Functional Group Adsorption on Calcite: II. Nitrogen and Sulfur

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Functional Group Adsorption on Calcite: II. Nitrogen and Sulfur Containing 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.6b01359 • 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: II. Nitrogen and Sulfur Containing 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 Sulfur and nitrogen are two common constituents of natural and synthetic organic molecules, especially in systems where organisms play a role. There is evidence in the literature that nitrogen and sulfur containing functional groups have an influence on adsorption of organic molecules to calcite surfaces. The purpose of this work was to investigate the interaction of these functional groups with CaCO3 and to explore how adsorption is affected by various side groups and the H atom. First, we used density functional theory with semiempirical dispersion corrections (DFT-D2) to determine the energy of adsorption on the dominant calcite face, {10.4} for molecules containing nitrogen (ammonia, methylamine, ethylamine, aniline, hydrogen cyanide, acetonitrile, propionitrile, benzonitrile, dimethylamine, pyrrole, trimethylamine and pyridine) and sulfur (hydrogen sulfide, methanethiol, ethanethiol, thiophenol, dimethyl sulfide and thiophene). Second, based on the determined adsorption energies, we predicted desorption temperature for each molecule within the transition state theory approximation. Finally, we used X-ray photoelectron spectroscopy (XPS) to determine the desorption temperature for four molecules for comparison with the predicted values. Our results show that ammonia and primary amines (R-NH2) adsorb more strongly than nitriles (R-CN) and hydrogen sulfide and thiols (RSH). On average, the adsorption energy of nitriles is slightly higher than hydrogen sulfide and thiols. Attachment of side groups or a H atom changes the strength of the surface-molecule interactions and significantly affects the adsorption behavior of all three functional groups.

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INTRODUCTION Calcium carbonate (CaCO3) is an abundant mineral in nature and is widely used by organisms to form shells and exoskeletons. Limestone and chalk are composed predominantly of calcite and synthetic material is a base ingredient in paper, paint, plastics, pharmaceuticals and a range of other products. Calcite scale formation is a common problem in cooling systems, oil production and refining, municipal water supplies and household tea kettles and water heaters. Because calcite is the most stable polymorph of CaCO3 in ambient conditions, it is used extensively as a model system to study complex physical and chemical phenomena that could equally affect other mineral and chemical compound systems. A detailed understanding of the properties of organic molecule-calcite interfaces in particular could provide valuable insights for a range of applications where interactions between organic molecules and calcite surfaces are central. We have a twofold motivation for studying the adsorption of organic molecules on calcite. First, we want to contribute data for use in predicting calcite behavior in the presence of organic molecules, to produce structures with superior material properties, such as in biomineralization, or to inhibit scale formation in industrial processes. Second, we want to gain fundamental understanding about interactions between complex organic fluids and natural mineral surfaces. For both aspects, the list of organic molecules that one could study is extensive. We needed a practical approach that would provide information about the patterns of behavior, that could be used for general predictions, across a wide range of systems. Our method was to calculate the adsorption energies of organic molecules on the calcite {10.4} surface and investigate in detail the effects of various side groups on the adsorption behavior of the functional groups that are commonly found in organic molecules.


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In the first paper1 of this pair, we investigated adsorption of eighteen oxygen containing and nonpolar molecules on calcite {10.4}. There, we demonstrated that there are three main types of interaction between the molecules and the surface: electrostatic interaction, hydrogen bonding and dispersion. On average, the adsorption energy for carboxylic acids (R-COOH), which have the strongest electrostatic and hydrogen bonding interactions with the surface, is 0.17 eV higher than for water and alcohols (R-OH) and 0.40 eV higher than for aldehydes (R-CHO). Aldehydes have the lowest adsorption energy because they cannot hydrogen bond with the surface. We also showed that attachment of a H atom or a methyl (-CH3), ethyl (-C2H5) or phenyl (-C6H5) side group does not significantly affect the adsorption behavior for the carboxyl functional group. For the hydroxyl and aldehyde functional groups, side groups have an effect. This paper sets out to extend that work. Oxygen containing molecules in general, and carboxyl, hydroxyl, and aldehyde functional groups in particular, are important for a large number of systems but they represent only a part of the vast family of organic molecules in nature. Amino acids, nucleic acids, peptides and proteins, which contain nitrogen and sulfur in their structures either in their backbone or as terminal groups, play an important role in determining adsorption properties and in controlling the structure of biominerals and the behavior of minerals in natural systems where organic molecules abound. A number of experimental and theoretical investigations that are reported in the literature demonstrated the direct involvement of amine groups in the adsorption of molecules to calcite2-7. The results of these studies show that amine or protonated amine groups in peptides and proteins form hydrogen bonds with the oxygen atoms of surface carbonate groups. The molecular dynamics (MD) simulations of Auscher et al.8 suggest that nitrogen atoms in the structure of a molecule cause attractive electrostatic interactions with surface calcium atoms and van der Waals interactions with surface oxygen atoms. Two experimental studies by Teng et al9 and Auscher et al.10 showed that amine groups in 3 ACS Paragon Plus Environment


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carboxyl containing molecules significantly affect the interaction between the molecules and the calcite surface. Sulfur atoms in organic molecules exist mostly as thiol (-SH), thioether (-S-) and disulfide (-S-S-) and these species have important effects on structural properties of the molecules, especially for proteins and peptides11. Thiol groups, in particular, are suitable candidates for anchoring biomolecules on surfaces12. In general, sulfur containing molecules have been neglected by the crystallization community but a recent study by13 Hamm et al. compared the effects of various functional groups on calcite mineralization and showed that thiol groups can have significant effects. Therefore, to have a more complete picture of calcite-organic molecule interactions, adsorption of nitrogen and sulfur containing molecules deserve attention. As in our first paper1, our aim is to answer two fundamental questions: How do the various functional groups interact with the calcite surface and what effect does attachment of a H atom or one of several side groups have on adsorption behavior? For this purpose, we used DFT-D2 to determine adsorption geometry and energy for twelve nitrogen and six sulfur containing molecules on calcite {10.4}. We explored the effects of adding a H atom or a methyl, ethyl or phenyl side group, on the adsorption behavior of primary amine (-NH2), nitrile (-CN) and thiol (-SH) functional groups. From calculated adsorption energies, within transition state theory, we predicted desorption temperature for each molecule. Then we chose four molecules (thiophene, pyrrole, pyridine, and aniline) and determined their desorption temperatures from XPS data so we could compare them with the predicted values. The very good agreement between predicted and measured desorption temperatures provides confidence in the modelling, suggesting that the computational approach and the parameters chosen are quite suitable for the system investigated here and most likely can be applied for adsorption on other ionic surfaces. 4 ACS Paragon Plus Environment

