Orientation Of Hydrogen Bonds Research Articles

Viscosity of Water under Electric Field: Anisotropy Induced by Redistribution of Hydrogen Bonds.

The viscosity of water under an external electric field of 0.00-0.90 V/nm was studied using both molecular dynamics simulations and atomistic modeling accounting for intermolecular potentials. For all temperatures investigated, the water viscosity becomes anisotropic under an electric field: the viscosity component parallel to the field increases monotonically with the field strength, E, while the viscosity perpendicular to the field first decreases and then increases with E. This anisotropy is believed to be mainly caused by the redistribution of hydrogen bonds under the electric field. The preferred orientation of hydrogen bonds along the field direction leads to an increase of the energy barrier of a water molecule to its neighboring site, and hence increases the viscosity in that direction. However, the probability of hydrogen bonds perpendicular to the electric field decreases with E, together with the increase of the average number of hydrogen bonds per molecule, causing the perpendicular component of water viscosity to first decrease and then increase with the electric field.

High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction

The matrix 2 (M2) protein from influenza A virus is a proton channel that uses His37 as a selectivity filter. Here we report high-resolution (1.10 Å) cryogenic crystallographic structures of the transmembrane domain of M2 at low and high pH. These structures reveal that waters within the pore form hydrogen-bonded networks or "water wires" spanning 17 Å from the channel entrance to His37. Pore-lining carbonyl groups are well situated to stabilize hydronium via second-shell interactions involving bridging water molecules. In addition, room temperature crystallographic structures indicate that water becomes increasingly fluid with increasing temperature and decreasing pH, despite the higher electrostatic field. Complementary molecular dynamics simulations reveal a collective switch of hydrogen bond orientations that can contribute to the directionality of proton flux as His37 is dynamically protonated and deprotonated in the conduction cycle.

Hydrogen bond network in the hydration layer of the water confined in nanotubes increasing the dielectric constant parallel along the nanotube axis.

The water confined in nanotubes has been extensively studied, because of the potential usages in drug delivery and desalination. The radial distribution of the dielectric constant parallel along the nanotube axis was obtained by molecular dynamics simulations in a carbon nanotube and a nanotube with a very small van der Waals potential. The confined water was divided into two parts, the middle part water and the hydration water. In both cases, the hydrogen bond orientation of the middle water is isotropic, while the hydrogen bonds in hydration layers are apt to parallel along the nanotube axis. Therefore, the hydration water has higher dipole correlations increasing the dielectric constant along the nanotube axis.

Electric control of magnetism in a multiferroic metal–organic framework

AbstractElectric control of magnetism is demonstrated in a multiferroic metal–organic framework with a perovskite structure. A moderate electric field of a few kV/cm applied during the cooling process is able to cause a large (more than 50%) change of the magnetization at low temperature. This significant magnetoelectric effect is ascribed to the electric field manipulation of orientation of hydrogen bonds that modify the superexchange interaction between metal ions.magnified imageElectric‐field cooling causes a large change in the magnetization of a multiferroic MOF.(© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Anisotropic Dielectric Relaxation of the Water Confined in Nanotubes for Terahertz Spectroscopy Studied by Molecular Dynamics Simulations

The dynamics and structure of the hydrogen-bond network in confined water are of importance in understanding biological and chemical processes. Recently, terahertz (THz) time domain spectroscopy was widely applied for studying the kinetics of molecules and the hydrogen-bond network in water. However, the characteristics of the THz spectroscopy varying with respect to the confinement and the mechanism underlying the variation are still unclear. Here, on the basis of molecular dynamics simulations, the relationship between the anisotropic dielectric relaxation and the structure of the water confined in a carbon nanotube (CNT) was investigated. The results show that there are two preferred hydrogen-bond orientations of the confined water in the nanotube: (1) parallel to the CNT axis and (2) perpendicular to the CNT axis, which are clearly different. Moreover, the response of the orientations to the increment of the CNT diameters is opposite, leading to the opposite variations of the dielectric relaxation times along the two directions. The anisotropy in the relaxation time can be presented by the anisotropic dielectric permittivity which is able to be observed through THz spectroscopy. The anormal behaviors above are attributed to the special structure of the water close to the nanotube wall due to the confinement and hydrophobicity of CNT. These studies contribute an important step in understanding the THz experiments of water in nanoscales, and designing a chamber for specific chemical and biological reactions by controlling the diameters and materials of the nanotube.

