Self-Organized Overlayers Formed by Alanine on Cu{311} Surfaces

Article pubs.acs.org/JPCC

Self-Organized Overlayers Formed by Alanine on Cu{311} Surfaces David C. Madden, Israel Temprano, Marco Sacchi, Maria Blanco-Rey,† Stephen J. Jenkins, and Stephen M. Driver* Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom S Supporting Information *

ABSTRACT: Chirality can manifest itself in diverse ways when a molecule adsorbs on a metal surface. A clear understanding of the interplay between molecular chirality, “footprint chirality”, and chirality in the long-range selforganization is crucial if metal surfaces are to be exploited for enantioselective heterogeneous catalysis or enantio-discriminating sensors. We have investigated the self-organization of Lalanine adsorbed as alaninate on Cu{311}, using reflection− absorption infrared spectroscopy in conjunction with firstprinciples calculations to determine bonding configurations, and low-energy electron diffraction and scanning tunnelling microscopy to elucidate structural features. Three ordered structures are seen. One has a symmetric lattice and 3-point adsorbate bonding (the “symmetric lattice” or SL phase); the others, occurring at higher coverage, have chiral lattices and also involve 2-point bonding (the “chiral lattice” or CL phase). Possible models for these structures are discussed, together with the roles of footprint chirality and of long-range chirality in the self-organization. These results set the forms of chirality seen in alaninate overlayers on Cu{110} and {100} surfaces into a wider context. The common underlying principles should help in establishing a general framework for understanding the behavior of chiral adsorbates on low-symmetry metal surfaces. With the idea of investigating the possibility of “switching off” the footprint chirality associated with μ3 bonding, we have chosen to investigate amino acid adsorption on Cu{311} surfaces. These closely resemble Cu{110} surfaces, in that both have a high density of close-packed steps running in a single direction, as shown in Figure 1. Cu{311}, however, has a larger row−row spacing than Cu{110} (4.23 Å, cf. 3.61 Å), and {100} microfacets alternate with {111} between the close-packed rows, such that the surface has no rotational symmetry and only one mirror plane (Figure 1b). Crucially, the registry between successive close-packed rows in Cu{311} defines bonding sites for alaninate in the form of isosceles triangles, in contrast to the bonding sites defined by the rectangular unit mesh of Cu{110}. One can therefore anticipate that alaninate can bond in a μ3 configuration on Cu{311} with a footprint which is not chiral. An exploratory investigation of alanine on Cu{311} using scanning tunnelling microscopy (STM) and low-energy electron diffraction (LEED) confirmed this expectation.11 In that study, we identified two distinct types of structural phase. One has an ordered periodic structure described by a (2,1;1,2) matrix (with respect to the lattice basis vectors defined in Figure 1b), and is the analogue of the (3 × 2) alaninate “phase IV” structure seen on Cu{110}.24 We inferred a structural model involving μ3-bonded alaninate at 0.33 ML coverage. In contrast to Cu{110} phase IV, in which each (3 × 2) unit mesh

1. INTRODUCTION Chirality can manifest itself at single-crystal metal surfaces in numerous ways,1−5 ranging from spontaneous chiral selforganization of simple achiral molecules on a high-symmetry surface,6,7 to the enantiospecific restructuring of an intrinsically chiral surface induced by a chiral adsorbate.8−11 Simple amino acids adsorbed on Cu surfaces have emerged as a model system for the interaction of chiral molecules with single-crystal fcc surfaces. The overlayers formed by glycine (NH 2 − α CH 2 −COOH) and alanine NH 2 − α CH(CH 3 )− COOH) on Cu{110} and {100} have been explored in particular depth.12−34 On Cu surfaces at 300 K, these amino acids adsorb in anionic form by deprotonation of the carboxylic acid group (the hydrogen atom associatively desorbing as H2). A characteristic bonding configuration, seen for a number of the structural phases that occur, involves the amine N atom and the two carboxylate O atoms bonding to three Cu atoms in nearatop positions. This bonding configurationwhich, following earlier papers, we denote as “μ3”is shown schematically for Lalaninate in the (3 × 2) “phase IV” structure on Cu{110} in Figure 1a. The bonding footprint can be represented by a rightangled triangle defined by the three Cu atoms, and thus occurs in one or the other of two enantiomeric forms. It is necessary to consider this “footprint chirality”, as well as the molecular chirality due to the chiral center in the amino acid (except glycine, which lacks a chiral center), when examining the factors controlling self-organization in the ordered overlayers. © 2014 American Chemical Society

Received: June 6, 2014 Published: July 23, 2014 18589

dx.doi.org/10.1021/jp505636v | J. Phys. Chem. C 2014, 118, 18589−18603

The Journal of Physical Chemistry C

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Figure 1. Schematic showing (a) the Cu{110} and (b) the Cu{311} surfaces. Indicated on the diagrams are the lattice basis vectors a1 and a2 used in the text, the surface mirror symmetry (red lines), and the {100} and {111} microfacets between ridge rows of the Cu{311} surface. L-Alaninate moieties are shown on both surfaces in μ3 bonding configurations (gray = C, red = O, blue = N, white = H). On Cu{110}, the (3 × 2) unit mesh of the phase IV structure (green) contains two alaninate moieties, which are molecularly homochiral but have a racemic pair of heterochiral footprints (yellow triangles). On Cu{311}, the bonding footprint is achiral, but could in principle be oriented in either of two symmetrically inequivalent directions (yellow triangles) within a (2,1;1,2) unit mesh (green).

earlier usage.) The lattices described by the (2,1;4,n)/(n,4;1,2) matrices break the mirror symmetry of the substrate: we therefore describe structures involving or based on the observed boundaries collectively as the “chiral lattice” (CL) phase. These postulated ordered lattices are the analogue of the alaninate “phase III” structure seen on Cu{110}.24 Here we report a systematic investigation of the selforganized overlayers formed when enantiopure L-alanine adsorbs on Cu{311}, building on our earlier, exploratory experiments. We have now employed reflection−absorption infrared spectroscopy (RAIRS), together with new LEED and STM measurements, to elucidate the preparation conditions leading to the different phases, and the local coverages and bonding configuration(s) of alaninate within them. We have gained new structural information about the high-coverage phase, resolving the apparent ambiguity in this regard in our earlier study. The experimental measurements are underpinned by first-principles calculations within the framework of density functional theory (DFT), allowing us to interpret the RAIR spectra by reference to calculated frequencies of normal modes of adsorbed alaninate.

contains two alaninate moieties whose chiral footprints form a racemic pair (even when all adsorbates have the same molecular chirality) as shown in Figure 1a, the smaller (2,1;1,2) unit mesh on Cu{311} contains a single alaninate, implying that all alaninate moieties adopt the same achiral μ3 footprint. The lattice described by the (2,1;1,2) matrix (as distinct from the molecular motif) retains the full substrate symmetry: we therefore describe this as the “symmetric lattice” (SL) phase. We subsequently found that the same SL phase forms with racemic alaninate and with glycinate.35 The other phase involves anisotropic islands of the (2,1;1,2) structure separated by a network of linear boundaries. These are translational domain boundaries, and have a high-packingdensity internal structure. The orientation of the boundaries breaks the substrate mirror symmetry, meaning that the boundaries are chiral; the boundary chirality switches with molecular chirality. In initial experiments with enantiopure alanine,11 and in experiments with racemic alanine and with glycine,35 we found that the boundaries were irregularly spaced. However, one could envisage the possibility of taking the boundary structure in isolation and using it as the repeat unit of a regular grating structure. Based on the details of the boundaries seen by STM, the resulting grating structure would be expected to have (2,1;4,6)/(6,4;1,2) periodicity for D-/L-alanine, whereas LEED data obtained in one series of experiments with D-alanine indicated instead that an ordered overlayer of (2,1;4,7) periodicity had formed;11 the equivalent structure for L-alanine would be (7,4;1,2). We suggested that the boundaries (and any associated ordered structures) probably involve, in addition to μ3-bonded alaninate, another alaninate bonding configuration in which one of the O atoms is detached from the surface, leaving the molecule bound through the other O atom and the N atom. Such a configuration has previously been reported for some of the amino acid structural phases (including phase III) on Cu{110}, and denoted as “μ2” bonding.23,24 (Strictly, the standard μ2 notation for a bridging ligand refers to the number of metal atoms coordinated to the ligand. If the N and/or O atom were to adsorb in bridge sites, the standard notation would be μ3 or μ4. Here, however, we use “μ2” to imply that two points on the adsorbate bond to the surface, in line with

2. EXPERIMENTAL DETAILS The experiments were performed in two separate ultrahigh vacuum (UHV) systems, one dedicated to RAIRS, the other to STM. Both systems are equipped with standard facilities for sample cleaning by Ar+ ion bombardment and annealing, and for characterization by LEED. Two separate Cu{311} crystals were used, due to the different mounting requirements in the two instruments. Note that in the RAIRS system, the thermocouple was mounted directly on the sample, whereas in the SPM system, the thermocouple is located at one of the spring clips for the detachable sample plates. Despite this, phase transitions were seen to occur at similar measured temperatures in both systems. The Cu{311} surfaces were prepared in UHV by cycles of Ar+ ion bombardment (typically 1 kV) and annealing (typically 900 K), until a sharp (1 × 1) LEED pattern was obtained. To prepare alaninate overlayers, solid L-alanine was heated in a capillary tube to around 340 K, at which temperature alanine sublimes. When the gate valve separating the (differentially 18590



