One-handed helical screw direction of homopeptide foldamer exclusively induced by cyclic α-amino acid side-chain chiral centers

Article abstract of DOI:10.1002/chem.201102902

Chiral cyclic α,α-disubstituted amino acids, (3S,4S)- and (3R,4R)-1-amino-3,4-(dialkoxy)cyclopentanecarboxylic acids ((S,S)- and (R,R)-Ac₅c^dOR; R: methyl, methoxymethyl), were synthesized from dimethyl L-(+)- or D-(-)-tartrate, and their homochiral homoligomers were prepared by solution-phase methods. The preferred secondary structure of the (S,S)-Ac₅c^dOMe hexapeptide was a left-handed (M) 3 ₁₀ helix, whereas those of the (S,S)-Ac₅c^dOMe octa- and decapeptides were left-handed (M) α helices, both in solution and in the crystal state. The octa- and decapeptides can be well dissolved in pure water and are more α helical in water than in 2,2,2-trifluoroethanol solution. The left-handed (M) helices of the (S,S)-Ac₅c ^dOMe homochiral homopeptides were exclusively controlled by the side-chain chiral centers, because the cyclic amino acid (S,S)-Ac ₅c^dOMe does not have an α-carbon chiral center but has side-chain γ-carbon chiral centers. Copyright

Full text of DOI:10.1002/chem.201102902

DOI: 10.1002/chem.201102902
One-Handed Helical Screw Direction of Homopeptide Foldamer Exclusively
Induced by Cyclic a-Amino Acid Side-Chain Chiral Centers
Yosuke Demizu,[b] Mitsunobu Doi,[c] Masaaki Kurihara,[b] Tokumi Maruyama,[d]
Hiroshi Suemune,[e] and Masakazu Tanaka*[a]
Abstract: Chiral cyclic a,a-disubstitut-
ed amino acids, (3S,4S)- and (3R,4R)-1-
amino-3,4-(dialkoxy)cyclopentanecar-
boxylic acids ((S,S)- and (R,R)-
Ac5cdOR; R: methyl, methoxymethyl),
were synthesized from dimethyl l-(+)-
or d-(ꢀ)-tartrate, and their homochiral
homoligomers were prepared by solu-
tion-phase methods. The preferred sec-
ondary structure of the (S,S)-Ac5cdOMe
hexapeptide was a left-handed (M) 310
helix, whereas those of the (S,S)-
Ac5cdOMe octa- and decapeptides were
left-handed (M) a helices, both in solu-
tion and in the crystal state. The octa-
and decapeptides can be well dissolved
in pure water and are more a helical in
water than in 2,2,2-trifluoroethanol so-
lution. The left-handed (M) helices of
the (S,S)-Ac5cdOMe homochiral homo-
peptides were exclusively controlled by
the side-chain chiral centers, because
the cyclic amino acid (S,S)-Ac5cdOMe
does not have an a-carbon chiral
center but has side-chain g-carbon
chiral centers.
Keywords: amino acids · chirality ·
conformation analysis
·
helical
structures · peptides
Introduction
proteins almost always have a right-handed (P) screw sense.
This right handedness is believed to result from the asym-
metric center at the a-carbon atom of proteinogenic l-a-
amino acids, because if peptides composed of l-a-amino
acids formed left-handed (M) helical structures, steric repul-
sion would arise between the carbonyl group and the side-
chain b-carbon atom of one residue.[5]
Among the l-a-amino acids, threonine and isoleucine ex-
clusively have an additional chiral center at the side-chain
b-carbon atom, as well as at the a-carbon atom; however,
only a little physiochemical attention has been paid to the
influence of side-chain asymmetric centers on the secondary
structure of peptides.[6,7] Scientists have believed that the a-
carbon chiral centers of l-a-amino acids affect the helical
screw bias of their peptides but that side-chain chiral centers
do not, and the physiochemical role of side-chain chiral cen-
ters has been overlooked. Herein, we describe the design
and synthesis of chiral cyclic a,a-disubstituted amino acids
in which chiral centers exist at the side-chain g-carbon
atoms but not at the a-carbon atoms, and we reveal that the
side-chain chiral centers of cyclic amino acid homochiral ho-
mopeptides can control the helical screw direction into one
handedness in organic solvent, in water, and also in the crys-
tal state.
Helices are life-science-related three-dimensional structures.
For instance, they are found in proteins as helical secondary
structures and in DNA as a double-helical structure. Recent-
ly, de novo designed helical structures of foldamers, such as
b peptides,[1] peptoids,[2] oligoarenes,[3] and urea oligomers,[4]
have attracted the attention of organic, medicinal, and pep-
tide chemists, and some have been used to design biological-
ly active molecules and organocatalysts. Helices are chiral,
and their helical screw senses result in two directions, right
handedness (P) and left handedness (M). The a helices in
[a] Prof. M. Tanaka
Graduate School of Biomedical Sciences
Nagasaki University
Nagasaki 852-8521 (Japan)
Fax: (81+)95-819-2423
E-mail: matanaka@nagasaki-u.ac.jp
[b] Dr. Y. Demizu, Dr. M. Kurihara
National Institute of Health Sciences
Tokyo 158-8501 (Japan)
[c] Prof. M. Doi
Osaka University of Pharmaceutical Sciences
Osaka 569-1094 (Japan)
[d] Prof. T. Maruyama
Faculty of Pharmaceutical Sciences
Kagawa Campus
Tokushima Bunri University
Kagawa 769-2193 (Japan)
Results and Discussion
[e] Prof. H. Suemune
Design and synthesis of chiral cyclic a,a-disubstituted a-
amino acids: We designed chiral cyclic a,a-disubstituted a-
amino acids, 1-amino-3,4-(dialkoxy)cyclopentanecarboxylic
acids (Ac5cdOR; R: methyl (Me) or methoxymethyl (MOM)),
having chiral centers at the side-chain g-carbon atoms but
Graduate School of Pharmaceutical Sciences
Kyushu University
Fukuoka 812-8582 (Japan)
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/chem.201102902.