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MATERIALS AND METHODS The experimental setup, the computational methods and the parameters were described in detail in Part 1 of this work1. The results presented herein were obtained using the same procedures so only a summary is provided.

Density Functional Theory The Quantum Espresso14 code was used for making the periodic plane wave density functional theory calculations within the generalized gradient approximation (GGA), with the revPBE functional15. Pseudopotentials from Quantum Espresso library16, which were generated using the projector augmented wave (PAW) method17,18, were implemented in all calculations. We included semiempirical dispersion corrections with the approach adopted in DFT-D219,20. The C6 parameters were modified to improve the model for ionic solid materials21. The reduction of C6 parameters for cations has been shown to perform well for the adsorption properties of molecules on ionic solid surfaces1,22. A 3 × 3 × 1 Monkhorst-Pack grid23 and a kinetic energy cutoff of 49 Ry were used for geometry optimization calculations for the conventional bulk unit cell of calcite. For all calculations, we set the density cutoff to ten times the energy cutoff. The converged (within 0.03 Å) unit cell dimensions that we derived, a = 5.06 Å and c = 17.25 Å, agree well with previous ab initio calculations, 5.03 Å, 17.17 Å24, and values derived from X-ray diffraction, 4.99 Å, 17.06 Å25. The plane wave energy cutoff was set to 37 Ry and we adopted only a single k-point (gamma) for adsorption geometry calculations. To model the {10.4} surface, we used a 2 × 2 four



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molecular layer slab separated by 25 Å of vacuum which corresponds to a coverage of 0.13 ML. The super cell dimensions were 16.40 × 10.12 × 35.80 Å3. All atoms of the adsorbed molecules and the first two molecular layers of the substrate were allowed to relax and the bottom two molecular layers were fixed to their bulk positions. The reported adsorption energy values were converged within 0.01 eV, with respect to the number of layers, the cutoff energy and the number of k-points. Molecular geometries reported in the NIST Computational Chemistry Database26 were used as starting points for geometry optimization calculations in a cubic cell with a side length of 25 Å. For all 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: ‫ܧ‬௔ௗ = −൫‫ܧ‬௠௢௟௘௖௨௟௘ି௦௨௥௙௔௖௘ − ‫ܧ‬௦௨௥௙௔௖௘ − ‫ܧ‬௠௢௟௘௖௨௟௘ ൯

(1)

where ‫ܧ‬௦௨௥௙௔௖௘ , ‫ܧ‬௠௢௟௘௖௨௟௘ , and ‫ܧ‬௠௢௟௘௖௨௟௘ି௦௨௥௙௔௖௘ represent the total energies of a clean slab, a molecule and a system with the molecule adsorbed on the slab. A positive adsorption energy value calculated in this way corresponds to an exothermic process. In addition to total energy, the Quantum Espresso program calculates the value of the dispersion contribution (Edc) to total energy for each step through the geometry optimization process. By replacing the terms in the right side of Equation 1 with the dispersion contribution values for each system, we obtained the dispersion contribution to the adsorption energy. For each set of molecules with a different functional group, the adsorption energy calculations began for the smallest member of the group. By changing the H atom of the most stable adsorption geometry for the smallest member, adsorption energies of the larger members of the set were calculated. The molecules with a phenyl side group required a more careful examination because atoms and delocalized electrons of the phenyl ring can induce further


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interactions with the surface. In Section S7 of Supporting Information, the systematic approach used for generating different starting geometries is further discussed.

X-ray Photoelectron Spectroscopy An Axis UltraDLD instrument from Kratos Analytical was used to make the XPS measurements. The three chambers of the instrument (load lock, sample treatment and analysis) are separated by gate valves. The typical base pressures were 3 × 10-8 torr (after overnight pumping) for the load lock, 9 × 10-10 torr for the sample treatment chamber and 1 × 10-9 torr for the analysis chamber. The manipulator in the sample analysis chamber, where XPS measurements were performed, was cooled by liquid nitrogen through a closed tubing system and heated using a filament. A K-type thermocouple attached to the manipulator ~5 mm from the sample is used to measure the sample temperature. Monochromated Al Kα X-rays (photon energy 1486.6 eV) were used. Pass energy for the electron energy analyzer was set to 10 eV, resulting in instrumental resolution ≥ 0.48 eV. Surface charge arising from photoemission was compensated by a neutralizer that uses magnetic confinement27. We calibrated the binding energy scale from the carbonate peak at 290.1 eV28. A gas line was installed to introduce the volatile molecules into the ultrahigh vacuum chamber. All of the molecules that we studied exist as liquids at room temperature. We purchased aniline (purity ≥ 99.5) from Merck and pyridine (purity ≥ 99.9), thiophene (purity ≥ 99) and pyrrole (purity ≥ 98) from Sigma-Aldrich. Iceland spar calcite, acquired from Ward’s Scientific USA, was cleaved to produce rods of approximately 3 × 5 × 10 mm3. These were placed into the cylindrical hole in stainless steel sample holders and held in place by a bit of cleaned Ta or Al foil. The rods that protruded from



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the sample holder were cleaved inside the load lock (at ~ 3 × 10-8 torr) and transferred to the analysis chamber (method described elsewhere28). We collected XPS spectra on each crystal at room temperature to verify that the samples were free of adventitious contamination. The crystals were cooled to ~ –140 °C and about 10 to 15 L of the desired molecule was leaked into the chamber. The surface with its adsorbed material was characterized at low temperature by XPS, then the temperature was slowly increased by steps of 5 °C for thiophene, 15 °C for pyridine and 20 °C for pyrrole and aniline. At each new temperature, we collected a spectrum after 10 minutes of stabilization time. Temperature was finally raised 40 to 70 °C above the point where the intensity of the peaks that represented the adsorbed molecules reached a minimum and stabilized.

