Autocatalysis
andSelf-Replication~ toward synthesis of THE LIFE ~Lit. Seminar
2011.1.8 (Sat)
Katsuya Sato (B4)1Outline of Topics
I.

Introduction~ Concept of Autocatalysis ~II. Asymmetric Autocatalysis~ Soai Reaction ~III. Organic Autocatalysis~ Synthetic Autocatalyst ~Today’s Keywords
asymmetric amplification / autocatalysis /homochirality /non-linear effect /ribozyme / RNA world / self-replication /Soai reaction /Today’s Key-persons

IV. Biological Autocatalysis~ Self-Replication of RNA ~K. Soai

V. Summary

J. Rebek, Jr.

G. F. Joyce

Recent Reports
K. Soai Science 2009, 324, 492-495
J. Rebek, Jr Proc. Natl. Acad. Sci. USA 2010, 107, 541-544
G. F. Joyce Science 2009, 323, 1229-1232
2

I. Introduction~ Concept of Autocatalysis ~✤ What is Autocatalysis?
✤ Examples✤ Scientific Importance3

Definition
Autocatalysis is...
catalysis of a chemical reaction by one of the
products of the reaction.
A

A
B

A

B

B

A B

A B
B

B

A

B

A
A

B

A

A

B A

A B

A B

B A

B A
B

A B

Fig.1 A simple image of autocatalysis

exponential increase of catalyst(=product)!!
Fig.2 Sigmoid variation of productconcentration in autocatalytic reactions
4

Examples of Autocatalysis• Bromination of ketone
H+ catalyzes formation of enol from ketone

O

+ Br2

H+

O

Br + HBr
HBr regenerates catalytic H+• Ley OxidationOH
water reduces
autocatalysis in
this reaction

R

R

n-Pr4NRuO4

O

NMO
CH2Cl2 / CH3CN
MS 4Å

R

R

activated catalyst

RuO4- + nRuO2
reduction

iPrOH

RuO4-•nRuO2
colloid
D. G. Lee J. Org. Chem. 1992, 57, 3276-3277
5

Examples of Autocatalysis• LDA-Mediated Ortholithiation

Web 11/25/2008

Diisopropylamide-MediatedN(i-Pr)
2
thiationsO. Hoepker, and David B. Collum*

N(i-Pr)2

O

O

O
i-Pr
Li
N
i-Pr
Li
F

iology, Baker Laboratory, Cornell UniVersity,
York 14853-1301

008; E-mail: dbc6@cornell.edu

F
1

N(i-Pr)2
OF4

propyl carbamate by lithium diisopropylamide (LDA)
ding linear decays of the carbamate, delayed formation
utocatalysis. A mechanistic model in conjunction withdependent changes in concentration. The two criticaler-based metalation of arylcarbamate, and (2) a ratethe LDA dimer to form two isomeric LDA-ArLi mixed-rate-limiting) metalation of aryl carbamate, in turn,ations of such autocatalysis are discussed.

i-Pr
Li
N i-Pri-Pr NLi
i-Pr

N(i-Pr)2
O

O
Li
F

2

in neat THF as monitored by 19F NMR spectroscopy. The solid and dashedlines represent least-squares fits to first- and second-order decays, respectively.

i-Pr
N i-PrLi

53

Figure 1. Reaction of 0.10 M carbamate 1 with 0.10 M LDA at -78 °C

O
Li

N(i-Pr)2
O

1

O

F

D. B. Collum J. Am. Chem. Soc. 2008, 130, 18008-18017
see also : D. B. Collum J. Am. Chem. Soc. 2010, 132, 15610-15623
6

Examples of Autocatalysis• Autocatalysis in Biological Systems

Figure 1. Autocatalysis at various scales: single molecule folding, autogeneous regulation, intracellular signaling pathways,
organ systems, collective motion and ecological scales.
Evolution as a response to the environment results in changes in the structure and function of single molecules. Not
shown are criss-crossing links that indicate the effect of intracellular signaling to community behavior, or single molecule folding to population dynamics for instance as seen in the effect of unfolded proteins in prion disease epidemiology. Figures except single molecule and autogeneous regulation are from wikipedia.com.

AIChE J. 2009, 55, 556-562
4

7

Scientific Importance• Chemical Oscillation
Belousov-Zhabotinskii(BZ) Reaction

Fig.2 Change of color in BZ reaction with Fe(phen)32+
Fig.1 Change of color in BZ reaction with Ce3+

8

Scientific Importance• Chemical Oscillation - BZ reaction Initial stepBr- + BrO3- + 2H+

HBrO2 + HOBr

(R1)

Br- + HOBr + H+

Br2 + H2O

(R2)

Br- + HBrO2 + H+

2HOBr

(R5)

2BrO2

+ H2O

Autocatalytic step
BrO3- + HBrO2 + H+
BrO2

+ Ce3+ + H+

HBrO2 + Ce4+

BrO3- + HBrO2 + 2Ce3+ + 3H+
2HBrO2(R3)(R4)

2HBrO2 + 2Ce4+ + H2O (!)

HOBr + BrO3- + H+

Oxidation of malonic acid}

Process A(R6)}

Process B

Br2 + CH2(CO2H)2

BrCH(CO2H)2 + H+ + Br- (R7)
6Ce3+ + HCO2H + CO2 + 6H+
6Ce4+ + CH2(CO2H)2 + 2H2O

4Ce4+ + BrCH(CO2H)2 + 2H2O

(R8)

Br- + 4Ce3+ + HCO2H + CO2 + 5H+(R9)

R. J. Field, E. Körös, R. M. Noyes J. Am. Chem. Soc. 1972, 94, 8649-8664
9

Scientific Importance• Origin of Life
Homochirality
COOH
H
NH2
L-Valine

RNA World

OH
HO
HO

O
OH

OH

D-Glucose“Autocatalysis”
Create a New Order ?
10II. Asymmetric Autocatalysis~ Soai Reaction ~✤ Asymmetric Amplification✤ Discovery of Soai Reaction✤ Mechanistic Study

11

Asymmetric Amplification
eeprod = ee0 · eeaux
eeprod | ee value of the productee0| the maximum ee value of the producteeaux | ee value of the chiral auxiliary

Fig.1 Non-linear effects (NLE) in asymmetric synthesis“asymmetric amplification” means ::eeprod > ee0×eeauxreview : H. B. Kagan Angew. Chem. Int. Ed. 1998, 37, 2922-2959
12

!"#$"%&!" #" $%&%' %'( )" *+,%,(-.+&/,0 12" 340 0'%'5+670,+8 0980:: 6; 540 <,6(/80( 0<69+(0! -!!<,6(2 =40' <>6550( %: % ;/'85+6' 6; 540 !! 6; -!2?@A3-!!%/92 =%: +'(00( &,0%50, 54%' 09<0850(" 340 /:0 6; % (+70,+8
4050,684+,%> :<08+0: 54%5 +: >0:: ,0%85+B0C %'( 54/: 76,0 :5%D>0C

Discover of (+)-/(-)-NLE!"#$"%&!" #" $%&%' %'( )" *+,%,(-.+&/,0 12" 340 0'%'5+670,+80980:: 6; 540 <,6(/80(
0<69+(0O(R,R)-(+)-DET! -!!<,6(2OH=40' <>6550(%: %4 (5%);/'85+6' 6; 540 !! 6; OH-!2?@A3
Ti(OiPr)-!!%/92 =%: +'(00( &,0%50, 54%' 09<0850(" 340 /:0 6; % (+70,+8
4050,684+,%> :<08+0: 54%5+: >0:: ,0%85+B0C %'( 54/: 76,0 :5%D>0C
tBuOOHCH2Cl2, -20 °C

S
CH3
H3C

(R,R)-(+)-DET
Ti(OiPr)4tBuOOH, H2O
CH2Cl2, -20 °C

S O
CH3
H3C

.+&/,0 S" -"2?EFA +' 540 %:H7705,+8 69+(%5+6' 6; :/>;+(0 # =+54 % 84+,%>5+5%'+/7 ,0%&0'5"

B%,+6/: %76/'5: 6; 0'%'5+670,: %>:6 &%B0 +';6,7%5+6' %D6/5
540 ,0%85+6' +5:0>;" Y5 D08%70 8>0%, 54%5 540 :0%,84 ;6,'6'>+'0%, 0;;085: +' % &+B0' :H:507 %>:6 D08670: % <,6D0 ;6,%'%>HZ+'& 540 '%5/,0 6; 540 8%5%>H5+8 :<08+0: 6, 540 '6',0%85+'&:<08+0: +'B6>B0( +' %' %:H7705,+8 :H'540:+:".+&/,0 1" -!2?EFA +' 540 G4%,<>0:: 0<69+(%5+6' 6; &0,%'+6> -"2".+&/,0 S" -"2?EFA +' 540 %:H7705,+8 69+(%5+6' 6; :/>;+(0 # =+54 % 84+,%>%&%& '()*+, -.) /01.213+*,
Fig.2 ,0%&0'5"(-)-NLE in the asymmetric oxidation of sulfide
5+5%'+/7

54%' +5: 467684+,%> 86/'50,<%,5: <,6B+(0: % =%H 6; /'(0,?
:5%'(+'& 540 -!2?EFA 6; 540 ,0%85+6'C :+'80 :670 ,%807+8@A3 =+>> D0 ,05%+'0( +' 540 +'%85+B0 867<>09" 34+: <,6<6:%> +:867<%5+D>0 =+54 540 G4%,<>0:: 7084%'+:7 6; %:H7705,+8
0<69+(%5+6'C =4+84 +'(+8%50: 540 +'50,B0'5+6' 6; % (+70,+8

36 &05 % D0550, /'(0,:5%'(+'& %'( 56 4%B0 :670 +':+&45 +'56
B%,+6/:%76/'5:
6; 0'%'5+670,:%>:6&%B0 6;+';6,7%5+6'
540 D04%B+6,
6; 8%5%>H:5:(/,+'& 540
86/,:0% ,0%85+6' %D6/5
54%5
H. %B.EFAC
Kagan
Am. Chem.
108,2353-2357
540+5:0>;" :+7<>+;+0(
Y5J.D08%70
8>0%, Soc.
54%5 1986,
540:0%,84;6,>0%(:,0%85+6'56
7%5407%5+8%>76(0>:=0,0
H. B. Kagan Angew. Chem.IW[LInt. Ed. 1998, 37, 2922-2959
76(0>:=0,0(0B0>6<0(0;;085:
DH $%&%'
05 %>" :H:507+' [RR1"%>:6 340:0'6'>+'0%,+' % &+B0'
D08670:% <,6D0;6,
13(+:8/::0( 540+' 5408+50(6;%,5+8>0%'( =+>>:<08+0:'65 D0 09<>%+'0(
40,0 +'%'%>HZ+'&'%5/,0540 8%5%>H5+8
6, 540 '6',0%85+'&

Fig.1 (+)-NLE in the Sharpless epoxidation

at
in
le.
re
yin
nty

se
uely
ric
stcts
ar
to
to
ric
he
he

ence between the two models is the nature of the active catalytic
species: in the Kagan ML2 model shown in Scheme 1a, the dimers
are themselves the catalysts, while in Noyori’s model shown in
Scheme 1b,
theAsymmetricactive single-ligandNLE
catalyst is in equilibrium with
Modelsforoff-cycle species containing two homochiral or heterochiralligands.
Kagan’s modelaNoyori’s modelb

Scheme 1. Models for non-linear effects.

