Theoretical Simulations of Structure and X-ray Photoelectron Spectra

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Theoretical Simulations of Structure and X‑ray Photoelectron Spectra of Glycine and Diglycine Adsorbed on Cu(110) Vincenzo Carravetta,*,† Susanna Monti,‡ Cui Li,† and Hans Ågren§ †

Institute of Chemical and Physical Processes, CNR-IPCF, via G. Moruzzi 1, I-56124 Pisa, Italy Institute of Chemistry of Organometallic Compounds, CNR-ICCOM, via G. Moruzzi 1, I-56124 Pisa, Italy § Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10044 Stockholm, Sweden ‡

ABSTRACT: The study of adsorption of glycine and glycylglycine (or diglycine) on a copper surface is an important step for the comprehension of mechanisms that determine the stability of biological functionalizers on metal substrates. These two molecules can be considered as prototypes and essential models to investigate, theoretically and experimentally, the adaptability of flexible short peptide chains to a definite interface. In this work, we have improved and updated earlier molecular dynamics simulations by including reactivity of the various species and the comparison of ab initio calculated C, N, and O core photoelectron chemical shifts with the ones found in previous studies. New diglycine−copper bonding is predicted, and the results of the chemical shift analysis are, in all cases, fully compatible with structural information obtained through experimental measurements. Moreover, we have found that the process of proton transfer, which is fundamental in the dynamics of amino acids and peptides, occurs mainly by intermolecular interaction between the first and second layer of the adsorbate.

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INTRODUCTION Knowledge of the organization of matter at the interface between different systems has always been of great interest in basic science. In the past decades it has gained increased importance in various technological applications in the fields of heterogeneous catalysis, chemical sensors, molecular electronics, and biocompatible materials. In this latter area the functionalization of metal surfaces with a great variety of biomolecular compounds has become a very promising technique to obtain materials of superior quality. Indeed, it is the subject of a large number of studies addressed to understand in detail the processes connected to the formation of the interfaces and their chemical physical dynamics. A very recent and interesting review1 illustrates with an extensive bibliography the main theoretical and experimental approaches that are currently used to study the adsorption process between biomolecules and metal surfaces. These investigations have a strong multidisciplinary character because they integrate specialized branches of learning such as materials science, biochemistry, physics, and, last but not least, computational simulations. As a matter of fact, molecular modeling may correlate the results of experimental investigations with models of increasing complexity which can describe, at the atomic level, the chemical components of the interfaces as well as their geometric and electronic structure. Surface science spectroscopies such as reflection absorption infrared spectroscopy (RAIRS), X-ray photoelectron diffraction, © 2013 American Chemical Society

X-ray photoelectron spectroscopy (XPS), and near edge X-ray absorption fine structure (NEXAFS) spectroscopy together with theoretical approaches such as density functional theory (DFT) have been used to date to study different hybrid materials, and among these, amino acids on metals have received special attention. In particular, the adsorption of glycine (Gly) on copper has been studied by various authors2−9 who have shown that the molecule has the general tendency to adsorb in its deprotonated glycinate (H2NCH2COO−) form preferentially locating both its carboxyl oxygens on top of two underlying copper atoms. However, from the examination of the literature it has been noted that most of the theoretical studies have been limited to the optimization of adsorbate structures suggested on the basis of chemical intuition and have been essentially used to verify their stability. Investigations of the dynamical aspects of the adsorption process are less frequent, and those dedicated to chemisorption of small peptides on well-defined surfaces have only recently appeared.3,10−26 From an experimental point of view, spectroscopies with photons in the infrared and X-rays regions can provide special information on the nature of the chemical species present at the interface and, at the same time, details regarding their Received: May 9, 2013 Revised: July 10, 2013 Published: July 15, 2013 10194

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portion of the system should be enlarged to the nanometer scale in order to obtain sensible results. In this case, the use of classical reactive force fields becomes fundamental. ReaxFF is one of these implementations; it has been used successfully to investigate large-complex reactive dynamics28−51 and has been confidently applied to characterize macromolecular selfassemblies in contact with inorganic substrates, in solution and in the gas phase, and to explore and predict the properties of new composite materials. Recently, these methods have been applied to study the adsorption of amino acids and small peptides on metal and metal oxide surfaces.25,26,52 The present work describes our most recent results obtained by modeling the adsorption of glycine and diglycine on the Cu(110) surface. Diglycine, which consists of two glycine residues joined by a single peptide bond, may be considered the most basic molecular model for understanding the adsorption processes of other peptides and more complex biomolecules. Following the approach applied in studying the interface between glycine and titanium dioxide,26,53 the reactivity, conformational properties, and dynamics of glycine and diglycine on Cu(110) have been explored by means of all-atom classical reactive molecular dynamics simulations performed with the ReaxFF code and a set of force fields recently parametrized by quantum calculations on model systems.52

