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Functional Group Adsorption on Calcite: I. Oxygen Containing and Nonpolar Organic Molecules Evren Ataman, Martin Peter Andersson, Marcel Ceccato, Nicolas Bovet, and Susan L. S. Stipp J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.6b01349 • Publication Date (Web): 23 Jun 2016 Downloaded from http://pubs.acs.org on July 5, 2016

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The Journal of Physical Chemistry

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

ABSTRACT Considerable interest in calcite crystallization has prompted many studies on organic molecule adsorption. However, each study has explored only a few compounds, using different methods and conditions, so it is difficult to combine the results into a general model that describes the fundamental mechanisms. Our goal was to develop a comprehensive adsorption model from the behavior of a range of organic compounds by exploring how common functional groups interact with calcite and the effects of various side groups and hydrogen on adsorption. We used density functional theory, with semiempirical dispersion corrections (DFT-D2), to determine adsorption energy on calcite {10.4} for nonpolar (benzene, ethane, carbon dioxide) and oxygen containing polar molecules (water, methanol, ethanol, phenol, formic acid, acetic acid, propanoic acid, benzoic acid, formaldehyde, acetaldehyde, propionaldehyde, benzaldehyde, dimethyl ether, acetone and furan). From the adsorption energies, within the transition state theory approximation, we derived desorption temperature for each molecule. Then we used X-ray photoelectron spectroscopy (XPS) to determine the desorption temperature for four representative molecules and compared the experimental results with those predicted. Carboxylic acids (RCOOH) adsorb more strongly than water and alcohols (R-OH), which in turn adsorb more strongly than the aldehydes (R-CHO). Attachment of a hydrogen atom or a side group changes adsorption behavior for hydroxyl and aldehyde functional groups but does not affect the carboxyl functional group significantly.

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INTRODUCTION A detailed understanding about the behavior of the interfaces between inorganic mineral surfaces and organic molecules has the potential to open new perspectives for a number of scientific questions and technological challenges. Among inorganic compounds, calcium carbonate (CaCO3) has a prominent place because it is ubiquitous in nature, it is common in industrial processes and it is frequently used by biological organisms to produce hard parts for support and protection. The results of numerous studies suggest that organic molecules, present during the biomineralization process, such as proteins and polysaccharides, have an important effect on the formation of the elaborate structures of these biominerals but the exact mechanisms are not yet fully understood. Consequently, during the past three decades, the interaction between organic molecules and the surfaces of the various CaCO3 polymorphs has attracted considerable interest1. CaCO3 is the main constituent of sedimentary rocks such as chalk and limestone, where a considerable proportion of the world’s oil reserves are found2. One of the most commonly applied methods to increase oil recovery (IOR), namely, water flooding to maintain pressure in an oil reservoir, still only results in producing a fraction of the oil in place so there is a strong financial incentive to enhance oil recovery (EOR) further. Different methods are used in EOR to change the properties of oil-water and oil-rock interfaces3. One method is to use surfactants. Another is to change the composition of the injected water. Although there are many successful applications of EOR in oil fields all over the world, clearer understanding of the actual physical and chemical processes that control oil release and what happens at water-organic compoundrock interfaces at the molecular level would provide clues for optimizing the effect for oil reservoirs and to shed light on solid-fluid interactions for a broad range of other applications.


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One of these applications is mineral scaling, where CaCO3 is a common culprit. It causes serious problems in industry, where growing minerals clog pipes, decrease heat dissipation efficiency and in some cases, enhance degradation of mechanical parts. The common solution to scaling is to use chemicals to inhibit mineral growth. Inhibition is achieved either through complex formation, which decreases the free ion concentration in solution, or through surface adsorption, which blocks the active growth sites. The search for new molecules that are economically feasible, harmless to the environment and have high inhibition efficiencies is an active field of research. Calcite is the most stable polymorph of CaCO3 in ambient conditions and the {10.4} family of faces represents the most stable surfaces. Calcite has been used extensively as a model substrate for organic-inorganic interfaces in both experimental and theoretical studies. Adsorption of various molecules has been investigated, ranging from small molecules such as water4-18, alcohols18-23, carboxylic acids4,19,24-34 and amino acids35-40, to bigger molecules such as polypeptides41-43, proteins41,44 and polysaccharides45,46. The problem is that all of these studies have focused on adsorption of a few selected molecules and reached conclusions that are appropriate for the particular study but that are limited in overall applicability. Also, in the computational studies, there are some contradictory results for adsorption energy and the most stable adsorption geometry for a particular molecule and for relative stabilities among different molecules. These inconsistencies mostly result from differences in the approaches used, the adsorption conditions (in vacuum or in liquid) and to some extent, the adsorption coverage that is considered. The purpose of our study was to gain a general understanding about how a range of organic molecules interact with calcite. For this, we aim to answer two fundamental questions: (i)

How do the various functional groups interact with calcite? 3 ACS Paragon Plus Environment


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(ii)

What is the effect of the side groups on adsorption behavior?

There are a few reports in the literature, where similar questions have been addressed but these are either focused on a limited number of functional groups4,18,26,38,47 or on a particular functional group with a range of side groups30,48. To provide answers to our two fundamental questions, we investigated the adsorption of organic molecules with a range of functional groups on calcite {10.4} and examined the differences in behavior arising from attachment of a hydrogen atom, (H) or methyl (-CH3), ethyl (-C2H5) or phenyl (-C6H5) side groups. In this paper, we focus on nonpolar and oxygen containing polar molecules. In a second paper49, we cover nitrogen and sulfur containing molecules.

