Templating irreversible covalent macrocyclization by using anions

Article abstract of DOI:10.1002/chem.201204306

Inorganic anions were used as templates in the reaction between a diamine and an activated diacid to form macrocyclic amides. The reaction conditions were found to perform the macrocyclization sufficiently slow to observe a template effect. A number of analytical methods were used to clarify the reaction mechanisms and to show that the structure of the intermediate plays a decisive role in determining the product distribution. For the macrocyclization under kinetic control, it was shown that the amount of a template, the conformational rigidity of building blocks, and the anion affinities of reaction components and intermediates are important parameters that one should take into consideration to achieve high yields. Copyright

Full text of DOI:10.1002/chem.201204306

DOI: 10.1002/chem.201204306
Templating Irreversible Covalent Macrocyclization by Using Anions
Evgeny A. Kataev,*[a] Grigory V. Kolesnikov,[b] Rene Arnold,[a] Herman V. Lavrov,[b] and
Victor N. Khrustalev[b]
Abstract: Inorganic anions were used
as templates in the reaction between a
diamine and an activated diacid to
form macrocyclic amides. The reaction
conditions were found to perform the
macrocyclization sufficiently slow to
observe a template effect. A number of
analytical methods were used to clarify
the reaction mechanisms and to show
that the structure of the intermediate
plays a decisive role in determining the
product distribution. For the macrocyc-
lization under kinetic control, it was
shown that the amount of a template,
the conformational rigidity of building
blocks, and the anion affinities of reac-
tion components and intermediates are
important parameters that one should
take into consideration to achieve high
yields.
Keywords: anions · macrocycles ·
peptides · self-assembly · template
synthesis
Introduction
mation of peptide bonds in the synthesis of cyclic peptides
and search for new artificial receptors and catalysts.[4]
Template synthesis in organic chemistry has attracted con-
siderable attention in recent years, since it has opened
access to large molecules and multicomponent one-pot syn-
thesis.[1] In nature, the use of templates is a major tool in the
transfer of information, for example, in DNA replication,
enzyme synthesis, and signal transduction, whereby recogni-
tion often occurs through hydrogen bonds. Anions are
known to form strong hydrogen bonds and they have often
Macrocyclization through irreversible covalent bonds was
initially used by Shur et al.[5] and Hawthorne et al.,[6] who
discovered the anion template effect. Although some prog-
ress on irreversible macrocyclization from preorganized
building blocks[7] and with the help of templates has been
made,[8] this type of macrocyclization is still rarely used be-
cause of low yields and complications in controlling the re-
action. There are only a few literature examples that deal
with the anion-templated macrocyclization through irrever-
sible bonds; they are the reactions of amines with alkyl
halides[9] or isocyanates.[10] To the best of our knowledge,
there is no literature precedent of templated macrocycliza-
tion through amide bonds in which different anions amplify
different products. Our recent attempt to treat diamines
with acid dichlorides in the presence of a template was not
successful because the reaction was too fast and the elimi-
nating chloride anion itself functioned as a template.[11]
Herein, we present the macrocyclization of a diamine
with activated diacids under mild conditions and a detailed
study of the template effect induced by inorganic anions.
We show that the amount of a template, the conformational
rigidity of building blocks, the anion affinities of compo-
nents, and the intermediates of the reaction are important
parameters that influence the product distribution. NMR
spectroscopy, ESI-MS, and fluorescence measurements pro-
vided a mechanistic insight into the anion-templated macro-
cyclization through amide bonds.
