Acceleration of an aromatic claisen rearrangement via a designed spiroligozyme catalyst that mimics the ketosteroid isomerase catalytic dyad

Article abstract of DOI:10.1021/ja409214c

A series of hydrogen-bonding catalysts have been designed for the aromatic Claisen rearrangement of a 1,1-dimethylallyl coumarin. These catalysts were designed as mimics of the two-point hydrogen-bonding interaction present in ketosteroid isomerase that has been proposed to stabilize a developing negative charge on the ether oxygen in the migration of the double bond.1 Two hydrogen bond donating groups, a phenol alcohol and a carboxylic acid, were grafted onto a conformationally restrained spirocyclic scaffold, and together they enhance the rate of the Claisen rearrangement by a factor of 58 over the background reaction. Theoretical calculations correctly predict the most active catalyst and suggest that both preorganization and favorable interactions with the transition state of the reaction are responsible for the observed rate enhancement.

Full text of DOI:10.1021/ja409214c

Article
pubs.acs.org/JACS
Open Access on 01/23/2015
Acceleration of an Aromatic Claisen Rearrangement via a Designed
Spiroligozyme Catalyst that Mimics the Ketosteroid Isomerase
Catalytic Dyad
Matthew F. L. Parker,§ Sílvia Osuna,‡ Guillaume Bollot,‡ Shivaiah Vaddypally,† Michael J. Zdilla,†
K. N. Houk,‡ and Christian E. Schafmeister*,†
†Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania, 19122, United States
‡Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
§Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
S
* Supporting Information
ABSTRACT: A series of hydrogen-bonding catalysts have
been designed for the aromatic Claisen rearrangement of a 1,1-
dimethylallyl coumarin. These catalysts were designed as
mimics of the two-point hydrogen-bonding interaction present
in ketosteroid isomerase that has been proposed to stabilize a
developing negative charge on the ether oxygen in the
migration of the double bond.1 Two hydrogen bond donating
groups, a phenol alcohol and a carboxylic acid, were grafted
onto a conformationally restrained spirocyclic scaffold, and
together they enhance the rate of the Claisen rearrangement by
a factor of 58 over the background reaction. Theoretical calculations correctly predict the most active catalyst and suggest that
both preorganization and favorable interactions with the transition state of the reaction are responsible for the observed rate
enhancement.
ketosteroid isomerase (KSI) in a small spiroligozyme and the
catalysis of an aromatic Claisen rearrangement of a 1,1-
dimethylallyl coumarin.
1. INTRODUCTION
One century after its discovery,2 the [3,3]-sigmatropic
rearrangement of allyl vinyl ethers (i.e., the Claisen rearrange-
ment) continues to be extensively investigated and applied in
the synthesis of natural products and complex organic
molecules.3,4 Many efforts have been devoted to develop
small molecule and biocatalysts for this synthetically powerful
reaction.5,6 Attractive noncovalent interactions are responsible
for much of the rate accelerations and stereoselectivities
observed in enzyme catalysis, and active site residues can
stabilize the transition state by electrostatic and noncovalent
interactions.7 A variety of dual hydrogen-bond donor organo-
catalysts such as ureas, thio-ureas, guanidinium groups, and bis-
imidazoliums have been reported in the literature for Claisen
rearrangements.6,8−13 Some biological catalysts have also been
identified,14−16 and de novo computational design strategies for
developing an aromatic Claisen biocatalyst have been carried
out.17 We are developing a new approach to the development
of organocatalysts called “spiroligozymes” wherein we use
transition state modeling to identify constellations of reactive
functional groups and then build those functional groups onto a
spiroligomer scaffold to see if they can act as organocatalysts.18
In this manuscript, we describe the design and synthesis of a
series of bis-amino acid monomers fused to amino acids
through diketopiperazines, that accelerate the Claisen rear-
rangement of 1,1-dimethylallyl coumarin. This paper reports
the successful mimicry of the catalytic dyad of bacterial
Aromatic Claisen rearrangements are typically performed in
the temperature range of 180−225 °C,19 and proceed through a
concerted pericyclic pathway followed by a keto/enol
tautomerization that restores aromaticity. The cyclic transition
state of the Claisen rearrangement is key for understanding a
number of phenomena. These include the effect of solvent on
the rate of the reaction,20−27 substituent effects, and stereo-
selectivity.4 There is one well-established enzyme-catalyzed
Claisen rearrangement, the chorismate to prephenate trans-
formation catalyzed by chorismate mutase.28−33 The Claisen
rearrangement of O-prenylated tyrosines in a prenyltransferase
from the TruF enzyme family has also been proposed,16 and
catalytic antibodies have been developed for the chorismate to
prephenate conversion.34−36
Considerable acceleration of the Claisen rearrangement can
be achieved by employing hydrogen-bonding solvents,
especially water.25,26,28,37−40 In 1987, Carpenter and co-workers
first reported the acceleration of the Claisen rearrangement of
chorismic acid and related compounds in aqueous media.28 The
rate of the aromatic Claisen rearrangement of allyl naphthyl
ether was also increased in aqueous suspensions relative to
Received: September 5, 2013
Published: January 23, 2014
© 2014 American Chemical Society
3817
dx.doi.org/10.1021/ja409214c | J. Am. Chem. Soc. 2014, 136, 3817−3827

Journal of the American Chemical Society
Article
other organic solvents such as toluene, dimethylformamide,
acetonitrile, and methanol.41 Sharpless reported “on-water”
catalysis of a Diels−Alder reaction and aromatic Claisen
rearrangement. Several examples from his lab illustrated the
substantial rate acceleration of the reactions when insoluble
reactants were stirred in aqueous suspension. This “on water”
catalysis has prompted several computational studies to unravel
the origin of the rate acceleration in water and hydrogen-
bonding solvents.20,21,26,28,38,42 It was found that the aqueous
acceleration of the Claisen rearrangement is due to a greater
stabilization of the transition state by specific interactions with
first shell solvent molecules.17,38,43−45 Jorgensen and co-
workers computationally studied the acceleration of the Claisen
rearrangement in water. The model consisted of two explicit
water molecules around the core heteroatom of the allyl vinyl
ether.21
Curran et al. discovered that dual hydrogen-bonding catalysts
such as ureas and thioureas accelerate the Claisen rearrange-
ment and measured modest rate accelerations using NMR
experiments.9 In addition, protonated catalysts including those
based on guanidinium,11 quinolinium thioamide,46 and
ammonium26,47 structures were also studied. The latter
positively charged catalysts tend to activate electrophiles
more strongly than the neutral compounds.10 Jacobsen and
co-workers have developed diphenylguanadinium salts as
stereoselective Claisen rearrangement catalysts for a variety of
substituted allyl vinyl ethers and β-ketoester derivatives.11,13
The mechanism by which the guanidinium catalysts promote
the Claisen rearrangement was also studied both experimentally
and theoretically.6,12 The catalysis is mainly achieved by
stabilization of the developing negative charge on the oxallyl
fragment, and by a secondary attractive interaction between the
π-system of the catalyst and the partially positive allyl cation
fragment.12 Kozlowski and co-workers designed a bisamidinium
catalyst salt able to catalyze the Claisen rearrangement through
a two-point hydrogen bonding stabilization of the negatively
charged ether oxygen in the transition state.8
The most prominent biological example of a Claisen
rearrangement is the enzyme Chorismate mutase, which
catalyzes the Claisen rearrangement of chorismate to
prephenate more than a million-fold relative to the uncatalyzed
process.15 Hilvert and co-workers have also studied the enzyme
catalyzed Cope rearrangement of carbachorismate to carbap-
rephenate in the enzyme Bacillus subtilis chorismate mutase
(BsCM).14 They showed that a positively charged residue at
position 88 or 90 is essential for stabilization of the transition
state of the enzymatic chorismate rearrangement.14 Borden and
Houk studied models for this rearrangement and tested
different theozymes to determine the effect of different side
chains in chorismate mutase.48 Bertran et al. performed a QM/
MM study where two different transition states were located for
the chorismate conversion to prephenate. It was found that the
enzyme stabilizes one of the transition states (TS) by means of
hydrogen bonding interactions, while the other TS located,
corresponded to the preferred one in vacuum and in water.49
They found that aqueous solution and BsCM active site
environments reduce the free energy barriers more than in the
gas phase for both reactions. The catalytic effect was mainly
attributed to the enhanced electrostatic stabilization of the
transition state relative to the starting substrate in the Claisen
rearrangement.50
prenylation of tyrosine, serine, and threonine in cyclic peptides.
