Construction of peptoids with all trans -amide backbones and peptoid reverse turns via the tactical incorporation of N -aryl side chains capable of hydrogen bonding

Article abstract of DOI:10.1021/jo101075a

Figure presented. The ability to design foldamers that mimic the defined structural motifs of natural biopolymers is critical for the continued development of functional biomimetic molecules. Peptoids, or oligomers of N-substituted glycine, represent a versatile class of foldamers capable of folding into defined secondary and tertiary structures. However, the rational design of discretely folded polypeptoids remains a challenging task, due in part to an incomplete understanding of the covalent and noncovalent interactions that direct local peptoid folding. We have found that simple, peptoid monomer model systems allow for the effective isolation of individual interactions within the peptoid backbone and side chains and can facilitate the study of the role of these interactions in restricting local peptoid conformation. Herein, we present an analysis of a set of peptoid monomers and an oligomer containing N-aryl side chains capable of hydrogen bonding with the peptoid backbone. These model peptoids were found to exhibit well-defined local conformational preferences, allowing for control of the ω, φ, and φ dihedral angles adopted by the systems. Fundamental studies of the peptoid monomers enabled the design and synthesis of an acyclic peptoid reverse-turn structure, in which N-aryl side chains outfitted with ortho-hydrogen bond donors were hypothesized to play a critical role in the stabilization of the turn. This trimeric peptoid was characterized by X-ray crystallography and 2D NMR spectroscopy and was shown to adopt a unique acyclic peptoid reverse-turn conformation. Further analysis of this turn revealed an n→π* _C-O interaction within the peptoid backbone, which represents the first reported example of this type of stereoelectronic interaction occurring exclusively within a polypeptoid backbone. The installation of N-aryl side chains capable of hydrogen bonding into peptoids is straightforward and entirely compatible with current solid-phase peptoid synthesis methodologies. As such, we anticipate that the strategic incorporation of these N-aryl side chains should facilitate the construction of peptoids capable of adopting discrete structural motifs, both turnlike and beyond, and will facilitate the continued development of well-folded peptoids.

Full text of DOI:10.1021/jo101075a

pubs.acs.org/joc
Construction of Peptoids with All Trans-Amide Backbones and Peptoid
Reverse Turns via the Tactical Incorporation of N-Aryl Side Chains
Capable of Hydrogen Bonding
Joseph R. Stringer, J. Aaron Crapster, Ilia A. Guzei, and Helen E. Blackwell*
Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison,
Wisconsin 53706-1322
blackwell@chem.wisc.edu
Received June 3, 2010
The ability to design foldamers that mimic the defined structural motifs of natural biopolymers is
critical for the continued development of functional biomimetic molecules. Peptoids, or oligomers of
N-substituted glycine, represent a versatile class of foldamers capable of folding into defined
secondary and tertiary structures. However, the rational design of discretely folded polypeptoids
remains a challenging task, due in part to an incomplete understanding of the covalent and
noncovalent interactions that direct local peptoid folding. We have found that simple, peptoid
monomer model systems allow for the effective isolation of individual interactions within the peptoid
backbone and side chains and can facilitate the study of the role of these interactions in restricting
local peptoid conformation. Herein, we present an analysis of a set of peptoid monomers and an
oligomer containing N-aryl side chains capable of hydrogen bonding with the peptoid backbone.
These model peptoids were found to exhibit well-defined local conformational preferences, allowing
for control of the ω, φ, and ψ dihedral angles adopted by the systems. Fundamental studies of the
peptoid monomers enabled the design and synthesis of an acyclic peptoid reverse-turn structure, in
which N-aryl side chains outfitted with ortho-hydrogen bond donors were hypothesized to play a
critical role in the stabilization of the turn. This trimeric peptoid was characterized by X-ray
crystallography and 2D NMR spectroscopy and was shown to adopt a unique acyclic peptoid
reverse-turn conformation. Further analysis of this turn revealed an nfπ*CdO interaction within the
peptoid backbone, which represents the first reported example of this type of stereoelectronic
interaction occurring exclusively within a polypeptoid backbone. The installation of N-aryl side
chains capable of hydrogen bonding into peptoids is straightforward and entirely compatible with
current solid-phase peptoid synthesis methodologies. As such, we anticipate that the strategic
incorporation of these N-aryl side chains should facilitate the construction of peptoids capable of
adopting discrete structural motifs, both turnlike and beyond, and will facilitate the continued
development of well-folded peptoids.
6068 J. Org. Chem. 2010, 75, 6068–6078
Published on Web 08/19/2010
DOI: 10.1021/jo101075a
2010 American Chemical Society
r

Stringer et al.
JOCFeatured Article
Introduction
R-chiral side chains. Such sterically demanding side chains
have been found to enforce largely cis-amide bond geome-
tries in peptoid backbone amides, thereby reducing overall
peptoid conformational flexibility. Recently, Kirshenbaum
and co-workers have reported complementary efforts to-
ward the design of peptoid helices that mimic the polyproline
type II helix.18 These strategies have focused on using achi-
ral, N-aryl side chains, which force the peptoid backbone
amides to adopt predominately trans-amide conformations,
primarily due to steric19,20 and electronic factors.18,20 In the
Kirshenbaum work, molecular modeling predicted that an
N-aryl peptoid hexamer could form extended right- and left-
handed polyproline type II helices, with approximately 3.1
Biomimicry by non-natural polymers remains a challen-
ging task. However, extensive efforts toward the develop-
ment of foldameric systems that mimic the structure and
function of Nature’s biopolymers have provided significant
insight into the folding propensities and functions of a variety
of abiotic polymers.1 Peptoids, or oligomers of N-substituted
glycine, have emerged as an important class of peptidomi-
metic foldamer, in part because they have shown the ability
to perform a range of relevant and specific biological func-
tions, including inhibiting certain protein-protein inter-
actions,2,3 acting as potent and selective antimicrobial
agents,4,5 and serving as molecular transporters.6,7 Addition-
ally, peptoids offer attractive advantages relative to native
R-peptide scaffolds due to their increased cellular perme-
ability,8,9 proteolytic stability,10 straightforward and mod-
ular synthesis,11 and ability to display a wide range of non-
native functionalities.12-14 For the continued development
of peptoids as functional mimics of biological macromole-
cules, however, there remains a need to generate peptoid oli-
gomers capable of folding into predictable and distinct three-
dimensional structures. Although it has been demonstrated
that well-defined structure is not essential for peptoid func-
tion in certain specific cases,2 the ability to accurately con-
struct peptoids with a variety of well-defined secondary (and
higher order) structures could open up new avenues for their
use in biological applications.
˚
residues per turn and a helical pitch of approximately 9 A per
turn. Experimental studies of these helices are ongoing and
are of significant interest as trans-amide polypeptoids may
adopt structures beyond the polyproline type II helix, such as
peptoid sheetlike structures.
In addition to peptoid helices, several recent investigations
have focused on the design and characterization of peptoid
loops and turns. The peptoid “threaded” loop represents a
secondary structure unique to peptoids and was first char-
acterized by Huang et al.21 This lasso-like motif appears to be
limited to a very small set of peptoid primary sequence space,
that is, peptoid nonamers of bulky R-chiral peptoid residues.
The loop is formed by the peptoid backbone doubling back
on itself via the formation of intramolecular hydrogen bonds
between the N-terminal amine and several backbone amides
and has been well characterized in solution by NMR spec-
troscopy. In contrast to loops, turn motifs are common
secondary structural elements in polypeptides,22-24 and the
development of peptoid turns is justifiably of significant
interest. Notable examples by Appella,25 Kirshenbaum,26
and co-workers highlight recent advancements in peptoid
turn design, including both cyclic peptoid turns and acyclic
peptide-peptoid hybrids. These initial studies demonstrate
that peptoids can fold into well-defined turn motifs that can
mimic naturally occurring turns in polypeptides.26 However,
further work is required to develop a standard set of design
strategies for the formation of acyclic peptoid turns in the
context of polypeptoid structures.
