Self-Assembly of Cysteine Dimers at the Gold Surface: A

Aug 26, 2013 - The only proteinogenic acid with a mercapto group, cysteine is the main participant in the binding of proteins and peptides to the surf...
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Self-Assembly of Cysteine Dimers at the Gold Surface: A Computational Study of Competing Interactions Chris R. L. Chapman, Elvis C.M. Ting, Ashley Kereszti, and Irina Paci* Department of Chemistry, University of Victoria, P.O. Box 3065, Victoria, British Columbia V8W 3V6, Canada ABSTRACT: The only proteinogenic acid with a mercapto group, cysteine is the main participant in the binding of proteins and peptides to the surfaces of noble metals. A chiral molecule, it becomes a major player in surface patterning for chiral amplification, biosensing, and chiral catalysis. Here, we examine the interplay of molecule−surface and molecule−molecule interactions in the selfassembly process of monomers, dimers, and trimers of L-cysteine on a (1 × 2)reconstructed Au(110) surface, and the implications for chiral recognition. Multiple adsorbed configurations of L-cysteine and L-cysteinate in neutral and zwitterionic forms were generated using molecular dynamics simulations, serving as starting points for further density functional theory (DFT)-based optimizations. We found that binding for both monomers and dimers was stronger at kink sites formed on the surface during the chemisorption process, and was unlikely to occur along the highly coordinated trough sites. In this, DFT calculations disagreed with MD simulations using centrosymmetric potentials, which tended to maximize coordination of the adsorbate groups, and ignore differences in reactivity of the various Au sites, unless specifically included in the force field. Kink-site bound homochiral L-cysteine dimers were particularly stable relative to both heterochiral and trimer structures, while molecules more weakly bound at more stable surface locations did not exhibit chiral recognition. If barriers to the diffusion of Au atoms along the surface can be overcome, the four-atom vacancy structures proposed by Kuhnle et al. (Nature 2002, 415, 891) provide reactive kink sites, ideally spaced for binding homochiral cysteinate dimers, with highly stable COOH-based hydrogen bonding.

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INTRODUCTION Chirality and chiral recognition have for many years been fascinating topics of investigation for chemists. With the advance of scientific research in surface nanopatterning, these issues have taken yet another facet. As it turns out, stereospecificity is ubiquitous in surface-supported selfassembly. Achiral molecules may form chiral patterns when deposited and assembled on an achiral surface. Racemic mixtures that do not undergo chiral separation at crystallization may nevertheless separate during a surface deposition process. Mixed monolayers may exhibit a wealth of chiral phases. Besides more obvious applications in chiral separations, either through a two-dimensional equivalent of Pasteur’s “conglomerate” formation or through various chiral amplification effects, chiral functionalized surfaces have possible applications in asymmetric catalysis,1 biomolecular sensing,2 and nonlinear optics.3 Generally speaking, chiral recognition and, consequently, chiral structure formation at adsorption, are facilitated by the underlying surface. Once molecules are evolving in the anisotropic potential of the surface which often confines them to two-dimensional motion, fewer degrees of freedom must be restricted to achieve the preferential binding that gives rise to chiral discrimination. On the other hand, the surface itself provides complexity in understanding the recognition process, by biasing molecular conformations, binding, and diffusion.4 Just as chiral segregation at crystallization in bulk © 2013 American Chemical Society

phases is not yet fully understood, much work remains to be done in developing a comprehensive description of chiral recognition, and its structural outcomes, in adsorbed phases. Chiral amino acids have been the molecules of choice in experimental and theoretical investigations of chiral selfassembly, because of their biochemical importance, relative structural simplicity, and ability to achieve chiral recognition through the formation of hydrogen-bonded supramolecular structures.5−8 Cysteine, the only proteinogenic amino acid with a mercapto functional group, can undergo chemisorption on gold substrates and has been particularly targeted, both as an archetypal chiral molecule, and as the entity that provides surface binding in peptides and proteins.9−24 A rich picture of the adsorption behavior of cysteine on gold surfaces has so far emerged through experimental studies, though much of this behavior is yet to be understood at a molecular level. The surface binding mode of the thiol group depends on the identity of the facet on which adsorption occurs.13,14,25 On Au(111), many unreacted SH groups are preserved at room temperature, and a large fraction of thiol molecules do not bind covalently to the substrate in these conditions. In contrast, system-wide chemisorption is observed in similar conditions on (1 × 2) reconstructed Au(110) Received: June 3, 2013 Revised: August 23, 2013 Published: August 26, 2013 19426