The Kagan mathematical model describing the system shown in
Scheme 1a contains two parameters, Kdimer and g. The former is a
G. Blackmond
Tetrahedron:
Asymmetry
2010, 21, 1630-1634
general property of the chemical D.species,
while
the latteris specific14

!"#$"%&!" #" $%&%' %'( )" *+,%,(-.+&/,0 12" 340 0'%'5+670,+8 0980:: 6; 540 <,6(/80( 0<69+(0! -!!<,6(2 =40' <>6550( %: % ;/'85+6' 6; 540 !! 6; -!2?@A3-!!%/92 =%: +'(00( &,0%50, 54%' 09<0850(" 340 /:0 6; % (+70,+8
4050,684+,%> :<08+0: 54%5 +: >0:: ,0%85+B0C %'( 54/: 76,0 :5%D>0C

Example of (+)-/(-)-NLE!"#$"%&!" #" $%&%' %'( )" *+,%,(-.+&/,0 12" 340 0'%'5+670,+80980:: 6; 540 <,6(/80(
0<69+(0O(R,R)-(+)-DET! -!!<,6(2OH=40' <>6550(%: %4 (5%);/'85+6' 6; 540 !! 6; OH-!2?@A3
Ti(OiPr)-!!%/92 =%: +'(00( &,0%50, 54%' 09<0850(" 340 /:0 6; % (+70,+8
4050,684+,%> :<08+0: 54%5+: >0:: ,0%85+B0C %'( 54/: 76,0 :5%D>0C
tBuOOHCH2Cl2, -20 °C

S
CH3
H3C

(R,R)-(+)-DET
Ti(OiPr)4tBuOOH, H2O
CH2Cl2, -20 °C

S O
CH3
H3C

.+&/,0 S" -"2?EFA +' 540 %:H7705,+8 69+(%5+6' 6; :/>;+(0 # =+54 % 84+,%>5+5%'+/7 ,0%&0'5"

B%,+6/: %76/'5: 6; 0'%'5+670,: %>:6 &%B0 +';6,7%5+6' %D6/5
540 ,0%85+6' +5:0>;" Y5 D08%70 8>0%, 54%5 540 :0%,84 ;6,'6'>+'0%, 0;;085: +' % &+B0' :H:507 %>:6 D08670: % <,6D0 ;6,%'%>HZ+'& 540 '%5/,0 6; 540 8%5%>H5+8 :<08+0: 6, 540 '6',0%85+'&:<08+0: +'B6>B0( +' %' %:H7705,+8 :H'540:+:".+&/,0 1" -!2?EFA +' 540 G4%,<>0:: 0<69+(%5+6' 6; &0,%'+6> -"2".+&/,0 S" -"2?EFA +' 540 %:H7705,+8 69+(%5+6' 6; :/>;+(0 # =+54 % 84+,%>%&%& '()*+, -.) /01.213+*,
Fig.2 ,0%&0'5"(-)-NLE in the asymmetric oxidation of sulfide
5+5%'+/7

EE467684+,%>= 1000, g<,6B+(0:= 0.35 % =%H 6; /'(0,?
0 = 95%, K
54%' +5:
86/'50,<%,5::5%'(+'& 540 -!2?EFA 6; 540 ,0%85+6'C :+'80 :670 ,%807+8@A3 =+>> D0 ,05%+'0( +' 540 +'%85+B0 867<>09" 34+: <,6<6:%> +:867<%5+D>0 =+54 540 G4%,<>0:: 7084%'+:7 6; %:H7705,+8
0<69+(%5+6'C =4+84 +'(+8%50: 540 +'50,B0'5+6' 6; % (+70,+8

complicatedis required...
36 &05more% D0550,/'(0,:5%'(+'& model%'( 56 4%B0:670 +':+&45 +'56
B%,+6/:%76/'5:
6; 0'%'5+670,:%>:6&%B0 6;+';6,7%5+6'
540 D04%B+6,
6; 8%5%>H:5:(/,+'& 540
86/,:0% ,0%85+6' %D6/5
54%5
H. %B.EFAC
Kagan
Am. Chem.
108,2353-2357
540+5:0>;" :+7<>+;+0(
Y5J.D08%70
8>0%, Soc.
54%5 1986,
540:0%,84;6,>0%(:,0%85+6'56
7%5407%5+8%>76(0>:=0,0
H. B. Kagan Angew. Chem.IW[LInt. Ed. 1998, 37, 2922-2959
76(0>:=0,0(0B0>6<0(0;;085:
DH $%&%'
05 %>" :H:507+' [RR1"%>:6 340:0'6'>+'0%,+' % &+B0'
D08670:% <,6D0;6,
15(+:8/::0( 540+' 5408+50(6;%,5+8>0%'( =+>>:<08+0:'65 D0 09<>%+'0(
40,0 +'%'%>HZ+'&'%5/,0540 8%5%>H5+8
6, 540 '6',0%85+'&

Fig.1 (+)-NLE in the Sharpless epoxidation

Soai Reaction• First Asymmetric Autocatalysis
O
H
N

OH

R2Zn
20 mol% producttoluene, r.t.

RN
R = Me, Et, iPr, nBu

R

catalyst ee (%)

product ee (%)

Me

42

7

Et

56

14

iPr

86

35

nBu

47

6

K. Soai J. Chem. Soc. Chem. Comm. 1990, 982-983
16

Soai Reaction• Asymmetric Autocatalysis with Amplification
O
N

H

iPr2Zn20 mol% product (5% ee)

NFig.1 Asymmetric autocatalysis ofchiral pyrimidyl alkanol.

toluene, 0 °C

OH
N
N

Fig.2 Relation between ee of catalyst
and ee of product.
K. Soai Nature 1995, 378, 767-768
17

Soai Reaction• 2-Alkynyl 5-Pyrimidyl Alkanol
O
N

H

OH

iPr2Zn20 mol% productNtoluene, 0 °C

N

N
R

R

R

catalyst ee (%)

product ee (%)

nBu

5.8

21.2

tBu

5.5

69.6

Me3Si

8.4

74.2

iPr3Si

8.6

8.8

Ph

5.9

47.3

K. Soai Angew. Chem. Int. Ed. 1999, 38, 659-661
18

configuration as the catalyst.
In the planning of further efficient asymmetric autocatalysts
possessing high autoamplification ability, the key feature is theinteraction between the enantiomers of the asymmetric autocatalyst. As mentioned in a previous section, fluorine-containing
compounds are expected to interact with each other, which canlead to self-purification. There is a trend in fluorine-containing
Other
Substrates ( = Catalysts ! )compounds for a larger difference between the energy of homochiral

Soai Reaction•

Fig. 12. Asymmetric autocatalysts, which produce amplification of ee in theenantioselective addition of i-Pr2Zn to the corresponding aldehydes.

of a pyrim
cation of
Not onlywith very
autocataly
a chiral in
23 with 7
induced thchiral com
functional
asymmetr
high ee. Ch
inducesreactionsenantiom
urations chydrocarb
allene [83Becausrene 42 w
detectablebutyl)ethy
nary hydr
over the ra

K. Soai J. Fluorine Chem. 2010, 131, 525-534
19

Soai Reaction• Various Chiral Initiators
O
N

H

OH

iPr2Znchiral trigger

N

N
tBu

N
tBu
T. Kawasaki, K. Soai / Journal of Fluorine Chemistry 131 (2010) 525–534

531

Fig. 14. Asymmetric autocatalysis initiated by chiral compounds.

polarized light (CPL) [11–13], inorganic crystals such as quartz
enantiomers poses the utmost difficulty. Their enantiomeric forms[14,15] and sodium chlorate [91,92], enantiomorphous organic
cannot be distinguished by applying any contemporary technique
crystals formed from achiral organic molecules [93–96] andand are called cryptochiral. Thus, asymmetric autocatalysis
spontaneous absolute asymmetric synthesis [97]. The enantiotriggered by cryptochiral compounds has been examined. Isotactic
meric imbalances that were induced by these proposed mechanpolystyrene 42 induced enantioselective addition of i-Pr2Zn toisms have usually been very small; therefore, a suitablepyrimidine-5-carbaldehyde 21 to afford the pyrimidyl alkanol 22
amplification process is required to reach homochirality ofwith the corresponding absolute configurations to that of
biological organic compounds. Asymmetric autocatalysis withcryptochiral polystyrene 42 and its enantiomer ent-42 [86]. In
amplificationof eeofgives
a strong correlation between the origin ofaddition, the reaction between pyrimidine-5-carbaldehyde
21 andFig. 15. Asymmetric autocatalysis
induced by
the proposed origins
chirality.
K. Soai J.
Chem. 2010,
131, 525-534
chirality and the homochirality
of Fluorine
organic compounds,
i.e.,
i-Pr2Zn in the presence of (R)-43 formed (S)-pyrimidyl alkanol 22
asymmetric autocatalysis can be initiated by these proposedwith high ee, whereas in the presence of (S)-43, the opposite (R)20
6. Isotopically chiral compound triggers asymmetricdirect correlation of the handedness of CPL with that of the organic

Soai Reaction• Isotope Chirality

Fig. 16. Asymmetric autocatalysis triggered by a chiral compound by carbon isotope substitution.

T. Kawasaki, K. Soai / Journal of Fluorine Chemistry 131 (2010) 525–534

13by carbon
12 isotope substitution.
Fig. 16. Asymmetric autocatalysis triggered by a chiral compoundcarbon isotopic effect ( C/ C)

hydrogen isotopic effect (D/H)

Fig. 17. Asymmetric autocatalysis triggered by a chiral compound by hydrogen isotope substitution.

formation of homochiral and heterochiraof the hydrogen isotopic chirality in meteoritic achiral molecules.
different physical properties. These dia
Therefore, we performed asymmetric autocatalysis initiated with
between the enantiomers promote se
the meteoritic achiral amino acids, glycine and a-methylalanine
enantiomers, thus it is possible for a cwith hydrogen (D/H) isotope chirality. When the i-Pr2Zn addition
ee of itself under achiral conditions such
was performed in the presence of the (S)-glycine-a-d (47) with an
K.
Soai
J.
Am.
Chem.
Soc.
2000, 122, 11739-11740
tion and column chromatography using aee of 93%, the (S)-5-pyrimidyl alkanol 22 was obtained in a 94%
containing
compounds
a strong dyield with an ee of 96% [117]. On the other hand, (R)-22 withan ee Chem.
K. SoaiComm.
2009,possess
4396-4398
the energy of homochiral and heteroof 95% was obtained in the presence of (R)-47. Next, the addition ofK.
Soai
Science 2009, 324, 492-495
fluorine-containing chiral compounds s
i-Pr2Zn to pyrimidine-5-carbaldehyde 21 using (R)- and (S)-aeffects
without
anotherchiralauxiliary.
methyl-d3-alanine (48) was performed. In the presence(R)-48,
K. Soaiof J.
Fluorine
Chem.
2010,
131,
525-534
Asymmetric amplification can be obs(S)-22 was induced, and the reaction of aldehyde 21 and i-Pr2Zn in
21even isotope chirality has ability
to act as a chiral trigger !

Summary of Soai Reaction
530

T. Kawasaki, K. Soai / Journal of Fluorine Chemistry 131 (2010) 525–534

K. Soai J. Fluorine Chem. 2010, 131, 525-534
22

red: itahesis,
el of
then,chiralactionsof theandgetherympersis-ble inwer,r atrobin ofunderropa-

Mechanism of Soai Reaction• Autocatalysis Aloneee= ee · ee

cat,0

cat,0

SPECIAL FEA TURE PERSPECTIVE

ation
ucts
e inents or

metry breaking is observable and persistent, as in the Soai reaction. The
Fig. 1. Simple asymmetric autocatalytic reactions (unlik
question is, what makes it observable inof ee over time. Plotted is the final product ee as a
autocatalytic reactions for two hypothetical of autoca
this case? In trying to find an answer,
enantioselectivity: a catalyst with an initial eecat,0 ! 0.99 eperhaps we have been focusing our atline), and a catalyst with an initial eecat,0 ! 0.88 exhibitin
tention on the wrong part of the probline).
lem: instead of pondering the origin of
the initial imbalance, we need to understand how this imbalance can be propaat an ee lower than their antecedents,
angated; that is, how can we prevent theserve as catalysts in further turnovers
te
prod
0
aux
mirror from repairing itself?
If theof
catalyst
is NOT(ee0 <
1) , thesubstrate
toperfect
product.
Thus,in eachtu
ee will be less than catalyst ee and theHere is where autocatalysis, such as inproductcycle,
the ee of the newly formed prod- au
eeprod | ee value of the productlowereeproducts
will be serving as catalysts inthe example of the Soai reaction, has auctdecreases
further. In terms of thepr
ee0 | the maximum ee value of the productfuturereactions!
role to play. To understand this idea, we total number of turnovers undertakenoreeaux| ee avalueof thechiraltakecloserlook
at auxiliaryFrank’s (5) modelin an autocatalytic reaction (TON, dem
for amplification in asymmetric autocafined as the moles of substrate conre
talysis. However, before we do this, weverted per mole of catalyst initiallyinneed to highlight a key point that haspresent), the final ee product (eeprod,f)
au
not received adequate attention in awill be given by Eq. 2 (16):lenumber of the recent discussions of amno
plification of ee in asymmetric autocaeeprod,f ! eecat,0!(TON # 1)(ee0 $ 1).
wetalysis. This point is: autocatalysis alone[2] inis not enough.
syFig. 1 demonstrates the results of any
Autocatalysis Alone
simple asymmetric autocatalytic reactu
The failure of autocatalysis by itself totion. Even an autocatalyst of very highinrationalize
amplification
Fig. 1. Simple asymmetricautocatalyticasymmetric
reactions (unlike the Soaireaction) necessarily show inan erosion
enantiopurity that is capable of producof ee over time. Plotted is the final product ee as a function of turnover number in asymmetricasautocatalytic
reactionswasdiscussed
autocatalytic reactions for two hypothetical of autocatalysts at different ee and different producting itself in 99% ee will experience anenantioselectivity: a catalyst with an initial ee! 0.99 exhibiting an enantioselectivity of 0.99 (solid blue
anqualitatively
byGirard
and
Kagan
(27),
line), and a catalyst with an initial ee! 0.88 exhibiting an enantioselectivity of 0.88 (shaded magenta
erosion of ee; after only 200 turnovers,line).
and Blackmond (28) has provided D.
a G.
theBlackmond
Proc. Nat.eeAcad.
Sci.
USA
2004,An
101,5732-5736du
this
catalyst
will
be
"94%.
88%
oretical derivation.an The
argument is simni
23
at an ee lower than their antecedents,‘‘anticatalyst’’ in self-replicating sysee catalyst that produces itself in 88%