Molecular Recognition in Different Environments: β-Cyclodextrin Dimer Formation in Organic Solvents

Electrostatic and van der Waals interactions as well as entropy contribute to the energetics governing macromolecular complexation in biomolecules. Hydrogen bonds play a particularly important role in such interactions. Here we use molecular dynamics (MD) simulations to investigate the hydrogen bond (HB) orientations of free beta-cyclodextrin (β-CD) and head-to-head dimerization of β-CD monomers with and without guest molecules in different environments, namely, in 10 different solvents covering a wide range of polarity. Potentials of mean force for the dimer dissociation are derived from umbrella sampling simulations, allowing determination of the binding affinity between monomers. The HB orientations are in good agreement with available experimental data in water and dimethyl sulfoxide, yielding confidence in the force field used. HB exchanges at the secondary rim of β-CD are observed with a fast rate in water and with a low rate or even no exchange in other solvents. Orientational preferences of interglucopyranose HBs and their effects on the β-CD structure in these solvents are discussed in detail. Polar solvents with stronger HB accepting abilities can interrupt intermolecular HBs more easily, resulting in a less stable dimer. Guest molecules included in the channel-type cavity strengthen the binding affinity between two monomers to some extent, particularly in polar solvents. Formation of the head-to-head dimer is therefore solvent-dependent and guest-modulated. There is only limited correlation between the dimer binding energies and solvent properties like the dielectric constant. This implies that implicit solvent models will not be capable of predicting important properties like binding energy for other solvents than water without a complete reparameterization. This work provides a deeper comprehension on the properties of β-CD, and implications for the application of cyclodextrins in aqueous and nonaqueous media are discussed.

Structure, energetics and vibrational spectra of protonated chlortetracycline in the gas phase: An experimental and computational investigation

Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy has been used to generate gas phase vibrational spectra for six protonated tetracycline derivatives: chlortetracycline, meclocycline, minocycline, doxycycline, tetracycline, and metacycline. The IRMPD spectrum for protonated chlortetracycline is compared here to theoretical gas phase vibrational spectra obtained from geometry optimization and frequency electronic structure calculations using the B3LYP hybrid density functional method with the 6-311+G(d,p) basis set. The most energetically favorable protonation sites, tautomer structures, and hydrogen bond orientations were determined. Protonation at the dimethyl amine functional group and an extensive hydrogen bonding network lead to the most energetically favourable structures. Calculated spectra directly resembled the IRMPD spectrum, supporting the conclusion that the probable gas phase structure of protonated chlortetracycline has been determined.

Crystallographic Characterization of 12-Helical Secondary Structure in β-Peptides Containing Side Chain Groups

Helices are the most extensively studied secondary structures formed by β-peptide foldamers. Among the five known β-peptide helices, the 12-helix is particularly interesting because the internal hydrogen bond orientation and macrodipole are analogous to those of α-peptide helices (α-helix and 3(10)-helix). The β-peptide 12-helix is defined by i, i+3 C═O···H-N backbone hydrogen bonds and promoted by β-residues with a five-membered ring constraint. The 12-helical scaffold has been used to generate β-peptides with specific biological functions, for which diverse side chains must be properly placed along the backbone and, upon folding, properly arranged in space. Only two crystal structures of 12-helical β-peptides have previously been reported, both for homooligomers of trans-2-aminocyclopentanecarboxylic acid (ACPC). Here we report five additional crystal structures of 12-helical β-peptides, all containing residues that bear side chains. Four of the crystallized β-peptides include trans-4,4-dimethyl-2-aminocyclopentanecarboxylic acid (dm-ACPC) residues, and the fifth contains a β(3)-hPhe residue. These five β-peptides adopt fully folded 12-helical conformations in the solid state. The new crystal structures, along with previously reported data, allow a detailed characterization of the 12-helical conformation; average backbone torsion angles of β-residues and helical parameters are derived. These structural parameters are found to be similar to those for i, i+3 C═O···H-N hydrogen-bonded helices formed by other peptide backbones generated from α- and/or β-amino acids. The similarity between the conformational behavior of dm-ACPC and ACPC is consistent with previous NMR-based conclusions that 4,4-disubstituted ACPC derivatives are compatible with 12-helical folding. In addition, our data show how a β(3)-residue is accommodated in the 12-helix, thus enhancing understanding of the diverse conformational behavior of this flexible class of β-amino acids.