It was found that at physiological temperature and in aqueous
buffer, O-prenylated tyrosine derivatives undergo spontaneous
Claisen rearrangements.
In recent years, novel enzyme catalysts for the Kemp
elimination,51 retro-aldol,52 and Diels−Alder53 reactions have
been designed, making use of the so-called “Inside-Out”
approach. The first step of this protocol involves quantum
mechanical calculations of the ideal arrangement of catalytic
groups around the transition state of a reaction; these
computed complexes are called theozymes (short for
theoretical enzymes).54−56 Theozymes serve as models for
active site structures and for the prediction of activation barriers
relative to the uncatalyzed reaction in aqueous solution. The
arrangement of functional groups in the theozyme geometry is
then incorporated into protein scaffolds from the Protein Data
Bank57 using the computational package RosettaMatch.58 The
active sites of the generated proteins are then minimized and
repacked, and amino acids in the vicinity of the active site are
mutated to stabilize the ideal transition state geometry. This
process is performed using the RosettaDesign package.59,60 The
Inside-Out approach has been satisfactorily applied in the
above-mentioned cases (Kemp elimination, retro-aldol, and
Diels−Alder reaction), but it has some important limitations.
Up until now, most active designed enzymes still perform quite
poorly in comparison with the natural existing enzymes (i.e.,
natural enzymes have average kcat/kuncat of ∼1011, whereas
artificial enzymes developed through computational modeling
and directed evolution have kcat/kuncat values that range from
102 to 105).51−53,61 In part, this is due to the difficulty of
designing a protein with the same ideal geometry of functional
groups present in the theozyme.
The design and testing of small-molecule “enzyme mimics”
has been a tempting but frustrating target for organic
chemists,62−66 and occasional success has been reported.10,67,68
We conceived the melding of the Inside-Out approach with
our recent successes in spiroligozyme syntheses to mount
catalytic groups from theozymes on a spiroligomer scaffold.69
Spiroligomers are shape-programmable macromolecules con-
structed by assembling stereochemically pure, cyclic, function-
alized bis-amino acids through pairs of amide bonds to create
rigidified scaffolds that present functional groups in controlled
three-dimensional constellations by virtue of the sequence,
shape, and stereochemistry inherent in each chiral building
block.70−72 Previously, spiroligomers have been utilized as
catalysts for the aldol reaction and transesterification
reaction.18,69 We now report a combined computational and
experimental approach to use spiroligozymes as catalysts for the
aromatic Claisen rearrangement.
2. RESULTS AND DISCUSSION
2.1. Design and Synthesis of Ketosteroid Isomerase-
Inspired Catalysts for the Aromatic Claisen Rearrange-
ment. Bacterial ketosteroid isomerase (KSI) is heavily utilized
as a model system for investigating fundamental aspects of
enzyme catalysis.1,73,74 Its natural function is the isomerization
of the position of a double bond in steroids. The mechanism
involves a general base that deprotonates the steroid forming a
dienolate, which is stabilized via hydrogen bonding with a
tyrosine-16 residue and a protonated aspartic acid-104 residue
(see Figure 1a). The stabilized intermediate is reprotonated and
the double bond isomerized. The hydrogen bonding catalytic
dyad was considered a promising modality for the stabilization
Very recently, LynF, a prenyltransferase from the TruF
enzyme family, was characterized.16 This enzyme performs O-
3818
dx.doi.org/10.1021/ja409214c | J. Am. Chem. Soc. 2014, 136, 3817−3827

Journal of the American Chemical Society
Article
Scheme 1. Synthetic Scheme for the Solid Phase Assembly of
Claisen Catalysts BPC1-10
Figure 1. (a) Molecular model overlay of the active site of KSI (pdb
code 3OWU1) with the spiroligomer mimetic BPC8. KSI is displayed
as a rainbow ribbon with Y16 and D103 shown in gray. Equilenin is
bound and also shown in gray. The spirocyclic catalyst BPC8 is
displayed as dark green and is overlaid matching the oxygens of the
catalytic residues. (b) The theoretical enzyme model for the KSI
catalytic dyad.
of the growing negative charge in the transition state of the
Claisen rearrangement (Figure 1). It was proposed by Gerlt
and Gassman that the formation of short, strong hydrogen
bonds (SSHB, also called low-barrier hydrogen bonds LBHB)
between the KSI oxyanion hole and the reaction intermediate
stabilizes the transition state of the reaction.75,76 There has
been an intense debate about the role of SSHBs in enzyme
catalysis.77,78
We designed a series of bioinspired spiroligozyme catalysts
that display a carboxylic acid and a phenol on a spiroligomer
backbone that resembles the hydrogen bonding catalytic dyad
of KSI (see Figure 1b). The use of a phenol and carboxylic acid
is a stark departure from the currently utilized organocatalysts
for the Claisen rearrangement, which generally rely on N−H
hydrogen-bond donors. The optimized theozyme for the
aromatic Claisen rearrangement using the KSI catalytic dyad
(i.e., Asp/Tyr; see Figure 1b) suggests that a 105-fold
acceleration with respect to the background reaction could be
achieved (at M06-2X/6-311+G(d,p)//M06-2X/6-31G(d) and
in CPCM implicit solvation for CH2Cl2 with ε = 4).
Selection of the scaffold to tether the catalytic residues was
accomplished by matching carboxylic acid/phenol function-
alized Amber 9479 minimized spiroligomer structural motifs
that we have synthetic access to against the crystal structure
data for KIS as shown in Figure 1a (pdb code 3OWU).1 A
scaffold previously used for studying electron transfer in water
was selected as a starting point for further optimization.80 The
scaffold features a single bis-amino acid building block with one
functional group introduced via a 2,5-dioxopiperazine (DKP)
ring and the other introduced via amide linkage at the
pyrrolidine nitrogen forming a well-defined cleft between the
two catalytic residues.