Thus far, the best-characterized peptoid secondary struc-
ture is the peptoid helix, which resembles a polyproline type I
helix with approximately three residues per turn and a helical
pitch of approximately 6.7 A per turn.15-17 These structures
˚
are limited to a relatively small set of peptoid primary seq-
uences, largely based on residues containing sterically bulky,
(1) Gellman, S. H. Acc. Chem. Res. 1998, 31, 173–180.
(2) Hara, T.; Durell, S. R.; Myers, M. C.; Appella, D. H. J. Am. Chem.
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Steinman, L.; Rothbard, J. B. Proc. Natl. Acad. Sci. U.S.A. 2000, 97,
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Despite the examples outlined above, the number of
reported peptoid secondary structures and studies thereof
remains relatively small in comparison to other foldameric
systems.27,28 This is largely due to the poor understanding of
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peptoid folding processes in general. To date, steric,15 hydro-
phobic,21 electrostatic,29 stereoelectronic,30 and hydrogen-
bonding interactions21,31 have been implicated in local and
global peptoid folding. Careful investigation of the specific
noncovalent interactions that govern peptoid folding would
undoubtedly aid in future peptoid design. Furthermore,
previous work has focused primarily on controlling amide
bond geometry (ω dihedral angle) in peptoids. However, in
addition to the ω angle, the φ and ψ dihedral angles are also
subject to change and thus contribute, in part, to the overall
conformational flexibility of peptoids. For example, the
recent modeling studies of Kirshenbaum and co-workers
have suggested that, in addition to cis/trans ω amide bond
isomerization, there exists considerable flexibility in ψ when
a trans ω geometry is present.32 Therefore, the installation of
side chains that are capable of predictably influencing the
rotational preferences of the φ and ψ dihedral angles, in
addition to the ω dihedral angle, may serve as a general tactic
for reducing overall conformational flexibility in polypep-
toids. To address these challenges, our group is studying the
mechanisms of peptoid folding by probing the effects of
various side chain-to-backbone and backbone-to-backbone
noncovalent interactions on ω, φ, and ψ dihedral angles in
model peptoid systems.30,31,33,34 We have focused our efforts
on monomers that are straightforward to synthesize and
install using established peptoid synthesis techniques, there-
by enabling their facile incorporation into polypeptoids. Using
this fundamental approach, we seek to contribute to a more
complete understanding of peptoid sequence-structure rela-
tionships and facilitate the future rational design of peptoids
with novel secondary and higher order structures.
Herein, we report the design, synthesis, and characteriza-
tion of a series of peptoids equipped with N-aryl side chains
capable of hydrogen bonding with the peptoid backbone.
These studies demonstrate that the presence of such hydro-
gen-bonding side chains can strongly affect local back-
bone conformational preferences in peptoid monomers and
oligomers;both in solution and in the solid state;and
allow for greater control over the ω, φ, and ψ dihedral angles
adopted by these systems relative to peptoids containing
analogous N-aryl side chains that are incapable of hydrogen
bonding. On the basis of these results, we rationally designed
and synthesized an acyclic peptoid reverse turn and char-
acterized its structure in solution by two-dimensional nucle-
ar magnetic resonance (2D NMR) spectroscopy and in the
solid state by single-crystal X-ray crystallography. Further
analysis of this peptoid reverse-turn structure revealed an
nfπ*CdO interaction within the peptoid backbone, which
represents the first reported example of this type of stereo-
electronic interaction occurring exclusively within a poly-
peptoid backbone.35 We anticipate that the design strategies
presented herein incorporating N-aryl side chains should
advance the understanding of peptoid folding and the on-
going development of a generalized set of peptoid folding
rules.
Results and Discussion
Motivation. We sought to examine whether noncovalent
interactions between substituted N-aryl peptoid side chains
and the peptoid backbone could be utilized to engender
predictable conformational motifs in peptoids. As high-
lighted above, recent investigations by Kirshenbaum and
co-workers had shown that N-aryl side chains enforce pre-
dominantly trans backbone amides in peptoids.18 We rea-
soned that substituents on the aryl ring could be utilized to
enforce additional, unique restrictions on local peptoid
conformation. Prior to designing such peptoids, further
scrutiny of the unsubstituted N-aryl systems was required,
and we sought to do so in the context of our previously re-
ported, peptoid monomer model system.30,34 We therefore
analyzed N-aryl monomer peptoid 1 (Figure 1A) as a control
compound. Previous studies in our laboratory have shown
that monomeric peptoids, such as 1, can be reliable model
systems for the isolation and examination of noncovalent
interactions in peptoids, while mimicking the local environ-
ment of typical polypeptoids.30,34
N-Aryl peptoid monomer 1 was synthesized according to
our previously reported method30 and characterized by
NMR spectroscopy and X-ray crystallography (see the Ex-
perimental Section for details of NMR and X-ray analyses).
The 1D-NOESY and 1H NMR spectra for 1 revealed that the
N-aryl amide bond displayed a >95% preference for the
trans-amide in CDCl3 at 25 °C (see the Supporting Infor-
mation). In turn, the X-ray crystal structure of 1 (Figure 1B)
revealed an N-terminal trans-amide bond and the N-aryl side
chain rotated out of the plane ∼66° relative to the peptoid
backbone. These data support those reported by Kirshen-
baum and co-workers and others for related peptoid18 and
amide model systems.19,20,37,38 Careful inspection of the solid-
state structure of 1 led us to speculate that ortho-substituted
N-aryl side chains may engender subtle, but distinct, local
rotational preferences among backbone dihedral angles
relative to those of previously studied N-aryl peptoids. We
hypothesized that the placement of a hydrogen-bond donor
at the ortho position could have a dramatic effect, as it would
offer a potential tunable strategy to effectively restrict rota-
tion about local single bonds and thus confer additional
conformational ordering to N-aryl peptoids. Specifically,
based on our studies of 1 in the solid state, we reasoned that
this functionality would be ideally suited to form an intra-
molecular 8-membered-ring hydrogen bond to the C-term-
inal carbonyl oxygen. However, we note that an alternate
hydrogen bond is also possible between the N-aryl hydrogen
bond donor and the N-terminal carbonyl oxygen, which
would result in a 7-membered ring instead (see Figure 1C).
We therefore set forth to design, synthesize, and characterize
peptoid monomer model systems and peptoid oligomers
(29) Shin, S. B. Y.; Kirshenbaum, K. Org. Lett. 2007, 9, 5003–5006.
(30) Gorske, B. C.; Bastian, B. L.; Geske, G. D.; Blackwell, H. E. J. Am.
Chem. Soc. 2007, 129, 8928–8929.
(31) Gorske, B. C.; Blackwell, H. E. J. Am. Chem. Soc. 2006, 128, 14378–
14387.
(32) Butterfoss, G. L.; Renfrew, P. D.; Kuhlman, B.; Kirshenbaum, K.;
Bonneau, R. J. Am. Chem. Soc. 2009, 131, 16798–16807.
(33) Fowler, S. A.; Luechapanichkul, R.; Blackwell, H. E. J. Org. Chem.
2009, 74, 1440–1449.
(34) Gorske, B. C.; Stringer, J. R.; Bastian, B. L.; Fowler, S. A.; Blackwell,
H. E. J. Am. Chem. Soc. 2009, 131, 16555–16567.
(35) On the basis of molecular modeling studies, nfπ*CdO interactions
between adjacent trans-amide bonds have been suggested as possible stabi-
lizing influences on a peptoid polyproline type II helix. See ref 18.
(36) Moehle, K.; Hofmann, H.-J. Biopolymers 1996, 38, 781–790.
(37) Itai, A.; Toriumi, Y.; Tomioka, N.; Kagechika, H.; Azumaya, I.;
Shudo, K. Tetrahedron Lett. 1989, 30, 6177–6180.
(38) Pedersen, B. F.; Pedersen, B. Tetrahedron Lett. 1965, 2995–3001.
