NMR studies of anion-induced conformational changes in diindolylureas and diindolylthioureas

Article abstract of DOI:10.3762/bjoc.7.140

The conformational properties of 1,3-diindolylureas and thioureas were studied by a combination of heteronuclear NMR spectroscopy and quantum mechanics calculations. NOE experiments showed that the anti-anti conformer along the C7-N7α bonds was predominant in DMSO-d₆ solution in the absence of anions. Anion-induced changes in the ¹H and ¹⁵N chemical shifts confirm the weak binding of chloride anions with negligible conformational changes. Strong deshielding of ureido protons and moderate deshielding of indole NH was observed upon the addition of acetate, benzoate, bicarbonate and dihydrogen phosphate, which indicated that the predominant hydrogen bond interactions occurred at the urea donor groups. Binding of oxo-anions caused conformational changes along the C7-N7α bonds and the syn-syn conformer was preferred for anion-receptor complexes. The conformational changes upon anion binding are in good agreement with energetic preferences established by ab initio calculations.

Full text of DOI:10.3762/bjoc.7.140

NMR studies of anion-induced conformational
changes in diindolylureas and diindolylthioureas
Damjan Makuc1,2, Jennifer R. Hiscock3, Mark E. Light3, Philip A. Gale*3
and Janez Plavec*1,2,4
Full Research Paper
Open Access
Address:
Beilstein J. Org. Chem. 2011, 7, 1205–1214.
1Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova
19, SI-1000 Ljubljana, Slovenia, 2EN→FIST Centre of Excellence,
Dunajska 156, SI-1000 Ljubljana, Slovenia, 3Chemistry, University of
Southampton, Southampton SO17 1BJ, United Kingdom and 4Faculty
of Chemistry and Chemical Technology, University of Ljubljana,
SI-1000 Ljubljana, Slovenia
doi:10.3762/bjoc.7.140
Received: 31 May 2011
Accepted: 03 August 2011
Published: 02 September 2011
This article is part of the Thematic Series "Supramolecular chemistry II".
Guest Editor: C. A. Schalley
Email:
Damjan Makuc - damjan.makuc@ki.si; Jennifer R. Hiscock -
J.Hiscock@soton.ac.uk; Mark E. Light - m.e.light@soton.ac.uk;
Philip A. Gale* - philip.gale@soton.ac.uk; Janez Plavec* -
janez.plavec@ki.si
© 2011 Makuc et al; licensee Beilstein-Institut.
License and terms: see end of document.
* Corresponding author
Keywords:
anion recognition; conformation analysis; host–guest systems; NMR
spectroscopy
Abstract
The conformational properties of 1,3-diindolylureas and thioureas were studied by a combination of heteronuclear NMR spec-
troscopy and quantum mechanics calculations. NOE experiments showed that the anti–anti conformer along the C7–N7α bonds was
predominant in DMSO-d6 solution in the absence of anions. Anion-induced changes in the 1H and 15N chemical shifts confirm the
weak binding of chloride anions with negligible conformational changes. Strong deshielding of ureido protons and moderate
deshielding of indole NH was observed upon the addition of acetate, benzoate, bicarbonate and dihydrogen phosphate, which
indicated that the predominant hydrogen bond interactions occurred at the urea donor groups. Binding of oxo-anions caused
conformational changes along the C7–N7α bonds and the syn–syn conformer was preferred for anion–receptor complexes. The con-
formational changes upon anion binding are in good agreement with energetic preferences established by ab initio calculations.
Introduction
In the last two decades, remarkable efforts have been made in research. Biomolecules such as the sulfate binding protein [14]
the field of the development of synthetic anion receptors, moti- and phosphate binding protein [15] employ hydrogen bonds as
vated by prospective applications in recognition, separation, the key driving force to bind or transport anions through cell
guest inclusion and catalysis [1-13]. The fundamental role of membranes. Hydrogen bonding interactions are extensively
anions in biological and chemical processes drives much of this employed in synthetic anion receptors comprising groups such
1205

Beilstein J. Org. Chem. 2011, 7, 1205–1214.
as amides, pyrroles, indoles, ureas and triazoles, as well as in has yet to be performed and may help shed light on the high
ammonium, guanidinium and imidazolium moieties used as affinity of these systems for oxo-anions. Therefore, in the
hydrogen bond donors [16-23]. Amongst neutral anion receptor current work the conformational preorganization of bis-indole
systems, indole and related heterocycles, such as carbazole, receptors 1–4 (Figure 1), as well as the conformational changes
2,2'-biindole and indolo[1,2-b]carbazoles, have recently of these systems upon binding of chloride and several oxo-
attracted significant attention [24-31]. Indole contains a single anions, were studied by NMR spectroscopy and supported by
hydrogen bond donor group, which is employed in biological energetic preferences established from ab initio calculations.
systems to bind anions such as chloride [32] and sulfate [14].
