Adsorption of organic molecules at the TiO2(110) surface: the effect of van der Waals interactions

Understanding the interaction of organic molecules with TiO2 surfaces is important for a wide range of technological applications. While density functional theory (DFT) calculations can provide valuable insight about these interactions, traditional DFT approaches with local exchange-correlation functionals suffer from a poor description of non-bonding van der Waals (vdW) interactions. We examine here the contribution of vdW forces to the interaction of small organic molecules (methane, methanol, formic acid and glycine) with the TiO2 (110) surface, based on DFT calculations with the optB88-vdW functional. The adsorption geometries and energies at different configurations were also obtained in the standard generalized gradient approximation (GGA-PBE) for comparison. We find that the optB88-vdW consistently gives shorter surface adsorbate-to-surface distances and slightly stronger interactions than PBE for the weak (physisorbed) modes of adsorption. In the case of strongly adsorbed (chemisorbed) molecules both functionals give similar results for the adsorption geometries, and also similar values of the relative energies between different chemisorption modes for each molecule. In particular both functionals predict that dissociative adsorption is more favourable than molecular adsorption for methanol, formic acid and glycine, in general agreement with experiment. The dissociation energies obtained from both functionals are also very similar, indicating that vdW interactions do not affect the thermodynamics of surface deprotonation. However, the optB88-vdW always predicts stronger adsorption than PBE. The comparison of the methanol adsorption energies with values obtained from a Redhead analysis of temperature programmed desorption data suggests that optB88-vdW significantly overestimates the adsorption strength, although we warn about the uncertainties involved in such comparisons.

Emulation of chiral hydrogenation catalysts by adsorbtion of small molecules onto Ni surfaces

Adsorption of small molecules on the Ni{111} and NiO{111} surfaces is investigated under UHV and elevated pressures (~10-1 mbar) of hydrogen and water. The molecules considered are chosen for their relevance to understanding the mechanism of enantioselective hydrogenation on Raney Nickel modified by chiral molecules. Adsorption of water onto, and its subsequent reaction with, oxygen-covered Ni{111} is dependent on the initial atomic oxygen coverage. An OH species (O1s binding energy 531.5eV), oriented perpendicular to the surface, forms at atomic oxygen coverages <0.25ML. The reaction does not consume all the adsorbed oxygen for coverages ≥0.12ML. The p(2×2) atomic oxygen uperstructure is unreactive, while an OH species is formed on the p(√3×√3) superstructure at binding energy 530.9eV. L-alanine is adsorbed on Ni{111} as a model chiral modifier molecule. At low coverages, alanine forms a presumed tridentate alaninate species for coverages ≥0.11ML at 250K. A minority, bidentate zwitterionic species forms at coverages >0.11ML, but was not observed at 300K. Saturation occurs at 0.25ML. At high alanine coverages (≥0.19ML) and H2 pressure (≥1×10-2 mbar), the tridentate L-alaninate converts to bidentate zwitterionic L-alanine at 300K. Thermal evolution of L-alanine on Ni{111} under varying hydrogen pressures is examined. Adsorption of L-alanine onto hydroxylated NiO{111} at 300K in UHV, mimicking a catalyst surface under aqueous conditions, yields the tridentate alaninate which is immune to the effects of elevated hydrogen pressure. Exposing the L-alanine/Ni{111} adsorption system to water (≤10-1 mbar) oxidises the surface and recreates the L-alanine/hydroxylated NiO{111} system. Pyruvic acid on Ni{111} is examined as a model for hydrogenation substrate adsorption. Behaviour is coverage dependent and several conformations are possible at low coverages (≤0.1ML). Annealing at coverages <0.2ML causes a condensation reaction, releasing water onto the surface. High coverages do not condense and a saturation coverage of ~0.35ML is found.

