Inclusion compounds of l,d-dipeptide with small sulfoxides: flexible sheet structure of (S)-phenylglycyl-(R)-phenylglycine

Article abstract of DOI:10.1016/j.tet.2007.07.061

A heterochiral l,d-dipeptide, (S)-phenylglycyl-(R)-phenylglycine (SR-1), formed inclusion compounds with some small dialkyl sulfoxides. By their single-crystal X-ray analyses, we observed monolayer structures, where SR-1 molecules are arranged in parallel

Full text of DOI:10.1016/j.tet.2007.07.061

Tetrahedron 63 (2007) 9933–9938
Inclusion compounds of L,D-dipeptide with small sulfoxides:
flexible sheet structure of (S)-phenylglycyl-(R)-phenylglycine
a,*
b
Motohiro Akazome, Atsushi Hirabayashi, Kyoko Senda and Katsuyuki Ogura
a
a,b,*
a
Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoicho, Inageku,
Chiba 263-8522, Japan
b
Graduate School of Science and Technology, Chiba University, 1-33 Yayoicho, Inageku, Chiba 263-8522, Japan
Received 26 May 2007; revised 18 July 2007; accepted 20 July 2007
Available online 26 July 2007
Abstract—A heterochiral L,D-dipeptide, (S)-phenylglycyl-(R)-phenylglycine (SR-1), formed inclusion compounds with some small dialkyl
sulfoxides. By their single-crystal X-ray analyses, we observed monolayer structures, where SR-1 molecules are arranged in parallel to con-
+
struct a wavy sheet. The sulfoxides were accommodated in a channel cavity between the monolayers of SR-1 by hydrogen bonding with NH
3
of SR-1. Notably, the sheet of SR-1 is so flexible to change its wavy degree in response to the volume of the included sulfoxides. Furthermore,
we could analyze the structure of crystalline SR-1 without any sulfoxide, which has a bilayer structure.
Ó 2007 Published by Elsevier Ltd.
1
. Introduction
Here, we wish to report that SR-1 also includes sulfoxides
like our homochiral dipeptides
molecules. In the inclusion crystals, guest sulfoxides dras-
tically change the sheet structure of SR-1 from wavy into
approximately flat.
1
–3
and other artificial host
8
Homochiral L,L-dipeptides have been well studied because
they are regarded as a partial structure of proteins. Hitherto,
we have reported molecular recognition of organic guest
1
molecules by (S)-leucyl-(S)-alanine, (R)-phenylglycyl-(R)-
phenylglycine (RR-1), and (R)-(1-naphthyl)glycyl-(R)-phe-
nylglycine, which are typical homochiral dipeptides. These
2
3
2. Results and discussion
dipeptides aggregate to construct a layer and include guest
molecules between the layers. In contrast, little attention
has been paid to heterochiral L,D-dipeptides, though the
chemistry of regularly alternating L,D-oligopeptides has
2.1. Crystal structures of inclusion compounds of SR-1
In the presence of relatively small sulfoxides as a guest mol-
ecule, SR-1 was crystallized from a methanol solution to af-
ford a 1:1 inclusion compound (vide infra). Fortunately, we
could analyze the inclusion compound of dimethyl sulfoxide
(DMSO), ethyl methyl sulfoxide, and diethyl sulfoxide by
single-crystal X-ray crystallography. As seen from Figure 2,
these inclusion crystals have a wavy sheet structure, which is
composed of the curved SR-1 molecules and their wave de-
gree depends on the guest size. The structure of inclusion
compound with DMSO is quite similar to that with DMF
(Fig. 1) in morphology. In the case of racemic ethyl methyl
sulfoxide, both of its enantiomers were included at the same
position in the cavity. The sulfoxide in the crystal has a mixed
structure of trigonal bipyramidal geometry having the sulfur
atom that occupies two coordination sites (S1 and S2). From
the ratio of S1/S2¼91:9, (S)-ethyl methyl sulfoxide is
revealed to be the major enantiomer. In order to estimate
the enantiomeric ratio of included ethyl methyl sulfoxide
by NMR, the recovered sulfoxide was converted to the
corresponding diastereomeric N-[(S)-methoxyphenylacetyl]-
4
been reported on their intriguing structures such as double
5
6
stranded helices or peptide nanotubes. Recently, we inves-
tigated the inclusion phenomena of (S)-phenylglycyl-(R)-
phenylglycine (SR-1) crystals that include small amides
such as N,N-dimethylformamide (DMF), acetamide, and
7
N,N-dimethylacetamide. The crystals have a wavy struc-
ture. As a typical example, the crystal structure of SR-1
with DMF is illustrated in Figure 1. These inclusion com-
pounds showed the same interlayer distances along the
˚
b axis (10.9–11.0 A). Interestingly, the length of c axis
˚
expands from 5.2 to 5.9 A when N,N-dimethylacetamide is
7
included instead of acetamide. This shows that the c-axis
of the SR-1 inclusion crystals is variable in response to the
volume of the guest amides.