We have recently analyzed the conformational preferences of
several 2,7-disubstituted indoles with amide substituents at C2
and urea substituents at C7, which showed preference for
distinct conformations in the presence and in the absence of
anions [33-35]. In addition, indole and urea groups were
strongly involved in hydrogen-bonding interactions with the
bound anionic guest, whilst the amide group interacted only
weakly with the bound anion. These observations led to the
design of diindolylureas and diindolylthioureas [36-38]. These
compounds have remarkably high affinities for oxo-anions such
as phosphate and sulfate for neutral receptors in DMSO-d6/
0.5% water and have been shown to perturb the pKa of bound
guests (Table 1) [38,39]. X-ray crystal structures of a variety of
complexes with anions revealed the adoption of the syn–syn
Figure 1: Anion receptors 1–4 together with their atomic numbering
scheme.
conformation in the solid state upon anion complexation. With
the urea analogues, such as 1, this is accompanied by higher
order complex formation with oxo-anions in the solid state. For
Results and Discussion
example, with dihydrogen phosphate, three equivalents of
receptor complex to a single anion, which has doubly deproto- Synthesis
nated, resulting in the formation of a complex in which twelve Compounds 1–3 were synthesized following a previously
hydrogen bonds stabilize the PO43− anion. In solution, the reported methodology [36-39]. Compound 4 was prepared by
thiourea analogues such as compound 2 show significantly reaction of 7-amino-N-phenyl-1H-indole-2-carboxamide
lower affinities for oxo-anions than do the urea analogues. We (0.27 g, 1.07 mM) with 7-isothiocyanato-N-phenyl-1H-indole-
had previously proposed that this may be due to the larger size 2-carboxamide (0.31 g, 1.07 mM) in pyridine in 27% yield (see
of the sulfur atom resulting in a lower propensity of these Supporting Information File 1 for details).
systems to adopt a planar conformation. Whilst the con-
formational properties of these compounds have been explored Structural features and NMR chemical shifts
by single crystal X-ray diffraction in the solid-state, a detailed The conformational properties of diindolylureas and diindolyl-
analysis of the conformational properties of the these com- thioureas 1–4, shown in Figure 1, were evaluated by means of
pounds in solution, in the absence and presence of oxo-anions, NMR spectroscopy. Proton and 13C NMR resonances were
Table 1: Stability constants of compound 1 measured in DMSO-d6/0.5% water, DMSO-d6/10% water and DMSO-d6/25% water and compound 2 in
DMSO-d6/0.5% water at 298 K by 1H NMR titration techniques [37].
Aniona
Compound 1 in
Compound 1 in
Compound 1 in
Compound 2 in
DMSO-d6/0.5% water
DMSO-d6/10% water
DMSO-d6/25% water
DMSO-d6/0.5% water
Cl−
128
17
–
74
CH3CO2−
C6H5CO2−
H2PO4−
>104
>104
>104
774
521
5170
20
1620
477
1630
precipitate
160
aAnions added as tetrabutylammonium salts.
1206

Beilstein J. Org. Chem. 2011, 7, 1205–1214.
assigned through 1D and 2D spectra, while 15N chemical shifts shifts of δH7α were observed upon addition of acetate, benzoate
were determined by 1H–15N correlations in HSQC and HMBC and bicarbonate anions (Δδ ≈ 2 ppm, Figures 2c–2e), which
spectra. Notable 1H and 15N NMR chemical shifts of 1–4 are suggested strong interaction of ureido NH protons with these
shown in Table 2. It should be noted that only one set of signals anions. In addition, the strong deshielding of indolyl H1 protons
was observed for both indole rings in all four receptors, due to corroborates its participation in the hydrogen bond formation
the symmetry of the compounds. The full NMR data set with carboxylate and bicarbonate moieties (Δδ ≈ 1 ppm). Planar
together with 13C NMR chemical shifts is reported in oxo-anions interact both with H1 and H7α due to their
Supporting Information File 1.
Y-shaped geometry. The tetrahedral geometry of the dihy-
drogen phosphate anion allows strong interaction with all four
Indole NH proton resonances were found between 10.8 and hydrogen bond donor groups, which is reflected in the substan-
11.7 ppm. Thioureido containing compounds 2 and 4 exhibited tial deshielding of the H1 and H7α protons (Figure 2f). Interest-
slight downfield shifts of H1 and H7α with respect to ureido ingly, one set of signals was observed for each type of anion on
receptors 1 and 3 (Table 2). N1 chemical shifts showed only
minor variations as a result of structural differences in 1–4. The
most significant differences in chemical shifts between the
ureido and thioureido functionalized receptors were observed
for H7α and N7α atoms (ΔδH = 0.8 and ΔδN = 22 ppm,
Table 2). Compounds 3 and 4 contain phenylamide substituents
at C2 and hence two more NH groups (Figure 1). Considerable
deshielding of the H3 and H6 resonances was observed in 3 and
4 with respect to the nonsubstituted indole moieties in 1 and 2.
The downfield shift of δH3 was attributed directly to the pres-
ence of the phenylamide group at C2. Deshielding of H6 (Δδ
0.4–0.5 ppm) in 3 and 4 with respect to 1 and 2, respectively,
was much larger than the deshielding of H4 (Δδ 0.1 ppm),
possibly due to a more efficient conjugation.
