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Sample records for intramolecular hydrogen-bonding studies

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

    Science.gov (United States)

    Qu, Peng; Tian, Dongxu

    2014-01-01

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

  2. Intramolecular Energy Transfer, Charge Transfer & Hydrogen Bond

    Indian Academy of Sciences (India)

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

  3. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    Directory of Open Access Journals (Sweden)

    Peter I. Nagy

    2014-10-01

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

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

    National Research Council Canada - National Science Library

    Nicholson, Jesse

    2001-01-01

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

  5. Evidence for excited-state intramolecular proton transfer in 4-chlorosalicylic acid from combined experimental and computational studies: Quantum chemical treatment of the intramolecular hydrogen bonding interaction

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Bijan Kumar [Department of Chemistry, University of Calcutta, 92 Acharya Prafulla Chandra Road, Calcutta 700009 (India); Guchhait, Nikhil, E-mail: nikhil.guchhait@rediffmail.com [Department of Chemistry, University of Calcutta, 92 Acharya Prafulla Chandra Road, Calcutta 700009 (India)

    2012-07-25

    Highlights: Black-Right-Pointing-Pointer Experimental and computational studies on the photophysics of 4-chlorosalicylic acid. Black-Right-Pointing-Pointer Spectroscopically established ESIPT reaction substantiated by theoretical calculation. Black-Right-Pointing-Pointer Quantum chemical treatment of IMHB unveils strength, nature and directional nature. Black-Right-Pointing-Pointer Superiority of quantum chemical treatment of H-bond over geometric criteria. Black-Right-Pointing-Pointer Role of H-bond as a modulator of aromaticity. -- Abstract: The photophysical study of a pharmaceutically important chlorine substituted derivative of salicylic acid viz., 4-chlorosalicylic acid (4ClSA) has been carried out by steady-state absorption, emission and time-resolved emission spectroscopy. A large Stokes shifted emission band with negligible solvent polarity dependence marks the spectroscopic signature of excited-state intramolecular proton transfer (ESIPT) reaction in 4ClSA. Theoretical calculation by ab initio and Density Functional Theory methods yields results consistent with experimental findings. Theoretical potential energy surfaces predict the occurrence of proton transfer in S{sub 1}-state. Geometrical and energetic criteria, Atoms-In-Molecule topological parameters, Natural Bond Orbital population analysis have been exploited to evaluate the intramolecular hydrogen bond (IMHB) interaction and to explore its directional nature. The inter-correlation between aromaticity and resonance assisted H-bond is also discussed in this context. Our results unveil that the quantum chemical treatment is a more accurate tool to assess hydrogen bonding interaction in comparison to geometrical criteria.

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

    Science.gov (United States)

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

    2018-01-01

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

  7. 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...

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

    Science.gov (United States)

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

    2017-09-28

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

  9. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

    Energy Technology Data Exchange (ETDEWEB)

    Mori, Yukie, E-mail: mori.yukie@ocha.ac.jp; Masuda, Yuichi

    2015-09-08

    Highlights: • MD simulations were performed to study dynamics of strong hydrogen bonds. • Nuclear magnetic relaxation times of proton were measured in solution. • The hydrogen bond of dibenzoylmethane enol is asymmetric in methanol solution. • Formation or breakage of intermolecular hydrogen bonds can trigger proton transfer. • Dimethylsulfoxide may form a bifurcated hydrogen bond with a hydrogen-bonded system. - Abstract: Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl{sub 4}, acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the {sup 17

  10. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

    International Nuclear Information System (INIS)

    Mori, Yukie; Masuda, Yuichi

    2015-01-01

    Highlights: • MD simulations were performed to study dynamics of strong hydrogen bonds. • Nuclear magnetic relaxation times of proton were measured in solution. • The hydrogen bond of dibenzoylmethane enol is asymmetric in methanol solution. • Formation or breakage of intermolecular hydrogen bonds can trigger proton transfer. • Dimethylsulfoxide may form a bifurcated hydrogen bond with a hydrogen-bonded system. - Abstract: Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl 4 , acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the 17 O and 1

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

    Directory of Open Access Journals (Sweden)

    Liliana Mammino

    2017-08-01

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

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

    Directory of Open Access Journals (Sweden)

    Paweł Misiak

    2018-01-01

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

  13. NMR study of conformational exchange and double-well proton potential in intramolecular hydrogen bonds in monoanions of succinic acid and derivatives.

    Science.gov (United States)

    Guo, Jing; Tolstoy, Peter M; Koeppe, B; Denisov, Gleb S; Limbach, Hans-Heinrich

    2011-09-08

    We present a (1)H, (2)H, and (13)C NMR study of the monoanions of succinic (1), meso- and rac-dimethylsuccinic (2, 3), and methylsuccinic (4) acids (with tetraalkylammonium as the counterion) dissolved in CDF(3)/CDF(2)Cl at 300-120 K. In all four monoanions, the carboxylic groups are linked by a short intramolecular OHO hydrogen bond revealed by the bridging-proton chemical shift of about 20 ppm. We show that the flexibility of the carbon skeleton allows for two gauche isomers in monoanions 1, 2, and 4, interconverting through experimental energy barriers of 10-15 kcal/mol (the process itself and the energy barrier are also reproduced in MP2/6-311++G** calculations). In 3, one of the gauche forms is absent because of the steric repulsion of the methyl groups. In all four monoanions, the bridging proton is located in a double-well potential and subject, at least to some extent, to proton tautomerism, for which we estimate the two proton positions to be separated by ca. 0.2 Å. In 1 and 3, the proton potential is symmetric. In 2, slowing the conformational interconversion introduces an asymmetry to the proton potential, an effect that might be strong enough even to synchronize the proton tautomerism with the interconversion of the two gauche forms. In 4, the asymmetry of the proton potential is due to the asymmetric substitution. The intramolecular H-bond is likely to remain intact during the interconversion of the gauche forms in 1, 3, and 4, whereas the situation in 2 is less clear.

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

    Science.gov (United States)

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

    2017-09-01

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

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

    DEFF Research Database (Denmark)

    Schrøder, Sidsel Dahl

    and 1,4-diaminobutane). Experimentally, the hydrogen bonds have been studied with vibrational spectroscopy in the infrared and near-infrared regions. The focus is primarily on spectra recorded in the near-infrared regions, which in these studies are dominated by O-H and N-H stretching overtones....... Overtone spectra have been recorded with intracavity laser photoacoustic laser spectroscopy and conventional long path absorption spectroscopy. Theoretically, a combination of electronic structure calculations and local mode models have been employed to guide the assignment of bands in the vibrational......,4-diaminobutane, no sign of intramolecular N-H···N hydrogen bonds were identified in the overtone spectra. However, theoretical analyzes indicate that intramolecular N-H···N hydrogen bonds are present in all three diamines if two hydrogen atoms on one of the methylene groups are substituted with triuoromethyl...

  16. Matrix-isolation FT-IR and DFT theoretical studies of the intramolecular hydrogen bonding in Mannich bases

    International Nuclear Information System (INIS)

    Pajak, J.; Rospenk, M.; Maes, G.; Sobczyk, L.

    2006-01-01

    FT-IR Ar-matrix isolated spectra were studied for dichloro- (Cl 2 -MB) and tetrachloroderivatives (Cl 4 -MB) of the ortho Mannich base. The spectra were analyzed based on the DFT calculated frequencies and intensities and compared with those recorded in CCl 4 solution in the region of the ν(OH) and ν(OD) vibrations. The matrix-isolated spectra are characterized by narrower ν(OH) and ν(OD) bands with much better resolved fine structure than in solution. The fine structure originates from the anharmonic coupling with the low frequency modes as well as from Fermi resonance. The ν(OD) band shapes can be reproduced exclusively by assuming the Fermi resonance with overtones and summation of the frequencies of modes into which the bridge atoms are involved. The frequency isotopic ratio (ISR) is for both compounds 1.33 while the half-width ratios are equal to 1.82 and 1.94, for Cl 2 -MB and Cl 4 -MB, respectively

  17. Spectral and cyclic voltammetric studies on some intramolecularly hydrogen bonded arylhydrazones: Crystal and molecular structure of 2-(2-(3-nitrophenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione

    Science.gov (United States)

    Sethukumar, A.; Arul Prakasam, B.

    2010-01-01

    A series of arylhydrazone derivatives ( 1- 7) were prepared by the coupling of acetylacetone/dimedone with respective aromatic diazonium salts and characterized by IR, 1H and 13C NMR spectra. The IR and NMR spectral data clearly manifests the effective intramolecular hydrogen bonding in all the cases. Cyclic voltammetric studies certainly indicate that in all the cases the reduced center is C dbnd N bond of hydrazonic moiety. The single crystal X-ray structural analysis of 2-(2-(3-nitrophenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione ( 6) is also reported. Single crystal X-ray analysis of 6 evidences the intramolecular hydrogen bonding with the N(2)⋯O(4) distance of 2.642(15) Å, which can be designated as S(6) according to Etter's graph nomenclature. The cyclohexane ring conformation in the molecule ( 6) can be described as an envelope. RAHB studies suggest that the resonance assistance for hydrogen bonding is significantly reduced for the compound ( 6) due to the non-planarity of the six atoms which are involved in resonant cycle S(6) of Etter's graph. The planarity of the resonant cycle S(6) is very much disturbed by the conformational requirement of the cyclohexane ring and hence RAHB concept is less operative in this case.

  18. Location of protons in N-H···N hydrogen-bonded systems: a theoretical study on intramolecular pyridine-dihydropyridine and pyridine-pyridinium pairs.

    Science.gov (United States)

    Mori, Yukie; Takano, Keiko

    2012-08-21

    Two-dimensional potential energy surfaces (PESs) were calculated for the degenerate intramolecular proton transfer (PT) in two N-H···N hydrogen-bonded systems, (Z)-2-(2-pyridylmethylidene)-1,2-dihydropyridine (1) and monoprotonated di(2-pyridyl) ether (2), at the MP2/cc-pVDZ level of theory. The calculated PES had two minima in both cases. The energy barrier in 1 was higher than the zero-point energy (ZPE) level, while that in 2 was close to the ZPE. Vibrational wavefunctions were obtained by solving time-independent Schrödinger equations with the calculated PESs. The maximum points of the probability density were shifted from the energy minima towards the region where the covalent N-H bond was elongated and the N···N distance shortened. The effects of a polar solvent on the PES were investigated with the continuum or cluster models in such a way that the solute-solvent electrostatic interactions could be taken into account under non-equilibrated conditions. A solvated contact ion-pair was modelled by a cluster consisting of one cation 2, one chloride ion and 26 molecules of acetonitrile. The calculation with this model suggested that the bridging proton is localised in the deeper well due to the significant asymmetry of the PES and the high potential barrier.

  19. NMR and IR Investigations of Strong Intramolecular Hydrogen Bonds

    Directory of Open Access Journals (Sweden)

    Poul Erik Hansen

    2017-03-01

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

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

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Spanget-Larsen, Jens

    2012-01-01

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

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

    International Nuclear Information System (INIS)

    Pal, H.; Mukherjee, T.

    1994-01-01

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

  2. NMR and IR investigations of strong intramolecular hydrogen bonds

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Spanget-Larsen, Jens

    2017-01-01

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

  3. Phase transition and intramolecular hydrogen bonding in nitro derivatives of ortho-hydroxy acetophenones

    Science.gov (United States)

    Filarowski, A.; Kochel, A.; Koll, A.; Bator, G.; Mukherjee, S.

    2006-03-01

    The crystal structures of two ortho-hydroxy aryl ketones (5-chloro-3-nitro-2-hydroxyacetophenone, 5-methyl-3-nitro-2-hydroxyacetophenone and the complex 5-chloro-3-nitro-2-hydroxyacetophenone with 2-aminobenzoic acid (anthranilic acid)) were determined by X-ray diffraction. The existence of an intramolecular hydrogen bond of enol character between the hydroxyl and acetyl groups was found by the X-ray method. The enol character was also confirmed by DFT (B3LYP/6-31+G(d,p)) calculations. A phase transition was found at 138 K in 5-chloro-3-nitro-2-hydroxyacetophenone. This phase transition was investigated by differential scanning calorimetry (DSC), dilatometry, and the dielectric method. A study of the nitro-group dynamics in the ortho-hydroxy acetophenones was carried out with DFT (B3LYP/6-31+G(d,p)) calculations.

  4. Rotational Isomers, Intramolecular Hydrogen Bond, and IR Spectra of o-Vinylphenol Homologs

    Science.gov (United States)

    Glazunov, V. P.; Berdyshev, D. V.; Balaneva, N. N.; Radchenko, O. S.; Novikov, V. L.

    2018-03-01

    The ν(OH) stretching-mode bands in solution IR spectra of five o-vinylphenol (o-VPh) homologs in the slightly polar solvents CCl4 and n-hexane were studied. Several rotamers with free OH groups were found in solutions of o-VPh and its methyl-substituted derivatives in n-hexane. The proportion of rotamers in o-VPh homologs with intramolecular hydrogen bonds (IHBs) O-H...π varied from 22 to 97% in the gas and cyclohexane according to B3LYP/cc-pVTZ calculations. The theoretically estimated effective enthalpies -ΔH of their IHBs varied in the range 0.20-2.24 kcal/mol.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    , 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......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...

  6. 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...

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

    Indian Academy of Sciences (India)

    Administrator

    C NMR, DEPT and aided by 2D HETCOR and HMBC heteronuclear correlation techniques. The UV-vis spectra of the Schiff bases have been systematically studied in organic solvents of different polarity, acidic and basic media and found useful in understanding of tautomeric equilibria (phenol-imine, O–H...N and ...

  8. Influence of intramolecular hydrogen bonds on the binding potential of methylated β-cyclodextrin derivatives

    Directory of Open Access Journals (Sweden)

    Gerhard Wenz

    2012-11-01

    Full Text Available Various heptasubstituted derivatives of β-cyclodextrin (β-CD bearing 1, 2 and 3 methyl substituents per glucose unit were synthesized by regioselective methods. Binding free energies and binding enthalpies of these hosts towards 4-tert-butylbenzoate and adamantane-1-carboxylate were determined by isothermal titration microcalorimetry (ITC. It was found that methyl substituents at the secondary positions of β-CD lead to a tremendous reduction of the binding potential, while methylation at the primary positions significantly improved binding. Stabilizing intramolecular hydrogen bonds between the glucose units were made responsible for the high binding potentials of those β-CD derivatives that possess secondary hydroxy groups.

  9. Hydrogen bond strengthening induces fluorescence quenching of PRODAN derivative by turning on twisted intramolecular charge transfer

    Science.gov (United States)

    Yang, Yonggang; Li, Donglin; Li, Chaozheng; Liu, YuFang; Jiang, Kai

    2017-12-01

    Researchers have proposed different effective mechanisms of hydrogen bonding (HB) on the fluorescence of 6-propionyl-2-dimethylaminonaphthalene (PRODAN) and its derivatives. Herein, excited state transition and dynamics analysis confirm that the fluorescence of PD (a derivative of PRODAN with ethyl replaced by 3-hydroxy-2,2-dimethylpropan) emits from the planar intramolecular charge transfer (PICT) state rather than twist ICT (TICT) state, because the fluorescence emission and surface hopping from the TICT state to the twist ground (T-S0) state is energy forbidden. Nevertheless, the strengthening of intramolecular-HB (intra-HB) and intermolecular-HB (inter-HB) of PD-(methanol)2 smooth the pathway of surface hopping from TICT to T-S0 state and the external conversion going to planar ground state by decreasing the energy difference of the two states. This smoothing changes the fluorescence state of PD-(methanol)2 to the TICT state in which fluorescence emission does not occur but surface hopping, leading to the partial fluorescence quenching of PD in methanol solvent. This conclusion is different from previous related reports. Moreover, the inter-HB strengthening of PD-methanol in PICT state induces the cleavage of intra-HB and a fluorescence red-shift of 54 nm compared to PD. This red-shift increases to 66 nm for PD-(methanol)2 for the strengthening of the one intra-HB and two inter-HBs. The dipole moments of PD-methanol and PD-(methanol)2 respectively increase about 10.3D and 8.1D in PICT state compared to PD. The synergistic effect of intra-HB and inter-HB induces partial quenching of PD in methanol solvent by turning on the TICT state and fluorescence red-shift. This work gives a reasonable description on the fluorescence red-shift and partial quenching of PD in methanol solvent, which will bring insight into the study of spectroscopic properties of molecules owning better spectral characteristics.

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

    Science.gov (United States)

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

    2017-04-01

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

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

    Indian Academy of Sciences (India)

    and V KRISHNAKUMARd. aPG & Research ... its related properties.6 12 The present work deals with ..... HOMA index can be analytically separated into two independent terms ..... Sweet Taste Enhancers US Patent 20090047379. 6. Kawski P ...

  12. The Strength of Hydrogen Bonds between Fluoro-Organics and Alcohols, a Theoretical Study.

    Science.gov (United States)

    Rosenberg, Robert E

    2018-05-10

    Fluorinated organic compounds are ubiquitous in the pharmaceutical and agricultural industries. To better discern the mode of action of these compounds, it is critical to understand the strengths of hydrogen bonds involving fluorine. There are only a few published examples of the strengths of these bonds. This study provides a high level ab initio study of inter- and intramolecular hydrogen bonds between RF and R'OH, where R and R' are aryl, vinyl, alkyl, and cycloalkyl. Intermolecular binding energies average near 5 kcal/mol, while intramolecular binding energies average about 3 kcal/mol. Inclusion of zero-point energies and applying a counterpoise correction lessen the difference. In both series, modest increases in binding energies are seen with increased acidity of R'OH and increased electron donation of R in RF. In the intramolecular compounds, binding energy increases with the rigidity of the F-(C) n -OH ring. Inclusion of free energy corrections at 298 K results in exoergic binding energies for the intramolecular compounds and endoergic binding energies for the intermolecular compounds. Parameters such as bond lengths, vibrational frequencies, and atomic populations are consistent with formation of a hydrogen bond and with slightly stronger binding in the intermolecular cases over the intramolecular cases. However, these parameters correlated poorly with binding energies.

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

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

    Science.gov (United States)

    Morishima, Fumiya; Inokuchi, Yoshiya; Ebata, Takayuki

    2013-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Danuta Rusinska-Roszak

    2017-03-01

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

  16. CMPO-calix[4]arenes with spacer containing intramolecular hydrogen bonding: Effect of local rigidification on solvent extraction toward f-block elements

    International Nuclear Information System (INIS)

    Chu, Hongzhu; He, Lutao; Jiang, Qian; Fang, Yuyu; Jia, Yiming; Yuan, Xiangyang; Zou, Shuliang; Li, Xianghui; Feng, Wen; Yang, Yuanyou; Liu, Ning; Luo, Shunzhong; Yang, Yanqiu; Yang, Liang; Yuan, Lihua

    2014-01-01

    Highlights: • Three CMPO-calix[4]arenes with spacer containing intramolecular hydrogen bonds were designed and synthesized. • The influence of local rigidification caused by intramolecular hydrogen bonds upon extraction of f-elements was investigated. • Selective extraction is realized via tuning local chelating surroundings by aid of intramolecular hydrogen bonds. -- Abstract: To understand intramolecular hydrogen bonding in effecting liquid–liquid extraction behavior of CMPO-calixarenes, three CMPO-modified calix[4]arenes (CMPO-CA) 5a–5c with hydrogen-bonded spacer were designed and synthesized. The impact of spacer rotation that is hindered by introduction of intramolecular hydrogen bonding upon extraction of La 3+ , Eu 3+ , Yb 3+ , Th 4+ , and UO 2 2+ has been examined. The results show that 5b and 5c containing only one hydrogen bond with a less hindered rotation spacer extract La 3+ more efficiently than 5a containing two hydrogen bonds with a more hindered rotation spacer, demonstrating the importance of local rigidification of spacer in the design of extractants in influencing the coordination environment. The large difference in extractability between La 3+ and Yb 3+ (or Eu 3+ ) by 5b (or 5c), and the small difference by 5a, suggests intramolecular hydrogen bonding do exert pronounced influence upon selective extraction of light and heavy lanthanides. Log–log plot analysis indicates a 1:1, 2:1 and 1:1 stoichiometry (ligand/metal) for the extracted complex formed between 5b and La 3+ , Th 4+ , UO 2 2+ , respectively. Additionally, their corresponding acyclic analogs 7a–7c exhibit negligible extraction toward these metal ions. These results reveal the possibility of selective extraction via tuning local chelating surroundings of CMPO-CA by aid of intramolecular hydrogen bonding

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

    OpenAIRE

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

    1996-01-01

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

  18. Conformational properties of oxazole-amino acids: effect of the intramolecular N-H···N hydrogen bond.

    Science.gov (United States)

    Siodłak, Dawid; Staś, Monika; Broda, Małgorzata A; Bujak, Maciej; Lis, Tadeusz

    2014-03-06

    Oxazole ring occurs in numerous natural peptides, but conformational properties of the amino acid residue containing the oxazole ring in place of the C-terminal amide bond are poorly recognized. A series of model compounds constituted by the oxazole-amino acids occurring in nature, that is, oxazole-alanine (L-Ala-Ozl), oxazole-dehydroalanine (ΔAla-Ozl), and oxazole-dehydrobutyrine ((Z)-ΔAbu-Ozl), was investigated using theoretical calculations supported by FTIR and NMR spectra and single-crystal X-ray diffraction. It was found that the main feature of the studied oxazole-amino acids is the stable conformation β2 with the torsion angles φ and ψ of -150°, -10° for L-Ala-Ozl, -180°, 0° for ΔAla-Ozl, and -120°, 0° for (Z)-ΔAbu-Ozl, respectively. The conformation β2 is stabilized by the intramolecular N-H···N hydrogen bond and predominates in the low polar environment. In the case of the oxazole-dehydroamino acids, the π-electron conjugation that is spread on the oxazole ring and C(α)═C(β) double bond is an additional stabilizing interaction. The tendency to adopt the conformation β2 clearly decreases with increasing the polarity of environment, but still the oxazole-dehydroamino acids are considered to be more rigid and resistant to conformational changes.

  19. The origin of enantioselectivity in the l-threonine-derived phosphine-sulfonamide catalyzed aza-Morita-Baylis-Hillman reaction: Effects of the intramolecular hydrogen bonding

    KAUST Repository

    Lee, Richmond

    2013-01-01

    l-Threonine-derived phosphine-sulfonamide 4 was identified as the most efficient catalyst to promote enantioselective aza-Morita-Baylis-Hillman (MBH) reactions, affording the desired aza-MBH adducts with excellent enantioselectivities. Density functional theory (DFT) studies were carried out to elucidate the origin of the observed enantioselectivity. The importance of the intramolecular N-H⋯O hydrogen-bonding interaction between the sulfonamide and enolate groups was identified to be crucial in inducing a high degree of stereochemical control in both the enolate addition to imine and the subsequent proton transfer step, affording aza-MBH reactions with excellent enantioselectivity. © 2013 The Royal Society of Chemistry.

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

    NARCIS (Netherlands)

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

    2004-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2018-01-01

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

  2. Experimental and Theoretical Studies in Hydrogen-Bonding Organocatalysis

    Directory of Open Access Journals (Sweden)

    Matej Žabka

    2015-08-01

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

  3. CMPO-calix[4]arenes with spacer containing intramolecular hydrogen bonding: effect of local rigidification on solvent extraction toward f-block elements.

    Science.gov (United States)

    Chu, Hongzhu; He, Lutao; Jiang, Qian; Fang, Yuyu; Jia, Yiming; Yuan, Xiangyang; Zou, Shuliang; Li, Xianghui; Feng, Wen; Yang, Yuanyou; Liu, Ning; Luo, Shunzhong; Yang, Yanqiu; Yang, Liang; Yuan, Lihua

    2014-01-15

    To understand intramolecular hydrogen bonding in effecting liquid-liquid extraction behavior of CMPO-calixarenes, three CMPO-modified calix[4]arenes (CMPO-CA) 5a-5c with hydrogen-bonded spacer were designed and synthesized. The impact of spacer rotation that is hindered by introduction of intramolecular hydrogen bonding upon extraction of La(3+), Eu(3+), Yb(3+), Th(4+), and UO2(2+) has been examined. The results show that 5b and 5c containing only one hydrogen bond with a less hindered rotation spacer extract La(3+) more efficiently than 5a containing two hydrogen bonds with a more hindered rotation spacer, demonstrating the importance of local rigidification of spacer in the design of extractants in influencing the coordination environment. The large difference in extractability between La(3+) and Yb(3+) (or Eu(3+)) by 5b (or 5c), and the small difference by 5a, suggests intramolecular hydrogen bonding do exert pronounced influence upon selective extraction of light and heavy lanthanides. Log-log plot analysis indicates a 1:1, 2:1 and 1:1 stoichiometry (ligand/metal) for the extracted complex formed between 5b and La(3+), Th(4+), UO2(2+), respectively. Additionally, their corresponding acyclic analogs 7a-7c exhibit negligible extraction toward these metal ions. These results reveal the possibility of selective extraction via tuning local chelating surroundings of CMPO-CA by aid of intramolecular hydrogen bonding. Copyright © 2013 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    Moosavi-Tekyeh, Zainab; Dastani, Najmeh

    2015-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-02-21

    Beginning with work in the 1950s at the first generation of research reactors, studies of hydrogen-bonded systems have been a prime application for single-crystal neutron diffraction. The range of systems studied was extended in the 1960s and 1970s, with the advent of high flux reactor sources, and beginning around 1980 studies at pulsed neutron sources have made increasingly important contributions. Recently at the Argonne Intense Pulsed Neutron Source (IPNS), working with collaborators, we completed two studies of hydrogen-bonded systems that will serve to illustrate topics of current interest. In the first study, on andrographolide, an active diterpenoid natural product, our neutron diffraction results definitively characterize the hydrogen-bonding interactions. The second IPNS study is on tetraacetylethane (TAE), a {beta}-diketone enol system with a very short, strong intramolecular O-H...O hydrogen bond. At IPNS, we have determined the neutron crystal structure of TAE at five temperatures between 20 and 298 K to investigate changes in the structure with temperature and to probe for disorder. Despite the successes illustrated by the two examples presented here and by many other studies, at present applications of single-crystal neutron diffraction continue to be extremely flux limited and constrained by the requirement for mm-size crystals for many problems. These limitations are being addressed through the realization of powerful instruments at a new generation of pulsed neutron sources, including in the USA the TOPAZ and MaNDi single-crystal diffractometers that are under development at the Spallation Neutron Source (SNS)

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

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

    International Nuclear Information System (INIS)

    Koetzle, Thomas F.; Piccoli, Paula M.B.; Schultz, Arthur J.

    2009-01-01

    Beginning with work in the 1950s at the first generation of research reactors, studies of hydrogen-bonded systems have been a prime application for single-crystal neutron diffraction. The range of systems studied was extended in the 1960s and 1970s, with the advent of high flux reactor sources, and beginning around 1980 studies at pulsed neutron sources have made increasingly important contributions. Recently at the Argonne Intense Pulsed Neutron Source (IPNS), working with collaborators, we completed two studies of hydrogen-bonded systems that will serve to illustrate topics of current interest. In the first study, on andrographolide, an active diterpenoid natural product, our neutron diffraction results definitively characterize the hydrogen-bonding interactions. The second IPNS study is on tetraacetylethane (TAE), a β-diketone enol system with a very short, strong intramolecular O-H...O hydrogen bond. At IPNS, we have determined the neutron crystal structure of TAE at five temperatures between 20 and 298 K to investigate changes in the structure with temperature and to probe for disorder. Despite the successes illustrated by the two examples presented here and by many other studies, at present applications of single-crystal neutron diffraction continue to be extremely flux limited and constrained by the requirement for mm-size crystals for many problems. These limitations are being addressed through the realization of powerful instruments at a new generation of pulsed neutron sources, including in the USA the TOPAZ and MaNDi single-crystal diffractometers that are under development at the Spallation Neutron Source (SNS).

  8. Chemical origin of blue- and redshifted hydrogen bonds: intramolecular hyperconjugation and its coupling with intermolecular hyperconjugation.

    Science.gov (United States)

    Li, An Yong

    2007-04-21

    Upon formation of a H bond Y...H-XZ, intramolecular hyperconjugation n(Z)-->sigma*(X-H) of the proton donor plays a key role in red- and blueshift characters of H bonds and must be introduced in the concepts of hyperconjugation and rehybridization. Intermolecular hyperconjugation transfers electron density from Y to sigma*(X-H) and causes elongation and stretch frequency redshift of the X-H bond; intramolecular hyperconjugation couples with intermolecular hyperconjugation and can adjust electron density in sigma*(X-H); rehybridization causes contraction and stretch frequency blueshift of the X-H bond on complexation. The three factors--intra- and intermolecular hyperconjugations and rehybridization--determine commonly red- or blueshift of the formed H bond. A proton donor that has strong intramolecular hyperconjugation often forms blueshifted H bonds.

  9. Numerical simulation of dynamic quenching of dual-split fluorescence of molecules with intramolecular hydrogen bonds

    International Nuclear Information System (INIS)

    Morozov, V.A.; Chuvulkin, N.D.; Smolenskij, E.A.; Dubina, Yu.M.

    2014-01-01

    The dynamic quenching of intensity pulses of the dual-split fluorescence (DSF) has been simulated using numerical solutions of the equations for the population matrix of five states of the model fluorescent molecule (FM). The state with the highest energy is considered as resonantly excited by irradiation, and two other excited states populated by subsequent relaxation processes are taken as initial states for the FM transitions with emission of the DSF photons. The FM model parameters are selected to fit typical parameters of the molecules with intramolecular proton photo transfer. Quenching is considered as a consequence of non-radiative decay of the FM excited states due to collisions with the quencher molecules. Examples of two types of the DSF quenching of the FM are given. The first type leads to an intramolecular radiationless decay of particular excited states of the FM, and the second one results in radiationless transitions from the same states to the quencher molecule states. (authors)

  10. Geometrical criteria versus quantum chemical criteria for assessment of intramolecular hydrogen bond (IMHB) interaction: A computational comparison into the effect of chlorine substitution on IMHB of salicylic acid in its lowest energy ground state conformer

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Bijan Kumar [Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Calcutta 700009 (India); Guchhait, Nikhil, E-mail: nikhil.guchhait@rediffmail.com [Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Calcutta 700009 (India)

    2013-02-01

    Highlights: ► Intramolecular hydrogen bonding (IMHB) in salicylic acid and its chloro derivatives. ► A complex effect of +R and −I effect of chlorine substituents on IMHB energy. ► Interplay between IMHB energy and aromaticity. ► Directional nature of IMHB from quantum chemical assessment. ► Quantum chemical treatment vs. geometrical criteria to assess weak interaction. - Abstract: Density functional theory based computational study has been performed to characterize intramolecular hydrogen bonding (IMHB) interaction in a series of salicylic acid derivatives varying in chlorine substitution on the benzene ring. The molecular systems studied are salicylic acid, 5-chlorosalicylic acid, 3,5-dichlorosalicylic acid and 3,5,6-tricholorosalicylic acid. Major emphasis is rendered on the analysis of IMHB interaction by calculation of electron density ρ(r) and Laplacian ∇{sup 2}ρ(r) at the bond critical point using atoms-in-molecule theory. Topological features, energy densities based on ρ(r) through perturbing the intramolecular H-bond distances suggest that at equilibrium geometry the IMHB interaction develops certain characteristics typical of covalent interaction. The interplay between aromaticity and resonance-assisted hydrogen bonding (RAHB) is discussed using both geometrical and magnetic criteria as the descriptors of aromaticity. The optimized geometry features, molecular electrostatic potential map analysis are also found to produce a consensus view in relation with the formation of RAHB in these systems.

  11. Geometrical criteria versus quantum chemical criteria for assessment of intramolecular hydrogen bond (IMHB) interaction: A computational comparison into the effect of chlorine substitution on IMHB of salicylic acid in its lowest energy ground state conformer

    International Nuclear Information System (INIS)

    Paul, Bijan Kumar; Guchhait, Nikhil

    2013-01-01

    Highlights: ► Intramolecular hydrogen bonding (IMHB) in salicylic acid and its chloro derivatives. ► A complex effect of +R and −I effect of chlorine substituents on IMHB energy. ► Interplay between IMHB energy and aromaticity. ► Directional nature of IMHB from quantum chemical assessment. ► Quantum chemical treatment vs. geometrical criteria to assess weak interaction. - Abstract: Density functional theory based computational study has been performed to characterize intramolecular hydrogen bonding (IMHB) interaction in a series of salicylic acid derivatives varying in chlorine substitution on the benzene ring. The molecular systems studied are salicylic acid, 5-chlorosalicylic acid, 3,5-dichlorosalicylic acid and 3,5,6-tricholorosalicylic acid. Major emphasis is rendered on the analysis of IMHB interaction by calculation of electron density ρ(r) and Laplacian ∇ 2 ρ(r) at the bond critical point using atoms-in-molecule theory. Topological features, energy densities based on ρ(r) through perturbing the intramolecular H-bond distances suggest that at equilibrium geometry the IMHB interaction develops certain characteristics typical of covalent interaction. The interplay between aromaticity and resonance-assisted hydrogen bonding (RAHB) is discussed using both geometrical and magnetic criteria as the descriptors of aromaticity. The optimized geometry features, molecular electrostatic potential map analysis are also found to produce a consensus view in relation with the formation of RAHB in these systems

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

    Science.gov (United States)

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

    2012-11-01

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

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

    Science.gov (United States)

    Papadopoulos, Anastasios G; Sigalas, Michael P

    2011-07-01

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

  14. Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1 complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern.

