Self-Folding Molecules: A Well Defined, Stable Loop Formed by a Carboxylate - Guanidinium Zwitterion in DMSO

Article abstract of DOI:10.1021/jo9915980

Two zwitterions 1a,b have been synthesized, in which a carboxylate group is attached via a flexible alkyl chain of different length (butylene and ethylene, respectively) to a guanidiniocarbonyl pyrrole cation moiety. For 1b, no signs for either an intra- or intermolecular association between these two groups in polar solution (DMSO) could be found. In contrast to this, the ¹H NMR spectrum of 1a shows clear evidence for a strong interaction between the carboxylate and the guanidiniocarbonyl pyrrole cation. According to variable-temperature and concentration-dependent NMR studies, this interaction stems from an intramolecular complexation. It was shown by ROESY and H/D-solvent exchange experiments that 1a, even in DMSO, folds into a well-defined intramolecular loop conformation held together by multiple weak interactions.

Full text of DOI:10.1021/jo9915980

2432
J . Org. Chem. 2000, 65, 2432-2437
Self-F old in g Molecu les: A Well Defin ed , Sta ble Loop F or m ed by a
Ca r boxyla te-Gu a n id in iu m Zw itter ion in DMSO
Carsten Schmuck*
Institut fu¨r Organische Chemie, Universita¨t zu Ko¨ln, Greinstrasse 4, 50939 Ko¨ln, Germany
Received October 13, 1999
Two zwitterions 1a ,b have been synthesized, in which a carboxylate group is attached via a flexible
alkyl chain of different length (butylene and ethylene, respectively) to a guanidiniocarbonyl pyrrole
cation moiety. For 1b, no signs for either an intra- or intermolecular association between these
1
two groups in polar solution (DMSO) could be found. In contrast to this, the H NMR spectrum of
1a shows clear evidence for a strong interaction between the carboxylate and the guanidiniocarbonyl
pyrrole cation. According to variable-temperature and concentration-dependent NMR studies, this
interaction stems from an intramolecular complexation. It was shown by ROESY and H/D-solvent
exchange experiments that 1a , even in DMSO, folds into a well-defined intramolecular loop
conformation held together by multiple weak interactions.
In tr od u ction
tural characterization of a conformationally flexible zwit-
terion 1a is reported. Without any built-in structural
bias, this zwitterion folds, even in a highly polar solvent
such as DMSO, into a well-defined loop conformation due
to strong intramolecular interactions between two self-
complementary groups.
The molecular properties and thus the function of a
given molecule depend not only on its chemical constitu-
tion but also on its specific conformation. The various
conformations accessible for a large and flexible molecule
are often associated with different molecular properties.
However, the basic principles that control such folding
processes are still poorly understood.1,2 Therefore, the
design of molecules that fold into a predictable, specific
conformation can help learn more about these self-
organization processes and design molecules with new,
tailored functions and properties (e.g., designer proteins,
new catalysts, and drug candidates). However, a lot of
systems reported so far3 either are rather rigid and
therefore structurally biased toward a particular con-
formation3e,4 or adopt their specific conformation only in
organic solvents of low polarity (e.g., chloroform),5 be-
cause their folding is mainly determined by hydrogen
bonds,6 which are easily disrupted when the polarity of
the solvent increases.3b,7 Here, the synthesis and struc-
It was shown recently that guanidiniocarbonyl pyrroles
are excellent receptors for carboxylates even in aqueous
solvents with association constants in the order of K ≈
103 mol-1 in 40% water-DMSO (v/v).8,9 By linking a
pyrrole carboxylate moiety to such a guanidiniocarbonyl
pyrrole receptor unit through a flexible spacer, molecules
capable self-organizing into higher ordered structures are
obtained. Depending on the length and flexibility of the
spacer, either monomolecular self-folding molecules or
supramolecular oligomers and polymers should result
(Scheme 1).1,10,11
(7) For solvent effects on the strengths of H-bonds in complexes,
see, e.g.: (a) Horvath, P.; Gergely, A.; Noszal, B. J . Chem. Soc., Perkin
Trans. 1 1996, 1419-1422. (b) Kelly, T. R.; Kim, M. H. J . Am. Chem.
Soc. 1994, 116, 7072-7080. (c) Ariga, K.; Anslyn, E. V. J . Org. Chem.
1992, 57, 417-419.
(8) (a) Schmuck, C. Chem. Commun. 1999, 843-844. (b) Schmuck,
C. Chem. Eur. J . 2000, 4, 709-718.
* To whom correspondence should be addressed. Fax: + 49 221
4705102. E-mail: carsten.schmuck@uni-koeln.de.
(1) (a) Lehn, J .-M. Supramolecular Chemistry; Concepts and Per-
spectives; VCH: Weinheim, 1995. (b) Whitesides, G. M.; Mathias, J .
P.; Seto, C. T. Science 1991, 254, 1312-1319. (c) Philp, D.; Stoddart,
J . F. Angew. Chem., Int. Ed. Engl. 1999, 38, 1154-1196.