1H and 15N NMR chemical shift changes in 1 upon
addition of anions
Figure 2 shows 1H chemical shift changes of 1 in the presence
of one equivalent of chloride, acetate, benzoate, bicarbonate and
dihydrogen phosphate anions. The protons that are most
affected by anion–receptor interaction were found to be H1, H6
and H7α. Only minor ΔδH7α and negligible differences of δH1
and δH6 were observed in the presence of chloride anions
(Figure 2a and Figure 2b). The very weak interactions between
Figure 2: 1H NMR spectra of 1 in the absence of anions (a) and upon
chloride and 1 could be due to competing interactions of the
polar DMSO molecules for the hydrogen bond donor groups of
the receptor, and the weak basicity of the chloride. This is
supported by the stability constant determinations previously
reported, and presented in Table 1. Considerable downfield
addition of one equivalent of the following anions: Chloride (b), acetate
(c), benzoate (d), bicarbonate (e) and dihydrogen phosphate (f). All
spectra were recorded in DMSO-d6 at 298 K. (g) 1H and 15N NMR
chemical shift changes, Δδ = δ (in the presence of anion) – δ (in the
absence of anions), induced by addition of one equivalent of different
anions to receptor 1.
Table 2: Selected 1H and 15N NMR chemical shifts for 1–4 (in ppm).a
H1
H2β
H7α
H2
H3
H6
N1
N2β
N7α
1
2
3
4
10.78
11.03
11.62
11.68
–
8.64
9.48
8.97
9.72
7.35
7.36
–
6.44
6.46
7.49
7.48
7.08
7.03
7.59
7.39
136.5
136.3
134.5
134.9
–
102.7
124.9
104.6
126.6
–
–
10.29
10.26
128.6
129.0
–
aIn DMSO-d6 at 298 K.
1207

Beilstein J. Org. Chem. 2011, 7, 1205–1214.
the NMR timescale, which suggested that the symmetry of the anti–anti and syn–anti, can be stabilized by intramolecular
receptor 1 is preserved upon interactions with anions. The NH–CO hydrogen bonds, which represent competition to
stability constant determinations presented in Table 1 also anion–receptor interactions and therefore make conformational
support the finding that this compound interacts selectively with studies even more appealing.
oxo-anions.
The conformational characteristics of diindolylurea 1 were
Anion–receptor interactions assessed by 1H chemical shift assessed by the use of 1D difference NOE experiments in the
changes were corroborated by 15N NMR data. Weak shielding absence and in the presence of anions. The orientation along the
of N1 in 1 was observed upon addition of acetate, benzoate and C7–N7α bonds was established by comparative evaluation of
bicarbonate anions, whereas addition of dihydrogen phosphate NOE enhancements of H7α with H1 and H6 protons. The satu-
anions led to deshielding of N1 (Figure 2g). In contrast, N7α ration of H7α in 1 gave strong NOE at H6 (10.4%) and
was deshielded upon addition of anions (Figure 2g). The moderate NOE at H1 (4.3%), which suggested that the anti
strongest deshielding of 11.2 ppm was observed for the 1·BzO− orientation prevails along the linkage between ureido moiety
complex.
and indole ring (Figure 4a). As the observed NOE enhance-
ments are primarily a function of the H6–H7α and H1–H7α
distances, we compared their values in the optimized anti–anti
(d(H6–H7α) = 2.28 Å) and syn–syn (d(H1–H7α) = 2.32 Å)
Conformational properties of 1 and its complexes
with anions
The rotational flexibility of the ureido moiety allows numerous structures and established a minor difference of 0.04 Å which
conformations of receptor 1. Among them three major, energeti- would be reflected in a 1% change in the NOE enhancements.
cally preferred, conformers are likely to be observed (Figure 3). The observed difference between NOE enhancements in the
The syn–syn conformer, where NH protons form a convergent uncomplexed form of receptor 1 was over 6%, which led us to
hydrogen-bonding array, is expected to be adopted in the pres- conclude that the anti–anti conformer is predominant in the
ence of bound anionic guests, based on the previous solid-state DMSO-d6 solution. In addition, the anti–anti conformer of 1
studies. On the other hand, this conformer is unlikely to be with its plane of symmetry along the carbonyl bond is in agree-
abundant in the absence of anions, due to repulsion between the ment with the single set of resonances in the NMR spectra. On
hydrogen bond donor groups. The other two rotamers, namely the other hand, the syn–anti rotamer shows a twofold rotational
Figure 3: Three representative conformational families of rotamers of 1. Notations refer to the orientations along [C6–C7–N7α–C7β] fragments.
Figure 4: NOE enhancements of 1 in the absence of anions (a) and upon addition of one equivalent of acetate anions (b).
