Enantiospecific Adsorption and Decomposition of Cysteine

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C: Surfaces, Interfaces, Porous Materials, and Catalysis

Enantiospecific Adsorption and Decomposition of Cysteine Enantiomers on the Chiral Cu{421} Surface R

Michael J Gladys, Kane M. O'Donnell, Anton Tadich, Hyunwoo Yook, Jeong Woo Han, and Lars Thomsen J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.9b03373 • Publication Date (Web): 08 Aug 2019 Downloaded from pubs.acs.org on August 20, 2019

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The Journal of Physical Chemistry

Enantiospecific Adsorption and Decomposition of Cysteine Enantiomers on the Chiral Cu{421}R Surface Michael J. Gladys1*, Kane O’Donnell2, Anton Tadich2,3, Hyunwoo Yook4, Jeong Woo Han4,5 and Lars Thomsen1,2 1School

of Mathematical and Physical Sciences, University of Newcastle, Callaghan, NSW 2308, Australia. 2Australian 3Department

4School

Synchrotron, Clayton, VIC 3168, Australia.

of Physics, La Trobe University, Bundoora, VIC 3083, Australia.

of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.

5Department

of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.

Abstract A detailed understanding of the bonding and molecular geometry characteristics of amino acids on chiral surfaces is vital towards discovering new pathways in chiral chemistry. Saturated layers of Dand L-cysteine amino acids were chemisorbed onto a chiral Cu{421}R surface. Although very little difference was observed in the molecular orientation of the two enantiomers as observed with NEXAFS, a large variation in the sulphur bond scission energy was measured using a HR-XPS thermal anneal sequence. As a result of this scission process, enantiomers of cysteine molecules completely dissociate into alaninate at temperatures separated by as much as 16 K or 0.06eV which is one of the largest stereo effects observed on chiral metal surfaces.

Corresponding Address: School of Mathematical and Physical Sciences University of Newcastle, Callaghan, NSW 2308, Australia. Email: [email protected]

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1. Introduction To provide the expertise in tailoring advanced functionalised materials, an understanding of the key properties, such as adsorption, stability and molecular alignment is crucial. Many technologies now incorporate functionalised materials into drug delivery and biosensor devices.1-4 In chiral catalysis, the molecular architecture on a surface may allow for cheaper and alternative separation techniques

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while in medicine the need for biocompatible materials has stimulated a great deal of

effort to understand the characteristics of biomolecules at metal surfaces.8-10 To elucidate any differences in enantiomer adsorption and stability, techniques such as Temperature Programmed Desorption (TPD) can be utilised to probe the molecular – surface bonding by measuring the desorption temperatures and desorption mechanisms.11-13 As an example, Cheong and Gellman13 reveal significant enantiomer differences in lysine on Cu{3,1,17} surfaces. This type of experiment works well if the molecule does not dissociate prior to desorption, however if it does dissociate then the product molecule may or may not show selectivity or not be chiral any longer. Any information about the intact molecular orientation and selectivity of the system will be obscured. As an alternative, measuring the molecular bonding regime with High-Resolution X-ray Photoelectron Spectroscopy (HRXPS) can illuminate any stereo effects prior to, or during, any thermally activated or kinetically driven dissociation. Thiol-containing molecules provide an important approach to interface technology due to their self-assembling nature; sulphur bonds strongly to noble metals.14 In heterogeneous chiral chemistry, the ability of a layer to self-assemble is important as it provides a regular repeating environment to synthesize or separate chiral compounds. To study the properties of chiral molecular structures on surfaces, simple molecules are needed. A significant effort has gone into investigating small amino acids on surfaces as they are building blocks for peptides, proteins and manufactured drugs.15-17 Our current research is focused on the adsorption characteristics and organizational properties of small chiral molecules on chiral metal surfaces. Cysteine, a small amino acid with a thiol side chain, is an ideal test bed for the study of small molecule adsorption properties in a chiral environment. Chiral metal surfaces are inherently chiral interfaces produced by cleaving the crystal at a particular angle to generate a set of miller indices that are non-zero and all different, such as {531}, or {643}, or even {1 5 17}. 15-21 These surfaces are non-symmetric due to the formation of step kinks as shown by the circled top layer atoms in figure 1. The chirality of these kinks are determined by the clockwise or anticlockwise combination of low index microfacets that make up the kink site 22, 23. Just


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like chiral molecules, the handedness of the surface is denoted by R and S or D and L, for example, Cu{531}R. The lock and key mechanism of the kink sites have been shown on numerous occasions to influence the adsorption and chemical reactions in a stereo-specific way.15, 23-32 However the majority of these studies have only observed weak selectivity. Our previous work illustrated that the sulphur containing molecules of L-cysteine and Lmethionine interact very differently with the chiral Cu{531}S surface.33,34 While cysteine bonds with both oxygen, nitrogen and sulphur atoms in a 4-point (quadrangular) “footprint”, the sulphur atom in methionine does not bond to the copper substrate atoms. Subsequent annealing showed the sulphur dissociate from the methionine at a much higher temperature than observed for the cysteine. Both molecules however formed alaninate on the surface as a consequence of annealing above the sulphur dissociation temperatures. No selectivity was observed for cysteine on Cu{531}. In this study cysteine is adsorbed onto Cu{421}. This surface was chosen as it offers a slightly larger unit cell than that of the Cu{531} and may offer a lock and key mechanism to generate selectivity effects. Figure 1 displays the bulk terminated Cu{421} surface as well as an inset of the Cu{531} for comparison. Interestingly, it should be noted that the Cu{421} surface produces a unit cell (just top layer atoms) that is perfectly rectangular, and therefore not chiral. Additional layers of Cu atoms produce the surface chirality in this case. If a chiral molecule were to adsorb onto the top layer atoms alone, no selectivity would be expected, however, the distance between first and second layer Cu atoms (see Fig. 1) is very close to the oxygen – oxygen distance in the carboxylate part of amino acids like cysteine. Previous studies of amino acids on Cu{531} and Cu{421} have shown that adsorption on first and second layer atoms to be the bonding configuration for alanine.29,35,36