    Science.gov (United States)

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

    2005-08-19

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-05-10

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

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

    Directory of Open Access Journals (Sweden)

    Esko Oksanen

    2017-04-01

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

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

    Science.gov (United States)

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

    2017-01-04

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

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

    Directory of Open Access Journals (Sweden)

    Malose Jack Mphahlele

    2017-01-01

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

  19. TD-DFT investigation of the potential energy surface for Excited-State Intramolecular Proton Transfer (ESIPT) reaction of 10-hydroxybenzo[h]quinoline: Topological (AIM) and population (NBO) analysis of the intramolecular hydrogen bonding interaction

    International Nuclear Information System (INIS)

    Paul, Bijan Kumar; Guchhait, Nikhil

    2011-01-01

    Here, we report a Density Functional Theoretical (DFT) study on the photophysics of a potent Excited-State Intramolecular Proton Transfer (ESIPT) molecular system, viz., 10-hydroxybenzo[h]quinoline (HBQ). Particular emphasis has been rendered on the assessment of the proton transfer reaction in HBQ in the ground and excited-states through elucidation and a careful perusal of the potential energy surfaces (PES). The non-viability of Ground-State Intramolecular Proton Transfer (GSIPT) process is dictated by a high-energy barrier coupled with no energy minimum for the proton transferred (K-form) form at the ground-state (S 0 ) PES. Remarkable reduction of the barrier along with thermodynamic stability inversion between the enol (E-form) and the keto forms (K-form) of HBQ upon photoexcitation from S 0 to the S 1 -state advocate for the operation of ESIPT process. These findings have been cross-validated on the lexicon of analysis of optimized geometry parameters, Mulliken's charge distribution on the heavy atoms, and molecular orbitals (MO) of the E- and the K-forms of HBQ. Our computational results also corroborate to experimental observations. From the modulations in optimized geometry parameters in course of the PT process a critical assessment has been endeavoured to delve into the movement of the proton during the process. Additional stress has been placed on the analysis of the intramolecular hydrogen bonding (IMHB) interaction in HBQ. The IMHB interaction has been explored by calculation of electron density ρ(r) and the Laplacian ∇ 2 ρ(r) at the bond critical point (BCP) using Atoms-In-Molecule (AIM) method and by calculation of interaction between σ* of OH with the lone pair of the nitrogen atom using Natural Bond Orbital (NBO) analysis. - Highlights: → Theoretical modelling of the photophysics of an ESIPT probe 10-hydroxybenzo[h]quinoline (HBQ). → Calculation of intramolecular hydrogen bond (IMHB) energy. → Role of hyperconjugative charge transfer

  20. Intramolecular hydrogen bonding

    DEFF Research Database (Denmark)

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

    2006-01-01

    The vibrational structure of the title compound (DBM) was investigated by FTIR spectroscopy in liquid solutions, by FTIR linear dichroism (LD) measurements, and by Raman spectroscopy. The results were supported by the application of theoretical model calculations and analyzed with particular atte...

  1. Intra- und intermolecular hydrogen bonds. Spectroscopic, quantum chemical and molecular dynamics studies

    International Nuclear Information System (INIS)

    Simperler, A.

    1999-03-01

    Intra- and intermolecular H-bonds have been investigated with spectroscopic, quantum chemical, and molecular dynamics methods. The work is divided into the following three parts: 1. Intramolecular interactions in ortho-substituted phenols. Theoretical and experimental data that characterizes the intramolecular hydrogen bonds in 48 different o-substituted phenols are discussed. The study covers various kinds of O-H ... Y -type interactions (Y= N, O, S, F, Cl, Br, I, C=C, C=-C, and C-=N). The bond strength sequences for several series of systematically related compounds as obtained from IR spectroscopy data (i.e., v(OH) stretching frequencies) are discussed and reproduced with several theoretical methods (B3LYP/6-31G(d,p), B3LYP/6-311G(d,p), B3LYP/6-31++G(d,p), B3LYP/DZVP, MP2/6-31G(d,p), and MP2/6-31++G(d,p) levels of theory). The experimentally determined sequences are interpreted in terms of the intrinsic properties of the molecules: hydrogen bond distances, Mulliken partial charges, van der Waals radii, and electron densities of the Y-proton acceptors. 2. Competitive hydrogen bonds and conformational equilibria in 2,6-disubstituted phenols containing two different carbonyl substituents. The rotational isomers of ten unsymmetrical 2,6-disubstituted phenols as obtained by combinations of five different carbonyl substituents (COOH, COOCH 3 , CHO, COCH 3 , and CONH 2 ) have been theoretically investigated at the B3LYP/6-31G(d,p) level of theory. The relative stability of four to five conformers of each compound were determined by full geometry optimization for free molecules as well as for molecules in reaction fields with dielectric constants up to ε=37.5. A comparison with IR spectroscopic data of available compounds revealed excellent agreement with the theoretically predicted stability sequences and conformational equilibria. The stability of a conformer could be interpreted to be governed by the following two contributions: (i) an attractive hydrogen bond

  2. Crystal structure, vibrational spectra and DFT studies of hydrogen bonded 1,2,4-triazolium hydrogenselenate

    Science.gov (United States)

    Arjunan, V.; Thirunarayanan, S.; Marchewka, M. K.; Mohan, S.

    2017-10-01

    The new hydrogen bonded molecular complex 1,2,4-triazolium hydrogenselenate (THS) is prepared by the reaction of 1H-1,2,4-triazole and selenic acid. This complex is stabilised by N-H⋯O and C-H⋯O hydrogen bonding and electrostatic attractive forces between 1H and 1,2,4-triazolium cations and hydrogen selenate anions. The XRD studies revealed that intermolecular proton transfer occur from selenic acid to 1H-1,2,4-triazole molecule, results in the formation of 1,2,4-triazolium hydrogenselenate which contains 1,2,4-triazolium cations and hydrogenselenate anions. The molecular structure of THS crystal has also been optimised by using Density Functional Theory (DFT) using B3LYP/cc-pVTZ and B3LYP/6-311++G** methods in order to find the whole characteristics of the molecular complex. The theoretical structural parameters such as bond length, bond angle and dihedral angle determined by DFT methods are well agreed with the XRD parameters. The atomic charges and thermodynamic properties are also calculated and analysed. The energies of frontier molecular orbitals HOMO, LUMO, HOMO-1, LUMO+1 and LUMO-HUMO energy gap are calculated to understand the kinetic stability and chemical reactivity of the molecular complex. The natural bond orbital analysis (NBO) has been performed in order to study the intramolecular bonding interactions and delocalisation of electrons. These intra molecular charge transfer may induce biological activities such as antimicrobials, antiinflammatory, antifungal etc. The complete vibrational assignments of THS have been performed by using FT-IR and FT-Raman spectra.

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

    Indian Academy of Sciences (India)

    total electronic density and its corresponding Laplacian in BCPs and RCPs. Consequently, in the RAHB sys- tems with N–H···N unit, these parameters are good descriptors for investigation of IHB energy. In correla- tion between IHB energy and ρN···H, figure 2(a), in spite of including the MA results, excellent correlation.

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

    Science.gov (United States)

    Miño, German; Barriga, Raul; Gutierrez, Gonzalo

    2014-08-28

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

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

    Science.gov (United States)

    Wimmer, Michael

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

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  7. Studies of Hydrogen Bonding Between N, N-Dimethylacetamide and Primary Alcohols

    Directory of Open Access Journals (Sweden)

    M. S. Manjunath

    2009-01-01

    Full Text Available Hydrogen bonding between N, N-dimethylacetamide (DMA and alcohols has been studied in carbon tetrachloride solution by an X-band Microwave bench at 936GHz. The dielectric relaxation time (τ of the binary system are obtained by both Higasi's method and Gopalakrishna method. The most likely association complex between alcohol and DMA is 1:1 stoichiometric complex through the hydroxyl group of the alcohol and the carbonyl group of amide. The results show that the interaction between alcohols and amides is 1:1 complex through the free hydroxyl group of the alcohol and the carbonyl group of amide and the alkyl chain-length of both the alcohols and amide plays an important role in the determination of the strength of hydrogen bond (O-H: C=O formed and suggests that the proton donating ability of alcohols is in the order: 1-propanol < 1-butanol < 1-pentanol and the accepting ability of DMA.

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

    International Nuclear Information System (INIS)

    Hanna, Gabriel; Geva, Eitan

    2010-01-01

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

  9. Cryosolution infrared study of hydrogen bonded halothane acetylene complex

    Science.gov (United States)

    Melikova, S. M.; Rutkowski, K. S.; Rospenk, M.

    2018-05-01

    The interactions between halothane (2-bromo-2-chloro-1,1,1-trifluoroethane) and acetylene (C2H2) are studied by FTIR spectroscopy. Results obtained in liquid cryosolutions in Kr suggest weak complex formation stabilized by H - bond. The complexation enthalpy (∼11 kJ/mol) is evaluated in a series of temperature measurements (T ∼ 120-160 K) of integrated intensity of selected bands performed in liquefied Kr. The quantum chemical MP2/6-311++G(2d,2p) calculations predict four different structures of the complex. The most stable and populated (94% at T∼120 K) structure corresponds to the H - bond between H atom of halothane and pi-electron of triple bond between C atoms of acetylene. Wave numbers of vibrational bands of the most stable structure are calculated in anharmonic approximation implemented in Gaussian program.

  10. 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.

  11. Photoinduced electron transfer through hydrogen bonds in a rod-like donor-acceptor molecule: A time-resolved EPR study

    International Nuclear Information System (INIS)

    Jakob, Manuela; Berg, Alexander; Stavitski, Eli; Chernick, Erin T.; Weiss, Emily A.; Wasielewski, Michael R.; Levanon, Haim

    2006-01-01

    Light-driven multi-step intramolecular electron transfer in a rod-like triad, in which two of the three redox components are linked by three hydrogen bonds, was studied by time-resolved electron paramagnetic resonance (TREPR) and optical spectroscopies. One part of the molecule consists of a p-methoxyaniline primary electron donor (MeOAn) covalently linked to a 4-aminonaphthalene-1, 8-dicarboximide (6ANI) chromophoric electron acceptor (MeOAn-6ANI). The unsubstituted dicarboximide of 6ANI serves as one half of a hydrogen bonding receptor pair. The other half of the receptor pair consists of a melamine linked to a naphthalene-1,8:4,5-bis(dicarboximide) (NI) secondary electron acceptor (MEL-NI). TREPR spectroscopy is used to probe the electronic interaction between the radicals within the photogenerated, spin-correlated radical ion pair MeOAn ·+ -6ANI/MEL-NI ·- . The results are compared to those obtained in earlier studies in which MeOAn-6ANI is covalently linked to NI through a 2,5-dimethylphenyl group (MeOAn-6ANI-Ph-NI). We show that the electronic coupling between the oxidized donor and reduced acceptor in the hydrogen-bonded radical ion pair MeOAn ·+ -6ANI/MEL-NI ·- is very similar to that of MeOAn ·+ -6ANI-Ph-NI ·-

  12. Rotational Spectrum, Conformational Composition, Intramolecular Hydrogen Bonding, and Quantum Chemical Calculations of Mercaptoacetonitrile (HSCH2C≡N), a Compound of Potential Astrochemical Interest.

    Science.gov (United States)

    Møllendal, Harald; Samdal, Svein; Guillemin, Jean-Claude

    2016-03-31

    The microwave spectra of mercaptoacetonitrile (HSCH2C≡N) and one deuterated species (DSCH2C≡N) were investigated in the 7.5-124 GHz spectral interval. The spectra of two conformers denoted SC and AP were assigned. The H-S-C-C chain of atoms is synclinal in SC and anti-periplanar in AP. The ground state of SC is split into two substates separated by a comparatively small energy difference resulting in closely spaced transitions with equal intensities. Several transitions of the parent species of SC deviate from Watson's Hamiltonian. Only slight improvements were obtained using a Hamiltonian that takes coupling between the two substates into account. Deviations from Watson's Hamiltonian were also observed for the parent species of AP. However, the spectrum of the deuterated species, which was investigated only for the SC conformer, fits satisfactorily to Watson's Hamiltonian. Relative intensity measurements found SC to be lower in energy than AP by 3.8(3) kJ/mol. The strength of the intramolecular hydrogen bond between the thiol and cyano groups was estimated to be ∼2.1 kJ/mol. The microwave work was augmented by quantum chemical calculations at CCSD and MP2 levels using basis sets of minimum triple-ζ quality. Mercaptoacetonitrile has astrochemical interest, and the spectra presented herein should be useful for a potential identification of this compound in the interstellar medium. Three different ways of generating mercaptoacetonitrile from compounds already found in the interstellar medium were explored by quantum chemical calculations.

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

    International Nuclear Information System (INIS)

    Luo, Y.

    2004-01-01

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

  14. Interstellar hydrogen bonding

    Science.gov (United States)

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

    2018-06-01

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

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

    Science.gov (United States)

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

    2017-11-09

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

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

    Science.gov (United States)

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

    2009-12-01

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

  17. Dynamic study of excited state hydrogen-bonded complexes of harmane in cyclohexane-toluene mixtures.

    Science.gov (United States)

    Carmona, Carmen; Balón, Manuel; Galán, Manuel; Guardado, Pilar; Muñoz, María A

    2002-09-01

    Photoinduced proton transfer reactions of harmane or 1-methyl-9H-pyrido[3,4-b]indole (HN) in the presence of the proton donor hexafluoroisopropanol (HFIP) in cyclohexane-toluene mixtures (CY-TL; 10% vol/vol of TL) have been studied. Three excited state species have been identified: a 1:2 hydrogen-bonded proton transfer complex (PTC), between the pyridinic nitrogen of the substrate and the proton donor, a hydrogen-bonded cation-like exciplex (CL*) with a stoichiometry of at least 1:3 and a zwitterionic exciplex (Z*). Time-resolved fluorescence measurements evidence that upon excitation of ground state PTC, an excited state equilibrium is established between PTC* and the cationlike exciplex, CL*, lambdaem approximately/= 390 nm. This excited state reaction is assisted by another proton donor molecule. Further reaction of CL* with an additional HFIP molecule produces the zwitterionic species, Z*, lambda(em) approximately/= 500 nm. From the analysis of the multiexponential decays, measured at different emission wavelengths and as a function of HFIP concentration, the mechanism of these excited state reactions has been established. Thus, three rate constants and three reciprocal lifetimes have been determined. The simultaneous study of 1,9-dimethyl-9H-pyrido[3,4-b]indole (MHN) under the same experimental conditions has helped to understand the excited state kinetics of these processes.

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

    Science.gov (United States)

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

    2017-10-01

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

  19. HR-EELS study of hydrogen bonding configuration, chemical and thermal stability of detonation nanodiamond films

    Energy Technology Data Exchange (ETDEWEB)

    Michaelson, Sh.; Akhvlediani, R. [Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000 (Israel); Petit, T.; Girard, H.A.; Arnault, J.C. [CEA, LIST, Diamond Sensors Laboratory, F-91191 Gif sur Yvette (France); Hoffman, A., E-mail: choffman@tx.technion.ac.il [Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000 (Israel)

    2014-06-01

    Nano-diamond films composed of 3–10 nm grains prepared by the detonation method and deposited onto silicon substrates by drop-casting were examined by high resolution electron energy loss spectroscopy (HR-EELS), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and secondary ion mass spectroscopy (SIMS). The impact of (i) ex-situ ambient annealing at 400 °C and (ii) ex-situ hydrogenation on hydrogen bonding and its thermal stability were examined. In order to clarify the changes in hydrogen bonding configuration detected on the different surfaces as a function of thermal annealing, in-situ hydrogenation by thermally activated atomic hydrogen was performed and examined. This study provides direct evidence that the exposure to ambient conditions and medium temperature ambient annealing have a pronounced effect on the hydrogen-carbon bonding configuration onto the nano-diamond surfaces. In-situ 1000 °C annealing results in irreversible changes of the film surface and partial nano-diamond silicidation.

  20. Competing intramolecular N-H⋯O=C hydrogen bonds and extended intermolecular network in 1-(4-chlorobenzoyl)-3-(2-methyl-4-oxopentan-2-yl) thiourea analyzed by experimental and theoretical methods

    Energy Technology Data Exchange (ETDEWEB)

    Saeed, Aamer, E-mail: aamersaeed@yahoo.com [Department of Chemistry, Quaid-I-Azam University, Islamabad 45320 (Pakistan); Khurshid, Asma [Department of Chemistry, Quaid-I-Azam University, Islamabad 45320 (Pakistan); Jasinski, Jerry P. [Department of Chemistry, Keene State College, 229 Main Street Keene, NH 03435-2001 (United States); Pozzi, C. Gustavo; Fantoni, Adolfo C. [Instituto de Física La Plata, Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 49 y 115, La Plata, Buenos Aires (Argentina); Erben, Mauricio F., E-mail: erben@quimica.unlp.edu.ar [CEQUINOR (UNLP, CONICET-CCT La Plata), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, C.C. 962, (1900) La Plata, Buenos Aires (Argentina)

    2014-03-18

    Highlights: • Two distinct N-H⋯O=C intramolecular competing hydrogen bonds are feasible in the title molecule. • Crystal structures and vibrational properties were determined. • The C=O and C=S double bonds of the acyl-thiourea group are mutually oriented in opposite directions. • A strong hyperconjugative lpO1 → σ{sup ∗}(N2-H) remote interaction was detected. • Topological analysis reveals a Cl⋯N interaction playing a relevant role in crystal packing. - Abstract: The synthesis of a novel 1-acyl-thiourea species (C{sub 14}H{sub 17}N{sub 2}O{sub 2}SCl), has been tailored in such a way that two distinct N-H⋯O=C intramolecular competing hydrogen bonds are feasible. The X-ray structure analysis as well as the vibrational (FT-IR and FT-Raman) data reveal that the S conformation is preferred, with the C=O and C=S bonds of the acyl-thiourea group pointing in opposite directions. The preference for the intramolecular N-H⋯O=C hydrogen bond within the -C(O)NHC(S)NH- core is confirmed. The Natural Bond Orbital and the Atom in Molecule approaches demonstrate that a strong hyperconjugative lpO → σ{sup ∗}(N-H) remote interaction between the acyl and the thioamide N-H groups is responsible for the stabilization of the S conformation. Intermolecular interactions have been characterized in the periodic system electron density and the topological analysis reveals the presence of an extended intermolecular network in the crystal, including a Cl⋯N interaction playing a relevant role in crystal packing.

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

    DEFF Research Database (Denmark)

    Olesen, Solveig Gaarn; Hammerum, Steen

    2009-01-01

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

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

    Science.gov (United States)

    Mondal, Anirban; Balasubramanian, Sundaram

    2015-02-05

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

  3. Hydrogen bond controlled adduct formation of meso-tetra(4-sulfonatophenyl)porphyrin with protic acids: a UV-vis spectroscopic study.

    Science.gov (United States)

    Zakavi, Saeed; Rahiminezhad, Hajar; Alizadeh, Robabeh

    2010-12-01

    Interaction of meso-tetra(4-sulfonatophenyl)porphyrin (H2tppS4) with weak and strong protic acid have been studied by UV-vis spectroscopy in water, dichloromethane and methanol. Different shifts of the Soret and Q(0,0) bands in the three solvents, the aggregation of diprotonated species and the stability of porphyrin-acid adducts in the solution, may be explained by the inter- and intramolecular hydrogen bonds. Whilst, the addition of excess amounts of tetra-n-butylammonium chloride to H2tppS4(Cl)2 in dichloromethane has little to no effect on the UV-vis spectrum of the dication, gradual addition of tetra-n-butylammonium hydrogen sulfate to the dichloromethane solution of H2tppS4(H2SO4)2 leads to the degradation of adducts and the release of porphryin. The results of this study clearly show the crucial role played by hydrogen bonds between the porphyrin diprotonated species and the counter ion in the stability of porphyrin diacids in solution. Copyright © 2010 Elsevier B.V. All rights reserved.

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

  5. BINDING OF THE RESPIRATORY CHAIN INHIBITOR ANTIMYCIN TO THE MITOCHONDRIAL bc1 COMPLEX: A NEW CRYSTAL STRUCTURE REVEALS AN ALTERED INTRAMOLECULAR HYDROGEN-BONDING PATTERN.

    OpenAIRE

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

    2005-01-01

    Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex. Structure-activity-relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding specificity, and suggested that a low pKa for the phenolic OH group and an intramolecular H-bond between that OH and the carbonyl O of the salicylamide linkage are important. Tw...

  6. Deuterium isotope effects on 13C and 15N chemical shifts of intramolecularly hydrogen-bonded enaminocarbonyl derivatives of Meldrum’s and Tetronic acid

    Science.gov (United States)

    Ullah, Saif; Zhang, Wei; Hansen, Poul Erik

    2010-07-01

    Secondary deuterium isotope effects on 13C and 15N nuclear shieldings in a series of cyclic enamino-diesters and enamino-esters and acyclic enaminones and enamino-esters have been examined and analysed using NMR and DFT (B3LYP/6-31G(d,p)) methods. One-dimensional and two-dimensional NMR spectra of enaminocarbonyl and their deuterated analogues were recorded in CDCl 3 and CD 2Cl 2 at variable temperatures and assigned. 1JNH coupling constants for the derivatives of Meldrum's and tetronic acids reveal that they exist at the NH-form. It was demonstrated that deuterium isotope effects, for the hydrogen bonded compounds, due to the deuterium substitution at the nitrogen nucleus lead to large one-bond isotope effects at nitrogen, 1Δ 15N(D), and two-bond isotope effects on carbon nuclei, 2ΔC(ND), respectively. A linear correlations exist between 2ΔC(ND) and 1Δ 15N(D) whereas the correlation with δNH is divided into two. A good agreement between the experimentally observed 2ΔC(ND) and calculated dσ 13C/dR NH was obtained. A very good correlation between calculated NH bond lengths and observed NH chemical shifts is found. The observed isotope effects are shown to depend strongly on Resonance Assisted Hydrogen bonding.

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

    Science.gov (United States)

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

    2018-06-01

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

  8. A spectroscopic study of the hydrogen bonding and pi-pi stacking interactions of harmane with quinoline.

    Science.gov (United States)

    Balón, M; Guardado, P; Muñoz, M A; Carmona, C

    1998-01-01

    A spectroscopic (UV-vis, Fourier transform IR, steady state, and time-resolved fluorescence) study of the interactions of the ground and excited singlet states of harmane (1-methyl-9H-pyrido/3,4-b/indole) with quinoline has been carried out in cyclohexane, toluene, and buffered pH=8.7 aqueous solutions. To analyze how the number of rings in the substrate influences these interactions, pyridine and phenanthridine have also been included in this study. In cyclohexane and toluene 1:1 stoichiometric hydrogen-bonded complexes are formed in both the ground and the excited singlet states. As the number of rings of the benzopyridines and the solvent polarity increase hydrogen-bonding interactions weaken and pi-pi van der Waals interactions become apparent.

  9. The thermodynamic stability of hydrogen bonded and cation bridged complexes of humic acid models-A theoretical study

    International Nuclear Information System (INIS)

    Aquino, Adelia J.A.; Tunega, Daniel; Pasalic, Hasan; Haberhauer, Georg; Gerzabek, Martin H.; Lischka, Hans

    2008-01-01

    Hydrogen bonded and cation bridged complexation of poly(acrylic acid) oligomers, representing a model compound for humic acids, with acetic acid and the herbicide (4-chloro-2-methylphenoxy) acetic acid (MCPA) have been studied by means of density functional theory. Solvation effects were computed by means of a combination of microsolvation (explicit insertion of water molecules) and global solvation (polarizable continuum approach). The stability of hydrogen bonded complexes in solution is characterized by a strong competition between solute and solvent molecules. The cation bridged complexes of the negatively charged (deprotonated) ligands were found to be strongly favored explaining the capability of humic acids to fixate anionic species from soil solutions and the ability to form cross-linking structures within the humic acid macromolecules

  10. Estimation of strength in different extra Watson-Crick hydrogen bonds in DNA double helices through quantum chemical studies.

    Science.gov (United States)

    Bandyopadhyay, D; Bhattacharyya, D

    2006-10-15

    It was shown earlier, from database analysis, model building studies, and molecular dynamics simulations that formation of cross-strand bifurcated or Extra Watson-Crick hydrogen (EWC) bonds between successive base pairs may lead to extra rigidity to DNA double helices of certain sequences. The strengths of these hydrogen bonds are debatable, however, as they do not have standard linear geometry criterion. We have therefore carried out detailed ab initio quantum chemical studies using RHF/6-31G(2d,2p) and B3LYP/6-31G(2p,2d) basis sets to determine strengths of several bent hydrogen bonds with different donor and acceptors. Interaction energy calculations, corrected for the basis set superposition errors, suggest that N-H...O type bent EWC hydrogen bonds are possible along same strands or across the strands between successive base pairs, leading to significant stability (ca. 4-9 kcal/mol). The N-H...N and C-H...O type interactions, however, are not so stabilizing. Hence, consideration of EWC N-H...O H-bonds can lead to a better understanding of DNA sequence directed structural features. Copyright (c) 2006 Wiley Periodicals, Inc.

  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)

    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 400×10?6 (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. A study on hydrogen bond in coal macerals with in situ diffuse reflectance FTIR by using a new experimental method

    Energy Technology Data Exchange (ETDEWEB)

    Li, D.T.; Li, W.; Sun, Q.L.; Li, B.Q. [Chinese Academy of Science, Taiyuan (China). Inst. for Coal Chemistry

    2003-04-01

    A new method using the small porcelain as the reactor combined with increasing the flow rate of carrier gas was proposed, which has the advantage of excluding the condensation of volatile produced by heated solid samples on the windows during in situ diffuse reflectance FTIR experiment. Moreover, the feasibility of this method was also discussed. Using this method, the distribution and thermal stability of hydrogen bonds in coal macerals obtained from two coals were studied. The results show that the differences between the distribution of hydrogen bonds formed by hydroxyl group in the macerals of two coals were very similar. For the vitrinites the thermal stability of SH-N, carboxylic acid dimmers and self-associated OH is higher than those in inertinites but for OH-N and hydroxyl tetramers and OH-OR{sub 2} there are no obvious laws. For OH-{pi}, its content increased with increasing temperature to 350-380{sup o}C, and then decreased with further heating. The variation of hydrogen bonds in macerals reflects the difference in their structure.

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

    International Nuclear Information System (INIS)

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

    1989-01-01

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

  14. Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics

    Science.gov (United States)

    Brela, Mateusz Z.; Boczar, Marek; Malec, Leszek M.; Wójcik, Marek J.; Nakajima, Takahito

    2018-05-01

    Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.

  15. A comparison of hydrogen-bonded and van der Waals isomers of phenolṡṡnitrogen and phenolṡṡcarbon monoxide: An ab initio study

    Science.gov (United States)

    Chapman, Darren M.; Müller-Dethlefs, Klaus; Peel, J. Barrie

    1999-08-01

    The hydrogen-bonded and van der Waals isomers of phenolṡṡnitrogen and phenolṡṡcarbon monoxide in their neutral electronic (S0) and cation ground state (D0) were studied using ab initio HF/6-31G*, MP2/6-31G*, and B3LYP/6-31G* methods. The hydrogen-bonded isomers have the ligand bound via the hydroxyl group of the phenol ring, while the van der Waals isomers studied have the ligand located above the aromatic ring. For both complexes, the hydrogen-bonded isomer was found to be the most stable form for both the S0 and the D0 states. For phenolṡṡcarbon monoxide, twice as many isomers as compared to phenolṡṡnitrogen were found. The hydrogen-bonded isomer with the carbon end bonded to the hydroxyl group was the most stable structure for both the S0 and the D0 states.

  16. A conformation-selective IR-UV study of the dipeptides Ac-Phe-Ser-NH2 and Ac-Phe-Cys-NH2: probing the SH···O and OH···O hydrogen bond interactions.

    Science.gov (United States)

    Yan, Bin; Jaeqx, Sander; van der Zande, Wim J; Rijs, Anouk M

    2014-06-14

    The conformational preferences of peptides are mainly controlled by the stabilizing effect of intramolecular interactions. In peptides with polar side chains, not only the backbone but also the side chain interactions determine the resulting conformations. In this paper, the conformational preferences of the capped dipeptides Ac-Phe-Ser-NH2 (FS) and Ac-Phe-Cys-NH2 (FC) are resolved under laser-desorbed jet cooling conditions using IR-UV ion dip spectroscopy and density functional theory (DFT) quantum chemistry calculations. As serine (Ser) and cysteine (Cys) only differ in an OH (Ser) or SH (Cys) moiety; this subtle alteration allows us to study the effect of the difference in hydrogen bonding for an OH and SH group in detail, and its effect on the secondary structure. IR absorption spectra are recorded in the NH stretching region (3200-3600 cm(-1)). In combination with quantum chemical calculations the spectra provide a direct view of intramolecular interactions. Here, we show that both FS as FC share a singly γ-folded backbone conformation as the most stable conformer. The hydrogen bond strength of OH···O (FS) is stronger than that of SH···O (FC), resulting in a more compact gamma turn structure. A second conformer is found for FC, showing a β turn interaction.

  17. Experimental and theoretical studies on the structural, spectroscopic and hydrogen bonding on 4-nitro-n-(2,4-dinitrophenyl) benzenamine

    Science.gov (United States)

    Subhapriya, G.; Kalyanaraman, S.; Jeyachandran, M.; Ragavendran, V.; Krishnakumar, V.

    2018-04-01

    Synthesized 4-nitro-N-(2,4-dinitrophenyl) benzenamine (NDPBA) molecule was confirmed applying the tool of NMR. Theoretical prediction addressed the NMR chemical shifts and correlated well with the experimental data. The molecule subjected to theoretical DFT at 6-311++G** level unraveled the spectroscopic and structural properties of the NDPBA molecule. Moreover the structural features proved the occurrence of intramolecular Nsbnd H· · O hydrogen bonding in the molecule which was further confirmed with the help of Frontier molecular orbital analysis. Vibrational spectroscopic characterization through FT-IR and Raman experimentally and theoretically gave an account for the vibrational properties. An illustration of the topology of the molecule theoretically helped also in finding the hydrogen bonding energy.

  18. Microscopic dynamics of the hydrogen bonded systems studied by quasi-elastic slow neutron scattering

    International Nuclear Information System (INIS)

    Padureanu, I.; Aranghel, D.; Radulescu, A.; Ion, M.; Lechner, R. E.; Desmedt, A.; Pieper, J.

    2002-01-01

    The detailed understanding of the dynamical properties in highly viscous liquids such as glycerol, as well the supercooled and glassy state has attracted a great deal of attention. Glycerol is a hydrogen bonded forming system considered as intermediate between fragile and strong glasses with a glass transition temperature T g ∼ 185 K, melting temperature T m 290 K and a sound velocity V S ∼ 3330 m/s. Incoherent neutron scattering experiments from glasses generally show a broad feature with a maximum around 2 to 10 meV. This large contribution of such unusual low frequency excitations obeying the Bose-Einstein statistics to the density of states is referred to as 'boson peak' (BP) with a maximum near a frequency of 1 THz. A very much-debated question is the dramatic changes in the properties as well as the nature of the boson peak and the acoustic modes occurring in the neighborhood of this frequency. So far the experiments were not able to give a definite answer concerning the excitations giving rise to the boson peak. The inelastic X-ray scattering across the liquid glass transition in glycerol revealed propagating collective excitations in the whole liquid-glass transition temperature range. This conclusion challenges the present understanding of glasses and supercooled liquids particularly with their thermal properties. New experiments at lower temperatures than those investigated so far where the phonon scattering processes are less hard have been proposed. The relationship between the low frequency features, the microscopic structure, the nature of the forces and the atomic motions taking place at low frequencies is still an open question. According to the mode coupling theory (MCT) the glass transition is interpreted as a two-step process where the glass structure is softened by fast local motions (β - process) until some temperature T c >T g , where the structure breaks down leading to diffusion (α-process). It is an open question, whether MCT can

  19. Fluorescence Correlation Spectroscopy to Study Diffusion of Polymer Chains within Layered Hydrogen-Bonded Polymer Films

    Science.gov (United States)

    Pristinski, Denis; Kharlampieva, Evguenia; Sukhishvili, Svetlana

    2002-03-01

    Fluorescence Correlation Spectroscopy (FCS) has been used to probe molecular motions within polymer multilayers formed by hydrogen-bonding sequential self-assembly. Polyethylene glycol (PEG) molecules were end-labeled with the fluorescent tags, and self-assembled with polymethacrylic acid (PMAA) using layer-by-layer deposition. We have found that molecules included in the top adsorbed layer have significant mobility at the millisecond time scale, probably due to translational diffusion. However, their dynamics deviate from classical Brownian motion with a single diffusion time. Possible reasons for the deviation are discussed. We found that motions were significantly slowed with increasing depth within the PEG/PMAA multilayer. This phenomena occured in a narrow pH range around 4.0 in which intermolecular interactions were relatively weak.

  20. Pressure dependence of hydrogen bonding in metal deuteroxides: a neutron powder diffraction study of Mn(OD)2 and β-Co(OD)2

    International Nuclear Information System (INIS)

    Parise, J.B.; Theroux, B.; Li, R.; Loveday, J.S.; Marshall, W.G.; Klotz, S.

    1998-01-01

    The structures of deuterated pyrochroite, Mn(OD) 2 and β-Co(OD) 2 have been refined using the Rietveld method and neutron powder diffraction data collected in an opposed-anvil high pressure (Paris-Edinburgh) cell from room pressure to 9 GPa. The equation of state for Mn(OD) 2 was determined (K=41(3) GPa for fixed K'=4.7) and found to be consistent with previous studies of the isostructural brucite, Mg(OD) 2 . The compressibility of β-Co(OD) 2 on the other hand is apparently anomalous. The c-axis initially decreases at 3 times the rate of decrease of the a-axis; the ratio decreases to about 1.5 at an estimated 6 GPa before increasing again beyond this pressure. There is no obvious corresponding anomaly in the details of the atomic structure. In both materials there is an increase in the D-site disorder with pressure. A split-site model for the D-positions best fits the data at pressures above 8 GPa. There is no statistically significant increase in the O-D interatomic distance at increased pressure while the hydrogen bonding interaction D..O appears to increase as this distance decreases and the O-D..O angle increases. The intramolecular O-D bond valences, determined indirectly from the intermolecular D..O distances, decrease steadily for both materials as pressure is increased. (orig.)

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2017-02-15

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

  3. Hydrogen bonded supramolecular materials

    CERN Document Server

    Li, Zhan-Ting

    2015-01-01

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

  4. First-principles study of hydrogen-bonded molecular conductor κ -H3(Cat-EDT-TTF/ST)2

    Science.gov (United States)

    Tsumuraya, Takao; Seo, Hitoshi; Kato, Reizo; Miyazaki, Tsuyoshi

    2015-07-01

    We theoretically study hydrogen-bonded molecular conductors synthesized recently, κ -H3(Cat-EDT-TTF) 2 and its diselena analog, κ -H3(Cat-EDT-ST) 2, by first-principles density functional theory calculations. In these crystals, two H(Cat-EDT-TTF/ST) units share a hydrogen atom with a short O-H-O hydrogen bond. The calculated band structure near the Fermi level shows a quasi-two-dimensional character with a rather large interlayer dispersion due to the absence of insulating layers, in contrast with conventional molecular conductors. We discuss effective low-energy models based on H(Cat-EDT-TTF/ST) units and its dimers, respectively, where the microscopic character of the orbitals composing them are analyzed. Furthermore, we find a stable structure which is different from the experimentally determined structure, where the shared hydrogen atom becomes localized to one of the oxygen atoms, in which charge disproportionation between the two types of H(Cat-EDT-TTF) units is associated. The calculated potential energy surface for the H atom is very shallow near the minimum points; therefore the probability of the H atom can be delocalized between the two O atoms.

