carbohydrate–aromatic π interactions: a test of density functionals and the dft-d method
TRANSCRIPT
Carbohydrate–aromatic p interactions: a test of density functionals
and the DFT-D methodw
Rajesh K. Raju, Anitha Ramraj, Ian H. Hillier,* Mark A. Vincent
and Neil A. Burton
Received 19th December 2008, Accepted 28th January 2009
First published as an Advance Article on the web 2nd March 2009
DOI: 10.1039/b822877a
The performance of a number of computational approaches based upon density functional theory
(DFT) for the accurate description of carbohydrate–p interactions is described. A database
containing interaction energies of a small number of representative complexes, computed at a
high ab initio level, is described, and is used to judge 18 different density functionals including the
M05 and M06 families as well as the DFT method augmented with empirical dispersive
corrections (DFT-D). The DFT-D method and the M06 functionals are found to perform
particularly well, whilst traditional functionals such as B3LYP perform poorly. The interaction
energies for 23 sugar–aromatic complexes calculated by the DFT-D method are compared with
the values from the 18 functionals. Again, the M06 class of functional is found to be superior.
Introduction
Weak interactions, particularly hydrogen bonds and dispersive
interactions, are central to many substrate–protein interactions,1
and as such their accurate description is needed to understand
structure–function relationships of proteins and to assist in the
associated problem of rational drug design.2 Thus, there is
much current interest in searching for the most appropriate
quantum mechanical model for quantifying these interactions
to a high level of accuracy. To achieve this using ab initio
methods requires methods beyond MP2, such as at the
CCSD(T) level, as well as the use of large basis sets, and basis
set superposition (BSSE) corrections.3 Calculations at this
level are still quite computationally demanding, but have been
used to establish databases containing complexes which
exemplify the varied range of such non-covalent interactions
found in biological systems. A variety of methods including
semiempirical Hartree Fock4 and DFT models,5 as well as
DFT-based approaches using different functionals,6–11 have
been explored in attempts to accurately predict these inter-
actions. Although the inadequacies of a number of popular
functionals such as B3LYP in describing non-covalent inter-
actions, particularly p–p stacking, have been noted, some
functionals, such as BH&H,12 and in particular the newer
meta and hybrid meta functionals of Zhao and Truhlar,6–8 are
considerably more successful. In addition, a particularly fruit-
ful approach13,14 has been to augment traditional DFT and
semiempirical15 methods with an empirical atom–atom
dispersive correction having the usual R�6 form. These various
methods have been used to study, in particular, hydrogen-
bonding and p–p stacking interactions. There have been far
fewer studies directed at the accurate modelling of those
interactions responsible for sugar–protein recognition, which
are important, for example, in the case of various amyloid-
forming proteins such as those associated with Alzheimer and
Creutzfeldt–Jacob diseases.16
We have recently shown17 that a density functional model
using a BLYP functional, when augmented with an empirical
dispersive term (DFT-D), is successful in describing a range of
complexes involving simple monosaccharides and analogues
of phenylalanine, tyrosine and tryptophan, when judged
against a very limited number of high level calculations. We
find that the important interactions involve the aliphatic C–H
and O–H groups which point toward the aromatic p system,
and that there can be a delicate balance between these
two classes of interaction. Thus, although crystal structures
display mainly C–H–p interactions, we find that for binary
fucose–toluene and a-methyl glucose–toluene complexes, the
most stable structures involve O–H–p interactions, which are
reflected in the infrared shift of the corresponding O–H
stretching frequency, our calculations being in good quantita-
tive agreement with experiment.18
It is thus important to find the most appropriate ways of
carrying out these calculations and this is the focus of the present
paper. We first construct a small database of high level calcula-
tions of monosaccharide–aromatic complexes, and then use these
data to assess the accuracy of a variety of DFT calculations,
particularly the newM05 andM06 families of functionals, as well
as the DFT-D approach. We then compare these DFT methods
to describe a larger set of monosaccharide–aromatic complexes.
In view of the importance of the aliphatic C–H and O–H–pinteractions in such complexes, and indications that such inter-
actions are somewhat stronger with tryptophan than with
phenylalanine,17 we have also studied the prototype complexes
of water and methane with benzene and 3-methylindole.