orientation. This is more easily obtained when the experimental results are combined with theoretical simulations of the spectra that are performed through quantum mechanical ab initio methods. In order to have an efficient and reliable model to interpret the experimental results and, possibly, predict the behavior of complex hybrid systems, like the ones made of the interface between the metal and a set of biomolecules, it is often necessary to use several computational methods. For a full description of the formation and stability of a complex interface, such computational models should take into account the reactivity of the various components, that is, the dynamical equilibrium between different chemical species. It is, in fact, evident that different chemical states of an adsorbed molecule can coexist on the surface and their relative abundance can greatly depend, apart from temperature and concentration, on the type of metal, the face exposed, the film thickness, and other factors. In the case of glycine, for example, while the deprotonated form is the predominant one on the Cu surfaces, experimental indications are in favor of the zwitterionic species for the adsorbate on Pd (111).27 This difference in the chemical state of the adsorbed glycine was also investigated from a theoretical point of view,6,7 and various explanations of the molecular behavior were proposed. These studies, based on single molecule DFT optimization of the structure of the different adsorbed species, could anyway indicate, by Monte Carlo simulations, that the aggregation of the glycines plays a very important role factor in the adsorption process. This underlines the need of using model systems with a large number of molecules on the metal surface and, at the same time, the need of computational methods that are able to describe the reactivity for this type of systems. Moreover, it should be observed that in the fields of heterogeneous catalysis, biosensing, or hybrid biomaterials, a biomolecule/metal interface is practically always exposed to a solvent, generally water. Only very recently interesting methodological advances have allowed to extend the experimental techniques of surface science, which generally require ultrahigh vacuum (UHV), to samples in which the adsorption occurs in the presence of water, with good prospects of being able to study, in the near future, film solutions deposited on the metal. With regard to the chemistry of glycine on various metal surfaces when coadsorbed with water, the X-ray spectroscopical studies of Held and co-workers8,9 have admirably highlighted as the aqueous environment greatly influences the balance between the different chemical forms of the adsorbate, its stability, and reactivity. The growing experimental evidence of a complex multicomponent nature of the interfaces between biomolecules and surfaces, even in the relatively more simple cases, requires the development of adequate theoretical models that go beyond the simple optimization of single adsorbed molecules. Classical molecular dynamics simulations of biomolecules in solution and in the gas phase are nowadays a well-established methodology to disclose the behavior of macromolecular systems and characterize the different interactions that determine their structure and supramolecular arrangements in the gas phase and in solution. Moreover, the combination of classical methods with quantum mechanical approaches (QM/ MD) has allowed computational scientists to achieve a more realistic picture of reactive environments, being able to accurately represent the reactive region and the influence of its surroundings on the reaction mechanism. However, these hybrid methodologies can be prohibitively expensive from a computational point of view, especially when the reactive

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COMPUTATIONAL DETAILS The ReaxFF version incorporated into the Amsterdam Density Functional (ADF)28 program was used for all the reactive dynamics simulations. The ReaxFF parameters for copper and for the molecules considered in the present investigation have been determined by quantum mechanical calculations performed in previous studies.26,35,52,53 The parameters for the interaction of Cu with O and H atoms were straightforwardly integrated into the glycine ReaxFF force field by following the suggestions of Gubbins et al.54 The C/Cu interaction was not explicitly optimized since such bonds were not expected to form, while the nonbonded interactions were taken into account by the standard combination rules. The N/Cu interaction was parametrized using small clusters optimized by quantum mechanical calculations as already described in an earlier paper.52 In order to simulate a physical sample that has been also investigated by X-ray spectroscopic measurements, which are performed in ultra high vacuum (UHV), the reactive molecular dynamics simulations were carried out in the gas phase. The system consisted of a six-layer slab with a (110) surface with size (22 × 31) Å2 in x (the close-packed Cu row [11̅0]) direction and y ([001]) direction, respectively, whereas different sets of glycines and diglycines were used to depict various surface coverages. The biomolecules were initially set at an average distance of about 3 Å from the surface, in their nonionic form (most stable species for the molecule in the gas phase). In the case of glycine the two sets consisted of 16 (low concentration = lc) and 34 (high concentration = hc) molecules, while for diglycine a set of 8 molecules was employed. Periodic boundary conditions were applied in all directions, and the height of the simulation box was fixed at 70 Å, in order to make negligible the influence of the adjacent z-image. The adsorption process was simulated by annealing the system to 400 K and then, when most of the molecules were deposited on top of the substrate, by lowering the temperature to 300 K. The characteristics and dynamics of the adsorbates were studied in the NVT ensemble with the temperature regulated by means of the Berendsen thermostat55 10195

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defining relatively small models where the direct interaction of the molecule with distant metal atoms and the other adsorbed molecules are neglected. Notwithstanding this, the methodology requires a great computational effort. However, intermolecular interactions were fully included in the molecular dynamics calculations and are reflected in the selected geometries (Figures 1 and 2). An example of the reduced models employed for the ab initio calculation of the spectra is presented in Figure 3.