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Chem. Eur. J. 2012, 18, 2430 – 2439

FULL PAPER
not at the a-carbon atoms.[8,9] The a-carbon atom of the
cyclic amino acid does not affect the screw direction of the
helix formed by the peptides because the a-carbon atom is
not an asymmetric center. Thus, we reasoned that the helical
screw sense of the Ac5cdOR homochiral homopeptides would
be exclusively affected by the side-chain chiral centers.[10–12]
We efficiently synthesized both enantiomers of the opti-
cally active cyclic amino acid[13] (S,S)- and (R,R)-Ac5cdOMe by
of the cyclic side chain, was synthesized from dimethyl l-
(+)-tartrate with protection of the secondary alcohols as the
MOM ethers (Scheme 1). Alkaline hydrolysis of the ester in
the cyclic amino acids 4a,b produced the free-C-terminal
amino acids Cbz-(Ac5cdOR)-OH (5a,b) in >99% yield. The
spectroscopic data of all compounds supported their struc-
tures.
starting
from
dimethyl
l-(+)-
or
d-(ꢀ)-tartrate
Preparation of homochiral homo-oligopeptides composed of
the cyclic amino acids (S,S)- and (R,R)-Ac5cdOMe and (S,S)-
Ac5cdOMOM: Homochiral homopeptides (up to decapeptide
11a for (S,S)-Ac5cdOMe and octapeptides 10a,b for (R,R)-
Ac5cdOMe and (S,S)-Ac5cdOMOM, respectively) were prepared
by solution-phase methods, with 1-ethyl-3-(3-dimethylami-
nopropyl)carbodiimide (EDC) hydrochloride and 1-hydrox-
ybenzotriazole (HOBt), or O-benzotriazol-1-yl-N,N,N’,N’-
tetramethyluronium hexafluorophosphate (HBTU), em-
ployed as the coupling reagents,[16] as illustrated in
Scheme 2. After removal of the Cbz protecting group in
Cbz-(Ac5cdOR)-OMe (4a,b) by hydrogenolysis with H2/5%
Pd-C, the resulting free-N-terminal amino acid was coupled
with the free-C-terminal amino acids Cbz-(Ac5cdOR)-OH
(5a,b) by EDC and HOBt to produce the dipeptides Cbz-
(Ac5cdOR)2-OMe (6a,b) in 61–71% yield. Alkaline hydrolysis
of 6a,b afforded free-C-terminal dipeptide acids 7a,b in
quantitative yields. After removal of the Cbz-protecting
group in the dipeptides 6a,b by hydrogenolysis, the resulting
free-N-terminal dipeptides were coupled with the dipeptide
acids 7a,b to give tetrapeptides 8a,b in 33–65% yield. Hexa-
peptides 9a,b, octapeptides 10a,b, and decapeptide (S,S)-
11a were prepared by two amino acid elongations in a simi-
lar manner to that used for the preparation of tetrapeptides
(Scheme 1).[14] Dimethyl tartrate was converted into diiodide
Scheme 1. Synthesis of the cyclic amino acids Cbz-(Ac5cdOR)-OMe (R:
Me, MOM). DIPEA: N,N-diisopropylethylamine; DPPA: diphenylphos-
phoryl azide; Bn: benzyl; Cbz: benzyloxycarbonyl.
2a in 70% yield through a three-step sequence of methyla-
tion of the secondary alcohols with MeI/Ag2O, reduction of
the methyl esters with LiAlH4, and substitution of the pri-
mary alcohols with iodide. Dialkylation of dimethylmalonate
with the diiodide 2a by KOtBu in dimethylsulfoxide
(DMSO) at room temperature
gave cyclic diester 3a in 53%
yield. Later, the yield of prod-
uct 3a was improved to 86%
by using K2CO3 in N,N-dime-
thylformamide
(DMF)
at
758C. Monohydrolysis of an
ester, followed by Curtius rear-
rangement with DPPA[15] and
work up with benzyl alcohol
produced the Cbz-protected
cyclic
amino
acid
Cbz-
(Ac5cdOMe)-OMe (4a) in 88%
yield. The synthesis from di-
methyl l-(+)-tartrate afforded
Cbz-[(S,S)-Ac5cdOMe]-OMe
((S,S)-4a), whereas that from
dimethyl d-(ꢀ)-tartrate gave
the enantiomeric Cbz-[(R,R)-
Ac5cdOMe]-OMe ((R,R)-4a) on
the gram scale. By a similar
procedure, the cyclic amino
acid
Cbz-[(S,S)-Ac5cdOMOM]-
OMe (4b), with two MOM
substituents at the g-position
Scheme 2. Synthesis of the homopeptides Cbz-(Ac5cdOR)n-OMe (R: Me, MOM; n=2–10).
Chem. Eur. J. 2012, 18, 2430 – 2439
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2431

M. Tanaka et al.
8a,b. Interestingly, the octapeptides 10a,b and decapeptide
11a could be dissolved in water because of the presence of
the ether functional groups. Removal of the MOM protect-
ing groups from hexapeptide 9b by treatment with concen-
trated HCl in MeOH gave a hexapeptide with twelve hy-
droxy groups, Cbz-[(S,S)-Ac5cdOH]6-OMe (9c), which was
well dissolved in pure water.
helices in solution, and are very different from the spectra
of diethylglycine (Deg)[19] and (S)-butylethylglycine[20] ho-
mochiral homopeptides, which assume fully extended planar
C5 conformations. The IR absorption spectra of homochiral
homopeptides composed of (S,S)-Ac5cdOMOM (Figure 1b)
show similar absorption spectra to those of (S,S)-Ac5cdOMe
homochiral homopeptides, but the absorption bands in the
3320–3360 cmꢀ1 region in the (S,S)-Ac5cdOMOM peptides are
slightly wider than those of the (S,S)-Ac5cdOMe peptides.
