van der Waals interactions of the benzene dimer: towards treatment of polycyclic aromatic hydrocarbon dimers
ABSTRACT Although density functional theory (DFT) in principle includes even long-range interactions, standard implementations employ local or semi-local approximations of the interaction energy and fail at describing the van der Waals interactions. We show how to modify a recent density functional that includes van der Waals interactions in planar systems [Phys. Rev. Lett. 91, 126402 (2003)] to also give an approximate interaction description of planar molecules. As a test case we use this modified functional to calculate the binding distance and energy for benzene dimers, with the perspective of treating also larger, flat molecules, such as the polycyclic aromatic hydrocarbons (PAH).
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ABSTRACT: Benzoxazole, 1,2-benzisoxazole and 2,1-benzisoxazole are biologically active molecules with potential applications in drug design. Their interaction with aqueous medium in biological systems may be simulated by considering their interaction with explicit water molecules. Such studies provide information on the structures, energies and type of interactions stabilizing the resulting geometric systems. The objective of the current study was to utilize theoretical approaches to investigate the structures, stabilization energy and binding energy of benzoxazole–water, 1,2-benzisoxazole–water and 2,1-benzisoxazole–water complexes. The calculations were performed utilizing the density functional theory (DFT)/M06-2X/6-311 ++ G(d,p) method and the DFT/ωB97XD method with both the 6-311 ++ G(d,p) and the aug-cc-pVDZ basis sets. The results suggest that the stability of the different clusters depends on interrelated factors including the rings formed by intermolecular hydrogen bonds and the proton affinity (PA) or acidity of the atoms forming the intermolecular hydrogen bonds with the water molecules. A comparison across methods indicates that the results follow similar trends with different methods. Read More: http://www.worldscientific.com/doi/abs/10.1142/S0219633613500703Journal of Theoretical and Computational Chemistry 11/2013; 12(7). · 0.52 Impact Factor
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ABSTRACT: Quinoxaline is a parent structure for a broad class of N-heteroaromatic compounds, many of which exhibit various biological activities. The interaction of quinoxaline with explicit water molecules or metal ions and the formation of quinoxaline dimer play important role in many of the biological activities of quinoxaline. This study investigates the structures, stabilization and binding energies of quinoxaline complexes with water, transition metal ions and quinoxaline dimer to provide information on the preferred geometries, interaction energies and type of non-covalent interactions accounting for the stability of the complexes. The investigations are performed in vacuo and in water solution using MP2 and DFT methods. The results of the study on the quinoxaline---(H2O)n show that the preferred adducts in vacuo involve one, two or three water molecules hydrogen bonded to the N atom and the neighboring H atom of the Csp2-H group. The results in water solution show a preference for water-water clustering. The dimers of quinoxaline are stabilized by either pi--pi stacking or weak C-H---N intermolecular hydrogen bonds. The relative stability of the quinoxaline---Cu complexes depends on the site on which the Cu ion binds and the binding strength depends on both the nature of the cation and the binding site.The Journal of Physical Chemistry A 01/2013; · 2.77 Impact Factor
arXiv:cond-mat/0406549v1 [cond-mat.soft] 23 Jun 2004
APPLIED PHYSICS REPORT 2004–17
van der Waals interactions of the benzene dimer: towards treatment of
polycyclic aromatic hydrocarbon dimers
Svetla D. Chakarova∗and Elsebeth Schr¨ oder
Department of Applied Physics, Chalmers University of
Technology and G¨ oteborg University, SE–412 96 G¨ oteborg, Sweden
(Dated: June 21, 2004)
Although density functional theory (DFT) in principle includes even long-range interactions,
standard implementations employ local or semi-local approximations of the interaction energy
and fail at describing the van der Waals interactions. We show how to modify a recent density
functional that includes van der Waals interactions in planar systems [Phys. Rev. Lett. 91, 126402
(2003)] to also give an approximate interaction description of planar molecules. As a test case we
use this modified functional to calculate the binding distance and energy for benzene dimers, with
the perspective of treating also larger, flat molecules, such as the polycyclic aromatic hydrocarbons
Keywords: van der Waals Interactions; Density Functional Theory; Benzene.
The benzene dimer is the prototype for aromatic interactions and has been studied extensively
both by theoretical [1, 2, 3, 4, 5, 6] and experimental [7, 8, 9] means. Describing benzene interactions
can be regarded as the first step toward describing interactions of polycyclic aromatic hydrocarbons
(PAHs). PAHs are planar molecules consisting of several aromatic rings, where the peripheral carbon
atoms are covalently bonded to hydrogen atoms. Both benzene and PAHs structurally resemble
graphite and exhibit very similar intra- and intermolecular bond lengths, particularly for (stacks of)
large PAHs. Like the interactions between the sheets in graphite, the interactions between parallel
benzene molecules or layers in PAH stacks are dominated by the weak, nonlocal van der Waals
(vdW) interaction. However, the description of the vdW interaction is absent in the traditional
implementations of density functional theory (DFT), implementations which have otherwise been
very successful in describing dense, hard materials on the atomic scale.