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Figure 1: Schematic model of the atoms on a bulk-terminated Cu{421}R. Added to the model at the bottom are the most relevant crystallographic directions along with the rectangular surface unit cell. At the top the {311} and {110} micro facets are specified. The insert is of Cu{531}R with its equivalent {311} and {110} micro facets. The {531} unit is also shown within the {421} surface below the insert. 2. Methods 2.1 Experimental Details Details of the Cu{421}R single crystal and UHV endstation at the Australian synchrotron are outlined in previous articles.18,37 Enantiopure D- and L-cysteine (≥98% pure, from Sigma-Aldrich) was deposited onto the Cu{421}R surface using a Knudsen cell. The evaporator was mounted behind a gate valve and the half-filled capillary was allowed to come to equilibrium at the required temperature before the surface was exposed to the evaporation source. At every deposition a saturated layer was adsorbed onto the Cu {421}R surface by dosing for a much longer time than required, based on smaller submonolayer dose measurements. XPS C1s, N1s, O1s and S2p spectra were collected at normal incidence to the analyser, at temperatures listed in the result section, using a photon energy of 630eV. The peaks were normalized with respect to the background signal and Gaussian-Lorentzian functions were then fitted to the spectra to find the integrated peak intensities. All binding energies (BE) were calibrated using the 4f7/2


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peak position (located at 84.0eV BE) of a gold reference sample. Step anneals were done by cooling the manipulator down with liquid nitrogen and ramping up to the desired temperature at approximately 5 oC per second. The cooled manipulator would cause the sample temperature to drop very rapidly after it had reached the temperature. The sample only remained at the desired temperature for a fraction of a second. The XPS signal was taken at a fresh spot each time to minimise beam damage. Carbon K-edge partial electron yield (PEY) NEXAFS spectra were recorded at room temperature (300 K) with the crystal surface plane perpendicular to the incident photon beam using a PEY retarding voltage of 50eV below the lowest photon energy in each spectrum. The angular rotation of the sample around the surface normal (the azimuthal angle) was varied throughout the experiment. This equates to rotating the polarization of the incident beam with respect to the surface plane, a technique widely used to determine the relative footprint of carboxylate-containing adsorbates on metal substrates.27,35 The π* and σ* transition states within the NEXAFS spectra were then identified and fitted with Gaussian-Lorentzian functions onto a step edge background. Again each NEXAFS scan was taken on a fresh spot on the surface. 2.2 Computational Details Our plane wave DFT calculations were performed with the Vienna ab initio simulation package (VASP).38,39 We employed the Perdew-Burke-Ernzerhof (PBE) generalized gradient functional 40,41 along with the projector augmented wave (PAW) method42,43 to describe ionic cores. In order to take into account the van der Waals (vdW) interaction, we used a DFT-D2 approach of Grimme,44 as implemented in VASP. A plane wave expansion with a cutoff of 400 eV was used with a 2  3  1 Monkhorst-Pack45 k-point sampling of the Brillouin zone for all calculations. Total energy calculations were conducted using the residual minimization method for electronic relaxation, accelerated using Methfessel-Paxton Fermi-level smearing46 with a width of 0.2 eV. Geometries were relaxed using a conjugate gradient algorithm until the forces on all unconstrained atoms were less than 0.03 eV/Å. The periodicity of the material in the plane of the surface was defined using the DFToptimized lattice parameter of Cu, 3.64 Å. The computational supercell contained (2  1) and (4  2) surface unit cells for Cu(421)R, respectively, with a vacuum spacing of 14 Å in the direction of the surface normal. The surface unit cell is shown as white dashed lines in Figs. 7(a) ~ 10(a). Our calculations were performed using slabs equivalent in thickness to six (111)-oriented layers.


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Calculations for adsorbed amino acids were performed for a coverage corresponding to one molecule per the surface unit cell we used. This gives an area of 60.6 Å2/molecule at p(2  1) and 242.6 Å2/molecule at p(4  2) for Cu(421)R, respectively, where the adsorbed molecules are well separated (Figs. 7 ~ 10). When examining adsorption, molecules were placed on only one side of the slab. Dipole corrections in the direction normal to the surface were therefore applied in computing all of the energies reported below.47,48 All degrees of freedom of all the metal atoms and the molecule were allowed to relax in all energy minimization calculations. The adsorption energy, Eads , for the deprotonated molecules is defined as Eads  EH2 NCHRCOO(ads)  ECu(s)  ( EH2 NCHRCOOH(g) 

1 EH (g) ) , 2 2

Where EH2 NCHRCOO(ads) is the total energy of the system containing the adsorbed deprotonated amino acid, ECu(s) the total energy for the optimized solid Cu surface, EH2 NCHRCOOH(g) the total energy for the amino acid in the gas phase, and EH2 (g) the total energy for the hydrogen molecule in the gas phase, respectively.[49,50] For the amino acids that contain deprotonated β-SH, we used the expression: Eads  EH2 NCHRCOO(ads)  ECu(s)  ( EH2 NCHRCOOH(g)  EH2 (g) ) .