(with a relaxation constant of 0.1 ps). The dynamics run was 1.2 ns long, and the time step was 0.25 fs, which is a reasonable value for reactive dynamics calculations where the bond orders are updated every time step.56 The equations of motion were solved with the Verlet leapfrog algorithm,57 and system configurations were sampled every 0.1 ps during the last 900 ps of the dynamics. The simulations were analyzed to estimate the fraction of each glycine and diglycine species, which could be neutral, zwitterionic, anionic, or cationic, and to count the number of hydrogen atoms within 1.3 Å of the nitrogens and within 1.2 Å of oxygens as a function of the simulation time. The fraction of each form is reported in Tables 1 and 2 for glycine and Table 1. Fraction of Different Forms of Glycine at the Beginning and End of the Sampling Period of the Reactive Dynamics time (ps)

neutral

0 982.45

0.81 0.75

0 350.2

0.47 0.44

anionic low concentration 0.13 0.13 high concentration 0.32 0.32

zwitterionic

cationic

0 0.06

0.06 0.06

0 0.03

0.18 0.18

Table 2. Fraction of Different Forms of Diglycine at the Beginning and End of the Sampling Period of the Reactive Dynamics time (ps)

neutral

anionic

0 500

0.875 0.875

0.125 0.125

Figure 1. Most representative adsorbate geometries of glycine on Cu(110).The x-axis (red) points along the close-packed Cu row [11̅0] direction, the y-axis (green) along the [001] direction, and the z-axis (blue) along the [110] direction.

The XPS spectra were computed by ΔSCF calculations of the core ionization potential at each N and O site for both molecules and also at C sites for diglycine, using the DALTON code59 with Ahlrichs VTZ basis set;60 more details can be

diglycine, respectively. The fractional values for diglycine do not add to 1 because one molecule dissociated during the annealing step in the early stage of the dynamics and was not considered anymore. Representative frames for the structures of the adsorbed molecules were extracted from the last portion of the trajectories (in the time intervals 450−500 and 850−900 ps for diglycine and glycine, respectively) because the distributions of the different chemical species in these regions were stable and remained such for the rest of the simulation time. Then, all the selected frames were grouped into clusters, using a distance cutoff of 0.2 Å for the glycine−copper and 0.6 Å for the diglycine−copper models, in order to get a more limited number of highly representative structures of the adsorbate configurations sampled during the dynamics. The final part of each trajectory obtained by the molecular dynamics was analyzed with the GROMACS tool “g_cluster”.58 In practice, the frames were divided into different “clusters” so that in each cluster are located only system structures that have a mutual distance less than the selected cutoff. The distance between two structures is calculated as the root-mean-square deviation of atom-pair distances. In the case of the adsorbed glycine three configurations for the neutral form, two for the anionic and one for the zwitterionic forms were obtained and employed, together with an 18-copper-atom cluster to represent the surface, in the calculation of the XPS spectra. For the diglycine adsorbate a larger slab of 24 copper atoms was employed together with six neutral and one anionic conformations of diglycine. The theoretical procedure for obtaining the XPS spectra consists of

Figure 2. Most representative adsorbate geometries of diglycine on Cu(110). The x-axis (red) points along the close-packed Cu row [11̅0] direction, the y-axis (green) along the [001] direction, and the z-axis (blue) along the [110] direction. 10196

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Figure 3. Examples of reduced models employed for the ab initio calculations of the XPS spectra.