School of Chemistry, University of Manchester, Oxford Road,M13 9PL Manchester, UK. E-mail: [email protected] Electronic supplementary information (ESI) available: Optimizedstructures of fucose–toluene complexes at DFT-D/TZV2D level(Fig. S1); optimized structures of glucose–3-methylindole and–p-hydroxytoluene complexes (Fig. S2); coordinates of the structuresfor which ‘benchmark’ calculations were carried out (Table S1);interaction energies for full dataset, for 18 functionals, DFT-D andMP2, the MUE values compared to the DFT-D values are also given(Table S2). See DOI: 10.1039/b822877a
This journal is �c the Owner Societies 2009 Phys. Chem. Chem. Phys., 2009, 11, 3411–3416 | 3411
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Computational details
A number of benchmark studies were carried out employing
the strategy of Hobza and co-workers.3 Here the MP2 energies
of the complex and monomers are extrapolated to the basis set
limit by the use of the aug-cc-pVDZ and aug-cc-pVTZ basis
sets giving the MP2/CBS energy. This value is then corrected
for higher order correlation effects obtained by computing
MP2 and CCSD(T) energies using a modified 6-31G** basis
followed by employing the difference between these energies to
obtain the correction. The modified 6-31G** basis used more
diffuse polarization functions than are standard, in order to
describe the long-range interactions.19,20 Basis set super-
position errors (BSSE) are also taken into account in the
calculation of the interaction energy. We note that in their
study of the benzene dimer, Sinnokrot and Sherrill20 found
that both the standard aug-cc-pVTZ and the larger modified
basis, aug-cc-pVQZ, gave a similar potential energy surface
when BSSE is taken into account, giving us confidence in our
basis set extrapolation procedure.
We have previously found14 that DFT-D calculations can
describe the extensive range of structures in the full JSCH-
2005 database3 with a mean unsigned error (MUE) of less than
1 kcal mol�1. Recently,17 we have shown that for a limited
number of structures, a similar accuracy is found for mono-
saccharide sugar complexes. Briefly, in the DFT-D method the
dispersion corrected total energy is given by
EDFT-D = EKS-DFT + Edisp (1)
where EKS-DFT is the normal self-consistent Kohn–Sham
energy, and Edisp is an empirical term involving pair-wise
dispersive interactions
Edisp = �s6P
i
Pj4i(C
ij6/R
6ij)fdmp(Rij) (2)
Here, the summation is over all atom pairs, Cij6 is the disper-
sion coefficient for the pair of atoms i and j (calculated from
the atomic C6 coefficients), s6 is a scaling factor that depends
on the density functional used and Rij is the interatomic
distance between atoms i and j. A damping function is used
in order to avoid near singularities for small distances. This
function is given by
fdmp(Rij) = 1/(1 + exp(�a(Rij/R0 � 1))) (3)
where R0 is the sum of atomic van der Waals radii and a is a
parameter determining the steepness of the damping function.
In order to obtain the composite dispersion coefficients Cij6, a
simple average of the form
Cij6 = 2Ci
6Cj6/(C
i6 + Cj
6) (4)
is used. We here use the BLYP functional together with the
values for the C6, R0, s6, and a parameters taken from the
original parameterization of the DFT-D method.13 Following
Grimme,13 we do not consider basis set superposition errors
(BSSE), as we use a basis of triple zeta quality for the valence
orbitals, complemented with two sets of polarization functions
(TZV2D).21
We have carried out calculations using our implementation
of the DFT-D method, as well as for a range of pure func-
tionals. We have used a number of functionals in everyday use
such as B3LYP, BLYP and BH&H, together with the four
hybrid meta GGA functionals, MPW1B95, MPWB1K,
PW6B95, and PWB6K, developed by Zhao and Truhlar,
and the five new meta and hybrid meta functionals (M05,
M05-2X, M06, M06-2X and M06-L) also developed by the
same group. In all we have used 18 functionals as well as the
MP2 method. Those functionals not available in Gaussian
release (G03)22 were implemented by us in this code. All
calculations employed a TZV2D basis and were not corrected
for BSSE.