Layer-by-layer electrostatic entrapment of protein molecules on superparamagnetic nanoparticle: new strategy to enhance adsorption capacity and maintain biological activity

There is a recent interest to use inorganic-based magnetic nanoparticles as a vehicle to carry biomolecules for various biophysical applications, but direct attachment of the molecules is known to alter their conformation leading to attenuation in activity. In addition, surface immobilization has been limited to monolayer coverage. It is shown that alternate depositions of negatively charged protein molecules, typically bovine serum albumin (BSA) with a positively charged aminocarbohydrate template such as glycol chitosan (GC) on magnetic iron oxide nanoparticle surface as a colloid, are carried out under pH 7.4. Circular dichroism (CD) clearly reveals that the secondary structure of the entrapped BSA sequential depositions in this manner remains totally unaltered which is in sharp contrast to previous attempts. Probing the binding properties of the entrapped BSA using small molecules (Site I and Site II drug compounds) confirms for the first time the full retention of its biological activity as compared with native BSA, which also implies the ready accessibility of the entrapped protein molecules through the porous overlayers. This work clearly suggests a new method to immobilize and store protein molecules beyond monolayer adsorption on a magnetic nanoparticle surface without much structural alteration. This may find applications in magnetic recoverable enzymes or protein delivery.

Normal coordinates for the planar vibrations of benzene

Force constants and normal coordinates have been recalculated for all of the in-plane vibrations of benzene, making use of the recently observed data on one of the Coriolis constants in the E2g species from the work of Callomon et al. The extent to which the force field is uniquely determined by the data is reviewed for each symmetry species in turn, and the results of a force constant refinement calculation are reported in which a modified valency force field was used based on the hybrid orbital model. The results show considerable differences from Whiffen's normal coordinates for benzene, but somewhat smaller differences from Scherer's recent calculations.

Sequence-selective assembly of tweezer-molecules on linear templates enables frameshift-reading of sequence information

Monomer-sequence information in synthetic copolyimides can be recognised by tweezer-type molecules binding to adjacent triplet-sequences on the polymer chains. In the present paper different tweezer-molecules are found to have different sequence-selectivities, as demonstrated in solution by 1H NMR spectroscopy and in the solid state by single crystal X-ray analyses of tweezer-complexes with linear and macrocyclic oligo-imides. This work provides clear-cut confirmation of polyimide chain-folding and adjacent-tweezer-binding. It also reveals a new and entirely unexpected mechanism for sequence-recognition which, by analogy with a related process in biomolecular information processing, may be termed "frameshift-reading". The ability of one particular tweezer-molecule to detect, with exceptionally high sensitivity, long-range sequence-information in chain-folding aromatic copolyimides, is readily explained by this novel process.

Formation of a one-dimensional helical alignment of water molecules within a water-mediated supramolecular helix using molecular self-assembly of a water-soluble short pseudopeptide

The reported pseudopeptide 1 adopts a double turn molecular conformation consisting of an intramolecular 9-membered turn together with a water-mediated 11-atom turn and this pseudopeptide 1 self-assembles to form a water-mediated supramolecular helical structure with internal water molecules, which are aligned in a ID helical array. (c) 2006 Elsevier Ltd. All rights reserved.

Intercalation of diiodine molecules in cis-Ru(bpy)(2)Cl-2

Reaction of diiodine with cis-Ru(bpy)(2)Cl-2 in methanol at room temperature yields a thermally stable intercalate cis-Ru(bpy)(2)Cl-2 center dot 1.7I(2) (1) which has been characterised by X-ray crystallography. Iodine is leeched from 1 as it reacts with acetone at room temperature. (C) 2005 Elsevier B.V. All rights reserved.

Selective catalytic oxidation of alkylaromatic molecules by nanosize water droplets containing Co2+ species in supercritical carbon dioxide fluid

Stabilized nano-sized water droplet carrying water-soluble Co2+ species is employed as a new catalyst system for the oxidation of the alkyl aromatics in the presence of a fluorinated surfactant. This stable system contains no labile C-H structure and can facilitate excellent mixing of catalytic Co(II)/NaBr species, hydrocarbon substrates and oxygen in supercritical carbon dioxide fluid, which is demonstrated to be an excellent alternative solvent system to acetic acid or nitric acid for air oxidation of a number of alkyl aromatic hydrocarbons using Co(II) species at mild conditions. As a result, potential advantages of this 'greener' catalytic method including safer operation, easier separation and purification, higher catalytic activity with selectivity and without using corrosive or oxidation unstable solvent are therefore envisaged.

Structure of adsorbed organometallic rhodium: model single atom catalysts

We have determined the structure of a complex rhodium carbonyl chloride [Rh(CO)(2)Cl] molecule adsorbed on the TiO2 (110) surface by the normal incidence x-ray standing wave technique. The data show that the technique is applicable to reducible oxide systems and that the dominant adsorbed species is undissociated with Rh binding atop bridging oxygen and to the Cl found close to the fivefold coordinated Ti ions in the surface. A minority geminal dicarboryl species, where Rh-Cl bond scission has occurred, is found bridging the bridging oxygen ions forming a high-symmetry site.

