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Hydrocarbon Adsorption on Carbonate Mineral Surfaces: A First-

Principles Study with van der Waals Interactions
Vagner A. Rigo,† Cigdem O. Metin,‡ Quoc P. Nguyen,‡ and Caetano R. Miranda*,†

Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil

Department of Petroleum and Geosystems Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
S Supporting Information

ABSTRACT: In this work, we study the adsorption of hydrocarbon

molecules on carbonate surfaces by means of first-principles calculations
based on Density Functional Theory (DFT) with and without van der
Waals (vdW) corrections. Energetic, electronic, and structural properties
have been determined for the adsorption of the representative
hydrocarbons (hexane and benzene) on calcite (CaCO3) and dolomite
[CaMg(CO3)2] (10−14) dry surfaces. Those hydrocarbons were
selected to represent aromatics and alkanes on surfaces, and for each
molecule the evaluated properties are similar for both surfaces. Due to
the obtained similarities in both surfaces, we have evaluated the vdW
corrections only for calcite. Our results suggest that Ca sites are the most
energetically favorable for hydrocarbon adsorption on both minerals.
This effect is mostly due to the electronic level ordering that leads to
charge differences in the possible adsorbed sites (Ca, Mg, and CO3) in the carbonate surfaces. The vdW corrections strengthen
the hydrocarbon−surface bond with a corresponding reduction in the bond distance between the benzene and the surface.
However, this reduction is not even for all atoms in the molecule, and the angle between the benzene aromatic ring and the
surface increases. The energy barrier, for the displacement of the hydrocarbons along the calcite surface, was determined for
representative surface direction, using the Nudged Elastic Band method, and adsorption energies for the most stable sites show
the same order of magnitude.

Carbonaceous systems are an abundant material in nature and
mainly employs classical force field models. For example,
Freeman et al.13,14 applied atomistic calculations to study the
represent a wide range of physical compounds. They are the interactions between mineral, water, and organic molecules
main component of minerals rocks, as well as shells and (namely, methanol, methanoic acid, methylamine, and dimethyl
skeletons,1−3 and have a central importance for CO2 exchange ether) and also provided comparisons between classical force
in seawater4 and oil accumulation in petroleum fields.5−8 fields and ab initio methods using the PW9115 functional. Some
Moreover, calcite (CaCO3) and dolomite [CaMg(CO3)2] differences in results obtained by first-principles and classical
represent 90% of sedimentary rocks,5 and in many cases interatomic potentials have been observed. In those classical
these minerals constitute hydrocarbon reservoirs.6−8 Addition- simulations, the ab initio data can be used to parametrize the
ally, most petroleum exploration takes place in carbonaceous oil interatomic potential. However, in many cases for ab initio, the
fields, and a knowledge about the interaction between the dispersion forces are not treated adequately. The inclusion of a
hydrocarbon molecules and the mineral surface is desirable.9 dispersion corrected functional to treat the van der Waals
The accurate description of the rock−hydrocarbon interaction interactions at the ab initio level is essential to accurately
is an important step to understand the mechanisms and parametrize a reliable classical model to describe the interaction
improve the Enhanced Oil Recovery in calcite and dolomite between molecules and the surface for further modeling of
minerals.10−12 biomineralization and oil exploration processes at larger scales.
One of the most interesting phenomena concerning calcium To the best of our knowledge, our work is the first one to
carbonates is the biomineralization processes, where the include van der Waals (vdW) corrections on ab initio
interaction between organic molecules and carbonates can calculations for carbonaceous surfaces interacting with organic
drive the mechanism for surface growth. Detailed and accurate molecules. Benzene and hexane have been chosen as the
information about the molecule−mineral interaction is of representative aromatic and alkane adsorbed molecules. The
central importance to model these systems, and efforts were
done to understand this process.2 First-principles calculations Received: June 19, 2012
represent an important and accurate tool to obtain information Revised: October 1, 2012
about the processes at atomistic level. However, the literature Published: November 2, 2012

© 2012 American Chemical Society 24538 | J. Phys. Chem. C 2012, 116, 24538−24548
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inclusion of vdW corrections in ab initio methods can improve were allowed to relax until the forces reached 1 × 10−3 au. For
the description of these systems,3,16 particularly the long-range bulk calculations the cell vectors were relaxed until the pressure
weak dipole−dipole interaction, as well as provide a fully on the cell reached 0.5 kbar.
electronic description for the interface of hydrocarbon Initially, the crystalline parameters (atomic positions and cell
molecules and mineral surfaces, which can be used to improve vectors) of bulk calcite and dolomite were fully relaxed. The
the force fields based on first-principles calculations. hexagonal structure of calcite is shown in Figure 1a and that for
We choose the (10−14) surface of the hexagonal calcite
structure in our study. This surface is charged neutral and
exhibits both Ca atoms and carbonate groups and has been
reported in the literature as the most stable one using different
theoretical methods: classical force fields17−19 and also by ab
initio calculations using the Density Functional Theory (DFT)
with both plane waves20 and a Local Combination of Numerical
Orbitals (LCAO).21 Other calcite terminations (more en-
ergetic) have also been recently considered in the literature:
{11−20} and {10−10}.22 An extensive experimental work using
ultrathin films by Archibald et al.23 suggests that other
orientations would also be favorable as a function of organic
surface modification, but the (10−14) surface was exper-
imentally found to be the most stable.
The (10−14) surface has also been considered as the most
common for dolomite, based on classical force fields including a
shell model for polarization.24,25 However, using the same
methodology and considering different surface terminations,
Titiloye et al.18 reported the {10−10} and {11−20} surfaces as
the most stable for dolomite. Pokrovsky et al.26 experimentally
showed that the calcite and dolomite surface speciation change
as a function of pH. The authors showed that for a given NaCl
concentration and CO2 pressure the CaOH2+ is favorable for
the calcite surface at low pH, and CaCO3− groups are favorable
at high pH. They also reported similar results for dolomite in
both cases, Ca or Mg, at the surface.
In this work, we first present the calcite and dolomite bulk
properties, followed by the calculated properties (energetics,
structural, and kinetics) for hydrocarbon adsorption on calcite Figure 1. Hexagonal crystal structure of calcite and dolomite and (10−
and dolomite (10−14) surfaces. The effect of vdW interactions 14) surface of calcite. Side view of calcite (a) and dolomite (b). The
on these properties is elaborated, followed by the results on the unit cell vectors are shown. Considering a cleaved (10−14) surface, we
adsorption and kinetics effects of hydrocarbons on carbona- present a side view along [42−1] (c) and [010] (d) directions and an
ceous surfaces. Our main goal is to understand the adsorption overview (e) of the irreducible cell of the calcite (10−14) surface. The
blue and dark balls represent the Ca and Mg atoms. The red and
of representative hydrocarbon molecules on carbonaceous yellow represent the O and C atoms, respectively.
surfaces by first-principles calculations including the vdW
dispersion forces, comparing the most used standard functional
(PW9127) with the most reliable vdW corrected one for a large dolomite in Figure 1b. The surfaces were constructed by
number of atoms.

