WorldWideScience

Sample records for blue-shifting hydrogen bonds

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

    Science.gov (United States)

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

    2016-05-01

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

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

    Science.gov (United States)

    Zhou, Pan-Pan; Qiu, Wen-Yuan

    2009-08-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Ab initio quantum chemistry methods were applied to study the bifurcated bent hydrogen bonds Y… H2CZ (Z = O, S, Se) and Y…H2CZ2 (Z = F, Cl, Br) (Y = Cl-, Br-) at the MP2/6-311++G(d,p) and MP2/6-311++G(2df,2p) levels. The results show that in each complex there are two equivalent blue-shifted H-bonds Y…H—C, and that the interaction energies and blue shifts are large, the energy of each Y…H—C H-bond is 15-27 kJ/mol, and Δr(CH) = -0.1 - -0.5 pm and Δv(CH) = 30 - 80 cm-1. The natural bond orbital analysis shows that these blue-shifted H-bonds are caused by three factors: large rehybridization; small direct intermolecular hyperconjugation and larger indirect intermolecular hy- perconjugation; large decrease of intramolecular hyperconjugation. The topological analysis of elec- tron density shows that in each complex there are three intermolecular critical points: there is one bond critical point between the acceptor atom Y and each hydrogen, and there is a ring critical point inside the tetragon YHCH, so these interactions are exactly H-bonding.

  4. On the Correlation between the Blue Shift of Hydrogen Bonding and the Proton Donor-Proton Acceptor Distance

    Institute of Scientific and Technical Information of China (English)

    WANG,Jin-Ti(王金姼); FENG,Yong(封勇); LIU,Lei(刘磊); LI,Xiao-Song(李晓松); GUO,Qing-Xiang(郭庆祥)

    2004-01-01

    It is demonstrated that in all types of hydrogen bonds (X-H…Y) there is a balance between the long-range attractive orbital interactions and short-range Pauli/nucleus repulsions. When the proton acceptor approaches the proton donor from distance, the hydrogen bonding energy becomes more negative at relatively large distance, goes through a minimum, and then starts to become less negative when the short-range repulsive forces come into effect.Meanwhile, the X-H bond length increases at relatively large distances, goes through a maximum and starts to shorten when the short-range repulsive forces come into effect. Whether the hydrogen bond is red or blue shifted is dictated by the energy minimum position. If at the energy minimum position the X-H bond length is shorter than that for the free monomer, the hydrogen bond is blue shifted and vice versa. Further studies demonstrate that the recent report about the correlation of C-H bond lengths with proton donor-acceptor distance in F3C-H…OH2 and F3C-H…Cl- is not fully correct because the authors conducted an inappropriate comparison. Furthermore, it is shown for the first time that the Pauli/nucleus repulsion theory is applicable to the blue-shifted hydrogen bonds in the X-H…π complexes and the blue-shifted lithium bonds in the X-Li…Y complexes.

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

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  6. Theoretical study of the N—H···O red-shifted and blue-shifted hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

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

  7. A PBE hybrid functional study of blue-shifting and red-shifting hydrogen bonds in p hydrocarbons

    Directory of Open Access Journals (Sweden)

    Boaz Galdino de Oliveira

    2009-07-01

    Full Text Available This study examines a selected group of p hydrocarbon complexes, represented by C2H4•••HCF3, C2H2•••HCF3, C2H4•••HCF3 and C2H2•••HCF3, from a theoretical point of view. From BPBE/6-311++G(d,p calculations, the geometrical results of these complexes revealed an elongation and shortening of the H—C bond lengths of chloroform (HCCl3 and fluoroform (HCF3, respectively. In terms of the infrared spectrum, the analysis of stretch frequencies revealed that the variations in the H—C modes are essentially recognized as red and blue-shifting modes. For the purposes of understanding the two vibrational phenomena of the p hydrocarbon complexes studied here, PBE/6-311++G(d,p calculations were carried out and partitioning of atomic charges derived from the ChelpG algorithm were also used. A theoretical justification of red- and blue-shift effects was drawn up using charge-transfer analysis, which is manifested in the p bonds of acetylene and ethylene to chloroform (H—CCl3 and fluoroform (H—CF3, respectively. Finally, a further debate regarding the distinct polarizability power of chloroform and fluoroform is presented, concluding that, in comparison with fluoroform, chloroform possesses the requisite features for conventional proton donors and a red-shift is therefore observed in the C2H4•••HCCl3 and C2H2•••HCCl3 complexes.

  8. Theoretical Study on N-H…O Blue-shifted H-Bond for HNO…H2O2 Complex

    Institute of Scientific and Technical Information of China (English)

    YANG, Yong; ZHANG, Wei-Jun; GAO, Xiao-Ming

    2006-01-01

    A theoretical study on the blue-shifted H-bond N-H…O and red-shifted H-bond O-H…O in the complex HNO…H2O2 was conducted by employment of both standard and counterpoise-corrected methods to calculate the geometric structures and vibrational frequencies at the MP2/6-31G(d), MP2/6-31 + G(d,p), MP2/6-311 + + G(d,p),B3LYP/6-31G(d), B3LYP/6-31 +G(d,p) and B3LYP/6-311 + +G(d,p) levels. In the H-bond N-H…O, the calculated blue shift of N-H stretching frequency is in the vicinity of 120 cm-1 and this is indeed the largest theoretical estimate of a blue shift in the X-H…Y H-bond ever reported in the literature. From the natural bond orbital analysis, the red-shifted H-bond O-H…O can be explained on the basis of the dominant role of the hyperconjugation.For the blue-shifted H-bond N-H…O, the hyperconjugation was inhibited due to the existence of significant electron density redistribution effect, and the large blue shift of the N-H stretching frequency was prominently due to the rehybridization of spn N-H hybrid orbital.

  9. Hydrogen bonded supramolecular structures

    CERN Document Server

    Li, Zhanting

    2015-01-01

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

  10. On some hydrogen bond correlations at high pressures

    Science.gov (United States)

    Sikka, S. K.

    2007-09-01

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

  11. Hydrogen bonding in polyanilines

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-11-29

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

  12. Water's Hydrogen Bond Strength

    CERN Document Server

    Chaplin, Martin

    2007-01-01

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

  13. Hydrogen Bonds Involving Metal Centers

    OpenAIRE

    Pavlović, G.; Raos, N.

    2006-01-01

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

  14. Photoinduced hydrogen-bonding dynamics.

    Science.gov (United States)

    Chu, Tian-Shu; Xu, Jinmei

    2016-09-01

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

  15. Quantum Confinement in Hydrogen Bond

    CERN Document Server

    Santos, Carlos da Silva dos; Ricotta, Regina Maria

    2015-01-01

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

  16. 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...

  17. Hydrogen Bonds in Polymer Folding

    OpenAIRE

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

    2000-01-01

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

  18. Why are Hydrogen Bonds Directional?

    Indian Academy of Sciences (India)

    ABHISHEK SHAHI; ELANGANNAN ARUNAN

    2016-10-01

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

  19. Blue-shifting van der Waals interaction

    CERN Document Server

    Arulsamy, Andrew Das

    2011-01-01

    The origin of attractive van der Waals (vdW) interaction between two identical neutral atoms is due to polarization, which has been solved exactly if the distance between the atoms is very large compared to atomic size. Therefore, by default the vdW interaction is always assumed to be long range. Here, we prove (i) the existence of a blue-shifting vdW interaction for both long and short distances, and (ii) the original vdW theory does not lead to an attractive interaction for large polarization.

  20. Hydrogen bonding in ionic liquids.

    Science.gov (United States)

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

    2015-03-01

    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

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

    Institute of Scientific and Technical Information of China (English)

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

    2006-01-01

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

  2. Hydrogen Bonding in Hydrogenated Amorphous Germanium

    Institute of Scientific and Technical Information of China (English)

    M.S.Abo-Ghazala; S. Al Hazmy

    2004-01-01

    Thin films of hydrogenated amorphous germanium (a-Ge:H) were prepared by radio frequency glow discharge deposition at various substrate temperatures. The hydrogen distribution and bonding structure in a-Ge:H were discussed based on infrared absorption data. The correlation between infrared absorption spectra and hydrogen effusion measurements was used to determine the proportionality constant for each vibration mode of the Ge-H bonds. The results reveal that the bending mode appearing at 835 cm?1 is associated with the Ge-H2 (dihydride) groups on the internal surfaces of voids. While 1880 cm?1 is assigned to vibrations of Ge-H (monohydride) groups in the bulk, the 2000 cm?1 stretching mode is attributed to Ge-H and Ge-H2 bonds located on the surfaces of voids. For films associated with bending modes in the infrared spectra, the proportionality constant values of the stretching modes near 1880 and 2000 cm?1 are found to be lower than those of films which had no corresponding bending modes.

  3. Physical Nature of Hydrogen Bond

    CERN Document Server

    Zhyganiuk, I V

    2015-01-01

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

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

    OpenAIRE

    Jeremy R. Wolf

    2014-01-01

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

  5. Imaging Hydrogen Bond in Real Space

    CERN Document Server

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

    2013-01-01

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

  6. Theoretical study of the intermolecular hydrogen bond interaction for furan-HCl and furan-CHCl3 complexes

    Institute of Scientific and Technical Information of China (English)

    李绛; 谢代前; 鄢国森

    2003-01-01

    The nature of the intermolecular hydrogen bond for the furan-HCl and furan-CHCl3 complexes has been studied using ab initio calculations with MP2 level of theory. The new hydrogen bond type of C(Cl)-H...O and C(Cl)-H... interactions are studied also. It is shown that, for the optimized geometries of furan-CHCl3, C-H bond lengths contract and vibrational frequencies are blue-shifted, while for the furan-HCl complex, H-Cl bond lengths elongate and vibrational frequencies are red-shifted. In addition, the NBO analysis indicates that, for the furan-CHCl3 complex, the charge transfers from the lone pair of the proton acceptor to both * (CH) antibonding MO and lone pairs of Cl atom.

  7. Contribution of Hydrogen Bonds to Protein Stability

    Science.gov (United States)

    Pace, Nick

    2014-03-01

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

  8. The effect of hydrogen bonding on torsional dynamics: A combined far-infrared jet and matrix isolation study of methanol dimer

    DEFF Research Database (Denmark)

    Kollipost, F.; Andersen, Jonas; Wallin Mahler Andersen, Denise;

    2014-01-01

    The effect of strong intermolecular hydrogen bonding on torsional degrees of freedom is investigated by far-infrared absorption spectroscopy for different methanol dimer isotopologues isolated in supersonic jet expansions or embedded in inert neon matrices at low temperatures. For the vacuum......-isolated and Ne-embedded methanol dimer, the hydrogen bond OH librational mode of the donor subunit is finally observed at ∼560 cm(-1), blue-shifted by more than 300 cm(-1) relative to the OH torsional fundamental of the free methanol monomer. The OH torsional mode of the acceptor embedded in neon is observed...

  9. Blue-shifted photoluminescence of Alq3 dispersed in PMMA

    Indian Academy of Sciences (India)

    J G Mahakhode; S J Dhoble; C P Joshi; S V Moharil

    2011-12-01

    Alq3 is known to emit bright green light under UV excitation. Blue shift of the emission was reported in recent literature. This was ascribed to the presence of various isomers/crystallographic modifications obtained through train sublimation. Here a blue shift was reported for Alq3 dispersed in PMMA. No isomers/phases, which were reponsible for blue-shift, separated and yet the emission maxima shift to shorter wavelengths as the concentration of Alq3 in PMMA decreases. The results were interpreted on the basis of cross relaxation between interacting Alq3 molecules.

  10. 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.

  11. 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.

  12. 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...

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

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

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

    Science.gov (United States)

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

    2010-03-01

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

  15. HYDROGEN BONDING IN POLYMERIC ADSORBENTS BASED ADSORPTION AND SEPARATION

    Institute of Scientific and Technical Information of China (English)

    XUMancai; SHIZuoqing; 等

    2000-01-01

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

  16. Hydrogen bonds in PC61BM solids

    Directory of Open Access Journals (Sweden)

    Chun-Qi Sheng

    2015-09-01

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

  17. First principles DFT study of weak C-H…O bonds in crystalline amino acids under pressure-alanine

    Science.gov (United States)

    Ramaniah, Lavanya M.; Kamal, C.; Sikka, S. K.

    2013-02-01

    Many crystalline solids containing C-H…O hydrogen bonds display blue shifting of the C-H stretching frequency under pressure. No agreed explanation is available for this. Here, we use first principles density functional theory, to determine the hydrogen atom positions to understand the cause of this blue shift. No neutron diffraction is feasible due to flux limitations for this purpose. As a first case, we have taken up the study of the amino acid, alanine. We find that the C_H_…O bond in it no longer remain isolated under compression as is case at ambient pressure. The hydrogen atom in the bond has now repulsive contacts with other atoms. This results in contraction of the C-H bond length and consequently to blue shifting as is found experimentally.

  18. Conjugation in hydrogen-bonded systems

    CERN Document Server

    Novakovskaya, Yulia V

    2012-01-01

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

  19. 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.

  20. Probing the Hydrogen Bond Strength at Single Bond Limit

    Science.gov (United States)

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

    2015-03-01

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

  1. Blue-shifted emission and enhanced quantum efficiency viaπ-bridge elongation in carbazole-carborane dyads.

    Science.gov (United States)

    Wang, Zhaojin; Jiang, Peng; Wang, Tianyu; Moxey, Graeme J; Cifuentes, Marie P; Zhang, Chi; Humphrey, Mark G

    2016-06-21

    Carbazole-carborane linear dyads and di(carbazole)-carborane V-shaped dyads with phenyleneethynylene-based bridges have been synthesized. The V-shaped dyads display the expected red-shifts in the location of their UV-Vis absorption maxima on bridge-lengthening, but show unusual blue-shifts in charge-transfer (CT) emission on the same π-system lengthening. These blue-shifts can be attributed to the 2n + 3 electron count within the carborane cluster in the excited state. The linear dyads luminesce via a combination of local excited (LE) and CT emission, with a red-shift in LE emission and a blue-shift in CT emission accompanying π-bridge elongation. A quantum efficiency as high as 86% in the solution state is achieved from the hybrid LE/CT emission. Time-dependent density functional theory (TD-DFT) calculations at the excited state of these compounds have clarified the photoluminescence blue-shift and suggested a typical cluster C-C bond elongation in the V-shaped dyads. Calculations on the elongated linear dyads have suggested that the electron density is localized at the phenyleneethynylene-containing bridge. PMID:27225829

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

    Science.gov (United States)

    2016-01-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    Photoabsorption of the hydrogen-bonded complex of a neutral and an anionic Green Fluorescent Protein chromophore has been studied using a new dual-detection approach to action-absorption spectroscopy. Following absorption of one photon, dissociation through a single channel ensures that the full...... absorption spectrum is measured. Our theoretical account of the spectral shape reveals that the anionic 0–0 transition (464 nm) is blue-shifted compared to that of the wild-type protein (478 nm) due to the stronger H-bond in the dimer, and represents an upper bound for that of the isolated anion. At the same...... time, the apparent effect of the H-bond for the neutral chromophore is as large as 0.5 eV, red-shifting the absorption maximum of the isolated neutral (340 nm) to that measured in the dimer (393 nm) and various proteins ([similar]395 nm). This shift results from changes in the topography of potential...

  5. 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...

  6. Hydrogen bonds in methane-water clusters.

    Science.gov (United States)

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

    2016-08-24

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

  7. Recodable surfaces based on switchable hydrogen bonds.

    Science.gov (United States)

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

    2016-07-01

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

  8. Characterization of Hydrogen Bonds by IR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Vojta, D.

    2012-05-01

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

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

    Institute of Scientific and Technical Information of China (English)

    WANG HaiJun; HONG XiaoZhong; GU Fang; BA XinWu

    2007-01-01

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

  10. Dispersion blue-shift in an aperiodic Bragg reflection waveguide

    CERN Document Server

    Fesenko, Volodymyr I

    2016-01-01

    A particular feature of an aperiodic design of cladding of Bragg reflection waveguides to demonstrate a dispersion blue-shift is elucidated. It is made on the basis of a comparative study of dispersion characteristics of both periodic and aperiodic configurations of Bragg mirrors in the waveguide system, wherein for the aperiodic configuration three procedures for layers alternating, namely Fibonacci, Thue-Morse and Kolakoski substitutional rules are considered. It was found out that, in a Bragg reflection waveguide with any considered aperiodic cladding, dispersion curves of guided modes appear to be shifted to shorter wavelengths compared to the periodic configuration regardless of the modes polarization.

  11. Soliton blue-shift in tapered photonic crystal fiber

    CERN Document Server

    Stark, S P; Russell, P St J

    2010-01-01

    We show that solitons undergo a strong blue shift in fibers with a dispersion landscape that varies along the direction of propagation. The experiments are based on a small-core photonic crystal fiber, tapered to have a core diameter that varies continuously along its length, resulting in a zero-dispersion wavelength that moves from 731 nm to 640 nm over the transition. The central wavelength of a soliton translates over 400 nm towards shorter wavelength. This accompanied by strong emission of radiation into the UV and IR spectral region. The experimental results are confirmed by numerical simulation.

  12. Dispersion blue-shift in an aperiodic Bragg reflection waveguide

    Science.gov (United States)

    Fesenko, Volodymyr I.; Tuz, Vladimir R.

    2016-04-01

    A particular feature of an aperiodic design of cladding of Bragg reflection waveguides to demonstrate a dispersion blue-shift is elucidated. It is made on the basis of a comparative study of dispersion characteristics of both periodic and aperiodic configurations of Bragg mirrors in the waveguide system, wherein for the aperiodic configuration three procedures for layers alternating, namely Fibonacci, Thue-Morse and Kolakoski substitutional rules are considered. It was found out that, in a Bragg reflection waveguide with any considered aperiodic cladding, dispersion curves of guided modes appear to be shifted to shorter wavelengths compared to the periodic configuration regardless of the modes polarization.

  13. Formaldoxime hydrogen bonded complexes with ammonia and hydrogen chloride

    Science.gov (United States)

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

    2015-02-01

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

  14. Spatial Orientation of Spin Vectors of Blue-shifted Galaxies

    CERN Document Server

    Yadav, S N; Saurer, W

    2016-01-01

    We present the analysis of the spin vector orientation of 5$\\,$987 SDSS galaxies having negative redshift from $-$87.6 to $-$0.3 km$\\,$s$^{-1}$. Two dimensional observed parameters are used to compute three dimensional galaxy rotation axes by applying `position angle--inclination' method. We aim to examine the non-random effects in the spatial orientation of blue-shifted galaxies. We generate 5$\\times$10$^6$ virtual galaxies to find expected isotropic distributions by performing numerical simulations. We have written MATLAB program to facilitate the simulation process and eliminate the manual errors in the process. Chi-square, auto-correlation, and the Fourier tests are used to examine non-random effects in the polar and azimuthal angle distributions of the galaxy rotation axes. In general, blue-shifted galaxies show no preferred alignments of galaxy rotation axes. Our results support Hierarchy model, which suggests a random orientation of angular momentum vectors of galaxies. However, local effects are noted...

  15. 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’.

  16. Fluorescence from Multiple Chromophore Hydrogen-Bonding States in the Far-Red Protein TagRFP675.

    Science.gov (United States)

    Konold, Patrick E; Yoon, Eunjin; Lee, Junghwa; Allen, Samantha L; Chapagain, Prem P; Gerstman, Bernard S; Regmi, Chola K; Piatkevich, Kiryl D; Verkhusha, Vladislav V; Joo, Taiha; Jimenez, Ralph

    2016-08-01

    Far-red fluorescent proteins are critical for in vivo imaging applications, but the relative importance of structure versus dynamics in generating large Stokes-shifted emission is unclear. The unusually red-shifted emission of TagRFP675, a derivative of mKate, has been attributed to the multiple hydrogen bonds with the chromophore N-acylimine carbonyl. We characterized TagRFP675 and point mutants designed to perturb these hydrogen bonds with spectrally resolved transient grating and time-resolved fluorescence (TRF) spectroscopies supported by molecular dynamics simulations. TRF results for TagRFP675 and the mKate/M41Q variant show picosecond time scale red-shifts followed by nanosecond time blue-shifts. Global analysis of the TRF spectra reveals spectrally distinct emitting states that do not interconvert during the S1 lifetime. These dynamics originate from photoexcitation of a mixed ground-state population of acylimine hydrogen bond conformers. Strategically tuning the chromophore environment in TagRFP675 might stabilize the most red-shifted conformation and result in a variant with a larger Stokes shift. PMID:27447848

  17. Studies on Hydrogen Bonding Network Structures of Konjac Glucomannan

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

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

    Science.gov (United States)

    Nishio, M.

    2012-06-01

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

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    of the mixed phase at metal surfaces. The surface bonding can be considered to be similar to accepting a hydrogen bond, and we can thereby apply general cooperativity rules developed for hydrogen-bonded systems. This provides a simple understanding of why water molecules become more strongly bonded...... to the surface upon hydrogen bonding to OH and why the OH surface bonding is instead weakened through hydrogen bonding to water. We extend the application of this simple model to other observed cooperativity effects for pure water adsorption systems and H3O+ on metal surfaces....

  20. AAA-DDD triple hydrogen bond complexes.

    Science.gov (United States)

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

    2009-10-01

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

  1. Electron collisions with hydrogen-bonded complexes

    International Nuclear Information System (INIS)

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

  2. Constructing supramolecular nanostructure by hydrogen-bonding

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    WU RongLiang; JI Qing; KONG Bin; YANG XiaoZhen

    2008-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hongyu; MA Ning; WANG Zhiqiang

    2005-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2000-01-01

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

  7. VIBRATIONAL RELAXATION ON HYDROGEN BONDING IN DINUCLEOSIDE PHOSPHATE

    OpenAIRE

    Yoshii, Giichi

    1983-01-01

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

  8. 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.

  9. 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.

  10. Binding of reactive organophosphate by oximes via hydrogen bond

    Indian Academy of Sciences (India)

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

    2013-07-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

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

  12. Predictions of Glass Transition Temperature for Hydrogen Bonding Biomaterials

    NARCIS (Netherlands)

    Sman, van der R.G.M.

    2013-01-01

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

  13. Microphase separation in hydrogen bonding polymer/surfactant melts

    NARCIS (Netherlands)

    Dormidontova, Elena; Brinke, Gerrit ten

    1999-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-10-23

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

  15. Molecular orbital analysis of the hydrogen bonded water dimer

    Science.gov (United States)

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

    2016-01-01

    As an essential interaction in nature, hydrogen bonding plays a crucial role in many material formations and biological processes, requiring deeper understanding. Here, using density functional theory and post-Hartree-Fock methods, we reveal two hydrogen bonding molecular orbitals crossing the hydrogen-bond’s O and H atoms in the water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. Our finding sheds light on the essential understanding of hydrogen bonding in ice, liquid water, functional materials and biological systems. PMID:26905305

  16. Recent progress in hydrogen-rich materials from the perspective of bonding flexibility of hydrogen

    International Nuclear Information System (INIS)

    The bonding flexibility of hydrogen is a source of various interesting functionalities in hydrides. Here, we illustrate the benefits of this flexibility through several selected examples of recent progress in the development of hydrogen storage materials. From the viewpoint of electronegativity, we discuss the diverse cohesion and materials science underlying the bonding flexibility of hydrogen in hydrides

  17. Effect of hydrogen bonds on protein stability

    CERN Document Server

    Bianco, Valentino; Franzese, Giancarlo

    2010-01-01

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

  18. 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.

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

    Science.gov (United States)

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

    2014-09-01

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

  20. Giantically blue-shifted visible light in femtosecond mid-IR filament in fluorides

    CERN Document Server

    Dormidonov, A E; Chekalin, S V; Kandidov, V P

    2015-01-01

    A giant blue shift of an isolated visible band of supercontinuum was discovered and studied in the single filament regime of Mid-IR femtosecond laser pulse at powers slightly exceeding critical power for self-focusing in fluorides.

  1. The effect of hydrogen bonding on torsional dynamics: A combined far-infrared jet and matrix isolation study of methanol dimer

    Energy Technology Data Exchange (ETDEWEB)

    Kollipost, F.; Heger, M.; Suhm, M. A. [Institut für Physikalische Chemie, Universität Göttingen, Tammannstr. 6, D-37077 Göttingen (Germany); Andersen, J.; Mahler, D. W.; Wugt Larsen, R., E-mail: rewl@kemi.dtu.dk [Department of Chemistry, Technical University of Denmark, Kemitorvet 206, DK-2800 Kgs. Lyngby (Denmark); Heimdal, J. [MAX-IV Laboratory, Lund University, P. O. Box 118, SE-22100 Lund (Sweden)

    2014-11-07

    The effect of strong intermolecular hydrogen bonding on torsional degrees of freedom is investigated by far-infrared absorption spectroscopy for different methanol dimer isotopologues isolated in supersonic jet expansions or embedded in inert neon matrices at low temperatures. For the vacuum-isolated and Ne-embedded methanol dimer, the hydrogen bond OH librational mode of the donor subunit is finally observed at ∼560 cm{sup −1}, blue-shifted by more than 300 cm{sup −1} relative to the OH torsional fundamental of the free methanol monomer. The OH torsional mode of the acceptor embedded in neon is observed at ∼286 cm{sup −1}. The experimental findings are held against harmonic predictions from local coupled-cluster methods with single and double excitations and a perturbative treatment of triple excitations [LCCSD(T)] and anharmonic. VPT2 corrections at canonical MP2 and density functional theory (DFT) levels in order to quantify the contribution of vibrational anharmonicity for this important class of intermolecular hydrogen bond vibrational motion.

  2. 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.

  3. 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.