Mechanism of Soai Reaction• Mutual Antagonism“anticatalyst” : autocatalyst must be capable not
only of producing itself but also of suppressing
Noyori’s model

Scheme 2. Models for including mutual antagonism in autocatalytic systems. (A) Specific mutual
antagonism: enantiomeric R and S catalysts form a reservoir of inactive heterochiral dimers. If the initialratio of S:R enantiomers is not 1:1, a greater fraction of the minor enantiomer is extracted into the dimer
reservoir, which has total S:total R ratio equal to 1:1. (B) Unspecific mutual antagonism: enantiomeric R
and S catalysts form a reservoir of inactive homochiral and heterochiral dimers in statistical proportions.

The Problem with Unspecific Mutual
Antagonismthat of the enant
2 and 3 show, thestudy revealed thkeeps pace excel
pure counterpart
unequivocally tha
agree with what
as the Frank modmutual antagonis
dox: the rate dat
there should be ncation in ee; but
the very phenommark of the Soai
Indeed, asymmet
observed experim
mond et al. (30)tiopure catalyst w

D.
G. 2.
Blackmond
Proc.
Nat. Acad. Sci.
101,
5732-5736
Fig.
Why is thatsignificant?
Let’sUSA 2004,The
Solution:Dim

consider the implications of this result

24

ht
istic
symn
aSR.
he
S,
then
erenThis
of
en R
29),
relactituagoranknsarily reflected in the rate, which is proportional to catalyst concentration. If
the racemic catalyst exhibits a bias toward the heterochiral dimer; as it must
if we are to observe amplification of ee,then part of the R and S enantiomer
pool is shunted off, not only into theinactive RR and SS reservoirs as it is forthe enantiopure catalyst but also into
the inactive SR reservoir that is significant for nonenantiopure catalysts only.
Thus, the rate of production in the racemic system should start to lag behindnism), and the R and S monomers
themselves are present only in kinetically insignificant concentrations. This
twist takes us full circle back to the earliest theoretical work on nonlinear effects in asymmetric catalysis by Kaganand coworkers (31, 32). The ML2model, modified in this case for autocatalysis (33), allows us to account for amplification of ee by adding one simple
constraint: the homochiral and heterochiral species must have different activities as catalysts. All we need to assume
to explain the amplification of ee is that

Mechanism of Soai Reaction• A Paradox Emerges

Racemic rate should start to lag behind theenantiopure (due to heterodimer) to cause anamplification in ee.

dox

dies
al.
n.
ed
nibthatpor-nFig. 2. Experimental reaction rate as a function of fraction conversion of the aldehyde 1b in the Soai
autocatalytic reaction shown in Scheme 1 employing enantiopure and racemic catalyst. The experimental
rate for the racemic catalyst has been multiplied by a factor of !2 (1.93).

0308363101

Paradox:the rate data fit a model that says there
should be no asymmetric amplification in ee;
but amplification in ee is the very
phenomenon that is the hallmark of the Soaireaction system !

Blackmond

Fig. 3. Schematic depicting how the catalyst concentration increases for enantiopure and racemic
catalysts as the autocatalytic reaction of Scheme 1 proceeds, as predicted by the experimentally measured
reaction rates shown in Fig. 2.

the homochiral species is better at cataSecond, we don’t have to give up on
asymmetric amplification, just because
lyzing the reaction than is the heterothe dimers are capable only of statisticalchiral species. As we discuss in the next
D. G.thisBlackmond
Acad.
Sci. USA
2004,
101, 5732-5736
formation.
Indeed,accounting
for amsection,
hybrid modelProc.
offers Nat.
a ratioplification of ee by assuming different 25
nalization of the Soai autocatalytic

we are trying
to describe is a world
beSupportive
evidencefortheirthatfeasibility
comes
from
the X-ray
re catalystchangessame rolein the prebiotic
chemistry
considerationinunderstandingthedefore a chiral pool existed. Design of spe- ultimately established homochirality.
velopmentof diethylnicotinamide
homochirality in biologicalof
7acrystal Statistics,
structureof ZnX2 complexes
cific stereochemical
inuouslychangingbias by modern
and one stroke of luck;a diffunction. The ‘‘minimal systems’’ formethods generally requires access to an
15 Theferenceinreactivity
that
ended
up
self-replication
developed
Kiedmacrocyclic
bimetallic
chelateof by8vonderivedfromasymmetric template, and today andwe can7b.working for us
instead of against us, arerowski (37, 38) and others for nucleic
draw on the chiral pool for our alcoholbuilding
all2thatexhibits
is required foran
us tohomologous
find ouracids arrangement,(39), peptides (40, 41), withsmall or- formally
blocks. Our proficiency in tuning desired selves in our homochiral world today.
(42), and ribozymes
16 Preliminary ganic
1H molecules
Mechanismof
Soai
Reaction
properties
isreflected
in
the
large
numNMR
studies systems
on these aretricoordinate
zinc.
gβ ber of efficient chiral ligands that have Outlook(43) all represent autocatalytic
based on core templates larger than(1)consistent
both
with
the
existenceof indimeric
Zn alkoxides
and abeen discovered for a wide varietyoffirst mechanistic studies on the Soai those
the Soai reactions.
However,+ β chemical transformations. In a prebiotic The
reaction thus implicated a trimeric spenone of those insystems
involveprochiral signal.17
lackof
selectivity
inassociation,
exhibited
the
Ar-CH
soup
of simple molecules, Dimeric
however, theciesCatalyst
as the transition state for the reacmolecules, meaning that the origin of3
Solution:)•resources for pulling
off such a feat2
would have been meager.

([SR])K ) Kagan’s ML model([RR])([SS])tion; that is, two molecules of alcohol!
alkoxide in the dimeric catalysts and2dx
ex[2] + eedx [1]02dx
[2] + [1]02(2)Scheme 3. ML2 model for autocatalysis. The monomeric R and S enantiomers form homochiral (RR andSS) and heterochiral (SR) dimers that themselves serve as the active catalysts in the autocatalytic reaction.

the first imbalance in asymmetric centers is not at issue in these cases; when
we examine von Kiedrowski’s (37, 38)
autocatalytic system based on DNA hexamers, for example, we know we are
already firmly committed and residing in
the camp of the L-amino acids and theD-sugars. We might agree with Cintas
and coworkers’ (44) view that the Soai
system represents a ‘‘triumph of reductionism’’ in helping us to understand thechemical origin of life in molecular
terms, but we also accept his statementthat there remains a ‘‘large gap between
molecular chirality and molecular evolution.’’ Thus, further studies ought to be
aimed at trying to provide informationthat might help close this gap.

ultaneously to the
In summary, a simple dimeric catalyst model explains the broad
1 gave thean hybrid
excellent
dimer model explains
theof
rate
data perfectly autocatalysis quite strikingly. The two Zn
featuresasymmetrictribution of dimers
atoms in compound 8 are nicely disposed toward bimetallic N,Or.12 Figure 3 shows All we coordinationa template for attack ofofexplainaldehyde
1,10a providing
need to assume tothe amplificationof ee is thattion of conversion the homochiralis better at catalyzing
the reaction thanis
The required
stereospecificityof thisprocess is under
ZnPri2. species
species.
culated from the fit the heterochiralactive investigation.
nd 2. The excellent
Acknowledgment. D.We
thank the J.EPSRC(two
grantsto D.G.B.),theffers further support
G. Blackmond
Am. Chem.
Soc.
2001, 123,
10103-10104
D. G. Blackmond
Nat.Central
Acad. Sci.Research
USA 2004, (D.G.B.)
101, 5732-5736
Leverhulme Foundation(J.M.B.),Proc.
Pfizerandification of enanti26
Blackmond

PNAS " April 20, 2004 " vol. 101 " no. 16 " 5735

Mechanism of Soai Reaction• Additional Mechanistic Evidence
rate = k[aldehyde][iPr2Zn][homochiraldimer]→

rate = k’[aldehyde]2[homochiraldimer]

Summary
The evolu
ity can bewhich an itiomers ismarkableessay hasnecessary
Althoughoccur arou
by virtue oof such antion by chspecial kin
Amplificat
Scheme 4. Proposed models for the Soai reaction based on trimeric (A) and tetrameric (B) transitionmeans exi
states, where the order refers to the number of prochiral aldehyde plus ex-aldehyde (alcohol!alkoxide or
action of t
nascent alkoxide species) that are brought together (although not simultaneously) in the reaction event.
lyst. Exper
reaction re
D. G. Blackmond J. Am. Chem. Soc. 2003, 125, 8978-8979
of dimer cBlackmond
Proc. Nat.
Another point comes to mind when D. G.pounds,
is unlikely
inAcad.
itselfSci.
to USA
have2004,
been101, 5732-5736
lower activ
27
of importance in an aqueous prebiotic
the Soai reaction is compared to com-ror image (right-hand side ofiomeric cycles are chemically conequilibrations of homo- and heterd zinc-saturated, dimers. The cataeterochiral dimer RS is not shown
oes not effectively compete with
Scheme 2. Proposed mechanism for the Soai autocatalytic reaction.
[10]s. Indeed, to observe chiral amat the heterochiral dimer is signifihe homochiral dimers. In this way
a trapof thes theion.[11]n, thetions, we proposed the mechanism shown in Scheme 2,talytic
where R2 and S2 are the homochiral dimers; RS is the hetermolecochiral dimer; Z is diisopropylzinc; (R2Z2)I and (R2Z2)II,where
is exand (RSZ2)II are type I and(S2Z2)I and (S2Z2)II, and (RSZ2)Irds
this istype II constitutional isomers of zinc-saturated dimers; A is
oposalthe aldehyde 1, and the abbreviations of the remaining comled at
plexes are self-explanatory.[10]s conThe mechanism consists of fully enantioselective catalytics andlocacycles driven by the homochiral dimer R2 (left-hand side ofof theScheme 2) and its mirror image (right-hand side ofo irre-

h the
3-R2,
les oft 4-R2. The
zationcataIIinindingyde 1(!
hexaR,antid thensitione twoZnor exthe 6irre-

Mechanism of Soai ReactionDFT Study Suggests a Mechanism

Scheme 2). The two enantiomeric cycles are chemically connected through statistical equilibrations of homo- and heterochiral, as well as free and zinc-saturated, dimers. The catalytic cycle driven by the heterochiral dimer RS is not shownin Scheme 2 because it does not effectively compete withthe two homochiral cycles.[10] Indeed, to observe chiral amplification it is required that the heterochiral dimer is significantly less reactive than the homochiral dimers. In this way
the heterodimer acts like a trapthat leaves the excess of the
majority enantiomer as thedominant catalyst in solution.[11]For the sake of illustration, thehomochiral “all-R” catalytic
cycle is translated at the molecular level in Scheme 3, where
the used nomenclature is explained below. To date this is

Scheme 2. Proposed mechanism for the Soai autocatalytic reaction.