A series of molecules of this scaffold type were synthesized
using solid phase synthesis on HMBA resin (Scheme 1).81 The
bis-amino acid82 1 was attached to HMBA resin with MSNT
and NMI in DCM. The benzyl carbamate and tert-butyl ester
were then removed by treatment with 33% HBr in AcOH as a
1:1 volumetric mixture with DCM. This treatment causes
acetylation of all remaining hydroxyl groups on the resin. The
benzoic acid derivative was introduced using HATU and
DIPEA in NMP. The C-2 carboxylic acid was converted to an
amide using PyAOP and the amine R3R4NH in NMP to form
the resin bound intermediate 2. The Fmoc group was removed
using a 20% solution of piperidine in DMF. The phenylalanine
derivative was then introduced using HATU and DIPEA in
NMP to produce intermediate 3. The tert-butyl carbamate,
(a) HMBA Resin (1.1 equiv), MSNT (2 equiv), NMI (2 equiv), DCM
(0.1 M); (b) 33% HBr in AcOH/DCM (1:1, 0.1 M); (c) Benzoic Acid
derivative (3 equiv), HATU (3 equiv), DIPEA (6 equiv), NMP (0.2
M); (d) Substituted Amine (6 equiv), PyAOP (3 equiv), NMP (0.2
M); (e) 20% Piperidine in DMF (0.1 M); (f) N-Boc-Amino Acid (3
equiv), HATU (3 equiv), DIPEA (6 equiv), NMP (0.2 M); (g) TFA/
DCM (1:1, 0.1 M); (h) 10% DIPEA in MeCN (0.05 M).
ester, and ether were removed with treatment with a 1:1
volumetric mixture of TFA and DCM. The DKP was closed
and subsequent cleavage from the resin was affected with a 10%
solution of DIPEA in MeCN. Purification with C18 reverse
phase HPLC yielded the pure catalysts BPC1−10 in 60−70%
isolated yields (Table 1).
The series of catalysts BPC1−10 and controls were tested
for acceleration of the aromatic Claisen rearrangement of the
1,1-dimethylallyl coumarin substrate 4. Catalyst was added at
20 mol % relative to the substrate 4 at 0.2 M in dichloroethane.
The reaction vessels were sealed and stirred magnetically at 60
°C for 84 h. High-density polypropylene vessels had to be used
because untreated glass vessels lead to decomposition of the
reagent, presumably catalyzed by trace acid. The reactions were
analyzed by HPLC-MS. Percent conversions were obtained by
comparison of the area contributions from the product 5 and
starting material peaks. Rate constants were determined by
fitting the concentration of product with respect to time using a
first-order kinetics model. Table 1 lists relative rate constants
for the catalysts as well as benzoic acid and diphenylguanidi-
nium BARF catalyst.11
The compound BPC1 displayed a 11-fold rate enhancement
relative to the background reaction (entries 1−2). BPC1 was
designed to display a terephthalic acid and a tyrosine in order to
project a carboxylic acid and a phenol alcohol toward each
other. Molecular modeling suggested that this would direct the
terephthalic acid and phenol toward each other so that they
could both simultaneously act as hydrogen bond donors to a
single ether oxygen atom. This close approach of these two
hydrogen-bonding groups is promoted by the stereochemistry
of the spirofused pyrrolidine and diketopiperazine ring onto
which the groups are mounted (Figure 1a). This close approach
is analogous to the close approach that is achieved when a
pyrene and a para-dimethylaniline group are displayed in place
of the terephthalic acid and phenol.80 The C-2 amide was
modified to primary and tertiary amides (entries 3 and 4) to
3819
dx.doi.org/10.1021/ja409214c | J. Am. Chem. Soc. 2014, 136, 3817−3827

Journal of the American Chemical Society
Article
Table 1. Kinetic Data for the Aromatic Claisen Rearrangement of 4 to 5
entry
catalyst
none
C-2
C-4
A
R1
R2
R3/R4
R5
R6
krel
1
-
-
-
-
-
-
-
-
1
11
10
10
2
2
BPC1
S
S
S
S
S
-
S
S
S
S
S
-
S
S
S
R
S
-
4-COOH
4-COOH
4-COOH
4-COOH
4-COOH
-
OH
iBu/H
H/H
H
H
H
H
H
-
H
H
H
H
H
-
3
BPC2
OH
4
BPC3
OH
iBu/iBu
iBu/H
iBu/H
-
5
BPC4
OH
6
BPC5
H
2
7
PhCOOH
BPC6
-
2
8
S
S
S
S
S
-
S
S
S
S
S
-
S
S
S
S
S
-
3-COOH
2-COOH
4-OH
OH
iBu/H
iBu/H
iBu/H
iBu/H
iBu/H
-
H
H
H
H
H
-
H
H
H
H
H
-
8
9
BPC7
OH
4
10
11
12
13
14
15
16
BPC8
COOH
COOH
COOH
-
30
6
BPC9
3-OH
BPC10
DPGB*
BPC11
BPC12
BPC13
2-OH
4
-
14
42
40
58
S
S
S
S
S
S
S
S
S
4-OH
COOH
COOH
COOH
iBu/H
iBu/H
iBu/H
H
Bn
Bn
Bn
H
Bn
4-OH
4-OH
create the catalysts BPC2 and BPC3 which are more soluble in
dichloroethane, and this does not effect the catalytic rate,
suggesting that the C2 amide is not involved in hydrogen bond
stabilization of the transition state. The cooperativity of the two
hydrogen bond donor groups was probed by altering the
stereochemistry of the bicyclic backbone to create BPC4, which
modeling suggests would pull the two donors away from each
other (entry 5)and the activity of BPC4 drops to 2-fold
above background, which is similar to the activity of benzoic
acid alone (entry 7). The cooperativity was further probed by
removing the phenol alcohol using phenylalanine in place of
tyrosine to form BPC5 (entry 6) and its activity is equivalent to
BPC4 and benzoic acid. Altering the substitution of the
carboxylic acid on the benzoic acid derivative to meta (BPC6)
and ortho (BPC7) leads to less well-aligned hydrogen bond
donor groups by modeling and leads to lower activity catalysts
(entries 8 and 9). Swapping the positions of the alcohol and the
carboxylic acid (BPC8) brings the carboxylic acid and phenol
alcohol in better alignment to simultaneously donate two
hydrogen bonds to a single oxygen and increased the relative
rate to 30-fold over background (entry 10). Altering the
position of the alcohol on the benzoic acid derivative to meta
(BPC9) and ortho (BPC10) also leads to less-well-aligned
hydrogen bond donor groups by modeling and led to less active
catalysts (entries 11 and 12). Diphenyl guanidinium BARF
(DPGB; entry 13) is a prototype of a series of asymmetric
catalysts of the Claisen rearrangement developed by the
Jacobsen group.11 Under these reaction conditions, DPGB
generated the product 5 with a krel of 14; however, concomitant
with product formation, significant amounts of side products
were formed, as observed by analytical reverse phase C18 HPLC
analysis during the course of the reaction. Among these side
products, the free coumarin was observed, indicating that the
guanidinium catalyst is effective, under these reaction
conditions, at breaking the ether linkage between the coumarin
oxygen and allylic carbon, possibly by acting as a Bronsted acid.
Modeling suggests that the diketopiperazine ring of the BPC
scaffold exists in a boat-like conformation. The boat
conformation and the rotamer preferences of the functional
groups could be altered through N-alkylation of the amide
nitrogens within the diketopiperazine ring, and this could alter
the presentation of the phenol and carboxylic acid groups and
change their catalytic activity. Dichloroethane solutions of
BPC1−10 are cloudy at room temperature, although clear at 60
°C, which we attributed to diketopiperazine-tape formation at
room temperature.83 N-Alkylation could also improve the
solubility of the catalysts in the dichloroethane solvent because
it would disrupt hydrogen-bonded tape-formation. We created
three N-alkylated versions of BPC8, the mono N-benzylated
catalysts BPC11 and BPC12, and the di-N-benzylated catalyst
BPC13. Unlike BPC1−10, these new catalysts were completely
soluble in dichloroethane at 40 mM at room temperature, as
well as at 60 °C, under the reaction conditions.