  4. Is electrostatics sufficient to describe hydrogen-bonding interactions?

    Science.gov (United States)

    Hoja, Johannes; Sax, Alexander F; Szalewicz, Krzysztof

    2014-02-17

    The stability and geometry of a hydrogen-bonded dimer is traditionally attributed mainly to the central moiety A-H⋅⋅⋅B, and is often discussed only in terms of electrostatic interactions. The influence of substituents and of interactions other than electrostatic ones on the stability and geometry of hydrogen-bonded complexes has seldom been addressed. An analysis of the interaction energy in the water dimer and several alcohol dimers--performed in the present work by using symmetry-adapted perturbation theory--shows that the size and shape of substituents strongly influence the stabilization of hydrogen-bonded complexes. The larger and bulkier the substituents are, the more important the attractive dispersion interaction is, which eventually becomes of the same magnitude as the total stabilization energy. Electrostatics alone are a poor predictor of the hydrogen-bond stability trends in the sequence of dimers investigated, and in fact, dispersion interactions predict these trends better. PMID:24453112

  5. Modelling of spreading process: effect from hydrogen bonds

    Institute of Scientific and Technical Information of China (English)

    Li Xin; Hu Yuan-Zhong; Jiang Lan

    2008-01-01

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

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

    OpenAIRE

    Swarbrick, Janine Cathy

    2006-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    王海军; 洪晓钟; 赵敏; 巴信武

    2001-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    庞小峰; 封原平

    2003-01-01

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

  9. Seeking hydrogen bonds- with and without neutron diffraction

    International Nuclear Information System (INIS)

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

  10. Alkyl Radicals as Hydrogen Bond Acceptors: Computational Evidence

    DEFF Research Database (Denmark)

    Hammerum, Steen

    2009-01-01

    , and gives rise to pronounced shifts of IR stretching frequencies and to increased absorption intensities. The hydrogen bond acceptor properties of alkyl radicals equal those of many conventional acceptors, e.g., the bond length changes and IR red-shifts suggest that tert-butyl radicals are slightly better...

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

    Science.gov (United States)

    Biswal, Himansu S; Wategaonkar, Sanjay

    2009-11-19

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

  12. Are hydrogen bonds responsible for glycine conformational preferences?

    Energy Technology Data Exchange (ETDEWEB)

    Cormanich, Rodrigo A.; Ducati, Lucas C. [Chemistry Institute, State University of Campinas, P.O. Box 6154, 13083-970 Campinas, SP (Brazil); Rittner, Roberto, E-mail: rittner@iqm.unicamp.br [Chemistry Institute, State University of Campinas, P.O. Box 6154, 13083-970 Campinas, SP (Brazil)

    2011-08-25

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

  13. Nature of Hydrogen Bond in Water

    CERN Document Server

    Makhlaichuk, Paul; Zhyganiuk, Igor

    2012-01-01

    The work is devoted to the investigation of physical nature of H-bond. The H-bond potential $\\Phi_{H} (r,\\Omega)$ is studied as an irreducible part of the interaction energy of water molecules. It is defined as a difference between generalized Stillinger-David potential and the sum of dispersive and multipole interaction potentials. Relative contribution of $\\Phi_{H} (r,\\Omega)$ to intermolecular potential does not exceed (10\\div15)%.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-09-15

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

  15. The correlation of blue shift of photoluminescence and morphology of silicon nanoporous

    Science.gov (United States)

    Al-Jumaili, Batool E. B.; Talib, Zainal A.; Josephine L., Y.; Paiman, Suriati B.; Ahmed, Naser M.; Al-Jumaily, Abdulmajeed H. J.; Ramizy, Asmiet; Abdulateef, Sinan A.; Muh'd, Ibrahim B.; Mofdal, Manahil E. E.

    2016-07-01

    Porous silicon with diameters ranging from 6.41 to 7.12 nm were synthesized via electrochemical etching by varied anodization current density in ethanoic solutions containing aqueous hydrofluoric acid up to 65mA/cm2.The luminescence properties of the nanoporous at room temperature were analyzed via photoluminescence spectroscopy. Photoluminescence PL spectra exhibit a broad emission band in the range of 360-700 nm photon energy. The PL spectrum has a blue shift in varied anodization current density; the blue shift incremented as the existing of anodization although the intensity decreased. The current blue shift is owning to alteration of silicon nanocrystal structure at the superficies. The superficial morphology of the PS layers consists of unified and orderly distribution of nanocrystalline Si structures, have high porosity around (93.75%) and high thickness 39.52 µm.

  16. Plasmon-controlled narrower and blue-shifted fluorescence emission in (Au-SiO2)SiC nanohybrids

    International Nuclear Information System (INIS)

    Fluorescent imaging is a key tool in biology. On one hand, organic dyes are subjected to bleaching; while, on the other hand II–VI semiconductor quantum dots are photostable, but may exhibit some toxicity. Silicon carbide nanoparticles (SiC NPs) are a good alternative as SiC is chemically inert and considered as biocompatible material. However, their fluorescence quantum yield is weak. Plasmon-controlled fluorescence appears as a mean to enhance SiC NPs fluorescence. To this aim, new fluorescent nanohybrids (NHs) involving a gold colloid surrounded by a silica shell and overcoated with SiC NPs have been engineered. Au-SiO2 particles were synthesized via a sol–gel method to obtain a controlled thickness of silica around gold colloid. Then, SiC NPs were immobilized onto silica by covalent bonding. TEM was used to study the structural properties of NHs. The influence of several parameters on NHs’ fluorescence properties was investigated. It reveals that excitation wavelength must be chosen as close as possible to the gold plasmon band to avoid quenching of emission due to energy transfer between gold absorption and SiC emission. Moreover, the silica thickness is a key parameter to obtain high enhancement; for gold colloids of 20 nm in diameter overcoated by a 25 nm shell, an enhancement factor as high as 12.5 was obtained with a narrower and blue-shifted emission band. This blue-shift can be attributed to the surface chemistry modification of SiC NPs when they are covalently bonded to silica.

  17. Optimising hydrogen bonding in solid wood

    DEFF Research Database (Denmark)

    Engelund, Emil Tang

    2009-01-01

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

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

    Science.gov (United States)

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

    2016-09-01

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

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

    CERN Document Server

    Narayanan, Chitra

    2013-01-01

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

  20. Infrared Spectra and Hydrogen Bonds of Biologically Active Benzaldehydes

    Science.gov (United States)

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

    2013-09-01

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

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

    Science.gov (United States)

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

    2016-07-01

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

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

    Institute of Scientific and Technical Information of China (English)

    DHARMALINGAM K.; RAMACHANDRAN K.; SIVAGURUNATHAN P.

    2006-01-01

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

  3. 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...

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

    Science.gov (United States)

    Chen, Yinshan; Zhang, Wei; Yu, Lian

    2016-08-18

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

  5. Templation in Noncovalent Synthesis of Hydrogen-Bonded Rosettes

    NARCIS (Netherlands)

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

    2005-01-01

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

  6. 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....

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

    NARCIS (Netherlands)

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

    2005-01-01

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

  8. Adhesion between silica surfaces due to hydrogen bonding

    Science.gov (United States)

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

    2016-09-01

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

  9. Adhesion between silica surfaces due to hydrogen bonding

    Science.gov (United States)

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

    2016-09-01

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

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

    Science.gov (United States)

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

    2014-09-01

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

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

    Science.gov (United States)

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

    2014-09-01

    Organic piezoelectric materials are promising targets in applications such as energy harvesting or mechanical sensors and actuators. In a recent paper (Werling, K. A.; et al. J. Phys. Chem. Lett. 2013, 4, 1365-1370), we have shown that hydrogen bonding gives rise to a significant piezoelectric response. In this article, we aim to find organic hydrogen bonded systems with increased piezo-response by investigating different hydrogen bonding motifs and by tailoring the hydrogen bond strength via functionalization. The largest piezo-coefficient of 23 pm/V is found for the nitrobenzene-aniline dimer. We develop a simple, yet surprisingly accurate rationale to predict piezo-coefficients based on the zero-field compliance matrix and dipole derivatives. This rationale increases the speed of first-principles piezo-coefficient calculations by an order of magnitude. At the same time, it suggests how to understand and further increase the piezo-response. Our rationale also explains the remarkably large piezo-response of 150 pm/V and more for another class of systems, the "molecular springs" (Marvin, C.; et al. J. Phys. Chem. C 2013, 117, 16783-16790.). PMID:24576213

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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. PMID:23829609

  17. Liquid state of hydrogen bond network in ice

    Science.gov (United States)

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

    2016-08-01

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

  18. Liquid state of hydrogen bond network in ice

    CERN Document Server

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

    2016-01-01

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

  19. Stabilization of quinapril by incorporating hydrogen bonding interactions

    Directory of Open Access Journals (Sweden)

    Roy B

    2009-01-01

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

  20. Rheology of miscible polymer blends with hydrogen bonding

    Science.gov (United States)

    Yang, Zhiyi

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

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

    OpenAIRE

    Hay, Benjamin P.; Bryantsev, Vyacheslav S.

    2008-01-01

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

  2. 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.

  3. Effect of quantum nuclear motion on hydrogen bonding

    Science.gov (United States)

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

    2014-05-01

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

  4. Shear Bond Strength of Resin Bonded to Bleached Enamel Using Different Modified 35% Hydrogen Peroxides

    Directory of Open Access Journals (Sweden)

    Moosavi H

    2015-12-01

    Full Text Available Statement of Problem: Bleaching systems with different concentrations and applications are widely used to improve the visual appearance of the teeth, but one of the complications of these materials is reduction of bond strength for immediately bonding to the bleached enamel. Objectives: The aim of this study was to evaluate the influence of using different modified hydrogen peroxide bleaching agents on the shear bond strength of composite resin bonded to the bleached enamel. Materials and Methods: Forty-eight sound extracted premolar teeth were collected, sectioned 1 mm below the CEJ to detach the root. The proximal surfaces of the teeth were flattened using diamond disks and silicon carbide papers to achieve flat homogeneous enamel surfaces without exposure to the dentin. The teeth were randomly divided into four groups as follows (n = 12: group 1: bleaching with 35% hydrogen peroxide gel; group 2: bleaching with 35% hydrogen peroxide gel contained (casein phosphopeptide-amorphous calcium phosphate (CPP-ACP; group 3: bleaching with 35% hydrogen peroxide gel combined with fluoride; and group 4: bleaching with 35% hydrogen peroxide applying one week before resin restoration placement. Composite resin, Clearfil AP-X (Kuraray, Tokyo, Japan, was bonded on each tooth in the mould (4 mm diameter × 3 mm height using Clearfil SE Bond (Kuraray, Tokyo, Japan. After 24 hours of storage and 1000 cycles of thermocycling, the shear bond strength of the specimens at a cross-head speed of 0.5 mm/min was measured in MPa. Data were analyzed using ANOVA and Tukey’s post-hoc test. Results: The minimum and maximum mean shear bond strength values were observed in groups 2 (15.82 ± 4.41 and 4 (21.00 ± 3.90, respectively. Multiple comparisons of groups revealed no significant differences among the groups except between group 4 and all the other groups. The most common type of failure was adhesive. Conclusions: Using modified bleaching agents decreased the bond

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

    CERN Document Server

    Ogawa, Takaya; Tamaki, Takanori; Yamaguchi, Takeo

    2016-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

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

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

    OpenAIRE

    Rychlewska Urszula; Francis Savarimuthu; Muthiah Packianathan; Warżajtis Beata

    2006-01-01

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

  8. The giant mottled eel, Anguilla marmorata, uses blue-shifted rod photoreceptors during upstream migration.

    Directory of Open Access Journals (Sweden)

    Feng-Yu Wang

    Full Text Available Catadromous fishes migrate between ocean and freshwater during particular phases of their life cycle. The dramatic environmental changes shape their physiological features, e.g. visual sensitivity, olfactory ability, and salinity tolerance. Anguilla marmorata, a catadromous eel, migrates upstream on dark nights, following the lunar cycle. Such behavior may be correlated with ontogenetic changes in sensory systems. Therefore, this study was designed to identify changes in spectral sensitivity and opsin gene expression of A. marmorata during upstream migration. Microspectrophotometry analysis revealed that the tropical eel possesses a duplex retina with rod and cone photoreceptors. The λmax of rod cells are 493, 489, and 489 nm in glass, yellow, and wild eels, while those of cone cells are 508, and 517 nm in yellow, and wild eels, respectively. Unlike European and American eels, Asian eels exhibited a blue-shifted pattern of rod photoreceptors during upstream migration. Quantitative gene expression analyses of four cloned opsin genes (Rh1f, Rh1d, Rh2, and SWS2 revealed that Rh1f expression is dominant at all three stages, while Rh1d is expressed only in older yellow eel. Furthermore, sequence comparison and protein modeling studies implied that a blue shift in Rh1d opsin may be induced by two known (N83, S292 and four putative (S124, V189, V286, I290 tuning sites adjacent to the retinal binding sites. Finally, expression of blue-shifted Rh1d opsin resulted in a spectral shift in rod photoreceptors. Our observations indicate that the giant mottled eel is color-blind, and its blue-shifted scotopic vision may influence its upstream migration behavior and habitat choice.

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

    Science.gov (United States)

    Ortiz de Urbina, Jordi; Sesé, Gemma

    2016-07-01

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

  10. Infrared intensities and charge mobility in hydrogen bonded complexes

    Science.gov (United States)

    Galimberti, Daria; Milani, Alberto; Castiglioni, Chiara

    2013-08-01

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

  11. Influence of hydrogen bonds and temperature on dielectric properties

    Science.gov (United States)

    Ortiz de Urbina, Jordi; Sesé, Gemma

    2016-07-01

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

  12. Photoluminescence blue shift of indium phosphide nanowire networks with aluminum oxide coating

    Energy Technology Data Exchange (ETDEWEB)

    Fryauf, David M.; Zhang, Junce; Norris, Kate J.; Diaz Leon, Juan J.; Oye, Michael M.; Kobayashi, Nobuhiko P. [Nanostructured Energy Conversion Technology and Research (NECTAR), Advanced Studies Laboratories, University of California, Santa Cruz, CA (United States); Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA (United States); NASA Ames Research Center, Moffett Field, CA (United States); Wei, Min [Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA (United States); School of Micro-Electronics and Solid-Electronics, University of Electronic Science and Technology of China, Chengdu (China)

    2014-07-15

    This paper describes our finding that optical properties of semiconductor nanowires were modified by depositing a thin layer of metal oxide. Indium phosphide nanowires were grown by metal organic chemical vapor deposition on silicon substrates with gold catalyst resulting in three-dimensional nanowire networks, and optical properties were obtained from the collective nanowire networks. The networks were coated with an aluminum oxide thin film deposited by plasma-enhanced atomic layer deposition. We studied the dependence of the peak wavelength of photoluminescence spectra on the thickness of the oxide coatings. A continuous blue shift in photoluminescence spectra was observed when the thickness of the oxide coating was increased. The observed blue shift is attributed to the Burstein-Moss effect due to increased carrier concentration in the nanowire cores caused by repulsion from intrinsic negative fixed charges located at the inner oxide surface. Samples were further characterized by scanning electron microscopy, Raman spectroscopy, transmission electron microscopy, and selective area diffractometry to better understand the physical mechanisms for the blue shift. (copyright 2014 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  13. Atomistic design of microbial opsin-based blue-shifted optogenetics tools

    Science.gov (United States)

    Kato, Hideaki E.; Kamiya, Motoshi; Sugo, Seiya; Ito, Jumpei; Taniguchi, Reiya; Orito, Ayaka; Hirata, Kunio; Inutsuka, Ayumu; Yamanaka, Akihiro; Maturana, Andrés D.; Ishitani, Ryuichiro; Sudo, Yuki; Hayashi, Shigehiko; Nureki, Osamu

    2015-05-01

    Microbial opsins with a bound chromophore function as photosensitive ion transporters and have been employed in optogenetics for the optical control of neuronal activity. Molecular engineering has been utilized to create colour variants for the functional augmentation of optogenetics tools, but was limited by the complexity of the protein-chromophore interactions. Here we report the development of blue-shifted colour variants by rational design at atomic resolution, achieved through accurate hybrid molecular simulations, electrophysiology and X-ray crystallography. The molecular simulation models and the crystal structure reveal the precisely designed conformational changes of the chromophore induced by combinatory mutations that shrink its π-conjugated system which, together with electrostatic tuning, produce large blue shifts of the absorption spectra by maximally 100 nm, while maintaining photosensitive ion transport activities. The design principle we elaborate is applicable to other microbial opsins, and clarifies the underlying molecular mechanism of the blue-shifted action spectra of microbial opsins recently isolated from natural sources.

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

    Science.gov (United States)

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

    2013-06-24

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

  15. 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.

  16. 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…

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

    Indian Academy of Sciences (India)

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

    2004-08-01

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

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

    Science.gov (United States)

    Sen, Ibrahim; Kara, Hulya; Azizoglu, Akın

    2016-10-01

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

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

    Science.gov (United States)

    Sen, Ibrahim; Kara, Hulya; Azizoglu, Akın

    2016-10-01

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

  20. Weak hydrogen bonding yields rigid, tough, and elastic hydrogels

    Science.gov (United States)

    Sheiko, Sergei; Hu, Xiaobo; Vatankhah-Varnosfaderani, Mohammad; Zhou, Jing; Li, Qiaoxi; Dobrynin, Andrey

    Unlike living tissues, synthetic hydrogels are inherently soft and brittle, particularly when built of hydrogen bonds. It remains challenging to design hydrogels that combine high rigidity, strength at break, extensibility, high elasticity. Through free-radical copolymerization of N , N -dimethylacrylamide and methacrylic acid, we have designed a network system based on tunable composition of covalent bonds (permanent cross-links) and hydrogen bonds (sacrificial and recoverable crosslinks) with the following rationale: 1) Maintain a high total number of cross-links to ensure high modulus; 2) Introduce a high fraction of H-bonding to ensure high energy dissipation; and 3) Incorporate a small fraction of permanent cross-links to ensure shape control. By tuning the chemical composition and microstructure we have obtained materials with superb mechanical properties. The hydrogels contain 70 wt% water (similar to living cartilage, skin, and ligaments), while display modulus of 28 MPa, strength of 2 MPa, fracture energy of 9300 J .m-2, extensibility of 800%, excellent fatigue-resistance, and great elasticity allowing for complete and fast strain recovery. The results agreed with theoretical predictions for modulus relaxation of dual networks with dynamic and permanent crosslinks. We gratefully acknowledge funding from the National Science Foundation (DMR 1122483, DMR 1407645, and DMR 1436201).

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

    Institute of Scientific and Technical Information of China (English)

    XUMancai; SHIZuoqing; 等

    2000-01-01

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

  2. 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...

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

    Science.gov (United States)

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

    2009-12-21

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

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

    Science.gov (United States)

    Kondo, Makoto; Kasahara, Yasutoshi; Ishikawa, Haruki

    2015-06-01

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

  5. Density Functional Calculations on a Double Hydrogen-bonded Dimer

    Institute of Scientific and Technical Information of China (English)

    建方方; 赵朴素; 汪庆祥

    2005-01-01

    Density functional theory (DFT) calculations on a double hydrogen-bonded dimer of o-hydroxybenzoic acid were carried out at the B3LYP/6-31G* level. The optimized geometry of the dimer closely resembles that of the crystal. The calculated results show that the total energy of the dimer is much lower than the sum energies of the two monomers, and the average strength of the double hydrogen bonds is about 38.37 kJ/mol. In order to probe the origin of the interactions in the dimer, natural bond orbital analyses were performed. The thermodynamic properties of the title compound at different temperatures have also been calculated on the basis of vibrational analyses and AGT, the change of Gibbs free energy for the aggregation from monomer to the dimmer, is 26.47 k J/mol at 298.15 K and 0. 1 Mpa, implying the spontaneous process of forming the dimer. The correlation graphics of Som, Hom and temperatures is depicted.

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

    Science.gov (United States)

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

    2014-01-21

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

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

    Science.gov (United States)

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

    1987-08-01

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

  8. Intramolecular hydrogen bonds in sulfur-containing aminophenols

    Science.gov (United States)

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

    2010-07-01

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

  9. Hydrogen-Bonding-Supported Self-Healing Antifogging Thin Films

    Science.gov (United States)

    Zhang, Xiaojie; He, Junhui

    2015-03-01

    Inspired by the repair of DNA through efficient reformation of hydrogen bonds (H-bonds), herein we report a facile one-step approach to construction of self-healing antifogging thin films on the basis of partly cross-linked poly(vinyl alcohol)(PVA) and poly(acrylic acid)(PAA). By designing the molar ratio of hydroxyl groups to carboxyl groups, the cross-linked polymer thin films maintain abundant free hydroxyl groups to present excellent antifogging property, which is derived from the hydrophilicity and hygroscopicity of the thin films. The thin films showed smart intrinsic self-healing characteristics towards wounds caused by external forces, which is attributed to sufficient free hydroxyl groups at the scratched interfaces to reform H-bonds across the interfaces and a sufficient chain mobility that is indispensable for chain diffusion across the interfaces and hydroxyl groups association to form H-bonds. No synthetic surfaces reported so far possess all the unique characteristics of the polymer thin films: intrinsic self-healing, long-term antifogging, excellent mechanical property, high transmittance and large-scale feasibility.

  10. A QTAIM exploration of the competition between hydrogen and halogen bonding in halogenated 1-methyluracil: Water systems

    Science.gov (United States)

    Huan, Guo; Xu, Tianlv; Momen, Roya; Wang, Lingling; Ping, Yang; Kirk, Steven R.; Jenkins, Samantha; van Mourik, Tanja

    2016-10-01

    Using QTAIM we show that the hydrogen bonding complexes of 5-halogenated-1-methyluracil (XmU; X = F, Cl, Br, I or At) with a water molecule were always stronger than the corresponding halogen bonds. The strength of the hydrogen bond decreased with increasing halogen size. The hydrogen bonds displayed an admixture of covalent character but all the halogen bonds were purely electrostatic in nature. An F---O halogen bond was found and was facilitated by an intermediate F---H bonding interaction. The metallicity ξ(rb) of the C = O bonds neighboring the hydrogen bonds and of the C-X bonds contiguous with the halogen bonds was explored.

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

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

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

  13. Gamma radiation-induced blue shift of resonance peaks of Bragg gratings in pure silica fibres

    Science.gov (United States)

    Faustov, A. V.; Gusarov, A. I.; Mégret, P.; Wuilpart, M.; Kinet, D.; Zhukov, A. V.; Novikov, S. G.; Svetukhin, V. V.; Fotiadi, A. A.

    2016-02-01

    We report the first observation of a significant gamma radiation-induced blue shift of the reflection/transmission peak of fibre Bragg gratings inscribed into pure-silica core fibres via multiphoton absorption of femtosecond pulses. At a total dose of ~100 kGy, the shift is ~20 pm. The observed effect is attributable to the ionising radiation-induced decrease in the density of the silica glass when the rate of colour centre formation is slow. We present results of experimental measurements that provide the key parameters of the dynamics of the gratings for remote dosimetry and temperature sensing.

  14. Rayleigh scattering and luminescence blue shift in tris(8-hydroxyquinoline)aluminum films

    International Nuclear Information System (INIS)

    The Rayleigh scattering (RS) by independent small particles is a well-known effect which also accounts for the blue color of the sky. Lately, the blue shift of the greenish emission band of thin films of Alq3, tris(8-hydroxyquinoline)aluminum, after thermal treatments of various nature has been attributed to RS. Here, we show that RS effects cannot account for the observed spectral features, which are attributed to the onset of various molecular aggregations in the otherwise amorphous films, a morphological model already utilized to explain the optical properties of Alq3

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

    DEFF Research Database (Denmark)

    Olesen, Solveig Gaarn; Hammerum, Steen

    2009-01-01

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

  16. Anharmonicity and hydrogen bonding in electrooptic sucrose crystal

    Science.gov (United States)

    Szostak, M. M.; Giermańska, J.

    1990-03-01

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

  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. DFT and AIM studies of intramolecular hydrogen bonds in dicoumarols

    International Nuclear Information System (INIS)

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

  19. Hydrogen bonding interaction of small acetaldehyde clusters studied with core-electron excitation spectroscopy in the oxygen K-edge region

    International Nuclear Information System (INIS)

    In order to examine inner-shell electron excitation spectra of molecular clusters with strong multipole interactions, excitation spectra and time-of-flight (TOF) fragment-mass spectra of small acetaldehyde (AA) clusters have been studied under the beam conditions. The TOF spectra at the oxygen K-edge region showed an intense growth of the protonated clusters, MnH+ (M=CH3CHO) in the cluster beams. 'cluster-specific' excitation spectra could be generated by monitoring partial-ion-yields of the protonated clusters. The most intense band of O1s→π*CO was found to shift to a higher energy by 0.15 eV relative to the monomer band upon clusterization. X-ray absorption spectra (XAS) were also calculated for the representative dimer configurations using a computer modelling program based on the density functional theory. The XAS prediction for the most stable (non-planar) configuration was found to give a close comparison with the cluster-band shift observed. The band shift was interpreted as being due to the HOMO-LUMO interaction within the complex where a contribution of vibrationally blue-shifting hydrogen bonding could be identified.

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

    Science.gov (United States)

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

    2016-03-01

    Substituent effects on the open shell N-H···O═C hydrogen-bond has never been reported. This study examines how 12 functional groups composed of electron donating groups (EDG), halogen atoms and electron withdrawing groups (EWG) affect the N-H···O═C hydrogen-bond properties in a six-membered cyclic model system of O═C(Y)-CH═C(X)N-H. It is found that group effects on this open shell H-bonding system are significant and have predictive trends when X = H and Y is varied. When Y is an EDG, the N-H···O═C hydrogen-bond is strengthened; and when Y is an EWG, the bond is weakened; whereas the variation in electronic properties of X group do not exhibit a significant impact upon the hydrogen bond strength. The structural impact of the stronger N-H···O═C hydrogen-bond are (1) shorter H and O distance, r(H···O) and (2) a longer N-H bond length, r(NH). The stronger N-H···O═C hydrogen-bond also acts to pull the H and O in toward one another which has an effect on the bond angles. Our findings show that there is a linear relationship between hydrogen-bond angle and N-H···O═C hydrogen-bond energy in this unusual H-bonding system. In addition, there is a linear correlation of the r(H···O) and the hydrogen bond energy. A short r(H···O) distance corresponds to a large hydrogen bond energy when Y is varied. The observed trends and findings have been validated using three different methods (UB3LYP, M06-2X, and UMP2) with two different basis sets. PMID:26855203

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

    Science.gov (United States)

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

    2016-03-01

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

  2. Quenching and blue shift of UV emission intensity of hydrothermally grown ZnO:Mn nanorods

    Energy Technology Data Exchange (ETDEWEB)

    Vinod, R. [Department of Physics, Cochin University of Science and Technology, Kochi 682022, Kerala (India); Junaid Bushiri, M., E-mail: junaidbushiri@gmail.com [Department of Physics, Cochin University of Science and Technology, Kochi 682022, Kerala (India); Achary, Sreekumar Rajappan; Muñoz-Sanjosé, Vicente [Departamento de FisicaAplicada y Electromagnetismo, Universitat de Valencia, c/Dr. Moliner 50, Burjassot, Valencia 46100 (Spain)

    2015-01-15

    Highlights: • Single crystalline ZnO:Mn nanorods. • Reduced optical active defects. • Quenching and blue shift of UV emission. - Abstract: ZnO:Mn alloyed nanorods (Mn nominal concentration – 3–5 wt%) were synthesized by using hydrothermal process at an optimized growth temperature of 200 °C and a growth time of 3 h. The XRD, SEM and Raman, FTIR investigations reveal that ZnO:Mn (Mn – 3–5 wt%) retained hexagonal wurtzite crystal structure with nanorod morphology. The HRTEM and SAED analysis confirm the single crystalline nature of hydrothermally grown ZnO and ZnO:Mn (5 wt%) nanorods. The ZnO:Mn nanorods (Mn – 0–5 wt%) displayed optical band gap in the range 3.23–3.28 eV. The blue shift of UV emission peak (PL) from 393 (ZnO) to 386 nm and quenching of photoluminescence emission in ZnO:Mn is due to the Mn incorporation in ZnO lattice. Relative increase in intensity of Raman band at 660 cm{sup −1} with nominal doping of Mn 3–5 wt% in ZnO indicate that defects are introduced in ZnO:Mn system as a result of doping that leads to the quenching of photoluminescence emission at 393 nm.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-12-16

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

  4. 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...