  5. Intramolecular CH···O hydrogen bonds in the AI and BI DNA-like conformers of canonical nucleosides and their Watson-Crick pairs. Quantum chemical and AIM analysis.

    Science.gov (United States)

    Yurenko, Yevgen P; Zhurakivsky, Roman O; Samijlenko, Svitlana P; Hovorun, Dmytro M

    2011-08-01

    The aim of this work is to cast some light on the H-bonds in double-stranded DNA in its AI and BI forms. For this purpose, we have performed the MP2 and DFT quantum chemical calculations of the canonical nucleoside conformers, relative to the AI and BI DNA forms, and their Watson-Crick pairs, which were regarded as the simplest models of the double-stranded DNA. Based on the atoms-in-molecules analysis (AIM), five types of the CH···O hydrogen bonds, involving bases and sugar, were detected numerically from 1 to 3 per a conformer: C2'H···O5', C1'H···O2, C6H···O5', C8H···O5', and C6H···O4'. The energy values of H-bonds occupy the range of 2.3-5.6 kcal/mol, surely exceeding the kT value (0.62 kcal/mol). The nucleoside CH···O hydrogen bonds appeared to "survive" turns of bases against the sugar, sometimes in rather large ranges of the angle values, pertinent to certain conformations, which points out to the source of the DNA lability, necessary for the conformational adaptation in processes of its functioning. The calculation of the interactions in the dA·T nucleoside pair gives evidence, that additionally to the N6H···O4 and N1···N3H canonical H-bonds, between the bases adenine and thymine the third one (C2H···O2) is formed, which, though being rather weak (about 1 kcal/mol), satisfies the AIM criteria of H-bonding and may be classified as a true H-bond. The total energy of all the CH···O nontraditional intramolecular H-bonds in DNA nucleoside pairs appeared to be commensurable with the energy of H-bonds between the bases in Watson-Crick pairs, which implies their possible important role in the DNA shaping.

  6. Weak hydrogen bond topology in 1,1-difluoroethane dimer: A rotational study

    Science.gov (United States)

    Chen, Junhua; Zheng, Yang; Wang, Juan; Feng, Gang; Xia, Zhining; Gou, Qian

    2017-09-01

    The rotational spectrum of the 1,1-difluoroethane dimer has been investigated by pulsed-jet Fourier transform microwave spectroscopy. Two most stable isomers have been detected, which are both stabilized by a network of three C—H⋯F—C weak hydrogen bonds: in the most stable isomer, two difluoromethyl C—H groups and one methyl C—H group act as the weak proton donors whilst in the second isomer, two methyl C—H groups and one difluoromethyl C—H group act as the weak proton donors. For the global minimum, the measurements have also been extended to its four 13C isotopologues in natural abundance, allowing a precise, although partial, structural determination. Relative intensity measurements on a set of μa-type transitions allowed estimating the relative population ratio of the two isomers as NI/NII ˜ 6/1 in the pulsed jet, indicating a much larger energy gap between these two isomers than that expected from ab initio calculation, consistent with the result from pseudo-diatomic dissociation energies estimation.

  7. A systematic structural study of halogen bonding versus hydrogen bonding within competitive supramolecular systems

    Directory of Open Access Journals (Sweden)

    Christer B. Aakeröy

    2015-09-01

    Full Text Available As halogen bonds gain prevalence in supramolecular synthesis and materials chemistry, it has become necessary to examine more closely how such interactions compete with or complement hydrogen bonds whenever both are present within the same system. As hydrogen and halogen bonds have several fundamental features in common, it is often difficult to predict which will be the primary interaction in a supramolecular system, especially as they have comparable strength and geometric requirements. To address this challenge, a series of molecules containing both hydrogen- and halogen-bond donors were co-crystallized with various monotopic, ditopic symmetric and ditopic asymmetric acceptor molecules. The outcome of each reaction was examined using IR spectroscopy and, whenever possible, single-crystal X-ray diffraction. 24 crystal structures were obtained and subsequently analyzed, and the synthon preferences of the competing hydrogen- and halogen-bond donors were rationalized against a background of calculated molecular electrostatic potential values. It has been shown that readily accessible electrostatic potentials can offer useful practical guidelines for predicting the most likely primary synthons in these co-crystals as long as the potential differences are weighted appropriately.

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

    Science.gov (United States)

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

    2016-06-01

    The purpose of this study is to confirm the impact of polar functional groups on inter and intra-molecular hydrogen bonding in haloperidol (HP) and droperidol (DP) and, hence, their effects on dissolution using a new approach. To confirm our theory, a new molecule: deshydroxy-haloperidol (DHP) was designed and its synthesis was requested from a contract laboratory. The molecule was then studied and compared to DP and HP. Unlike DHP, both the HP and DP molecules have hydrogen donor groups, therefore, DHP was used to confirm the relative effects of the hydrogen donor group on solubility and crystal packing. The solid dispersions of the three structurally related molecules: HP, DP, and DHP were prepared using PVPK30, and characterized using XRPD and IR. A comparative dissolution study was carried out in aqueous medium. The absence of a hydrogen bonding donor group in DHP resulted in an unexpected increase in its aqueous solubility and dissolution rate from solid dispersion, which is attributed to weaker crystal pack. The increased dissolution rate of HP and DP from solid dispersions is attributed to drug-polymer hydrogen bonding that interferes with the drug-drug intermolecular hydrogen bonding and provides thermodynamic stability of the dispersed drug molecules. The drug-drug intermolecular hydrogen bond is the driving force for precipitation and crystal packing.

  9. 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.

  10. 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.

  11. Supramolecular network through Nsbnd H…O, Osbnd H…O and Csbnd H…O hydrogen bonding interaction and density functional theory studies of 4-methylanilinium-3-carboxy-4-hydroxybenzenesulphonate crystal

    Science.gov (United States)

    Rajkumar, M.; Muthuraja, P.; Dhandapani, M.; Chandramohan, A.

    2018-02-01

    By utilizing the hydrogen bonding strategy, 4-methylanilinium-3-hydroxy-4-corboxy-benzenesulphonate (4MABS), an organic proton transfer molecular salt was synthesized and single crystals of it were successfully grown by slow solvent evaporation solution growth technique at ambient temperature. The 1H and 13C NMR spectra were recorded to establish the molecular structure of the title salt. The single crystal XRD analysis reveals that the title salt crystallizes in monoclinic crystal system with centrosymmetric space group, P21/n. Further, the title salt involves extensive intermolecular Nsbnd H…O, Osbnd H…O and Csbnd H…O as well as intramolecular Osbnd H…O hydrogen bonding interactions to construct supramolecular architecture. All quantum chemical calculations were performed at the level of density functional theory (DFT) with B3LYP functional using 6-311G (d,p) basis atomic set. The photoluminescence spectrum was recorded to explore the emission property of the title crystal. The presence of the various vibrational modes and functional groups in the synthesized salt was confirmed by FT-IR studies. The thermal behaviour of title crystal was established employing TG/DTA analyses. The mechanical properties of the grown crystal were determined by Vicker's microhardness studies. Dielectric measurements were carried out on the grown crystal at a different temperature to evaluate electrical properties.

  12. Influence of intramolecular hydrogen bonds on regioselectivity of glycosylation. Synthesis of lupane-type saponins bearing the OSW-1 saponin disaccharide unit and its isomers.

    Science.gov (United States)

    Kuczynska, Kinga; Cmoch, Piotr; Rárová, Lucie; Oklešťková, Jana; Korda, Anna; Pakulski, Zbigniew; Strnad, Miroslav

    2016-03-24

    A series of lupane-type saponins bearing OSW-1 disaccharide unit as well as its regio- and stereoisomers were prepared and used for the structure-activity relationships (SAR) study. Unexpected preference for 1→4-linked regioisomers and an unusual inversion of the conformation of the sugar rings were noted. Cytotoxic activity of new lupane compounds was evaluated in vitro and revealed that some saponins exhibited an interesting bioactivity profile against human cancer cell lines. Influence of the protecting groups on the cytotoxicity was investigated. These results open the way to the synthesis of various lupane-type triterpene and saponin derivatives as potential anticancer compounds. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Intramolecular hydrogen bonding in myricetin and myricitrin

    DEFF Research Database (Denmark)

    Vojta, Danijela; Dominkovic, Katarina; Miljanic, Snezana

    2017-01-01

    The molecular structures of myricetin (3,3’,4’,5,5’,7-hexahydroxyflavone; MCE) and myricitrin (myricetin 3-O-rhamnoside; MCI) are investigated by quantum chemical calculations (B3LYP/6-311G**). Two preferred molecular rotamers of MCI are predicted, corresponding to different conformations of the ...

  14. The role of hydrogen bonds in the crystals of 2-amino-4-methyl-5-nitropyridinium trifluoroacetate monohydrate and 4-hydroxybenzenesulfonate - X-ray and spectroscopic studies.

    Science.gov (United States)

    Bryndal, I; Marchewka, M; Wandas, M; Sąsiadek, W; Lorenc, J; Lis, T; Dymińska, L; Kucharska, E; Hanuza, J

    2014-04-05

    Two new organic-organic salts, 2-amino-4-methyl-5-nitropyridinium trifluoroacetate monohydrate (AMNP-TFA), and 2-amino-4-methyl-5-nitropyridinium 4-hydroxybenzenesulfonate (AMNP-HBS), were obtained and characterized by means of FT-IR, FT-Raman and single crystal X-ray crystallography. In the former crystal, the cations, anions and water molecules are linked into layers by three types of hydrogen bonds, NPH⋯O, NAH⋯O and OH⋯O. These layers are connected by weaker CH⋯O hydrogen bonds. In the latter crystal, the cations and anions form one-dimensional structure through a number of hydrogen-bonding interactions involving the OH, NH(+) and NH2 groups as donors. In this case the NPH⋯O and NAH⋯O hydrogen bonds are formed. The combination of interactions between cations and anions results in the formation of columns. Additionally, there are π-π stacking interactions between the columns. The obtained X-ray structural data are related to the vibrational spectra of the studied crystals. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. On the importance of hydrogen bonding in the promotion of Diels-Alder reactions of unactivated aldehydes: a computational study

    Science.gov (United States)

    Chemouri, Hafida; Mekelleche, Sidi Mohamed

    2014-03-01

    The kinetic solvent effects on the Diels-Alder (DA) reaction of N,N-dimethylamino-3-trimethylsilyl butadiene with p-anisaldehyde are studied by density functional calculations at the B3LYP/6-31C(d) level of theory. Experimentally, it has been found that the acceleration of this reaction is not due to the increase of the polarity of the solvent but it is rather due to hydrogen bonding (HB). Intrinsic reaction coordinate calculations combined with electron localisation function analysis show that this reaction follows a one-step two-stage mechanism with a highly asynchronous sigma bond formation process. The calculations, performed using an explicit solvent model based on the coordination of the carbonyl group with one molecule of the solvent, show a considerable decrease of the activation energy when going from the gas phase (ɛ = 1) to solution phase and this diminution is found to be more important in isopropyl alcohol (ɛ = 18.3) in comparison with acetonitrile (ɛ = 37.5). Our calculations also show that the acceleration of this DA reaction is due to the increase of the electrophilicity power of the solvated carbonyl compound and consequently the increase of the polarity of the reaction in the presence of protic solvents. The obtained results put in evidence the relevance of HB in the promotion of DA reactions of unactivated ketones as experimentally expected.

  16. A Raman spectroscopy study on the effects of intermolecular hydrogen bonding on water molecules absorbed by borosilicate glass surface

    Science.gov (United States)

    Li, Fabing; Li, Zhanlong; Wang, Ying; Wang, Shenghan; Wang, Xiaojun; Sun, Chenglin; Men, Zhiwei

    2018-05-01

    The structural forms of water/deuterated water molecules located on the surface of borosilicate capillaries have been first investigated in this study on the basis of the Raman spectral data obtained at different temperatures and under atmospheric pressure for molecules in bulk and also for molecules absorbed by borosilicate glass surface. The strongest two fundamental bands locating at 3063 cm-1 (2438 cm-1) in the recorded Raman spectra are assigned here to the Osbnd H (Osbnd D) bond stretching vibrations and they are compared with the corresponding bands observed at 3124 cm-1 (2325 cm-1) in the Raman spectrum of ice Ih. Our spectroscopic observations have indicated that the structure of water and deuterated water molecules on borosilicate surface is similar to that of ice Ih (hexagonal phase of ice). These observations have also indicated that water molecules locate on the borosilicate surface so as to construct a bilayer structure and that strong and weak intermolecular hydrogen bonds are formed between water/deuterated molecules and silanol groups on borosilicate surface. In accordance with these findings, water and deuterated water molecules at the interface of capillary have a higher melting temperature.

  17. Hydrogen bond interactions in sulfamerazine: DFT study of the O-17, N-14, and H-2 electric field gradient tensors

    International Nuclear Information System (INIS)

    Aghazadeh, Mustafa; Mirzaei, Mahmoud

    2008-01-01

    Hydrogen bond (HB) interactions are studied in the real crystalline structure of sulfamerazine by density functional theory (DFT) calculations of the electric field gradient (EFG) tensors at the sites of O-17, N-14, and H-2 nuclei. One-molecule (single) and four-molecule (cluster) models of sulfamerazine are created by available crystal coordinates and the EFG tensors are calculated in both models to indicate the influence of HB interactions on the tensors. Directly relate to the experiments, the calculated EFG tensors are converted to the experimentally measurable nuclear quadrupole resonance (NQR) parameters, quadrupole coupling constant (qcc) and asymmetry parameter (η Q ). The evaluated NQR parameters reveal that due to contribution of the target molecule to N-H...N and N-H...O types of HB interactions, the EFG tensors at the sites of various nuclei are influenced from single model to the target molecule in cluster. Additionally, O2, N4, and H2 nuclei of the target molecule are significantly influenced by HB interactions, consequently, they have the major contributions to HB interactions in cluster model of sulfamerazine. The calculations are performed employing B3LYP method and 6-311++G** basis set using GAUSSIAN 98 suite of program

  18. A tensegrity model for hydrogen bond networks in proteins

    OpenAIRE

    Bywater, Robert P.

    2017-01-01

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

  19. Are the hydrogen bonds of RNA (.U) stronger than those of DNA (A.T)? A quantum mechanics study

    Czech Academy of Sciences Publication Activity Database

    Pérez, A.; Šponer, Jiří; Jurečka, Petr; Hobza, Pavel; Luque, Javier F.; Orozco, Modesto

    2005-01-01

    Roč. 11, č. 17 (2005), s. 5062-5066 ISSN 0947-6539 R&D Projects: GA ČR(CZ) GA203/05/0009 Institutional research plan: CEZ:AV0Z50040507 Keywords : density functional calculations * DNA * hydrogen bonds Subject RIV: BO - Biophysics Impact factor: 4.907, year: 2005

  20. Dynamics of circular hydrogen bond array in calix[4]arene in a nonpolar solvent: A nuclear magnetic resonance study

    Czech Academy of Sciences Publication Activity Database

    Lang, J.; Deckerová, V.; Czernek, Jiří; Lhoták, P.

    2005-01-01

    Roč. 122, - (2005), 044506/1-044506/11 ISSN 0021-9606 R&D Projects: GA AV ČR KJB4050311 Institutional research plan: CEZ:AV0Z40500505 Keywords : hydrogen bonds * organic compounds * spin-spin relaxation Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.138, year: 2005

  1. O hydrogen bonds in alkaloids

    Indian Academy of Sciences (India)

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

  2. Distance criterion for hydrogen bond

    Indian Academy of Sciences (India)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-03-21

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

  4. Optimising hydrogen bonding in solid wood

    DEFF Research Database (Denmark)

    Engelund, Emil Tang

    2009-01-01

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

  5. Report of the specialists' workshop on phase transition studies on hydrogen-bonded crystals by neutron and X-ray diffractometries

    International Nuclear Information System (INIS)

    Tokunaga, M.; Shibuya, I.

    1989-01-01

    The report carries a total of 15 studies on hydrogen-bonded crystals made by means of neutron/X-ray diffraction which were presented at a technical study meeting held on December 12 and 13, 1988, at the Research Reactor Institute of Kyoto University. The report covers 'introduction', 'linear relation between transition temperature and hydrogen-bond length in KDP type crystals', 'X-ray study of crystal structure under high pressure in DKDP', 'crystal structure of ADP in the paraelectric phase', 'crystal structure of Rochelle salt in the paraelectric phase', 'distortion of AsO 4 in KDA', 'study of phase transition in KDP family by dielectric dispersion', 'dielectric relaxation and phase transition in ice Ih', 'Raman scattering study of KDP', 'mechanism of phase transition in KDP by Raman scattering study under high pressure-reinvestigation of the Peercy's conclusion', 'localized modes of proton in KDP', 'hyper-Raman scattering study of hydrogen-bonded crystals', 'phase transition of CDP', 'the 180deg law in phase diagram', and 'comments'. (N.K.)

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

    Science.gov (United States)

    Kole, Goutam Kumar; Kumar, Mukesh

    2018-07-01

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

  7. Substituent effif ects on hydrogen bonding in Watson-Crick base pairs. A theoretical study

    NARCIS (Netherlands)

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

    2005-01-01

    We have theoretically analyzed Watson-Crick AT and GC base pairs in which purine C8 and/or pyrimidine C6 positions carry a substituent X = H, F, Cl or Br, using the generalized gradient approximation (GGA) of density functional theory at BP86/TZ2P. The purpose is to study the effects on structure

  8. Dielectric and conformational studies of hydrogen bonded 2-ethoxyethanol and ethyl methyl ketone system

    Science.gov (United States)

    Pattebahadur, Kanchan. L.; Deshmukh, S. D.; Mohod, A. G.; Undre, P. B.; Patil, S. S.; Khirade, P. W.

    2018-05-01

    The Dielectric constant, density and refractive index of binary mixture of 2-ethoxy ethanol (2-EE) with ethyl methyl ketone (EMK) including those of the pure liquids were measured for 11 concentrations at 25°C temperature. The experimental data is used to calculate the Excess molar volume, Excess dielectric constant, Kirkwood correlation factor and Bruggemann factor. The excess parameters results were fitted to the Redlich-Kister type polynomial equation to derive its fitting coefficient. The Kirkwood correlation factor of the mixture has been discussed to yield information about solute solvent interaction. The Bruggeman plot shows a deviation from linearity. The FT-IR spectra of pure and their binary mixtures are also studied.

  9. NQR application to the study of hydrogen dynamics in hydrogen-bonded molecular dimers

    Energy Technology Data Exchange (ETDEWEB)

    Asaji, Tetsuo, E-mail: asaji@chs.nihon-u.ac.jp [Nihon University, Department of Chemistry, College of Humanities and Sciences (Japan)

    2016-12-15

    The temperature dependences of {sup 1}H NMR as well as {sup 35}Cl NQR spin-lattice relaxation times T{sub 1} were investigated in order to study the hydrogen transfer dynamics in carboxylic acid dimers in 3,5-dichloro- and 2,6-dichlorobenzoic acids. The asymmetry energy A/ k{sub B} and the activation energy V/ k{sub B} for the hydrogen transfer were estimated to be 240 K and 900 K, and 840 K and 2500 K, respectively, for these compounds. In spite of a large asymmetric potential the quantum nature of hydrogen transfer is recognized in the slope of the temperature dependence of T{sub 1} on the low-temperature side of the T{sub 1} minimum. The NQR T{sub 1} measurements was revealed to be a good probe for the hydrogen transfer dynamics.

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

    Science.gov (United States)

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

    2010-07-01

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

  11. Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

    Science.gov (United States)

    Tiwari, Rakesh K.; Ojha, Rajendra P.; Tiwari, Gargi; Pandey, Vishnudatt; Mall, Vijaysree

    2018-05-01

    In order to elucidate the structural activity of hydrophobic modified DNA, the DMMO2-D5SICS, base pair is introduced as a constituent in different set of 12-mer and 14-mer DNA sequences for the molecular dynamics (MD) simulation in explicit water solvent. AMBER 14 force field was employed for each set of duplex during the 200ns production-dynamics simulation in orthogonal-box-water solvent by the Particle-Mesh-Ewald (PME) method in infinite periodic boundary conditions (PBC) to determine conformational parameters of the complex. The force-field parameters of modified base-pair were calculated by Gaussian-code using Hartree-Fock /ab-initio methodology. RMSD Results reveal that the conformation of the duplex is sequence dependent and the binding energy of the complex depends on the position of the modified base-pair in the nucleic acid strand. We found that non-bonding energy had a significant contribution to stabilising such type of duplex in comparison to electrostatic energy. The distortion produced within strands by such type of base-pair was local and destabilised the duplex integrity near to substitution, moreover the binding energy of duplex depends on the position of substitution of hydrophobic base-pair and the DNA sequence and strongly supports the corresponding experimental study.

  12. An Ab Initio MP2 Study of HCN-HX Hydrogen Bonded Complexes

    Directory of Open Access Journals (Sweden)

    Araújo Regiane C.M.U.

    1998-01-01

    Full Text Available An ab initio MP2/6-311++G** study has been performed to obtain geometries, binding energies and vibrational properties of HCN-HX H-bonded complexes with X = F, Cl, NC, CN and CCH. These MP2/6-311++G** results have revealed that: (i the calculated H-bond lengths are in very good agreement with the experimental ones; (ii the H-bond strength is associated with the intermolecular charge transfer and follows the order: HCN-HNC ~ HCN-HF > HCN-HCl ~ HCN-HCN > HCN-HCCH; (iii BSSE correction introduces an average reduction of 2.4 kJ/mol on the MP2/6-311++G** binding energies, i.e. 11% of the uncorrected binding energy; (iv the calculated zero-point energies reduce the stability of these complexes and show a good agreement with the available experimental values; (v the H-X stretching frequency is shifted downward upon H-bond formation. This displacement is associated with the H-bond length; (vi The more pronounced effect on the infrared intensities occurs with the H-X stretching intensity. It is much enhanced after complexation due to the charge-flux term; (vii the calculated intermolecular stretching frequencies are in very good agreement with the experimental ones; and, finally, (viii the results obtained for the HCN-HX complexes follow the same profile as those found for the acetylene-HX series but, in the latter case, the effects on the properties of the free molecules due to complexation are less pronounced than those in HCN-HX.

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

    Science.gov (United States)

    Binoy, J.; Prathima, N. B.; Murali Krishna, C.; Santhosh, C.; Hubert Joe, I.; Jayakumar, V. S.

    2006-08-01

    Acetanilide, a compound of pharmaceutical importance possessing pain-relieving properties due to its blocking the pulse dissipating along the nerve fiber, is subjected to vibrational spectral investigation using NIR FT Raman, FT-IR, and SERS. The geometry, Mulliken charges, and vibrational spectrum of acetanilide have been computed using the Hartree-Fock theory and density functional theory employing the 6-31G (d) basis set. To investigate the influence of intermolecular amide hydrogen bonding, the geometry, charge distribution, and vibrational spectrum of the acetanilide dimer have been computed at the HF/6-31G (d) level. The computed geometries reveal that the acetanilide molecule is planar, while twisting of the secondary amide group with respect to the phenyl ring is found upon hydrogen bonding. The trans isomerism and “amido” form of the secondary amide, hyperconjugation of the C=O group with the adjacent C-C bond, and donor-acceptor interaction have been investigated using computed geometry. The carbonyl stretching band position is found to be influenced by the tendency of the phenyl ring to withdraw nitrogen lone pair, intermolecular hydrogen bonding, conjugation, and hyperconjugation. A decrease in the NH and C=O bond orders and increase in the C-N bond orders due to donor-acceptor interaction can be observed in the vibrational spectra. The SERS spectral analysis reveals that the flat orientation of the molecule on the adsorption plane is preferred.

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

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

    Indian Academy of Sciences (India)

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

  16. Why are Hydrogen Bonds Directional?

    Indian Academy of Sciences (India)

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

  17. dimensional architectures via hydrogen bonds

    Indian Academy of Sciences (India)

    Administrator

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

  18. 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...

  19. 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...

  20. What is a hydrogen bond?

    Indian Academy of Sciences (India)

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

  1. Quantum mechanical study on hydrogen bonds between 3-aminophenol and CH{sub x}Cl{sub 4-}x (x=1, 2, 3): Effect of the number of halogen atoms

    Energy Technology Data Exchange (ETDEWEB)

    Lee, So Young; Kang, Hyuk [Dept. of Chemistry, Ajou University, Suwon (Korea, Republic of)

    2015-03-15

    Hydrogen bonds between 3-aminophenol and three chlorine-substituted methanes (CHCl{sub 3}, CH{sub 2}Cl{sub 2}, and CH{sub 3}Cl) were quantum mechanically studied at MP2/aug-cc-pVDZ level. Several low-energy structures with a hydrogen bond were identified for all chlorinated methanes, and the properties of their C[BOND]H stretching vibrations were investigated. When it is hydrogen-bonded to 3-aminophenol (3AP), the C[BOND]H stretching frequency of CHCl{sub 3} is blue-shifted by 18–54 cm−1, and its IR absorption intensity is 48–74 times increased, depending on the isomer. The symmetric and antisymmetric C[BOND]H stretches of CH{sub 2}Cl{sub 2} and CH{sub 3}Cl are shifted in either direction by a few cm−1 upon hydrogen-bonding to 3AP, and their IR intensity was increased by a few times. It is concluded that all chlorinated methanes can make a π-hydrogen bond to 3AP but only CHCl{sub 3}, the one with the most chlorine atoms, makes a blue-shifting hydrogen bond, or an “antihydrogen bond”.

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

    Directory of Open Access Journals (Sweden)

    Eric Morssing Vilén

    2013-08-01

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

  3. EPR-spin probe studies of model polymers: separation of covalent cross-linking effects from hydrogen bonding effects in swelled Argonne Premium Coal samples

    Energy Technology Data Exchange (ETDEWEB)

    Spears, D.R.; Sady, W.; Tucker, D.; Kispert, L.D. (University of Alabama, Tuscaloosa, AL (United States). Chemistry Dept.)

    The swelling behaviour of 2-12% cross-linked polystyrene-divinylbenzene (PSDVB) copolymers was examined by an EPR-spin probe technique. It was observed that the mechanism of spin probe inclusion was the intercalation into the matrix rather than diffusion into the pores. The disruption of van der Waals forces between adjacent aromatic rings appeared to be the primary mechanism for pyridine swelling of PSDVB. By comparing the data to results from coal swelling studies it was also inferred that the extent of hydrogen bonding in coal will have a much greater impact on its swelling properties than its covalently cross-linked character. 24 refs., 6 figs.

  4. Proton transfer and hydrogen bonding in the organic solid state: a combined XRD/XPS/ssNMR study of 17 organic acid-base complexes.

    Science.gov (United States)

    Stevens, Joanna S; Byard, Stephen J; Seaton, Colin C; Sadiq, Ghazala; Davey, Roger J; Schroeder, Sven L M

    2014-01-21

    The properties of nitrogen centres acting either as hydrogen-bond or Brønsted acceptors in solid molecular acid-base complexes have been probed by N 1s X-ray photoelectron spectroscopy (XPS) as well as (15)N solid-state nuclear magnetic resonance (ssNMR) spectroscopy and are interpreted with reference to local crystallographic structure information provided by X-ray diffraction (XRD). We have previously shown that the strong chemical shift of the N 1s binding energy associated with the protonation of nitrogen centres unequivocally distinguishes protonated (salt) from hydrogen-bonded (co-crystal) nitrogen species. This result is further supported by significant ssNMR shifts to low frequency, which occur with proton transfer from the acid to the base component. Generally, only minor chemical shifts occur upon co-crystal formation, unless a strong hydrogen bond is formed. CASTEP density functional theory (DFT) calculations of (15)N ssNMR isotropic chemical shifts correlate well with the experimental data, confirming that computational predictions of H-bond strengths and associated ssNMR chemical shifts allow the identification of salt and co-crystal structures (NMR crystallography). The excellent agreement between the conclusions drawn by XPS and the combined CASTEP/ssNMR investigations opens up a reliable avenue for local structure characterization in molecular systems even in the absence of crystal structure information, for example for non-crystalline or amorphous matter. The range of 17 different systems investigated in this study demonstrates the generic nature of this approach, which will be applicable to many other molecular materials in organic, physical, and materials chemistry.

  5. Proton transfer in a short hydrogen bond caused by solvation shell fluctuations: an ab initio MD and NMR/UV study of an (OHO)(-) bonded system.

    Science.gov (United States)

    Pylaeva, Svetlana; Allolio, Christoph; Koeppe, Benjamin; Denisov, Gleb S; Limbach, Hans-Heinrich; Sebastiani, Daniel; Tolstoy, Peter M

    2015-02-14

    We present a joint experimental and quantum chemical study on the influence of solvent dynamics on the protonation equilibrium in a strongly hydrogen bonded phenol-acetate complex in CD2Cl2. Particular attention is given to the correlation of the proton position distribution with the internal conformation of the complex itself and with fluctuations of the aprotic solvent. Specifically, we have focused on a complex formed by 4-nitrophenol and tetraalkylammonium-acetate in CD2Cl2. Experimentally we have used combined low-temperature (1)H and (13)C NMR and UV-vis spectroscopy and showed that a very strong OHO hydrogen bond is formed with proton tautomerism (PhOH···(-)OAc and PhO(-)···HOAc forms, both strongly hydrogen bonded). Computationally, we have employed ab initio molecular dynamics (70 and 71 solvent molecules, with and without the presence of a counter-cation, respectively). We demonstrate that the relative motion of the counter-cation and the "free" carbonyl group of the acid plays the major role in the OHO bond geometry and causes proton "jumps", i.e. interconversion of PhOH···(-)OAc and PhO(-)···HOAc tautomers. Weak H-bonds between CH(CD) groups of the solvent and the oxygen atom of carbonyl stabilize the PhOH···(-)OAc type of structures. Breaking of CH···O bonds shifts the equilibrium towards PhO(-)···HOAc form.

  6. Hydrogen Bonding in Proteins and Water Studied by Far-IR and Low-Wavenumber Raman Spectroscopy

    International Nuclear Information System (INIS)

    Greve, Tanja Maria; Birklund Andersen, Kristine; Engdahl, Anders; Nelander, Bengt; Faurskov Nielsen, Ole

    2008-01-01

    Far-IR spectra with a synchrotron radiation source were for the first time recorded through a microscope coupled to an FTIR-spectrometer. A comparison with spectra recorded with an ordinary globar source revealed that no artifacts occurred with synchrotron radiation. A comparison of ATR (Si-prism) and transmission spectra of a tetrapeptide showed that the ATR-microscope technique could be applied. ATR- and transmission spectra were recorded of polyglycine and compared to the low wavenumber Raman spectrum in the R(v)-representation. A protein band at 115-125 cm -1 was assigned to hydrogen bond modes. Collectively these modes might drive conformational changes in proteins. Based mainly on previously published results the determination of water with a structure like that in bulk liquid water was performed for human and animal skin samples. Changes in water content were reported for freezing and thawing of human skin biopsies and for human skin with benign or malignant skin diseases.

  7. Zinc-coordinated MOFs complexes regulated by hydrogen bonds: Synthesis, structure and luminescence study toward broadband white-light emission

    Science.gov (United States)

    Duan, Hui; Dan, Wenyan; Fang, Xiangdong

    2018-04-01

    Two new compounds, namely {[Zn(apc)2]·H2O}n (1) and [Zn(apc)2(H2O)2] (2), have been designed and synthesized with a multi-functional ligand 2-aminopyrimidine-5-carboxylic acid (Hapc). Both compounds were characterized by single crystal X-ray diffraction analysis (SC-XRD), elemental analysis (EA), infrared spectroscopy (IR), and thermogravimetric analysis (TG). In solid-state structures, 1 features a two-fold interpenetrating pillared-layer 3D framework with point symbol {83}2{86}, referring to tfa topology; while 2 exhibits a 3D framework based on super unit of Zn(apc)2(H2O)2 interconnected via hydrogen bonds. Furthermore, the luminescent properties of 1 and 2 were discussed.

  8. Di-ureasil hybrids doped with LiBF{sub 4}: Spectroscopic study of the ionic interactions and hydrogen bonding

    Energy Technology Data Exchange (ETDEWEB)

    Fernandes, Mariana [Departamento de Quimica/CQ-VR, Universidade de Tras-os-Montes e Alto Douro, 5001-801 Vila Real (Portugal); Barbosa, Paula C.; Manuela Silva, M.; Smith, Michael J. [Departamento de Quimica/Centro de Quimica, Universidade do Minho, Campus de Gualtar, 4710-057 Braga (Portugal); Zea Bermudez, Veronica de, E-mail: vbermude@utad.pt [Departamento de Quimica/CQ-VR, Universidade de Tras-os-Montes e Alto Douro, 5001-801 Vila Real (Portugal)

    2011-09-15

    Highlights: {yields} FT-IR and FT-Raman spectroscopy were used to characterize cation interactions in two LiBF{sub 4}-doped di-ureasil networks incorporating POE chains with different length. {yields} Over the range of salt content analyzed the cations bond to amorphous POE chains and form ion contact pairs with BF{sub 4}{sup -}. {yields} A crystalline POE/LiBF{sub 4} complex of unknown stoichiometry emerges at high salt concentration. - Abstract: In the present work Fourier transform infrared and Raman spectroscopy were used to characterize the cation/polymer, cation/cross-link, cation/anion and hydrogen bonding interactions in hybrid electrolytes composed of lithium tetrafluoroborate (LiBF{sub 4}) and di-urea cross-linked poly(oxyethylene) (POE)/siloxane hybrid networks (di-ureasils) designated as d-U(2000) and d-U(600) and incorporating polyether chains with ca. 40.5 and 8.5 oxyethylene repeat units, respectively. Samples with {infinity} > n {>=} 2.5 (where n, composition, is the molar ratio of CH{sub 2}CH{sub 2}O units per Li{sup +} ion) were analyzed. In both di-ureasil systems over the whole range of salt content examined the Li{sup +} ions bond to the ether oxygen atoms of amorphous POE chains and to BF{sub 4}{sup -} ions forming ion contact pairs. Spectroscopic evidences and SEM images confirm the presence of a crystalline POE/LiBF{sub 4} complex of unknown stoichiometry at n < 20 and 25, respectively. Ionic association is particularly important in the case of the d-U(600)-based materials, as a result of the presence of strong hydrogen-bonded aggregates that prevent the establishment of Li{sup +}/urea carbonyl oxygen atom interactions.