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surfaces.13,14 The charging state of the molecule also depends on environmental factors and substrate symmetry, with repercussions over the nature and extent of hydrogen bonding, and therefore short- and long-range order in the monolayer. Experimental reports on charging states are tentative. Overall, it appears that cysteine adsorbs in a mixture of neutral and zwitterionic forms on Au(111), even in ultrahigh vacuum (UHV) conditions.19,26 The general consensus is that cysteine chemisorbed in UHV conditions at the Au(110) surface is neutral at low coverages, though zwitterionic forms have been proposed at high coverage.11,13,27−29 Adsorption of solvated cysteine results in predominantly zwitterionic structures regardless of the substrate.30,31 Self-assembled geometries also vary widely with surface features, annealing temperature and coverage, due to the interplay of surface−molecule and intermolecular binding strengths. The structural behavior and stereospecificity in adsorbed phases obtained in the deposition of cysteine on Au(110)(1 × 2) is particularly complex. Random, physisorbed cysteine aggregates form in lowcoverage, low-temperature UHV deposition. Upon annealing to 270 K, small, uniform, and highly stereospecific nanoclusters are observed, even when racemic mixtures of cysteine are deposited.12,13 Despite their uniformity, the structures are thought to be thermodynamically unstable as they can be easily translated on the surface. When annealing is performed to 340 K, a new phase of homochiral, strongly bound dimers is observed.10,12,13 The reorganization of the molecular clusters is accompanied by changes in the underlying surface at these temperatures, and in the presence of the adsorbate molecule: Au atoms neighboring the binding site along the top row are displaced to other sites on the surface, and the reconstruction of the (110) facet is locally removed. Individual cysteine molecules appear to be chemically bound at the emerging kink sites of the new surface. As coverage is increased at high annealing temperatures, well-ordered molecular double rows are observed, and their uniformity has been explained as an extension of the surface reorganization starting from the kink sites, accompanied by the relocation of entire top rows of Au atoms.13 In this paper, we examine L-cysteine binding on reconstructed Au(110)(1 × 2) surfaces from a computational standpoint. The formation and stability of dimers is considered with an eye to understanding the various regions of the adsorbed monolayer phase space discussed above. The competition between and relative importance of surface binding and intermolecular binding are explored by comparisons between dimer and monomer binding. The particular stability of homochiral dimer structures, a required first step in chiral structure formation, is also considered, by examining binding in chemisorbed heterochiral dimers and in homochiral trimers.

additional energy to the system using temperature. This can be achieved with molecular dynamics (MD) simulations, using a temperature relevant to experimental conditions, and, if necessary, simulated annealing conditions. MD Simulations. Besides the empirical nature of the force field, a challenge in using classical MD for chemisorbed systems such as cysteine on gold is that bond breaking and formation are not well dealt with by the usual force fields, although they are important factors in the chemisorption process. Available force fields are also mainly optimized for liquid or gas phase simulations, with very few exceptions. In this study, we employed a strong nonbonded potential to treat the S−Au bonds, in order to afford thiol or thiolate groups some freedom of movement. We then improved on the structural outcomes of the classical MD simulations by performing further optimization using quantum chemical methods. We used the Groningen Machine for Chemical Simulations (GROMACS) program version 4.0.7.32 Simulations were run in the NVT ensemble, at 50 K set by a Berendsen thermostat, and with annealing to 370 K. A total simulation time of 1 ns was used, with 0.02 ps time steps. A 3-layer Au(110)(1 × 2) reconstructed slab of 200 atoms was used. Because of the low molecular density, no periodic boundary conditions were used. The GROMOS96 45A3 force field33 was used for molecules, incorporating intramolecular parameters, as well as dispersive and electrostatic terms for intermolecular interactions. The interaction between the cysteine molecules and the atomistic gold surface was described by a regular 12-6 LennardJones potential. Most of the molecule−surface parameters were derived by fitting to the Dreiding force field parameters of Jang et al.34 An exception was made for the N−Au interaction parameters which in ref 34 were directly imported from the Unified Force Field, and mixed with Lorentz−Berthelot rules. The resulting potential was weaker than expected given the n− d interaction between amines and gold surfaces. For this atomic pair, we used the empirical observation of D’Iorio et al.35 that the N−Au interaction strength should be about 1/8 of the S− Au minimum. This argumentation for our parameter choices is admittedly highly qualitative; however, we were only pursuing physically reasonable structures, to be further optimized and compared using higher levels of theory. The resulting parameters are given in Table 1. Table 1. Lennard-Jones Parameters for the Interaction of Cysteine and Gold