been used as templates in self-assembly reactions.[2]
A
number of effective and selective receptors have been gen-
erated using dynamic covalent chemistry. Mainly, reversible
covalent bonds have been employed to connect building
blocks in the presence of anionic, neutral, and cationic spe-
cies.[3] However, the use of irreversible bonds in the synthe-
sis of artificial receptors is scarce. If one could control the
synthesis of receptors through irreversible covalent bonds,
this would give access to chemically and kinetically stable
structures such as proteins. It is well known that proteins
are only active when in a certain kinetically stabilized con-
formation. Thus, it is of particular interest to control the for-
[a] Prof. E. A. Kataev, R. Arnold
Institut fꢀr Chemie, Technische Universitꢁt Chemnitz
Strasse der Nationen, 62, 09111 Chemnitz (Germany)
Fax : (+49)371-531-839841
E-mail: evgeny.kataev@chemie.tu-chemnitz.de
[b] Dr. G. V. Kolesnikov, H. V. Lavrov, Prof. V. N. Khrustalev
A. N. Nesmeyanov Institute of Organoelement Compounds
Russian Academy of Sciences, Vavilov St., 28
Results and Discussion
Moscow, 119991 (Russian Federation)
Supporting information for this article contains synthetic and charac-
terization details of compounds, as well as kinetic experiments and
calculations, and is available on the WWW under http://dx.doi.org/
10.1002/chem.201204306.
Diamine 1 and diacid 2 were chosen to study a macrocycli-
zation reaction in the presence of an anion as a template.
The building blocks react to form a mixture of macrocyclic
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FULL PAPER
oligomers of different sizes. In contrast to our previous
work, in which aromatic amines were used, diamine 1 bears
two aliphatic amino groups to mimic natural aminoacids.
Additionally, the bipyrrole-based diamine is able to bind
anions. Chloroform and dichloromethane were used as sol-
vents in coupling reactions because these aprotic solvents
have low solvation energies and facilitate the formation of
tight host–anion complexes even with rather hydrophobic
anions such as nitrate and iodide. Thus, it was expected that
we would observe a template effect for anions of different
nature and form.
presence of tetrabutylammonium chloride (1.5 equiv) turned
the reaction toward a [1+1] product. Thus, it was concluded
that there is the anion-template effect in the system. The re-
action was screened by using the following templates: ClÀ,
À
À
À
BrÀ, IÀ, CH3COOÀ, HSO4 , H2PO4 , and NO3 . Analysis of
product distributions was performed by using LC-ESI-MS
with a UV/Visible detector at 320 nm in the presence of a
reference.
Inspection of Table 1 reveals that the best templates are
chloride, acetate, hydrogen sulfate, and dihydrogen phos-
phate. They amplify the [1+1] product with a yield up to
The important part of the first screening experi-
ments was to search for coupling reactions that take
place in chloroform and are relatively slow to allow
the interaction between the reaction components
Table 1. Yields of major macrocyclization products determined by LC-ESI-MS analy-
sis with UV/Visible detector (320 nm: absorption of the bipyrrole core) with various
template anions and without a template.[a]
Yield[b] [%]
HSO4
and a template. Standard peptide coupling condi-
tions, including activating reagents for acids like di- Product Without template H2PO4
À
À
À
OAcÀ ClÀ
BrÀ IÀ
7.5 0.6
NO3
2.9
cyclohexyl carbodiimide (DCC), 1-ethyl-3-(3-di-
methylaminopropyl) carbodiimide (EDC), 1-hy-
R
11.7
20.2
4.3
55.0
5.4
0.7
34.0
0.6
0.1
0
63.8
11.9
1.6
47.8
E
11.7 20.0 21.3 20.0
1.5
0.2
A
ACHTUNGTRENNUNG
N
3.0
0.4
4.0
0.9
4.4
0.9
droxybenzotriazole (HOBt), and O-(benzotriazol-1-
yl)-N,N,N’,N’-tetramethyluronium hexafluorophos-
phate (HBTU) were not efficient because either
only a [1+1] macrocycle was formed or a polymer
was formed. By applying diacid dichloride 3 to the
G
0.9
0.1
0.4
[a] The reaction was carried out in CHCl3 by mixing 1, 4, and a template in chloro-
form for 12 h; [1]=[4]=0.01m, [tetrabutylammonium salt]=0.015m. [b] Yields were
determined from integration of peak areas by using absorption coefficients of products
and internal reference: ethyl 2-(7-methoxy-2-oxo-2H-chromen-4-yl)acetate (error
macrocyclization reaction in THF or dichloro
ane, we observed the formation of a [1+1] product
in 60% yield. The addition of a template (tetrabu-
ACHTUNGTRENUNmNG eth- 0.5%).