Water transportation across narrow channel of nanometer dimension

Since the discovery of the carbon nanotube and aquaporin, the study of the transportation of water across nanochannels has become one of the hot subjects. When the radius of a nanochannel is only about one nanometer or a little larger, water confined in those nanoscale channels usually exhibits dynamics different from those in bulk system, such as the wet–dry transition due to the confinement, concerted hydrogen-bond orientations and flipping, concerted motion of water molecules, and strong interactions with external charges. Those dynamics correlate with the unique behavior of the water transportation across the channels, such as the extra-high permeability, excellent on–off gating behavior with response to the external mechanical and electrical signals and noises, enhancement by structure outside the channel, directional transportation driven by charges close to a channel or electric field. In this article, we review some of the recent progress on the study of the water molecules inside those narrow nanochannels.

Synthesis, structure and spectroelectrochemical property of (2,2′-bipyridine)–metal (M = Pt, Pd) dichloride with 4,4′-bis(fluorous-ponytail) on bipyridine

The 4,4′-bis(R fCH 2OCH 2)-2,2′-bpy ligands [R f = n-C 3F 7 ( 1a), HCF 2(CF 2) 3 ( 1b)] were prepared and then treated with [MCl 2(CH 3CN) 2] (M = Pt or Pd) to result in the corresponding metal complexes, [MCl 2(4,4′-bis(R fCH 2OCH 2)-2,2′-bpy)] (M = Pt 2a–b; Pd 3a–b). Both ligands and metal complexes were fully characterized by multi-nuclei NMR ( 1H, 19F and 13C), FTIR, and mass (GC/MS or HR-FAB) methods. The X-ray structures of 2a–b and 3a–b were studied. With terminal CF 3, the structures of 2a and 3a exhibit disordered polyfluorinated regions in solid state. With terminal HCF 2, the structures of 2b and 3b show a π–π stacking of the bpy planes, five-membered C–H···O hydrogen bond and an unusual intramolecular blue-shifting C–H···F–C hydrogen bond system, whereas without terminal HCF 2, the structures of 2a and 3a show the similar π–π stacking, five-membered C–H···O hydrogen bond and typical orientation of polyfluorinated ponytails, but not the C–H···F–C hydrogen bond system. The CV and UV/Vis studies were also carried out.

Orientation of hydrogen bond in H-complexes of sulfones and sulfonamides

According to the data of quantum chemical calculations using the DFT method (B3LYP/6-311G*), dimethylsulfone (I), N,N-dimethylmethanesulfonamide (II) and N,N-dimethyltrifluoromethanesulfonamide (III) form with methanol and phenol H-complexes of two types: (1) having nonlinear structure and (2) bidentate complexes with participation of both oxygen atom lone pairs in the formation of the H-bond. The angle determining the directionality of the hydrogen bond with respect to the axis of the nearest lone electron pair of the SO2 group oxygen atom in the conformational isomers of these complexes falls within the range 3°–100°. Variation of the calculated values of Δν(OH) in the H-complexes is parallel to that observed in their IR spectra and reflects the decrease of basicity of the sulfonyl group in the order I > II > III.

Thermally Responsive Fluid Behaviors in Hydrophobic Nanopores

A fundamental understanding of the thermal effects on nanofluid behaviors is critical for developing and designing innovative thermally responsive nanodevices. Using molecular dynamics (MD) simulation and experiment, we investigate the temperature-dependent intrusion/adsorption of water molecules into hydrophobic nanopores (carbon nanotubes and nanoporous carbon) and the underlying mechanisms. The critical infiltration pressure is reduced for elevated temperature or increased pore size. The variation of wettability is related to the thermally responsive fluid characteristics, such as the surface tension and contact angle, which arise from the variations of multiple atomic variables including the confined water density, hydrogen bond, and dipole orientation. With thermal perturbation, most of these physical quantities are found to be more significantly influenced in the confined nanoenvironment than in the bulk. By utilizing the prominent thermal effect at the nanoscale, the feasibility and prospective efficiency of employing nanofluidics for energy storage, actuation, and thermal monitoring are discussed.