  9. A tensegrity model for hydrogen bond networks in proteins

    Directory of Open Access Journals (Sweden)

    Robert P. Bywater

    2017-05-01

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

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

    Science.gov (United States)

    Bywater, Robert P

    2017-05-01

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

  11. Synthesis, spectral characterization and structural studies of a novel O, N, O donor semicarbazone and its binuclear copper complex with hydrogen bond stabilized lattice

    Science.gov (United States)

    Layana, S. R.; Saritha, S. R.; Anitha, L.; Sithambaresan, M.; Sudarsanakumar, M. R.; Suma, S.

    2018-04-01

    A novel O,N,O donor salicylaldehyde-N4-phenylsemicarbazone, (H2L) has been synthesized and physicochemically characterized. Detailed structural studies of H2L using single crystal X-ray diffraction technique reveals the existence of intra and inter molecular hydrogen bonding interactions, which provide extra stability to the molecule. We have successfully synthesized a binuclear copper(II) complex, [Cu2(HL)2(NO3)(H2O)2]NO3 with phenoxy bridging between the two copper centers. The complex was characterized by elemental analysis, magnetic susceptibility and conductivity measurements, FT-IR, UV-Visible, mass and EPR spectral methods. The grown crystals of the copper complex were employed for the single crystal X-ray diffraction studies. The complex possesses geometrically different metal centers, in which the ligand coordinates through ketoamide oxygen, azomethine nitrogen and deprotonated phenoxy oxygen. The extensive intermolecular hydrogen bonding interactions of the coordinated and the lattice nitrate groups interconnect the complex units to form a 2D supramolecular assembly. The ESI mass spectrum substantiates the existence of 1:1 complex. The g values obtained from the EPR spectrum in frozen DMF suggest dx2 -y2 ground state for the unpaired electron.

  12. Theoretical study of γ-aminobutyric acid conformers: Intramolecular interactions and ionization energies

    Science.gov (United States)

    Wang, Ke-Dong; Wang, Mei-Ting; Meng, Ju

    2014-10-01

    Allowing for all combinations of internal single-bond rotamers, 1,296 unique trial structures of γ-Aminobutyric acid (GABA) are obtained. All of these structures are optimized at the M06-2X level of theory and a total of 68 local minimal conformers are found. The nine low-lying conformers are used for further studies. According to the calculated relative Gibbs free energies at M06-2X level of theory, we find that the dispersion is important for the relative energy of GABA. The intramolecular hydrogen bonds and hyperconjugative interaction and their effects on the conformational stability are studied. The results show that both of them have great influence on the conformers. The vertical ionization energies (VIE) are calculated and match the experimental data well. The results show that the neutral GABA in the gas phase is a multi-conformer system and at least four conformations exist.

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

    Science.gov (United States)

    Koenig, S; Müller, L; Smith, D K

    2001-03-02

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

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

    Indian Academy of Sciences (India)

    Administrator

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

  15. Conformation and hydrogen bonding in 4-Aminobutanol

    Science.gov (United States)

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

    2017-06-01

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

  16. Probing hydrogen bonding interactions and proton transfer in proteins

    Science.gov (United States)

    Nie, Beining

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

  17. On the Catalytic Effect of Water in the Intramolecular Diels–Alder Reaction of Quinone Systems: A Theoretical Study

    Directory of Open Access Journals (Sweden)

    Renato Contreras

    2012-11-01

    Full Text Available The mechanism of the intramolecular Diels–Alder (IMDA reaction of benzoquinone 1, in the absence and in the presence of three water molecules, 1w, has been studied by means of density functional theory (DFT methods, using the M05-2X and B3LYP functionals for exploration of the potential energy surface (PES. The energy and geometrical results obtained are complemented with a population analysis using the NBO method, and an analysis based on the global, local and group electrophilicity and nucleophilicity indices. Both implicit and explicit solvation emphasize the increase of the polarity of the reaction and the reduction of activation free energies associated with the transition states (TSs of this IMDA process. These results are reinforced by the analysis of the reactivity indices derived from the conceptual DFT, which show that the increase of the electrophilicity of the quinone framework by the hydrogen-bond formation correctly explains the high polar character of this intramolecular process. Large polarization at the TSs promoted by hydrogen-bonds and implicit solvation by water together with a high electrophilicity-nucleophilicity difference consistently explains the catalytic effects of water molecules.

  18. Hydrogen bonding interactions in PN...HX complexes: DFT and ab initio studies of structure, properties and topology.

    Science.gov (United States)

    Varadwaj, Pradeep Risikrishna

    2010-05-01

    Spin-restricted DFT (X3LYP and B3LYP) and ab initio (MP2(fc) and CCSD(fc)) calculations in conjunction with the Aug-CC-pVDZ and Aug-CC-pVTZ basis sets were performed on a series of hydrogen bonded complexes PN...HX (X = F, Cl, Br) to examine the variations of their equilibrium gas phase structures, energetic stabilities, electronic properties, and vibrational characteristics in their electronic ground states. In all cases the complexes were predicted to be stable with respect to the constituent monomers. The interaction energy (Delta E) calculated using a super-molecular model is found to be in this order: PN...HF > PN...HCl > PN...HBr in the series examined. Analysis of various physically meaningful contributions arising from the Kitaura-Morokuma (KM) and reduced variational space self-consistent-field (RVS-SCF) energy decomposition procedures shows that the electrostatic energy has significant contribution to the over-all interaction energy. Dipole moment enhancement (Delta mu) was observed in these complexes expected of predominant dipole-dipole electrostatic interaction and was found to follow the trend PN...HF > PN...HCl > PN...HBr at the CCSD level. However, the DFT (X3LYP and B3LYP) and MP2 levels less accurately determined these values (in this order HF 0, nabla(2)rho(c) > 0 and H(c) > 0 at the BCP) whilst the bonds in PN (rho(c) > 0, nabla(2)rho(c) > 0 and H(c) 0, nabla(2)rho(c) BD*(HX) delocalization.

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

    Science.gov (United States)

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

    2012-08-02

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

  20. Proton transfer through hydrogen bonds in two-dimensional water layers: A theoretical study based on ab initio and quantum-classical simulations

    International Nuclear Information System (INIS)

    Bankura, Arindam; Chandra, Amalendu

    2015-01-01

    The dynamics of proton transfer (PT) through hydrogen bonds in a two-dimensional water layer confined between two graphene sheets at room temperature are investigated through ab initio and quantum-classical simulations. The excess proton is found to be mostly solvated as an Eigen cation where the hydronium ion donates three hydrogen bonds to the neighboring water molecules. In the solvation shell of the hydronium ion, the three coordinated water molecules with two donor hydrogen bonds are found to be properly presolvated to accept a proton. Although no hydrogen bond needs to be broken for transfer of a proton to such presolvated water molecules from the hydronium ion, the PT rate is still found to be not as fast as it is for one-dimensional chains. Here, the PT is slowed down as the probability of finding a water with two donor hydrogen bonds in the solvation shell of the hydronium ion is found to be only 25%-30%. The hydroxide ion is found to be solvated mainly as a complex anion where it accepts four H-bonds through its oxygen atom and the hydrogen atom of the hydroxide ion remains free all the time. Here, the presolvation of the hydroxide ion to accept a proton requires that one of its hydrogen bonds is broken and the proton comes from a neighboring water molecule with two acceptor and one donor hydrogen bonds. The coordination number reduction by breaking of a hydrogen bond is a slow process, and also the population of water molecules with two acceptor and one donor hydrogen bonds is only 20%-25% of the total number of water molecules. All these factors together tend to slow down the hydroxide ion migration rate in two-dimensional water layers compared to that in three-dimensional bulk water

  1. Femtosecond laser studies of ultrafast intramolecular processes

    Energy Technology Data Exchange (ETDEWEB)

    Hayden, C. [Sandia National Laboratories, Livermore, CA (United States)

    1993-12-01

    The goal of this research is to better understand the detailed mechanisms of chemical reactions by observing, directly in time, the dynamics of fundamental chemical processes. In this work femtosecond laser pulses are used to initiate chemical processes and follow the progress of these processes in time. The authors are currently studying ultrafast internal conversion and subsequent intramolecular relaxation in unsaturated hydrocarbons. In addition, the authors are developing nonlinear optical techniques to prepare and monitor the time evolution of specific vibrational motions in ground electronic state molecules.

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

    Science.gov (United States)

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

    2016-05-20

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

  3. Structural, photophysical, and theoretical studies of imidazole-based excited-state intramolecular proton transfer molecules

    Science.gov (United States)

    Somasundaram, Sivaraman; Kamaraj, Eswaran; Hwang, Su Jin; Park, Sanghyuk

    2018-02-01

    Imidazole-based excited state intramolecular proton transfer (ESIPT) blue fluorescent molecules, 2-(1-(4-chlorophenyl)-4,5-diphenyl-1H-imidazol-2-yl)phenol (BHPI-Cl) and 2-(1-(4-bromophenyl)-4,5-diphenyl-1H-imidazol-2-yl)phenol (BHPI-Br) were designed and synthesized by Debus-Radziszewski method through a one-pot multicomponent reaction in high yield. The synthesized compounds were fully characterized by 1H NMR, 13C NMR, FT-IR, FT-Raman, GC-Mass, and elemental analysis. The molecular structures in single crystal lattice were studied by X-ray crystallographic analysis. Because of the intramolecular hydrogen bonding, hydroxyphenyl group is planar to the central imidazole ring, while the other phenyl rings gave distorted conformations to the central heterocyclic ring. BHPI-Cl and BHPI-Br molecules showed intense ESIPT fluorescence at 480 nm, because the two twisted phenyl rings on 4- and 5-positions have reduced intermolecular interaction between adjacent molecules in each crystal through a head-to-tail packing manner. Quantum chemical calculations of energies were carried out by (TD-)DFT using B3LYP/6-31G(d, p) basis set to predict the electronic absorption spectra of the compounds, and they showed good agreement between the computational and the experimental values. The thermal analyses of the synthesized molecules were also carried out by TGA/DSC method.

  4. Theoretical study of the changes in the vibrational characteristics arising from the hydrogen bonding between Vitamin C ( L-ascorbic acid) and H 2O

    Science.gov (United States)

    Dimitrova, Yordanka

    2006-02-01

    The vibrational characteristics (vibrational frequencies, infrared intensities and Raman activities) for the hydrogen-bonded system of Vitamin C ( L-ascorbic acid) with five water molecules have been predicted using ab initio SCF/6-31G(d, p) calculations and DFT (BLYP) calculations with 6-31G(d, p) and 6-31++G(d, p) basis sets. The changes in the vibrational characteristics from free monomers to a complex have been calculated. The ab initio and BLYP calculations show that the complexation between Vitamin C and five water molecules leads to large red shifts of the stretching vibrations for the monomer bonds involved in the hydrogen bonding and very strong increase in their IR intensity. The predicted frequency shifts for the stretching vibrations from Vitamin C taking part in the hydrogen bonding are up to -508 cm -1. The magnitude of the wavenumber shifts is indicative of relatively strong OH···H hydrogen-bonded interactions. In the same time the IR intensity and Raman activity of these vibrations increase upon complexation. The IR intensity increases dramatically (up to 12 times) and Raman activity increases up to three times. The ab initio and BLYP calculations show, that the symmetric OH vibrations of water molecules are more sensitive to the complexation. The hydrogen bonding leads to very large red shifts of these vibrations and very strong increase in their IR intensity. The asymmetric OH stretching vibrations of water, free from hydrogen bonding are less sensitive to the complexation than the hydrogen-bonded symmetric O sbnd H stretching vibrations. The increases of the IR intensities for these vibrations are lower and red shifts are negligible.

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

    OpenAIRE

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

    2012-01-01

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

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

    NARCIS (Netherlands)

    Engberts, Jan B.F.N.

    1995-01-01

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

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

    NARCIS (Netherlands)

    Engberts, J.B.F.N.

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

  8. Ab initio and DFT study of hydrogen bond interactions between ascorbic acid and dimethylsulfoxide based on FT-IR and FT-Raman spectra

    Science.gov (United States)

    Niazazari, Naser; Zatikyan, Ashkhen L.; Markarian, Shiraz A.

    2013-06-01

    The hydrogen bonding of 1:1 complexes formed between L-ascorbic acid (LAA) and dimethylsulfoxide (DMSO) has been studied by means of ab initio and density functional theory (DFT) calculations. Solutions of L-ascorbic acid (AA) in dimethylsulfoxide (DMSO) have been studied by means of both FT-IR (4000-220 cm-1) and FT-Raman spectroscopy. Ab initio Hartree-Fock (HF) and DFT methods have been used to determine the structure and energies of stable conformers of various types of L-AA/DMSO complexes in gas phase and solution. The basis sets 6-31++G∗∗ and 6-311+G∗ were used to describe the structure, energy, charges and vibrational frequencies of interacting complexes in the gas phase. The optimized geometric parameters and interaction energies for various complexes at different theories have been estimated. Binding energies have been corrected for basis set superposition error (BSSE) and harmonic vibrational frequencies of the structures have been calculated to obtain the stable forms of the complexes. The self-consistent reaction field (SCRF) has been used to calculate the effect of DMSO as the solvent on the geometry, energy and charges of complexes. The solvent effect has been studied using the Onsager models. It is shown that the polarity of the solvent plays an important role on the structures and relative stabilities of different complexes. The results obtained show that there is a satisfactory correlation between experimental and theoretical predictions.

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

    Science.gov (United States)

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

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

  10. Hydrogen bond dynamics in bulk alcohols

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  11. Theoretical Characterization of Hydrogen Bonding Interactions ...

    Indian Academy of Sciences (India)

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

  12. Hydrogen bond dynamics in bulk alcohols.

    Science.gov (United States)

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

    2015-06-07

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

  13. Study of variation in thermal width of nematic and induced smectic ordering phase of citric acid (CA) and 4-heptyloxybenzoic acid (7OBA) hydrogen bonded liquid crystal complexes

    Science.gov (United States)

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

    2018-01-01

    Hydrogen-bonded liquid crystals (HBLCs) have been derived from nonmesogenic citric acid (CA) and mesogenic 4-heptyloxybenzoic acid (7OBA) yielding a highly ordered smectic C (Sm C) phase along with the new smectic X (Sm X) phase which has been identified as fingerprint-type texture. Optical (polarizing optical microscopy), thermal (differential scanning calorimetry) and structural (Fourier transform infrared spectroscopy and nuclear magnetic resonance spectroscopy) properties are studied. A noteworthy observation is that the intermolecular H-bond (between CA and 7OBA) influences on its melting point and clearing temperature of the HBLCs which exhibits lower value than those of the individual compounds. A typical extended mesophase region has been observed in the present complex while varying the mixture ratio (1:1 to 1:3) than those of individual compounds. The change in the ratio of the mesogenic compound in the mixture alters thermal properties such as enthalpy value and thermal span width in nematic (N) region of HBLC complex. Optical tilt angle measurement of CA+7OBA in Sm C phase has been discussed to identify the molecular position in the mesophase.

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

    Science.gov (United States)

    Tabayashi, K.; Chohda, M.; Yamanaka, T.; Tsutsumi, Y.; Takahashi, O.; Yoshida, H.; Taniguchi, M.

    2010-06-01

    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.

  15. Experimental evidence for blue-shifted hydrogen bonding in the fluoroform-hydrogen chloride complex: a matrix-isolation infrared and ab initio study.

    Science.gov (United States)

    Gopi, R; Ramanathan, N; Sundararajan, K

    2014-07-24

    The 1:1 hydrogen-bonded complex of fluoroform and hydrogen chloride was studied using matrix-isolation infrared spectroscopy and ab initio computations. Using B3LYP and MP2 levels of theory with 6-311++G(d,p) and aug-cc-pVDZ basis sets, the structures of the complexes and their energies were computed. For the 1:1 CHF3-HCl complexes, ab initio computations showed two minima, one cyclic and the other acyclic. The cyclic complex was found to have C-H · · · Cl and C-F · · · H interactions, where CHF3 and HCl sub-molecules act as proton donor and proton acceptor, respectively. The second minimum corresponded to an acyclic complex stabilized only by the C-F · · · H interaction, in which CHF3 is the proton acceptor. Experimentally, we could trap the 1:1 CHF3-HCl cyclic complex in an argon matrix, where a blue-shift in the C-H stretching mode of the CHF3 sub-molecule was observed. To understand the nature of the interactions, Atoms in Molecules and Natural Bond Orbital analyses were carried out to unravel the reasons for blue-shifting of the C-H stretching frequency in these complexes.

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

    Science.gov (United States)

    Miller, Kathryn; Kim, Thomas

    2017-09-01

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

  17. Alkyl Radicals as Hydrogen Bond Acceptors: Computational Evidence

    DEFF Research Database (Denmark)

    Hammerum, Steen

    2009-01-01

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

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

    Science.gov (United States)

    Bespalov, S V; Tolpygo, K B

    1993-01-01

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

  19. New insights into the dual fluorescence of methyl salicylate: effects of intermolecular hydrogen bonding and solvation.

    Science.gov (United States)

    Zhou, Panwang; Hoffmann, Mark R; Han, Keli; He, Guozhong

    2015-02-12

    In this paper, we propose a new and complete mechanism for dual fluorescence of methyl salicylate (MS) under different conditions using a combined experimental (i.e., steady-state absorption and emission spectra and time-resolved fluorescence spectra) and theoretical (i.e., time-dependent density function theory) study. First, our theoretical study indicates that the barrier height for excited state intramolecular proton transfer (ESIPT) reaction of ketoB depends on the solvent polarity. In nonpolar solvents, the ESIPT reaction of ketoB is barrierless; the barrier height will increase with increasing solvent polarity. Second, we found that, in alcoholic solvents, intermolecular hydrogen bonding plays a more important role. The ketoB form of MS can form two hydrogen bonds with alcoholic solvents; one will facilitate ESIPT and produce the emission band in the blue region; the other one precludes ESIPT and produces the emission band in the near-UV region. Our proposed new mechanism can well explain previous results as well as our new experimental results.

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

    International Nuclear Information System (INIS)

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

    2003-01-01

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

  1. Structure and Hydrogen Bonding of 2-aminopyridine·(H2O)n (n=1,2) Studied by Infrared Ion Depletion Spectroscopy

    Czech Academy of Sciences Publication Activity Database

    Wu, R.; Nachtigall, Petr; Brutschy, B.

    2004-01-01

    Roč. 6, č. 3 (2004), s. 515-521 ISSN 1463-9076 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : hydrogen bonding * electronic and vibrational spectra * spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.076, year: 2004

  2. Adenine versus Guanine Quartets in Aqueous Solution. Dispersion-Corrected DFT Study on the Differences in π-Stacking and Hydrogen-Bonding Behavior

    NARCIS (Netherlands)

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

    2010-01-01

    We have investigated the performance of the dispersion-corrected density functionals (BLYP-D, BP86-D and PBE-D) and the widely used B3LYP functional for describing the hydrogen bonds and the stacking interactions in DNA base dimers. For the gas-phase situation, the bonding energies have been

  3. Infrared and Raman spectroscopy and quantum chemistry calculation studies of C-H...O hydrogen bondings and thermal behavior of biodegradable polyhydroxyalkanoate

    Czech Academy of Sciences Publication Activity Database

    Sato, H.; Dybal, Jiří; Murakami, R.; Noda, I.; Ozaki, Y.

    744-747, - (2005), s. 35-46 ISSN 0022-2860 R&D Projects: GA AV ČR IAA4050208 Keywords : infrared and Raman spectroscopy * quantum chemical calculation * C-H...O hydrogen bonding Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.440, year: 2005

  4. Ultrafast Hydrogen-Bonding Dynamics in Amyloid Fibrils.

    Science.gov (United States)

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

    2018-06-08

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

  5. Competitive intramolecular hydrogen bonding in oligo(ethylene oxide) substituted quadruple hydrogen bonded systems

    NARCIS (Netherlands)

    Greef, de T.F.A.; Nieuwenhuizen, M.M.L.; Sijbesma, R.P.; Meijer, E.W.

    2010-01-01

    A series of oligo(ethylene oxide) (oligoEO) substituted 2-ureido-pyrimidinones (UPy), differing in the number of ethylene oxide units and the length of the aliphatic spacer connecting the oligoEO side chain with the UPy group, have been prepared. It was found that variation in these structural

  6. 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.

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

    NARCIS (Netherlands)

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

    2002-01-01

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

  8. Structural, vibrational and theoretical studies of anilinium trichloroacetate: New hydrogen bonded molecular crystal with nonlinear optical properties

    Science.gov (United States)

    Tanak, H.; Pawlus, K.; Marchewka, M. K.; Pietraszko, A.

    2014-01-01

    In this work, we report a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of the potential nonlinear optical (NLO) material anilinium trichloroacetate. The FT-IR and FT-Raman spectra of the compound have been recorded together between 4000-80 cm-1 and 3600-80 cm-1 regions, respectively. The compound crystallizes in the noncentrosymmetric space group of monoclinic system. The optimized molecular structure, vibrational wavenumbers, IR intensities and Raman activities have been calculated by using density functional method (B3LYP) with 6-311++G(d,p) as higher basis set. The obtained vibrational wavenumbers and optimized geometric parameters were seen to be in good agreement with the experimental data. DSC measurements on powder samples do not indicate clearly on the occurrence of phase transitions in the temperature 113-293 K. The Kurtz and Perry powder reflection technique appeared to be very effective in studies of second-order nonlinear optical properties of the molecule. The non-linear optical properties are also addressed theoretically. The predicted NLO properties of the title compound are much greater than ones of urea. In addition, DFT calculations of the title compound, molecular electrostatic potential, frontier orbitals and thermodynamic properties were also performed at 6-311++G(d,p) level of theory. For title crystal the SHG efficiency was estimated by Kurtz-Perry method to be deff = 0.70 deff (KDP).

  9. The Comparative Studies of Binding Activity of Curcumin and Didemethylated Curcumin with Selenite: Hydrogen Bonding vs Acid-Base Interactions

    Science.gov (United States)

    Liao, Jiahn-Haur; Wu, Tzu-Hua; Chen, Ming-Yi; Chen, Wei-Ting; Lu, Shou-Yun; Wang, Yi-Hsuan; Wang, Shao-Pin; Hsu, Yen-Min; Huang, Yi-Shiang; Huang, Zih-You; Lin, Yu-Ching; Chang, Ching-Ming; Huang, Fu-Yung; Wu, Shih-Hsiung

    2015-12-01

    In this report, the in vitro relative capabilities of curcumin (CCM) and didemethylated curcumin (DCCM) in preventing the selenite-induced crystallin aggregation were investigated by turbidity tests and isothermal titration calorimetry (ITC). DCCM showed better activity than CCM. The conformers of CCM/SeO32- and DCCM/SeO32- complexes were optimized by molecular orbital calculations. Results reveal that the selenite anion surrounded by CCM through the H-bonding between CCM and selenite, which is also observed via IR and NMR studied. For DCCM, the primary driving force is the formation of an acid-base adduct with selenite showing that the phenolic OH group of DCCM was responsible for forming major conformer of DCCM. The formation mechanisms of selenite complexes with CCM or DCCM explain why DCCM has greater activity than CCM in extenuating the toxicity of selenite as to prevent selenite-induced lens protein aggregation.

  10. 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.

  11. Structural and vibrational spectroscopic studies on charge transfer and ionic hydrogen bonding interactions of melaminium benzoate dihydrate

    Science.gov (United States)

    Kanagathara, N.; Marchewka, M. K.; Drozd, M.; Gunasekaran, S.; Rajakumar, P. R.; Anbalagan, G.

    2015-06-01

    Single crystals of melaminium benzoate dihydrate (MBDH) have been grown from aqueous solution by the slow solvent evaporation method at room temperature. Crystalline nature of the grown crystal has been confirmed by X-ray powder diffraction studies. The optimized geometry, frequency and intensity of the vibrational bands of MBDH were obtained by the Hartree-Fock and density functional theory using B3LYP/cam-B3LYP with 6-311++G(d,p) basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with the experimental FT-IR and FT-Raman spectral values. The obtained vibrational wavenumbers and optimized geometric parameters are found to be in good agreement with the experimental data. UV-Visible spectrum was recorded in the region 200-400 nm and the electronic properties, HOMO-LUMO energies and other related electronic parameters are calculated. The isotropic chemical shifts computed by 1H and 13C NMR analysis also show good agreement with experimental observation. Natural bond orbital (NBO) analysis has been performed on MBDH compound to analyze the stability of the molecule arising from hyperconjugative interactions and charge delocalization. Molecular electrostatic potential surface (MEP) has also been performed by DFT/cam-B3LYP method with 6-311++G(d,p) basis set. Differential scanning calorimetric measurements performed on the powder sample indicate the phase transition point approximately at 368 and 358 K for heating and cooling, respectively.

  12. Multicomponent DFT study of geometrical H/D isotope effect on hydrogen-bonded organic conductor, κ-H3(Cat EDT-ST)2

    Science.gov (United States)

    Yamamoto, Kaichi; Kanematsu, Yusuke; Nagashima, Umpei; Ueda, Akira; Mori, Hatsumi; Tachikawa, Masanori

    2017-04-01

    We theoretically investigated a significant contraction of the hydrogen-bonding O⋯O distance upon H/D substitution in our recently developed purely organic crystals, κ-H3(Cat-EDT-ST)2 (H-ST) and its isotopologue κ-D3(Cat-EDT-ST)2 (D-ST), having π-electron systems coupled with hydrogen-bonding fluctuation. The origin of this geometrical H/D isotope effect was elucidated by using the multicomponent DFT method, which takes the H/D nuclear quantum effect into account. The optimized O⋯O distance in H-ST was found to be longer than that in D-ST due to the anharmonicity of the potential energy curve along the Osbnd H bond direction, which was in reasonable agreement with the experimental trend.

  13. Functional chiral hydrogen-bonded assemblies

    NARCIS (Netherlands)

    Mateos timoneda, Miguel

    2005-01-01

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

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

    NARCIS (Netherlands)

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

    2005-01-01

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

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

    NARCIS (Netherlands)

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

    2010-01-01

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

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

    Indian Academy of Sciences (India)

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

  17. Phase transition scheme of isolated hydrogen-bonded material h-MeHPLN studied by neutron and X-ray diffraction

    International Nuclear Information System (INIS)

    Kiyanagi, Ryoji; Kimura, Hiroyuki; Watanabe, Masashi; Noda, Yukio; Kojima, Akiko; Mochida, Tomoyuki; Sugawara, Tadashi

    2005-01-01

    The antiferroelectric material with an isolated hydrogen-bond, h-MeHPLN (5-methyl-9-hydroxyphenalenon), was structurally investigated by X-ray and neutron diffraction experiments in the low-temperature phase (T c =42K). The formation of a superlattice of 2 x b was found below T c , and the space group was identified to be P2 1 /c transformed from C2 c . Accordingly, the number of crystallographically independent molecules became two. The electron density distribution and the nuclear density distribution revealed some significant features below T c . One of the independent molecules exhibits an ordering of the hydrogen atom in the hydrogen-bond region, a conformational ordering of the methyl group and a molecular rotation around the a-axis. Moreover, a static electronic dipole moment is found in the hydrogen-bond region in this molecule. In contrast, the other molecule shows a disordered hydrogen atom, disordered conformation of the methyl group, no molecular rotation and a disordered electronic dipole moment. These features can be described simply in terms of a modulation wave of an order parameter. (author)

  18. Hydrogen Bonds and Life in the Universe

    Directory of Open Access Journals (Sweden)

    Giovanni Vladilo

    2018-01-01

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

  19. Hydrogen Bonds and Life in the Universe

    Science.gov (United States)

    2018-01-01

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

  20. Hydrogen Bonds and Life in the Universe.

    Science.gov (United States)

    Vladilo, Giovanni; Hassanali, Ali

    2018-01-03

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

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

    International Nuclear Information System (INIS)

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

    1983-01-01

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

  2. Hydrogen bonding in ionic liquids.

    Science.gov (United States)

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

    2015-03-07

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

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

    Science.gov (United States)

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

    2016-03-03

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

  4. [Study of hydrogen bonds in the "catalytic triad" of trypsin by NMR spectra at 1H, 13C, and 15N nuclei].

    Science.gov (United States)

    Golubeb, N S; Gindin, V A; Ligaĭ, S S; Smirnov, S N

    1994-05-01

    The 1H and 13C NMR of trypsin stabilized by chemical modification with a hydrophilic polymer have been obtained in a wide range of pH (1.0-11.0). The spectral features referred to some nuclei of the "catalytic triad" have been identified using different NMR techniques as well as chemical modification with selective reagents. It was found that the monoprotonation of this system results in a quasi-symmetrical hydrogen bond formed between the basic groups which provided explanation for the discrepancies between the experimental findings obtained by different authors concerning the protonation site in this catalytic system. Simulation of the catalytic triad by a 15N-labelled low molecular model suggests that an increase in the OH-group acidity is unaccompanied by a discrete double proton transfer; however, a smooth shift of the bridging protons from one basic atom to another occurs with quasi-symmetrical hydrogen bonds formed in intermediate cases. On the basis of experimental data a new concept has been proposed for the mechanism of acid-base catalysis performed by pains of weak basic groups, such as His-Im and Asp(Glu)-COO- (pKa = 3-7) which are not capable of proton abstraction from alcoholic or water OH-groups (pKa > 13). The catalysis may consist in changing the charge densities on the reacting groups due to strong H-bonding and, on the other hand, in facilitating the free movement of a proton in the field of several basic atoms when going along the reaction coordinate. The energy of very strong hydrogen bonds thus formed diminishes the activation energy of the reaction.

  5. A theoretical study of the hydrogen bonding between the vic-, cis- and trans-C 2H 2F 2 isomers and hydrogen fluoride

    Science.gov (United States)

    Rusu, Victor H.; da Silva, João Bosco P.; Ramos, Mozart N.

    2009-04-01

    MP2/6-31++G(d,p) and B3LYP/6-31++G(d,p) theoretical calculations have been employed to investigate the hydrogen bonding formation involving the vic-, cis- and trans-C 2H 2F 2 isomers and hydrogen fluoride. Our calculations have revealed for each isomer the preferential existence of two possible hydrogen-bonded complexes: a non-cyclic complex and a cyclic complex. For all the three isomers the binding energies for the non-cyclic and cyclic hydrogen complexes are essentially equal using both the MP2 and B3LYP calculations, being that the cyclic structure is slightly more stable. For instance, the binding energies including BSSE and ZPE corrections for the non-cyclic and cyclic structures of cis-C 2H 2F···HF are 8.7 and 9.0 kJ mol -1, respectively, using B3LYP calculations. The cyclic complex formation reduces the polarity, in contrast to what occurs with the non-cyclic complex. This result is more accentuated in vic-C 2H 2F 2···HF. In this latter, Δ μ(cyclic) is -3.07 D, whereas Δ μ(non-cyclic) is +1.92 D using B3LYP calculations. Their corresponding MP2 values are +0.44 D and -1.89 D, respectively. As expected, the complexation produces an H sbnd F stretching frequency downward shift, whereas its IR intensity is enhanced. On the other hand, the vibrational modes of the vic-, cis- and trans-C 2H 2F 2 isomers are little affected by complexation. The new vibrational modes due to hydrogen bonding formation show several interesting features, in particular the HF bending modes which are pure rotations in the free molecule.

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

    Science.gov (United States)

    Srivastava, Abhinav; Debnath, Ananya

    2018-03-01

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

  7. FT-IR spectroelectrochemical study of the reduction of 1,4-dinitrobenzene on Au electrode: Hydrogen bonding and protonation in proton donor mixed media

    International Nuclear Information System (INIS)

    Tian Dexiang; Jin Baokang

    2011-01-01

    Highlights: → 1,4-Dinitrobenzene electrochemical reduction on the Au electrode is explored. → Radical anion (PNB· - ) is found both in aprotic media and in proton donors mixed media. → The H-bonding forming between PNB· - , PNB 2- and proton donors in low donors concentration. → The protonation of PNB 2- occurs in high concentration proton donor mixed media. - Abstract: The electrochemical behavior of 1,4-dinitrobenzene (1,4-PNB) on the Au electrode was investigated by cyclic voltammetry (CV), in situ FT-IR spectroelectrochemistry, cyclic voltabsorptometry (CVA) and derivative cyclic voltabsorptometry (DCVA) techniques. In aprotic media, 1,4-dinitrobenzene is reversibly reduced in two-step one-electron transfer. A series of IR absorption bands at 1056, 1210, 1341, 1356, 1464 and 1549 cm -1 , tracing to PNB; PNB· - and PNB 2- are observed. In the presence of proton donors mixed media, with increasing concentrations of proton donors, hydrogen-bonding and protonation process are found successively. The values of combining proton donors with per PNB 2- to form hydrogen-bonding are estimated by using electrochemical parameters. The result of forming aromatic nitroso compound is supported by tracing the change of IR absorption bands at 1149 and 1587 cm -1 at high concentration of proton donors. Based on CVA and DCVA techniques, it is clearly distinguished that the mechanisms of electrochemical reduction of PNB are elaborated in different systems.

  8. {sup 2}H NMR study of phase transition and hydrogen dynamics in hydrogen bonded organic antiferroelectric 55DMBP-H{sub 2}ca

    Energy Technology Data Exchange (ETDEWEB)

    Asaji, Tetsuo, E-mail: asaji@chs.nihon-u.ac.jp; Hara, Masamichi; Fujimori, Hiroki [Nihon University, Department of Chemistry, College of Humanities and Sciences (Japan); Hagiwara, Shoko [Nihon University, Department of Chemistry, Graduate School of Integrated Basic Sciences (Japan)

    2016-12-15

    Hydrogen dynamics in one-dimensional hydrogen bonded organic antiferroelectric, co-crystal of 5,5’-dimethyl-2,2’-bipyridine (55DMBP) and chloranilic acid (H{sub 2}ca), was investigated by use of {sup 2}H high resolution solid-state NMR. The two types of hydrogen bonds O-H …N and N{sup +}-H …O{sup −} in the antiferroelectric phase were clearly observed as the splitting of the side band of the {sup 2}H MAS NMR spectra of the acid-proton deuterated compound 55DMBP-D {sub 2}ca. The temperature dependence of the spin-lattice relaxation time was measured of the N{sup +}-H and O-H deuterons, respectively. It was suggested that the motion of the O-H deuteron is already in the antiferroelectric phase in the fast-motion regime in the NMR time scale, while that of the N{sup +}-H deuteron is a slow motion. In the high-temperature paraelectric phase, the both deuterons become equivalent and the fast motion of the deuterons in the NMR time scale is taking place with the activation energy of 7.9 kJ mol{sup −1}.