ACHTUNGTRENNUNG
tylammonium salts) in both cases did not influence the
product distribution according to the data obtained from
liquid chromatography coupled with electrospray mass de-
tection (LC-ESI-MS). The series of anions were also tested
to template the macrocyclization reaction (Figure 1) be-
tween 1 and 2-mercaptothiazoline derivative 4, and only in
this case different distributions of products for each anion
were observed. Surprisingly, the reaction without a template
led to [2+2] macrocycle as a major product; however, the
64%. Bromide and nitrate did not have a remarkable influ-
ence on the reaction, although iodide shifts the product dis-
tribution towards the formation of [2+2] and [3+3] prod-
ucts; the yield of the [1+1] product is almost negligible in
this case.
Attempts to grow crystals from isolated [1+1] and [2+2]
products were successful only for the [2+2] macrocycle. The
structure of the cyclic product is rather unusual owing to the
presence of a network of intramolecular hydrogen bonds
Figure 1. Suggested reaction pathways explaining the template effect.
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3711

E. A. Kataev et al.
tate, and chloride. However, there is no agreement between
the good affinities of the [1+1] macrocyclization product for
bromide and iodide and their template effects.
UV/Visible titrations revealed that the diamine self-aggre-
gates in solution, and this fact could be also the reason for
the formation of a [2+2] product in the absence of a tem-
plate. Since the bipyrrole unit emits light around 425 nm
under excitation at 390 nm, we followed fluorescence
changes upon dilution of the diamine. The data obtained
was fitted to the dimerization process with constants logK=
4.83(2) and logK=3.10(1) in CHCl3 and DMSO, respective-
ly. According to the mass spectra, the diamine can even
form trimer, tetramer, and pentamer aggregates in chloro-
form (see the Supporting Information). All these facts led
us to the conclusion that the diamine is prone to form aggre-
gates even in rather polar organic solvents such as DMSO.
Because it was not possible to grow suitable crystals from
diamine 1, we carried out DFT modeling[14] to understand
possible ways of dimerization. The optimized dimer is
formed by a pair of NHACTHNUTRGENN(UG pyrrole)···OAHCTUNGTRNEN(UGN amide) hydrogen
bonds similar to those observed in the secondary structure
of peptides (Figure 3). We also hypothesized that free pyr-
role rings could be the connection points for further aggre-
gations (shown as arrows). Of particular interest in this
structure is the distance between the amino residues, which
is rather long (ca. 11 ꢃ), and could be one of the possible
reasons for the formation of the [2+2] product in the ab-
sence of a template.
Figure 2. Molecular structure of the [2+2] product showing intramolecu-
lar hydrogen bonds according to the X-ray analysis. Most of the hydrogen
atoms and solvent molecules are omitted for clarity.[15]
(Figure 2). The amido group (O2) that belongs to the pyri-
dine core is involved in the formation of hydrogen bonds
with bipyrrole NH donors (N1, N3, and N14). The bipyrrole
amido group (O4) forms in return a hydrogen bond with the
pyridine NH donor (N4). Thus, the overall structure of the
[2+2] product is rigidified.
To gain insight into the structural and mechanistic factors
that may be at play in the anion-templated reaction, we fol-
lowed the macrocyclization process more closely. There
could be several reasons for the template effect: a relation-
ship between anion affinities of the diamine and the prod-
ucts, particularities of the structure of the diamine in solu-
tion, or structures of intermediates. In anion-templated reac-
tions, in which building blocks react with each other through
reversible covalent bonds, macrocyclization is controlled by
the thermodynamic stability of the formed host–anion com-
plex. Thus, the outcome of the macrocyclization reaction
can be proposed on the basis of
Figure 3. Optimized geometry of the dimer formed from diamine 1. Hy-
drogen atoms are omitted for clarity. Arrows show the direction of fur-
ther aggregation to form a trimer or tetramer.