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can provide only a partial insight into the boundary structure(s), and we have no evidence regarding the strength of any H-bonding between neighboring adsorbates. To avoid unjustified assumptions about unknown nearest-neighbor configurations and interactions, we chose to perform calculations for isolated μ2-bonded alaninate at 1/6 ML coverage in a (3,3;−1,1) unit mesh, as a basis for calculating μ2-bonded alaninate normal modes. We also performed calculations for isolated μ3-bonded alaninate in the same unit mesh, in order to compare directly the relative energies of the two bonding configurations in the absence of intermolecular Hbonding. The calculations were performed at the generalized gradient approximation (GGA) level of theory with the Perdew Burke Ernzerhof exchange-correlation functional.38 The plane wave basis set was expanded to a 360 eV energy cutoff and reciprocal space was sampled with a (3 × 3 × 1) Monkhorst−Pack kpoint grid.39 Electron−ion interactions were included within the ultrasoft pseudopotential scheme.40 In its original formulation, DFT explicitly ignores long-range dispersion interactions (van der Waals (vdW) forces) in the total ground state energy calculations. In computational surface science this limitation is particularly dramatic when calculating weak physisorption bonding between closed shell molecules and inert substrates, but it can also be important when modeling small aromatic molecules or amino acids adsorbed on metal surfaces.41−44 In this work, we account for vdW interactions between alaninate and the Cu{311} surface by employing the dispersion force correction methodology (TS) developed by Tkatchenko and Scheffler,45 in which the pair-potential interatomic coefficients are calculated from the electron density derived by DFT. The force tolerance for the structural calculations was set to 0.04 eV Å−1, while the electronic energy was minimized up to a tolerance of 10−7 eV. Calculation of phonon spectra via the finite displacement method46 entails systematic distortion of each equilibrium geometry to obtain a matrix of force constants. In our work, displacements of individual atoms were imposed in (arbitrarily oriented) Cartesian directions, with magnitude 0.01 bohr, and forces on all atoms (the single displaced atom and all the nondisplaced atoms) were recorded in those same Cartesian directions. Combining the force constant matrix with the mass matrix of the system allows the determination (subject to an assumption of harmonic motion) of the so-called dynamical matrix, whose diagonalization leads to the phonon frequencies (square roots of the eigenvalues) and displacement patterns (the eigenvectors). The effects of anharmonicity were incorporated through multiplication of the frequencies by scaling facotrs of 0.99 (below 1800 cm−1) and 0.96 (above 1800 cm−1) as per the procedure given in Halls et al.47 Assignment of particular displacement patterns to local-mode descriptions (e.g., CO2 symmetric stretch, NH2 scissor, etc.) is achieved by visual inspection and the corresponding eigenvalues labeled accordingly (some of the most significant local-mode group vibrations and their symbols are shown schematically in Figure S1 of the Supporting Information). Our calculations assume in-phase motion between one unit cell and the next (i.e., we calculate only the zone-center phonon modes) but this is entirely appropriate for comparison with RAIRS experiments (which probe only this region of the Brillouin zone). For quantitative LEED analysis of the clean Cu{311} surface orientation, diffracted beam intensities as a function of primary

pumped) doser from the UHV chamber was opened, a pressure rise, typically to 3 × 10−9 mbar, was observed; a rising mass 41 signal, monitored by a quadrupole mass spectrometer, verified the presence of a flux of gas-phase alanine. Exposure values in langmuir units (1 L = 10−6 Torr s) were calculated from the overall pressure rise; it was not found necessary to have line-ofsight between the capillary tube and the surface. Surface temperatures during exposure were as stated in the text. RAIR spectra were acquired with a Mattson RS2 Fourier transform infrared (FTIR) spectrometer and external mercury cadmium telluride (MCT) detector, capable of detecting frequencies in the range 4000−570 cm−1. The incident and reflected infrared beams were transmitted in and out of UHV via KBr viewports, and the beam paths linking the UHV chamber to the spectrometer and detector were purged with dry N2(g). Each spectrum shown was obtained by averaging 400 individual spectra, each recorded at a resolution of 4 cm−1, and dividing by a similarly averaged background spectrum previously obtained from the clean surface. Spectra as a function of exposure were recorded continuously while exposing the surface to alanine, typically at a background pressure of 3 × 10−9 mbar. Spectra recorded as a function of temperature were obtained by heating the surface to successively higher temperatures, in each case holding the targeted temperature for 2 min and then reducing back to 300 K before recording the corresponding spectrum. STM images were recorded at 78 K with an Omicron lowtemperature scanning probe microscope (LT-SPM). Electrochemically etched W tips were used, and the instrument was operated in constant-current (topographic) mode, with the bias voltage applied to the tip and the sample at earth potential. Lateral miscalibration of the instrument has been corrected for in high-resolution images where stated in the figure captions; the (2,1;1,2) structure, for which the true periodicity is verified by the LEED pattern, was taken as the reference point for the calibration. All STM images are shown at the same azimuthal orientation as the corresponding LEED patterns. LEED measurements on both instruments were made at very low beam energies (typically 23 eV), which are found to be below the threshold for electron beam damage, to which these overlayers are sensitive. We were unable to obtain very sharp LEED patterns using the optics on the RAIRS instrument; this is attributed to poor focusing of the electron beam, rather than poor surface order (we have found this performance to be characteristic over a wide range of surfaces). The quality was nevertheless sufficient to establish the correspondences between structural phases and RAIR spectra. The surface orientation of the Cu{311} crystal in the SPM instrument was verified by quantitative LEED analysis of the (1 × 1) structure of the clean surface. Data for this analysis were obtained by recording a series of LEED patterns from 30 to 300 eV in steps of 2 eV, with the sample at 300 K (the minimum temperature available at the sample stage of the manipulator in the STM instrument).

3. CALCULATION DETAILS DFT calculations were performed for D-alaninate (although the results, mirror-imaged appropriately, should be equally applicable to L-alaninate), using the CASTEP code,36,37 for both μ3- and μ2-bonding on Cu{311}. Led by RAIRS evidence of pure μ3 bonding (discussed below), the SL phase was modeled with a single μ3-bonded alaninate within a (2,1;1,2) unit mesh at 1/3 ML coverage. For the CL phase, STM images 18591



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beam energy (experimental “I(V) curves”) were extracted from the recorded movies by digital image processing. All I(V) curves were 3-point smoothed prior to analysis. Corresponding I(V) curves for trial structures were calculated by using the CLEED code,48 using the Pendry reliability factor RP to evaluate the fit with experiment.49 CLEED implements automated structural refinement, using the downhill simplex method to search for the RP-factor minimum that is nearest in parameter space to the initial structure, and performing a full multiple-scattering calculation for each iteration of the search.

4. RESULTS 4.1. Overview of Phases and Transformations. To facilitate detailed discussion of our results, we first present a summary overview of the most important outcomes. The key features of the behavior all become apparent in the course of two series of measurements: exposure of the Cu{311} surface to alanine up to saturation with the sample at 300 K, and subsequent heating of the alaninate-saturated surface. Overlayer phases were identified primarily through their LEED patterns (additional structural details being determined by STM), while the corresponding bonding configurations were determined from RAIR spectra and associated DFT calculations. Figure 2 shows the evolution of the RAIR spectrum while exposing the sample at 300 K to alanine. A detailed interpretation of the various absorption bands is presented in Section 4.4. Here we focus on the band at 1408 cm−1, which is diagnostic of the symmetric O−C−O stretch mode, νs(CO2), of the carboxylate group in μ3-bonded alaninate, and on the band at 1618 cm−1. Although the latter absorption band has previously been assigned to the antisymmetric O−C−O stretch mode, νa(CO2), of μ2-bonded alaninate, we argue in Sections 4.3 and 4.4 that as a consequence of the inequivalent bonding of the two O atoms, the carboxylate-group vibrations can be better described as individual CO (double bond) and CO (single bond) modes. The band at 1618 cm−1 is assigned to the CO stretch mode, ν(CO), and its presence/absence is a signature of the presence/absence of μ2 bonding. A set of absorption bands which includes the symmetric OCO stretch but not the CO stretch can be seen in the RAIR spectrum from 0.7 L exposure, with growing intensity as the exposure increases to around 2 L. The appearance of these bands is accompanied by the appearance of a (2,1;1,2) LEED pattern corresponding to the SL phase (Figure 3a). We can therefore associate the SL phase with pure μ3 bonding. With increasing exposure above 2 L, the CO stretch appears as an additional absorption band in the spectrum, and there is a corresponding change in the LEED to a streaky multispot pattern (which sharpens slightly on annealing up to around 410 K, Figure 3b) that we attribute to a mixed (6,4;1,2)/(7,4;1,2) structure within the CL phase. From the coexistence in the RAIR spectra of the CO stretch with existing μ3 bands, we can associate the CL phase with both μ3 and μ2 bonding. No further development in the RAIR spectrum was observed with exposures beyond 8 L: the surface appears to be saturated, with both μ2- and μ3-bonded alaninate present. Figure 4 shows the further evolution of the RAIR spectrum, starting from saturation alaninate coverage, as the surface is subjected to flash anneals (2 min each) to successively higher temperatures. In the temperature window between 440 and 460 K, the CO stretch at 1618 cm−1 is progressively lost, the spectrum reverting to that associated with pure μ3 bonding. The LEED pattern correspondingly reverts to (2,1;1,2). We can

Figure 2. Evolution of RAIR spectra as Cu{311} is exposed at 300 K to alanine. Exposures (in langmuir) are marked.