MATERIALS AND METHODS Density Functional Theory Periodic plane wave density functional theory calculations were performed using the Quantum Espresso code50. Electronic exchange-correlation effects were modeled within the generalized gradient approximation (GGA) by the revPBE functional51. In all calculations, we used the projector augmented wave (PAW) method52,53, with pseudopotentials available in the Quantum Espresso pseudopotential library54. London dispersion corrections were included through the semiempirical DFT-D2 approach55,56 with modified C6 parameters for ionic solids57, which perform well for adsorption properties of molecules on ionic solid surfaces18. First, geometry optimization calculations for the conventional bulk unit cell of calcite were performed where we used a 3 × 3 × 1 Monkhorst-Pack grid58, with a kinetic energy cutoff of 49 Ry. For all calculations reported in this paper, the density cutoff was set to ten times the energy cutoff. The convergence of unit cell dimensions with respect to both the k-point grid and


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the cutoff energy was checked and the lattice parameters were converged within 0.03 Å. The converged bulk unit cell dimensions, a = 5.06 Å and c = 17.25 Å, fit well with previous ab initio calculations59, 5.03 Å, 17.17 Å, and experimental values derived from X-ray diffraction60, 4.99 Å, 17.06 Å. All of the adsorption energies reported here were calculated for the {10.4} surface, that we created from this converged bulk unit cell. For adsorption energy calculations, the plane wave energy cutoff was set to 37 Ry and only a single k-point (gamma) was used. The {10.4} surface was modeled using a 2 × 2 slab consisting of 4 molecular layers and 25 Å of vacuum, resulting in a super cell with the dimensions of 16.40 × 10.12 × 35.80 Å3 (Figure 1). Assuming that each Ca atom on the surface is an adsorption site for a molecule, this configuration corresponds to 0.13 ML coverage. All atoms in the first two molecular layers of the substrate and the adsorbed molecules were allowed to relax and the bottom two molecular layers were fixed in their bulk positions. The most stable adsorption geometry for the water molecule was used to check the convergence of adsorption energy with respect to the number of layers, the cutoff energy and the k-points. The adsorption energies converged within 0.01 eV. Single molecule geometries in vacuum were optimized in a cubic cell with side length of 25 Å. For these calculations, we started with the molecular geometries presented in the NIST Computational Chemistry Database61. For all geometry optimization calculations, the electronic energy, total energy and force convergence thresholds were set to 10–8, 10–4 and 10–3 in atomic Rydberg units. The adsorption energy was determined from: = −

− −

(1)

where , , and

represent the total energies of a clean slab, a molecule, and a system with the molecule adsorbed on the slab. A positive adsorption energy



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determined in this way corresponds to an exothermic process and a larger adsorption energy indicates stronger interaction with the surface. The Quantum Espresso code reports the value of dispersion contribution to total energy for every step during the geometry optimization process. Accordingly, the dispersion contribution to adsorption energy (Edc) was determined using Equation 1, by replacing the terms on the right side with the dispersion contribution value for converged geometry of each structure. To find the most stable adsorption geometry for a particular molecule, calculations were made for a number of starting geometries, where the molecule was placed on the surface to promote possible interactions between the functional group and the surface atoms. For each set of molecules with different functional groups, we determined the adsorption energy for the smallest member of the series, i.e. the molecule with an H atom. Based on that, we exchanged the H atom with the side groups to model the larger members of the series. Because the atoms and delocalized electrons of the phenyl ring can have strong dispersion and electrostatic interactions with the surface, additional adsorption configurations were considered for the molecules that had a side group consisting of a phenyl ring. The systematic approach for generating different starting geometries is further discussed in Section S7 of Supporting Information. Dissociative adsorption of molecules on calcite {10.4} is a possibility, particularly for carboxylic acids and water. To elucidate this point, various geometry optimization calculations were performed for water and formic acid, in which the H atom and the residual molecule were adsorbed to the surface separately. In the case of water, dissociated species always recombined during the geometry optimization, to form water molecules. In the case of formic acid however, more than one exothermic dissociated adsorption geometry was found (shown in Figure S5 in the Supporting Information). The most stable dissociated geometry has a significantly lower adsorption energy than the most stable geometry for the full molecule adsorption. 6 ACS Paragon Plus Environment