(9) Selected examples of other synthetic receptors that function in
polar solvents: (a) Hossain, A.; Schneider, H.-J . J . Am. Chem. Soc.
1998, 120, 11208-11209. (b) Davies, M.; Bonnat, M.; Gullier, F.;
Kilburn, J . D.; Bradley, M. J . Org. Chem. 1998, 63, 8696-8703. (c)
Berger, M.; Schmidtchen, F. P. Angew. Chem., Int. Ed. Engl. 1998,
37, 2694-2696. (d) J agessar, R. C.; Shang, M.; Scheldt, W. R.; Burns,
D. H. J . Am. Chem. Soc. 1998, 120, 11684-11692. (e) Niikura, K.;
Metzger, A.; Anslyn, E. V. J . Am. Chem. Soc. 1998, 120, 8533-8534.
(f) Peczuh, M. W.; Hamilton, A. D.; Sanchez-Qesada, J .; deMendoza,
J .; Haak, T.; Giralt, E. J . Am. Chem. Soc. 1997, 119, 9327-9328. (g)
Buhlmann, P.; Nishizawa, S.; Xiao, K. P.; Umewaza, Y. Tetrahedron
1997, 53, 1647-1654. (h) Berger, M.; Schmidtchen, F. P. J . Am. Chem.
Soc. 1996, 118, 8947-8948. (i) LaBrenz, S. R.; Kelly, J . W. J . Am.
Chem. Soc. 1995, 117, 1655-1656. (j) Albert, J . S.; Goodman, M. S.;
Hamilton, A. D. J . Am. Chem. Soc. 1995, 117, 1143-1144. (k) Kato,
Y.; Conn, M. M.; Rebek, J . J r. J . Am. Chem. Soc. 1994, 116, 3279-
3284. (l) Schiessl, P.; Schmidtchen, F. P. Tetrahedron Lett. 1993, 2449-
2452. (m) Fan, E.; Anslyn, E. V. J . Am. Chem. Soc. 1993, 115, 10042-
10055.
(2) Gellman, S. H. Chem. Rev. 1997, 97, 1231-1232.
(3) For selected reviews and articles on this area see: (a) Nowick,
J . S.; Tsai, J . H.; Bui, Q.-C. D.; Maitra, S. J . Am. Chem. Soc. 1999,
121, 8409-8410. (b) Nowick, J . S. Acc. Chem. Res. 1999, 32, 287-296.
(c) Gellman, S. H. Acc. Chem. Res. 1998, 31, 173-180. (d) Nowick, J .
S.; Smith, E. M.; Pairish, M. Chem. Soc. Rev. 1996, 401-415. (e)
Schneider, J . P.; Kelly, J . W. Chem. Rev. 1995, 95, 2169-2187.
(4) (a) Feigel, M. J . Am. Chem. Soc. 1986, 108, 181-182. (b) Wagner,
G.; Feigel, M. Tetrahedron 1993, 49, 10831-10842. (c) Brandmeier,
V.; Sauer, W. H. B.; Feigel, M. Helv. Chim. Acta 1994, 77, 70-85.
(5) Recently, short artificial peptides have been shown to form stable
helices and sheets in aqueous solvents, e.g.: (a) Apella, D. H.; Barchi,
J . J ., J r.; Durell, S. R.; Gellman, S. H. J . Am. Chem. Soc. 1999, 121,
2309-2310. (b) Seebach, D.; Abele, S.; Gademann, K.; J aun, B. Angew.
Chem., Int. Ed. Engl. 1999, 38, 1595-1597. (c) See also: Blanco, F.;
Ramirez-Alvarado, M.; Serrano, L. Curr. Opin. Struct. Biol. 1998, 8,
107-111.
(10) For a sampling of hydrogen-bonded self-assembled dimers in
nonpolar solvents, see, e.g.: (a) Kang, J .; Rebek, J ., J r. Nature 1997,
385, 50-52. (b) Kang, J .; Rebek, J ., J r. Nature 1996, 382, 239-241.
(c) Meissner, R. S.; de Mendoza, J .; Rebek, J ., J r. Science 1995, 270,
1485-1488. (d) For a comprehensive review article, see: Conn, M. M.;
Rebek, J ., J r. Chem. Rev. 1997, 97, 1647-1668.
(6) Another approach is persued by Hoffmann et al., who use gauche
interactions within 2,4-dimethyl pentane units to induce specific
conformations in acyclic hydrocarbons in unpolar solvents: Schopfer,
U.; Stahl, M.; Brandl, T.; Hoffmann, R. W. Angew. Chem., Int. Ed. Engl.
1997, 36, 1745-1747 and references therein.