This mechanism is consistent
with kinetic results

G. Ercolani Chem. Eur. J. 2010, 16, 3147-3156
28

III. Organic Autocatalysis~ Synthetic Autocatalyst ~✤ Self-Replicating System✤ Ability to Catalyze Other Reaction

29

ationo its
s rewithucleic
nforears,
hetic
quesn demouireions,
From
maand
hierg thison ofcrecient
thers
that
ation

Replication Models
Minimal model

A. Vidonne, D. Philp

Figure 1. The minimal model of self-replication. Reagents A and B
can react through three pathways – an uncatalyzed bimolecular
reaction, a recognition-mediated pseudounimolecular pathway mediated by a binary complex [A·B] and a recognition-mediated pseudounimolecular autocatalytic cycle mediated by a ternary complex[A·B·T].

The first channel is the uncatalyzed bimolecular reaction
between reagents A and B to afford the template T. A key
requirement of the minimal model is that A and B bear
complementary recognition sites such that A and B can associate with each other to form a binary complex, [A·B].
The presence of this complex opens a second reaction chan-ence in template complementarity between minimal and reciprocal self-replication is a key distinction between these
two types of system. In a minimal system, the template isself-complementary, whereas in a reciprocal system a pairof templates are complementary to each other. Therefore,
reciprocal replicating systems rely on two interlinked crosscatalytic cycles in which the two templates catalyze the formation of each other. The processes involved in reciprocal
replication are encapsulated schematically in Figure 2.

Additioncross-cat

3. AnalOne oinvestiga
zation ofstudy. Fo
Reciprocal modelstages ofslowly th
will exhib
tion of T
significanthe autoc
the cycletion, thetially, besumed. T
system s
curve. Th
iour of t
In ordlar prodiour, it isFirstly, itpossesses
blocks of
Figure 2. The reciprocal model of self-replication. Compounds C
and D can react to form the template TCD, and, similarly, coming in an
pounds E and F can react to form template TEF. TCD and TEF arecontrolmutually complementary. TCD is capable of assembling E and F
structed
into the ternary complex [E·F·TCD] which catalyses the formationof TEF. Similarly, TEF is capable of assembling C and D into the this contternary complex [C·D·TEF] catalyzing the formation of TCD. These all of thetwo interlinked cross-catalytic cycles represent a formal reciprocal
tion ofreplication cycle.
binding
is import
D. Philip Eur. J. Org. Chem. 2009, 593-610
In these systems, compounds C and D can react to form molecula30
the template T , and, similarly, compounds E and F can inhibitor

The Art of Self-Replicator
+
A

→
B

AB

AB

AB

→
A

B

AB

link: 有機化学美術館（http://www.org-chem.org/yuuki/replica/replica.html）
31

1st Generation of Self-Replicating System• Discovery of Synthetic Self-Replicator

interaction by hydrogen bonding
between adenine and imide
J. Rebek, Jr J. Am. Chem. Soc. 1990, 112, 1249-1250
32

-

5

catalytic effects, control 9 perfo
catalysis, whatever its source,geometricfit implied by the struct
5 in Scheme 1.

6

i

0

the "southern"
40
80 Since 80
100 control 7
time, minnot catalysts, whereas control
aminolysis,mightbetween
suspect th
Figure 2. Time course for formation of amide
4 in the one
reaction
9 (the amide group) plays a key
amine 1 and cster 2 in CDCl3 in the presence of amide 4, amide 9, and2case. 2-Naphthoamide (0.5 equmonitored
forA
N-methylpropionamide (all at 0.03 M). Reactions
standard wereconditions
by 13%.
25.0 "C. almost
Error ininitialthe production of amide 4 by IH N M R at catalysis
as the
large
as th
0
rates
is
estimatedtobe*15%. Note that the
rates
in
the
latterpart(compare Figures 1B and 1D).of N
0
10
20
30
40
the reaction
provides a 3 1%rate increase by 1
time, min(unexamined by Rebek') are identical.
(Figure 2) within experimental e
Figure 1. Initial rates of pcntafluorophenol formation in the reaction of
Scheme2amide 1 (0.03 M ) with ester 2 (0.03 M ) in CDCI3 in the presence of:catalysis can be achieved using fo
A, no additive: B, 0.03 M amide 4; C, 0.03 M control 9; and D, 0.03 M
based mechanism for amide 4 bacetamide.
Reactionsweremonitored
by
19F
NMR
at
25.0
"C.
Communications to the Editor
3614 J. Am. Chem. SOC.,Vol. 116, No. 8, 1994
Although catalyses of less th
15
10
integration was achieved with the aid of an internal standard.warrant a detailed mechanistic r
Hardly any observable difference exists between the amide 4 andM. Litvinenko*osegxirelevanttothat carboxamidesare effectiveca
control 9 additives over a 100-min trace. In the world of smallby acid chlorides in benzene.
8H 9 performs well. And Rebek's autocatalytic effects, control
catalysis, although
one cannot diIcatalysis,
Z'O whatever its source, does not require the precise
among
ionic
tetrahedral
intermE
geometric
fit implied by the structure of the termolecular complexWhatever the precise mechanism
5 6
5 in eScheme 1.
or more were obtained with ami
Since the "southern" control 7 and the "northern" control 8 areours. The 2040% catalyses obse
5 5
4
not catalysts,
whereas 7control 9 does indeed accelerate themost readily explained by a sim
aminolysis, one might suspect that the central portion of controlmagnitude owing, no doubt, to theacid derivative). Note that Litv
8
9 (the amide group) plays a key role. This turned
out to be theimides, consistent with our obs
2case. 2-Naphthoamide (0.5 equiv) catalyzes the reaction underaccelerate the Rebek acylations
0 conditions by 13%. Acetamide (1 equiv) manifests a
standard
40 as that
80 of the80 amide
100 4 "template" Our reasoning,
0 therefore, reduc
catalysis 0almost20as large
0time, minaccelerateacylations.
Rebek's(compare Figures 1B and 1D). N-Methylpropionamide(1 equiv)
0
10
20
30
40
Figure 2. Time course for formation of amide 4 in the reaction between
Therefore,
the catalyzed
acylatiprovides
a
3
1%
rate
increaseby
19F
NMRandalong-term
profileOOtime, minanalog,
9,
is
seen
even
more
strikingly
inFigure2,inwhichamine 1 and cster 2 in CDCl3 in the presence of amide 4, amide 9, andthe presence of the amide.the(Figure 2) within(allexperimental
error
of
amide
4.
Since
Rebek's
Figure 1. Initial rates of pcntafluorophenol formation in the reaction of N-methylpropionamide
werewasmonitoredforat 0.03 M). Reactions
productionof amide
monitoredby 1H NMR.8 Accurate
amide 1 (0.03 M ) with ester 2 (0.03 M ) in CDCI3 in the presence of: the catalysis
summary,
control 9N(a nonc
2
4 by IHusing
N M R fourat 25.0"C. Error
in the initial
productioncanof amidebe achieveddifferent
amides?
a template- InNH
Hcharact
A, no additive: B, 0.03 M amide 4; C, 0.03 M control 9; and D, 0.03 M ratesbasedis estimatedto be *15%.
Note thatthe rates insuperfluous.
the latter part of4)
shows
similar kinetic
mechanismfor(8)
amide
4 becomesIt
wasconsidereddesirabletoutilizetwo
independent
methodsofthe reaction (unexamined by Rebek') are identical.
acetamide. Reactions were monitored by 19F NMR at 25.0 "C.
acetamide
duplicatesthecatalyThus,monitoringamide
4 production
by 'H NMR was carried out
analysis.
Although catalysesof lessthan
2-fold may
be toofeeble topremature toat thisThepoininadditiontomonitoring
pcntafluorophenol
production
byassume
l9F NMR.
Scheme2 a detailed mechanistic rationale, the classic work of L.
15
warrant
predicated upon a template-dirlatter was the more precise.
M. Litvinenko*osegxirelevantto the problem. Litvinenkoshowedunder the conditions of our exp
that carboxamidesare effectivecatalysts in the acylationof amines
simple amide can play a role of catalyst
by acid chlorides in benzene. He favored an 0-nucleophilic
Acknowledgment. This workin Rebek’s self-replicating system catalysis, although one cannot discount assisted proton transfersScience
Foundation.
Z'O
among
ionic
tetrahedral
intermediatesintheaprotic
media.
H
E
I
Whatever the precise mechanism, rate enhancementsof 10-folde(9) The Rebek mechanism is comp
or
more
were
obtainedwithamide
concentrations
equivalent
to
HNYo
the
reactants60,
can beperturb the rate ap
F. M. Menger J. Am. Chem.
Soc. 1994, 116, 3613-3614; J. Org. Chem. 1995,
2870-2878
ours. The 2040% catalyses observed with the Rebek system areThisis why westudiedsimpleamideaddi
to temost readily explained by a similar effect (although smaller inbinding sites (see l l b in ref lb), 33

54

z

0

20

1st Generation of Self-Replicating System• Simple Amide as Catalyst

-

i
5

z

-

i

-

i

HNYo

"

1st Generation of Self-Replicating System
3

4• A Non-Self-Replicative Mechanism

J. Org. Chem., Vol. 60,No. 9, 1995

Alternative Mechanism to a Self-Replicating System

2876

Scheme 2. A Non-Self-ReplicativeMechanism
J. Org. Chem., Vol. 60,No. 9, 1995 2871

Alternative Mechanism to a Self-Replicating System

Scheme 1. Rebek's Self-ReplicativeMechanism
J. Org. Chem., Vol. 60,No. 9, 1995 2871

cating System

me 1. Rebek's Self-ReplicativeMechanism

““Q
\ N
NL N

-

-

J. Org. Chem., Vol. 60,No. 9, 1995 2871

+ to a Self-Replicating System
Alternative Mechanism

7

1+4===

2 or 8)
Scheme 1. Rebek's Self-Replicative(orMechanism

I

"
"
5

plus 0.5 equiv ofd concentrations
will become clear
his group was(Scheme 1)at 2.2
g amide catalysis
ugh a change ofon range seemedd. This is, after
experimentation

3

5

r. J.Am. Chem. Soc.

I I :

3
4

amide works as a base?

4

6

10

9

sites. Such esters cannot, obviously, engage in theformation of a termolecular complex. On the other hand,the amide-catalysis alternative predicts that 4 might
indeed catalyze the+ aminolysis of nonbinding esters
because a termolecular complex is not invoked. These
considerations prompted us, therefore, to investigate thebehavior of the two non-hydrogen-bondingesters shown
below. Experiments with these two esters should settle
the question conclusively.
"

HN

P

3

0

1 + 2 + 4 =nd definitive test
echanism is pre) in which amine
en-bonded to eachnds that catalysis
ydrogen-bonding

=

4

r
7

i

8

A Critiqueof Scheme 1
ing pentafluorophenol as a bonafide product had to be

confronted
directly,and inthe
any factors
case,6 a second independ6
It is instructive
to examine
in moredetailent analytical method is always beneficial. Thus, we
5

11

12

F. M. Menger J. Org. Chem. 1995, 60, 2870-2878

trations mentioned earlier. Rather, the experiments
under the exact Rebek conditions were required to test
the claim that the mechanism changes from 8 to 2 mM.

34

1st Generation of Self-Replicating System• Control Experimentexclude the function of self-replicator
as a simple chemical catalysis
J. Rebek, Jr J. Am. Chem. Soc. 1994, 116, 8823-8824; J. Org. Chem. 1995, 60, 7997-8001
35

1st Generation of Self-Replicating System• Exclusion of Internal Amide Catalysis

O
NH2

O
NH2

cis amide and primary amide cancatalyze the formation of amide
BUT self-replicator is trans amide
J. Rebek, Jr J. Am. Chem. Soc. 1994, 116, 8823-8824; J. Org. Chem. 1995, 60, 7997-8001
366886 J. Am. Chem. Soc., Vol. 118, No. 29, 1996

Reinhoudt et al.

1st Generation of Self-Replicating System
Chart 2
6886 J. Am. Chem. Soc., Vol. 118, No. 29, 1996

6886
Chem.
Soc.,Vol.
Vol.118,
118,No.
No.29,
29,1996
1996
6886
J. J.
Am.
Chem.
Soc.,
Chart
2Am.

Reinhoudt et al.