Figure 3. Examples of the (2,1;1,2) LEED pattern of the SL phase (left) and a multispot LEED pattern of the CL phase (right) obtained with L-alaninate overlayers on Cu{311}. The beam energy was low (23 eV) to minimize electron beam damage.

therefore infer that the surface has reverted on heating to the SL phase. Above 470 K, the RAIRS absorption bands diminish and the fractional-order LEED spots likewise become fainter. By 490 K, there is no evidence from RAIRS or LEED of any 18592



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Figure 5. Summary of the coverages and surface annealing temperatures under which the SL and CL alaninate phases are observed on Cu{311}. The horizontal arrows denote experiments in which RAIR spectra were recorded as a function of exposure, with the surface held at constant temperature throughout the recording. The vertical and sloping arrows denote experiments involving a series of annealing cycles to successively higher temperatures; the surface was held for 2 min at the target temperature in each case, before cooling back to 300 K and recording a spectrum.

4.2. Other Preparation Routes. Other preparation routes that we have explored are indicated by the arrows in Figure 5. When the surface is held at 400 K during exposure, the results are similar to those seen at 300 K, the only significant difference being that the intensities of the absorption bands characteristic of μ2 bonding at the highest exposures are smaller relative to those characteristic of μ3 bonding than in the 300 K experiment. When the surface is held at 440 K during exposure, the SL phase is again seen, but only small bands characteristic of μ2 bonding are seen at the highest exposures, and there is no transformation of the (2,1;1,2) LEED pattern to the multispot pattern. If the surface at 300 K is exposed to alanine until a (2,1;1,2) LEED pattern and a pure μ3 RAIR spectrum are obtained, and the surface is then annealed, no further change is seen in LEED or RAIRS until the onset of desorption/ dissociation above 470 K as before. 4.3. DFT Structural Models. Six generic models, shown after convergence in Figure S2 of the Supporting Information, were evaluated for μ3-bonded D-alaninate in the (2,1;1,2) SL phase on Cu{311}. These were chosen to probe (i) the orientation of the bonding footprint on the surface (the two possible directions indicated in Figure 1b) and (ii) the angle that the N−αC−COO− backbone plane makes to the surface, and the corresponding tilt of the αC−CH3 bond relative to the surface normal. The lowest-energy structure is shown in Figure 6a. The backbone plane is perpendicular to the surface and coincident with the surface mirror plane. The projection of the backbone onto the surface is therefore linear, and the αC−CH3 bond is tilted by around 50° relative to the surface normal. This places the two carboxylate C−O bonds symmetrically about the surface mirror plane, and the two C−O bond lengths are accordingly identical at 1.27 Å. These compare to values of 1.24−1.26 and 1.26−1.27 Å for the two bonds, determined experimentally and theoretically for solid-phase zwitterionic alanine (the slight inequality arises from one of the O atoms bonds interacting with the nearby NH3+ group).50−53 The O− C−O plane is tilted approximately 55° from the surface normal.

Figure 4. Evolution of RAIR spectra as a function of the temperatures of successive annealing steps (see text), starting from the alaninatesaturated (8 L) surface at 300 K.

alaninate or order remaining in the overlayer: we attribute this to a combination of dissociation and desorption of alaninate. Figure 5 summarizes diagrammatically the conditions of coverage and surface annealing temperature that were found to lead to the SL and CL alaninate phases in our experiments. The justification for the coverage values given on the horizontal axis is described later in the paper. We stress that this figure is not intended to be read as an equilibrium phase diagram in the conventional sense. In particular, it is likely, though we have not investigated this explicitly, that at temperatures where reversion from the CL to the SL phase occurs, or where coverage within the SL phase decreases, the extent of change will show some dependence upon the annealing time. We also stress that in general the phase boundaries are not sharp: there will be, for example, a progressive transition from the SL to the fully developed CL phase as the coverage increases above 0.33 ML. The positions of the boundary lines should therefore be thought of as broadly indicative, rather than marking abrupt phase transitions. 18593



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details), implying that a range of backbone tilts and C−CH3 orientations will coexist at typical experimental temperatures (300−470 K). The energy cost of reversing the footprint orientation was more significant (0.06−0.08 eV), sufficient that a single orientation would be expected at comparable temperatures. The energy cost of neglecting vdW interactions was comparable to that of the structural changes (up to 0.07 eV), confirming that vdW interactions should not be neglected; indeed, more than half of the preference for the orientation shown in Figure 6a can be attributed to the vdW contribution. Exploratory calculations for isolated μ2-bonded D-alaninate on Cu{311} showed a clear preference for the O atom that is bonded to the surface to move from an atop site to a short bridge site after convergence. Four models incorporating this O site, shown in Figure S4 of the Supporting Information, were investigated in detail. These represent (i) the two possible orientations of the bonding footprint and (ii) the direction in which the backbone plane tilts away from the surface mirror plane, which dictates whether the αC−CH3 bond tilts toward or away from the surface relative to its orientation in μ3-bonded alaninate. The lowest-energy structure is shown in Figure 6b. The footprint orientation is opposite to that of the μ3-bonded structure shown in Figure 6a, and the αC−CH3 bond is nearly perpendicular to the surface plane. In this model, the C−O

Figure 6. (Left) The most stable μ3-bonded D-alaninate geometry in the (2,1;1,2) SL phase as calculated by DFT. (Right) The most stable μ2-bonded D-alaninate geometry calculated by DFT in a (3,3;−1,1) unit cell. The other configurations considered in this work are shown in Section 2 of the Supporting Information.

This structure was used in subsequent vibrational mode calculations to obtain the frequencies for the SL phase shown in Table 1. The energy cost of tilting the backbone plane (which implies changing the torsion angle between the N lone pair and the backbone plane) was small (0.005−0.021 eV, with vdW forces incorporated; see Section 2 of the Supporting Information for

Table 1. Absorption Band Frequencies (in cm−1) Seen Experimentally in the Pure μ3 (“Low θ Data”) and in the μ3 + μ2 Spectra (“High θ Data”), Correlated with Frequencies Calculated for Pure μ3 in the (2,1;1,2) Structural Phase (“μ3 calcd”) and for Pure μ2 As Isolated Molecules (“μ2 calcd”)a low θ data

μ3 calcd

2974 2931 2877

3363.47 3300.21 2989.88 2978.88 2935.51 2883.94

νa(NH2) νs(NH2) νa(CH3) νa(CH3) ν(αCH) νs(CH3)

1591.74

δ(NH2)

1567.42 1469.25 1461.51

νa(CO2) δa(CH3) δa(CH3)

1408 1371

1393.35 1380.35 1356.63

νs(CO2) + δs(CH3) + ν(αC−CO2) ν(αC−CO2) + (νs(CO2)) + δ(αCH) τ(NH2) + δ(αCH) + δs(CH3)

1296

1316.47 1249.22

ρ(αCH) + (νa(CO2)) τ(NH2) + δ(αCH) + δa(CH3)

1146

1129.11

ρ(CH3) + ν(αCN)

1076

1075.59 1042.36 1038.97

ν(αC−CH3) + ω(NH2) + ρ(CH3) ν(αC−CH3) + δ(αCH) + ρ(CH3) ω(NH2) + δ(αCH)

908.4 862.93 773.09

δ(CO2) + ν(αC−CO2) + ν(αCN) δ(CO2) + ν(αCN) ω(CO2)

mode

high θ data

μ2 calcd

2974 2931 2877 1618

3423.21 3322.76 2978.75 2970.58 2910.59 2884.47 1657.52

νa(NH2) νa(NH2) νa(CH3) νa(CH3) ν(αCH) νs(CH3) + ν(αCH) ν(CO)

1408 1375

1516.05 1467.72 1450.80 1399.22 1351.84

δ(NH2) δa(CH3) δa(CH3) δs(CH3) ρ(αCH) + ν(αC−CO2) + τ(NH2)

1323 1296

1339.11 1233.91

δ(αCH) ρ(αCH) + τ(NH2) + ν(C−O)

1182 1146 1090 1076 1047 1038 1024

1174.05 1158.68 1095.64

τ(NH2) + ρ(αCH) + ρ(CH3) τ(NH2) + ρ(αCH) ρ(CH3) + ν(αC−CH3) + τ(NH2)