To obtain more detailed information on the preferred
Conformation analysis in solution: The dominant conforma-
tions of the Ac5cdOR homopeptides in solution were studied
by using IR, 1H NMR, and CD spectroscopies. Figure 1
1
conformation, the H NMR spectra of the Ac5cdOR hexapep-
tides (S,S)-9a,b and octapeptides (S,S)-10a,b were measured
1
in CDCl3 solution. In the H NMR spectra of Ac5cdOMe ho-
mopeptides 9a and 10a, the N(1)H signals at the N terminus
could be unambiguously determined by their high-field posi-
tions at d=5.54 ppm (brs, 1H) in 9a and d=5.53 ppm (brs,
1H) in 10a, due to their urethane structure,[21] but the re-
maining five or seven NH protons could not be assigned at
this stage. Also, the N(1)H signals at the N terminus of 9b
and 10b were assigned as signals at d=6.66 ppm (brs, 1H)
in 9b and d=6.51 ppm (brs, 1H) in 10b by their high-field
positions. Figure 2 and Figure 3 illustrate the results of sol-
vent perturbation experiments by the addition of the strong
H-bond acceptor solvent DMSO (0–10% v/v) or the para-
magnetic free radical 2,2,6,6-tetramethylpiperidin-1-yloxyl
(TEMPO; 0–5ꢁ10ꢀ2 % w/v).[18a,b] Two NH chemical shifts of
9a,b and 10a,b were sensitive (solvent-exposed NH group)
to the addition of the perturbing reagent DMSO, although
one NH signal of 10b could not be analyzed perfectly be-
cause of overlapping with the signals of the Cbz protecting
group. Also, with the addition of the TEMPO radical, the
Figure 1. IR absorption spectra of a) Cbz-[(S,S)-Ac5cdOMe]n-OMe (n=2:
6a; 4: 8a; 6: 9a; 8: 10a, 10: 11a) and b) Cbz-[(S,S)-Ac5cdOMOM]n-OMe
(n=2: 6b; 4: 8b; 6: 9b; 8: 10b) in CDCl3 solution. Peptide concentra-
tion: 1.0 mm.
shows the IR absorption spectra of Cbz-[(S,S)-Ac5cdOMe]n-
OMe (n=2 (6a), 4 (8a), 6 (9a), 8 (10a), 10 (11a)) and Cbz-
[(S,S)-Ac5cdOMOM]n-OMe (n=2 (6b), 4 (8b), 6 (9b), 8 (10b))
in the 3500–3250 cmꢀ1 region at a peptide concentration of
1.0 mm in CDCl3 solution. In the IR absorption spectra of
Cbz-[(S,S)-Ac5cdOMe]n-OMe (Figure 1a), the weak bands at
3420–3440 cmꢀ1 region are assigned to free (solvated) pep-
tide NH groups and the strong bands at 3320–3360 cmꢀ1 are
ꢀ
assigned to peptide NH groups with N H···O=C intramolec-
ular hydrogen bonds of different strengths. As the peptide
chain length increases, the strong band observed at
3360 cmꢀ1 in 8a shifts to slightly lower wavenumbers
(3320 cmꢀ1 in 11a) and the relative intensity of the bands in
the 3320–3360 cmꢀ1 region gradually increases. These IR ab-
sorption spectra are very similar to those of achiral 1-amino-
cyclopentanecarboxylic acid (Ac5c) homopeptides[17] and a-
aminoisobutyric acid (Aib) homopeptides,[18] which form 310
Figure 2. Plots of N H chemical shifts in the 1H NMR spectra of the ho-
ꢀ
mopeptides
a) Cbz-[(S,S)-Ac5cdOMe]6-OMe
(9a),
b) Cbz-[(S,S)-
Ac5cdOMOM]6-OMe (9b), c) Cbz-[(S,S)-Ac5cdOMe]8-OMe (10a), and d) Cbz-
[(S,S)-Ac5cdOMOM]8-OMe (10b) as a function of increasing percentage of
DMSO added to the CDCl3 solution.
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Side-Chain Control of Homopeptide Helical Structures
FULL PAPER
ꢀ
Figure 3. Plots of bandwidth of the N H protons of the homopeptides
a) Cbz-[(S,S)-Ac5cdOMe]6-OMe (9a), b) Cbz-[(S,S)-Ac5cdOMOM]6-OMe (9b),
c) Cbz-[(S,S)-Ac5cdOMe]8-OMe (10a), and d) Cbz-[(S,S)-Ac5cdOMOM]8-OMe
(10b) as a function of increasing percentage of TEMPO added to the
CDCl3 solution. Peptide concentration: 1.0 mm.
bandwidth of two NH signals broadened in the case of 9a,
9b, and 10a, although one NH signal of 10b overlapped
with the signals of the Cbz protecting group. These results
mean that two NH protons are solvent exposed, which sug-
gests that two NH protons are not intramolecularly hydro-
gen bonded. These data are in accordance with a 310-helical
structure, in which two NH groups at the N terminus of the
peptide are freely solvated (not intramolecularly hydrogen-
bonded) peptide NH groups.
1
Figure 4 shows the 2D ROESY H NMR spectra of hexa-
peptides 9a and 9b in CDCl3 solution. Both ROESY
1H NMR spectra show a complete series of sequential NH
(i!i+1) dipolar interactions, from the N-terminal N(1)H to
the C-terminal N(6)H, respectively. Sequential NH (i!i+1)
dipolar interactions are used to diagnose helical structures;
however, these interactions alone do not enable assessment
of whether a 310- or a-helical conformation is present. In l-
a-amino acid peptides and proteins, two NOE constraints
[daN (i!i+2)] and [daN (i!i+4)] are believed to be charac-
teristic of the 310- and a-helical structures, respectively;[22]
however, these interactions do not occur in the case of the
Ac5cdOR homopeptides because the cyclic a,a-disubstituted
amino acids lack an a-hydrogen atom. The NH (i!i+1) in-
teractions of octapeptide 10a could not be analyzed with
Figure 4. Rotating-frame nuclear Overhauser effect spectroscopy
(ROESY) 1H NMR spectra of a) Cbz-[(S,S)-Ac5cdOMe]6-OMe (9a) and
b) Cbz-[(S,S)-Ac5cdOMOM]6-OMe (9b).
