S. Haq

A study of glycine adsorption on a Cu{110} surface using reflection absorption infrared spectroscopy

Abstract The chemisorption of glycine (NH 2 CH 2 COOH) and its fully deuterated analogue d 5 -glycine, vacuum deposited on a clean Cu{110} surface, have been investigated using reflection absorption infrared spectroscopy (RAIRS). At room temperature (300xa0K) a saturated monolayer is dissociatively adsorbed producing glycine in its anionic form; a glycinate species. The orientation of the adsorbed species changes as the coverage increases with bonding occurring initially via equivalent oxygen atoms of the carboxylate group, orientated broadly perpendicular to the surface, similar to the bonding found in simple carboxylic acids. At saturation coverage, at 300xa0K, a different orientation of the carboxylate group is observed with the carboxylate binding in a more unidentate fashion. The IR spectra are then very similar to those of solid copper glycinate. Low energy electron diffraction (LEED) shows a poor (3×2)g pattern. On annealing this fully covered surface to 420xa0K, there is no significant desorption and the IR spectra show dramatic changes in relative band intensities with the spectra becoming more similar to those obtained at low coverage. The (3×2)g LEED pattern sharpens considerably. At this stage, we suggest that anionic glycine (glycinate) species are adsorbed with the O 2 –C–C–N backbone essentially parallel to the surface with interadsorbate bonding dominated by CH⋯O and N–H⋯O hydrogen bonds similar to those found in bulk glycine. The (3×2) structure is a compromise between optimal adsorbate site, intermolecular hydrogen bonding and maximum adsorbate density. With the substrate held just below room temperature, multilayers of the zwitterionic glycine form which desorb in two stages with the second layer leaving the surface at a higher temperature than the other layers. At liquid nitrogen temperatures (85xa0K), some of the glycine is present on the surface in its acid form, as evidenced by the presence of a carbonyl (Cue605O) stretch.

Methanol oxidation on Cu(110)

The mechanism of reaction and surface structures for the adsorption and partial oxidation of methanol on the oxygen precovered Cu(110) surface have been studied with a variety of surface sensitive techniques. Molecular beam reaction measurements and TPD have been used to determine the chemical nature of the adsorbed species and the products formed. LEED and STM have been employed to determine the surface structure of both the oxygen covered surface and the structures formed by reaction with methanol. The kinetics are shown to be dependent on the initial oxygen precoverage and the surface temperature during reaction. The mechanism shows three distinct temperature regimes; at low temperatures (< 330 K) stable methoxy species are formed on the surface in a 2:1 ratio to preadsorbed oxygen atoms while at intermediate temperatures (330–450 K) the stoichiometry is the same, but the methoxy is unstable, decomposing to formaldehyde and hydrogen. At high temperatures (

A one-dimensional ice structure built from pentagons

450 K) the stoichiometry of reaction changes to 1:1 with no hydrogen production. STM and LEED show a previously unreported (5 × 2) structure for methoxy adsorbed on this surface. It is clear from the combination of techniques that a dual site combination is crucial for high reactivity. This dual site consists of an oxygen atom and a Cu0; the fully oxygen covered surface with partially oxidised Cu atoms is poisoned in activity for the reaction, whereas the partly covered surface is the most active. The proposed active sites are located at the short side of the rectangular oxygen islands.

Growth of thin crystalline ice films on Pt(111)

Heterogeneous ice nucleation has a key role in fields as diverse as atmospheric chemistry and biology. Ice nucleation on metal surfaces affords an opportunity to watch this process unfold at the molecular scale on a well-defined, planar interface. A common feature of structural models for such films is that they are built from hexagonal arrangements of molecules. Here we show, through a combination of scanning tunnelling microscopy, infrared spectroscopy and density-functional theory, that about 1-nm-wide ice chains that nucleate on Cu(110) are not built from hexagons, but instead are built from a face-sharing arrangement of water pentagons. The pentagon structure is favoured over others because it maximizes the water-metal bonding while maintaining a strong hydrogen-bonding network. It reveals an unanticipated structural adaptability of water-ice films, demonstrating that the presence of the substrate can be sufficient to favour non-hexagonal structural units.