Computational results
Complexes of water and methane with benzene and
3-methylindole
We first discuss the results for the complexes of water and
methane with benzene. For the water–benzene complex
we have investigated three possible structures in which one
or both hydrogen atoms point towards the benzene ring. Two
are of C2v symmetry and one of Cs symmetry (Fig. 1). At the
DFT-D level it was possible to locate only the symmetric C2v
structures, and a number of stationary structures were found
to have one or more imaginary frequencies for various func-
tionals (Table 1). A similar situation was found for the
hydrogen sulfide–benzene complex studied with a variety of
functionals.9 The DFT-D structure of the water–benzene
complex (Fig. 1f) has a ‘benchmark’ interaction energy
of �3.35 kcal mol�1 (Table 2), close to the complete basis
set limit value of �3.33 kcal mol�1 of Min et al.23 for a Cs
structure. All the nine functionals of Zhao and Truhlar, as well
as the MP2 method, give interaction energies within
1 kcal mol�1 of the benchmark value, most being within
0.2 kcal mol�1 of this value. Of these M05, M06-L, MPWB1K
and PW6B95 can be singled out, all giving interaction energies
within 0.1 kcal mol�1 of the benchmark value. The three
structures we have studied are very close in energy, all methods
Fig. 1 Structures of methane–benzene (a–d) and water–benzene (e–g)
complexes.
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giving corresponding interaction energies which differ by less
than 0.1 kcal mol�1. To investigate the energetics of the
different structures further we have optimized both the C2v
and Cs structures at the MP4(SDQ)/TZV2D level, followed by
evaluation of their energies at the CCSD(T)/TZV2D level.
This procedure gave the Cs structure (Fig. 1g) to be lower in
energy by 0.05 kcal mol�1 than the C2v structure (Fig. 1f).
For the methane–benzene complex we have studied four
possible C3v structures, which have either three or a single
hydrogen atom pointing towards the benzene ring (Table 3,
Fig. 1). We find that the two structures having a single hydrogen
interacting with the benzene ring are preferred, with these two
structures, (c) and (d), having essentially the same energy. Our
benchmark value of �1.52 kcal mol�1, again for the DFT-D
Table 1 Interaction energy (I.E) (kcal mol�1) for benzene–water complex (Fig. 1), and distance between the centroid of benzene ring and centre ofmass of water molecule (A). The number of imaginary frequencies (I.F.) is also given. Blanks indicate that a structure could not be located
C2V (e) C2V (f) Cs (g)
I.E I.F. Distance I.E I.F. Distance I.E I.F. Distance
MP2 �4.17 2 3.22 �4.17 1 3.21 �4.21 1 3.24DFT-D �3.76 0 3.26 �3.77 1 3.25 — — —M05 �3.39 1 3.36 �3.40 1 3.36 �3.41 0 3.37M05-2X �4.09 0 3.17 �4.09 0 3.17 �4.13 2 3.20M06 �3.41 2 3.21 �3.43 2 3.20 �3.47 0 3.28M06-2X �4.40 0 3.13 �4.41 0 3.12 �4.41 1 3.13M06-L �3.26 0 3.16 �3.28 0 3.16 �3.19 1 3.21MPWB1K �3.23 0 3.20 �3.22 0 3.19 �3.26 0 3.24MPW1B95 �3.13 0 3.21 �3.13 2 3.24 �3.16 1 3.27PW6B95 �3.33 0 3.21 �3.35 2 3.26 �3.35 1 3.29PWB6K �3.74 0 3.21 �3.74 0 3.19 �3.79 0 3.23