Keywords: Crystal engineering; Inclusion compounds; Dipeptides; Sulf-
oxides; Molecular recognition.
*
Corresponding authors. Tel.: +81 43 290 3388; fax: +81 43 290 2402;
e-mail: katsuyuki@faculty.chiba-u.jp
4
sulfoximine and the diastereomeric ratio was 85:15. The
0
040–4020/$ - see front matter Ó 2007 Published by Elsevier Ltd.
doi:10.1016/j.tet.2007.07.061

9934
M. Akazome et al. / Tetrahedron 63 (2007) 9933–9938
Figure 1. (a) Structure of (S)-phenylglycyl-(R)-phenylglycine (SR-1). (b)
Crystal structure of the inclusion crystals of SR-1 with dimethylformamide.
L.D. is a layer distance measured by PXRD.
Figure 2. Layer structure of inclusion compounds of SR-1 (a-c plane). L.D.
is a layer distance measured by PXRD: (a) with dimethyl sulfoxide
ratio was close to that of S1/S2 in the crystal structure. In the
inclusion crystals with DMSO and ethyl methyl sulfoxide,
two phenyl groups of SR-1 are apart from each other, but
they interact with the phenyl group of SR-1 in the adjacent
sheet. Since the wavy sheets are piled up in antiparallel di-
rection, these crystals have a space group P2 2 2 (Fig. 2a
(
DMSO); (b) with ethyl methyl sulfoxide; (c) with diethyl sulfoxide.
capture of the sulfoxide guests that are accommodated in
the cavity between the layers.
1
1 1
and b). Interestingly, the sheets of SR-1 in the inclusion com-
pound with diethyl sulfoxide are so approximately flat to
stack in parallel (Fig. 2c). Thus, the space group of the crys-
The hydrogen bonding distances of the inclusion compounds
are summarized in Figure 3. As shown in Figure 3, the
glycylglycine backbones of the dipeptides are arranged in
parallel by the ionic pairing of carboxyl and amino groups
tal becomes P2 . In this case, two phenyl groups of the SR-1
1
ꢀ
molecule are close to one another and, as a result, do not con-
tact with the phenyl ring of SR-1 in the adjacent sheet. Prob-
ably, no benzene–benzene interaction between the layers
allows the sheets of SR-1 to stack in the same direction.
via hydrogen-bonding network: one terminal COO bridges
two NH of adjacent dipeptides and the NH is also bound
+
+
3
3
ꢀ
with two adjacent COO groups (O/N). The hydrogen-
bonding network of SR-1 resembles to that of a homochiral
D,D-dipeptide (RR-1) with sulfoxides.
2
All of the inclusion crystals described above have a mono-
layer structure with a cavity surrounded by the phenyl
groups of SR-1. Two of three ammonio protons of the SR-1
take part in the construction of the sheet structure by hydro-
gen bonding. The third ammonio proton contributes to the
In Figure 4, the sheet structures are shown with CPK models.
As the alkyl group of the guest sulfoxide increases in vol-
ume, the phenyl group of the same SR-1 molecule seems
to be pushed out more strongly, so that the SR-1 sheet

M. Akazome et al. / Tetrahedron 63 (2007) 9933–9938
9935
Figure 3. Dipeptide backbone and atomic distances of intermolecular hy-
drogen bonds.
changes from wavy to approximately flat and the unit cell
˚
expands from 14.5 to 15.7 A in a axis direction. It should
be noted that, if the sheet was flat, the volume of the cavity
would become maximum. This is the case when diethyl sulf-
oxide is the guest. Indeed, larger sulfoxides such as ethyl
propyl sulfoxide and ethyl isopropyl sulfoxide were not
included at all.
The wall of the cavity consists of two phenyl groups of SR-1.
The C-terminal phenyl groups of SR-1 always adopt the
same conformation on the backbone sheet. On the other
hand, the conformation of N-terminal phenyl group of SR-
1
sulfoxide. The similar flipping of the N-terminal phenyl
is drastically changed according to the size of the guest
2
b,c
groups was observed in the inclusion crystals of RR-1.
