Functional Group Adsorption on Calcite: I. Oxygen Containing and Nonpolar Organic Molecules

Transcription

1 SUPPORTING INFORMATION Functional Group Adsorption on Calcite: I. Oxygen Containing and Nonpolar Organic Molecules E. Ataman*, M. P. Andersson, M. Ceccato, N. Bovet, S. L. S. Stipp Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark S1. DFT calculations, in the absence of dispersion corrections To obtain a fuller understanding of the extent of dispersion interactions on adsorption energies, we performed geometry optimization calculations without dispersion corrections. For these calculations, the PBE exchange-correlation functional and PAW pseudopotentials were used. We chose PBE because it is one of the most widely used exchange-correlation functionals in the solid state physics and materials science communities. First, optimized bulk unit cell parameters of calcite were derived. The lattice parameters, a = 5.04 Å and c = Å, are in agreement with the values calculated using the DFT-D2 method. From this converged bulk unit cell, a 2 2, four molecular layer slab of {10.4} surface was created. For adsorption energy calculations, the plane wave cutoff was set to 37 Ry and only the gamma point was used. Geometry optimization calculations were started from converged DFT-D2 geometries. Figure S1 shows the adsorption energy for eighteen molecules, calculated using DFT-D2 and DFT methods. Four main conclusions can be derived from these data: i) The adsorption energies calculated using the DFT-D2 method are higher than those calculated by DFT, except for water, formic and acetic acids. ii) The differences between adsorption energies calculated using different methods are lowest for carboxylic acids, followed by alcohols and highest for aldehydes. The difference becomes larger with increasing size of the molecule. S1

2 iii) The trends and the conclusions drawn in the main paper, from the DFT-D2 calculations, concerning the effects of side groups on adsorption behavior of the different functional groups, are mostly supported by DFT calculations. Different carboxylic acids have similar adsorption energies. The adsorption energy of formaldehyde is lower than acetaldehyde and propionaldehyde. Benzaldehyde has the lowest adsorption energy because of its flat adsorption geometry. Among the alcohols, water has the highest adsorption energy because of its additional hydrogen bond, followed by the methanol and ethanol. Phenol has the lowest adsorption energy. iv) If we were to use the adsorption energy values calculated using DFT to predict desorption temperatures, then the predictions for furan and acetone would be off by ~40 C and not change for water and acetic acid. Thus, DFT-D2 with revpbe functional predicts a desorption temperature that is more consistent with experimental values than the DFT predictions made with the PBE functional. S2

3 Figure S1. Adsorption energy for eighteen nonpolar and oxygen containing polar molecules, calculated using DFT (red circles) and DFT-D2 (black squares). S2. C 1s fits, coverage estimation and residual carbon The left panels of Figure S2 show XPS spectra and fits for furan, acetone and acetic acid, together with the individual peaks for the various carbon species. The spectra were calibrated to the carbonate peak from calcite, at ev. A Shirley background fit was made for all spectra and we used Voigt profiles for peak fitting. The following constraints were applied in the fitting procedure: (i) for the furan spectrum, the areas of the two molecular carbon species were set equal; (ii) for the acetone spectrum, the area of the carbonyl peak was set to be half the area of the methyl peak and the binding energy difference between the two peaks was set to 3.3 ev [S1,S2]; (iii) for the acetic acid spectrum, the areas of the two molecular carbon species were set to be equal and the binding energy difference between the two peaks was set to 3.8 ev [S3]. S3

4 As we see in the right panels of Figure S2, some amount of residual carbon remained after desorption of acetone and acetic acid. The binding energy of the peaks suggests -C y H x species. Dissociative desorption of both acetone and acetic acid has been observed previously [S4,S5] and the results show that some of the molecules desorb from the Pd(111) surface intact. The experimental desorption temperatures we have reported and used for comparison with theoretical calculations in the main paper are for those intact molecules. S4

5 Figure S2. Left panels: C 1s X-ray photoelectron spectra of furan, acetone and acetic acid on calcite {10.4} at 135 C. Dots represent experimental data and lines represent the fits. For each spectrum, the individual components of various carbon species are represented by shaded peaks and marked by arrows. Right panels: X-ray photoelectron spectra of calcite {10.4} after the adsorbed molecules were desorbed. S5