By our definition, a negative value is favorable to the adsorption. To characterize the enantiospecificity of adsorption in each example, we used the enantiospecific difference in adsorption energies, Eenantio , defined as the total energy of the most stable structure of the adsorbed L enantiomer minus the total energy of the most stable structure of the adsorbed D enantiomer.

47,48,51,52

With this

definition, a positive value indicates that the D enantiomer is more strongly adsorbed to the surface than the L enantiomer. For the quantitative comparison of sulphur dissociation between the enantiomers of cysteine in μ3 geometry, the dissociation energy is estimated as Ediss  EAft  EBef ,

where EAft is total energy of system after the decomposition and EBef is total energy of system before the decomposition. If the value is negative, the structures after the decomposition are more stable. We calculated the dissociation energy by searching for the most stable co-adsorption site of sulphur and alanine.


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3. Results and Discussion 3.1 Experimental observations Figure 2 shows comparison of C1s (panel (a)) and S2p (panel (b)) spectra for saturated L and D-cysteine dosed at 300K and reveals spectra displaying an appearance typically observed for these molecules that have bonded to the surface with oxygen, nitrogen and sulphur. The molecule is now cysteinate as it has lost the hydrogen from the carboxylate group. Based on the binding energies observed in the S2p spectra has also lost the hydrogen atom when bonding to the Cu surface.33 Based on several saturated doses of each enantiomer, the average dose was calculated by comparing the intensity of the C1s signal. For L-cysteinate the normalized average was 0.85 ± 0.10 while Dcysteinate was 0.74 ± 0.04. This observed difference in intensity is much larger than other molecules investigated on similar surfaces and may be indicative of a difference in packing density on the surface with L-cysteinate being able to orient itself in a more efficient way or assist in additional molecules finding areas to adsorb on the Cu surface atoms. The S2p spectra reveal the molecular and atomic doublets. The small amount of atomic sulphur observed is a combination of thermal dissociation and beam damage during the scan itself. The scans were done in the shortest possible time to allow good statistics. A typical scan would generate an approximate dose of 0.1 secondary electrons/molecule, based on the photon load and area of illumination on the surface to produce about a 5% loss to the molecular peak per spectrum.

Molecular Sulphur

Carboxylate

a) b) Atomic Sulphur


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Figure 2: HRXPS comparison of adsorbed cysteine enantiomers at room temperature. a) Carbon 1s spectra show slight differences in overall intensity, however individual peak positions for the C atoms in the molecule are shown as grey dotted lines. Four peaks are distinguishable, for the C-S bond at 285.6eV, the chiral backbone carbon atom at 284.7eV and the carboxylate carbon atom at 286.45eV. The feature at approximately 288eV is a shake-up satellite peak. b) Sulphur 2p spectra which contain both S2p 3/2 and ½ peaks for two species, molecular (Sulphur – Carbon bond) and atomic. These dosed samples were then step annealed until only carbon fragments were visible on the surface. Figure 3 shows the step anneal while probing the S2p signal with HR-XPS. Fitting the S2p peaks identified two species of sulphur corresponding to a molecular form (covalently bonded to both carbon and copper) and an atomic form (only bound to the surface Cu atoms). The error in temperature is approximately ±3oC based on repeated experiments. As the temperature is increased, the molecular form of the sulphur is transformed into an atomic form. The figure shows a large difference in the decomposition temperature between the two enantiomers with D-cysteine decomposing roughly on average 16 K less than L-cysteine. The derivatives of the S2p XPS peak areas vs temperature are approximately proportional to d(SMol)/dT, (ignoring photoelectron diffraction effects), i.e. the change in the amount of C-S bond, d(SMol) with temperature, T. This allows the determination of the decomposition rate at constant cysteine coverage. The derivative of the molecular form of the S2p spectra produces a peak at 89 ± 5oC (362 ± 5 K) and 105 ± 7oC (378 ± 7 K) for D and L-cysteinate respectively. Using a similar equation as Redhead used for desorption and assuming first order dissociation (i.e. only the sulphur bond to the Cu atoms is breaking with temperature) 37, the energy for dissociation of the sulphur from cysteinate was estimated at 1.12 ± 0.02 eV (108 kJ/mol) and 1.18 ± 0.02 eV (114 kJ/mol) for D- and L-cysteine respectively.


