals are stable in the monoclinic space group P2(1)/n. The molecules are O-H...O hydrogen bonded into dimers, which in turn interact via a unique pattern of halogen...halogen contacts. Between 0.1 and 1.4 GPa the OH...O bond is squeezed from 2.674 (13) to 2.632 (9) A. Within the pressure range investigated the hydrogen bonds are squeezed and the shear displacement of the molecules compensate, and the H atoms remain ordered.

  19. Anions of the hydrogen-bonded thymine dimer: ab initio study

    Science.gov (United States)

    Jalbout, Abraham F.; Smets, Johan; Adamowicz, Ludwik

    2001-11-01

    Theoretical calculations have been performed to determine the ability of the hydrogen-bonded thymine dimer to form stable anions. The major conclusions of this work are: (i) three of the hydrogen-bonded conformers of the thymine dimer can form stable dipole-bound anions with excess electrons; (ii) thymine dimer can form a covalent anion that has a structure dissimilar from the structures of the neutral dimer; (iii) in the covalent thymine-dimer anion the excess electron is localized in a π-orbital on one of the thymine molecules and this molecule shows an out-of-plane distortion; (iv) the covalent thymine-dimer anion is stable with respect to an adiabatic electron detachment.

  20. Comparative study of halogen- and hydrogen-bond interactions between benzene derivatives and dimethyl sulfoxide.

    Science.gov (United States)

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

    2015-08-24

    The halogen bond, similar to the hydrogen bond, is an important noncovalent interaction and plays important roles in diverse chemistry-related fields. Herein, bromine- and iodine-based halogen-bonding interactions between two benzene derivatives (C6 F5 Br and C6 F5 I) and dimethyl sulfoxide (DMSO) are investigated by using IR and NMR spectroscopy and ab initio calculations. The results are compared with those of interactions between C6 F5 Cl/C6 F5 H and DMSO. First, the interaction energy of the hydrogen bond is stronger than those of bromine- and chlorine-based halogen bonds, but weaker than iodine-based halogen bond. Second, attractive energies depend on 1/r(n) , in which n is between three and four for both hydrogen and halogen bonds, whereas all repulsive energies are found to depend on 1/r(8.5) . Third, the directionality of halogen bonds is greater than that of the hydrogen bond. The bromine- and iodine-based halogen bonds are strict in this regard and the chlorine-based halogen bond only slightly deviates from 180°. The directional order is iodine-based halogen bond>bromine-based halogen bond>chlorine-based halogen bond>hydrogen bond. Fourth, upon the formation of hydrogen and halogen bonds, charge transfers from DMSO to the hydrogen- and halogen-bond donors. The CH3 group contributes positively to stabilization of the complexes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Selective Nitrate Binding in Competitive Hydrogen Bonding Solvents: Do Anion–π Interactions Facilitate Nitrate Selectivity?**

    Science.gov (United States)

    Watt, Michelle M.; Zakharov, Lev N.

    2013-01-01

    New tripodal urea receptors demonstrate preferential binding of anions over competitive hydrogen bonding solvents. 1H NMR titrations in 10% DMSO-d6/CDCl3 show a higher affinity for nitrate over the halides for the fluorinated receptor, which is lost when the fluorines are removed. An “anion–π” interaction between the nitrate and the π-system of the ethynyl-substituted arene is proposed as the source of this selectivity. PMID:23939999

  2. 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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Hydrogen-Bonded Liquids: Effects of Correlations of Orientational Degrees of Freedom

    OpenAIRE

    Franzese, G.; Yamada, M.; Stanley, H. E.

    2000-01-01

    We improve a lattice model of water introduced by Sastry, Debenedetti, Sciortino, and Stanley to give insight on experimental thermodynamic anomalies in supercooled phase, taking into account the correlations between intra-molecular orientational degrees of freedom. The original Sastry et al. model including energetic, entropic and volumic effect of the orientation-dependent hydrogen bonds (HBs), captures qualitatively the experimental water behavior, but it ignores the geometrical correlatio...

  4. Hydrogen-Bond Dynamics in a Protic Ionic Liquid: Evidence of Large-Angle Jumps.

    Science.gov (United States)

    Hunger, Johannes; Sonnleitner, Thomas; Liu, Liyuan; Buchner, Richard; Bonn, Mischa; Bakker, Huib J

    2012-10-18

    We study the molecular rotation of the protic room-temperature ionic liquid ethylammonium nitrate with dielectric relaxation spectroscopy and femtosecond-infrared spectroscopy (fs-IR) of the ammonium N-H vibrations. The results suggest that the rotation of ethylammonium ion takes place via large angular jumps. Such nondiffusive reorientational dynamics is unique to strongly hydrogen-bonded liquids such as water and indicates that the intermolecular interaction is highly directional in this class of ionic liquids.

  5. The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease

    OpenAIRE

    Trylska, Joanna; Grochowski, Paweł; McCammon, J. Andrew

    2004-01-01

    The hydrogen-bond network in various stages of the enzymatic reaction catalyzed by HIV-1 protease was studied through quantum-classical molecular dynamics simulations. The approximate valence bond method was applied to the active site atoms participating directly in the rearrangement of chemical bonds. The rest of the protein with explicit solvent was treated with a classical molecular mechanics model. Two possible mechanisms were studied, general-acid/general-base (GA/GB) with Asp 25 protona...

  6. Control of a two-dimensional molecular structure by cooperative halogen and hydrogen bonds

    OpenAIRE

    Yasuda, Satoshi; Furuya, Atom; Murakoshi, Kei

    2014-01-01

    The cooperative effect of hydrogen and halogen bonds on the two-dimensional (2D) molecular arrangement on highly oriented pyrolytic graphite (HOPG) was studied by scanning tunneling microscopy. The terephthalic acid (TPA) molecule, which has two carboxyl groups attached at the para positions of a benzene ring, formed a one-dimensional (1D) linear non-covalent network structure on HOPG by hydrogen bonds between the carboxyl groups of neighboring molecules. However, unlike the TPA molecule, Br ...