release of the carboxyl hydrogen becomes much more probable in the presence of multilayers and can be described as a multistep mechanism, which takes the molecules from a partially adsorbed orientation to the final tridentate chemisorption of the anions. Intermediate zwitterionic or even cationic species can coexist inside the multilayer but are less frequently observed at low concentration when a glycinate monolayer is firmly established. Such species have a protonated amine group that cannot efficiently interact with a Cu atom. In agreement with previous experimental62 and theoretical studies,63−65 it was also observed that in the most stable tridentate conformation, when the molecules are close to each other, a network of hydrogen bonds among the adsorbed glycine molecules is more easily established and leads to the formation of stable heterochiral domains. A more detailed description of the results of the reactive dynamics of glycine on Cu(110) can be found elsewhere.52 As far as the dynamics of diglycine is concerned, as in the case of glycine, the molecules reached the surface very quickly and established a series of favorable interactions with the substrate coordinating both their oxygens and nitrogen atoms to the metal sites. This appears clearly from the examination of the plot of Figure 4, showing the evolution of the distance of the center of mass of each molecule from the surface during the first 500 ps of the sampling time. It is evident that it took almost 350 ps for most of the molecules to find a relatively stable arrangement on the surface and reduce their movements to damped oscillations around an average distance. These final positions, which are very close to each other (within the range 2.5−3.2 Å), primarily depend on the starting location of the various units, their intramolecular conformation, and their mutual orientation. Similarly to glycine, the adsorbed diglycines tried to establish the maximum number of contacts with the copper top atoms in order to settle stably on the substrate. The fluctuations of the center of mass distances are more marked for larger separations, that is, when the molecules are only slightly attracted by the interface, whereas at closer distances self-interactions and the impediment of the substrate diminish their mobility. As Figure 4 shows, only GG7 remained in an upright orientation with its center of mass at about 4 Å from

found in ref 61. For comparison, the XPS spectra of the most important conformers of glycine and diglycine in the gas phase, already investigated in our previous study,61 were also computed.

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RESULTS AND DISCUSSION Molecular Dynamics. In the first part of the dynamics of glycine, all of the molecules moved spontaneously toward the Cu(110) surface and reached it after about 300 ps. The competition between interglycine interactions and interactions of the molecules with the surface is such that in the lc case less than two-thirds of the interface is covered with a glycine layer at the end of the simulation, whereas in the hc case the surface is more densely occupied (70%). The two sets can be considered representative examples of a submonolayer coverage. The analysis of the reactive dynamics also shows that different forms of glycine: neutral, anionic, zwitterionic, and cationic are present at the end of the simulation, although at the beginning of the simulations all the glycine molecules were in their neutral form. The anionic species are more strongly bound to the surface and adopt a characteristic tridentate bonding orientation with the two oxygens and the nitrogen atom coordinated to three copper sites. As shown in Table 1, the fraction of molecules converted from a neutral to an ionic form grows through the lc sample to the hc one. A direct analysis of the dynamics allows to rationalize this behavior as due to the fact that the proton transfer is realized essentially through the interaction between the glycine molecules of the first and second layer, which, of course, is most active in the hc sample. The deprotonation for a direct transfer to the surface is not highlighted by the present reactive simulations within the sampled time interval (1.2 ns). In agreement with experimental and theoretical studies, different adsorption geometries are observed during the simulations. They involve bidentate interactions, with the two oxygen atoms or with one oxygen and the nitrogen atom both in contact with two copper atoms of the substrate, or even a single interaction site through one of the oxygen atoms, as shown in Figure 1. These configurations tend, however, to be transformed into more favorable tridentate conformations in the long term. The calculations show that the 10197

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Figure 5. Z-density profiles as a function of the distance from the substrate for diglycine.

Figure 4. Distance of the center of mass of the diglycine molecules from the surface as a function of the simulation time.

highest peaks, located at a distance from the interface in the range of 1.8−2.1 Å, identify the chemisorbed heavy atoms. The attachment through the equivalent oxygens of the carboxylic group in a perpendicular orientation is, instead, less frequently observed. It could be speculated that the horizontal adsorption, where the maximum number of effective interactions takes place, could be due to the low coverage regime, whereas at high concentration, packing and self-assembling forces could induce the molecule to adopt upright orientations in order to reach a suitable balance between conformational confinement and surface−molecule connection. On the other hand, it was already suggested66 that a dense upright conformation of glycines would entail repulsion between molecular dipoles. We tend to agree with this second hypotheses, which is also supported by some of our ongoing calculations, for a system with a much larger number of cysteines, which will be presented elsewhere. Those simulations show that at higher coverage a second layer starts to develop rather than converting the molecules to an upright structure. In order to have a more complete picture of the adsorption geometry, the distributions of the backbone torsion angles ϕ and ψ (Figures 7 and 8) were analyzed in detail. These data reflect the variability of the diglycine backbone conformation, which, due to the presence of the substrate, should be limited to selected regions. It is well-known that, having no chiral centers, polyglycine is the most flexible peptide, and its backbone torsion angles, in solution and in the gas phase, present a considerably larger conformational variability than any other amino acid. This high flexibility is responsible for the fact that specific arrangements are highly entropically unfavorable. However, because of the influence of the surface the flexibility of the chain is reduced and the molecules can adopt geometries not sterically allowed for other amino acids. The conformations of the adsorbed molecules slowly evolved in their conformational space folding into various secondary structure arrangements which were induced by the morphology of the interface. As can be seen in the Ramachandran and distribution plots (Figures 7 and 8), diglycine explores all the quadrants of the map throughout the simulation. It presents a Ramachandran map with distinct high probability peaks in the [(−120°, −60°); (−180°, −150°)], [(−120°, −60°); (150°, 180°)], [(−180°, −150°); (−180°, −150°)], [(−180°, −150°); (150°, 180°)], [(−180°, −120°); (−70°, −30°)], [(60°, 100°); (−180°, −150°)], [(60°, 100°); (150°, 180°)] intervals. This means significant population of α-helical and β-sheet structures but also coils, turns, and planar arrangements.