cleaving the bulk calcite and dolomite in the hexagonal form
along the (10−14) surface, and they contain the same number
METHODS of metal atoms (Ca/Mg) and carbonate groups (CO3) to keep
Calculations without vdW Dispersion. Our calculations the total charge neutral.
were based on density functional theory,27,28 using the Perdew Since we are using periodic boundary conditions, surfaces are
and Wang (PW91)29 approximation to the exchange and represented by a finite number of CaCO3 or CaMg(CO3)2
correlation energy term. This functional is a common choice for layers. The optimal surface thickness was determined by
calcite and was used to parametrize classical potentials.13,14 checking the changes in geometry and energy as a function of
Ultrasoft pseudopotentials29 were used to describe the core− the number of layers, for 3, 4, 5, and 6 layers. For these
valence electron interaction, and the valence electrons are geometries, only atoms in the bottom layer were fixed to
described by plane wave expansions with an energy cutoff of simulate the bulk part, while the remaining atoms were allowed
544 eV. This cutoff value was tested with a calculation using to relax. Geometries with two fixed bottom layers were also
680 eV, giving a small difference of approximately 5 meV in evaluated. These results for a surface composed by a total of
adsorption energy. The gamma centered Monkhost−Pack three layers do not show significant differences compared to the
method30 was used for the Brillouin-zone sampling integration. other ones, with geometry and energy deviations lower than
For the minimal supercell, a total of seven inequivalent k-points 1%. We adopted the model with three layers (one of them
were used, while the isolated hydrocarbons were simulated at fixed) to study the interactions of hydrocarbons with calcite and
the gamma point only. The geometry optimizations were dolomite surfaces. To avoid interaction between the periodic
performed using the bfgs minimization algorithm as imple- images, we have used a vacuum of at least 11 Å in the
mented in the QUANTUM ESPRESSO package.31 Structures simulations.
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Figure 1c,d shows the irreducible unit cell of the calcite avoid the interaction between periodic images. The gamma
surface along the [42−1] and [010] directions, respectively. point was used for the Brillouin zone sampling integration, and
Figure 1e presents the top view of the (10−14) surface, where an energy cutoff of 1088 eV was applied.
the lines show the irreducible unit cell (just one layer). In the
adsorption process, we used a geometry composed by two
surface irreducible unit cells (a 2 × 1 supercell, according to
Bulk Properties. Calcite and dolomite have a hexagonal
Figure 1e). In this calculation, we used a surface model with 20 crystalline form (shown in Figure 1). Considering calcite, we
atoms per layer, amounting to 60 atoms. For adsorbed benzene, have obtained optimized unit cell vectors presented in Figure
a total of 72 atoms were used. Considering a benzene molecule 1a as: a = b = 5.042 Å and c = 17.220 Å (3.415*a). With the
lying parallel to this calcite surface geometry model, the closest inclusion of vdW, these values are a = b = 5.121 Å and c =
distance between the molecule and its own image due to the 17.512 Å (3.419*a). The slight increase in the lattice
periodic boundary conditions is 5.80 and 3.25 Å along the two parameters with vdW is in agreement with the DCACP
periodic directions, according to the coordinate system theory.36 Quantum chemistry calculations by Villegas-Jiménez
depicted in Figure 1e (for vdW calculations we used a larger et al.42 with a Gaussian basis using RHF/6-31G(d,p) level give
supercell, see below). We have done calculations using a large a Ca−O bond length of 2.37 Å, which is very close to our
supercell (3 × 2), to check the size effects of the supercell. calculated value of 2.38 Å using the PW91 functional.
Comparing the results of the minimal cell (2 × 1) with the Comparing this result with vdW ones, they show deviations
large one (3 × 2), we obtained adsorption energy changes of of only about 1% for bulk calcite. In Table 1, we summarize our
approximately only 10 meV for the evaluated sites.
For hexane adsorption, we used three different geometries: Table 1. Calcite and Dolomite Structural Parameters
(i) a (2 × 1) geometry (similar to benzene adsorption) for top Obtained in This Work from First-Principles Calculations
sites and a (ii) (3 × 1) and (iii) (2 × 2) surface for hexane (Without and With van der Waals) and Compared with
adsorption. Those geometries were used to consider the Other Methods and Experimental Values
nonsymmetric alignments of hexane on the surface. These
supercells contain 80, 110, and 140 atoms, respectively. calcite
To determine the energy barriers involved in diffusion of unit cell vectors PW91 B3LYP45 van der Waals EXPT43
both benzene and hexane on the calcite surface, we have used a (Å) 5.042 5.049 5.122 4.9880
the Nudge Elastic Band (NEB) method.32 The first NEB image c (Å) 17.220 17.343 17.512 17.0680
represents the most stable adsorption site for each hydrocarbon c/a 3.4151 3.4350 3.4191 3.4220
on the calcite surface. The energy barriers were obtained along bond length
the periodic directions along the surfaces, namely, [42−1], C−O 1.298 1.305 1.29
[48−1], and [010]. Calculations were converged until all forces Ca−O 2.381 2.430 2.36
were less than 0.05 eV/Å. dolomite
Calculations Including vdW Dispersion. To take into unit cell vectors PW91 B3LYP46 EXPT44
account the van der Waals dispersion forces, we used the DFT
a (Å) 4.833 4.838 4.8069
with the Dispersion-Corrected Atom-Centered Potentials
c (Å) 16.022 16.276 16.0020
model (DCACP).16 This model introduces London dispersion c/a 3.3153 3.3640 3.3290
forces applied as an atom-electron potential, and this is
included in the system in a self-consistent way using a nonlocal
form, similar to that applied for pseudopotentials. We adopt the results compared with experimental43,44 and other theoretical
actual methodology to be a consistent way to obtain the values based on different functionals.45,46 These values show a
electronic properties of the systems, to evaluate the bond deviation close to 1% compared with experimental values, as
formations between the molecules and the surface for a van der well as our calculations without and with vdW.
Waals calculation with more than a hundred atoms. It was We have also determined the structural properties of bulk
shown that this methology is superior to the standard atom− dolomite. It can be clearly observed from Figure 1b that the
atom corrections; for example, using DCACP Lin et al. showed geometry for the dolomite crystal is similar to that for the
that the description of liquid water can be improved over other calcite crystal. The main difference between the calcite and
vdW corrections that just include an atom−atom potential,33 dolomite structures comes from the substitution of a Ca atom
and recently, an accurate potential for water has been fitted for a Mg atom in dolomite (Figure 1b), keeping only Ca atoms
using DCACP results.34 With this method, we applied the vdW in calcite (Figure 1a). This creates a slight difference in the
correction to all atoms in the calcite surface, except for Ca. A lattice parameters of the two minerals. Our first-principles
similar procedure was used by Aeberhard et al., for molecules calculations for dolomite also show a very good agreement with
containing sulfur, where the inclusion of vdW in C, O, and H the experimental values. The electronic properties of the bulk
atoms provides satisfactory results.35 This is in agreement with calcite and dolomite are here analyzed and appear in Figure
Lin et al. where they showed that the vdW is most relevant for S1a−c in the Supporting Information. Results with and without
molecules composed by C, O, and H atoms.36 The vdW vdW in bulk electronic structure do not present any changes
dispersion calculations were performed with the CPMD and are presented in Figure S2a,b in the Supporting
package, 37 using the BLYP38,39 approximation for the Information.
exchange-correlation energy term and Troullier−Martins Hydrocarbon Adsorption. For hydrocarbon adsorption
pseudopotentials.40 This functional is the most transferable on calcite and dolomite, a critical point in our study is to
one considering the DCACP methodology and provides the determine the most favorable sites where adsorption can occur.
best results, compared with other functionals.41 The computa- To determine some possibilities, we analyze the charge density
tional supercell was doubled with respect to the minimal one to slice of a calcite surface of a three-layer surface, as described in
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the Methods section. For surfaces, the charge density profiles