  9. In situ ultra-small-angle X-ray scattering study under uniaxial stretching of colloidal crystals prepared by silica nanoparticles bearing hydrogen-bonding polymer grafts

    Directory of Open Access Journals (Sweden)

    Ryohei Ishige

    2016-05-01

    Full Text Available A molded film of single-component polymer-grafted nanoparticles (SPNP, consisting of a spherical silica core and densely grafted polymer chains bearing hydrogen-bonding side groups capable of physical crosslinking, was investigated by in situ ultra-small-angle X-ray scattering (USAXS measurement during a uniaxial stretching process. Static USAXS revealed that the molded SPNP formed a highly oriented twinned face-centered cubic (f.c.c. lattice structure with the [11−1] plane aligned nearly parallel to the film surface in the initial state. Structural analysis of in situ USAXS using a model of uniaxial deformation induced by rearrangement of the nanoparticles revealed that the f.c.c. lattice was distorted in the stretching direction in proportion to the macroscopic strain until the strain reached 35%, and subsequently changed into other f.c.c. lattices with different orientations. The lattice distortion and structural transition behavior corresponded well to the elastic and plastic deformation regimes, respectively, observed in the stress–strain curve. The attractive interaction of the hydrogen bond is considered to form only at the top surface of the shell and then plays an effective role in cross-linking between nanoparticles. The rearrangement mechanism of the nanoparticles is well accounted for by a strong repulsive interaction between the densely grafted polymer shells of neighboring particles.

  10. TDDFT study on excited state intramolecular proton transfer mechanism in 2-amino-3-(2‧-benzazolyl)-quinolines

    Science.gov (United States)

    Jia, Xueli; Li, Chaozheng; Li, Donglin; Liu, Yufang

    2018-03-01

    The intramolecular proton transfer reaction of the 2-amino-3-(2‧-benzoxazolyl)-quinoline (ABO) and 2-amino-3-(2‧-benzothiazolyl)-quinoline (ABT) molecules in both S0 and S1 states at B3LYP/6-311 ++G(d,p) level in ethanol solvent have been studied to reveal the deactivation mechanism of the tautomers of the two molecules from the S1 state to the S0 state. The results show that the tautomers of ABO and ABT molecules may return to the S0 state by emitting fluorescence. In addition, the bond lengths, angles and infrared spectra are analyzed to confirm the hydrogen bonds strengthened upon photoexcitation, which can facilitate the proton transfer process. The frontier molecular orbitals (MOs) and natural bond orbital (NBO) are also calculated to indicate the intramolecular charge transfer which can be used to explore the tendency of ESIPT reaction. The potential energy surfaces of the ABO and ABT molecules in the S0 and S1 states have been constructed. According to the energy potential barrier of 9.12 kcal/mol for ABO molecule and 5.96 kcal/mol for ABT molecule, it can be indicated that the proton transfer may occur in the S1 state.

  11. 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.

  12. Intra- versus Intermolecular Hydrogen Bonding: Solvent-Dependent Conformational Preferences of a Common Supramolecular Binding Motif from 1 H NMR and Vibrational Circular Dichroism Spectra.

    Science.gov (United States)

    Demarque, Daniel P; Merten, Christian

    2017-12-19

    When predicting binding properties of small molecules or larger supramolecular aggregates, intra- and intermolecular hydrogen bonds are often considered the most important factor. Spectroscopic techniques such as 1 H NMR spectroscopy are typically utilized to characterize such binding events, but interpretation is often qualitative and follows chemical intuition. In this study, we compare the effects of intramolecular hydrogen bonding and solvation on two chiral 2,6-pyridinediyl-dialkylamides. In comparison with 1 H NMR spectroscopy, vibrational circular dichroism (VCD) spectroscopy proved to be more sensitive to conformational changes. In fact, the change of the solvent from CDCl 3 to [D 6 ]DMSO generates mirror-image VCD spectra for the same enantiomer. Here, the common sense that the sterically less hindered group is more prone to solvation proved to be wrong according predicted VCD spectra, which clearly show that both asymmetric amide hydrogens are equally likely to be solvated, but never simultaneously. The competition between intra- and intermolecular hydrogen bonding and their importance for a correct prediction of spectral properties are discussed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Vibrational polarizabilities of hydrogen-bonded water

    International Nuclear Information System (INIS)

    Torii, Hajime

    2013-01-01

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

  14. Hydrogen bonding in cytosinium dihydrogen phosphite

    OpenAIRE

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

    2009-01-01

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

  15. Hydrogen bonding in cytosinium dihydrogen phosphite

    Directory of Open Access Journals (Sweden)

    Nourredine Benali-Cherif

    2009-05-01

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

  16. 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

  17. Improper, Blue-Shifting Hydrogen Bond

    Czech Academy of Sciences Publication Activity Database

    Hobza, Pavel; Havlas, Zdeněk

    2002-01-01

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

  18. Nuclear quantum effects and hydrogen bond fluctuations in water

    Science.gov (United States)

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

    2013-01-01

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

  19. Finite size effects on hydrogen bonds in confined water

    International Nuclear Information System (INIS)

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

    2008-01-01

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

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

    Science.gov (United States)

    O'Neal, Kristi L; Weber, Stephen G

    2009-01-08

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

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

    Science.gov (United States)

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

    2015-08-01

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

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

    Indian Academy of Sciences (India)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-05-21

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

  4. 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.

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

    OpenAIRE

    Jović, Branislav; Nikolić, Aleksandar; Petrović, Slobodan

    2012-01-01

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

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

    Science.gov (United States)

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

    2016-08-05

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

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

    OpenAIRE

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

    2015-01-01

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

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

    OpenAIRE

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

    2015-01-01

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

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

    NARCIS (Netherlands)

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

    2014-01-01

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

  10. Experimental and theoretical studies of solvent effects on the hydrogen bonds in homoconjugated cations of substituted 4-halo (Cl, Br) pyridine N-oxide derivatives

    International Nuclear Information System (INIS)

    Gurzynski, Lukasz; Puszko, Aniela; Makowski, Mariusz; Chmurzynski, Lech

    2007-01-01

    Hydrogen bond OHO-type bridges formed between six substituted 4-halo (Cl, Br) pyridine N-oxide systems and their simple cations have been investigated by using the potentiometric titration method. The formation constants of these complexes (expressed as lgK BHB + ) have been determined in two non-aqueous aprotic solvents with different polarity, i.e., acetone (AC) and acetonitrile (AN). It has been observed that tri- and tetra-substituted pyridine N-oxides [B] and their cationic acids [BH + ] form stable homocomplexed cations [BHB + ] stabilized by O...H...O bridges in both solvents used. It has been found that the most stable homocomplexed system is formed by 3,5-dimethyl-4-chloropyridine N-oxide (3,5Me 2 4ClPyO). The lgK BHB + values for this compound in acetone and acetonitrile are 3.15 and 2.82, respectively. Furthermore, by using ab initio methods at the RHF and MP2 levels utilizing the Gaussian 6-31++G ** basis set, the energies of formation of the homocomplexed cations and Gibbs free energies have been determined in vacuo. The calculated energy parameters in vacuo have been compared with the cationic homoconjugation constants determined potentiometrically in acetone and acetonitrile to establish a correlation between these magnitudes. Additionally, the results of potentiometric measurements have been used to determine the acidity constants of the conjugate acids of N-oxides

  11. Study on dioxygen reduction by mutational modifications of the hydrogen bond network leading from bulk water to the trinuclear copper center in bilirubin oxidase

    Energy Technology Data Exchange (ETDEWEB)

    Morishita, Hirotoshi; Kurita, Daisuke; Kataoka, Kunishige; Sakurai, Takeshi, E-mail: tsakurai@se.kanazawa-u.ac.jp

    2014-07-18

    Highlights: • Proton transport pathway in bilirubin oxidase was mutated. • Two intermediates in the dioxygen reduction steps were trapped and characterized. • A specific glutamate for dioxygen reduction by multicopper oxidases was identified. - Abstract: The hydrogen bond network leading from bulk water to the trinuclear copper center in bilirubin oxidase is constructed with Glu463 and water molecules to transport protons for the four-electron reduction of dioxygen. Substitutions of Glu463 with Gln or Ala were attributed to virtually complete loss or significant reduction in enzymatic activities due to an inhibition of the proton transfer steps to dioxygen. The single turnover reaction of the Glu463Gln mutant afforded the highly magnetically interacted intermediate II (native intermediate) with a broad g = 1.96 electron paramagnetic resonance signal detectable at cryogenic temperatures. Reactions of the double mutants, Cys457Ser/Glu463Gln and Cys457Ser/Glu463Ala afforded the intermediate I (peroxide intermediate) because the type I copper center to donate the fourth electron to dioxygen was vacant in addition to the interference of proton transport due to the mutation at Glu463. The intermediate I gave no electron paramagnetic resonance signal, but the type II copper signal became detectable with the decay of the intermediate I. Structural and functional similarities between multicopper oxidases are discussed based on the present mutation at Glu463 in bilirubin oxidase.

  12. Study on dioxygen reduction by mutational modifications of the hydrogen bond network leading from bulk water to the trinuclear copper center in bilirubin oxidase

    International Nuclear Information System (INIS)

    Morishita, Hirotoshi; Kurita, Daisuke; Kataoka, Kunishige; Sakurai, Takeshi

    2014-01-01

    Highlights: • Proton transport pathway in bilirubin oxidase was mutated. • Two intermediates in the dioxygen reduction steps were trapped and characterized. • A specific glutamate for dioxygen reduction by multicopper oxidases was identified. - Abstract: The hydrogen bond network leading from bulk water to the trinuclear copper center in bilirubin oxidase is constructed with Glu463 and water molecules to transport protons for the four-electron reduction of dioxygen. Substitutions of Glu463 with Gln or Ala were attributed to virtually complete loss or significant reduction in enzymatic activities due to an inhibition of the proton transfer steps to dioxygen. The single turnover reaction of the Glu463Gln mutant afforded the highly magnetically interacted intermediate II (native intermediate) with a broad g = 1.96 electron paramagnetic resonance signal detectable at cryogenic temperatures. Reactions of the double mutants, Cys457Ser/Glu463Gln and Cys457Ser/Glu463Ala afforded the intermediate I (peroxide intermediate) because the type I copper center to donate the fourth electron to dioxygen was vacant in addition to the interference of proton transport due to the mutation at Glu463. The intermediate I gave no electron paramagnetic resonance signal, but the type II copper signal became detectable with the decay of the intermediate I. Structural and functional similarities between multicopper oxidases are discussed based on the present mutation at Glu463 in bilirubin oxidase

  13. Halocarbons as hydrogen bond acceptors: a spectroscopic study of haloethylbenzenes (PhCH2CH2X, X = F, Cl, Br) and their hydrate clusters.

    Science.gov (United States)

    Robertson, Patrick A; Villani, Luigi; Dissanayake, Uresha L M; Duncan, Luke F; Abbott, Belinda M; Wilson, David J D; Robertson, Evan G

    2018-03-28

    The electronic spectra of 2-bromoethylbenzene and its chloro and fluoro analogues have been recorded by resonant two-photon ionisation (R2PI) spectroscopy. Anti and gauche conformers have been assigned by rotational band contour analysis and IR-UV ion depletion spectroscopy in the CH region. Hydrate clusters of the anti conformers have also been observed, allowing the role of halocarbons as hydrogen bond acceptors to be examined in this context. The donor OH stretch of water bound to chlorine is red-shifted by 36 cm -1 , or 39 cm -1 in the case of bromine. Although classed as weak H-bond acceptors, halocarbons are favourable acceptor sites compared to π systems. Fluorine stands out as the weakest H-bond acceptor amongst the halogens. Chlorine and bromine are also weak H-bond acceptors, but allow for more geometric lability, facilitating complimentary secondary interactions within the host molecule. Ab initio and DFT quantum chemical calculations, both harmonic and anharmonic, aid the structural assignments and analysis.

  14. 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.

  15. 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.

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

    Science.gov (United States)

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

    2014-06-01

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

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

    Science.gov (United States)

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

    2001-08-01

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

  18. Experimental and theoretical studies of solvent effects on the hydrogen bonds in homoconjugated cations of substituted 4-halo (Cl, Br) pyridine N-oxide derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Gurzynski, Lukasz [Department of General and Inorganic Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Puszko, Aniela [Department of Organic Chemistry, School of Economics, Wroclaw (Poland); Makowski, Mariusz [Department of General and Inorganic Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland); Chmurzynski, Lech [Department of General and Inorganic Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk (Poland)], E-mail: lech@chem.univ.gda.pl

    2007-09-15

    Hydrogen bond OHO-type bridges formed between six substituted 4-halo (Cl, Br) pyridine N-oxide systems and their simple cations have been investigated by using the potentiometric titration method. The formation constants of these complexes (expressed as lgK{sub BHB{sup +}}) have been determined in two non-aqueous aprotic solvents with different polarity, i.e., acetone (AC) and acetonitrile (AN). It has been observed that tri- and tetra-substituted pyridine N-oxides [B] and their cationic acids [BH{sup +}] form stable homocomplexed cations [BHB{sup +}] stabilized by O...H...O bridges in both solvents used. It has been found that the most stable homocomplexed system is formed by 3,5-dimethyl-4-chloropyridine N-oxide (3,5Me{sub 2}4ClPyO). The lgK{sub BHB{sup +}} values for this compound in acetone and acetonitrile are 3.15 and 2.82, respectively. Furthermore, by using ab initio methods at the RHF and MP2 levels utilizing the Gaussian 6-31++G{sup **} basis set, the energies of formation of the homocomplexed cations and Gibbs free energies have been determined in vacuo. The calculated energy parameters in vacuo have been compared with the cationic homoconjugation constants determined potentiometrically in acetone and acetonitrile to establish a correlation between these magnitudes. Additionally, the results of potentiometric measurements have been used to determine the acidity constants of the conjugate acids of N-oxides.

  19. mPW1PW91 Calculated Conformational Study of Calix[n]arene (n = 4,5,6): Hydrogen Bond

    International Nuclear Information System (INIS)

    Kim, Kwang Ho; Choe, Jong In

    2009-01-01

    We have performed mPW1PW91 calculations to investigate the conformational characteristics and hydrogen bonds of p-tert-butylcalix[4]arene, p-tert-butylcalix[5]arene, calix[6]arene and p-tertbutylcalix[ 6]arene. The structures of the different conformers of 1-3 were optimized by using mPW1PW91/ 6-31+G(d,p) method. The relative stability of the four conformers of 1 is in the following order: cone (most stable) > partial-cone > 1,2-alternate > 1,3-alternate. The relative stability of the conformers of 2 is in the following order: cone (most stable) > 1,2-alternate > partial-cone > 1,3-alternate. The relative stability of the various conformers of 3 is in the following order: cone (pinched: most stable) > partial-cone > cone (winged) ∼ 1,2-alternate ∼ 1,2,3-alternate > 1,4-alternate > 1,3-alternate > 1,3,5-alternate. The structures of the various conformers of 4 were optimized by using the mPW1PW91/6-31G(d,p) method followed by single point calculation of mPW1PW91/6-31+G(d,p). The relative stability of the conformers of 4 is in the following order: cone (pinched) > 1,2-alternate > cone (winged) > 1,4-alternate ∼ partial-cone > 1,2,3-alternate > 1,3,5-alternate > 1,3-alternate

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

    Science.gov (United States)

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

    2002-04-23

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

  1. Characterization of the hydrogen bond in molecular systems of biological interest by neutron scattering

    International Nuclear Information System (INIS)

    Cavillon, F.

    2004-10-01

    This work presents a methodology for the analysis of the scattering spectra of neutrons on molecular liquids. This method is based on the adjustment of the molecular form factor concerning great momentum transfer. The subtraction of the intra-molecular contributions gives access to information on inter-molecular interactions such as the hydrogen bond. 3 systems with increasing levels of difficulty have been studied: the ammonia molecule, the N-methyl-formamide (NMF) and the N-methyl-acetamide (NMA). The value we get for the N-D intermolecular distance of the liquid ammonia molecule is 1.7 angstrom, this value is different from the value generally admitted (2.3 angstrom) but we have validated it by studying the isotopic substitution N 14 /N 15 . The adjustment to the NMF is obtained with a good accuracy but the characterization of the hydrogen bound is more delicate to infer. A preliminary study of the NMA molecule shows that this method can give relevant results on complex molecules

  2. Mixed quantum-classical molecular dynamics study of the hydroxyl stretch in methanol/carbon-tetrachloride mixtures II: excited state hydrogen bonding structure and dynamics, infrared emission spectrum, and excited state lifetime.

    Science.gov (United States)

    Kwac, Kijeong; Geva, Eitan

    2012-03-08

    We present a mixed quantum-classical molecular dynamics study of the hydrogen-bonding structure and dynamics of a vibrationally excited hydroxyl stretch in methanol/carbon-tetrachloride mixtures. The adiabatic Hamiltonian of the quantum-mechanical hydroxyl is diagonalized on-the-fly to obtain the ground and first-excited adiabatic energy levels and wave functions which depend parametrically on the instantaneous configuration of the classical degrees of freedom. The dynamics of the classical degrees of freedom are determined by Hellmann-Feynman forces obtained by taking the expectation value of the force with respect to the ground or excited vibrational wave functions. Polarizable force fields are used which were previously shown to reproduce the experimental infrared absorption spectrum rather well, for different isotopomers and over a wide composition range [Kwac, K.; Geva, E. J. Phys. Chem. B 2011, 115, 9184]. We show that the agreement of the absorption spectra with experiment can be further improved by accounting for the dependence of the dipole moment derivatives on the configuration of the classical degrees of freedom. We find that the propensity of a methanol molecule to form hydrogen bonds increases upon photoexcitation of its hydroxyl stretch, thereby leading to a sizable red-shift of the corresponding emission spectrum relative to the absorption spectrum. Treating the relaxation from the first excited to the ground state as a nonadiabatic process, and calculating its rate within the framework of Fermi's golden rule and the harmonic-Schofield quantum correction factor, we were able to predict a lifetime which is of the same order of magnitude as the experimental value. The experimental dependence of the lifetime on the transition frequency is also reproduced. Nonlinear mapping relations between the hydroxyl transition frequency and bond length in the excited state and the electric field along the hydroxyl bond axis are established. These mapping relations

  3. Hydrogen Bond Basicity Prediction for Medicinal Chemistry Design.

    Science.gov (United States)

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

    2016-05-12

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

  4. Tetrahedrality and hydrogen bonds in water

    Science.gov (United States)

    Székely, Eszter; Varga, Imre K.; Baranyai, András

    2016-06-01

    We carried out extensive calculations of liquid water at different temperatures and pressures using the BK3 model suggested recently [P. T. Kiss and A. Baranyai, J. Chem. Phys. 138, 204507 (2013)]. In particular, we were interested in undercooled regions to observe the propensity of water to form tetrahedral coordination of closest neighbors around a central molecule. We compared the found tetrahedral order with the number of hydrogen bonds and with the partial pair correlation functions unfolded as distributions of the closest, the second closest, etc. neighbors. We found that contrary to the number of hydrogen bonds, tetrahedrality changes substantially with state variables. Not only the number of tetrahedral arrangements increases with lowering the pressure, the density, and the temperature but the domain size of connecting tetrahedral structures as well. The difference in tetrahedrality is very pronounced between the two sides of the Widom line and even more so between the low density amorphous (LDA) and high density amorphous (HDA) phases. We observed that in liquid water and in HDA, the 5th water molecule, contrary to ice and LDA, is positioned between the first and the second coordination shell. We found no convincing evidence of structural heterogeneity or regions referring to structural transition.

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

    Science.gov (United States)

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

    2008-01-01

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

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

    Indian Academy of Sciences (India)

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

  7. Influence of Intramolecular Charge Transfer and Nuclear Quantum Effects on Intramolecular Hydrogen Bonds in Azopyrimidines

    Czech Academy of Sciences Publication Activity Database

    Bártová, Kateřina; Čechová, Lucie; Procházková, Eliška; Socha, Ondřej; Janeba, Zlatko; Dračínský, Martin

    2017-01-01

    Roč. 82, č. 19 (2017), s. 10350-10359 ISSN 0022-3263 R&D Projects: GA ČR GA15-11223S Institutional support: RVO:61388963 Keywords : pyrimidines * NMR spectroscopy * DFT calculations Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 4.849, year: 2016

  8. Performance of Several Density Functional Theory Methods on Describing Hydrogen-Bond Interactions.

    Science.gov (United States)

    Rao, Li; Ke, Hongwei; Fu, Gang; Xu, Xin; Yan, Yijing

    2009-01-13

    We have investigated eleven density functionals, including LDA, PBE, mPWPW91, TPSS, B3LYP, X3LYP, PBE0, O3LYP, B97-1, MPW1K, and TPSSh, for their performances on describing hydrogen bond (HB) interactions. The emphasis has been laid not only on their abilities to calculate the intermolecular hydrogen bonding energies but also on their performances in predicting the relative energies of intermolecular H-bonded complexes and the conformer stabilities due to intramolecular hydrogen bondings. As compared to the best theoretical values, we found that although PBE and PBE0 gave the best estimation of HB strengths, they might fail to predict the correct order of relative HB energies, which might lead to a wrong prediction of the global minimum for different conformers. TPSS and TPSSh did not always improve over PBE and PBE0. B3LYP was found to underestimate the intermolecular HB strengths but was among the best performers in calculating the relative HB energies. We showed here that X3LYP and B97-1 were able to give good values for both absolute HB strengths and relative HB energies, making these functionals good candidates for HB description.

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

    Science.gov (United States)

    Hachuła, Barbara

    2018-01-01

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

  10. 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.

  11. 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.

  12. Porous Hydrogen-Bonded Organic Frameworks

    Directory of Open Access Journals (Sweden)

    Yi-Fei Han

    2017-02-01

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

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

    Science.gov (United States)

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

    2017-09-20

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

  14. Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol

    Directory of Open Access Journals (Sweden)

    Hailiang Zhao

    2016-12-01

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

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

    Science.gov (United States)

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

    2016-12-30

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

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

    Science.gov (United States)

    van der Sman, R G M

    2013-12-19

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

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

    Directory of Open Access Journals (Sweden)

    Lingjia Xu

    2007-04-01

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

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

    Science.gov (United States)

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

    2014-06-04

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

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

    Indian Academy of Sciences (India)

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

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

    International Nuclear Information System (INIS)

    Rekik, Najeh

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Jović Branislav

    2012-01-01

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

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

    Science.gov (United States)

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

    2018-03-01

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

  3. Study of first electronic transition and hydrogen bonding state of ultra-thin water layer of nanometer thickness on an α-alumina surface by far-ultraviolet spectroscopy

    Science.gov (United States)

    Goto, Takeyoshi; Kinugasa, Tomoya

    2018-05-01

    The first electronic transition (A˜ ← X˜) and the hydrogen bonding state of an ultra-thin water layer of nanometer thickness between two α-alumina surfaces (0.5-20 nm) were studied using far-ultraviolet (FUV) spectroscopy in the wavelength range 140-180 nm. The ultra-thin water layer of nanometer thickness was prepared by squeezing a water droplet ( 1 μL) between a highly polished α-alumina prism and an α-alumina plate using a high pressure clamp ( 4.7 MPa), and the FUV spectra of the water layer at different thicknesses were measured using the attenuated total reflection method. As the water layer became thinner, the A˜ ← X˜ bands were gradually shifted to higher or lower energy relative to that of bulk water; at thicknesses smaller than 4 nm, these shifts were substantial (0.1-0.2 eV) in either case. The FUV spectra of the water layer with thickness lost at thicknesses below 4 nm, because of steric hydration forces between the α-alumina surfaces.

  4. Evaluation of coupling terms between intra- and intermolecular vibrations in coarse-grained normal-mode analysis: Does a stronger acid make a stiffer hydrogen bond?

    Science.gov (United States)

    Houjou, Hirohiko

    2011-10-01

    Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m-1 for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules.

  5. The influence of hydrogen bonding on partition coefficients

    Science.gov (United States)

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

    2017-02-01

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

  6. Near-infrared analysis of hydrogen-bonding in glass- and rubber-state amorphous saccharide solids.

    Science.gov (United States)

    Izutsu, Ken-ichi; Hiyama, Yukio; Yomota, Chikako; Kawanishi, Toru

    2009-01-01

    Near-infrared (NIR) spectroscopic analysis of noncrystalline polyols and saccharides (e.g., glycerol, sorbitol, maltitol, glucose, sucrose, maltose) was performed at different temperatures (30-80 degrees C) to elucidate the effect of glass transition on molecular interaction. Transmission NIR spectra (4,000-12,000 cm(-1)) of the liquids and cooled-melt amorphous solids showed broad absorption bands that indicate random configuration of molecules. Heating of the samples decreased an intermolecular hydrogen-bonding OH vibration band intensity (6,200-6,500 cm(-1)) with a concomitant increase in a free and intramolecular hydrogen-bonding OH group band (6,600-7,100 cm(-1)). Large reduction of the intermolecular hydrogen-bonding band intensity at temperatures above the glass transition (T(g)) of the individual solids should explain the higher molecular mobility and lower viscosity in the rubber state. Mixing of the polyols with a high T(g) saccharide (maltose) or an inorganic salt (sodium tetraborate) shifted both the glass transition and the inflection point of the hydrogen-bonding band intensity to higher temperatures. The implications of these results for pharmaceutical formulation design and process monitoring (PAT) are discussed.

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

    International Nuclear Information System (INIS)

    Karyakin, A.V.

    1985-01-01

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

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

    Science.gov (United States)

    Bespalova, S V; Tolpygo, K B

    1991-11-21

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

  9. 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

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-05-10

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

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  13. Molecular Dynamics Investigation of the Effects of Concentration on Hydrogen Bonding in Aqueous Solutions of Methanol, Ethylene Glycol and Glycerol

    International Nuclear Information System (INIS)

    Zhang, Ning; Li, Weizhong; Chen, Cong; Zuo, Jianguo; Weng, Lindong

    2013-01-01

    Hydrogen bonding interaction between alcohols and water molecules is an important characteristic in the aqueous solutions of alcohols. In this paper, a series of molecular dynamics simulations have been performed to investigate the aqueous solutions of low molecular weight alcohols (methanol, ethylene glycol and glycerol) at the concentrations covering a broad range from 1 to 90 mol %. The work focuses on studying the effect of the alcohols molecules on the hydrogen bonding of water molecules in binary mixtures. By analyzing the hydrogen bonding ability of the hydroxyl (-OH) groups for the three alcohols, it is found that the hydroxyl group of methanol prefers to form more hydrogen bonds than that of ethylene glycol and glycerol due to the intra-and intermolecular effects. It is also shown that concentration has significant effect on the ability of alcohol molecule to hydrogen bond water molecules. Understanding the hydrogen bonding characteristics of the aqueous solutions is helpful to reveal the cryoprotective mechanisms of methanol, ethylene glycol and glycerol in aqueous solutions

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

    Indian Academy of Sciences (India)

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

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

    NARCIS (Netherlands)

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

    2000-01-01

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

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

    NARCIS (Netherlands)

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

    1999-01-01

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

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

    NARCIS (Netherlands)

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

    2000-01-01

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

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

    Indian Academy of Sciences (India)

    TECS

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

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

    Science.gov (United States)

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

    2003-04-07

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

  20. 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 ...

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

    Science.gov (United States)

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

    2012-01-01

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

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

    International Nuclear Information System (INIS)

    Cierpicki, Tomasz; Otlewski, Jacek

    2001-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  5. X-ray and Hydrogen-bonding Properties of 1-((1H-benzotriazol-1-ylmethylnaphthalen-2-ol

    Directory of Open Access Journals (Sweden)

    Jaime Ríos-Motta

    2009-03-01

    Full Text Available The solid state structure of 1-((1H-benzotriazol-1-ylmethylnaphthalen-2-ol, C17H13N3O, shows that this Mannich base crystallizes forming intermolecular N···HO hydrogen bonds, rather than intramolecular ones. Factors contributing to this choice of hydrogen-bonding mode are discussed. The compound crystallizes in the monoclinic system, P21/c space group, with lattice constants: a = 11.7934(9 Å, b = 14.3002(14 Å, c = 8.4444(8 Å, β = 106.243(5 deg, V = 1367.3(2 Å3, Z = 4, F(000 = 576, R1 = 6.96%, wR2 = 11.4%.

  6. Bodipy–C60 triple hydrogen bonding assemblies as heavy atom-free triplet photosensitizers: preparation and study of the singlet/triplet energy transfer† †Electronic supplementary information (ESI) available: Syntheses, structure characterization data, and UV/vis absorption and emission spectra. See DOI: 10.1039/c4sc03865g

    Science.gov (United States)

    Guo, Song; Xu, Liang; Xu, Kejing; Küçüköz, Betül; Karatay, Ahmet; Yaglioglu, Halime Gul; Hayvali, Mustafa; Elmali, Ayhan

    2015-01-01

    Supramolecular triplet photosensitizers based on hydrogen bonding-mediated molecular assemblies were prepared. Three thymine-containing visible light-harvesting Bodipy derivatives (B-1, B-2 and B-3, which show absorption at 505 nm, 630 nm and 593 nm, respectively) were used as H-bonding modules, and 1,6-diaminopyridine-appended C60 was used as the complementary hydrogen bonding module (C-1), in which the C60 part acts as a spin converter for triplet formation. Visible light-harvesting antennae with methylated thymine were prepared as references (B-1-Me, B-2-Me and B-3-Me), which are unable to form strong H-bonds with C-1. Triple H-bonds are formed between each Bodipy antenna (B-1, B-2 and B-3) and the C60 module (C-1). The photophysical properties of the H-bonding assemblies and the reference non-hydrogen bond-forming mixtures were studied using steady state UV/vis absorption spectroscopy, fluorescence emission spectroscopy, electrochemical characterization, and nanosecond transient absorption spectroscopy. Singlet energy transfer from the Bodipy antenna to the C60 module was confirmed by fluorescence quenching studies. The intersystem crossing of the latter produced the triplet excited state. The nanosecond transient absorption spectroscopy showed that the triplet state is either localized on the C60 module (for assembly B-1·C-1), or on the styryl-Bodipy antenna (for assemblies B-2·C-1 and B-3·C-1). Intra-assembly forward–backward (ping-pong) singlet/triplet energy transfer was proposed. In contrast to the H-bonding assemblies, slow triplet energy transfer was observed for the non-hydrogen bonding mixtures. As a proof of concept, these supramolecular assemblies were used as triplet photosensitizers for triplet–triplet annihilation upconversion. PMID:29218142

  7. "Anomalous" excitation in hydrogen-bonded molecular crystals - a Raman scattering study of specifically deuterated acetanilide (C 6D 5-CONH-CD 3)

    Science.gov (United States)

    Sauvajol, J. L.; De Nunzio, G.; Almairac, R.; Moret, J.; Barthés, M.; Bataillon, Place E.

    1991-01-01

    The focus of experimental and theoretical works about crystalline Acetanilide has been the "anomalous" temperature-dependent ir absorption and Raman peaks at about 1650 cm -1 and the multiband structure in the N-H stretch region. A lively discussion about the assignment of these "anomalous" bands has arisen and is still in progress. The present Raman experiments should be placed in this context as an attempt to identify the molecular degrees of freedom which originate the "anomalous" bands. In this aim Raman experiments have been performed on specifically deuterated Acetanilide [C 6D 5-CONH-CD 3] single crystal in the low-frequency (phonon) and C=O stretching regions. On cooling a distinct band at about 1495 cm -1 increases in intensity. We assign this peak to the equivalent of the 1650 cm -1 band in Acetanilide. The temperature dependence of this Raman line was studied. The results are discussed in the light of the models proposed to explain the anomalous behaviour of the 1650 cm -1 Raman line in Acetanilide.

  8. Blue-shifted and red-shifted hydrogen bonds: Theoretical study of the CH3CHO· · ·HNO complexes

    Science.gov (United States)

    Yang, Yong; Zhang, Weijun; Gao, Xiaoming

    The blue-shifted and red-shifted H-bonds have been studied in complexes CH3CHO?HNO. 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, the geometric structures and vibrational frequencies of complexes CH3CHO?HNO are calculated by both standard and CP-corrected methods, respectively. Complex A exhibits simultaneously red-shifted C bond H?O and blue-shifted N bond H?O H-bonds. Complex B possesses simultaneously two blue-shifted H-bonds: C bond H?O and N bond H?O. From NBO analysis, it becomes evident that the red-shifted C bond H?O H-bond can be explained on the basis of the two opposite effects: hyperconjugation and rehybridization. The blue-shifted C bond H?O H-bond is a result of conjunct C bond H bond strengthening effects of the hyperconjugation and the rehybridization due to existence of the significant electron density redistribution effect. For the blue-shifted N bond H?O H-bonds, the hyperconjugation is inhibited due to existence of the electron density redistribution effect. The large blue shift of the N bond H stretching frequency is observed because the rehybridization dominates the hyperconjugation.

  9. The Born-Oppenheimer molecular simulations of infrared spectra of crystalline poly-(R)-3-hydroxybutyrate with analysis of weak Csbnd H⋯Odbnd C hydrogen bonds

    Science.gov (United States)

    Brela, Mateusz Z.; Boczar, Marek; Wójcik, Marek J.; Sato, Harumi; Nakajima, Takahito; Ozaki, Yukihiro

    2017-06-01

    In this letter we present results of study of weak Csbnd H⋯Odbnd C hydrogen bonds of crystalline poly-(R)-3-hydroxybutyrate (PHB) by using Born-Oppenheimer molecular dynamics. The polymeric structure and IR spectra of PHB result from the presence of the weak hydrogen bonds. We applied the post-molecular dynamics analysis to consider a Cdbnd O motion as indirectly involved in the hydrogen bonds. Quantization of the nuclear motion of the oxygens was done to perform detailed analysis of the strength and properties of the Cdbnd O bands involved in the weak hydrogen bonds. We have also shown the dynamic character of the weak hydrogen bond interactions.