Reinhoudt et al.
Reinhoudt• Settlement of The Controversy : Kinetic Study

Chart
Chart
2 2

dependence on the concentration of catalyst

Table 2. Calculated Initial Rates for Equimolar Amounts ofand time. In all cases, the above derived rate constants were
1 and 2aused for the pathways depicted in Chart 2: background via I
contribution to(k1 ) 0.035 M-1 min-1 ), preassociatiVe via complex II (k2 )initial rate (%)-10.0044 min ), termolecular via complex III (k3 ) 0.030
II III IV V
[2]o [1]o [3]o (dP/dt)calcd (dP/dt)obsdb I-1), actiVated bimolecular via complex IV (k ) 0.130 M-1
min
4 Reinhoudt et al.
o. 29, 1996
Reinhoudt et al.
1.67 1.67
0.10
9.5 90.5 0.0 0.0 0.0
min-1), and bimolecular via complex V (k5 ) 0.020 M-1 min-1).
1.67 1.67 1.67
0.14
7.0 56.4 33.7 2.5 0.4
In the case where both starting compounds A and E have a
2.2
2.2
0.17
10.1 89.9 0.0 0.0 0.0
2.2
2.2
2.2
0.24
7.2 52.5 36.8 3.0 0.5hydrogen-bonding site, which is the case for 2 and 1, the relevant
8.2
8.2
1.5
1.4
15.8
84.2 0.0 0.0 0.0
equilibrium constants are (Vide supra): K1 ) K2 ) K3 ) K4 )
8.2
8.2
4.1
2.2
2.0
10.7 46.6 36.9 5.0 0.8
K5 ) K10 ) K11 ) K12 ) K14 ) K15 ) K16 ) K17 ) K18 ) 100
8.2
8.2
8.2
2.5
9.6 35.8 45.9 7.5 1.2
M-1, K8 ) 200 M-1, K9 ) 0.3 M-1, K6 ) 60 M-1, K7 ) 10 000
16.5 16.5
4.4
4.1c
21.9 78.1 0.0 0.0 0.0
16.5 33.0
6.9
8.2
27.7 72.3 0.0 0.0 0.0
M-2, and K13 ) 0.03 M-1. The calculated initial rates (dP/
33.0 16.5
6.9
7.9
27.7 72.3 0.0 0.0 0.0dt)t)0 and also the contribution (%) of the different pathways
c
16.5
16.5
8.2
6.9
5.7
13.7
38.3 38.5 8.3 1.3
Table
Initial Rates for Equimolar Amounts ofviaallI-V
to thethe above
product
formation
are compiled
2.222.a Calculated
and time. In
cases,
derivedrate constants
were in Table
16.5 16.5 11.5
7.4
5.9
12.9 33.2 42.4 10.0 1.5
1 and 2
results depictedshow theinfollowing.
First of all, themodel
predicts
used for theThepathways
Chart 2: background
viaTable
I Table16.5
16.5
7.8 Amounts
6.2
12.2 28.1 45.7 12.2 1.9
2. Calculated
Initial16.5
Rates
for Equimolarof
2. Calculated
InitialRates
for
Equimolar
Amountsofcontribution
to 70.3 0.0 0.0 0.0
and
time.
In
all
cases,
theabove
derivedrate
constants
were
-1
-1
and
time.
In
all
cases,
theabove
derivedrate
constants
were
Table
2.
Calculated
InitialRates
for
Equimolar
Amounts
of
a
a
30
30
10.6
12.9
29.7
formationofderived
product
3via
ascomplex
a function
time
with
M
min
), preassociatiVe)
1a2 and2 a
1 and1 ) 0.035
and(ktime.
In allthe
cases,
the aboverate constants
were II (k2ofinitial
rate
(%)
2
used
depictedin fitChart
2: thebackground
via )
Ivia
usedforforthe
thepathways
pathways
depictedin withChart
2: experimental
backgroundI1 and
-1
30
30
15
18.2
17.4 31.1 37.2 12.5 1.9),
termolecularvia
complex
III
(k
0.030
surprisingly
good
data
in
the
concenused0.0044
for the minpathways
depicted
in
Chart
2:
backgroundvia
I
3
contribution
to II toIII IV Vb contribution
-1
-1
-1
-1
[1]
[3]
(dP/dt)(dP/dt)
I
[2]
)
0.035
M
min
),
preassociatiVeviacomplex
II
(k
)
(k(k
30o
30 calcd30 contribution
20.7
16.3
15.2 22.0 42.2 17.9 2.8
o
o
obsd
)
0.035
min
), preassociatiVe
via IV
complexII(k )to rate-1),-1M
initialrateinitial(%)(%)
actiVated
(k
0.130
M-1
)1 10.035
M-1
min-1bimolecular), preassociatiVevia
II4(k)2 22)(k1 mintrationrange
upviatovia
30complex
mMcomplex(see(kTable
and2 Figures3-7). At
initial
rate
(%)
-1
50
50
22.9
47.0
0.0 0.0 0.0),
termolecularcomplexIII)
0.030
0.0044min
3 (k3 )-10.030-1), termolecularvia complex
III
0.0044
min
-1
1.67
0.10
9.5
90.5
0.0 38.3
0.0 61.7
0.0-1bbII I III II),
termolecularvia
complex
III
(k
)
0.030
0.0044min[1]oo 1.67
[3]
(dP/dt)(dP/dt)
I
IV
V
[2]
min
),
and
bimolecularvia
complex
V
(k
)
0.020
M
min
).
3
o
o
calcd
obsd
[1]
[3]
(dP/dt)(dP/dt)
III
IV
V
5
[2]
50
mM
the
actualrates
arehigherthan
predicted(probably
due
-1
-1
o 50
calcd
b 25I obsd II 41.3
500.14-1-1 [2]o), ),actiVatedbimolecular
via via
complex
IV (k
0.130
M
min
[1]o 1.67[3]o o 1.67
(dP/dt)III 7.0
IV 56.4
V 33.7 21.2
4)
calcd
obsd
1.67(dP/dt)
2.5 25.3
0.4 33.8 17.2 2.6
actiVatedbimolecularcomplex
IV
(k
min
-1 M
4 ) 0.130),
actiVatedbimolecularvia
complex
IV
(k
)
0.130
M
min-1
7,8
4
1.67
1.67
0.10
9.5
90.5
0.0
0.0
0.0
-1
-1
-1
18.2
In-1
case
where
both
starting
AM
andErelative
have
).
The
to
generalbase
amide
1.672.21.67 2.2 0.1050 0.10500.17 509.5 90.5 48.1
9.50.090.5
0.0
0.0-1 min-1). a contribution
min
),the
bimolecularvia
complexV (kcompounds
)
M
min
10.1
89.9
0.00.00.0 17.0
0.0 37.1 24.0 3.7
min
),and
and
bimolecularvia
complex
V5catalysis(k50.020) 0.020
1.67
0.0
0.0
-1
-1 min-1).).
1.67 1.67
1.67
1.67
0.14
7.0
56.4
33.7
2.5
0.4
minhydrogen-bonding), andbimolecularvia
complexV(k5 ) 0.020 M
1.672.21.67
1.67 2.21.67
56.4
33.7
2.5
0.4
2.2 0.14 0.24 7.0 56.4 7.0
7.2
52.5
36.8
site,
which iscompounds
thecase for
2and
and
the
of
the bothbackgroundreactionincreases
whentheconcentration
1.67
0.14
33.7
2.5
0.4
-1 ×3.05.0.5
b Average rate over
InInthewherestarting
A
E 1,
have
arelevant
2.2
2.2
0.17 a 0.17
10.1 in
89.9
0.0rates
0.0in0.0
0.0
Concentrations
mM;
M‚min
10
thecase
case
where
both
starting
compoundsAEand
E ahavea 1.67
2.2
2.2
10.1
89.9
0.0
0.0
Inequilibrium
the casewhere
bothstarting
compounds
A
and
have
8.2
8.2
1.5
1.4
15.8
84.2
0.0
0.0
0.0
23
2.2
2.2
0.17
10.1
89.9
0.0
0.0
0.0
)the
K2relevant) K3 ) K
constantsaresupra):
K1 preassociative
2.2
2.2 The2.2
0.24the first 100 min.
7.2 c 52.5
36.8
3.0 0.5
increases
atwhichtheexpensethemechanism.
4 )hydrogen-bonding
site,
which
is(Videthecaseforof2forandUsed
for52.5
parametrization.
2.2
2.2
36.8
3.0 0.5hydrogen-bondingsite,
iscase
the
case
21,1,
and
1,
the relevant
8.22.2
8.22.2
4.1 0.24 1.4
2.2 15.8
2.0 7.2
10.7
2.2
2.2
0.24
7.2 52.5
36.8
3.0
0.5
hydrogen-bonding
site,
which
is
the
for
2
and
the
relevant
8.2
8.2
1.5
84.2
0.0
0.0 46.6
0.0 36.9 5.0 0.8
K
)
K
)
K
)
K
)
K
)
K
)
K
)
100
Kequilibrium
)
K
K
)
K
)
equilibrium
constantsare(Videsupra):K5 ) K10 )
11
12
14
15
16
17
18
1 at 8.25
2
3
4
template
effectis highest
andconcentrations
8.2 8.28.2 8.2 1.5 8.2 1.5 1.42.5 15.8
1.4
15.80.084.2
0.0
0.0 0.0
0.0
0.0
9.6
K
)K
K416.5) KmM
constantsare (Videsupra):
3)4 ) 8.2
8.2 8.2
8.2
4.1
2.2
2.0
10.7 84.2
46.6 36.9
5.0 35.8
0.8 45.9 7.5 1.2
K1K))
K23K-1)equilibrium
constantsare(Videsupra):
KK1 ))K2)-1,KK )
-1,)
-1
c
8.2
8.2
4.1
2.2
2.0
10.7
46.6
36.9
5.0
0.80.0 0.0 +
)
K
)
K
K
)
K
)
)
100
KM
)
200
M
K
)
0.3
M
,
K
)
60
M
,
K
)
10
000
5
108
11
15 the 16
17
8.2
8.2
2.04.4in hydrogen
10.7
5.0
0.8
9 14K In6
7 equimolar
4.1 36.9
21.9
0.0
to12
presenceof18
anof16.5 2.2
8.2 amount
8.216.54.1
8.2
2.5 involved
9.6 46.6
35.8
45.9
7.5 78.1
1.2
interaction
bondingvia
a
CdO‚‚‚HsN
K10K11)(up
K11K-112)
K46%).
)
)
K
)
K
)
K
)
K
)
100
12
14
15
16
17
18
)K-15-2
K,)
)
)
)
K
)
K
)
K
)
K
)
K
)
100
K5 M
10
14
15
16
17
18
-1
-1
8.2
8.2
8.2
2.5
9.6
35.8
45.9
7.5
1.2
-1
c
8.2
8.2
8.2 33.0 2.5
9.6 35.8
45.9
7.5
1.2
K
)
200
M
,
K
)
0.3
M
,
K
)
60
M
,
K
)
10
000
16.5
6.9
8.2
27.7
72.3
0.0
0.0
0.0
8
9
6
7
16.5
16.5
4.4
4.1
21.9
78.1
0.0
0.0
0.0
,
and
K
)
0.03
M
.
The
calculated
initial
rates
(dP/
M
24
-1
-1
-1
-1
13
-1,M
-1, M
-1
template,thecontribution
complexIII,)K200200, K0.30.3,K60, theM7 )termolecular, 10
K7 000) 10 00016.5
Mc
Atc 30mM,
it 0.0contributes
almost
7 times as much
(Figure8).
,-2K,8 andK9 )Kcalculated
606 )
Mof
K
M-1
8)M
9 )M
16.5
16.5to4.4 4.1
4.1
21.9
0.0
0.0
6)
-1
4.4
21.9
78.1
0.0
0.0
16.5 16.5
33.033.0
6.9
8.2
27.7
72.3
0.078.1
0.0 72.3
0.0 0.0
16.5
6.9
7.9
27.7
0.0
0.0
0.0
K
)
0.03
M
.
The
initial
rates
(dP/
M
13
and
also
the
contribution
(%)
of
the
different
pathwaysdt)-2-1t)0, and
16.5
33.0 16.5 6.9
6.9 8.2
8.2
0.0
0.0
0.08.3 In
16.5
72.3
0.0
0.0
in therange
ofinitial
34%(1.67(dP/mM)
to 33.0
46%(16.5
K)initial
0.03
MThe.is(%)
The
calculated
rates
M
c 0.0
, and
K13also)the
0.03
M-1.rate
calculated
initial
rates
(dP/
M-2
to theoverallinitial
rate
than
13the
33.0
16.516.5
6.98.2
7.9
27.7
72.3
0.072.3
0.0 at0.01.67
6.9 27.7
5.727.7
13.7
38.3
38.5mM.
1.3reactions where
andcontributionofthedifferent
pathways
dt)
22
t)0
c
via
I-V
to
the
product
formationarecompiled
in
Table
2.
33.0
16.5
6.9
7.9
27.7
72.3
0.0
0.0
0.0
33.0
16.5
6.9
7.9
27.7
72.3
0.0
0.0
0.0
D.
N.
Reinhoudt
J.
Am.
Chem.
Soc.
1996,
118,
6880-6889
16.5
16.5
8.2
6.9
5.7
13.7
38.3
38.5
8.3
1.3
also
the
contribution(%) ofthepathwaysdt)viaalso
the contribution(%)
ofdifferent
thethedifferentdt)and22
16.5 the16.5 11.5
7.4
5.9a recognition
12.9 33.2site
42.4(e.g.,
10.02 1.5mM).
Thecontributionofcatalysis”
throught)0t)0 andonly6.9the+4) threeof thecaminechas
I-V
to theproduct
formationarecompiled
in“amide
Tablepathways
2.
16.5
16.5
8.2
6.9
5.7
13.7
38.3
38.5
8.3
1.3
16.5
16.5
8.2
5.7
13.7
38.3
38.5
8.3
1.3
16.5
16.5
11.5
7.4
5.9
12.9
33.2
42.4
10.0
1.5
The
results
show
theformation
following.
Firstof all,model
16.5 16.5 16.5
7.8
6.2
12.2 the28.1preassociative
45.7 12.2 1.9pathway via II,
viaTheI-V
to theproduct
areIV
compiled
in theTable
2.22 predicts
37
via
I-V
to
thetheproduct
formation
inTable
2.2216.5
activatedcomplexincreaseswithincreasing
concentration.
pathways
are33.2
excluded:
results
show
following.
First
ofare
all,compiled
the model
predicts
16.5
7.4 five7.4
5.9
12.9
42.433.2
10.042.4
1.5 10.0 1.5
16.5 11.5
16.5 11.5
5.9
12.9

