Structures of Glycine, Enantiopure Alanine, and Racemic Alanine

We have determined the structures of dense adlayers of glycine and alanine on the Cu(110) and Cu(100) surfaces using plane wave density functional the...
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16764

J. Phys. Chem. B 2005, 109, 16764-16773

Structures of Glycine, Enantiopure Alanine, and Racemic Alanine Adlayers on Cu(110) and Cu(100) Surfaces Rees B. Rankin and David S. Sholl* Department of Chemical Engineering, Carnegie Mellon UniVersity, Pittsburgh, PennsylVania 15213 ReceiVed: June 30, 2005

We have determined the structures of dense adlayers of glycine and alanine on the Cu(110) and Cu(100) surfaces using plane wave density functional theory. These calculations resolve several experimental controversies regarding these structures. Glycine exists on Cu(110) as a single adlayer structure, while on Cu(100) two distinct glycine adlayers coexist. The glycine structures serve as useful starting points for constructing alanine adlayer structures. We considered separately the adsorption of enantiopure alanine and racemic alanine on each surface. Adlayers of enantiopure alanine are found to be closely related to the adlayers observed for glycine. Racemic alanine adlayers on Cu(110) are structurally analogous to those observed for glycine on this surface and adopt a pseudo-racemate ordering. On Cu(100), in contrast to glycine, racemic alanine is found to adopt a single adlayer structure that is an ordered racemate. Spontaneous segregation of molecular enantiomers does not occur in racemic adsorbed mixtures on either surface. Consideration of the orientationally distinct domains that may exist for each adlayer on these surfaces provides important information for the interpretation of the adlayer domain boundaries that are commonly observed in scanning tunneling microscopy images of amino acid adlayers. Examining this set of amino acid adlayers provides useful insight into the range of subtle behaviors that can arise in these and related systems where chiral molecules form ordered adlayers on flat metal surfaces.

1. Introduction Solid surfaces that exhibit net chirality have many potential applications in chirally specific chemical processing.1 A variety of physical means can be used to create chiral solid surfaces. Surfaces of materials whose bulk crystal structure is enantiomorphic (e.g., quartz and calcite) are frequently chiral.2 Surfaces of highly symmetric materials that are aligned away from low Miller index planes are also typically chiral.3-7 An alternative route to the creation of chirality in a surface is to adsorb chiral organic species onto otherwise achiral surfaces. The small number of effective chiral heterogeneous catalysts fall into this class by modifying supported metal catalysts with adsorbed chiral species.8-10 Examining the adsorption of amino acids on flat metal surfaces offers an excellent means to explore the possible phenomena that can arise when chiral molecules form surface adlayers on achiral substrates. A large number of experiments have probed the formation of amino acid adlayers on flat Cu surfaces11-19 and other surfaces.18,20-35 In many (although not all) cases, highly structured adlayers exist. Scanning tunneling microscopy (STM) experiments frequently reveal the existence of multiple domains within these ordered adlayers.11-13,15-17,19,36,37 Examples have been reported where the presence of adsorbed amino acids induces faceting of the underlying surface into high Miller index facets that have chiral characteristics.16,17 A natural objective in studying ordered amino acid adlayers on flat surfaces is to describe the detailed atomic structure of the adlayers. This objective has proven to be challenging to achieve. The adlayers formed by glycine on Cu(110)11-14 provide a good example of this situation. Glycine is a prochiral * Corresponding author. E-mail: [email protected].

molecule that becomes locally chiral upon adsorption onto a surface.11-14,38 Initial experimental studies of dense glycine adlayers on Cu(110) suggested that two distinct adlayers with (3 × 2) periodicity coexisted on the surface, giving rise to the distinct domains seen with STM.12 Subsequent photoelectron diffraction (PhD) experiments suggested an alternative interpretation in which only one adlayer structure is present on the surface.14 Density functional theory (DFT) calculations examining both structures suggested experimentally established that a single adlayer structure does indeed predominate on Cu(110) and that the domain boundaries observed with STM arise from distinct domains that are structurally equivalent but have distinct orientations with respect to the surface.38 We have also recently used DFT to determine the structure of dense alanine adlayers on Cu(110).39 Several low coverage and metastable alanine structures have been observed on Cu(110) experimentally, but the stable high coverage adlayer has the same (3 × 2) periodicity as glycine.19,39,40 Because alanine is a chiral species, unlike glycine, the adsorption of enantiopure and racemic alanine can be considered separately. Experimental studies have focused primarily on enantiopure adlayers.19,41 The structure formed by racemic alanine on Cu(110) is very closely related to the dense glycine adlayer on the same surface, as might be expected from the geometric similarity of the two molecules.39 There is no driving force for molecular enantiomers of alanine to either segregate or order on Cu(110), so dense adlayers of alanine on this surface form a pseudo-racemate in which the local geometry of each molecule is similar to the adsorption of glycine.39 A variety of experiments have been used to study the adsorption of glycine and alanine on Cu(100),15-17,42,43 and like Cu(110), highly ordered adlayers are observed. As with Cu-

10.1021/jp0535700 CCC: $30.25 © 2005 American Chemical Society Published on Web 08/12/2005