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a)

b)

Figure 3: (a) Step anneal of D-cysteinate, illustrating the consistency of the step anneal process with the S2p signal. (b) Step anneal comparing both enantiomers of cysteine while observing the S2p signal. As the temperature increases the molecular form changes into atomic sulphur. A clear difference in the decomposition rate is observed. To illustrate the selectivity, the C1s spectra for D and L-cysteine annealed to 100 oC (373 K) are shown in Figure 4(a). There are enantiomer differences in the spectra, for example the L-cysteinate has shoulder at approximately 283.6 eV revealing that the surface still contains a reasonable proportion of intact cysteine. The D-cysteine spectra resemble more closely to the spectra for alaninate on Cu surfaces, and shows the sulphur has been removed from the adsorbed molecule. While the spectra is very similar to Alaninate from deposited Analysis of the C1s does not allow us to resolve the difference between the R group of the alaninate to be CH3 or CH2ˉ, however there are two hydrogen atoms per molecule sitting on the surface from the adsorption of cysteine and could easily fill the extra bond in the ion state. This occurs for the L-form of cysteine at a higher temperature. This process of forming alaninate on the surface of Cu has been shown previously.31 This study of Lcysteine on Cu{531}S showed that the C-S bond severed around 370 K (100 oC) similar to the temperature observed here for L-cysteine on Cu{421}. The D-cysteine spectra also contains a small ACS Paragon Plus Environment

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new peak at 282.1 eV. Following the C1s peak signal with temperature shows little difference between the enantiomers.

Amine

b)

a)

Carboxylate Methyl (CH3 or CH2-)

Figure 4: Comparison of a) C1s spectra and b) S2p for D- and L-Cysteine taken at hv = 630eV with a temperature of 100oC. The C1s spectra is almost identical to that seen for alaninate on Cu surfaces.29 There also appears to be a small amount of atomic carbon located at 282.15eV. The S2p doublet shows the significant difference in the amount of molecular sulphur left on the D-cysteinate as compared to the L molecule. Figure 5 shows the temperature evolution of the N1s and O1s spectra for the L-enantiomer of cysteinate. The N1s spectra remain consistent at 399.3 eV until after 150 oC where the signal centre shifts by +0.22 eV and corresponds to the decomposition of the alaninate species decomposing. The D-cysteinate N1s spectrum show a similar shift but after 175 oC indicate a slightly larger stability of the alaninate on the surface when which may be due to intermolecular interactions or with the coadsorbed sulphur or a combination of both. However the spectrum are 25 oC apart and the temperature difference is most likely much closer.

A small amount of atomic nitrogen (at

approximately 398 eV) was left on the surface at 225 oC. The O1s spectra in Figure 5b show multiple shifts at different temperatures. A 0.1 eV shift around 125 oC is followed by a second shift of 0.25 eV after 150 oC. The first shift occurs just after the cysteinate conversion to alaninate while the second


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shift is consistent with the shift observed in the N1s signal when alaninate begins to dissociate and fragments start to desorb from the surface. This is consistent with the dissociation observed for cysteinate on Cu{531}.31 The D-enantiomer of cysteinate shifts by a small amount at 175oC consistent with the N1s spectra. No real shift was observed at lower temperatures.

a)

b)

Figure 5: Step anneal spectra for L-cysteine a) N1s and b) O1s.

The numbers in the legend

correspond to the temperature in degrees Celsius. Binding energy shifts can be seen in both series of spectra as indicated by the dotted line. Carbon K-edge NEXAFS found relatively little difference in the carboxylate geometries between enantiomers. Figure 6(a) shows the intensity of the * resonance within the carboxylate group bound to the surface Cu atoms as a function of E-vector angle. The intensity of the * resonance (I*) is linked to the polarization angle of the incoming electromagnetic radiation such that for a single molecule, I* will be at a minimum when the E-field is in the plane of the triangle formed by the carboxylate group and similarly I* will be at a maximum when the E-field is perpendicular.


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[53] The angular dependence of the * resonance is proportional to cos2(  , where  is the angle between the surface projection of the normal from the plane of the carboxylate triangle and the horizontal axis of the of the crystal, in this case the [1,-1,-2] direction as shown in the insert in Figure 6(a) and  is the azimuthal angle. If there is only one molecular orientation adsorbed on the surface then the * intensity should fluctuate between zero and a given maximum as the azimuthal angle fluctuates. More than one orientation prevents the intensity to go to zero. Many molecular orientations of the carboxylate group will show up as a very flat fluctuation. Figure 6(a) shows about 50% fluctuation of the * intensity which indicates the majority of adsorption is taking place with two molecular orientations.

a)


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b) Figure 6: a) Comparison of NEXAFS between L (red triangles) and D (black circles) enantiomers of cysteinate. The golden band indicates the parameter range to produce the cos squared modelling for the L-cysteinate data. b) NEXAFS comparison of L-cysteinate on Cu{421} (black squares) and Lcysteinate on Cu{531} (red circles). The angular dependence can be fitted to the following expression for two molecular orientations:29,33,53 I*(f) = A1 cos2(    A21 cos2(   A1 and A2 are multiplication factors that take into account factors such as differences in coverages and/or differences from the polar angle of the normal from the plane of the carboxylate triangle for the different microfacetted adsorption sites.  and  describe the orientations of two carboxylate triangles with respect to the [1,-1,-2]. The fit in the L and D-cysteinate both give orientation angles of approximately 54 ± 8º and – 32 ± 6º. The fact that there is little difference in the NEXAFS results between the enantiomers may be due to beam damage, and the data is therefore measuring a proportion of the orientation of alaninate and cysteinate on Cu{421}. The values for the carboxylate triangle orientations are very similar to those found for alanine on Cu{421} [mono and sub] The electron dose for a NEXAFS scan is approximately 0.25 electrons / molecule, which is about 5 times more than for the HR-XPS scans. This damage issue however may not change the molecular alignment measurement by NEXAFS. The carboxylate group