do not show deviations between the vacuum exposed layer and
the surface inner layer, as shown in Figure S3 in the Supporting
To evaluate the energetic properties for different adsorption
sites, we adsorb the hydrocarbons on nonequivalent sites on
calcite and dolomite. As we present along the paper, the calcite
and dolomite show similar adsorption characteristics, and we
incorporated vdW interactions only for calcite.
The adsorption energies (Eads) of the hydrocarbons on the
surface systems were obtained by the equation
Eads = E(surface + H) − Esurface − E H
where Esurface and E(surface+H) are the total energies of the pristine
surface and of the surface plus adsorbate, respectively, and EH is
the total energy of the isolated adsorbate.
Benzene Adsorption. A benzene molecule was placed in
different nonequivalent sites above the surfaces. For the initial
configurations with the benzene aromatic ring parallel to the
surface (hole sites), all benzene carbon atoms are at the same
distance from the calcite surface. The adsorption of benzene on
calcite can occur above either a Ca atom or a carbonate group.
For the dolomite surface, the benzene adsorption can also
occur above a Mg site. Top sites (where just one benzene C
atom is closest to the surface) and bridge sites (sites with a C−
C bond of benzene above the surface sites) were also
considered. An overview of representative geometries is
schematically presented in Figure 2, where the Ca_hole_a
and Ca_hole_b, CO3_hole_a and CO3_hole_b represent hole
configurations. The Top_a and Top_b sites represent top
configurations. Finally, Ca_bridge and CO3_bridge represent
the bridge sites. The hole, top, and oblique geometries
considering a Mg site (not shown) correspond to similar
configurations presented for Ca sites in Figure 2. Figure 2. Representation of benzene adsorption sites on the calcite
Table 2 presents the adsorption energies for benzene (10−14) surface (similar to the dolomite (10−14) surface, where the
adsorbed on the calcite and dolomite surfaces. The Ca_hole_b Mg sites are analogous to the presented Ca ones). The site labels are
(a) Ca_hole_a, (b) Ca_hole_b, (c) Top_a, (d) Top_b, (e)
adsorption site represents the most stable one for a benzene Ca_bridge, (f) CO3_bridge, (g) CO3_hole_a, and (h) CO3_hole_b.
molecule on the calcite (10−14) surface with an adsorption The blue balls represent the Ca atoms, and the ticks represent the
energy of −0.13 eV. The Ca_bridge site has an adsorption carbonate groups.
energy of −0.11 eV. Adsorption on a CO3 surface site is less
favorable compared to adsorption on Ca sites. The most stable Table 2. Adsorption Energies for a Benzene Molecule
adsorption site on a CO3 group is the CO3_hole geometry, Adsorbed on Calcite and Dolomite (10−14) Surfaces
where CO3_hole_a and CO3_hole_b have an adsorption
energy of −0.06 and −0.08 eV, respectively. Top configurations Eads (eV)
(Top_a and Top_b) have an adsorption energy close to zero. configuration calcite (DFT) calcite (DFT + vdW) dolomite (DFT)
This adsorption energy value (around 0.1 eV) is of the same Ca_hole_a −0.11 −0.34 −0.15
order as obtained for HCA organic molecules adsorbed on Ca_hole_b −0.13 −0.33 −0.13
calcite using DFT calculations with Local Density Approx- Top_a −0.00 −0.05 −0.02
imation (LDA) functional.47 Top_b −0.01 −0.13 −0.05
Figure 3a−d shows the optimized adsorption geometry and Ca_bridge −0.11 −0.23 −0.11
charge density maps on slices along the benzene and calcite CO3_bridge −0.02 −0.08 −0.03
surface, for benzene adsorbed on calcite over Ca_hole_b and CO3_hole_a −0.06 −0.20 −0.05
CO3_hole sites, respectively. Energetically, Ca_hole_b is the CO3_hole_b −0.08 −0.23 −0.07
most stable site, and CO3_hole_b is a representative case for Mg_bridge - - −0.06
adsorption on a CO3 site. After the optimization of forces and Mg_top_a - - −0.01
energies, the Ca_hole_b configuration shows a small displace- Mg_hole_a - - −0.07
ment from the initial fully planar configuration. In particular, Mg_hole_b - - −0.08
the angle formed between the benzene aromatic ring and the
surface is approximately 15° in the Ca_hole_b geometry
(Figure 3a). The benzene with Ca_hole_a geometry (not the CO3_hole_b (Figure 3d) configurations show that the
shown) presents an angle of 9° with the surface. interaction between the calcite surface and the benzene
The charge density maps of the region between the surface molecule is stronger for adsorption on a Ca site, compared
Ca and benzene C atoms on the Ca_hole_b (Figure 3b) and to adsorption over a CO3 group. The low charge density along
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Figure 3. Geometry details (a) and slice on surface charge density (b)
for a benzene adsorbed on the calcite (10−14) surface at Ca_hole_b
and geometry (c) and surface charge density slice (d) for CO3_hole_b
configuration on calcite. The figures present only one surface layer;
however, the calculations were carried out using three layers. The
distances are in Å, and the scale for surface charge density slices is
linear between 0 and 0.1 electrons/bohr2.