1208

Beilstein J. Org. Chem. 2011, 7, 1205–1214.
symmetry and is expected to exhibit distinct shielding of nuclei, Conformational analysis of 1 and its anion
imposed by the orientations of H6 and H1 protons in the two complexes by quantum mechanics calculations
indole rings with respect to the carbonyl group. However, the The observations on the conformational equilibria in the
populations of the two distinct conformational families are aver- absence and in the presence of anions were corroborated by
aged on the NMR time scale.
quantum mechanical calculations at the B3LYP/6-311+G(d,p)
level of theory by means of the Gaussian 03 [40] and Gaussian
Only minor changes in the NOE enhancements were observed 09 [41] programs. Indole rings represent the rigid part of the
upon addition of chloride anions to 1. The strongest NOE was anion receptors, while the substituents on the ureido moiety in 1
observed between H7α and H6 (9.9%), which was of compa- exhibit conformational freedom. [C6–C7–N7α–C7β] torsion
rable magnitude to the NOE between the same protons in the angles were defined to follow energetic changes induced by
absence of anions (Table 3). On the other hand, stronger NOE reorientation of the indolyl moieties along the C7–N7α bonds.
enhancement between H7α and H1 (7.0%) suggested predomi- The energy surface for the [C6–C7–N7α–C7β] torsion angles,
nance of the syn–anti rotamer of 1 in the presence of chloride with 30° resolution, shows that the conformer with the lowest
anions in DMSO-d6 solution. Interestingly, the syn–syn rotamer energy is in the anti–anti region (Figure 5).
was observed in the crystal structure, where conformational
preferences are dictated by other forces, such as crystal packing.
These observations are in agreement with minute 1H chemical
shift changes and the weak stability constant of 1 for the
binding of chloride anions.
Table 3: Selected NOE enhancements for 1 in the absence and in the
presence of different anions (in %).
Saturated:
Enhanced:
H1
H6
H7α
H7α
H7α
H1
H6
no anion
Cl–
3.2
4.2
7.2
7.2
–a
3.8
2.2
1.0
0.9
0.0
0.0
4.3
7.0
10.4
9.9
4.8
4.8
4.7
2.8
AcO–
12.0
10.4
–a
BzO–
HCO3–
H2PO4–
4.2
5.3
aBroad NH signals in the baseline.
Figure 5: Surface plot of the relative potential energy of 1 as a func-
tion of the two constitutive [C6–C7–N7α–C7β] torsion angles. Indi-
vidual geometries were optimized at the B3LYP/6-311+G(d,p) level of
theory at 30° resolution.
Considerable changes in the NOE enhancements were observed
upon addition of acetate anions to 1. The saturation of H7α
resulted in a much stronger NOE at H1 (12.0%) with respect to
H6 (4.8%), which suggested that addition of acetate anions led
to conformational changes along the C7–N7α bond (Table 3).
The syn–syn conformer is preferred for the 1·AcO− complex in
solution (Figure 4b). In a similar manner, significant changes in
the NOEs were observed upon addition of benzoate anions. The
saturation of H7α gave much stronger NOE at H1 (10.4%) with
respect to H6 (4.8%, Table 3). Broad NH proton signals
prevented the study of the conformation of the 1·HCO3− com-
plex through NOE experiments. NOE enhancements between
H1 and H7α (4.2–5.3%) were considerably stronger with
respect to NOE between H7α and H6 (0–2.8%) upon addition of
dihydrogen phosphate to 1. The observed NOE enhancements
for 1·H2PO4− complex suggest a preference for the syn–syn
conformer in DMSO-d6.
Energy minimization of the anti–anti conformer of 1 was
performed without any constraints, whereas syn orientations in
the syn–anti as well as the syn–syn cases were restrained along
the [C6–C7–N7α–C7β] torsion angle, while other degrees of
freedom were freely optimized. The relative energies for the
three representative conformers are reported in Table 4. The
anti–anti conformer of 1 was found to be the lowest in energy,
while the syn–syn conformer showed considerably higher
energy (11.6 kcal·mol−1). The angle between the two indolyl
rings in the freely optimized anti–anti conformer was 53.9°
(Figure 6a). The relative energies of the three representative
conformers were also computed for complexes of 1 with chlo-
ride, acetate and bicarbonate anions. The syn–syn conformer
exhibited the lowest relative energy for all three anion–receptor
1209

Beilstein J. Org. Chem. 2011, 7, 1205–1214.
Figure 6: Freely optimized structure at the B3LYP/6-311+G(d,p) level of theory and side view showing deviation from coplanarity defined by the angle
between the indolyl rings of receptor 1 in the absence of anions (a) and for the 1·AcO− complex (b).
complexes (Table 4). The anti–anti conformers of of Tomasi's polarized continuum model [42,43]. Preferences
anion–receptor complexes exhibited considerably higher ener- amongst the three rotamers were retained (Table 4). Only small
gies between 6.2 and 7.3 kcal·mol−1. The angle between the two differences below 1.2 kcal·mol−1 were found between the three
indolyl rings in the freely optimized syn–syn conformer of the distinct conformers in the case of the 1·Cl− complex. In particu-
1·AcO− complex was found to be 21.6° (Figure 6b). The opti- lar, the negligible energy differences between syn–syn and
mized structure, shown in Figure 6b, shows a single acetate syn–anti rotamers are in agreement with the NOE data that
anion bound to the four NH groups in the receptor 1 with N···O suggested predominance of the syn–anti conformer upon ad-
distances in the range from 2.75 to 2.95 Å and N–H···O angles dition of chloride. The energetic preference of the syn–syn over
in the range 170–176°.
the anti–anti conformer of 3.8 and 3.0 kcal·mol−1 was observed
for the 1·AcO− and the 1·HCO3− complexes, respectively
(Table 4). The energetic preferences of the 1·AcO–complex are
in excellent agreement with the NOE experiments, which
showed conformational reorganizations of 1 upon addition of
acetate anions.