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remains attached to the same Cu adatoms before and after the transition from cysteinate to alaninate, however the backbone of the molecules will cause different relaxations based on their handedness. Figure 6b shows a comparison of the angular NEXAFS scans for L-cysteinate adsorbed onto Cu{421} and Cu{531}. There is approximately a 10° shift in the carboxylate angle due to the difference in angle of the two surface planes. The important differences between the two spectra are the peak to trough intensity changes. Even if beam damage were occurring on both surfaces during acquisition, the result shows that L-cysteinate on the {421} surface has a much larger amplitude suggesting the ‘molecules’ are more aligned than observed on the {531} plane. This may be due to the top layer sites situated further apart and therefore reducing intermolecular forces. 3.2 Theoretical Simulations Using DFT calculations, we examine in detail the adsorption geometries and energetics of cysteine on Cu{421}R. Figure 7 shows our results for the most stable structures in μ3 geometries of each enantiomer of cysteine with their Eads, Eenantio and bond lengths between S and Cu atoms. The most stable configuration of D-cysteine favors a quadridentate configuration with an N atom on top of the Cu kink atom and two O atoms on the kink and nearby step edge in the one atomic lower height, respectively (Fig. 7(a) and (c)). An S atom additionally binds onto the step edge (Fig. 7(c)). This corresponds to the adsorption on {110} microfacet.33,35 For L-cysteine, however, a tridentate adsorption configuration is favored through an N atom on top of the Cu kink atom, an O atom on Cu bridge site of the nearby step edges, and a S atom on the Cu kink atom in the one atomic higher height, respectively (Fig. 7(b) and (d)). The Eads of the adsorbed D-cysteine is -1.87 eV/mole while that of L-cysteine is -1.92 eV/mole, which makes Eenantio = -0.05 eV/mole. The distance between S atom and the nearby C atom in cysteine (d(S-C)) is 1.85 Å for D-enantiomer and the 1.83 Å for Lenantiomer, respectively. This indicates that d(S-C) is stretched upon the adsorption of both enantiomers, compared to 1.82 Å in the DFT optimized geometry of cysteine in the gas phase. Compared to our previous study of alanine adsorption, cysteine is more strongly adsorbed on Cu{421}R.

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Both enantiomers of alanine were adsorbed on {311} microfacets of Cu{421}R, where

Eads was -1.13 eV/mole and -1.16 eV/mole for D- and L-alanine, respectively. Therefore, the adsorption strength of cysteine in μ3 geometry was much stronger for D-form by 0.74 eV/mole and for L-form by 0.76 eV/mole than that of alanine. This indicates that the thiol group in cysteine strengthens the adsorption compared to the alanine adsorption.


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Figure 7: (a, b) Top and (c, d) side views of the most favorable μ3 adsorption configurations of D- and L-cysteine with p(2  1) structures on Cu(421)R. Cu atoms are shown as red-yellow spheres, O atoms as red spheres, H atoms as white spheres, C atoms as gray spheres, N atoms as blue spheres, S atoms as yellow spheres, respectively. The white dashed lines in (a) indicate the surface unit cell. The most stable configurations in μ4 geometries of each enantiomer of cysteine are shown in Fig. 8 with their Eads, Eenantio, and bond lengths between S and Cu atoms. Both enantiomers prefer to bind in the quadridentate fashion. In μ4 geometries, D-cysteine adsorbs onto the {110} microfacet while L-cysteine binds onto {311} microfacet, which is consistent with our previous report for alanine adsorption on Cu{421}R.35 In addition, the S atom in D-cysteine binds onto the four-fold site of {100} microfacet (Fig. 8(c)) and the one in L-cysteine adsorbs on the bridge site of {110} microfacet (Fig. 8(d)), respectively. The Eads of the adsorbed D-cysteinate is -2.41 eV/mole while that of L-cysteinate is -2.40 eV/mole, showing the small enantiospecific energy difference of 0.01 eV/mole. Since most kind of quantum chemistry calculations are challenging to accurately resolve the energy differences at the level of 0.01 eV, the minimum DFT energy difference that can be meaningful should be above


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~0.01 eV. Thus, the energy difference may be negligible. The d(S-C) is 1.86 Å for D-enantiomer and 1.85 Å for the L-enantiomer, respectively. Again, this indicates that d(S-C) is stretched upon the adsorption of both enantiomers of cysteine.