the surface and benzene in Figure 3b shows that even at the

most stable benzene site on calcite (Ca_hole_b) the binding Figure 4. Benzene adsorbed on the dolomite (10−14) surface. The
between the aromatic hydrocarbon and the surface is weak. geometry and charge density slice are presented for Ca_hole_a site (a)
For benzene adsorption on the dolomite (10−14) surface, in and (b), CO3_hole_a (c) and (d), and Mg_hole_a (e) and (f),
addition to the adsorption sites presented in Figure 2, we also respectively. The distances are in Å, and the scale for charge density
evaluated geometries with the benzene above a surface Mg slices is the same as Figure 3.
atom. In this way, hole and bridge configurations above the Mg
atom were considered. Table 2 shows the adsorption energies
for all evaluated benzene−dolomite surface systems. The maps of CO3_hole (Figure 4d) and Mg_hole_a (Figure 4f)
Ca_hole_a site is the most stable, with adsorption energies of configurations do not show isolines between the benzene and
−0.15 eV. The Mg_hole_b site shows a lower adsorption the dolomite surface, indicating low adsorption energy.
energy considering adsorption over a surface Mg atom (−0.08 Considering calculations without vdW, the most stable site
eV). The Mg_hole_a site is similar to the Mg_hole_b, differing on calcite (Ca_hole_b) and on dolomite (Ca_hole_a) presents
by a rotation of the benzene molecule on the surface. The an adsorption energy difference of 20 meV. This small
adsorption on a carbonate group represents the less stable difference in adsorption energy suggests a similar bond strength
configuration. for a benzene molecule on both surfaces. On the basis of this
In Figure 4a,b, we present the geometry and charge density result, we only use the calcite surface to study the effects of
map for the Ca_hole_a adsorption site on dolomite. This is the vdW interactions and to find the energy barriers for
most stable site for benzene adsorption on dolomite. In this hydrocarbon displacement on these surfaces.
configuration the benzene carbon atom closest to the surface When we include the vdW interactions in the systems, by
Ca atom shows a bond length of 3.31 Å. This distance is shorter means of DCACP calculations for adsorbing surfaces, the
than that for Ca_hole_b on calcite (3.53 Å). This is an energetic preference for adsorption over Ca sites is preserved.
indication of a slight stronger binding of benzene to the As a general trend, the vdW interactions increase the
dolomite surface, compared to the calcite surface. The charge adsorption energies for all sites and reduce the bond length
density map along the surface Ca atom supports this and the between the benzene and the surface.
closest benzene carbon atom on dolomite (Figure 4b), where The hole sites on Ca atoms were found to be the most
isolines suggest a higher charge density between them, stables ones, regardless of vdW interactions. The Ca_hole_a
compared to the calcite−benzene system (Figure 3b). The configuration is the most stable for benzene adsorption with
bond lengths for benzene adsorbed on both surfaces are greater vdW interactions (adsorption energy of −0.34 eV), while the
than those for methanoic acid on calcite (10−14), around 2.21 Ca_hole_b is the most stable without vdW calculations. These
and 3.01 Å, computed using a classical potential.48 results represent an increase of more than 60% in the
Figure 4c−f shows the geometries and charge density maps adsorption energy, by comparing the calculations without and
for CO3_hole_b and Mg_hole_a geometries. As we can see in with vdW correction for these sites. A similar increase in the
Figure 4c,e, the respective distances from the surface increase adsorption energy (more than 60%) is obtained for adsorption
for benzene above the CO3_hole and Mg sites, as compared to on the CO3_hole site. In this case, the vdW results provide an
adsorption above the Ca atom (Figure 4a). The charge density adsorption energy of −0.20 eV.
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Considering adsorptions on a Ca atom or a CO3 group, the analysis (Figures 5b, e, and h) indicates a pronounced
Ca site kept as the most stable when the vdW correction was modification for benzene adsorption on Ca (Figure 5b),
included. Considering only the Ca_hole_a and Ca_hole_b compared to adsorption on Mg (Figure 5e) and CO3 sites
sites, without vdW interactions the Ca_hole_b site is the most (Figure 5h), respectively. These results are in agreement with
stable for benzene adsorption on a Ca atom. When the vdW the observed bond between a benzene and Mg and Ca isolated
correction is included, the most stable sites are the Ca_hole_a. cations.50 The metal atom−benzene bond is explained in terms
Indeed, according the Figure 2, the Ca_hole_a and Ca_hole_b of the charge rearranging after adsorption.
sites differ by a rotation of the benzene on the surface, and in Additionally to the atomic structure information, we have
this way we can consider these as equivalent sites, where the also studied the electronic structure for Ca_hole_a, Mg_ho-
first one corresponds to the global energy minimum le_a, and CO3_hole_b pristine and adsorbed sites. The
(Ca_hole_a). Projected Density of States (PDOS) and orbital population
The hydrocarbon adsorption on the dolomite surface (by means of Löwdin population analysis) were considered.
provides information concerning the Ca, Mg, and CO3
The benzene molecule has a similar total orbital population
adsorption sites. The adsorption energies suggest an increase
after adsorption on Ca_hole_a, Mg_hole_a, and CO3_hole_b
in the stability for hydrocarbon adsorption on a Ca site,
compared to Mg and CO3 ones, where the adsorption on Mg is dolomite surface sites, 29.52, 29.52, and 29.53 electrons,
slightly more favorable than on a CO3 site. The benzenes respectively. Those charges provide us a qualitative indication
adsorbed on Ca_hole_a, Mg_hole_a, and CO3_hole_b sites that the adsorbed benzene loses electrons when compared with
are used to understand the differences within carbonate surface the isolated molecule (30 valence electrons). This is in
adsorption. Figures 5a−i show the structure (as balls and sticks, agreement with the benzene interaction with isolated Mg and
Ca cations.50
The PDOS for the adsorbed sites on the pristine surface
(Figure 6a) indicates that the Highest Occupied Molecular
Orbital (HOMO) is composed by a sharp oxygen p-orbital, and
the conduction level contains a major contribution from 3d and
4s Ca orbitals. A closer inspection of the position of the first

Figure 5. Geometry as balls and sticks, slice on charge density

difference, and geometry as vdW radii representation for a benzene on
the dolomite surface, on Ca_hole_a (a), (b), and (c); Mg_hole_a (d),
(e), and (f); and CO3_hole_b (g), (h), and (i) configurations,
respectively. The yellow and red balls in carbonates represent C and O
atoms, respectively, and dark and cyan (light gray) balls represent the
Mg and Ca atom, respectively. The same linear scale is used in all
charge difference slices and presents positive (light) and negative
(dark) values between 0 and 0.01 electrons/bohr2. The charge density
difference is obtained as ρ = ρ(Surface+H) − ρSurface − ρH, where
ρ(Surface+H), ρSurface, and ρH represent the surface plus adsorbate, the
surface, and the adsorbate charge density, respectively.

Figures 5a, d, and g), the charge differences (Figures 5b, e, and
h), and the structure considering the van der Waals radii
(Figures 5c, f, and i) for each different chemical species.49 The
vdW spheres from the molecule and surface touch each other Figure 6. Ca, Mg, and outermost O projected electronic density of
only for Figure 5c (adsorption on Ca) and do not overlap with states for the (a) pristine and (b) benzene directly adsorbed dolomite
the neighbor surface sites in any case. The charge difference surface. The Fermi level is at zero energy.