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

    Science.gov (United States)

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

    2015-05-22

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

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

    Science.gov (United States)

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

    2018-05-08

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

  12. 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)

  13. The role of hydrogen bonding on kinetics of rearrangement of heterocyclic aldoximes in perchloric acide

    International Nuclear Information System (INIS)

    Azzouz, A.S.; Abdullah, K.A.; Al-Niemi, I.

    1995-01-01

    Four paris of syn and anti aromatic heterocyclic aldoximes as 2-thiophenealdoxime, 2- furfuraladoxime, 2-pyridinealdoxime and 2-pyrrolealdoxime are prepared. The strcutures of these geometrical isomers are confirmed by the meaasurements of their U.V. I, R and melting points. Experiments show the existence of these aldoximers in an intramolecular hy-drogen bonding with variable strength depending on the hetero ztoms in the aldoximes. The first order rate constants of the rearrangement of syn aldoximes follow the order of hetero S>O>N, while the anti aldoximes show irregular order, Factors governing the aniti constants of the rearrangement of syn and anti aldoximes are analysed. Activation parameters are estimated and discussed on the basis of isokinetic relation-ship. The differences in physical and spectroscpic behavior of aldoximes lead to an important suggestion regarding the configuration of oxime. (author). 27 refs., 2 figs., 2 tabs

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

    Directory of Open Access Journals (Sweden)

    VLADIMIR LESKOVAC

    2008-04-01

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

  15. Hydrogen bonding characterization in water and small molecules

    Science.gov (United States)

    Silvestrelli, Pier Luigi

    2017-06-01

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

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

    Science.gov (United States)

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

    2014-05-01

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

  17. Reassigning hydrogen-bond centering in dense ice

    International Nuclear Information System (INIS)

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

    2002-01-01

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

  18. Trimeric Hydrogen Bond in Geometrically Frustrated Hydroxyl Cobalt Halogenides

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  19. Positively charged phosphorus as a hydrogen bond acceptor

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Chaya Rapp

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

  1. Crystal Structure and Hydrogen Bonding Study of (10E-2,2-Dimethyl-3,4-dihydro-2H-benzo[g]chromene-5,10-dione 10-Oxime Derived From a-Lapachone

    Directory of Open Access Journals (Sweden)

    Lorenzo C. Visentin

    2011-01-01

    Full Text Available The compound (10E-2,2-dimethyl-3,4-dihydro-2H-benzo[g]chromene-5,10-dione-10-oxime (1 was synthesized from a-lapachone and hydroxylamine chloride in alkaline medium. Single-crystals suitable for X-ray diffraction measurements were grown from an ethanol solution, and the crystal structure of the title molecule is reported for the first time. The title molecule was also characterized by 1H- and 13C-NMR in CDCl3 solution, FTIR and MS. The crystal structure of 1 shows an E stereochemistry and dimers formed through classical hydrogen bonds.

  2. Bane of Hydrogen-Bond Formation on the Photoinduced Charge-Transfer Process in Donor–Acceptor Systems

    KAUST Repository

    Alsam, Amani Abdu

    2017-03-14

    Controlling the ultrafast dynamical process of photoinduced charge transfer at donor acceptor interfaces remains a major challenge for physical chemistry and solar cell communities. The process is complicated by the involvement of other complex dynamical processes, including hydrogen bond formation, energy transfer, and solvation dynamics occurring on similar time scales. In this study, we explore the remarkable impact of hydrogen-bond formation on the interfacial charge transfer between a negatively charged electron donating anionic porphyrin and a positively charged electron accepting pi-conjugated polymer, as a model system in solvents with different polarities and capabilities for hydiogen bonding using femtosecond transient absorption spectroscopy. Unlike the conventional understanding of the key role of hydrogen bonding in promoting the charge-transfer process, our steadystate and time-resolved results reveal that the intervening hydrogen-bonding environment and, consequently, the probable longer spacing between the donor and acceptor molecules significantly hinders the charge-transfer process between them. These results show that site-specific hydrogen bonding and geometric considerations between donor and acceptor can be exploited to control both the charge-transfer dynamics and its efficiency not only at donor acceptor interfaces but also in complex biological systems.

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

    International Nuclear Information System (INIS)

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

    2006-12-01

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

  4. Effect of cationic substitution on the double-well hydrogen-bond potential in [K1-x(NH4)x]3H(SO4)2 proton conductors: a single-crystal neutron diffraction study.

    Science.gov (United States)

    Choudhury, R R; Chitra, R; Selezneva, E V; Makarova, I P

    2017-10-01

    The structure of the mixed crystal [K 1-x (NH 4 ) x ] 3 H(SO 4 ) 2 as obtained from single-crystal neutron diffraction is compared with the previously reported room-temperature neutron structure of crystalline K 3 H(SO 4 ) 2 . The two structures are very similar, as indicated by the high value of their isostructurality index (94.8%). It was found that the replacement of even a small amount (3%) of K + with NH 4 + has a significant influence on the short strong hydrogen bond connecting the two SO 4 2- ions. Earlier optical measurements had revealed that the kinetics of the superionic transition in the solid solution [K 1-x (NH 4 ) x ] 3 H(SO 4 ) 2 are much faster than in K 3 H(SO 4 ) 2 ; this reported difference in the kinetics of the superionic phase transition in this class of crystal is explained on the basis of the difference in strength of the hydrogen-bond interactions in the two structures.

  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, eve...... studies, which is clarified in the present work. New hydrogen bonding data based on infrared spectroscopy are reported for seven binary mixtures of alcohols and alkanes. (C) 2007 Elsevier B.V. All rights reserved....... though pure-component liquid densities and vapour pressures are predicted equally accurately for the associating compound. As was the case in the study of pure components, there exists some confusion in the literature about the correct interpretation and comparison of experimental data and theoretical...

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  7. Supramolecular materials based on hydrogen-bonded polymers

    NARCIS (Netherlands)

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

    2007-01-01

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

  8. 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....

  9. Binding of reactive organophosphate by oximes via hydrogen bond

    Indian Academy of Sciences (India)

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

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

    Science.gov (United States)

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

    2014-03-07

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

  11. Amplification of Chirality in Hydrogen-Bonded Tetrarosette Helices

    NARCIS (Netherlands)

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

    2006-01-01

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

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

    Indian Academy of Sciences (India)

    WINTEC

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

  13. Polarization-induced sigma-holes and hydrogen bonding

    Czech Academy of Sciences Publication Activity Database

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

    2012-01-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2011-01-01

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

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

    NARCIS (Netherlands)

    Dijkstra - Vinken, E.

    2008-01-01

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

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

    Indian Academy of Sciences (India)

    Unknown

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

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

    Science.gov (United States)

    Mountain, Raymond D

    2010-12-16

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

  18. 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

  19. Crystal structure and hydrogen bonding in N-(1-deoxy-β-d-fructopyranos-1-yl-2-aminoisobutyric acid

    Directory of Open Access Journals (Sweden)

    Valeri V. Mossine

    2018-01-01

    Full Text Available The title compound, alternatively called d-fructose-2-aminoisobutyric acid (FruAib, C10H19NO7, (I, crystallizes exclusively in the β-pyranose form, with two conformationally non-equivalent molecules [(IA and (IB] in the asymmetric unit. In solution, FruAib establishes an equilibrium, with 75.6% of the population consisting of β-pyranose, 10.4% β-furanose, 10.1% α-furanose, 3.0% α-pyranose and <0.7% the acyclic forms. The carbohydrate ring in (I has the normal 2C5 chair conformation and the amino acid portion is in the zwitterion form. Bond lengths and valence angles compare well with the average values from related pyranose structures. All carboxyl, hydroxy and ammonium groups are involved in hydrogen bonding and form a three-dimensional network of infinite chains that are connected through homodromic rings and short chains. Intramolecular hydrogen bonds bridge the amino acid and sugar portions in both molecules. A comparative Hirshfeld surfaces analysis of FruAib and four other sugar–amino acids suggests an increasing role of intramolecular heteroatom interactions in crystal structures with an increasing proportion of C—H bonds.

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

    Science.gov (United States)

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

    2005-07-01

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

  1. The contribution of the hydrogen bond acidity on the lipophilicity of drugs estimated from chromatographic measurements.

    Science.gov (United States)

    Pallicer, Juan M; Pascual, Rosalia; Port, Adriana; Rosés, Martí; Ràfols, Clara; Bosch, Elisabeth

    2013-02-14

    The influence of the hydrogen bond acidity when the 1-octanol/water partition coefficient (log P(o/w)) of drugs is determined from chromatographic measurements was studied in this work. This influence was firstly evaluated by means of the comparison between the Abraham solvation parameter model when it is applied to express the 1-octanol/water partitioning and the chromatographic retention, expressed as the solute polarity p. Then, several hydrogen bond acidity descriptors were compared in order to determine properly the log P(o/w) of drugs. These descriptors were obtained from different software and comprise two-dimensional parameters such as the calculated Abraham hydrogen bond acidity A and three-dimensional descriptors like HDCA-2 from CODESSA program or WO1 and DRDODO descriptors calculated from Volsurf+software. The additional HOMO-LUMO polarizability descriptor should be added when the three-dimensional descriptors are used to complement the chromatographic retention. The models generated using these descriptors were compared studying the correlations between the determined log P(o/w) values and the reference ones. The comparison showed that there was no significant difference between the tested models and any of them was able to determine the log P(o/w) of drugs from a single chromatographic measurement and the correspondent molecular descriptors terms. However, the model that involved the calculated A descriptor was simpler and it is thus recommended for practical uses. Copyright © 2012 Elsevier B.V. All rights reserved.

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

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  3. A Direct Proof of the Resonance-Impaired Hydrogen Bond (RIHB) Concept.

    Science.gov (United States)

    Lin, Xuhui; Wu, Wei; Mo, Yirong

    2018-01-24

    The concept of resonance-enhanced hydrogen bond (RAHB) has been widely accepted and applied as it highlights the positive impact of π-conjugation on intramolecular H-bonds. However, electron delocalization is directional and there is a possibility that π-resonance goes from the H-bond acceptor to the H-bond donor, leading to a negative impact on H-bonds. Here we used the block-localized wavefunction (BLW) method which is a variant of ab initio valence bond (VB) theory and able to derive strictly electron-localized structures self-consistently, to quantify the interplay between H-bond and π-resonance in the terms of geometry, energetics and spectral properties. The comparison of geometrical optimizations with and without π-resonance shows that conjugation can indeed either enhance or weaken intramolecular H-bonds. We further experimented with various substituents attached to either the H-bond acceptor and/or H-bond donor side(s) to tune the H-bonding strength in both directions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

    Science.gov (United States)

    Prisk, T. R.; Hoffmann, C.; Kolesnikov, A. I.; Mamontov, E.; Podlesnyak, A. A.; Wang, X.; Kent, P. R. C.; Anovitz, L. M.

    2018-05-01

    Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factor reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10-100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.

  5. 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.

  6. Spectroscopic Studies of a Three-dimensional, Five-coordinated Copper(Ⅱ) Complex via Hydrogen Bonds: [Cu(PDA)(H2O)2](H2PDA=Pyridine-2,6-dicarboxylic Acid)

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    A new copper(Ⅱ) complex [Cu(PDA)(H2O)2] was synthesized and its structure was determined. Cu(Ⅱ) is five-coordinated in a tetragonal pyramid geometry. The two coordinating water molecules are different and the two Cu-O bond lengths differ by nearly 0.02 nm. The whole crystal is linked to form a three-dimensional network by means of hydrogen bonds. The X-band ESR spectrum shows three different g tensors with a well-resolved hyperfine structure in the gz signal, giving the ESR parameters gx=2.05, gy=2.065 and gz=2.29. The covalency of the coordinate bonds and the deviation from tetragonal pyramid geometry for the complex are discussed based on the ESR spectra.

  7. Coherent pulse and environmental characteristics of the intramolecular proton-transfer lasers based on 3-hydroxyflavone and fisetin

    Science.gov (United States)

    Parthenopoulos, Dimitri A.; Kasha, Michael

    1988-04-01

    Coherent stimulated emission and laser beams of good quality are reported for 3-hydroxyfiavone (3-HF) and a polyhydroxyfiavone, risetin, acting as intramolecular proton-transfer lasers. The laser beam quality of these materials is comparable to that observed for rhodamine-6G. Studies of amplified spontaneous emission of 3-hydroxyflavone in highly polar solvents are also reported. The very large changes in dipole moment upon electronic excitation of 3-HF expected according to ZINDO semiempirical molecular orbital calculations fail to give rise to spectral shifts in the high dielectric constant solvents. The results are interpreted as a masking spectral effect caused by specific hydrogen bonding by the solvent.

  8. Structure and weak hydrogen bonds in liquid acetaldehyde

    Directory of Open Access Journals (Sweden)

    Cordeiro Maria A. M.

    2004-01-01

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

  9. 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.

  10. Quantum confinement in hydrogen bond of DNA and RNA

    International Nuclear Information System (INIS)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2014-12-14

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

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

    Science.gov (United States)

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

    2017-02-01

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

  13. Anion-assisted trans-cis isomerization of palladium(II) phosphine complexes containing acetanilide functionalities through hydrogen bonding interactions.

    Science.gov (United States)

    Lu, Xiao-Xia; Tang, Hau-San; Ko, Chi-Chiu; Wong, Jenny Ka-Yan; Zhu, Nianyong; Yam, Vivian Wing-Wah

    2005-03-28

    The anion-assisted shift of trans-cis isomerization equilibrium of a palladium(II) complex containing acetanilide functionalities brought about by allosteric hydrogen bonding interactions has been established by UV/Vis, 1H NMR, 31P NMR and ESI-MS studies.

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

    Science.gov (United States)

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

    1998-01-01

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

  15. Spectroscopic study of 2-, 4- and 5-substituents on p Ka values of imidazole heterocycles prone to intramolecular proton-electrons transfer

    Science.gov (United States)

    Eseola, Abiodun O.; Obi-Egbedi, Nelson O.

    2010-02-01

    New 2-(1H-imidazol-2-yl)phenols ( L1Et- L8tBuPt) bearing a phenolic proton in the vicinity of the imidazole base were prepared and characterized. Experimental studies of the dependence of their protonation/deprotonation equilibrium on substituent identities and intramolecular hydrogen bonding tendencies were carried out using electronic absorption spectroscopy at varying pH values. In order to make comparison, 2-(anthracen-10-yl)-4,5-diphenyl-1H-imidazole ( L9Anthr) bearing no phenolic proton and 4,5-diphenyl-2-(4,5-diphenyl-1H-imidazol-2-yl)-1H-imidazole ( L10BisIm) bearing two symmetrical imidazole base fragments were also prepared and experimentally investigated. DFT calculations were carried out to study frontier orbitals of the investigated molecules. While electron-releasing substituents produced increase in protonation-deprotonation p Kas for the hydroxyl group, values for the imidazole base were mainly affected by polarization of the imidazole ring aromaticity across the 2-imidazole carbon and the 4,5-imidazole carbons axis of the imidazole ring. It was concluded that electron-releasing substituents on the phenol ring and/or electron-withdrawing substituents on 4,5-imidazole carbons negatively affects donor strengths/coordination chemistries of 2-(1H-imidazol-2-yl)phenols, and vice versa. Change of substituents on the phenol ring significantly altered the donor strength of the imidazole base. The understanding of p Ka variation on account of electronic effects of substituents in this work should aid the understanding of biochemical properties and substituent environments of imidazole-containing biomacromolecules.

  16. Intramolecular hydrogen bond: Can it be part of the basis set of ...

    Indian Academy of Sciences (India)

    However, we know that IMHB is a weak bond and hence its RFC has to be a measure of bond strength. .... oxalic acid, 1,4-butanediol, and 1,2-ethanediol, where .... −59.0. −56.2. −62.8. −165.8 −59.4 −179.4 −170.9. Relative energies∗∗. HF.

  17. Non-equivalent Role of Inter- and Intramolecular Hydrogen Bonds in the Insulin Dimer Interface

    Czech Academy of Sciences Publication Activity Database

    Antolíková, Emília; Žáková, Lenka; Turkenburg, J. P.; Watson, C. J.; Hančlová, Ivona; Šanda, Miloslav; Cooper, A.; Kraus, Tomáš; Brzozowski, A. M.; Jiráček, Jiří

    2011-01-01

    Roč. 286, č. 42 (2011), s. 36968-36977 ISSN 0021-9258 R&D Projects: GA MŠk(CZ) LC06077 Institutional research plan: CEZ:AV0Z40550506 Keywords : insulin * dimer * analog Subject RIV: CC - Organic Chemistry Impact factor: 4.773, year: 2011

  18. Hydrogen bonding strength of diblock copolymers affects the self-assembled structures with octa-functionalized phenol POSS nanoparticles.

    Science.gov (United States)

    Lu, Yi-Syuan; Yu, Chia-Yu; Lin, Yung-Chih; Kuo, Shiao-Wei

    2016-02-28

    In this study, the influence of the functional groups by the diblock copolymers of poly(styrene-b-4-vinylpyridine) (PS-b-P4VP), poly(styrene-b-2-vinylpyridine) (PS-b-P2VP), and poly(styrene-b-methyl methacrylate) (PS-b-PMMA) on their blends with octa-functionalized phenol polyhedral oligomeric silsesquioxane (OP-POSS) nanoparticles (NPs) was investigated. The relative hydrogen bonding strengths in these blends follow the order PS-b-P4VP/OP-POSS > PS-b-P2VP/OP-POSS > PS-b-PMMA/OP-POSS based on the Kwei equation from differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopic analyses. Small-angle X-ray scattering and transmission electron microscopic analyses show that the morphologies of the self-assembly structures are strongly dependent on the hydrogen bonding strength at relatively higher OP-POSS content. The PS-b-P4VP/OP-POSS hybrid complex system with the strongest hydrogen bonds shows the order-order transition from lamellae to cylinders and finally to body-centered cubic spheres upon increasing OP-POSS content. However, PS-b-P2VP/OP-POSS and PS-b-PMMA/OP-POSS hybrid complex systems, having relatively weaker hydrogen bonds, transformed from lamellae to cylinder structures at lower OP-POSS content (50 wt%).

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

    Science.gov (United States)

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

    2004-12-01

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

  20. Anharmonicity and hydrogen bonding in electrooptic sucrose crystal

    Science.gov (United States)

    Szostak, M. M.; Giermańska, J.

    1990-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-09-01

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

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  3. X-ray Absorption Spectroscopy and Density Functional Theory Studies of [(H3buea)FeIII-X]n1 (X= S2-, O2-,OH-): Comparison of Bonding and Hydrogen Bonding in Oxo and Sulfido Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Dey, Abhishek; Hocking, Rosalie K.; /Stanford U., Chem. Dept.; Larsen, Peter; Borovik, Andrew S.; /Kansas U.; Hodgson, Keith O.; Hedman, Britt; Solomon, Edward I.; /SLAC,

    2006-09-27

    Iron L-edge, iron K-edge, and sulfur K-edge X-ray absorption spectroscopy was performed on a series of compounds [Fe{sup III}H{sub 3}buea(X)]{sup n-} (X = S{sup 2-}, O{sup 2-}, OH{sup -}). The experimentally determined electronic structures were used to correlate to density functional theory calculations. Calculations supported by the data were then used to compare the metal-ligand bonding and to evaluate the effects of H-bonding in Fe{sup III}-O vs Fe{sup III-}S complexes. It was found that the Fe{sup III-}O bond, while less covalent, is stronger than the FeIII-S bond. This dominantly reflects the larger ionic contribution to the Fe{sup III-}O bond. The H-bonding energy (for three H-bonds) was estimated to be -25 kcal/mol for the oxo as compared to -12 kcal/mol for the sulfide ligand. This difference is attributed to the larger charge density on the oxo ligand resulting from the lower covalency of the Fe-O bond. These results were extended to consider an Fe{sup IV-}O complex with the same ligand environment. It was found that hydrogen bonding to Fe{sup IV-}O is less energetically favorable than that to Fe{sup III-}O, which reflects the highly covalent nature of the Fe{sup IV-}O bond.

  4. Collision-Induced Dissociation Study of Strong Hydrogen-Bonded Cluster Ions Y-(HF) n (Y=F, O2) Using Atmospheric Pressure Corona Discharge Ionization Mass Spectrometry Combined with a HF Generator.

    Science.gov (United States)

    Sakamoto, Kenya; Sekimoto, Kanako; Takayama, Mitsuo

    2017-01-01

    Hydrogen fluoride (HF) was produced by a homemade HF generator in order to investigate the properties of strong hydrogen-bonded clusters such as (HF) n . The HF molecules were ionized in the form of complex ions associated with the negative core ions Y - produced by atmospheric pressure corona discharge ionization (APCDI). The use of APCDI in combination with the homemade HF generator led to the formation of negative-ion HF clusters Y - (HF) n (Y=F, O 2 ), where larger clusters with n ≥4 were not detected. The mechanisms for the formation of the HF, F - (HF) n , and O 2 - (HF) n species were discussed from the standpoints of the HF generator and APCDI MS. By performing energy-resolved collision-induced dissociation (CID) experiments on the cluster ions F - (HF) n ( n =1-3), the energies for the loss of HF from F - (HF) 3 , F - (HF) 2 , and F - (HF) were evaluated to be 1 eV or lower, 1 eV or higher, and 2 eV, respectively, on the basis of their center-of-mass energy ( E CM ). These E CM values were consistent with the values of 0.995, 1.308, and 2.048 eV, respectively, obtained by ab initio calculations. The stability of [O 2 (HF) n ] - ( n =1-4) was discussed on the basis of the bond lengths of O 2 H-F - (HF) n and O 2 - H-F(HF) n obtained by ab initio calculations. The calculations indicated that [O 2 (HF) 4 ] - separated into O 2 H and F - (HF) 3 .

  5. N-(N-[2-(3,5-Difluorophenyl)acetyl]-(S)-alanyl)-(S)-phenylglycine tert-butyl ester (DAPT): an inhibitor of γ-secretase, revealing fine electronic and hydrogen-bonding features

    Energy Technology Data Exchange (ETDEWEB)

    Czerwinski, Andrzej; Valenzuela, Francisco [Peptides International Inc., 11621 Electron Drive, Louisville, KY 40299 (United States); Afonine, Pavel [Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 64R0121, Berkeley, CA 94720 (United States); Dauter, Miroslawa, E-mail: dauter@anl.gov [Basic Research Program, SAIC-Frederick Inc., Synchrotron Radiation Research Section, MCL, NCI, Argonne National Laboratory, Biosciences Division, Building 202, Argonne, IL 60439 (United States); Dauter, Zbigniew [Synchrotron Radiation Research Section, MCL, NCI, Argonne National Laboratory, Biosciences Division, Building 202, Argonne, IL 60439 (United States); Peptides International Inc., 11621 Electron Drive, Louisville, KY 40299 (United States)

    2010-12-01

    The title compound, C{sub 23}H{sub 26}F{sub 2}N{sub 2}O{sub 4}, is a dipeptidic inhibitor of γ-secretase, one of the enzymes involved in Alzheimer’s dis@@ease. The mol@@ecule adopts a compact conformation, without intra@@molecular hydrogen bonds. In the crystal structure, one of the amide N atoms forms the only inter@@molecular N—H⋯O hydrogen bond; the second amide N atom does not form hydrogen bonds. High-resolution synchrotron diffraction data permitted the unequivocal location and refinement without restraints of all H atoms, and the identification of the characteristic shift of the amide H atom engaged in the hydrogen bond from its ideal position, resulting in a more linear hydrogen bond. Significant residual densities for bonding electrons were revealed after the usual SHELXL refinement, and modeling of these features as additional inter@@atomic scatterers (IAS) using the program PHENIX led to a significant decrease in the R factor from 0.0411 to 0.0325 and diminished the r.m.s. deviation level of noise in the final difference Fourier map from 0.063 to 0.037 e Å{sup −3}.

  6. Multiple Hydrogen Bond Tethers for Grazing Formic Acid in Its Complexes with Phenylacetylene.

    Science.gov (United States)

    Karir, Ginny; Kumar, Gaurav; Kar, Bishnu Prasad; Viswanathan, K S

    2018-03-01

    Complexes of phenylacetylene (PhAc) and formic acid (FA) present an interesting picture, where the two submolecules are tethered, sometimes multiply, by hydrogen bonds. The multiple tentacles adopted by PhAc-FA complexes stem from the fact that both submolecules can, in the same complex, serve as proton acceptors and/or proton donors. The acetylenic and phenyl π systems of PhAc can serve as proton acceptors, while the ≡C-H or -C-H of the phenyl ring can act as a proton donor. Likewise, FA also is amphiprotic. Hence, more than 10 hydrogen-bonded structures, involving O-H···π, C-H···π, and C-H···O contacts, were indicated by our computations, some with multiple tentacles. Interestingly, despite the multiple contacts in the complexes, the barrier between some of the structures is small, and hence, FA grazes around PhAc, even while being tethered to it, with hydrogen bonds. We used matrix isolation infrared spectroscopy to experimentally study the PhAc-FA complexes, with which we located global and a few local minima, involving primarily an O-H···π interaction. Experiments were corroborated by ab initio computations, which were performed using MP2 and M06-2X methods, with 6-311++G (d,p) and aug-cc-pVDZ basis sets. Single-point energy calculations were also done at MP2/CBS and CCSD(T)/CBS levels. The nature, strength, and origin of these noncovalent interactions were studied using AIM, NBO, and LMO-EDA analysis.

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

    Science.gov (United States)

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

    2017-03-01

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

  8. Performance of wave function and density functional methods for water hydrogen bond spin-spin coupling constants.

    Science.gov (United States)

    García de la Vega, J M; Omar, S; San Fabián, J

    2017-04-01

    Spin-spin coupling constants in water monomer and dimer have been calculated using several wave function and density functional-based methods. CCSD, MCSCF, and SOPPA wave functions methods yield similar results, specially when an additive approach is used with the MCSCF. Several functionals have been used to analyze their performance with the Jacob's ladder and a set of functionals with different HF exchange were tested. Functionals with large HF exchange appropriately predict 1 J O H , 2 J H H and 2h J O O couplings, while 1h J O H is better calculated with functionals that include a reduced fraction of HF exchange. Accurate functionals for 1 J O H and 2 J H H have been tested in a tetramer water model. The hydrogen bond effects on these intramolecular couplings are additive when they are calculated by SOPPA(CCSD) wave function and DFT methods. Graphical Abstract Evaluation of the additive effect of the hydrogen bond on spin-spin coupling constants of water using WF and DFT methods.

  9. Hydrogen bonding donation of N-methylformamide with dimethylsulfoxide and water

    Science.gov (United States)

    Borges, Alexandre; Cordeiro, João M. M.

    2013-04-01

    20% N-methylformamide (NMF) mixtures with water and with dimethylsulfoxide (DMSO) have been studied. A comparison between the hydrogen bonding (H-bond) donation of N-methylformamide with both solvents in the mixtures is presented. Results of radial distribution functions, pair distribution energies, molecular dipole moment correlation, and geometry of the H-bonded species in each case are shown. The results indicate that the NMF - solvent H-bond is significantly stronger with DMSO than with water. The solvation shell is best organized in the DMSO mixture than in the aqueous one.

  10. Competition of hydrogen bonds and halogen bonds in complexes of hypohalous acids with nitrogenated bases.

    Science.gov (United States)

    Alkorta, Ibon; Blanco, Fernando; Solimannejad, Mohammad; Elguero, Jose

    2008-10-30

    A theoretical study of the complexes formed by hypohalous acids (HOX, X = F, Cl, Br, I, and At) with three nitrogenated bases (NH 3, N 2, and NCH) has been carried out by means of ab initio methods, up to MP2/aug-cc-pVTZ computational method. In general, two minima complexes are found, one with an OH...N hydrogen bond and the other one with a X...N halogen bond. While the first one is more stable for the smallest halogen derivatives, the two complexes present similar stabilities for the iodine case and the halogen-bonded structure is the most stable one for the hypoastatous acid complexes.

  11. Thermal generation and mobility of charge carriers in collective proton transport in hydrogen-bonded chains

    International Nuclear Information System (INIS)

    Peyrard, M.; Boesch, R.; Kourakis, I.

    1991-01-01

    The transport of protons in hydrogen-bonded systems is a long standing problem which has not yet obtained a satisfactorily theoretical description. Although this problem was examined first for ice, it is relevant in many systems and in particular in biology for the transport along proteins or for proton conductance across membranes, an essential process in cell life. The broad relevance makes the study of proton conduction very appealing. Since the original work of Bernal and Fowler on ice, the idea that the transport occurs through chains of hydrogen bonds has been well accepted. Such ''proton wires'' were invoked by Nagle and Morowitz for proton transport across membranes proteins and more recently across lipid bilayers. In this report, we assume the existence of such an hydrogen-bonded chain and discuss its consequences on the dynamics of the charge carriers. We show that this assumption leads naturally to the idea of soliton transport and we put a special emphasis on the role of the coupling between the protons and heavy ions motions. The model is presented. We show how the coupling affects strongly the dynamics of the charge carriers and we discuss the role it plays in the thermal generation of carriers. The work presented has been performed in 1986 and 87 with St. Pnevmatikos and N. Flyzanis and was then completed in collaboration with D. Hochstrasser and H. Buettner. Therefore the results presented in this part are not new but we think that they are appropriate in the context of this multidisciplinary workshop because they provide a rather complete example of the soliton picture for proton conduction. This paper discusses the thermal generation of the charge carriers when the coupling between the protons and heavy ions dynamics is taken into account. The results presented in this part are very recent and will deserve further analysis but they already show that the coupling can assist for the formation of the charge carriers

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

    Wang, Yuhao; Sukhishvili, Svetlana

    2015-03-01

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

  15. 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.

  16. Effect of quantum nuclear motion on hydrogen bonding

    International Nuclear Information System (INIS)

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

    2014-01-01

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

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

    DEFF Research Database (Denmark)

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

    2017-01-01

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

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

    International Nuclear Information System (INIS)

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

    1999-01-01

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

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

    Science.gov (United States)

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

    2014-02-01

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

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

    DEFF Research Database (Denmark)

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

    2017-01-01

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

  1. A novel chalcone-analogue as an optical sensor based on ground and excited states intramolecular charge transfer: A combined experimental and theoretical study

    International Nuclear Information System (INIS)

    Fayed, Tarek A.

    2006-01-01

    Steady-state absorption and emission spectroscopic techniques as well as semiempirical quantum calculations at the AM1 and ZINDO/S levels have been used to investigate the intramolecular charge transfer (ICT) behaviour of a novel chalcone namely; 1-(2-pyridyl)-5-(4-dimethylaminophenyl)-penta-2,4-diene-1-one, DMAC. The ground state DMAC has a significant ICT character and a great sensitivity to the hydrogen bond donating ability of the medium as reflected from the change of the absorption spectra in pure and mixed organic solvents. On the other hand, its excited singlet state exhibits high ICT characters as manifested by the drastic solvatochromic effects. These results are consistent with the data of charge density calculations in both the ground and excited state, which indicates enhancement of the charge transfer from the dimethyl-amino group to the carbonyl oxygen upon excitation. Also, the dipole moment calculations indicates a highly dipolar excited singlet state (Δμ eg = 15.5 D). The solvent dependence of the fluorescence quantum yield of DMAC was interpreted on the basis of positive and negative solvatokinetic as well as the hydrogen bonding effects. Incorporation of the 2-pyridyl group in the chemical structure of the present DMAC led to design of a potential optical sensor for probing acidity of the medium and metal cations such as Zn 2+ , Cd 2+ and Hg 2+ . This was concluded from the high acidochromic and metallochromic behaviour of DMAC on adding such cations to its acetonitrile solutions

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

    Science.gov (United States)

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

    2016-11-01

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

  3. Hydrogen bond based smart polymer for highly selective and tunable capture of multiply phosphorylated peptides.

    Science.gov (United States)

    Qing, Guangyan; Lu, Qi; Li, Xiuling; Liu, Jing; Ye, Mingliang; Liang, Xinmiao; Sun, Taolei

    2017-09-06

    Multisite phosphorylation is an important and common mechanism for finely regulating protein functions and subsequent cellular responses. However, this study is largely restricted by the difficulty to capture low-abundance multiply phosphorylated peptides (MPPs) from complex biosamples owing to the limitation of enrichment materials and their interactions with phosphates. Here we show that smart polymer can serve as an ideal platform to resolve this challenge. Driven by specific but tunable hydrogen bonding interactions, the smart polymer displays differential complexation with MPPs, singly phosphorylated and non-modified peptides. Importantly, MPP binding can be modulated conveniently and precisely by solution conditions, resulting in highly controllable MPP adsorption on material surface. This facilitates excellent performance in MPP enrichment and separation from model proteins and real biosamples. High enrichment selectivity and coverage, extraordinary adsorption capacities and recovery towards MPPs, as well as high discovery rates of unique phosphorylation sites, suggest its great potential in phosphoproteomics studies.Capture of low-abundance multiply phosphorylated peptides (MPPs) is difficult due to limitation of enrichment materials and their interactions with phosphates. Here the authors show, a smart polymer driven by specific but tunable hydrogen bonding interactions can differentially complex with MPPs, singly phosphorylated and non-modified peptides.

  4. Hydrogen bonding in (substituted benzene)·(water)n clusters with n≤4

    International Nuclear Information System (INIS)

    Barth, H.-D.; Buchhold, K.; Djafari, S.; Reimann, B.; Lommatzsch, U.; Brutschy, B.

    1998-01-01

    Infrared ion-depletion spectroscopy, a double resonance method combining vibrational predissociation with resonant two-photon ionization (R2PI) spectroscopy, has been applied to study mixed clusters of the type (substituted benzene)·(H 2 O) n with n≤4. The UV chromophores were p-difluorobenzene, fluorobenzene, benzene, toluene, p-xylene and anisole. From the IR depletion spectra in the region of the OH stretching vibrations it could be shown that the water molecules are attached as subclusters to the chromophores. Size and configuration of the subclusters could be deduced from the IR depletion spectra. In the anisole·(H 2 O) 1 a nd 2 complexes the water clusters form an ordinary hydrogen bond to the oxygen atom of the methoxy group. In all other mixed complexes a π-hydrogen bond is formed between one of the free OH groups of a water subcluster and the π-system of the chromophore. According to the strength of this interaction the frequency of the respective absorption band exhibits a characteristic red-shift which could be related to the total atomic charges in the aromatic ring. (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

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

    Science.gov (United States)

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

    2014-05-01

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

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

    KAUST Repository

    El-Mellouhi, Fedwa

    2016-09-08

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

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

    KAUST Repository

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2002-08-14

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

  9. Photophysical study of a cyclophane displaying intramolecular exciplex emission

    International Nuclear Information System (INIS)

    Galindo, Francisco; Isabel Burguete, M.; Luis, Santiago V.