Figure 8: (a, b) Top and (c, d) side views of the most favorable μ3 adsorption configurations of D- and L-cysteine with p(2  1) structures on Cu(421)R. Cu atoms are shown as orange spheres, O atoms as red spheres, H atoms as white spheres, C atoms as gray spheres, N atoms as blue spheres, S atoms as yellow spheres, respectively. The white dashed lines in (a) indicate the surface unit cell. To confirm the existence of lateral interaction, we performed additional DFT calculations for the low coverage adsorption of cysteine. The unit cell was expanded from p(2  1) (8.92 Å  6.80 Å) to p(4  2) (17.84 Å  13.60 Å), which allows the adsorbates to be separate enough to avoid the lateral intermolecular interaction on the surface. For μ3 configuration, the adsorption strength of L-cysteine was reduced by 0.16 eV upon decreasing the surface coverage while that of D-cysteine was rather increased by 0.14 eV (Figs. 7 and 9). This indicates that the lateral interaction of L-cysteine stabilizes


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the adsorption, which is attributed to the attractive hydrogen bonding between oxygen atom unbound with surface in one molecules and amine group in the other molecule (Fig. 7(b)). On the other hand, all oxygen atoms in D-cysteine are bound to the surface and one of them prefers rather to form the intramolecular interaction with the nitrogen atom in the same molecule, not others (Fig. 7(a)). In this case, stronger adsorption to the surface stabilizes the system, and thus the adsorption strength increases at the lower coverage (Fig. 9(a)). Consequently, the enantiospecific difference in adsorption, Eenantio, was changed from 0.25 eV at low coverage to -0.05 eV at high coverage, implying that Lcysteine becomes more stabilized at high coverage. We therefore believe that in our experimental results, the adsorption coverage was not very low, but high enough to have some lateral interaction, especially for L-cysteine.

Figure 9: (a, b) Top and (c, d) side views of the most favorable μ3 adsorption configurations of D- and L-cysteine with p(4  2) structures on Cu(421)R. Cu atoms are shown as red-yellow spheres, O atoms as red spheres, H atoms as white spheres, C atoms as gray spheres, N atoms as blue spheres, S atoms as yellow spheres, respectively. The white dashed lines in (a) indicate the surface unit cell. ACS Paragon Plus Environment

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Similarly to the D-cysteine in μ3 geometry, both enantiomers in μ4 geometries are adsorbed in a quadridentate fashion. Thus, the effect of lateral interaction is not significant, where the differences of Eads and Eenantio between the two coverage are relatively small. The adsorption strength was increased by 0.05 eV for D-cysteine and 0.03 eV for L-cysteine. In addition, Eenantio was slightly increased from 0.01 eV at p(2  1) to 0.03 eV at p(4  2) – both favour D-cysteine.

Figure 10: (a, b) Top and (c, d) side views of the most favorable μ4 adsorption configurations of Dand L-cysteine with p(4  2) structures on Cu(421)R. Cu atoms are shown as orange spheres, O atoms as red spheres, H atoms as white spheres, C atoms as gray spheres, N atoms as blue spheres, S atoms as yellow spheres, respectively. The white dashed lines in (a) indicate the surface unit cell.

To assess the stability of configuration after the decomposition, we should compare the energy state between the adsorbed cysteine in μ3 and the co-adsorbed alanine and dissociated sulphur. ACS Paragon Plus Environment

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For this, we additionally calculated Ediss of μ3 cysteine. Ediss and the configuration of both enantiomers before and after the decomposition are shown in Fig. 11. In the case of D-cysteine, the dissociated sulphur is adsorbed at kink bridge site and alanine is adsorbed on {311} microfacets. On the other hand, for L-cysteine, the dissociated sulphur is adsorbed at 4-fold hollow site near the step edge and alanine have bidentate configuration. The dissociation energies were -1.93 eV and -1.88 eV for Dcysteine and L-cysteine, respectively, which implies that the decomposition was energetically preferred in both enantiomers of cysteine. This indicates that the stability of the dissociated form (coadsorbed alanine and atomic sulphur) is better than that before the decomposition (adsorbed cysteine). Although the adsorption strength of cysteine is stronger than that of alanine, the dissociation of large thiol group and its separate co-adsorption with alanine are more favourable than the adsorption of cysteine in the system. In addition, D-cysteine has more favourable dissociation energy than Lcysteine by 0.05 eV/mole. Based on Brønsted−Evans−Polanyi (BEP) relation which is a linear relation between reaction energy (dissociation energy, here) and activation barrier, therefore, the activation barrier for the dissociation in D-cysteine should be lower than that in L-cysteine. This confirms our experimental results that D-cysteine requires 0.06 eV less energy for the dissociation than L-cysteine.


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Figure 11: Top view of D- and L-cysteine configurations in μ3 geometries before and after decomposition of sulphur on Cu{421}R and the dissociation energy per molecule. The inset shows the side view. 4. Conclusion Stereo effects were observed for the molecular decomposition of L and D – cysteine on the chiral Cu{421} surface using HRXPS and compared to theoretical calculations. The decomposition temperature is different for the enantiomers by 16 K, which is one of the largest chiral effects occurring on a chiral metal surface. The DFT calculations confirmed that the activation barrier for the dissociation in D-cysteine would be lower than that in L-cysteine. Acknowledgement This research was undertaken on the soft x-ray beamline at the Australian Synchrotron, Victoria, Australia. The authors are thankful to the staff at the Australian Synchrotron for providing us ACS Paragon Plus Environment