In irreversible and kinetically controlled reactions, the
product distribution is controlled by the stability of reaction
intermediates.[13] Thus, structures of intermediates formed in
the absence and in the presence of a template could be dif-
ferent. This idea becomes evident after careful analysis of
the X-ray structure of the [2+2] product, which contains an
anion affinities of products. To
Table 2. Binding constants logK11 and logK12 (where appropriate) of macrocyclization products and diamine 1
for anions determined in dichloroethane (2% methanol) at 238C.
find any relationship between
anion affinities of starting mate-
rial and products, we conducted
binding studies by using UV/
Visible titrations. Analysis of
Table 2 reveals that all the com-
pounds have excellent affinities
À
À
À
H2PO4
HSO4
OAcÀ
6.44(3) (1:1)
3.36(4) (1:2)
>6[a]
11.14(3) (1:2)
ClÀ
BrÀ
IÀ
NO3
U
>6
4.44(1)
>6
4.50(1)
4.34(1)
4.30(1)
[b]
N
>6[a]
>6[a]
4.76(1)
11.34(10) (1:2)
4.56(1)
9.68(1) (1:2)
n.d.[c]
n.d.[c]
n.d.[c]
1
>6
n.d.[c]
[a] 1:1 and 1:2 simultaneous binding events were observed. [b] Calculations were not possible owing to the low
for dihydrogen phosphate, ace- affinity and iodide absorption. [c] Binding was not detected.
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Irreversible Covalent Macrocyclization
FULL PAPER
intramolecular hydrogen-bond network. We hypothesized
that the formation of the [2+2] product proceeds through
intermediate INT1 and the formation of the [1+1] product
proceeds through intermediate INT2 (Figure 1). INT1 has
the same intramolecular hydrogen-bond network as that
found in the structure of the [2+2] product. This network
makes the structure of INT1 very rigid and places the amino
group and the activated ester far away from each other. The
rigidity of the structure hinders further coupling to a [1+1]
product. In contrast, the presence of a template turns the
pyridine ring around so that the cyclization to a [1+1] prod-
uct is sterically favorable. Density functional theory (DFT)
modeling of both structures of the intermediates showed
that the presence of the hydrogen-bond network as ob-
served in the [2+2] product is sterically allowed and ener-
getically favorable (see the Supporting Information).
To provide experimental evidence for the existence of the
intermediates, we investigated the reaction using fluores-
cence. The fluorescence intensity of the bipyrrole subunit is
dependent on its structural rigidity. The intermediates are
more rigid structures than the diamine, and hence their
emission intensity should be higher than that of the diamine.
The online monitoring of the fluorescence emission of the
reaction between 1 and 4 indeed showed nonlinear changes
over a duration of 15 min. Moreover, it was found that the
amount of tetrabutylammonium chloride had a significant
influence on the reaction rate. After approximately 200 s,
the fluorescence of the reaction mixture reaches its maxi-
mum and then slowly goes down (Figure 4). This observa-
tion was interpreted as an indication of the existence of in-
termediate INT1. Performing the reaction with different
amounts of tetrabutylammonium chloride as a template (1,
5, and 10 equiv) led to an increase of the fluorescence, thus
indicating the accumulation of intermediate INT2. However,
10 equiv of the template was not enough to identify the in-
termediate with the help of ESI-MS. Thus, we used 50 equiv
of TBACl, and in this case the cyclization step was suffi-
ciently slow for us to observe the intermediate in the mass
spectrum. The major peak of the reaction mixture corre-
sponded to the chloride complex similar to INT2 but with a
carboxylate group instead of 2-marcaprothiazoline group,
formed through the hydrolysis in the spectrometer (m/z
794.21 [M+2H+Cl]+ ; see the Supporting Information).
