Molecular Physics

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Theoretical study on complexation

of the perchlorate, permanganate,
pertechnate and perrhenate anions with
dodecabenzylbambus[6]uril

Stanislav Böhm, Emanuel Makrlík & Petr Vaňura

To cite this article: Stanislav Böhm, Emanuel Makrlík & Petr Vaňura (2017): Theoretical study
on complexation of the perchlorate, permanganate, pertechnate and perrhenate anions with
dodecabenzylbambus[6]uril, Molecular Physics, DOI: 10.1080/00268976.2017.1299235

To link to this article: http://dx.doi.org/10.1080/00268976.2017.1299235

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Published online: 16 May 2017.

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Download by: [Cornell University Library] Date: 16 May 2017, At: 07:37
MOLECULAR PHYSICS, 
https://doi.org/./..

RESEARCH ARTICLE

Theoretical study on complexation of the perchlorate, permanganate,

pertechnate and perrhenate anions with dodecabenzylbambus[]uril
Stanislav Böhma , Emanuel Makrlíkb and Petr Vaňuraa
a
University of Chemistry and Technology, Prague, Czech Republic; b Faculty of Environmental Sciences, Czech University of Life Sciences, Prague,
Czech Republic

ABSTRACT ARTICLE HISTORY

By using quantum chemical calculations, the most probable structures of the anionic Received  January 
complex species dodecabenzylbambus[6]uril–ClO4 − , dodecabenzylbambus[6]uril–MnO4 − , Accepted  February 
dodecabenzylbambus[6]uril–TcO4 − and dodecabenzylbambus[6]uril–ReO4 − were derived. In these
KEYWORDS
four complexes, each of the considered anions, included in the macrocyclic cavity, is bound by 12 Dodecabenzylbambus[]uril;
weak hydrogen bonds between methine hydrogen atoms on the convex face of glycoluril units anions; complexation; DFT
and the respective anion. Further, the corresponding interaction energies of the investigated four calculations; structures
anionic complexes were calculated; the absolute values of these calculated energies increase in the
series of ReO4 − < TcO4 − < MnO4 − < ClO4 − .

1. Introduction [16]. In contrast to previously published macrocycle

Me12 BU[6], which does not dissolve in any organic sol-
Cucurbit[n]urils are macrocyclic compounds consisting
vents, Bn12 BU[6] is easily soluble in chloroform. Besides,
of n glycoluril units connected by 2n methylene bridges.
Bn12 BU[6] has very great affinity for some univalent
The shape of the macrocycle resembles a hollow bar-
anions as well [16], so that this macrocycle can be con-
rel with a hydrophobic interior and partially negative
sidered quite justifiably as very effective supramolecu-
charged rims of carbonyls on both sides of the macrocy-
lar anionic receptor. However, up to now, the accurate
cle. This structure makes the macrocycle suitable to bind
structures of the formed anionic complexes have not
organic guests bearing one or more positive charges in
been solved mostly in detail. Therefore, in the current
their structures [1–14].
work, employing DFT calculations, the most probable
The synthesis of a cyclic hexamer dodecamethyl-
structures of the anionic complexes 1·ClO4 − , 1·MnO4 − ,
bambus[6]uril (Me12 BU[6]) has been first published
1·TcO4 − and 1·ReO4 − (1 = Bn12 BU[6]) were derived in
in 2010 [15]. Dodecabenzylbambus[6]uril, denoted also
detail. In this context, we must add that the 1·ClO4 − com-
by Bn12 BU[6] (abbrev. 1; see Scheme 1), in which 12
plex is extraordinarily stable in chloroform, as reported
methyl groups of Me12 BU[6] are substituted by 12 benzyl
recently [17].
groups, has been described by Sindelar and co-workers