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with beam. We thank Dr B. Watts (Paul Scherrer Inst, SLS, CH-5232 Villigen, Switzerland) for supplying us with Whooshka – a MatLab based GUI used in the NEXAFS analysis. JWH acknowledges the financial support from the Ministry of Trade, Industry & Energy (MOTIE) of the Republic of Korea (No. 20173010032120) and the National Research Foundation of Korea (NRF2019M3E6A1064913), and the supercomputing resource including technical support from Supercomputing Center/Korea Institute of Science and Technology Information (KSC-2016-C30032). References 1. Petkar, K. C.; Chavhan, S. S.; Agatonovik-Kustrin, S.; Sawant, K. K.; Critical Reviews™ in Therapeutic Drug Carrier Systems, 2011, 28, 101 – 164. 2. Ampuero, S.; Bosset, J.O.; Sensors and Actuators B, The Electronic Nose Applied to Dairy

Products: A Review, 2003, 94, 1–12. 3. Göpel, W.; Electronic noses for gas and odor sensing in food industries: state-of-the-art and new concepts, in: R. Stute (Ed.), Food and science Wissenschaft im Dienste der Ernährung, Bestfoods, Heilbronn, 1997. 4. Trojanowicz, M.; Kaniewska, M.; Electrochemical Chiral Sensors and Biosensors, Electroanalysis 2009, 21, 229 – 238. 5. Barlow, S. W.; Raval, R. Complex organic molecules at metal surfaces: bonding, organization and chirality, Surf. Sci. Rep. 2003, 50, 201-341. 6. Gellman, A. J.; Chiral Surfaces: Accomplishments and Challenges, ACS Nano, 2010, 4, 5 - 10. 7. Gross, E.; Liu, J. H.; Alayoglu, S.; Marcus, M. A.; Fakra, S. C.; Dean Toste, F.; Somorjai, G. A. J.Am.Chem.Soc. 2013, 135, 3881− 3886. 8. H. F. Hildebrand, N. Blanchemain, G. Mayer, F. Chai, M. Lefebvre, F. Boschin Surface & Coatings Technology, 2006, 200, 6318–6324. 9. Salata, O. V.; “Applications of nanoparticles in biology and medicine”, Journal of Nanobiotechnology 2004, 2-3. 10. Balasundaram, G.; Webster, T. J.; Nanotechnology and biomaterials for orthopedic medical applications, Nanomedicine, 2006, 1, 169 – 176. 11. Mahapatra, M.; Tysoe, W. T. Adsorption and Structure of Chiral Epoxides on Pd(111): Propylene Oxide and Glycidol. J. Phys. Chem C, 2018, 122, 1215 – 1222. 12. Gellman A. J.; Ernst, K-H; Chiral autocatalysis and mirror symmetry breaking, Catalysis Lett. 2018, 148, 1610 – 1621.


21


Page 22 of 25

13. Cheong W. Y.; and Gellman A. J.; Energetics of chiral imprinting of Cu(100) by lysine, J. Phys. Chem C, 2011, 115, 1031 – 1035. 14. Preuss, M.; Schmidt, W. G.; Bechstedt, F.; Coulombic amino group-metal bonding: Adsorption of adednine on Cu(110), Phys. Rev. Lett. 2005, 94, 236102. 15. Baddeley, C. J.; Held, G.; Chiral molecules on surfaces. In: Andrews, D. L., Scholes, G. D. and Wiederrecht, G. P. (eds.) Comprehensive nanoscience and technology. Elsevier, London, 2010, 105133. and references therein. 16. Hazen R. M.; Sholl D. S.; Chiral selection on inorganic crystalline surfaces, Nature materials, 2003, 2, 367 – 374. 17. Rampulla, D. M.; Gellman, A. J.; “Enantioselectivity on Surfaces with Chiral Nanostructures” in Dekker Encyclopedia of Nanoscience and Nanotechnology, by Marcel Dekker, Inc. 2004, 1113 – 1123. 18. McFadden, C. F.; Cremer P. S., Gellman, A. J.; Adsorption of chiral alcohols on chiral metal surfaces, Langmuir, 1996, 12, 2483. 19. Pratt, S. J.; Jenkins S. J. King, D. A.; The symmetry and structure of crystalline surfaces, Surf. Sci. 2005, 585, L159. 20. Tadich, A.; Riley, J.; Thomsen, L.; Cowie, B.C.C., Gladys, M. J.; Determining the orientation of a chiral substrate using full-hemisphere angle-resolved photoelectron spectroscopy, PRL, 2011, 107, 175501. 21. Jones, G.; Gladys, M. J.; Ottal, J.; Jenkins S. J.; Held, G.; Surface geometry of Cu{531}, Phys. Rev. B, 2009, 79, 165420. 22. Sholl, D. S.; Asthagiri A.; Power T. D.; Naturally chiral metal surfaces as enantiospecific adsorbents, J. Phys. Chem. B 2001, 105, 4771. 23. Ahmadi, A.; Attard, G.; Feliu J.; Rodes, A; Surface reactivity at chiral platinum surfaces, Langmuir, 1999, 15, 2420. 24. C. Karageorgaki, C.; Ernst,K. H.; A metal surface with chiral memory, Chem. Commun., 2014, 50, 1814-1816. 25. Kuhnle, A.; Linderoth, T. R.; Hammer B.; Besenbacher F.; Chiral recognition in dimerization of adsorbed cystein obseved by scanning tunnelling microscopy, Nature, 2002, 415, 891 – 893. 26. Greber, T.; Sljivancanin, S.; Wider, J.; Hammer, Chiral recognition of organic molecules by atomic kinks on surfaces, B. Phys. Rev. Lett. 2006, 96, 056103. 27. Easson L. H.; Stedman, E.; Studies on the relationship between chemical constitutional and physiological action: Molecular dissymmetry and physiological activity, Biochem. J. 1933, 27, 1257. 28. Kuhnle, A.; Linderoth T. R.; Besenbacher, F.; Enantiospecific adsorption of cysteine at chiral kink sites on Au(110) – (1x2), J. Am. Chem. Soc. 2006, 128, 1076-1077.