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FIGURE 1. (A) Chemical structure of peptoid monomer model system 1 showing dihedral angles as previously described in peptoids.32,36 (B)
X-ray crystal structure of 1 showing the trans-amide geometry and the N-aryl side chain rotated out of the amide plane. (C) Chemical structure
showing a hypothetical 7-membered-ring (left) and 8-membered-ring (right) hydrogen bond (solid green line) in a peptoid monomer containing
an o-aryl hydrogen-bond donor.
2-7 in solution using NMR spectroscopy. In order to be
applicable as a modular design strategy in polypeptoids, an
ideal hydrogen-bonding interaction in the substituted N-aryl
peptoids would involve both a unique hydrogen-bond donor
and a unique acceptor. Again, an intramolecular hydrogen
bond in monomers 2 and 3 could involve either the C-terminal
carbonyl oxygen or the N-terminal carbonyl oxygen as a
hydrogen-bond acceptor (see Figure 1C). In the latter case,
the N-aryl amide bond must be in the cis-amide geometry for
the resulting intramolecular 7-membered-ring hydrogen bond
to occur. Such a geometry would be unexpected in light of the
data above for peptoid 1 indicating it adopted a predomin-
antly trans-amide geometry. NOESY experiments in CDCl3 at
room temperature confirmed the N-aryl amide bond in 2
displayed a 93% preference for the trans-amide, while 3 dis-
played a >95% preference for the trans-amide. These NMR
data suggest that since the N-aryl amide bonds in 2 and 3
exist almost entirely as trans-amides, conformational states
containing an intramolecular 7-membered-ring hydrogen
FIGURE 2. Chemical structures of peptoid monomer model sys-
tems 2-7.
bond to the N-terminal carbonyl oxygen are not significantly
populated in 2 or 3 under these conditions.
containing hydrogen-bonding N-aryl side chains to probe
our hypotheses. The results and implications of these studies
To further examine the nature of potential hydrogen-
are reported below.
Design and Synthesis of N-Aryl Peptoid Monomers. We
examined six N-aryl peptoid monomer model systems in this
study (2-7; shown in Figure 2). Monomers 2 and 3 were
designed to investigate potential interactions of o-acetamide
and o-hydroxyl hydrogen-bond donors, respectively. Pep-
toid monomers 4 and 5 were generated as control com-
pounds in order to characterize the nature of any potential
hydrogen-bonding interactions observed in monomers 2 and
3. The para positioning of the hydrogen-bonding substitu-
ents in both 4 and 5 precludes the formation of an intramo-
lecular hydrogen bond but allows for the possibility of
intermolecular hydrogen-bonding interactions.
For comparison to the hydrogen-bonding monomers 2-5,
we also sought to investigate the effects of non-hydrogen-
bonding interactions in peptoid monomers 2 and 3, we utili-
zed variable-concentration 1H NMR studies. Such 1H NMR
studies can provide insight into the presence of inter- vs intra-
molecular hydrogen-bonding interactions in solution and are
frequently utilized for this purpose in foldamer research.39-42
Protons involved in intermolecular hydrogen bonding most
commonly display concentration-dependent chemical shift
values, while protons involved in intramolecular hydrogen
bonding exhibit chemical shifts that are concentration inde-
pendent.43 Variable concentration 1H NMR studies of mono-
mers 2 and 3, along with control monomers 4 and 5, were
carried out at 0.1-100 mM in CDCl3 at room temperature
(Figure 3). Over this concentration range, Δδ (2)-NH = 0.0
and Δδ (3)-OH = 0.0, consistent with intramolecular hydro-
gen bonding. In contrast, Δδ (4)-NH = 3.2 and Δδ (5)-OH =
1.3 over the same concentration range, consistent with inter-
molecular hydrogen bonding. Additionally, the significant
bonding, ortho-substituted N-aryl side chains on peptoid
local conformation. We therefore synthesized monomers 6
and 7, which contain methyl-substituted N-aryl side chains
that cannot participate in hydrogen bonding and differ only
in the substitution pattern on their aryl ring, as controls. All
six monomers were generated in high purity using our
previously reported, straightforward synthetic route to dia-
mide peptoid model systems.30,34
(39) Dado, G. P.; Gellman, S. H. J. Am. Chem. Soc. 1993, 115, 4228–4245.
(40) Prabhakaran, P.; Kale, S. S.; Puranik, V. G.; Rajamohanan, P. R.;
Chetina, O.; Howard, J. A. K.; Hofmann, H.-J.; Sanjayan, G. J. J. Am.
Chem. Soc. 2008, 130, 17743–17754.
(41) Eyman, D. P.; Drago, R. S. J. Am. Chem. Soc. 1966, 88, 1617–1620.
(42) Gellman, S. H.; Dado, G. P.; Liang, G. B.; Adams, B. R. J. Am.
Chem. Soc. 1991, 113, 1164–1173.
Characterization of Peptoid Monomers 2-7 in Solution.
We first characterized the structures of peptoid monomers
(43) Haque, T. S.; Little, J. C.; Gellman, S. H. J. Am. Chem. Soc. 1994,
116, 4105–4106.
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FIGURE 3. NMR chemical shifts of the hydrogen-bond donor protons in peptoids 2-5 plotted as a function of the logarithm of peptoid
concentration (in CDCl3, 25 °C). Data for peptoid 5 at concentrations g60 mM are not reported due to its lowered solubility at these
concentrations.
FIGURE 4. X-ray crystal structures of peptoid monomers (A) 2 and (B) 3. Hydrogen bonds (solid green lines) and interatomic distance (black
˚
dashed line) are shown. Hydrogen bond in 2: N O distance = 2.79 A. Hydrogen bond in 3: O O distance = 2.66 A.
˚
3 3 3
3 3 3
downfield chemical shifts of (2)-NH and (3)-OH, relative to
the upfield shifts of (4)-NH and (5)-OH, are consistent with
intramolecular hydrogen-bonding interactions. These NMR
data support our initial hypothesis that an intramolecular
8-membered-ring hydrogen bond is present in peptoid monomers
2 and 3 and that intermolecular hydrogen-bonding interactions
exist, at least to some degree, in control monomers 4 and 5.
Our NMR analysis also revealed that the methylene pro-
tons in the ortho-substituted N-aryl peptoid monomers 2, 3,
6, and 7 are all diastereotopic (see the Supporting Informa-
tion for spectra). These observations are in agreement with
previously reported studies by Siddall et al. on ortho-sub-
stituted acetanilides structurally similar to 6 and 7.44-47 This
phenomenon is a result of atropisomerism due to restricted
rotation of the ortho-substituted N-aryl moiety around the
nitrogen-aryl bond. Our NMR data suggest that ortho-
substitution of the N-aryl side chain, as in monomers 2, 3,
6, and 7, results in atropisomerism, regardless of the hydro-
gen-bonding capability of the side chain. Therefore, it may
be possible to use ortho-substituted N-aryl side chains that do
not contain a hydrogen-bond donor, such as those in 6 and 7,
to restrict side chain rotation and potentially influence local
torsions within the peptoid backbone. Unfortunately, our
inability to characterize monomers 6 or 7 by X-ray crystal-
lography hindered further structural comparisons to the
hydrogen-bond-containing monomers 2 and 3.
Characterization of Peptoid Monomers 2 and 3 in the Solid
State. To provide additional supporting evidence that the
N-aryl side chains in peptoid monomers 2 and 3 influence local
peptoid conformations, we analyzed their solid-state con-
formations by single-crystal X-ray crystallography. Crystals
of 2 and 3 were grown by slow evaporation from a CH2Cl2/n-
hexane solution at room temperature (see the Experimental
Section). Notably, monomers 2 and 3 each crystallized as
single enantiomers throughout their respective crystal lat-
tices. The X-ray crystal structure of peptoid monomer 2
revealed an intramolecular 8-membered-ring hydrogen bond
between the side chain amide proton and C-terminal carbo-
nyl oxygen (Figure 4A). Similarly, the X-ray crystal structure
of 3 showed an intramolecular 8-membered-ring hydrogen
bond between the side chain hydroxyl proton and C-terminal
carbonyl oxygen (Figure 4B). In both monomers, the C-terminal
carbonyl oxygen acts as the sole hydrogen-bond acceptor in
the intramolecular hydrogen bond. Further, the hydrogen
bonds in 2 and 3 are exclusively intramolecular in their
(44) Siddall, T. H.; Prohaska, C. A. Nature 1965, 208, 582–583.