Table 4: Relative energiesa (in kcal·mol−1) of receptor 1 in vacuo and
in DMSO, in the absence and in the presence of anions.
anion
conformer
in vacuo
in DMSO
anti–anti
syn–anti
syn–syn
0.00
5.09
11.61
0.00
2.74
6.60
Conformational features of receptors 2–4
no anion
The choice of thio (2 and 4) versus oxo (1 and 3) ureido func-
tionalities, as well as the C2 functionalization of the indole scaf-
folds with pendant phenyl amides in 3 and 4, allows tuning of
the binding affinities of the receptors. Negligible Δδ values
were observed for 2 upon interaction with chloride anions
(Figure 7a), which suggests a very weak interaction between
chloride and 2, similar to the weak interactions observed
between chloride and 1. Chemical shift changes showed that the
main interaction between receptor 2 and trigonal planar anions
(acetate, benzoate and bicarbonate) occurred at the H7α protons
(Figure 7a). Addition of dihydrogen phosphate anions caused
considerable deshielding of the H1 and H7α protons. Compari-
son of the Δδ values for 1 and 2 upon interaction with the
anions showed that the urea derivative 1 exhibited a higher pref-
erence for anion binding relative to thiourea 2 (the data were
supported by the stability constant determinations performed
previously and shown in Table 1). The larger sulfur atom can
anti–anti
syn–anti
syn–syn
6.50
1.84
0.00
1.20
0.12
0.00
Cl−
anti–anti
syn–anti
syn–syn
7.26
2.82
0.00
3.75
1.74
0.00
AcO−
HCO3−
anti–anti
syn–anti
syn–syn
6.21
2.02
0.00
2.97
1.31
0.00
aRelative energies are reported with respect to the lowest energy (arbi-
trarily set to 0.00 kcal/mol) in the absence and in the presence of
anions. Geometry optimizations were carried out at B3LYP/6-
311+G(d,p).
In order to evaluate the role of DMSO on the energetic prefer- prevent the receptor 2 from adopting a planar conformation,
ences of rotamers, relative energies were calculated with the use which may reduce the affinity of this receptor for anionic
1210

Beilstein J. Org. Chem. 2011, 7, 1205–1214.
guests. Conformational studies of 2 with the use of NOE
enhancements showed that the anti–anti conformer is the
preferred conformation in the absence of anions. No apparent
conformational changes were observed upon addition of chlo-
ride anions to 2. The overlap of the proton signals as well as the
broad line-width of the H1 and H7α NMR resonances prevented
conformational analysis of 2 upon addition of other anions used
in the study. The conformational preferences of 2 were evalu-
ated by quantum mechanical calculations at the B3LYP/6-
311+G(d,p) level of theory. The freely optimized anti–anti
conformer of 2 exhibited the lowest energy and the syn–syn
conformer was 8.0 kcal·mol−1 higher in energy, in vacuo. Inter-
estingly, the two indolyl rings were not coplanar, with the angle
between the two indolyl planes found to be 98.9° (Figure 8a). In
the case of 2·AcO− complex the syn–syn conformer exhibited
the lowest energy, while the anti–anti conformer was
7.4 kcal·mol−1 higher in energy, in vacuo. The optimized struc-
ture of 2·AcO− complex is shown in Figure 8b, where the two
acetate oxygen atoms are hydrogen bonded to the four NH
groups, with N···O distances in the range from 2.76 to 2.94 Å
and N–H···O angles in the range 168–177°. The angle between
the indolyl rings in the freely optimized syn–syn conformer of
the 2·AcO− complex was 68.0°.
Bis-amide functionalized diindolylurea 3 exhibits two extra NH
groups, which introduces additional possibilities for interac-
tions with anions. The addition of chloride anions to 3 induced
negligible chemical shifts, suggesting only weak interactions
with this anion (Figure 7b). The strong deshielding of H7α and
moderate deshielding of H1 protons in the 3·AcO− and 3·BzO−
complexes suggests a significant interaction between the anions
and the ureido functionality. Interestingly, negligible
deshielding of H2β in 3 was observed and this suggests that the
amide protons do not participate in the interaction with acetate
Figure 7: 1H NMR chemical shift changes, Δδ = δ (in the presence of
anions) – δ (in the absence of anions), induced by addition of one
equivalent of different anions to receptors 2 (a), 3 (b) and 4 (c). Note,
there is no H2β proton in 2.
Figure 8: Freely optimized structures at the B3LYP/6-311+G(d,p) level of theory and side view showing deviation from coplanarity defined by the
angle between the indolyl rings of 2 (a) and 2·AcO− complex (b).