22

Page 23 of 25 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


29. 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. 30. Yun Y.; Gellman, A. J.; Enantioselective separation on naturally chiral metal surfaces: D,L-Aspartic acid on Cu(3,1,17) R&S surfaces, Angew Chem. Int. Ed. 2013, 52, 3394 – 3397. 31. Gellman, A. J.; Huang, Y.; Xu, F.; Pushkarev, V. V.; Holsclaw, B.; Mhatre, B. S.; Superenantioselective chiral surface explosions, J. Am. Chem. Soc., 2013, 135, 19208-19214. 32. Eralp, T.; Levins, A.; Shavorskiy, A.; Jenkins, S. J.; Held, G.; The importance of attractive three-point interaction in enantioselective surface chemistry: Sterospecific adsorption of serine on the intrinsically chiral Cu{531} surface, JACS, 2012, 134, 9615-9621. 33. Thomsen, L.; Riley, D. P.; Wharmby, M. T.; Held G.; Gladys, M. J.; The adsorption and stability of sulphur containing amino acids on Cu{531}, Surf. Sci. 2009, 603, 1253-1261. 34. Gladys M. J.; et al. In preparation. 35. Thomsen, L.; Tadich, A.; Riley, D. P.; Cowie

B. C. C.; Gladys, M. J.; Investigating the

enantioselectivity of alanine on a chiral Cu{421}R surface, J. Phys. Chem. C, 2012, 116, 9472. 36. Held, G.; Gladys, M., The chemistry of intrinsically chiral surfaces, J. Top. Catal. 2008, 48, 128. 37. Slater, N. B.; General molecular models which give the Arrhenius form of first order dissociation rate, Trans. Faraday Soc., 1959, 55, 5-8. 38. Kresse, G.; Furthmuller, Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set, J. Comput. Mater. Sci. 1996, 6, 15. 39. Kresse, G.; Furthmuller, Efficient iterative schemes for ab-initio total-energy calculation using a plane wave basis set, J. Phys. Rev. B, 1996, 54, 11169. 40. Perdew, J. P.; Burke, K.; Ernzerhof, M., Generalized gradient approximation made simple, Phys. Rev. Lett. 1996, 77, 3865. 41. Perdew, J. P.; Burke, K.; Ernzerhof, Generalized gradient approximation made simple ;erratum, M. Phys. Rev. Lett. 1997, 78, 1396. 42. Blöchl, P. E., Projector augmented-wave method, Phys. Rev. B 1994, 50, 17953. 43. Kresse, G.; Joubert, D., From ultrasoft pseudopotentials to the projector augmented-wave method, Phys. Rev. B 1999, 59, 1758. 44. Grimme, S. Semiempirical GGA-type density functional constructed with a long range dispersion correction, J. Comput. Chem. 2006, 27, 1787. 45. Monkhorst, H. J.; Pack, J. D. , Special points for Brillouin-zone integrations, Phys. Rev. B 1976, 13, 5188. 46. Methfessel, M.; Paxton, A. T. , High-precision sampling for Brillouin-zone integration in metals, Phys. Rev. B 1989, 40, 3616.


23


Page 24 of 25

47. Šljivancanin, Ž.; Gothelf, K. V.; Hammer, B. , Density functional theory study of enantiospecif adsorption at chiral surfaces, J. Am. Chem. Soc. 2002, 124, 14789. 48. Blankenburg, S.; Schmidt, W. G., Steric effects and chirality in the adsorption of glycine and phenylglycine on Cu(110), Nanotechnology 2007, 18, 424030. 49. Bhatia, B.; Sholl, D. S. J., Characterization of enatiospecific chemisorption on chiral surfaces vicinal to Cu(111) and Cu(100) using density functional theory, Chem. Phys. 2008, 128, 144709. 50. Han, J. W.; Sholl, D. S., Enatiospecific adsorption of amino acids on hydroxylated quartz (0001) Langmuir 2009, 25, 10737. 51. Han, J. W.; Sholl, D. S., Enantiospecific adsorption of amino acids on hydroxlated quartz (1010), Phys. Chem. Chem. Phys. 2010, 12, 8024. 52. Han, J. W. , Enantiospecific chemisorption of amino acids on step decorated chiral Cu surfaces, Top. Catal. 2012, 55, 243. 53. Stöhr, J. NEXAFS Spectroscopy, 2nd. Ed. Springer Series in Surface Sciences, Springer: Berlin, 1996. 54. Gladys, M. J; Han, J. W.; Pedersen, T. S.; Tadich, A.; O’Donnell, K. M.; Thomsen, L.; Adsorption differences between low coverage enantiomers of alanine on the chiral Cu{421}R surface, Phys. Chem. Chem. Phys. 2017, 19, 13562 – 13570.


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Enantiospecific Adsorption and Decomposition of Cysteine

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