Autocatalysis and organocatalysis with synthetic structures

Article abstract of DOI:10.1073/pnas.0912769107

The discovery of ribozymes led to the proposal of an RNA world, where a single type of molecule was supposedly capable of selfreplication and chemical catalysis. We show here that both autocatalysis and organocatalysis can be engineered into a synthetic structure. The compound is shown to selectively accelerate its own formation and catalyze either hydrogenation or nucleophilic addition to α,β-unsaturated aldehydes. The observed reactivity indicates that the components of a purported pre-RNA world conceivably include smaller organic molecules. imidazolidinone catalysis self-replication template effects.

Full text of DOI:10.1073/pnas.0912769107

Autocatalysis and organocatalysis
with synthetic structures
1
Seiji Kamioka, Dariush Ajami, and Julius Rebek Jr.
The Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road,
La Jolla, CA 92037
Contributed by Julius Rebek, November 5, 2009 (sent for review September 8, 2009)
The discovery of ribozymes led to the proposal of an RNA world,
where a single type of molecule was supposedly capable of self-
replication and chemical catalysis. We show here that both auto-
catalysis and organocatalysis can be engineered into a synthetic
structure. The compound is shown to selectively accelerate its
own formation and catalyze either hydrogenation or nucleophilic
addition to α,β-unsaturated aldehydes. The observed reactivity
indicates that the components of a purported pre-RNA world
conceivably include smaller organic molecules.
proline itself requires extensive synthetic sequences, but creation
of an imidazolidinone in the space between the recognition
elements as in 2a could be contemplated in a single step—the
same step that assembles the autocatalyst. This functional group,
devised by MacMillan and coworkers (16, 17) is a versatile
organocatalyst that operates through reversibly formed covalent
intermediates (18).
In the experiment, 2a could be obtained from condensation of
aldehyde 3 with thymine-derived amino acid 4a in hot benzene
(
Fig. 1 and SI Appendix). The desired cis 2a was accompanied
imidazolidinone catalysis ∣ self-replication ∣ template effects
by the trans isomer 2c. The N-methyl thymine derivatives 2b
and 2d were also prepared and used as controls because their
inability to “base pair” abrogates molecular recognition during
their reactions with the diaminotriazine subunit.
The earliest evidence that recognition-based reactions were
involved in the final steps of the synthesis came from the yields
of reactions involving closely related structures. Specifically, the
cis 2a (38%) was obtained in higher yield than trans 2c (18%),
whereas the N-methyl 2b (19%) and 2d (15%) were produced
in comparable amounts. The preference for 2a was diminished
in a polar solvent such as MeOH, which competes for hydrogen
bonds, and was eliminated entirely in the reaction of 4a and 4b
with the ester 5, which lacks a hydrogen-bonding site complemen-
tary to the imide function of 4a (SI Appendix).
tudies of prebiotic chemistry raise questions concerning which
S
functions came nearer the origin of life—genetics or metabo-
lism (1). The discovery of the catalytic activity of ribozymes pro-
vided an answer in which both functions could be accounted for in
an “RNA world” (2). Although no one doubted that RNA could
carry genetic information, some 15 years lapsed before an RNA
molecule was shown to self-replicate (3), and this type of catalysis
has since been developed to an extraordinary level of efficiency
(
4). Short, self-complementary DNA strands were shown to self-
replicate in 1986 (5), and autocatalysis based on molecular recog-
nition was found in simplified organic molecules (6) and even
peptides (7). At the present time, many types of self-replicating
structures are known (8). These systems function like their nu-
cleic acid counterparts in that the self-complementary structures
operate as templates for their own formation. However, unlike
ribozymes, the synthetic self-replicating systems are not known
to catalyze other chemical reactions. The wholly synthetic struc-
tures act as either organocatalysts or autocatalysts, but published
evidence for both activities in a single molecule is limited (9). This
research was undertaken to find molecules that could perform in
both capacities, and we report here an imidazolidinone-based
compound and its properties as a catalyst and autocatalyst.
A consistent and quantitative measure of autocatalysis was
obtained through kinetic studies. The condensation reaction of
3
with 4a was analyzed by HPLC and the results are shown in
Fig. 2 Left. The initial rate for the coupling reaction (blue line)
is shown with that of 0.25 equiv (red line) and 0.50 equiv (green
line) cis 2a added. The yields were corrected for the addition of
the catalysts and are determined with respect to an internal stan-
dard. Clearly, 2a accelerates its own formation. That this process
is grounded in self-recognition was shown by parallel studies
monitoring trans 2c as a function of added 2a (Fig. 2 Right). Here,
no acceleration of the rate occurred; cis 2a is, accordingly, a self-
ish (8) replicator because it catalyzes its own formation but not
that of its structurally related diastereomer trans 2c. By compar-
ison, trans 2c also accelerates its own formation and, unexpect-
edly, the formation of the cis 2a as well (S.I.). Thus, trans 2c is
a cooperative (19) replicator. The trans arrangement of alkyl
groups on an imidazolidinone is not expected to be advantageous
for organocatalysis so trans 2c was not tested in those capacities.
