C-H...O hydrogen bonding in 4-phenyl-benzaldehyde: a comprehensive crystallographic, spectroscopic and computational study

The crystal structure of 4-phenyl-benzaldehyde reveals the presence of a dimer linked by the C=O and C( 9)-H groups of adjacent molecules. In the liquid phase, the presence of C-(HO)-O-... bonded forms is revealed by both vibrational and NMR spectroscopy. A Delta H value of - 8.2 +/- 0.5 kJ mol(-1) for the dimerisation equilibrium is established from the temperature-dependent intensities of the bands assigned to the carbonyl-stretching modes. The NMR data suggest the preferential engagement of the C(2,6)-H and C(10/12)/C(11)-H groups as hydrogen bond donors, instead of the C(9)-H group. While ab initio calculations for the isolated dimers are unable to corroborate these NMR results, the radial distribution functions obtained from molecular dynamics simulations show a preference for C(2,6)-H and C(10/12)/C(11)-(HO)-O-... contacts relative to the C(9)-(HO)-O-... ones.

Reactions of hydroxyl radicals with trichloroethene and tetrachloroethene in argon matrices at 12 K

Irradiation of argon matrices at 12 K containing hydrogen peroxide and tetrachloroethene using the output from a medium-pressure mercury lamp gives rise to the carbonyl compound trichloroacetyl chloride (CCl3CClO). Similarly trichloroethene gives dichloroacetyl chloride ( CCl2HCClO) - predominantly in the gauche form - under the same conditions. It appears that the reaction is initiated by homolysis of the O-O bond of H2O2 to give OH radicals, one of which adds to the double bond of an alkene molecule. The reaction then proceeds by abstraction of the H atom of the hydroxyl group and Cl-atom migration. This mechanism has been explored by the use of DFT calculations to back up the experimental findings. The mechanism is analogous to that shown by the simple hydrocarbon alkenes.

The adsorbed conformation of globular proteins at the air/water interface

External reflection FTIR spectroscopy and surface pressure measurements were used to compare conformational changes in the adsorbed structures of three globular proteins at the air/water interface. Of the three proteins studied, lysozyme, bovine serum albumin and P-lactoglobulin, lysozyme was unique in its behaviour. Lysozyme adsorption was slow, taking approximately 2.5 h to reach a surface pressure plateau (from a 0.07 mM solution), and led to significant structural change. The FTIR spectra revealed that lysozyme formed a highly networked adsorbed layer of unfolded protein with high antiparallel beta-sheet content and that these changes occurred rapidly (within 10 min). This non-native secondary structure is analogous to that of a 3D heat-set protein gel, suggesting that the adsorbed protein formed a highly networked interfacial layer. Albumin and P-lactoglobulin adsorbed rapidly (reaching a plateau within 10 min) and with little chance to their native secondary structure.

Protein-lipid interactions at the air/water interface

Surface pressure measurements and external reflection FTIR spectroscopy have been used to probe protein-lipid interactions at the air/water interface. Spread monomolecular layers of stearic acid and phosphocholine were prepared and held at different compressed phase states prior to the introduction of protein to the buffered subphase. Contrasting interfacial behaviour of the proteins, albumin and lysozyme, was observed and revealed the role of both electrostatic and hydrophobic interactions in protein adsorption. The rate of adsorption of lysozyme to the air/water interface increased dramatically in the presence of stearic acid, due to strong electrostatic interactions between the negatively charged stearic acid head group and lysozyme, whose net charge at pH 7 is positive. Introduction of albumin to the subphase resulted in solubilisation of the stearic acid via the formation of an albumin-stearic acid complex and subsequent adsorption of albumin. This observation held for both human and bovine serum albumin. Protein adsorption to a PC layer held at low surface pressure revealed adsorption rates similar to adsorption to the bare air/water interface and suggested very little interaction between the protein and the lipid. For PC layers in their compressed phase state some adsorption of protein occurred after long adsorption times. Structural changes of both lysozyme and albumin were observed during adsorption, but these were dramatically reduced in the presence of a lipid layer compared to that of adsorption to the pure air/water interface.