the interface but engaged favorable interactions with the Cu atoms by means of its carboxyl group. All the other structures were flatly adsorbed. The simulation of the dynamics of the adsorption process led to the identification of a number of possible modes of anchorage of glycine and diglycine to the surface, including those which, suggested by chemical intuition, have been in the past the subject of optimizations by quantum calculations. The G4 structure in Figure 1, for example, has the same footprint (tridentate chemisorption) of the most stable structure optimized in several previous investigations using DFT calculations, such as those presented in ref 66. In that case the distances at the three contact points of the adsorbate were estimated as Cu−O (2.07 Å) and Cu−N (2.13 Å), while the present results, as shown in Figure 1, are Cu−O (2.0, 2.1 Å) and Cu−N (2.0 Å). As regards diglycine, the comparison can be made between the most stable structure GG8 in Figure 2, which shows four points of contact with the surface and the structure AN2, with the same footprint, in Figure 2 of ref 61, optimized with DFT calculations. The values obtained by quantum calculationsCu−Ocarbox (2.0, 2.1 Å), Cu−Opept (2.2 Å), and Cu−N (2.2 Å)can be compared to the valuesCu− Ocarbox (1.9, 2.0 Å), Cu−Opept (2.0 Å), and Cu−N (2.0 Å) reported in Figure 2. Considering the differences between the models used in the two investigations and, most importantly, the profound differences between the computational methods employed, the deviations observed in the surface/molecule bond lengths can be considered, in our opinion, acceptable. Further investigations may lead to a refinement of the reactive force fields used in the dynamics, but the present computational approach certainly looks promising for the simulation of more complex biomolecules on metal surfaces. The location of the different atoms of diglycine was analyzed by means of the Z-density profiles shown in Figure 5 and by visual inspection of the trajectory. Some of the sampled binding modes are displayed in Figure 6. The most frequently observed and stable adsorbates seem to be the ones where both the terminus regions and the peptide bond are in touch with the substrate. Indeed, this kind of arrangement induced the molecule to lay in an extended conformation on the top copper atoms and, as a consequence, to align all the oxygens with the copper sites, at a distance of about 1.88 Å, and place all the nitrogens (amine and peptide bond nitrogens) at about 1.96 Å from other Cu atoms of the surface. This clearly appears in the Z-density profiles, shown in Figure 5, where the three 10198

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Figure 7. Distributions of peptide backbone torsion angles ϕ and ψ for diglycine.

Figure 6. Typical binding modes of diglycine. (a) Diglycine in an extended conformation adsorbed through a four-atom coordination to the copper sites of the surface, namely carboxyl oxygen atoms, carbonyl oxygen, and terminus nitrogen atom; distances are highlighted in green. (b) Adsorption of diglycine through a threeatom coordination, namely the nonprotonated oxygen atom of the COOH group, carbonyl oxygen, and terminus nitrogen; in this structure the carboxyl hydrogen points out of the surface. (c) Orientation of another diglycine structure similar to (b) where the carboxyl hydrogen points toward the surface. (d) Diglycine adsorbed in a upright orientation through the nonprotonated atom of the carboxyl group.

Figure 8. Ramachandran map for diglycine adsorbed on Cu(110).

Table 3. O 1s and N 1s Binding Energies (eV) of Glycine in Different Adsorbate Configurations and Isolated

Computed Core Photoemission Spectra. The computed ionization potentials of the O 1s and N 1s cores, for both glycine and diglycine adsorbates, and C 1s, for diglycine adsorbates, are listed in Tables 3, 4, and 5 for the different structures shown in Figures 1 and 2. Both glycine and diglycine molecules have been studied experimentally by X-ray photoemission spectroscopy.2,61 In this kind of study the comparison of experimental results and theoretical values provides valuable information on the geometrical structure of the adsorbate and allows to rationalize the observed chemical shifts in terms of charge transfer in the final state leading to a more or less efficient screening of the core hole. In such a comparison it is

core holes

config

O1

O2

N

G1 G2 G3 G4a G5a G6 gas phase

neutral neutral neutral anionic anionic zwitterionic neutral

539.94 539.93 539.37 537.27 536.37 536.61 540.40

537.30 537.14 536.03 536.81 535.84 536.82 538.31

406.01 406.18 406.05 406.85 406.36 408.62 405.72

a

One proton was added to the cluster model of the surface covered with a glycine in anionic form to make the adsorbate globally neutral.