6 The area ratios for the molecular and carbonate C 1s peaks (C mol /C car ) were used to estimate the surface coverage. First, the expected C mol /C car ratio for a monolayer of a particular molecule was calculated from theoretical values. By comparing this number to the experimental value, the experimental coverage was estimated. It is important to point out that the coverages calculated in this way are only estimates. To calculate the C mol /C car ratio for each equivalent molecular layer, three quantities are needed; the thickness of the monolayer, inelastic mean free path (IMFP) for electrons in that particular molecular layer and the IMFP of electrons in calcite. Once these values are known, the Beer-Lambert law, =exp, can be used to calculate the expected C mol /C car ratio.,,, and represent initial and reduced intensity of emitted photoelectrons, IMFP and thickness of the layer. The NIST electron inelastic mean free path software [S6] was used to predict the IMFP of electrons in various materials. This program can calculate IMFP by using either one of two predictive formulae, TPP-2M or G1. We chose the comparatively less complicated G1 method mainly because the TPP-2M method requires the energy gap (HOMO-LUMO) of the material under investigation as an input. This is difficult to estimate for a material adsorbed on a surface. In contrast, the G1 method calculates IMFP simply from the chemical formula of the molecule and the density. All geometric parameters were extracted from calculated adsorption geometries by considering that in one monolayer, two molecules would associate with each unit cell of calcite. Using the G1 method, the following values were obtained for acetic acid, acetone and furan: the thickness of the equivalent layers was 3.05 Å, 2.48 Å and 2.68 Å; calculated IMFP was 27.1 Å, 19.8 Å and 20.8 Å; and the C mol /C car area ratio was 0.22, 0.33 and The distance between the layers in the calcite crystal is 3.14 Å and its calculated IMFP value is 30.7 Å. From S6

7 these values, the equivalent layer coverage was estimated to be ~1.5 ML for acetic acid and ~0.5 ML for acetone and furan. Adsorption of water on calcite {10.4} has been investigated previously. The published results are not consistent for the degree of adsorbed water dissociation and the thickness of the adsorbed layer. In spite of the discrepancies about the details, the calcite surface is hydrated and the water is structured by the underlying mineral surface. Our experimental results suggest that within the reported temperature range, water adsorbs and desorbs from the surface as intact molecules. O 1s spectra in Figure 5c in the main paper show that for the water layer formed on the calcite {10.4} surface, three discrete desorption processes occur, one at 110 ± 10 C, another at 30 ± 10 C and finally one at 10 ± 10 C. We speculate that the first stage is desorption or sublimation of bulk water, the second is the desorption of the structured water and the last is the desorption of the water that is strongly associated with calcite. S3. Effect of coverage on adsorption energy In the main paper, we reported on adsorption energy calculations for a low coverage (0.13 ML), that is, for almost fully isolated molecules on the surface because our main focus was on molecule-surface interactions rather than molecule-molecule interactions. As the number of molecules on a surface increases, intermolecular dispersion interactions and steric hindrance begin to affect the adsorption energy. However, it can be difficult to predict the net result of these two opposing interactions. To investigate the effects of interaction, we performed adsorption energy calculations for water, acetic acid, acetone and furan for different coverages; from two to eight molecules in a 2 2 unitcell, which corresponds to coverages of 0.25, 0.38, 0.50, 0.63, 0.75, 0.88 and 1 ML. To generate starting geometries for these calculations, we adopted two S7

8 different methods. The first was the bottom to top approach, in which we started from the converged 0.13 ML geometry reported in the main paper, added one molecule to each unique adsorption site and optimized the resulting structures to find the most stable adsorption geometry for 0.25 ML. The most stable geometry for 0.25 ML was then used in the same way to find the most stable adsorption geometry for 0.33 ML and so on, up to 1 ML coverage. The second approach was top to bottom, where, based on the converged 0.13 ML geometry, we created 1 ML and optimized this structure. From the optimized geometry at 1 ML, we removed one molecule from each unique site and re-optimized the resulting structures to find the most stable adsorption geometry for 0.88 ML. We continued in this way until we got the same geometries as for the bottom to top approach. From the most stable adsorption geometries, we calculated adsorption energy per molecule for a particular coverage. The results are presented in Table S1 and discussed in the main paper. Table S1. Adsorption energy per molecule (ev) for water, acetic acid, acetone and furan on calcite {10.4} for various coverages. Molecule/ Coverage (ML) water acetic acid acetone furan S8