Table 2 Interaction energies (kcal mol�1) at ‘benchmark’, DFT-D and MP2 levels, and for 18 functionals, for database of 7 DFT-D structures.The MUE values with respect to the CCSD(T) values are given
Complex ‘Benchmark’ DFT-D BLYP B3LYP B97-2 B98 BMK BH and H BH and HLYP PBE VSXC
II �6.81 �6.52 2.09 0.55 0.61 �1.28 �2.37 �7.65 �0.80 �1.61 �27.02I �9.21 �9.28 �0.36 �1.92 �1.58 �3.78 �4.59 �11.05 �3.28 �4.33 �31.88V �7.69 �7.97 0.44 �0.87 �0.61 �2.65 �3.16 �9.04 �1.98 �3.28 �28.10III �5.92 �5.14 2.07 0.67 0.61 �0.99 �1.72 �6.27 �0.57 �1.12 �23.42Benzene–H2O �3.35 �3.76 �1.33 �1.91 �1.85 �2.70 �2.56 �5.44 �2.44 �2.96 �10.26Benzene–CH4 �1.52 �0.97 0.93 0.44 0.36 �0.28 0.21 �1.98 0.02 �0.32 �5.28IV �7.42 �7.30 1.91 0.35 0.48 �1.58 �2.35 �8.23 �1.01 �2.00 �29.35MUE — 0.36 6.81 5.60 5.71 4.10 3.62 1.11 4.55 3.76 16.20
Complex MPW1B95 MPWB1K PWB6K PW6B95 MP2 M05 M05-2X M06 M06-2X M06-LII �2.99 �3.41 �4.41 �3.33 �8.94 �2.99 �5.46 �6.26 �6.39 �6.06I �5.09 �5.46 �6.62 �5.51 �11.61 �5.81 �8.23 �9.21 �8.93 �8.72V �3.77 �4.04 �5.17 �4.24 �10.02 �4.53 �6.64 �7.41 �7.48 �7.11III �2.59 �2.97 �3.89 �2.93 �7.73 �2.55 �4.77 �5.21 �5.60 �5.14Benzene–H2O �3.26 �3.38 �3.90 �3.44 �4.18 �3.41 �4.18 �3.56 �4.38 �3.29Benzene–CH4 �0.52 �0.64 �1.10 �0.72 �1.87 �0.81 �1.19 �0.91 �1.27 �0.80IV �3.1 �3.5 �4.6 �3.5 �10.0 �3.5 �6.00 �6.80 �6.80 �6.60MUE 2.94 2.66 1.90 2.63 1.78 2.64 1.01 0.43 0.45 0.60
Table 3 Interaction energy (I.E) (kcal mol�1) for benzene–methane complex (Fig. 1), and the distance between the centroid of benzene ring andcarbon atom of methane (A). The number of imaginary frequencies (I.F.) is also given. Blanks indicate that the structure could not be located
C3V (a) C3V (b) C3V (c) C3V (d)
I.E I.F. Distance I.E I.F. Distance I.E I.F. Distance I.E I.F. Distance
MP2 �1.62 2 3.58 �1.62 2 3.57 �1.90 0 3.68 �1.90 0 3.68DFT-D �0.71 2 3.67 �0.71 2 3.67 �0.97 0 3.82 �0.97 0 3.81M05 �0.66 2 3.80 �0.69 0 3.78 �0.94 1 3.95 �0.89 0 3.95M05-2X — — — �0.93 1 3.65 �1.15 2 3.77 �1.15 2 3.76M06 �0.62 6 3.59 �0.79 0 3.63 �0.88 2 3.83 �0.88 2 3.83M06-2X — — — �1.01 2 3.47 �1.34 3 3.63 �1.33 3 3.63M06-L — — — �0.85 1 3.65 �0.78 2 3.75 �0.81 1 3.75MPWB1K �0.37 0 3.90 �0.37 2 3.90 �0.61 0 3.79 �0.61 0 3.79MPW1B95 �0.34 1 3.90 �0.28 0 3.79 �0.50 0 3.81 �0.50 0 3.80PW6B95 — — — �0.54 0 3.78 — — — �0.80 1 3.98PWB6K — — — — — — �1.07 0 3.77 — — —
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structure (Fig. 1d), is very close to the value of Hobza et al.3 Other
estimates of the interaction energy are slightly less than this value,
at �1.4324 and �1.45 kcal mol�1.25 All of the nine functionals, as
well as the DFT-D method, give a value up to 1 kcal mol�1 less
than these values, with both M05-2X and M06-2X being in error
by less than 0.5 kcal mol�1, and the DFT-D value, 0.6 kcal mol�1,
being too small.