Both cis 2a and trans 2c are stable under the reaction conditions;
they neither interconvert nor racemize.
Results and Discussion
To realize an autocatalytic/organocatalytic molecule, we made
modifications in the structure of compound 1, a molecule
that bears self-complementary hydrogen-bonding subunits—a
diaminotriazine and cyclic imide—that allow for dimerization
in noncompeting organic media (Fig. 1). The arrangement of
these subunits in 1 was earlier shown to allow its action as an
autocatalyst (10): It acts as a template for its own synthesis, gath-
ering two subunits on its surface to facilitate the formation of the
amide bond. The insertion of a functional group known to cata-
lyze organic transformations into 1 was a prospect to be explored.
We initially inserted a thiourea into the framework of 1 (11).
Although the thiourea function is a widely used organocatalyst
Taken together, these results show that autocatalysis based on
recognition—replication—takes place during the formation of
the cis 2a, and the likely process is illustrated in Fig. 3. The two
complementary hydrogen-bonding sites of 2a (diaminotriazine
and thymine) can assemble the starting materials into the
(12), its applications were limited in the present context: The
same hydrogen bonding that accounts for the thiourea’s activity
requires the use of solvents that also lead to tight dimerization
of the template. This effect minimizes the fraction of the mono-
meric compound that operates as the organocatalyst. To avoid
this limitation we sought an organocatalytic function that oper-
ates through reversible formation of covalent bonds, such as
the venerable proline-based catalysts (13–15). Insertion of
Author contributions: S.K., D.A., and J.R. designed research; S.K. and D.A. performed
research; S.K., D.A., and J.R. analyzed data; S.K., D.A., and J.R. wrote the paper.
The authors declare no conflict of interest.
1
To whom correspondence should be addressed. Email: jrebek@scripps.edu.
This article contains supporting information online at www.pnas.org/cgi/content/full/
0912769107/DCSupplemental.
www.pnas.org/cgi/doi/10.1073/pnas.0912769107
PNAS ∣ January 12, 2010 ∣ vol. 107 ∣ no. 2 ∣ 541–544

Fig. 1. Line drawings and synthesis of autocatalytic molecules. The previously reported self-replicator 1, was modified to contain an embedded
imidazolidinone in 2a. The condensation of aldehyde 3 with thymine-derived amino acid 4a results in both the cis 2a and the trans 2c. The N-methyl derivatives
(
2b, 2d, and 4b) and aldehyde 5 lack the corresponding hydrogen bond motifs (recognition elements) and were used as controls.
termolecular complex 6 to template the reaction. This complex
places the two reacting sites, aldehyde and amine, in close proxi-
mity and accelerates the rate of their condensation reaction.
The imidazolidinone site in the self-replicating molecule 2a is
capable of activating α,β-unsaturated aldehydes via the reversible
formation of iminium ions (20). This catalytic functional group
forms during the syntheses of the replicator. The organocatalytic
activity of 2a was demonstrated in a hydride transfer reaction
The imidazolidinone motif is also known to catalyze the cou-
pling of indoles and α,β-unsaturated aldehydes in Friedel–Crafts
alkylations (21) (Fig. 5). Compound 2a was also effective in this
context: The addition of N-methylindole 10 to 7 was catalyzed by
2a and control experiments with 3 and 4a clearly illustrated that
the catalytic activity of 2a is not housed in its diaminopyridine or
imide functional groups.
In the present study, neither the catalyst nor the reaction con-
ditions are conventionally prebiotic, and the replication does not
involve an “informational” oligomer though such synthetic struc-
tures do exist and are capable of information transfer and pairing
with RNA (22, 23). There are also synthetic cyclic phosphates
embedded in chiral microenvironments that feature the same
functional group as the phosphodiesters of RNA and DNA.
Although the cyclic phosphates are widely used organocatalysts
(24), the minimalist dinucleotide monophosphates counterparts
have, to our knowledge, yet to show activity in this regard. The
departure for the cases at hand is the postulate that autocatalytic
(
Fig. 4) to (E)-cinnamaldehyde 7. The substrate was reduced
in high yield (91%) using 2a, the Hantzsch ester 8 as the hydride
source and catalytic amount of an acid (DCl). The course of
1
the reaction was followed with H NMR spectroscopy in which
the downfield doublet of cinnamaldehyde changed to a trip-
let of dihydrocinnamaldehyde 9; the corresponding signals of
imidazolidinone catalyst 2a did not change. No reduction was
observed in the absence of 2a. Neither the thymine-derived
amino amide 4a nor the aldehyde 3 acted as a reduction catalyst
under these conditions.