9 S4. Various alternatives for deriving desorption temperature To make a prediction for the desorption temperature from the calculated adsorption energies, we used the Polanyi-Wigner equation: =, where represents surface coverage,, time, represents a prefactor,, the adsorption energy,, the Boltzmann constant, and, the desorption temperature. We assume that adsorption does not require an activation energy, that is, absolute values of adsorption and desorption energies are equal and that adsorption energy does not depend on coverage. The values reported in Figure 6 in the main paper were calculated using: = h, where initial,, and final,, coverage are set to 1 ML and 0.01 ML, i.e. 99% of the monolayer is desorbed. The prefactor,, was approximated to be /h, where h represents Planck's constant. The value in the upper limit of the time integral reflects the experimental conditions. During the XPS measurements, the system was kept at a particular temperature for 600 seconds before the spectrum was collected. The results of this calculation are shown as black dots in Figure S3 (the same values are reported in Figure 6 in the main paper). To test the robustness of our approach, we also calculated the desorption temperatures using other parameters. In Figure S3, red squares show the calculated desorption from 1 ML to 0.1 ML (90% percent of the monolayer is desorbed); green triangles show the results from 0.5 ML to 0.01 ML and blue diamonds show desorption from 1 ML to 0.01 ML but for these, the prefactor was set to the commonly used value, s 1. As we see in Figure S3, the differences between temperatures calculated using different parameters are very small (between 4 7 C). S9

10 Figure S3. Desorption temperatures calculated using the DFT-D2 adsorption energies and the Polanyi-Wigner equation with a variety of parameters. To calculate the desorption temperature above, we assumed that the adsorption energy does not change with coverage. As we showed in Section S3, this is not true in general. Coverage can affect the adsorption energy and therefore the desorption temperature. To investigate the effect, we calculated the desorption temperature for water, acetic acid, acetone and furan with the coverage dependent adsorption energy values. For these calculations we assumed that desorption of a ML takes place within 600 seconds and used = h, where the limits of the integration on the left side of the equation represent the various coverages, each with corresponding adsorption energy per molecule, given by. The desorption temperatures calculated in this way for water, acetic acid, acetone and furan are 10, 75, 61 and 90 C. These can be compared with the values calculated above, namely, 8, 57, 55 and 115 C. S10

11 The difference between desorption temperatures calculated using different methods are highest for acetic acid and furan, for which adsorption energy increase ~0.11 ev from 0.13 to 1 ML. S5. Additional adsorption geometries The most stable adsorption geometries for water, phenol and benzaldehyde cannot be used to assess the effects of particular side groups on adsorption behavior because of relatively strong side group-surface interactions. For formaldehyde, the carbon atom of the molecule has a strong dispersion interaction with a surface oxygen atom. Therefore for these four molecules we made additional geometry optimization calculations in which the molecules have upright adsorption geometries. The results of these calculations are presented in Figure S4. Figure S4. Adsorption geometries and energies (E ad ) for water, phenol, formaldehyde and benzaldehyde on calcite {10.4}. These were used for assessing the effect of particular side groups on adsorption behavior for the hydroxyl and aldehyde functional groups. For each geometry, the difference between adsorption energy and dispersion contribution (E ad E dc ) and distances between some atoms in the molecules and the surface are given. Ca is represented by green spheres, C, by gray, O, by red, and H, by white. For water and formic acid, we tried dissociative adsorption geometries. In these calculations, we removed one of the H atoms from water and the H atom of the carboxyl group from formic acid, placed the H atom close to a surface O atom and the rest of the molecule on S11