Structures of Glycine and Alanine Adlayers

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TABLE 1: Projected distances between N and O atoms in adsorbed glycine and alanine molecules and surface Cu atoms on Cu(110) and Cu(100), with all distances in angstroms (the available experimental data for glycine on each surface is listed) system experiment14 heterochiral homochiral racemic enantiopure system experiment37 pseudo-heterochiral homochiral racemic pseudo-heterochiral enantiopure pseudo-heterochiral racemic homochiral enantiopure homochiral

N-Cu offset in 〈1h10〉 Glycine/Cu(110) 0.24 ( 0.10 0.20 0.17, 0.20 Alanine/Cu(110) 0.11, 0.11 0.14, 0.20 N-Cu offset in 〈010〉 Glycine/Cu(100) N/A 0.23 0.17 Alanine/Cu(100) 0.25 0.24 0.18 0.17

(110), a variety of different structures have been proposed on the basis of experimental data.15-17,42,43 Morikawa and Mae have recently used DFT to determine the structure of glycine on Cu(100).44 Unlike glycine on Cu(110), two distinct adlayers were found to coexist on Cu(100), one of which has local chirality but one which does not. In this paper, we present DFT calculations that determine the surface structure of glycine, enantiopure alanine, and racemic alanine adsorbed as dense, ordered adlayers on Cu(110) and Cu(100). Examining these adlayers together is a useful means to explore the commonalities between them and to illustrate the range of subtle features that can arise in these chiral adlayers. It also suggests useful ways to predict related structures of other amino acid adlayers. For example, we have investigated whether parallels can be drawn between the structures that are observed on these flat metal surfaces and the crystal faces that are expressed in bulk crystals of amino acids. 2. Methodology All results in our calculations were obtained using plane wave density functional theory (DFT) as implemented in the Vienna Ab Initio Simulation Package (VASP).45-47 The calculations presented employed the ultrasoft pseudopotentials available in VASP and the PW-91 functional48-50 within the generalized gradient approximation. A cutoff energy of 29.2 Ry was used in truncation of the plane wave expansion for all calculations. Total energy calculations utilized the residual minimization method for electronic relaxation, with a Methfessel Paxton Fermi-level smearing51 width of 0.2 eV. Geometric relaxations were performed using the conjugate gradient algorithm until the forces on each unconstrained atom where less than 0.03 eV/Å. All calculations for Cu(110) used seven metal layers with the bottom three layers constrained in their bulk positions. For Cu(100), we used three metal layers and constrained only the bottom layer. The DFT-optimized lattice parameter for Cu was used in all calculations. Unless otherwise stated, the calculations used a 4 × 4 × 1 (5 × 5 × 1) k-point mesh for alanine (glycine) on the metal surfaces. All calculations used a vacuum spacing of 12 (9.5) Å along the surface normal for calculations involving Cu(110) (Cu(100)). Dipole corrections were applied to remove the small artificial energy contributions in our asymmetric slabs.38,39,52,53 Experiments show unambiguously that glycine and alanine are adsorbed on the Cu(110) and Cu(100) surfaces in a deprotonated form.11,12,36,37,40,54 As a result, all of our calcula-

O-Cu offset in 〈001〉 0.68 ( 0.09, 0.97 ( 0.08 0.70, 0.98 0.76, 0.87, 0.23, 1.10 1.04, 0.63, 1.03, 0.58 0.99, 0.70, 1.09, 0.45 O-Cu offset in 〈100〉 0.32 ( 0.07 (dir. unknown) 0.34, 0.36, 0.33, 0.34 0.34, 0.27 0.36, 0.31, 0.32, 0.34 0.33, 0.28, 0.36, 0.26 0.33, 0.29, 0.34, 0.26 0.33, 0.28, 0.33, 0.27

tions have represented these molecules on the surface in this deprotonated form, namely, glycinate (NH2CH2CO2) and alaninate (NH2C(CH3)HCO2). For convenience, we will refer to adlayers of these deprotonated amino acids simple as glycine and alanine. Prior to examination of the amino acid adlayers on the surface, we performed gas phase structural optimizations of these molecules in supercells of corresponding size. The results for glycine showed good agreement with previously published theoretical structure information.55 3. Results and Discussion 3.a. Glycine/Cu(110). Experimental characterizations of glycine on Cu(110) initially led to conflicting interpretations on the nature of the molecular adlayers formed upon adsorption. Low energy electron diffraction (LEED) experiments revealed an adlayer with (3 × 2) periodicity.12 STM images indicated this adlayer had two molecules within each unit cell and were interpreted as showing the coexistence of two distinct adlayers.12 One proposed structure had glide plane symmetry and as a result was termed heterochiral. The other proposed structure was denoted homochiral as a result of the lack of glide plane symmetry. Subsequent PhD experiments suggested, however, that only one type of adlayer existed.11,12,14 Our DFT calculations38 were performed to gain further understanding of the energetic and geometric properties of the adlayers proposed to occur for the adsorption of glycine on Cu(110). Initial calculations examined candidate glycine monomers within (3 × 2) surface cells. This situation can be thought of as the adsorption of isolated molecules on the surface. All initial monomer configurations we examined converged to the same final configuration, a tridentate configuration in which the amine group and the two O atoms in the molecule sit on top of separate Cu atoms.38 From this stable configuration, a number of candidate structures for the dense heterochiral and homochiral adlayers were examined. The results support the idea that only the heterochiral adlayer is present on the surface in large areas under practical experimental conditions. This conclusion stems from two observations. First, the projected O-Cu distances from the final heterochiral adlayer structure are in quantitative agreement with PhD measurements, while the analogous distances from the homochiral layer contradict with the PhD data. The experimental and DFT-derived values for these projected distances are listed in Table 1. Second, the heterochiral adlayer is predicted by DFT to be energetically more favorable than the homochiral adlayer at a level where >80% of the