Fig. 2. Kinetics of autocatalytic reactions. (Left) Appearance of cis compound 2a as a function of time: blue line, no additive; red line, 0.25 equiv product
added; green line, 0.50 equiv product added. Initial concentrations were aldehyde 3 (8.0 mM) and amine 4a (9.6 mM) in benzene. (Right) Appearance of trans
compound 2c as a function of time: blue line, no additive; red line, 0.25 equiv 2a added; green line, 0.50 equiv 2a added. Initial concentrations were aldehyde
3
(8.0 mM) and amine 4a (9.6 mM) in benzene.
5
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Kamioka et al.

Fig. 3. Autocatalytic reaction through a proposed termolecular complex. The recognition sites of 2a act through hydrogen bonding and stacking to provide a
template for assembly 6. The reactive groups (circled) can be brought into proximity and the condensation reaction is accelerated. A modeled structure of the
dimeric 2a.2a is also shown.
reproduction of catalytic capabilities (25) can be a useful and
expanded definition of the chemistry at life’s origins. Compound
5 (2 mM) in benzene (2.0 mL) at room temperature. After 2 d of stirring
at 70 °C, the reaction mixture was concentrated in vacuo. The residue was
purified by column chromatography on silica gel, eluting with 30% acetone
in chloroform to afford the cis and trans imidazolidinones. The coupling
reaction of 3 and 4a gave 53% of cis 2a and 24% of trans 2c. The character-
ization data for 2a and 2c are as follows.
2
a acting as both autocatalyst and organocatalyst provides a
working example. Such organocatalysts could even be envisioned
to assist in building up the molecular components from which
they are composed, for example, the synthesis of the pyrimidine
heterocyclic subunits featured here. Such compounds provide a
starting point for a “bottom up” approach to creating molecular
complexity and establishing catalytic reaction cycles (26). There
is also the possibility for mutations (27) in these synthetic
replicators. The ultimate aim is the generation of accessible
synthetic systems that are potential precursors to the RNA world.
Cis 2a: 1H NMR (600 MHz, DMSO-d6) δ 11.26 (s, 1H), 7.75 (s, 1H), 7.67
(
(
1
(
s, 1H), 7.39 (s, 1H), 7.38 (s, 1H), 7.25 (s, 1H), 7.05 − 6.95 (m, 3H), 6.78
d, J ¼ 6.9 Hz, 2H), 6.20 (s, 1H), 4.37 − 4.30 (m, 2H), 4.14 (d, J ¼ 14.9 Hz,
H), 4.09 − 4.00 (s, 1H), 3.85 − 3.80 (m, 2H), 3.75 (s, 3H), 1.71 (s, 3H), 1.60
s, 3H), 1.59 (s, 3H), 1.32 (s, 9H), 1.19 (s, 9H); 13C NMR (151 MHz, DMSO-d6)
δ 172.8, 171.8, 168.0, 165.1, 152.1, 147.4, 146.6, 146.0, 145.4, 142.8, 137.8,
1
1
31.2, 129.9, 128.6, 127.6, 127.2, 127.1, 126.4, 125.8, 124.8, 124.3, 123.6,
08.6, 67.8, 57.7, 49.9, 44.5, 35.3, 35.1, 35.0, 33.8, 32.2, 32.1, 31.2, 13.0;
Materials and Methods
high-resolution mass spectrometry (HRMS) [matrix-assisted laser desorption/
General Experimental. All reagents were obtained from commercial suppliers
and used without further purification. NMR spectra were recorded on a
Bruker DRX-600 spectrometer at 300 K. HPLC for analysis was performed
on a Hewlett–Packard HP-1100 series system with following gradients:
þ
ionization–Fourier transform mass spectrometry (MALDI-FTMS): MH ] calcu-
þ
lated for C42H50N9O4 744.3998, found 744.3975.