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X-ray Photoelectron Spectroscopy XPS measurements were performed using an Axis UltraDLD instrument from Kratos Analytical. The instrument has three chambers separated by gate valves for sample loading (load lock), treatment and analysis. The load lock is equipped with a blade that is used for cleaving calcite crystals in vacuum. The whole instrument is pumped by only dry (scroll, turbo molecular, ion or titanium sublimation) pumps to minimize hydrocarbon contamination. The typical base pressures were 3 × 10–8 torr (overnight pumping) in the load lock, 9 × 10–10 torr in the sample treatment chamber and 1 × 10–9 torr in the analysis chamber. A Hidden Analytical mass spectrometer is installed both in the sample treatment and the analysis chambers. Residual gas analysis showed only trace amounts of water, carbon monoxide and carbon dioxide, which are typical species in leak free, well baked, ultrahigh vacuum (UHV) chambers. No other species less than the m/e ratio of 90 were detected. Samples were introduced into the analysis chamber and placed on the sample manipulator for XPS analysis. The manipulator was cooled by liquid nitrogen using a closed tubing system and heated from the back using a filament. The temperature was measured with a K-type thermocouple attached to the manipulator, ~5 mm from the sample. We used a stainless steel sample holder (diameter 15 mm) with a cylindrical hole (diameter 6 mm) drilled in the center. Calcite rods of approximately 3 × 5 × 10 mm3 were prepared outside the vacuum chamber, by cleaving with a scalpel (method described elsewhere62), then fitted into the hole of the sample holder and wedged there using a clean bit of Al or Ta foil. Almost half of each crystal protruded from the top of the sample holder. This upper part was cleaved away inside the vacuum chamber, to produce a fresh, clean face. All crystals were visually inspected for faults created during cleavage, such as macroscopic steps and small,



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adhering calcite particles. XPS measurements were made only on macroscopically flat regions of crystals that were free of calcite dust. Small amounts of gas of the selected molecules were introduced into the UHV chamber through a gas line that was pumped by a turbomolecular pump and baked separately from the instrument chamber. All of the molecules that we investigated are liquid at room temperature. A glass tube containing the liquid was attached to the gas line and on the opposite end, was a stainless steel flange at a port on the vacuum system sealed with a metal gasket: silver, when we used acetic acid, and copper otherwise. The liquids were initially degassed through three pumpthaw cycles to remove possible dissolved contaminant gases, then the gas line was filled and pumped three times with the vapor of the liquid. Acetic acid (purity ≥ 99.7) was purchased from Merck, furan (purity ≥ 99.7) and acetone (purity ≥ 99.5) were acquired from Sigma-Aldrich. These were used without further purification. Ultrapure water (Milli-Q) was obtained using a Millipore Academic water purification system. A mass spectrum was recorded for each molecule before dosing to the surface and compared with literature data63. Iceland spar calcite was purchased from Ward’s Scientific USA. The crystal rods were prepared in air but the fresh surface used for dosing was cleaved in the load lock (at 3–5 × 10–8 torr) and immediately transferred to the analysis chamber for the base scan. That is, before each experiment, an XPS analysis was made at room temperature to verify the cleanness of the crystals. All of the freshly cleaved samples were free of carbon contamination, within XPS detection limits. After the initial XPS analysis, the crystals were cooled to ~ –135 °C on the sample manipulator and the chamber was filled with gas of the desired molecule. Once the dosage reached 10 to 15 L, the valve to the gas line was closed and residual gas in the chamber was evacuated. An XPS analysis was performed at this temperature to characterize the adsorbed molecules. Then the temperature was gradually increased in a stepwise manner (5 °C per step for 8 ACS Paragon Plus Environment

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furan, 15 °C, for acetone and 20 °C, for water and acetic acid). At every new temperature, after a stabilization period of 10 minutes, a new spectrum was recorded. The temperature was increased 60–80 °C above the first point where the C 1s peak intensity had stabilized, which we defined as the desorption temperature. Monochromated Al Kα radiation (photon energy 1486.6 eV) was used as the X-ray source, at a power of 150 W. Analyzer pass energy was set to 10 eV, resulting in an ultimate instrument resolution ≥ 0.48 eV. Because calcite is an insulator, charge compensation was used to minimize peak width and simplify data interpretation. The Axis UltraDLD is equipped with a neutralizer, which uses the magnetic confinement method64 for charge compensation. The binding energies of C 1s and O 1s spectra were calibrated to their corresponding carbonate peaks at 290.1 and 531.9 eV62.

Desorption Temperature Calculations The molecules considered in this study do not form a chemical (covalent or ionic) bond with the surface so it is reasonable to expect that no activation energy is required for adsorption. Consequently, the absolute value of the adsorption and desorption energies can be considered to be equal and calculated adsorption energies can be used to estimate desorption temperatures by using the Polanyi-Wigner equation65:

− = ,

(2)

where represents surface coverage, represents time, is a prefactor, represents the value of adsorption (desorption) energy, , the Boltzmann constant and , the desorption temperature. In this way, the desorption temperatures measured using XPS can be directly compared to the desorption temperatures predicted by DFT-D2 calculations. 9 ACS Paragon Plus Environment


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RESULTS AND DISCUSSION Adsorption Energy Calculations Calcite consists of positively charged calcium (Ca2+), ionically bonded with negatively charged carbonate (CO32–). In the bulk structure, each Ca atom is coordinated by six O atoms and each O atom is bound covalently to one C atom and coordinated with two Ca atoms (Figure 3 in reference 66). The Ca-O distance derived from our model, 2.39 Å, is close to the experimentally measured Ca-O distance for the bulk structure, 2.36 Å60. The cleavage plane {10.4} is formed by rupture of the ionic bonds. With respect to the cleavage plane, the trigonal planar carbonate ions are tipped, resulting in a molecular structure, where C, Ca and one third of the O lie in a plane, a third of the O are located slightly above this plane and a third of the O are slightly below it (Figure 1b). On the {10.4} surface, Ca and the upper level O atoms are undercoordinated compared with the bulk. The number of the undercoordinated O and Ca atoms is equal (two per unit cell) so the {10.4} surface is overall neutral. However, the chemical reactivity of the surface arises from these undercoordinated atoms, or “dangling” bonds, where the partial negative charge on O and the partial positive charge on Ca attract species with positive and negative charge (net or partial).