CONTACT Emanuel Makrlík makrlik@centrum.cz

Supplemental data for this article can be accessed http://dx.doi.org/./...
©  Informa UK Limited, trading as Taylor & Francis Group
2 S. BÖHM ET AL.
2. Computational details
The theoretical calculations were performed at the den-
sity functional level of theory (DFT, B3LYP) [18,19],
employing the Gaussian 09 suite of programs [20]. The
LanL2DZ basis set was used and the optimisations were
unconstrained. In order to increase the numerical accu-
racy and to reduce oscillations during the molecular
geometry optimisation, two-electron integral and their
derivatives were calculated by using the pruned (99,590)
integration grid, having 99 radial shells and 590 angu-
lar points per shell, which was requested by means of the
Gaussian 09 keyword ‘integral(ultrafinegrid).’
The most probable structures of the anionic complexes
1·ClO4 − , 1·MnO4 − , 1·TcO4 − and 1·ReO4 − were pre-
dicted on the basis of the thorough conformational anal-
yses (i.e. in each of the four cases studied, six very dif-
ferent initial mutual positions of the ligand 1 and the X−
anion, where X− = ClO4 − , MnO4 − , TcO4 − and ReO4 − ,
were considered during the geometry optimisation) and
the respective vibrational frequency analyses.
3. Results and discussion
In the model calculations, we optimised the molecular
geometries of the parent macrocycle 1 and its anionic
complexes with X− (X− = ClO4 − , MnO4 − , TcO4 − and
ReO4 − ) using previously published CIF files [15,16]
(however, predominantly by means of their suitable mod-
ifications), similarly as in our previous papers [21–26].
The optimised structure of the free macrocyclic recep-
tor 1, having a symmetry very close to C3 , is illustrated
in Figure 1. At this point, it should be noted that the six
glycoluril units in this macrocycle adopt alternate confor-
mations; the methine hydrogen atoms on the convex face
of each unit point into the cavity – its diameter is 8.49 Å
Scheme . Structural formula of dodecabenzylbambus[]uril
(abbrev. 1).
(see Figure 1). This macrocycle can be divided into two
identical parts by a plane defined by the carbon atoms of
the six methine bridges, and besides, the carbons of the six
carbonyl groups are arranged alternately above and below
the mentioned plane in a ‘zigzag’ manner.
In Figures 2–5, the lowest-energy-level structures of
the anionic complex species 1·X- , where X− = ClO4 − ,
MnO4 − , TcO4 − , ReO4 − , are shown, together with the
lengths of the corresponding hydrogen bonds (in Å).
No other conformations of the complexes 1·X- (X− =
ClO4 − , MnO4 − , TcO4 − , ReO4 − ) were found using the
above-mentioned theoretical procedure. In this context,
it should be stated that the respective vibrational calcula-
tions found no imaginary frequencies. In these four com-
plexes, each of the considered anions, located in the cen-
tre of the macrocyclic cavity, is bound by 12 weak hydro-
gen bonds between the methine hydrogen atoms on the
convex face of the glycoluril units and the respective three
oxygen atoms of the anion. The diameters of the cavities
in 1·ClO4 − , 1·MnO4 − , 1·TcO4 − and 1·ReO4 − are 8.26,
8.22, 8.31 and 8.35 Å, respectively. This means that the
diameters of the cavities in these four investigated anionic
complexes increase in the sequence of MnO4 − < ClO4 −
< TcO4 − < ReO4 − . For this reason, the macrocycle 1
is somewhat flexible because its cavity size adapts to the
size of the considered anion. Cartesian coordinates (in
Å) of the ligand 1 and the anionic complexes 1·ClO4 − ,
1·MnO4 − , 1·TcO4 − and 1·ReO4 − are given in supple-
mental data.
Finally, the interaction energies, E(int), of the anionic
complexes 1·ClO4 − , 1·MnO4 − , 1·TcO4 − and 1·ReO4 − ,
involving the 7-point correction for the basis set of super-
position error [27,28], were found to be −259.7, −252.0,
−219.2 and −215.9 kJ/mol, respectively. Thus, the abso-
lute values of these calculated energies increase in the
order of ReO4 − < TcO4 − < MnO4 − < ClO4 − , which
means that the stabilities of the anionic complexes under
study in vacuo increase in the same sequence.
4. Concluding remarks
In this work, employing quantum chemical DFT cal-
culations, the most probable structures of the anionic
complexes 1·ClO4 − , 1·MnO4 − , 1·TcO4 − and 1·ReO4 −
(1 = dodecabenzylbambus[6]uril) were predicted. It was
proven that in these four anionic complex species, each of
the considered anions, included in the macrocyclic cavity
of the parent receptor 1, is bound by 12 weak hydrogen
bonds between methine hydrogen atoms on the convex
face of the glycoluril units of 1 and the respective three
oxygens of the investigated anion. Moreover, from the cal-
culated interaction energies of the four complexes under
study, it follows that the absolute values of these energies
 MOLECULAR PHYSICS 3

Figure . Two projections of the DFT optimised structure of free macrocycle 1 (BLYP/LanLDZ). The diameter of the cavity in 1 is . Å.
4 S. BÖHM ET AL.

Figure . Two projections of the DFT optimised structure of the 1·ClO − complex (BLYP/LanLDZ); distances/Å. The diameter of the cavity
in 1·ClO − is . Å.
 MOLECULAR PHYSICS 5

Figure . Two projections of the DFT optimised structure of the 1·MnO − complex (BLYP/LanLDZ); distances/Å. The diameter of the
cavity in 1·MnO − is . Å.
6 S. BÖHM ET AL.

Figure . Two projections of the DFT optimised structure of the 1·TcO − complex (BLYP/LanLDZ); distances/Å. The diameter of the cavity
in 1·TcO − is . Å.
 MOLECULAR PHYSICS 7

Figure . Two projections of the DFT optimised structure of the 1·ReO − complex (BLYP/LanLDZ); distances/Å. The diameter of the
cavity in 1·ReO − is . Å.
8 S. BÖHM ET AL.
increase in the series of ReO4 − < TcO4 − < MnO4 − <
ClO4 − . On the other hand, the diameters of the cavities
in these anionic complexes increase in the sequence of
MnO4 − < ClO4 − < TcO4 − < ReO4 − , as follows from
Figures 2–5. Therefore, the macrocycle 1 is somewhat
flexible because its cavity size adapts to the size of the con-
sidered anion. From the previous results, it follows that
the present study may be an important contribution pre-
dominantly to the investigated macrocyclic receptor, as
well as to supramolecular chemistry in general.
Disclosure statement
No potential conflict of interest was reported by the authors.
Funding
This work was supported by the Grant Agency of Faculty of
Environmental Sciences, Czech University of Life Sciences,
Prague [grant number 42,900/1312/3114]; Czech Ministry of
Education, Youth, and Sports [grant number MSMT 20/2015].
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