In the cavity, the alkyl group of the guest sulfoxide is close to
the phenyl group of SR-1: the shortest distances between the
alkyl group of the guest and the phenyl group of SR-1 are
indicated in red arrows (Fig. 4). The conventional van der
˚
˚
Waals limit is ca. 3.7 A for the C/C (ca. 2.9 A for the
Figure 4. Top views of inclusion crystals (CPK model, a-c plane): (a) with
dimethyl sulfoxide; (b) with ethyl methyl sulfoxide; (c) with diethyl
sulfoxide.
˚
˚
H/C) distance, which is the sum of 2.0 A for CH (1.2 A
3
˚
for H) and 1.7 A for Csp . Judging from these values,
2 9
˚
the distances, 3.72(2.93) A (dimethyl sulfoxide) and
˚
.76(2.90) A (diethyl sulfoxide), meet the criteria of van
3
der Waals contact. It is noteworthy that the C/C distance
summarized in Figure 5. The hydrogen-bonding network
of glycylglycine’s backbones assembles to form a bilayer
structure (Fig. 5a). This is in sharp contrast to the monolayer
structure of the above inclusion crystals of SR-1. As seen
from Figure 5b, the hydrogen-bonding network sheet con-
sists of three hydrogen bonds (A–C), which correspond to
˚
3.43 A) in the inclusion crystal with ethyl methyl sulfoxide
(
is shorter than the sum of van der Waals radii, suggesting the
1
0
presence of CH–p interaction.
.2. Crystal structure of SR-1 host
2
0
0
the hydrogen-bonds (A –C ) of its opposite sheet. A central
amide group, whose trans conformation keeps the glycylgly-
cine backbone linear, does not take part in this hydrogen-
bonding network. Two of three ammonio hydrogens are
We were interested in the crystal structure of SR-1 without
any guest, since we could not obtain a single crystal of
RR-1, that is, suitable to X-ray crystallography. Fortunately,
we could obtain good-quality single crystals of SR-1 that
made us achieve their single-crystal X-ray analysis. In the
crystallization of SR-1 in the presence of ethyl isopropyl
sulfoxide, SR-1 itself deposited as good-quality crystals
that did not include the sulfoxide. The results are
ꢀ
bound with two adjacent COO groups to construct the sheet
˚
structure (A: 2.67 A and B: 3.04 A). The residual one of the
˚
ꢀ
ammonio hydrogens binds with COO group of SR-1 in the
˚
opposite sheet (C: 2.79 A). Thus, the salt formation between
the amino and carboxyl groups constructs the sequence of

9936
M. Akazome et al. / Tetrahedron 63 (2007) 9933–9938
herringbone packing (Fig. 5c). The herringbone motif
is a well-known arrangement of phenyl rings in crystal
engineering.
1
2
3. Conclusion
A heterochiral L,D-dipeptide, (S)-phenylglycyl-(R)-phenyl-
glycine (SR-1), has an ability to form inclusion compounds
with relatively small sulfoxides such as DMSO, ethyl methyl
sulfoxide, and diethyl sulfoxide. In these inclusion com-
pounds, SR-1 molecules arrange in parallel to construct
a monolayer sheet. The guest sulfoxides are linked to
NH of SR-1 via hydrogen bonding in channel cavity be-
+
3
tween the layers. In particular, these monolayer sheets of
SR-1 are wavy and their wave degree depends on the size
of the guest. It is noteworthy that the conformation of the
phenyl groups, which construct the sidewall of the cavity,
changes in response to the guest volume to make the cavity
suitable to the shape of the guest. Furthermore, we could
obtain a single crystal of SR-1 without a sulfoxide, which
was revealed by its X-ray crystallographic analysis to be a
bilayer structure.
4. Experimental
4
.1. General methods
1
NMR spectra were recorded at 300 MHz for H NMR. Melt-
ing points (decomposition) were measured on a TG-DTA.
Elemental analyses were performed at Chemical Analysis
Center, Chiba University, Japan. Both of (S)- and (R)-phe-
nylglycine (99% ee) were purchased from Tokyo Chemical
Industry.
4
.1.1. X-ray analyses. X-ray powder diffractions were
obtained with a MAC Science MXP diffractometer using
graphite-monochromated Cu Ka radiation (30 kV, 200 mA).
The spectra were measured at room temperature between
ꢁ
ꢁ ꢁ
and 50 in the 2q/q-scan mode with steps of 0.01 in 2q
2
and 4 min
ꢁ
ꢀ1
.