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empty state for Ca, Mg, and O surface sites reveals that the Mg- Figures 7c−f show the charge density maps for the
3s and O-2p orbitals are located 0.05 and 0.6 eV above the Ca- Ca_hole_b geometry at different positions, respectively.
4s peak, respectively. The pristine PDOS indicates that the Ca These maps correspond to vertical slices in the geometries
orbital would be the first available during the benzene−surface shown in Figure 7a,b. In Figure 7c,d, the slices were obtained in
interaction followed by the Mg one. the Ca position without and with vdW, respectively. The
In Figure 6b, the PDOS for Ca, Mg, and O surface absorbed inclusion of vdW interaction enhances the charge transfer
sites are shown. For Ca PDOS, a reduction in the intensity of between the Ca atom and the benzene, increasing the surface−
the first 4s peak is observed with respect to the pristine surface. benzene binding. We remind that the vdW forces are not
Considering the Mg PDOS, intensity peak reduction on the included in the Ca atoms. This procedure has been used by
first empty 3s and 3p orbitals is also observed compared to the Aeberhard et al., where the inclusion of vdW in O, C, and H
pristine surface (Figure 6a). The empty d orbitals for Ca and atoms results in a satisfactory description of a molecular
Mg are not significantly affected. system.35 A similar result was observed for a slice in the oxygen
Our results for vdW dispersion forces indicate a reduction in position and the benzene (Figures 7e,f). All observed effects on
the bond distance between the benzene molecule and the charge transfer, adsorption energy, and bond length deviations
calcite surface and an increase in the adsorption energy. This is obtained with vdW correction indicate some improvement on
in agreement with the DCACP method16 that slightly increases the description of the molecule−surface interaction. Consider-
the electron density between the surface and the adsorbing ing the adsorption on the CO3_hole_b site, we also obtained
molecule. However, this bond length reduction does not have a an increase in the strength of the surface−benzene bond after
systematic deviation from the calculations without vdW the inclusion of vdW, as presented in Figure S4a−d in the
interactions. Figure 7a,b shows the representative bond lengths Supporting Information.
for Ca_hole_b sites, without and with vdW, respectively. The Hexane Adsorption. The fully relaxed hexane (C6H14)
bond length displays a slight reduction, and the angle formed molecule shows a long axis (8.183 Å) and a short axis (1.429
by the benzene aromatic ring and the surface increases as the Å). Some rotations along these molecular axes define different
vdW dispersion forces are taken into account. sites of adsorption on surfaces. Figure 8 presents the evaluated
alignments of the hexane molecule with respect to the calcite
surface for some rotations along the hexane axes, similarly for

Figure 7. Geometry and charge density slices for the Ca_hole_b

configuration, without and with van der Waals, in the left and right
side, respectively. We present geometrical details (in Å for distances
and degrees for angles) obtained without (a) and (b) with van der Figure 8. Representation of hexane adsorption sites on the calcite
Waals and charge density slice between the Ca surface atom and the (10−14) surface. The evaluated Mg adsorption sites on dolomite are
most close benzene C atoms for calculation (c) without and (d) with analogous to the presented Ca ones where the vertical aligned Ca
van der Waals. A slice between a surface O atom and closest benzene atoms (blue) represent alternate positions for Ca or Mg in the
C atom is presented (e) without and (f) with van der Waals dolomite case. The site labels are (a) Ca_top, (b) CO3_top, (c) side-
correction. The same linear scale for charge density slices is presented on_Ca_[010], (d) end-on_Ca_[010], (e) side-on_[42−1], (f) end-
for all pictures and shows values between 0 and 0.06 electrons/bohr2. on_[42−1], and (g) end-on_CO3_[42−1].