1
the 2D ROESY H NMR spectrum because significant NH
proton signals overlapped and showed poor signal disper-
sion.
The CD spectra of (S,S)-Ac5cdOMe peptides 9a, 10a, and
11a in 2,2,2-trifluoroethanol (TFE) show positive maxima at
approximately 208 and 222 nm (207, 223 nm for 9a; 208,
225 nm for 10a; 210, 225 nm for 11a), which indicates that
the helical screw sense is left handed (M), although hexa-
peptide 9a lacks the negative maximum at approximately
200 nm (Figure 5a). The R ratios (q222/q208) suggest that the
secondary structure of hexapeptide 9a (R=0.4) is a 310 helix
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2433

M. Tanaka et al.
cate that the a-helical structure is more stable in water than
in organic solvents.
The CD spectra of (S,S)-Ac5cdOMOM peptides 9b and 10b,
with the MOM ether, in TFE showed similar patterns to
those of (S,S)-Ac5cdOMe peptides 9a and 10a, which indicates
that the helical screw sense is left handed (Figure 6a). Fig-
ure 6b shows the CD spectra of (S,S)-Ac5cdOH hexapeptide
9c with 12 deprotected hydroxy groups. On the basis of the
CD spectra, the (S,S)-Ac5cdOH peptide 9c does not form a
helical structure in TFE solution but instead seems to have
a random-chain conformation. However, in water, positive
maxima are shown at 208 and 225 nm (R>1.0) in the CD
spectrum, although the intensities are weak, which suggests
a left-handed (M) a-helical structure as a partially occurring
conformation in water.
Conformations of (S,S)-Ac5cdOMe homochiral homopeptides
in the crystal state: X-ray crystallographic analyses unam-
biguously revealed the molecular structures and conforma-
tions of the terminally protected (S,S)-Ac5cdOMe peptides in
the crystal state. The (S,S)-Ac5cdOMe peptides formed good
crystals for X-ray crystallographic analysis upon slow evapo-
ration of the solvent at room temperature (9a: EtOH/H2O;
10a: MeOH/H2O; 11a: CHCl3/iPrOH). The crystal and dif-
fraction parameters of hexapeptide 9a, octapeptide 10a, and
decapeptide 11a are summarized in Table 1.[25–27] The molec-
ular structures are illustrated in Figures 7–11. Relevant
backbone and side-chain torsion angles[24] and the intra- and
intermolecular hydrogen-bond parameters are listed in
Table 2 and Table 3, respectively.
Figure 5. CD spectra of (S,S)- and (R,R)-Ac5cdOMe homochiral homopepti-
des: a) (S,S)-Ac5cdOMe homochiral homopeptides (9a, 10a, and 11a) in
TFE solution (0.50 mm), b) (S,S)-Ac5cdOMe and (R,R)-Ac5cdOMe homochi-
ral octapeptides ((S,S)- and (R,R)-10a) in TFE solution (0.50 mm),
c) (S,S)-Ac5cdOMe homochiral octa- and decapeptides (10a and 11a) in
pure water (0.50 mm), and d) (R,R)-Ac5cdOMe homochiral octapeptide
(R,R)-10a in various solutions (0.5 mm; A: TFE; B: MeCN; C: MeCN/
H2O (10/90); D: MeCN/H2O (50/50); E: H2O).
Three crystallographically independent molecules, A, B,
and C, existed in the asymmetric unit of (S,S)-Ac5cdOMe
hexapeptide 9a. Three methoxy groups, that is, an ether
oxygen atom of the methoxy group at residues 3 and 6 in
molecule B and the methoxy group at residue 4 in mole-
cule C, were disordered. Molecules A–C were all folded into
left-handed (M) 310-helical structures and, thus, displayed
positive signs of the f and y torsion angles at each amino
acid residue, as illustrated in Figure 7. The average values of
torsion angles f and y are +57.88, +28.98 in molecule A,
+58.58, +32.18 in molecule B, and +59.28, +30.58 in mole-
and that those of octapeptide 10a (R=1.4) and decapeptide
11a (R=1.5) are a helices.[23] The CD spectrum of the enan-
tiomeric (R,R)-Ac5cdOMe octapeptide (R,R)-10a shows nega-
tive maxima at 208 nm and 225 nm, which indicates a right-
handed (P) a helix (Figure 5b). Measurement of the CD
spectra of (R,R)-10a at different temperatures (30–708C) in
TFE solution did not change the shape (maxima at 208 nm
and 225 nm), although the intensities of the maxima slightly
decreased. These results indicated that the right-handed a-
helical structure of 10a is
stable even at high tempera-
ture (708C).[24] Interestingly,
the intensity of the maxima at
210 nm and 225 nm in the CD
spectra of the (S,S)-Ac5cdOMe
octapeptide 10a and decapep-
tide 11a were stronger in
water than in TFE solution,
which indicates that these pep-
tides are more a helical in
water (Figure 5c). Figure 5d
shows the CD spectra of the
(R,R)-Ac5cdOMe
octapeptide
Figure 6. CD spectra of a) (S,S)-Ac5cdOMOM homochiral homopeptides 9b and 10b in TFE (0.50 mm) and
b) (S,S)-Ac5cdOH hexapeptide 9c in TFE (0.50 mm) and water (0.50 mm).