Methane–indole complexes have been studied at the
CCSD(T) level by Ringer et al.25 They have located a number
of structures, the lowest energy configuration, with an inter-
action energy of �2.08 kcal mol�1, having one hydrogen atom
pointing to each of the two rings. At the DFT-D level, we
find such a methane–3-methylindole structure to be the most
stable, with an interaction energy of �1.69 kcal mol�1
(Table 4). For the water–methylindole complex our p-complex
at the DFT-D level has one hydrogen atom pointing
towards each of the two rings, with an interaction energy of
�5.31 kcal mol�1, in contrast to the structure given by the
B3LYP functional in which water binds to a single ring.26 We
have also studied the more stable structure having the water
molecule hydrogen bonded to the indole nitrogen atom, but
do not discuss these results further. We have carried out
benchmark ab initio calculations of the interaction energy
of the water–methylindole and methane–methylindole
complexes using the DFT-D structures, yielding values
of �4.83 and �2.36 kcal mol�1, respectively. We have again
studied the performance of the nine functionals of Zhao
and Truhlar, the interaction energies for the corresponding
optimized structures are given in Table 4. The values for the
methane–indole complex are all greater by B0.5 kcal mol�1
than the corresponding ones for the methane–benzene
complex (Table 3), but for both complexes the trends in the
values for different functionals are very similar. A similar
picture emerges for the water–methylindole complex
(Table 4), where the trend is close to that for the water–
benzene complex (Table 1), although the interaction energies
are again greater, now by 1–2 kcal mol�1. All values
are within 0.5 kcal mol�1 of the benchmark value
(�4.83 kcal mol�1), except for the M05-2X and M06-2X
values, which are noticeably larger. The performance of
the MPW1B95, MPWB1K, PW6B95 and PWB6K functionals
in describing the complexes of water with benzene and methyl-
indole has been investigated by Zhao et al.,27 who find similar
interaction energies to the ones reported here.
Sugar–aromatic complexes
Benchmark studies
We have previously17 studied the fucose–toluene system at the
DFT-D level and have located ten minimum energy structures
which are close in energy, involving the three low energy con-
formers of fucose which differ in the orientation of O–H1 or
O–H2, which in turn leads to different interactions with the
p-system of toluene. We have described these structures in
Fig. S1 of ref. 17, and use the same labelling, 1–10, in this paper.
For convenience, we show these structures again in Fig. S1 (ESIw)of the present paper. In these structures, the aromatic group
interacts with either the upper or the lower face of the sugar. The
most stable group of complexes (8, 9, 10) involves the interaction
with one O–H and one C–H group of the upper face of the sugar.
The next group of complexes, (1, 2, 3, 5, 6), is higher in energy by
1–3 kcal mol�1, and involve the interaction of only C–H groups
of the lower face of the sugar. We have also studied 11 complexes
of glucose with 3-methylindole and p-hydroxytoluene (Fig. S2 of
ref. 17), which we have optimized at the DFT-D level, initial
structures being based upon crystal structures. Here, we number
these structures 11–21, and they are again shown in Fig. S2 (ESIw)of the present paper. Again, these structures can be characterized
in terms of the interaction of the C–H and O–H groups of the
sugar with the aromatic ring. In addition there is the possibility of
OH� � �N hydrogen bonding in the case of the indole systems.
We have chosen five complexes (I–V) shown in Fig. 2,
together with the water–benzene and methane–benzene com-
plexes, to be members of our small database, and have
evaluated the corresponding interaction energies at the high
ab initio level previously outlined, using structures optimized
at the DFT-D level. The coordinates of these seven structures
are given in Table S1 (ESIw). Structures I and II are 8 and 5,
respectively, from Fig. S1 (ESIw), and involve the interaction
of toluene with the upper and lower faces, respectively, of
fucose. Complex II has three C–H–p interactions, whilst
complex I has one C–H–p and one O–H–p interaction. The
p-hydroxytoluene–glucose complex IV is structure 17 from
Fig. S2 (ESIw), and also has three C–H–p interactions, and an
interaction energy close to that of II. We have chosen two
other sugar–aromatic complexes for our small database, a
galactose–benzene complex (III), which also has three C–H–pinteractions, and a a-methyl glucose–toluene complex (V)
which has two O–H–p interactions and a single C–H–pinteraction, with an interaction energy 1–2 kcal mol�1 less
than that of (I). Thus, in this small database we included five
quite diverse structures with interaction energies in the
range �5.9 to �9.2 kcal mol�1. It is to be expected that the
accurate prediction of these values, both absolute and relative,
will be a quite severe test of the various DFT methods.