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Figure 1. Structure of the calcite {10.4} surface predicted with the model. (a) Top view: for clarity; only the atoms of the first molecular layer are represented by spheres. The layer below is drawn with sticks. The dashed rectangle shows a surface unit cell. (b) Side view: the molecular structure of calcite {10.4} surface where Ca, C and one third of O are in the same plane, one third of the O atoms are above the plane and one third are below the plane. The O atoms that lie above the plane and the Ca atoms are undercoordinated compared with the bulk structure. Ca is represented by green spheres, C by gray and O by red.

Figures 2 and 3 show converged adsorption geometries for eighteen molecules on the calcite {10.4} surface. For each molecule, the adsorption energy (Ead), the difference between adsorption energy and dispersion contribution (Ead – Edc) and distances between selected atoms of the surface and the molecules are presented. In general, there are three main contributions to the adsorption energy: (i)

electrostatic interactions between the electronegative O atom of the molecule and a surface Ca atom,

(ii)

hydrogen bonds, which form between a H atom of the molecule and an O atom of a surface carbonate group,

(iii)

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Figure 2. Predicted adsorption energy (Ead) and geometry for the oxygen containing polar molecules on the calcite {10.4} surface. Also included is the difference between adsorption energy and dispersion contribution (Ead – Edc) and distances between certain atoms in the molecules and the surface. Ca is represented by green spheres, C, gray, O, red, and H, white.


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Figure 3. Predicted adsorption energy (Ead) and geometry for the oxygen containing polar and nonpolar molecules on

the calcite {10.4} surface. Also included is the difference between adsorption energy and dispersion contribution (Ead – Edc) and distances between certain atoms in the molecules and the surface. Ca is represented by green spheres, C, gray, O, red, and H, white.



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The oxygen containing polar molecules considered in this study can be categorized in two groups, depending on whether a molecule can form a hydrogen bond with the surface in addition to an electrostatic interaction. For the molecules that cannot form a hydrogen bond, the adsorption energies range from 0.46 eV for furan to 0.68 eV for benzaldehyde. For these molecules, the dispersion contribution to the adsorption energy is in the range of 36 to 76%. The molecules that can form a hydrogen bond have significantly higher adsorption energies, ranging from 0.79 eV for methanol to 1.03 eV for benzoic acid. For these molecules the dispersion contribution to the adsorption energy is lower, in 20 to 58% range. Among the three nonpolar molecules, ethane and benzene adsorb completely as a result of dispersion. That the contribution for dispersion interaction is higher than the adsorption energy suggests that a calculation without the dispersion correction would result in an unstable structure for these two molecules. Indeed, geometry optimization calculations for ethane and benzene, which are initiated from the geometries shown in Figure 3, without the dispersion correction but with the same parameters, converged to different configurations. The optimized geometry (not shown) for ethane resulted in a configuration where the molecule moved ~0.5 Å away from the surface and for benzene, a configuration where the molecule moved ~0.7 Å away from the surface. Carbon dioxide is different from other nonpolar molecules in that both the fraction of dispersion contribution to adsorption energy (66%) and the adsorption geometry (Ca-O distance of 2.68 Å) suggest a significant electrostatic contribution to the adsorption energy. Our results compare well with some of the previously published adsorption data for small organic molecules on calcite {10.4}. Villegas-Jimenés et al.13 used the Hartree-Fock (HF) method to investigate water adsorption and reported adsorption energy of 0.79 eV for one monolayer, which is close to our value, 0.83 eV, but smaller than 0.91 eV, predicted with DFT by Lardge et al.14. Duffy et al.10 calculated adsorption energies with DFT and HF. Our values are 14 ACS Paragon Plus Environment

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comparable with their DFT adsorption energies for water, 0.89, and formic acid, 1.01 eV. Our results are also similar to those reported by Duffy et al.10 for surface-molecule distances for water (Ca-O = 2.38 Å, O-H = 1.71 Å) and formic acid (Ca-O = 2.35 Å, O-H = 1.48 Å). Freeman et al.19 used force fields and predicted adsorption energies of 0.54 eV for dimethyl ether, 0.72 eV for methanol and 0.89 eV for formic acid. Our values are ~0.07 eV higher than theirs but the adsorption energy differences are remarkably similar. Rigo et al.67 studied adsorption of benzene and hexane on calcite {10.4} with and without dispersion corrections. Although they used a different method to include dispersion interactions in their calculations, their predictions for benzene adsorption energy (0.34 eV) and geometry (Ca-C = 3.12 Å) were very similar to ours, 0.31 eV and 3.13 Å. Sánchez and Miranda34 studied adsorption of propionic acid and coadsorption of propionic acid and water on calcite {10.4}. Their propionic acid adsorption energy was higher (1.12 eV) than our value (0.99 eV) but the adsorption geometry was very similar (Ca-O = 2.32 Å, O-H = 1.57 Å). Recently, Okhrimenko et al.18 studied the adsorption of water, ethanol and acetic acid at a range of surface densities on several CaCO3 polymorphs, including calcite. The results of their DFT calculations suggest that adsorption of ethanol is stronger than water and acetic acid. In contrast, our results show that interaction of acetic acid with calcite is stronger than ethanol and water. The reason for the apparent discrepancy between two studies lies in the different reference state of acetic acid in the gas phase in the two experimental setups. For the pressures of acetic acid used in18, acetic acid forms a dimer and thus the adsorption energy was calculated relative to the dimer. In our experimental conditions (UHV), dimer formation is unlikely and therefore our calculated adsorption energy is relative to a free acetic acid molecule in vacuum. The difference in water adsorption energy is low (0.05 eV) and most likely is a result of slightly different parameters used in the calculations. 15 ACS Paragon Plus Environment