3D surface point and wireframe reconstruction from multiview photographic images

This paper describes a new method for reconstructing 3D surface points and a wireframe on the surface of a freeform object using a small number, e.g. 10, of 2D photographic images. The images are taken at different viewing directions by a perspective camera with full prior knowledge of the camera configurations. The reconstructed surface points are frontier points and the wireframe is a network of contour generators. Both of them are reconstructed by pairing apparent contours in the 2D images. Unlike previous works, we empirically demonstrate that if the viewing directions are uniformly distributed around the object's viewing sphere, then the reconstructed 3D points automatically cluster closely on a highly curved part of the surface and are widely spread on smooth or flat parts. The advantage of this property is that the reconstructed points along a surface or a contour generator are not under-sampled or under-represented because surfaces or contours should be sampled or represented with more densely points where their curvatures are high. The more complex the contour's shape, the greater is the number of points required, but the greater the number of points is automatically generated by the proposed method. Given that the viewing directions are uniformly distributed, the number and distribution of the reconstructed points depend on the shape or the curvature of the surface regardless of the size of the surface or the size of the object. The unique pattern of the reconstructed points and contours may be used in 31) object recognition and measurement without computationally intensive full surface reconstruction. The results are obtained from both computer-generated and real objects. (C) 2007 Elsevier B.V. All rights reserved.

Experimental structure determination of the chemisorbed overlayers of chlorine and iodine on Au{111}

We have performed an experimental structure determination of the ordered p(sqrt[3] x sqrt[3])R30 degrees structures of chlorine and iodine on Au{111} using low-energy electron diffraction (LEED). Despite great similarities in the structure of the underlying substrate, which shows only minor deviations from the bulk positions in both cases, chlorine and iodine are found to adsorb in different adsorption sites, fcc and hcp hollow sites, respectively. The experimental Au-Cl and Au-I bond lengths of 2.56 and 2.84 A are close to the sums of the covalent radii, supporting the view that the bond is essentially covalent in nature; however, they are significantly shorter than predicted theoretically.

On the structure of Langmuir turbulence

The Stokes drift induced by surface waves distorts turbulence in the wind-driven mixed layer of the ocean, leading to the development of streamwise vortices, or Langmuir circulations, on a wide range of scales. We investigate the structure of the resulting Langmuir turbulence, and contrast it with the structure of shear turbulence, using rapid distortion theory (RDT) and kinematic simulation of turbulence. Firstly, these linear models show clearly why elongated streamwise vortices are produced in Langmuir turbulence, when Stokes drift tilts and stretches vertical vorticity into horizontal vorticity, whereas elongated streaky structures in streamwise velocity fluctuations (u) are produced in shear turbulence, because there is a cancellation in the streamwise vorticity equation and instead it is vertical vorticity that is amplified. Secondly, we develop scaling arguments, illustrated by analysing data from LES, that indicate that Langmuir turbulence is generated when the deformation of the turbulence by mean shear is much weaker than the deformation by the Stokes drift. These scalings motivate a quantitative RDT model of Langmuir turbulence that accounts for deformation of turbulence by Stokes drift and blocking by the air–sea interface that is shown to yield profiles of the velocity variances in good agreement with LES. The physical picture that emerges, at least in the LES, is as follows. Early in the life cycle of a Langmuir eddy initial turbulent disturbances of vertical vorticity are amplified algebraically by the Stokes drift into elongated streamwise vortices, the Langmuir eddies. The turbulence is thus in a near two-component state, with suppressed and . Near the surface, over a depth of order the integral length scale of the turbulence, the vertical velocity (w) is brought to zero by blocking of the air–sea interface. Since the turbulence is nearly two-component, this vertical energy is transferred into the spanwise fluctuations, considerably enhancing at the interface. After a time of order half the eddy decorrelation time the nonlinear processes, such as distortion by the strain field of the surrounding eddies, arrest the deformation and the Langmuir eddy decays. Presumably, Langmuir turbulence then consists of a statistically steady state of such Langmuir eddies. The analysis then provides a dynamical connection between the flow structures in LES of Langmuir turbulence and the dominant balance between Stokes production and dissipation in the turbulent kinetic energy budget, found by previous authors.

Charge transfer in Cr adsorption and reaction at the rutile TiO2(110) surface

The rutile TiO2(110) surface has been doped with sub-monolayer metallic Cr, which oxidises and donates charge to specific surface Ti ions. X-Ray and ultra violet photoemission spectroscopy and first principles density functional theory with Hubbard U are used to assign the oxidation states of Cr and surface Ti and we find that Cr2+ forms on bridging oxygen ions and a 5-fold coordinated surface Ti atom is reduced to Ti3+ and the Cr ions readily react with oxygen (to Cr3+), which leads to depletion of surface Ti3+ 3d electrons.