The past few years a number of publications [10, 11, 12, 13, 14, 15, 16, 17, 18] have addressed
the problem of consistently extending the common DFT implementations to also include the vdW
interaction. For the mutual interactions of planar sheets or surfaces a functional was obtained in
Refs. [13, 15]. For example, a relatively good estimate of the binding distance between two graphite
planes (graphene) was obtained with this planar functional , while the usual generalized gradient
approximations (GGA) fail to bind the graphene layers or do so at an unphysical binding distance and
energy. Since benzene and PAHs are similar to graphite, the correction to the regular calculations
will be significant also in dimers of these molecules.
In this work, we study dimers of benzene (C6H6) by modifying and approximating the planar
nonlocal density functional [13, 15] in order to treat molecules of finite size. We here concentrate on
dimers where the molecules are placed directly on top of each other (“AA stacking”). The method
we use is developed with the aim of being able to study also PAH molecules, and it is described
below. The results for some of the small PAH molecules naphthalene, anthracene, and pyrene
(C10H8, C14H10, and C16H10) will be reported in a forthcoming publication .
∗Corresponding author: Tel. +46 31 772 3632; Fax +46 31 772 8426; E-mail firstname.lastname@example.org
DFT in principle does include even long-range interactions, such as the vdW interactions, but
those are a part of the exchange-correlation functional Excwhich is approximated in the implementa-
tions of DFT. The most commonly used approximations to Excare the local density approximation
(LDA) and the generalized gradient approximation (GGA), both of which are local or semi-local
and do not include the vdW interaction. However, GGA (and to some extend LDA) has proven
very successful in describing the interactions within dense matter, e.g., within a molecule, and a
consistent correction scheme that includes the long-range intermolecular vdW interactions must not
change the short-range intramolecular interaction.
A. The graphite interactions
In the vdW correction scheme for planar sheets and surfaces, defined and described in Refs.
[13, 15, 16], the exchange energy from GGA is retained, and the correlation energy is determined as
a sum of the local correlation (obtained from LDA) and the nonlocal correlation Enl
described below. For the exchange part the GGA revPBE flavor of Zhang and Yang  is chosen
because it is fitted to exact exchange for atoms. Thus the (vdW-corrected) total energy is written
c, which will be
EvdW−DF= EGGA− EGGA,c+ ELDA,c+ Enl
where all energy terms are functionals of the electron charge density n(r), and EGGA,cand ELDA,care
the correlation from GGA and LDA, respectively. These energy terms are directly available from
our DFT calculations. Our DFT calculations are performed by the plane-wave pseudo-potential
based program Dacapo .
The nonlocal correlation, per area A, for a planar, translationally invariant system such as
graphite is given by 
c/A = − lim
where φ(z) fulfills the differential equation (ǫkφ′)′= k2ǫ2
φ(L) = 0, and φ0(z) is the vacuum solution. The system is enclosed in a long box of length L
along the direction perpendicular to the graphite plane(s). ǫkis the dielectric function of graphite,
Fourier-transformed in the plane of the graphite sheet
kφ with boundary conditions φ(0) = 0 and
ǫk(z,iu) = 1 +
⊥)2/3 + (k2+ q2
The plasmon frequency ωpis defined by ω2
n(z) is the planarly averaged electron density varying in the z-direction perpendicular to the plane,
and iu is the imaginary frequency. We use atomic units unless otherwise noted.
The parameter q⊥is introduced to compensate for the locality of ǫk in the z-direction. The
value of q⊥is materials dependent, and it is found from a separate set of GGA DFT calculations
with an applied, static electric field across the graphite layer.
In Figure 1(a) we show the interaction curve of graphene-graphenein the AA stacking according
to (1). These results of graphene in the AA stacking allow us to directly compare to our results of
benzene, and later PAHs, also in AA stacking. The binding separation 4.0˚ A of graphene (AA) is
larger than for graphene in the physically correct AB stacking (3.76˚ A), calculated within the same
vdW correction scheme . We used the value q⊥= 0.756 in atomic units for a graphene sheet
p(z) = 4πn(z), the Fermi velocity by νF(z) = (3π2n(z))
B.Extending the functional to treat planar molecules
It is a natural next step to modify Enl
large, but not infinitely extended molecules. The PAH molecules are pieces of graphene, passivated
c for planar, translational invariant sheets to treat planar,
by hydrogen atoms at the broken carbon-carbon bonds.
appropriate approximations in order to apply the functional to planar, large, finite molecules.