Drastic symmetry breaking in supramolecular organization of enantiomerically unbalanced monolayers at surfaces

Adsorption of water on Pt(1xa01xa01) at 135 K or above proceeds by a Stranski–Krastanov mechanism to form crystalline ice films. The structure of thin films reflects a conflict between maximising the binding to the surface and minimising the stress in the multilayer film. The first bilayer of water forms an ordered hexagonal overlayer which shows a ()R16.1° LEED pattern. Water condensation on this overlayer is initially slow, accelerating as second layer nucleation sites form and allow multilayer growth. Adsorption continues to grow the ()R16.1° structure until the film reaches a thickness of ≈xa05 bilayers at 137 K, after which further adsorption reorients the overlayer to form an incommensurate hexagonal film aligned at 30° to the Pt(1xa01xa01) close packed direction. Thermal desorption measurements reveal a change in the water desorption rate as the multilayer re-crystallises during heating, formation of the hexagonal R30° structure stabilising the multilayer film at the cost of reducing the binding of the first layer of water to the Pt(1xa01xa01) surface. The ()R16.1° overlayer becomes increasingly unstable to electron exposure as its thickness increases towards five bilayers, the ice rapidly restructuring to form islands with the R30° structure and exposing bare Pt.

The bonding and orientation of the amino acid l-alanine on Cu{110} determined by RAIRS

There is considerable interest in skewing the transmission of chirality, or handedness, from the molecular to the supramolecular level so that single-handed superstructures are created from mixed enantiomer systems. One approach is to flip the chirality of all the molecular building blocks to the same handedness. However, manipulation of molecular chirality is not possible for non-interconvertible enantiomers, and mechanisms that skew such systems are unclear. Here, we track the molecule-to-supramolecular chiral transfer in such systems at the nanoscale by probing molecular monolayers at surfaces. Scanning tunnelling microscopy and theoretical modelling show that enantiomeric imbalances lead to nonlinear symmetry breaking in organization, driven by configurational entropy effects. Thus, the majority enantiomer readily organizes into its superstructure with the minority left fragmented and disorganized, and thus impeded from realizing its superstructure. Such effects promise new strategies in chiral separations and enantioselective processes, and may have contributed to the homochiral evolution of complex matter from prebiotic environments.

The adsorption and decomposition of formic acid on Cu {110}

Reflection absorption infrared spectra have been obtained for the amino-acid l-alanine on Cu{110} as a function of exposure at 300 K. The RAIR spectra reveal a complicated set of vibrational bands which can be interpreted with reference to Cu-(ala)2 complexes. A detailed analysis in terms of the individual functional groups present in the molecule yields a detailed geometry of the adsorbed species. Two chemisorbed phases are identified: a thermodynamically stable phase which forms at low exposures, in which both the carboxylate oxygen atoms are equidistant from the surface, and a second phase, created by diffusion-limited adsorption processes, in which a differently oriented alanine species is accommodated at the surface, possessing titled carboxylate groups where the two oxygen atoms are no longer equidistant from the surface.

The structure and crystallization of thin water films on Pt(111)