2nd Generation of Self-Replicating System• Modification of Spacer

strategy : reduce the pre-associative bimolecular pathway

Hoogsteen-type

Watson-Crick-type

Watson-Crick-type

Watson-Crick-type
long

long

Communications to the Editor
have a sigmoidal
character

J . Am. Chem. Soc., Vol. 113, No. 24, 1991 9423

have no catalytic activity

short

0

20

40

60

80

100

Time (Min)have no catalytic activity

showed the appropriate curvature. The lines represent the best
fit of the data to von Kiedrowski’s) square root law for autocatalysis. The coupling of N-methyl imide 3b, which is incapableof base pairing, shows normal (linear) product growth with amine
2 but is slower than 3a. Therefore, the mechanism involving
bimolecular base paired species such as 7 is still operative. (Thiswas the major pathway in molecules bearing shorter naphthyl or
phenyl spacer surfaces.’,*)The sigmoidality of the autocatalyzed reaction curve is aconsequence of the self-replicating pathway via termolecularcomplex 8. Efficient autocatalysis results when template 1, theproduct of the coupling reaction, is added to the reaction medium.
For example, when 0.2 equiv of 1 is present at to, the rate enhancement observed is nearly 2-fold. N M R titrations of ester 3aand 5’-acetyl-2’,3’-isopropylideneadenosine indicate a K , forcomplex 7 of -280 M-I, and the estimated K, for the termolecularspecies 8 is about 78 000 M-2. Dimerization of the template wasmeasured as ca. 80000 M-I. Thus the concentration of termolecular complex 8 at 25% completion is only 3%, yet its presence
increases the rate of product formation 2-fold.

Figure 1. Plots of appearance of la and l b vs time as determined by
HPLC for a representative run. Initial concentrations of 2, 3a, and 3b
were 50 mM in CHC13 with 9 equiv of Et,N added: (a) reaction of 2
and 3 and (b) reaction of 2 and 3b. Boxes represent approximate uncertainty (hO.1 mmol). The lines drawn represent the best fit of the vonKiedrowski rate law expression.

Scheme 11

need a moderate long spacer

J. Rebek, Jr J. Am. Chem. Soc. 1991, 113, 9422-9423
38

2nd Generation of Self-Replicating System• Modification of Backbone
Hoogsteen-type
Hoogsteen-type

Watson-Crick-type

combineWatson-Crick-type

Ka = 105 M-1

associate constant Ka = 60 M-1

J. Rebek, Jr J. Am. Chem. Soc. 1994, 116, 8877-8884
39

2nd Generation of Self-Replicating System• Improvement of Autocatalytic Activity

J. Rebek, Jr J. Am. Chem. Soc. 1994, 116, 8877-8884
40

Reciprocal Self-Replicating System↑components of reciprocal self-replicating system

J. Rebek, Jr Tetrahedron 1995, 51, 485-498
41

Autocatalyst as Organocatalyst• Strategy
insertion of a functional group known to catalyze organic
transformations into already known autocatalyst 1a
candidates of functional groups

S
R

N
H

N
H

R

thiourea!

conversion to catalytic active group

autocatalyst reported by Rebek and co-workers

O R

N
O
H
prolineO

R
N

N
H
imidazolidinone
J. Rebek, Jr Proc. Natl. Acad. Sci. USA 2010, 107, 541-544
42

Autocatalyst as Organocatalyst

View Onlin
Fig. 3 Effects of catalysts on Michael additions using 2,5-pentanedione as a nucleophile. The concentration of the product (mM) is
plotted against time (hours).

• Auto-/Organocatalyst with Thiourea

Fig. 2 The synthesis of autocatalytic and organocatalytic molecules.
Both 2b and 5 lack recognition sites and were used as controls.

Table 1 Competition reactions between thymine isothiocyanate 4aand N-methylated thymine isothiocyanate 4b with xanthene diaminopyridine unit 3a
Entry

Catalyst 2a (%)

Yield of 2a + 2b (%)aRatio (2a : 2b)b

1
2
3c
4
5c

0
25
25
50
50

91
94
95
92
87

68 : 32
74 : 26
90 : 1074 : 26
92 : 8Isolation by column chromatography. b Ratios were determined by
HPLC after column chromatography. c These reactions were
performed using high dilution conditions of isothiocyanates 4. The
yields and ratios of products have been corrected for the addition of 2aat the start of the experiments.

on http://pubs.rsc.org | doi:10.1039/B916836Baalone did not show catalysis of these reactions, but the
combination of 3a and 4a showed the same activity as 2a
itself. Accordingly, the organocatalytic activity requires thethiourea function and the formation of 2a is much faster thanFig. 4Fig.The
reductionof a nitroolefin.
3 organocatalyzed
Effects of catalysts
on Michael
additions The
usingconcentration
2,5-pentanethe Michael reactions. In these cases, the reaction conditionsof thedione
resulting(mM)Theis plottedagainst reaction
progress(mM)(days).
as a productnucleophile.
concentrationof the productisFig. 2 The synthesis of autocatalytic and organocatalytic molecules.
for autocatalysis
andorganocatalysis
similar;to ourplotted against time (hours).
Both 2b and5 lackrecognition sitesare
andquitewere used
as controls.
knowledge, a system in which the product of an autocatalytic
should, be considered as starting points for the autocatalytic
Comm.
7324-7326
reaction Table
is ableto catalyze
otherbetween
unrelated
reactionsis 4a reproduction ofJ. Rebek,
catalyticJr Chem.
capabilities
as2009,proposedby
1 Competition
reactions
thymineisothiocyanate
15
and N-methylated thymine isothiocyanate 4b with xanthene diamino- Eschenmoser.
unprecedented.
In the meantime a ‘‘top down’’ approach43

a Hewlett–Packard
HP-1100
seriessystem with following gradients:
synthetic systems that on
are potential
precursors to
the RNA
world.
108.6,
67.8,
131.2, 129.9, 128.6, 127.6, 127.2, 127.1,
124.3,7.25
123.6,
7.38126.4,(d, J125.8,¼ 2.0124.8,
Hz, 1H),(s, 1H),
7.0
Materials
and100%
Methods
5–40% over 7 min, 40–100% over 25 min,
and
then
over
5
min
high-resoluti
108.6, 67.8, 57.7, 49.9, 44.5, 35.3, 35.1,
35.0,
33.8,
32.2,
32.1,
31.2,
13.0;
(m, 3H),(d, Jsuppliers¼ 6.9 Hz, 2H), 6.78
Materials and Methods
GeneralExperimental.
Allreagents
from 6.82
commercial[CH3 CN in H2 O (0.1% TFA)], with the flowrate
of 0.5 mL∕min
on a were
GL obtained
ionization–F
high-resolutionmassspectrometry(HRMS) [matrix-assisted laser desorption/

Autocatalyst as Organocatalyst

CHEMISTRY

4.19− 4.12were(m,recorded
2H), 4.12
usedwithoutPeak
furtherpurification.
NMR
spectraon−a4.08 (m, 1H),
General Experimental. All reagentsfrom commercial
Sciences,were
Inc.obtained
Inertsil-ODS-1HO,
4.6suppliers
× 150 andmmionization–Fouriercolumn.
areas
werelated for C42transform
mass spectrometry (MALDI-FTMS): MHþ ] calcuat 300 K. HPLC
for analysis
was performed
and used without further purification. NMR spectra were recorded on aBruker DRX-600 spectrometer
J
¼
7.1,
13.5
Hz,
1H),
3.44
(dd,
J ¼ 9.8,
þ
integrated at 254 nm. The details of the synthetic
procedures
character-found 744.3975.
Trans
2c:
lated
for C42 H50 Nand
9 OHP-1100
4 744.3998,
seriessystemwithfollowing
gradients:
Bruker DRX-600 spectrometer at 300 K. HPLC for analysis was performedon a Hewlett–Packard
13
1(s, 6H),
1.33
9H),(s,(m,9H);
C NMR
Trans 2c: H NMR(600acids
MHz,4aDMSO-d6)
δ 11.28(s, (s,1H),
7.611.17− 7.552H),
7.38(d, J ¼(1izations of the aldehydes 3 and 5, as well as thymine-derived
amino
on a Hewlett–Packard HP-1100 series system with following gradients:5–40% over 7 min, 40–100% over 25 min, and then 100% over 5 min
7.38 (d, J ¼ 2.0 Hz, 1H), 7.25 (s, 1H),167.2,
7.08 (d,164.4,
J ¼ 1.9151.0,
Hz, 1H),
7.06 −145.9,
6.96(m, 3H),
6.8
146.4,
145.3,
and 4bare25described
SI Appendix.
5–40% over 7 min, 40–100%
overmin, and inthen
100% over 5 min[CH3 CN in H2 O (0.1% TFA)], with the flow rate of 0.5 mL∕ min on a GL(m, 3H),(d, J ¼ 6.9 Hz,4.62H),(s,column.
4H),
6.18
(d,areas
J 126.0,
¼ 6.5
Hz,
1H),
4.19
− 4.1212(127.8,
127.1,
126.6,
124.8,
124.4,
Inc. 6.82
Inertsil-ODS-1HO,× 1506.78
mm
Peak
were
[CH3 CN in H2 O (0.1% TFA)], with the flow rate of 0.5 mL∕ min on a GLSciences,
4.19 − 4.12(m,
2H),
− 4.08(m,synthetic
1H),
4.06procedures(s, J ¼
16.0
Hz,character1H),
3.6931.4,(dd,
J ¼31.3,
7.1, 13.5
integrated
at 254nm.
The4.12detailsof theandSciences, Inc. Inertsil-ODS-1HO,× 150 mm forcolumn.
Peak areas
44.0,
34.5,
34.3,
34.2,
31.5,
31.
General4.6
Procedure
the Synthesisof wereImidazolidinones
2.
Thymine-derived
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
(
þ
izationsofthealdehydes
3
and
5,
as
well
as
thymine-derived
amino
acids
4a
þ
integrated at 254 nm. Theamino
details of
the4asynthetic
andtreatedcharacter-with a solution of aldehyde 3 oracid
or 4b procedures(3 mM) was
MH ) calculated for C42 H50 N9 O4 744.399
13
1.33 (s, 9H),(s, 9H); C NMR (151 MHz, DMSO-d6) δ 172.3, 171.8,
167.2, 164.4
4b 6H),are describedin 1.17SI Appendix.
izations of the aldehydes 3 and 5, as well as thymine-derived amino acids 4aand (s,167.2, 164.4, 151.0, 146.4, 145.9, 145.3, 144.6, 142.5, 136.8, 130.3, 129.6,
127.8, 127.1,
and 4b are described in SI Appendix.
127.8,
127.1, 126.6,
126.0,
124.8,of124.4,
124.0, 123.0,2.121.9,
107.7, 57.0, 49.4,
44.0, 34.5, 34
GeneralProcedure
for theSynthesis
Imidazolidinones
Thymine-derived
44.0,
34.5,
34.3,
31.5,
31.3,with
31.3,a 31.1,
12.0;ofHRMS(MALDI-FTMS:
acid
4a or
4b 34.2,(3 mM)
was31.4,
treatedsolution
aldehyde
3 orMHþ ) calcula
General Procedure for the Synthesis of Imidazolidinones 2. Thymine-derivedamino
amino acid 4a or 4b (3 mM) was treated with a solution of aldehyde 3 orMHþ ) calculated for C42 H50 N9 Oþ
4 744.3998, found 744.3982.