1211

Beilstein J. Org. Chem. 2011, 7, 1205–1214.
and benzoate (Figure 7b). The observed Δδ values support the (Figure 7c). The conformational properties of the 4·AcO– and
idea that carboxylates were strongly bound to the urea H7α 4·BzO– complexes could not be determined due to the broad
protons which prevented interaction between the anions and the and overlapped proton signals. Unfortunately, excessively broad
amide H2β protons. Analogously, large chemical shift changes and overlapped 1H signals for the 4·HCO3− and 4·H2PO4−
of up to 1 ppm were observed for the H7α and H1 protons upon complexes prevented unambiguous assignment of the NMR
the addition of bicarbonate anions to 3. Strong deshielding of resonances and hence the conformational studies of these
H1, H2β and H7α protons in the 3·H2PO4− complex suggests complexes. In the solid state compound 4 crystallized with
that all the NH donor groups are involved in interactions with tetrabutylammonium dihydrogen phosphate as the monohy-
the dihydrogen phosphate anions (Figure 7b).
drogen phosphate complex (see Supporting Information File 2
for more details).
The conformational properties of 3 and of its complexes with
different anions were studied by NOE measurements. The satu- Conclusion
ration of the H1 protons resulted in moderately negative NOEs The bis-indole receptors 1–4 were characterized by heteronu-
at the H7α and H2β protons. The cross peaks in the 2D NOESY clear NMR spectroscopy. NOE based conformational analysis
spectra between the NH protons and bulk water suggest chem- was supported by quantum mechanics calculations and revealed
ical exchange that complicated the conformational study along that diindolylurea 1 exhibited conformational preorganization in
the C2–C2α and C7–N7α bonds. Nevertheless, strong NOE DMSO-d6 solution. The anti–anti conformer, which could be
enhancements between the H2β and H3 protons suggest an stabilized by intramolecular hydrogen bonds between the C7β
orientation along the C2–C2α bond where the H2β and H3 carbonyl group and indole NH proton, was predominant for 1 in
protons are spatially close and the C2α carbonyl group is the absence of anions. The energetically minimized structure of
oriented towards the indole H1 proton. NOE enhancements anti–anti conformer showed a plane of symmetry along the
between H2β and H3 protons were observed also in the 3·AcO− ureido carbonyl group and deviation from coplanarity amongst
and 3·BzO− complexes, which suggests that the orientation of the indolyl rings. Anion-induced chemical shift changes
the carboxamide group along the C2–C2α bond is retained in 3 suggested weak binding of chloride anions and negligible con-
upon addition of carboxylate anions. This observation was formational changes for 1. Addition of acetate, benzoate, bicar-
supported by negligible Δδ values for the H2β protons in the bonate and dihydrogen phosphate resulted in strong deshielding
3·AcO− and 3·BzO− complexes with respect to 3. The con- of the ureido protons and moderate deshielding of the indole
formational preferences and the proposed binding mode in the H1, which indicated that the main hydrogen bond interaction
3·AcO− complex are shown in Figure 9. A conformational study occurred at the urea donor groups of 1. Furthermore, binding of
of 3 in the presence of bicarbonate and dihydrogen phosphate anions caused conformational changes along the C7–N7α
anions was hindered by the broadened and overlapped 1H bonds, and the syn–syn conformer was predominant in the
signals. In the solid state compound 3 crystallized with tetra- anion–receptor complexes according to both NOE enhance-
butylammonium dihydrogen phosphate as the monohydrogen ments and ab initio calculations in solution. The freely opti-
phosphate complex [38].
mized syn–syn conformer of the 1·AcO− complex retained a
plane of symmetry along the carbonyl bond and showed a
smaller deviation from indole ring coplanarity than did the
anti–anti conformer of 1. The conformational preferences for 2
were analogous to those observed for receptor 1. Unfortunately,
excessively broad and overlapped 1H signals prevented a
detailed conformational analysis of the anion–receptor
complexes for 3 and 4.
Experimental
NMR experiments
Figure 9: Conformational preferences and proposed binding mode for
the 3·AcO− 1:1 complex.
1H, 13C and 15N NMR spectra were acquired on a Varian Unity
Inova 300 MHz NMR spectrometer. All data were recorded in
Only negligible chemical shifts were observed for 4 upon ad- DMSO-d6 at 298 K. Chemical shifts were referenced to the
dition of chloride anions (Figure 7c). Considerable deshielding residual solvent signal of DMSO-d6 at δ 2.50 ppm for 1H
of H7α protons in 4 by up to 2.3 ppm in the 4·AcO− and 4·BzO− (297.801 MHz) and δ 39.50 ppm for 13C (76.190 MHz), while
complexes suggested that the major interactions between 15N (30.188 MHz) chemical shifts were referenced relative to
carboxylates and receptor 4 occurred at the ureido functionality external benzamide (δ 103.55 ppm). Individual resonances were
1212

Beilstein J. Org. Chem. 2011, 7, 1205–1214.
assigned on the basis of their chemical shifts, signal intensities, Acknowledgements
multiplicity of resonances, H–H coupling constants as well as We gratefully acknowledge the financial support of the
by means of a series of 2D NMR experiments (COSY, gHSQC Slovenian Research Agency (ARRS, program no. P1-0242),
and gHMBC). The saturation delay in the 1D difference NOE COST D-31, EAST-NMR (grant no. 228461) and Bio-NMR
experiment was 5.0 s. All anions were added as tetrabutylam- (grant no. 261863) FP7 projects. PAG thanks the EPSRC for
monium salts except bicarbonate which was added as a support and the access to the crystallographic facilities at the
tetraethylammonium salt. NOESY spectra were acquired with University of Southampton.
mixing time of 100 and 300 ms.