10.1021/jo9915980 CCC: $19.00 © 2000 American Chemical Society
Published on Web 03/18/2000

Self-Folding Molecules
J . Org. Chem., Vol. 65, No. 8, 2000 2433
Sch em e 1. Sch em a tic Rep r esen ta tion of P ossible
Self-Assem bled Str u ctu r es for Zw itter ion s Su ch a s 1
pyrrole (Figure 1; all peaks were clearly assigned with
the help of 2D NMR experiments): A broad signal for
the two CH2 groups at δ ) 3.4, multiplets for the four
pyrrole CHs around δ ) 6.7, a broad signal for the four
guanidinium protons NHf,g at δ ) 7.3, two signals for the
amide NHs at δ ) 8.4 (NHb) and 8.6 (NHc), respectively,
and signals for the two pyrrole protons NHa and NHd and
the guanidinium amide NHe around δ ) 11.7. These
shifts are identical with similar, more simple guanidin-
iocarbonyl pyrroles, which lack any possible complemen-
tary binding group.8,16 It is well-known that any com-
plexation between a guanidiniocarbonyl group and a
carboxylate group causes significant complexation-
induced shift changes in the 1H NMR spectrum.8,16,17
Therefore, the absence of any such shift changes in the
spectrum of 1b clearly shows that at least under these
experimental conditions (millimolar solution in DMSO)
no complexation, neither inter- nor intramolecular of the
carboxylate and the guanidiniocarbonyl pyrrole, occurs.
In contrast to this, the spectrum of zwitterion 1a is
completely different: The signal for the four guanidin-
iocarbonyl pyrrole protons splits into two signals (two
protons each), at δ ) 8.0 (NHg) and 9.9 (NHf), respec-
tively. The two amide NHs give signals at δ ) 8.6 (NHb)
and 9.5 (NHc). One of the two pyrrole NHs is shifted
downfield by 1.4 ppm relative to 1b and resonates at δ
) 13.2 (NHd), the other resonating at δ ) 11.8 (NHa).
And perhaps most strikingly, the guanidinio amide NHe
gives a signal at δ ) 14.8 that corresponds to a downfield
Resu lts a n d Discu ssion
Syn th esis. The C4-linked zwitterion 1a (n ) 4) along
with the C2-linked control compound 1b (n ) 2) was
synthesized according to Scheme 2. The acid 212 is reacted
with the mono tBoc-protected diamines 313 in methylene
chloride with DCC as the coupling reagent and catalytic
amounts of DMAP. After deprotection with TFA, the
amine 5 is reacted with the acyl chloride 6,8 prepared
from the corresponding acid by reaction with oxalyl
chloride in the presence of catalytic amounts of DMF in
methylene chloride. The resulting methyl ester 7 can
then be hydrolyzed with LiOH in aqueous THF to give
the desired zwitterions 1. Alternatively, the diamide 10
can be prepared from the acyl chloride 8 and the
diamines 9.14 Guanidinylation15 of compound 10 with
guanidinium chloride in sodium methoxide gives the
same mono ester 7 as before. However, the yields
following this second route are lower (especially the
guanidinylation step is low yielding), and the workup and
purification of the products is more difficult so that the
first synthetic alternative, though being slightly longer,
is preferred.
1
shift of more than 3 ppm (relative to 1b). This H NMR
pattern is exactly the same as already known from
intermolecular complexes between simple carboxylates
and guanidiniocarbonyl pyrrole receptors.8,19 In these
complexes, the guanidinium cation forms an ion pair with
the carboxylate that is simultaneously hydrogen bonded
by the pyrrole NH and the various amide NHs. The two
guanidinium protons Hg, which do not form hydrogen
bonds to the carboxylate, resonate more or less at the
same field as in 1b, whereas the other two guanidinium
protons Hf, the amide NHe and the pyrrole NHd, all of
which take part in the complexation process, give signals
at much lower field relative to the corresponding signals
in uncomplexed guanidiniocarbonyl pyrrole compounds
(e.g., the spectrum of 1b), indicating strong hydrogen
bonding interactions. This clearly shows that even in
DMSO complexation of the carboxylate by the guanidin-
iocarbonyl pyrrole moiety takes place.8
Str u ctu r a l Ch a r a cter iza tion . According to molecu-
lar modeling calculations, zwitterion 1a with its C4 linker
should be capable of folding intramolecularly into a loop
conformation, whereas in zwitterion 1b the C2 linker is
much too short to allow such a self-folding. And indeed,
In principle, such a complexation can occur inter- or
intramolecularly. However, the principal binding interac-
tions between the carboxylate and the guanidiniocarbonyl
1
the H NMR spectra of these two compounds in DMSO
are remarkably different. Zwitterion 1b shows the “nor-
(16) Dixon, R. D.; Geib, S. J .; Hamilton, A. D. J . Am. Chem. Soc.
1992, 114, 365-366.