Anion Receptors with 2-Imidazolidone Molecular Scaffold

Manyanions have diverse geometries that require shape-selectiverecognition. Therefore, many researchers have used hydro-gen bonds as a recognition element as they are directional.The correct orientation of hydrogen bonds can differentiatebetween anionic guests with different geometries.In nature, the hydrogen bonds are most often utilized toachieve anion binding by proteins.

Theoretical Investigation of the Hydrogen Abstraction Reaction of the OH Radical with CH2FCH2F (HFC-152): A Dual-Level Direct Dynamics Study

The hydrogen abstraction reaction of the OH radical with CH(2)FCH(2)F (HFC-152) is studied theoretically over the 150-3000 K temperature range. In this study, the two most recently developed hybrid density functional theories, namely, BB1K and MPWB1K, are applied, and their efficiency in reaction dynamics calculation is discussed. The BB1K/6-31+G(d,p) method gives the best result for the potential energy surface (PES) calculations, including barrier heights, reaction path information (the first and second derivatives of PES), geometry of transition state structures, and even weak hydrogen bond orientations. The rate constants were obtained by the dual-level direct dynamics with the interpolated single-point energy method (VTST-ISPE) using the BB1K/MG3S//BB1K/6-31+G(d,p) quantum model. The canonical variational transition state theory (CVT) with the small-curvature tunneling correction methods are used to calculate the rate constants in comparison to the experimental data. The total rate constant and its temperature dependency in the form of a fitted three-parameter Arrhenius expression is k(T) = 5.4 x 10(-13)(T/298)3.13 exp{-322/T} cm3 molecule(-1) s(-1). A significant variational effect, which is not common generally for hydrogen-transfer reactions, is reported and analyzed.

Structural studies of methyl brevifolincarboxylate in solid state by means of NMR spectroscopy and DFT calculations

Methyl brevifolincarboxylate isolated from the herb of Potentilla argentea L. (Rosaceae) is a representative of the naturally occurring polyphenols. The compound is of pharmaceutical interest mainly because of its antiviral and antioxidant properties. 13C NMR spectra were recorded for solution and solid phase. 13C CPMAS spectra were assigned by comparison with solution data, dipolar dephasing and short contact time experiments. The correctness of assignments was verified by GIAO DFT calculations of shielding constants. The differences between the solution and solid state chemical shift values were explained in terms of orientation of OH groups and intramolecular hydrogen bonds. The splitting of the C1 O resonance shows that there exists a polymorphism in the solid phase, which might be due to the formation of intramolecular hydrogen bond involving carbonyl or methoxy oxygen (i.e. C10 OH⋯O C or C10 OH⋯OCH 3).

Fluorescent Anion Receptor with Two Methylene Bridged Bis‐imidazolium Ring on Anthracene.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Fluorescent Anion Receptor with Two Methylene Bridged Bis-imidazolium Ring on Anthracene