  7. Water on Silicene: Hydrogen Bond Autocatalysis Induced Physisorption-Chemisorption-Dissociation Transition

    OpenAIRE

    Hu, Wei; Li, Zhenyu; Yang, Jinlong

    2016-01-01

    A single water molecule has nothing special. However, macroscopic water displays many anomalous properties at the interface, such as a high surface tension, hydrophobicity and hydrophillicity. Although the underlying mechanism is still elusive, hydrogen bond is expected to have played an important role. An interesting question is if the few-water molecule clusters will be qualitatively different from a single molecule. Using adsorption behavior as an example, by carefully choosing two-dimensi...

  8. Matrix isolation infrared spectra of OH··· π Hydrogen bonded ...

    Indian Academy of Sciences (India)

    Mid infrared spectra of two O–H· · · π hydrogen-bonded binary complexes of acetic acid (AA) and trifluoroacetic acid (F₃AA) with benzene (Bz) have been measured by isolating the complexes in an argon matrix at ∼8 K. In a matrix isolation condition, the O–H stretching fundamentals (νO−H) of the carboxylic acid groups of ...

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

    Science.gov (United States)

    Wen, Jialin; Jiang, Jun; Zhang, Xumu

    2016-09-16

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

  10. Self-Healing Gelatin Hydrogels Cross-Linked by Combining Multiple Hydrogen Bonding and Ionic Coordination.

    Science.gov (United States)

    Zhang, Guangzhao; Lv, Lei; Deng, Yonghong; Wang, Chaoyang

    2017-06-01

    Self-healing hydrogels have been studied by many researchers via multiple cross-linking approaches including physical and chemical interactions. It is an interesting project in multifunctional hydrogel exploration that a water soluble polymer matrix is cross-linked by combining the ionic coordination and the multiple hydrogen bonds to fabricate self-healing hydrogels with injectable property. This study introduces a general procedure of preparing the hydrogels (termed gelatin-UPy-Fe) cross-linked by both ionic coordination of Fe3+ and carboxyl group from the gelatin and the quadruple hydrogen bonding interaction from the ureido-pyrimidinone (UPy) dimers. The gelatin-UPy-Fe hydrogels possess an excellent self-healing property. The effects of the ionic coordination of Fe3+ and quadruple hydrogen bonding of UPy on the formation and mechanical behavior of the prepared hydrogels are investigated. In vitro drug release of the gelatin-UPy-Fe hydrogels is also observed, giving an intriguing glimpse into possible biological applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Effect of hydrogen bonds on pKa values: importance of networking.

    Science.gov (United States)

    Shokri, Alireza; Abedin, Azardokht; Fattahi, Alireza; Kass, Steven R

    2012-06-27

    The pK(a) of an acyclic aliphatic heptaol ((HOCH(2)CH(2)CH(OH)CH(2))(3)COH) was measured in DMSO, and its gas-phase acidity is reported as well. This tertiary alcohol was found to be 10(21) times more acidic than tert-butyl alcohol in DMSO and an order of magnitude more acidic than acetic acid (i.e., pK(a) = 11.4 vs 12.3). This can be attributed to a 21.9 kcal mol(-1) stabilization of the charged oxygen center in the conjugate base by three hydrogen bonds and another 6.3 kcal mol(-1) stabilization resulting from an additional three hydrogen bonds between the uncharged primary and secondary hydroxyl groups. Charge delocalization by both the first and second solvation shells may be used to facilitate enzymatic reactions. Acidity constants of a series of polyols were also computed, and the combination of hydrogen-bonding and electron-withdrawing substituents was found to afford acids that are predicted to be extremely acidic in DMSO (i.e., pK(a) acids represent an attractive class of Brønsted acid catalysts.

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

    Science.gov (United States)

    Jezierska, Aneta; Panek, Jarosław J

    2015-06-22

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

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

    Science.gov (United States)

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

    2014-07-01

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

  14. Lipid carbonyl groups terminate the hydrogen bond network of membrane-bound water.

    Science.gov (United States)

    Ohto, Tatsuhiko; Backus, Ellen H G; Hsieh, Cho-Shuen; Sulpizi, Marialore; Bonn, Mischa; Nagata, Yuki

    2015-11-19

    We present a combined experimental sum-frequency generation (SFG) spectroscopy and ab initio molecular dynamics simulations study to clarify the structure and orientation of water at zwitterionic phosphatidylcholine (PC) lipid and amine N-oxide (AO) surfactant monolayers. Simulated O-H stretch SFG spectra of water show good agreement with the experimental data. The SFG response at the PC interface exhibits positive peaks, whereas both negative and positive bands are present for the similar zwitterionic AO interface. The positive peaks at the water/PC interface are attributed to water interacting with the lipid carbonyl groups, which act as efficient hydrogen bond acceptors. This allows the water hydrogen bond network to reach, with its (up-oriented) O-H groups, into the headgroup of the lipid, a mechanism not available for water underneath the AO surfactant. This highlights the role of the lipid carbonyl group in the interfacial water structure at the membrane interface, namely, stabilizing the water hydrogen bond network.

  15. Microwave spectroscopy of 2-(trifluoromethyl)pyridine⋯water complex: Molecular structure and hydrogen bond

    Science.gov (United States)

    Li, Xiaolong; Zheng, Yang; Gou, Qian; Feng, Gang; Xia, Zhining

    2018-01-01

    In order to explore the -CF3 substitution effect on the complexation of pyridine, we investigated the 2-(trifluoromethyl)pyridine⋯water complex by using pulsed jet Fourier transform microwave spectroscopy complemented with quantum chemical calculations. Experimental assignment and ab initio calculations confirmed that the observed complex is stabilized through N⋯H-O and O⋯H-C hydrogen bonds forming a five-membered ring structure. The bonding distance in N⋯H-O is determined to be 2.027(2) Å, whilst that in O⋯H-C interaction is 2.728(2) Å. The quantum theory of atoms in molecules analysis indicates that the interaction energy of N⋯H-O hydrogen bond is ˜22 kJ mol-1 and that for O⋯H-C hydrogen bond is ˜5 kJ mol-1. The water molecule lies almost in the plane of the aromatic ring in the complex. The -CF3 substitution to pyridine quenches the tunneling splitting path of the internal motion of water molecule.