Desorption Temperature Calculations Because the molecules considered in this study do not form a chemical (covalent or ionic) bond with the calcite surface, it is reasonable to expect that adsorption does not require an activation energy. Therefore, the absolute values for the adsorption and desorption energies are considered equal so we can use the Polanyi-Wigner equation29: ௗఏ

ಶೌ೏

− ௗ௧ = ߠߥ଴ ݁ ି ೖ೅

(2)

to determine desorption temperature. In this equation, ߠ represents surface coverage, ‫ ݐ‬represents time, ߥ଴ is a prefactor, ‫ܧ‬௔ௗ denotes the absolute value of adsorption (desorption) energy, ݇ represents the Boltzmann constant, and ܶ, desorption temperature. The details of calculations and effects of the various parameters on the desorption temperature are presented in the Supporting Information for Part 1 of this study1 and are therefore not discussed further here.

RESULTS AND DISCUSSION 8 ACS Paragon Plus Environment

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Adsorption Energy Calculations Calcite is an ionic compound that consists of positively charged Ca2+ and negatively charged CO32- ions. Calcium is coordinated octahedrally by O from the covalently bound, trigonal planar CO32- units. Each oxygen atom is bound ionically with two Ca2+ ions and our calculated Ca-O distance, 2.39 Å, agrees well with the experimental value for the bulk calcite structure, 2.36 Å25. The net charge on the {10.4} surface is zero but locally, partial charge is relatively high so the mineral surface provides sites that are attractive to both positive and negatively charged species. Because the plane of carbonate ions is at an angle to the surface, the O atoms are located at different heights relative to the {10.4} plane (Figure 1 in1). The topmost O atoms are undercoordinated and their high partial negative charge makes them good hydrogen bond acceptors. The middle layer of O atoms is in the plane with C and Ca atoms. Calcium is underbonded so its partial positive charge makes it an anchor point for negatively charged species. The remaining O atoms are completely bonded with the next molecular layer. The converged adsorption geometries of eighteen nitrogen and sulfur containing molecules on the calcite {10.4} surface are shown in Figures 1 and 2. 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 for each molecule. In general, there are three main contributions to adsorption energy: (i)

electrostatic interactions between the electronegative atom (N or S) 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 and

(iii)

dispersion interactions between all atoms of the molecule and surface.



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Figure 1. Predicted adsorption energy (Ead) and geometry for eight of the nitrogen containing molecules on the calcite {10.4} surface. Also included is the difference between adsorption energy and dispersion contribution (Ead –


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Edc) and distance between certain atoms in the molecules and the surface. Ca is represented by green spheres, C, gray, O, red, N dark blue, and H, white.

Figure 2. Predicted adsorption energy (Ead) and geometry for four of the nitrogen and sulfur containing 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, N dark blue, S, yellow, and H, white.



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The molecules investigated in this study can be categorized in two groups based on their adsorption energies. The first group consists of nitriles, sulfur containing molecules and pyrrole, with adsorption energies between 0.34 and 0.65 eV. For these molecules the dispersion contribution to adsorption energy is about 41 to 100%. The second group consists of amines and pyridine, with adsorption energies between 0.73 and 0.88 eV. For these molecules the dispersion contribution to adsorption energy is about 27 to 68%. Some of the molecules (thiols, pyrrole and hydrogen cyanide) in the low adsorption energy group have weak electrostatic interactions and form weak hydrogen bonds with the surface and the others (nitriles and dimethyl sulfide) cannot form hydrogen bonds and only have weak electrostatic interaction. Thiophene is different than the rest of the molecules in this group because the adsorption results from only dispersion interaction. The stronger surface-molecule interactions for the molecules in the high adsorption energy group result from a combination of effects. Primary amines interact with the surface through electrostatic interactions and two hydrogen bonds. Dimethylamine, in addition to electrostatic interaction, forms a single hydrogen bond with the surface but it has a similar adsorption energy to primary amines because of the high dispersion interaction. Although pyridine and trimethylamine cannot form hydrogen bonds, they are in the high adsorption energy group because the electrostatic interaction of pyridine and the dispersion interaction of trimethylamine with the surface are strong. Compared with reports of investigations on oxygen containing molecules, the number of computational studies of the adsorption of nitrogen and sulfur containing molecules on calcite is limited. Hwang et al.30 made MD simulations to study the calcite-pyridine interface and their results show that the N atoms of most of the molecules at the interface were coordinated to Ca on 12 ACS Paragon Plus Environment

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the surface, in an adsorption geometry very similar to what is shown in Figure 2. De Leeuw et al.31 used MD to calculate the adsorption energy for four oxygen and nitrogen containing molecules on several calcite faces. Their adsorption energy values for methylamine, 0.58 eV, and formic acid, HCOOH, 0.87 eV, are lower than ours, 0.86 eV for methylamine and 0.97 eV for formic acid1. The differences are not surprising because different computational methods were used but the main point is that formic acid adsorbs somewhat more strongly than methylamine. Freeman et al.32 also investigated adsorption of methylamine and formic acid on various calcite faces. They considered adsorption of molecules from a water phase so their values are not directly comparable but again, they show that formic acid adsorbs more strongly than methylamine. The main motivation for this study was investigation of general differences in surfacemolecule interactions for a range of molecules and therefore the adsorption energy values were calculated for a fixed and relatively low coverage (0.13 ML). However, as shown in Part 1 of this work1, for some oxygen containing molecules, the adsorption energy changes with coverage. To investigate the effect of coverage for the molecules discussed in this paper, additional adsorption energy calculations were performed for higher coverages of aniline, pyrrole, pyridine and thiophene. The results are presented in Section S3 in Supporting Information. The most significant effect is observed for aniline; the adsorption energy per molecule increases 0.21 eV from 0.13 to 0.75 ML and decreases thereafter. For pyrrole, adsorption energy per molecule increases 0.11 eV from 0.13 to 0.50 ML and slowly decreases up to 1 ML. For pyridine, adsorption energy per molecule continuously increases ~0.07 eV up to 1 ML. For thiophene, the effect is weakest but the behavior is similar to aniline, namely adsorption energy per molecule increases 0.05 eV up to 0.75 ML and decreases thereafter.