The reaction between 1 and 4 can be considered a two-
step process that involves the conversion of the diamine to
the intermediate (k1), followed by the conversion of the in-
termediate to the cyclic product (k2). The quasi-stationary
approximation was used to access the rate constants and the
influence of the amount of the template on the reaction
rates. The curves shown in Figure 4 were fitted using Excel
Solver, and the calculated rates versus amount of TBACl
are shown in Figure 4. Interestingly, after 2 equiv of the tem-
plate, k1 and k2 started to differ from each other; 10 equiv is
enough to have one order of magnitude difference. These
results urged us to perform the next experiment, in which
we determined absolute yields of templated reactions by
using different amounts of a template. The results confirmed
Figure 4. a) Fluorescence changes of the reaction mixture 1 and 4 in the
presence of different amounts of chloride. Insert: calculated rate con-
stants k1 and k2 versus the amount of chloride. b) Fluorescence changes
of the reaction of 1 and 5 in the presence of chloride.
that the formation of more intermediate leads to higher
yields: 0.5, 5, and 10 equiv of TBACl led to 37, 79, and 95%
yields of [1+1] product.
With sufficient evidence for the existence of intermediates
INT1 and INT2, we turned to the question of whether or
not it is really the intramolecular hydrogen bond in the 2-
pyridine carboxamide fragment that rigidifies the overall
structure of intermediate INT1. To make a direct compari-
son, activated acid 5 with a benzene ring instead of a pyri-
dine ring was synthesized and tested in the macrocyclization
reaction with 1. In the isophthalimide unit there is no possi-
bility of forming an intramolecular hydrogen bond because
of the absence of the nitrogen atom. Analysis of the reaction
mixture between 1 and 5 revealed that the [1+1] product
was formed in 90% yield, and the presence of different tem-
plates did not have any significant influence on the product
distribution. Interestingly, the dependence of the fluores-
cence of the reaction mixture upon the time was linear and
did not provide any evidence of the formation of an inter-
mediate. In contrast to the reaction with activated acid 4,
the reaction with 5 was much slower than that with 4, and
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E. A. Kataev et al.
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the macrocyclization was slightly accelerated by the addition
of TBACl (Figure 4).
The progress of reactions with activated acids 4 and 5 was
additionally monitored by using 1H NMR spectroscopy. A
remarkable difference between the templated and nontem-
plated reactions was observed for activated acid 4. Without
TBACl as a template, all signals were broadened because of
the formation of a mixture of products. If TBACl was
added, the signals were sharp and it was possible to observe
the formation of the [1+1] product, which reached an 85%
yield in 4 min. A similar reaction with 50 equiv of TBACl
resulted in double the number of aromatic signals, thus indi-
cating the formation of an open structure of intermediate
INT2. In contrast, the reaction with activated acid 5 pro-
ceeded almost identically in the presence and in the absence
of TBACl, thereby leading to the [1+1] product in 80%
yield after 60 min of reaction time (see the Supporting Infor-
mation).
Conclusion
In summary, we have shown that it is possible to control ir-
reversible macrocyclization through amide bonds by using
anions as templates. The reaction conditions were found to
perform the macrocyclization sufficiently slow to observe a
template effect. Mechanistic investigations revealed that the
reaction is kinetically controlled and the structure of the in-
termediate plays a decisive role in determining the product
distribution. The knowledge obtained in this work is of high
importance for the synthesis of cyclic peptides or natural
cyclic compounds. Currently, we are applying our strategy to
the synthesis of large cyclic and cagelike molecules.
Acknowledgements
[14] D. N. Laikov, Y. A. Ustynyuk, Russ. Chem. Bull. 2005, 54, 820–826.
[15] CCDC-907743 ([2+2] product) contains the supplementary crystal-
lographic data for this paper. These data can be obtained free of
charge from The Cambridge Crystallographic Data Centre via
www.ccdc.cam.ac.uk/data_request/cif.
We thank Fonds der Chemischen Industrie and Technische Universitꢁt
Chemnitz for funding.
[1] F. Diederich, P. J. Stang, R. R. Tykwinski, Modern Supramolecular
Chemistry: Strategies for Macrocycle Synthesis, Wiley-VCH, Wein-
heim, 2008.
Received: December 4, 2012
Published online: January 31, 2013
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Chem. Eur. J. 2013, 19, 3710 – 3714