1029.47 1014.16

ω(NH2) + ρ(CH3) + ν(αC−CH3) τ(NH2) + ρ(CH3) + ν(αCN)

929.37 839.75 725.08

ν(αCN) + ρ(CH3) δ(CO2) + ν(αC−CO2) + ρ(CH3) ω(CO2)

mode

1576

1460

1038 1013 916

1460

916

a

The vibrational modes found in the calculations to be associated with the various frequencies are identified. Modes given in parentheses are weak components. 18594



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In Figures 2 and 4, the strong absorption band at 1408 cm−1 arises from the symmetric O−C−O stretch of μ3-bonded alaninate, coupled to the symmetric deformation (umbrella) mode of the methyl group, δs(CH3), and the stretch mode of the bond between the αC and carboxylate C atoms, ν(αC− CO2). For the symmetric O−C−O stretch to be RAIRS-active (i.e., for its dynamic dipole to have a nonzero component normal to the surface), the O−C−O plane must be tilted out of the surface plane. With the two carboxylate O atoms located in equivalent sites equidistant from the surface (as indicated by the DFT calculations), the tilting of the O−C−O plane must be about the axis defined by the two O atoms. In this geometry, the antisymmetric O−C−O stretch mode has its dynamic dipole parallel to the surface plane, and is therefore RAIRSinactive, consistent with the absence in the experimental spectra up to 2 L exposure of a νa(CO2) band (calculated to lie at 1567 cm−1 for μ3-bonded alaninate). The prominent absorption band at 1038 cm−1 is due to the wag mode of the amine group, ω(NH2), coupled to the bending mode δ(αCH) of the αCH group. For the amine wag to be RAIRS-active, the H−N−H plane, to which the dynamic dipole is perpendicular, must be nonperpendicular to the surface. The absence from the spectra of the symmetric H−N−H stretch, νs(NH2), at 3300 cm−1 (not shown) and the H−N−H scissors mode, δ(NH2), at 1590 cm−1 is consistent with the H−N−H plane being close to parallel to the surface plane, as these modes will then be RAIRS-inactive (although we note that the νs(NH2) mode would be likely to be masked by background noise in the relevant spectral region of our data). Taken together, the behavior of the O−C−O stretch modes and the various NH2 modes are the core evidence for a μ3-bonding configuration. Three other prominent bands appear in the fingerprint region of the spectrum. The band at 1296 cm−1 can be assigned to the rocking mode ρ(αCH) of the αCH group (which is RAIRS-active if the αC−H bond is tilted away from the surface normal), weakly coupled to the antisymmetric CO2 stretch. The band at 1146 cm−1 is due to the rocking mode of the methyl group, ρ(CH3), coupled with the backbone αC−N stretch, ν(αCN). The band at 1076 cm−1 is due to stretching of the bond between the αC and methyl C atoms, ν(αC−CH3), coupled with the methyl group rock and the wag mode ω(NH2) of the amine group. The αC−CH3 stretch is RAIRSactive if the bond is tilted out of the surface plane. Weaker features can also be seen in this region. The band at 1460 cm−1 is due to the antisymmetric deformation mode of the methyl group, δa(CH3). The band at 1371 cm−1 is due to the αC−CH3 stretch and αCH bend, weakly coupled to symmetric O−C−O stretch. The band at 916 cm−1 is due to the O−C−O scissors mode of the carboxylate group, δ(CO2), coupled with the αC− CO2 and αC−N stretches, ν(αC−CO2) and ν(αCN). The presence of the O−C−O scissors mode is consistent with the orientation of the carboxylate group, as discussed above. Turning to the high-frequency range, three distinct bands appear. The bands at 2974 and 2877 cm−1 are due to antisymmetric and symmetric stretching modes of the methyl group, νa(CH3) and νs(CH3), respectively, while the intervening band at 2931 cm−1 is due to the backbone αCH stretch, ν(αCH), implying that the αC−H bond is not parallel to the surface. 4.4.2. The μ3 + μ2 CL Phase. At exposures above 2 L, the most obvious change to the spectrum is the addition of the C O stretch band at 1618 cm−1 (Figure 2). In our simulations of vibrational modes of isolated μ2-bonded alaninate, the motions

bond length for the surface-bonded O is 1.31 Å, whereas the C−O bond length for the O atom that is not surface-bonded is 1.23 Å (the nonbonded O lying some 3.03 Å from the nearest Cu atom). Experimental and theoretical studies of gas-phase neutral alanine find values of 1.32−1.37 Å for the COH bond and 1.19−1.24 Å for the CO bond.54−58 For the structure in Figure 6b, we therefore infer essentially CO double bonding for the O atom that is not surface-bonded, and CO single bonding for the surface-bonded O. This structure was used in subsequent vibrational mode calculations for μ2-bonded alaninate, although we emphasize that the bonding configuration and vibrational frequencies may be modified when the μ2-bonded alaninate moiety has adjacent neighbors in the CL phase. (In particular, as we argue below, we expect that the surface-bonded carboxylate O atom in the CL phase bonds in a near-atop position, rather than at the bridge site found for the isolated monomer.) The other isolated μ2-bonded monomer structures were 0.04−0.06 eV less stable; all of these structures were around 0.3 eV less stable than the lowest-energy model for an isolated μ3-bonded alaninate monomer in the same unit mesh (see Figure S3 of the Supporting Information). 4.4. Normal Modes and RAIRS Band Assignments. In Section 4.1, we focused on the symmetric OCO stretch and CO stretch modes of the carboxylate group, νs(CO2) at 1408 cm−1 and ν(CO) at 1618 cm−1, asserting that the latter in particular is diagnostic of μ2 bonding. Here, we examine all of the principal features and changes seen in the RAIR spectra, assigning the absorption bands to specific vibrational modes by reference to our DFT calculations. The modes considered are shown schematically in Figure S1 of the Supporting Information, and the band assignments are summarized in Table 1. The calculations are based on vibration of the whole alaninate moiety: contributions to a given vibrational frequency from coupled normal modes are therefore accounted for where these occur. For almost all of the vibrational modes examined, the agreement between the calculated and measured vibrational frequencies turned out to be remarkably close, allowing us to assign the various absorption bands to their corresponding modes with a high degree of confidence. 4.4.1. The Pure μ3 SL Phase. We first examine the RAIRS evidence supporting the μ3-bonding configuration of the alaninate species in the SL phase. Carbonyl stretching bands in the 1600−1800 cm−1 spectral region, consistent with neutral intact alanine, were observed for multilayers adsorbed at 100 K (the upper spectrum of Figure S5 of the Supporting Information). For exposures up to 2 L with the surface at 300 K or above, however, the absence in the spectrum of any absorption due to the CO stretch is indicative of alanine adsorbing in the deprotonated alaninate (anionic) form, as previously reported for Cu{110} and {100}.12,15,22,30 The possibility that adsorption is zwitterionic, with the proton lost from the carboxylic acid group being transferred to an adjacent amine group, is more difficult to evaluate, as RAIR spectra are not clearly diagnostic of the state of the amine group in this respect. In view of the structural parallels, described below, between the phases formed by alanine on Cu{311} and the phases formed by glycine and alanine on Cu{110} and {100}, we draw the same conclusion as that reached in the previous studies, that the amino acid adsorbs in anionic, rather than zwitterionic, form. Hydrogen is assumed to desorb from the various Cu surfaces at or close to room temperature in all cases. 18595



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Figure 7. (a) STM image (500 × 500 Å2) of the SL phase of L-alaninate on Cu{311}, showing the (2,1;1,2) structure with occasional translational domain boundaries within each terrace. A spontaneous tip change occurs about 3/4 of the way up the image, leading to enhanced resolution. (b) High-resolution STM image (100 × 100 Å2, corrected for scanner miscalibration) showing boundaries between adjacent translational domains of the (2,1;1,2) structure within the SL phase of L-alaninate on Cu{311}. Each (2,1;1,2) domain is terminated by a laterally shifted bright row at its lower right-hand edge, and by a less bright row at its upper left-hand edge. (Both images: +1.0 V tip bias, 1.0 nA, 78 K sample temperature.)