• Auto-/Organocatalyst with Imidazolidinone

ngs and synthesis of autocatalytic molecules. The previously reported self-replicator 1, was modified to contain an embeddeda. 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
aldehyde 5 lack the corresponding hydrogen bond motifs (recognition elements) and were used as controls.

plex 6 to template the reaction. This complex
The imidazolidinone motif is also known to catalyze the couacting sites, aldehyde and amine, in close proxipling of indoles and α,β-unsaturated aldehydes in Friedel–Crafts
ates the rate of their condensation reaction.
alkylations (21) (Fig. 5). Compound 2a was also effective in thisinone site in the self-replicating molecule 2a iscontext: The addition of N-methylindole 10 to 7 was catalyzed bying α,β-unsaturated aldehydes via the reversible
Fig. experiments
4. The organocatalyzed
cinnamaldehyde:
red line, 0.2 equiv
2a and control
withreduction
3 andof4aclearly illustrated
that2a; green l
Fig.
4.
The
organocatalyzed
reductionofcinnamaldehyde:
red
line,
0.2
equiv
2a;
green
line,
0.2
eqiv
3;
blue
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. line, 0.2
nium ions (20).Fig.This
catalytic functional groupthe catalytic activity of 2a is not housed in its diaminopyridine or
Kamioka groups.
et al.
syntheses of the replicator. The organocatalytic
imide functional
Kamioka et al.
PNAS ∣ January 12, 2010 ∣ vol. 107 ∣ PNAS
no. 2 ∣ ∣ 543
Kamioka et al.
January 12
s demonstrated in a hydride transfer
reactionIn the present
study,
neitherthecatalystnorthereaction
J. Rebek, Jr Proc. Natl. Acad. Sci. USA 2010, 107,con541-544
innamaldehyde 7. The substrate was reduced
ditions are conventionally prebiotic, and the replication does not 44

IV. Biological Autocatalysis~ Self-Replication of RNA ~✤ Evidence for RNA World

45

What is the RNA World ?
RNA World is...
a self-replicating system consisting of RNA(NOT
DNA/Protein), thought to exist in earlier time on
the earth.
However...
There are some points to be discussed in RNA
World hypothesis.
1) No evidence for forming RNA from many other nucleotide
2) Unstable structure of RNA compared to DNA
3) Never discovery of self-replicating RNA

46

catalytic
and fication
varying
rates
ofin5
exponential
catalytic
partners
without
markedlyaffectingrate wasandvessel
1.05Six
hour,containsrespectively.
after
hours.
cross-replicating
werecontains
varied,the rule
thatactivity
eachenzymes
ferredgrowth
to a newreactionthata fresh
shown
Fig.
1CThe
had various
the following
regiononeadoptingG•C and
three
A•U
pairs
so
supplyof0.92
substrates.
successive
reactionswereends
REPORTS
growth
(fig.
S1).
The
pair
shown
in
Fig.
1B
(now
replication
efficiency.
These
regionsarelocatedExponential
growthcanbecontinued
inderank
orderofreplication
efficiency:
E1,
E10,
E5, following
that
there
would
be
no
substantial
differencesincarriedoutinthisfashion,
each
5
hours
in
durationshown
in Fig. 1C had theregion contains
one G•C
andthree A•U
pairs so enzymes
supply of substrates.
Six successive
reactionswereand demonstrated
varying
levelsof rate ofthe(Fig.
cross-1B).tested
the transfer
enzymes experiment
E and E′, thedesignatedE1 andE1′)
hadE12,thefastestatgions
the of5′ Watson-Crickand3′ ends pairingof stability.
thebetween
enzymefinitelyrate.
in aForserialin exponential
which
a one
E4,
E6,
E3,
E7,
E9,
E8,
E2,
E11.
The
top
five
base-pairing
Of
the
32
possible
pairs
of
and
transferring
4%
of
the
material
fromreac–1
rank
order
of
replication
E1, E10, E5,
that
there
wouldatbenotheaffecting
substantial
differences
invarying
carriedoutgrowth
in
each
hours
intransduration
activity andrates ofexponential
catalytic
partners
without
markedly
ratefashion,
was 0.92reaction
and
1.055
hour
, respectively.
exponential
growth,achievingabout
20-fold
ampli-thanefficiency:
Fournucleotide
positionsboth
5′ forand each
3′catalytic
portionof thisamixturecompletedmixturereplicators
allachieved
more
10-fold amplicomplementary
sequences
region,12The
tion
togrowth
the next.
The
firstismixture
contained
growth
(fig.
S1).
pair
shown
in
Fig.
1B
(now
replication
efficiency.
These
regionsarelocatedExponential
canbecontinued
indeE6, E3,
E12, E7, E9, E8, E2, E11. The top fivebase-pairingstability.
Of thatthe 32and transferringof thematerial
froma one
ficationpairs
after 5ofhours. E4,
The various
cross-replicatingends werevaried, adopting
the rule
eachpossible
ferred to a new4%
reaction
vesselthat contains
fresh reacfication
5 hours,
werechosena set of(Fig.
designatedpairingsE1(Fig.
0.1 mM
andtransfer
0.1 mME′, but
all subsequentand E1′)
had theafter
fastestrate ofand all except E11 achieved
3′ endsof theasenzyme
1B). designatedfinitelyin a Eserial
experimentin whicha at the 5′ andenzymes
shown
in
Fig.
1C
had
the
following more than 10-fold ampliregion
contains
one
G•C
and
three
A•U
pairs
so
supplyofsubstrates.
Sixsuccessive
reactionswerereplicators
all achieved
complementary
sequences
region,tion mixture
to theThe reaction
first mixture
contained
exponential
growth, 12achievingabout
20-foldamplification
amplinucleotide
at boththe 5′associatedand for3′ eachportionof anext.
completedmixtureistrans-thatFour
at least
fivefold
1C). positions
Eachpairing
waswith
a orderparticmixturescontained
only
those
enzymes
were
rank
of
replication
efficiency:
E1,
E10, E5,after 5 hours.
that
there
would
be
no
substantial
differencesincarriedferred
out intothis
fashion,
each
5
hours
in
duration
after
5both
hours.
The various
cross-replicating
ends
were
varied,adopting
the
rule
that
each fication
aover
new inreaction
vesselbutthat
contains
a freshficationafter
5
hours,
and all except E11 achieved
werechosenasasetof
designatedpairings(Fig.
0.1 mM
E
and
0.1
mM
E′,
all
subsequentA
serial-transfer
experimentular
sequence
withinthecatalytic
coreofcarriedthetransfer.
Exponential
growthwas
E4, E6,
E3, E12,
E7,1C
E9,had
E8,theE2,following
E11. The top five was initiated with astability.
Ofandthethree
32 possible
pairs
and transferring
4% of theSix
materialfrom
one reacshownin Fig.
region contains
one G•CA•U pairs
so ofenzymes
supply of substrates.
successive
reactionswere base-pairing
at moreleast
fivefold
amplification
5 hours.
1C).
Eachpairing
associatedwitha replication
particmixturescontained
only
those
enzymesthat
were
0.1efficiency:
mM
concentrationof E1 to E4 afterand E1′tomembersa cross-replicating
Twelvemaintained
throughout30
total
of incubation,
replicators
all achievedthan
10-fold
amplicomplementary
sequences
for waseachregion,12ranktion mixture
toouttheinnext.
The
first
mixtureorder ofpairs
E1,
E10,
E5,eachthat there
would
be no ofsubstantial
differencesin pair.
carriedthisfashion,each
5hourshourscontainedin duration
8
E4′
and
a
5.0
mM
concentration
of
each
of
the
16
of
cross-replicating
enzymes
weresynthesized,withanoverall
amplificationofgreaterthan
10A
serial-transfer
experimentwas
initiatedwith aular
sequence
withinthecatalytic
core
of
both
carriedoverinthetransfer.
Exponential
growthwasfication
after
hours,
andE11.
all except
chosen stability.
as a set Ofof designatedpairings
0.1 mMand 0.1 4%
mMof E′,but all from
subsequentE3, E12,E7,5 E9,
E8, E2,The topE11
five achieved
base-pairing
the 32 possible
pairs of(Fig.E4, E6,
andEtransferring
the material
one reac- werereplicators
allachieved
morethan
10-fold
amplicomplementary
sequencesfor
each
region,12
tion
mixture
to
the
next.
The
first
mixturecontained
corresponding
substrates.
Sixteensuccessive
as
well
as
the
48
substrates
(12
each
of
A,
A′,
B,
fold
for
each
of
the
two
enzymes
(Fig.
2B).
at
least
fivefold
amplification
after
5
hours.
1C).
Eachpairing
wasassociatedwithaparticmixturescontained
only
those
enzymesthat
weremaintained throughout 30 hours total of incubation, members of a cross-replicating pair. Twelve pairs 0.1 mM concentration each of E1 to E4 and E1′ toficationafter
5 hours, andallexceptE11
achievedchosenandaswithina B′)
set ofnecessary
designatedpairings(Fig.
0.1
Epossible
and
0.1 tomME′, but all
subsequentA serial-transfer
experimentwas
initiatedwith 70
a hours, transferring
thecatalytic
coreof bothovermMthetransfer.
Exponential
growthwas
8weretransfers
werecarriedout
overtosupporttheir
exponential
Itinisamplification
constructvariantsof theularcrossato5.0
mM
concentrationof each of the 16
ofofcross-replicating
enzymes
weresynthesized,with carriedan overallofgreaterthan- sequenceat least
fivefold
amplificationE4′
afterand5 hours.
1C).
Eachpairing
was associatedpair.
witha partic-pairs
mixturescontained30only
those
enzymesthatwere10members
0.1
mM
concentration
each
of
E1
E4
and
E1′
to
a
cross-replicating
Twelvemaintained
throughout
hours
total
of
incubation,
replicating RNA enzymes that differ8 in the re- amplification. Each replicator was individually 5% of the material from one reaction mixture to theAserial-transfer
experimentwas
initiated
with
a
ular
sequence
withinthecatalytic
core
of
both
carriedoverinthetransfer.
Exponential
growthwascorresponding
substrates.
Sixteensuccessive
as
well
as
the
48
substrates
(12
each
of
A,
A′,
B,
fold for
each
of
the
two
enzymes(Fig.
2B).
with an overall amplification of greater than 10 - of cross-replicating enzymes were synthesized, E4′ and a 5.0 mM concentration of each of the 16
maintained throughout 30 hours total of incubation, members of a cross-replicating pair. Twelve pairs 0.1 mM concentration each of E1 to E4 and E1′ toSixteenas well andas theB′)48 substrates(12 eachof A, A′, B,
for each oftothe
two enzymes(Fig. 2B).
transfers
were successive
carried out over 70 hours, transferring
necessaryto support
theircorresponding
exponentialsubstrates.
Itfoldis possible
constructvariantsof the crosswith an overall amplification of greater than 108- of cross-replicating enzymes were synthesized, E4′ and a 5.0 mM concentration of each of the 16transfers
werecarriedout
over
70
hours,
transferringandB′)
necessary
tosupporttheir
exponentialItispossibletoconstructvariants
ofthecrossof thematerial from one reaction mixture to theEachindividually
replicatingfold
RNA
enzymesthat differ
in the re-as wellamplification.
corresponding
substrates. 5%
Sixteensuccessive
as the 48 substrates (12eachreplicatorof A, A′, B, wasfor eachof the two enzymes(Fig. 2B).
5% wereof thecarriedmaterial
from70one
reaction
mixture to the
Eachto replicator
wasexponential
individuallytransfers
replicatingIt isRNA
enzymesthat variants
differ inthecrossre- amplification.
out
overhours,
transferringandB′)
necessary
supporttheirpossibletoconstruct
of
the
A
B
5% of the material from one reaction mixture to the