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Figure 1. (a) DFT-optimized structure of the dense heterochiral adlayer of glycine/Cu(110). The white lines indicate a (3 × 2) surface cell with the corners of the cell on top of Cu atoms in the surface. (b) An illustration of one of many possible domain boundaries between domains of glycine heterochiral adlayers on Cu(110).

surface would be covered by the former under the annealing temperatures used experimentally. The DFT calculated energy difference between the heterochiral and homochiral adlayers is 6.3 kJ/mol/unit cell. Although we feel that this calculated energy difference is reliable, assessing the reliability of DFT-computed energy differences this small is difficult. We show below that most of the energy differences used in determining the most stable adlayer for the other amino acid structures we consider are larger than this one. The structure of the heterochiral glycine adlayer on Cu(110) is illustrated in Figure 1a. It is important to note that our DFT does not contradict with the basic observation from STM images that distinct glycine adlayers can coexist on Cu(110). The adlayer shown in Figure 1a has each molecule oriented with the NH2 group on the left and the COO group on the right. As can be seen by viewing Figure 1a upside down, there is a completely equivalent structure in which this direction is reversed. It is natural to expect that, during the initial stages of molecular organization on the surface, separated domains with both possible orientations will form with equal probability. In the final dense adlayer, distinct domain boundaries will form between these regions that have identical local structures but different orientations of the molecules in the adlayer. An example of one of the many possible domain boundaries of this type is shown in Figure 1b. This description implies that the surface area covered by each possible orientation should be approximately equal, and this is indeed what is observed in STM experiments that identified two domains on this surface.12 3.b. Glycine/Cu(100). As with glycine on Cu(110), the adsorption characteristics of glycine on the Cu(100) surface have also been characterized experimentally and theoretically.15,37 As was the case for Cu(110), interpreting the available experimental data for glycine on Cu(110) in a consistent manner was initially difficult. STM experiments revealed distinct domains with (2 × 4) and c(2 × 4) periodicity on the surface.16 However, PhD measurements37 suggested that just one domain existed on the surface. Morikawa and Mae44 examined glycine on Cu(100) using DFT and found that two distinct adlayer structures have very similar energies and thus should be expected to coexist on the surface. Around the time Mae and Morikawa’s DFT calculations appeared, we performed independent calculations for a similar set of adlayers. Our results are entirely consistent with those reported by Mae and Morikawa.44 We report our results below to demonstrate this consistency and, more importantly, to address the agreement between DFT-optimized

structures of the data available from PhD experiments, an issue not addressed by Mae and Morikawa. We have based our naming of the adlayers on the nomenclature introduced by Efstathiou and Woodruff.37 We examined all four dense adlayer structures proposed by Efstathiou and Woodruff:37 the c(4 × 2) homochiral adlayer, the (2 × 2) pseudo-heterochiral adlayer, the (4 × 2)-pg heterochiral adlayer, and the (2 × 2) homochiral adlayer. The latter structure was not examined by Mae and Morikawa. The (2 × 2) pseudo-heterochiral adlayer can also be denoted as a (4 × 2)pg heterochiral structure, but the former notation is more convenient. The description of these adlayers as homochiral or heterochiral is made by analogy with the binding footprints of the glycine adlayers on Cu(110) discussed above. The prefix “pseudo” is used when the spatial organization of the molecules in the adlayer differs from that of the related structure of glycine on Cu(110). In agreement with the calculations of Mae and Morikawa, the c(4 × 2) homochiral structure and the (2 × 2) pseudo-heterochiral adlayer are energetically favored over the (4 × 2)-pg heterochiral adlayer. We found the two stable adlayers to be favored relative to the (4 × 2)-pg heterochiral adlayer by more than 50 kJ/mol/unit cell using the (4 × 2) unit cell. These two adlayers are more stable than the (2 × 2) homochiral adlayer by more than 18 kJ/mol. It is interesting to note that these energy differences are considerably larger than those observed between the two adlayers examined for glycine/ Cu(110). The energy difference between the two favored structures is very small; in our calculations, we found an energy difference of only 1.5 kJ/mol/unit cell on the basis of a (4 × 2) unit cell. These two structures are shown in Figure 2. In both structures, the adsorbed molecules adopt a tridentate bonding configuration in which the N and O atoms are on top of Cu atoms in the surface. A comparison between the projected O-Cu distances in our DFT-optimized structures and the results obtained experimentally with PhD is made in Table 1. Within the resolution of the experimental data, only one distinct projected O-Cu distance is observed. Crucially, all of the projected O-Cu distances for both energetically preferred adlayers are consistent with the experimental measurement. That is, the single projected distance observed in this experiment is entirely consistent with the coexistence of two distinct glycine adlayers on Cu(100). One distinction between glycine adlayers on Cu(110) and Cu(100) is the number of orientations each domain can take on each surface. As discussed above, if glycine is thought of as