  16. Spectroscopic and Ab-Initio Studies of π -Type Hydrogen Bonding in Cyclic Alcohols and Amines

    Science.gov (United States)

    Ocola, Esther; Laane, Jaan

    2011-10-01

    Infrared and Raman spectroscopy have been used to investigate several molecules capable of intramolecular π-type hydrogen bonding. Ab-initio calculations have been utilized to complement the experimental work. The cyclic alcohols, 3-cyclopenten-1-ol (3CYPO), 2-cyclopenten-1-ol, 2-cyclohexen-1-ol, and the cyclic amines, 3-cyclopenten-1-amine, 2-aminoindan, 2-cyclopenten-1-amine, 1-aminoindan, and 2-hydroxytetralin have been studied. 3CYPO can exist in four different conformational forms and all were observed in the infrared and Raman spectra. The conformer with the weak π-type intramolecular hydrogen bonding is about 400 cm-1 (1.1 kcal/mole) lower in energy than the other three conformations to which the lowest energy form can interconvert through ring-puckering or internal rotation vibrations. The interconversions and relative energies of all the other molecules were also investigated. In each case the conformation with the lowest energy had a π-type hydrogen bonding.

  17. Measuring the relative hydrogen-bonding strengths of alcohols in aprotic organic solvents.

    Science.gov (United States)

    Tessensohn, Malcolm E; Lee, Melvyn; Hirao, Hajime; Webster, Richard D

    2015-01-12

    Voltammetric experiments with 9,10-anthraquinone and 1,4-benzoquinone performed under controlled moisture conditions indicate that the hydrogen-bond strengths of alcohols in aprotic organic solvents can be differentiated by the electrochemical parameter ΔEp (red) =|Ep (red(1)) -Ep (red(2)) |, which is the potential separation between the two one-electron reduction processes. This electrochemical parameter is inversely related to the strength of the interactions and can be used to differentiate between primary, secondary, tertiary alcohols, and even diols, as it is sensitive to both their steric and electronic properties. The results are highly reproducible across two solvents with substantially different hydrogen-bonding properties (CH3 CN and CH2 Cl2 ) and are supported by density functional theory calculations. This indicates that the numerous solvent-alcohol interactions are less significant than the quinone-alcohol hydrogen-bonding interactions. The utility of ΔEp (red) was illustrated by comparisons between 1) 3,3,3-trifluoro-n-propanol and 1,3-difluoroisopropanol and 2) ethylene glycol and 2,2,2-trifluoroethanol. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. 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.

  19. 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.

  20. Hydrogen-bond Specific Materials Modification in Group IV Semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Tolk, Norman H. [Vanderbilt Univ., Nashville, TN (United States); Feldman, L. C. [Vanderbilt Univ., Nashville, TN (United States); Luepke, G. [College of William and Mary, Williamsburg, VA (United States)

    2015-09-14

    Executive summary Semiconductor dielectric crystals consist of two fundamental components: lattice atoms and electrons. The former component provides a crystalline structure that can be disrupted by various defects or the presence of an interface, or by transient oscillations known as phonons. The latter component produces an energetic structure that is responsible for the optical and electronic properties of the material, and can be perturbed by lattice defects or by photo-excitation. Over the period of this project, August 15, 1999 to March 31, 2015, a persistent theme has been the elucidation of the fundamental role of defects arising from the presence of radiation damage, impurities (in particular, hydrogen), localized strain or some combination of all three. As our research effort developed and evolved, we have experienced a few title changes, which reflected this evolution. Throughout the project, ultrafast lasers usually in a pump-probe configuration provided the ideal means to perturb and study semiconductor crystals by both forms of excitation, vibrational (phonon) and electronic (photon). Moreover, we have found in the course of this research that there are many interesting and relevant scientific questions that may be explored when phonon and photon excitations are controlled separately. Our early goals were to explore the dynamics of bond-selective vibrational excitation of hydrogen from point defects and impurities in crystalline and amorphous solids, initiating an investigation into the behavior of hydrogen isotopes utilizing a variety of ultrafast characterization techniques, principally transient bleaching spectroscopy to experimentally obtain vibrational lifetimes. The initiative could be divided into three related areas: (a) investigation of the change in electronic structure of solids due to the presence of hydrogen defect centers, (b) dynamical studies of hydrogen in materials and (c) characterization and stability of metastable hydrogen

  1. Hydrogen bond, electron donor-acceptor dimer, and residence dynamics in supercritical CO(2)-ethanol mixtures and the effect of hydrogen bonding on single reorientational and translational dynamics: A molecular dynamics simulation study.

    Science.gov (United States)

    Skarmoutsos, Ioannis; Guardia, Elvira; Samios, Jannis

    2010-07-07

    The hydrogen bonding and dynamics in a supercritical mixture of carbon dioxide with ethanol as a cosolvent (X(ethanol) approximately 0.1) were investigated using molecular dynamics simulation techniques. The results obtained reveal that the hydrogen bonds formed between ethanol molecules are significantly more in comparison with those between ethanol-CO(2) molecules and also exhibit much larger lifetimes. Furthermore, the residence dynamics in the solvation shells of ethanol and CO(2) have been calculated, revealing much larger residence times for ethanol molecules in the ethanol solvation shell. These results support strongly the ethanol aggregation effects and the slow local environment reorganization inside the ethanol solvation shell, reported in a previous publication of the authors [Skarmoutsos et al., J. Chem. Phys. 126, 224503 (2007)]. The formation of electron donor-acceptor dimers between the ethanol and CO(2) molecules has been also investigated and the calculated lifetimes of these complexes have been found to be similar to those corresponding to ethanol-CO(2) hydrogen bonds, exhibiting a slightly higher intermittent lifetime. However, the average number of these dimers is larger than the number of ethanol-CO(2) hydrogen bonds in the system. Finally, the effect of the hydrogen bonds formed between the individual ethanol molecules on their reorientational and translational dynamics has been carefully explored showing that the characteristic hydrogen bonding microstructure obtained exhibits sufficiently strong influence upon the behavior of them.

  2. The Effect of Hydrogen Bonding on Radical Semi-Batch Copolymerization of Butyl Acrylate and 2-Hydroxyethyl Acrylate

    National Research Council Canada - National Science Library

    Jan E S Schier; David Cohen-Sacal; Owen R Larsen; Robin A Hutchinson

    2017-01-01

    The radical copolymerization of butyl acrylate (BA) and 2-hydroxyethyl acrylate (HEA) was investigated under batch and semi-batch operations, with a focus on the influence of hydrogen-bonding on acrylate backbiting...