(45) Siddall, T. H., III; Prohaska, C. A. J. Am. Chem. Soc. 1966, 88, 1172–
1176.
(46) Siddall, T. H., III; Stewart, W. E. J. Org. Chem. 1969, 34, 2927–2933.
(47) Siddall, T. H., III; Stewart, W. E. J. Phys. Chem. 1969, 73, 40–45.
6072 J. Org. Chem. Vol. 75, No. 18, 2010

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TABLE 1. Dihedral Angles Observed in X-ray Crystal Structures of
Peptoid Monomers 1-3
peptoid
φ (deg)
ψ (deg)
χ1 (deg)
ω (deg)
1
2
3
101.00
-79.21
74.55
167.79
162.45
-165.27
114.71
82.92
106.33
179.05
-179.31
-179.36
respective crystal lattices, again with the C-terminal carbonyl
oxygens acting as the lone hydrogen-bond acceptors. These
solid-state data for peptoid monomers 2 and 3 corroborate
the corresponding NMR data discussed above and suggest
that the conformational state containing an intramolecular
8-membered-ring hydrogen bond is highly populated by these
two peptoid monomers, both in solution and in the solid state.
The dihedral angles observed in the X-ray crystal struc-
tures of peptoid monomers 1-3 are listed in Table 1 (see
Figure 1 for angle designations in peptoids). We note that
since either enantiomer of 1-3 could potentially exist in
solution or in the solid state, only absolute values need be
considered when comparing the dihedral angles in Table 1.
All three peptoid monomers have trans-amide bonds17,18,48
(ω) with values (∼179° each) near planarity. The ψ values in
1-3 are also similar, ranging from 162.45° to 167.79°, but the
φ values in ortho-substituted monomers 2 (-79.21°) and 3
(74.55°) differ from the unsubstituted aryl peptoid monomer
1 (101.00°). This difference in φ values in 2 and 3 relative to
1 may be a result of the intramolecular hydrogen bond,
which stabilizes the backbone orientations in 2 and 3. Fur-
ther comparisons to other previously reported N-aryl pep-
toid structures are complicated, as these N-aryl structures are
either part of a peptoid macrocycle or contain intermolecular
hydrogen bonding.18 We therefore chose to directly compare
the values in Table 1 to a peptoid oligomer (9, see below) con-
taining side chains derived from monomers 1-3, and we
return to this comparison below.
FIGURE 5. Chemical structure of peptoid 9 with individual resi-
dues color-coded: green, derived from monomer 1; red, derived
from monomer 2; blue, derived from monomer 3.
to position the termini backbone atoms directly opposite
each other in an approximate antiparallel orientation. Ac-
cordingly, we selected the unsubstituted and o-hydroxyl
N-aryl residues (derived from peptoid monomers 1 and 3)
for the N- and C-termini (residues 1 and 3), respectively.
Again, the central o-amide N-aryl side chain would consti-
tute part of the actual turn backbone, with the third N-aryl
residue coupled to the o-amide substituent. Notably, this
turn design would allow us to study not only the ability of the
o-acetamide N-aryl unit to induce a turn in peptoids but also
the effects of the three N-aryl side chains of monomers 1-3
on peptoid backbone amide geometries in an actual oligo-
meric peptoid system (vide infra).
We developed a solid-phase synthetic route to peptoid
turn 9 on a Rink amide linker-derivatized resin that built on
our previously reported, microwave-assisted peptoid synth-
esis procedure (Scheme 1).11,51 This route uses the two-step
submonomer method to generate each peptoid unit via a
bromoacetic acid coupling and a subsequent nucleophilic
displacement with a primary amine.11 Peptoid trimer 9 was
thus constructed using three iterative acid and amine cou-
plings. Due to the low nucleophilicity of aryl amines, bro-
moacetylation and amination reactions required extended
reaction times relative to those typical for N-alkyl peptoid
syntheses (1.5 and 16 h at rt vs ∼20 min and ∼20 min at rt,
respectively).11 We found that performing the amination
reactions at 60 °C using microwave irradiation for 1 h
expedited the installation of the two flanking N-aryl side
chains in 9.18,51 The central turn-inducing motif was installed
using N-Fmoc-protected 2-amino aniline 8, which was read-
ily synthesized in solution on gram scale. We chose to per-
form this amination at room temperature for 16 h to reduce
potential thermal cleavage of the N-Fmoc group. Acetyla-
tion of the central turn inducing motif, and ultimately the
N-terminus, was achieved via bromoacetylation and subse-
quent reduction using NaBH4.51 Crude peptoid 9 was iso-
lated by acid-mediated resin cleavage (using TFA), purified
by flash silica gel chromatography, and characterized by MS
to confirm its identity (see the Experimental Section). Using
these methods, pure 9 could be generated on a ∼20 mg scale.
Characterization of Peptoid 9 in Solution. We evaluated the
solution-phase conformation of peptoid 9 in CDCl3 at 10
mM using NMR spectroscopy. 1D 1H NMR data suggested
that 9 exists as a mixture of one major conformer family
(∼70% populated based on integration) and several minor
Further inspection of the X-ray crystal structure of
o-acetamide monomer 2 indicated that the distance between
the N-terminal methyl carbon and C-terminal piperidinyl
˚
carbon R to the nitrogen is 5.7 A (Figure 4A). Interestingly,
this distance is within the distance constraints of typical
peptide turns (CR CR distance e 7 A).49,50 We therefore
˚
3 3 3
envisaged that the o-acetamide N-aryl side chain in 2 could
be used as a novel reverse-turn-forming motif in peptoid
oligomers, in which the turn backbone would continue from
the o-acetamide nitrogen as opposed to the adjacent, “na-
tive” N-terminus. Such an acyclic turn structure had yet to be
evaluated in peptoids and could be straightforward to im-
plement. We outline our application of this new design
strategy below.
Design and Synthesis of a Peptoid Reverse Turn. We
designed an acyclic, trimeric peptoid turn (9) containing
the o-amide N-aryl side chain from peptoid monomer 2 as
a turn-inducing motif (Figure 5). We then flanked this
central unit (residue 2) with two N-aryl peptoid residues that
would enforce trans-amide geometries in the peptoid back-
bone. These flanking trans-amide residues were anticipated
(48) Sui, Q.; Borchardt, D.; Rabenstein, D. L. J. Am. Chem. Soc. 2007,
129, 12042–12048.
(49) Lewis, P. N.; Momany, F. A.; Scheraga, H. A. Biochim. Biophys.
Acta, Protein Struct. 1973, 303, 211–229.
(50) Ball, J. B.; Hughes, R. A.; Alewood, P. F.; Andrews, P. R. Tetra-
hedron 1993, 49, 3467–3478.
(51) Shah, N. H.; Kirshenbaum, K. Org. Biomol. Chem. 2008, 6, 2516–2521.
J. Org. Chem. Vol. 75, No. 18, 2010 6073

Stringer et al.