In order to synthesize these, an alternative solid phase
synthesis had to be devised to assemble the tetra- and penta-
substituted DKP rings shown in Scheme 2. The bis-amino acid
derivative82 6 was attached to an isobutyl amine modified
formyl resin via HATU promoted acylation. The pyrollidine
Alloc group was removed using palladium catalyst in the
presence of a scavenger and then acylated with the t-butyl-
protected 4-hydroxy benzoic acid. The C-4 amino acid
protecting group was then removed followed by reductive
alkylation to the C-4 nitrogen with benzaldehyde to form 7.
The carboxy-phenylalanine derivative was introduced via
HATU promoted acylation. Treatment of the resin with neat
TFA was used to cleave the intermediate from the resin, which
led to spontaneous diketopiperazine formation and concom-
itant removal of all protecting groups. Purification with reverse
3820
dx.doi.org/10.1021/ja409214c | J. Am. Chem. Soc. 2014, 136, 3817−3827

Journal of the American Chemical Society
Article
Scheme 2. Synthetic Scheme for the Solid Phase Assembly of
Spiroligomer Claisen Catalysts BPC11−13
Figure 3. X-ray crystal structure of BPC1 illustrates the proposed
catalytically active conformation of the tyrosine side chain and one of
the two possible amide rotamers of the terphthalic acid. This X-ray
observed conformation is very similar to BPC1a (Figure 4b), one of
the lowest energy predicted structures of BPC1.
tyrosine alcohol of another molecule of BPC1. The X-ray
crystal structure is very similar to the predicted conformation
BPC1a in Figure 4b.
(a) Substituted Amino Resin (1 equiv), HATU (1 equiv), DIPEA (2
equiv), NMP (0.2 M); (b) (P(Ph3)4)Pd(0) (0.3 equiv), BH3:DMA (6
equiv), DCM (0.1 M); (c) Benzoic Acid Derivative (3 equiv), HATU
(3 equiv), DIPEA (6 equiv), NMP (0.2 M); (d) 20% Piperidine in
DMF (0.1 M); (e) PhCHO (2 equiv); NaH3BCN (2 equiv); DMF
(0.1 M); (f) Boc-Amino Acid (3 equiv); HATU (3 equiv), DIPEA (6
equiv); NMP (0.2 M); (g) TFA.
phase HPLC yielded the pure catalysts in 75−80% yields
relative to solid support loading.
Kinetic studies of catalysts BPC1, BPC8, and BPC11−13 are
shown in Figure 2. Improvement in catalytic rate was observed
Figure 4. M06-2X/6-31G(d) optimized structures for the lowest
energy conformers for BPC8, BPC1a, and BPC1b. M06-2X/6-
311+G(d,p)//M06-2X/6-31G(d) relative Gibbs free energies have
been computed using the thermal corrections at M06-2X/6-31G(d)
level (ΔGrel are relative to BPC8(a) which can be calculated given that
BPC1 and BPC8 have the same number of atoms, all distances are
represented in Å).
Figure 2. Claisen rearrangement product formation as a function of
time and catalyst (0.2 M substrate in dichloroethane, 60 °C, 0.02 M
catalyst).
over the course of each catalyst generation with BPC13 (krel
58) providing the largest rate enhancement relative to the
background reaction.
=
2.2. Quantum Mechanical and Molecular Dynamics
Evaluation of the Catalysts. We have explored the catalysis
by BPC1, BPC8, and BPC11−13 using molecular dynamics
(MD) to explore the conformational space of each catalyst and
used quantum mechanics (QM) to evaluate transition states.
We performed a conformational analysis of BPC1, BPC8, and
BPC11−13 using the Monte Carlo (MCMM) method and the
OPLS-AA force field as implemented in the MacroModel
computational package (see SI for a detailed description of the
computational methods used).84,85 In each case, 20 or more
lower energy conformers were further reoptimized using the
hybrid meta exchange-correlation DFT functional M06-2X,86
which includes medium-range correlation, with the standard 6-
The catalyst BPC1 was crystallized from water/acetonitrile
1:1 at room temperature and its crystal structure was
determined (Figure 3). In the crystal structure the tyrosine
side chain is observed to fold back over the diketopiperazine
and pyrrolidine rings in the conformation that was proposed for
dual hydrogen bonded catalysis. The terephthalic acid is rotated
away from the tyrosine in one of the two available amide
rotamers. The preference of this rotamer of the terephthalic
acid in the crystal structure can be understood in terms of
crystal packing forces and an intermolecular hydrogen bond
between the amide carbonyl of the terephthalic acid and the
3821
dx.doi.org/10.1021/ja409214c | J. Am. Chem. Soc. 2014, 136, 3817−3827

Journal of the American Chemical Society
Article
31G(d) basis set.87,88 Solvent effects were included with the
conductor-like polarizable continuum model (CPCM)89 with
dichloroethane as the solvent. M06-2X/6-31G(d) energies
indicated that the lowest energy conformer for BPC8 is from
6.5 up to 18.6 kcal/mol more stable than the rest of the
computed conformers. The situation for BPC1 is slightly
different as the lowest energy conformer (BPC1a) is only 0.2
kcal/mol more stable than BPC1b, with the rest of the
computed conformers being from 4 up to 15 kcal/mol higher in
energy (see Figure 4). BPC8 and BPC1b both present close
approaching, preorganized carboxylic acid and phenol groups
for catalysis, while BPC1a has these two functional groups far
separated (see Figure 4).
The optimized transition state structures with catalytic
conformations of BPC8, BPC1a, and BPC1b are shown in
Figure 6. The computed activation barrier for the Claisen
rearrangement catalyzed by BPC8 is 28.1 kcal/mol with respect
to isolated reactants (i.e., BPC8 and the coumarin reactant). As
a reference, the computed activation barrier in terms of free
Gibbs energy for the background reaction is 30.0 kcal/mol at
the M06-2X/6-311+G(d,p)//M06-2X/6-31G(d) level of
theory in CPCM dichloroethane (see Figure 5). The catalyzed
Figure 6. M06-2X/6-311+G(d,p)//M06-2X/6-31G(d) optimized
transition state structures for the Claisen rearrangement catalyzed by
(a) BPC8, (b) BPC1a, and (c) BPC1b in dichloroethane using
CPCM implicit solvation model. The uncatalyzed reaction has a Gibbs
free activation barrier of 30.0 kcal/mol. All distances are represented in
Å.
approximately 3.3 Å). An enantiomer bound to the same
catalyst was also found, but was 0.2 kcal/mol higher in energy.
The transition state involving BPC1b, which has both hydroxyl
groups in a closer disposition, presents an activation barrier that
is 0.5 kcal/mol higher than the previous TS for BPC1a (the
Gibbs free activation barrier compared to isolated reactants is
31.4 kcal/mol; see Figure 6c). This slightly higher activation
barrier is mainly attributed to the fact that only the hydroxyl
group of the phenol moiety is stabilizing the negative charge of
the ether oxygen, and more importantly the favorable π-
stacking interaction between the coumarin derivative and the
benzoic acid moiety is lost (see Figure 6c). In both BPC1a and
BPC1b cases, the computed Gibbs activation barriers are
slightly larger than background reaction.
We have also studied the more active catalysts BPC11−13.
The conformational analysis and the subsequent optimization
at M06-2X/6-31G(d) level indicated that the lowest energy
conformers for all three cases present the proper arrangement
for catalysis with the carboxyl and the phenol group in close
proximity (see Figure 7, Figure S1 and SI for more details).