  3. Isotope dependent, temperature regulated, energy repartitioning in a low-barrier, short-strong hydrogen bonded cluster

    NARCIS (Netherlands)

    Li, X. H.; Oomens, J.; Eyler, J. R.; Moore, D. T.; Iyengar, S. S.

    2010-01-01

    We investigate and analyze the vibrational properties, including hydrogen/deuterium isotope effects, in a fundamental organic hydrogen bonded system using multiple experimental (infrared multiple photon dissociation and argon-tagged action spectroscopy) and computational techniques. We note a

  4. Thermodynamic and dynamic dielectric properties of one-dimensional hydrogen bonded ferroelectric of PbHPO4-type

    National Research Council Canada - National Science Library

    I.R. Zachek; R.R. Levitskii; Ya. Shchur; O.B. Bilenka

    2014-01-01

    Within the modified model of proton ordering of one-dimensional ferroelectric having hydrogen bonds of PbHPO4-type, their thermodynamic and dynamic characteristics are studied and calculated taking...

  5. The Effect of Hydrogen Bonding on Radical Semi-Batch Copolymerization of Butyl Acrylate and 2-Hydroxyethyl Acrylate

    National Research Council Canada - National Science Library

    Jan E S Schier; David Cohen-Sacal; Owen R Larsen; Robin A Hutchinson

    2017-01-01

    .... The effect of hydrogen bonding on HEA to BA relative incorporation rates during copolymerization, previously seen in low-conversion kinetic studies, was also observed under high-conversion semi-batch conditions...

  6. Hydrogen-Bond Strength of CC and GG Pairs Determined by Steric Repulsion: Electrostatics and Charge Transfer Overruled.

    Science.gov (United States)

    van der Lubbe, Stephanie C C; Fonseca Guerra, Célia

    2017-08-01

    Theoretical and experimental studies have elucidated the bonding mechanism in hydrogen bonds as an electrostatic interaction, which also exhibits considerable stabilization by charge transfer, polarization, and dispersion interactions. Therefore, these components have been used to rationalize the differences in strength of hydrogen-bonded systems. A completely new viewpoint is presented, in which the Pauli (steric) repulsion controls the mechanism of hydrogen bonding. Quantum chemical computations on the mismatched DNA base pairs CC and GG (C=cytosine, G=guanine) show that the enhanced stabilization and shorter distance of GG is determined entirely by the difference in the Pauli repulsion, which is significantly less repulsive for GG than for CC. This is the first time that evidence is presented for the Pauli repulsion as decisive factor in relative hydrogen-bond strengths and lengths. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  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. Role of Surface Molecular Architecture and Energetics of Hydrogen Bonding Sites in Adsorption of Polymers and Surfactants.

    Science.gov (United States)

    Bjelopavlic, Mick; Singh, Pankaj K.; El-Shall, Hassan; Moudgil, Brij M.

    2000-06-01

    Hydrogen bonding is generally thought to be an ubiquitous adsorption mechanism, which often foils selective adsorption schemes. Through investigation of hydrogen bonding energy and its dependence on surface molecular architecture, it may be possible to develop new methodologies to control the adsorption of surfactants and polymeric flocculants, depressants, and dispersants used in particulate processing industries. A model system using Stöber silica spheres and polyethylene oxide, a polymer known for its ability to form hydrogen bonds, was examined. The effect of two different surface treatments of the silica particles, calcination and rehydroxylation, upon the adsorption of two polymer molecular weights was studied. The adsorption behavior was then linked to the respective surface structures via characterization of the surfaces using FTIR, NMR, and Raman techniques. In this paper role of hydrogen bonding sites and surface architecture on adsorption is discussed. Copyright 2000 Academic Press.

  9. Car-Parrinello Molecular Dynamics Simulations of Infrared Spectra of Crystalline Vitamin C with Analysis of Double Minimum Proton Potentials for Medium-Strong Hydrogen Bonds.

    Science.gov (United States)

    Brela, Mateusz Z; Wójcik, Marek J; Boczar, Marek; Witek, Łukasz; Yasuda, Mitsuru; Ozaki, Yukihiro

    2015-06-25

    We studied proton dynamics of a hydrogen bonds of the crystalline l-ascorbic acid. Our approach was based on the Car-Parrinello molecular dynamics. The focal point of our study was simulation of the infrared spectra of l-ascorbic acid associated with the O-H stretching modes that are very sensitive to the strength of hydrogen bonding. In the l-ascorbic acid there are four kinds of hydrogen bonds. We calculated their spectra by using anharmonic approximation and the time course of the dipole moment function as obtained from the Car-Parrinello simulation. The quantization of the nuclear motion of the protons was made to perform detailed analysis of strength and properties of hydrogen bonds. We presented double minimum proton potentials with small value of barriers for medium-strong hydrogen bonds. We have also shown the difference character of medium-strong hydrogen bonds compared to weaker hydrogen bonds in the l-ascorbic acid.

  10. Effect of hydrogen bond networks on the nucleation mechanism of protein folding.

    Science.gov (United States)

    Djikaev, Y S; Ruckenstein, Eli

    2009-12-01

    We have recently developed a kinetic model for the nucleation mechanism of protein folding (NMPF) in terms of ternary nucleation by using the first passage time analysis. A protein was considered as a random heteropolymer consisting of hydrophobic, hydrophilic (some of which are negatively or positively ionizable), and neutral beads. The main idea of the NMPF model consisted of averaging the dihedral potential in which a selected residue is involved over all possible configurations of all neighboring residues along the protein chain. The combination of the average dihedral, effective pairwise (due to Lennard-Jones-type and electrostatic interactions), and confining (due to the polymer connectivity constraint) potentials gives rise to an overall potential around the cluster that, as a function of the distance from the cluster center, has a double-well shape. This allows one to evaluate the protein folding time. In the original NMPF model hydrogen bonding was not taken into account explicitly. To improve the NMPF model and make it more realistic, in this paper we modify our (previously developed) probabilistic hydrogen bond model and combine it with the former. Thus, a contribution due to the disruption of hydrogen bond networks around the interacting particles (cluster of native residues and residue in the protein unfolded part) appears in the overall potential field around a cluster. The modified model is applied to the folding of the same model proteins that were examined in the original model: a short protein consisting of 124 residues (roughly mimicking bovine pancreatic ribonuclease) and a long one consisting of 2500 residues (as a representative of large proteins with superlong polypeptide chains), at pH=8.3 , 7.3, and 6.3. The hydrogen bond contribution now plays a dominant role in the total potential field around the cluster (except for very short distances thereto where the repulsive energy tends to infinity). It is by an order of magnitude stronger for

  11. Spectroscopic Investigation of the Formation and Disruption of Hydrogen Bonds in Pharmaceutical Semicrystalline Dispersions.