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These results demonstrate that the adsorption energy can be significantly influenced by coverage. In general, increasing intermolecular dispersion interaction and steric hindrance among the adsorbed molecules affects the adsorption energy in two opposing ways and the net effect depends on the structure and adsorption geometry of the molecule. For large molecules which can adsorb to the surface in an upright position, such as furan, acetic acid1, aniline and pyridine, the adsorption energy per molecule increases. For small molecules, such as water1, no effect is observed and for molecules with a branched structure with respect to the binding moiety, such as acetone, the adsorption energy per molecule decreases with coverage.

Effects of Side Groups on Adsorption Behavior In general, side groups influence the adsorption energy of a particular functional group in two ways: (i) by changing the electronic structure of the functional group so that either or both the strength of electrostatic interaction and hydrogen bonding change and (ii) by changing the strength of dispersion interaction between the adsorbed molecule and the surface. Estimating the change in the strength of dispersion interaction is relatively easy because in general, dispersion increases with the size of the side group and decreases with the distance between the side group and the surface. The changes in the electronic structure of a functional group however, might be different for different functional groups and affect the strength of electrostatic and hydrogen bonding (nondispersive) interactions differently. In addition, for molecules where both types of interactions with the surface are important, the net effect can be hard to predict. Therefore, how the attachment of H or the various side groups influences the strength of nondispersive interactions of different functional groups is the main focus of this paper. This is what we referred to as adsorption behavior and discussed in detail in the rest of this section.


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The adsorption energy as a function of side group and functional group (primary amine, thiol and nitrile) are displayed in Figure 3. Irrespective of the side group, primary amines adsorb stronger than nitriles and thiols. On average, the adsorption energy of primary amines is 0.3 eV higher than nitriles and 0.33 eV higher than thiols. The average adsorption energy of nitriles (0.54 eV) is slightly higher than for thiols (0.51 eV). Except for the smallest member (hydrogen cyanide) the other three nitriles adsorb more strongly than the corresponding thiols. Figure 3 also shows that except for aniline, adsorption energy increases with the size of the side group. This is the same trend observed for oxygen containing molecules1 and results from the increase of dispersion interaction that accompanies increase in size of the side group. The reason for aniline not fitting the general trend is discussed below.

Figure 3. The energy of adsorption on calcite, in relation to the functional and side groups. Blue triangles, represent primary amine, blue squares, nitrile and yellow circles, thiol functional groups.



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To determine the effect of the side groups on the electronic structure of the functional groups and therefore, the adsorption behavior, two basic assumptions were made. First, the strength of nondispersive interactions was assumed to be proportional to the distances between the atoms of the molecules and the surface. In other words, longer O-H distances for hydrogen bonds and longer Ca-N or Ca-S distances for electrostatic interactions were considered to be weaker. Second, the total strength of nondispersive interactions for a particular adsorption geometry is estimated by the difference between the adsorption energy and the dispersion contribution (Ead – Edc). For hydrogen cyanide, hydrogen sulfide, benzonitrile and thiophenol, the H atom or the phenyl ring of the molecules is strongly involved in adsorption and this results in adsorption geometries where it is not possible to separate the influence of the side group on the electronic structure of the functional group. To overcome this problem, for these molecules, different optimized adsorption geometries were considered, where the side group-surface interactions were decreased. One possible way to assess the change in electronic structure and the strength of electrostatic interaction and hydrogen bonding is to compare the partial charges of atoms for different molecules. For this purpose, a partial charge analysis was performed and the results for H and N or S atoms of the molecules, together with corresponding electrostatic interaction distances and hydrogen bond lengths are presented in Section S6 in Supporting Information. In addition, pKa values are compiled for molecules that can hydrogen bond with the surface. In summary, the results indicate that the partial charge on the N or S atom correlates with the electrostatic interaction distance, that is the strength of the electrostatic interaction. However, the charge for the H atom of different molecules does not fully correlate with the hydrogen bond strength except for a few cases.


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Primary Amines and Ammonia: In addition to electrostatic interaction, primary amines are able to form two hydrogen bonds with the surface, which is the reason they have the highest adsorption energies. One of these hydrogen bonds is strong, with O-H distances in the 1.95 to 2.14 Å range, while the other is weak, with O-H distances in the 2.40 to 2.48 Å range. Among primary amines, aniline has the strongest hydrogen bonds and the weakest electrostatic interaction with the surface. This indicates that the phenyl side group decreases the electron density of the amine functional group compared with the H atom and alkyl side groups, which is a similar effect observed for the hydroxyl (-OH) functional group1. The strength of electrostatic interactions is similar for ammonia and the other two amines. However, the hydrogen bonds of ethylamine are slightly weaker compared with methylamine, which indicates that the ethyl side group increases the electron density of the amine group more than the methyl group. A similar behavior was also observed for methanol (CH3-OH) and ethanol (C2H5-OH), namely, ethanol has a slightly weaker hydrogen bond (1.77 Å) than methanol (1.74 Å)1. The fact that primary amines interact with the surface through two hydrogen bonds and an electrostatic interaction results in high adsorption energies and also limits geometric freedom. A clear manifestation of this geometric hindrance is observed in the case of aniline adsorption, where decreased nondispersive interactions cannot be compensated by the dispersion interaction because the molecule adsorbs in an upright position with the phenyl ring far from the surface. We made several other geometry optimization calculations, where aniline was tilted toward the surface. Although some arrangements with higher dispersion contribution were found, they all had lower adsorption energy than the one shown in Figure 1. Indeed, among all molecules considered in this pair of papers, aniline is the only molecule with a phenyl side group that does not have the highest adsorption energy in the family of molecules with the same functional group.