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

    Science.gov (United States)

    Ghosh, Sanat; Bhattacharyya, Surjendu; Wategaonkar, Sanjay

    2015-11-01

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

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

    Science.gov (United States)

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

    2007-10-15

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

  7. Hydrogen bond competition in the ethanol-methanol dimer.

    Science.gov (United States)

    Finneran, Ian A; Carroll, P Brandon; Mead, Griffin J; Blake, Geoffrey A

    2016-08-10

    Previous theoretical work on the ethanol-methanol dimer has been inconclusive in predicting the preferred hydrogen bond donor/acceptor configuration. Here, we report the microwave spectrum of the dimer using a chirped pulse Fourier transform microwave spectrometer from 8-18 GHz. In an argon-backed expansion, 50 transitions have been assigned to a trans-ethanol-acceptor/methanol-donor structure that is likely stabilized by a secondary weak C-HO hydrogen bond. A higher energy conformer was observed in a helium-backed expansion and tentatively assigned to a gauche-ethanol-acceptor/methanol-donor structure. No ethanol-donor/methanol-acceptor dimers have been found, suggesting such interactions are energetically disfavored. A preliminary analysis of the A-E splitting due to the internal rotation of the methanol methyl group in the ground state species is also presented. We find evidence of the Ubbelohde effect in the measured A-E splittings of three deuterated isotopologues and the normal species of this conformer. PMID:27472828

  8. 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.

  9. Infrared Spectroscopy of Hydrogen Bonds in Benzoic Acid Derivatives

    Science.gov (United States)

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

    2014-03-01

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

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

    Indian Academy of Sciences (India)

    K Sivashankar

    2000-12-01

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

  11. Probing backbone hydrogen bonding in PDZ/ligand interactions by protein amide-to-ester mutations

    DEFF Research Database (Denmark)

    Pedersen, Søren W; Pedersen, Stine B; Anker, Louise;

    2014-01-01

    via backbone hydrogen bonds; however, little is known about the role of these hydrogen bonds due to experimental challenges with backbone mutations. Here we address this interaction by generating semisynthetic PDZ domains containing backbone amide-to-ester mutations and evaluating the importance...... of individual hydrogen bonds for ligand binding. We observe substantial and differential effects upon amide-to-ester mutation in PDZ2 of postsynaptic density protein 95 and other PDZ domains, suggesting that hydrogen bonding at the carboxylate-binding site contributes to both affinity and selectivity....... In particular, the hydrogen-bonding pattern is surprisingly different between the non-canonical and canonical interaction. Our data provide a detailed understanding of the role of hydrogen bonds in protein-protein interactions....

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

    OpenAIRE

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

    2002-01-01

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

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

    OpenAIRE

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

    2007-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

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

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

    Indian Academy of Sciences (India)

    Rajnikant; Dinesh; Kamni

    2005-06-01

    An overview of general classification scheme, medicinal importance and crystal structure analysis with emphasis on the role of hydrogen bonding in some alkaloids is presented in this paper. The article is based on a general kind of survey while crystallographic analysis and role of hydrogen bonding are limited to only those alkaloids whose three-dimensional structure has been reported by us. The C–H…O hydrogen bonding in the solid state in alkaloids has been found to be predominant and this observation makes the role of hydrogen bonding in organic molecular assemblies very important.

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

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

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

  17. Quantum hydrogen-bond symmetrization in the superconducting hydrogen sulfide system

    Science.gov (United States)

    Errea, Ion; Calandra, Matteo; Pickard, Chris J.; Nelson, Joseph R.; Needs, Richard J.; Li, Yinwei; Liu, Hanyu; Zhang, Yunwei; Ma, Yanming; Mauri, Francesco

    2016-04-01

    The quantum nature of the proton can crucially affect the structural and physical properties of hydrogen compounds. For example, in the high-pressure phases of H2O, quantum proton fluctuations lead to symmetrization of the hydrogen bond and reduce the boundary between asymmetric and symmetric structures in the phase diagram by 30 gigapascals (ref. 3). Here we show that an analogous quantum symmetrization occurs in the recently discovered sulfur hydride superconductor with a superconducting transition temperature Tc of 203 kelvin at 155 gigapascals—the highest Tc reported for any superconductor so far. Superconductivity occurs via the formation of a compound with chemical formula H3S (sulfur trihydride) with sulfur atoms arranged on a body-centred cubic lattice. If the hydrogen atoms are treated as classical particles, then for pressures greater than about 175 gigapascals they are predicted to sit exactly halfway between two sulfur atoms in a structure with symmetry. At lower pressures, the hydrogen atoms move to an off-centre position, forming a short H–S covalent bond and a longer H···S hydrogen bond in a structure with R3m symmetry. X-ray diffraction experiments confirm the H3S stoichiometry and the sulfur lattice sites, but were unable to discriminate between the two phases. Ab initio density-functional-theory calculations show that quantum nuclear motion lowers the symmetrization pressure by 72 gigapascals for H3S and by 60 gigapascals for D3S. Consequently, we predict that the phase dominates the pressure range within which the high Tc was measured. The observed pressure dependence of Tc is accurately reproduced in our calculations for the phase, but not for the R3m phase. Therefore, the quantum nature of the proton fundamentally changes the superconducting phase diagram of H3S.

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

    OpenAIRE

    Gamble, Stephanie Nicole

    2016-01-01

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

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

    Science.gov (United States)

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

    2010-12-01

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

  20. Revealing the multi-bonding state between hydrogen and graphene-supported Ti clusters

    CERN Document Server

    Takahashi, Keisuke; Omori, Kengo; Mashoff, Torge; Convertino, Domenica; Miseikis, Vaidotas; Coletti, Camilla; Tozzini, Valentina; Heun, Stefan

    2016-01-01

    Hydrogen adsorption on graphene-supported metal clusters has brought much controversy due to the complex nature of the bonding between hydrogen and metal clusters. The bond types of hydrogen and graphene-supported Ti clusters are experimentally and theoretically investigated. Transmission electron microscopy shows that Ti clusters of nanometer-size are formed on graphene. Thermal desorption spectroscopy captures three hydrogen desorption peaks from hydrogenated graphene-supported Ti clusters. First principle calculations also found three types of interaction: Two types of bonds with different partial ionic character and physisorption. The physical origin for this rests on the charge state of the Ti clusters: when Ti clusters are neutral, H2 is dissociated, and H forms bonds with the Ti cluster. On the other hand, H2 is adsorbed in molecular form on positively charged Ti clusters, resulting in physisorption. Thus, this work clarifies the bonding mechanisms of hydrogen on graphene-supported Ti clusters.

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

    Science.gov (United States)

    Smedley, Sarah Black

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

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

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

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

  3. Hydrogen bonding in microsolvation: photoelectron imaging and theoretical studies on Au(x)(-)-(H2O)(n) and Au(x)(-)-(CH3OH)(n) (x = 1, 2; n = 1, 2) complexes.

    Science.gov (United States)

    Wu, Xia; Tan, Kai; Tang, Zichao; Lu, Xin

    2014-03-14

    We have combined photoelectron velocity-map imaging (VMI) spectroscopy and theoretical calculations to elucidate the geometry and energy properties of Aux(-)(Solv)n clusters with x = 1, 2; n = 1, 2; and Solv = H2O and CH3OH. Besides the blue-shifted vertical electron detachment energies (VDEs) of the complexes Au1,2(-)(Solv)n with the increase of the solvation number (n), we independently probed two distinct Au(-)(CH3OH)2 isomers, which combined with MP2/aug-cc-pVTZ(pp) calculations represent a competition between O···H-O hydrogen bonds (HBs) and Au···H-O nonconventional hydrogen bonds (NHBs). Complementary calculations provide the total binding energies of the low-energy isomers. Moreover, the relationship between the total binding energies and total VDEshift is discussed. We found that the Au1,2(-) anions exhibit halide-analogous behavior in microsolvation. These findings also demonstrate that photoelectron velocity map imaging spectroscopy with the aid of the ab initio calculations is an effective tool for investigating weak-interaction complexes. PMID:24469385

  4. Blue shift of CdSe/ZnS nanocrystal-labels upon DNA-hybridization

    Directory of Open Access Journals (Sweden)

    Palme Klaus

    2008-05-01

    Full Text Available Abstract Luminescence color multiplexing is one of the most intriguing benefits, which might occur by using semiconductor Quantum Dots (QDs as labels for biomolecules. It was found, that the luminescence of QDs can be quenched, and replaced by a luminescence peak at approximately 460 nm on hybridization with certain regions of Arabidopsis thaliana tissue. This effect is site selective, and it is unclear whether it occurs due to an energy transfer process, or due to quenching and scattering of the excitation light. The article describes methods for phase-transfer of differently coloured, hydrophobically ligated QDs, coupling of DNA strands to the QD's surface, and hybridization of the labelled DNA to different cell types of Arabidopsis thaliana. The reason for the luminescence blue-shift was studied systematically, and narrowed down to the above mentioned causes.

  5. Giantically blue-shifted visible light in femtosecond mid-IR filament in fluorides.

    Science.gov (United States)

    Dormidonov, A E; Kompanets, V O; Chekalin, S V; Kandidov, V P

    2015-11-01

    A giant blue shift (more than 3000 nm) of an isolated visible band of supercontinuum was discovered and studied in the single filament regime of Mid-IR femtosecond laser pulse at powers slightly exceeding critical power for self-focusing in fluorides. At the pulse central wavelength increasing from 3000 nm to 3800 nm the spectral maximum of the visible band is shifted from 570 nm and 520 nm up to 400 nm and 330 nm for BaF(2) and CaF(2), respectively, its spectral width (FWHM) being reduced from 50 - 70 nm to 14 nm. It is shown that the formation of this narrow visible wing is a result of the interference of the supercontinuum components in the anomalous group velocity dispersion regime. PMID:26561190

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

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

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

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

    CERN Document Server

    Sharley, John N

    2016-01-01

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

  8. Effect of quantum nuclear motion on hydrogen bonding

    CERN Document Server

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

    2014-01-01

    This work considers how the properties of hydrogen bonded complexes, D-H....A, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor (D) and acceptor (A) have the same proton affinity, is carried out. For quantitative comparisons, a parametrization specific to the O-H....O complexes is used. The vibrational energy levels of the one-dimensional ground state adiabatic potential of the model are used to make quantitative comparisons with a vast body of condensed phase data, spanning a donor-acceptor separation (R) range of about 2.4-3.0 A, i.e., from strong to weak bonds. The position of the proton and its longitudinal vibrational frequency, along with the isotope effects in both are discussed. An analysis of the secondary geometric isotope effects, using a simple extension of the two-state model, yields an improved agreement of the predicted variation with R of frequency isotope effects. The role of the b...

  9. Plasmon-controlled narrower and blue-shifted fluorescence emission in (Au-SiO{sub 2})SiC nanohybrids

    Energy Technology Data Exchange (ETDEWEB)

    Sui Ning; Monnier, Virginie, E-mail: virginie.monnier@ec-lyon.fr [Institut des Nanotechnologies de Lyon-INL, UMR CNRS 5270, Site Ecole Centrale de Lyon, Universite de Lyon (France); Zakharko, Yuriy [Institut des Nanotechnologies de Lyon-INL-UMR 5270-CNRS, Site INSA Lyon, Universite de Lyon (France); Chevolot, Yann [Institut des Nanotechnologies de Lyon-INL, UMR CNRS 5270, Site Ecole Centrale de Lyon, Universite de Lyon (France); Alekseev, Sergei [Kiev National Taras Schevchenko University, Faculty of Chemistry (Ukraine); Bluet, Jean-Marie; Lysenko, Vladimir [Institut des Nanotechnologies de Lyon-INL-UMR 5270-CNRS, Site INSA Lyon, Universite de Lyon (France); Souteyrand, Eliane [Institut des Nanotechnologies de Lyon-INL, UMR CNRS 5270, Site Ecole Centrale de Lyon, Universite de Lyon (France)

    2012-08-15

    Fluorescent imaging is a key tool in biology. On one hand, organic dyes are subjected to bleaching; while, on the other hand II-VI semiconductor quantum dots are photostable, but may exhibit some toxicity. Silicon carbide nanoparticles (SiC NPs) are a good alternative as SiC is chemically inert and considered as biocompatible material. However, their fluorescence quantum yield is weak. Plasmon-controlled fluorescence appears as a mean to enhance SiC NPs fluorescence. To this aim, new fluorescent nanohybrids (NHs) involving a gold colloid surrounded by a silica shell and overcoated with SiC NPs have been engineered. Au-SiO{sub 2} particles were synthesized via a sol-gel method to obtain a controlled thickness of silica around gold colloid. Then, SiC NPs were immobilized onto silica by covalent bonding. TEM was used to study the structural properties of NHs. The influence of several parameters on NHs' fluorescence properties was investigated. It reveals that excitation wavelength must be chosen as close as possible to the gold plasmon band to avoid quenching of emission due to energy transfer between gold absorption and SiC emission. Moreover, the silica thickness is a key parameter to obtain high enhancement; for gold colloids of 20 nm in diameter overcoated by a 25 nm shell, an enhancement factor as high as 12.5 was obtained with a narrower and blue-shifted emission band. This blue-shift can be attributed to the surface chemistry modification of SiC NPs when they are covalently bonded to silica.

  10. 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

  11. Chiral shift reagent for amino acids based on resonance-assisted hydrogen bonding.

    Science.gov (United States)

    Chin, Jik; Kim, Dong Chan; Kim, Hae-Jo; Panosyan, Francis B; Kim, Kwan Mook

    2004-07-22

    [structure: see text] A chiral aldehyde that forms resonance-assisted hydrogen bonded imines with amino acids has been developed. This hydrogen bond not only increases the equilibrium constant for imine formation but also provides a highly downfield-shifted NMR singlet for evaluating enantiomeric excess and absolute stereochemistry of amino acids. PMID:15255698

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

    Science.gov (United States)

    Ikeda, Noriaka; Okada, Tadashi; Mataga, Noboru

    1980-01-01

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

  13. Hydrogen bonding strength of interfacial water determined with surface sum-frequency generation

    NARCIS (Netherlands)

    M. Sovago; R. Kramer Campen; H.J. Bakker; M. Bonn

    2009-01-01

    We demonstrate that marked variations exist in hydrogen bonding interactions of interfacial water at different aqueous interfaces. The average hydrogen bond strength and its distribution are inferred from surface sum-frequency generation (SFG) spectra through the center frequency and width, respecti

  14. 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…

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

    International Nuclear Information System (INIS)

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

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

    CERN Document Server

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

    2015-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2003-01-01

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

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

    Science.gov (United States)

    Hristova, Kalina; Sarabipour, Sarvenaz

    2013-03-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2002-01-01

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

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

    Indian Academy of Sciences (India)

    Amalendu Chandra; Snehasis Chowdhuri

    2001-10-01

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

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

    Science.gov (United States)

    Schmiedekamp, Ann; Nanda, Vikas

    2009-07-01

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

  2. 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.

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

    Indian Academy of Sciences (India)

    Sunil K Panigrahi; Gautam R Desiraju

    2007-06-01

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

  4. Replacing the hydrogen in the intermolecular hydrogen bond of the cyanuric acid-bipyridyl adduct by Ag(I)

    Indian Academy of Sciences (India)

    K Sivashankar; Anupama Ranganathan; V R Pedireddi

    2000-04-01

    A complex between cyanuric acid (CA), 4,4′-bipyridyl (BP) and Ag(I), with the composition, [Ag2(C3H2N3O3-N)2 (C10H8N2-N)] has been prepared. Crystal structure analysis shows that it has a chain structure in which the CA molecules are linked to the BP units through silver atoms by the formation of N-Ag-N bonds, wherein one of the hydrogens of CA is replaced by Ag(I), showing thereby the chains connected to one another by N-H${\\ldots}$O hydrogen bonds formed between the CA molecules. This intermolecular chain structure resembles the chain structure of the CA.BP adduct where CA-BP-CA chains formed by N-H${\\ldots}$N hydrogen bonds are linked to one another by N-H${\\ldots}$O hydrogen bonds between the CA molecules.

  5. NMR study of the FH⋯F hydrogen bond. Relation between hydrogen atom position and FH⋯F bond length

    Science.gov (United States)

    Panich, A. M.

    1995-07-01

    1H and 19F NMR study of (NH 4) 3BiBr 6NH 4Br·2NH 4HF 2 shows the bifluoride ion in this compound to be asymmetric with distances r( HF) = 1.042 ± 0.002 and R( FF) = 2.373 ± 0.008 Å. Existing NMR and neutron diffraction data for the FH⋯F hydrogen bond in solids have been studied to find a relation between the position of the hydrogen atom and FH⋯F bond length. Such a relation has been established and explained in the framework of the two-dimensional dynamic model of the hydrogen bond. The dependencies of r(AH) on R(AB) for the OH⋯O and FH⋯F bonds are shown to be similar.

  6. 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.

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

    Science.gov (United States)

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

    2016-05-20

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

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

    Institute of Scientific and Technical Information of China (English)

    WANG HaiJun; GU Fang; HONG XiaoZhong; BA XinWu

    2007-01-01

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

  9. Red and blue shift of liquid water's excited states: A many body perturbation study

    Science.gov (United States)

    Ziaei, Vafa; Bredow, Thomas

    2016-08-01

    In the present paper, accurate optical absorption spectrum of liquid H2O is calculated in the energy range of 5-20 eV to probe the nature of water's excited states by means of many body perturbation approach. Main features of recent inelastic X-ray measurements are well reproduced, such as a bound excitonic peak at 7.9 eV with a shoulder at 9.4 eV as well as the absorption maximum at 13.9 eV, followed by a broad shoulder at 18.4 eV. The spectrum is dominated by excitonic effects impacting the structures of the spectrum at low and higher energy regimes mixed by single particle effects at high energies. The exciton distribution of the low-energy states, in particular of S1, is highly anisotropic and localized mostly on one water molecule. The S1 state is essentially a HOCO-LUCO (highest occupied crystal orbital - lowest unoccupied crystal orbital) transition and of intra-molecular type, showing a localized valence character. Once the excitation energy is increased, a significant change in the character of the electronically excited states occurs, characterized through emergence of multiple quasi-particle peaks at 7.9 eV in the quasi-particle (QP) transition profile and in the occurring delocalized exciton density distribution, spread over many more water molecules. The exciton delocalization following a change of the character of excited states at around 7.9 eV causes the blue shift of the first absorption band with respect to water monomer S1. However, due to reduction of the electronic band gap from gas to liquid phase, following enhanced screening upon condensation, the localized S1 state of liquid water is red-shifted with respect to S1 state of water monomer. For higher excitations, near vertical ionization energy (11 eV), quasi-free electrons emerge, in agreement with the conduction band electron picture. Furthermore, the occurring red and blue shift of the excited states are independent of the coupling of resonant and anti-resonant contributions to the

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

    International Nuclear Information System (INIS)

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

  11. 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

  12. 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.

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

    Institute of Scientific and Technical Information of China (English)

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

    2013-01-01

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

  14. 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.

  15. Electrooptic Kerr effect of porphyrin H-aggregates in polymer films: Polymer specific spectral blue shift

    Science.gov (United States)

    Suzuki, Masaya; Nakata, Kazuaki; Kuroda, Reiko; Kobayashi, Takayoshi; Tokunaga, Eiji

    2016-05-01

    J- and H-aggregates of porphyrin molecules (TPPS4) in spin-coated polymer films have been studied by electroabsorption and circular dichroism (CD) spectroscopy. A spectral blue shift of the H-band due to the electrooptic Kerr effect was observed for the first time. This occurs only for a polyvinylpyrrolidone (PVP) film, with negligibly small spectral shift observed in polyvinyl alcohol (PVA), polyvinyl sulfate (PVS), and polyacrylic acid (PAA) films, in contrast to the red shift of the J-band which is commonly observed for any host polymers. Accordingly, the CD activity in both of J- and H-bands is more enhanced in PVP films than in PVA films. The mechanism of the blue and red shifts of the respective H- and J-bands is discussed by invoking a helical structure in micro-aggregates, which is compatible with the CD spectra, based on the molecular rearrangement model. It is proved that blue- and red-shifts occur evenly to cancel each other in the H-band if a simple helical structure is assumed, in good agreement with no spectral shifts in the H-band in PVA, PVS, and PAA films.

  16. 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…

  17. H2XP:OH2 Complexes: Hydrogen vs. Pnicogen Bonds

    Directory of Open Access Journals (Sweden)

    Ibon Alkorta

    2016-02-01

    Full Text Available A search of the Cambridge Structural Database (CSD was carried out for phosphine-water and arsine-water complexes in which water is either the proton donor in hydrogen-bonded complexes, or the electron-pair donor in pnicogen-bonded complexes. The range of experimental P-O distances in the phosphine complexes is consistent with the results of ab initio MP2/aug’-cc-pVTZ calculations carried out on complexes H2XP:OH2, for X = NC, F, Cl, CN, OH, CCH, H, and CH3. Only hydrogen-bonded complexes are found on the H2(CH3P:HOH and H3P:HOH potential surfaces, while only pnicogen-bonded complexes exist on H2(NCP:OH2, H2FP:OH2, H2(CNP:OH2, and H2(OHP:OH2 surfaces. Both hydrogen-bonded and pnicogen-bonded complexes are found on the H2ClP:OH2 and H2(CCHP:OH2 surfaces, with the pnicogen-bonded complexes more stable than the corresponding hydrogen-bonded complexes. The more electronegative substituents prefer to form pnicogen-bonded complexes, while the more electropositive substituents form hydrogen-bonded complexes. The H2XP:OH2 complexes are characterized in terms of their structures, binding energies, charge-transfer energies, and spin-spin coupling constants 2hJ(O-P, 1hJ(H-P, and 1J(O-H across hydrogen bonds, and 1pJ(P-O across pnicogen bonds.

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

    Science.gov (United States)

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

    2016-04-01

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

  19. 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.

  20. 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...

  1. Continuum in the X-Z---Y weak bonds: Z= main group elements.

    Science.gov (United States)

    Joy, Jyothish; Jose, Anex; Jemmis, Eluvathingal D

    2016-01-15

    The Continuum in the variation of the X-Z bond length change from blue-shifting to red-shifting through zero- shifting in the X-Z---Y complex is inevitable. This has been analyzed by ab-initio molecular orbital calculations using Z= Hydrogen, Halogens, Chalcogens, and Pnicogens as prototypical examples. Our analysis revealed that, the competition between negative hyperconjugation within the donor (X-Z) molecule and Charge Transfer (CT) from the acceptor (Y) molecule is the primary reason for the X-Z bond length change. Here, we report that, the proper tuning of X- and Y-group for a particular Z- can change the blue-shifting nature of X-Z bond to zero-shifting and further to red-shifting. This observation led to the proposal of a continuum in the variation of the X-Z bond length during the formation of X-Z---Y complex. The varying number of orbitals and electrons available around the Z-atom differentiates various classes of weak interactions and leads to interactions dramatically different from the H-Bond. Our explanations based on the model of anti-bonding orbitals can be transferred from one class of weak interactions to another. We further take the idea of continuum to the nature of chemical bonding in general.

  2. Quantification of hyperconjugative effect on the proton donor X-H bond length changes in the red- and blueshifted hydrogen-bonded complexes

    Science.gov (United States)

    Zhou, Pan-Pan; Qiu, Wen-Yuan; Jin, Neng-Zhi

    2012-08-01

    A whole dataset containing 55 hydrogen bonds were studied at the MP2/aug-cc-pVTZ level of theory. The changes of geometries and stretching vibrational frequencies show that there are 31 redshifted and 24 blueshifted hydrogen-bonded complexes. Natural bond orbital analysis was carried out at the B3LYP/aug-cc-pVTZ level of theory to obtain the electron densities in the bonding and antibonding orbitals of the proton donor X-H bond, which are closely associated with its bond length. Based on their relationship, a generally applicable method considering both the electron densities in the bonding and antibonding orbitals of the proton donor X-H bond has been developed to quantitatively describe the hyperconjugative effect on the X-H bond length changes in these hydrogen-bonded complexes.

  3. Halogen Bonding in Iodo-perfluoroalkane/Pyridine Mixtures

    Science.gov (United States)

    Fan, Haiyan; Eliason, Jeffrey K.; Moliva A., C. Diane; Olson, Jason L.; Flancher, Scott M.; Gealy, M. W.; Ulness, Darin J.

    2009-12-01

    Mole fraction and temperature studies of halogen bonding between 1-iodo-perfluorobutane, 1-iodo-perfluorohexane, or 2-iodo-perfluoropropane and pyridine were performed using noisy light-based coherent anti-Stokes Raman scattering (I(2) CARS) spectroscopy. The ring breathing mode of pyridine both is highly sensitive to halogen bonding and provides a strong I(2) CARS signal. As the lone pair electrons from the pyridinyl nitrogen interact with the σ-hole on the iodine from the iodo-perfluoroalkane, the ring breathing mode of pyridine blue-shifts proportionately with the strength of the interaction. The measured blue shift for halogen bonding of pyridine and all three iodo-perfluoroalkanes is comparable to that for hydrogen bonding between pyridine and water. 2-Iodo-perfluoropropane displays thermodynamic behavior that is different from that of the 1-iodo-perfluoroalkanes, which suggests a fundamental difference at the molecular level. A potential explanation of this difference is offered and discussed.