cm−1 gains a contribution from the amine group twist coupled to the αCH rock. The band at 1038 cm−1 gains a contribution which again involves the amine group wag, but now coupled to the methyl group rock and the αC−CH3 stretch, although the shoulder at 1024 cm−1 is a new feature involving a coupling of the amine group twist, the methyl group rock, and the αC−N stretch, ν(αCN). Finally, the band at 916 cm−1 gains a contribution involving coupling of the αC−N stretch and methyl group rock. Four of the bands associated with the μ3-bound molecule, at 1146, 1076, 1038, and 916 cm−1, decrease in intensity at these higher exposures. In principle, this could indicate subtle conformation changes in μ3-bonded alaninate that reduce the components of the relevant dynamic dipole moments perpendicular to the surface. Alternatively, it could indicate a reduction in the surface concentration of μ3-bound molecules, although, as already noted, the intensities of the bands at 1408 and 1296 cm−1, also mainly associated with μ3-bonded alaninate, do not decrease. We address these observations below, after examining evidence in the STM data relating to coverage. On annealing above 440 K, the RAIR spectrum for the most part reverts to the pure μ3 spectrum seen at lower exposures (Figure 4). In particular, the CO stretch band at 1618 cm−1 disappears, signifying the loss of μ2-bonded alaninate. Most of the other changes seen with increasing coverage are similarly reversed. For reasons that are not at present clear, however, three absorption bands remain somewhat more prominent than they were in the initial low coverage data: the antisymmetric CH3 deformation at 1460 cm−1; the band at 1371 cm−1; and the backbone αCH bend at 1323 cm−1. 4.5. LEED and STM Measurements of SL and CL Structures. 4.5.1. The SL Phase. When the preparation conditions that gave rise to a (2,1;1,2) LEED pattern and the most intense pure μ3-bonded alaninate RAIR spectrum were reproduced in the LT-STM instrument, a sharp (2,1;1,2) LEED pattern was obtained, and STM images showed large, flat terraces of (2,1;1,2) periodicity (corresponding to 0.33 ML coverage), exhibiting excellent atomic-scale order within the overlayer. Figures 3a and 7a, for example, show LEED and STM data obtained from a surface that had been exposed to Lalanine and annealed to 470 K. In the STM image, a

of the two CO bonds were found to be essentially decoupled, to the point that recognizable symmetric and antisymmetric OCO stretches are not seen. This is consistent with the calculated bond lengths indicating CO and CO bonding for the now-inequivalent O atoms. The stretch mode of the CO bond is seen at 1658 cm−1 in the calculations, while the stretch mode of the CO bond, coupled with the αCH group rock, ρ(αCH), and the amine group twist, τ(NH2), is seen at 1234 cm−1. Accordingly we assign the experimental band at 1618 cm−1 and a probable additional contribution to the existing band at 1296 cm−1, respectively, to these two modes; use of the isolated-monomer μ2 model in the calculations, and thus the neglect of H-bonding interactions, may account for the discrepancies with experimental frequencies. The band at 1408 cm−1, diagnostic of the symmetric OCO stretch mode of μ3-bonded alaninate, does not significantly change in intensity at these higher exposures. Its presence indicates the continued presence of μ3bonded alaninate in the CL phase. Other new spectral features associated with μ2-bonded alaninate appear in the fingerprint region at these higher coverages. The band at 1576 cm−1 we attribute to the NH2 scissor mode, δ(NH2), although the calculated frequency for this mode, 1516 cm−1, differs significantly from the measured value. This discrepancy may again arise from the use of isolated μ2-bonded alaninate in the calculations. The shoulder at 1323 cm−1 on the band at 1296 cm−1 is the αCH group bend, δ(αCH). The band at 1375 cm−1 involves coupling of the αCH rock, the backbone αC−CO2 stretch, ν(αC−CO2), and the amine group twist, τ(NH2) (which has no dynamic dipole moment, so does not contribute to the IR absorption). The band at 1182 cm−1 involves a coupling of the amine group twist to the ρ(αCH) and ρ(CH3) rocking modes. The band at 1090 cm−1 involves a coupling of the methyl group rocking mode, ρ(CH3), the αC−CH3 stretch, ν(αC−CH3), and the amine group twist. Meanwhile, several of the existing bands associated with μ3bonded alaninate gain additional contributions from μ2-bonded alaninate. The band at 1296 cm−1 has already been discussed; bands at 1460 and 1408 cm−1 gain contributions respectively from antisymmetric and symmetric (umbrella) deformations, δa(CH3) and δs(CH3), of the methyl group. The band at 1146 18596



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Figure 8. High-resolution STM images showing (a) ordered (6,4;1,2) and (b) ordered (7,4;1,2) structures of L-alaninate in the CL phase on Cu{311}. (Both images: 200 × 200 Å2, +1.0 V, 0.2 nA, 78 K, corrected for scanner miscalibration.)

spontaneous tip change can be seen about 3/4 of the way up the frame, giving rise to enhanced resolution in the top part of the image. The appearance of the point defects indicates that there was a slight double tip prior to the tip change. The bright features in the image can be attributed to μ3-bonded alaninate in the SL phase. Occasional translational domain boundaries were seen running in [1 −3 0] directions. This symmetry-breaking direction and the structure within the boundaries, shown at high resolution in Figure 7b, are identical with those reported in our previous work,11 where we identified such boundaries as separating adjacent translational domains of the (2,1;1,2) structure. Each (2,1;1,2) domain is terminated on its lower right side (as oriented in the image) by a laterally shifted molecular row, and on its upper left side by a molecular row that images at lower height in the STM. 4.5.2. The CL Phase. In none of the high-exposure experiments reported here was a LEED pattern obtained that could be characterized as pure (6,4;1,2) or pure (7,4;1,2). Some degree of spot elongation and streaking, as exemplified in Figure 3b and indicative of some form of surface disorder, was always present. STM images reveal clearly the origin of the ambiguity in the LEED data for the CL phase: two distinct, well-defined structures coexist on the surface within the CL phase. Extended, well-ordered regions of both phases were found, which would be expected to give rise to a superposition of the individual LEED patterns. In principle this would lead to two sets of discrete fractional-order beams, although in practice they would be sufficiently closely spaced that they would be hard to distinguish. One of the structures, shown in Figure 8a, is indeed the (6,4;1,2) structure that we previously predicted on the basis of STM data.11 The other structure, shown in Figure 8b, has the (7,4;1,2) periodicity that we previously anticipated on the basis of LEED data.11 Equally typical, however, were terraces in which coexisting, smaller domains of both structures could be seen abutting, as shown in Figure 9. Such images prove that the two observed structures are not simply the same phase imaged under different tip/tunnelling conditions, and allow some details of the (7,4;1,2) structure to be determined by reference to the (6,4;1,2) structure. In these regions, the domains are small enough relative to the LEED transfer width (which is of order 100 Å) that one would expect interference between contributions to the outgoing electron wave function arising

Figure 9. High-resolution STM image showing a boundary between domains of (7,4;1,2) (upper left) and (6,1;4,2) (lower right) structures within a single terrace of Cu{311}. (100 × 100 Å2, +1.0 V, 0.2 nA, 78 K, corrected for scanner miscalibration.)

from the two structures. This is entirely consistent with the observed streaking and elongation of the LEED spots. The (6,4;1,2) structure can be readily understood in terms of the translational domain boundaries separating adjacent (2,1;1,2) domains in the SL phase discussed above, by taking the local structure of the boundary in isolation and repeating it to form a periodic structure. Thus, the repeating structural motif comprises two bright molecular rows and one less bright row, with exactly the same lateral alignments as those seen at the (2,1;1,2) domain boundaries of the SL phase in, as indicated by the unit mesh marked in Figure 7b. The (6,4;1,2) unit mesh contains three moieties, corresponding to a local coverage of 3/8 or 0.375 ML. Key features of the (7,4;1,2) structure can be determined by extrapolation from the (6,4;1,2) phase across the boundaries between the two phases in images such as Figure 10. The (7,4;1,2) unit mesh contains four moieties, corresponding to a local coverage of 4/10 or 0.4 ML. 18597



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Figure 10. STM image (to scale) and models of the (6,4;1,2) L-alaninate structure on Cu{311}. The STM image (a) has been corrected for miscalibration and lattice averaged; a (6,4;1,2) lattice has been superposed. In the models, solid white and yellow circles represent the two bright rows, dashed white circles the less bright row; the (6,4;1,2) unit mesh is marked in red. Models b and c relate to the two possible orientations for the μ3 alaninate footprint in the SL phase (see text).

Figure 11. STM image (to scale) and models of the (7,4;1,2) L-alaninate structure on Cu{311}. The STM image (a) has been corrected for miscalibration and lattice averaged; a (7,4;1,2) lattice has been superposed. In the model, solid white and yellow circles represent the bright rows, dashed white circles the less bright rows; the (7,4;1,2) unit mesh is marked in red. Models b and c relate to the two possible orientations for the μ3 alaninate footprint in the SL phase (see text).

structural optimization led to an overall RP value of 0.26, and layer-spacing relaxations consistent with those obtained in a previous LEED study.59 In the other orientation, the overall RP value after optimization was 0.69, and the corresponding layer spacings were not physically plausible. (Examples of calculated fits to the experimental I(V) curves, after structural optimization, and details of the layer spacings are given in Section 4 of the Supporting Information.) On this basis, the LEED analysis unambiguously determines the orientation of the Cu{311} surface corresponding to the STM images; Figures 1, 10, and 11 show the surface oriented consistently with the STM images. With the surface orientation known from LEED and the boundary orientation from STM, the orientation of the boundaries relative to the surface is determined uniquely. Analysis of the local structure of isolated boundaries within the SL phase, such as those shown in Figure 7a, allows the (2,1;1,2) structure to be taken as a reference point. The footprint orientation of μ3-bonded alaninate within the (2,1;1,2) unit mesh must correspond to one or the other of the two possibilities shown in Figure 1b. The bonding sites of the shifted and less bright rows within the boundary relative to the adjacent (2,1;1,2) rows can then be determined, at least to a first approximation, directly from the relative positions of the rows in the STM image. Figure 10 shows the result of applying this method of analysis to the (6,4;1,2) structure. The STM image in Figure