12 different sites on the surface. In the case of water, the H atom combined with the OH group and formed an intact water molecule. In the case of formic acid, we found a few exothermic adsorption geometries. In Figure S5 we show the two most stable of them. Figure S5. The two most stable dissociated absorption geometries for formic acid on calcite {10.4}. For both geometries, adsorption energies and distances between some atoms in the molecules and the surface are given. Ca is represented by green spheres, C, by gray, O, by red, and H, by white. S6. Partial Charge Calculations and pk a In the main paper we stated that the side groups affect the adsorption energy by changing the electronic structure of the functional group and therefore the strength of electrostatic and hydrogen bonding interactions. One way to assess the changes in the electronic structure is to investigate the partial charges of different atoms for different molecules. For this purpose we calculated Löwdin partial charges [S7,S8] for the polar molecules and in Table S2 we present the results for H and O atoms of the molecules that interact with calcite surface along with the corresponding interaction distances (from Figures 2 and 3 in the main paper). S12

13 Table S2. Calculated charges for the H and O atoms of the polar molecules and corresponding hydrogen bond lengths and electrostatic interaction distances (from Figures 2 and 3 in the main paper, * from Figure S4). For alcohols and carboxylic acids, the pk a values are also reported [S9]. Molecule pk a molecule and corresponding hydrogen bond length Partial charge of the H atom of the Löwdin Charge O surf -H mol Distance Partial charge of the O atom of the molecule and corresponding electrostatic interaction distance Löwdin Charge (e) (Å) (e) Water* Methanol Ethanol Phenol* Formic Acid Acetic Acid Propanoic Acid Benzoic Acid Formaldehyde* Acetaldehyde Propionaldehyde Benzaldehyde* Dimethyl Ether Furan Acetone Ca surf -O mol Distance (Å) There are two important points that we observe from the data. The first is that the charges of the H atom for alcohols and carboxylic acids are similar, in contrast to relatively shorter hydrogen bond lengths for carboxylic acids. One possible explanation for the disagreement is that for alcohols and water, in addition to hydrogen bonding, the hydroxyl functional group is electrostatically attracted to the Ca atom of the surface and therefore the geometry is influenced by two opposing forces. In other words, a gain in the strength of hydrogen bonding results in a loss in the strength of the electrostatic interactions. A similar effect is probably much weaker for the carboxyl functional group because of its relatively larger size. It is also possible that the partial charge calculation with the computational method that we used is not accurate enough for capturing the charge differences for the H atoms. In Table S2, we list the pk a values for alcohols and carboxylic acids. The hydrogen bond lengths for the different molecules are correlated with S13

14 their pk a values. This is a strong indication that the amount of positive charge on the H atom of a molecule is proportional to the strength of the hydrogen bond that the molecule forms with the surface. The second observation is that if the alcohols are excluded, because of the competing hydrogen bonding and electrostatic interactions that were discussed above, then there is a linear trend between increasing Ca-O (electrostatic interaction) distance and decreasing negative charge of the O atom of the molecules. In Figure S6 we show how the calculated charges for the O atom of the molecules correlate with the electrostatic interaction distances for carboxylic acids, aldehydes, dimethyl ether, furan and acetone. Figure S6. The plot for the partial charge of the O atom of the molecules versus corresponding Ca-O (electrostatic interaction) distance for carboxylic acids, aldehydes, dimethyl ether, furan and acetone (the values are from Table S2). S7. Generation of starting geometries The top layer of the calcite {10.4} surface consists of undercoordinated Ca and O atoms. The Ca atoms have positive and O atoms have negative partial charge and attract oppositely charged species. In particular, for the molecules studied in this work (except ethane and benzene) the O atom of the molecules is attracted to a surface Ca atom and if possible, the molecules form a S14