(R,R)-10a in a variety of sol-
vents. These spectra also indi-
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Chem. Eur. J. 2012, 18, 2430 – 2439

Side-Chain Control of Homopeptide Helical Structures
FULL PAPER
Table 1. Crystal and diffraction parameters of the (S,S)-Ac5cdOMe peptides
9a, 10a, and 11a.
Hexapeptide 9a Octapeptide 10a
Decapeptide 11a
empirical
formula
Mr
C57H88O21N6
C73H114O27N8·3H2O C89H140O33N10
1193.34
1589.77
1878.11
crystal
0.50ꢁ0.30ꢁ0.15 0.60ꢁ0.40ꢁ0.30
0.30ꢁ0.25ꢁ0.15
dimensions
[mm]
crystal
monoclinic
monoclinic
monoclinic
system
a, b, c [ꢂ]
22.854, 11.880,
15.639, 16.431,
15.989
90, 95.85, 90
4087.2
P21
14.480, 20.886,
33.632
90, 91.995, 90
9182.0
P21
16.904
90, 111.64, 90
4751.9
P21
a, b, g [8]
V [ꢂ3]
space group
Z value
6
2
2
Dcalcd [gcmꢀ3
]
1.295
0.99
1.292
1.00
1.313
1.00
m (MoKa
[cmꢀ1
no. of
)
]
Figure 7. Secondary structure of (S,S)-Ac5cdOMe hexapeptide 9a, as deter-
mined by X-ray crystallographic analysis: a) The three crystallographical-
ly independent molecules (A–C), as viewed perpendicular to the 310-heli-
cal axis, b) the structure of molecule A, as viewed along the 310-helical
axis, and c) the superimposed structures of molecules A–C.
31196
2300
16850
1023
15457
357
observations
(I>ꢀ10.0sI)
no. of varia-
bles
R1, Rw
solvent
0.075, 0.1972
EtOH/H2O
0.0579, 0.140
MeOH/H2O
0.1469, 0.2848
CHCl3/iPrOH
cule C. These torsion angles are in good agreement with the
ideal torsion angles (+608, +308) of the (M) 310-helical
structure.[28] The three molecules have generally similar sec-
ondary structures but show small differences in the confor-
mation of the side chain and the peptide backbone, as
shown in the superimposed structures in Figure 7c. Four
successive intramolecular hydrogen bonds of the i i+3
type, which correspond to the 310-helical structure, are found
in each molecule. Molecule A shows four intramolecular hy-
Table 2. Selected torsion angles w, f, and y [8] for 9a (A–C), 10a, and
11a, as determined by X-ray crystallographic analysis.
Torsion
angle
9a A
9a B
9a C
10a
11a
!
q0
178.6
175.1
169.9
61.4
35.9
178.5
58.1
27.8
175.4
63.1
21.3
179.4
56.6
27.5
176.9
58.6
29.7
167.5
53.1
50.1
172.9
–
175.1
180.0
ꢀ170.8
160.0
60.1
46.6
173.2
63.5
43.4
177.6
55.4
53.1
174.5
60.5
47.4
173.8
59.8
48.8
171.9
63.0
43.7
179.3
56.8
46.1
175.8
56.2
w0
f1
y1
w1
f2
y2
w2
f3
y3
w3
f4
y4
w4
f5
y5
w5
f6
y6
w6
f7
y7
w7
f8
y8
w8
f9
y9
w9
f10
y10
w10
170.0
56.4
42.0
171.7
64.8
17.4
ꢀ175.1
57.2
25.6
178.5
60.0
17.6
ꢀ176.8
59.6
22.8
179.6
48.7
47.8
ꢀ179.0
–
164.8
66.1
25.3
ꢀ179.1
54.7
34.0
175.0
58.4
27.4
174.9
53.5
33.2
173.1
67.4
17.1
177.0
55.1
46.2
178.2
–
168.1
60.5
43.7
173.5
57.0
50.1
172.8
60.7
47.1
175.5
59.5
46.8
174.8
58.4
46.7
176.9
65.6
49.4
171.3
64.8
43.7
ꢀ171.9
ꢀ54.2
ꢀ43.9
ꢀ174.2
–
ꢀ
drogen bonds between H N(3a) and the C(0a)=O(0a)
oxygen atom of the Cbz group (with an N(3a)···O(0a) dis-
ꢀ
tance of 3.03 ꢂ), between H N(4a) and C(1a)=O(1a)
ꢀ
(N(4a)···O(1a): 2.98 ꢂ), between H N(5a) and C(2a)=O(2a)
ꢀ
(N(5a)···O(2a): 3.04 ꢂ), and between H N(6a) and C(3a)=
O(3a) (N(6a)···O(3a): 2.99 ꢂ). Molecule B similarly shows
ꢀ
four intramolecular hydrogen bonds between H N(3b) and
ꢀ
C(0b)=O(0b) (N(3b)···O(0b): 2.98 ꢂ), between H N(4b)
ꢀ
H
and C(1b)=O(1b) (N(4b)···O(1b): 3.08 ꢂ), between
N(5b) and C(2b)=O(2b) (N(5b)···O(2b): 3.15 ꢂ), and be-
ꢀ
tween H N(6b) and C(3b)=O(3b) (N(6b)···O(3b): 3.09 ꢂ).