Structures of Glycine and Alanine Adlayers

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Figure 2. DFT-optimized structure of the (a) c(4 × 2) homochiral adlayer and (b) the (2 × 2) pseudo-heterochiral adlayer of glycine/Cu(100). The white lines indicate a (4 × 2) unit cell in both parts a and b. A (x2 × x2)R45° unit cell is also shown in part a. (c) A schematic illustration of coexisting glycine domains, each with multiple possible orientations, on a Cu(100) surface. The white (grey) domains indicate the pseudo-heterochiral (homochiral) adlayers, and the black arrows indicate the orientation of molecules within the domain.

being oriented from the NH2 group toward the COO group, two orientationally distinct versions of the heterochiral glycine adlayer on Cu(110) exist. This gives rise to domain boundaries such as those illustrated in Figure 1b. On Cu(100), similar reasoning shows that each possible adlayer has four orientationally distinct structures. This observation implies that, on large length scales, many domain boundaries between the possible orientations of the two coexisting glycine adlayers on Cu(100) should be expected. A schematic illustration of this effect is shown in Figure 2c. 3.c. Alanine/Cu(110). Glycine is not a chiral molecule, although it can become chiral upon adsorption on a surface.11,12,16 The inherent molecular chirality of alanine makes it an interesting candidate for understanding the range of chiral phenomena available in the adsorption of amino acids on welldefined surfaces. There has been some work done to qualitatively describe the nature of adsorbed L-, di-L-, and tri-L-alanine structures on Cu(110).19,41,56-58 It is known, for example, that L-alanine adsorbs on Cu(110) in a deprotonated form and that the most stable dense adlayer has a (3 × 2) periodicity.19,40,41,57 These experiments have not, however, allowed the construction of quantitative models for the adlayer structure of these systems.

We have tackled this issue using DFT calculations. Our DFT calculations for the adsorption of alanine on Cu(110) have been reported in detail elsewhere39 and are summarized here for completeness. We have used DFT calculations to explore two complementary situations related to the adsorption of alanine on Cu(110). First, we consider the adsorption of enantiopure alanine. This is the situation that has been explored in previous experiments.19,41,57 Second, we consider the adsorption of racemic alanine. In discussions of bulk chiral crystallization and in work on the deposition of racemic mixtures on surfaces,42,59-63 two possibilities are typically considered: the segregation of enantiomers into separate domains and the formation of ordered racemic structures. A number of direct experimental observations of chiral domain segregation have been made,42,59-63 and STM images of racemic mixtures of alanine on Cu(100)42 have been interpreted in this way. Many examples are known of bulk crystallization where ordered racemic crystals coexist or are thermodynamically preferred over enantiopure crystals.64,65 This is the case for bulk alanine in its zwitterionic form.43 Our DFT calculations with both isolated adsorbed alanine molecules and dense alanine adlayers showed that the geometry

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Figure 3. (a) DFT-optimized structure of the energetically favored enantiopure adlayer of alanine/Cu(110). The white lines indicate a (3 × 2) surface cell with the corners of the cell on top of Cu atoms in the surface. (b) The same as part a but for the energetically favored racemate adlayer.

of alanine molecules on Cu(110) is very similar to that for glycine on the same surface. As a result, the structure of alanine adlayers can be described in terms of the footprint of the atoms bound to the surface using the same terminology as for glycine. The geometry of isolated alanine molecules on Cu(110) predicted by DFT is in good agreement with the quantitative data that are available from experimental sources.14,57 We first consider the adsorption of enantiopure alanine on Cu(110). The most energetically stable structure was found to have the same “heterochiral” structure with respect to the atoms bonded to the surface. The overall adlayer lacks glide plane symmetry and has a net chirality because the methyl groups on the two molecules within each (3 × 2) surface unit cell are distinct. This structure is illustrated in Figure 3a. The DFT energy difference between the favored structure for enantiopure alanine and the structure based on the “homochiral” footprint previously discussed for glycine is 10.5 kJ/mol/unit cell. This energy difference is larger than the analogous energy difference for the two possible glycine adlayers on Cu(110). To predict the structures formed by the deposition of racemic alanine on Cu(110), it is necessary to compare the energies of enantiopure adlayers that could form following the segregation of enantiomers to adlayers in which the molecular enantiomers are mixed. We examined the structures of racemate adlayers with (3 × 2) periodicity. A racemate structure is one in which each repeat unit contains an ordered array of D and L molecules in equal proportion.64 In this case, each (3 × 2) unit cell contains one D-alanine molecule and one L-alanine molecule. As with the enantiopure adlayers, racemate alanine adlayers can be usefully characterized in terms of their footprint on the surface in the same notation as that used for glycine adlayers. We found that the racemate adlayer with the same bonding footprint as the glycine heterochiral adlayer is energetically preferred over the racemate adlayer based on the glycine homochiral adlayer by 26.3 kJ/mol/unit cell. This energy difference is considerably larger than the energy differences observed for either glycine or enantiopure alanine on this surface. As for glycine, this energetically preferred racemate alanine structure satisfies glide plane symmetry. Perhaps the most interesting feature of the enantiopure and racemate adlayers described above is that they have essentially the same energy.39 The implication of this observation is that the deposition of a racemic mixture of alanine on Cu(110) will not lead to either the segregation of enantiomers or to the