    Science.gov (United States)

    Van Duong, Tu; Reekmans, Gunter; Venkatesham, Akkaladevi; Van Aerschot, Arthur; Adriaensens, Peter; Van Humbeeck, Jan; Van den Mooter, Guy

    2017-05-01

    We recently found that indomethacin (IMC) can effectively act as a powerful crystallization inhibitor for polyethylene glycol 6000 (PEG) despite the fact that the absence of interactions between the drug and the carrier in the solid state was reported in the literature. However, in the present study, we investigate the possibility of drug-carrier interactions in the liquid state to explain the polymer crystallization inhibition effect of IMC. We also aim to discover other potential PEG crystallization inhibitors. Drug-carrier interactions in both liquid and solid state are characterized by variable temperature Fourier transform infrared spectroscopy (FTIR) and cross-polarization magic angle spinning (13)C nuclear magnetic resonance spectroscopy (CP/MAS NMR). In the liquid state, FTIR data show evidence of the breaking of hydrogen bonding between IMC molecules to form interactions of the IMC monomer with PEG. The drug-carrier interactions are disrupted upon storage and polymer crystallization, resulting in segregation of IMC from PEG crystals that can be observed under polarized light microscopy. This process is further confirmed by (13)C NMR since in the liquid state, when the IMC/PEG monomer units ratio is below 2:1, IMC signals are undetectable because of the loss of cross-polarization efficiency in the mobile IMC molecules upon attachment to PEG chains via hydrogen bonding. This suggests that each ether oxygen of the PEG unit can form hydrogen bonds with two IMC molecules. The NMR spectrum of IMC shows no change in solid dispersions with PEG upon storage, indicating the absence of interactions in the solid state, hence confirming previous studies. The drug-carrier interactions in the liquid state elucidate the crystallization inhibition effect of IMC on PEG as well as other semicrystalline polymers such as poloxamer and Gelucire. However, hydrogen bonding is a necessary but apparently not a sufficient condition for the polymer crystallization inhibition

  12. Hydrogen bonding and transportation properties of water confined in the single-walled carbon nanotube in the pulse-field

    Science.gov (United States)

    Zhou, Min; Hu, Ying; Liu, Jian-chuan; Cheng, Ke; Jia, Guo-zhu

    2017-10-01

    In this paper, molecular dynamics simulations were performed to investigate the transportation and hydrogen bonding dynamics of water confined in (6, 6) single-walled carbon nanotube (SWCNT) in the absence and presence of time-dependent pulse-field. The effects of pulse-field range from microwave to ultraviolet frequency on the diffusivity and hydrogen bonding of confined water were analyzed. The significant confinement effect due to the narrow space inside SWCNT was observed.

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

    Science.gov (United States)

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

    2015-01-01

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

  14. Helix Stability of Oligoglycine, Oligoalanine and Oligo-β-alanine Dodecamers Reflected by Hydrogen-Bond Persistence

    Science.gov (United States)

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

    2014-01-01

    Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of α- and β-amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by β-amino acids are experimentally more stable than those formed by α-amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead to entropic destabilization. In this study, molecular dynamics simulations using the second-generation force field, AMOEBA [1], explored the stability and hydrogen-bonding patterns of capped oligo-β-alanine, oligoalanine and oligoglycine dodecamers in water. The MD simulations showed that oligo-β-alanine has strong acceptor+2 hydrogen bonds, but surprisingly did not contain a large content of 312-helical structures, possibly due to the sparse distribution of the 312-helical structure and other structures with acceptor+2 hydrogen bonds. On the other hand, despite its backbone flexibility, the β-alanine dodecamer had more stable and persistent hydrogen bonds. Its structure was dominated more by multicentered hydrogen bonds than either oligoglycine and oligoalanine helices. The 31 (PII) helical structure, prevalent in oligoglycine and oligoalanine, does not appear to be stable in oligo-β-alanine indicating its competition with other structures (stacking structure as indicated by MD analyses). These differences are among the factors that shape helical structural preferences and the relative stabilities of these three oligopeptides. PMID:25116421

  15. Cooperative Hydrogen-Bond Dynamics at a Zwitterionic Lipid/Water Interface Revealed by 2D HD-VSFG Spectroscopy.

    Science.gov (United States)

    Inoue, Ken-Ichi; Singh, Prashant C; Nihonyanagi, Satoshi; Yamaguchi, Shoichi; Tahara, Tahei

    2017-10-19

    Molecular-level elucidation of hydration at biological membrane interfaces is of great importance for understanding biological processes. We studied ultrafast hydrogen-bond dynamics at a zwitterionic phosphatidylcholine/water interface by two-dimensional heterodyne-detected vibrational sum frequency generation (2D HD-VSFG) spectroscopy. The obtained 2D spectra confirm that the anionic phosphate and cationic choline sites are individually hydrated at the interface. Furthermore, the data show that the dynamics of water at the zwitterionic lipid interface is not a simple sum of the dynamics of the water species that hydrate to the separate phosphate and choline. The center line slope (CLS) analysis of the 2D spectra reveals that ultrafast hydrogen-bond fluctuation is not significantly suppressed around the phosphate at the zwitterionic lipid interface, which makes the hydrogen-bond dynamics look similar to that of the bulk water. The present study indicates that the hydrogen-bond dynamics at membrane interfaces is not determined only by the hydrogen bond to a specific site of the interface but is largely dependent on the water dynamics in the vicinity and other nearby moieties, through the hydrogen-bond network.