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Okhrimenko et al.18 also investigated the effect of coverage on adsorption energy and their results show that the adsorption energy increases with coverage for ethanol and acetic acid. In the current work however, we determined adsorption energy for a fixed and relatively low coverage (0.13 ML) because our aim was to map the general differences in behavior for a range of molecules. That is, we focus on molecule-surface interactions rather than molecule-molecule interactions. Nevertheless, for comparison we performed additional adsorption energy calculations for water, acetic acid, acetone and furan for increasing coverage and we present the results in Section S3 in Supporting Information. In general, we observed three different trends. For acetic acid and furan, adsorption energy per molecule increases, approximately 0.11 eV, from 0.13 ML to 1 ML. For water, adsorption energy per molecule is constant (within 0.01 eV) over the full coverage range and for acetone it is constant (within 0.02 eV) up to 0.75 ML and decreases from 0.75 ML to 1 ML. The different trends can be understood in terms of two competing effects, namely, increasing intermolecular dispersion interactions and steric hindrance between the adsorbed molecules. In particular, the adsorption energy per molecule for acetic acid and furan increase because the adsorption geometry and the size of the molecules allow an increase in dispersion interaction among closest neighbors but cause no or little steric hindrance. For water, adsorption energy per molecule does not change because the molecule is small and therefore there is no steric hindrance or increase in dispersion interactions among adsorbed molecules. For acetone, however, the shape and the size of the molecule cause steric hindrance among closest neighbors and increased dispersion interactions cannot balance this effect for coverages over 0.75 ML. In general, the adsorption energies and geometries we determined agree well with previous studies. This provides confidence that the model works well so we can apply it to understand behavior in the systems where less experimental data are available. 16 ACS Paragon Plus Environment

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Effects of Side Groups on Adsorption Behavior Side groups affect the adsorption energy in two ways: (i) by changing the electronic structure of the functional group, which changes the strength of electrostatic interactions and hydrogen bonding and (ii) by changing the strength of the dispersion interaction between the adsorbed molecule and the surface. An increase in the electron density of a functional group generally causes the electrostatic interactions to be stronger and hydrogen bonding to be weaker. For a functional group that can have both kinds of interactions with the surface, the net effect remains to be investigated. The strength of the dispersion interaction however, is easier to predict because it increases with the number of atoms in the side group and decreases with the distance between two interacting atoms. Therefore it is mainly the strength of electrostatic and hydrogen bonding, i.e., the nondispersive interactions, that determine the behavior differences resulting from the various side groups. That is what we refer to as adsorption behavior in this paper. In other words, the strength of the interaction between the molecule and the surface, i.e. the adsorption energy, is the value that can be compared with experimental measurements but it is the strength of the nondispersive interactions that determines the differences in adsorption behavior. Figure 4 shows adsorption energies for the series of molecules that are formed by attachment of a H atom or various side groups to carboxyl, hydroxyl and aldehyde functional groups. Irrespective of the side group, carboxylic acids (R-COOH) adsorb more strongly than alcohols (R-OH) and water, on average by 0.17 eV. These in turn adsorb more strongly than aldehydes (R-CHO), by 0.23 eV. Figure 4 also shows that adsorption energy increases with the size of the side group. This is a result of higher dispersion interaction. Water is the only



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exception. The H atom attaches to the hydroxyl functional group, hydrogen bonding to a surface oxygen atom, which results in relatively high adsorption energy.

Figure 4. The energy of adsorption on calcite, as a function of the main functional group and the side groups. Triangles, represent carboxyl, squares, hydroxyl, and circles, aldehyde functional groups.

In the following discussion, two basic assumptions were made to determine the effects of side groups on the electronic structure of functional groups and adsorption behavior. First, the atomic distances between the molecules and the surface were used to compare the strength of various molecule-surface interactions. Specifically, relatively longer Ca-O distances for the electrostatic interactions and relatively longer O-H distances for hydrogen bonds correspond with relatively weaker interactions. Second, the difference between the adsorption energy and the dispersion contribution (Ead – Edc) for a particular adsorption geometry was used as an estimate for the total strength of the nondispersive interactions. One drawback of this approach is that for some molecules, the H atom and phenyl ring are involved in the adsorption. This results in