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dolomite, where the Mg sites were also considered. The most energy of −60 meV, and the adsorption on the carbonate
representative orientations are the top, end-on, and side-on groups represents the less stable configurations, with adsorption
alignments. The top sites are evaluated with the hexane above a energy of −20 meV for end-on_CO3_[42−1] and unbound for
Ca and a CO3 group on the calcite surface. These sites are CO3_top configuration.
named as Ca_top and CO3_top. For the dolomite surface, the Figure 9a shows the geometry of the end-on_Ca_[010]
hexane above a Mg site (Mg_top) is considered in addition to configuration on the calcite surface (most stable site). The
Ca_top and CO3_top.
As the surface periodical directions are not identical with
respect to the atomic sites, there are two representative
orientations of the end-on and side-on surface positions above
the surface. Figure 8 presents different orientations for hexane
above the calcite surface. Only one calcite surface layer is
presented, and the vertical aligned Ca atoms in Figure 8
indicate the successive position of Ca and Mg atoms in the
dolomite case.
When the long axis of hexane is oriented along the [42−1]
direction, the hexane molecule can adsorb over both Ca and
Mg atoms. Due to these geometrical details, we denote side-
on_[42−1] and end-on_[42−1] as the sites on which the
hexane long axis is oriented along the [42−1] direction on the
surfaces. In addition, in the [42−1] direction, the adsorption of
the hexane above a CO3 site was considered in the end-
on_CO3_[42−1] configuration as a representative case for
adsorption on the carbonate group.
The adsorption of the hexane molecule with the long axis
along the [010] direction of the surfaces was done over the line
of consecutive Ca atoms, considering the side-on and end-on Figure 9. Optimized geometry and charge density map for a hexane
orientations (named as side-on_Ca_[010] and end- molecule adsorbed on a calcite surface on end-on_Ca_[010]
on_Ca_[010] configurations). The adsorption above Mg sites configuration without van der Waals (a) and (c), respectively, and
(dolomite case) is evaluated in the end-on_Mg_[010] with van der Waals corrections (b) and (d), respectively. In (a) the
geometry presented corresponds to the calcite surface; however, the
configuration. The evaluation of these configurations com- hexane on the same site of dolomite shows a similar geometry. The
pletely characterizes the hexane adsorption on calcite and bond lengths are presented (in Å) for calcite (outside of parentheses)
dolomite. and dolomite (inside parentheses). The charge density map (c)
Table 3 presents the values of adsorption energies for the represents the adsorption on calcite, where the adsorption on dolomite
adsorption of hexane on calcite and dolomite. For the shows qualitatively identical results. The scale is linear between 0 and
0.08 electrons/bohr2.
Table 3. Adsorption Energies Considering a Hexane
Molecule Adsorbed on Calcite and Dolomite (10−14) bond length between the closest hexane C atom and the calcite
Surfaces (dolomite) surface Ca atom is 3.57 Å (3.50 Å). The charge
Eads (eV) density profiles between the hexane molecule and the surfaces
(calcite and dolomite) are similar for the end-on_Ca_[010]
calcite calcite dolomite
configuration (DFT) (DFT + vdW) (DFT) configurations. Figure 9c shows the charge density slice to the
end-on_Ca_[010] geometry for the hexane molecule on calcite
Ca_top −0. 06 −0.12 −0.04
(similar to the dolomite case). This figure shows that the
CO3_top −0.00 −0.09 −0.01
binding between the hexane molecule and the surface is weak as
Mg_top - - −0.02
indicated by a low charge density between them.
side-on_Ca_[010] −0.09 −0.32 −0.07
Considering top sites on calcite, like Ca_top and CO3_top,
end-on_Ca_[010] −0.11 −0.35 −0.10
the distance between a closest C atom from hexane to the
end-on_Mg_[010] - - −0.06
surface Ca atom or the CO3 group is 3.10 and 3.31 Å,
side-on_[42−1] −0.10 −0.30 −0.09
respectively. On the dolomite surface, the distance between the
end-on_[42−1] −0.11 −0.32 −0.09
surface and the closest carbon atom in the hexane on Ca_top is
end-on_CO3_[42−1] −0.02 −0.12 −0.03
3.58 Å, and the Mg_top site shows a distance of 3.41 Å. The
top sites calculated in this work show high adsorption energies,
adsorption on calcite, the end-on_Ca_[010] and end- compared to the end-on and side-on adsorption sites.
on_[42−1] configurations are the most stable (Eads = −0.11 Another interesting observation is at the end-on_[42−1] site
eV). This result indicates that the nonequivalent end-on hexane on calcite and dolomite. For these configurations we found an
orientations on the calcite surface (along the [010] or [42−1] adsorption energy of −0.11 eV for calcite and −0.09 eV for
directions) are energetic degenerates. This result also shows dolomite. This difference in adsorption energies is most likely
that the two different surface directions do not have any due to the differences between the calcite and the dolomite
significant effect on the surface−hexane binding. The side-on surface sites. The end-on_[42−1] site on calcite and dolomite
orientations (side-on_Ca_[010] and side-on_[42−1]) are occurs on different chemical elements. On calcite the
more energetic by 20 and 10 meV than the end-on ones, adsorption is on the Ca atom only; however, on dolomite the
respectively. The Ca_top configuration shows an adsorption adsorption is on Ca and Mg atoms. From the adsorption purely
24545 | J. Phys. Chem. C 2012, 116, 24538−24548