References
1. Bianchi, A.; Bowman-James, K.; García-España, E., Eds.
Ab initio calculations
Initial structures were generated by Chem3D Pro 10.0 software
Supramolecular Chemistry of Anions; Wiley-VCH: New York, 1997.
2. Schmidtchen, F. P.; Berger, M. Chem. Rev. 1997, 97, 1609.
and energy minimization at the B3LYP/6-311+G(d,p) level was
doi:10.1021/cr9603845
performed for 1 and 2 without any constraints for the anti–anti
3. Beer, P. D. Acc. Chem. Res. 1998, 31, 71. doi:10.1021/ar9601555
conformers, by means of Gaussian 03 [40] and Gaussian 09
4. Kavallieratos, K.; Bertao, C. M.; Crabtree, R. H. J. Org. Chem. 1999,
[41]. Syn orientations in the syn–anti as well as the syn–syn
conformers of 1 and 2 were restrained along the
[C6–C7–N7α–C7β] torsion angle while other degrees of
freedom were freely optimized. Ab initio calculations of
anion–receptor complexes were carried out without any
constraints for the syn–syn conformers, where anions were
placed initially at the expected equilibrium distance to the H1
and H7α protons. The positions of the anions were freely opti-
mized. Energy minimizations of the syn–anti and anti–anti
conformers of the anion–receptor complexes were restrained
along the [C6–C7–N7α–C7β] torsion angle while other degrees
of freedom were freely optimized. The tetrabutylammonium
countercation was omitted in the geometry optimization of the
anion–receptor complexes. Frequency calculations verified that
the optimized geometries were stable points on the potential
energy surface. Relative energies in solution were calculated by
means of Tomasi's polarized continuum model, where the
dielectric constant of DMSO was used (ε = 46.7).
64, 1675. doi:10.1021/jo982382l
5. Beer, P. D.; Gale, P. A. Angew. Chem., Int. Ed. 2001, 40, 486.
doi:10.1002/1521-3773(20010202)40:3<486::AID-ANIE486>3.0.CO;2-
P
6. Wiskur, S. L.; Ait-Haddou, H.; Lavigne, J. J.; Anslyn, E. V.
Acc. Chem. Res. 2001, 34, 963. doi:10.1021/ar9600796
7. Vilar, R. Angew. Chem., Int. Ed. 2003, 42, 1460.
doi:10.1002/anie.200200551
8. Bowman-James, K. Acc. Chem. Res. 2005, 38, 671.
doi:10.1021/ar040071t
9. Gale, P. A. Acc. Chem. Res. 2006, 39, 465. doi:10.1021/ar040237q
10.Sessler, J. L.; Gale, P. A.; Cho, W. S. Anion Receptor Chemistry; Royal
Society of Chemistry: Cambridge, 2006.
11.Albrecht, M. Naturwissenschaften 2007, 94, 951.
doi:10.1007/s00114-007-0282-7
12.Lankshear, M. D.; Beer, P. D. Acc. Chem. Res. 2007, 40, 657.
doi:10.1021/ar7000217
13.Vilar, R. Eur. J. Inorg. Chem. 2008, 357. doi:10.1002/ejic.200701017
14.Pflugrath, J. W.; Quiocho, F. A. Nature 1985, 314, 257.
doi:10.1038/314257a0
15.Luecke, H.; Quiocho, F. A. Nature 1990, 347, 402.
doi:10.1038/347402a0
16.Bondy, C. R.; Loeb, S. J. Coord. Chem. Rev. 2003, 240, 77.
doi:10.1016/S0010-8545(02)00304-1
Supporting Information
17.Gómez, D. E.; Fabbrizzi, L.; Licchelli, M.; Monzani, E.
Org. Biomol. Chem. 2005, 3, 1495. doi:10.1039/b500123d
18.Kang, S. O.; Begum, R. A.; Bowman-James, K. Angew. Chem., Int. Ed.
2006, 45, 7882. doi:10.1002/anie.200602006
Supporting Information File 1
Experimental for the synthesis of compound 4 and details
of the crystal structure of the HPO42− complex of 4, 1H and
13C NMR data for 1–4, 1D difference NOE spectra for 1 in
the absence and upon addition of one equivalent of acetate
anions.