Our benchmark consists of these five sugar–aromatic com-
plexes as well as the benzene–water and benzene–methane
complexes previously discussed. We have not included the
water–3-methylindole and methane–3-methylindole complexes
since these are similar to the corresponding benzene com-
plexes. We have evaluated the interaction energies of these
seven complexes at the DFT-D optimal geometry using the
DFT-D method, 18 functionals and MP2. These energies and
Table 4 Methane–3-methylindole and water–3-methylindole inter-action energies (kcal mol�1) using different functionals
Methane–3-methylindole Water–3-methylindole
DFT-D �1.69 �5.31M05 �1.26 �4.60M05-2X �1.89 �5.86M06 �2.01 �5.16M06-2X �2.49 �6.21M06-L �1.88 �4.91MPW1B95 �0.87 �4.44MPWB1K �0.95 �4.56PW6B95 �1.16 �4.63PWB6K �1.50 �5.12MP2 �3.25 �6.42
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the corresponding MUE values are given in Table 2. Of the
computational schemes used we see that the DFT-D method
performs the best, with a MUE of 0.36 kcal mol�1. The
traditional functionals, with the exception of BH&H, perform
particularly poorly. Of the Zhao and Truhlar functionals
tested, the newer M06 family performs much better than the
older M05 functionals, with MUE values only slightly greater
than for the DFT-D method.
Density functional studies of 23 sugar–aromatic complexes
We have studied the performance of the 18 functionals in
predicting the interaction energies of the 21 sugar–aromatic
complexes previously reported,17 together with structures
III and V. Since we have benchmark values for only five of
these complexes, we judge the interaction energies against the
corresponding DFT-D values, which we have found to repro-
duce those energies of our benchmark to better than
0.5 kcal mol�1. The interaction energies of these 23 complexes,
using a variety of functionals, are shown in Table S2 (ESIw),
the corresponding MUE values being shown in Table 5, which
also include the water–benzene and methane–benzene inter-
action energies. The inadequacy of the traditional functionals is
evident, all of which, except VSXC and BH&H, underestimate
the interaction energies by 3–7 kcal mol�1 whilst VSXC over-
estimates the interaction energy by a much larger amount, and
BH&H is again more successful, overestimating the inter-
action by only 1.5 kcal mol�1. The four hybrid meta GGA
functionals, MPW1B95, MPWB1K, PWB6K and PW6B95,
are generally more successful than the previous functionals,
apart from BH&H, and underestimate the interaction energies
by between 2.9 and 4.0 kcal mol�1, with PWB6K being the
more accurate. Of the two newer M05 functionals investigated,
M05-2X is the better performer, giving interaction energies
within B1 kcal mol�1 of the DFT-D values, whilst the
corresponding value for M05 is B3 kcal mol�1. We find the
M06 group of new functionals to perform even better, with all
three giving average interaction energies within 0.7 kcal mol�1
of the DFT-D values, with M06 and M06-2X performing
the best.
In these studies of the sugar–aromatic complexes using
different functionals, we have employed the DFT-D optimized
structures. As a check of this procedure we have optimized the
structures of the fucose–toluene complexes (3, 8) and evalu-
ated the corresponding interaction energies. We find values
of (�5.42, �5.82 kcal mol�1) for the M05 functional, and
values of (�7.72, �8.86 kcal mol�1) for the M06 functional.
These are close to the corresponding values obtained with the
DFT-D optimized structures of �5.32 and �5.81 kcal mol�1
for M05, and �7.98 and �9.21 kcal mol�1 for M06 (Table S2,
ESIw). We note, for comparison, that the DFT-D interaction
energies are �8.11 and �9.28 kcal mol�1 for 3 and 8,
respectively.
Conclusions
We have here shown that a small database of complexes
involving the interaction of –OH and –CH groups with
Fig. 2 DFT-D structures used in ‘benchmark’ calculations.
Table 5 Mean unsigned error (MUE, kcal mol�1) of interactionenergies for full dataset (25 structures, Table S2, ESIw), for 18functionals and MP2, compared to DFT-D values
Functional MUE
BLYP 8.12B3LYP 6.64B97-2 6.83B98 4.97BMK 4.12BH and H 1.48BH and HLYP 5.35PBE 4.57VSXC 18.62MPW1B95 3.62MPWB1K 3.24PWB6K 2.23PW6B95 3.26MP2 2.44M05 3.24M05-2X 1.00M06 0.40M06-2X 0.36M06-L 0.73
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aromatic p systems can be used to judge the performance of
both the DFT-D scheme and of a range of traditional and
newer density functionals. The studies we have reported here
reinforce previous findings concerning the application of DFT
methods to study non-covalent interactions of biological
importance. Thus, the DFT-D method is here particularly
successful with a MUE value of less than 1 kcal mol�1, a
similar value being found previously for a range of different
interactions.14 The poor performance of traditional func-
tionals is again evident, with the newer set of functionals of
Zhao and Truhlar being definitely superior. However, it is only
the latest M06 family which here gives MUE values less than
1 kcal mol�1, and is thus competitive with the DFT-D
approach.