    2004-01-01

    The photophysical behavior of cyclophane 1, comprised by two L-valine units and one naphthalene ring, has been studied. It displays exciplex (EX) emission with a maximum in the range 390-460 nm, depending on solvent polarity. From this dependence a dipole moment of 19.4 D for the excited charge-transfer state has been calculated. Fluorescence quantum yields in organic media ranging from 0.012 to 0.038 have been measured. This phenomenon has been interpreted taking into account the rigidity imposed by the cyclophane framework which could pre-orient the donor and the acceptor subunits for a favorable interaction

  10. Photophysical study of a cyclophane displaying intramolecular exciplex emission

    Energy Technology Data Exchange (ETDEWEB)

    Galindo, Francisco; Isabel Burguete, M.; Luis, Santiago V

    2004-07-12

    The photophysical behavior of cyclophane 1, comprised by two L-valine units and one naphthalene ring, has been studied. It displays exciplex (EX) emission with a maximum in the range 390-460 nm, depending on solvent polarity. From this dependence a dipole moment of 19.4 D for the excited charge-transfer state has been calculated. Fluorescence quantum yields in organic media ranging from 0.012 to 0.038 have been measured. This phenomenon has been interpreted taking into account the rigidity imposed by the cyclophane framework which could pre-orient the donor and the acceptor subunits for a favorable interaction.

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

    NARCIS (Netherlands)

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

    1999-01-01

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

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

    NARCIS (Netherlands)

    Guerra, Célia Fonseca; Bickelhaupt, F. Matthias

    2006-01-01

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

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

    NARCIS (Netherlands)

    Guerra, Célia Fonseca; Bickelhaupt, F. Matthias

    2006-01-01

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

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

    DEFF Research Database (Denmark)

    Luo, Jiangshui

    2016-01-01

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

  15. 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…

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

    NARCIS (Netherlands)

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

    2006-01-01

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

  17. Hydrogen Bonding, (1)H NMR, and Molecular Electron Density Topographical Characteristics of Ionic Liquids Based on Amino Acid Cations and Their Ester Derivatives.

    Science.gov (United States)

    Rao, Soniya S; Bejoy, Namitha Brijit; Gejji, Shridhar P

    2015-08-13

    Amino acid ionic liquids (AAILs) have attracted significant attention in the recent literature owing to their ubiquitous applications in diversifying areas of modern chemistry, materials science, and biosciences. The present work focuses on unraveling the molecular interactions underlying AAILs. Electronic structures of ion pairs consisting of amino acid cations ([AA(+)], AA = Gly, Ala, Val, Leu, Ile, Pro, Ser, Thr) and their ester substituted derivatives [AAE(+)] interacting with nitrate anion [NO3(-)] have been obtained from the dispersion corrected M06-2x density functional theory. The formation of ion pair is accompanied by the transfer of proton from quaternary nitrogen to anion facilitated via hydrogen bonding. The [Ile], [Pro], [Ser], and [Thr] and their esters reveal relatively strong inter- as well as intramolecular hydrogen-bonding interactions. Consequently, the hierarchy in binding energies of [AA][NO3] ion pairs and their ester analogues turns out to be [Gly] > [Ala] > [Ser] ∼ [Val] ∼ [Ile] > [Leu] ∼ [Thr] > [Pro]. The work underlines how the interplay of intra- as well as intermolecular hydrogen-bonding interactions in [AA]- and [AAE]-based ILs manifest in their infrared and (1)H NMR spectra. Substitution of -OCH3 functional group in [AA][NO3] ILs lowers the melting point attributed to weaker hydrogen-bonding interactions, making them suitable for room temperature applications. As opposed to gas phase structures, the presence of solvent (DMSO) does not bring about any proton transfer in the ion pairs or their ester analogues. Calculated (1)H NMR chemical shifts of the solvated structures agree well with those from experiment. Correlations of decomposition temperatures in [AA]- and [AAE]-based ILs with binding energies and electron densities at the bond critical point(s) in molecular electron density topography, have been established.

  18. Conformational Effects through Hydrogen Bonding in a Constrained γ-Peptide Template: From Intraresidue Seven-Membered Rings to a Gel-Forming Sheet Structure.

    Science.gov (United States)

    Awada, Hawraà; Grison, Claire M; Charnay-Pouget, Florence; Baltaze, Jean-Pierre; Brisset, François; Guillot, Régis; Robin, Sylvie; Hachem, Ali; Jaber, Nada; Naoufal, Daoud; Yazbeck, Ogaritte; Aitken, David J

    2017-05-05

    A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.

  19. Theoretical Study of H/D Isotope Effects on Nuclear Magnetic Shieldings Using an ab initio Multi-Component Molecular Orbital Method

    Directory of Open Access Journals (Sweden)

    Masanori Tachikawa

    2013-05-01

    Full Text Available We have theoretically analyzed the nuclear quantum effect on the nuclear magnetic shieldings for the intramolecular hydrogen-bonded systems of σ-hydroxy acyl aromatic species using the gauge-including atomic orbital technique combined with our multi-component density functional theory. The effect of H/D quantum nature for geometry and nuclear magnetic shielding changes are analyzed. Our study clearly demonstrated that the geometrical changes of hydrogen-bonds induced by H/D isotope effect (called geometrical isotope effect: GIE is the dominant factor of deuterium isotope effect on 13C chemical shift.

  20. Peptide-Driven Charge-Transfer Organogels Built from Synergetic Hydrogen Bonding and Pyrene-Naphthalenediimide Donor-Acceptor Interactions.

    Science.gov (United States)

    Bartocci, Silvia; Berrocal, José Augusto; Guarracino, Paola; Grillaud, Maxime; Franco, Lorenzo; Mba, Miriam

    2018-02-26

    The peptide-driven formation of charge transfer (CT) supramolecular gels featuring both directional hydrogen-bonding and donor-acceptor (D-A) complexation is reported. Our design consists of the coassembly of two dipeptide-chromophore conjugates, namely diphenylalanine (FF) dipeptide conveniently functionalized at the N-terminus with either a pyrene (Py-1, donor) or naphthalene diimide (NDI-1, acceptor). UV/Vis spectroscopy confirmed the formation of CT complexes. FTIR and 1 H NMR spectroscopy studies underlined the pivotal role of hydrogen bonding in the gelation process, and electronic paramagnetic resonance (EPR) measurements unraveled the advantage of preorganized CT supramolecular architectures for charge transport over solutions containing non-coassembled D and A molecular systems. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

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

    2014-09-04

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

  2. Electronic dipole moment and tunneling state of hydrogen atom in hydrogen-bond materials revealed by neutron and X-ray structure analyses

    International Nuclear Information System (INIS)

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

    2007-01-01

    The isolated hydrogen-bonded materials, 5-methyl-9-hydroxyphenalenone (MeHPLN) and 5-bromo-9-hydroxyphenalenone (Br-HPLN), were studied by means of X-ray and neutron diffraction methods. It was found that the position of the nucleus of the hydrogen atom in the hydrogen-bond region does not agree with the center of mass of the electron cloud of the hydrogen atom. This leads to a local electronic dipole moment in the hydrogen-bond region. Using the experimentally obtained dipole moment, phase transition temperatures for MeHPLN and BrHPLN were calculated based on a tunneling model. Result shows good agreement with the ones obtained by a dielectric measurement. (author)

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

    Science.gov (United States)

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

    2018-06-01

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

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

    Science.gov (United States)

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

    2017-06-12

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

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

    Science.gov (United States)

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

    2015-12-10

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

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

    Science.gov (United States)

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

    2012-02-15

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

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

    Directory of Open Access Journals (Sweden)

    Boaz Galdino Oliveira

    2009-08-01

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

  8. Probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation.

    Science.gov (United States)

    Zheng, Zhong-liang; Ye, Mao-qing; Zuo, Zhen-yu; Liu, Zhi-gang; Tai, Keng-chang; Zou, Guo-lin

    2006-05-01

    Hydrogen bonds occurring in the catalytic triad (Asp32, His64 and Ser221) and the oxyanion hole (Asn155) are very important to the catalysis of peptide bond hydrolysis by serine proteases. For the subtilisin NK (nattokinase), a bacterial serine protease, construction and analysis of a three-dimensional structural model suggested that several hydrogen bonds formed by four residues function to stabilize the transition state of the hydrolysis reaction. These four residues are Ser33, Asp60, Ser62 and Thr220. In order to remove the effect of these hydrogen bonds, four mutants (Ser33-->Ala33, Asp60-->Ala60, Ser62-->Ala62, and Thr220-->Ala220) were constructed by site-directed mutagenesis. The results of enzyme kinetics indicated that removal of these hydrogen bonds increases the free-energy of the transition state (DeltaDeltaG(T)). We concluded that these hydrogen bonds are more important for catalysis than for binding the substrate, because removal of these bonds mainly affects the kcat but not the K(m) values. A substrate, SUB1 (succinyl-Ala-Ala-Pro-Phe-p-nitroanilide), was used during enzyme kinetics experiments. In the present study we have also shown the results of FEP (free-energy perturbation) calculations with regard to the binding and catalysis reactions for these mutant subtilisins. The calculated difference in FEP also suggested that these four residues are more important for catalysis than binding of the substrate, and the simulated values compared well with the experimental values from enzyme kinetics. The results of MD (molecular dynamics) simulations further demonstrated that removal of these hydrogen bonds partially releases Asp32, His64 and Asn155 so that the stability of the transition state decreases. Another substrate, SUB2 (H-D-Val-Leu-Lys-p-nitroanilide), was used for FEP calculations and MD simulations.

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

    Science.gov (United States)

    Alkorta, Ibon; Elguero, José; Elguero, Eric

    2017-11-01

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

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

    Science.gov (United States)

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

    2009-06-04

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

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

    Science.gov (United States)

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

    2014-12-15

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

  12. Substituent Effects on the Hydrogen Bonding Between Phenolate and HF, H2O and NH3

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    B3LYP/6-31+g(d) calculations were performed on the hydrogen bonded complexes between substituted phenolates and HF, H2O as well as NH3. It was found that some properties of the non-covalent complexes, including the interaction energies, donor-acceptor (host-guest) distances, bond lengths, and vibration frequencies, could show well-defined substituent effects. Thus, from the substituent studies we can not only understand the mechanism of a particular non-covalent interaction better, but also easily predict the interaction energies and structures of a particular non-covalent complex, which might otherwise be very hard or resource-consuming to be known. This means that substituent effect is indeed a useful tool to be used in supramolecular chemistry and therefore, many valuable studies remain to be carried out.

  13. Proton conductivity in quasi-one dimensional hydrogen-bonded systems: A nonlinear approach

    International Nuclear Information System (INIS)

    Tsironis, G.; Phevmatikos, S.

    1988-01-01

    Defect formation and transport in a hydrogen-bonded system is studied via a two-sublattice soliton-bearing one-dimensional model. Ionic and orientational defects are associated with distinct nonlinear topological excitations in the present model. The dynamics of these excitations is studied both analytically and with the use of numerical simulations. It is shown that the two types of defects are soliton solutions of a double Sine--Gordon equation which describes the motion of the protons in the long-wavelength limit. With each defect there is an associated deformation in the ionic lattice that, for small speeds, follows the defect dynamically albeit resisting its motion. Free propagation as well as collision properties of the proton solitons are presented. 33 refs., 10 figs

  14. Twisted intramolecular charge transfer investigation of semi organic L-Glutamic acid hydrochloride single crystal for organic light-emitting and optical limiting applications

    Science.gov (United States)

    Joy, Lija K.; George, Merin; Alex, Javeesh; Aravind, Arun; Sajan, D.; Vinitha, G.

    2018-03-01

    Single crystals of L-Glutamic acid hydrochloride (LGHCl) were grown by slow evaporation solution technique and good crystalline perfection was confirmed by Powder X-ray diffraction studies. The complete vibrational studies of the compound were analyzed by FT-IR, FT-Raman and UV-visible spectra combined with Normal Coordinate Analysis (NCA) following the scaled quantum mechanical force field methodology and density functional theory (DFT). Twisted Intramolecular Charge Transfer (ICT) occurs due to the presence of strong ionic intra-molecular Nsbnd H⋯O hydrogen bonding was confirmed by Hirshfeld Surface analysis. The existence of intermolecular Nsbnd H⋯Cl hydrogen bonds due to the interaction between the lone pair of oxygen with the antibonding orbital was established by NBO analysis. The Z-scan result indicated that the title molecule exhibits saturable absorption behavior. The attractive third-order nonlinear properties suggest that LGHCl can be a promising candidate for the design and development devices for optical limiting applications. LGHCL exhibits distinct emission in the blue region of the fluorescence lifetime which proves to be a potential candidate for blue- Organic light-emitting diodes (OLEDs) fabrication.

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

    Science.gov (United States)

    Takahashi, Masae; Ishikawa, Yoichi

    2013-06-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2018-01-12

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

  18. Electron detachment of the hydrogen-bonded amino acid side-chain guanine complexes

    Science.gov (United States)

    Wang, Jing; Gu, Jiande; Leszczynski, Jerzy

    2007-07-01

    The photoelectron spectra of the hydrogen-bonded amino acid side-chain-guanine complexes has been studied at the partial third order (P3) self-energy approximation of the electron propagator theory. The correlation between the vertical electron detachment energy and the charge distributions on the guanine moiety reveals that the vertical electron detachment energy (VDE) increases as the positive charge distribution on the guanine increases. The low VDE values determined for the negatively charged complexes of the guanine-side-chain-group of Asp/Glu suggest that the influence of the H-bonded anionic groups on the VDE of guanine could be more important than that of the anionic backbone structure. The even lower vertical electron detachment energy for guanine is thus can be expected in the H-bonded protein-DNA systems.

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

    Science.gov (United States)

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

    2018-01-01

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

  20. A low-barrier hydrogen bond mediates antibiotic resistance in a noncanonical catalytic triad

    Science.gov (United States)

    2018-01-01

    One group of enzymes that confer resistance to aminoglycoside antibiotics through covalent modification belongs to the GCN5-related N-acetyltransferase (GNAT) superfamily. We show how a unique GNAT subfamily member uses a previously unidentified noncanonical catalytic triad, consisting of a glutamic acid, a histidine, and the antibiotic substrate itself, which acts as a nucleophile and attacks the acetyl donor molecule. Neutron diffraction studies allow for unambiguous identification of a low-barrier hydrogen bond, predicted in canonical catalytic triads to increase basicity of the histidine. This work highlights the role of this unique catalytic triad in mediating antibiotic resistance while providing new insights into the design of the next generation of aminoglycosides. PMID:29632894

  1. Studies on the syntheses, structural characterization, antimicrobial-, and DPPH radical scavenging activity of the cocrystals caffeine:cinnamic acid and caffeine:eosin dihydrate

    Science.gov (United States)

    Suresh Kumar, G. S.; Seethalakshmi, P. G.; Bhuvanesh, N.; Kumaresan, S.

    2013-10-01

    Two organic cocrystals namely, caffeine:cinnamic acid [(caf)(ca)] (1) and caffeine:eosin dihydrate [(caf)(eos)]·2H2O (2) were synthesized and studied by FT-IR, TGA/DTA, and single crystal XRD. The crystal system of cocrystal 1 is triclinic with space group P-1 and Z = 2 and that of cocrystal 2 is monoclinic with space group P21/C and Z = 4. An imidazole-carboxylic acid synthon is observed in the cocrystal 1. The intermolecular hydrogen bond, O-H⋯N and π-π interactions play a major role in stabilizing 1 whereas the intermolecular hydrogen bonds, O-H⋯O, O-H⋯N, and intramolecular hydrogen bond, O-H⋯Br; along with π-π interactions together play a vital role in stabilizing the structure of 2. The antimicrobial- and DPPH radical scavenging activities of both the cocrystals were studied.

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-01-17

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

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  6. Adaptive polymeric nanomaterials utilizing reversible covalent and hydrogen bonding

    Science.gov (United States)

    Neikirk, Colin

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

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

    Science.gov (United States)

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

    2012-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Fifield, Leonard S.; Grate, Jay W.

    2010-06-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2016-01-01

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

  10. Quantum mechanics models of the methanol dimer: O-H…O hydrogen bonds of ß-D-glucose moieties from crystallographic data.

    Science.gov (United States)

    In this study, a survey of the Cambridge Crystal Structure Database for all donor-acceptor interactions in ß-D-glucose moieties was performed to examine the similarities and differences among the different hydroxyl groups and ether oxygen atoms that participate in hydrogen bonds. Comparable behavior...

  11. Hydrogen bonds of DsrD protein revealed by neutron crystallography

    International Nuclear Information System (INIS)

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

    2008-01-01

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

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

    Science.gov (United States)

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

    2016-07-28

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

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

    International Nuclear Information System (INIS)

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

    2016-01-01

    In RNA secondary structure determination, it is essential to determine whether a nucleotide is base-paired and not. Base-pairing of nucleotides is mediated by hydrogen bonds. The NMR characterization of hydrogen bonds relies on experiments correlating the NMR resonances of exchangeable protons and can be best performed for structured parts of the RNA, where labile hydrogen atoms are protected from solvent exchange. Functionally important regions in RNA, however, frequently reveal increased dynamic disorder which often leads to NMR signals of exchangeable protons that are broadened beyond 1 H detection. Here, we develop 13 C direct detected experiments to observe all nucleotides in RNA irrespective of whether they are involved in hydrogen bonds or not. Exploiting the self-decoupling of scalar couplings due to the exchange process, the hydrogen bonding behavior of the hydrogen bond donor of each individual nucleotide can be determined. Furthermore, the adaption of HNN-COSY experiments for 13 C direct detection allows correlations of donor–acceptor pairs and the localization of hydrogen-bond acceptor nucleotides. The proposed 13 C direct detected experiments therefore provide information about molecular sites not amenable by conventional proton-detected methods. Such information makes the RNA secondary structure determination by NMR more accurate and helps to validate secondary structure predictions based on bioinformatics.

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

    International Nuclear Information System (INIS)

    Henchman, Richard H

    2016-01-01

    A model is proposed for liquid water that is a continuum between the ordered state with predominantly tetrahedral coordination, linear hydrogen bonds and activated dynamics and a disordered state with a continuous distribution of multiple coordinations, multiple types of hydrogen bond, and diffusive dynamics, similar to that of normal liquids. Central to water’s heterogeneous structure is the ability of hydrogen to donate to either one acceptor in a conventional linear hydrogen bond or to multiple acceptors as a furcated hydrogen. Linear hydrogen bonds are marked by slow, activated kinetics for hydrogen-bond switching to more crowded acceptors and sharp first peaks in the hydrogen-oxygen radial distribution function. Furcated hydrogens, equivalent to free, broken, dangling or distorted hydrogens, have barrierless, rapid kinetics and poorly defined first peaks in their hydrogen-oxygen radial distribution function. They involve the weakest donor in a local excess of donors, such that barrierless whole-molecule vibration rapidly swaps them between the linear and furcated forms. Despite the low number of furcated hydrogens and their transient existence, they are readily created in a single hydrogen-bond switch and free up the dynamics of numerous surrounding molecules, bringing about the disordered state. Hydrogens in the ordered state switch with activated dynamics to make the non-tetrahedral coordinations of the disordered state, which can also combine to make the ordered state. Consequently, the ordered and disordered states are both connected by diffusive dynamics and differentiated by activated dynamics, bringing about water’s continuous heterogeneity. (paper)

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

    Science.gov (United States)

    Mondal, Abhisek; Datta, Saumen

    2017-06-01

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

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

    International Nuclear Information System (INIS)

    Sarma, Rahul; Paul, Sandip

    2012-01-01

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

  17. Inversion symmetry and local vs. dispersive interactions in the nucleation of hydrogen bonded cyclic n-mer and tape of imidazolecarboxamidines

    Directory of Open Access Journals (Sweden)

    2008-07-01

    Full Text Available Substitutional changes to imidazolecarboxamidine that preserved intermolecular hydrogen bonding in the solid state were used to study the relationship between packing and the hydrogen bond motif. Various motifs competed, but the most common imidazolecarboxamidine crystalline phase was a Ci symmetric dimer that established inversion centers by associating enantiomeric tautomers. Counter to intuition, the calculated gas-phase energies per molecule of the solid state atomic coordinates of the Ci dimer motifs were higher than those of the C1 dimer, trimer, tetramer and tape motifs, while the packing densities of Ci dimers were found to be higher. This result was interpreted as an enhanced ability of the Ci dimers to pack. If other motifs competed, the hydrogen bonds and conformations should be lower in energy than the Ci dimer. The results detail the effect of packing on the conformation in these molecules. The results are interpreted as a rough measure of the energetic compromise between packing and the energies related to the coordinates involving one dihedral angle and hydrogen bonding. The results establish a connection between solution and solid phase conformation.

  18. Hydrogen bond dynamics and water structure in glucose-water solutions by depolarized Rayleigh scattering and low-frequency Raman spectroscopy

    Science.gov (United States)

    Paolantoni, Marco; Sassi, Paola; Morresi, Assunta; Santini, Sergio

    2007-07-01

    The effect of glucose on the relaxation process of water at picosecond time scales has been investigated by depolarized Rayleigh scattering (DRS) experiments. The process is assigned to the fast hydrogen bonding dynamics of the water network. In DRS spectra this contribution can be safely separated from the slower relaxation process due to the sugar. The detected relaxation time is studied at different glucose concentrations and modeled considering bulk and hydrating water contributions. As a result, it is found that in diluted conditions the hydrogen bond lifetime of proximal water molecules becomes about three times slower than that of the bulk. The effect of the sugar on the hydrogen bond water structure is investigated by analyzing the low-frequency Raman (LFR) spectrum sensitive to intermolecular modes. The addition of glucose strongly reduces the intensity of the band at 170cm-1 assigned to a collective stretching mode of water molecules arranged in cooperative tetrahedral domains. These findings indicate that proximal water molecules partially lose the tetrahedral ordering typical of the bulk leading to the formation of high density environments around the sugar. Thus the glucose imposes a new local order among water molecules localized in its hydration shell in which the hydrogen bond breaking dynamics is sensitively retarded. This work provides new experimental evidences that support recent molecular dynamics simulation and thermodynamics results.

  19. Improvement of hydrogen bond geometry in protein NMR structures by residual dipolar couplings - an assessment of the interrelation of NMR restraints

    Energy Technology Data Exchange (ETDEWEB)

    Jensen, Pernille Rose; Axelsen, Jacob Bock [University of Copenhagen, Institute of Molecular Biology (Denmark); Lerche, Mathilde Hauge [Amersham Health (Sweden); Poulsen, Flemming M. [University of Copenhagen, Institute of Molecular Biology (Denmark)], E-mail: fmp@apk.molbio.ku.dk

    2004-01-15

    We have examined how the hydrogen bond geometry in three different proteins is affected when structural restraints based on measurements of residual dipolar couplings are included in the structure calculations. The study shows, that including restraints based solely on {sup 1}H{sup N}-{sup 15}N residual dipolar couplings has pronounced impact on the backbone rmsd and Ramachandran plot but does not improve the hydrogen bond geometry. In the case of chymotrypsin inhibitor 2 the addition of {sup 13}CO-{sup 13}C{sup {alpha}} and {sup 15}N-{sup 13}CO one bond dipolar couplings as restraints in the structure calculations improved the hydrogen bond geometry to a quality comparable to that obtained in the 1.8 A resolution X-ray structure of this protein. A systematic restraint study was performed, in which four types of restraints, residual dipolar couplings, hydrogen bonds, TALOS angles and NOEs, were allowed in two states. This study revealed the importance of using several types of residual dipolar couplings to get good hydrogen bond geometry. The study also showed that using a small set of NOEs derived only from the amide protons, together with a full set of residual dipolar couplings resulted in structures of very high quality. When reducing the NOE set, it is mainly the side-chain to side-chain NOEs that are removed. Despite of this the effect on the side-chain packing is very small when a reduced NOE set is used, which implies that the over all fold of a protein structure is mainly determined by correct folding of the backbone.

  20. Intramolecular and nonlinear dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Davis, M.J. [Argonne National Laboratory, IL (United States)

    1993-12-01

    Research in this program focuses on three interconnected areas. The first involves the study of intramolecular dynamics, particularly of highly excited systems. The second area involves the use of nonlinear dynamics as a tool for the study of molecular dynamics and complex kinetics. The third area is the study of the classical/quantum correspondence for highly excited systems, particularly systems exhibiting classical chaos.

  1. Characterization of the hydrogen bond in molecular systems of biological interest by neutron scattering; Caracterisation de la liaison hydrogene dans des systemes moleculaires d'interet biologique par diffusion de neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Cavillon, F

    2004-10-15

    This work presents a methodology for the analysis of the scattering spectra of neutrons on molecular liquids. This method is based on the adjustment of the molecular form factor concerning great momentum transfer. The subtraction of the intra-molecular contributions gives access to information on inter-molecular interactions such as the hydrogen bond. 3 systems with increasing levels of difficulty have been studied: the ammonia molecule, the N-methyl-formamide (NMF) and the N-methyl-acetamide (NMA). The value we get for the N-D intermolecular distance of the liquid ammonia molecule is 1.7 angstrom, this value is different from the value generally admitted (2.3 angstrom) but we have validated it by studying the isotopic substitution N{sup 14}/N{sup 15}. The adjustment to the NMF is obtained with a good accuracy but the characterization of the hydrogen bound is more delicate to infer. A preliminary study of the NMA molecule shows that this method can give relevant results on complex molecules.

  2. Removal of distal protein-water hydrogen bonds in a plant epoxide hydrolase increases catalytic turnover but decreases thermostability.

    Science.gov (United States)

    Thomaeus, Ann; Naworyta, Agata; Mowbray, Sherry L; Widersten, Mikael

    2008-07-01

    A putative proton wire in potato soluble epoxide hydrolase 1, StEH1, was identified and investigated by means of site-directed mutagenesis, steady-state kinetic measurements, temperature inactivation studies, and X-ray crystallography. The chain of hydrogen bonds includes five water molecules coordinated through backbone carbonyl oxygens of Pro(186), Leu(266), His(269), and the His(153) imidazole. The hydroxyl of Tyr(149) is also an integrated component of the chain, which leads to the hydroxyl of Tyr(154). Available data suggest that Tyr(154) functions as a final proton donor to the anionic alkylenzyme intermediate formed during catalysis. To investigate the role of the putative proton wire, mutants Y149F, H153F, and Y149F/H153F were constructed and purified. The structure of the Y149F mutant was solved by molecular replacement and refined to 2.0 A resolution. Comparison with the structure of wild-type StEH1 revealed only subtle structural differences. The hydroxyl group lost as a result of the mutation was replaced by a water molecule, thus maintaining a functioning hydrogen bond network in the proton wire. All mutants showed decreased catalytic efficiencies with the R,R-enantiomer of trans-stilbene oxide, whereas with the S,S-enantiomer, k (cat)/K (M) was similar or slightly increased compared with the wild-type reactions. k (cat) for the Y149F mutant with either TSO enantiomer was increased; thus the lowered enzyme efficiencies were due to increases in K (M). Thermal inactivation studies revealed that the mutated enzymes were more sensitive to elevated temperatures than the wild-type enzyme. Hence, structural alterations affecting the hydrogen bond chain caused increases in k (cat) but lowered thermostability.

  3. Site-specific binding of a water molecule to the sulfa drugs sulfamethoxazole and sulfisoxazole: a laser-desorption isomer-specific UV and IR study.

    Science.gov (United States)

    Uhlemann, Thomas; Seidel, Sebastian; Müller, Christian W

    2018-03-07

    To determine the preferred water molecule binding sites of the polybasic sulfa drugs sulfamethoxazole (SMX) and sulfisoxazole (SIX), we have studied their monomers and monohydrated complexes through laser-desorption conformer-specific UV and IR spectroscopy. Both the SMX and SIX monomer adopt a single conformer in the molecular beam. On the basis of their conformer-specific IR spectra in the NH stretch region, these conformers were assigned to the SMX and SIX global minimum structures, both exhibiting a staggered sulfonamide group and an intramolecular C-HO[double bond, length as m-dash]S hydrogen bond. The SMX-H 2 O and SIX-H 2 O complexes each adopt a single isomer in the molecular beam. Their isomeric structures were determined based on their isomer-specific IR spectra in the NH/OH stretch region. Quantum Theory of Atoms in Molecules analysis of the calculated electron densities revealed that in the SMX-H 2 O complex the water molecule donates an O-HN hydrogen bond to the heterocycle nitrogen atom and accepts an N-HO hydrogen bond from the sulfonamide NH group. In the SIX-H 2 O complex, however, the water molecule does not bind to the heterocycle but instead donates an O-HO[double bond, length as m-dash]S hydrogen bond to the sulfonamide group and accepts an N-HO hydrogen bond from the sulfonamide NH group. Both water complexes are additionally stabilized by a C ph -HOH 2 hydrogen bond. Interacting Quantum Atoms analysis suggests that all intermolecular hydrogen bonds are dominated by the short-range exchange-correlation contribution.

  4. Density functional for van der Waals forces accounts for hydrogen bond in benchmark set of water hexamers

    DEFF Research Database (Denmark)

    Kelkkanen, Kari André; Lundqvist, Bengt; Nørskov, Jens Kehlet

    2009-01-01

    A recent extensive study has investigated how various exchange-correlation (XC) functionals treat hydrogen bonds in water hexamers and has shown traditional generalized gradient approximation and hybrid functionals used in density-functional (DF) theory to give the wrong dissociation-energy trend...... of low-lying isomers and van der Waals (vdW) dispersion forces to give key contributions to the dissociation energy. The question raised whether functionals that incorporate vdW forces implicitly into the XC functional predict the correct lowest-energy structure for the water hexamer and yield accurate...

  5. The hydrogen bond between N-H or O-H and organic fluorine: favourable yes, competitive no.

    Science.gov (United States)

    Taylor, Robin

    2017-06-01

    A study was made of X-H...F-C interactions (X = N or O) in small-molecule crystal structures. It was primarily based on 6728 structures containing X-H and C-F and no atom heavier than chlorine. Of the 28 451 C-F moieties in these structures, 1051 interact with X-H groups. However, over three-quarters of these interactions are either the weaker components of bifurcated hydrogen bonds (so likely to be incidental contacts) or occur in structures where there is a clear insufficiency of good hydrogen-bond acceptors such as oxygen, nitrogen or halide. In structures where good acceptors are entirely absent, there is about a 2 in 3 chance that a given X-H group will donate to fluorine. Viable alternatives are X-H...π hydrogen bonds (especially to electron-rich aromatics) and dihydrogen bonds. The average H...F distances of X-H...F-C interactions are significantly shorter for CR 3 F (R = C or H) and Csp 2 -F acceptors than for CRF 3 . The X-H...F angle distribution is consistent with a weak energetic preference for linearity, but that of H...F-C suggests a flat energy profile in the range 100-180°. X-H...F-C interactions are more likely when the acceptor is Csp 2 -F or CR 3 F, and when the donor is C-NH 2 . They also occur significantly more often in structures containing tertiary alcohols or solvent molecules, or with Z' > 1, i.e. when there may be unusual packing problems. It is extremely rare to find X-H...F-C interactions in structures where there are several unused good acceptors. When it does happen, there is often a clear reason, e.g. awkwardly shaped molecules whose packing isolates a donor group from the good acceptors.

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

    Science.gov (United States)

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

    2018-02-08

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

  7. Microsolvation effect and hydrogen-bonding pattern of taurine-water TA-(H2O)n (n = 1-3) complexes.

    Science.gov (United States)

    Dai, Yumei; Wang, Yuhua; Huang, Zhengguo; Wang, Hongke; Yu, Lei

    2012-01-01

    The microsolvation of taurine (TA) with one, two or three water molecules was investigated by a density functional theory (DFT) approach. Quantum theory of atoms in molecules (QTAIM) analyses were employed to elucidate the hydrogen bond (H-bond) interaction characteristics in TA-(H(2)O)(n) (n = 1-3) complexes. The results showed that the intramolecular H-bond formed between the hydroxyl and the N atom of TA are retained in most TA-(H(2)O)(n) (n = 1-3) complexes, and are strengthened via cooperative effects among multiple H-bonds from n = 1-3. A trend of proton transformation exists from the hydroxyl to the N atom, which finally results in the cleavage of the origin intramolecular H-bond and the formation of a new intramolecular H-bond between the amino and the O atom of TA. Therefore, the most stable TA-(H(2)O)(3) complex becomes a zwitterionic complex rather than a neutral type. A many-body interaction analysis showed that the major contributors to the binding energies for complexes are the two-body energies, while three-body energies and relaxation energies make significant contributions to the binding energies for some complexes, whereas the four-body energies are too small to be significant.

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

    African Journals Online (AJOL)

    monomer A) and 2,6-diaminopyridine-3,5-dialdehyde (monomer B) was performed using the AM1 method to obtain its binding energy. A series of complexes 2 to 9 were designed by changing the R-groups on monomer A in complex 1 into C6H5, ...

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

    African Journals Online (AJOL)

    the complexes were optimized employing the AM1 method [14] in the GAUSSIAN 03 program. [15] to accomplish the binding energies. Based on the optimized geometries, the electronic spectra of the complexes were computed using the INDO/CIS method [16-22] to obtain absorption wavelengths λ and oscillator strength f.

  10. Theoretical investigation on hydrogen bond interaction of diketo/keto-enol form uracil and thymine tautomers with intercalators.

    Science.gov (United States)

    Anithaa, V S; Vijayakumar, S; Sudha, M; Shankar, R

    2017-11-06

    The interaction of diketo and keto-enol form of thymine and uracil tautomers with acridine (Acr), phenazine (Phen), benzo[c]cinnoline (Ben), 1,10-phenanthroline (1,10-Phe), and 4,7-phenenthroline (4,7-Phe) intercalating drug molecules was studied using density functional theory at B3LYP/6-311++G** and M05-2×/6-311++G** levels of theory. From the interaction energy, it is found that keto-enol form tautomers have stronger interaction with intercalators than diketone form tautomers. On complex formation of thymine and uracil tautomers with benzo[c]cinnoline the drug molecules have high interaction energy values of -20.14 (BenT3) and -20.55 (BenU3) kcal mol -1 , while phenazine has the least interaction energy values of -6.52 (PhenT2) and -6.67 (PhenU2) kcal mol -1 . The closed shell intermolecular type interaction between the molecules with minimum elliptical value of 0.018 and 0.019 a.u at both levels of theory has been found from topological analysis. The benzo[c]cinnoline drug molecule with thymine and uracil tautomers has short range intermolecular N-H…N, C-H…O, and O-H...N hydrogen bonds (H-bonds) resulting in higher stability than other drug molecules. The proper hydrogen bonds N-H..N and O-H..N have the frequency shifted toward the lower side (red shifted) with the elongation in their bond length while the improper hydrogen bond C-H...O has the frequency shifted toward the higher side (blue shifted) of the spectral region with the contraction in their bond length. Further, the charge transfer between proton acceptor and donor along with stability of the bond is studied using natural bond orbital (NBO) analysis. Graphical abstract Hydrogen bond interaction of diketo/keto-enol form uracil and thymine tautomers with intercalators.