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Overall, the differences between adsorption energy and dispersion contributions show that the total strength of nondispersive interactions is equal for ammonia and methylamine (0.58 eV), lower for ethylamine (0.55 eV) and significantly lower for aniline (0.42 eV). This indicates that although side groups affect the electronic structure of primary amine and hydroxyl functional groups similarly, in the case of the phenyl side group, there is a slight difference in adsorption behavior. For phenol (C5H6-OH), the decrease in the strength of electrostatic interaction is nearly balanced by the increase in the strength of the hydrogen bond1 but for aniline, it is not the case and hence the reduction in total strength of nondispersive interactions is more pronounced. This observation is supported by the results of the charge analysis, namely, from ethanol to phenol, the charge on the O atom decreases by 0.08 e and the charge on the H atom increases by 0.02 e1 and similarly from ethylamine to aniline, the charge on the N atom decreases by 0.07 e and the charge on the H atom increases by 0.03 e. Yet the changes in the total strength of nondispersive interactions are different. Nitriles: Adsorption properties of nitriles are similar to aldehydes in that the molecules cannot form hydrogen bond (except hydrogen cyanide) and the dispersion contribution to adsorption energy is in a similar range, i.e. 36 to 76 % for aldehydes1 and 41 to 68 % for nitriles. However, for the same side groups, each aldehyde adsorbs slightly stronger than the corresponding nitrile, mostly as a result of stronger electrostatic interactions. The most stable adsorption geometry for hydrogen cyanide and benzonitrile shown in Figure 1 cannot be used to assess the effects of the H atom and the phenyl ring on the electronic structure and hence the adsorption behavior of the nitrile functional group. This is because both adsorption geometries are highly influenced by side group-surface interactions, namely the H atom of hydrogen cyanide forms a hydrogen bond and the phenyl ring of benzonitrile has a high dispersion interaction with the surface which tilts the benzonitrile molecule toward the surface. 18 ACS Paragon Plus Environment

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Therefore, for each molecule, an additional geometry optimization calculation was performed from the converged propionitrile geometry (Figure S3 in the Supporting Information). The calculation for hydrogen cyanide resulted in an adsorption geometry with slightly lower adsorption energy (0.37 eV) and higher nondispersive contribution (0.22 eV) and a significantly reduced Ca-N distance (2.59 Å). The benzonitrile calculation also resulted in a lower adsorption energy (0.59 eV), with a higher nondispersive contribution (0.32 eV) and a slightly shorter Ca-N distance (2.54 Å). The differences between the adsorption energy and the dispersion contribution for nitriles suggest that hydrogen cyanide has significantly lower electrostatic interaction with the surface (0.22 eV) than other nitriles and there is not a significant difference among acetonitrile (0.32 eV), propionitrile (0.30 eV) and benzonitrile (0.32 eV). The Ca-N distances for the different molecules also supports this conclusion, namely Ca-N distance is highest for hydrogen cyanide (2.59 Å) and similar for other nitriles (2.53–2.54 Å). The effect of the H atom and the side groups on the adsorption behavior of nitriles is very similar to aldehydes1, where the H atom reduces electron density and hence the strength of electrostatic interactions compared with the alkyl and phenyl side groups. Thiols and Hydrogen Sulfide: Thiols (R-SH) are structurally similar to alcohols (R-OH) and because S is one period away from O in the periodic table, they have similar chemical properties. However two important differences significantly affect the strength of moleculesurface interactions for thiols and alcohols; the S atom is larger and its electronegativity is lower than for the O atom so both electrostatic interactions and hydrogen bonding are expected to be stronger for alcohols than for thiols. This is also what our calculated adsorption geometries and energies show. For alcohols, the Ca-O distances are in the 2.40 to 2.54 Å range and O-H distances are in the 1.64 to 1.79 Å range1. For thiols, both are higher. Ca-S distances are in the 19 ACS Paragon Plus Environment


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3.04 to 3.09 Å range and O-H distances are in the 1.92 to 2.06 Å range. On average, the adsorption energy of alcohols is 0.31 eV higher than that of thiols. The smaller adsorption energy for thiols results in another difference between thiols and alcohols. The dispersion contribution to adsorption energy for the alcohols is significantly lower, 26 to 58 %1, than for thiols, 51 to 94 %. In other words, dispersion interactions have a major effect on the adsorption geometry of thiols on calcite. This is consistent with results for thiol adsorption on gold surfaces, where 65% of the adsorption energy results from dispersion interactions33. Similar to the case for hydrogen cyanide and benzonitrile, the adsorption geometry for hydrogen sulfide and thiophenol is strongly influenced by side group-surface interactions. Therefore for a correct assessment of the effect of the H atom and the phenyl group on the electronic structure of the thiol functional group, two geometry optimization calculations were performed that were initiated from converged adsorption geometry of ethanethiol (Figure S3). The calculation for hydrogen sulfide resulted in a lower adsorption energy (0.41 eV), the same nondispersive contribution (0.22 eV) and distances that are similar for Ca-S (3.06 Å) and slightly higher for O-H (1.95 Å). The converged thiophenol geometry has significantly lower adsorption energy (0.48 eV), higher nondispersive contribution (0.10 eV) and higher Ca-S (3.11 Å) and O-H (1.97 Å) distances. From hydrogen sulfide to methanethiol and ethanethiol, the strength of electrostatic interactions between the molecules and the surface slightly increases and the hydrogen bonds become weaker. This indicates an increase in the electron density of the thiol functional group from H atom to methyl and ethyl side groups. Thiophenol has the weakest electrostatic interaction with the surface and a relatively strong hydrogen bond, which suggests that the phenyl group decreases the electron density of the thiol group. This behavior is similar to that observed for hydroxyl1 and primary amine functional groups. Overall, the difference between adsorption 20 ACS Paragon Plus Environment