Abstract The reactive adsorption of formic acid (HCOOH) on oxygen dosed Cu(110) has been studied using a molecular beam system, TPD, LEED and STM. At low temperature the reaction is strongly oxygen coverage dependent. All coverages result in high reaction probability (0.8 at room temperature) for formic acid and, for less than 0.25 monolayers of oxygen there is complete oxygen clean-off, leaving formate on the surface in a c(2 × 2) structure. At higher coverages the situation is more complex, with some oxygen remaining coadsorbed with the formate. The two adsorbates are then mainly phase separated into islands of c(6 × 2) oxygen and (3 × 1) formate. The two phases mutually compress each other due to pressure at the phase boundaries. The reaction stoichiometry is 2:1 formic acid:oxygen atoms in this temperature range. At higher temperatures (> 450 K) the formate itself is unstable and decomposes during adsorption which results in a change of stoichiometry of the reaction; one molecule of formic acid removes an oxygen atom as water, and hydrogen evolution ceases. There is a range of temperature between 350 and 420 K for which the reaction becomes very difficult, and the reaction probability drops to ∼ 0.1. It is proposed that this is due to rapid compression of much of the oxygen adlayer into the unreactive c(6 × 2) structure by small amounts of formate. The reaction proceeds through a highly mobile, weakly held, “precursor” state on the surface, which is able to seek out the active sites on the surface, which are low in coverage at high levels of oxygen. These active sites are the terminal oxygen atoms in the oxygen islands (in the [001] direction), which are only present at step edges or phase boundaries at 0.5 monolayers coverage of oxygen.

Bonding and assembly of the chiral amino acid S-proline on Cu(1 1 0): the influence of structural rigidity

When water is adsorbed on Pt(111) above 135 K several different ice structures crystallize, depending on the thickness of the ice layer. At low coverage water forms extended islands of ice with a (square root(37) x square root(37))R25(o) unit cell, which compresses as the monolayer saturates to form a (square root(39) x square root(39))R16(o) structure. The square root(39) low-energy electron diffraction (LEED) pattern becomes more intense as the second layer grows, remaining bright for films up of 10-15 layers and then fading and disappearing for films more than ca. 40 layers thick. The ice multilayer consists of an ordered square root(39) wetting layer, on which ice grows as a crystalline film which progressively loses its registry to the wetting layer. Ice films more than ca. 50 layers thick develop a hexagonal LEED pattern, the entire film and wetting layer reorienting to form an incommensurate bulk ice. These changes are reflected in the vibrational spectra which show changes in line shape and intensity associated with the different ice structures. Thin amorphous solid water films crystallize to form the same phases observed during growth, implying that these structures are thermodynamically stable and not kinetic phases formed during growth. The change from a square root(39) registry to incommensurate bulk ice at ca. 50 layers is associated with a change in crystallization kinetics from nucleation at the Pt(111) interface in thin films to nucleation of incommensurate bulk ice in amorphous solid water films more than 50 layers thick.

Face specificity and the role of metal adatoms in molecular reorientation at surfaces

Abstract The adsorption of S -proline, vacuum deposited on a clean Cu(1xa01xa00) surface held at room temperature, has been investigated using reflection absorption infrared spectroscopy and low energy electron diffraction. Throughout the adsorption regime at 300 K, a (4×2) phase is formed in which the molecule bonds to the copper surface in an anionic form, via the oxygen atoms of the carboxylate (COO − ) functionality and the nitrogen of the imino (NH) group which forms part of a pyrrolidine ring. Both carboxylate oxygen atoms are found to be equidistant from the surface while the pyrrolidine ring is held at a small angle to the surface plane. Unlike other amino acids, the molecule does not show a range of different phases with varying coverage or temperature conditions and does not significantly reorient at high coverage or on annealing. This difference in behaviour is attributed to the structural rigidity of the molecular structure which severely restricts the degrees of freedom generally associated with amino acid end and side groups. As a result, the proline is forced to adopt the same footprint at the copper surface at all coverages, which also requires slightly more physical space than other amino acids. The bonding of the proline layer to Cu(1xa01xa00) is strong, creating a robust adlayer which is stable up to 450 K, after which the molecule dehydrogenates and, subsequently, decomposes. Finally, this strong and defined mode of interaction with the metal surface must play an important role in the use of this molecule as a chiral modifier in heterogeneous diastereoselective catalysis, where its attachment to an organic molecule determines the adsorption and orientation adopted by the latter at a surface, thus creating a strong inequality in the probability of hydrogen addition at the two prochiral faces of the reactant.