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

    Science.gov (United States)

    Auvil, Tyler Jay

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

  17. Does fluoride disrupt hydrogen bond network in cationic lipid bilayer? Time-dependent fluorescence shift of Laurdan and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Pokorna, Sarka; Jurkiewicz, Piotr; Hof, Martin, E-mail: martin.hof@jh-inst.cas.cz [J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8 (Czech Republic); Vazdar, Mario [Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, P.O.B. 180, HR-10002 Zagreb (Croatia); Cwiklik, Lukasz [J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8 (Czech Republic); Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic); Jungwirth, Pavel [Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic); Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere (Finland)

    2014-12-14

    Time-dependent fluorescence shift (TDFS) of Laurdan embedded in phospholipid bilayers reports on hydration and mobility of the phospholipid acylgroups. Exchange of H{sub 2}O with D{sub 2}O prolongs the lifetime of lipid-water and lipid-water-lipid interactions, which is reflected in a significantly slower TDFS kinetics. Combining TDFS measurements in H{sub 2}O and D{sub 2}O hydrated bilayers with atomistic molecular dynamics (MD) simulations provides a unique tool for characterization of the hydrogen bonding at the acylgroup level of lipid bilayers. In this work, we use this approach to study the influence of fluoride anions on the properties of cationic bilayers composed of trimethylammonium-propane (DOTAP). The results obtained for DOTAP are confronted with those for neutral phosphatidylcholine (DOPC) bilayers. Both in DOTAP and DOPC H{sub 2}O/D{sub 2}O exchange prolongs hydrogen-bonding lifetime and does not disturb bilayer structure. These results are confirmed by MD simulations. TDFS experiments show, however, that for DOTAP this effect is cancelled in the presence of fluoride ions. We interpret these results as evidence that strongly hydrated fluoride is able to steal water molecules that bridge lipid carbonyls. Consequently, when attracted to DOTAP bilayer, fluoride disrupts the local hydrogen-bonding network, and the differences in TDFS kinetics between H{sub 2}O and D{sub 2}O hydrated bilayers are no longer observed. A distinct behavior of fluoride is also evidenced by MD simulations, which show different lipid-ion binding for Cl{sup −} and F{sup −}.

  18. Polymer Soft-Landing Isolation of Acetylene on Polystyrene and Poly(vinylpyridine): A Novel Approach to Probing Hydrogen Bonding in Polymers.

    Science.gov (United States)

    Li, Yike; Samet, Cindy

    2015-09-17

    Hydrogen-bonded complexes of acetylene (Ac) with the polymers polystyrene (PS), poly(4-vinylpyridine) (P4VP), and poly(2-vinylpyridine) (P2VP) have been characterized for the first time at 16 K in a "polymer soft-landing isolation" experiment which is being pioneered in our research laboratory. In particular, changes in vibrational modes of Ac provide ample evidence for hydrogen-bonded complexes between Ac and the phenyl groups of PS or the pyridyl groups of P4VP and P2VP. With PS, the proton on the top Ac molecule of the classic T-shaped Ac dimer interacts with the π cloud of the benzene (Bz) ring to form a C-H---π interaction, while the π cloud of the lower Ac forms a second C-H---π interaction with a proton on the Bz ring. An analogous (ring)1-(Ac)2 double interaction occurs between an Ac dimer and the pyridine (Pyr) rings on both P2VP and P4VP, yielding a C-H---N and C-H---π interaction. With P4VP and P2VP a second bridged (ring)2-(Ac)2 product is formed, with the Ac dimer forming nearly collinear C-H---N hydrogen bonds to adjacent Pyr rings. On P2VP this bridged product is the only one after extensive annealing. These complexes in which Ac acts as both proton donor and acceptor have not previously been observed in conventional matrix isolation experiments. This study is the second from our laboratory employing this method, which represents a slight modification of the traditional matrix isolation technique.

  19. Recognition through self-assembly. A quadruply-hydrogen-bonded, strapped porphyrin cleft that binds dipyridyl molecules and a [2]rotaxane.

    Science.gov (United States)

    Shao, Xue-Bin; Jiang, Xi-Kui; Zhao, Xin; Zhao, Cheng-Xue; Chen, Yan; Li, Zhan-Ting

    2004-02-06

    Quadruply-hydrogen-bonded porphyrin homodimer Zn1.Zn1 has been designed, assembled, and evaluated as a supramolecular cleft-featured receptor for its ability to bind dipyridyl guests in chloroform-d. Monomer Zn1 consists of a 2-ureidopyrimidin-4(1H)-one unit, which was initially reported by Meijer et al., and a zinc porphyrin unit. The zinc porphyrin is strapped with an additional aliphatic chain for controlling the atropisomerization of porphyrin. The 2-ureidopyrimidin-4(1H)-one unit dimerizes exclusively in chloroform even at the dilute concentration of 10(-)(4) M, while the two "strapped" zinc porphyrin units of the homodimer provide additional binding sites for selective guest recognition. (1)H NMR studies indicate that the new homodimer Zn1.Zn1 adopts an S-type conformation due to strong donor-acceptor interaction between the electron-rich porphyrin units and the electron-deficient 2-ureidopyrimidin-4(1H)-one unit. (1)H NMR, UV-vis, and vapor pressure osmometry investigations reveal that Zn1.Zn1 could function as a new generation of assembled supramolecular cleft, to be able to not only efficiently bind linear dipyridyl molecules 14-17, resulting in the formation of stable termolecular complexes, with K(aasoc) values ranging from 3.8 x 10(6) to 8.9 x 10(7) M(-)(1), but also strongly complex a hydrogen-bond-assembled [2]rotaxane, 18, which consists of a rigid fumaramide thread and a pyridine-incorporated tetraamide cyclophane, with K(aasoc) = 1.2 x 10(4) M(-)(1). (1)H NMR competition experiments reveal that complexation to the dipyriyl guests also promotes the stability of the quadruply-hydrogen-bonded dimeric receptor.

  20. Theoretical Prediction of Hydrogen-Bond Basicity pKBHX Using Quantum Chemical Topology Descriptors

    Science.gov (United States)

    2014-01-01

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

  1. Evaluation of one-dimensional potential energy surfaces for prediction of spectroscopic properties of hydrogen bonds in linear bonded complexes.