We have studied the spiroligozyme catalyzed Claisen
rearrangement of the lowest energy conformers of the catalysts
(i.e., 4 for BPC11, 4 for BPC12, and 4 for BPC13). It should
be emphasized here that the main differences between the 4
different conformers studied for each case arise mainly from
different conformations of the benzyl and isopropyl sub-
stituents (see Figure S1). The difference in energy between the
different conformers is less than 4 kcal/mol in all cases. We
calculated the energy of each catalyst bound to the substrate
relative to the energy of the lowest energy conformer of each
unbound catalyst and substrate. The energies are 8.7, 6.9, and
5.2 kcal/mol for BPC11, BPC12, and BPC13, respectively (see
Figure S2). For BPC11 the OH hydrogen bond (2.2 Å) is
substantially longer than for the other two cases (1.85 Å). The
OH in BPC11 is also hydrogen bonded to the CO of the
Figure 5. M06-2X/6-31G(d) optimized structures for the (a)
theozyme with the Asp/Glu and Tyr motif and (b) the uncatalyzed
reaction (all distances are represented in Å).
reaction is bimolecular, and the rate of rearrangement is
considerably faster than the background, but there is
unfavorable entropy of association of the substrate and catalyst.
The reactant complex between BPC8 and the 1,1-dimethylallyl
coumarin ether is 3.9 kcal/mol higher in Gibbs free energy than
isolated reactants; that is, the nearly 10 kcal/mol binding is
counteracted by −TΔS for the bimolecular association. In the
transition state, both hydroxyl groups of BPC8 are stabilizing
the partial negative charge on the ether oxygen and are
approximately 1.7 Å away (see Figure 6). The breaking O−C
and the forming C−C bond distances are 2.274 and 2.416 Å,
respectively. For BPC1a, the catalysis of the aromatic Claisen
rearrangement could be assessed considering two different
approaches. The phenol group and the benzoic acid moiety are
not in close contact. Instead, the hydroxyl group of the phenol
is interacting with a carbonyl group of the bis-peptide backbone
(see Figures 4b and 6b). Therefore, the BPC1a catalyzed
reaction was studied using either the phenol or the carboxylic
group individually hydrogen bonded to the ether oxygen of the
coumarin transition state. A lower energy transition state was
found for the phenol-mediated catalysis. This single hydrogen-
bonding TS has a computed Gibbs free activation barrier of
30.9 kcal/mol relative to isolated reactants, BPC1a and the
coumarin ether. At the TS, the hydrogen bond distance
between the ether oxygen and the hydrogen of the phenol is
1.743 Å, and the C−O breaking and C−C forming bond are
2.159 and 2.279 Å, respectively. The coumarin analogue is
nicely π-stacked to the benzoic acid moiety (the distance
between the center of mass of the benzene rings is
3822
dx.doi.org/10.1021/ja409214c | J. Am. Chem. Soc. 2014, 136, 3817−3827

Journal of the American Chemical Society
Article
conformational change (see plots in Figure 8). MD simulations
indicate that the correct arrangement for catalysis is present
68.5% of the simulation time for BPC8. In this suitable
arrangement, the averaged OOH−OOH distance is 4.41 0.79 Å,
which is still substantially longer than the QM value of 2.84 Å.
The distance between hydroxyl groups is less than 4 Å 14.5% of
the simulation time. The introduction of a benzyl substituent
on the amide backbone leads to a substantial improvement.
BPC11 adopts the proper conformation for catalysis ca. 74% of
the simulation time, and the averaged OOH−OOH distance for
this arrangement is 3.73 0.51 Å. The arrangement stays close
to the QM value (i.e., less than 3 Å) 55.5% of the time. The
benzoic acid moiety in BPC12 stays in the proper orientation
ca. 99% of the time; however, the OOH−OOH distance is close
to the QM value 32.1% of the simulation time. BPC13, which
has benzyl substituents on both amide backbone nitrogens,
adopts the correct arrangement ca. 94% of the time during the
MD trajectory. The averaged OOH−OOH distance for the
BPC13 suitable arrangement for catalysis is 4.41 0.79 Å; the
OOH−OOH distance is less than 4 Å 31.9% of the time. The MD
simulations performed on the free catalysts have shown that the
ideal arrangement for catalysis is substantially modified,
especially in the case of BPC8. In the case of BPC11,
BPC12, and BPC13, those conformers with the suitable
arrangement for catalysis present averaged OOH−OOH distances
closer to the optimized QM value. These simulations indicate
the fraction of conformers that have the catalytic groups
properly preorganized for catalysis.
Figure 7. M06-2X/6-31G(d) optimized structures for the lowest
energy conformers for (a) BPC11, (b) BPC12, and (c) BPC13. The
benzyl substituents have been marked in light green for clarity. All
distances are represented in Å.
We have also computed the Gibbs free activation energies for
the spiroligozyme catalyzed Claisen rearrangement involving
BPC11, BPC12, and BPC13. In Figure 10, the M06-2X/6-
31G(d) optimized transition state structures for the lowest
activation barrier with each catalyst are shown. The computed
activation barriers for BPC11, BPC12, and BPC13 are 28.8,
29.1, and 25.7 kcal/mol referred to the reactants: the isolated
spiroligozyme, each in their lowest energy conformer, and the
coumarin ether. Minor differences are observed among the
computed activation barriers, especially in the case of BPC11
and BPC12. As mentioned earlier for BPC1 and BPC8, the
optimized reactant complexes are ca. 7−9 kcal/mol higher in
Gibbs-free energy than isolated reactants in the case of BPC11
and BPC12, and ca. 5 kcal/mol in BPC13. In all cases, the
breaking O−C and the forming C−C bond distances are
approximately 2.260 and 2.390 Å (see Figure 10). The
hydrogen bonds formed between the ether oxygen and the
phenol and benzoic acid moieties to stabilize the partial
negative charge are 1.710 and 1.692, and 1.734 and 1.640 Å in
BPC11 and BPC12, respectively. Interestingly, BPC13
presents slightly shorter hydrogen bond distances of 1.620
and 1.718 Å.
carboxylic moiety (2.1 Å). The hydrogen bond length for
COOH to the substrate is progressively decreased from BPC11
to BPC13. BPC13 has similar hydrogen bond lengths for both
OH and COOH, so the reactant complex for BPC13 presents a
closer arrangement to the TS structure (Figure 10), which
presents hydrogen bond distances of ca. 1.7 Å.