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energy and dispersion contribution indicates that nondispersive interactions are highest for hydrogen sulfide (0.22 eV) and slightly lower for methanethiol (0.20 eV) and ethanethiol (0.19 eV) and lowest for thiophenol (0.10 eV). Other Molecules: The 6 most common functional groups, in the organic molecules that contain O, N or S, together with an H atom and the 3 different side groups, form a set of 24 molecules. The adsorption behavior of these and 3 nonpolar compounds has been discussed in detail in the first paper1 and continued here. In the discussion that follows, we focus on the remaining 8 molecules, which are shown in Figure 4. A comparison of the adsorption behavior of these molecules can offer ideas about how O, N and S as heteroatoms affect adsorption behavior.

Figure 4. Furan, pyrrole, thiophene and pyridine are the four heterocyclic and aromatic molecules and dimethyl ether, dimethylamine, dimethyl sulfide and trimethylamine are the aliphatic counterparts.

Pyridine has the highest adsorption energy (0.76 eV) and nondispersive interaction (0.46 eV) which suggests that the partial negative charge of the N atom of pyridine is higher than other heteroatoms in other heterocyclic compounds. This is in agreement with the results of charge analysis; the partial charge of the N atom of pyridine, –0.22 e, is higher than that of pyrrole, – 0.20 e, and the O atom of furan, –0.17 e1. Pyridine is also the only molecule that adsorbs almost perfectly perpendicular to the surface. The other N containing molecule, pyrrole, is different than the rest of the heterocyclic compounds in that it has the possibility to hydrogen bond with the 21 ACS Paragon Plus Environment


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surface. Indeed, the adsorption geometry presented in Figure 2 shows that pyrrole forms a hydrogen bond (1.94 Å) with a surface O atom. The Ca-N distance (3.26 Å), on the other hand, suggests that the contribution of electrostatic interaction to the adsorption energy for pyrrole is very small. The strength of its nondispersive interaction is very similar to that of furan (0.16 eV)1 and the difference in adsorption energy between the two molecules results from the difference in dispersion interaction. Pyrrole has a more flat adsorption geometry and therefore a stronger dispersion interaction with the surface compared with furan. The S containing heterocyclic compound, thiophene, has the lowest adsorption energy and the net attractive interaction between the molecule and the surface results only from dispersion interaction. The difference between the adsorption behaviors of furan and thiophene resembles the difference that is observed for thiol and hydroxyl functional groups. The lower electronegativity of the S atom compared with the O atom makes the electrostatic interaction of thiophene significantly lower than furan. Dimethylamine has the highest adsorption energy among the aliphatic molecules (0.84 eV) followed by trimethylamine (0.73 eV). This is the opposite behavior observed for the heterocyclic counterparts, namely, pyridine has the highest adsorption energy followed by pyrrole. There are two reasons for this behavior. First, dimethylamine has a significantly stronger nondispersive interaction with the surface than pyrrole. A comparison of Ca-N distances (Figure 2) indicates that electrostatic interaction for dimethylamine is stronger than for pyrrole. Second, the electrostatic interaction for trimethylamine is significantly lower than for pyridine, which can be seen from both the increased Ca-N distance for trimethylamine and the difference between adsorption energy and dispersion contribution values (Figure 2). Both observations agree well with partial charge analysis, namely the partial charge of the N atom of dimethylamine, –0.39 e, is significantly higher than that of pyrrole, –0.20 e and the partial charge on the N atom of pyridine, –0.22 e, is higher than that of trimethylamine, –0.18 e. Among aliphatic molecules, 22 ACS Paragon Plus Environment

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dimethyl sulfide has the lowest adsorption energy (0.54 eV), followed by the O containing molecule, dimethyl ether (0.61 eV). This behavior is also observed for heterocyclic counterparts, such as thiophene, which has the lowest adsorption energy followed by furan. The difference between dimethyl ether and dimethyl sulfide adsorption is purely electrostatic, which agrees well with our findings based on differences in electronegativity of O and S atoms and partial charges, –0.32 e for O and 0.12 e for S.

Desorption Temperature Measurements and Comparison with Predictions The adsorption energies determined with the DFT-D2 method were used in the Polanyi-Wigner equation (Equation 2) to calculate a desorption temperature for each molecule and the results were compared to values derived from XPS experiments. Figure 5 shows X-ray photoelectron spectra of thiophene, pyrrole, pyridine and aniline on calcite {10.4} for increasing temperature. At the lowest temperatures, the surface coverages are 0.7 monolayer (ML) for thiophene, 3 ML for pyrrole, 0.8 ML for pyridine and 1 ML for aniline. One ML is defined as two molecules per one calcite {10.4} surface unit cell, which naturally contains two adsorption sites per molecule. The way that coverage is estimated from experimental data is discussed in Section S2 of the Supporting Information.



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Figure 5. X-ray photoelectron spectra. C 1s and S 2p spectra for (a) thiophene and C 1s and N 1s spectra for (b) pyrrole, (c) pyridine and (d) aniline on calcite {10.4} as a function of temperature.