15 hydrogen bond (in case of water two hydrogen bonds) with a surface O atom. For each Ca atom on the surface, we considered three O atoms that can act as a hydrogen bond acceptor (Figure S7a). In addition to the top layer, the O atom beneath the surface Ca atom is also shown in Figure S7. The most stable adsorption geometries of water (Figure S7b), furan (Figure S7c) and benzaldehyde (Figure S7d) show that the O atom of the molecules is positioned on the opposite site of the O atom underneath, to complete octahedral coordination of the surface Ca atom. For alcohols, water and carboxylic acids, different possible hydrogen bonding configurations are considered as different starting geometries. Because of its size and delocalized electrons, the phenyl ring as a side group can have strong interaction with the surface and offer an adsorption site for the molecule in addition to its functional group. For phenol, acetic acid and benzaldehyde, additional adsorption geometries have been considered, where the phenyl group of the molecules is pushed toward the surface for several different orientations of the molecule, to introduce a possible interaction between the phenyl ring and the surface. In their most stable adsorption geometry, phenol and benzaldehyde bend toward the surface while for acetic acid, bent geometry resulted lower adsorption energy. Aldehydes, dimethyl ether, acetone, furan and carbon dioxide cannot hydrogen bond with the surface. Therefore, the only possibility for these molecules to attach are electrostatic and dispersion interactions. To generate different staring geometries for these molecules, we placed the O atom of molecule close to a surface Ca atom and tried different adsorption geometries where the molecules were rotated around themselves and around the axis defined by Ca-O. In addition, we tried the geometries where the O atom of the molecules coordinated to two surface Ca atoms. S15

16 Benzene and ethane are two nonpolar molecules that consist of only C and H and have very small structural charge separation. For these molecules the interaction with the surface is mainly dispersive and therefore it is a challenge to predict their adsorption geometries. For these two molecules alone, we have tried 25 different starting geometries in which we placed the molecules parallel to and approximately 3 Å away from the surface (Figure S7e and S7f) and moved the molecules in steps of their lateral size above the surface to generate different starting geometries. Figure S7. Top view of the calcite {10.4} surface without (a) and with (b-f) molecules. For the surface Ca atom at the center, the O atom underneath is also shown. (a) Possible hydrogen bond acceptors nearby a particular surface Ca atom. Converged (b) water, (c) furan, (d) benzaldehyde geometries. In (c) and (d) the Ca-O axis around which the molecules were rotated is also shown. A starting geometry for (e) benzene and (f) ethane. Ca is represented by green spheres, C, by gray, O, by red, and H, by white. S16

17 References for Supporting Information [S1] In Sparks, S. C.; Szabo, A.; Szulczewski, G. J.; Junker K.; White, J. M. Thermal, Electron, and Photon Induced Chemistry of Acetone on Ag(111). J. Phys. Chem. B 1997, 101, The binding energy difference between methyl and carbonyl carbon species was measured as 2.8 ev. [S2] In Senanayake, S. D.; Gordon, W. O.; Overbury, S. H.; Mullins, D. R. Adsorption and Reaction of Acetone over CeO x (111) Thin Films. J. Phys. Chem. C 2009, 113, and in Starr, D. E.; Pan, D.; Newberg, J. T.; Ammann, M.; Wang, E. G.; Michaelides, A.; Bluhm, H. Acetone adsorption on ice investigated by X-ray spectroscopy and density functional theory. Phys. Chem. Chem. Phys. 2011, 13, The binding energy difference between methyl and carbonyl carbon species was measured as 3 ev. [S3] Krepelová, A.; Bartels-Rausch, T.; Brown, M. A.; Bluhm, H.; Ammann, M. Adsorption of Acetic Acid on Ice Studied by Ambient-Pressure XPS and Partial-Electron-Yield NEXAFS Spectroscopy at K. J. Phys. Chem. A 2013, 117, [S4] Davis J. L.; Barteau, M. A. The influence of temperature and surface composition upon the coordination of acetone to the Pd(111) surface. Surf. Sci. 1989, 208, [S5] Haley, R. D.; Tikhov, M. S.; Lambert, R. M. The surface chemistry of acetic acid on Pd{111}, Catal. Lett. 2001, 3-4, [S6] Powell, C. J.; Jablonski, A. NIST Electron Inelastic-Mean-Free-Path Database, Version 1.2, National Institute of Standards and Technology, Gaithersburg, MD (2010). [S7] Löwdin, P. O. Quantum Theory of Many-Particle Systems. I. Physical Interpretations by Means of Density Matrices, Natural Spin-Orbitals, and Convergence Problems in the Method of Configurational Interaction. Phys. Rev. 1955, 97, S17

18 [S8] Löwdin, P. O. On the Non Orthogonality Problem Connected with the Use of Atomic Wave Functions in the Theory of Molecules and Crystals. J. Chem. Phys. 1950, 18, [S9] CRC Handbook of Chemistry and Physics. 94th ed. CRC Press, pp. 5-94, S18