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METHODOLOGY One of the main challenges in simulations of patterned surfaces is that the potential energy surface on which the system evolves is very complex. There are many competing minima that can be significantly different in energy, but steep enough that low- or zero-temperature modeling (such as molecular mechanics or density functional theory) will be easily trapped in metastable minima neighboring the initial structure. In principle, experimental structures also get trapped in metastable states, but it is this dependence on the initial, guessed structure that is problematic for computations. One avenue to more broadly explore the available configurational space is to provide

pair

σ (Å)

ε (kJ/mol)

S−Au N−Au C−Au O−Au H−Au

2.38 3.09 3.17 3.02 2.74

38.286 4.760 0.270 0.202 0.173

Density Functional Theory (DFT) Calculations. A number of low-energy snapshots from the MD simulations were further optimized using the DFT implementation in the Spanish Initiative for Electronic Simulations with Thousands of Atoms (SIESTA) code, version 3.1.36,37 The Perdew−Burke− Erzenhof 38 (PBE) generalized gradient functional was employed along with norm-conserving nonlocal Troullier− Martins pseudopotentials39 for all atoms. The PBE exchangecorrelation functional was found previously to perform well, with consistent results for metal surfaces,40 thiol−gold 19427

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Figure 1. (a) Regular missing row Au(110)-(1 × 2) surface that contains troughs (blue arrow) and ridges (red arrow). (b) Missing row Au(110)-(1 × 2) surface with a four-atom vacancy (blue arrow). The red arrow indicates the relocation of the four atoms. (c) A model of the L-cysteine molecule.

interactions,41,42 and hydrogen bonding in various molecular types,43,44 all of which are relevant phenomena for the systems investigated here. The gold surface was modeled using a 120-atom missing-row (1 × 2) reconstructed Au(110) slab with periodic boundary conditions, see Figure 1a. To examine the removal of the reconstruction upon chemisorption proposed in ref 13, the 4atom-vacancy slab of Figure 1b was also used. In Figure 1b, the vacancy was created by moving the respective gold atoms into a trough of the reconstructed surface. Thus, by conserving the number of atoms, the total energies of the two surfaces can be compared directly. Previous work with gold surfaces in DFT calculations has shown that the number of layers in the Au slab has a minimal effect on the adsorption energy if there are more than two layers present.45 We confirmed this conclusion by comparing monomer binding strengths on regular and vacancy surfaces with three and six layers, comprising 120 and 264 gold atoms, respectively. Accordingly, a three layer slab with periodic boundary conditions was used to efficiently model the surface in all of the calculations discussed below. In all geometry optimizations, the bottom layer of gold atoms was kept frozen, while the top two layers were allowed to optimize. Models and Binding Energies. In this work, we considered the stability of adsorbed monomers, dimers, and trimers as an indication of the likelihood that a given structural motif represents the outcome of the self-assembly process. We investigated structural outcomes of the chemisorption and physisorption of the L-cysteine enantiomer, dimerization, and the relative stability of LL and LD dimers, and several possible like (LLL) trimer configurations. Two possible adsorption processes were considered: one in which the mercapto group undergoes homolytic fission when adsorbed (a chemisorption process), the other in which the molecule is adsorbed without decomposition (a physisorption process):

ESb = Ecomplex − Ecysteine − EAun +

1 EH 2 2

(1)

Similarly, the adsorption energy for a cysteine mercaptan is ESHb = Ecomplex − Ecysteine − EAun

(2)

The stabilization energy of an adsorbed molecule in an mmer (dimer or trimer) on the surface is, in the case of thiolate adsorption Em − S =

⎞ 1 ⎛⎜ m Ecomplex − mEcysteine − EAun + E H2⎟ ⎠ m⎝ 2

(3)

and for thiols it is Em − SH =

1 (Ecomplex − mEcysteine − EAun) m

(4)

In all equations, EAun is the calculated energy of the surface, Ecysteine is the gas-phase energy of a neutral cysteine molecule, Ecomplex is the total energy of the adsorbed molecule−surface complex, and EH2 is the gas-phase energy of a hydrogen molecule. In the results presented below, all participants in a given reaction were considered at the same level of theory, and with the same basis set. Mechanistic aspects were outside of the interest area of the present work, mainly because of major computational challenges that need to be overcome in order to provide proper treatment to an otherwise very important investigation direction. In considering the chemisorption process, we ignored the possible adsorbed H radicals, because they did not alter the outcomes of the present study: we were seeking relative energies of the various adsorption motifs of the cysteine radical, whereas the Au−H entity would be involved in the baseline calculation and would not change from one motif to another. One important note regards the nomenclature convention used in this work. In the following pages, we will refer to the product of the chemisorption process as the cysteinate form (due to the formation of a thiolate bond in the process, and the accompanying charge transfer process).18,19,46 As only stable products and reactants were considered, the cysteinyl radical did not appear in our calculations. Where necessary, we will refer to the relevant functional group as a thiolate group. To distinguish the product of the physisorption process from generic references to cysteine, we will refer to cysteine mercaptan or the mercapto group, indicating that the thiol group is kept intact in this case. Basis Set Effects. The standard basis set for valence electrons in pseudopotential periodic boundary conditions codes is double-ζ plus polarization (DZP), and this basis set was used for the majority of the calculations reported here. A