These measured coverages, and that of the SL phase, were used to calibrate the horizontal axis of the diagram in Figure 5. Possible models for the (6,4;1,2) and (7,4;1,2) structures are discussed below. 4.5.3. Structural Observations. STM imaging cannot reliably determine the molecular orientation, nor the absolute surface orientation (recalling that Cu{311} does not possess 180° rotational symmetry). Full structural analysis of the molecular overlayer with use of quantitative LEED would require special precautions to minimize the impact of electron beam damage, and lies beyond the scope of the work reported here; moreover, the sizes of the CL phase unit meshes are prohibitive for LEED multiple scattering calculations, even if the (6,4;1,2) and (7,4;1,2) structures could be prepared in isolation. Nevertheless, knowledge of the surface orientation would be helpful in constraining possible models for the (6,4;1,2) and (7,4;1,2) structures drawn from the STM data. To address this question, we performed a quantitative LEED analysis, using data measured in situ in the LT-SPM UHV system, of the clean surface structure of the Cu{311} crystal used in the STM experiments. Our multiple scattering calculations were based on a model structure that was unreconstructed, consistent with the (1 × 1) LEED pattern, and was initially unrelaxed. Two sets of calculations were performed, which differed in that the experimental I(V) curves were indexed according to the two possible orientations of the sample. In one orientation, 18598



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our analysis of vibrational modes indicates that this band is better interpreted in terms of a CO stretch. We also propose alternative band assignments in the following cases. Williams et al. assigned a band at 1086 cm−1 to the (CCN) backbone stretching vibration,22 on the basis of a previous assignment of a band at 1121 cm−1 for a Cu-ala complex.60 By contrast, our assignment of this mode to the coupling of ν(αC−CH3), ρ(CH3), and ω(NH2) in μ3-bonded alaninate puts the calculated frequency, 1076 cm−1, much closer to the experimental values for Cu{311} (1076 cm−1) and Cu{110} (1086 cm−1). Correspondingly, we assign the band at 1146 cm−1 to ρ(CH3) + ν(αCN) rather than ω(NH2) + νs(OCO). Another difference relates to the band at 1036−1038 cm−1 for both Cu{110} and Cu{311}. Williams et al. assigned this to a combination of C−N stretch and O−C−O symmetric stretch modes, again on the basis of a previous assignment of a band at 1078 cm−1 for a Cu-ala complex.22,60 We assign this instead to modes involving ω(NH2), with a calculated frequency of 1029−1039 cm−1. For the band at 1296 cm−1 in the CL phase, our calculations suggest that it contains a contribution from the C−O stretch, rather than the symmetric O−C−O stretch, of μ2-bonded alaninate. Finally, we assign the bands at 2931 and 2877 cm−1 to ν(αCH) and νs(CH3), respectively, rather than to νs(CH3) and δ (CH3). 5.2. The CL Phase on Cu{311}. The apparent conflict in our earlier work,11 between the (6,4;1,2) structure for L-alanine proposed on the basis of STM data, and the (7,4;1,2) phase identified by LEED, is resolved by our new STM observations: both of these high-coverage structures occur. In all of the highexposure experiments we report here, the two structures were found to coexist, leading to a slightly ill-defined multispot LEED pattern. Only in the original LEED experiment did we succeed in isolating a pure (2,1;4,7) phase for D-alanine. The exact conditions needed to obtain one or the other of these two structures in isolation remain to be established. The (2,1;4,7) phase corresponds to the highest coverage that we have observed on Cu{311}, 0.4 ML. We also note that these ordered phases were not seen at all with comparable preparation in experiments with racemic alanine or glycine;35 only irregularly spaced boundaries, similar to those seen in initial experiments with enantiopure alanine, were observed.11 A simple rationalization for the progression from the SL to the CL phase can be obtained by assuming that, in each of the ordered structures, all surface-layer Cu atoms are bonded to either a carboxylate O or an amine group. In the (2,1;1,2) structure, at 0.33 ML coverage and with pure μ3 bonding, this is clearly the case. In the (6,4;1,2) and (7,4;1,2) structures, for which the STM data establish coverages of 0.375 and 0.4 ML, the assumption holds if we have μ3:μ2 ratios of 2:1 and 2:2, respectively. STM images of the (6,4;1,2) structure (Figure 8a) show two bright features and one less bright one per unit mesh, consistent with an interpretation in terms of μ3- and μ2bonded moieties in a 2:1 ratio. Similarly, images of the (7,4;1,2) phase (Figure 8b) show two bright and two less bright features per unit mesh, consistent with two μ3-bonded and two μ2bonded moieties. With increasing exposure, therefore, the μ3 coverage decreases from its initial value of 0.33 ML in the SL phase to values of 0.25 and 0.2 ML (i.e., a drop of 0.08−0.13 ML) in the two structures of the CL phase, freeing up the Cu atoms required to allow further adsorption and increased total coverage. The intensity decreases observed in the RAIRS bands associated with μ3-bonded alaninate at 1146, 1076, 1038, and

10a has been corrected for scanner miscalibration and latticeaveraged by using a self-correlation method to reduce the scan noise. A (6,4;1,2) lattice has then been superposed with its vertices centered on what, for an isolated boundary, would be the terminal rows of the (2,1;1,2) structure (compare the unit mesh marked in Figure 7b). Panels b and c of Figure 10 show this row (solid white circles) placed according to the two footprint orientations. The relative positions of the shifted and less bright rows, marked as yellow circles and dashed white circles, respectively, are then taken directly from the STM image. It can be seen that the shifted row appears to occupy similar sites to the unshifted row, whereas the less bright row appears to be located over either bridge or atop sites. We comment on these observations, and on the details of the model, in Section 5.2. Figure 11 shows the result of applying a similar analysis to the (7,4;1,2) structure. The STM image in Figure 11a has again been corrected for miscalibration and lattice-averaged, and a (7,4;1,2) lattice superposed with its vertices centered on a row of bright features assumed to correspond to μ3 alaninate moieties. Panels b and c of Figure 11 show this row (solid white circles) placed according to the two possible footprint orientations. The other row of bright features is marked as yellow circles, while the two less bright rows are marked as dashed white circles, the relative positions again being taken from the STM image. On this basis, the two bright rows correspond to one unit mesh of (2,1;1,2), whereas the two less bright rows correspond plausibly to long bridge positions straddling the trough between adjacent close-packed rows, consistent with μ2 bonding geometry. Again, we discuss the details of this model in Section 5.2.

5. DISCUSSION 5.1. RAIRS Assignments. The assignment of experimental RAIRS absorption bands to vibrational modes presented in Section 4.4 is based entirely on the DFT-based calculations of normal modes summarized in Table 1. The agreement between calculated and experimental frequencies is mostly excellent (the average error is about 9 cm−1). Only for μ2-bonded alaninate do we see significant mismatches between calculated and experimental frequencies for three of the bands involving the surface-bonding groups. The most obvious explanation is the use of an isolated-monomer model in evaluating modes, and thus the neglect of H-bonding interactions that are expected to occur within the CL phase. In previous RAIRS studies of amino acids on Cu{110}, absorption bands have been assigned by reference to other studies in which the amino acid was in solid form, in an argon or nitrogen matrix, or in a complex with Cu or Ni in solution.12,22 In subsequent RAIRS studies of amino acids on Cu{100} and {111}, band assignments have been made primarily by reference to the work on Cu{110}.30,34 In principle, the reliability of such an approach can be affected by the fact that vibrational frequencies may be influenced by the bonding between the molecules and the surface, either through charge-transfer effects, or through intermolecular bonding (Hbonding in this case). In fact, our assignments in most cases agree closely with those of Williams et al. for alaninate on Cu{110}.22 The most significant exception is the assignment of the band at 1618 cm−1 for μ2-bonded alaninate. Whereas this has previously been assigned to the antisymmetric OCO stretch, our DFT calculations indicate different bond lengths, implying different bond orders, for the two CO bonds, and 18599



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916 cm−1 as the CL phase develops are consistent with a decrease in μ3-bonded alaninate coverage. Corresponding decreases are not seen in the intensities of the 1408 and 1296 cm−1 bands, but these gain additional contributions from μ2-bonded alaninate modes, and there may also be subtle conformational variations (such as an increased tilt of the CO2 group out of the surface plane) in the remaining μ3-bonded alaninate that increase the perpendicular components of the relevant dynamic dipoles. With regard to the details of the (6,4;1,2) and (7,4;1,2) structures, we stress that the schematics shown in Figures 10 and 11 do not purport to be full structural models, but simply represent coarse structural features that can be directly inferred from the STM data. In the (6,4;1,2) structure, the simplest assumption is that both bright rows (solid white and yellow circles) correspond to μ3-bonded alaninate (hence their similar appearance), while the less bright row (dashed white circles) corresponds to μ2-bonded alaninate. The relative positions of the two bright rows in the STM images, however, imply that one Cu atom in the unit mesh, located where the solid white and yellow circles are in closest proximity, bonds to an amino group and a carboxylate O. This applies to the registries shown in both panels b and c of Figure 10, and is shown explicitly for the first of these in Figure 12a. Multiple coordination to a single