Acknowledgements
We thank Dr Y Zhao for advice on the M0X functionals.
References
1 E. A. Meyer, R. K. Castellano and F. Diederich, Angew. Chem.,Int. Ed., 2003, 42, 1210.
2 H. J. Gabius, H. C. Siebert, S. Andre, J. Jimenez-Barbero andH. Rudiger, ChemBioChem, 2004, 5, 740.
3 P. Jurecka, J. Sponer, J. Cerny and P. Hobza, Phys. Chem. Chem.Phys., 2006, 8, 1985.
4 T. J. Giese, E. C. Sherer, C. J. Cramer and D. M. York, J. Chem.Theory Comput., 2005, 1, 1275.
5 M. Elstner, D. Porezag, G. Jungnickel, J. Elstner, M. Haugk,T. Frauenheim, S. Suhai and G. Seifert, Phys. Rev. B: Condens.Matter, 1998, 58, 7260.
6 Y. Zhao and D. G. Truhlar, J. Phys. Chem. A, 2005, 109, 5656.7 Y. Zhao and D. G. Truhlar, Theor. Chem. Acc., 2008, 120, 215.8 Y. Zhao and D. G. Truhlar, Acc. Chem. Res., 2008, 41, 157.9 H. R. Leverentz and D. G. Truhlar, J. Phys. Chem. A, 2008, 112,6009.
10 Y. Zhao and D. G. Truhlar, J. Chem. Theory Comput., 2007, 3,289.
11 T. v. Mourik, J. Chem. Theory Comput., 2008, 4, 1610.12 M. P. Waller, A. Robertazzi, J. A. Platts, D. E. Hibbs and
P. A. Williams, J. Comput. Chem., 2006, 27, 491.
13 S. Grimme, J. Comput. Chem., 2004, 25, 1463.14 C. Morgado, M. A. Vincent, I. H. Hillier and X. Shan, Phys.
Chem. Chem. Phys., 2007, 9, 448.15 J. P. McNamara and I. H. Hillier, Phys. Chem. Chem. Phys., 2007,
9, 2362.16 J. McLaurin, T. Franklin, P. E. Fraser and A. Chakrabartty,
J. Biol. Chem., 1998, 273, 4506.17 R. K. Raju, A. Ramraj, M. A. Vincent, I. H. Hillier and
N. A. Burton, Phys. Chem. Chem. Phys., 2008, 10, 6500.18 E. C. Stanca-Kaposta, D. P. Gamblin, J. Screen, B. Liu,
L. C. Snoek, B. G. Davis and J. P. Simons, Phys. Chem. Chem.Phys., 2007, 9, 4444.
19 J. Sponer, J. Leszczynski and P. Hobza, J. Phys. Chem., 1996, 100,1965.
20 M. O. Sinnokrot and C. D. Sherrill, J. Phys. Chem. A, 2004,108, 10200.
21 A. Shaefer, C. Huber and R. Ahlrichs, J. Chem. Phys., 1994, 100,5829.
22 M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria,M. A. Robb, J. R. Cheeseman, J. A. Montgomery Jr, T. Vreven,K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi,V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega,G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K.Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima,Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox,H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo,R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin,R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala,K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg,V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain,O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari,J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford,J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz,I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham,C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill,B. Johnson, W. Chen, M. W. Wong, C. Gonzalez and J. A. Pople,GAUSSIAN 03 (Revision C.02), Gaussian, Inc., Wallingford,CT, 2004.
23 S. K. Min, E. C. Lee, H. M. Lee, D. Y. Kim, D. Kim andK. S. Kim, J. Comput. Chem., 2008, 29, 1208.
24 K. Shibasaki, A. Fujii, N. Mikami and S. Tsuzuki, J. Phys. Chem.A, 2006, 110, 4397.
25 A. L. Ringer, M. S. Figgs, M. O. Sinnokrot and C. D. Sherrill,J. Phys. Chem. A, 2006, 110, 10822.
26 T. v. Mourik, Chem. Phys., 2004, 304, 317.27 Y. Zhao, O. Tishchenko and D. G. Truhlar, J. Phys. Chem. B,
2005, 109, 19046.
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