(17) Recent review articles on the binding of carboxylates by
artificial receptors including guanidinium-based systems: (a) Schmidt-
chen, F. P.; Berger, M. Chem. Rev. 1997, 97, 1609-1646. (b) Schmidtch-
en, F. P. Artificial Anion Hosts: Concepts for Structure and Guest
Binding in Supramolecular Chemistry of Anions; Bianchi, A., Bowman-
J ames, K., Garc´ıa-Espan˜a, E., Eds.; Wiley-VCH: New York, 1997; pp
79-146. (c) Atwood, J . L.; Steed, J . W. Structural and Topological
Aspects of Anion Coordination. In Supramolecular Chemistry of Anions;
Bianchi, A., Bowman-J ames, K., Garc´ıa-Espan˜a, E., Eds.; Wiley-
VCH: New York, 1997; pp 147-216. (d) Seel, C.; Gala´n, A.; de
Mendoza, J . Top. Curr. Chem. 1995, 175, 101-132.
mal” spectrum expected for a simple guanidiniocarbonyl
(11) For selected examples of the formation of supramolecular
oligomers in nonpolar solvents, see, e.g.: (a) Yamaguchi, N.; Gibson,
H. W. Angew. Chem., Int. Ed. Engl. 1999, 38, 143-147. (b) Ashton, P.
R.; Parson, I. W.; Raymo, F. M.; Stoddart, J . F.; White, A. J . P.;
Williams, D. J .; Wolf, R. Angew. Chem., Int. Ed. Engl. 1998, 37, 1913-
1916. (c) Yamaguchi, N.; Nagvekar, D. S.; Gibson, H. W. Angew. Chem.,
Int. Ed. Engl. 1998, 37, 2361-2364.
(12) Barker, P.; Gendler, P.; Rapoport, H. J . Org. Chem. 1978, 43,
4849-4853 and references therein.
(18) The 1H NMR spectrum of a saturated solution of 1b (ca. 50
mM) in DMSO at 20 °C shows two but still overlapping signals for the
guanidinium NHs (in contrast to more dilute solutions which only show
one signal, see Figure 1). This might be a first hint to the formation of
oligomers in such highly concentrated solutions.
(13) Pons, J .-F.; Fauche`re, J .-L.; Lamaty, F.; Molla, A.; Lazaro, R.
Eur. J . Org. Chem. 1998, 3, 853-859.
(14) Shama, S. A.; Tran, T. L. J . Chem. Educ. 1978, 55, 816.
(15) Bicking, J . B.; Robb, C. M.; Kwong, S. F.; Cragoe, E. J . J . Med.
Chem. 1967, 10, 598-602.
(19) Schmuck, C. Eur. J . Org. Chem. 1999, 2397-2403.

2434 J . Org. Chem., Vol. 65, No. 8, 2000
Sch em e 2. Syn th esis of Zw itter ion s 1a a n d 1ba
Schmuck
a
Key: (a) DCC, DMAP (cat.), THF/CH2Cl2 (1:1), 0 °C then rt, 70-80%; (b) TFA, CH2Cl2, 0 °C, quant; (c) NEt3, THF, 0 °C, 12 h, rt,
30-45%; (d) LiOH, THF/water (4:1), rt; (e) C6H6, reflux, 24 h, 35-45%; (f) guanidinium chloride, MeONa, MeOH, reflux, 24 h, 18-25%.
F igu r e 2. Proposed structure for zwitterion 1a that folds into
a loop stabilized by multiple intramolecular weak interactions
(shown here in form of dashed lines).
group on the one end of the molecule interacts with the
guanidiniocarbonyl pyrrole moiety on the other.
Furthermore, such an intramolecular self-folding is
concentration independent, whereas with increasing
dilution the formation of intermolecular self-associated
oligomers or polymers becomes less and less favorable.
1
As the H NMR splitting pattern and shifts observed in
the spectrum of 1a do not change in the concentration
range from 100 mM to as low as 0.01 mM oligomer
1
F igu r e 1. Downfield part of the H NMR spectra (300 MHz,
DMSO-d6, 1 mM, 298 K) of zwitterions 1a and 1b clearly
formation can most likely be ruled out. The C2-linked
zwitterion 1b cannot self-fold intramolecularly due to
geometric reasons and could only oligomerize intermo-
lecularly.18 Accordingly, in contrast to 1a the zwitterion
1b is much less soluble. Whereas 1a can be recrystallized
from water and is readily soluble in methanol, 1b is
nearly completely insoluble in these solvents. Even in
DMSO 1b is only very poorly soluble and immediately
precipitates from the solution upon addition of chloro-
form, whereas 1a readily forms millimolar solutions even
in 10% DMSO-CHCl3.
Therefore, 1b probably forms oligomers in the solid
state that dissociate in polar solutions, whereas 1a most
likely folds monomolecularly into a loop conformation
(Figure 2). In this conformation, the carboxylate is bound
by the guanidiniocarbonyl pyrrole unit in the same way
as already known from intermolecular complexes be-
tween carboxylates and guanidiniocarbonyl pyrrole re-
showing the complexation of the carboxylate group by the
guanidiniocarbonyl pyrrole moiety in the case of 1a in contrast
to 1b.
pyrrole group are the same in 1a and 1b, but only in 1a
and not in 1b an interaction between the carboxylate and
the guanidiniocarbonyl pyrrole group can be seen. If the
above-described features in the NMR spectrum of 1a
were due to intermolecular oligomerization, both 1a and
1b should show similar spectra, which is not the case.