Instead, the yellow circles could be located half a lattice spacing to the right, in which case the alaninate orientation on the surface would be rotated through 180°. For the registry shown in Figure 12c, this avoids Cu atom sharing by adjacent μ3 alaninate moieties, whereas for the other registry (Figure 12d) it does not. Based on the STM data alone, therefore, the model shown in Figure 12c is the most plausible, especially if one assumes that the STM images the methyl group (the most prominent part of the molecule), which may not be located directly above the centroid of the bonding footprint indicated by the circles in the schematic. Indeed, inequivalence of the two μ3-bonded alaninate moieties may be the origin of the indications in the RAIRS fingerprint region of possible variations in the μ3 conformation. The lowest-energy DFT model for the (2,1;1,2) phase (Figure 6a), however, favors the registry shown for the solid white circles in Figure 10c and the solid white triangles in Figure 12d. We also note that the CL models in panels c and d of Figure 10 both reduce much of the scope for the intermolecular H-bonding that helps stabilize the (2,1;1,2) structure. Further work will be needed to establish the correct model. The less bright features in the STM image appear to be located at either short bridge (Figure 10b) or atop (Figure 10c) sites, neither of which is an expected bonding position for μ2bonded alaninate. This may again simply be a consequence of the STM imaging a part of the molecule (perhaps the O atom that is not surface-bonded) that does not coincide with the centroid of its bonding footprint. Based on the STM data, one cannot rule out the alternative possibility that the two bright rows correspond to a μ3/μ2 pair (which could account for their proximity, although not their similar appearance), while the less bright row corresponds to some other, as yet unidentified, bonding configuration (e.g., bonded through the carboxylate group alone in an upright position, as observed with formate on Cu{110}, for example61,62) or species (e.g., decomposition fragment). However, the RAIRS data show no significant evidence of species other than μ3- and μ2-bonded alaninate, which clearly argues against this possibility. Turning to the (7,4;1,2) structure, the registry shown in Figure 11b allows the positions of the features in the STM image to correspond rather naturally to sites consistent with a combination of μ3 and μ2 bonding, without Cu atom sharing. However, the (2,1;1,2)-like part of this model is inconsistent with the lowest-energy DFT structure for (2,1;1,2) alaninate. The registry shown in Figure 11c is consistent with the DFT results, but introduces Cu atom sharing by the two μ2-bonded moieties, and by one of the μ2-bonded and one of the μ3bonded moieties. Again, further work is needed to resolve this question. 5.3. Growth of the (6,4;1,2) Structure from the (2,1;1,2) Structure. Because a (2,1;1,2) unit mesh contains three surface-layer Cu atoms, three translational domains of this lattice are possible on Cu{311}. Random nucleation and growth of the SL phase should lead to equal areas of all three domains: as expected, translational domain boundaries between adjacent (2,1;1,2) domains are seen (e.g., Figure 7). As discussed above, the boundary structure is identical with the repeat unit of the (6,4;1,2) structure (even in the SL phase, the occasional boundaries thus presumably contain μ2-bonded alaninate). In principle, therefore, the (6,4;1,2) structure develops via the nucleation, growth, and stacking of a set of translational domain boundaries within the pre-existing (2,1;1,2) phase.

Figure 12. (a) Bright rows (solid white and yellow triangles) spaced as in STM images: Cu atoms shared between alaninate molecules; one bare Cu atom per mesh. (b) Bright rows spaced in locally (2,1;1,2)like arrangement: inconsistent with STM images. (c) Orientation of the shifted row (yellow triangles) reversed: our preferred model. (d) Whole lattice shifted to the right by half a lattice spacing: effectively reverses orientation of bright row(s). See the text.

substrate atom does not normally occur for molecular adsorbates on metal surfaces, and thus seems unlikely here; it would also contradict the coordination arguments set out above. Moving the yellow circles one lattice spacing to the right (e.g., Figure 12b) would return the stacking of these two rows to that of the (2,1;1,2) structure. This would eliminate the Cu atom sharing, but is clearly inconsistent with the relative positions of the two bright rows in the STM images. 18600



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SL phase occurs above 440 K. On Cu{110}, by contrast, it is phases I and II, which show no long-range order (although short-range order is apparent in STM images of phase II), that form at 300 K. Raval and co-workers indicate that the ordered phase III is only observed after annealing to 430 K, and the ordered phase IV either after further annealing to 470 K or by deposition above 430 K.24 (These observations apply to enantiopure alaninate; racemic alaninate behaves differently in some respects, the differences being greater on Cu{110} than on Cu{311}.25,35) It is clear from the temperature dependence of the phases observed on both surfaces that μ3 bonding is more stable than μ2, which is unsurprising given the higher coordination to surface-layer Cu atoms associated with μ3 bonding. This is borne out by our DFT finding that μ3 bonding is about 0.3 eV more stable than μ2 bonding for an isolated monomer. Raval and co-workers attribute the onset of μ2 bonding at high exposure and temperatures below 430 K on Cu{110} to kinetic factors, implying that there is a barrier to forming a high-coverage ordered overlayer with pure μ3 bonding.24 Any such barrier is evidently lower on Cu{311}, given that the SL phase forms readily at 300 K; likewise, any barriers to formation of the ordered high-coverage structures and reversion to the pure μ3-bonded structures are similarly lower on Cu{311} than {110}. One possible factor contributing to these differences would be any energy barriers that may need to be overcome when forming the racemic pairs of chiral μ3 footprints in the (3 × 2) structure on Cu{110}. Another relates to the 17% larger (1 × 1) unit mesh of Cu{311} compared to {110}. This suggests that at a given coverage (e.g., 0.33 ML), intermolecular H-bonds are likely to be longer and consequently weaker on Cu{311},63 implying lower barriers to any restructuring process that involves breaking these bonds. Steric interactions during any restructuring process will also tend to be smaller on Cu{311} because of the lower packing density. A chiral footprint and μ3 bonding are also features of the ordered alaninate overlayer seen on Cu{100}.17,18,21,29−32 There is ongoing debate as to the detailed structure (including the disposition of footprints), and as to whether the periodicity is (2 × 4) or c(2 × 4)both of which would be described as symmetric-lattice phases. However, the coverage in the ordered overlayer is accepted to be 0.25 ML, implying that 25% of surface-layer Cu atoms are not bonded to alaninate. This corresponds to a packing density (in molecules per unit area) that lies between the corresponding values for 0.33 and 0.375 ML on Cu{110}, and close to that for 0.4 ML on Cu{311}. The fact that no higher-coverage structures have been reported on Cu{100}, and there are no reports of μ2 bonding, can thus be understood as being due to steric constraints: 0.25 ML represents a practical maximum in the packing density. This in turn precludes the formation of any chiral-lattice phases involving μ2 bonding on Cu{100}.

This does, however, pose a mechanistic problem. Suppose a translational domain boundary nucleates and grows across a (2,1;1,2) domain. Thereafter, the (2,1;1,2) regions to either side of the boundary are no longer the same domain: one of them has been displaced by one lattice parameter from its original position. The simultaneous displacement of many adsorbates is a high-energy process; moreover, it may cause the shifted domain to impinge upon a neighboring domain. Such behavior seems physically unlikely. By contrast, a set of three boundaries growing across a (2,1;1,2) domain leaves the (2,1;1,2) regions to either side in registry with each other, i.e., the same domain. If the individual boundaries were spatially separated, their growth would still involve displacive shifts of the intervening (2,1;1,2) islands. If, however, the three boundaries grow next to each other, a region of the (6,4;1,2) structure can form, via adsorption and reconfiguration processes confined to this area, without disturbing the adjacent (2,1;1,2) regions. To illustrate the latter principle, section 5 of the Supporting Information describes in detail an example of a sequence of changes that would lead to one of the suggested models for the (6,4;1,2) structure. Such a sequence of changes seems physically plausible, and we therefore speculate that the (6,4;1,2) structure forms through a process of this type. It does, however, require significant local movement of adsorbed moieties in a confined space between immediate neighbors. Dynamic steric effects during the local restructuring process can therefore be expected to be important, and one can expect the methyl group to play a significant role. 5.4. Cu{311} Compared to Higher-Symmetry Cu Surfaces. A key point of comparison for our results for Lalaninate on Cu{311} is the known behavior of enantiopure alaninate on Cu{110}. There are evidently strong parallels between the two. The (2,1;1,2) SL phase on Cu{311} can be seen as the analogue of the (3 × 2) phase IV on Cu{110}. A μ3-bonding configuration and the scope for intermolecular hydrogen bonding to help stabilize the ordered structure are common to both, although the absence of footprint chirality on Cu{311} allows all alaninate moieties to bond identically, rather than forming racemic footprint pairs as on Cu{110}. The overlayer lattice preserves the substrate surface symmetry in both cases: both can be described as symmetric-lattice phases. Similarly, the (6,4;1,2) and (7,4;1,2) structures of the CL phase on Cu{311} can be seen as the analogues of phase III on Cu{110} (which itself shows some structural variability24). In each of these cases, μ2 bonding coexists with μ3, and the overlayer is characterized by a network of chiral boundaries, whose chirality switches with molecular chirality, leading to a chiral lattice or lattices. On Cu{311}, the onset of μ2 bonding at higher coverage can be understood in terms of alaninate coordination to surface-layer Cu atoms. Similar considerations most likely apply to the phases involving μ2 bonding Cu{110}: phase III is thought to correspond to around 0.375 ML coverage, while phase II probably corresponds to a similar local coverage within the semiordered islands.24 Where clear differences between the behavior on Cu{311} and on {110} emerge is in the temperatures needed for selforganization to emerge. On Cu{311} at 300 K, a clear (2,1;1,2) LEED pattern indicating long-range periodic order emerges at essentially the same point as the corresponding μ3 absorption bands in the RAIR spectra. Transformation into the CL phase also occurs readily at 300 K (although ordering seems to be improved by warming to around 410 K), while reversion to the