Also, molecule C shows four intramolecular hydrogen bonds
ꢀ
between H N(3c) and C(0c)=O(0c) (N(3c)···O(0c): 3.00 ꢂ),
ꢀ
between H N(4c) and C(1c)=O(1c) (N(4c)···O(1c): 3.00 ꢂ),
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
ꢀ
between H N(5c) and C(2c)=O(2c) (N(5c)···O(2c): 3.19 ꢂ),
ꢀ
and between H N(6c) and C(3c)=O(3c) (N(6c)···O(3c):
2.98 ꢂ). In packing mode, molecules A–C are connected by
two intermolecular hydrogen bonds, respectively, to form a
head-to-tail alignment of (M) 310 helices of molecules A, B,
and C, that is, ···A···B···C···A···B···C··· chains.[24]
45.7
173.8
60.5
–
–
–
–
48.2
173.2
ꢀ63.7
ꢀ14.6[a]
ꢀ172.0[a]
In the asymmetric unit of (S,S)-Ac5cdOMe octapeptide 10a,
only one conformer of peptide molecule existed, together
with three water molecules. Although it has been reported
that a,a-disubstituted a-amino acid containing homopepti-
des prefer to form a 310 helix over an a helix (3.613 helix),[29]
–
–
–
–
–
–
–
–
–
–
[a] Disorder of the torsion angles (y10 =166.8, w10 =ꢀ148.5) of 11a was
observed.
Chem. Eur. J. 2012, 18, 2430 – 2439
ꢀ 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
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2435

M. Tanaka et al.
Table 3. Intra- and intermolecular H-bond parameters for 9a, 10a, and 11a.
ꢀ
cal molecule of 10a. These are shown between H
N(4) and the C(0)=O(0) oxygen atom of the Cbz
Peptide[a] Donor,
Acceptor, Distance [ꢂ], Angle [8], Symmetry
ꢀ
D H
ꢀ
A
D···A
D H···A
operations
group (with an N(4)···O(0) distance of 3.10 ꢂ), be-
ꢀ
9a:
tween H N(5) and C(1)=O(1) (N(5)···O(1):
ꢀ
A (M)
B (M)
C (M)
N3a
ꢀ
N4a
H
H
O0a
O1a
O2a
O3a
O0b
O1b
O2b
O3b
O0c
O1c
O2c
O3c
O5a
O6a
O5b
O6b
O5c’
O6c’
3.03
2.98
3.04
2.99
2.98
3.08
3.15
3.09
3.00
3.00
3.19
2.98
2.75
2.93
2.87
3.00
2.81
3.08
153.6
164.2
165.2
170.2
149.1
159.9
165.5
171.4
155.1
156.9
160.9
167.1
170.6
159.4
165.7
146.7
173.1
164.8
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
ꢀ
2.95 ꢂ), between H N(6) and C(2)=O(2)
ꢀ
(N(6)···O(2): 3.08 ꢂ), between H N(7) and C(3)=
O(3) (N(7)···O(3): 2.87 ꢂ), and between H N(8)
ꢀ
N5a
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
ꢀ
ꢀ
N6a
N3b
and C(4)=O(4) (N(8)···O(4): 2.98 ꢂ). In packing
mode, the chains of the intermolecularly hydrogen-
bonded (M) a helices are formed in a head-to-tail
alignment along the b-axis direction (Figure 9).[24]
The (S,S)-Ac5cdOMe decapeptide 11a, which has a
molecular weight of 1878, crystallized in space
group P21 to form one left-handed (M) a-helical
conformer in the asymmetric unit (Figure 10). We
could not obtain good reflection data because of
the high molecular weight and conformational flex-
ibility of the methoxy groups. Thus, least-squares
refinement of the crystal structure was performed
by using reflection data at the maximal value of
1.2 ꢂ resolution, and the carbon atoms were re-
fined as isotropic displacement factors. The signs
(negative) of the f and y torsion angles (ꢀ63.78,
ꢀ14.68) of the C-terminal residue (residue 10) are
opposite to those (positive) of the preceding resi-
dues (1–9), that is, a reversal of the C terminus was
observed. The mean values of the f and y torsion
angles of amino acid residues 1–9 are +59.58 and
+47.08. There are seven intramolecular hydrogen
ꢀ
ꢀ
N4b
ꢀ
N5b
ꢀ
N6b
ꢀ
N3c
ꢀ
N4c
ꢀ
N5c
ꢀ
N6c
ꢀ
N1b
ꢀ
N2b
ꢀ
N1c
ꢀ
N2c
ꢀ
N1a
x+1,y,zꢀ1
ꢀ
N2a
x+1,y,zꢀ1
ꢀ
10a (M):
N4
N5
N6
N7
N8
N1
N2
H
O0
O1
O2
O3
O4
O8’
Ow(a)
Om5
Ow(c’)
O6’
3.10
2.95
3.08
2.87
2.98
2.91
2.92
2.78
2.83
2.89
2.89
2.81
2.84
167.4
164.6
164.2
162.5
166.8
156.3
169.6
177.8
165.8
171.5
175.9
174.2
174.4
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y+1,z
x,y,z
ꢀ
H
ꢀ
H
ꢀ
H
H
ꢀ
ꢀ
H
ꢀ
H
[b]
[b]
ꢀ
Ow(b)
H
H
H
H
H
H
x,y,z
ꢀ
Ow(a)
Ow(c)
Ow(a)
Ow(c)
Ow(b)
ꢀx+2,y+1/2,ꢀz
ꢀx+2,y+1/2,ꢀz
x,y+1,z
x,y,zꢀ1
ꢀ
ꢀ
O7’
Ow(b’)
Om2’
ꢀ
!
bonds of the i i+4 type, which corresponds to an
a-helical structure; these hydrogen bonds were be-
tween H N(4) and the C(0)=O(0) oxygen atom of
the Cbz group (with an N(4)···O(0) distance of
3.04 ꢂ), between H N(5) and C(1)=O(1)
(N(5)···O(1): 3.00 ꢂ), between H N(6) and C(2)=
O(2) (N(6)···O(2): 2.96 ꢂ), between H N(7) and
C(3)=O(3) (N(7)···O(3): 3.03 ꢂ), between H N(8)
ꢀ
ꢀx+2,yꢀ1/2,z+1
ꢀ
11a (M):
N4
N5
N6
N7
N8
N9
H
O0
O1
O2
O3
O4
O5
O6
O8’
O9’
3.04
3.00
2.96
3.03
3.07
3.21
3.18
2.92
3.00
165.7
165.2
160.0
166.5
161.7
156.3
162.5
170.7
152.3
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
x,y,z
ꢀ
ꢀ
H
H
ꢀ
ꢀ
ꢀ
H
ꢀ
ꢀ
H
ꢀ
H
ꢀ
H
ꢀ
N10
N1
ꢀ
ꢀ
H
H
x,y,zꢀ1
ꢀ
and C(4)=O(4) (N(8)···O(4): 3.07 ꢂ), between H
N(9) and C(5)=O(5) (N(9)···O(5): 3.21 ꢂ), and be-
ꢀ
N2
x,y,zꢀ1
[a] The number of the amino acid residues begins at the N terminus of the peptide
chain. [b] Ow: water (a, b, c); Om: methoxy.