Any intermolecular complexation is possible in both
compounds in exactly the same manner as far as the
binding interactions are concerned and should even be
more favorable in 1b due to its less flexible nature.
Therefore, the complexation-induced shift changes in the
NMR spectrum of 1a cannot be caused by dimerization
or oligomerization but rather indicate that 1a forms a
specifically folded monomer, in which the carboxylate

Self-Folding Molecules
J . Org. Chem., Vol. 65, No. 8, 2000 2435
F igu r e 3. Key NOEs (arrows) detected by ROESY studies
(500 MHz, DMSO-d6, rt) of zwitterion 1a (dashed lines indicate
intramolecular hydrogen bonds; hydrogens attached to carbon
atoms are omitted for clarity).
F igu r e 4. 1H NMR H/D-exchange experiment of 1a (D2O
added to a 1 mM solution of 1a in 10% DMSO-CDCl3 (v/v) at
room temperature, 300 MHz).
ceptors,8 consistent with the observed shifts for the
various NH protons in the 1H NMR spectrum as de-
scribed above. In addition to these binding interactions
between the carboxylate and the guanidiniocarbonyl
moiety, the pyrrole NHa and the amide NHb of the first
pyrrole moiety can form hydrogen bonds to the carbonyl
oxygen next to the guanidiniocarbonyl pyrrole further
stabilizing this conformation (Figure 2).
ROESY experiments also indicate that 1a folds into a
well-defined loop. In this conformation, amide NHb points
inward and is involved in hydrogen bonding to the
opposite carbonyl group, whereas amide NHc points
outward toward the solvent. Therefore, as expected,
amide NHb shows NOE signals to all four CH2 groups of
the linker and the neighboring pyrrole NHa (Figure 3).
Amide NHc, however, only exhibits NOEs with the two
nearest CH2 groups and no NOE with its neighboring
pyrrole NHd. Even a weak NOE signal between the two
pyrrole NHs a and d is observed, which indicates that
both pyrrole units, though being located at the opposite
ends of a rather long and flexible alkyl chain, obviously
are quite close to each other. Therefore, 1a in contrast
to 1b does not exist in a linear extended conformation or
a random coil. In that case, both amide NHs should give
similar NOEs to the methylene groups in the linker and
no NOE between the pyrrole NHs would be expected. All
observed NOEs, however, are in full agreement with the
proposed intramolecular loop structure for 1a .
The difference between the two amide protons b and
c, one forming intramolecular hydrogen bonds (NHb) the
other being only exposed to the solvent (NHc), can also
be proved by variable-temperature and H/D-solvent
exchange NMR studies. Protons that form stable in-
tramolecular hydrogen bonds show a much smaller shift
change upon increase in temperature and also exchange
much more slowly with the solvent than protons that are
only exposed to the solvent.3d And indeed the temperature
gradient for the shift change of amide NHc is more than
twice as large as that of amide proton NHb. In DMSO,
the signal for amide NHc shifts from δ ) 9.4 at 30 °C to
8.0 at 170 °C, whereas the signal for amide NHb shifts
from δ ) 8.5 only to 7.9. Furthermore, upon addition of
D2O to a 1 mM solution of 1a in 10% DMSO-d6 in CDCl3
at room temperature, amide proton NHc has completely
exchanged after 2 h and its signal has disappeared while
amide NHb is still detectable even after 2 days (see Figure
4). These observed differences in solvent exchange rate
and temperature gradient clearly reflect a strinkingly
different chemical environment to which the two amide
NHs b and c are exposed. This rules out any extended or
random coil-like structure, but again is in total agree-
ment with the self-folded loop structure proposed for 1a .
To probe the stability of this intramolecular complex-
ation in 1a , NMR studies were done at 140 °C to see
whether dissociation could be seen. Opening up of this
folded conformation should lead to a random coil struc-
ture with an NMR spectrum similar to that of the
nonassociated zwitterion 1b. However, though the signals
become increasingly broad and difficult to detect at
higher temperatures, the spectrum of 1a does not change
its appearance accordingly. Hence, it seems as if the loop
is conformationally completely stable in DMSO even at
elevated temperatures. This is remarkable as very often
small molecules adopt their specific conformation only
in rather unpolar solvents and are completely unfolded
in polar solvents.3 From earlier NMR titration studies,
we already know that the intermolecular complexation
of pyrrole carboxylate (NMe4+ salt) with [5-(methoxycar-
bonyl)-1H-pyrrole-2-carbonyl]guanidinium (picrate salt)
in DMSO has an association constant of K ≈ 106 mol-1
,
and even in 40% water-DMSO (v/v) it still has K ≈ 5 ×
103 mol-1 19
As the intramolecular association in 1a
.
should entropically be more favorable, it is expected that
the association constant is even K g 106 mol-1. Therefore,
it is not surprising that, under the conditions studied
here, no unfolding of the molecule could be seen.