chemisorption: C3H6O2 N−SH + Au120 1 = C3H6O2 N−S−Au120 + H 2 2 physisorption: C3H6O2 N−SH + Au120 = C3H6O2 N−SHAu120

For both types of sorption, zwitterionic and “neutral” forms of the adsorbate were considered, though very few zwitterionic forms were found to be stable. Binding energies were calculated on the basis of the reaction enthalpies corresponding to the individual binding process. The chemisorption energy of a cysteinate monomer is 19428

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larger basis set (triple-ζ plus polarization, TZP) was also considered in a few cases, to understand its effect on the binding energy. One issue that became apparent during calculations was that binding energies, particularly for physisorbed (thiol) species, were strongly overestimated due to basis set superposition errors (BSSE).47 One approach to correct such errors is to estimate a counter-poise correction as detailed in ref 47. This is problematic for chemisorbed systems, where the entire molecule is in close proximity to the surface (so prone to BSSE), yet the definition of molecular fragments is ambiguous. Another approach is to use large basis sets, which exhibit less BSSE. In pseudoatomic orbital (PAO) codes such as SIESTA, one can essentially increase the size of the basis set by extending the confinement radius of the PAOs. We evaluated changes in binding energies for one of our chemisorbed systems with increasing confinement radius (implemented by decreasing the PAO confinement energy from its default value of 20 mRy down to 0.5 mRy).48 Figure 2 displays the dependence of the

Figure 3. Optimized chemisorbed geometries at different pseudoorbital cutoff radii. In parts a and b, Rc values for the carbon atom ζ1 pseudo-orbitals are 4.1 and 5.8 Å, respectively.

large cutoff radii. Chemisorption bond lengths and most N−Au bonds did not, however, change with cutoff radii. The PBE/DZP procedure detailed here was tested for consistency with higher-level quantum calculations by comparing our results for the CH3−SH−Au2 complex with those of Krueger et al.49 Both CP-corrected binding energies and bond lengths were consistent within 10%, despite methodological and code differences.

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RESULTS AND DISCUSSION Monomer Structure and Binding. Simulated annealing MD was used to generate initial configurations for further DFT optimizations and binding energy calculations. A minimum annealing temperature of 70 K was required to allow the thiolate group to migrate along the Au substrate and find its own force-field-based equilibrium position. This is a sliding, rather than a desorption, temperature, and is thus significantly lower than previously reported thermal desorption energies relevant to monolayer repair in alkylthiols,50 or usual annealing temperatures for cysteine self-assembly.13 Moreover, it relates to experimentally relevant temperatures only to the extent that the Lennard-Jones potential is related to the S−Au binding energy, particularly as no attempt has been made to fit barriers to sliding along the surface. Annealing temperatures below 70 K led to equilibrated Lcysteinate geometries in which the thiolate group was bound at the initial (user input) location. Such semiequilibrated structures were used to examine the possibility of binding along the top of the ridge or at kink sites, which, due to their lower coordination, are expected to be more reactive than sites within the trough. All runs with annealing temperatures over 70 K led to L-cysteinate bound to multiple gold atoms inside the trough. These structures were stable within the classical MD force field, because the thiolate group maximized its Au neighbors, and thus its LJ binding energy, at locations inside the trough. Several monomer configurations were examined further from the MD optimizations. Besides those corresponding to energy minima, configurations bound at other surface sites were retained. PBE/DZP binding energies of these monomers are presented in Table 2. Basis set effects, examined using TZP basis sets, are included in the table. For molecules retaining their thiol hydrogen, the effect of BSSE is reported as well. Given the relatively large size of the BSSE correction, only corrected energies are considered in the discussion below. Several observations can be made on the basis of Table 2 and Figures 3b and 4, which present the relevant adsorbed geometries obtained upon PBE-optimization. Despite the fact that L-cysteinates were overall more strongly bound than Lcysteine mercaptans, they exhibited structurally similar minima (apart from the specifics of the sulfur−gold bond formation). In