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adsorption geometries where it is not possible to isolate the effect of the side group on the electronic structure of the functional group and therefore, the strength of the interactions. This effect was observed most strongly for water, phenol and benzaldehyde. In these cases, different optimized adsorption geometries were considered, where the side group-surface interactions did not strongly affect the adsorption geometry. Carboxylic acids: Among the carboxylic acids (Figure 2), formic acid has the strongest hydrogen bond and the weakest electrostatic interaction with the surface, which indicates that the H atom decreases the electron density of the carboxyl functional group more than either the alkyl or the phenyl side groups. The strength of electrostatic interaction and hydrogen bonding are quite similar for acetic, propanoic, and benzoic acids. As expected, the dispersion contribution increases with the size of the side group. Nevertheless, as a result of large side group-surface distances, the increase in dispersion interaction is relatively small. This has two causes: i) the upright adsorption geometry for the carboxylic acids and ii) the side groups attached to the carbon atom of the functional group that is away from the surface. For benzoic acid, the adsorption energies for a couple of different geometries were calculated, where the molecule was bent to bring the phenyl group close to the surface. Although a few stable adsorption geometries were found with higher dispersion contributions, the adsorption energies were slightly lower. Overall, the difference between adsorption energy and dispersion contribution for formic and benzoic acids (0.77 eV) is slightly higher than for acetic and propanoic acids (0.75 eV). This indicates that there is not a significant difference in the nondispersive interactions and that for carboxylic acids, the changes in the strength of the electrostatic interactions and hydrogen bonds balance each other. Alcohols and Water: For phenol and water, the most stable adsorption geometries shown in Figure 2 are strongly influenced by side group-surface interactions and therefore cannot be 19 ACS Paragon Plus Environment


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used to assess the effect of the H atom or phenyl group on adsorption behavior of the hydroxyl functional group. In the case of phenol, the strong dispersion interaction between the phenyl ring and the surface results in a flat adsorption geometry and this affects the interaction between the hydroxyl group and the surface. In the case of water, the effect is more significant. The H atom attaches to the hydroxyl group, hydrogen bonding with a surface O atom. This is also the reason why water, in spite of being the smallest of the molecules that has a hydroxyl functional group, does not have the lowest adsorption energy. Consequently, we made two additional geometry optimization calculations for phenol and water that were started from the converged adsorption geometry of ethanol (Figure S4 in Supporting Information). The calculation for phenol resulted in an upright adsorption geometry with a smaller adsorption energy (0.80 eV) and significantly higher nondispersive interaction (0.50 eV), with much shorter Ca-O (2.47 Å) and slightly longer O-H distances (1.67 Å). The calculation for water resulted in an adsorption geometry in which the molecule forms only one hydrogen bond, with a smaller adsorption energy (0.73 eV), and nondispersive interaction (0.56 eV), with similar Ca-O (2.44 Å) and shorter O-H distances (1.72 Å). Among alcohols and water, phenol has the strongest hydrogen bond and the weakest electrostatic interaction with the surface, which indicates that the phenyl ring decreases the electron density of the hydroxyl group more than alkyl groups and the H atom. The electrostatic interactions of methanol and ethanol with the surface are quite similar but the hydrogen bond for methanol is stronger. This implies that the ethyl side group increases the electron density of the H in the hydroxyl functional group more than the methyl group. For water, the electrostatic interaction is weaker than methanol and ethanol but not as weak as phenol and the hydrogen bond is stronger than methanol and ethanol but not as strong as phenol.


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An important difference between alcohols and carboxylic acids is that the adsorption geometry of alcohols is less constrained in terms of molecule-surface orientation. This is because a change of the angle between the surface and an alcohol molecule would probably affect the electrostatic interaction but not the hydrogen bonding because the molecule can rotate around the axis of the hydrogen bond itself. In contrast, changing the molecule-surface angle for a carboxylic acid would affect both types of interaction. This effect is visible in the adsorption of phenol, where the molecule adsorbs to the surface in a flat geometry, inducing a higher dispersion contribution (0.49 eV) than benzoic acid (0.26 eV). The differences between the adsorption energy and the dispersion contribution for the alcohols and water show that the nondispersive interactions are similar for water (0.56 eV) and methanol (0.55 eV) and higher than ethanol and phenol (0.50 eV). In contrast to carboxylic acids, for alcohols and water, the changes in the strength of the electrostatic interactions and hydrogen bonding is not fully balanced and there is a more pronounced difference in the total strength of the nondispersive interactions. Aldehydes: As in the case for phenol adsorption, the high dispersion interaction introduced by the phenyl ring makes benzaldehyde adsorb flat on the surface and this affects the functional group-surface interaction. Therefore to correctly assess the effect of the phenyl side group on the aldehyde functional group, a geometry optimization calculation for benzaldehyde, which was initiated from the converged adsorption geometry of acetaldehyde, was performed. The calculation (Figure S4 in Supporting Information) resulted in an upright adsorption geometry with a smaller adsorption energy (0.62 eV), a much larger nondispersive interaction (0.37 eV) and a slightly shorter Ca-O distance (2.45 Å). For the adsorption geometry of formaldehyde shown in Figure 3 the molecule has the shortest Ca-O distance (2.43 Å) among the aldehydes, which suggests the strongest electrostatic interaction. However, the nondispersive interaction 21 ACS Paragon Plus Environment