The Journal of Physical Chemistry C Article

on Ca or Mg surface atoms (Ca_top and Mg_top sites), we

found that the adsorption on Ca atoms is more favorable than
on Mg atoms as indicated by lower adsorption energies for end-
on_[42−1] sites on calcite than dolomite.
Regarding vdW calculations, the most stable sites with and
without vdW do not change (end-on_Ca_[010]). However,
the adsorption energy increases by approximately 69% if vdW is
taken into account. Figures 9b,d present the geometry and the
charge density map, respectively, for the end-on_Ca_[010],
hexane adsorbed site on calcite for vdW calculations. As
similarly observed for benzene on calcite, the inclusion of vdW
reduces the bond length between hexane and the surface and
improves the hexane−surface charge transference, compared to
that without vdW (Figures 9a,c), respectively.
Headen et al.9 have considered an asphaltene molecule
adsorbed on the calcite surface by means of computational
simulations using a classical force field. The authors reported an
optimum calcite−asphaltene bond length of 3.5 Å. This result is
far from our result with vdW calculation for hexane (3.27 Å)
but closer to that for the benzene (approximately 3.4 Å).
However, the authors emphasized the necessity of more
accurate calculations due to the presence of different types of
atoms in the simulations (a typical difficulty with classical force
fields). Our vdW calculations are able to deal with this difficulty
and can be used as reference results.
Energy Barriers. To better characterize the hydrocarbon−
mineral surface energetics, we have also determined the energy
barriers involved in the displacement of hydrocarbon molecules
along the mineral surface. These energy barriers are important
to quantify the energetic cost of hydrocarbon adsorption,
migration, and diffusion on these surfaces. Those are crucial
parameters for a more realistic description of this kind of
system and can be used to derive a classical or semiclassical Figure 10. Directions for energy barrier evaluation on calcite, for (a)
force field. benzene and (b) hexane adsorption. The paths were chosen so as to
The energetics of adsorption of the hydrocarbons considered have the end points on an equivalent Ca atom. For benzene, paths lie
along the nonequivalent [010], [42−1], and [48−1] directions, and
in this work over the calcite and dolomite surfaces presents, in a
for benzene, paths lie along the [010] and [42−1] directions.
closer look, important similarities. The first one is that the most Hydrocarbons are shown only over the initial point in the path.
stable adsorption site, for all mineral−hydrocarbon combina-
tions, is over a Ca atom. Moreover, the differences in
adsorption energies for a given hydrocarbon over the Ca differences can be seen. Thus, it is very important to take
atom of both mineral surfaces are very small, amounting to 40 vdW dispersion effects into account for a proper description of
meV for benzene and 10 meV for hexane. This suggests that the interaction of the molecules with the surfaces, and this
energy barriers should qualitatively display the same behavior should make a difference in classical and/or semiclassical
and be furthermore very close quantitatively. Therefore, we potentials for MD and MC calculations.
focus on the energy barriers for the displacement of the For hexane, Figure 12 shows the energy barriers for the
hydrocarbons over the calcite surface only. displacement along the paths indicated in Figure 10, and
To compute the energy barriers, we consider densely energies and energy differences for the GGA and vdW
sampled nonequivalent paths along the calcite (10−14) surface, calculations for the points of energy extrema are summarized
as shown in Figure 10. Since the inclusion of the computa- in Table 5. The results are different from the ones obtained for
tionally expensive vdW dispersion shifts the adsorption energies benzene displacement, where [010] is the direction with the
up but trends are generally conserved, we initially calculate the largest barrier. This is due to the presence of a carbonate group
barriers with plain GGA and only consider vdW effects, self- along the path: for the [010] direction, hexane is always above
consistently, for the points corresponding to each minimum Ca atoms. Benzene, in its turn, would diffuse over a carbonate
and maximum energy value along the path. From now on, we group along its path, hence the different paths for the highest
will refer to these points (maxima and minima) as extrema. energy barrier.
Figure 11 shows the energy barriers to displace the benzene The calculated energy barriers are comparable to the
molecule along the [010], [42−1], and [48−1] directions on adsorption energy in these systems. A hydrocarbon molecule
the calcite surface. The extrema in each curve are labeled and diffuses along the surface as soon as it has enough energy to
marked by arrows, and energy values for both, GGA and vdW desorb, and in typical conditions found in oil wells, thermal
calculations on these points, as well as the corresponding energy could supply this activation energy. Hence, diffusion of
energy differences, are shown in Table 4. As can be seen from hydrocarbon molecules is very likely to occur, and it is
these results, the net effect of including vdW interactions is to important to take into account the energy barriers in a
shift energies up homogeneously, and significant energy semiclassical potential, to provide a better description of the
24546 | J. Phys. Chem. C 2012, 116, 24538−24548
The Journal of Physical Chemistry C Article