Figure 2. Cutoff radius dependence of the binding energy. Data is presented for the cutoff radius of the first ζ pseudo-orbital of the carbon atom; cutoff radii of other pseudo-orbitals present a similar impact on binding energy.

binding energy on the cutoff radius of the first ζ pseudo-orbital of the carbon atom. The data was calculated for one chemisorbed configuration where the molecule lies in the surface trough. The convergence value of the binding energy in this particular case is about −0.3 eV. As discussed below, other types of molecular attachment to the surface produced stronger binding. Overall, the value is comparable with the dominant S− Au contribution that was used in our MD simulations, which was roughly −0.4 eV (see Table 1). The vagaries involved in the determination of LJ parameters, surface geometry differences, and molecular attachment points defy any attempts to quantitatively match LJ energy parameters to quantum chemical estimates for the molecular binding energy. However, the consistency between the two values offers some confidence in the ability of the present formalism to adequately treat binding in chemisorbed systems. The results presented in the following pages were obtained with PAO confinement energy set to 1 mRy. In addition to the significant reduction in binding energy upon extension of the basis set cutoffs, the geometry of the adsorbed system also changed. Low-cutoff structures overbound the entire molecule on the surface, which particularly affected the geometry of the carboxylic group relative to the surface. Figure 3 presents adsorbed geometries of the L-cysteine monomer chemisorbed within the trough at ζ1 cutoffs of 4.1 and 6.1 Å, with the height of the COOH group increasing at 19429

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chemisorption on nonuniform surfaces, that the uneven surface energy is properly accounted for in the force field. Our quantum calculations revealed that L-cysteine monomers bound most strongly to kink sites on vacancy surfaces. This preference was due to the sites’ low in-surface coordination, despite the lower stability of the surface itself in this geometry. L-Cysteinate structures adsorbed at kink sites accommodated well both the thiolate and the amino groups (Figure 4a), with the thiolate group bound in a bridge location to the kink site and a neighboring atom along the exposed (110) surface. The amino group pointed toward the surface, forming a physical bond to another atom along the newly exposed (110) plane, while the backbone atoms and the carboxyl group were parallel to the surface. The undissociated mercaptan also bound at the kink site, in an off-centered bridge location, which allowed the molecule to more easily bind the amino group to the substrate than an atop location would have. As seen in Table 2, however, the mercapto group was only bound to one Au atom in this case, accounting for the 40% weaker binding energy. Relatively strong binding was also achieved at ridge locations. In this case, the optimized configurations presented a unique feature: the L-cysteinate and the corresponding mercaptan adsorbed structures were visually identical (Figure 4b,c), despite numerical differences in the S−Au bond lengths presented in Table 2. The thiolate bound in an atop position, with a very short bond length, in order to accommodate the surface binding of the amino group, also along the ridge. The overall binding energy at ridge locations was identical for the mercaptan and the cysteinate forms: to the extent that the product stability is a predictor of a chemical process, mixed mercaptan/cysteinate monolayers would be expected at ridge sites. Chemisorbed configurations along the trough bottom presented two S−Au bonds (to the trough walls), as well as binding by the amino group (Figure 3b). Despite the apparent geometric fit of the molecule in the trough, weak binding at this location was due to (i) the high coordination (low reactivity) of the Au(111) facets at the trough walls and (ii) the inability of

Table 2. Binding Energies for Adsorbed L-Cysteine Monomers in Various Configurations geometry Mercaptan Form vacancy ridge ridge along trough trough, N-up trough, COOH-up Thiolate Form vacancy ridge ridge trough, COOH-up along trough trough, N-up trough, zwitterion

EDZPa −0.99 −0.65 −0.35 −0.28 −0.51 −1.20 −0.59 −0.34 −0.31 −0.10 −0.18

ETZP

EDZP;CPb

−0.31

−0.73 −0.59 −0.17 −0.10 −0.32

−0.31

(d1, d2)c (2.6, (2.6, (2.8, (3.2, (2.7,

3.4) 4.4) 3.1) 3.6) 3.6)

(2.5, (2.4, (2.5, (2.6, (2.5, (2.5,

2.5) 3.4) 2.7) 2.6) 2.7) 2.7)

a Energies are in eV. bEnergies after a counterpoise correction for BSSE. cDistances between S and its nearest Au atoms (Å), in the DZP optimization.