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SCHEME 1. Synthesis of Peptoid Trimer 9a
aReagents and conditions: Fmoc-OSu = 9-fluorenylmethyl N-succinimidyl carbonate; DMF = N,N-dimethylformamide; BrAcOH = bromoacetic
acid; DIC = N,N-diisopropylcarbodiimide; DMSO = dimethyl sulfoxide; TFA = trifluoroacetic acid; μW = microwave irradiation; rt = room
temperature.
the C1 methyl protons to the ortho-aromatic protons in resi-
due 1 and an interresidue NOE from the C4 methylene and
the C16 methyl protons to the N6 amide proton. We were not
able to unambiguously assign an NOE from the C10 methy-
lene protons to the ortho-aromatic proton in residue 3 due to
peak overlap in this region of the spectrum. However, we did
not observe an interresidue NOE from the C10 methylene
protons to the C13 methylene protons, which suggests that
residue 3 does not adopt a cis-amide conformation. We also
note the significant downfield chemical shift of the N6 amide
proton at 10.67 ppm, which implies that this proton is invol-
ved in a hydrogen bond, presumably to the C11 carbonyl
FIGURE 6. Chemical structure of peptoid 9. Observed NOEs of
the major conformer family are indicated by red arrows.
oxygen (vide supra). The presence of such a hydrogen bond
would most likely orient the peptoid backbone termini in an
approximate antiparallel fashion, as illustrated by the che-
mical structure in Figure 6 and similar to the solid-state
structure of peptoid monomer 2 (Figure 4A). In view of this
possible structure, we also anticipated observing a weak
NOE between the C13 and C4 hydrogens in peptoid 9; such
a NOE was not apparent, however, even when the ROESY
experiment was performed with an extended number of
transients and at lower temperature (0 °C; see below).
Characterization of Peptoid 9 in the Solid State. The
structure of peptoid turn 9 was further characterized using
single-crystal X-ray crystallography. Crystals of 9 were
grown by slow evaporation from a mixture of acetone/n-
hexane. We were pleased to observe that peptoid 9 resembles
a reverse-turn structure in the solid state (see Figure 7). This
turn can be classified as a δ or C8 turn in the context of
conformer families in CDCl3 at room temperature. 2D
rotating-frame Overhauser effect spectroscopy (ROESY)
was next utilized to detect NOEs between backbone and
side-chain protons on 9 to obtain information about its
solution-phase structure. Figure 6 shows important NOEs
for the major conformer family of peptoid 9 that indicate the
presence of trans-amide bonds throughout the peptoid back-
bone. In N-aryl peptoids, a backbone trans-amide confor-
mation is characterized by an interresidue NOE from the
backbone methylene protons of one residue (i) to the ortho-
aromatic protons of an adjacent residue (i þ 1), while a back-
bone cis-amide conformation is characterized by an inter-
residue NOE between the backbone methylene protons of
one residue (i) to the backbone methylene protons of an
adjacent residue (i-1).18 In peptoid 9, there is an NOE from
6074 J. Org. Chem. Vol. 75, No. 18, 2010

Stringer et al.
JOCFeatured Article
FIGURE 7. X-ray crystal structure of peptoid 9. (A) Side view of 9 showing C4 C13 distance. (B) End view of 9 showing nfπ*CdO
backbone interaction. Hydrogen bonds (solid green lines) and interatomic distances (black dashed lines) are shown.
3 3 3
TABLE 2. Dihedral Angles Observed in X-ray Crystal Structure of
Peptoid 9
R-peptides, which is defined by an 8-atom hydrogen-bond
ring between the amide proton and the carbonyl oxygen of
two adjacent residues (ifi ( 1 interaction).52,53 The distance
between the ends of the 10-atom turn spanning the C4
methylene carbon to the C13 methylene carbon of peptoid
residue
φ (deg)
ψ (deg)
χ1 (deg)
ω (deg)
1
2
3
-67.75
73.71
82.97
140.09
-158.88
178.44
116.26
103.96
103.73
177.58
176.70
-176.05
˚
˚
9 is 6.2 A, within the 7 A maximum limit of typical peptide
turns.49,50 Based on the solid-state structure of 9, we note
that the interproton distance between the methylene protons
trans-amides of tertiary amides.54-56 Previously, we had
characterized a related nfπ*CdO interaction in the solid-
state structure of a peptoid monomer system. This interac-
tion occurred between a carbonyl oxygen in the peptoid
backbone and an adjacent p-NO2 anilide carbonyl in the side
chain.30 To our knowledge, the nfπ*CdO interaction in 9
represents the first solid-state example of an nfπ*CdO
interaction occurring exclusively within a peptoid backbone.
Note, this nfπ*CdO interaction is absent in the solid-state
structure of monomer 1, presumably due to the poorer
electron accepting ability of the carbonyl π* orbital of the
tertiary piperidinyl amide in 1 relative to the carbonyl π*
orbital of the secondary aryl amide in oligomer 9.34 While the
nfπ* interaction is not as energetically significant as other
noncovalent interactions (typically <1 kcal/mol in a peptoid
monomer),30,34 the crystal structure of 9 illustrates that the
nfπ*CdO interaction can exist in polypeptoids containing
trans-amides and should be considered among the repertoire
of noncovalent interactions that influence overall peptoid
structure.
˚
on C13 and the methylene protons on C4 is ∼4.5 A, which is
near the approximate threshold distance for NOE observa-
tions and may be a contributing factor in our inability to
observe a NOE between these two pairs of methylene pro-
tons in CDCl3 (as mentioned above). Two intramolecular
8-membered-ring hydrogen bonds are present: one between
the side chain hydroxyl proton and C14 carbonyl oxygen and
the other between the N6 amide proton and C11 carbonyl
oxygen. Notably, both hydrogen bonds in the crystal struc-
ture of 9 are also present in the crystal structures of their
respective monomers (2 and 3), suggesting that these N-aryl
side chains can also form predictable, intraresidue hydrogen
bonds to the peptoid backbone when incorporated into
peptoid oligomers. These X-ray crystallographic data are
significant, as 9 represents the first acyclic peptoid turn, to
our knowledge, to be characterized in the solid state.
Further analysis of the solid-state structure of 9 revealed
an nfπ*CdO stereoelectronic interaction occurring within
the peptoid backbone, from the C2 N-terminal carbonyl
Lastly, we note that peptoid 9 is an approximate modular
assembly of the peptoid residues studied in model systems
1-3, even in view of the nonstandard backbone linkage of
residues 1 and 2 via the side chain. Thus, we compared the
oxygen to the C5 anilide carbonyl (O CdO distance and
3 3 3
˚
angle of 2.9 A and 109°, respectively; Figure 7B). The
nfπ*CdO interaction is defined by donation of electron den-
sity from a carbonyl oxygen lone pair into the π* orbital of an
adjacent amide carbonyl and has been shown to stabilize the
(54) Choudhary, A.; Gandla, D.; Krow, G. R.; Raines, R. T. J. Am.
Chem. Soc. 2009, 131, 7244–7246.
(55) Hodges, J. A.; Raines, R. T. Org. Lett. 2006, 8, 4695–4697.
(56) Horng, J.-C.; Raines, R. T. Protein Sci. 2006, 15, 74–83.
(52) Chou, K.-C. Anal. Biochem. 2000, 286, 1–16.
(53) Stroup, A. N.; Rockwell, A. L.; Rheingold, A. L.; Gierasch, L. M.
J. Am. Chem. Soc. 1988, 110, 5157–5161.
J. Org. Chem. Vol. 75, No. 18, 2010 6075

Stringer et al.
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backbone dihedral angles in the solid-state structures of
monomers 1-3 versus those in trimer 9 to acquire insights
into the local torsional preferences of each N-aryl side chain
in monomeric versus oligomeric peptoids (Tables 1 and 2).
Analysis of the dihedral angles in peptoid oligomer 9 reveals
that the ψ and φ angles for the N-terminal residue 1, which
contains an unsubstituted N-aryl side chain, deviate the most
relative to the corresponding peptoid monomer (1). Specifi-
cally, there is a 33.25° difference in the φ angle and a 27.70°
difference in the ψ angle between 1 and the corresponding
residue in peptoid oligomer 9. Residues 2 and 3, both com-
prising ortho-substituted hydrogen-bonding N-aryl side chains,
show a less significant change in their respective ψ and φ dihe-
dral angles compared to the corresponding monomers. In re-
sidue 2 of 9, there is a 5.50° difference in the φ angle and a
3.57° difference in the ψ angle compared to model peptoid 3.