Theoretical calculations also support the high stability
of this loop. Molecular dynamics calculations were per-
formed using the Amber* force field and the GB/SA water
solvation treatment as implemented in Macromodel 6.5.20
Molecule 1a was allowed to thermally equilibrate at 300
K for 5 ps and was then heated to 500 K within 20 ps.
After another equilibration period of 100 ps at this
temperature, the molecule was slowly cooled to 300 K
again (over 50 ps) and equilibrated for another 10 ps. This
procedure enables the molecule to overcome any possible
conformational energy barriers on its hypersurface before
optimizing the final structure. The resulting conforma-
(20) Mohamadi, F.; Richards, N. G. J .; Guida, W. C.; Liskamp, R.;
Lipton, M.; Caufiled, C.; Chang, G.; Hendrickson, T.; Still, W. C. J .
Comput. Chem. 1990, 11, 440-467.

2436 J . Org. Chem., Vol. 65, No. 8, 2000
Schmuck
38.65, 39.75 (both CH2), 51.64 (CH3), 112.50 (CH), 115.22 (CH),
124.18, 131.43, 138.99, 159.33, 160.72 (all quat C). Anal. Calcd
for C16H25N3O5 (339.18): C, 56.61;, H, 7.43; N, 12.39. Found:
1
C, 56.46; H, 7.24; N, 12.24. 4b (8.2 g, 71%): mp 148 °C; H
NMR (300 MHz, DMSO-d6) δ 1.32 (s, 9 H, tBu), 3.02 (m, 2 H,
CH2), 3.25 (m, 2 H, CH2), 3.78 (s, 3 H, CH3), 6.68 (m, 2 H,
pyrrole CH), 6.91 (t, 2 H, amide NH), 8.32 (t, 1 H, amide NH),
12.07 (s, 1 H, pyrrole NH); 13C NMR (75.5 MHz, DMSO-d6) δ
28.39 (tBu), 39.09, 39.45 (both CH2), 51.63 (CH3), 112.48 (CH),
115.21 (CH), 124.22, 131.35, 155.85, 159.62, 160.70 (all quat
C). Anal. Calcd for C14H21N3O5 (311.15): C, 53.99; H, 6.80; N,
13.50. Found: C, 53.94; H, 6.85; N, 13.49.
Gen er a l P r oced u r e for th e P r ep a r a tion of Meth yl
Ester s 7. The tBoc-protected amide 4 (30 mmol) was dissolved
in CH2Cl2 (100 mL) and the solution cooled to 0 °C. Over a
period of 3 h, TFA (10 mL) was added, and the mixture was
stirred at room temperature for 24 h. After removal of the
solvent under reduced pressure, the residue was extracted with
acetone and the resulting white precipitate of the crude amine
salt was filtered off and dried over phosphorus pentoxide. The
amine 5 (4.4 mmol) was then reacted without further purifica-
tion with acyl chloride 619 (4 mmol) in the presence of NEt3
(1.82 g, 18 mmol) in THF (30 mL), following a procedure
already described.8 After removal of the solvent under reduced
pressure, the residue was purified by chromatography on
alumina (eluent: CH2Cl2/MeOH, 4:1, with 0.1% NEt3). The
yields were generally in the range from 30 to 45%. 7a : 1H
NMR (300 MHz, DMSO-d6) δ 1.51 (m, 4 H, CH2), 3.21 (m, 4
H, CH2), 3.81 (s, 3 H, CH3), 6.71 (m, 2 H, pyrrole CH), 6.83
(m, 1 H, pyrrole CH), 7.49 (m, 1 H, pyrrole NH), 8.29 (t, 1 H,
amide NH), 8.45 (t, 1 H, amide NH), 8.52 (brs, 4 H, guani-
dinium NH2), 11.81 (s, 1 H, amide NH), 12.09, 12.35 (both, s,
1 H, pyrrole NH); 13C NMR (75.5 MHz, DMSO-d6) δ 26.74,
26.77, 38.55, 38.63 (all CH2), 51.63 (CH3), 112.53, 115.22, 116.
09, 118.42 (all CH), 124.19, 125.49, 131.39, 133.12, 155.0.58,
159.18, 159.38, 159.80, 160.71 (all quat C). 7b: 1H NMR (300
MHz, DMSO-d6) δ 3.32 (m, 4 H, CH2), 3.75 (s, 3 H, CH3), 6.72
(m, 2 H, pyrrole CH), 6.85 (m, 1 H, pyrrole CH), 7.41 (m, 1 H,
pyrrole CH), 8.30 (brs, 4 H, guanidinium NH2), 8.50, (t, 1 H,
amide NH), 8.68 (t, 1 H, amide NH), 11.81 (brs, 1 H, pyrrole
NH), 12.12 (s, amide NH), 12.31 (s, 1 H, pyrrole NH); 13C NMR
(75.5 MHz, DMSO-d6) δ 38.68, 39.45 (both CH2), 51.67 (CH3),
112.65 (CH), 115.28 (CH), 124.35, 131.28, 159.55, 159.74,
160.71 (all quat C).