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When the number of glycines increases, the intermolecular and/or intramolecular proton transfer, between the first and second layers, as observed in the present reactive molecular dynamics results, increases, and the presence of a COO− group allows a stronger anchoring through the oxygens. This is accomplished in the G4−G5 anionic structures and in the G6 zwitterion. In the latter case the on top adsorption of the two O atoms is particularly strong, but, on the other hand, the protonation of the amino group prevents an effective interaction of the N atom with the surface. In the G4−G5 anions the nitrogen lone pair, not engaged with the proton, can interact with an atom of Cu and lead to a more stable adsorbate. The core ionization of the two oxygen atoms in the anionic species, although they are not strictly equivalent due to the constraints imposed by the molecular bonds, lead to a single unresolved peak in the XPS experimental spectrum.2 The fact that the bonding between N and Cu is realized through an electron charge transfer from the lone pair to the surface is also suggested by the spectra in Figure 8B, in which a positive shift in the binding energy for any structure is highlighted, in particular for the tridentate ones G4 and G5, corresponding to a reduced capability of the environment to screen the core hole. The even stronger positive shift observed for the zwitterionic adsorbate G6 is evidently due to the presence of the NH3+ group. The zwitterion, having a bidentate interaction with the surface, does not provide the most stable adsorbate, and in the long run the anionic form prevails. The preparation of the experimental sample normally proceeds through a deposition of a multilayer which is then reduced to a monolayer by desorption of the upper layers caused by a rise in temperature. This procedure makes the deprotonation of the carboxylic group more likely, and even more easily of the NH3+ group by intermolecular interactions, leading to a high yield of the anionic form. Molecular dynamics runs in conditions of submonolayer adsorption may show this evolutionary trend (see our results in Table 1 for the cases of low and high concentration of glycine) but do not reproduce quantitatively the preponderance of anionic species, which, however, is predicted as the most stable one through the theoretical investigation. The spectra calculated at the O 1s, N 1s, and C 1s edges of diglycine for the various adsorption structures illustrated in Figure 2 and for the isolated molecule are collected in Figure 10. The experimental XPS spectra of diglycine on Cu (110) have recently been collected for samples in different coverage conditions, and their interpretation has been addressed by

Table 4. O 1s and N 1s Binding Energies (eV) of Diglycine in Different Adsorbate Configurations and Isolated core holes

config

O1

O2

O3

N1

N2

GG1 GG3 GG4 GG6 GG7 GG8a gas phase

neutral neutral neutral neutral neutral anionic neutral

540.23 540.05 539.81 539.79 540.22 537.39 540.28

536.88 536.46 536.66 537.14 537.60 536.52 538.28

536.58 537.71 537.49 536.13 538.14 538.49 536.24

406.39 406.37 406.09 405.98 405.50 406.43 405.70

407.25 407.76 407.67 406.23 406.42 407.67 405.83

a

One proton was added to the cluster model of the surface covered with a glycine in anionic form to make the adsorbate globally neutral.

Table 5. C 1s Binding Energies (eV) of Diglycine in Different Adsorbate Configurations and Isolated core holes

C1

C2

C3

C4

GG7 GG8a gas phase

293.18 295.46 297.07

293.79 293.95 293.16

295.75 294.21 294.98

292.82 294.39 292.74

a

One proton was added to the cluster model of the surface covered with a glycine in anionic form to make the adsorbate globally neutral.

important to recall that the theoretical values of the ionization potentials measured for an adsorbate cannot be directly related to the experimental data because of the missing “work function” for the emitted electron which amounts to about 5 eV. The theoretical results are more directly comparable to the gas phase results. In Tables 3, 4, and 5 we also report the core binding energies computed for the isolated glycine and diglycine molecules in the gas phase, which are the values that we should refer to in order to define the chemical shifts in the molecule that interacts with the surface. Figure 9 shows the O 1s and N1S photoemission spectra of glycine in different adsorption geometries and in the gas phase. The energy shift toward lower BE observed for each adsorbate indicates that the mechanism of binding between the oxygen atoms and the surface is such as to give an improved electron charge transfer toward the molecule. The two peaks corresponding to hydroxyl (O1) and carbonyl (O2) oxygens remain well separated in the adsorbates G1−G3 in which glycine maintains its neutral form. As already suggested in previous experimental and theoretical investigations,66 these structures can be considered as intermediate steps toward a complete adsorption of glycine on the surface and are more likely to occur under conditions of submonolayer adsorption.