Molecular dynamics (MD) simulations using AMBER1190
and a 10 Å truncated octahedral box with explicit chloroform
molecules (see SI for further details) were performed in order
to determine the relative free energies of catalytic and
noncatalytic conformers of the catalyst. In Figure 8, the average
distances between both oxygen atoms of the phenol and
benzoic acid moieties of the spiroligozymes (dist OOH−OOH
)
along the 1 μs MD simulation are represented. In Figure 9, the
histograms for the OOH−OOH distance are provided. The
standard deviation is also shown using a shaded area and has
been computed every 20 ps. For each catalyst analyzed in this
way (i.e., BPC8 and BPC11−13), 250 superimposed MD
snapshots have also been included where both the open and
closed conformations have been marked using two different
colors. The ideal arrangement for catalysis is substantially
altered along the simulation for BPC8, BPC11, and BPC13
catalysts (see Figures 8 and 10). The distance between the
hydroxyl groups of both the phenol and benzoic acid moieties
(d(OOH−OOH)) along the MD trajectory for BPC8 and
BPC11−13 are 5.86 2.87, 5.16 2.61, 4.39 0.88, and 4.68
1.80 Å, respectively. These distances are substantially longer
than the optimized QM value of 2.84 Å, especially for BPC8
and BPC11 cases. The higher distance and deviation found for
BPC8 and BPC11 is due to a conformational change that leads
to an arrangement where both benzoic acid and phenol
moieties are not interacting (see snapshots in Figure 8, and
histograms in Figure 9). Interestingly, in most cases more than
100 ns of simulation is needed to observe the latter
The computed activation barriers for the uncatalyzed and
BPC1, BPC8, and BPC11−13 catalyzed Claisen rearrange-
ments at 333 K are 30.0, 30.9, 28.1, 28.8, 29.1, and 25.7 kcal/
mol, respectively. MD simulations have shown that BPC8 and
BPC11−13 adopt the appropriate conformation for catalysis
(the hydroxyl distance is less than 4 Å) 14.5%, 55.5%, 32.1%,
and 31.9% of the simulation time, respectively. The latter
fraction of conformers (f) in the catalytic conformation must
be used to estimate the experimental rate constant (kcat = f·
kcat,computed). Each value kcat,computed is calculated from ΔG‡
calculated
using transition state theory. This leads to a computed kcat/
kuncat of ca. 3 and 210 for BPC8 and BPC13 with respect to the
background reaction, respectively. We calculated quantum
3823
dx.doi.org/10.1021/ja409214c | J. Am. Chem. Soc. 2014, 136, 3817−3827

Journal of the American Chemical Society
Article
Figure 8. Representation of 250 superimposed MD snapshots for (a) BPC8 (magenta), (b) BPC11 (cyan), (c) BPC12 (purple), and (d) BPC13
(gold). The plots monitoring the OOH−OOH distance along the 1 μs MD trajectory for these catalysts are also included. The computed QM distance
at M06-2X/6-31G(d) is ca. 2.836 Å. The mean (dark line) and standard deviation of the OOH−OOH distance is represented using a shaded area
(width is 1 std dev) and have been calculated every 10 steps of the simulation (i.e., 20 ps) (all distances are expressed in Å).
mechanical distortion energies by removing the substrate from
each transition state structure and carrying out a single-point
energy calculation at this geometry and subtracting the
minimum energy conformation of each catalyst. The distortion
energies were 6.8, 5.1, 8.8, and 3.6 kcal/mol for BPC8, BPC11,
BPC12, and BPC13, respectively. The lower activation barrier
observed for BPC13 is attributed to the lower distortion energy
needed to distort the catalyst to adopt the TS geometry.
Using transition state theory we calculated the ΔΔG‡
expt
values from the relative rate enhancements and plotted them
against the ΔΔG‡
values (Table 2). The calculations
calc
correctly predict that BCP13 will be the most active catalyst,
that BPC8, BPC11, and BCP12 will have intermediate activity,
3824
dx.doi.org/10.1021/ja409214c | J. Am. Chem. Soc. 2014, 136, 3817−3827

Journal of the American Chemical Society
Article
Figure 10. M06-2X/6-311+G(d,p)//M06-2X/6-31G(d) optimized
transition state structures for the Claisen rearrangement catalyzed by
(a) BPC11, (b) BPC12, and (c) BPC13 in dichloroethane using
CPCM implicit solvation model. The uncatalyzed reaction has a Gibbs
free activation barrier of 30.0 kcal/mol. All distances are represented in
Å.
Table 2. Comparison of Experimentally Derived Relative
Activation Barriers to Prediction
Figure 9. Distribution of the OOH−OOH distance during the 1 μs MD
trajectory for (a) BPC8 (magenta), (b) BPC11 (cyan), (c) BPC12
(purple), and (d) BPC13 (gold). All distances are expressed in Å.
and that BPC1 will have the lowest activity. A linear fit of the
two sets of values has a slope of 4.0, and so while the
calculations predict the trend of activity, they predict higher
activity of the catalysts than is observed. The calculations of
reaction rates are based upon separated reactants in solution as
the reference. Since hydrogen bonding groups, especially
carboxylic acids, are known to form observable complexes
with ca. 380 μM dissociation constants in non-hydrogen-
bonding solvents (carboxylic acid dimers),91 the catalysts and
substrates are expected to form stabilized hydrogen bonding
complexes in solution, thus increasing the activation barriers as
compared to the calculations reported here.
CONCLUSIONS
■
a
b
From Figures 6 and 10. Derived using transition state theory.
We have developed a series of dual hydrogen-bond donor
catalysts for the aromatic Claisen rearrangement modeled on
the active site of Ketosteroid Isomerase. These catalysts are
designed to present a carboxylic acid and a phenol alcohol that
each simultaneously donate one hydrogen bond donor to a
single ether oxygen of the 1,1-dimethylallyl coumarin substrate
to stabilize the developing negative charge on the ether oxygen
in the transition state of the Claisen rearrangement. The
catalysts provide increasing reactivity as they better organize
their hydrogen bonding groups and more closely approximate
the functional group display observed in Ketosteroid Isomerase
and as they are better able to stabilize the transition state as
determined by transition state modeling. The first designed
catalyst BPC1 accelerates the reaction 11-fold relative to
background, while the best catalyst, BPC13, accelerates the
reaction 58-fold. The combined QM and MD computational
study of these systems established that BPC13 gives a higher
acceleration of the reaction due to an optimal disposition of the
hydroxyl groups of both the phenol and benzoic acid moieties
in both the TS and the reactant complex. This optimal
3825
dx.doi.org/10.1021/ja409214c | J. Am. Chem. Soc. 2014, 136, 3817−3827

Journal of the American Chemical Society
Article
(2) Claisen, L. Chem. Ber. 1912, 43, 3157.
arrangement is induced by the benzyl substituents of the amide
backbone, which limit the movement of the benzoic acid and
phenol moieties. MD simulations have determined that this
arrangement is better conserved in the case of BPC13 and
BPC11. The higher efficiency of BPC13 compared to BPC8,
BPC11, and BPC12 is due to the combination of a lower
activation barrier due to a lower distortion energy, and a better
preorganization of BPC13, which maintains both hydrogen
donors in close proximity ca. 94% of the time during the 1 μs
MD simulation. Comparison of the experimentally determined
activation barrier lowering to calculated values demonstrates
that calculations overestimate the catalytic power of the two
hydrogen bond catalysis by 4-fold: this is most likely due to our
lack of understanding and the difficulty modeling how solvation
and self-association affect the energies of the ground states and
transition states.
(3) (a) Martín Castro, A. M. Chem. Rev. 2004, 104, 2939.
(b) Rehbein, J.; Hiersemann, M. Synthesis 2013, 45, 1121. (c) Kirsten,
M.; Rehbein, J.; Hiersemann, M.; Strassner, T. J. Org. Chem. 2007, 72,
4001.
(4) Ziegler, F. E. Chem. Rev. 1988, 88, 1423.
(5) Majumdar, K. C.; Alam, S.; Chattopadhyay, B. Tetrahedron 2008,
64, 597.
(6) Knowles, R. R.; Jacobsen, E. N. Proc. Natl. Acad. Sci. U.S.A. 2010,
107, 20678.
(7) Warshel, A.; Sharma, P. K.; Kato, M.; Xiang, Y.; Liu, H.; Olsson,
M. H. M. Chem. Rev. 2006, 106, 3210.
(8) Annamalai, V. R.; Linton, E. C.; Kozlowski, M. C. Org. Lett. 2008,
11, 621.