XPS peak intensities for the adsorbed molecules decrease with increasing temperature as a result of desorption. For each molecule, the molecular signal abruptly decreases to minimum intensity at a specific temperature and does not change further. This is the temperature at which all intact molecules have desorbed from the surface. Therefore, the midpoint between the last temperature at which there were still some molecules on the surface and the first temperature at which all intact molecules had been desorbed is designated as the desorption temperature for that particular molecule. When the temperature was increased 40 to 70 °C above the desorption temperature, the XPS spectrum for the clean surface was not restored for any of the molecules. This behavior is similar to what we observed for acetone and acetic acid on the calcite {10.4}


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surface1 and was interpreted to result from strongly bound fragments of molecules that had dissociated during heating. In Figure 5a, C 1s and S 2p spectra are shown for thiophene which, among the four molecules studied, had the lowest desorption temperature, –137.5 ± 2.5 °C. As we increased the temperature, the C 1s peak slightly shifted to higher binding energy while the S 2p peak shifted to lower binding energy. In Figure 5b, C 1s and N 1s spectra are shown for pyrrole, which desorbed at –90 ± 10°C. Pyrrole was the only molecule that formed a multilayer and our results indicate that the multilayer desorbs between –140 °C and –100 °C. Similar to thiophene, for pyrrole, as the temperature increased, the C 1s peak shifts to higher binding energy and the N 1s peak shifts to lower binding energy. In addition, the shoulder at the low binding energy side of the C 1s peak disappeared. In Figure 5c, the C 1s and N 1s spectra are shown for pyridine, which desorbed at – 17.5 ± 7.5 °C. For pyridine, both the N 1s and C 1s peaks shifted toward lower binding energies. After the molecules desorbed, the species that remained on the surface had significantly lower binding energy compared with the intact molecules. Finally, in Figure 5d, the C 1s and N 1s spectra for aniline desorbed at 10 ± 10 °C. Aniline behaves differently from the rest of the molecules in that both the C 1s and N 1s peaks shift to higher binding energy. Adsorption and thermal desorption of thiophene, pyrrole, pyridine and aniline on different surfaces have been investigated in detail previously34-42. Although possible chemical changes that result from heating are interesting, they are not relevant for comparison with our calculated desorption energies. In Section S2 of the Supporting Information, the results from fitting the Xray photoelectron spectra for the four molecules are shown and details about the specific results are briefly discussed. Figure 6 summarizes the results. The black circles represent the predicted desorption temperatures for the eighteen molecules of this study, calculated using the Polanyi-Wigner 25 ACS Paragon Plus Environment


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equation (Equation 2). The desorption temperature for each molecule was determined for 99 % of a hypothetical ML of the molecule desorbed from calcite {10.4} within the 10 minutes of the experiment, which was chosen to reflect the waiting time in XPS measurements. We assumed that the magnitude of desorption and adsorption energy is equal and that adsorption energy is constant over the whole coverage range and equal to the value calculated for 0.13 ML using DFT-D2. In Section S4 of Supporting Information, the results for desorption temperature calculations for coverage dependent adsorption energy values are presented and briefly discussed. The prefactor in Equation 2, ߥ଴ , was approximated by the term ݇ܶ/ℎ43, where ݇ and ℎ represent the Boltzmann and Planck constants and ܶ denotes temperature. The changes in desorption temperature predictions depending on the values of prefactor and coverage were discussed in the first paper1. In summary, using 1013 s–1 (a commonly used value) for the prefactor, reducing the initial coverage to 0.5 ML or the remaining coverage to 0.1 ML changes the desorption temperature prediction by only 4 to 7 °C. The desorption temperature for thiophene, pyrrole, pyridine and aniline, determined from XPS data, are represented by red squares in Figure 6. There is good agreement between the measured and predicted desorption temperatures, which together with the results from the first paper1, strongly suggest that the adsorption energies determined using DFT-D2 with revPBE functional and modified C6 parameters are in good agreement with experimental values.


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Figure 6. Temperature of desorption for 99 % of a monolayer for eighteen molecules, predicted by DFT-D2 calculations (black circles), with experimental data for thiophene, pyrrole, pyridine and aniline derived from XPS measurements (red squares).

CONCLUSIONS We have determined the adsorption energy and geometry for twelve nitrogen and six sulfur containing molecules on the calcite {10.4} surface using DFT-D2 with C6 parameters modified for ionic solids. We have investigated in detail the changes in adsorption behavior resulting from the attachment of a H atom, methyl, ethyl or phenyl side group, for primary amine, nitrile and thiol functional groups. The results presented in this paper indicate that there are three types of interaction between molecules and the calcite surface: electrostatic, hydrogen bonding and dispersion. Irrespective of the side group, primary amines adsorb more strongly than nitriles and thiols and on average, the adsorption energy of nitriles is slightly higher than thiols. As expected, the dispersion interaction between the molecules and the surface increases with the size of the side group. For primary amines, the nondispersive interaction is highest for ammonia and methylamine, followed by ethylamine and significantly lower for aniline. Among the nitriles, the



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strength of the electrostatic interaction is slightly higher for acetonitrile and benzonitrile compared with propionitrile and significantly lower for hydrogen cyanide. For thiols, the total nondispersive interaction is highest for hydrogen sulfide, slightly lower for methanethiol and ethanethiol and lowest for thiophenol. The results for the heterocyclic aromatic molecules and the structurally similar aliphatic counterparts show that surface-molecule interaction is strongest for nitrogen containing molecules, followed by the oxygen containing ones and lowest for the sulfur containing molecules. The difference between oxygen and sulfur containing molecules results solely from differences in the strength of electrostatic interactions but for the nitrogen containing molecules, both dispersive and nondispersive interactions play a role. The adsorption energy values determined by DFT-D2 calculations were used in the Polanyi-Wigner equation to predict the desorption temperature for each molecule from calcite {10.4}. For thiophene, pyrrole, pyridine and aniline, the desorption temperatures were determined experimentally from XPS measurements. The experimental values and predictions agree well, which provides confidence that the DFT-D2 method with modified C6 parameters is reliable and the results presented here can be used as a benchmark for adsorption of organic molecules on calcite in particular and on ionic surfaces in general. Considering the lack of data available in the literature for adsorption energies of nitrogen and sulfur containing molecules on calcite {10.4}, the results presented in this paper will hopefully be useful for experimental and computational studies in the field. The results obtained in this paper and in Part 11 show that it is possible to group the molecules with different functional groups into three categories based on their adsorption energies: the first group, strong bonding, consists only of carboxylic acids with adsorption energies in the 1.03 to 0.97 eV range; the second group, moderate bonding, consists of primary 28 ACS Paragon Plus Environment

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amines and ammonia and alcohols and water with adsorption energies in the 0.88 to 0.79 eV range; and the third group, weak bonding, consists of aldehydes, nitriles, and thiols and hydrogen sulfide with adsorption energies in the 0.68 to 0.38 eV range. Our results show that in general, attachment of the H atom or a side group affects the adsorption behavior of the nitrogen and sulfur containing functional groups more significantly than for the oxygen containing functional groups. In particular, the total strength of nondispersive interactions is considerably decreased when a H atom is attached to nitrile and aldehyde functional groups and when a phenyl group is attached to primary amine and thiol functional groups. Except on this one point, it is difficult to generalize the effect of the various side groups on the adsorption behavior of different functional groups and each side group and functional group must be investigated individually.