formation of a racemate adlayer. Instead, the preferred structure for racemic alanine on Cu(110) is a pseudo-racemate structure in which all of the adsorbed molecules have the same bonding footprint as glycine in its favored adlayer on this surface but the molecular chirality within the adlayer is random on all length scales. Pseudo-racemates are also known for some bulk crystals.64 As with glycine/Cu(110), two distinct orientations of the preferred adlayer exist with identical energies, so domains similar to those illustrated in Figure 1a should be expected when either enantiopure or racemic alanine is adsorbed on Cu(110). The positions of the N and O atoms in the enantiopure and racemate adlayers relative to the Cu atoms in the surface are summarized in Table 1. While there are subtle differences between the enantiopure and racemate adlayers, it appears to be extremely unlikely that PhD experiments could distinguish between the enantiopure adlayer and the pseudo-racemate layer if experiments performed following enantiopure and racemic deposition were compared. These experiments, however, could potentially detect the differences in projected O-Cu distances that exist between glycine adlayers and enantiopure alanine adlayers on Cu(110). 3.d. Alanine/Cu(100). A number of experiments have examined the adsorption of racemic or enantiopure alanine on Cu(100).15,42 The application of STM and LEED to enantiopure alanine on Cu(100) has indicated the presence of c(4 × 2) analogous to those observed for glycine on the same surface.15 STM images of racemic alanine deposited on Cu(100) have shown the existence of distinct domains on the surface, an observation interpreted as arising from spontaneous segregation of enantiomers into enantiopure surface domains.42 We have shown above that the existence of multiple surface domains is a ubiquitous feature of ordered amino acid adlayers, so the observation of domain boundaries with STM in this example is at best circumstantial evidence for chiral segregation. We have performed DFT calculations to examine possible adlayers of alanine on Cu(100) following methods very similar to those described above. Our study of glycine and alanine on Cu(110) indicated that the bonding footprint of alanine is extremely similar to that of glycine. We therefore constructed candidate adlayer structures for alanine on Cu(100) using all four of the glycine adlayers we examined above on the same surface. In each case, we separately examined adlayers of enantiopure alanine and racemate adlayers in which each (4 × 2) unit cell contained one D-alanine molecule and one L-alanine

Structures of Glycine and Alanine Adlayers

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Figure 4. DFT-optimized structure of (a) the (2 × 2) pseudo-heterochiral adlayer of enantiopure alanine/Cu(100), (b) the c(4 × 2) homochiral adlayer of enantiopure alanine/Cu(100), (c) the c(4 × 2) homochiral adlayer of racemic alanine/Cu(100), and (d) the (2 × 2) pseudo-heterochiral adlayer of racemic alanine/Cu(100). In each frame, the white lines indicate a (4 × 2) surface cell with the corners of the cell on top of Cu atoms in the surface. A (x2 × x2)R45° unit cell is also shown in part b. (e) Illustration of the possible domain boundary orientation and adlayer character of racemic alanine on Cu(100). The arrows within each domain indicate the orientation of the adsorbed molecules.

molecule. For each structure, we performed a series of calculations to explore the possible orientation of the methyl group that differentiates alanine from glycine. As might be expected from inspection of Figure 2, only structures where the methyl group of alanine was oriented roughly away from the surface were found to be feasible. We first consider the structure of enantiopure alanine on Cu(100). It is useful to recall that when the adsorption of enantiopure alanine on Cu(110) was compared to glycine on Cu(100), each molecule was found to adopt the same adlayer structure. This observation also applies to the comparison of enantiopure alanine on Cu(100) and glycine on Cu(100). Our

calculations show that the c(4 × 2) homochiral adlayer and the (2 × 2) pseudo-heterochiral adlayer differ in energy by only 1.8 kJ/mol/unit cell, with the c(4 × 2) homochiral adlayer being the more stable of the two. The other two adlayers we examined are considerably less favorable, differing by more than 12 kJ/ mol/unit cell from the c(4 × 2) homochiral adlayer. The two favored adlayers are shown in Figure 4a,b. It is important to note that the designation of one of these adlayers as heterochiral stems from the similarity of the bonding footprint to the heterochiral glycine adlayer on Cu(110); every molecule in this adlayer has the same molecular chirality. Similar to glycine on Cu(100), the two favorable adlayers of enantiopure alanine on