(9) Curran, D. P.; Lung, H. K. Tetrahedron Lett. 1995, 36, 6647.
(10) Rodriguez, A. A.; Yoo, H.; Ziller, J. W.; Shea, K. J. Tetrahedron
Lett. 2009, 50, 6830.
(11) Uyeda, C.; Jacobsen, E. N. J. Am. Chem. Soc. 2008, 130, 9228.
(12) Uyeda, C.; Jacobsen, E. N. J. Am. Chem. Soc. 2011, 133, 5062.
These catalysts represent the first examples of synthetic
Claisen rearrangement catalysts that utilize O−H hydrogen
bond donors as found in the Ketosteroid Isomerase enzyme
rather than N−H hydrogen bond donors observed in urea-,
thiourea-, guanidinium-, and bisimidazolium-based catalysts of
the Claisen rearrangement.
(13) Uyeda, C.; Rotheli, A. R.; Jacobsen, E. N. Angew. Chem., Int. Ed.
̈
2010, 49, 9753.
(14) Aemissegger, A.; Jaun, B.; Hilvert, D. J. Org. Chem. 2002, 67,
6725.
(15) Andrews, P. R.; Smith, G. D.; Young, I. G. Biochemistry 1973,
12, 3492.
(16) McIntosh, J. A.; Donia, M. S.; Nair, S. K.; Schmidt, E. W. J. Am.
Chem. Soc. 2011, 133, 13698.
(17) Osuna, S.; Kim, S.; Bollot, G.; Houk, K. N. Eur. J. Org. Chem.
2013, 2013, 2823.
(18) Zhao, Q.; Lam, Y. H.; Kheirabadi, M.; Xu, C.; Houk, K. N.;
Schafmeister, C. E. J. Org. Chem. 2012, 77, 4784.
(19) Claisen, L. Chem. Ber. 1912, 43, 3157.
(20) Cramer, C. J.; Truhlar, D. G. J. Am. Chem. Soc. 1992, 114, 8794.
(21) Severance, D. L.; Jorgensen, W. L. J. Am. Chem. Soc. 1992, 114,
10966.
(22) White, W. N.; Wolfarth, E. F. J. Org. Chem. 1970, 35, 2196.
(23) Coates, R. M.; Rogers, B. D.; Hobbs, S. J.; Curran, D. P.; Peck,
D. R. J. Am. Chem. Soc. 1987, 109, 1160.
(24) Grieco, P. A.; Brandes, E. B.; McCann, S.; Clark, J. D. J. Org.
Chem. 1989, 54, 5849.
(25) Brandes, E.; Grieco, P. A.; Gajewski, J. J. J. Org. Chem. 1989, 54,
515.
(26) Gajewski, J. J. Acc. Chem. Res. 1997, 30, 219.
(27) Sehgal, A.; Shao, L.; Gao, J. J. Am. Chem. Soc. 1995, 117, 11337.
(28) Gajewski, J. J.; Jurayj, J.; Kimbrough, D. R.; Gande, M. E.;
Ganem, B.; Carpenter, B. K. J. Am. Chem. Soc. 1987, 109, 1170.
(29) Pawlak, J. L.; Padykula, R. E.; Kronis, J. D.; Aleksejczyk, R. A.;
Berchtold, G. A. J. Am. Chem. Soc. 1989, 111, 3374.
(30) Guilford, W. J.; Copley, S. D.; Knowles, J. R. J. Am. Chem. Soc.
1987, 109, 5013.
(31) Stewart, J.; Wilson, D. B.; Ganem, B. J. Am. Chem. Soc. 1990,
112, 4582.
(32) Bartlett, P. A.; Johnson, C. R. J. Am. Chem. Soc. 1985, 107, 7792.
(33) Ganem, B. Tetrahedron 1978, 34, 3353.
(34) Hilvert, D.; Nared, K. D. J. Am. Chem. Soc. 1988, 110, 5593.
(35) Jackson, D. Y.; Jacobs, J. W.; Sugasawara, R.; Reich, S. H.;
Bartlett, P. A.; Schultz, P. G. J. Am. Chem. Soc. 1988, 110, 4841.
(36) Hilvert, D.; Carpenter, S. H.; Nared, K. D.; Auditor, M. T. Proc.
Natl. Acad. Sci. U.S.A. 1988, 14, 4953.
(37) Acevedo, O.; Armacost, K. J. Am. Chem. Soc. 2010, 132, 1966.
(38) Repasky, M. P.; Guimaraes, C. R. W.; Chandrasekhar, J.; Tirado-
Rives, J.; Jorgensen, W. L. J. Am. Chem. Soc. 2003, 125, 6663.
(39) Kincaid, J. F.; Tarbell, D. S. J. Am. Chem. Soc. 1939, 61, 3085.
(40) Chanda, A.; Fokin, V. V. Chem. Rev. 2009, 109, 725.
(41) Narayan, S.; Muldoon, J.; Finn, M. G.; Fokin, V. V.; Kolb, H. C.;
Sharpless, K. B. Angew. Chem., Int. Ed. 2005, 44, 3275.
(42) Ganem, B. Angew. Chem., Int. Ed. 1996, 35, 936.
(43) Copley, S. D.; Knowles, J. R. J. Am. Chem. Soc. 1987, 109, 5008.
ASSOCIATED CONTENT
* Supporting Information
■
S
Synthesis of reaction substrate and BPC1−13, kinetic measure-
ments, computation details, Cartesian coordinates, absolute
energies, and 3D representations of all optimized structures,
snapshots from molecular dynamics simulations, and crystallo-
graphic data. This material is available free of charge via the
Internet at http://pubs.acs.org.
AUTHOR INFORMATION
Corresponding Author
*E-mail address: meister@temple.edu.
■
Funding
This work was supported by the Defense Threat Reduction
Agency (DOD-DTRA) (HDTRA1−09−1−0009) and we are
grateful to the National Institute of General Medical Sciences,
the National Institutes of Health Grant (GM-36700 and
GM067866), and the Defense Advanced Research Projects
Agency for additional financial support of this research.
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
This work used the Extreme Science and Engineering
Discovery Environment (XSEDE), which is supported by
National Science Foundation grant number OCI-1053575. S.O.
acknowledges the European Community for the postdoctoral
fellowship PIOF-GA-2009-252856. This research was sup-
ported by an allocation of advanced computing resources
provided by the National Science Foundation (TG-
CHE100059). The computations were performed on Kraken
at the National Institute for Computational Sciences (http://
www.nics.tennessee.edu/). We thank Professor David Dalton
for helpful discussions regarding kinetics experiments.
REFERENCES
■
(1) Fafarman, A. T.; Sigala, P. A.; Schwans, J. P.; Fenn, T. D.;
Herschlag, D.; Boxer, S. G. Proc. Natl. Acad. Sci. U.S.A. 2012, 109,
E299.
3826
dx.doi.org/10.1021/ja409214c | J. Am. Chem. Soc. 2014, 136, 3817−3827

Journal of the American Chemical Society
Article
(44) Guest, J. M.; Craw, J. S.; Vincent, M. A.; Hillier, I. H. J. Chem.
Soc., Perkin Trans. 2 1997, 2, 71.
(81) Brown, Z. Z.; Alleva, J.; Schafmeister, C. E. Pept. Sci. 2011, 96,
578.
(82) Schafmeister, C. E.; Brown, Z. Z.; Gupta, S. Acc. Chem. Res.
2008, 41, 1387.