    Science.gov (United States)

    Jouypazadeh, Hamidreza; Farrokhpour, Hossein; Solimannejad, Mohammad

    2017-05-01

    This work evaluated the reliability of the one-dimensional potential energy surface for calculating the spectroscopic properties (rovibrational constants and rotational line energies) of hydrogen bonds in linear bonded complexes by comparing theoretical results with the corresponding experimental results. For this purpose, two hydrogen bonded complexes were selected: the HCN···HCN homodimer and the HCN···HF heterodimer. The one-dimensional potential energy surfaces related to the hydrogen bonds in these complexes were calculated using different computational methods and basis sets. The calculated potential curve of each complex was fitted to an analytical one-dimensional potential function to obtain the potential parameters. The obtained analytical potential function of each complex was used in a two-particle Schrödinger equation to obtain the rovibrational energy levels of the hydrogen bond. Using the calculated rovibrational levels, the rovibrational spectra and constants of each complex were calculated and compared with experimental data available from the literature. Compared with experimental data, the calculated one-dimensional potential energy surface at the QCISD/aug-cc-pVDZ level of theory was found to predict the spectroscopic properties of hydrogen bonds better than the potential curves obtained using other computational methods, especially for the HCN···HCN homodimer complex. Generally, the results obtained for the HCN···HCN homodimer complex were closer to experimental data than those obtained for the HCN···HF heterodimer complex. The investigation performed in this work showed that the one-dimensional potential curve related to the hydrogen bond between two linear molecules can be used to predict the spectroscopic constants of hydrogen bonds. Graphical abstract Potential energy curves of HCN···HCN and HCN···HF complexes calculated at the different computational levels.

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

    Science.gov (United States)

    Netzel, Jeanette; van Smaalen, Sander

    2009-10-01

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

  3. Hydrogen bond mediated aglycone delivery: synthesis of linear and branched α-glucans.

    Science.gov (United States)

    Yasomanee, Jagodige P; Demchenko, Alexei V

    2014-09-22

    A Hydrogen bond mediated aglycone delivery (HAD) method was applied to the synthesis of α-glucans, which are abundant in nature, but as targets represent a notable challenge to chemists. The synthesis of linear oligosaccharide sequences was accomplished in complete stereoselectivity in all glycosylations. The efficacy of HAD may diminish with the increased bulk of the glycosyl acceptor, and may be an important factor for the syntheses of oligomers beyond pentasaccharides. The synthesis of a branched structure proved more challenging, particularly with bulky trisaccharide acceptors. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. (±-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 ++−−.

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

    Science.gov (United States)

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

    2008-10-30

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

  6. 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.

  7. Large angular jump mechanism observed for hydrogen bond exchange in aqueous perchlorate solution.

    Science.gov (United States)

    Ji, Minbiao; Odelius, Michael; Gaffney, K J

    2010-05-21

    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 NaClO4 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 extracted an average jump angle of 49 +/- 4 degrees, in qualitative agreement with the jump angle observed in molecular dynamics simulations of the same aqueous NaClO4 solution.

  8. Asymmetric Hydrogen Bonding Catalysis for the Synthesis of Dihydroquinazoline-Containing Antiviral, Letermovir.

    Science.gov (United States)

    Chung, Cheol K; Liu, Zhijian; Lexa, Katrina W; Andreani, Teresa; Xu, Yingju; Ji, Yining; DiRocco, Daniel A; Humphrey, Guy R; Ruck, Rebecca T

    2017-08-09

    A weak Brønsted acid-catalyzed asymmetric guanidine aza-conjugate addition reaction has been developed. C2-symmetric, dual hydrogen-bond donating bistriflamides are shown to be highly effective in activating α,β-unsaturated esters toward the intramolecular addition of a pendant guanidinyl nucleophile. Preliminary mechanistic investigation, including density functional theory calculations and kinetics studies, support a conjugate addition pathway as more favorable energetically than an alternative electrocyclization pathway. This methodology has been successfully applied to the synthesis of the 3,4-dihydroquinazoline-containing antiviral, Letermovir, and a series of analogues.

  9. Study of hydrogen bonding in ethanol-water binary solutions by Raman spectroscopy

    Science.gov (United States)

    Li, Fabing; Men, Zhiwei; Li, Shuo; Wang, Shenghan; Li, Zhanlong; Sun, Chenglin

    2018-01-01

    Raman spectra of ethanol-water binary solutions have been observed at room temperature and atmospheric pressure. We find that with increasing ethanol concentration, the symmetric and asymmetric Osbnd H stretching vibrational mode (3286 and 3434 cm- 1) of water are shifted to lower frequency and the weak shoulder peak at 3615 cm- 1 (free OH) disappears. These results indicate that ethanol strengthens hydrogen bonds in water. Simultaneously, our experiment shows that Raman shifts of ethanol reverses when the volume ratio of ethanol and the overall solution is 0.2, which demonstrates that ethanol-water structure undergoes a phase transition.

  10. Rational Design for Complementary Donor-Acceptor Recognition Pairs Using Self-Complementary Hydrogen Bonds.

    Science.gov (United States)

    Sikder, Amrita; Ghosh, Boyli; Chakraborty, Saptarshi; Paul, Ankan; Ghosh, Suhrit

    2016-02-01

    An adaptable and efficient molecular recognition pair has been established by taking advantage of the complementary nature of donor-acceptor interactions together with the strength of hydrogen bonds. Such distinct molecular recognition propagates in orthogonal directions to effect extended alternating co-assembly of two different appended molecular entities. The dimensions of the assembled structures can be tuned by stoichiometric imbalance between the donor and acceptor building blocks. The morphology of the self-assembled material can be correlated with the ratio of the two building blocks. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Physical Properties and Hydrogen-Bonding Network of Water-Ethanol Mixtures from Molecular Dynamics Simulations.

    Science.gov (United States)

    Ghoufi, A; Artzner, F; Malfreyt, P

    2016-02-04

    While many numerical and experimental works were focused on water-ethanol mixtures at low ethanol concentration, this work reports predictions of a few physical properties (thermodynamical, interfacial, dynamical, and dielectrical properties) of water-ethanol mixture at high alcohol concentrations by means of molecular dynamics simulations. By using a standard force field a good agreement was found between experiment and molecular simulation. This was allowed us to explore the dynamics, structure, and interplay between both hydrogen-bonding networks of water and ethanol.

  12. Effect of cooperative hydrogen bonding in Azo-Hydrazone Tautomerism of Azo Dyes

    OpenAIRE

    Özen, Alimet Sema; Ozen, Alimet Sema; Doruker, Pemra; Aviyente, Viktorya

    2007-01-01

    Azo-hydrazone tautomerism in azo dyes has been modeled by using density functional theory (DFT) at the B3LYP/6-31+G(d,p) level of theory. The most stable tautomer was determined both for model compounds and for azo dyes Acid Orange 7 and Solvent Yellow 14. The effects of the sulfonate group substitution and the replacement of the phenyl group with naphthyl on the tautomer stability and on the behavior in solvent have been discussed. Intramolecular hydrogen bond energies have been estimated f...