In residue 3 of peptoid 9, there is a 8.42° difference in the
φ angle and a 13.17° difference in the ψ angle compared to
model peptoid 3. Overall, these comparisons of torsional
angles in peptoids 1-3 and 9 suggest that there is more
rotational flexibility in the ψ and φ dihedral angles of
residues containing an unsubstituted N-aryl side chain re-
lative to residues with ortho-substituted hydrogen-bonding
N-aryl side chains. These data support the work of Butterfoss
et al.,32 whose previous survey of (experimentally determined)
N-alkyl and N-aryl peptoid structures illustrated the flex-
ibility of the ψ angle in peptoids when the backbone amide
bond is in the trans conformation. The greater variations in
the dihedral angles of residue 1, relative to residues 2 and 3 in
peptoid 9, may be a result of the backbone orientation re-
quired for residue 1 to participate in the observed nfπ*CdO
interaction. In peptoid 9, residue 1 contains an unsubstituted
N-aryl side chain that cannot participate in intramolecular
hydrogen bonding. Presumably, the absence of an ortho-
positioned hydrogen bond permits more rotational freedom
in the backbone of residue 1, relative to the hydrogen-bond
containing residues 2 and 3, thus allowing residue 1 to as-
sume a proper orientation for an nfπ*CdO interaction.
Summary and Outlook. We have outlined a new design
strategy for the construction of discretely folded peptoids
that utilizes N-aryl side chains with ortho-substituents cap-
able of hydrogen-bond donation. These N-aryl side chains
enforce trans-amide geometries within the peptoid backbone
and participate in localized hydrogen bonds to their respec-
tive intraresidue backbone carbonyl oxygens. Conforma-
tional analyses of a series of peptoid monomers in solution
and in the solid state revealed that hydrogen-bonding N-aryl
side chains can be used to effectively modulate local dihedral
angles in peptoids. We examined these side chains in the
context of a peptoid trimer and demonstrated that they can
be used to effectively introduce a reverse-turn conformation.
Together, our results reveal a new tactic for the design of
well-folded peptoids that should be applicable to the assem-
bly of peptoids with distinct secondary structures. Specifi-
cally, we envisage peptoids that contain multiple N-aryl side
chains with ortho-hydrogen-bond donors could adopt highly
stable, polyproline-type II peptoid helices. Even more inter-
esting may be the incorporation of adjacent R-chiral and
N-aryl side chains into peptoids, which could potentially
enforce a particular N-aryl atropisomer, and thereby further
reduce overall conformational heterogeneity. Ongoing work
in our laboratory is focused on optimizing and applying
these design strategies to generate novel peptoid architec-
tures and expand the known, three-dimensional peptoid
structure space.
Experimental Section
General Methods. All reagents and solvents were purchased
from commercial sources and used without further purification,
with the exception of dichloromethane (CH2Cl2) and hex-
anes, which were distilled immediately prior to use. Thin-layer
chromatography (TLC) was performed on silica gel 60 F254
plates. Silica gel 60 (40-63 μm) was used for flash column
chromatography.57
1H NMR (500 MHz) and 13C NMR (125 MHz) spectra were
recorded on 500 MHz spectrometers in deuterated solvents.
1H NMR (300 MHz) and 13C NMR (75 MHz) spectra were
recorded on 300 MHz spectrometers in deuterated solvents.
Rotating-frame Overhauser effect spectroscopy (ROESY) NMR
experiments were performed on a 600 MHz spectrometer using a
5 mm hcn probe and were referenced to solvent. Chemical shifts
are reported in parts per million (ppm, δ) using tetramethylsi-
lane (TMS) as a reference (0.0 ppm). Couplings are reported in
hertz. All NMR data were manipulated and processed using
standard NMR software.58
Attenuated total reflectance (ATR)-IR spectra were recorded
with an IR spectrometer outfitted with a single-reflection ATR
unit and a ZnSe crystal with a spectral range of 20000 to 650
cm-1. Electrospray ionization (ESI) mass spectra were obtained
on a mass spectrometer equipped with a time-of-flight analyzer.
Samples were dissolved in methanol and sprayed with a sample
cone voltage of 20. Perfluorokerosene (PFK) was used for
calibration. Matrix-assisted laser desorption/ionization time-
of-flight (MALDI-TOF) mass spectra were obtained on a mass
spectrometer equipped with a 337 nm laser and a reflectron. In
positive-ion mode, the acceleration voltage was 25 kV.
Analytical HPLC analyses were performed using a laboratory
HPLC system equipped with a UV/vis detector. Purities were
determined by integration of peaks at 220 nm. A C18 column
(4.6 mm ꢀ 250 mm) was used for all analytical HPLC work.
Standard HPLC conditions were as follows: flow rate = 1 mL/
min; mobile phase A = 0.1% trifluoroacetic acid (TFA) in
water; mobile phase B = 0.1% TFA in acetonitrile. LC-MS
data were obtained using a laboratory HPLC system equipped
with an UV/vis diode array detector and a single quadrupole
analyzer (ESI). A C18 wide-pore column (15 cm ꢀ 2.1 mm) was
used for all LC-MS work. Standard HPLC conditions for
LC-MS were as follows: flow rate =200 μL/min; mobile phase
A = 0.1% formic acid in water; mobile phase B = 0.1% formic
acid in acetonitrile.
Representative Synthetic Route to Model Peptoids 1-7. 2-
Bromo-1-(piperidin-1-yl)ethanone (200 mg, 0.97 mmol; pre-
pared according to our previously reported method)30 was
dissolved in dry DMF (2 mL) in a dry 50 mL flask equipped
with a dropping funnel. Aniline (88 μL, 0.97 mmol) was dis-
solved in dry DMF (5 mL) and added dropwise via the dropping
funnel to the stirred solution. The reaction mixture was allowed
to stir for 6 h at room temperature. The DMF was removed in
vacuo, and the resulting crude oil was redissolved in CH2Cl2 (10
mL) and cooled to 0 °C under stirring. Triethylamine (406 μL,
2.91 mmol) was added to the stirred solution, followed by the
dropwise addition of an acetyl chloride/CH2Cl2 solution (429
μL, 1.96 mmol in ∼5 mL of CH2Cl2). The reaction mixture was
allowed to return to room temperature and stirred for an addi-
tional 15 min. Thereafter, the reaction mixture was transferred
(57) Still, W. C.; Kahn, M.; Mitra, A. J. Org. Chem. 1978, 43, 2923–2925.
(58) Goddard, T. D.; Kneller, D. G. SPARKY, v. 3.110; University of
California, San Francisco.
6076 J. Org. Chem. Vol. 75, No. 18, 2010

Stringer et al.
JOCFeatured Article
to a separatory funnel, washed with 10% w/v aq citric acid (1ꢀ),
satd aq NaHCO3 (1ꢀ), and dried over anhydrous MgSO4. The
solvent was removed in vacuo, and the crude peptoid product
was purified to homogeneity by flash silica gel chromatography
(EtOAc).57 To generate model peptoids 2 and 4, the aryl hydro-
xyl groups (protected as methoxyl groups) were deprotected
using BBr3 in a final step according to a literature procedure.59
Isolated yields: 1, 70%; 2, 45%; 3, 37%; 4, 51%; 5, 40%, 6, 78%;
7, 73%.
906, 844, 826, 795, 777, 771, 760, 743, 707, 667, 649. HRMS
(ESI): calcd for C15H20N2O3Na m/z 299.1367, found m/z
299.1359.
1
Peptoid 6. TLC: Rf = 0.25 (EtOAc). H NMR (300 MHz,
CDCl3): δ 7.67-7.64 (m, 1H), 7.29-7.20 (m, 3H), 5.08 (d, J =
15.7 Hz, 1H), 3.62 (d, J = 15.7 Hz, 1H), 3.57-3.28 (m, 4H), 2.27
(s, 3H), 1.84 (s, 3H), 1.69-1.45 (m, 6H). 13C NMR (75 MHz,
CDCl3, 1H broadband-decoupled): δ 171.3, 165.9, 142.6, 135.5,
131.3, 130.0, 128.6, 127.6, 50.1, 46.1, 43.4, 26.4, 25.6, 24.6, 22.1,
17.8. IR (ATR, cm-1): 3004, 2999, 2934, 2855, 1653, 1601, 1581,
1492, 1456, 1414, 1386, 1358, 1276, 1260, 1227, 1198, 1158, 1139,
1125, 1037, 1024, 1015, 985, 954, 923, 853, 805, 765, 750, 733,
632, 627. HRMS (ESI): calcd for C16H22N2O2Na m/z 297.1574,
found m/z 297.1567.