ꢀ
tween H N(10) and C(6)=O(6) (N(10)···O(6):
3.18 ꢂ). In packing mode, two intermolecular hy-
ꢀ
drogen bonds are formed between the H N(1)
the homochiral (S,S)-Ac5cdOMe octapeptide 10a was folded
into a left-handed (M) a helix in the crystal state. A reversal
of the C-terminal torsion angles occurred, that is, the signs
(negative) of the f and y torsion angles (ꢀ54.28, ꢀ43.98) of
the C-terminal residue (residue 8) were opposite to those
(positive) of the preceding residues (1–7). This phenomenon
is frequently observed in the 310-helical peptides of 2-amino-
isobutyric acid.[30] The mean values of the f and y torsion
angles of amino acid residues 1–7 are +60.98 and +46.88,
values that are close to those for the ideal left-handed (M)
a helix (+608 and +458).[28a] Figure 8 shows the secondary
structure of the (M) a-helical molecule perpendicular to and
along the a-helical axis. Five intramolecular hydrogen
Figure 8. a-Helical secondary structure of the (S,S)-Ac5cdOMe octapeptide
10a, as determined by X-ray crystallographic analysis: a) View perpen-
dicular to the a-helical axis and b) view along the a-helical axis.
bonds, in which each hydrogen bond forms a 13-membered
!
(atom) pseudo-ring of the i i+4 type, existed in the a-heli-
2436
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Chem. Eur. J. 2012, 18, 2430 – 2439

Side-Chain Control of Homopeptide Helical Structures
FULL PAPER
Figure 9. Packing of 10a in the crystalline state. Intermolecular hydrogen
bonds are indicated as dashed lines.
Figure 12. Superimposed structures determined by X-ray crystallographic
analysis (black) and the calculated minimum-energy conformation (light
gray): a,b) 310 helix of the (S,S)-Ac5cdOMe hexapeptide 9a and c,d) a helix
of the (S,S)-Ac5cdOMe octapeptide 10a.
Figure 10. a-Helical secondary structure of the (S,S)-Ac5cdOMe decapep-
tide 11a, as determined by X-ray crystallographic analysis: a) View per-
pendicular to the a-helical axis and b) view along the a-helical axis.
shown by the superimpositions in Figure 12. A right-handed
(P) 310 helix (+2.03 kcalmolꢀ1) and a right-handed (P) a
helix (> +15.00 kcalmolꢀ1) were obtained as local mini-
mum-energy conformations.
peptide donor and C(8’)=O(8’) of a symmetry-related mole-
ꢀ
cule (x, y, zꢀ1; N(1)···O(8’): 2.91 ꢂ), and between the H
N(2) peptide donor and C(9’)=O(9’) of a symmetry-related
molecule (x, y, zꢀ1; N(2)···O(9’): 3.00 ꢂ), to form the chains
The calculation for the (S,S)-Ac5cdOMe octapeptide 10a af-
forded a left-handed (M) a helix as a global minimum-
energy conformation. The main-chain structure of the calcu-
lated (M) a helix matches the structure determined by X-
ray crystallographic analysis (Figure 12), although some dif-
ferences in the side-chain cyclopentane ring and protecting
group were observed. A left-handed (M) 310 helix (+
4.16 kcalmolꢀ1), a right-handed (P) a helix (> +15.00 kcal
molꢀ1), and a (P) 310 helix (+4.06 kcalmolꢀ1) were produced
as local minimum-energy conformations.
Figure 11. Packing of 11a in the crystalline state. Intermolecular hydro-
gen bonds are indicated as dashed lines.
Discussion: The preferred secondary structure of the (S,S)-
Ac5cdOMe hexapeptide 9a was a left-handed (M) 310 helix
and those of the (S,S)-Ac5cdOMe octa- and decapeptides 10a
and 11a were left-handed (M) a helices, both in solution
and in the crystalline state. Empirically, the increasing per-
centage of a,a-disubstituted amino acid in the peptide se-
quence and the decreasing length of the peptide preferen-
tially induces the formation of a 310 helix, and a,a-disubsti-
tuted amino acid homochiral homopeptides usually prefer a
310 helix over an a helix.[18d,31] Toniolo and co-workers re-
cently reported that interconversion between a and 310 heli-
ces might be allowed, even in a homochiral homo-heptapep-
tide amide exclusively composed of the chiral a,a-disubsti-
tuted amino acid l-aMeVal, by the selection of the solvent
MeOH or the strong hydrogen-bonding donor 1,1,1,3,3,3-
hexafluoropropan-2-ol (HFIP).[29] They reported a 310-helical
structure recrystallized from MeOH and an a-helical struc-
ture from HFIP by X-ray crystallographic analysis. Herein,
both the (S,S)-Ac5cdOMe octapeptide 10a and the decapep-
tide 11a formed a helices, even in TFE or water, without
of intermolecularly hydrogen-bonded left-handed (M) a
helices in a head-to-tail alignment (Figure 11).