19.Gale, P. A.; García-Garrido, S. E.; Garric, J. Chem. Soc. Rev. 2008,
37, 151. doi:10.1039/b715825d
20.Caltagirone, C.; Gale, P. A. Chem. Soc. Rev. 2009, 38, 520.
doi:10.1039/b806422a
21.Gale, P. A. Chem. Commun. 2005, 3761. doi:10.1039/b504596g
22.Gale, P. A. Chem. Soc. Rev. 2010, 39, 3746. doi:10.1039/c001871f
23.Gale, P. A. Chem. Commun. 2011, 47, 82. doi:10.1039/c0cc00656d
24.Chmielewski, M. J.; Charon, M.; Jurczak, J. Org. Lett. 2004, 6, 3501.
doi:10.1021/ol048661e
[http://www.beilstein-journals.org/bjoc/content/
supplementary/1860-5397-7-140-S1.pdf]
Supporting Information File 2
Crystallographic data of the complex of compound 4 with
tetrabutylammonium dihydrogen phosphate
(4·TBA2·HPO4).
25.Piatek, P.; Lynch, V. M.; Sessler, J. L. J. Am. Chem. Soc. 2004, 126,
16073. doi:10.1021/ja045218q
26.Chang, K.-J.; Moon, D.; Lah, M. S.; Jeong, K.-S.
Angew. Chem., Int. Ed. 2005, 44, 7926. doi:10.1002/anie.200503121
27.Curiel, D.; Cowley, A.; Beer, P. D. Chem. Commun. 2005, 236.
doi:10.1039/b412363h
[http://www.beilstein-journals.org/bjoc/content/
supplementary/1860-5397-7-140-S2.cif]
1213

Beilstein J. Org. Chem. 2011, 7, 1205–1214.
28.Pfeffer, F. M.; Lim, K. F.; Sedgwick, K. J. Org. Biomol. Chem. 2007, 5,
1795. doi:10.1039/b702804k
29.Chmielewski, M. J.; Zhao, L. Y.; Brown, A.; Curiel, D.;
Sambrook, M. R.; Thompson, A. L.; Santos, S. M.; Felix, V.;
Davis, J. J.; Beer, P. D. Chem. Commun. 2008, 3154.
doi:10.1039/b804941f
30.Suk, J.-m.; Chae, M. K.; Kim, N.-K.; Kim, U.-I.; Jeong, K.-S.
Pure Appl. Chem. 2008, 80, 599. doi:10.1351/pac200880030599
31.Zhao, L.; Mullen, K. M.; Chmielewski, M. J.; Brown, A.; Bampos, N.;
Beer, P. D.; Davis, J. J. New J. Chem. 2009, 33, 760.
doi:10.1039/b818854h
32.Verschueren, K. H. G.; Seljée, F.; Rozeboom, H. J.; Kalk, K. H.;
Dijkstra, B. W. Nature 1993, 363, 693. doi:10.1038/363693a0
33.Makuc, D.; Lenarčič, M.; Bates, G. W.; Gale, P. A.; Plavec, J.
Org. Biomol. Chem. 2009, 7, 3505. doi:10.1039/b908947k
34.Makuc, D.; Triyanti; Albrecht, M.; Plavec, J.; Rissanen, K.;
Valkonen, A.; Schalley, C. A. Eur. J. Org. Chem. 2009, 2009, 4854.
doi:10.1002/ejoc.200900721
35.Makuc, D.; Albrecht, M.; Plavec, J. Supramol. Chem. 2010, 22, 603.
doi:10.1080/10610278.2010.506544
36.Caltagirone, C.; Gale, P. A.; Hiscock, J. R.; Brooks, S. J.;
Hursthouse, M. B.; Light, M. E. Chem. Commun. 2008, 3007.
doi:10.1039/b806238b
37.Caltagirone, C.; Hiscock, J. R.; Hursthouse, M. B.; Light, M. E.;
Gale, P. A. Chem.–Eur. J. 2008, 14, 10236.
doi:10.1002/chem.200801639
38.Gale, P. A.; Hiscock, J. R.; Moore, S. J.; Caltagirone, C.;
Hursthouse, M. B.; Light, M. E. Chem.–Asian J. 2010, 5, 555.
doi:10.1002/asia.200900230
39.Gale, P. A.; Hiscock, J. R.; Jie, C. Z.; Hursthouse, M. B.; Light, M. E.
Chem. Sci. 2010, 1, 215. doi:10.1039/c0sc00202j
40.Gaussian 03, Revision B.3; Gaussian, Inc.: Pittsburgh PA, 2004.
41.Gaussian 09, Revision A.5; Gaussian, Inc.: Wallingford CT, 2009.
42.Miertus, S.; Scrocco, E.; Tomasi, J. Chem. Phys. 1981, 55, 117.
doi:10.1016/0301-0104(81)85090-2
43.Miertus, S.; Tomasi, J. Chem. Phys. 1982, 65, 239.
doi:10.1016/0301-0104(82)85072-6
License and Terms
This is an Open Access article under the terms of the
Creative Commons Attribution License
(http://creativecommons.org/licenses/by/2.0), which
permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.
The license is subject to the Beilstein Journal of Organic
Chemistry terms and conditions:
(http://www.beilstein-journals.org/bjoc)
The definitive version of this article is the electronic one
which can be found at:
doi:10.3762/bjoc.7.140
1214