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

    Science.gov (United States)

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

    2016-06-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-03-31

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

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

    Science.gov (United States)

    Xin-Jun, Zhao; Zhi-Fu, Gao

    2016-07-01

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

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

    Institute of Scientific and Technical Information of China (English)

    赵新军; 高志福

    2016-01-01

    By employing molecular theory, we systematically investigate the shift of solubility of poly(N-isopropylacrylamide) (PNIPAM) brushes in sodium halide solutions. After considering PNIPAM–water hydrogen bonds, water–anion hydro-gen bonds, and PNIPAM–anion bonds and their explicit coupling to the PNIPAM conformations, we find that increasing temperature lowers the solubility of PNIPAM, and results in a collapse of the layer at high enough temperatures. The combination of the three types of bonds would yield a decrease in the solubility of PNIPAM following the Hofmeister se-ries:NaCl>NaBr>NaI. PNIPAM–water hydrogen bonds are affected by water–anion hydrogen bonds and PNIPAM–anion bonds. The coupling of polymer conformations and the competition among the three types of bonds are essential for de-scribing correctly a decrease in the solubility of PNIPAM brushes, which is determined by the free energy associated with the formation of the three types of bonds. Our results agree well with the experimental observations, and would be very im-portant for understanding the shift of the lower critical solution temperature of PNIPAM brushes following the Hofmeister series.

  8. Seeking for ultrashort "non-bonded" hydrogen-hydrogen contacts in some rigid hydrocarbons and their derivatives

    CERN Document Server

    Firouzi, Rohoullah

    2013-01-01

    In this communication a systematic computational survey is done on some rigid hydrocarbon skeletons and their chlorinated derivatives in order to seek for the so-called ultrashort "non-bonded" hydrogen-hydrogen contacts. It is demonstrated that upon a proper choice of the main hydrocarbons backbone and adding some bulky chlorine atoms instead of the original hydrogen atoms in parts of the employed hydrocarbons, the resulting strain triggers structural changes that yields ultrashort hydrogen-hydrogen contacts with distances as small as 1.38 Angstrom. Such ultrashort contacts is clearly less than the world record of a ultrashort non-bonded hydrogen-hydrogen contact, 1.56 Angstrom, very recently realized experimentally by Pascal and coworkers in in,in-bis(hydrosilane) [J. Am. Chem. Soc. 135, 13235 (2013)]. Accordingly, it is demonstrated that various backbones, e.g. half-cage pentacyclododecanes and tetracyclododecanes, after proper structural modifications, are capable to reveal ultrashort non-bonded hydrogen-h...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-02-15

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

  10. 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.

  11. 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...

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

    International Nuclear Information System (INIS)

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

  13. 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...

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

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

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

    Science.gov (United States)

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

    2001-08-01

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

  16. 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.

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

    Science.gov (United States)

    Titantah, John Tatini; Karttunen, Mikko

    2013-10-21

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

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

    Institute of Scientific and Technical Information of China (English)

    史福强; 安静仪; 俞稼镛

    2005-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

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

    2008-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

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

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

    OpenAIRE

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

    2012-01-01

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

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

    OpenAIRE

    Sreekumar Janardhnan; Mohini Sain

    2011-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    WANG Haijun; HONG Xiaozhong; GU Fang; BA Xinwu

    2006-01-01

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

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

    CERN Document Server

    McKenzie, Ross H

    2011-01-01

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

  6. Co-existing Intermolecular Halogen Bonding and Hydrogen Bonding in the Compound Trans-5,10-bis(1-bromodifluoroacetyl-1-ethoxycarbonyl-methylidene)thianthrene

    Institute of Scientific and Technical Information of China (English)

    ZHU Shi-Fa祝诗发; ZHU Shi-Zheng朱士正; LIAO Yuan-Xi廖远熹; HUANG Chao-Feng黄超峰; LI Zhan-Ting黎占亭

    2004-01-01

    Trans-5,10-bis(1-bromodifluoroacetyl-1-ethoxycarbonyl-methylidene)thianthrene (1b) was prepared from the reaction of BrCF2COC(N2)CO2Et with thianthrene. X-ray single crystal diffraction analysis showed that the intermolecular halogen bonding and hydrogen bonding coexisted in this compound. The bromine atom acted as an electron acceptor in the halogen bond and an electron donor in the hydrogen bond. It is the first example that the bromine atom acted as such a dual role in the hydrogen and halogen bond.

  7. A mixed quantum-classical molecular dynamics study of the hydroxyl stretch in methanol/carbon tetrachloride mixtures III: nonequilibrium hydrogen-bond dynamics and infrared pump-probe spectra.

    Science.gov (United States)

    Kwac, Kijeong; Geva, Eitan

    2013-06-27

    We present a mixed quantum-classical molecular dynamics study of the nonequilibrium hydrogen-bond dynamics following vibrational energy relaxation of the hydroxyl stretch in a 10 mol % methanol/carbon tetrachloride mixture and pure methanol. The ground and first-excited energy levels and wave functions are identified with the eigenvalues and eigenfunctions of the hydroxyl's adiabatic Hamiltonian and as such depend parametrically on the configuration of the remaining, classically treated, degrees of freedom. The dynamics of the classical degrees of freedom are in turn governed by forces obtained by taking the expectation value of the force with respect to the ground or excited vibrational wave functions. Polarizable force fields and nonlinear mapping relations between the hydroxyl transition frequencies and dipole moments and the electric field along the hydroxyl bond are used, which were previously shown to quantitatively reproduce the experimental infrared steady-state absorption spectra and excited state lifetime [Kwac, K.; Geva, E. J. Phys. Chem. B 2011, 115, 9184; 2012, 116, 2856]. The relaxation from the first-excited state to the ground state is treated as a nonadiabatic transition. Within the mixed quantum-classical treatment, relaxation from the excited state to the ground state is accompanied by a momentum-jump in the classical degrees of freedom, which is in turn dictated by the nonadiabatic coupling vector. We find that the momentum jump leads to breaking of hydrogen bonds involving the relaxing hydroxyl, thereby blue-shifting the transition frequency by more than the Stokes shift between the steady-state emission and absorption spectra. The subsequent nonequilibrium relaxation toward equilibrium on the ground state potential energy surface is thereby accompanied by red shifting of the transition frequency. The signature of this nonequilibrium relaxation process on the pump-probe spectrum is analyzed in detail. The calculated pump-probe spectrum is found

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-12-28

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

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

    Science.gov (United States)

    Lee, Myeong H.; Sankey, Otto F.

    2009-05-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    McKenzie, Ross H., E-mail: r.mckenzie@uq.edu.au [School of Mathematics and Physics, University of Queensland, Brisbane 4072 (Australia); Athokpam, Bijyalaxmi; Ramesh, Sai G. [Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012 (India)

    2015-07-28

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

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

    Science.gov (United States)

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

    2005-06-01

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

  12. 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.

  13. 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...

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

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2013-05-18

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

  17. Bending of Light Near a Star and Gravitational Red/Blue Shift Alternative Explanation Based on Refraction of Light

    CERN Document Server

    Gupta, D R C

    2004-01-01

    Many of the general-relativity-tests such as bending of light near a star and gravitational red/blue shift are explained without general-relativity and without Newtonian-approach. The author first casts doubts on both, the Newtonian and the relativistic approach; and proposes a novel alternative-explanation. The new alternative-explanation is based on refraction-phenomenon of optics. It predicts that as the ray passes through/near the stars atmospheric-medium, it bends due to refraction-phenomenon towards star-core, like a ray bends while passing through a prism or water-drop. A semi-empirical estimation of the atmospheric-height and its refractive-index are made to find the refraction-results. The refraction-based theory also suggests new explanation for gravitational red/blue shift; it tells that frequency remains constant (as it is so in refraction-phenomenon) and the red/blue shift is due to change in wavelength due to change in velocity of light in the medium . Estimated results for bending of light and ...

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

    Directory of Open Access Journals (Sweden)

    Jarosław Poznański

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

  19. Selective Breaking of Hydrogen Bonds of Layered Carbon Nitride for Visible Light Photocatalysis.

    Science.gov (United States)

    Kang, Yuyang; Yang, Yongqiang; Yin, Li-Chang; Kang, Xiangdong; Wang, Lianzhou; Liu, Gang; Cheng, Hui-Ming

    2016-08-01

    Selective breaking of the hydrogen bonds of graphitic carbon nitride can introduce favorable features, including increased band tails close to the band edges and the creation of abundant pores. These features can simultaneously improve the three basic processes of photocatalysis. As a consequence, the photocatalytic hydrogen-generation activity of carbon nitride under visible light is drastically increased by tens of times.

  20. 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

    . The number of AA side groups (hydrogen-bonding groups) after hydrolysis is determined from NMR measurements. We show that using the theoretical dependency of modulus and reptation time on the packing length, we can account for the changes in linear viscoelasticity due to transformation of nBA side groups...... 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...

  1. Delicate balance of hydrogen bonding forces in D-threoninol.

    Science.gov (United States)

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

    2014-09-01

    The seven most stable conformers of D-threoninol (2(S)-amino-1,3(S)-butanediol), a template used for the synthesis of artificial nucleic acids, have been identified and characterized from their pure rotational transitions in the gas phase using chirped-pulse Fourier transform microwave spectroscopy. D-Threoninol is a close analogue of glycerol, differing by substitution of an NH2 group for OH on the C(β) carbon and by the presence of a terminal CH3 group that breaks the symmetry of the carbon framework. Of the seven observed structures, two are H-bonded cycles containing three H-bonds that differ in the direction of the H-bonds in the cycle. The other five are H-bonded chains containing OH···NH···OH H-bonds with different directions along the carbon framework and different dihedral angles along the chain. The two structural types (cycles and chains of H-bonds) are in surprisingly close energetic proximity. Comparison of the rotational constants with the calculated structures at the MP2/6-311++G(d,p) level of theory reveals systematic changes in the H-bond distances that reflect NH2 as a better H-bond acceptor and poorer donor, shrinking the H-bond distances by ∼0.2 Å in the former case and lengthening them by a corresponding amount in the latter. Thus revealed is the subtle effect of asymmetric substitution on the energy landscape of a simple molecule, likely to be important in living systems.

  2. 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...

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

    Science.gov (United States)

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

    2009-02-01

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

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

    CERN Document Server

    McKenzie, Ross H; Ramesh, Sai

    2015-01-01

    If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor $\\Phi$ is correlated with the strength of the intramolecular hydrogen bonds. This correlation has been used to determine the length of the H-bonds (donor-acceptor separation) in a diverse range of enzymes and has been argued to support the existence of short low-barrier H-bonds. Starting with a potential energy surface based on a simple diabatic state model for H-bonds we calculate $\\Phi$ as a function of the proton donor-acceptor distance $R$. For numerical results, we use a parameterization of the model for symmetric O-H.... O bonds. We consider the relative contributions of the O-H stretch vibration, O-H bend vibrations (both in plane and out of plane), tunnelling splitting effects at...

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

    Indian Academy of Sciences (India)

    Mehdi Yoosefian; Hassan Karimi-Maleh; Afsaneh L Sanati

    2015-06-01

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

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

    Indian Academy of Sciences (India)

    Damanjit Kaur; Shweta Khanna

    2014-11-01

    Ab initio and DFT methods have been employed to study the hydrogen bonding ability of formamide, urea, urea monoxide, thioformamide, thiourea and thiourea monoxide with one water molecule and the homodimers of the selected molecules. The stabilization energies associated with themonohydrated adducts and homodimers’ formation were evaluated at B3LYP/6-311++G** and MP2/6-311++G∗∗ levels. The energies were corrected for zero-point vibrational energies and basis set superposition error using counterpoise method. Atoms in molecules study has been carried out in order to characterize the hydrogen bonds through the changes in electron density and laplacian of electron density. A natural energy decomposition and natural bond orbital analysis was performed to understand the nature of hydrogen bonding.

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

    Science.gov (United States)

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

    2016-07-01

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

  8. Intramolecular Hydrogen Bonding in (2-Hydroxybenzoyl)benzoylmethane Enol

    DEFF Research Database (Denmark)

    Hansen, Bjarke Knud Vilster; Winther, Morten; Spanget-Larsen, Jens

    2014-01-01

    In the stable enol tautomer of the title compound (OHDBM), one carbonyl group is flanked by two β-hydroxy groups, giving rise to bifold intramolecular H-bonding. A similar situation is found in other β,β'-dihydroxy carbonyl compounds like chrysazin, anthralin, 2,2'-dihydroxybenzophenone, and the ......In the stable enol tautomer of the title compound (OHDBM), one carbonyl group is flanked by two β-hydroxy groups, giving rise to bifold intramolecular H-bonding. A similar situation is found in other β,β'-dihydroxy carbonyl compounds like chrysazin, anthralin, 2,2'-dihydroxybenzophenone......, and the dienol form of 1,3-dibenzoylacetone. But in these examples the two H-bonds are equivalent, while in the case of OHDBM they are chemically different, involving one enolic and one phenolic hydroxy group. OHDBM is thus an interesting model compound with two competing H-bonds to the same carbonyl group...

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

    Science.gov (United States)

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

    2013-12-01

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

  10. Density functional theory, natural bond orbital and quantum theory of atoms in molecule analyses on the hydrogen bonding interactions in tryptophan-water complexes

    Indian Academy of Sciences (India)

    Xiqian Niu; Zhengguo Huang; Lingling Ma; Tingting Shen; Lingfei Guo

    2013-07-01

    The tryptophan-water (Trp-H2O) complexes formed by hydrogen bonding interactions were investigated at the B97XD/6-311++G(d,p) level. Five Trp-H2O complexes possessing various types of hydrogen bonds (H-bonds) were characterized by geometries, energies, vibrational frequencies. The nature of the H-bonds were characterized by the natural bond orbital (NBO) and the quantum theory of atoms in molecule (QTAIM) analyses as well. The intramolecular H-bond formed between the amino and carboxyl oxygen atom of tryptophan was retained in most of the complexes, and the cooperativity between the intra and intermolecular H-bonds exist in some complexes. The intramolecular H-bond and some intermolecular H-bonds are strong and have partial covalent character. The H-bonds formed between carboxyl and oxygen/nitrogen atoms are stronger than other H-bonds. The H-bonds involving methylene of tryptophan as H-donor are weak H-bonds. For all complexes,ele and ex makes major contributions to the total interaction energy (MP2), while disp is the smallest component of the interaction energy. Both hydrogen bonding interaction and structural deformation play important roles in the relative stabilities of the complexes. Regardless of strong H-bonds, the stabilities of some complexes are weakened by the serious structural deformations.

  11. 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....

  12. Calculation of Bond-length, Bond-energy and Force Constant of Hydrogen Molecule by Classical Mechanics

    Institute of Scientific and Technical Information of China (English)

    ChenJing

    2004-01-01

    Until recently the hydrogen molecule structural parameters are calculated with the methods of quantum mechanics. To achieve results close to experimental values, the wave function used is complicated and has no clear physical meaning. Because the distribution of the electron probability density is a statistical rule, the macro-time has actually been used in the concept on a electron cloud graph. Here are obtained three formulas with a classical mechanics method on the bond-length re , bond-energy De and force constant k of the ground state hydrogen molecule, which have a clear physical meaning but no artificial parameters, and compared with experimental values, the relative errors are respectively less than 1% , 2% and 4% .

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

    Directory of Open Access Journals (Sweden)

    Sreekumar Janardhnan

    2011-01-01

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

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

    Science.gov (United States)

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

    2014-03-01

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

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

    Science.gov (United States)

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

    2006-05-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Gomes, Jose R.B. [Centro de Investigacao em Quimica, Departamento de Quimica, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto (Portugal); Ribeiro da Silva, Manuel A.V. [Centro de Investigacao em Quimica, Departamento de Quimica, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto (Portugal)], E-mail: risilva@fc.up.pt

    2006-05-31

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

  17. Excitation wavelength and intensity dependence of photo-spectral blue shift in single CdSe/ZnS quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Xingbo, E-mail: shixingbo123@aliyun.com; Zheng, Shu; Gao, Wenli; Wei, Wei; Chen, Meiling; Deng, Fangming; Liu, Xia; Xiao, Qian [Hunan Agricultural University, Hunan Provincial Key Laboratory of Food Science and Biotechnology, College of Food Science and Technology (China)

    2014-12-15

    The influence of excitation wavelength and intensity on core/shell CdSe/ZnS quantum dots (QDs) photo-spectral blue shift was investigated by spectral imaging. Analysis of the evolution of the distance between the zeroth-order spot and the first-order spectral streak, we found that the extent of blue shift strongly depends on the excitation wavelength and QDs sizes, but not on the excitation intensity. Converted the extent of blue shift into the decreased QDs volume at a series of time, the core oxidation kinetics of CdSe/ZnS QDs was uncovered that provided a quantitative comparison method for study the excitation wavelength and intensity dependence of single QDs blue shift. The core oxidation rate is almost proportional to the excitation intensity. These results are explained by a fact that higher energy excitation wavelength can accelerate individual exciton formation and higher excitation intensity can induce more amount of exciton formation per a unit time.

  18. Excitation wavelength and intensity dependence of photo-spectral blue shift in single CdSe/ZnS quantum dots

    International Nuclear Information System (INIS)

    The influence of excitation wavelength and intensity on core/shell CdSe/ZnS quantum dots (QDs) photo-spectral blue shift was investigated by spectral imaging. Analysis of the evolution of the distance between the zeroth-order spot and the first-order spectral streak, we found that the extent of blue shift strongly depends on the excitation wavelength and QDs sizes, but not on the excitation intensity. Converted the extent of blue shift into the decreased QDs volume at a series of time, the core oxidation kinetics of CdSe/ZnS QDs was uncovered that provided a quantitative comparison method for study the excitation wavelength and intensity dependence of single QDs blue shift. The core oxidation rate is almost proportional to the excitation intensity. These results are explained by a fact that higher energy excitation wavelength can accelerate individual exciton formation and higher excitation intensity can induce more amount of exciton formation per a unit time

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-05-06

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

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

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    DU Ping; XU YunXiang; JIANG XiKui; LI ZhanTing

    2009-01-01

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

  3. Synthesis of oxocarbon-encapsulated gold nanoparticles with blue-shifted localized surface plasmon resonance by pulsed laser ablation in water with CO2 absorbers

    Science.gov (United States)

    Del Rosso, T.; Rey, N. A.; Rosado, T.; Landi, S.; Larrude, D. G.; Romani, E. C.; Freire Junior, F. L.; Quinteiro, S. M.; Cremona, M.; Aucelio, R. Q.; Margheri, G.; Pandoli, O.

    2016-06-01

    Colloidal suspensions of oxocarbon-encapsulated gold nanoparticles have been synthesized in a one-step procedure by pulsed-laser ablation (PLA) at 532 nm of a solid gold target placed in aqueous solution containing CO2 absorbers, but without any stabilizing agent. Multi-wavelength surface enhanced Raman spectroscopy allows the identification of adsorbed amorphous carbon and graphite, Au-carbonyl, Au coordinated CO2-derived bicarbonates/carbonates and hydroxyl groups around the AuNPs core. Scanning electron microscopy, energy dispersive x-ray analysis and high resolution transmission electron microscopy highlight the organic shell structure around the crystalline metal core. The stability of the colloidal solution of nanocomposites (NCs) seems to be driven by solvation forces and is achieved only in neutral or basic pH using monovalent hydroxide counter-ions (NaOH, KOH). The NCs are characterized by a blue shift of the localized surface plasmon resonance (LSPR) band typical of metal-ligand stabilization by terminal π-back bonding, attributed to a core charging effect caused by Au-carbonyls. Total organic carbon measurements detect the final content of organic carbon in the colloidal solution of NCs that is about six times higher than the value of the water solution used to perform PLA. The colloidal dispersions of NCs are stable for months and are applied as analytical probes in amino glycoside antibiotic LSPR based sensing.

  4. Hydrogen Bond Formation between the Carotenoid Canthaxanthin and the Silanol Group on MCM-41 Surface.

    Science.gov (United States)

    Gao, Yunlong; Xu, Dayong; Kispert, Lowell D

    2015-08-20

    The formation of one or two hydrogen bonds (H-bonds) between canthaxanthin (CAN), a dye, and the silanol group(s) on the MCM-41 surface has been studied by density functional theory (DFT) calculations and calorimetric experiments. It was found that the formation of the H-bond(s) stabilized the CAN molecule more than its radical cation (CAN(•+)). The charge distribution, bond lengths, and the HOMO and LUMO energies of CAN are also affected. The formation of the H-bond(s) explains the lower photoinduced electron transfer efficiency of CAN imbedded in Cu-MCM-41 versus that for β-carotene (CAR) imbedded in Cu-MCM-41 where complex formation with Cu(2+) dominates. These calculations show that to achieve high electron transfer efficiency for a dye-sensitized solar cell, H-bonding between the dye and the host should be avoided. PMID:26230844

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2015-03-30

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

  7. Blue-shift of E{sub 2} critical point resonance in optical second-harmonic spectrum of Si nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Mendoza, Bernardo S. [Department of Photonics, Centro de Investigaciones en Optica, A. C. Leon, Guanajuato (Mexico); Wei, Junwei; Downer, Michael C. [Department of Physics, The University of Texas at Austin, Austin, Texas 78712-1081 (United States)

    2012-06-15

    The E{sub 2} critical point (CP) resonance in the second-harmonic spectrum of silica-embedded Si nanocrystals (NCs) of 3 and 5 nm average diameter is observed to be blue-shifted by 0.5 eV from its energy (4.4 eV) in the linear dielectric response {epsilon}({omega}) of the same samples. In contrast, the E{sub 1} CP resonance (3.4 eV) and a third resonance intermediate in energy (3.8 eV) between E{sub 1} and E{sub 2} occur at nearly the same energy in both linear and nonlinear spectra. We explain the anomalous E{sub 2} blue-shift by calculating the second-harmonic response function {delta}({omega}) of the NCs analytically from the measured {epsilon}({omega}) using a dipolium model. The analysis shows that the E{sub 2} blue-shift originates from the screening factors of the form [{epsilon}(2{omega})+2]{sup -1} and [2{epsilon}(2{omega})+3]{sup -1} that are unique to second-harmonic generation (SHG) from nanospheres. Strong interaction between E{sub 2} and E'{sub 1} (5.3 eV in bulk c-Si) resonant contributions to this factor pulls the E{sub 2} peak response toward the higher E'{sub 1} energy while negligibly influencing lower energy resonances. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

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

    Science.gov (United States)

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

    2016-05-01

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

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

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei; HUANG Shengyou; YU Tao; ZOU Xianwu

    2007-01-01

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

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

    CERN Document Server

    Gasparotto, Piero; Ceriotti, Michele

    2016-01-01

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

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

    CERN Document Server

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

    2012-01-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Anthony W Fitzpatrick

    2011-10-01

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

  14. Effect of superalkali substituents on the strengths and properties of hydrogen and halogen bonds.

    Science.gov (United States)

    Tian, Wenkai; Huang, Xin; Li, Qingzhong; Li, Wenzuo; Cheng, Jianbo; Gong, Baoan

    2013-03-01

    Quantum chemical calculations have been performed for the complexes Li(3)OCCX-Y (X = Cl, Br, H; Y = NH(3), H(2)O, H(2)S) and Li(3)OCN-X'Y' (X'Y' = ClF, BrCl, BrF, HF) to study the role of superalkalis in hydrogen and halogen bonds. The results show that the presence of an Li(3)O cluster in a Lewis acid weakens its acidity, while its presence in a Lewis base enhances its basicity. Furthermore, the latter effect is more prominent than the former one, and the presence of an Na(3)O cluster causes an even greater effect than Li(3)O. The strengths of hydrogen and halogen bonds were analyzed using molecular electrostatic potentials. The contributions of superalkalis to the strength of hydrogen and halogen bonds were elucidated by analyzing differences in electron density. PMID:23179773

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

    Science.gov (United States)

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

    2006-11-10

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

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

    Science.gov (United States)

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

    2004-08-01

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

  17. The role of backbone hydrogen bonds in the transition state for protein folding of a PDZ domain

    DEFF Research Database (Denmark)

    Pedersen, Søren W; Hultqvist, Greta; Strømgaard, Kristian;

    2014-01-01

    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...

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

    Science.gov (United States)

    Houriez, Céline; Masella, Michel; Ferré, Nicolas

    2010-09-01

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

  19. Obtaining mass parameters of compact objects from red-blue shifts emitted by geodesic particles around them

    CERN Document Server

    Becerril, Ricardo; Nucamendi, Ulises

    2016-01-01

    The mass parameters of compact objects such as Boson Stars, Schwarzschild, Reissner Nordstrom and Kerr black holes are computed in terms of the measurable redshift-blueshift (zred, zblue) of photons emitted by particles moving along circular geodesics around these objects and the radius of their orbits. We found bounds for the values of (zred, zblue) that may be observed. For the case of Kerr black hole, recent observational estimates of SrgA\\* mass and rotation parameter are employed to determine the corresponding values of these red-blue shifts.

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

    CERN Document Server

    Gasparotto, Piero

    2014-01-01

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

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

    CERN Document Server

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

    2016-01-01

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

  2. 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.

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

    Institute of Scientific and Technical Information of China (English)

    XUMancai; OUZhize; 等

    2000-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    PANG XIAO-FENG; LI PING

    2000-01-01

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

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

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

    Science.gov (United States)

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

    2016-05-01

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

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

    CERN Document Server

    McKenzie, Ross H

    2014-01-01

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

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

    OpenAIRE

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

    2012-01-01

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

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

    CERN Document Server

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

    2013-01-01

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

  10. Learning Probabilistic Models of Hydrogen Bond Stability from Molecular Dynamics Simulation Trajectories

    KAUST Repository

    Chikalov, Igor

    2011-04-02

    Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. H-bonds involving atoms from residues that are close to each other in the main-chain sequence stabilize secondary structure elements. H-bonds between atoms from distant residues stabilize a protein’s tertiary structure. However, H-bonds greatly vary in stability. They form and break while a protein deforms. For instance, the transition of a protein from a nonfunctional to a functional state may require some H-bonds to break and others to form. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor. Other local interactions may reinforce (or weaken) an H-bond. This paper describes inductive learning methods to train a protein-independent probabilistic model of H-bond stability from molecular dynamics (MD) simulation trajectories. The training data describes H-bond occurrences at successive times along these trajectories by the values of attributes called predictors. A trained model is constructed in the form of a regression tree in which each non-leaf node is a Boolean test (split) on a predictor. Each occurrence of an H-bond maps to a path in this tree from the root to a leaf node. Its predicted stability is associated with the leaf node. Experimental results demonstrate that such models can predict H-bond stability quite well. In particular, their performance is roughly 20% better than that of models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a given conformation. The paper discusses several extensions that may yield further improvements.