Trans 2c: 1H NMR (600 MHz, DMSO-d6) δ 11.28 (s, 1H), 7.61 − 7.55 (m, 2H),
7
.38 (d, J ¼ 2.0 Hz, 1H), 7.25 (s, 1H), 7.08 (d, J ¼ 1.9 Hz, 1H), 7.06 − 6.96
m, 3H), 6.82 (d, J ¼ 6.9 Hz, 2H), 6.78 (s, 4H), 6.18 (d, J ¼ 6.5 Hz, 1H),
.19 − 4.12 (m, 2H), 4.12 − 4.08 (m, 1H), 4.06 (s, J ¼ 16.0 Hz, 1H), 3.69 (dd,
J ¼ 7.1, 13.5 Hz, 1H), 3.44 (dd, J ¼ 9.8, 13.5 Hz, 1H), 1.71 (s, 3H), 1.59
s, 6H), 1.33 (s, 9H), 1.17 (s, 9H); 13C NMR (151 MHz, DMSO-d6) δ 172.3, 171.8,
167.2, 164.4, 151.0, 146.4, 145.9, 145.3, 144.6, 142.5, 136.8, 130.3, 129.6,
27.8, 127.1, 126.6, 126.0, 124.8, 124.4, 124.0, 123.0, 121.9, 107.7, 57.0, 49.4,
44.0, 34.5, 34.3, 34.2, 31.5, 31.4, 31.3, 31.3, 31.1, 12.0; HRMS (MALDI-FTMS:
5
–40% over 7 min, 40–100% over 25 min, and then 100% over 5 min
(
4
[
CH3CN in H2O (0.1% TFA)], with the flow rate of 0.5 mL∕ min on a GL
Sciences, Inc. Inertsil-ODS-1HO, 4.6 × 150 mm column. Peak areas were
integrated at 254 nm. The details of the synthetic procedures and character-
izations of the aldehydes 3 and 5, as well as thymine-derived amino acids 4a
and 4b are described in SI Appendix.
(
1
General Procedure for the Synthesis of Imidazolidinones 2. Thymine-derived
amino acid 4a or 4b (3 mM) was treated with a solution of aldehyde 3 or
þ
þ
MH ) calculated for C42H50N9O4 744.3998, found 744.3982.
Fig. 4. The organocatalyzed reduction of cinnamaldehyde: red line, 0.2 equiv 2a; green line, 0.2 eqiv 3; blue line, 0.2 equiv 4a; black line, no additive.
Kamioka et al.
PNAS
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data for cis 2b, 12a, and 12b, as well as trans 2d, 12c, and 12d are described in
SI Appendix.
General Procedure for Kinetic Studies of Autocatalyzed Coupling Reactions of
Aldehyde 3 with Amino Acid 4a. A solution of aldehyde 3 (8.0 mM), thymine-
derived amino acid 4a (9.6 mM), and an internal standard such as biphenyl
(
0
8.0 mM) in benzene was treated with (no additive, 0.25 equiv of 2a, or
.50 equiv of 2a) at room temperature. While stirring at 70 °C, the mixture
was periodically analyzed by HPLC through comparison of the peak areas of
the internal standard with products (254 nm).
General Procedure for Competition Studies for Coupling Reactions of Aldehyde
3
or 5 with Thymine-Derived Amino Acids 4a and 4b. Thymine-derived amino
acids 4a and 4b (8.0 mM each) were mixed with a solution of aldehyde 3 or 5
8.0 mM) in benzene or methanol at room temperature. After 2 d of stirring
(
at 70 °C, the mixture was analyzed by HPLC using the peak areas (254 nm).
General Procedure for Organocatalytic Hydride Reduction. The trans-
cinnamaldehyde 7 (5.0 mM) was added to a solution of imidazolidinone
2
a (1.0 mM), Hantzsch ester 8 (50.0 mM), and a catalytic amount of conc.
DCl in CD2Cl2 at 0 °C. The reaction was allowed to come to room tempera-
ture, and the mixture was periodically analyzed by 1H NMR.
Fig. 5. The organocatalyzed Friedel-Crafts alkylation: red line, 0.2 equiv 2a;
green line, 0.5 eqiv 3; blue line, 0.2 equiv 4a; black line, no additive.
General Procedure for Organocatalytic Friedel–Crafts Alkylations. The trans-
cinnamaldehyde 7 (5.0 mM) and camphorsulfonic acid (50.0 mM) were added
to a solution of imidazolidinone 2a (2.5 mM) and N-methylindole (50.0 mM)
in CDCl3 at 0 °C. While stirring at room temperature, the mixture was
analyzed by 1H NMR analysis.
The stereochemistry of above compounds was determined from a 2D
rotating frame nuclear Overhauser effect spectroscopy spectrum. An NOE
cross-peak was observed for the benzylic proton of the xanthene and the
α-proton of the amino acid in cis 2a, whereas the trans 2c showed NOE
cross-peaks for the benzylic proton of the xanthene with the β-proton of
the amino acid and methyl protons at thymine. The yields and spectroscopy
ACKNOWLEDGMENTS. We are grateful to The Skaggs Institute for support
and Prof. A. Eschenmoser for encouragement and advice. S.K. is a Skaggs
Postdoctoral Fellow.
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