Artificial receptors for selective anion recognition is an area of intensive investigation as anions play a fundamental role in a wide range of chemical and biological process. Receptors based on guest anion induced changes of color or fluorescence seems to be attractive due to their high sensitivity and low detection limit. In many cases, hydrogen bonds are utilized as anion recognition element as host-guest complementarity could be achieved from the directionality of hydrogen bonds. The orientation of hydrogen bonds can differentiate anionic guests with different geometries. While most of hydrogen bond anion receptors utilize N-H---X− or O-H---X− hydrogen bonds, 1,3-disubstituted imidazolium groups are recently introduced as new anion binding hydrogen bond moiety by forming (C-H)--X hydrogen bonds between C(2)-H in imidazolium rings and the guest anion. Depending on the spatial arrangement of 1,3-disubstituted imidazolium groups, halide, dihydrogen phosphate, dicarboxylate, sulfate selective receptors have been reported. To extend the scope of imidazolium anion receptor, we have designed and synthesized the receptor 1, bearing two methylene bridged bis-imidazolium ring on 1,8-positions of anthracene. For the synthesis of anthracene receptor 1, methylene bridged bis-imidazole 2 was synthesized in 64% yield from the reaction of imidazole and bromochloromethane. Then the bis-imidazole 2 was reacted with 0.3 equivalents of ethyl bromide to give imidazolium ion 3 in 37% yield. This intermediate was refluxed in acetonitrile for 4 hours with 1,8-bis(bromomethyl)anthracene. Anion exchange with ammonium hexafluorophosphate gave receptor 1 bearing two methylene bridged bis-imidazolium ring on 1,8-positions of anthracene (Scheme 1). All compounds were characterized by H NMR, C NMR and high resolution mass spectrum. The complexation abilitiy of receptor 1 to the halides was measured by standard H NMR titration experiments in 10% DMSO-d6 in CD3CN using a constant host concentration(4 mM) and increasing concentrations of anions (1-10 equivalents). The chemical shift data were analyzed by EQNMR. The addition of tetrabutylammonium halide salts to the solution of 1 in 10% DMSO-d6 in CD3CN resulted in downfield shifts in two C(2) proton peaks of imidazolium ring. In case of iodide ion, two C(2) protons originally resonating at δ = 9.10 and 9.05 were shifted to δ = 9.50 and 9.47 upon the addition of 5 equivalents of iodide ion, which indicates that all C(2) protons are involved in binding events. Assuming 1 : 1 binding stoichiometry, the association constant calculated from the chemical shift change of C(2)H of imidazolium ring was 103 ± 11. The anthracene receptor 1 displayed strong fluorescence emission in 10% DMSO in acetonitrile solution as shown in Figure 1. The excitation and emission wavelength were 365 nm and 413 nm respectively. The associations between the anthracene receptor 1 and spherically shaped halides were investigated by fluorescence titration. The fluorescence change of the receptor 1 was monitored in 10% DMSO in acetonitrile. The intensity of emission spectrum from 10 μM solution of the anthracene receptor 1 decreased as the concentration of tetrabutylammonium halides salts was increased, which indicates the association between the receptor 1 and halides. The stoichiometry between host and guest was determined by fluorescence Job plot, which

Simulation of the Effect of Reorientation of Hydrogen Bonds in Proteins on Long-Range Electron Transfer

We present Monte Carlo simulations illustrating the influence of reorientation of hydrogen bonds in proteins on long-range interprotein electron transfer. The lattice protein model employed mimics the electron donor (or acceptor) interacting with an antiparallel β sheet. In addition, we take into account harmonic vibrations of the medium and also the dependence of the coupling matrix element on orientation of hydrogen bonds near the donor and/or acceptor. The results obtained show that the interaction between the tunneling electron and amino-acid residues, which are responsible for the formation of hydrogen bonds, may result in broadening the parabolic dependence of the electron-transfer rate constant on the reaction exothermicity and also in deviations from this dependence especially in the cases when the β sheet is linked with the electron donor.

Structure-configurational entropy and its effect on the thermodynamic stability of uranyl phases: With special application for geological disposal of nuclear waste

Spent UO 2 fuel will rapidly be altered to U 6+ phases in nuclear waste repositories. Because most uranyl phases are based on sheet or chain structures and usually contain several molecular water groups, site-mixing, vacancies, as well as disorder in the orientation of hydrogen bonds may occur. A systematic survey of the published crystallographic data for uranates, uranyl oxide hydrates, phosphates, silicates, carbonates, and sulfates demonstrates that site-mixing apparently occurs in the structures of at least 31 uranyl phases. Calculations of the ideal site-mixing entropy indicate that the residual contribution that arises from substitution and vacancies to the third-law entropies of some uranyl phases is large. A brief examination of the crystal chemistry of water molecules in uranyl phases suggests that considerable residual entropy may be caused by the disorder of hydrogen bonds associated with interstitial H 2 O groups. In the geochemical environment that expected to occur in the near-field of nuclear waste repositories, the existence of structure-configurational entropy may reduce the uranium concentration of several log units in solutions equilibrated with some uranyl phases. Therefore, compositional analysis and structural determinations must be made on the samples used in calorimetric measurements, and the calorimetric data must be combined with solubility data to evaluate the thermodynamic stability of the interested phases.

Structure of high-density amorphous ice under pressure.

We report in situ neutron diffraction studies of high-density amorphous ice (HDA) at 100 K at pressures up to 2.2 GPa. We find that the compression is achieved by a strong contraction ( approximately 20%) of the second neighbor coordination shell, so that at 2.2 GPa it closely approaches the first coordination shell, which itself remains intact in both structure and size. The hydrogen bond orientations suggest an absence of hydrogen bonding between first and second shells and that HDA has increasingly interpenetrating hydrogen bond networks under pressure.