Gen er a l P r oced u r e for th e P r ep a r a tion of th e Zw it-
ter ion s 1. The methyl ester 7 (0.5 mmol) was stirred with
LiOH monohydrate (63 mg, 1.5 mmol) in THF/water (4 mL,
4:1, v/v) overnight at room temperature. According to TLC,
the conversion was quantitative. After evaporation of the
solvent, the residue was taken up in water and the pH
adjusted to pH ) 6 with hydrochloric acid. The resulting white
precipitate was filtered off, washed with water, and in the case
of 1a recrystallized from methanol. 1a : mp 300 °C dec; 1H
NMR (300 MHz, DMSO-d6) δ 1.51 (m, 2 H, CH2), 1.62 (m, 2
H, CH2), 3.28 (m, 2 H, CH2), 3.51 (m, 2 H, CH2), 6.51, 6.63,
7.00, 7.03 (all, m, 1 H, pyrrole CH), 7.95 (brs, 2 H, guanidinium
NH2), 8.61 (t, 1 H, amide NH), 9.53 (t, 1 H, amide NH), 9.98
(brs, 2 H, guanidinium NH2), 11.80 (s, 1 H, pyrrole NH), 13.21
(s, 1 H, pyrrole NH), 14.82 (s, 1 H, amide NH); 13C NMR (75.5
MHz, DMSO-d6) δ 24.08, 25.15, 35.15, 36.61 (all CH2), 111.65,
112.34, 1113.76, 117.93 (all CH), 127.36, 128.43, 130.04,
130.75, 156.94, 159.30, 161.29, 165.95 (all quat C). 1b: mp
300 °C dec; 1H NMR (300 MHz, DMSO-d6) δ 3.35 (m, 2 H,
CH2), 3.48 (m, 2 H, CH2), 6.72 (m, 4 H, pyrrole CH), 7.32 (brs,
4 H, guanidinium NH2), 8.41 (t, 1 H, amide NH), 8.62 (t, 1 H,
amide NH), 11.70 (s, 1 H, pyrrole NH), 11.89 (s, 1 H, pyrrole
NH), 12.02 (s, 1 H, amide NH); 13C NMR (75.5 MHz, DMSO-
d6) δ 38.89, 38.92 (all CH2), 111.96, 112.5, 113.68, 114.14 (all
CH), 127.37, 129.12, 129.92, 131.63, 160.04, 160.34, 160.57,
163.16 (all quat C).
F igu r e 5. Superposition of 15 structures of 1a , sampled from
a Molecular Dynamics calculation over a time period of 100
ps at 300 K.
tion, which was the same as the energy minimum found
by a conventional Monte Carlo simulation, corresponds
to the loop already deduced from the NMR studies and
shown in Figure 2. As a constant temperature MD
calculation on this energy minimum conformation shows
(100 ps simulation at 300 K; Figure 5), the structure is
well defined and rather stable. At least during the time
period of this simulation, only the inner methylene
groups of the linker show some flexibility, but none of
the bonding interactions is lost, nicely illustrating the
high thermal stability of this conformation.
Con clu sion s
In conclusion, a novel self-folding motif based on
multiple weak interactions within a zwitterion, in prin-
ciple expected to be rather flexible, has been identified
and structurally characterized. It could be shown here
by NMR studies with H/D solvent exchange and ROESY
experiments that zwitterion 1a , in contrast to the very
similar 1b, folds into a well-defined loop, which is
conformationally completely stable even in DMSO. This
folding motif can be useful for the design of supramo-
lecular polymers by varying the linker length and its
flexibility.