Figure 9. O 1s (A) and N 1s (B) computed XPS spectra of glycine. Full lines are obtained by convolution of the theoretically calculated spectrum (bars) with a Gaussian function of fwhm = 0.5 eV. 10200

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Figure 10. N 1s (A), O 1s (B), and C 1s (C) computed XPS spectra of diglycine. Full lines are obtained by convolution of the theoretically calculated spectrum (bars) with a Gaussian function of fwhm = 0.75 eV.

ΔSCF calculations based on a limited number of structures optimized by DFT calculations.61 We refer to this previous work by one of us for a detailed comparison with experiment. The experimental spectrum of diglycine in the gas phase67 at the O 1s edge shows three broad bands covering an energy range of about 5 eV. The spectrum calculated for the gaseous phase in Figure 10 can explain these data as due to the ionization, with increasing BE, of the carbonyl oxygen in the peptide bond (O3), from the carbonyl oxygen of the carboxyl group (O2), and from that of the hydroxyl group (O1). In the monolayer or multilayer adsorbate oxygen core ionization leads to a single asymmetric broad band with a fwhm of about 2 eV where the individual contribution of the three oxygen atoms cannot be resolved. Despite the rather large bandwidth, there is an evident contraction of the spectral range in the adsorbate compared to the gas phase. This can intuitively be attributed to the disappearance of the O1 contribution due to the deprotonation of the carboxylic group. The results of the present calculations for the diglycine/Cu (110) system, shown in Figure 10, complies with this notion, since for almost all the neutral structures they predict a spectral range significantly larger than that observed experimentally in the adsorbate. For the GG8 structure, corresponding to the adsorption of the anionic form, we find instead a difference between the minimum and maximum values of the BE of about 2 eV. The asymmetric shape of the experimental band,61 with larger intensity on the high BE side, suggests, however, that a small part of the adsorbate may consist in diglycine in neutral or zwitterionic forms. This last form is not discussed here in detail because the result is an O 1s spectrum very similar to that of the anionic species. The presence of some diglycine zwitterions on the surface is, as predicted by the present molecular

dynamics and confirmed by the experimental data in Figure 4 of ref 61, more relevant in the multilayer adsorbate. The experimental N 1s spectrum of the isolated diglycine67 shows a single broad band despite the fact that the molecule contains two chemically nonequivalent N atoms. The result of the calculations in Table 4 and Figure 10 shows that this is justified by a relative chemical shift (0.13 eV) which does not permit the resolution of the two contributions. The width of the band, a little more than 1 eV in the gas phase, grows significantly in the adsorbate spectrum to 2 eV, suggesting an increase in the relative chemical shift deriving from a different interaction with the surface of the amine nitrogen (N1) and of the peptide nitrogen (N2). The calculations for the adsorbate support this hypothesis, since in almost any adsorbate spectrum, in Figure 10 an increased separation of the two contributions to the spectrum, that ranges from 0.8 to 1.6 eV, is observed. This differential chemical shift is compatible with the experimental bandwidth of about 2 eV.61 The weaker shoulder at about +3 eV with respect to the main band in the experimental spectrum61 is, instead, easily attributable to N 1s ionization of the protonated amino group of the zwitterion, as also indicated by the fact that this contribution, which is very weak in the monolayer spectrum, grows significantly on passing to the multilayer. These conclusions for the O 1s and N 1s spectra are in substantial agreement with those deduced from our previous theoretical analysis of the diglycine/Cu(110) core photoemission spectra.61 The results of the present calculations allow instead a more complete interpretation of the C 1s spectra. At this edge the experimental spectrum for diglycine in gas phase shows three bands67 despite that the molecule contains four chemically inequivalent C atoms. Also in this case theory provides an adequate interpretation based on the values of the 10201