1
Peptoid 1. TLC: Rf = 0.33 (EtOAc). H NMR (500 MHz,
CDCl3): δ 7.44-7.38 (m, 4H), 7.33 (tt, J = 7.0, 1.7 Hz, 1H), 4.48
(s, 3H), 3.56 (m, 2H), 3.37 (m, 2H), 1.95 (s, 3H), 1.69-1.54 (m,
6H). 13C NMR (75 MHz, CDCl3, 1H broadband-decoupled): δ
171.0, 166.0, 144.0, 129.7, 128.4, 128.1, 51.3, 46.0, 43.4, 26.4,
25.6, 24.6, 22.5. IR (ATR, cm-1): 3006, 2938, 2864, 2821, 1646,
1596, 1494, 1477, 1461, 1443, 1418, 1390, 1359, 1346, 1265, 1253,
1237, 1225, 1156, 1142, 1227, 1108, 1056, 1033, 1011, 902, 855,
844, 834, 803, 772, 729, 701, 647, 617. HRMS (ESI): calcd for
C15H20N2O2Na m/z 283.1417, found m/z 283.1420.
1
Peptoid 7. TLC: Rf = 0.15 (EtOAc). H NMR (300 MHz,
CDCl3): δ 7.30-7.12 (m, 4H), 4.44 (s, 2H), 3.54 (m, 2H), 3.36 (m,
2H), 2.37 (s, 3H), 1.93 (s, 3H), 1.68-1.51 (m, 6H). 13C NMR (75
MHz, CDCl3, 1H broadband-decoupled): δ 171.1, 166.1, 144.1,
139.8, 129.5, 128.9 (broad), 125.4, 51.3, 46.1, 43.4, 26.4, 25.6,
24.7, 22.5, 21.5. IR (ATR, cm-1): 2932, 2853, 1654, 1604, 1588,
1489, 1443, 1314, 1253, 1227, 1186, 1138, 1111, 1090, 1038, 1015,
988, 954, 925, 892, 853, 787, 760, 720, 702. HRMS (ESI): calcd
for C16H22N2O2Na m/z 297.1574, found m/z 297.1567.
Synthesis of Amine 8 (9H-Fluoren-9-yl)methyl 2-Aminophe-
nylcarbamate). 1,2-Phenylenediamine (200 mg, 1.85 mmol) was
dissolved in dry DMF (10 mL) in a dry 50 mL flask equipped
with a dropping funnel. 9-Fluorenylmethyl N-succinimidyl
carbonate (Fmoc-OSu, 624 mg, 1.85 mmol) was dissolved in
dry DMF (10 mL) and added dropwise via the dropping funnel
to the stirred solution. The reaction mixture was allowed to stir
for 2 h at room temperature. The solvent was removed in vacuo,
and the crude product was purified to homogeneity by flash
silica gel chromatography (2:1 hexanes/EtOAc) to give 200 mg
of 8 as a white solid. Isolated yield: 33%.
1
Peptoid 2. TLC: Rf = 0.29 (EtOAc). H NMR (500 MHz,
CDCl3): δ 11.20 (s, 1H), 8.43 (d, J = 8.3 Hz, 1H), 7.36 (m, 1H),
7.10 (m, 2H), 5.18 (d, J = 16.0 Hz, 1H), 3.60 (m, 2H), 3.55 (d,
J = 16.0 Hz, 1H), 3.45 (ddd, J = 13.6, 7.5, 3.5 Hz, 2H), 3.36
(ddd, J = 13.6, 7.5, 3.5 Hz, 2H), 2.25 (s, 3H), 1.84 (s, 3H),
1.76-1.50 (m, 6H). 13C NMR (75 MHz, CDCl3, 1H broadband-
decoupled): δ 171.8, 170.1, 167.5, 137.4, 132.8, 129.8, 128.1,
124.3, 122.5, 51.6, 46.2, 43.8, 26.3, 25.6, 24.7, 24.5, 21.5. IR
(ATR, cm-1): 2936, 1700, 1659, 1634, 1541, 1456, 1387, 1311,
1257, 1022, 799, 768, 749, 688. HRMS (ESI): calcd for
C17H23N3O3Na m/z 340.1632, found m/z 340.1628.
Peptoid 3. TLC: Rf = 0.4 (3:1 EtOAc/hexane). 1H NMR (500
MHz, CDCl3): δ 10.85 (s, 1H), 7.28 (td, J = 7.8, 1.6 Hz, 1H),
7.05 (dd, J = 4.4, 1.6 Hz, 1H), 7.03 (dd, J = 4.4, 1.6 Hz, 1H),
6.87 (td, J = 7.8, 1.4 Hz, 1H), 5.25 (d, J = 16.1 Hz, 1H),
3.65-3.55 (m, 2H), 3.55 (d, J = 16.1 Hz, 1H), 3.45 (ddd, J =
13.4, 7.7, 3.5 Hz, 2H), 3.37 (ddd, J = 13.4, 7.7, 3.5 Hz, 2H), 1.90
Amine 8. TLC: Rf = 0.3 (2:1 hexane/EtOAc). 1H NMR (300
MHz, DMSO-d6): δ 8.70 (brs, 1H), 7.90 (d, J = 7.3 Hz, 2H), 7.74
(m, 2H), 7.43 (t, J = 7.3 Hz, 2H), 7.34 (t, J = 7.3 Hz, 2H), 7.12
(m, 1H), 6.89 (td, J = 7.5,1.4 Hz, 1H), 6.71 (dd, J = 7.9,1.4 Hz,
1H), 6.53 (td, J = 7.5,1.4 Hz, 1H), 4.87 (s, 2H), 4.40 (d, J = 6.9
Hz, 2H), 4.29 (t, J = 6.9 Hz, 1H). 13C NMR (75 MHz, DMSO-
d6, 1H broadband-decoupled): δ 155.1, 144.5, 142.6, 141.5,
128.3, 127.8, 126.3, 126.0 (broad), 123.7, 120.8, 116.9, 116.3,
66.4, 47.4. IR (ATR, cm-1): 3428, 3352, 1680, 1648, 1623, 1597,
1530, 1498, 1465, 1454, 1311, 1291, 1272, 1254, 1233, 1161, 1106,
1094, 1051, 1041, 987, 938, 860, 799, 755, 751, 682. MS (ESI):
calcd m/z 330.1, found m/z 330.9 [M þ H]þ.
1
(s, 3H), 1.77-1.50 (m, 6H). 13C NMR (75 MHz, CDCl3, H
broadband-decoupled): δ 172.3, 168.6, 155.1, 130.8, 130.6,
128.7, 120.5, 119.0, 51.2, 46.3, 44.1, 26.3, 25.5, 24.4, 21.5. IR
(ATR, cm-1): 2951, 2856, 1663, 1624, 1494, 1453, 1406, 1314,
1293, 1256, 1140, 1021, 988, 835, 799, 761, 751, 628. HRMS
(ESI): calcd for C15H20N2O3Na m/z 299.1367, found m/z
299.1364.
1
Peptoid 4. TLC: Rf = 0.3 (12% MeOH/EtOAc). H NMR
(300 MHz): δ 8.49 (s 1H), 7.56 (AA0XX0 peak, Jax = 8.6, Jaa
0
=
Jxx = 2.4, Jax = 0.2 Hz, 2H), 7.32 (AA0XX0 peak, Jax = 8.6,
0
0
0
0
0
Jaa = Jxx = 2.4, Jax = 0.2 Hz, 2H), 4.46 (s, 2H), 3.52 (m, 2H),
C
Synthesis and Characterization of Peptoid 9. Peptoid 9 was
synthesized using a modified version of a previously reported,
microwave-assisted solid-phase method on Rink-amide deriva-
tized polystyrene resin.51 The crude peptoid was purified by
flash silica gel chromatography (eluent: 10% MeOH/EtOAc,
Rf = 0.31) and characterized by MS to confirm its identity.