Exp er im en ta ls:
Gen er a l Rem a r k s. Solvents were dried and distilled under
argon before use. All other reagents were used as obtained
from either Aldrich or Fluka. All experiments were run in
oven-dried glassware under argon unless otherwise stated. 1H
and 13C NMR shifts are reported relative to the deuterated
solvents. Peak assignments are based on DEPT, 2D NMR
studies and comparison with literature data.8,16
Gen er a l P r oced u r e for t h e P r ep a r a t ion of t Boc-
P r otected Am id es 4. To a suspension of acid 2 (37 mmol)
and amine 313 (37 mmol) in THF-CH2Cl2 (300 mL, 1:1
mixture, v/v) were added DCC (8.4 g, 41 mmol) and DMAP
(0.25 g, 2 mmol) at 0 °C, and the resulting mixture was stirred
at room temperature for 24 h. After filtration and removal of
the solvent under reduced pressure, the crude product was
purified by flash chromatography on silica gel (eluent: ethyl
acetate/hexane, 2:1, with 0.1% NEt3). 4a (9.9 g, 79%): mp 108
1
°C; H NMR (300 MHz, DMSO-d6) δ 1.41 (s, 9 H, tBu), 1.45
Gen er a l P r oced u r e for th e P r ep a r a tion of Dia m id es
10. Acyl chloride 8 (20 mmol) was prepared from the corre-
sponding acid12 (3.4 g, 20 mmol) by reaction with oxalyl
chloride (5.1 g, 40 mmol) in the presence of DMF (three drops)
in CH2Cl2 (50 mL) for 2 h. After removal of the solvent under
(m, 4 H, CH2), 2.92 (m, 2 H, CH2), 3.28 (m, 2 H, CH2), 3.78 (s,
3 H, CH3), 6.70 (m, 2 H, pyrrole CH), 6.81 (t, 2 H, amide NH),
8.25 (t, 1 H, amide NH), 12.08 (s, 1 H, pyrrole NH); 13C NMR
(75.5 MHz, DMSO-d6) δ 26.63, 27.26 (both CH2), 28.46 (tBu),

Self-Folding Molecules
J . Org. Chem., Vol. 65, No. 8, 2000 2437
reduced pressure, the crude acyl chloride was taken up in
benzene (50 mL) and the diamine 9 (10 mmol) was added. The
reaction mixture was refluxed for 48 h. After the HCl evolution
ceased, the solvent was evaporated and the residue either
recrystallized from methanol (10a ) or purified by flash chro-
matography on silica gel (eluent: CH2Cl2/MeOH, 9:1, with
0.1% NEt3) (10b). 10a (1.67 g, 43%): mp 190 °C dec; 1H NMR
(300 MHz, DMSO-d6) δ ) 1.51 (m, 4 H, CH2), 3.38 (m, 4 H,
CH2), 3.81 (s, 6 H, CH3), 6.72 (m, 4 H, pyrrole CH), 8.38 (t, 2
H, amide NH), 12.08 (s, 2 H, pyrrole NH); 13C NMR (75.5 MHz,
DMSO-d6) δ 26.83 (CH2), 38.60 (CH2), 51.69 (CH3), 112.55
(CH), 115.27 (CH), 124.25, 131.43, 159.41, 160.75 (all quat C).
Anal. Calcd for C18H22N4O6 (390.40): C, 55.38; H, 5.68; N,
14.35. Found: C, 55.10; H, 5.88; N, 14.20. 10b (1.31 g, 36%):
mp 240 °C dec; 1H NMR (300 MHz, DMSO-d6) δ 3.37 (m, 4 H,
CH2), 3.77 (s, 6 CH3), 6.78 (m, 4 H, pyrrole CH), 8.45 (t, 2 H,
amide NH), 12.11 (s, 2 H, pyrrole NH); 13C NMR (75.5 MHz,
DMSO-d6) δ 38.75 (CH2), 51.17 (CH3), 112.61 (CH), 115.28
(CH), 124.34 (quat C), 131.28, 159.72, 160.70 (all quat C). Anal.
Calcd for C16H18N4O6‚1/2H2O (371.13): C, 51.73; H, 5.16; N,
15.09. Found: C, 51.75; H, 4.81; N, 14.92.
of the solvent under reduced pressure, the residue was purified
by chromatography on alumina (eluent: CH2Cl2/MeOH, 4:1,
with 0.1% NEt3) in the same way as already described above.
The yields were in the range of 18-25%.
Molecu la r Mod elin g. All calculations described in this
paper were performed on an SGI O2 workstation using the
software package Macromodel 6.5.20 Monte Carlo conforma-
tional searches were performed with at least 1000 steps until
the energy minimum structure had been found several times.
Molecular dynamics calculations were carried out as described
in the text. The Amber* force field and the GB/SA water
solvation model implemented in Macromodel were used in all
studies.
Ackn owledgm en t. Financial support from the Fonds
der Chemischen Industrie (Liebig fellowship) is grate-
fully acknowledged. The author thanks Dr. Hans
Schmickler, Ko¨ln, for the ROESY studies and Professor
Dr. Albrecht Berkessel, Ko¨ln, for his generous support
and helpful discussions.
Gen er a l P r oced u r e for th e P r ep a r a tion of Meth yl
Ester s 7 by Gu a n id in yla tion of Dia m id e 10. Compound
10 (4 mmol) was dissolved in a solution of sodium methoxide
(prepared by dissolving sodium (176 mg, 8 mmol) in 20 mL of
methanol). Guanidinium chloride (764 mg, 8 mmol) was added,
and the reaction mixture was refluxed for 12 h. After removal
Su p p or t in g In for m a t ion Ava ila b le: 1H and 13C NMR
and DEPT spectra for compounds 1a ,b, 4a ,b, 7a ,b, and 10a ,b
and the ROESY spectrum of 1a . This material is available free
of charge via the Internet at http://pubs.acs.org.
J O9915980