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stable heterochiral domains. Also for diglycine, it is found that the most frequently observed and stable adsorption events are the ones where both the terminus regions and the peptide bond are in touch with the substrate. This kind of interaction induces a configuration where diglycine tends to lay in an extended conformation with all the oxygens almost on top of the copper sites. The analysis of the chemical shifts computed for the main bands of the XPS spectra at the O 1s, N 1s, and C 1s edges shows that the O−Cu bonding involves an electron charge transfer from the metal surface, while the molecule acts as a charge donor in the N−Cu bonding (through the N lone pair). Accordingly, the protonated amine group of the zwitterionic species cannot efficiently interact with Cu atoms. This mechanism, together with the strong interaction of the deprotonated carboxylic group with two neighboring Cu atoms along the close packed [11̅0] direction, deriving from a good matching of the O−O and Cu−Cu distances, leads to a preference for the anionic form of the diglycine adsorbate on the Cu(110) surface. The results of the present reactive molecular dynamics simulations suggests that both in the case of glycine and diglycine the formation of the anionic units is due to proton transfer between the first and second layer of the adsorbate. In the gas phase the zwitterionic form is stable only in a multilayer regime and is converted to the anionic form when the coverage is reduced to a monolayer or submonolayer. A clear effect of the surface is also to reduce the flexibility of diglycine. Indeed, the geometries of the adsorbed molecules slowly evolved in their conformational space, folding into various secondary structure arrangements which were induced by the morphology of the interface. The present classical reactive molecular dynamics have succeeded in describing realistically a biometal interface and in providing information on the chemical nature of the adsorbed species, their orientation, and bonding interactions with the surface. Together with the theoretical simulation of the spectroscopic data, it could be a powerful tool to identify possible mechanisms of the adsorption process at atomic level. In the present case, the analysis of the C 1s, N 1s, and O 1s chemical shifts in the photoelectron spectra of glycine and diglycine on Cu(110) reinforces, in all important aspects, the structural findings of the MD simulations and validates the abundance of the anionic form of glycine and diglycine with distinctly different chemical shifts.

relative chemical shifts. The broader band at low BE collects the contributions of core ionization of carbons C2 and C4 which have a similar chemical environment with sp3 hybridization and four single bonds with two H atoms, one C atom, and one N atom. A higher BE peak is due to carbon C3 of the peptide group that reflects the transfer of electronic charge from C3 toward the oxygen atom O3, to which it is directly linked. An even greater transfer is that experienced by C1, which belongs to the carboxyl group and which gives origin to the highest BE band. The interpretation of the C 1s spectrum of the molecule in the gas phase is then easily understood as due to the different effect of screening of the core hole ionization in the different sites. When the diglycine is adsorbed on the surface of Cu (110), the spectrum of C 1s is reduced to two bands separated by about 2.5 eV with the lower BE band having a greater width and also an evidently greater intensity in the case of a monolayer adsorbate. The present calculations for the two most representative structures GG7 (neutral) and GG8 (anionic) presented in Figure 10 and Table 4 provide a good interpretation of the variation of the spectral profile in terms of different energy shifts of the four contributions to the spectrum. In both cases the greatest shift of the BE with respect to the isolated diglycine is observed for C1; this shift is negative and originates from a more efficient screening due to the transfer of electronic charge from the surface to the carboxylic oxygen atoms and, indirectly, to C1 which belongs to the same group. The chemical shift for the other contributions to the spectrum can be instead positive or negative; both for the GG7 and GG8 adsorbates they lead to close contributions to form a single broad and intense band. The best agreement of the presently calculated C 1s spectrum with the experiment, which could not have been obtained in the previous survey,61 is attributed to a more accurate modeling of the system in the ab initio calculations. In the present calculations a larger cluster of Cu atoms was used to represent the surface, also including atoms of the second layer of the slab. The interaction of diglycine with the Cu atoms of the second layer can, in a first approximation, be considered a small fraction of the stronger interaction with the Cu atoms of the first layer in the case of atoms (O, N) directly bound to the surface. In contrast, it is not negligible in comparison with the interaction with the first layer, in the case of C atoms that are located at a larger distance from the surface.

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CONCLUSIONS In order to gain more understanding of glycine and diglycine mono- and multilayer adsorption on the Cu(110) surface, we have generalized our previous molecular dynamics simulations by using a reactive force field and by adding the results of quantum mechanical calculations of the X-ray photoelectron chemical shifts. Reactivity, conformational properties, and dynamics of glycine and diglycine on copper have been explored by means of all-atom classical reactive molecular dynamics simulations carried out with the ReaxFF code and a force field recently parametrized by means of quantum calculations on model systems. Our results lead to some salient conclusions about the structure and dynamics of the studied adsorbates. In agreement with previous experimental62 and theoretical studies,63−65 it was confirmed that in the most stable tridentate adsorption conformation glycine molecules, which are close to each other in the high coverage condition, tend to form a network of intermolecular hydrogen bonds and be arranged as

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected] (V.C.). Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS Adri C. T. van Duin is gratefully acknowledged for the serial version of the reactive dynamics program (ReaxFF) and for his useful comments and suggestions. C.L. and V.C. are grateful for the contribution of the “Ministero della Istruzione della Universita’ e della Ricerca, Direzione Generale per la Internazionalizzazione della Ricerca” of the Republic of Italy. V.C. and H.Å. dedicate this work to the colleague and friend Trygve Helgacker on the occasion of his 60th birthday. 10202

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