The effect of dopant molecules on the molecular order of electrically-conducting films of polypyrrole

X-ray scattering curves have been measured for a range of electrochemically-prepared conducting polypyrrole films employing a variety of counterions in aqueous solutions. Films containing counterions based on aromatic rings exhibit an anisotropic molecular organization. The degree of anisotropy is enhanced through the use of highly planar counterions. The electrical conductivity of such films is also improved if the charge/volume ratio of the counterion is maintained at a high level. Polypyrrole films prepared using ‘spherically’ shaped counterions such as SO42− do not display such anisotropic molecular organizations, and exhibit lower electrical conductivities. The competing structural roles of the counterions within these molecular composites are discussed.

Elucidating the structure of chiral molecules by using amplified vibrational circular dichroism: from theory to experimental realization

Recent experimental observations of enhanced vibrational circular dichroism (VCD) in molecular systems with low-lying electronically excited states suggest interesting new applications of VCD spectroscopy. The theory describing VCD enhancement through vibronic coupling schemes was derived by Nafie in 1983, but only recently experimental evidence of VCD amplification has demonstrated the extent to which this effect can be exploited as a structure elucidation tool to probe local structure. In this Concept paper, we give an overview of the physics behind vibrational circular dichroism, in particular the equations governing the VCD amplification effect, and review the latest experimental developments with a prospective view on the application of amplified VCD to locally probe biomolecular structure.

The calculation of force constants and normal coordinates IV: XH4 and XH3 molecules

Normal coordinate calculations of XH4 and XH3 molecules are reviewed and discussed. It is shown that for most of these molecules the true values of the force constants in the most General Harmonic Force Field can be uniquely determined only by making use of vibration-rotation interaction constants. It is emphasized that without these extra data the GFF is not determined. The results are compared with various model force fields for these molecules.

Rotational spectra induced by vibrations

Mizushima and Venkateswarlu showed in 1953 that certain molecules have the property that excited vibrational states may possess rotational spectra even when the rotational spectrum of the ground vibrational state is forbidden by symmetry. We call such a spectrum a vibrationally induced rotational spectrum, and have made a systematic examination of the point groups which permit such behaviour. We also give formulae for the approximate line frequencies and intensities in these spectra, and discuss some of the problems involved in observing them. The spectra can only arise from degenerate vibrational states, and are of three possible types: i) symmetric top perpendicular spectra, shown by molecules belonging to the point groups Dnh, Dn and Cnh, where n is odd; (ii) symmetric top parallel spectra, shown by molecules belonging to Dnd and S2n, where n is even; and (iii) spherical top spectra, shown by molecules belonging to T or Td. Excited vibrational states of polar molecules of point groups Cnv or Cn, where n is odd, may also possess vibrationally induced perpendicular components of type (i), in addition to their ordinary parallel spectra. In addition to the above limitations on the point groups there are, in general, limitations on the symmetry species of the degenerate vibrational states.

Sonogashira coupling on an extended gold surface in vacuo: reaction of phenylacetylene with iodobenzene on Au(111)

Temperature-programmed reaction measurements supported by scanning tunneling microscopy have shown that phenylacetylene and iodobenzene react on smooth Au(111) under vacuum conditions to yield biphenyl and diphenyldiacetylene, the result of homocoupling of the reactant molecules. They also produce diphenylacetylene, the result of Sonogashira cross-coupling, prototypical of a class of reactions that are of paramount importance in synthetic organic chemistry and whose mechanism remains controversial. Roughened Au(111) is completely inert toward all three reactions, indicating that the availability of crystallographically well-defined adsorption sites is crucially important. High-resolution X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy show that the reactants are initially present as intact, essentially flat-lying molecules and that the temperature threshold for Sonogashira coupling coincides with that for C−I bond scission in the iodobenzene reactant. The fractional-order kinetics and low temperature associated with desorption of the Sonogashira product suggest that the reaction occurs at the boundaries of islands of adsorbed reactants and that its appearance in the gas phase is rate-limited by the surface reaction. These findings demonstrate unambiguously and for the first time that this heterogeneous cross-coupling chemistry is an intrinsic property of extended, metallic pure gold surfaces: no other species, including solvent molecules, basic or charged (ionic) species are necessary to mediate the process.