Computational analysis of the (S,S)-Ac5cdOMe hexapeptide
and octapeptide: Conformational search calculations were
performed with the MacroModel Ver. 8.1 package (Schro-
dinger, Inc.) on an SGI workstation. The Monte Carlo mul-
tiple minimum method and an AMBER* force field were
used for finding the global and local minimum-energy con-
formations. As initial structures, extended, (P), and (M) 310-
helical and a-helical structures were used, and more than
50000 conformers were optimized.
The calculation for the (S,S)-Ac5cdOMe hexapeptide 9a
produced an (M) a helix as a global minimum-energy con-
formation (0 kcalmolꢀ1), and an (M) 310 helix was obtained
as a local minimum-energy conformation, which exhibited
an energy of +3.22 kcalmolꢀ1. The peptide main-chain
structure of the calculated (M) 310-helical conformer was
similar to those of the conformers in the crystal state, as
Chem. Eur. J. 2012, 18, 2430 – 2439
ꢀ 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.chemeurj.org
2437

M. Tanaka et al.
being dissolved in the strong hydrogen-bonding solvent
HFIP. Furthermore, X-ray crystallographic analyses showed
a-helical structures recrystallized from MeOH/H2O or
CHCl3/iPrOH. Thus, the chiral cyclic amino acids (S,S)-
Ac5cdOR have a stronger propensity to form a helices than l-
aMeVal. The a-helical properties of the (S,S)-Ac5cdOR ho-
mopeptides were also supported by the computational anal-
ysis.
trolled the helical screw sense of the peptides, without an a-
carbon chiral center. Although it is already known that side-
chain chiral centers affect the helical screw direction of
polymers such as poly(alkylisocyanates), and poly(alkylsi-
lanes),[32] no detailed research on the relationship between
the helical screw handedness of polymers and asymmetric
centers in the side chains of the monomers with high-resolu-
tion analysis has been reported so far. Furthermore, these
results imply that the chiral center at the side-chain b-
carbon atom of isoleucine and threonine would affect the
secondary structure of their peptides, although these resi-
dues also exhibit a strong screw sense bias due to their
chiral a-carbon atom and they are poorly helicogenic resi-
dues.[6,7] The design of new chiral cyclic amino acids and
their foldamers as well as the application of such molecules
as asymmetric catalysts or biologically active molecules are
currently underway in our group.[14,33]
The cyclic amino acid (S,S)-Ac5cdOR homochiral homopep-
tides do not have a-carbon chiral centers, but they formed
left-handed (M) helices. Thus, the one-handed helical screw
sense was exclusively controlled by the side-chain chiral cen-
ters. One of the factors that controls the helical screw direc-
tion of the (S,S)-Ac5cdOR homochiral homopeptides to form
the left handedness might be steric repulsions among the
side-chain substituents. If the (S,S)-Ac5cdOMe homopeptides
formed right-handed (P) 310 helices, unfavorable contact be-
tween an alkoxy group of amino acid residue i and an
alkoxy group of residue i+3 would arise because these two
residues are positioned one on top of each other in the ter-
nary helix, although a bicyclic amino acid homo-hexapeptide
showed both diastereomeric right-handed (P) and left-
handed (M) 310 helices.[11] The one-handed helical screw
sense was also found in the a-helical (S,S)-Ac5cdOMe octapep-
tide and decapeptide. These results may be attributed to the
existence of an equilibrium between the a helix and 310
helix. The right-handed (P) 310 helices of the (S,S)-Ac5cdOMe
peptides, which are in equilibrium with the (P) a helix, may
be unfavorable, and then the left-handed (M) helix may be
preferred. Furthermore, a one-handed helical screw sense
was also found with the hydroxy substituent on the cyclo-
pentane ring; the OH group is small enough to eliminate
large steric repulsion between two substituents. Thus, be-
sides the steric repulsion between the substituents at the
two amino acid residues i and i+3, the absolute configura-
tion of the substituent chiral centers at the cyclopentane
ring of amino acid residue i would affect the f and y torsion
angles of residue i through bond and/or space effects and
would control the homochiral homopeptides in a one-
handed helical screw direction. Furthermore, the measure-
ment of CD spectra of (S,S)-Ac5cOH 9c in different solvents
indicated that the hydrogen bonding of solvents may be cru-
cial for the formation of the secondary structure, including
helical screw control.
Experimental Section
The cyclic amino acids (S,S)-Ac5cdOMe ((S,S)-4a), (R,R)-Ac5cdOMe ((R,R)-
4a), and (S,S)-Ac5cdOMOM (4b) were synthesized from dimethyl l-(+)- or
d-(ꢀ)-tartrate. The syntheses of the homochiral homopeptides were car-
ried out according to solution-phase segment condensation methods, by
using EDC and HOBt, or HBTU, as coupling reagents. All compounds
were purified by column chromatography on silica gel. Full experimental
details are available in the Supporting Information.
Acknowledgements
This work was supported in part by a Grant-in-Aid (B) (22390022) and a
Grant-in-Aid for Young Scientists (B) from JSPS.
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We synthesized chiral cyclic a,a-disubstituted a-amino acids
(S,S)- and (R,R)-Ac5cdOR from l-(+)- or d-(ꢀ)-dimethyl tar-
trate and prepared the homochiral homopeptides up to the
decamer. The dominant conformation of the (S,S)-Ac5cdOMe
hexapeptide 9a was an (M) 310-helical structure and those of
octapeptide (S,S)-10a and decapeptide (S,S)-11a were (M)
a-helical structures, both in solution and in the crystal state.
We demonstrated that chiral centers at the side chain g-
carbon atoms of the cyclic a-amino acid exclusively con-
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Chem. Eur. J. 2012, 18, 2430 – 2439

Side-Chain Control of Homopeptide Helical Structures
FULL PAPER
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Received: September 16, 2011
Published online: January 20, 2012
Chem. Eur. J. 2012, 18, 2430 – 2439
ꢀ 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.chemeurj.org
2439