4.1.2. Synthesis of SR-1. The preparation of (S)-phenyl-
glycyl-(R)-phenylglycine [SR-1] was described in the
7
13
previous paper. According to the DCC–HOBt method,
coupling between (S)-N-(benzyloxycarbonyl)phenylgly-
Figure 5. Crystal structure of SR-1. (a) A bilayer structure (a-c plane). L.D.
is a layer distance measured by PXRD. (b) The offset between two hydrogen
14
cine and (R)-phenylglycine benzyl ester p-toluenesulfo-
nate provided the protected dipeptide. The deprotection
by hydrogenolysis proceeded in the presence of Pd black
0
0
bonding layers (a-b plane). Hydrogen bonds are labelled by A–C and A –C .
c) Packing (CPK model) of phenyl groups (a-b plane).
1
5
(
ꢁ
to afford SR-1. SR-1: colorless crystals, mp (dec) 223 C;
0
C in Fig. 5b). These 10-membered rings are often observed
25
1
1
0-membered rings via four hydrogen bonds (A, C, B , and
[a]D ꢀ19.6 (c 0.94, MeOH); H NMR (300 MHz,
0
in the helical hydrogen-bonding columns (2 -column) of
D O+DCl) 7.37 (m, 10H), 5.60 (s, 1H), 5.29 (s, 1H); IR
2
ꢀ1
(KBr) 3400, 1693, 1608, 1587, 1496, 1365 (cm ). Powder
˚
X-ray analysis [A(I/I )] 15.4(1.00), 7.58(0.17), 4.59(0.15),
1
1
1
amine salts of carboxylic acids. As a result, two sheets
are close face-to-face via hydrogen bonding to make a bila-
yer structure. In other words, the bilayer structure in SR-1
crystals changes to a monolayer when they include a sulfox-
ide guest via hydrogen bonding. Finally, we wish to describe
the arrangement of the phenyl groups of SR-1, which stand
perpendicular to the sheet of glycylglycine backbones. Inter-
estingly, all of the phenyl groups stack each other through
an edge-to-face benzene–benzene interaction to make the
0
3.76(0.44); Anal. Calcd for C H N O : C, 59.65; H,
1
6.12; N, 7.73. Found: C, 59.41; H, 6.06; N, 7.58.
6 16 2 3
4.1.2.1. Preparation of inclusion compound of SR-1.
SR-1 was dissolved in MeOH. After the addition of a sulfox-
ide (20 equiv) to the solution of SR-1, the resulting mixture
was allowed to stand at an ambient temperature. Then the
deposited crystals were collected by filtration and washed

M. Akazome et al. / Tetrahedron 63 (2007) 9933–9938
9937
with diethyl ether. The ratios were confirmed by single-
crystal X-ray analyses and elemental analyses.
atoms refined anisotropically, residual electron density
0.29/ꢀ0.29.
ꢁ
KBr) 3365, 1680, 1498, 1587, 1377, 1024 (cm ). Powder
SR-1$dimethyl sulfoxide: colorless crystals; dec 164 C; IR
(
X-ray analysis [A(I/I )] 11.2(1.00), 5.19(0.33), 3.80(0.58).
4.1.3.3. The inclusion compound of diethyl sulfoxide.
C H N O S, M¼390.50, crystal dimensions 0.40ꢂ0.30ꢂ
ꢀ
1
2
0 26 2 4
˚
˚
0.05 mm, monoclinic, P2 , T¼298 K, a¼11.520(4) A, b¼
0
1
˚ ˚ ˚
ꢁ
3
Anal. Calcd for C H N O $1.00C H SO: C, 59.65; H,
3
15.787(5) A, c¼5.686(2) A, b¼93.37(3) , V¼1032.2(6) A ,
ꢀ
calcd
1
6
16
2
2 6
3
6
.12; N, 7.73. Found: C, 59.41; H, 6.06; N, 7.58.
Z¼2, d
¼1.256 g cm , 2192 reflections measured, 2019
independent, R¼0.042 (1961 reflections with I>1.00s(I)),
Rw¼0.042, 329 parameters, with heavy atoms refined aniso-
tropically, residual electron density 0.28/ꢀ0.21.
ꢁ
KBr) 3377, 1686, 1592, 1495, 1370, 1010 (cm ). Powder
SR-1$diethyl sulfoxide: colorless crystals; dec 142 C; IR
(
X-ray analysis [A(I/I )] 11.5(0.59), 11.1(0.10), 5.77(0.13),
ꢀ
1
˚
0
3
6
.84(1.00). Anal. Calcd for C H N O $1.00C H SO: C,
4 10
1.52; H, 6.71; N, 7.17. Found: C, 61.14; H, 6.64; N, 7.13.