16770 J. Phys. Chem. B, Vol. 109, No. 35, 2005 Cu(100) have essentially the same energies. Thus, our DFT calculations predict that enantiopure alanine will form two coexisting adlayers on Cu(100), with the same bonding footprints as glycine on the same surface. Racemate adlayers of alanine on Cu(100) were examined in a similar manner. The same two bonding footprints, namely, the c(4 × 2) homochiral adlayer and the (2 × 2) pseudoheterochiral adlayer, emerged as being energetically favorable as for glycine and enantiopure alanine. These two adlayers are shown in Figure 4c,d. The energies of these adlayers reveal some interesting differences between the adsorption of racemic alanine on Cu(100) and on Cu(110). In the latter case, we found that the enantiopure and racemate adlayers had essentially equal energies, leading to the prediction that the deposition of racemic alanine on Cu(110) will lead to the formation of pseudoracemate adlayers. This observation also appears to apply to alanine on Cu(100) if one considers only the racemate c(4 × 2) homochiral adlayer. We find that this adlayer was essentially the same as the enantiopure (2 × 2) pseudo-heterochiral adlayer on this surface. Surprisingly, however, this is not the case for the racemate (2 × 2) pseudo-heterochiral adlayer. Our calculations show that this adlayer is 5.6 kJ/mol/unit cell more stable than the most stable enantiopure adlayer and the racemate c(4 × 2) homochiral adlayer. That is, our DFT calculations predict that the deposition of racemic alanine on Cu(100) has a single adlayer structure that is energetically favored. The energy difference between this adlayer and the other possible adlayers is not large, but it is comparable to the energy difference we interpreted above as giving rise to a single adlayer structure over other possible structures in glycine/Cu(110).38 We can now address the possibility raised by experiment42 that racemic alanine will spontaneously segregate into enantiopure domains. Our DFT results make a strong case that this segregation will not occur, as they predict that a racemate adlayer characterized as a (2 × 2) pseudo-heterochiral adlayer will be the energetically preferred structure. This adlayer has four possible orientations on Cu(100) for the same reasons that the glycine adlayers discussed above have four possible orientations. Thus, even though the local structure of the adlayer is identical everywhere on the surface, an STM image showing a large region of the surface will exhibit multiple domains with distinct domain boundaries. A schematic illustration of a set of domains of this type is shown in Figure 4e. The similarity between the bonding footprints of glycine and alanine on Cu(100) can be reinforced by examining the positions of the N and C atoms in the favored adlayers of each molecule. Information on these positions is summarized in Table 1. These results show that, within the resolution available in PhD experiments, the atoms that bond glycine and alanine to Cu(100) have essentially the same positions with respect to the surface atoms. This observation strongly suggests that these tridentate bonding configurations will also govern the adsorption of other amino acids for which the terminal group does not favor bonding with the surface and can be oriented away from the surface without severe steric hindrance between adjacent molecules. This category of amino acids includes valine and leucine but would exclude, for example, cysteine. 3.e. Bulk Alanine Crystal Structures. It is interesting to explore whether the structural motifs observed for the surface adlayers described above are related to the surfaces expressed in bulk crystals of amino acids. If relationships of this type can be established, they could prove useful in the analysis of other amino acid adlayers. We focus here on a comparison between L-alanine and DL-alanine crystals and alanine adlayers on Cu(110) and Cu(100). Crystals of L-alanine have space group

Rankin and Sholl TABLE 2: Surface packing densities of alanine adlayers on Cu surfaces and on selected surfaces of the bulk DL-alanine crystal surface

packing density (Å2/molecule)

alanine/Cu(110) alanine/Cu(100) DL-alanine(100) DL-alanine(010) DL-alanine(110) DL-alanine(101) DL-alanine(111)

26.21 29.26 35.19 35.09 24.85 24.88 24.88

P212121 with cell parameters 6.032, 12.343, and 5.784 Å.66,67 The crystal is known to express (011) and (120) faces.66,67 Similarly, racemate crystals of DL-alanine crystals have space group Pna21 with cell parameters of 12.026, 6.032, and 5.829 Å and are known to expose the (210) face.43,68 Aside from the inevitable internal symmetry differences between L-alanine and DL-alanine crystals, the two structures have very similar packings. As a result, we focus below solely on the surfaces of DLalanine crystals, noting that the (hkl) surfaces of DL-alanine are very similar to the (khl) surfaces of L-alanine. Using the bulk DL-alanine crystal structure, we examined the (100), (010), (001), (110), (101), (011), (111), and (210) surfaces of DL-alanine. These surfaces were chosen either because they are expressed experimentally66,68 or simply because they are the lowest Miller index surfaces of this crystal. Since our aim is to explore possible connections between the bulk crystals and the surface adlayers rather than to rigorously describe the true surface structures of the bulk crystals, we considered surfaces of DL-alanine simply by terminating the bulk structure. For surfaces that exhibit multiple surface terminations as the termination plane is moved with respect to the surface normal, all possible terminations that included planar termination of the surface and included only entire molecules were considered. Several of the surfaces listed above were immediately removed from further consideration because they bore no relationship to the planar structures observed on Cu(110) and Cu(100). Ideally terminated DL-alanine(210), for example, is a stepped surface. The (001) and (011) surfaces both have molecules oriented roughly along the surface normals rather than in the plane of the surface. An initial comparison between the bulk crystal surfaces and the Cu adlayers can be made using the molecular packing density for each structure. The packing density of each surface we considered is listed in Table 2. The DL-alanine(111), (101), and (110) surfaces have packing densities that are similar to those for alanine/Cu(110). None of the faces of DL-alanine that we examined have packing densities particularly similar to those of alanine/Cu(100). We also examined several quantities besides packing density that characterize molecular geometries within the surface layers. These include the angle of the C-C backbone of the amino acid relative to the surface normal with the bond defined as being oriented from the carboxylate end to the amino end of the molecule, ΘCC, the average orientational angles of methyl groups relative to the surface normal, ΘCH3, and the angle between the carboxylate plane and the surface normal, ΘCOO. The flatness of the surfaces was characterized using the deviation of the individual molecular centers of mass from the layer averaged center of mass, δcm, and the height differences between N and O atoms on neighboring molecules projected onto the surface normal, δN-01 and δN-02. The values of each of these quantities for the surfaces of interest are listed in Table 3. A careful analysis of Table 3 shows that none of the surfaces of bulk DL-alanine are particularly similar to the adlayers