MALDI-TOF MS: calcd m/z 531.2, found m/z 554.1 [M þ Na]þ.
See the Supporting Information for HPLC, MS, and NMR data
for peptoid 9.
NMR Analysis for Peptoid Monomers 1-7. 1D-NOESY
spectra were used to identify cis/trans amide rotameric peaks,
as reported in our previous studies.30,34 The cis/trans amide
ratios were determined by integration of 1D 1H NMR spectra.
NMR Analyses for Peptoid 9. Peptoid 9 was dissolved in
CDCl3 to give a ∼10-20 mM solution. 2D-ROESY experi-
ments on 9 was performed at 25 °C using the following para-
meter values: mix time = 200 ms; spectral width = 8000 Hz;
number of transients (nt) = 16; number of increments (ni) =
400. The number of points (np) was 2048, and 192 points were
obtained by linear prediction in the f1 dimension. Square cosine
window functions were applied in both dimensions. The spectra
were zero-filled to generate f1f2 matrices of 4096 ꢀ 4096 points.
3.36 (m, 2H), 2.17 (s, 3H), 1.92 (s, 3H), 1.72-1.45 (m, 6H). 13
1
NMR (75 MHz, CDCl3, H broadband-decoupled): δ 171.2,
168.8, 166.1, 139.6, 138.0, 129.0, 120.9, 51.3, 46.1, 43.4, 26.4,
25.6, 24.7, 24.6, 22.5. IR (ATR, cm-1): 3435, 3302, 3265, 3194,
3123, 3069, 3008, 2942, 2855, 1692, 1662, 1636, 1606, 1539, 1513,
1455, 1409, 1390, 1371, 1312, 1254, 1233, 1140, 1126, 1112, 1035,
1015, 989, 954, 905, 853, 797, 765, 666, 578, 555. HRMS (ESI):
calcd for C17H23N3O3Na m/z 340.1632, found m/z 340.1639.
1
Peptoid 5. TLC: Rf = 0.2 (19:1 EtOAc/MeOH). H NMR
(300 MHz, CDCl3): δ 7.53 (brs, 1H), 7.15 (AA0XX0 peak, Jax
=
8.8, Jaa = Jxx = 2.5, Jax = 0.2 Hz, 2H), 6.72 (AA0XX0 peak,
0
0
0
0 0 0
Jax = 8.8, Jaa = Jxx = 2.5, Jax = 0.2 Hz, 2H), 4.49 (s, 2H), 3.82
(s, 3H), 3.54 (m, 2H), 3.42 (m, 2H), 1.91 (s, 3H), 1.71-1.49 (m,
1
6H). 13C NMR (75 MHz, CDCl3, H broadband-decoupled):
δ 174.0, 168.1, 158.8, 136.6, 130.3, 117.2, 52.6, 47.1, 44.5, 27.4,
26.8, 25.5, 22.3. IR (ATR, cm-1): 3271, 3028, 3010, 2945, 2861,
1643 (broad), 1594, 1514, 1447, 1393, 1317, 1274, 1264, 1254, 1229,
1219, 1214, 1165, 1140, 1127, 1114, 1098, 1034, 1015, 990, 954,
(59) Vickery, E. H.; Pahler, L. F.; Eisenbraun, E. J. J. Org. Chem. 1979,
44, 4444–4446.
J. Org. Chem. Vol. 75, No. 18, 2010 6077

Stringer et al.
JOCFeatured Article
NOE intensities for 9 were classified according to their relative
cross-peak integrations in the 2D-ROESY spectrum.
nitrogen atoms were located in the difference map and were
refined independently.
X-ray crystal data for (9): C31H35N5O7, triclinic, P1, a =
X-ray Crystal Structure Data for 1-3 and 9. Model peptoids
1-3 and oligomer 9 (∼10 mg) were each dissolved in n-hexane
with a minimal amount of either CH2Cl2 (1-3) or HPLC-grade
acetone (9). Slow evaporation afforded crystals suitable for
X-ray analysis after ∼2-3 days. For all four X-ray structures,
non-hydrogen atoms were refined with anisotropic displace-
ment coefficients. All hydrogen atoms were included in the
structure factor calculations at idealized positions and were
allowed to ride on the neighboring atoms with relative iso-
tropic displacement coefficients. All software and sources of
the scattering factors are contained in the program suite
SHELXL.60
˚
˚
˚
10.7078(10) A, b = 12.1574(13) A, c = 13.2918(12) A, R =
3
˚
107.653(7)°, β = 109.664(7)°, γ = 93.441(8)°, V = 1527.1(3) A ,
Z = 2, T = 100(2) K, Dcalc =1.282 mg/m3, R(F) based on F2 for
I g 2σ = 9.26% for 5293 independent reflections (3.88° e θ e
69.05°).
Acknowledgment. We thank the NSF (CHE-0449959),
ONR (N000140710255), Greater Milwaukee Foundation,
Burroughs Welcome Fund, and Research Corporation for
financial support of aspects of this work. H.E.B. is an Alfred
P. Sloan Foundation fellow. Support for the NMR facilities
at UW;Madison by the NIH (1 S10 RR13866-01 and 1 S10
RR08389-01) and the NSF (CHE-0342998 and CHE-
9629688) is gratefully acknowledged. X-ray crystal struc-
tures were visualized using the UCSF Chimera package from
the Resource for Biocomputing, Visualization, and Infor-
matics at the University of California, San Francisco
(supported by NIH P41 RR-01081). We thank Dr. Charlie
Fry and Dr. Monika Ivancic for assistance with NMR
spectroscopy, Lara Spencer for X-ray crystallographic work,
and Prof. Hans Reich, Prof. Samuel Gellman, and Dr.
Benjamin Gorske for many contributive discussions.
X-ray crystal data for 1: C15H20N2O2, monoclinic, P21, a =
˚
˚
˚
8.116(3) A, b = 8.813(3) A, c = 10.402(3) A, β = 112.059(4)°,
V = 689.6(4) A , Z = 2, T = 100(2) K, Dcalc = 1.254 mg/m3,
3
˚
R(F) based on F2 for I g 2σ = 4.27% for 3873 independent
reflections (2.11° e θ e 30.02°).
X-ray crystal data for 2: C15H20N2O3, monoclinic, P21/c, a =
˚
˚
˚
8.6600(2) A, b = 29.0866(7) A, c = 11.5414(3) A, β = 91.7060-
3
˚
(10)°, V = 2905.87(12) A , Z = 8, T = 103(2) K, Dcalc = 1.263
mg/m3, R(F) based on F2 for I g 2σ = 3.49% for 5465 indepen-
dent reflections (3.04° e θ e 69.92°).
X-ray crystal data for 3: C17H23N3O3, triclinic, P1, a =
˚
˚
˚
8.7424(3) A, b = 12.4268(4) A, c = 15.4933(5) A, R =
3
˚
81.016(2)°, β = 81.487(2)°, γ = 84.078(2)°, V = 1638.70(9) A ,
Z = 4, T = 103(2) K, Dcalc =1.286 mg/m3, R(F) based on F2 for
I g 2σ = 3.69% for 5875 independent reflections (2.91° e θ e
69.76°). The hydrogen atoms H(3N) and H(6N) attached to
Supporting Information Available: NMR data for com-
pounds 1-9, HPLC data for peptoid 9, and X-ray crystal-
lographic data (CIF). This material is available free of charge
via the Internet at http://pubs.acs.org.
(60) Sheldrick, G. M. Acta Crystallogr. 2008, A64, 112–122.
6078 J. Org. Chem. Vol. 75, No. 18, 2010