all mercaptans, the SH group bound to a single Au atom, and the formed S−Au bonds were longer than in cysteinate structures, as observed in previous thiol−gold binding calculations.49,51 A second point has to do with the most stable surface locations of the L-cysteine monomer. In this regard, marked differences arose between MD-calculated preferences and those obtained using PBE. In MD simulations, binding was primarily determined by the centrosymmetric Lennard-Jones interaction of the thiolate group with the surface atoms. These interactions were optimal in trough locations, where the thiolate maximized its number of gold atom neighbors. In reality, however, surface atoms in the trough have large coordination numbers themselves, within the surface, and are less reactive than lower-coordinated ridge and kink sites. Care must be taken therefore when using classical force field simulations of

Figure 4. Equilibrium structures of surface-adsorbed L-cysteine monomers: (a) cysteinate adsorbed at a kink site in a 4-atom vacancy; (b) cysteinate along the ridge; (c) cysteine mercaptan along the ridge; (d) mercaptan along the trough bottom (the corresponding cysteinate structure is given in Figure 3b); (e) cysteinate chemisorbed in the trough bottom, with the COOH group pointing away from the surface; (f) cysteinate zwitterion along trough. Colors represent carbon (gray), nitrogen (blue), oxygen (red), sulfur (green), hydrogen (white), and gold (yellow). Gold atoms in the top layer are colored in a lighter shade. 19430

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the molecule to arrange in flat position (i.e., with the backbone parallel to the surface) in this case. Chemisorbed monomers with either the amino or the carboxylic group pointing away from the surface were also considered at trough locations, as possible participants in across-a-ridge dimer configurations. Both of these monomer configurations were relatively weakly bound (see Table 2 and Figure 4e). Because of its weak binding, the NH2-up configuration was not considered further in this study (Table 2). Zwitterion configurations were considered for both Lcysteinate and mercaptan forms, adsorbed in all of the surface locations discussed above. Optimizations of zwitterionic structures led to nonbonding structures, proton transfer back to the neutral form or the break-up of the molecule in all cases, with the exception of the zwitterionic L-cysteinate bound in a trough location (Figure 4f). This structure was more weakly bound than the neutral cysteinate, having achieved surface binding through thiolate and the carboxylate groups. Given the clear instability of zwitterion adsorbed structures, either chemisorbed or physisorbed, zwitterionic dimers and trimers were not considered. None of the surface structures and locations considered here were chiral. As a result, no chirality aspects enter the discussion of monomer binding at the Au(110)(1 × 2) surface. Even at the more anisotropic kink sites, a simple reflection normal to the vacancy line produces the D-cysteine enantiomer bound at the opposite kink site, with no changes in molecule−surface interactions. Like (LL) Dimers: Hydrogen Bonding and Surface Binding Considerations. Cysteine contains two substituent groups capable of hydrogen bonding: the carboxyl group and the amino group. Consequently, there are a number of possible ways for cysteine molecules to form hydrogen-bonded dimers. We considered a number of MD-generated initial structures for PBE-optimization, with L-cysteines bound at various surface sites, and where hydrogen bonding was achieved through the carboxyl groups, or through carboxyl and amino groups. Binding energies calculated per molecule are reported in Table 3. The difference between values given in Table 3 and the values for similar structures in Table 2 corresponds to the energy of the interaction between the two molecules bound to

the surface, plus that of any configurational changes that take place as a result of this interaction. The strongest hydrogen bonds were formed by the COOH groups of the two molecules. Dimers that converged with hydrogen bonds involving the amino groups were generally weakly bound (see Table 3). Besides being good hydrogen bond sites, carboxyl and amino groups may interact with the gold substrate. The two interactions can destabilize each other. For example, hydrogen bonding between carboxyl groups prevents the oxygen atoms from binding to the surface. Added rigidity within the dimer upon H-bonding may alter the conformation of the amino group (thus its ability to bind to the surface). As a result, sampling the potential energy surface of cysteine dimer adsorption on Au(110)(1 × 2) is a complex process, despite the availability of MD simulations to obtain starting configurations. Snapshots of the most strongly bound like (LL) cysteinate dimer configurations at the various surface locations are presented in Figure 5. As in monomer adsorption, binding

Figure 5. Most stable equilibrium structures of LL cysteinate dimers: (a) at a 4-atom vacancy site; (b) along the ridge, thiolate groups 3 Au atoms apart; (c) along the ridge, with thiolate groups bound 2 Au atoms apart; (d) along trough, with thiolate groups bound 3 Au atoms apart.