Structures of Glycine and Alanine Adlayers

J. Phys. Chem. B, Vol. 109, No. 35, 2005 16771

TABLE 3: Structural parameters for racemic alanine on Cu(110) and Cu(100) and surfaces of bulk

DL-alaninea

surface

layer

ΘCC

ΘCH3

ΘCOO

δcm

δN-01

δN-02

alanine/Cu(110) alanine/Cu(100) DL-alanine(100) DL-alanine(110) DL-alanine(010) DL-alanine(010) DL-alanine(101) DL-alanine(101) DL-alanine(111) DL-alanine(111) DL-alanine(111)

all all all all layer 1 layer 2 layer 1 layer 2 layer 1 layer 2 layer 3

58.3 67.5 81.3 110.9 110.7 69.3 56.9 40.6 88.7, 90.5, 107.0 68.2, 88.7, 106.6 90.0, 88.7, 84.8

26.2 0.9 81.5 110.4 36.5 143.5 121.9 74.1 150.1, 29.9, 98.5 81.5, 150.1, 98.5 95.2, 150.1, 73.0

122.8 113.3 55.4 80.4 110.2 69.8 56.5 40.6 88.7, 90.7, 106.6 68.2, 88.7, 106.6 88.4, 88.7, 105.4

0 0 0 (0.05, (0.24 0 0 0 0 -0.26, 0.68, -0.42 0.87, -0.35, -0.52 0.85, -0.34, -0.51

0.40 0.28 0.60 0.80 -0.53 0.53 1.39 2.23 0.3, 0.3, 0.8 0.5, 0.3, 0.8 0.8, 0.3, 0.8

0.22 0.12 0.56 1.24 1.19 -1.19 2.77 1.98 0.0, 0.0, 1.0 1.3, 0.0, 1.0 1.0, 0.0, 1.0

a See text for definition of symbols. All angles are reported in degrees, and all distances are reported in angstroms. In cases where multiple numerical results are presented, molecules with each of the presented values are present in the layer. Several of the surfaces have multiple possible terminations. In these cases, results for the geometrically distinct termination layers are shown.

TABLE 4: Summary of the favored adlayers for glycine and alanine on Cu(110) and Cu(100) as predicted by DFT (the number of domains is the number of orientationally distinct versions of an individual adlayer available on the surface multiplied by the number of geometrically distinct adlayers coexisting on the surface) adsorbate

surface

favored adlayer

glycine glycine alanine (enantiopure) alanine (racemic) alanine (enantiopure) alanine (racemic)

Cu(110) Cu(100) Cu(110) Cu(110) Cu(100) Cu(100)

heterochiral c(4 × 2) homochiral + (2 × 2) pseudo-heterochiral heterochiral pseudo-racemate heterochiral c(4 × 2) homochiral + (2 × 2) pseudo-heterochiral racemate (2 × 2) pseudo-heterochiral

observed on Cu(110) or Cu(100). To give just one example, the DL-alanine(101) surface looks superficially similar to alanine/ Cu(110) in terms of the molecular density and ΘCC. The values of δN-01 and δN-02, however, differ greatly between the molecular crystal’s surface and the adlayer on Cu(110), quantifying the qualitative observation that the molecules in the DL-alanine(101) surface are strongly inclined with respect to the surface plane. Similar observations can be made for all of the other DL-alanine surfaces we examined. There are simple reasons why there is a lack of similarity between the molecular crystal and the adsorbed layers on Cu. First, in the molecular crystal, the molecules are zwitterionic, while, on the Cu surfaces, the molecules are anionic. More crucially, we have shown previously that bonding with the metal surface and intramolecular distortions are the dominant contributions to the overall energy of glycine and alanine adlayers on Cu, with intermolecular interactions playing only a minor role.38 The situation is quite different for the molecular crystal, where of course the contributions due to metal bonding are absent and intermolecular interactions play a crucial role. Thus, the disappointing although perhaps unsurprising conclusion from these comparisons is that knowledge of the molecular crystal structure of amino acids will be of limited value in describing or predicting the structure of these molecules once they are adsorbed on metal surfaces. 4. Conclusions We have used plane wave DFT calculations to examine dense adlayers of glycine and alanine adsorbed on two flat Cu surfaces, Cu(110) and Cu(100). These calculations have resolved several issues that are challenging to assess experimentally. Our predictions for the favored adlayer in each system we have considered are summarized in Table 4. These predictions present a fascinating view of the diverse phenomena that can occur when amino acids are deposited on metal surfaces. Glycine adopts a single adlayer structure on Cu(110), but two distinct glycine structures will coexist on Cu(100). The adsorption of enantiopure alanine on Cu(110) or Cu(100) is very similar to the adsorption of glycine on the same surfaces in that the adlayer structure(s)