(83) Palacin, S.; Chin, D. N.; Simanek, E. E.; MacDonald, J. C.;
Whitesides, G. M. J. Am. Chem. Soc. 1997, 119, 11807.
(84) Maestro Ligprep, Macromodel, Glide and QikProp; Schrodinger,
LLC; New York, NY, 2011; http://www.schrodinger.com.
(85) Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem.
Soc. 1996, 118, 11225.
(45) Paton, R. S.; Mackey, J. L.; Kim, W. H.; Lee, J. H.; Danishefsky,
S. J.; Houk, K. N. J. Am. Chem. Soc. 2010, 132, 9335.
(46) Ganesh, M.; Seidel, D. J. Am. Chem. Soc. 2008, 130, 16464.
(47) Huang, J.; Corey, E. J. Org. Lett. 2004, 6, 5027.
(48) Vance, R. L.; Rondan, N. G.; Houk, K. N.; Jensen, F.; Borden,
W. T.; Komornicki, A.; Wimmer, E. J. Am. Chem. Soc. 1988, 110, 2314.
(49) Marti, S.; Andres, J.; Moliner, V.; Silla, E.; Tunon, I.; Bertran, J.
J. Am. Chem. Soc. 2003, 126, 311.
(86) Zhao, Y.; Truhlar, D. G. Acc. Chem. Res. 2008, 41, 157.
(87) Hehre, W. J.; Ditchfield, R.; Pople, J. A. J. Chem. Phys. 1972, 56,
2257.
(50) Claeyssens, F.; Ranaghan, K. E.; Lawan, N.; Macrae, S. J.;
Manby, F. R.; Harvey, J. N.; Mulholland, A. J. Org. Biomol. Chem.
2011, 9, 1578.
(88) Hariharan, P. C.; Pople, J. A. Theor. Chim. Acta 1973, 28, 213.
(89) Barone, V.; Cossi, M. J. Phys. Chem. A 1998, 102, 1995.
(90) Case, D. A.; Darden, T. A.; Cheatham, T. E.; Simmerling, C. L.;
Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.;
(51) Rothlisberger, D.; Khersonsky, O.; Wollacott, A. M.; Jiang, L.;
Dechancie, J.; Betker, J.; Gallaher, J. L.; Althoff, E. A.; Zanghellini, A.;
Dym, O.; Albeck, S.; Houk, K. N.; Tawfik, D. S.; Baker, D. Nature
2008, 453, 190.
(52) Jiang, L.; Althoff, E. A.; Clemente, F. R.; Doyle, L.;
Rothlisberger, D.; Zanghellini, A.; Gallaher, J. L.; Betker, J. L.;
Tanaka, F.; Barbas, C. F.; Hilvert, D.; Houk, K. N.; Stoddard, B. L.;
Baker, D. Science 2008, 319, 1387.
(53) Siegel, J. B.; Zanghellini, A.; Lovick, H. M.; Kiss, G.; Lambert, A.
R.; St.Clair, J. L.; Gallaher, J. L.; Hilvert, D.; Gelb, M. H.; Stoddard, B.
L.; Houk, K. N.; Michael, F. E.; Baker, D. Science 2010, 329, 309.
(54) DeChancie, J.; Clemente, F. R.; Gunaydin, H.; Smith, A. J. T.;
Zhang, X.; Zhao, Y.-L.; Houk, K. N. J. Org. Chem. 2007, 16, 1851.
(55) Tantillo, D. J.; Jiangang, C.; Houk, K. N. Curr. Opin. Chem. Biol.
1998, 2, 743.
́
Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossvary,
I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.;
Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak,
V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.;
Kollman, P. A. AMBER 11; University of California, San Francisco,
2011.
(91) Waterhous, D. V.; Muccio, D. D. Magn. Reson. Chem. 1990, 28,
223.
NOTE ADDED AFTER ASAP PUBLICATION
Figure 2 has been updated. The revised version was re-posted
on March 3, 2014.
■
(56) Ujaque, G.; Tantillo, D. J.; Hu, Y.; Houk, K. N.; Hotta, K.;
Hilvert, D. J. Comput. Chem. 2003, 24, 98.
(57) Berman, H.; Henrick, K.; Nakamura, H. Nat. Struct. Mol. Biol.
2003, 10, 980.
(58) Zanghellini, A.; Jiang, L.; Wollacott, A. M.; Cheng, G.; Meiler, J.;
Althoff, E. A.; Rothlisberger, D.; Baker, D. Protein Sci. 2006, 15, 2785.
̈
(59) Das, R.; Baker, D. Annu. Rev. Biochem. 2008, 77, 363.
(60) Richter, F.; Leaver-Fay, A.; Khare, S. D.; Bjelic, S.; Baker, D.
PLoS ONE 2011, 6, e19230.
(61) Zhang, X.; Houk, K. N. Acc. Chem. Res. 2005, 38, 379.
(62) Breslow, R.; Dong, S. D. Chem. Rev. 1998, 98, 1997.
(63) Cram, D. J. Angew. Chem., Int. Ed. 1988, 27, 1009.
(64) Rebek, J. Science 1987, 235, 1478.
(65) Wiester, M. J.; Ulmann, P. A.; Mirkin, C. A. Angew. Chem., Int.
Ed. 2011, 50, 114.
(66) Meeuwissen, J.; Reek, J. N. H. Nat. Chem. 2010, 2, 615.
(67) Dalko, P. I.; Moisan, L. Angew. Chem., Int. Ed. 2001, 40, 3726.
(68) Hastings, C. J.; Pluth, M. D.; Bergman, R. G.; Raymond, K. N. J.
Am. Chem. Soc. 2010, 132, 6938.
(69) Kheirabadi, M.; Celebi-Olcum, N.; Parker, M. F. L.; Zhao, Q.;
Kiss, G.; Houk, K. N.; Schafmeister, C. E. J. Am. Chem. Soc. 2012, 134,
18345.
(70) Brown, Z. Z.; Schafmeister, C. E. J. Am. Chem. Soc. 2008, 130,
14382.
(71) Gupta, S.; Schafmeister, C. E. J. Org. Chem. 2009, 74, 3652.
(72) Brown, Z. Z.; Schafmeister, C. E. Org. Lett. 2010, 12, 1436.
(73) Sigala, P. A.; Kraut, D. A.; Caaveiro, J. M. M.; Pybus, B.; Ruben,
E. A.; Ringe, D.; Petsko, G. A.; Herschlag, D. J. Am. Chem. Soc. 2008,
130, 13696.
(74) Schwans, J. P.; Sunden, F.; Gonzalez, A.; Tsai, Y.; Herschlag, D.
J. Am. Chem. Soc. 2011, 133, 20052.
(75) Gerlt, J. A.; Gassman, P. G. Biochemistry 1993, 32, 11943.
(76) Gerlt, J. A.; Gassman, P. G. J. Am. Chem. Soc. 1993, 115, 11552.
(77) Guthrie, J. P. Chem. Biol. 1996, 3, 163.
(78) Warshel, A.; Papazyan, A.; Kollman, P. A.; Cleland, W. W.;
Kreevoy, M. M.; Frey, P. A. Science 1995, 269, 102.
(79) Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K.
M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.;
Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179.
(80) Chakrabarti, S.; Parker, M. F. L.; Morgan, C. W.; Schafmeister,
C. E.; Waldeck, D. H. J. Am. Chem. Soc. 2009, 131, 2044.
3827
dx.doi.org/10.1021/ja409214c | J. Am. Chem. Soc. 2014, 136, 3817−3827