The (semi-)local part of the total energy in (1), EGGA−EGGA,c+ELDA,c, can be determined
directly from a usual DFT implementation. Such calculations provide us, besides the energy terms,
with a three-dimensional electron density n(r). In the formalism for Enl
n(z) is assumed translationally invariant along the molecule.
n(z) = A−1
?dxdy n(x,y,z) where Amol is the size of the molecular area that affects the vdW
interactions; this area must be estimated.
For carbon-dominated molecules such as benzene and PAH the dominating contribution to the
vdW correction comes from the carbon atoms. We thus assume that the dielectric function for the
molecules is well described by the functional form (3) with the graphene value q⊥= 0.756 a.u. By
comparing the dacapo-calculated static (u = 0) electric response of the isolated molecule with that
found from the model dielectric function (3), with Amolas a parameter, we can determine Amol. For
benzene we find that Amol= 51.7˚ A2reproduces the static response.
Given the model dielectric function (3) with the parameter Amol determined as described
above, the calculation of the Enl
contribution follows from (2). The physical analogy of using the
molecularly averaged n(z) in (2) is that of molecules moved together such that they each take up the
lateral area Amol. Enl
for molecules calculated this way therefore somewhat overcounts the vdW
interaction by including not only the physically correct interaction of one dimer molecule with its
partner, but also the interaction with the partner’s neighbors. Because the vdW attraction falls off
with distance this effect decreases as the molecule size increases. The other energy terms of (1) are
We stress that Amolis larger than the area of the same amount of carbon atoms in a graphene
plane. In our procedure of finding Amol we compare the (static) response of a molecule isolated
in all three directions. We make sure that our Dacapo-calculated response really does come from
an isolated molecule by checking the convergence of the response with increasing lateral unit cell
size. The response of the low-density charge distribution region within the molecular plane is thus
included in our description, and therefore the vdW interaction of these sheets of close molecules is
different than the vdW interaction of two sheets of graphite, even though the molecules are mostly
composed of carbon atoms.
With the assumptions introduced above, necessary for applying the vdW planar functional to
finite molecules, the quality of the vdW interaction calculations increases with increasing molecular
size. We emphasize that in this sense, the benzene molecule is an extreme molecule, and we do not
expect full quantitative agreement of our results with full-powered quantum-chemistry calculations
[1, 6] or with results in our new (more costly) general-geometry formulation of the vdW-DF .
We would therefore like to introduce
in (2) the density profile
For the finite molecules we take
We here present the results of applying the modified vdW functional to the benzene dimer in
the AA stacking. The first step is to determine the structure of the isolated molecule, the static
response to an applied electric field, the (semi-)local energy contributions to the dimer binding,
and the electron density of the dimer. This step is carried out in a standard DFT program. The
second step is to calculate the nonlocal correlation energy contribution, Enl
The standard DFT calculations were performed with the plane-wave pseudopotential code
Dacapo  with periodic boundary conditions. We performed the self-consistent calculations (before
c) using the revPBE GGA functional. The choice of unit cell size involves a trade-off
between manageable calculations on the one hand, and large lateral and vertical separations between
periodically repeated images of the molecules (or dimers) on the other hand. When deciding on the
unit cell size we also benefit from the short-range nature of the traditional DFT-implementations.
In our calculations we used a hexagonal unit cell of size (17.112˚ A, 17.112˚ A, 26˚ A).
In the plane-wave code the number of plane waves is determined by a cutoff in the plane-
wave energy. A preliminary analysis showed a cutoff at 450 eV to be sufficient. However, as we
discuss below, there is a small energy difference between dimers within the same unit cell at very
large separation and two isolated molecules in two separate unit cells. This offset depends on the
plane-wave cutoff in a non-trivial way. We emphasize that the offset in the total energy difference
is unrelated to Enl
c, with the approximations
FIG. 1: Energy curves for graphene and benzene dimers in the AA stacking as a function of separation dis-
tance. Panel (a) shows the graphene-graphene interaction, panel (b) shows the benzene-benzene interaction.
The dashed lines are the self-consistently determined revPBE total energies, the dotted lines show the Enl
correction, and the solid lines show the EvdW−DF total energy curves obtained according to Eq. (1). The
circles on the EvdW−DF curves indicate the calculations performed.
A.Benzene-benzene interaction energy
The benzene dimer interaction is calculated by fixing the relative atomic positions within of
each of the two molecules of the dimer and varying the distance between them, while keeping the
size of the unit cell constant. Figure 1(b) shows the total-energy curves for benzene: the revPBE
curve (which shows no binding at all), the nonlocal correlation Enl
includes nonlocal correlation. The reference energy is the benzene dimer at large (11˚ A) separation.