Table 3. Binding Energies per Molecule for Adsorbed Cysteine Dimers surface locationa

E2−S;DZPb

vacancy site ridge, 3-atom spacingc ridge, 2-atom spacing ridge, NH2 H-bonds trough, 3-atom spacing trough, 2-atom spacing trough, 1-atom spacing trough, dimer formed across ridge trough, NH2 H-bonds unlike dimer, vacancy site unlike dimer ridge (2-atom spacing) unlike dimer trough (2-atom spacing)

−1.68 −1.04 −0.87 −0.57 −0.60 −0.61 −0.57 −0.42 −0.30 −1.30 −1.11 −0.60

a

E2−SH;DZP E2−SH;CP−DZP −1.57

−1.43

−0.74

−0.65

−0.91 −0.84

−0.78 −0.72

−0.83

−0.73

was strongest when the L-cysteine molecules were chemisorbed within a four-atom surface vacancy, with thiolate groups bound at the opposite kink sites. In fact, a four-atom vacancy created two kink sites that were ideally spaced for a like cysteinate dimer with H-bonding through the COOH groups (bonding OO distance of about 2.5 Å, Figure 5a), also accommodating N−Au binding. The adsorbed conformation of individual Lcysteinate molecules in the dimer was virtually unchanged from the monomer structure. The dimer stabilization energy of 0.5 eV per molecule in the vacancy case was attributed entirely to hydrogen bonding. Like dimer binding along the ridge occurred most efficiently when thiolate groups were attached three Au atoms apart, with the amino groups binding to Au atoms in the spacing. In this structure, presented in Figure 5b, COOH-based H-bonding provided a stabilization energy of about 0.45 eV. Dimers bound

like dimers were considered; LD dimers considered if unlike. b2-S refers to the chemisorbed dimer; 2-SH refers to physisorbed dimer. Energies are in eV. cThe number of Au atoms between those bound to mercapto or thiolate groups are indicated. LL

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further apart established weaker H-bonds. Those closer together underwent significant configurational distortion. In Figure 5c, both L-cysteinate molecules were lifted off the surface to accommodate the smaller spacing when thiolate groups were 2 Au atoms apart, as well as some hydrogen bonding between the COOH groups. The result was weaker molecular binding to the surface, (one amino group is desorbed) as well as weaker hydrogen bonding, as the COOH groups were not well aligned. Overall, the dimer stabilization energy in the 2-atom spacing case was about 0.3 eV. When the two molecules were even closer together, sites were unavailable for amino group adsorption. This, in addition to crowding effects, eventually led to upright molecules, unable to form COOH-based Hbonds, weak NH2-based H-bonds, and no dimer stabilization (see Table 3). At trough sites, like dimers formed three Au-atoms apart established the strongest COOH-based H-bonds (OO distances of roughly 2.5 Å). Dimers bound closer together experienced configurational crowding that brought the molecules further away from the surface in order to align the COOH groups (see Table 3 and Figure 5d). Binding along the troughs was, however, quite restrictive. The proper alignment of the COOH groups for the formation of H-bonds was achieved by torsional changes that brought NH2 groups away from the surface. Note that, in the most stable trough like dimer, one molecule had the amino group in syn conformation with the CO group of the COOH, while the other had an anti conformation: dimers formed at less crowded sites were mostly found in syn conformations. In the end, stabilization through dimer formation for trough-adsorbed dimers was up to 0.25 eV/molecule. Among the other configurations reported in Table 3, dimers formed across the ridge with thiolate groups bound in adjacent troughs established weak H-bonds due to the distance between binding locations. The dimer stabilization energy was about 0.1 eV in this case. Like dimers of the upright cysteinate monomers (COOH-up and NH2-up) discussed in the previous section formed weak amino-group based H-bonds, with no overall dimer stabilization. Stability of Unlike (LD) Dimers. Chiral discrimination was estimated by optimizing the structures of unlike dimers corresponding to the more stable like dimers discussed above. Binding energies for unlike dimers are included in Table 3, with the corresponding equilibrium structures presented in Figure 6. The data indicates a preference for homochiral structure formation only in the most stable dimer configuration, where the adsorption of the like dimer created a vacancy in the gold surface. The homochiral preference in this case was due to weaker hydrogen bonding in the unlike dimer. This was a result of conformational changes in one monomer, to reduce steric repulsion between the hydrogen atom on the chiral carbon and the substrate. For surface locations leading to the formation of more frustrated adsorbed dimer and monomer conformations (atop the ridge or along the trough), the binding energies of unlike dimers were competitive with those of like dimers. Adsorption at such locations is not expected to lead to preferential homochirality, to the limited extent that dimer behavior may be a predictor of chiral structure formation in extended systems.4,52 Extension to Homochiral Trimers. Experimental studies of UHV cysteine adsorption indicate that like dimer conformations are particularly stable.9−11,13 We examined the

Figure 6. Equilibrium structures of unlike (LD) cysteinate dimers: (a) at a 4-atom vacancy site; (b) along the ridge; (c) along trough.