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(0.27 eV) is significantly lower than other aldehydes. This discrepancy results from an additional interaction between the carbon atom of the molecule and the surface oxygen atom, with C-O distance of 2.52 Å. We did not observe any difference for the molecular bond lengths and angles for formaldehyde in this adsorption geometry and the free molecule. It is likely that there is a dispersive interaction between the carbon atom of the molecule and the surface oxygen atom. Therefore to correctly estimate the effect of the H atom on the aldehyde functional group, we performed a geometry optimization calculation for formaldehyde which was initiated from the converged adsorption geometry of acetaldehyde. The calculation (Figure S4 in Supporting Information) resulted in adsorption geometry with very similar adsorption energy (0.51 eV)68, a larger nondispersive interaction (0.31 eV) and a longer Ca-O distance (2.49 Å). Aldehydes are different from alcohols and carboxylic acids in that they cannot hydrogen bond with the surface. Consequently, the adsorption energies are lower and the contribution from dispersion is higher. The Ca-O distances for the various aldehydes show that the electrostatic interaction is lowest for formaldehyde and similar for the other three aldehydes. This indicates that a H atom decreases the electron density of the aldehyde functional group compared with the other side groups. The differences between the adsorption energy and the dispersion contribution for aldehydes agree with the conclusions from bond length comparisons, namely, the electrostatic interaction is lowest for formaldehyde (0.31 eV) and similar for acetaldehyde (0.37 eV), propionaldehyde (0.38 eV) and benzaldehyde (0.37 eV). One way to estimate the changes in the electronic structure for adsorbed molecules is to investigate the partial charges for the different atoms. In Section S6 of the Supporting Information, we show the results of partial charge analysis for the polar molecules and pKa values for alcohols and carboxylic acids. In short, the results indicate that the partial charge on the H atom for the carboxylic acids and alcohols are similar and it does not fully correlate with the 22 ACS Paragon Plus Environment

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hydrogen bond lengths. However, we observe a correlation between the pKa values and hydrogen bond lengths for these molecules. In addition, the results also indicate that there is a linear relationship between the increasing Ca-O distance and the decreasing negative charge on the O atom for carboxylic acids, aldehydes, dimethyl ether, furan and acetone.

Desorption Temperature Measurements and Comparison with Predictions One experimental quantity that can be compared with the calculated adsorption energies is the temperature at which the adsorbed molecules desorb from the calcite surface. For this purpose, among the eighteen molecules considered in this study, we chose four to investigate with desorption temperature measurements by XPS. We chose organic compounds that would serve as representatives for the various types of functional groups, that have high vapor pressure at ambient temperature and that somewhat covered the adsorption energy range. Figure 5 shows C 1s and O 1s spectra for furan, acetone, water and acetic acid on calcite {10.4} as a function of temperature. The highest coverage (at the lowest temperature) was 0.5 monolayer (ML) for furan and acetone and 1.5 ML for acetic acid. Water is the only molecule that formed a relatively thick multilayer at the lowest temperature available with our equipment (~ –135 °C). In this work, 1 ML is defined as two molecules per calcite {10.4} surface unit cell because there are two adsorption sites (i.e. two Ca atoms) per unit cell. The method used to estimate coverage from the experimental data is described in Section S2.



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Figure 5. C 1s and O 1s spectra for (a) furan, (b) acetone, (c) water, and (d) acetic acid adsorbed on the calcite {10.4} surface as a function of temperature. Insets show the binding energy region where the effect of desorption is most visible.

It can be seen from the spectra of furan and water (Figure 5), that as the temperature increases, the intensity of the XPS peaks that represent the adsorbed molecules decrease, in parallel with desorption of the molecules. Above a certain temperature, the peaks disappeared completely and the clean calcite surface was recovered. We designated the midpoint between the last temperature at which there were still some molecules on the surface and the first temperature at which all molecules were desorbed, as the desorption temperature. Accordingly, for furan, the desorption temperature was –115 ± 5 °C and for water, –10 ± 10 °C. The C 1s peaks for acetone and acetic acid both decreased in intensity and shifted toward low binding energy as temperature increased. At a certain temperature, the peaks representing the adsorbed molecules stabilized at a specific intensity and binding energy and the clean surface was 24 ACS Paragon Plus Environment

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not recovered. For both acetone and acetic acid, stepwise heating continued for 60 to 80 °C above the temperature where C 1s peaks remained unchanged and residual species were still observed. This suggests that some of the adsorbed acetone and acetic acid molecules desorb intact from the surface and some dissociate and leave fragments behind. Thermal dissociation of acetone and acetic acid on other solid surfaces has been observed69-74 but the details of dissociation and the chemical species created during the dissociation process are beyond the scope of this paper (a brief discussion is included in Section S2). Our aim was to determine the desorption temperatures for the intact molecules so as to be able to compare them with the DFT predictions. Therefore, for acetic acid and acetone, we defined the desorption temperature as the midpoint between the first temperature where the peaks representing the molecules become stable and the measurement point immediately before that. Thus, for acetone, we interpreted the desorption temperature to be –42.5 ± 7.5 °C and for acetic acid, 50 ± 10 °C. Figure 5c shows that water desorbs from calcite at ~ –10 °C. This means that as soon as the sample temperature is below –10 °C, residual water in the UHV chamber can condense on the surface. A clear observation of this effect is visible in the O 1s spectra of furan in Figure 5a. As the temperature increases, furan desorbs from the surface and the peak at the high binding energy side (~535 eV), which represents the furan on the surface, decreases in intensity. Simultaneously, the intensity of a shoulder at the lower binding energy side (~534 eV) increases and when furan leaves the surface completely at –110 °C, the low binding energy shoulder becomes clearly visible. The shapes and positions of the furan C 1s peaks did not change during the heating process. Therefore, it is unlikely that oxygen containing species remain on the surface as a result of furan dissociation. The shoulder in the spectrum at ~534 eV is very similar to the XPS peak for water, which indicates that as furan desorbs, water adsorbs to take its place. This phenomenon is not visible in the acetone spectra, most likely because the desorption temperature of acetone is 25 ACS Paragon Plus Environment