Gas-phase reactions of NO3 and N2O5 with (Z)-hex-4-en-1-ol, (Z)-hex-3-en-1-ol ('leaf alcohol'), (E)-hex-3-en-1-ol, (Z)-hex-2-en-1-ol and (E)-hex-2-en-1-ol

The night-time atmospheric chemistry of the biogenic volatile organic compounds (Z)-hex-4-en-1-ol, (Z)-hex-3-en-1-ol ('leaf alcohol'), (E)-hex-3-en-1-ol, (Z)-hex-2-en-1-ol and (E)-hex-2-en-1-ol, has been studied at room temperature. Rate coefficients for reactions of the nitrate radical (NO3) with these stress-induced plant emissions were measured using the discharge-flow technique. We employed off-axis continuous-wave cavity-enhanced absorption spectroscopy (CEAS) for the detection of NO3, which enabled us to work in excess of the hexenol compounds over NO3. The rate coefficients determined were (2.93 +/- 0.58) x 10(-13) cm(3) molecule(-1) s(-1), (2.67 +/- 0.42) x 10(-13) cm(3) molecule(-1) s(-1), (4.43 +/- 0.91) x 10(-13) cm(3) molecule(-1) s(-1), (1.56 +/- 0.24) x 10(-13) cm(3) molecule(-1) s(-1), and (1.30 +/- 0.24) x 10(-13) cm(3) molecule(-1) s(-1) for (Z)-hex-4-en-1-ol, (Z)-hex-3en-1-ol, (E)-hex-3-en-1-ol, (Z)-hex-2-en-1-ol and (E)-hex-2-en-1-ol. The rate coefficient for the reaction of NO3 with (Z)-hex-3-en-1-ol agrees with the single published determination of the rate coefficient using a relative method. The other rate coefficients have not been measured before and are compared to estimated values. Relative-rate studies were also performed, but required modification of the standard technique because N2O5 (used as the source of NO3) itself reacts with the hexenols. We used varying excesses of NO2 to determine simultaneously rate coefficients for reactions of NO3 and N2O5 with (E)-hex-3-en-1-ol of (5.2 +/- 1.8) x 10(-13) cm(3) molecule(-1) s(-1) and (3.1 +/- 2.3) x 10(-18) cm(3) molecule(-1) s(-1). Our new determinations suggest atmospheric lifetimes with respect to NO3-initiated oxidation of roughly 1-4 h for the hexenols, comparable with lifetimes estimated for the atmospheric degradation by OH and shorter lifetimes than for attack by O-3. Recent measurements of [N2O5] suggest that the gas-phase reactions of N2O5 with unsaturated alcohols will not be of importance under usual atmospheric conditions, but they certainly can be in laboratory systems when determining rate coefficients.

Kinetic studies of reactions of the nitrate radical (NO3) with peroxy radicals (RO2): an indirect source of OH at night?

A discharge-flow system, coupled to cavity-enhanced absorption spectroscopy (CEAS) detection systems for NO3 at lambda = 662 nm and NO2 at lambda = 404 nm, was used to investigate the kinetics of the reactions of NO3 with eight peroxy radicals at P similar to 5 Torr and T similar to 295 K. Values of the rate constants obtained were (k/10(-12) cm(3) molecule(-1) s(-1)): CH3O2 (1.1 +/- 0.5), C2H5O2 (2.3 +/- 0.7), CH2FO2 (1.4 +/- 0.9), CH2ClO2 (3.8(-2.6)(+1.4)), c-C5H9O2 (1.2(-0.5)(+1.1)), c-C6H11O2 (1.9 +/- 0.7), CF3O2 (0.62 +/- 0.17) and CF3CFO2CF3 (0.24 +/- 0.13). We explore possible relationships between k and the orbital energies of the reactants. We also provide a brief discussion of the potential impact of the reactions of NO3 with RO2 on the chemistry of the night-time atmosphere.

Gas-phase rate coefficients for the reactions of nitrate radicals with (Z)-pent-2-ene, (E)-pent-2-ene, (Z)-hex-2-ene, (E)-hex-2-ene, (Z)-hex-3-ene, (E)-hex-3-ene and (E)-3-methylpent-2-ene at room temperature