figure 1a 2 3 3 4a,b 4d

no. of distinct domains 2 8 2 2 8 4

favored by glycine are also favored by enantiopure alanine. This similarity between glycine and alanine also extends to the adsorption of racemic mixtures of alanine on Cu(110), where the bonding footprint of alanine molecules in these mixtures is the same as that for glycine on Cu(110). This similarity breaks down, however, for racemic mixtures of alanine on Cu(100), where, unlike glycine or enantiopure alanine on the same surface, a single adlayer structure is favored. The appearance of this diverse set of outcomes can be understood in a general way by noting that the overall energy of an amino acid adlayer is a combination of the strength of the surface bonding, the energy incurred distorting intramolecular degrees of freedom in the adlayer, and intermolecular interactions. Our analysis of these systems38,39 and analyses of similar examples44 indicates that the differences between the total energy of two adlayers can be small even when the factors contributing to these energies are quite different. This conclusion supports the notion that a range of different outcomes can be observed among superficially similar systems and also suggests that efforts to predict adlayer structures focusing on just one of the contributions to the energy are likely to be unproductive. Our calculations also allow us to predict the fate of racemic mixtures of adsorbed alanine in terms of the local chirality of the resulting adlayers. At least one experiment of this type has been interpreted previously as showing spontaneous segregation of molecular enantiomers on the surface.42 Our calculations argue strongly against this conclusion. For racemic alanine adsorbed on Cu(100), we find that a racemate crystal structure, that is, a structure with an ordered pattern of D and L molecules within the surface unit cell, is favored over segregation of the enantiomers. For racemic alanine on Cu(110), neither enantiomeric segregation or formation of an ordered racemate are favorable. Instead, a pseudo-racemate, a structure in which the spatial distribution of the molecular enantiomers is random, is favored. An important general feature of the amino acid adlayers we have considered is that these adlayers exist on each surface in multiple geometrically distinct orientations. This observation

16772 J. Phys. Chem. B, Vol. 109, No. 35, 2005 is illustrated in Figure 1b, which shows a domain boundary between the two distinct orientations of the glycine adlayer that is favored on Cu(110). On Cu(100), four distinct orientations of each possible adlayer can coexist separated by domain boundaries. The number of distinct domains, defined as the number of locally distinct adlayers multiplied by the number of distinct orientations of each adlayer, for each system we have considered is summarized in Table 4. Because the existence of these domain boundaries appears to be quite general, the appearance of domain boundaries in STM images cannot be taken as the primary evidence for the existence of multiple adlayer structures or for the segregation of enantiomers in a racemic mixture without further supporting evidence that characterizes the local structure of the regions forming the separate domains. All of the adlayers we have considered deal with flat Cu surfaces. A number of experiments have indicated that the adsorption of amino acids onto flat Cu surfaces can induce highly ordered facets to appear on the surface that have specific high Miller index orientations.15-17 The best known example is the appearance of Cu(3 1 17) facets on Cu(100) surfaces in the presence of amino acids.15-17 A particularly interesting feature of these facets is that they are intrinsically chiral. A variety of experimental and theoretical studies of intrinsically chiral high Miller index metal surfaces has shown that they can exhibit enantiospecific adsorption properties.1,2,4,6,69,70 The adsorption-induced formation of high Miller index facets on Cu(100) indicates that the energy gain due to adsorbing amino acids on these facets more than compensates for the energy incurred in creating these facets from the flat surface. The observation that this facet formation can be homochiral when enantiopure amino acids are used15 indicates that the adsorption of these amino acids on high Miller index facets can be highly enantiospecific. A topic of considerable future interest will be to extend the types of calculations we have presented here to examine the detailed structure of amino acids adsorbed on the high Miller index facets that exist in these adsorption-induced faceting transitions. Plane wave DFT calculations are well suited to examine the adsorption of molecules on ordered facets formed by high Miller index surfaces.6,71-75 Our calculations have only been applied to dense adlayers on Cu(110) and Cu(100), that is, adlayers containing two adsorbed molecules per surface unit cell. There is compelling experimental evidence that the delicate balance between the various contributions to adlayer ordering can give rise to interesting phenomena when adlayers with changing surface coverages are created. Barlow and co-workers have recently shown that varying the coverage and temperature for the adlayer adsorption of enantiopure alanine on Cu(110) causes the adlayer character to change from disordered to chainlike to 2-d chiral cluster arrays.57 Similar effects are seen in the coverage dependent adsorption of glycine on Cu(110),16 Cu(111),37 glycine on Au(110),27 and cysteine on Au(111).76 An important challenge when determining a series of adlayer structures is to envision how these structures can be used to predict structures in related systems. We have shown that pursuing a connection between amino acid adlayers and the bulk crystal structures of amino acids is unlikely to be fruitful. The close similarity between the adsorption footprints of glycine and alanine on each surface we examined, however, suggests that thinking of this footprint as a template for constructing other amino acids adlayers may be viable. This approach can be applied with two caveats. First, the functional groups in the amino acids must be small enough that they can be accom-

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