  11. Blue-shift of Eu²⁺ emission in (Ba,Sr)₃Lu(PO₄)₃:Eu²⁺ eulytite solid-solution phosphors resulting from release of neighbouring-cation-induced stress.

    Science.gov (United States)

    Wang, Ziyuan; Xia, Zhiguo; Molokeev, Maxim S; Atuchin, Victor V; Liu, QuanLin

    2014-11-28

    A series of iso-structural eulytite-type (Ba,Sr)3Lu(PO4)3:Eu(2+) solid-solution phosphors with different Sr/Ba ratios were synthesized by a solid-state reaction. Crystal structures of (Ba,Sr)3Lu(PO4)3:Eu(2+) were resolved by the Rietveld method, which shows an eulytite-type cubic Bi4(SiO4)3 structure with cations disordered in a single C3 site while the oxygen atoms were distributed over two partially occupied sites. The emission peaks of Ba((3-x))Sr(x)Lu(PO4)3:Eu(2+) (0 ≤ x ≤ 3) phosphors were blue-shifted, from 506 to 479 nm, with increasing Sr/Ba ratio upon the same excitation wavelength of 365 nm, and such interesting luminescence behaviours can also be found in other eulytite-type (Ba,Sr)3Ln(PO4)3:Eu(2+) (Ln = Y, Gd) solid-solution phosphors. The blue-shift of the Eu(2+) emission with increasing Sr/Ba ratio was ascribed to the variation of the crystal field strength that the 5d orbital of Eu(2+) ion experiences, and a new model based on the Eu-O bond length and released neighboring-cation stress in disordered Ba(2+)/Sr(2+)/Ln(3+) sites is proposed.

  12. Electron-electron interactions in the chemical bond: ``1/3” Effect in the bond length of hydrogen molecule

    Indian Academy of Sciences (India)

    P Ganguly

    2001-10-01

    The prominent ``1/3” effect observed in the Hall effect plateaus of twodimensional electron gas (2DEG) systems has been postulated to indicating 1/3 fractional charge quasiparticle excitations arising from electron-electron interactions. Tunneling shot-noise experiments on 2DEF exhibiting fractional quantum Hall effect (FQHE) shows evidence for tunnelling of particles with and /3 charges for a constant band mass. A ``1/3” effect in the hydrogen molecule is seen in as much as its internuclear distance, - = - + +, with |+/-| = 1/3. This is examined in terms of electron-electron interactions involving electron- and hole quasiparticles, (-) and (ℎ+), equivalent to those observed in FQHE shot-noise experiments. The (/) ratio of the (-) and (ℎ+) quasiparticles is kept at 1: -3. Instead of a 2DEG, these particles are treated as being in flat Bohr orbits. A treatment in the language of charge-flux tube composites for the hydrogen atom as well as the hydrogen molecule is attempted. Such treatment gives important insights into changes in chemical potential and bond energy on crossing a phase boundary during the atom-bond transition as well as on models for FQHE itself.

  13. Kerr black hole parameters in terms of red/blue shifts of photons emitted by geodesic particles

    CERN Document Server

    Herrera-Aguilar, Alfredo

    2015-01-01

    We are motivated by the recently reported dynamical evidence of stars with short orbital periods moving around the center of the Milky Way and the corresponding hypothesis about the existence of a supermassive black hole hosted at its center. In this paper we show how the mass and rotation parameters of a Kerr black hole (assuming that the putative supermassive black hole is of this type), as well as the distance that separates the black hole from the Earth, can be estimated in a relativistic way in terms of i) the red and blue shifts of photons that are emitted by geodesic massive particles (stars and galactic gas) and travel along null geodesics towards a distant observer, and ii) the radius of these star/gas orbits. As a concrete example and as a first step towards a full relativistic analysis of the above mentioned star orbits around the center of our galaxy, we consider stable equatorial circular orbits of stars and express their corresponding red/blue shifts in terms of the metric parameters (mass and a...

  14. Time-Translation Invariance of Scattering Maps and Blue-Shift Instabilities on Kerr Black Hole Spacetimes

    CERN Document Server

    Dafermos, Mihalis

    2015-01-01

    In this paper, we provide an elementary, unified treatment of two distinct blue-shift instabilities for the scalar wave equation on a fixed Kerr black hole background: the celebrated blue-shift at the Cauchy horizon (familiar from the strong cosmic censorship conjecture) and the time-reversed red-shift at the event horizon (relevant in classical scattering theory). Our first theorem concerns the latter and constructs solutions to the wave equation on Kerr spacetimes such that the radiation field along the future event horizon vanishes and the radiation field along future null infinity decays at an arbitrarily fast polynomial rate, yet, the local energy of the solution is infinite near any point on the future event horizon. Our second theorem constructs solutions to the wave equation on rotating Kerr spacetimes such that the radiation field along the past event horizon (extended into the black hole) vanishes and the radiation field along past null infinity decays at an arbitrarily fast polynomial rate, yet, th...

  15. Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories

    KAUST Repository

    Chikalov, Igor

    2011-02-15

    Background: Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. They form and break while a protein deforms, for instance during the transition from a non-functional to a functional state. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor.Methods: This paper describes inductive learning methods to train protein-independent probabilistic models of H-bond stability from molecular dynamics (MD) simulation trajectories of various proteins. The training data contains 32 input attributes (predictors) that describe an H-bond and its local environment in a conformation c and the output attribute is the probability that the H-bond will be present in an arbitrary conformation of this protein achievable from c within a time duration ?. We model dependence of the output variable on the predictors by a regression tree.Results: Several models are built using 6 MD simulation trajectories containing over 4000 distinct H-bonds (millions of occurrences). Experimental results demonstrate that such models can predict H-bond stability quite well. They perform roughly 20% better than models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a conformation. In most tests, about 80% of the 10% H-bonds predicted as the least stable are actually among the 10% truly least stable. The important attributes identified during the tree construction are consistent with previous findings.Conclusions: We use inductive learning methods to build protein-independent probabilistic models to study H-bond stability, and demonstrate that the models perform better than H-bond energy alone. 2011 Chikalov et al; licensee BioMed Central Ltd.

  16. Computational insights into the photocyclization of diclofenac in solution: effects of halogen and hydrogen bonding.

    Science.gov (United States)

    Bani-Yaseen, Abdulilah Dawoud

    2016-08-21

    The effects of noncovalent interactions, namely halogen and hydrogen bonding, on the photochemical conversion of the photosensitizing drug diclofenac (DCF) in solution were investigated computationally. Both explicit and implicit solvent effects were qualitatively and quantitatively assessed employing the DFT/6-31+G(d) and SQM(PM7) levels of theory. Full geometry optimizations were performed in solution for the reactant DCF, hypothesized radical-based intermediates, and the main product at both levels of theories. Notably, in good agreement with previous experimental results concerning the intermolecular halogen bonding of DCF, the SQM(PM7) method revealed different values for d(ClO, Å) and ∠(C-ClO, °) for the two chlorine-substituents of DCF, with values of 2.63 Å/162° and 3.13 Å/142° for the trans and cis orientations, respectively. Employing the DFT/6-31+G(d) method with implicit solvent effects was not conclusive; however, explicit solvent effects confirmed the key contribution of hydrogen and halogen bonding in stabilizing/destabilizing the reactant and hypothesized intermediates. Interestingly, the obtained results revealed that a protic solvent such as water can increase the rate of photocyclization of DCF not only through hydrogen bonding effects, but also through halogen bonding. Furthermore, the atomic charges of atoms majorly involved in the photocyclization of DCF were calculated using different methods, namely Mulliken, Hirshfeld, and natural bond orbital (NBO). The obtained results revealed that in all cases there is a notable nonequivalency in the noncovalent intermolecular interactions of the two chlorine substituents of DCF and the radical intermediates with the solvent, which in turn may account for the discrepancy of their reactivity in different media. These computational results provide insight into the importance of halogen and hydrogen bonding throughout the progression of the photochemical conversion of DCF in solution. PMID:27424600

  17. 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...

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

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

  19. 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…

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

    Science.gov (United States)

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

    2016-05-01

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

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

    Institute of Scientific and Technical Information of China (English)

    PANG Xiao-feng; YU Jia-feng

    2004-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Graham Smith

    2015-11-01

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

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

    Science.gov (United States)

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

    2016-05-21

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

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

    DEFF Research Database (Denmark)

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

    2004-01-01

    We study discrete topological solitary waves (kinks and antikinks) in two nonlinear diatomic chain models that describe the collective dynamics of proton transfers in one-dimensional hydrogen-bonded networks. The essential ingredients of the models are (i) a realistic (anharmonic) ion-proton inte...

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

    Institute of Scientific and Technical Information of China (English)

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

    2012-01-01

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

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

    DEFF Research Database (Denmark)

    Sen, Anjana; Nielsen, Peter E

    2009-01-01

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

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

    Science.gov (United States)

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

    2000-12-15

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

  8. 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.

  9. 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…

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

    Indian Academy of Sciences (India)

    José Teixeira

    2008-10-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

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

    Science.gov (United States)

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

    2012-12-01

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

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

    Institute of Scientific and Technical Information of China (English)

    PANGXiao-feng; YUJia-feng

    2004-01-01

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

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

    Science.gov (United States)

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

    2015-11-01

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

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

    NARCIS (Netherlands)

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

    2003-01-01

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

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

    NARCIS (Netherlands)

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

    2001-01-01

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

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

    Indian Academy of Sciences (India)

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

    2004-07-01

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

  18. Si-H bond dynamics in hydrogenated amorphous silicon

    Science.gov (United States)

    Scharff, R. Jason; McGrane, Shawn D.

    2007-08-01

    The ultrafast structural dynamics of the Si-H bond in the rigid solvent environment of an amorphous silicon thin film is investigated using two-dimensional infrared four-wave mixing techniques. The two-dimensional infrared (2DIR) vibrational correlation spectrum resolves the homogeneous line shapes ( 4ps waiting times. The Si-H stretching mode anharmonic shift is determined to be 84cm-1 and decreases slightly with vibrational frequency. The 1→2 linewidth increases with vibrational frequency. Frequency dependent vibrational population times measured by transient grating spectroscopy are also reported. The narrow homogeneous line shape, large inhomogeneous broadening, and lack of spectral diffusion reported here present the ideal backdrop for using a 2DIR probe following electronic pumping to measure the transient structural dynamics implicated in the Staebler-Wronski degradation [Appl. Phys. Lett. 31, 292 (1977)] in a-Si:H based solar cells.

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

    International Nuclear Information System (INIS)

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

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

    Directory of Open Access Journals (Sweden)

    Batista VictorS.

    2013-03-01

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

  1. Theoretical Study of the Red-Shifting and Blue-Shifting Hydrogen Bonding Between Pyridine and CHX3 (X=F,Cl ,Br or I)%吡啶与CHX3(X=F,Cl,Br,I)形成分子间红移和蓝移氢键的理论研究

    Institute of Scientific and Technical Information of China (English)

    王素纹; 黎安勇

    2007-01-01

    运用量子化学从头算方法研究了复合物C5H5N…CHX3(X=F,Cl,Br,I)分子间C-H…N和C-H…π氢键.研究表明,在MP2/SDD水平下,分子间C-H…N氢键的形成均使CHX3分子中C-H键伸长,伸缩振动频率减小,形成红移氢键;分子间C-H…π氢键的形成均使CHX3分子中C-H键收缩,伸缩振动频率增大,形成蓝移氢键.振动光谱分析表明,不能根据质子供体分子CHX3的固有偶极矩对C-H键长的导数来判断红移氢键和蓝移氢键.NBO分析表明,超共轭效应占优势,因此形成C-H…N红移氢键;重杂化效应占优势,因此形成C-H…π蓝移氢键.

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

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

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

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

    Science.gov (United States)

    Słowikowska, Joanna Maria; Woźniak, Krzysztof

    1996-01-01

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

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

    Science.gov (United States)

    Sukumaran, S.; Beaucage, G.

    2000-03-01

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

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

    Institute of Scientific and Technical Information of China (English)

    LI Quan

    2006-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    LI Quan; ZHAO Keqing

    2009-01-01

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

  7. Chemical bonding in hydrogen and lithium under pressure.

    Science.gov (United States)

    Naumov, Ivan I; Hemley, Russell J; Hoffmann, Roald; Ashcroft, N W

    2015-08-14

    Though hydrogen and lithium have been assigned a common column of the periodic table, their crystalline states under common conditions are drastically different: the former at temperatures where it is crystalline is a molecular insulator, whereas the latter is a metal that takes on simple structures. On compression, however, the two come to share some structural and other similarities associated with the insulator-to-metal and metal-to-insulator transitions, respectively. To gain a deeper understanding of differences and parallels in the behaviors of compressed hydrogen and lithium, we performed an ab initio comparative study of these systems in selected identical structures. Both elements undergo a continuous pressure-induced s-p electronic transition, though this is at a much earlier stage of development for H. The valence charge density accumulates in interstitial regions in Li but not in H in structures examined over the same range of compression. Moreover, the valence charge density distributions or electron localization functions for the same arrangement of atoms mirror each other as one proceeds from one element to the other. Application of the virial theorem shows that the kinetic and potential energies jump across the first-order phase transitions in H and Li are opposite in sign because of non-local effects in the Li pseudopotential. Finally, the common tendency of compressed H and Li to adopt three-fold coordinated structures as found is explained by the fact that such structures are capable of yielding a profound pseudogap in the electronic densities of states at the Fermi level, thereby reducing the kinetic energy. These results have implications for the phase diagrams of these elements and also for the search for new structures with novel properties. PMID:26277151

  8. Chemical bonding in hydrogen and lithium under pressure

    Energy Technology Data Exchange (ETDEWEB)

    Naumov, Ivan I.; Hemley, Russell J. [Geophysical Laboratory, Carnegie Institution of Washington, 5251 Broad Branch Rd. NW, Washington, DC 20015 (United States); Hoffmann, Roald [Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 (United States); Ashcroft, N. W. [Laboratory of Atomic and Solid State Physics and Cornell Center for Materials Research, Cornell University, Clark Hall, Ithaca, New York 14853 (United States)

    2015-08-14

    Though hydrogen and lithium have been assigned a common column of the periodic table, their crystalline states under common conditions are drastically different: the former at temperatures where it is crystalline is a molecular insulator, whereas the latter is a metal that takes on simple structures. On compression, however, the two come to share some structural and other similarities associated with the insulator-to-metal and metal-to-insulator transitions, respectively. To gain a deeper understanding of differences and parallels in the behaviors of compressed hydrogen and lithium, we performed an ab initio comparative study of these systems in selected identical structures. Both elements undergo a continuous pressure-induced s-p electronic transition, though this is at a much earlier stage of development for H. The valence charge density accumulates in interstitial regions in Li but not in H in structures examined over the same range of compression. Moreover, the valence charge density distributions or electron localization functions for the same arrangement of atoms mirror each other as one proceeds from one element to the other. Application of the virial theorem shows that the kinetic and potential energies jump across the first-order phase transitions in H and Li are opposite in sign because of non-local effects in the Li pseudopotential. Finally, the common tendency of compressed H and Li to adopt three-fold coordinated structures as found is explained by the fact that such structures are capable of yielding a profound pseudogap in the electronic densities of states at the Fermi level, thereby reducing the kinetic energy. These results have implications for the phase diagrams of these elements and also for the search for new structures with novel properties.

  9. Chemical bonding in hydrogen and lithium under pressure.

    Science.gov (United States)

    Naumov, Ivan I; Hemley, Russell J; Hoffmann, Roald; Ashcroft, N W

    2015-08-14

    Though hydrogen and lithium have been assigned a common column of the periodic table, their crystalline states under common conditions are drastically different: the former at temperatures where it is crystalline is a molecular insulator, whereas the latter is a metal that takes on simple structures. On compression, however, the two come to share some structural and other similarities associated with the insulator-to-metal and metal-to-insulator transitions, respectively. To gain a deeper understanding of differences and parallels in the behaviors of compressed hydrogen and lithium, we performed an ab initio comparative study of these systems in selected identical structures. Both elements undergo a continuous pressure-induced s-p electronic transition, though this is at a much earlier stage of development for H. The valence charge density accumulates in interstitial regions in Li but not in H in structures examined over the same range of compression. Moreover, the valence charge density distributions or electron localization functions for the same arrangement of atoms mirror each other as one proceeds from one element to the other. Application of the virial theorem shows that the kinetic and potential energies jump across the first-order phase transitions in H and Li are opposite in sign because of non-local effects in the Li pseudopotential. Finally, the common tendency of compressed H and Li to adopt three-fold coordinated structures as found is explained by the fact that such structures are capable of yielding a profound pseudogap in the electronic densities of states at the Fermi level, thereby reducing the kinetic energy. These results have implications for the phase diagrams of these elements and also for the search for new structures with novel properties.

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

    Science.gov (United States)

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

    2016-05-01

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

  11. Mobility and chemical bond of hydrogen in titanium and palladium hydrides

    International Nuclear Information System (INIS)

    The probabilities for π- meson capture by hydrogen are measured at 25, 155 and 200 deg C in TiHsub(1.65) hydride and at 25, -120 and -196 deg C in PdHsub(0.67) hydride. An analysis of the results obtained shows that within the accuracy of the measurements (approximately 10%) a sharp (up to 1012) change in the mobility of hydrogen in the hydrides induced by temperature changes within the ranges indicated does not noticeably affect the probabilities for π- meson capture by bound hydrogen, i.e. does not lead to appreciable changes in the Me-H bond. A comparison of the capture probabilities for palladium hydride and hydrides of neighboring transition metals shows that there are no pronounced anomalies in the Pd-H bond

  12. 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...

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

    Science.gov (United States)

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

    2015-03-01

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

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

    Science.gov (United States)

    Angelina, Emilio L; Peruchena, Nélida M

    2011-05-12

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

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

    Science.gov (United States)

    Angelina, Emilio L; Peruchena, Nélida M

    2011-05-12

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

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

    Science.gov (United States)

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

    2013-08-29

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  18. Molecular structure and intramolecular hydrogen bonding in 2-hydroxybenzophenones: A theoretical study

    Indian Academy of Sciences (India)

    Mansoureh Zahedi-Tabrizi; Sayyed Faramarz Tayyari; Farideh Badalkhani-Khamseh; Reihaneh Ghomi; Fatemeh Afshar-Qahremani

    2014-07-01

    The intramolecular hydrogen bonding (IHB) in a series of 3-, 4- and 5-substituted 2-hydroxybenzophenone (HBP) is studied using density functional theory calculations. All calculations are performed at the B3LYP level, using 6-311++G∗∗ basis set. To understand the substitution effects on the nature of IHB and the electronic structure of the chelated ring system, the vibrational frequencies, 1H chemical shift, topological parameters, natural bond orders and natural charges over atoms involved in the chelated ring of HBP and its derivatives were calculated. TheWiberg bond indices and the natural charges over atoms involved in the chelated ring have been computed using the natural bond orbital (NBO) analysis. The computations were further complemented with an atoms-in-molecules (AIM) topological analysis to characterize the nature of the IHB in the considered molecules. Several correlations between geometrical parameters, 1H NMR chemical shift and topological parameters with the IHB strength are obtained.

  19. Large Angular Jump Mechanism Observed for Hydrogen Bond Exchange in Aqueous Perchlorate Solution

    Energy Technology Data Exchange (ETDEWEB)

    Ji, Minbiao; /SLAC, PULSE /Stanford U., Phys. Dept.; Odelius3, Michael; /Stockholm U.; Gaffney1, K.J.; /aff SLAC, PULSE

    2010-06-11

    The mechanism for hydrogen bond (H-bond) switching in solution has remained subject to debate despite extensive experimental and theoretical studies. We have applied polarization-selective multidimensional vibrational spectroscopy to investigate the H-bond exchange mechanism in aqueous NaClO{sub 4} solution. The results show that a water molecule shifts its donated H-bonds between water and perchlorate acceptors by means of large, prompt angular rotation. Using a jump-exchange kinetic model, we extract an average jump angle of 49 {+-} 4{sup o}, in qualitative agreement with the jump angle observed in molecular dynamics simulations of the same aqueous NaClO{sub 4} solution.

  20. Hydrogen bond dynamics in liquid water: Ab initio molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Cheolhee; Kim, Eunae [College of Pharmacy, Chosun University, Gwangju (Korea, Republic of); Yeom, Min Sun [Korea Institute of Science and Technology Information, Daejeon (Korea, Republic of)

    2016-01-15

    The effect of intermolecular interaction on the distribution of the harmonic vibrational frequencies of water molecules was investigated through ab initio molecular dynamics simulations based on the Born-Oppenheimer approach. For single water, the effect of the dynamics of the oxygen atom in single water and the simulation time step on the frequency distribution were examined. The distributions of the OH stretching and HOH bending vibrational frequencies of liquid water were compared to those of single water. The probability distributions of the change in OH bond length and the lifetime of the dangling OH bond were also obtained. The distribution of the frequencies was strongly affected by the long lifetime of the dangling OH bond, resulting in the formation of hydrogen bonds between water molecules.

  1. Growth mechanism and blue shift of Mn2+ luminescence for wurtzite ZnS : Mn2+ nanowires

    International Nuclear Information System (INIS)

    Wurtzite-type ZnS : Mn2+ nanowires were prepared by a hydrothermal method at 180 0C without any surface-active agent. The structure and morphology of the samples were characterized by x-ray diffraction, transmission electron microscopy, high-resolution transmission electron microscopy, Fourier transform infrared spectroscopy and energy dispersive spectroscopy. The average diameter of the nanowires was about 10 nm. An ethylenediamine-mediated template was observed and employed to explain the growth mechanism in detail. A strong yellow-orange emission from the Mn2+4T1-6A1 transition was observed in the photoluminescence spectra, which exhibited blue shift as the Mn2+ doped ratio increased.

  2. Geometric phase and o-mode blue shift in a chiral anisotropic medium inside a Fabry-P\\'erot cavity

    CERN Document Server

    Timofeev, I V; Sutormin, V S; Myslivets, S A; Arkhipkin, V G; Vetrov, S Ya; Lee, W; Zyryanov, V Ya

    2015-01-01

    Anomalous spectral shift of transmission peaks is observed in a Fabry--P\\'erot cavity filled with a chiral anisotropic medium. The effective refractive index value resides out of the interval between the ordinary and the extraordinary refractive indices. The spectral shift is explained by contribution of a geometric phase. The problem is solved analytically using the approximate Jones matrix method, numerically using the accurate Berreman method and geometrically using the generalized Mauguin--Poincar\\'e rolling cone method. The $o$-mode blue shift is measured for a 4-methoxybenzylidene-4'-$n$-butylaniline twisted--nematic layer inside the Fabry--P\\'erot cavity. The twist is electrically induced due to the homeoplanar--twisted configuration transition in an ionic-surfactant-doped liquid crystal layer. Experimental evidence confirms the validity of the theoretical model.

  3. Highly Selective Hg (II Ion Detection Based on Linear Blue-Shift of the Maximum Absorption Wavelength of Silver Nanoparticles

    Directory of Open Access Journals (Sweden)

    Li Ping Wu

    2012-01-01

    Full Text Available A new method of detecting Hg (II ion with silver nanoparticles (AgNPs is developed in this contribution. When Hg (II ions were added into AgNPs solution, the solution displayed rapid color change and blue shift of the maximum absorption wavelength (Δλ, which was in proportion to the Hg (II ion concentration over the range of 2.0 × 10−7–6.0 × 10−6 mol/L, with detection limit (3σ of 6.6 × 10−9 mol/L. Under the same experimental conditions, other metal ions did not interfere. Thus, we propose a rapid, simple and highly selective method for detecting Hg (II ion.

  4. 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 equilibria and predict the fraction of nonhydrogen bonded molecules in various hydrogen bonding mixtures. Carefully selected binary mixtures, which include water-hydrocarbon, 1-alkanol-hydrocarbon, water-1-alkanol, and glycol-hydrocarbon, were used to benchmark the accuracy of the models. Both models yielded...... 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....

  5. 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.

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

    Indian Academy of Sciences (India)

    Mark Johnson

    2008-11-01

    We have combined neutron scattering and a range of numerical simulations to study hydrogen bonds in condensed matter. Two examples from a recent thesis will be presented. The first concerns proton transfer with increasing temperature in short inter-molecular hydrogen bonds [1,2]. These bonds have unique physical and chemical properties and are thought to play a fundamental role in processes like enzymatic catalysis. By combining elastic and inelastic neutron scattering results with ab initio, lattice dynamics and molecular dynamics simulations, low frequency lattice modes are identified which modulate the potential energy surface of the hydrogen bond proton and drive proton transfer. The second example concerns base-pair opening in DNA which is the fundamental physical process underlying biological processes like denaturation and transcription. We have used an emprical force field and a large scale, all-atom phonon calculation to gain insight into the base-pair opening modes and the apparent `energy gap' between the accepted frequencies for these modes (∼ 100 cm-1 or ∼ 140 K) and the temperature of the biological processes (room temperature to 100° C) [3]. Inelastic neutron scattering spectra on aligned, highly crystalline DNA samples, produced at the ILL, provide the reference data for evaluating the precision of these simulation results.

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

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ye; LI Ting; TENG Qi-Wen

    2008-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

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

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

    Science.gov (United States)

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

    2015-05-21

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

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

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Spanget-Larsen, Jens

    2012-01-01

    in the harmonic and PT2 anharmonic approximations, as well as on experimental NMR parameters, i.e., proton chemical shifts (δH) and two-bond deuterium isotope effects on 13C chemical shifts (2ΔCOD). The procedures are applied in a discussion of the spectra of 2,6-dihydroxy-4-methylbenzaldehyde and 8......OH stretching frequencies are investigated for a series of non-tautomerizing systems with intramolecular hydrogen bonds. Effective OH stretching wavenumbers are predicted by the application of empirical correlation procedures based on the results of B3LYP/6-31G(d) theoretical calculations...