Self-Replication of RNA•Discovery of Self-Sustained Replication of RNA
amplification. Each replicator was individually

replicating RNA enzymes that differ in the re-

A

A A

A

A

AA

A

B

B

B

E´

A

B

E´

E´ B

E´

B

E´

E

E
E
B´

A´

A´

3´- C U U A

E

U

AG

G
E´
UGU
G U U C AE´

3´- C U U A U A A G U A C G

E

E
A´

UUCA

U
A

E1A A G U

G

A

UU
U

A
UUU CGCUUCAAGA GUUUAGU
AE7U U UCC GAU

A A AG

A

G
U
GU

B´

B´

C

E1C

GCAACUU

G
U
U
UU
GA
A

G

GC
UU
U
U
GU
A

E2
G

E2UU

A´

A´

U
A
C
A
G
G GA- 5´ U
A U E´ G
G
U
A
C
G C
G A U UA
ppp G UGA A CA GGC
GGUU
G A A U OHU GACC
A U
U G
G C
U A
U
G
GU U G G
CCA
UUUG
U GA U
A
G
A
G
G U U
A A U G
A
A U U
C G U
C G G
U
A U
A U A
A
U
A U
A U C
G
A
G
C
G C
A U
A U
G
A U
A
U
U A
U A
U
C
U A G
U A U
U
C G A
C G
A
A
G U
U
A U
A
G
U A
G
A U
C G

A

U
G

G
U
U
G U
AUCU
GA
U UCA
GG
G UU AU AGA

E2U U AGA
U
CU
AU
G
UU G
E8 C U GCGUAA A UA
GAA

B´

U

UCUU

G

A U
U

A

E3
U
G

AU AG

A
E4
U
UC AU
U
U A
G U
AGU A
C
U GA
AU AG A U
U
U
A AU
U
A

G
E5
U
GAAU
U
C
G U
CUUA
A
C C
G G UC AU
U A
A U
C
A

U
G

G
C
U
G U
G
U GU
C
UU A G

E6

A U

C AUU

G

U
A

G
U
C
GU U GCG G C UU A UAG
E4
E3
E5 G U A A
UU A U C
G
AU
G AE6
E4
E5
U
C
C AUU
GAAU
G UA U A G
G U
G UC
UA U
G U
U
U
U
CUUA C G G
U AUC
C G
C G U GC U
G GG UG GU
U AGU AU G
GU
E9 U A U C AC UG
E10U A G
E11
U AA CA U C GE12GAUUAUAA C
C
U UA
G
U
U A
A
U
A
U GU AC AU AU AGU
U U AG

E3

A´

U

AAUC

G

U
A
U

AUC A

G

UU A
U

AC AU

G

UU
C

A

GU AU

A

U
U

U

G
U catalyze
G
E1 copies that can
E2 reaction. (B)U SequenceanotherandE3secondaryB
GCAACUU

U portionA
C The
G corresponding
iable
of 12
different E enzymes.
E4
E5 E′ enzymes UhaveGa

A - 3´UGUUGAAG G - 5´
G
C
U
C
G

A
U
A U
C G
A U
A U
G C
E6
A UU
G
U AA
C AU
U
U
U AG
C
GU A
U
CA GC
G
A
GU
A
A U
U
GE12
A
C AU A
U

C G
G
U G
U C
G G
U G C G
E8 U UU G AA E9
E7 U
E9
E10
E11 E12 CUUA GA G
U
U GG
U
U U
AE8
A U
A U
A U C UG G U A GE11U A U GE7AAU
UAU UUCAGU GU AU U A G E10
U
U
A
A
A
A
U
U
A
UUUC
U GU UC AU A U AU AUG UUUU A GU AGA AU
U enzyme E′ (gray) catalyzes
U
U wobble pairs that provide
U
U
the
site
of
ligation.
Solid
boxes
indicate
criticalFig. 1. Cross-replicatingRNA
enzymes.
(A)
The
G U
G U
G U
G C A U
G U
G C
UU U
G U AUC A
G C
G U
AGA AUG A U
A C A U G UCAandA A U Cenhanced
DashedAboxes
ligationand GB U(black)form
E,Cwhereas
A Gsubstrates
AGU indicate
A C activity.
UGcatalytic
A Aof
C U U toU U
U AA A UCCC AU
GCcatalytic
U G
A the enzymeG
C G paired regions
C G
C GE
U A (C)AC G
U G thatCwere
nucleotides
variouscatalyzes ligationU of AA′ andUB′ toA form E′. TheUtwoAenzymesU dissociate
to provideU
A cross replicators.
G altered to construct
U VarAU G

A - 3´UGUUGAAG G - 5´GE´A´in vitro evolution :a technique used to explore thefunctional capabilities of RNA andDNA in a rapid, systematic, anddirected fashion.

B

AU U U UG UACUA GG UAU G GGU UUGGGGU U GUAGAUGUGG- 5´A A

A´

B´

C

5´- G

AG

CCAG

U AAGU ACG

E

E´

B´

E1

CCAG

3´- C U U A U A A G U A C G

E

C

B
U
C U A
GG
C CUA GUUGG
UUUG
G U AUA G
A U A C G ppp
3´- C GU UGAAGA A - 3´
G
5´- G
G
A
A
A A U OHC
ppp
G AGCACG G UGUGCAACUU A
G
3´
5´- G
GG A AGU U C A U G U
A -G
GACC
GGUU
G A A U OH
GUUCAUGUGCAACUU

E´

E´

E

E
B´

E

AA

E´

E´

B´

EE´´

E

U A
G
A
C G
A U
U A
U A
U A
A
U G
A
G U
C A
G
A
C G
U GA
A
C A
G U
U CG G
A U
U A
A U
U A
U A
AU U
U A
UU A
G G
C C
G
U U
A A
C UG AU U
G GU GA CU U
A AAC UA A
U U
G G
U U
U UG
C C
G G
G
A
ppp G
AG U
U5´- AG A
UG GAU U C A U G U
GGUU
BG A A U OH A G A C C
C
A

B

B

B

A
A

B

B

GU AU

E6

A
C
U

G
U
C
U
G
A
G
U
U
U
G
A

U

G

A

U
U
U
G
A

U The
A U RNA enzymes.
G (A)U of ligation.
U Solidcritical
G thatC provide pairs
A U
A
A indicate
the siteligation.
boxes
indicate
criticalFig.
RNA
enzyme(gray)
catalyzes
the
site
pairs
Fig. 1.structure(A)
enzymeE′ (gray)catalyzes
G
U C1.AU Aenzymes.
UCross-replicatingA
G complementary
Athe
UboxesU U provide
C Athat
G
AAU
AE′
U(E′,
USolidCinof
sequence
pairedregionandthe wobble
same
sequenceofU wobble
of Cross-replicating
the complex
betweentheATheenzymeandsubstrates
Uandformed
U its two E,C
U catalytic
U indicate
enhanced
activity.
Dashedboxes
pairedregionsandcatalytic
ligationA,of
substrates
A
B(black)toform
theenzymewhereasEenhancedcatalytic
activity.
Dashedboxes
indicatepairedregionsandcatalytic
ligationofsubstrates
AandB(black)toform
theenzymeE,
whereasE
and B are shown;
E, A′, and B′ are the reciprocal).
G U
G TheUcurved arrow indicates catalytic
G U
G U
G U nucleotides (alterations relative
G to
U the E1 enzyme are highlighted).
Ctwo
U E′.
Uform
A G U ligation
AThe
Aligation
U Athat
G U A A (C)CVarUUAU A U C to
A Galterednucleotides
that
were
to
constructvariouscrossreplicators.
Var-replicators.
catalyzes
of CA′ andB′ A′
to andformB′
E′.toenzymesdissociate
todissociateprovidenucleotides
to C
constructvariouscrosscatalyzes
The G
two
enzymes
G ofCG
C provideG
C wereG alteredC G (C)iable
12 different
E′ enzymes
copies copies
that canthat
catalyzeanother reaction.
secondary
U aA
USequence
A (B) andU Aportion ofiable
U12 different
A The corresponding
Ucorresponding
A have a E′ enzymes have
UcanA catalyze
portion Eofenzymes.
E enzymes. The
another (B)reaction.
Sequenceand secondary
27 enzyme
FEBRUARY2009
VOL 323SCIENCEwww.sciencemag.org
1230
complementary
sequence in thesequencepaired region
the samesequenceof same sequence ofstructureof the complex
formed between
andenzyme
its
two substrates(E′,substrates
in theandpaired
regionand thestructureof the complex
formedthe
between theand its two(E′, complementary(alterations
to the E1relative
enzyme to
areU
highlighted).
A, and BA,are
shown;
A′,GandE,B′A′,
areandthe B′
reciprocal).
curved arrow
indicates
UThe GG
U G
U relative
G(alterations
U
G nucleotides
catalytic
nucleotides
theE1 enzyme are highlighted).
andB areUE,shown;
are the reciprocal).
The curved
arrowcatalytic
indicates

E7

1230

1230

UUUC

A

A A AG

G
U
U

U
U
U
G
A

E8

E9

U
U U AG A U
U
U
G U
G U
27
2009
VOL
323
SCIENCEUUUC
U CFEBRUARYAAU FEBRUARY
A
C 323
G
27
2009 VOL
U A
U G
AGA A

A

E10

A

E11

U
U GU AU
G U
www.sciencemag.org
AC AU
AUC A C GSCIENCE www.sciencemag.org
C G
U AGU

A

G
C
U

U
U
C
G
A

E12

C AU A

G. CAF. Joyce Science 2009, 323, 1229-1232

GU AU

U

47

resulting in 64
replicators were dehave a binding adv
mole as compared
S2C), but once a mligated, it forms a r
cross-replicate. Re
recombinants, as w
sigmoidal curve
x25 amplification !
ABbinants. Based on
510
are expected to be
primarily involvin
4
among certain B c
1
A second seria3
with a 0.1 mM con
cross-replicating e2
0.1
tion of each of the
mixture allowed 1
1cross-replicating enonrecombinant c
0
0.01
0
2
4
6
8
10
0
5
10
15
20
25
30
sive reactions weTime (h)Time (h)transferring 5% oFig. 2. Self-sustained amplification of cross-replicating RNA enzymes. (A) The yield of both E mixture to the n(black curve) and E′ (gray curve) increased exponentially before leveling off as the supply of amplification of g
substrates became exhausted. (B) Amplification was sustained by performance of a serial transfer Of 100 clones i
experiment, allowing approximately 25-fold amplification before transferring 4% of the mixture to (sequencing 50 E
a new reaction vessel that contained a fresh supply of substrates. The concentrations of E and E′ recombinants (Fignonuniform, with
were measured at the end of each incubation.
containing compo(and reciprocal co
A 10C5A12′).
The most fr
G. F. Joyce Science 2009, 323,
1229-1232
were A5 and B348

next (fig. S2A). Individuals were cloned from the
population after the final reaction and sequenced.
Among 25 clones (sequencing E′ only), there was
no dominant replicator (fig. S2B). E1′, E2′, E3′, andE4′ all were represented, as well as 17 clones thatwere the result of recombination between aparticular A′ substrate and one of the three B′
substrates other than its original partner (or similarly
for A and B). Recombination occurs when an
enzyme binds and ligates a mismatched substrate. In
principle, any A could become joined to any B orB′, and any A′ could become joined to any B′ or B,

Self-Replication of RNA(µM)[E] or [E´ ] (µM)[E] or [E´ ] (µM)• Self-Sustained amplification of RNA

4

V. Summary

49

Summary of Today’s Topics• Asymmetric Autocatalysis → Homochirality• Organic Autocatalysis → Synthetic Biology• Biological Autocatalysis → RNA World Hypothesis}“bottom up”
approach to life

• Can We Utilize Autocatalytic Reactions toAccomplish More Efficient Organic Synthesis ?

50