6. CONCLUSIONS We have explored the effect of substrate crystallography on the self-assembly of amino acids by comparing the development and transitions of several 2-D phases of enantiopure L-alaninate on Cu{311} with the well-established “phase diagram” of enantiopure alaninate on Cu{110}. We have determined that the SL phase forms at surface temperatures of 300 K and above. It has (2,1;1,2) periodicity, corresponding to a coverage of 0.33 ML, with no chirality in the μ3 bonding footprint. At higher coverages and temperatures between 300 and 440 K, the CL 18601



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phase involves mixed μ3 and μ2 bonding, and two distinct ordered structures. These have (6,4;1,2) and (7,4;1,2) periodicities for L-alaninate, their coexistence resolving an apparent discrepancy in our earlier work. Heating the CL phase above 440 K causes it to revert to the SL phase. DFT-based calculations of normal-mode frequencies allow us to interpret alaninate RAIR spectra from first principles. With only a few exceptions, our assignments support those made in previous studies. The various structural phases, and the occurrence of the two bonding configurations, can be rationalized in terms of packing strategies involving all available outermost-layer Cu atoms. The STM data reveal key features of the (6,4;1,2) and (7,4;1,2) structures. Establishing the surface orientation with use of LEED and the boundary orientation from the STM data allows us to outline plausible models for these structures, using boundaries within the (2,1;1,2) structure as a reference point. Ordering and reordering processes appear to be more facile for alaninate on Cu{311} than on Cu{110}. Both steric factors and the removal of the necessity for μ3-bonded alaninate to adopt a chiral bonding footprint are likely to underlie this observation. These results give new insight into the influence that substrate crystallography has in controlling not only the bonding configurations of the adsorbed molecules, but also the evolution of long-range ordered networks and surface chirality.

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(6) Zhang, T.; Liu, Z.-P.; Driver, S. M.; Pratt, S. J.; Jenkins, S. J.; King, D. A. Stabilizing CO on Au with NO2: electronegative species as promoters on coinage metals? Phys. Rev. Lett. 2005, 95, 266102-1−4. (7) Zhang, T.; King, D. A.; Driver, S. M. Structural phases formed by NO2/CO co-adsorption on Au{111} surfaces. J. Chem. Phys. 2012, 137, 074703-1−5. (8) Gladys, M. J.; Stevens, A. V.; Scott, N. R.; Jones, G.; Batchelor, D.; Held, G. Enantiospecific adsorption of alanine on the chiral Cu{531} surface. J. Phys. Chem. C 2007, 111, 8331−8336. (9) Thomsen, L.; Wharmby, M. T.; Riley, D. P.; Held, G.; Gladys, M. J. The adsorption and stability of sulphur containing amino acids on Cu{531}. Surf. Sci. 2009, 603, 1253−1261. (10) Eralp, T.; Shavorskiy, A.; Zheleva, Z. V.; Dhanak, V. R.; Held, G. Hydrogen bond-induced pair formation of glycine on the chiral Cu{531} surface. Langmuir 2010, 26, 10918−10923. (11) Clegg, M. L.; Morales de la Garza, L.; Karakatsani, S.; King, D. A.; Driver, S. M. Chirality in amino acid overlayers on Cu surfaces. Top. Catal. 2011, 54, 1429−1444. (12) Barlow, S. M.; Kitching, K. J.; Haq, S.; Richardson, N. V. A study of glycine adsorption on a Cu{110} surface using reflection absorption infrared spectroscopy. Surf. Sci. 1998, 401, 322−335. (13) Hasselström, J.; Karis, O.; Weinelt, M.; Wassdahl, N.; Nilsson, A.; Nyberg, M.; Pettersson, L. G. M.; Samant, L. G.; Stöhr, J. The adsorption structure of glycine adsored on Cu(110); comparison with formate and acetate/Cu(110). Surf. Sci. 1998, 407, 221−236. (14) Booth, N. A.; Woodruff, D. P.; Schaff, O.; Gießel, T.; Lindsay, R.; Baumgärtel, P.; Bradshaw, A. M. Determination of the local structure of glycine adsorbed on Cu(110). Surf. Sci. 1998, 397, 258− 269. (15) Nyberg, M.; Hasselström, J.; Karis, O.; Wassdahl, N.; Weinelt, M.; Nilsson, A.; Pettersson, L. G. M. The electronic structure and surface chemistry of glycine adsorbed on Cu(110). J. Chem. Phys. 2000, 112, 5420−5427. (16) Chen, Q.; Frankel, D. J.; Richardson, N. V. Chemisorption induced chirality: glycine on Cu{110}. Surf. Sci. 2002, 497, 37−46. (17) Toomes, R. L.; Kang, J.-H.; Woodruff, D. P.; Polcik, M.; Kittel, M.; Hoeft, J.-T. Can glycine form homochiral structural domains on low-index copper surfaces? Surf. Sci. 2003, 522, L9−L14. (18) Kang, J.-H.; Toomes, R. L.; Polcik, M.; Kittel, M.; Hoeft, J.-T.; Efstathiou, V.; Woodruff, D. P.; Bradshaw, A. M. Structural investigation of glycine on Cu(100) and comparison to glycine on Cu(110). J. Chem. Phys. 2003, 118, 6059−6071. (19) Nyberg, M.; Odelius, M.; Nilsson, A.; Pettersson, L. G. M. Hydrogen bonding between adsorbed deprotonated glycine molecules on Cu(110). J. Chem. Phys. 2003, 119, 12577−12585. (20) Rankin, R. B.; Sholl, D. S. Assessment of heterochiral and homochiral glycine adlayers on Cu(110) using density functional theory. Surf. Sci. 2004, 548, 301−308. (21) Rankin, R. B.; Sholl, D. S. Structures of glycine, enantiopure alanine, and racemic alanine adlayers on Cu(110) and Cu(100) surfaces. J. Phys. Chem. B 2005, 109, 16764−16773. (22) Williams, J.; Haq, S.; Raval, R. The bonding and orientation of the amino acid L-alanine on Cu{110} determined by RAIRS. Surf. Sci. 1996, 368, 303−309. (23) Barlow, S. M.; Louafi, S.; Le Roux, D.; Williams, J.; Muryn, C.; Haq, S.; Raval, R. Supramolecular assembly of strongly chemisorbed size- and shape-defined chiral clusters: S- and R-alanine on Cu(110). Langmuir 2004, 20, 7171−7176. (24) Barlow, S. M.; Louafi, S.; Le Roux, D.; Williams, J.; Muryn, C.; Haq, S.; Raval, R. Polymorphism in supramolecular chiral structures of R- and S-alanine on Cu(110). Surf. Sci. 2005, 590, 243−263. (25) Haq, S.; Massey, A.; Moslemzadeh, N.; Robin, A.; Barlow, S. M.; Raval, R. Racemic versus enantiopure alanine on Cu(110): an experimental study. Langmuir 2007, 23, 10694−10700. (26) Rankin, R. B.; Sholl, D. S. Structure of enantiopure and racemic alanine adlayers on Cu(110). Surf. Sci. 2005, 574, L1−L8. (27) Sayago, D. I.; Polcik, M.; Nisbet, G.; Lamont, C. L. A.; Woodruff, D. P. Local structure determination of a chiral adsorbate: alanine on Cu(110). Surf. Sci. 2005, 590, 76−87.

ASSOCIATED CONTENT

S Supporting Information *

Schematic showing vibrational modes of alaninate; all structural models considered in DFT calculations for the (2,1;1,2) structure and for isolated μ3- and μ2-bonded monomers; RAIR spectrum showing multilayer alanine adsorption at low temperature; details of quantitative LEED analysis of clean Cu{311}; description of a possible mechanism of the (2,1;1,2) → (6,4;1,2) structural transition. This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Present Address †

Departamento de Fisica de Materiales UPV/EHU and Donostia International Physics Center, Paseo Manuel de Lardizabal, 4, 20018 Donostia-San Sebastian, Spain.

Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We acknowledge financial support from the Engineering and Physical Sciences Research Council. REFERENCES

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Self-Organized Overlayers Formed by Alanine on Cu{311} Surfaces

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