  11. Hydrogen-induced rupture of strained Si─O bonds in amorphous silicon dioxide

    OpenAIRE

    El-Sayed, Al-Moatasem; Watkins, Matthew B.; Grasser, Tibor; Afanas'ev, Valery; Shluger, Alexander L

    2015-01-01

    Using ab initio modeling we demonstrate that H atoms can break strained Si─O bonds in continuous amorphous silicon dioxide (a-SiO(2)) networks, resulting in a new defect consisting of a threefold-coordinated Si atom with an unpaired electron facing a hydroxyl group, adding to the density of dangling bond defects, such as E' centers. The energy barriers to form this defect from interstitial H atoms range between 0.5 and 1.3 eV. This discovery of unexpected reactivity of atomic hydrogen may hav...

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

    OpenAIRE

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

    2016-01-01

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

  13. 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

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

    Indian Academy of Sciences (India)

    Bhabani S Mallik; Amalendu Chandra

    2012-01-01

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

  15. Synthesis of Zn-Cu-In-S/ZnS Core/Shell Quantum Dots with Inhibited Blue-Shift Photoluminescence and Applications for Tumor Targeted Bioimaging

    OpenAIRE

    Weisheng Guo, Na chen, Yu Tu, Chunhong Dong, Bingbo Zhang, Chunhong Hu, Jin Chang

    2013-01-01

    A facile strategy is reported here for synthesis of Zn-Cu-In-S/ZnS (ZCIS/ZnS) core/shell QDs to address the synthetic issues that the unexpected blue-shift of CuInS2-based nanocrystals. In this strategy, Zn2+ ions are intentionally employed for the synthesis of alloyed ZCIS core QDs before ZnS shell coating, which contributes to the reduced blue-shift in photoluminescence (PL) emission. The experimental results demonstrate this elaborate facile strategy is effective for the reduction of blue-...

  16. 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.

  17. Bond topography and nanostructure of hydrogenated fullerene-like carbon films: A comparative study

    Science.gov (United States)

    Wang, Yongfu; Gao, Kaixiong; Shi, Jing; Zhang, Junyan

    2016-09-01

    Fullerene-like nanostructural hydrogenated amorphous carbon (FL-C:H) films were prepared by dc- and pulse- plasma enhanced chemical vapor deposition technique (PECVD). Both the films exhibit relatively stresses (0.63 GPa) in spite of their FL features and nanostructural bonding configurations, especially the pentagonal carbon rings. The creation of pentagonal rings is not fully driven by thermodynamics, but is closely related to compressive stress determined by the ion bombardment at the discharged state of the pulse- and dc- discharged plasmas methods. The dc method leads to FL's basal planes which contain less cross-linkages, and causes amorphous strongly hydrogenated structures.

  18. O-H···C hydrogen bond in the methane-water complex

    Science.gov (United States)

    Isaev, A. N.

    2016-10-01

    Quantum chemical calculations were performed at different levels of theory (SCF, DFT, MP2, and CCSD(T)) to determine the geometry and electronic structure of the HOH···CH4 complex formed by water and methane molecules, in which water is a proton donor and methane carbon ( sp 3) is an acceptor. The charge distribution on the atoms of the complex was analyzed by the CHelpG method and Hirshfeld population analysis; both methods revealed the transfer of electron charge from methane to water. According to the natural bond orbital (NBO) analysis data, the charge transfer upon complexation is caused by the interaction between the σ orbital of the axial C-H bond of methane directed along the line of the O-H···C hydrogen bridge and the antibonding σ* orbital of the O-H bond of the water molecule. Topological analysis of electron density in the HOH···CH4 complex by the AIM method showed that the parameters of the critical point of the bond between hydrogen and acceptor (carbon atom) for the O-H···C interaction are typical for H-bonded systems (the magnitude of electron density at the critical point of the bond, the sign and value of the Laplacian). It was concluded that the intermolecular interaction in the complex can be defined as an H bond of O-H···σ(C-H) type, whose energy was found to be 0.9 kcal/mol in MP2/aug-cc-pVQZ calculations including the basis set superposition error (BSSE).

  19. Chemical Bonding States of TiC Films before and after Hydrogen Ion Irradiation

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    TiC films deposited by rf magnetron sputtering followed by Ar+ ion bombardment were irradiated with a hydrogen ion beam. X-ray photoelectron spectroscopy (XPS) was used for characterization of the chemical bonding states of C and Ti elements of the TiC films before and after hydrogen ion irradiation, in order to understand the effect of hydrogen ion irradiation on the films and to study the mechanism of hydrogen resistance of TiC films. Conclusions can be drawn that ion bombardment at moderate energy can cause preferential physical sputtering of carbon atoms from the surface of low atomic number (Z) material. This means that ion beam bombardment leads to the formation of a non-stoichiometric composition of TiC on the surface.TiC films prepared by ion beam mixing have the more excellent characteristic of hydrogen resistance. One important cause, in addition to TiC itself, is that there are many vacant sites in TiC created by ion beam mixing.These defects can easily trap hydrogen and effectively enhance the effect of hydrogen resistance.

  20. Improvement of silicon direct bonding using surfaces activated by hydrogen plasma treatment

    CERN Document Server

    Choi, W B; Lee Jae Sik; Sung, M Y

    2000-01-01

    The plasma surface treatment, using hydrogen gas, of silicon wafers was studied as a pretreatment for silicon direct bonding. Chemical reactions of the hydrogen plasma with the surfaces were used for both surface activation and removal of surface contaminants. Exposure of the silicon wafers to the plasma formed an active oxide layer on the surface. This layer was hydrophilic. The surface roughness and morphology were examined as functions of the plasma exposure time and power. The surface became smoother with shorter plasma exposure time and lower power. In addition, the plasma surface treatment was very efficient in removing the carbon contaminants on the silicon surface. The value of the initial surface energy, as estimated by using the crack propagation method, was 506 mJ/M sup 2 , which was up to about three times higher than the value for the conventional direct bonding method using wet chemical treatments.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction en...... vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent, compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible....... energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and 3 or more imaginary frequencies using PM6-D3H+ implemented...

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    Inositol, 1,2,3,4,5,6-hexahydroxycyclohexane, exists in nine stereoisomers with different crystal structures and melting points. In a previous paper on the relationship between the melting points of the inositols and the hydrogen-bonding patterns in their crystal structures [Simperler et al. (2006...... ▶). CrystEngComm 8, 589], it was noted that although all inositol crystal structures known at that time contained 12 hydrogen bonds per molecule, their melting points span a large range of about 170 °C. Our preliminary investigations suggested that the highest melting point must be corrected for the effect...... of molecular symmetry, and that the three lowest melting points may need to be revised. This prompted a full investigation, with additional experiments on six of the nine inositols. Thirteen new phases were discovered; for all of these their crystal structures were examined. The crystal structures of eight...

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

    Energy Technology Data Exchange (ETDEWEB)

    Hay, Benjamin [ORNL; Pedzisa, Lee [ORNL

    2009-01-01

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

  4. 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.

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

    Science.gov (United States)

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

    2016-08-26

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

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

    Science.gov (United States)

    Jansson, Helén; Bergman, Rikard; Swenson, Jan

    2010-05-01

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

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

    Science.gov (United States)

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

    2011-05-01

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

  8. Hydrogen Dissociation in Generalized Hartree-Fock Theory: Breaking the diatomic bond

    Science.gov (United States)

    Jerke, Jonathan; Masood, Samina; Tymczak, Cj

    Generalized Hartree Fock theory predicts molecular Hydrogen dissociation without correlation. A variational Gaussian-Sinc linear superposition is the basis of 50 calculations with 3-4 significant digits of quality. The spin singlet covalent bond spontaneously breaks into a pair of uncorrelated doublets at atomic separation of 1.22 Angstroms. Quantum spin numbers and energetic comparison with Configuration Interaction theory--correlation--point to a first order phase transition in the molecular Hydrogen bond without correlation. Welch Foundation (Grant J-1675), the ARO (Grant W911Nf-13-1-0162), the Texas Southern University High Performance Computing Center (http:/hpcc.tsu.edu/; Grant PHY-1126251) and NSF-CREST CRCN project (Grant HRD-1137732).

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

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

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

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

    Science.gov (United States)

    Low, John N; Glidewell, Christopher

    2002-04-01

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2016-09-01

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

  13. 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 potential plays the role of the proton potential in the hydrogen bond. The system supports a rich variety of stationary kink solutions with different symmetry properties. We study the stability and bifurcation structure of all these stationary kink states. An exactly solvable model with a piecewise...... "parabola-constant" approximation of the double-Morse potential is suggested and studied analytically. The dependence of the Peierls-Nabarro potential on the system parameters is studied. Discrete traveling-wave solutions of a narrow permanent profile are shown to exist, depending on the anharmonicity...

  14. Hydrogen-bond-directed giant unilamellar vesicles of guanosine derivative: preparation, properties, and fusion.

    Science.gov (United States)

    Sawayama, Jun; Sakaino, Hirotoshi; Kabashima, Shin-ichiro; Yoshikawa, Isao; Araki, Koji

    2011-07-19

    By mixing a small volume of THF containing guanosine derivative 1 and tetraethylenegrycol dodecyl ether (TEGDE) with water and subsequently removing TEGDE by gel permeation chromatography, micrometer-sized giant unilamellar vesicles (GUV) of 1 were successfully prepared. The vesicle membrane was a 2-D sheet assembly of thickness 2.5 nm, composed of a 2-D inter-guanine hydrogen-bond network. The GUV dispersion showed high stability because of a large negative zeta potential, which allowed repeated sedimentation and redispersion by centrifugation and subsequent gentle agitation. TEGDE-triggered fusion of GUVs took place within 350 ms, which proceeded by fusion of the vesicle membranes in contact. These unique static and dynamic properties of the GUV membrane assembled by the 2-D hydrogen-bond network are discussed. PMID:21649445

  15. Spectroscopic examinations of hydrogen bonding in hydroxy-functionalized ADMET chemistry.

    Science.gov (United States)

    Thompson, Donovan L; Wagener, Kenneth B; Schulze, Ulrich; Voit, Brigitte; Jehnichen, Dieter; Malanin, Mikhail

    2015-01-01

    Wide-angle X-ray scattering (WAXS) and temperature-dependent Fourier transform infrared spectroscopy (FTIR) spectroscopy are used to study hydrogen bonding interactions of a hydroxyl-functionalized polyethylene (PE) prepared by acyclic diene metathesis (ADMET) chemistry. The hydroxyl polymer exhibits an orthorhombic unit cell structure with characteristic reflection planes at (110) and (200), comparable to pure crystalline PE. These data unequivocally demonstrate that the OH branch is excluded from the PE lamellae. Furthermore, the polymer melts 100 °C higher than all previous analogous polymers possessing precision placed long aliphatic branches that also are excluded from PE lamellae. Temperature-dependent FTIR spectroscopy from ambient to 150 °C, followed by cooling to 125 °C supports exclusion of the hydroxyl group from the crystalline lattice. It is concluded that these hydroxyl groups form stable physical networks in the amorphous region via hydrogen bonding and are important for the overall morphology of such polymers. PMID:25393938

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

    Science.gov (United States)

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

    2008-05-28

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

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

    Science.gov (United States)

    Pagola, Silvina; Stephens, Peter W

    2009-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Pagola, S.; Stephens, P

    2009-01-01

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

  19. Transfer Hydrogenation of C= C Double Bonds Catalyzed by Ruthenium Amido-Complexes:Scopes, Limitation and Enantioselectivity

    Institute of Scientific and Technical Information of China (English)

    XUE,Dong; CHENG,Ying-Chun; CUI,Xin; WANG,Qi-Wei; ZHU,Jin; DENG,Jin-Gen

    2004-01-01

    @@ The reduction of C = C double bonds is one of the most fundamental synthetic transformations and plays a key role in the manufacturing of a wide variety of bulk and fine chemicals. Hydrogenation of olefinic substrates can be achieved readily with molecular hydrogen in many cases, but transfer hydrogenation methods using suitable donor molecules such as formic acid or alcohols are receiving increasing attention as possible synthetic alternatives because it requires no special equipment and avoids the handling of potentially hazardous gaseous hydrogen.

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

    International Nuclear Information System (INIS)

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

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

    Indian Academy of Sciences (India)

    Okram Mukherjee Singh; Laishram Ronibala Devi; Neeladri Das

    2013-09-01

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

  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.

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

    Science.gov (United States)

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

    2011-10-13

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Koetzle, Thomas F. [IPNS Division, Argonne National Laboratory, Argonne, IL 60439 (United States)], E-mail: tkoetzle@anl.gov; Piccoli, Paula M.B.; Schultz, Arthur J. [IPNS Division, Argonne National Laboratory, Argonne, IL 60439 (United States)

    2009-02-21

    Beginning with work in the 1950s at the first generation of research reactors, studies of hydrogen-bonded systems have been a prime application for single-crystal neutron diffraction. The range of systems studied was extended in the 1960s and 1970s, with the advent of high flux reactor sources, and beginning around 1980 studies at pulsed neutron sources have made increasingly important contributions. Recently at the Argonne Intense Pulsed Neutron Source (IPNS), working with collaborators, we completed two studies of hydrogen-bonded systems that will serve to illustrate topics of current interest. In the first study, on andrographolide, an active diterpenoid natural product, our neutron diffraction results definitively characterize the hydrogen-bonding interactions. The second IPNS study is on tetraacetylethane (TAE), a {beta}-diketone enol system with a very short, strong intramolecular O-H...O hydrogen bond. At IPNS, we have determined the neutron crystal structure of TAE at five temperatures between 20 and 298 K to investigate changes in the structure with temperature and to probe for disorder. Despite the successes illustrated by the two examples presented here and by many other studies, at present applications of single-crystal neutron diffraction continue to be extremely flux limited and constrained by the requirement for mm-size crystals for many problems. These limitations are being addressed through the realization of powerful instruments at a new generation of pulsed neutron sources, including in the USA the TOPAZ and MaNDi single-crystal diffractometers that are under development at the Spallation Neutron Source (SNS)

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

    International Nuclear Information System (INIS)

    Beginning with work in the 1950s at the first generation of research reactors, studies of hydrogen-bonded systems have been a prime application for single-crystal neutron diffraction. The range of systems studied was extended in the 1960s and 1970s, with the advent of high flux reactor sources, and beginning around 1980 studies at pulsed neutron sources have made increasingly important contributions. Recently at the Argonne Intense Pulsed Neutron Source (IPNS), working with collaborators, we completed two studies of hydrogen-bonded systems that will serve to illustrate topics of current interest. In the first study, on andrographolide, an active diterpenoid natural product, our neutron diffraction results definitively characterize the hydrogen-bonding interactions. The second IPNS study is on tetraacetylethane (TAE), a β-diketone enol system with a very short, strong intramolecular O-H...O hydrogen bond. At IPNS, we have determined the neutron crystal structure of TAE at five temperatures between 20 and 298 K to investigate changes in the structure with temperature and to probe for disorder. Despite the successes illustrated by the two examples presented here and by many other studies, at present applications of single-crystal neutron diffraction continue to be extremely flux limited and constrained by the requirement for mm-size crystals for many problems. These limitations are being addressed through the realization of powerful instruments at a new generation of pulsed neutron sources, including in the USA the TOPAZ and MaNDi single-crystal diffractometers that are under development at the Spallation Neutron Source (SNS).

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

    Science.gov (United States)

    Koetzle, Thomas F.; Piccoli, Paula M. B.; Schultz, Arthur J.

    2009-02-01

    Beginning with work in the 1950s at the first generation of research reactors, studies of hydrogen-bonded systems have been a prime application for single-crystal neutron diffraction. The range of systems studied was extended in the 1960s and 1970s, with the advent of high flux reactor sources, and beginning around 1980 studies at pulsed neutron sources have made increasingly important contributions. Recently at the Argonne Intense Pulsed Neutron Source (IPNS), working with collaborators, we completed two studies of hydrogen-bonded systems that will serve to illustrate topics of current interest. In the first study, on andrographolide, an active diterpenoid natural product, our neutron diffraction results definitively characterize the hydrogen-bonding interactions. The second IPNS study is on tetraacetylethane (TAE), a β-diketone enol system with a very short, strong intramolecular O-H⋯O hydrogen bond. At IPNS, we have determined the neutron crystal structure of TAE at five temperatures between 20 and 298 K to investigate changes in the structure with temperature and to probe for disorder. Despite the successes illustrated by the two examples presented here and by many other studies, at present applications of single-crystal neutron diffraction continue to be extremely flux limited and constrained by the requirement for mm-size crystals for many problems. These limitations are being addressed through the realization of powerful instruments at a new generation of pulsed neutron sources, including in the USA the TOPAZ and MaNDi single-crystal diffractometers that are under development at the Spallation Neutron Source (SNS).

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

    Institute of Scientific and Technical Information of China (English)

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

    2001-01-01

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

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

    Science.gov (United States)

    Tutughamiarso, Maya; Wagner, Guido; Egert, Ernst

    2012-08-01

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

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

    OpenAIRE

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

    2013-01-01

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

  10. 2D-IR spectroscopy of hydrogen-bond-mediated vibrational excitation transfer.

    Science.gov (United States)

    Chuntonov, Lev

    2016-05-18

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

  11. Controlling Secondary Structures of Bio-Polymers with Hydrogen-Like Bonding

    OpenAIRE

    J. Krawczyk; Owczarek, A. L.; Prellberg, T.; Rechnitzer, A.

    2007-01-01

    We present results for a lattice model of bio-polymers where the type of $\\beta$-sheet formation can be controlled by different types of hydrogen bonds depending on the relative orientation of close segments of the polymer. Tuning these different interaction strengths leads to low-temperature structures with different types of orientational order. We perform simulations of this model and so present the phase diagram, ascertaining the nature of the phases and the order of the transitions betwe...

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

    Science.gov (United States)

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

    1993-09-01

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

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

    Science.gov (United States)

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

    2015-12-10

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Yokoyama, Takeshi, E-mail: tyokoya3@pha.u-toyama.ac.jp; Mizuguchi, Mineyuki; Nabeshima, Yuko [University of Toyama, 2630 Sugitani, Toyama 930-0914 (Japan); Kusaka, Katsuhiro; Yamada, Taro [Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan); Hosoya, Takaaki [Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan); Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511 (Japan); Ohhara, Takashi [Comprehensive Research Organization for Science and Society, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan); Kurihara, Kazuo [Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195 (Japan); Tanaka, Ichiro [Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan); Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511 (Japan); Niimura, Nobuo [Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106 (Japan)

    2013-11-01

    The neutron crystal structure of human transthyretin is presented. Transthyretin (TTR) is a tetrameric protein. TTR misfolding and aggregation are associated with human amyloid diseases. Dissociation of the TTR tetramer is believed to be the rate-limiting step in the amyloid fibril formation cascade. Low pH is known to promote dissociation into monomer and the formation of amyloid fibrils. In order to reveal the molecular mechanisms underlying pH sensitivity and structural stabilities of TTR, neutron diffraction studies were conducted using the IBARAKI Biological Crystal Diffractometer with the time-of-flight method. Crystals for the neutron diffraction experiments were grown up to 2.5 mm{sup 3} for four months. The neutron crystal structure solved at 2.0 Å revealed the protonation states of His88 and the detailed hydrogen-bond network depending on the protonation states of His88. This hydrogen-bond network is involved in monomer–monomer and dimer–dimer interactions, suggesting that the double protonation of His88 by acidification breaks the hydrogen-bond network and causes the destabilization of the TTR tetramer. Structural comparison with the X-ray crystal structure at acidic pH identified the three amino acid residues responsible for the pH sensitivity of TTR. Our neutron model provides insights into the molecular stability related to amyloidosis.

  15. 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.

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

    Institute of Scientific and Technical Information of China (English)

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

    2006-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2006-01-01

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

  18. 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.

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

    Science.gov (United States)

    Chipman, Daniel M

    2006-01-28

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

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

    Science.gov (United States)

    Kacar, Gokhan; de With, Gijsbertus

    2016-04-14

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-08-01

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

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

    Science.gov (United States)

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

    2002-12-01

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

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

    CERN Document Server

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

    2003-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-07-01

    The hydrogen bond and π-π stacking are two non-covalent interactions able to support cooperative magnetic ordering between paramagnetic centers. This contribution reports the crystal structure and related magnetic properties for VO[Fe(CN)5NO]·2H2O, which has a layered structure. This solid crystallizes with an orthorhombic unit cell, in the Pna21 space group, with cell parameters a=14.1804(2), b=10.4935(1), c=7.1722(8) Å and four molecules per unit cell (Z=4). Its crystal structure was solved and refined from powder X-ray diffraction data. Neighboring layers remain linked through a network of hydrogen bonds involving a water molecule coordinated to the axial position for the V atom and the unbridged axial NO and CN ligands. An uncoordinated water molecule is found forming a triple bridge between these last two ligands and the coordinated water molecule. The magnetic measurements, recorded down to 2 K, shows a ferromagnetic interaction between V atoms located at neighboring layers, with a Curie-Weiss constant of 3.14 K. Such ferromagnetic behavior was interpreted as resulting from a superexchange interaction through the network of strong OH····OH2O, OH····NCN, and OH····ONO hydrogen bonds that connects neighboring layers. The interaction within the layer must be of antiferromagnetic nature and it was detected close to 2 K.

  6. The Contrasting Character of Early and Late Transition Metal Fluorides as Hydrogen Bond Acceptors.

    Science.gov (United States)

    Smith, Dan A; Beweries, Torsten; Blasius, Clemens; Jasim, Naseralla; Nazir, Ruqia; Nazir, Sadia; Robertson, Craig C; Whitwood, Adrian C; Hunter, Christopher A; Brammer, Lee; Perutz, Robin N

    2015-09-16

    The association constants and enthalpies for the binding of hydrogen bond donors to group 10 transition metal complexes featuring a single fluoride ligand (trans-[Ni(F)(2-C5NF4)(PR3)2], R = Et 1a, Cy 1b, trans-[Pd(F)(4-C5NF4)(PCy3)2] 2, trans-[Pt(F){2-C5NF2H(CF3)}(PCy3)2] 3 and of group 4 difluorides (Cp2MF2, M = Ti 4a, Zr 5a, Hf 6a; Cp*2MF2, M = Ti 4b, Zr 5b, Hf 6b) are reported. These measurements allow placement of these fluoride ligands on the scales of organic H-bond acceptor strength. The H-bond acceptor capability β (Hunter scale) for the group 10 metal fluorides is far greater (1a 12.1, 1b 9.7, 2 11.6, 3 11.0) than that for group 4 metal fluorides (4a 5.8, 5a 4.7, 6a 4.7, 4b 6.9, 5b 5.6, 6b 5.4), demonstrating that the group 10 fluorides are comparable to the strongest organic H-bond acceptors, such as Me3NO, whereas group 4 fluorides fall in the same range as N-bases aniline through pyridine. Additionally, the measurement of the binding enthalpy of 4-fluorophenol to 1a in carbon tetrachloride (-23.5 ± 0.3 kJ mol(-1)) interlocks our study with Laurence's scale of H-bond basicity of organic molecules. The much greater polarity of group 10 metal fluorides than that of the group 4 metal fluorides is consistent with the importance of pπ-dπ bonding in the latter. The polarity of the group 10 metal fluorides indicates their potential as building blocks for hydrogen-bonded assemblies. The synthesis of trans-[Ni(F){2-C5NF3(NH2)}(PEt3)2], which exhibits an extended chain structure assembled by hydrogen bonds between the amine and metal-fluoride groups, confirms this hypothesis.

  7. Silver-catalyzed silicon-hydrogen bond functionalization by carbene insertion.

    Science.gov (United States)

    Iglesias, M José; Nicasio, M Carmen; Caballero, Ana; Pérez, Pedro J

    2013-01-28

    The catalytic functionalization of silicon-hydrogen bonds by means of the insertion of carbene units :CHCO(2)Et from ethyl diazoacetate (EDA) has been achieved using a silver-based catalyst, constituting the first example of this metal to promote this transformation. Competition experiments have revealed that the relative reactivity of substituted silanes depends on the bond dissociation energy of the Si-H bond (tertiary > secondary > primary for ethyl substituted). In the presence of bulky substituents such order reverts to secondary > primary ≈ tertiary (for phenyl substituted). Screening with other diazo compounds has shown that N(2)C(Ph)CO(2)Et displays similar reactivity to that of EDA, whereas other N(2)C(R)CO(2)Et (R = Me, CO(2)Et) gave lower conversions. PMID:23114570

  8. Hydrogen-bonded complexes of 2-aminopyrimidine-parabenzoquinone in an argon matrix

    Science.gov (United States)

    Plokhotnichenko, A. M.; Stepanian, S. G.; Karachevtsev, V. A.; Adamowicz, L.

    2006-02-01

    The H-bonded complexes of 2-aminopyrimidine (NH2Py) with parabenzoquinone (Qu) in a low-temperature argon matrix are investigated by the method of IR spectroscopy. The IR absorption spectra in the spectral range 400-3600cm-1 are obtained for different concentration ratios of these compounds at a temperature of 11K. The molar integrated absorption coefficients in the bands of the stretching modes of the free and H-bonded NH2 group are determined. Quantum-mechanical calculations of the IR spectra of the NH2Py and Qu molecules and their dimers are carried out. A comparison of the experimental and calculated results permits the conclusion that NH2Py-Qu dimers in an argon matrix have a planar structure with two weak hydrogen bonds, NH ⋯O and CH ⋯N.

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

    Science.gov (United States)

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

    2016-08-01

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

  10. Estimation of Abraham solvation equation coefficients for hydrogen bond formation from Abraham solvation parameters for solute acidity and basicity.

    Science.gov (United States)

    van Noort, Paul

    2013-01-01

    Abraham solvation equations find widespread use in environmental chemistry and pharmaco-chemistry. The coefficients in these equations, which are solvent (system) descriptors, are usually determined by fitting experimental data. To simplify the determination of these coefficients in Abraham solvation equations, this study derives equations, based on Abraham solvation parameters for hydrogen acidity and basicity of the solvents involved, to estimate the value of the coefficients for hydrogen bond formation. These equations were applied to calculate Abraham solvation parameters for hydrogen acidity and basicity for polyoxymethylene, polyacrylate, sodium dodecylsulfate, some ionic liquids, alkanoyl phosphatidyl cholines, and lipids for which fitted values for Abraham coefficients for hydrogen bond formation were available. PMID:22892357

  11. Electronic structure of planar-quasicycled organic molecules with intramolecular hydrogen bond

    Directory of Open Access Journals (Sweden)

    ALEXEI N. PANKRATOV

    2007-03-01

    Full Text Available By means of the HF/6-311G(d,p method, the electronic structure of the series of organic molecules, among which are malonaldehyde, acetylacetone, thiomalonaldehyde,’the derivatives of aniline 2-XC6H4NH2, phenol 2-XC6H4OH, benzenethiol 2-XC6H4SH (X = CHO, COOH, COO-, NO, NO2, OH, OCH3, SH, SCH3, F, Cl, Br, 8-hydroxyquinoline, 8-mercaptoquinoline, tropolone, has been studied. The intramolecular hydrogen bond (IHB has been established to lead to a local electron redistribution in quasicycle, and primarily to the electron density transfer between the direct IHB participants – from the hydrogen atom toward the proton-aceptor atom. On forming the IHB of the S–H···O type, the electron density in general decreases on the sulphohydryl hydrogen atom and increases on the sulphur atom.