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

    Science.gov (United States)

    Simončič, Matjaž; Urbic, Tomaz

    2018-05-01

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

  12. DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson-Crick pairing near graphite surfaces.

    Science.gov (United States)

    Shankar, Akshaya; Jagota, Anand; Mittal, Jeetain

    2012-10-11

    Single- and double-stranded DNA are increasingly being paired with surfaces and nanoparticles for numerous applications, such as sensing, imaging, and drug delivery. Unlike the majority of DNA structures in bulk that are stabilized by canonical Watson-Crick pairing between Ade-Thy and Gua-Cyt, those adsorbed on surfaces are often stabilized by noncanonical base pairing, quartet formation, and base-surface stacking. Not much is known about these kinds of interactions. To build an understanding of the role of non-Watson-Crick pairing on DNA behavior near surfaces, one requires basic information on DNA base pair stacking and hydrogen-bonding interactions. All-atom molecular simulations of DNA bases in two cases--in bulk water and strongly adsorbed on a graphite surface--are conducted to study the relative strengths of stacking and hydrogen bond interactions for each of the 10 possible combinations of base pairs. The key information obtained from these simulations is the free energy as a function of distance between two bases in a pair. We find that stacking interactions exert the dominant influence on the stability of DNA base pairs in bulk water as expected. The strength of stability for these stacking interactions is found to decrease in the order Gua-Gua > Ade-Gua > Ade-Ade > Gua-Thy > Gua-Cyt > Ade-Thy > Ade-Cyt > Thy-Thy > Cyt-Thy > Cyt-Cyt. On the other hand, mutual interactions of surface-adsorbed base pairs are stabilized mostly by hydrogen-bonding interactions in the order Gua-Cyt > Ade-Gua > Ade-Thy > Ade-Ade > Cyt-Thy > Gua-Gua > Cyt-Cyt > Ade-Cyt > Thy-Thy > Gua-Thy. Interestingly, several non-Watson-Crick base pairings, which are commonly ignored, have similar stabilization free energies due to interbase hydrogen bonding as Watson-Crick pairs. This clearly highlights the importance of non-Watson-Crick base pairing in the development of secondary structures of oligonucleotides near surfaces.

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

    Science.gov (United States)

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

    2015-05-06

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

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

    KAUST Repository

    Ajitha, Manjaly John; Huang, Kuo-Wei

    2016-01-01

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

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

    Science.gov (United States)

    Bushey, Mark Lawrence

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

  16. Molecular Dynamics Simulation of Barnase: Contribution of Noncovalent Intramolecular Interaction to Thermostability

    Directory of Open Access Journals (Sweden)

    Zhiguo Chen

    2013-01-01

    Full Text Available Bacillus amyloliquefaciens ribonuclease Barnase (RNase Ba is a 12 kD (kilodalton small extracellular ribonuclease. It has broad application prospects in agriculture, clinical medicine, pharmaceutical, and so forth. In this work, the thermal stability of Barnase has been studied using molecular dynamics simulation at different temperatures. The present study focuses on the contribution of noncovalent intramolecular interaction to protein stability and how they affect the thermal stability of the enzyme. Profiles of root mean square deviation and root mean square fluctuation identify thermostable and thermosensitive regions of Barnase. Analyses of trajectories in terms of secondary structure content, intramolecular hydrogen bonds and salt bridge interactions indicate distinct differences in different temperature simulations. In the simulations, Four three-member salt bridge networks (Asp8-Arg110-Asp12, Arg83-Asp75-Arg87, Lys66-Asp93-Arg69, and Asp54-Lys27-Glu73 have been identified as critical salt bridges for thermostability which are maintained stably at higher temperature enhancing stability of three hydrophobic cores. The study may help enlighten our knowledge of protein structural properties, noncovalent interactions which can stabilize secondary peptide structures or promote folding, and also help understand their actions better. Such an understanding is required for designing efficient enzymes with characteristics for particular applications at desired working temperatures.

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

    International Nuclear Information System (INIS)

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

    2005-01-01

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

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

    DEFF Research Database (Denmark)

    Kuznetsov, A.M.; Ulstrup, Jens

    2004-01-01

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    Science.gov (United States)

    Hemp, Sean T; Long, Timothy E

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-02-01

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

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

    Directory of Open Access Journals (Sweden)

    Hana Bourara

    2014-10-01

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

  3. Increased helix and protein stability through the introduction of a new tertiary hydrogen bond.

    Science.gov (United States)

    Peterson, R W; Nicholson, E M; Thapar, R; Klevit, R E; Scholtz, J M

    1999-03-12

    In an effort to quantify the importance of hydrogen bonding and alpha-helix formation to protein stability, a capping box motif was introduced into the small phosphocarrier protein HPr. Previous studies had confirmed that Ser46, at the N-cap position of the short helix-B in HPr, serves as an N-cap in solution. Thus, only a single-site mutation was required to produce a canonical S-X-X-E capping box: Lys49 at the N3 position was substituted with a glutamic acid residue. Thermal and chemical denaturation studies on the resulting K49E HPr show that the designed variant is approximately 2 kcal mol-1 more stable than the wild-type protein. However, NMR studies indicate that the side-chain of Glu49 does not participate in the expected capping H-bond interaction, but instead forms a new tertiary H-bond that links helix-B to the four-stranded beta-sheet of HPr. Here, we demonstrate that a strategy in which new non-native H-bonds are introduced can generate proteins with increased stability. We discuss why the original capping box design failed, and compare the energetic consequences of the new tertiary side-chain to main-chain H-bond with a local (helix-capping) side-chain to main-chain H-bond on the protein's global stability. Copyright 1999 Academic Press.

  4. Supra-molecular hydrogen-bonding patterns in the N(9)-H protonated and N(7)-H tautomeric form of an N(6) -benzoyl-adenine salt: N (6)-benzoyl-adeninium nitrate.

    Science.gov (United States)

    Karthikeyan, Ammasai; Jeeva Jasmine, Nithianantham; Thomas Muthiah, Packianathan; Perdih, Franc

    2016-02-01

    In the title molecular salt, C12H10N5O(+)·NO3 (-), the adenine unit has an N (9)-protonated N(7)-H tautomeric form with non-protonated N(1) and N(3) atoms. The dihedral angle between the adenine ring system and the phenyl ring is 51.10 (10)°. The typical intra-molecular N(7)-H⋯O hydrogen bond with an S(7) graph-set motif is also present. The benzoyl-adeninium cations also form base pairs through N-H⋯O and C-H⋯N hydrogen bonds involving the Watson-Crick face of the adenine ring and the C and O atoms of the benzoyl ring of an adjacent cation, forming a supra-molecular ribbon with R 2 (2)(9) rings. Benzoyl-adeninum cations are also bridged by one of the oxygen atoms of the nitrate anion, which acts as a double acceptor, forming a pair of N-H⋯O hydrogen bonds to generate a second ribbon motif. These ribbons together with π-π stacking inter-actions between the phenyl ring and the five- and six-membered adenine rings of adjacent mol-ecules generate a three-dimensional supra-molecular architecture.

  5. Conserved hydrogen bonds and water molecules in MDR HIV-1 protease substrate complexes

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhigang [Wayne State Univ., Detroit, MI (United States); Case Western Reserve Univ., Cleveland, OH (United States); Harbor Hospital Baltimore, MD (United States); Wang, Yong [Wayne State Univ., Detroit, MI (United States); Yedidi, Ravikiran S. [Wayne State Univ., Detroit, MI (United States); National Institutes of Health, Bethesda, MD (United States); Dewdney, Tamaria G. [Wayne State Univ., Detroit, MI (United States); Reiter, Samuel J. [Wayne State Univ., Detroit, MI (United States); Brunzelle, Joseph S. [Northwestern Univ. Feinberg School of Medicine, Chicago, IL (United States); Kovari, Iulia A. [Wayne State Univ., Detroit, MI (United States); Kovari, Ladislau C. [Wayne State Univ., Detroit, MI (United States)

    2012-12-19

    Success of highly active antiretroviral therapy (HAART) in anti-HIV therapy is severely compromised by the rapidly developing drug resistance. HIV-1 protease inhibitors, part of HAART, are losing their potency and efficacy in inhibiting the target. Multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, 90) was selected for the present study to understand the binding to its natural substrates. The nine crystal structures of MDR769 HIV-1 protease substrate hepta-peptide complexes were analyzed in order to reveal the conserved structural elements for the purpose of drug design against MDR HIV-1 protease. Our structural studies demonstrated that highly conserved hydrogen bonds between the protease and substrate peptides, together with the conserved crystallographic water molecules, played a crucial role in the substrate recognition, substrate stabilization and protease stabilization. Additionally, the absence of the key flap-ligand bridging water molecule might imply a different catalytic mechanism of MDR769 HIV-1 protease compared to that of wild type (WT) HIV-1 protease.

  6. Ab initio study on the electronic transport properties of carbon nanotube intramolecular junctions

    Energy Technology Data Exchange (ETDEWEB)

    Wang, R.N. [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China); Graduate School of the Chinese Academy of Sciences, 19A Yu Quan Rd, Beijing 100049 (China); Zheng, X.H.; Zeng, Z. [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China); Song, L.L. [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China); Graduate School of the Chinese Academy of Sciences, 19A Yu Quan Rd, Beijing 100049 (China); School of Electronic Science and Applied Physics, Hefei University of Technology, Hefei 230009 (China)

    2011-12-15

    The effects of electron doping and molecule adsorption on the electronic transport properties of carbon nanotube (CNT) junctions CNT(3,3)/n-CNT(6,0)/CNT(3,3) (n = 1-5) are simulated by first-principles calculations combined with a non-equilibrium Green's function technique. The doping effects are investigated by N substitution for the carbon atom while the molecule adsorption effects are studied by adsorbing a H{sub 2}O molecule or an OH group on the top of one carbon atom, respectively. The transmission function around the Fermi level is highly dependent on the doping or adsorption site. The effects are negligible when the site is at the interface, while it always forms a scattering barrier which causes a valley of the transmission spectra around the Fermi level when the doping/adsorption site is inside the sandwiched CNT(6,0). The conductance of CNT intramolecular junctions is very sensitive to the environment, which may provide potential of application in future nanoelectronic devices and gas sensors. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

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

    Science.gov (United States)

    Isaev, A. N.

    2016-03-01

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

  8. High-fidelity in vivo replication of DNA base shape mimics without Watson–Crick hydrogen bonds

    Science.gov (United States)

    Delaney, James C.; Henderson, Paul T.; Helquist, Sandra A.; Morales, Juan C.; Essigmann, John M.; Kool, Eric T.

    2003-01-01

    We report studies testing the importance of Watson–Crick hydrogen bonding, base-pair geometry, and steric effects during DNA replication in living bacterial cells. Nonpolar DNA base shape mimics of thymine and adenine (abbreviated F and Q, respectively) were introduced into Escherichia coli by insertion into a phage genome followed by transfection of the vector into bacteria. Genetic assays showed that these two base mimics were bypassed with moderate to high efficiency in the cells and with very high efficiency under damage-response (SOS induction) conditions. Under both sets of conditions, the T-shape mimic (F) encoded genetic information in the bacteria as if it were thymine, directing incorporation of adenine opposite it with high fidelity. Similarly, the A mimic (Q) directed incorporation of thymine opposite itself with high fidelity. The data establish that Watson–Crick hydrogen bonding is not necessary for high-fidelity replication of a base pair in vivo. The results suggest that recognition of DNA base shape alone serves as the most powerful determinant of fidelity during transfer of genetic information in a living organism. PMID:12676985

  9. Thermodynamics of single polyethylene and polybutylene glycols with hydrogen-bonding ends: A transition from looped to open conformations

    Science.gov (United States)

    Lee, Eunsang; Paul, Wolfgang

    2018-02-01

    A variety of linear polymer precursors with hydrogen bonding motifs at both ends enable us to design supramolecular polymer systems with tailored macroscopic properties including self-healing. In this study, we investigate thermodynamic properties of single polyethylene and polybutylene glycols with hydrogen bonding motifs. In this context, we first build a coarse-grained model of building blocks of the supramolecular polymer system based on all-atom molecular structures. The density of states of the single precursor is obtained using the stochastic approximation Monte Carlo method. Constructing canonical partition functions from the density of states, we find the transition from looped to open conformations at transition temperatures which are non-monotonously changing with an increasing degree of polymerization due to the competition between chain stiffness and loop-forming entropy penalty. In the complete range of chain length under investigation, a coexistence of the looped and open morphologies at the transition temperature is shown regardless of whether the transition is first-order-like or continuous. Polyethylene and polybutylene glycols show similar behavior in all the thermodynamic properties but the transition temperature of the more flexible polybutylene glycol is shown to change more gradually.

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

    Science.gov (United States)

    Cha, Seoncheol; Kim, Doseok

    2018-05-01

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

  11. Interpretation of IR and Raman spectra of dopamine neurotransmitter and effect of hydrogen bond in HCl

    Science.gov (United States)

    Yadav, T.; Mukherjee, V.

    2018-05-01

    The potential energy scanning with respect to the different dihedral angles were performed to search possible numbers of dopamine (neutral) conformers and further, fifteen conformers of dopamine were identified on the basis of energy minima. Vibrational frequencies were calculated for all the conformers of dopamine. Density functional theory was employed to carry out all the computations. The exchange correlation functional B3LYP and the basis set 6-31++G(d,p) were included in DFT calculation. The FTIR and FT-Raman spectra of dopamine hydrochloride were also recorded in the spectral region 400-4000 cm-1 and 50-4000 cm-1 respectively. The normal coordinate analysis was also performed to scale DFT calculated force constants and to calculate potential energy distributions. The detailed vibrational spectral analysis and the assignments of the bands, done on the best-fit basis comparison of the experimentally obtained and theoretically calculated IR and Raman spectra, match quite well indicating DFT calculations as very accurate source of normal mode assignments. The interaction of the most stable conformer of dopamine with HCl was also studied to know the effect of hydrogen bond on its geometry and dynamics. The stability of the dopamine in isolated and protonated forms arising from hyperconjugative interactions was also analyzed by natural bond orbital analysis.

  12. Comparison of hydrogen bonding in 1-octanol and 2-octanol as probed by spectroscopic techniques.

    Science.gov (United States)

    Palombo, Francesca; Sassi, Paola; Paolantoni, Marco; Morresi, Assunta; Cataliotti, Rosario Sergio

    2006-09-14

    Liquid 1-octanol and 2-octanol have been investigated by infrared (IR), Raman, and Brillouin experiments in the 10-90 degrees C temperature range. Self-association properties of the neat liquids are described in terms of a three-state model in which OH oscillators differently implicated in the formation of H-bonds are considered. The results are in quantitative agreement with recent computational studies for 1-octanol. The H-bond probability is obtained by Raman data, and a stochastic model of H-bonded chains gives a consistent picture of the self-association characteristics. Average values of hydrogen bond enthalpy and entropy are evaluated. The H-bond formation enthalpy is ca. -22 kJ/mol and is slightly dependent on the structural isomerism. The different degree of self-association for the two octanols is attributed to entropic factors. The more shielded 2-isomer forms larger fractions of smaller, less cooperative, and more ordered clusters, likely corresponding to cyclic structures. Signatures of a different cluster organization are also evidenced by comparing the H-bond energy dispersion (HBED) of OH stretching IR bands. A limiting cooperative H-bond enthalpy value of 27 kJ/mol is found. It is also proposed that the different H-bonding capabilities may modulate the extent of interaggregate hydrocarbon interactions, which is important in explaining the differences in molar volume, compressibility, and vaporization enthalpy for the two isomers.

  13. Heat conduction in chain polymer liquids: molecular dynamics study on the contributions of inter- and intramolecular energy transfer.

    Science.gov (United States)

    Ohara, Taku; Yuan, Tan Chia; Torii, Daichi; Kikugawa, Gota; Kosugi, Naohiro

    2011-07-21

    In this paper, the molecular mechanisms which determine the thermal conductivity of long chain polymer liquids are discussed, based on the results observed in molecular dynamics simulations. Linear n-alkanes, which are typical polymer molecules, were chosen as the target of our studies. Non-equilibrium molecular dynamics simulations of bulk liquid n-alkanes under a constant temperature gradient were performed. Saturated liquids of n-alkanes with six different chain lengths were examined at the same reduced temperature (0.7T(c)), and the contributions of inter- and intramolecular energy transfer to heat conduction flux, which were identified as components of heat flux by the authors' previous study [J. Chem. Phys. 128, 044504 (2008)], were observed. The present study compared n-alkane liquids with various molecular lengths at the same reduced temperature and corresponding saturated densities, and found that the contribution of intramolecular energy transfer to the total heat flux, relative to that of intermolecular energy transfer, increased with the molecular length. The study revealed that in long chain polymer liquids, thermal energy is mainly transferred in the space along the stiff intramolecular bonds. This finding implies a connection between anisotropic thermal conductivity and the orientation of molecules in various organized structures with long polymer molecules aligned in a certain direction, which includes confined polymer liquids and self-organized structures such as membranes of amphiphilic molecules in water.

  14. Intramolecular Diels-Alder reactions of pyrimidines, a synthetic and computational study

    NARCIS (Netherlands)

    Stolle, W.A.W.

    1992-01-01

    This thesis deals with an investigation on the ringtransformation reactions of 2and 5-(ω-alkynyl)pyrimidine derivatives, which undergo upon heating an intramolecular Diels-Alder reaction and subsequently a spontaneous retro Diels- Alder reaction. To get a better insight into the

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

    Directory of Open Access Journals (Sweden)

    Batista VictorS.

    2013-03-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    is a superior hydrogen bond acceptor. The class of large-amplitude donor OH librational motion is shown to account for up to 5.1 kJ mol-1 of the destabilizing change of vibrational zero-point energy upon intermolecular OH...O hydrogen bond formation. The experimental findings are supported by complementary...

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

    DEFF Research Database (Denmark)

    Mackeprang, Kasper; Kjærgaard, Henrik Grum

    2017-01-01

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

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

    NARCIS (Netherlands)

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

    1999-01-01

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

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

    Indian Academy of Sciences (India)

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

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

    NARCIS (Netherlands)

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

    2008-01-01

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

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

    NARCIS (Netherlands)

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

    2012-01-01

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

  2. 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…

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

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

    Science.gov (United States)

    Weinhold, Frank; Klein, Roger A.

    2014-01-01

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

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

    Science.gov (United States)

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

    2015-01-28

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

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

    Science.gov (United States)

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

    2011-01-01

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

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

    Science.gov (United States)

    Amtul, Zareen; Rahman, Atta-Ur

    2016-02-01

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

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

    Czech Academy of Sciences Publication Activity Database

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

    2006-01-01

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

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

    NARCIS (Netherlands)

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

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

  10. 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.

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

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

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

    NARCIS (Netherlands)

    2004-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-05-15

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

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

    Czech Academy of Sciences Publication Activity Database

    Kříž, Jaroslav; Dybal, Jiří

    2008-01-01

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

  15. Influence of hydrogen bonding on the generation and stabilization

    Indian Academy of Sciences (India)

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

  16. The effect of the flexibility of hydrogen bonding network on low-frequency motions of amino acids. Evidence from Terahertz spectroscopy and DFT calculations

    Science.gov (United States)

    Li, Yin; Lukács, András; Bordács, Sándor; Móczár, János; Nyitrai, Miklós; Hebling, János

    2018-02-01

    Low-frequency modes of L-Asp and L-Asn were studied in the range from 0.1 to 3.0 THz using time-domain Terahertz spectroscopy and density functional theory calculation. The results show that PBE-D2 shows more success than BLYP-D2 in prediction of THz absorption spectra. To compare their low-frequency modes, we adopted ;vibrational character ID strips; proposed by Schmuttenmaer and coworkers [Journal of Physical Chemistry B, 117, 10444(2013)]. We found that the most intense THz absorption peaks of two compounds both involve severe distortion of their hydrogen bonding networks. Due to less rigid hydrogen bonding network in L-Asp, the side chain (carboxyl group) of L-Asp exhibits larger motions than that (carboxamide group) of L-Asn in low-frequency modes.

  17. Stability of Hydrogen-Bonded Supramolecular Architecture under High Pressure Conditions: Pressure-Induced Amorphization in Melamine-Boric Acid Adduct

    International Nuclear Information System (INIS)

    Wang, K.; Duan, D.; Wang, R.; Lin, A.; Cui, Q.; Liu, B.; Cui, T.; Zou, B.; Zhang, X.

    2009-01-01

    The effects of high pressure on the structural stability of the melamine-boric acid adduct (C3N6H6 2H3BO3, M 2B), a three-dimensional hydrogen-bonded supramolecular architecture, were studied by in situ synchrotron X-ray diffraction (XRD) and Raman spectroscopy. M 2B exhibited a high compressibility and a strong anisotropic compression, which can be explained by the layerlike crystal packing. Furthermore, evolution of XRD patterns and Raman spectra indicated that the M 2B crystal undergoes a reversible pressure-induced amorphization (PIA) at 18 GPa. The mechanism for the PIA was attributed to the competition between close packing and long-range order. Ab initio calculations were also performed to account for the behavior of hydrogen bonding under high pressure.

  18. Versatile supramolecular reactivity of zinc-tetra(4-pyridylporphyrin in crystalline solids: Polymeric grids with zinc dichloride and hydrogen-bonded networks with mellitic acid

    Directory of Open Access Journals (Sweden)

    Sophia Lipstman

    2009-12-01

    Full Text Available Crystal engineering studies confirm that the zinc-tetra(4-pyridylporphyrin building block reveals versatile supramolecular chemistry. In this work, it was found to be reactive in the assembly of both (a a 2D polymeric array by a unique combination of self-coordination and coordination through external zinc dichloride linkers and (b an extended heteromolecular hydrogen-bonded network with mellitic acid sustained by multiple connectivity between the component species.

  19. 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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-07-15

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  2. XRD, vibrational spectra and quantum chemical studies of an anticancer drug: 6-Mercaptopurine.

    Science.gov (United States)

    Kumar, S Suresh; Athimoolam, S; Sridhar, B

    2015-07-05

    The single crystal of the hydrated anticancer drug, 6-Mercaptopurine (6-MP), has been grown by slow evaporation technique under room temperature. The structure was determined by single crystal X-ray diffraction. The vibrational spectral analysis was carried out using Laser Raman and FT-IR spectroscopy in the range of 3300-100 and 4000-400 cm(-1). The single crystal X-ray studies shows that the crystal packing is dominated by N-H⋯O and O-H⋯N classical hydrogen bonds leading to a hydrogen bonded ensemble. This classical hydrogen bonds were further connected through O-H⋯S hydrogen bond to form two primary ring R4(4)(16) and R4(4)(12) motifs. These two primary ring motifs are interlinked with each other to build a ladder like structure. These ladders are connected through N-H⋯N hydrogen bond along c-axis of the unit cell through chain C(5) motifs. Further, the strength of the hydrogen bonds is studied through vibrational spectral measurements. The shifting of bands due to the intermolecular interactions was also analyzed in the solid crystalline state. Geometrical optimizations of the drug molecule were done by Density Functional Theory (DFT) using the B3LYP function and Hartree-Fock (HF) level with 6-311++G(d,p) basis set. The optimized molecular geometry and computed vibrational spectra are compared with experimental results which show significant agreement. The natural bond orbital (NBO) analysis was carried out to interpret hyperconjugative interaction and intramolecular charge transfer (ICT). The chemical hardness, electro-negativity and chemical potential of the molecule are carried out by HOMO-LUMO plot. In which, the frontier orbitals has lower band gap value indicating the possible pharmaceutical activity of the molecule. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Thermodynamics of hydrogen bonding and van der Waals interactions of organic solutes in solutions of imidazolium based ionic liquids: “Structure-property” relationships

    Energy Technology Data Exchange (ETDEWEB)

    Varfolomeev, Mikhail A., E-mail: vma.ksu@gmail.com; Khachatrian, Artashes A.; Akhmadeev, Bulat S.; Solomonov, Boris N.

    2016-06-10

    Highlights: • Solution enthalpies of organic solutes in imidazolium based ionic liquids were measured. • van der Waals interactions scale of imidazolium based ionic liquids was proposed. • Enthalpies of solvation of organic solutes in ionic liquids were determined. • Hydrogen bond enthalpies of organic solutes with ionic liquids were calculated. • Relationships between structure of ionic liquids and thermochemical data were obtained. - Abstract: In the present work thermochemistry of intermolecular interactions of organic compounds in solutions of imidazolium based ionic liquids (ILs) has been studied using solution calorimetry method. Enthalpies of solution at infinite dilution of non-polar (alkanes, aromatic hydrocarbons) and polar (alcohols, amides, and etc.) organic solutes in two ionic liquids 1-butyl-3-methylimidazolium tetrafluoroborate and 1-butyl-3-methylimidazolium trifluoromethanesulfonate were measured at 298.15 K. The scale of van der Waals interactions of imidazolium based ILs has been proposed on the basis of solution enthalpies of n-alkanes in their media. The effect of the cation and anion structure of ILs on the enthalpies of solvation was analyzed. Enthalpies of hydrogen bonding of organic solutes with imidazolium based ILs were determined. It has been shown that these values are close to zero for proton acceptor solutes. At the same time, enthalpies of hydrogen bonding of proton donor solutes with ionic liquids are increased depending the anion: tetrafluoroborate ≈ bis(trifluoromethylsulfonyl)imide < 2-(2-methoxyethoxy)ethyl sulfate < trifluoromethanesulfonate. Enthalpies of van der Waals interactions and hydrogen bonding in the solutions of imidazolium based ionic liquids were compared with the same data for molecular solvents.

  4. Thermodynamics of hydrogen bonding and van der Waals interactions of organic solutes in solutions of imidazolium based ionic liquids: “Structure-property” relationships

    International Nuclear Information System (INIS)

    Varfolomeev, Mikhail A.; Khachatrian, Artashes A.; Akhmadeev, Bulat S.; Solomonov, Boris N.

    2016-01-01

    Highlights: • Solution enthalpies of organic solutes in imidazolium based ionic liquids were measured. • van der Waals interactions scale of imidazolium based ionic liquids was proposed. • Enthalpies of solvation of organic solutes in ionic liquids were determined. • Hydrogen bond enthalpies of organic solutes with ionic liquids were calculated. • Relationships between structure of ionic liquids and thermochemical data were obtained. - Abstract: In the present work thermochemistry of intermolecular interactions of organic compounds in solutions of imidazolium based ionic liquids (ILs) has been studied using solution calorimetry method. Enthalpies of solution at infinite dilution of non-polar (alkanes, aromatic hydrocarbons) and polar (alcohols, amides, and etc.) organic solutes in two ionic liquids 1-butyl-3-methylimidazolium tetrafluoroborate and 1-butyl-3-methylimidazolium trifluoromethanesulfonate were measured at 298.15 K. The scale of van der Waals interactions of imidazolium based ILs has been proposed on the basis of solution enthalpies of n-alkanes in their media. The effect of the cation and anion structure of ILs on the enthalpies of solvation was analyzed. Enthalpies of hydrogen bonding of organic solutes with imidazolium based ILs were determined. It has been shown that these values are close to zero for proton acceptor solutes. At the same time, enthalpies of hydrogen bonding of proton donor solutes with ionic liquids are increased depending the anion: tetrafluoroborate ≈ bis(trifluoromethylsulfonyl)imide < 2-(2-methoxyethoxy)ethyl sulfate < trifluoromethanesulfonate. Enthalpies of van der Waals interactions and hydrogen bonding in the solutions of imidazolium based ionic liquids were compared with the same data for molecular solvents.

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

    Science.gov (United States)

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

    2017-08-01

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

  6. The specific cleavage of lactone linkage to open-loop in cyclic lipopeptide during negative ESI tandem mass spectrometry: the hydrogen bond interaction effect of 4-ethyl guaiacol.

    Directory of Open Access Journals (Sweden)

    Mengzhe Guo

    Full Text Available Mass spectrometry is a valuable tool for the analysis and identification of chemical compounds, particularly proteins and peptides. Lichenysins G, the major cyclic lipopeptide of lichenysin, and the non-covalent complex of lichenysins G and 4-ethylguaiacol were investigated with negative ion ESI tandem mass spectrometry. The different fragmentation mechanisms for these compounds were investigated. Our study shows the 4-ethylguaiacol hydrogen bond with the carbonyl oxygen of the ester group in the loop of lichenysins G. With the help of this hydrogen bond interaction, the ring structure preferentially opens in lactone linkage rather than O-C bond of the ester-group to produce alcohol and ketene. Isothermal titration 1H-NMR analysis verified the hydrogen bond and determined the proportion of subject and ligand in the non-covalent complex to be 1∶1. Theoretical calculations also suggest that the addition of the ligand can affect the energy of the transition structures (TS during loop opening.

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

    Science.gov (United States)

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

    2017-09-01

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

  8. Ferroelectric phase transition in hydrogen-bonded 2-aminopyridine phosphate (NC sub 4 H sub 4 NH sub 2)centre dot H sub 3 PO sub 4

    CERN Document Server

    Czapla, Z; Waskowska, A

    2003-01-01

    A new crystal of 2-aminopyridine phosphate (NC sub 4 H sub 4 NH sub 2)centre dot H sub 3 PO sub 4 has been grown and its x-ray structure and physical properties were studied. At room temperature the crystals are monoclinic, space group C2/c. The flat 2-aminopyridine cations are hydrogen bonded to the anionic [PO sub 4 ] groups. The interesting feature of the crystal structure is the three-dimensional network of hydrogen bonds including, among others, two strong, symmetrical O centre dot centre dot centre dot H, H centre dot centre dot centre dot O interactions with disordered proton locations. Symmetrically related PO sub 4 anions linked through these protons form infinite (PO sub 4) subinfinity chains along the crystal a-axis. The anomalies in the temperature dependence of the electric permittivity showed that the crystal undergoes ferroelectric phase transition at T sub c = 103.5 K. The spontaneous polarization takes place along the crystal a-axis, being parallel to the chains of the hydrogen-bonded PO sub ...

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

    Directory of Open Access Journals (Sweden)

    Yin Long

    2015-07-01

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

  10. 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.

  11. Synthesis, growth, structural, optical, thermal, electrical and mechanical properties of hydrogen bonded organic salt crystal: Triethylammonium-3, 5-dinitrosalicylate

    Science.gov (United States)

    Rajkumar, Madhu; Chandramohan, Angannan

    2017-04-01

    Triethylammonium-3, 5-dinitrosalicylate, an organic salt was synthesized and single crystals grown by slow solvent evaporation solution growth technique using methanol as a solvent. The presence of various functional groups and mode of vibrations has been confirmed by FT-IR spectroscopic technique. The UV-vis-NIR Spectrum was recorded in the range 200-1200 nm to find optical transmittance window and lower cut off wavelength of the title crystal. The formation of the salt and the molecular structure was confirmed by NMR spectroscopic technique. Crystal system, crystalline nature, cell parameters and hydrogen bonding interactions of the grown crystal were determined by single crystal x-ray diffraction analysis. The thermal characteristics of grown crystal were analyzed by thermo gravimetric and differential thermal analyses. Dielectric studies were carried out to study the distribution of charges within the crystal. The mechanical properties of the title crystal were studied by Vicker's microhardness technique.

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

    Directory of Open Access Journals (Sweden)

    Søren W. Pedersen

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

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

    Science.gov (United States)

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

    2015-03-06

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

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

    Directory of Open Access Journals (Sweden)

    Fangjun Yao

    2017-03-01

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

  15. Density functional study of uranyl (VI) amidoxime complexes

    International Nuclear Information System (INIS)

    Chi Fang-Ting; Xiong Jie; Hu Sheng; Xia Xiu-Long; Wang Xiao-Lin; Li Peng; Gao Tao

    2012-01-01

    Uranyl (VI) amidoxime complexes are investigated using relativistic density functional theory. The equilibrium structures, bond orders, and Mulliken populations of the complexes have been systematically investigated under a generalized gradient approximation (GGA). Comparison of (acet) uranyl amidoxime complexes ([UO 2 (AO) n ] 2−n , 1 ≤ n ≤ 4) with available experimental data shows an excellent agreement. In addition, the U−O(1), U−O(3), C(1)−N(2), and C(3)−N(4) bond lengths of [UO 2 (CH 3 AO) 4 ] 2− are longer than experimental data by about 0.088, 0.05, 0.1, and 0.056 Å. The angles of N(3)−O(3)−U, O(2)−N(1)−C(1), N(3)−C(3)−N(4), N(4)−C(3)−C(4), and C(4)−C(3)−N(3) are different from each other, which is due to existing interaction between oxygen in uranyl and hydrogen in amino group. This interaction is found to be intra-molecular hydrogen bond. Studies on the bond orders, Mulliken charges, and Mulliken populations demonstrate that uranyl oxo group functions as hydrogen-bond acceptors and H atoms in ligands act as hydrogen-bond donors forming hydrogen bonds within the complex

  16. Quantum chemical study of the structure and properties of citrinin

    Science.gov (United States)

    Citrinin is a well known polyketide mycotoxin produced by fungal species that naturally occur in certain agricultural commodities, including red yeast rice. This toxin possesses complex intramolecular hydrogen bonding interactions which influence its mode of action and selective detection. Detailed ...

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

    Science.gov (United States)

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

    2018-03-01

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

  18. 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.

  19. Vibrational tug-of-war: The pKA dependence of the broad vibrational features of strongly hydrogen-bonded carboxylic acids

    Science.gov (United States)

    Van Hoozen, Brian L.; Petersen, Poul B.

    2018-04-01

    of strongly hydrogen-bonded structures depend on the relative pKA and other structural parameters will guide studies of biological structures and analysis of proton transfer studies using photoacids.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2003-08-01

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