  13. Cα-H carries information of a hydrogen bond involving the geminal hydroxyl group: a case study with a hydrogen-bonded complex of 1,1,1,3,3,3-hexafluoro-2-propanol and tertiary amines.

    Science.gov (United States)

    Pal, Uttam; Sen, Sudeshna; Maiti, Nakul Chandra

    2014-02-13

    Experimental measurement of the contribution of H-bonding to intermolecular and intramolecular interactions that provide specificity to biological complex formation is an important aspect of macromolecular chemistry and structural biology. However, there are very few viable methods available to determine the energetic contribution of an individual hydrogen bond to binding and catalysis in biological systems. Therefore, the methods that use secondary deuterium isotope effects analyzed by NMR or equilibrium or kinetic isotope effect measurements are attractive ways to gain information on the H-bonding properties of an alcohol system, particularly in a biological environment. Here, we explore the anharmonic contribution to the C-H group when the O-H group of 1,1,1,3,3,3-hexafluoro-2-propanol (HFP) forms an intermolecular H-bond with the amines by quantum mechanical calculations and by experimentally measuring the H/D effect by NMR. Within the framework of density functional theory, ab initio calculations were carried out for HFP in its two different conformational states and their H-bonded complexes with tertiary amines to determine the (13)C chemical shielding, change in their vibrational equilibrium distances, and the deuterium isotope effect on (13)C2 (secondary carbon) of HFP upon formation of complexes with tertiary amines. When C2-OH was involved in hydrogen bond formation (O-H as hydrogen donor), it weakened the geminal C2-H bond; it was reflected in the NMR chemical shift, coupling constant, and the equilibrium distances of the C-H bond. The first derivative of nuclear shielding at C2 in HFP was -48.94 and -50.73 ppm Å(-1) for anti and gauche conformations, respectively. In the complex, the values were -50.28 and -50.76 ppm Å(-1), respectively. The C-H stretching frequency was lower than the free monomer, indicating enhanced anharmonicity in the C-H bond in the complex form. In chloroform, HFP formed a complex with the amine; δC2 was 69.107 ppm for HFP

  14. 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.

  15. Bane of Hydrogen-Bond Formation on the Photoinduced Charge-Transfer Process in Donor–Acceptor Systems

    KAUST Repository

    Alsam, Amani Abdu

    2017-03-14

    Controlling the ultrafast dynamical process of photoinduced charge transfer at donor acceptor interfaces remains a major challenge for physical chemistry and solar cell communities. The process is complicated by the involvement of other complex dynamical processes, including hydrogen bond formation, energy transfer, and solvation dynamics occurring on similar time scales. In this study, we explore the remarkable impact of hydrogen-bond formation on the interfacial charge transfer between a negatively charged electron donating anionic porphyrin and a positively charged electron accepting pi-conjugated polymer, as a model system in solvents with different polarities and capabilities for hydiogen bonding using femtosecond transient absorption spectroscopy. Unlike the conventional understanding of the key role of hydrogen bonding in promoting the charge-transfer process, our steadystate and time-resolved results reveal that the intervening hydrogen-bonding environment and, consequently, the probable longer spacing between the donor and acceptor molecules significantly hinders the charge-transfer process between them. These results show that site-specific hydrogen bonding and geometric considerations between donor and acceptor can be exploited to control both the charge-transfer dynamics and its efficiency not only at donor acceptor interfaces but also in complex biological systems.

  16. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure.

    Science.gov (United States)

    Boobbyer, D N; Goodford, P J; McWhinnie, P M; Wade, R C

    1989-05-01

    An empirical energy function designed to calculate the interaction energy of a chemical probe group, such as a carbonyl oxygen or an amine nitrogen atom, with a target molecule has been developed. This function is used to determine the sites where ligands, such as drugs, may bind to a chosen target molecule which may be a protein, a nucleic acid, a polysaccharide, or a small organic molecule. The energy function is composed of a Lennard-Jones, an electrostatic and a hydrogen-bonding term. The latter is dependent on the length and orientation of the hydrogen bond and also on the chemical nature of the hydrogen-bonding atoms. These terms have been formulated by fitting to experimental observations of hydrogen bonds in crystal structures. In the calculations, thermal motion of the hydrogen-bonding hydrogen atoms and lone-pair electrons may be taken into account. For example, in a alcoholic hydroxyl group, the hydrogen may rotate around the C-O bond at the observed tetrahedral angle. In a histidine residue, a hydrogen atom may be bonded to either of the two imidazole nitrogens and movement of this hydrogen will cause a redistribution of charge which is dependent on the nature of the probe group and the surrounding environment. The shape of some of the energy functions is demonstrated on molecules of pharmacological interest.

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

    Science.gov (United States)

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

    2015-10-14

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

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

    Science.gov (United States)

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

    2015-07-28

    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.

  19. 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.

  20. Hydrogen bonding in aqueous solution of NaClO4

    Science.gov (United States)

    Bondarenko, G. V.; Gorbaty, Y. E.

    2011-03-01

    The ternary system NaClO4-H2O-D2O has been studied, using the Raman spectroscopy. Analysis of the uncoupled OD band of HDO clearly shows that the contour of the band consists of two components only. A new approach has been developed for the quantitative evaluation of the mole fraction of bonded OD groups as a function of perchlorate concentration. It is practically impossible to measure the absolute intensity of Raman scattering. Nevertheless, it is feasible to obtain the specific coefficients of scattering per bonded OD group from the ratio of integrated intensities of the components. For this purpose, the concept of negative 'phantom' concentration was introduced, at which all the OD groups must be bonded. As a result, the concentration dependence of the mole fraction of bonded OD groups has been derived. It was found that the infinite network of hydrogen bonds in bulk water ceases to exist at a mole fraction of NaClO4 above ∼0.03-0.035. At higher concentration of perchlorate only residual finite clusters of water molecules can take place. However, the infinite percolation in the system remains. The important fact resulting from the data treatment is that the average number of hydrogen bonds per water molecule in pure water is 2.6 ± 0.2.