  12. Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics.

    Science.gov (United States)

    Lee, Hyelee; Fischer, Marcus; Shoichet, Brian K; Liu, Shih-Yuan

    2016-09-21

    Protein crystallography and calorimetry were used to characterize the binding of 1,2-azaborines to model cavities in T4 lysozyme in direct comparison to their carbonaceous counterparts. In the apolar L99A cavity, affinity for Ab dropped only slightly versus benzene. In the cavity designed to accommodate a single hydrogen bond (L99A/M102Q), Gln102═O···H-N hydrogen bonding for Ab and BEtAb was observed in the crystallographic complexes. The strength of the hydrogen bonding was estimated as 0.94 and 0.64 kcal/mol for Ab and BEtAb, respectively. This work unambiguously demonstrates that 1,2-azaborines can be readily accommodated in classic aryl recognition pockets and establishes one of 1,2-azaborine's distinguishing features from its carbonaceous isostere benzene: its ability to serve as an NH hydrogen bond donor in a biological setting. PMID:27603116

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

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

  15. Hydrogen bonds in 1-indanone: Charge density analysis and simulation of the inelastic neutron scattering spectrum in solid phase

    International Nuclear Information System (INIS)

    The influence of the intermolecular interactions on the vibrational dynamics of 1-indanone has been checked by simulating the INS spectrum from molecular and DFT periodic calculations, showing that, even in the case of weak hydrogen bonds, those modes associated with lower energy transfer are affected in the solid state. The electron charge distribution of solid 1-indanone has also been studied from a DFT periodic calculation. In order to obtain some insight into the intermolecular interactions Bader's atoms in molecules theory has been used. After a careful analysis of the topological properties of the calculated electron density, bond paths, critical points and other related properties, most of the C-H...π and C-H...O weak hydrogen bonds predicted in the experimental X-ray structure are confirmed. In addition some new H?H interactions were found. Furthermore, a natural bond orbital analysis was performed describing each hydrogen bond as donor-acceptor interactions

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

    Science.gov (United States)

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

    2006-06-01

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

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

    Science.gov (United States)

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

    2013-05-01

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

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

    International Nuclear Information System (INIS)

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

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

    Indian Academy of Sciences (India)

    INES RIGANE; SIWAR WALHA; ABDELHAMID BEN SALAH

    2016-09-01

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

  20. Structural, hydrogen bonding and in situ studies of the effect of hydrogen dilution on the passivation by amorphous silicon of n-type crystalline (100) silicon surfaces

    OpenAIRE

    Meddeb, H.; Bearda, T.; Abdelraheem, Y.; Ezzaouia, H.; Gordon, I.; Szlufcik, J.; Poortmans, Jef

    2015-01-01

    Hydrogenated amorphous silicon (a-Si : H) layers deposited by chemical vapour deposition provide an attractive route to achieve high-performance crystalline silicon (c-Si) solar cells due to their deposition at low temperatures and their superior passivation quality. Hydrogen certainly plays an additional crucial role by passivating the dangling bonds, and thus improving the electrical and optical properties. In this work, we present the variation of the effective lifetime with the hydrogen d...

  1. Ice Regelation: Hydrogen-bond extraordinary recoverability and water quasisolid-phase-boundary dispersivity

    Science.gov (United States)

    Zhang, Xi; Huang, Yongli; Sun, Peng; Liu, Xinjuan; Ma, Zengsheng; Zhou, Yichun; Zhou, Ji; Zheng, Weitao; Sun, Chang Q.

    2015-09-01

    Regelation, i.e., ice melts under compression and freezes again when the pressure is relieved, remains puzzling since its discovery in 1850’s by Faraday. Here we show that hydrogen bond (O:H-O) cooperativity and its extraordinary recoverability resolve this anomaly. The H-O bond and the O:H nonbond possesses each a specific heat ηx(T/ΘDx) whose Debye temperature ΘDx is proportional to its characteristic phonon frequency ωx according to Einstein’s relationship. A superposition of the ηx(T/ΘDx) curves for the H-O bond (x = H, ωH ~ 3200 cm-1) and the O:H nonbond (x = L, ωL ~ 200 cm-1, ΘDL = 198 K) yields two intersecting temperatures that define the liquid/quasisolid/solid phase boundaries. Compression shortens the O:H nonbond and stiffens its phonon but does the opposite to the H-O bond through O-O Coulomb repulsion, which closes up the intersection temperatures and hence depress the melting temperature of quasisolid ice. Reproduction of the Tm(P) profile clarifies that the H-O bond energy EH determines the Tm with derivative of EH = 3.97 eV for bulk water and ice. Oxygen atom always finds bonding partners to retain its sp3-orbital hybridization once the O:H breaks, which ensures O:H-O bond recoverability to its original state once the pressure is relieved.

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

    Science.gov (United States)

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

    2014-06-01

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

  3. Electronic structure, stacking energy, partial charge, and hydrogen bonding in four periodic B-DNA models

    Science.gov (United States)

    Poudel, Lokendra; Rulis, Paul; Liang, Lei; Ching, W. Y.

    2014-08-01

    We present a theoretical study of the electronic structure of four periodic B-DNA models labeled (AT)10,(GC)10, (AT)5(GC)5, and (AT-GC)5 where A denotes adenine, T denotes thymine, G denotes guanine, and C denotes cytosine. Each model has ten base pairs with Na counterions to neutralize the negative phosphate group in the backbone. The (AT)5(GC)5 and (AT-GC)5 models contain two and five AT-GC bilayers, respectively. When compared against the average of the two pure models, we estimate the AT-GC bilayer interaction energy to be 19.015 Kcal/mol, which is comparable to the hydrogen bonding energy between base pairs obtained from the literature. Our investigation shows that the stacking of base pairs plays a vital role in the electronic structure, relative stability, bonding, and distribution of partial charges in the DNA models. All four models show a highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) gap ranging from 2.14 to 3.12 eV with HOMO states residing on the PO4 + Na functional group and LUMO states originating from the bases. Our calculation implies that the electrical conductance of a DNA molecule should increase with increased base-pair mixing. Interatomic bonding effects in these models are investigated in detail by analyzing the distributions of the calculated bond order values for every pair of atoms in the four models including hydrogen bonding. The counterions significantly affect the gap width, the conductivity, and the distribution of partial charge on the DNA backbone. We also evaluate quantitatively the surface partial charge density on each functional group of the DNA models.

  4. Discovery of a red and blue shifted iron disk line in the galactic jet source GRO J1655-40

    CERN Document Server

    Balucinska-Church, M

    1999-01-01

    We report the discovery of emission features in the X-ray spectrum of GRO J1655-40 obtained with RXTE during the observation of 1997, Feb 26. We have fitted the features firstly by two Gaussian lines which in four spectra analysed have average energies of 5.85 +/- 0.08 keV and 7.32 +/- 0.13 keV, strongly suggestive that these are the red and blue shifted wings of an iron disk line. These energies imply a velocity of ~0.33 c. The blue wing is less bright than in the calculated profiles of disk lines near a black hole subject to Doppler boosting, however known Fe absorption lines in GRO J1655-40 at energies between ~7 and 8 keV can reduce the apparent brightness of the blue wing. Secondly, we have fitted the spectra using the disk line model of Laor based on a full relativistic treatment plus an absorption line, and show that good fits are obtained. This gives a restframe energy of the disk line between 6.4 and 6.8 keV indicating that the line is iron K_alpha emission probably of significantly ionized material....

  5. Neutron Crystallography, Molecular Dynamics, and Quantum Mechanics Studies of the Nature of Hydrogen Bonding in Cellulose I beta

    Science.gov (United States)

    In the crystal structure of cellulose Ibeta, disordered hydrogen (H) bonding can be represented by the average of two mutually exclusive H bonding schemes that have been designated A and B. An unanswered question is whether A and B interconvert dynamically, or whether they are static but present in ...

  6. Vibrational dephasing in ionic liquids as a signature of hydrogen bonding.

    Science.gov (United States)

    Chatzipapadopoulos, Susana; Zentel, Tobias; Ludwig, Ralf; Lütgens, Matthias; Lochbrunner, Stefan; Kühn, Oliver

    2015-08-24

    Understanding both structure and dynamics is crucial for producing tailor-made ionic liquids (ILs). We studied the vibrational and structural dynamics of medium versus weakly hydrogen-bonded CH groups of the imidazolium ring in ILs of the type [1-alkyl-3-methylimidazolium][bis(trifluoromethanesulfonyl)imide] ([Cn mim][NTf2 ]), with n=1, 2, and 8, by time-resolved coherent anti-Stokes Raman scattering (CARS) and quantum-classical hybrid (QCH) simulations. From the time series of the CARS spectra, dephasing times were extracted by modeling the full nonlinear response. From the QCH calculations, pure dephasing times were obtained by analyzing the distribution of transition frequencies. Experiments and calculations reveal larger dephasing rates for the vibrational stretching modes of C(2)H compared with the more weakly hydrogen-bonded C(4,5)H. This finding can be understood in terms of different H-bonding motifs and the fast interconversion between them. Differences in population relaxation rates are attributed to Fermi resonance interactions. PMID:26175228

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

    Science.gov (United States)

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

    2016-01-01

    The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice. Project supported by the National Natural Science Foundation of China (Grant Nos. 11275008, 91021007, and 10974012) and the China Postdoctoral Science Foundation (Grant No. 2014M550005).

  8. On the Importance of CP-corrected Gradient Optimization in the Study of Hydrogen Bonded Systems

    Institute of Scientific and Technical Information of China (English)

    王伟周; 蒲雪梅; 郑文旭; 黄宁表; 田安民

    2003-01-01

    Geometries, harmonic vibrational frequencies and interaction energies of the water-hydrogen sulfide dimer, hydrogen fluoride dimer and glycine zwitterion-water dimer were determined by the counterpoise-corrected (CP-corrected) gradient optimization that explicitly corrects for the basis set superpusition error (BSSE) and CP-uncorrected (normal) gradient opfimization respectively at the B3LYP and MP2 levels of theory, employing the popular Pople's standard 6-31G(d), 6-31G(d,p) and 6-311+ +G(d,p) basis sets in order to assess the importance of CP-corrected gradient optimiTation in the study of hydrogen bonded systems. The normal optimization of these three H-bonded systems obtained using these popular basis sets all yielded erratic results, whereas use of CP-corrected gradient optimization led to consistent results with those from larger basis sets. So this CP receipt becomes useful and necessary to correctly describe large systems, where the use of small basis sets may be necessary.

  9. Molecular dynamics simulation of the formation of sp3 hybridized bonds in hydrogenated diamondlike carbon deposition processes.

    Science.gov (United States)

    Murakami, Yasuo; Horiguchi, Seishi; Hamaguchi, Satoshi

    2010-04-01

    The formation process of sp3 hybridized carbon networks (i.e., diamondlike structures) in hydrogenated diamondlike carbon (DLC) films has been studied with the use of molecular-dynamics simulations. The processes simulated in this study are injections of hydrocarbon (CH3 and CH) beams into amorphous carbon (a-C) substrates. It has been shown that diamondlike sp3 structures are formed predominantly at a subsurface level when the beam energy is relatively high, as in the "subplantation" process for hydrogen-free DLC deposition. However, for hydrogenated DLC deposition, the presence of abundant hydrogen at subsurface levels, together with thermal spikes caused by energetic ion injections, substantially enhances the formation of carbon-to-carbon sp3 bonds. Therefore, the sp3 bond formation process for hydrogenated DLC films essentially differs from that for hydrogen-free DLC films.

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

    Directory of Open Access Journals (Sweden)

    Dallakyan Sargis

    2008-08-01

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

  11. Dynamical Binding of Hydrogen Bond Surrogate-Derived Bak Helices to Anti-apoptotic Protein Bcl-xL

    OpenAIRE

    Bao, Ju; Dong, Xiao Y.; John Z. H. Zhang; Arora, Paramjit S.

    2009-01-01

    A new peptide modification strategy was recently developed to replace the i to i+4 hydrogen bond of the main chain of an a-helix with a carbon-carbon covalent bond to afford highly stable constrained α-helices, termed Hydrogen Bond Surrogate (HBS) helices. HBS helices that mimic the Bak BH3 domains were experimentally demonstrated to target protein Bcl-xL with high affinity. In this study, molecular dynamics (MD) simulation is used to understand how the covalent modification of the natural Ba...

  12. The blue shift

    Energy Technology Data Exchange (ETDEWEB)

    Berner, Joachim

    2010-07-01

    Established coating companies have strongly expanded their production capacities and new players have started up production. Further companies are working on new absorber coatings. Bluetec is meanwhile setting up a second line of business outside the sector.

  13. B-H···π Interaction: A New Type of Nonclassical Hydrogen Bonding.

    Science.gov (United States)

    Zhang, Xiaolei; Dai, Huimin; Yan, Hong; Zou, Wenli; Cremer, Dieter

    2016-04-01

    For the first time, nonclassical hydrogen (H)-bonding involving a B-H···π interaction is described utilizing both quantum chemical predictions and experimental realization. In the gas phase, a B-H···π H-bond is observed in either B2H6···benzene (ΔE = -5.07 kcal/mol) or carborane···benzene (ΔE = -3.94 kcal/mol) complex at reduced temperatures. Ir-dimercapto-carborane complexes [Cp*Ir(S2C2B10H10)] are designed to react with phosphines PR3 (R = C6H4X, X = H, F, OMe) to give [Cp*Ir(PR3)S2C2B10H10] for an investigation of B-H···π interactions at ambient temperatures. X-ray diffraction studies reveal that the interaction between the carborane BH bonds and the phosphine aryl substituents involves a BH···π H-bond (H···π distance: 2.40-2.76 Å). (1)H NMR experiments reveal that B-H···π interactions exist in solution according to measured (1)H{(11)B} signals at ambient temperatures in the range 0.0 ≤ δ ≤ 0.3 ppm. These are high-field shifted by more than 1.5 ppm relative to the (1)H{(11)B} signals obtained for the PMe3 analog without B-H···π bonding. Quantum chemical calculations suggest that the interaction is electrostatic and the local (B)H···ring stretching force constant is as large as the H-bond stretching force constant in the water dimer. PMID:26910602

  14. Hydrogen-bonding interactions in thiosemicarbazones of carboxylic acids: Structure of 2-ketobutyric acid thiosemicarbazone hemihydrate

    International Nuclear Information System (INIS)

    2-Thiosemicarbazonobutanoic acid hemihydrate, C5H9N3O2S.0.5H2O, Mr=184.22, triclinic, Panti 1, a=8.163(2), b=8.868(2), c=12.438(2) A, α=72.99(2), β=79.47(2), γ=84.06(2)deg, V=845.3(3) A3, Z=4, Dx=1.447 Mg m-3, λ(Mo Kα)=0.71073 A, μ=0.332 mm-1, F(000)=392, T=296 K, R=0.038 for 3830 independent reflections with I>3σ(I). Three hydrogen bonds link the two crystallographically independent molecules in a pairwise fashion. The two molecules both have E configurations about each C-N and N-N bond, but differ by nearly 180deg in the orientation of the -COOH group. (orig.)

  15. Stretchable gas barrier achieved with partially hydrogen-bonded multilayer nanocoating.

    Science.gov (United States)

    Holder, Kevin M; Spears, Benjamin R; Huff, Molly E; Priolo, Morgan A; Harth, Eva; Grunlan, Jaime C

    2014-05-01

    Super gas barrier nanocoatings are recently demonstrated by combining polyelectrolytes and clay nanoplatelets with layer-by-layer deposition. These nanobrick wall thin films match or exceed the gas barrier of SiOx and metallized films, but they are relatively stiff and lose barrier with significant stretching (≥ 10% strain). In an effort to impart stretchability, hydrogen-bonding polyglycidol (PGD) layers are added to an electrostatically bonded thin film assembly of polyethylenimine (PEI) and montmorillonite (MMT) clay. The oxygen transmission rate of a 125-nm thick PEI-MMT film increases more than 40x after being stretched 10%, while PGD-PEI-MMT trilayers of the same thickness maintain its gas barrier. This stretchable trilayer system has an OTR three times lower than the PEI-MMT bilayer system after stretching. This report marks the first stretchable high gas barrier thin film, which is potentially useful for applications that require pressurized elastomers. PMID:24700525

  16. Hydrogen-induced rupture of strained Si─O bonds in amorphous silicon dioxide.

    Science.gov (United States)

    El-Sayed, Al-Moatasem; Watkins, Matthew B; Grasser, Tibor; Afanas'ev, Valery V; Shluger, Alexander L

    2015-03-20

    Using ab initio modeling we demonstrate that H atoms can break strained Si─O bonds in continuous amorphous silicon dioxide (a-SiO(2)) networks, resulting in a new defect consisting of a threefold-coordinated Si atom with an unpaired electron facing a hydroxyl group, adding to the density of dangling bond defects, such as E' centers. The energy barriers to form this defect from interstitial H atoms range between 0.5 and 1.3 eV. This discovery of unexpected reactivity of atomic hydrogen may have significant implications for our understanding of processes in silica glass and nanoscaled silica, e.g., in porous low-permittivity insulators, and strained variants of a-SiO(2). PMID:25839289

  17. Reorientation of Isomeric Butanols: The Multiple Effects of Steric Bulk Arrangement on Hydrogen-Bond Dynamics.

    Science.gov (United States)

    Mesele, Oluwaseun O; Vartia, Anthony A; Laage, Damien; Thompson, Ward H

    2016-03-01

    Molecular dynamics simulations are used to investigate OH reorientation in the four isomeric butanols in their bulk liquid state to examine the influence of the arrangement of the steric bulk on the alcohol reorientational and hydrogen-bond (H-bond) dynamics. The results are interpreted within the extended jump model in which the OH reorientation is decomposed into contributions due to "jumps" between H-bond partners and "frame" reorientation of the intact H-bonded pair. Reorientation is fastest in iso-butanol and slowest in tert-butanol, while sec- and n-butanol have similar reorientation times. This latter result is a fortuitous cancellation between the jump and frame reorientation in the two alcohols. The extended jump model is shown to provide a quantitative description of the OH reorientation times. A detailed analysis of the jump times shows that a combination of entropic, enthalpic, and dynamical factors, including transition state recrossing effects, all play a role. A simple model based on the liquid structure is proposed to estimate the energetic and entropic contributions to the jump time. This represents the groundwork for a predictive model of OH reorientation in alcohols, but additional studies are required to better understand the frame reorientation and transition state recrossing effects.

  18. Isomorphous Crystals from Diynes and Bromodiynes Involved in Hydrogen and Halogen Bonds

    Directory of Open Access Journals (Sweden)

    Pierre Baillargeon

    2016-04-01

    Full Text Available Isomorphous crystals of two diacetylene derivatives with carbamate functionality (BocNH-CH2-diyne-X, where X = H or Br have been obtained. The main feature of these structures is the original 2D arrangement (as supramolecular sheets or walls in which the H bond and halogen bond have a prominent effect on the whole architecture. The two diacetylene compounds harbor neighboring carbamate (Boc protected amine and conjugated alkyne functionalities. They differ only by the nature of the atom located at the penultimate position of the diyne moiety, either a hydrogen atom or a bromine atom. Both of them adopt very similar 2D wall organizations with antiparallel carbamates (as in antiparallel beta pleated sheets. Additional weak interactions inside the same walls between molecular bricks are H bond interactions (diyne-H···O=C or halogen bond interactions (diyne-Br···O=C, respectively. Based on crystallographic atom coordinates, DFT (B3LYP/6-31++G(d,p and DFT (M06-2X/6-31++G(d,p calculations were performed on these isostructural crystals to gain insight into the intermolecular interactions.

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

    Science.gov (United States)

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

    2010-04-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

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

    OpenAIRE

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

    2001-01-01

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

  2. Innovative Catalysis in Organic Synthesis Oxidation, Hydrogenation, and C-X Bond Forming Reactions

    CERN Document Server

    Andersson, Pher G

    2012-01-01

    Authored by a European team of leaders in the field, this book compiles innovative approaches for C-X bond forming processes frequently applied in organic synthesis. It covers all key types of catalysis, including homogeneous, heterogeneous, and organocatalysis, as well as mechanistic and computational studies. Special attention is focused on the improvement of efficiency and sustainability of important catalytic processes, such as selective oxidations, hydrogenation and cross-coupling reactions.The result is a valuable resource for both advanced researchers in academia and industry, as well a

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

    International Nuclear Information System (INIS)

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2003-01-01

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

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

    Science.gov (United States)

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

    2003-09-01

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

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

    Science.gov (United States)

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

    2002-03-01

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

  7. 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.

  8. Hydrogen bond removal of pterin derivative whose structure is similar to nucleic acid bases.

    Science.gov (United States)

    Nonogawa, Mitsuru; Arai, Toshiyuki; Endo, Nobuyuki; Pack, Seung Pil; Kodaki, Tsutomu; Makino, Keisuke

    2005-01-01

    Pterin, an analog of guanine, is an electron transfer compound in biological systems. Among the analogs, 6-formylpterin (6FP) has been demonstrated to have many marked physiological and pharmacological activities and it is, therefore, worthwhile to elucidate whole mechanism of its activities. Unfortunately, however, 6FP is hardly soluble in water and organic solvents. Like nucleic acid bases, 6FP makes intermolecular hydrogen bonds and forms stacking structure causing such drawback nature. This has made mechanistic studies on 6FP activities extremely difficult. In this study, we carried out derivatization for 6FP and succeeded in increasing water solubility with maintaining its physiological activities. PMID:17150758

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

    Science.gov (United States)

    Paarmann, Alexander

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

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

    Indian Academy of Sciences (India)

    Lalit Rajput; Madhushree Sarkar; Kumar Biradha

    2010-09-01

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

  11. Statistics and Dynamics for the Aa-Dd Type hydrogen Bonding System

    Institute of Scientific and Technical Information of China (English)

    王海军; 洪晓钟; 巴信武

    2003-01-01

    The kinetics and dynamics for the growth of hydrogen bonding clusters in the Aa-Dd system are considered. The explicit relations between conversions of proton-acceptors and proton-donors and Gibbs free energy are deduced,and then the sol-gel phase transition is predicted to take place and the generalized scaling laws satisfied by the k-th moment and k-th radius near the critical point are given. The conclusions obtained from which are consistent with the statistical descriptions on the system under investigation.

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

    Institute of Scientific and Technical Information of China (English)

    Zeper Abliz; Hiroshi Moriyama; Junji Aoki; Toyotoshi Ueda

    1996-01-01

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

  13. Bonding titanium on multi-walled carbon nanotubes for hydrogen storage: An electrochemical approach

    Energy Technology Data Exchange (ETDEWEB)

    Brieno-Enriquez, K.M.; Ledesma-Garcia, J. [Centro de Investigacion y Desarrollo Tecnologico en Electroquimica, S.C., Parque Tecnologico Queretaro-Sanfandila, Pedro Escobedo, Qro, C.P. 76703 (Mexico); Perez-Bueno, J.J., E-mail: jperez@cideteq.mx [Centro de Investigacion y Desarrollo Tecnologico en Electroquimica, S.C., Parque Tecnologico Queretaro-Sanfandila, Pedro Escobedo, Qro, C.P. 76703 (Mexico); Godinez, Luis A. [Centro de Investigacion y Desarrollo Tecnologico en Electroquimica, S.C., Parque Tecnologico Queretaro-Sanfandila, Pedro Escobedo, Qro, C.P. 76703 (Mexico); Terrones, H. [Instituto Potosino de Investigacion Cientifica y Tecnologica, Division de Materiales Avanzados, Camino a la Presa San Jose 2055, Col. Lomas 4o Seccion C.P. 78216, San Luis Potosi (Mexico); Angeles-Chavez, C. [Instituto Mexicano del Petroleo, Programa de Ingenieria Molecular, Eje Central Lazaro Cardenas 152, A.P. 14-805, 07730 Mexico D.F. (Mexico)

    2009-06-15

    This work explores the use of some procedures, involving electrochemistry, in order to bond atomic Ti on the outer surface of multi-walled carbon nanotubes (MWNTs). It is assumed that each titanium atom has the potential of host up to four hydrogen molecules and relinquish them by heated. As a way to spread and stick nanotubes on an electrode, a tested route was drying a solution with nanotubes on a glassy carbon flat electrode. The MWNTs were treated by anodic polarization in organic media. Dichloromethane was selected as the medium and titanium tetrachloride as the precursor for attaching atomic Ti onto the nanotubes. The hydrogen adsorption, estimated from voltamperometry was five times higher on Ti-MWNTs that on bare nanotubes. The use of anodic polarization during the preparation of Ti-MWNTs may represent great significance in procedure, which was manifest during the voltamperometric evaluation of samples.

  14. Effects of dimethyl sulfoxide on the hydrogen bonding structure and dynamics of aqueous N-methylacetamide solution

    Indian Academy of Sciences (India)

    APRAMITA CHAND; SNEHASIS CHOWDHURI

    2016-06-01

    Effects of dimethyl-sulfoxide (DMSO) on the hydrogen bonding structure and dynamics in aqueousN-methylacetamide (NMA) solution are investigated by classical molecular dynamics simulations. Themodifications of structure and interaction between water and NMA in presence of DMSO molecules are calculatedby various site-site radial distribution functions and average interaction energies between these speciesin the solution. It is observed that the aqueous peptide hydrogen bond interaction is relatively stronger withincreasing concentration of DMSO, whereas methyl-methyl interaction between NMA and DMSO decreasessignificantly. The DMSO molecule prefers to interact with amide-hydrogen of NMA even at lower DMSO concentration.The lifetimes and structural-relaxation times of NMA-water, water-water and DMSO-water hydrogenbonds are found to increase with increasing DMSO concentration in the solution. The slower translationaland rotational dynamics of NMA is observed in concentrated DMSO solution due to formation of strongerinter-species hydrogen bonds in the solution.