Rate coefficients for reactions of nitrate radicals (NO3) with (Z)-pent-2-ene, (E)-pent-2-ene, (Z)-hex-2-ene, (E)-hex-2-ene, (Z)-hex-3-ene, (E)-hex-3-ene and (E)-3-methylpent-2-ene were determined to be (6.55 +/- 0.78) x 10(-13) cm(3) molecule(-1) s(-1), (3.78 +/- 0.45) x 10(-13) cm(3) molecule(-1) s(-1), (5.30 +/- 0.73) x 10(-13) cm(3) molecule(-1) s(-1), (3.83 +/- 0.47) x 10(-13) cm(3) molecule(-1) s(-1), (4.37 +/- 0.49) x 10(-13) cm(3) molecule(-1) s(-1), (3.61 +/- 0.40) x 10(-13) cm(3) molecule(-1) s(-1) and (8.9 +/- 1.5) x 10(-12) cm(3) molecule(-1) s(-1), respectively. We performed kinetic experiments at room temperature and atmospheric pressure using a relative-rate technique with GC-FID analysis. The experimental results demonstrate a surprisingly large cis-trans (Z-E) effect, particularly in the case of the pent-2-enes, where the ratio of rate coefficients is ca. 1.7. Rate coefficients are discussed in terms of electronic and steric influences, and our results give some insight into the effects of chain length and position of the double bond on the reaction of NO3 with unsaturated hydrocarbons. Atmospheric lifetimes were calculated with respect to important oxidants in the troposphere for the alkenes studied, and NO3-initiated oxidation is found to be the dominant degradation route for (Z)-pent-2-ene, (Z)-hex-3-ene and (E)-3-methylpent-2-ene.

The climatology of the middle atmosphere in a vertically extended version of the Met Office's climate model. Part I: mean state

The climatology of a stratosphere-resolving version of the Met Office’s climate model is studied and validated against ECMWF reanalysis data. Ensemble integrations are carried out at two different horizontal resolutions. Along with a realistic climatology and annual cycle in zonal mean zonal wind and temperature, several physical effects are noted in the model. The time of final warming of the winter polar vortex is found to descend monotonically in the Southern Hemisphere, as would be expected for purely radiative forcing. In the Northern Hemisphere, however, the time of final warming is driven largely by dynamical effects in the lower stratosphere and radiative effects in the upper stratosphere, leading to the earliest transition to westward winds being seen in the midstratosphere. A realistic annual cycle in stratospheric water vapor concentrations—the tropical “tape recorder”—is captured. Tropical variability in the zonal mean zonal wind is found to be in better agreement with the reanalysis for the model run at higher horizontal resolution because the simulated quasi-biennial oscillation has a more realistic amplitude. Unexpectedly, variability in the extratropics becomes less realistic under increased resolution because of reduced resolved wave drag and increased orographic gravity wave drag. Overall, the differences in climatology between the simulations at high and moderate horizontal resolution are found to be small.

Palladium-coated nickel nanoclusters: new Hiyama cross-coupling catalysts

The advantages of bimetallic nanoparticles as C - C coupling catalysts are discussed, and a simple, bottom- up synthesis method of core - shell Ni - Pd clusters is presented. This method combines electrochemical and 'wet chemical' techniques, and enables the preparation of highly monodispersed structured bimetallic nanoclusters. The double- anode electrochemical cell is described in detail. The core - shell Ni - Pd clusters were then applied as catalysts in the Hiyama cross- coupling reaction between phenyltrimethoxysilane and various haloaryls. Good product yields were obtained with a variety of iodo- and bromoaryls. We found that, for a fixed amount of Pd atoms, the core - shell clusters outperform both the monometallic Pd clusters and the alloy bimetallic Ni - Pd ones. THF is an excellent solvent for this process, with less than 2% homocoupling by-product. The roles of the stabiliser and the solvent are discussed.

Time-resolved gas-phase kinetic study of the germylene addition reaction, GeH2 + C2D2

Time-resolved studies of germylene, GeH2, generated by laser. ash photolysis of 3,4-dimethyl-1-germacyclopent-3-ene, have been carried out to obtain rate coefficients for its bimolecular reaction with C2D2. The reaction was studied in the gas phase, mainly at a total pressure of 1.3 kPa (in SF6 bath gas) at five temperatures in the range 298-558 K. Pressure variation measurements over the range 0.13-13 kPa ( SF6) at 298, 397 and 558 K revealed a small pressure dependence but only at 558 K. After correction for this, the second-order rate coefficients gave the Arrhenius equation: log(k(infinity)/cm(3) molecule(-1) s(-1)) = (-10.96 +/- 0.05) + ( 6.16 +/- 0.37 kJ mol(-1))/RT ln 10 Comparison with the reaction of GeH2 + C2H2 (studied earlier) showed a similar behaviour with almost identical rate coefficients. The lack of a significant isotope effect is consistent with a rate-determining addition process and is explained by irreversible decomposition of the reaction intermediate to give Ge(P-3) + C2H4. This result contrasts with that for GeH2 + C2H4/C2D4 and those for the analogous silylene reactions. The underlying reasons for this are discussed.