We find in vdW-DF the binding energy 100 meV at the distance 4.1˚ A. These results are in
agreement with our results for the AA stacked graphene dimer as we expect the binding distance
there to be similar to that of the benzene dimer and PAH dimers in the AA stacking. Both the
benzene separation distance and interaction energy are in reasonable, although not perfect agreement
with experiments and other calculations. For instance, Refs. [2, 4, 5] report calculating binding
separations of around 3.8˚ A and binding energies in the range of 64–92 meV. As mentioned earlier,
we expect the quality of our results to improve for larger molecules.
As previously mentioned, no binding arises in the revPBE flavor of GGA. We note that GGA
Perdew-Wang 91 (PW91)  calculations (not shown) exhibit an unphysically small binding energy
of the benzene dimer (12 meV) at separation 4.7˚ A. However, this PW91 binding arises from the
unphysical interactions mediated by the exchange contribution in the manner previously documented
for graphite .
c, and the full EvdW−DF that
B.Discussion of the energy reference level
During the course of this benzene and PAH study we encountered a technical problem in
determining an appropriate reference level for our (traditional) total energy calculations based on
All dimer energies presented in this paper, whether revPBE or vdW-DF energies, are given
with reference to the energy of two molecules far apart. Thus the energies that we report, and which
we for now generally denote Ediff, are total energy differences given by
Ediff(d) = Etot(d) − Eref
where Etot(d) is the total energy of the dimer determined at separation d, and Eref is the energy
of two molecules far apart. This applies both to the benzene molecules and the graphite sheets.
The reference level Erefcan be calculated either by removing one molecule to find half the reference
energy, or by keeping both molecules within the unit cell and moving them “far apart” within the
box. In both cases, we make sure that the periodic cell is sufficiently large that the molecule does
not interact (electrostatically) with its periodic images. In our underlying GGA-DFT calculations
it turned out that these two seemingly equivalent ways of determining Eref lead to two slightly
different results. Numerically, the difference is more significant for the benzene molecules than for
In Fig. 1(b) we report curves of interaction energies of dimers with increasing separation. The
natural choice of reference energy Erefis therefore the dimer with the two molecules “far apart”, by
which we mean 11–12˚ A separation in boxes of length of 24–26˚ A. However, the problem merits an
In Figure 2 we show the difference in reference energies δEref — defined as the energy of a
pair of molecules “far apart” subtracted by the energy of two separate molecules — as a function
of the choice of DFT convergence parameters. In Dacapo, besides the plane-wave energy cutoff for
the wave functions, it is possible to set a different (larger) cutoff for the charge density, to enhance
the description of the charge density at the price of only a modest increase in the calculational size.
Most of the calculations in Figure 2 use a larger charge-density cutoff than the wave-function cutoff.
In order to analyze δEref also for large charge-density cutoff energies we carried out a number of
calculations in a unit cell with reduced lateral size (10˚ A).
A few immediate conclusions can be drawn on the basis of Figure 2. By comparing the single-
cutoff and the double-cutoff results at charge-density cutoff 500 eV and 550 eV we find that the
quality of the wave-function description does not affect δEref. We see this in Figure 2 by the collapsed
data points (indicated by arrows) for the revPBE total energy, but it is true also for the exchange
and the correlation parts of the energy, as well as for PW91 (not shown). This indicates that the
(noninteracting) kinetic part of the total energy, which is calculated from the wave functions, does
not contribute to δEref.
In contrast, δErefdepends non-trivially on the charge-density cutoff. It is not clear that a very
high cutoff value will yield good results, rather, δErefseems to oscillate with charge-density cutoff.
By comparing the results for the usual box size with the small-box results we further notice that
δErefdecreases with the amount of low-density (vacuum) region in the box. δErefthus seems to be
mainly affected by contributions from the low-density regions. A major part of δEref comes from
the exchange part of the total energy. Not shown in the figure are δEreffor the PW91 total energy
and for correlation (revPBE and PW91). These energies all give a finite, but smaller value of δEref.
Unfortunately the problems are worse exactly for the revPBE-GGA that enters our subsequent
vdW-DF calculations in (1).
Besides the ever-present risk of undetected programming errors, we speculate on three pos-
sible origins for the finite δEref that affects our underlying GGA-DFT calculations: (i) numerical
instabilities and formal inaccuracies arising from the implementation of the exchange-correlation
approximation; (ii) the mixing of different exchange-correlation approximations for creation of pseu-
dopotentials and use in calculations; and (iii) the use and/or implementation of ultrasoft pseudopo-
tentials. The possibility of formal problems in the exchange-correlation term borrows some support
from the work by Lacks and Gordon in 1993 : PW91 exchange, and a number of other exchange
approximations, were shown to give values of |δEref| for noble gas dimers far exceeding those from
exact exchange. The deviation arises from contributions in the low-density, large-gradient regions
of space, which is precisely the regions that dominate our system. If this will turn out to be the