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

    Science.gov (United States)

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

    2016-11-01

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

  16. Theoretical modeling of infrared spectra of the hydrogen and deuterium bond in aspirin crystal

    Science.gov (United States)

    Ghalla, Houcine; Rekik, Najeh; Michta, Anna; Oujia, Brahim; Flakus, Henryk T.

    2010-01-01

    An extended quantum theoretical approach of the ν IR lineshape of cyclic dimers of weakly H-bonded species is proposed. We have extended a previous approach [M.E.-A. Benmalti, P. Blaise, H.T. Flakus, O. Henri-Rousseau, Chem. Phys. 320 (2006) 267] by accounting for the anharmonicity of the slow mode which is described by a "Morse" potential in order to reproduce the polarized infrared spectra of the hydrogen and deuterium bond in acetylsalicylic acid (aspirin) crystals. From comparison of polarized IR spectra of isotopically neat and isotopically diluted aspirin crystals it resulted that centrosymmetric aspirin dimer was the bearer of the crystal main spectral properties. In this approach, the adiabatic approximation is performed for each separate H-bond bridge of the dimer and a strong non-adiabatic correction is introduced into the model via the resonant exchange between the fast mode excited states of the two moieties. Within the strong anharmonic coupling theory, according to which the X-H→⋯Y high-frequency mode is anharmonically coupled to the H-bond bridge, this model incorporated the Davydov coupling between the excited states of the two moieties, the quantum direct and indirect dampings and the anharmonicity for the H-bond bridge. The spectral density is obtained within the linear response theory by Fourier transform of the damped autocorrelation functions. The evaluated spectra are in fairly good agreement with the experimental ones by using a minimum number of independent parameters. The effect of deuteration has been well reproduced by reducing simply the angular frequency of the fast mode and the anharmonic coupling parameter.

  17. Doping dependent blue shift and linewidth broadening of intersubband absorption in non-polar m-plane AlGaN/GaN multiple quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Kotani, Teruhisa, E-mail: tkotani@iis.u-tokyo.ac.jp [Institute for Nano Quantum Information Electronics, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Advanced Technology Research Laboratories, Sharp Corporation, 2613-1 Ichinomoto-cho, Tenri, Nara 632-8567 (Japan); Arita, Munetaka [Institute for Nano Quantum Information Electronics, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Arakawa, Yasuhiko [Institute for Nano Quantum Information Electronics, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan)

    2015-09-14

    Blue shift and broadening of the absorption spectra of mid-infrared intersubband transition in non-polar m-plane AlGaN/GaN 10 quantum wells were observed with increasing doping density. As the doping density was increased from 6.6 × 10{sup 11} to 6.0 × 10{sup 12 }cm{sup −2} per a quantum well, the intersubband absorption peak energy shifted from 274.0 meV to 302.9 meV, and the full width at half maximum increased from 56.4 meV to 112.4 meV. Theoretical calculations reveal that the blue shift is due to many body effects, and the intersubband linewidth in doped AlGaN/GaN QW is mainly determined by scattering due to interface roughness, LO phonons, and ionized impurities.

  18. On the mean kinetic energy of the proton in strong hydrogen bonded systems

    Energy Technology Data Exchange (ETDEWEB)

    Finkelstein, Y. [Nuclear Research Center–Negev, Beer-Sheva 84190 (Israel); Moreh, R. [Physics Department, Ben-Gurion University of the Negev, Beer-Sheva 84105 (Israel); Shang, S. L.; Wang, Y.; Liu, Z. K. [Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Shchur, Ya. [Institute for Condensed Matter Physics, 1 Svientsitskii str., L’viv 79011 (Ukraine)

    2016-02-07

    The mean atomic kinetic energies of the proton, Ke(H), and of the deuteron, Ke(D), were calculated in moderate and strongly hydrogen bonded (HB) systems, such as the ferro-electric crystals of the KDP type (XH{sub 2}PO{sub 4}, X = K, Cs, Rb, Tl), the DKDP (XD{sub 2}PO{sub 4}, X = K, Cs, Rb) type, and the X{sub 3}H(SO{sub 4}){sub 2} superprotonic conductors (X = K, Rb). All calculations utilized the simulated partial phonon density of states, deduced from density functional theory based first-principle calculations and from empirical lattice dynamics simulations in which the Coulomb, short range, covalent, and van der Waals interactions were accounted for. The presently calculated Ke(H) values for the two systems were found to be in excellent agreement with published values obtained by deep inelastic neutron scattering measurements carried out using the VESUVIO instrument of the Rutherford Laboratory, UK. The Ke(H) values of the M{sub 3}H(SO{sub 4}){sub 2} compounds, in which the hydrogen bonds are centro-symmetric, are much lower than those of the KDP type crystals, in direct consistency with the oxygen-oxygen distance R{sub OO}, being a measure of the HB strength.

  19. Hydrogen bonding and orientation effects on the accommodation of methylamine at the air-water interface

    Science.gov (United States)

    Hoehn, Ross D.; Carignano, Marcelo A.; Kais, Sabre; Zhu, Chongjing; Zhong, Jie; Zeng, Xiao C.; Francisco, Joseph S.; Gladich, Ivan

    2016-06-01

    Methylamine is an abundant amine compound detected in the atmosphere which can affect the nature of atmospheric aerosol surfaces, changing their chemical and optical properties. Molecular dynamics simulation results show that methylamine accommodation on water is close to unity with the hydrophilic head group solvated in the interfacial environment and the methyl group pointing into the air phase. A detailed analysis of the hydrogen bond network indicates stronger hydrogen bonds between water and the primary amine group at the interface, suggesting that atmospheric trace gases will likely react with the methyl group instead of the solvated amine site. These findings suggest new chemical pathways for methylamine acting on atmospheric aerosols in which the methyl group is the site of orientation specific chemistry involving its conversion into a carbonyl site providing hydrophilic groups for uptake of additional water. This conversion may explain the tendency of aged organic aerosols to form cloud condensation nuclei. At the same time, formation of NH2 radical and formaldehyde is suggested to be a new source for NH2 radicals at aerosol surfaces, other than by reaction of absorbed NH3. The results have general implications for the chemistry of other amphiphilic organics, amines in particular, at the surface of atmospherically relevant aerosols.

  20. Hydrogen bonding of single acetic acid with water molecules in dilute aqueous solutions

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In separation processes,hydrogen bonding has a very significant effect on the efficiency of isolation of acetic acid (HOAc) from HOAc/H2O mixtures. This intermolecular interaction on aggregates composed of a single HOAc molecule and varying numbers of H2O molecules has been examined by using ab initio molecular dynamics simulations (AIMD) and quantum chemical calculations (QCC). Thermodynamic data in aqueous solution were obtained through the self-consistent reaction field calculations and the polarizable continuum model. The aggregation free energy of the aggregates in gas phase as well as in aqueous system shows that the 6-membered ring is the most favorable structure in both states. The relative stability of the ring structures inferred from the thermodynamic properties of the QCC is consistent with the ring distributions of the AIMD simulation. The study shows that in dilute aqueous solution of HOAc the more favorable molecular interaction is the hydrogen bonding between HOAc and H2O molecules,resulting in the separation of acetic acid from the HOAc/H2O mixtures with more difficulty than usual.

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

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

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

  2. Water-containing hydrogen-bonding network in the active center of channelrhodopsin.

    Science.gov (United States)

    Ito, Shota; Kato, Hideaki E; Taniguchi, Reiya; Iwata, Tatsuya; Nureki, Osamu; Kandori, Hideki

    2014-03-01

    Channelrhodopsin (ChR) functions as a light-gated ion channel in Chlamydomonas reinhardtii. Passive transport of cations by ChR is fundamentally different from the active transport by light-driven ion pumps such as archaerhodopsin, bacteriorhodopsin, and halorhodopsin. These microbial rhodopsins are important tools for optogenetics, where ChR is used to activate neurons by light, while the ion pumps are used for neural silencing. Ion-transport functions by these rhodopsins strongly depend on the specific hydrogen-bonding networks containing water near the retinal chromophore. In this work, we measured protein-bound water molecules in a chimeric ChR protein of ChR1 (helices A to E) and ChR2 (helices F and G) of Chlamydomonas reinhardtii using low-temperature FTIR spectroscopy at 77 K. We found that the active center of ChR possesses more water molecules (9 water vibrations) than those of other microbial (2-6 water vibrations) and animal (6-8 water vibrations) rhodopsins. We conclude that the protonated retinal Schiff base interacts with the counterion (Glu162) directly, without the intervening water molecule found in proton-pumping microbial rhodopsins. The present FTIR results and the recent X-ray structure of ChR reveal a unique hydrogen-bonding network around the active center of this light-gated ion channel. PMID:24512107

  3. Hydrogen-bond interaction assisted branched copolymer HILIC material for separation and N-glycopeptides enrichment.

    Science.gov (United States)

    Shao, Wenya; Liu, Jianxi; Yang, Kaiguang; Liang, Yu; Weng, Yejing; Li, Senwu; Liang, Zhen; Zhang, Lihua; Zhang, Yukui

    2016-09-01

    Hydrophilic interaction chromatography (HILIC) has attracted increasing attention in recent years due to its efficient application in the separation of polar compounds and the enrichment of glycopeptides. However, HILIC materials are still of weak hydrophilicity and thereby present weak retention and selectivity. In this work, branched copolymer modified hydrophilic material Sil@Poly(THMA-co-MBAAm), with high hydrophilicity and unique "claw-like" polyhydric groups, were prepared by "grafting from" thiol-ene click reaction. Due to the abundant functional groups provided by branched copolymer, the material showed excellent retention for nucleosides, necleobases, acidic compounds, sugars and peptides. Furthermore, Sil@Poly(THMA-co-MBAAm) was also applied for the N-glycosylation sites profiling towards the digests of the mouse brain, and 1997N-glycosylated peptides were identified, corresponding to 686 glycoprotein groups. Due to the assisted hydrogen-bond interaction, the selectivity for glycopeptide enrichment in the real sample reached 94.6%, which was the highest as far as we know. All these results indicated that such hydrogen-bond interaction assisted branched copolymer HILIC material possessed great potential for the separation and large scale glycoproteomics analysis. PMID:27343616

  4. Hydrogen bonding in (substituted benzene)·(water)n clusters with n≤4

    International Nuclear Information System (INIS)

    Infrared ion-depletion spectroscopy, a double resonance method combining vibrational predissociation with resonant two-photon ionization (R2PI) spectroscopy, has been applied to study mixed clusters of the type (substituted benzene)·(H2O)n with n≤4. The UV chromophores were p-difluorobenzene, fluorobenzene, benzene, toluene, p-xylene and anisole. From the IR depletion spectra in the region of the OH stretching vibrations it could be shown that the water molecules are attached as subclusters to the chromophores. Size and configuration of the subclusters could be deduced from the IR depletion spectra. In the anisole·(H2O)1and2 complexes the water clusters form an ordinary hydrogen bond to the oxygen atom of the methoxy group. In all other mixed complexes a π-hydrogen bond is formed between one of the free OH groups of a water subcluster and the π-system of the chromophore. According to the strength of this interaction the frequency of the respective absorption band exhibits a characteristic red-shift which could be related to the total atomic charges in the aromatic ring. (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

  5. The influence of hydrogen bonding on the diffusion behaviour of diastereoisomeric tripeptide derivatives

    Science.gov (United States)

    Gröbel, Angela; Plass, Monika

    1999-05-01

    The diffusion behaviour of the diastereoisomers of Z-Ala-Phe-Val-OMe and Z-Ala-Leu-Val-OMe was studied in solutions of carbon tetrachloride and toluene. The capillary method according to Anderson was used for the diffusion experiment. The loss of the concentration of the tripeptide derivatives in the course of the time was monitored by infrared spectroscopy using their NH stretching vibrations. In general, the diffusion rate of the substances in toluene was 50-100 times larger than in carbon tetrachloride. Also the diastereoisomers differ in their diffusion properties. In carbon tetrachloride this effect is very small but still significant. It can be explained by the strong intramolecular hydrogen bonding of the peptides which leads to C 5 and C 7 rings. In toluene the different configuration of the compounds whose changes are connected with the change in their polar properties are responsible for the observed diffusion rates. The diffusion rate will be discussed in terms of equilibrium constants describing the intramolecular association behaviour and molecular descriptors of the tripeptide derivatives obtained from HPLC measurements in polar solvents. It will be shown that the diffusion rate correlates with the McGowan volume Vx and in part with the effective hydrogen bond acidity ∑ α2H.

  6. Levoglucosan formation from crystalline cellulose: importance of a hydrogen bonding network in the reaction.

    Science.gov (United States)

    Hosoya, Takashi; Sakaki, Shigeyoshi

    2013-12-01

    Levoglucosan (1,6-anhydro-β-D-glucopyranose) formation by the thermal degradation of native cellulose was investigated by MP4(SDQ)//DFT(B3LYP) and DFT(M06-2X)//DFT(B3LYP) level computations. The computational results of dimer models lead to the conclusion that the degradation occurs by a concerted mechanism similar to the degradation of methyl β-D-glucoside reported in our previous study. One-chain models of glucose hexamer, in which the interchain hydrogen bonds of real cellulose crystals are absent, do not exhibit the correct reaction behavior of levoglucosan formation; for instance, the activation enthalpy (Ea =≈38 kcal mol(-1) ) is considerably underestimated compared to the experimental value (48-60 kcal mol(-1) ). This problem is solved with the use of two-chain models that contain interchain hydrogen bonds. The theoretical study of this model clearly shows that the degradation of the internal glucosyl residue leads to the formation of a levoglucosan precursor at the chain end and levoglucosan is selectively formed from this levoglucosan end. The calculated Ea (56-62 kcal mol(-1) ) agrees well with the experimental value. The computational results of three-chain models indicate that this degradation occurs selectively on the crystalline surface. All these computational results provide a comprehensive understanding of several experimental facts, the mechanisms of which have not yet been elucidated.

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

    Science.gov (United States)

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

    2007-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Yagang Zhang

    2012-04-01

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

  9. DNA-triplex conformation from normal mode and hydrogen bond stability calculations.

    Science.gov (United States)

    Chen, Y. Z.; Prohofsky, E. W.; Powell, J. W.; White, A. P.

    1996-03-01

    Triple-stranded DNAs are of potential applications in genome mapping and in the treatment of genetic disorders with little side-effect. Despite significant interests, structural information of DNA triplexes is limited and sometimes conflicting. For instance, two structural models with different conformation have been proposed for a DNA-triplex Poly(dA)\\cdot2Poly(dT). We propose that the sensitivity of normal modes and hydrogen-bond stability on conformation can be used to determine the structure of biomolecules difficult to access by other methods. The structural model representative of the true conformation should have normal modes in agreement with observations, and have most stable hydrogen bonds which melt at observed temperatures. We carried out calculations on the two models of Poly(dA)\\cdot2Poly(dT) and found that one model is consistent with observations at high humidity and thus most likely a good approximation to the true conformation in that environment. Our method has potential application in structural prediction for other biomolecules.

  10. Nonadiabatic dynamics of floppy hydrogen bonded complexes: the case of the ionized ammonia dimer.

    Science.gov (United States)

    Chalabala, Jan; Slavíček, Petr

    2016-07-27

    In the case of the ammonia dimer, we address the following questions: how ultrafast ionization dynamics is controlled by hydrogen bonding and whether we can control the products via selective ionization of a specific electron. We use quantum chemical calculations and ab initio non-adiabatic molecular dynamics simulations to model the femtosecond dynamics of the ammonia dimer upon ionization. The role of nuclear quantum effects and thermal fluctuations in predicting the structure of the dimer is emphasized; it is shown that the minimum energy and vibrationally averaged structures are rather different. The ground state structure subsequently controls the ionization dynamics. We describe reaction pathways, electronic population transfers and reaction yields with respect to ionization from different molecular orbitals. The simulations showed that the ionized ammonia dimer is highly unstable and its decay rate is primarily driven by the position of the electron hole. In the case of ground state ionization (i.e. the HOMO electron is ionized), the decay is likely to be preceded by a proton transfer (PT) channel yielding NH4(+) and NH2˙ fragments. The PT is less intense and slower compared with the ionized water dimer. After ionizing deeper lying electrons, mainly NH3(+)˙ and NH3 fragments are formed. Overall, our results show that the ionization dynamics of the ammonia and water dimers differ due to the nature of the hydrogen bond in these systems. PMID:27402376

  11. Origins of IR Intensity in Overtones and Combination Bands in Hydrogen Bonded Systems

    Science.gov (United States)

    Horvath, Samantha; McCoy, Anne B.

    2010-06-01

    As the infrared spectra of an increasing number of hydrogen bonded and ion/water complexes have been investigated experimentally, we find that they often contain bands with significant intensity that cannot be attributed to fundamental transitions. In this talk, we explore several sources of the intensity of these overtone and combination bands. A common source of intensity is mode-mode coupling, as is often seen between the proton transfer coordinate and the associated heavy atom vibration. A second important mechanism involves large changes in the dipole moment due the loss of a hydrogen bond. This results in intense overtone transitions involving non-totally symmetric vibrations as well as the introduction of intense combination bands involving intramolecular bending coupled to hindered rotations. These effects will be discussed in the context of several systems, including the spectra of complexes of argon atoms with {H}_3{O}^+, F^-\\cdotH_2O, Cl^-\\cdotH_2O, protonated water clusters,^a and HOONO. T. Guasco, S. Olesen and M. A. Johnson, private communication S. Horvath, A. B. McCoy, J. R. Roscioli and M. A. Johnson, J. Phys. Chem. A, 112, 12337-44 (2008) S. Horvath, A. B. McCoy, B. M. Eliot, G. H. Weddle, J. R. Roscioli and M. A. Johnson, J. Phys. Chem. A, 115, 1556-68 (2010). A. B. McCoy, M. K. Sprague and M. Okumura, J. Phys. Chem. A, 115, 1324-33 (2010)

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

    Science.gov (United States)

    Ramegowda, Mariyappa

    2015-02-01

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

  13. Infrared spectroscopic studies of hydrogen-bonded complexes in cryogenic sulutions

    Science.gov (United States)

    Iskanderov, T. A.; Kimel'fel'd, Ya. M.; Smirnova, E. M.

    1987-03-01

    We have measured the ν s(OH) band parameters of the IR absorption spectra for a wide variety of hydrogen-bonded (HB) complexes of CH 3OH(D), CF 3CH 2OH, and (CF 3) 3COH(D) with some simplest representatives of various classes of bases in Xe and Kr in the temperature range 120-270 K. The ν s(OH) absorption bands of the HB complexes in solution in atomic solvents have been demonstrated to be narrower by a factor of 2 to 4 than in molecular solvents at the same temperature. The fact that the ν s(OH) bandwidths in Xe and in the gas phase at similar temperatures are practically the same indicates that these bandwidths are in both cases governed mainly by the contribution of "hot transitions" from a sequence of excited levels of the ν β low-frequency bending mode of the hydrogen bond. The other characteristic features revealed for the complexes under study in liquid Xe and Kr at ν s(OH) frequency shifts up to 500 cm -1 include: (1) slight temperature dependence of the ν s(OH) bandwidth (0.1-0.3 cm -1/K), (2) almost "normal" isotope frequency ratio ν s(OH)/ν s(OD) (1.34-1.36) and (3) low ν s(OH) temperature shift values (0.1-0.4 cm -1/K).

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

    Science.gov (United States)

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

    2005-04-01

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

  15. ADSORPTION OF TANNIN FROM AQUEOUS SOLUTION ONTO MACROPOROUS CROSSLINKED POLY(N—VINYL—ACETAMIDE)VIA HYDROGEN BONDING

    Institute of Scientific and Technical Information of China (English)

    XUMancai; XUMingcheng; 等

    2000-01-01

    A Strongly hydrophilic hydrogen-bonding adsorbent-macroporous crosslinked Poly(Nvinyl-acetamide),which contain both hydrogen bond acceptor and donator,was synthesized.Adsorption mechanism and dynamic adsorption of tannin from aqueous solution onto the adsorbent were investigated.Most of the differntial adsorption heats for various adsorption capacities calculated from the adsorption isotherms according to Clapeyron-Clausius equation lay in the range of hydrogen bond energy(8-50J/mol).Adsorption properties of the adsorbent were studied in detail.These results revealed a hydrogen bonding mechanism of the adsorption of tannin from aqueous solution onto the adsorbent.The result of the dynamic adsorption of tanning with the initial concentration under 600mg/L showed that the adsorption rate of tannin exceeded 90% when the flow rate was 3BV/h and the effluent volume reached 100BV.Therefore,the developed hydrogen-bonding adsorbent-macroporous crosslinked poly(N-vinyl-acetamide)-is an excellent adsorbent to remove tannin from extract of natural products,and has great value in application.

  16. Synthesis of Zn-Cu-In-S/ZnS Core/Shell Quantum Dots with Inhibited Blue-Shift Photoluminescence and Applications for Tumor Targeted Bioimaging

    Directory of Open Access Journals (Sweden)

    Weisheng Guo, Na chen, Yu Tu, Chunhong Dong, Bingbo Zhang, Chunhong Hu, Jin Chang

    2013-01-01

    Full Text Available A facile strategy is reported here for synthesis of Zn-Cu-In-S/ZnS (ZCIS/ZnS core/shell QDs to address the synthetic issues that the unexpected blue-shift of CuInS2-based nanocrystals. In this strategy, Zn2+ ions are intentionally employed for the synthesis of alloyed ZCIS core QDs before ZnS shell coating, which contributes to the reduced blue-shift in photoluminescence (PL emission. The experimental results demonstrate this elaborate facile strategy is effective for the reduction of blue-shift during shell growth. Particularly, a hypothesis is proposed and proved for explanation of this effective strategy. Namely, both cation exchange inhibition and ions accumulation are involved during the synthesis of ZCIS/ZnS QDs. Furthermore, the obtained near infrared (NIR ZCIS/ZnS QDs are transferred into aqueous phase by a polymer coating technique and coupled with cyclic Arg-Gly-Asp peptide (cRGD peptides. After confirmation of biocompability by cytotoxicity test on normal 3T3 cells, these QDs are injected via tail vein into nude mice bearing U87 MG tumor. The result indicates that the signals detected in the tumor region are much more distinguishing injected with ZCIS/ZnS-cRGD QDs than that injected with ZCIS/ZnS QDs.

  17. Six hydrogen-bonded supramolecular frameworks assembled from organic acids and p-dimethylaminobenzaldehyde

    Science.gov (United States)

    Jin, Shouwen; Wang, Lanqing; Lou, Yulei; Liu, Li; Li, Bin; Li, Linyu; Feng, Chao; Liu, Hui; Wang, Daqi

    2016-03-01

    Cocrystallization of the commonly available organic compound, p-dimethylaminobenzaldehyde, with a series of organic acids gave a total of six molecular adducts with the compositions: p-dimethylaminobenzaldehyde : (3,5-dinitrosalicylic acid) [(L) · (Hdsa), Hdsa = 3,5-dinitrosalicylic acid] (1), p-dimethylaminobenzaldehyde : (3-nitrophthalic acid) [(L) · (3-H2npa), 3-H2npa = 3-nitrophthalic acid] (2), p-dimethylaminobenzaldehyde : (4-nitrophthalic acid) [(L) · (4-H2npa), 4-H2npa = 4-nitrophthalic acid] (3), p-dimethylaminobenzaldehyde : (1,5-naphthalenedisulfonic acid) : (NH3)2 [NH4 · (HL) · (nds2-) · NH3, nds- = 1,5-naphthalenedisulfonate] (4), p-dimethylaminobenzaldehyde : (oxalic acid)0.5 [(L) · (H2oa)0.5, H2oa = oxalic acid] (5), and p-dimethylaminobenzaldehyde : (fumaric acid)0.5 [(L) · (H2fum)0.5, H2fum = fumaric acid] (6). The six molecular adducts have been characterized by X-ray diffraction technique, IR, and elemental analysis, and the melting points of all adducts were also reported. And their structural and supramolecular aspects are fully analyzed. Of the six adducts, only 4 is an organic salt and the other five are cocrystals. The crystal packing is interpreted in terms of the strong classical hydrogen bonds as well as other weak non-classical hydrogen bonds. The different families of non-covalent bonds contribute to the stabilization and expansion of the total high-dimensional (2D-3D) frameworks.

  18. Metal-and hydrogen-bonding competition during water absorption on Pd(111) and Ru(0001)

    International Nuclear Information System (INIS)

    The initial stages of water adsorption on the Pd(111) and Ru(0001) surfaces have been investigated experimentally by Scanning Tunneling Microscopy in the temperature range between 40 K and 130 K, and theoretically with Density Functional Theory (DFT) total energy calculations and STM image simulations. Below 125 K water dissociation does not occur at any appreciable rate and only molecular films are formed. Film growth starts by the formation of flat hexamer clusters where the molecules bind to the metal substrate through the O-lone pair while making H-bonds with neighboring molecules. As coverage increases, larger networks of linked hexagons are formed with a honeycomb structure, which requires a fraction of the water molecules to have their molecular plane perpendicular to the metal surface with reduced water-metal interaction. Energy minimization favors the growth of networks with limited width. As additional water molecules adsorb on the surface they attach to the periphery of existing islands, where they interact only weakly with the metal substrate. These molecules hop along the periphery of the clusters at intermediate temperatures. At higher temperatures they bind to the metal to continue the honeycomb growth. The water-Ru interaction is significantly stronger than the water-Pd interaction, which is consistent with the greater degree of hydrogen-bonded network formation and reduced water-metal bonding observed on Pd relative to Ru.

  19. Inverse Ubbelohde effect in the short hydrogen bond of photosystem II: Relation between H/D isotope effect and symmetry in potential energy profile.

    Science.gov (United States)

    Kanematsu, Yusuke; Tachikawa, Masanori; Takano, Yu

    2016-09-01

    The short hydrogen bond between tyrosine Yz and D1-His190 of photosystem II (PSII) was investigated using multicomponent quantum mechanics, where the quantum fluctuation of a hydrogen nucleus was incorporated into electronic structure calculation. Our computation demonstrated that the deuteration for hydrogen in the short hydrogen bond of PSII led to the reduction of the O…N distance. It indicated an inverse Ubbelohde effect typically recognized in strong and symmetric hydrogen-bonding clusters such as FHF(-) and H3O2-. We confirmed that the relation between the geometric isotope effect and the symmetry of the potential energy profile of FHF(-) was reasonably agreed with that of PSII. According to this agreement, the short hydrogen bond in PSII can be regarded as a short strong hydrogen bond. © 2016 Wiley Periodicals, Inc. PMID:27349328

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

    Science.gov (United States)

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

    2016-09-01

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