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higher than for furan and water has a lower sticking probability at this temperature. The important question here is if a small amount of residual water can affect the furan-calcite interaction and hence, desorption temperature? In the predicted adsorption geometry (Figure 2), O and both H atoms of water interact with the surface. This means that although an adsorbed water would block an adsorption site for furan, thus affecting its coverage, the water cannot create a new adsorption site where furan could interact more strongly than through electrostatic interaction with surface Ca. Thus it is unlikely that a small amount of residual or adsorbed water could significantly affect furan-calcite interactions. Figure 6 presents the desorption temperature for the eighteen molecules predicted with our DFT-D2 calculations. Superimposed are the data derived from the XPS experiments, for the four molecules studied. The desorption temperatures were determined using the Polanyi-Wigner equation (Equation 2). The calculations were made for desorption of 99% of a monolayer from the {10.4} surface, using the energies predicted with DFT-D2. The prefactor in the PolanyiWigner equation, , was replaced by /ℎ, where and ℎ represent the Boltzmann and Planck constants and

denotes temperature. The prefactor is most commonly approximated as75 1013 s-1

but here we use /ℎ to try to capture the temperature dependence76. The calculation of desorption temperature for different initial and final coverages, prefactor and coverage dependent adsorption energy values are discussed in the Supplementary Information, S4. Figure 6 shows that the molecules, for which the desorption temperatures have been experimentally measured, are well distributed on the temperature scale and the agreement between predicted and measured desorption temperatures is quite good.


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Figure 6. Desorption temperature for loss of 99% of a monolayer for eighteen molecules predicted by DFT-D2 calculations (black circles), and experimental data for four molecules derived from XPS data (red squares).

CONCLUSIONS Adsorption energies for three nonpolar and fifteen oxygen containing polar molecules on the calcite {10.4} surface were calculated using the DFT-D2 method with C6 parameters modified for ionic solids. The most stable adsorption geometries of the molecules reveal that in general, there are three types of interaction between molecules and the surface: electrostatic, hydrogen bonding and dispersion. We investigated the effects on adsorption behavior associated with the attachment of either the H atom or a side group, namely methyl, ethyl or phenyl, for the three most common oxygen containing functional groups. The results demonstrate that, irrespective of the side group, carboxylic acids adsorb more strongly than alcohols, which in turn adsorb more strongly than aldehydes. The dispersion contribution to adsorption energy increases with the size of the side group, as expected. Side groups affect the electronic structure of the functional groups and this changes the strength of the electrostatic interactions and hydrogen bonding (nondispersive). Nondispersive interactions in total do not change significantly for the various carboxylic acids. Among the alcohols and water, nondispersive interactions are similar for water



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and methanol and higher than ethanol and phenol. Among aldehydes, electrostatic interaction, i.e., the only nondispersive interaction, is lowest for formaldehyde and similar for acetaldehyde, propionaldehyde and benzaldehyde. From calculated adsorption energies, a prediction for desorption temperature of each molecule was made using the Polanyi-Wigner equation. Desorption temperatures for four of the molecules were measured using XPS and the experimental values agreed well with predictions. The match of the experimental data with the values derived from theory and the match of our results with those found in the literature, provides confidence that the predicted values are robust and can be used as a benchmark for adsorption of organic molecules on ionic surfaces in general and on calcite in particular.

ASSOCIATED CONTENT Supporting Information For comparison, adsorption energy calculations were performed with the most common exchange-correlation functional, PBE, without the dispersion corrections. The results are presented in Section S1. To estimate the coverage for furan, acetone and acetic acid, C 1s XPS spectra were fit and the results are presented in Section S2. The effect of coverage on adsorption energy is reported in Section S3. The results of the desorption temperature calculations are presented in Section S4. Adsorption geometries for water, phenol, formaldehyde and benzaldehyde in upright geometries, that were used to assess the effect of the H atom and the phenyl side group on adsorption behavior of hydroxyl and aldehyde functional groups, are presented in Section S5. The two most stable dissociative adsorption geometries for formic acid


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are also presented in Section S5. The results of partial charge analysis are reported in Section S6 and the methods for generating different starting geometries are discussed in Section S7.

AUTHOR INFORMATION *Corresponding Author E-mail: [email protected] Tel: +45 211 81 260

ACKNOWLEDGMENTS We warmly thank Akin Budi for invaluable discussions and critical comments to the manuscript. Funding was provided by the Maersk Oil Research and Technology Centre, Qatar. Additional funding was provided by the Engineering and Physical Sciences Research Council, EPSRC of the UK [Grant Number EP/I001514/1] for the MIB (Materials Interface with Biology) Consortium. Access to computing facilities was provided by a grant from the Danish Center for Scientific Computing (DCSC), which has since changed name to the Danish e-Infrastructure Consortium (DeIC).



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Functional Group Adsorption on Calcite: I. Oxygen ... - ACS Publications

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