ASSOCIATED CONTENT Supporting Information Adsorption energy calculations were performed with PBE functional without the dispersion corrections for comparison and the results are presented in Section S1. X-ray photoelectron spectra together with the fits and the coverage calculations for thiophene, pyrrole, pyridine and aniline are presented in Section S2. Adsorption energy calculations for various coverages are presented in Section S3 and the desorption temperature calculations with coverage dependent adsorption energy values are presented in Section S4. Adsorption geometries for hydrogen cyanide, benzonitrile, hydrogen sulfide and thiophenol in upright geometries are presented in Section S5. Results of partial charge analysis are presented and discussed in Section S6. Generation of different starting geometries is explained in Section S7.



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

ACKNOWLEDGMENTS We thank Mats H. M. Olsson for helpful comments to the manuscript and other members of the NanoGeoScience Research Group for discussion. 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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(26) At the NIST Computational Chemistry Database (http://cccbdb.nist.gov/) calculations for various molecules are performed with B3LYP exchange-correlation functional by using 6-31G* basis set and optimized geometries are reported. (27) Metson, J. B. Charge Compensation and Binding Energy Referencing in XPS Analysis. Surf. Interface Anal. 1999, 27, 1069-1072. (28) Stipp, S. L.; Hochella JR., M. F. Structure and Bonding Environments at the Calcite Surface as Observed with X-Ray Photoelectron Spectroscopy (XPS) and Low Energy Electron Diffraction (LEED). Geochim. Cosmochim. Acta 1991, 55, 1723–1736. (29) Ibach, H. Adsorption. Physics of Surfaces and Interfaces; Springer-Verlag Berlin, 2006; pp 273-284. (30) Hwang, S.; Blanco, M.; Goddard III, W. A. Atomistic Simulations of Corrosion Inhibitors Adsorbed on Calcite Surfaces I. Force Field Parameters for Calcite. J. Phys. Chem. B 2001, 105, 10746-10752. (31) de Leeuw, N. H.; Cooper, T. G. A Computer Modeling Study of the Inhibiting Effect of Organic Adsorbates on Calcite Crystal Growth. Cryst. Growth Des. 2004, 4, 123–133. (32) Freeman, C. L.; Asteriadis, I.; Yang, M.; Harding, J. H. Interactions of Organic Molecules with Calcite and Magnesite Surfaces. J. Phys. Chem. C 2009, 113, 3666–3673. (33) Andersson, M. P.; Density Functional Theory with Modified Dispersion Correction for Metals Applied to Self-Assembled Monolayers of Thiols on Au(111). Journal of Theoretical Chemistry 2013, 327839. (34) Baumgartner, K. M.; Volrner-Uebing, M.; Taborski, J.; Bäuerle, P.; Umbach, E. Adsorption and Polymerization of Thiophene on a Ag(111) Surface. Ber. Bunsen. Phys. Chem. 1991, 95, 1488-1495. 34 ACS Paragon Plus Environment

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(35) Rodriguez, J. A.; Dvorak, J.; Jirsak, T. Chemistry of Thiophene on Mo(110), MoCx and MoSx Surfaces: Photoemission Studies. Surf. Sci. 2000, 457, L413-L420. (36) Cao, X.; Coulter, S. K.; Ellison, M. D.; Liu, H.; Liu, J.; Hamers, R. J. Bonding of NitrogenContaining Organic Molecules to the Silicon(001) Surface: The Role of Aromaticity. J. Phys. Chem. B 2001, 105, 3759-3768. (37) Qiao, M.; Tao, F.; Cao, Y.; Xu, G. Adsorption and Thermal Dissociation of Pyrrole on Si(100)-2×1. Surf. Sci. 2003, 544, 285-294. (38) Kishi, K.; Chinomi, K.; Inoue, Y.; Ikeda, S. X-Ray Photoelectron Spectroscopic Study of the Adsorption of Benzene, Pyridine, Aniline, and Nitrobenzene on Evaporated Nickel and Iron. J. Catal. 1979, 60, 228-240. (39) Davies, P. R.; Newton, N. G. The Chemisorption and Decomposition of Pyridine and Ammonia at Clean and Oxidised Al(111) Surfaces. Surf. Sci. 2003, 546, 149-158. (40) Serafin, J. G.; Friend, C. M.; Reactivity of Pyridine on Mo(110): C-H and C-N Bond Activation. J. Phys. Chem. 1989, 93, 1998-2004. (41) Isvoranu, C.; Wang, B.; Ataman, E.; Schulte, K.; Knudsen, J.; Andersen, J. N.; Bocquet, M.L.; Schnadt, J. Pyridine Adsorption on Single-Layer Iron Phthalocyanine on Au(111). J. Phys. Chem. C 2011, 113, 3666–3673. (42) Xu, X.; Friend, C. M. The Adsorption and Reactions of Aniline on Rh (111). J. Vac. Sci. Technol. A 1991, 9, 1599-1603. (43) Ibach, H. Diffusion. Physics of Surfaces and Interfaces; Springer-Verlag: Berlin, 2006; pp 498–500.



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Functional Group Adsorption on Calcite: II. Nitrogen and Sulfur

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