changes brought on by the adsorption of a new L-cysteine molecule in the vicinity of the most stable like dimers. Binding energies per molecule in the equilibrated homochiral trimers are presented in Table 4, and a few representative snapshots are presented in Figure 7. Table 4. Binding Energies per Molecule for Adsorbed Cysteinate Trimers surface location

E2;thiolate;DZPa

vacancy ridgeb vacancy ridgec along ridged along ridgee along ridgef troughg troughh

−1.33 −1.25 −0.89 −0.95 −0.87 −0.59 −0.50

a

Energies are in eV. bVacancy structure with weak COOH-based Hbonds to third molecule, Figure 7a. cAlternate vacancy structure with little third molecule impact. dCOOH-NH2 binding to third molecule, Figure 7b. eWeak COOH-based H-bonds with third molecule. fSmall impact from third molecule. gCOOH-NH2 H-bonds with third molecule. hNH2−NH2 H-bonds with third molecule, Figure 7c.

The availability of favorable binding sites for a third molecule depended on surface location. Dimers formed at vacancy sites could interact laterally with a ridge-adsorbed third molecule. Top-of-ridge dimers could interact with a third molecule along the same ridge, or laterally, with a molecule adsorbed atop a nearby ridge. Analogous “linear” possibilities were considered for dimers chemisorbed within a trough. 19432

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fit of a homochiral cysteinate dimer with COOH-based hydrogen bonding. These chemisorbed structures were highly stable, with respect to both competing heterochiral dimers, and the inclusion of a third homochiral cysteinate in the molecular cluster. Less stable monomers, dimers, and trimers were formed along ridge sites and in troughs, and dimers adsorbed at such locations did not exhibit chiral recognition. Zwitterionic monomer structures were found to be unstable or weakly bound in all cases. In pursuing an understanding of chiral recognition through self-assembly at solid surfaces, it is important to examine the effects of temperature on the overall process. An essential follow-up of the present study will be to explore the impact of temperature on the surface-bound structures presented here, and in extended systems. The DFT methodology presented here does not directly treat temperature, and ab initio MD calculations, while possible, are very computationally intensive for large systems. On the other hand, classical simulations as the ones discussed here suffer from the highly imperfect centrosymmetric potential used to describe molecule−surface interactions. We are in the process of developing more appropriate coordination-dependent force-fields, which will allow us to use classical simulations to treat temperature effects and extended self-assembly systems on nonuniform surfaces.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected].

Figure 7. Stable equilibrium structures of LLL cysteinate trimers: (a) at a 4-atom vacancy site; (b) along the ridge, with binding to the third molecule; (c) along trough, NH2-based H-bonds to third molecule.

Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS Funding was provided by the National Science and Engineering Research Council of Canada, the Canada Foundation for Innovation, the British Columbia Knowledge Development Fund, and the University of Victoria. This research was performed in part using the WestGrid computing resources, which are funded in part by the Canada Foundation for Innovation, Alberta Innovation and Science, BC Advanced Education, and the participating research institutions. Mr. Ryan Hanson’s contribution in setting up initial MD simulations is gratefully acknowledged.

Generally speaking, linear trimers had either a noninteracting third molecule, or one with a weak destabilizing effect. Stable dimers, bound with COOH-based H-bonds and with sufficient binding site spacing to accommodate strong N−Au interactions, were mainly inert to the vicinity of an additional molecule. No additional intermolecular bonds were observed in these trimers, and binding energies per molecule were virtually unchanged from the dimer values (see, for example, Figure 7d and all trough configurations in Table 4). Trimers in lateral geometries were more stable (per molecule) than dimers only if the third molecule could form H-bonds with one of the dimer’s NH2 groups (see for example Figure 7b). When H-bonding with the third molecule distorted the strong H-bonding in the dimer, or the third molecule was crowding the dimer, the overall trimer effect was destabilizing (see Figure 7a and other vacancy results in Table 4).

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REFERENCES

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CONCLUSIONS In the present work, we undertook a combined MD/DFT study of the physisorbed and chemisorbed states of L-cysteine on (2 × 1)-reconstructed Au(110) surfaces. The process has been shown previously to lead to highly selective homochiral assembly of the cysteine molecules. We pursued here a molecular-level understanding of the effects of the complex competitive interactions that arise in this system and their relationships with the chiral recognition outcomes of the selfassembly process. Cysteine monomers were stabilized on the surface by the presence of kink sites formed upon moving some of the ridge Au atoms, with the creation of four-atom vacancies as noted by Kuhnle et al.10 The four-atom vacancy created a spacing between two surface kink sites that allowed for an ideal 19433

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