Table 5. Energy Values for GGA and vdW Calculations on

the Geometries of Hexane, On the Points Labeled in Figure
direction point EGGA EvdW ΔEvdW‑GGA
[010] Ha1 0.07 0.11 0.04
[42−1] Hb1 0.16 0.20 0.04
Hb2 0.16 0.20 0.04
All energies are given in eV.

hydrocarbon/mineral interaction at hydrocarbon reservoir

conditions, for longer time scales.

We have studied the adsorption of hydrocarbons molecule
(benzene and hexane) on calcite and dolomite (10−14)
surfaces. These molecules are representative of aromatic and
alkane hydrocarbons, and our calculations show that those
molecules weakly adsorb on both calcite and dolomite surfaces.
Our results suggest that Ca sites are the most energetically
favorable for hydrocarbon adsorption on both minerals. This
effect is mostly due to the electronic level ordering that leads to
charge differences in the possible adsorbed sites (Ca, Mg, and
CO3) in the carbonate surfaces. The van der Waals correction
Figure 11. Energy barriers for benzene displacements along (a) [010] increases the stability for those systems. For benzene adsorbed
and (b) [42−1] and (c) [48−1] directions on the calcite surface,
on Ca sites, we obtain an increase in the stability by 0.21 eV
according to Figure 8a. Labeled arrows mark the points of energy
maxima. (63%) including van der Waals, compared to the calculation
result without van der Waals. In addition, the shortest distance
Table 4. Energy Values for GGA and vdW Calculations on between carbon in benzene and the Ca surface atom is 3.12 Å
the Geometries of Benzene, On the Points Labeled in Figure (with vdW) compared with 3.69 Å (without vdW). The angle
11a with respect to the surface increases from 15 to 27° with the
inclusion of vdW. For adsorption on carbonate sites, this energy
direction point EGGA EvdW ΔEvdW‑GGA difference is 0.16 eV (67%), and distances between the closest
[010] Ba1 0.16 0.24 0.08 carbon and oxygen atoms were found to be 3.64 Å (vdW)
[42−1] Bb1 0.07 0.11 0.04 compared with 3.77 Å (without vdW). The vdW corrections
Bb2 0.08 0.13 0.05 resulted in an increase in the hydrocarbon−surface binding and
[48−1] Bc1 0.12 0.20 0.08 a decrease in the distance between benzene and the surface.
Bc2 0.13 0.21 0.08 Evaluating the hydrocarbon migration on the calcite surface, the
All energies are given in eV. highest energy barriers associated with the hydrocarbon
displacements on the surfaces are of the same order of the
adsorption energies for the most stable sites.
Finally, the obtained energy barriers in complement to
adsorption energies and geometries including van der Waals
interaction point out that this methodology must be taken into
account in the evaluated systems. In this way, the comparison
and parametrization of classical methods is also an important
issue that can be important for studies in biomineralization and
to describe the hydrocarbons/mineral rocks interaction in oil
fields, providing a more realistic description for those systems.

S Supporting Information
Additional figures showing charge density for bulk, surface, and
benzene adsorbed on a dolomite carbonate surface are showed.
This material is available free of charge via the Internet at

Figure 12. Energy barriers for hexane displacements along (a) [010]
Corresponding Author
and (b) [42−1] directions on the calcite surface, as shown in Figure *E-mail:
10b. Labeled arrows mark the points of maxima.
The authors declare no competing financial interest.
24547 | J. Phys. Chem. C 2012, 116, 24538−24548
The Journal of Physical Chemistry C


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