Cucurbit[6]uril Complexation
FULL PAPER
program suites. Only minor changes in the resulting struc-
ture were observed using Hartree–Fock method with 6-
31G*[18] basis set, with
a root-mean-square deviation
(RMSD) of 0.46 ꢁ between the initial and optimized struc-
tures (Figure 3C). A similar difference (RMSD=0.50 ꢁ)
was observed using density functional theory (B3LYP[19]
)
and larger basis set (cc-pVDZ[20]). These results reveal very
small impact of the crystal field on the complex but still
they do not say anything about the situation in solution.
Therefore, the complex was immersed into a box containing
about 6000 water molecules. Owing to the extreme complex-
ity of such system, quantum chemical computations had to
be replaced by a faster empirical molecular mechanics ap-
proach. This change also permits to study the dynamic be-
havior of the system by means of molecular dynamics. For
this purpose, the sander program from the AMBER pack-
age[21] was used. The complex was described using the
GAFF[22] force field, which is well tuned for the simulation
of small organic molecules, whereas water molecules were
described using TIP3P[23] potential. At the beginning of the
simulation, the system was heated up to 300 K with pressure
maintained at 1 bar (for detailed description of used proto-
cols, see the Supporting Information section). After system
equilibration, the simulation was run for an additional 10 ns
with temperature and pressure maintained at 300 K and
1 bar, respectively. During this period, the complex was
stable showing the same structural features as those ob-
served by X-ray diffraction and proposed from the interpre-
tation of NMR spectra. To avoid possible computational ar-
tifacts coming from for example, interlocked structure, the
simulation was re-run using different initial complex struc-
ture. [C4mim]+ was moved along axial axis of complex in
such a way that 3-methyl group was roughly situated in the
cavity centre and the butyl chain was outside of CB6. This
complex arrangement was stable only for ꢀ600 ps. After
this period, [C4mim]+ was moved back and the resulting
complex was stable until the end of the simulation.
We were also able to obtain the single crystals of the
[C2mim]+-CB6 complex. The crystal structure contains two
different types of complexes.[16] The first type contains
[C2mim]+ located within the CB6 cavity (Figure 4A,B). The
second one is composed of two superimposed structures,
both containing [C2mim]+ within the CB6 cavity, but with
opposite head-to-tail orientations. In all cases, the imidazoli-
um moiety is located inside the CB6 cavity, contrary to our
findings with the [C4mim]+-CB6 complex, where imidazoli-
um sits on top of one of the carbonyl portals. One might
argue that the small molecule [C2mim]+ is pushed into the
cavity by packing forces dominating in the crystal. However,
structure optimization of this complex by quantum chemical
methods reveals that the structure is stable even without the
crystal field (Figure 4C). Furthermore, the calculated com-
plex formation energy is about 5 kcalmolÀ1 smaller (B3LYP/
cc-pVDZ) than that for [C4mim]+-CB6 complex, which is in
agreement with our expectations and with the lower stability
of [C2mim]+-CB6 complex detected by NMR. Lower com-
plex stability is also observed in molecular dynamics simula-
Figure 4. Crystal structure of [C2mim]+-CB6 complex: A) side and
B) front views and C) comparison of crystal structure (black) and struc-
ture optimized using HF/6-31G* method (gray).
tions. The complex dissociates after 3–5 ns (proved by three
simulations starting from different conditions).
Our results from crystallographic measurements and com-
putations strongly support a 1:1 binding mode between
[C2mim]+ and CB6. However, our findings contrast with a
recent report on the formation of a 2:1 complex between
[C2mim]+ and CB6.[14a] Therefore, to further support our re-
sults, we constructed a Job plot using UV-visible spectrosco-
py. A maximum was found at c [C2mim]+ =0.5, which also
indicates a 1:1 stoichiometry between the host and the
guest. Furthermore, a major signal at 1107 m/z correspond-
ing to 1:1 [C2mim]+-CB6 complex was observed in the
MALDI TOF MS spectrum, when the complex solution in
the presence of more than fourfold excess of the guest was
analyzed with no sign of the 2:1 complex. Similar MALDI
TOF MS spectra indicating the presence of 1:1 complex
were obtained for the remaining guests upon the complexa-
tion with CB6 (see the Supporting Information).
The complexation between [C5mim]+ and CB6 was also
investigated using 15N NMR spectroscopy. We anticipated
that the shift of electron density in the imidazolium ring pre-
sumably induced by complexation with CB6 should affect
both 15N resonances on the imidazolium skeleton. A solu-
tion containing 1 equiv of [C5mim]+ and 0.5 equiv of CB6
was used for the 15N NMR measurements.[24] Two sets of sig-
nals corresponding to the free and bound forms of the guest
were observed because of the slow exchange process. 15N
resonances were assigned unequivocally to the N1 and N3
atoms by using 1H-15N GSQMBC experiments.[25] Interac-
tions of the protons on the methyl group with N1 and pro-
Chem. Eur. J. 2009, 15, 6926 – 6931
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