4.1.4. SR-1 host structure. In the course of our trial to make
inclusion compounds (vide infra), ethyl isopropyl sulfoxide
was not included, but SR-1 crystals suitable for single-
crystal X-ray analysis were obtained. C H N O ,
1
6
16
2
3
ꢁ
ꢀ
SR-1$ethyl methyl sulfoxide: colorless crystals; dec 136 C;
IR (KBr) 3379, 1676, 1589, 1504, 1375, 1012 (cm ).
˚
Powder X-ray analysis [A(I/I )] 10.9(1.00), 5.02(0.26),
4.66(0.56), 4.21(0.48), 3.80(0.69). Anal. Calcd for
C H N O $1.00(C H SO)$0.10H O: C, 60.33; H, 6.45;
N, 7.41. Found: C, 60.14; H, 6.44; N, 7.17.
1
6 16 2 3
1
M¼284.31, crystal dimensions 0.50ꢂ0.10ꢂ0.05 mm,
˚
monoclinic, P21, T¼298 K, a¼15.028(6) A, b¼
0
˚
˚
ꢁ
˚
3
5.815(2) A, c¼7.952(2) A, b¼95.40(0) , V¼691.8(4) A ,
ꢀ
calcd
3
Z¼2, d
¼1.365 g cm , 1551 reflections measured,
1
6
16
2
3
3
8
2
1444 independent, R¼0.070, (1444 reflections with
I>1.00s(I)), Rw2¼0.175, 191 parameters, with heavy
atoms refined anisotropically, residual electron density
0.47/ꢀ0.46.
1
6
According to the Kusumi’s methodology, ethyl methyl N-
(S)-methoxyphenylacetyl]sulfoximine was obtained from
the recovered ethyl methyl sulfoxide by a one pot reaction
ethyl methyl sulfoxide/O-mesitylsulfonylhydroxylamine/
[
(
Crystallographic data (excluding structure factors) for
the structure in this paper have been deposited with
the Cambridge Crystallographic Data Centre as supple-
mentary publication number CCDC 648530–648533.
Copies of the data can be obtained, free of charge, on ap-
plication to CCDC, 12 Union Road, Cambridge CB2 1EZ,
UK [fax: +44-(0)1223-336033 or e-mail: deposit@ccdc.
cam.ac.uk].
CHCl then (S)-methoxyphenylacetic acid/PyBOP/HOBt/
3
4
pyridine). Ethyl methyl N-[(S)-methoxyphenylacetyl]-
sulfoximine (S/R¼85:15 by NMR); colorless oil; H NMR
1
(
300 MHz, CDCl ) d 7.51–7.24 (m, 5.0H), 4.75 (s, 0.85H,
3
S major), 4.74 (s, 0.15H, R minor), 3.48–3.20 (m, 2.0H, S
major and R minor), 3.42 (s, 3.0H, S major and R minor),
3
0
.19 (s, 2.55H, S major), 3.12 (s, 0.45H, R minor), 1.31 (t,
.45H, J¼7.42 Hz, R minor), 1.18 (t, 2.55H, J¼7.49 Hz,
S major).
Acknowledgements
4
.1.3. Crystallograpic data for the inclusion compounds.
Data collection was performed on a Mac Science MXC18
four-circle diffractmetor with graphite-monochromated Cu
Ka (l¼1.54178) radiation using the 2q-u scan technique,
This work was supported by a Grant-in-Aid for Scientific
Research (C) (no. 18550117) from the Japan Society for
the Promotion of Science.
ꢁ
and the X-ray intensities were measured up to 2q¼140 .
1
7
The structures were solved by a direct method SIR-92 or
SHELXS-97 and refined by a computer program package,
1
8
References and notes
1
9
20
maXus from MAC Science or SHELXTL from Bruker
AXS. Hydrogen atoms were calculated in the appropriate
position.
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.1.3.1. The inclusion compound of DMSO.
C H N O S, M¼362.45, crystal dimensions 0.80ꢂ
1
8 22 2 4
0
.05ꢂ0.05 mm, orthorhombic, P2 2 2 , T¼298 K, a¼
1
1 1
˚ ˚ ˚ ˚
3
1
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ꢀ
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3
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¼1.316 g cm , 2122 reflections measured,
1
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9 24 2 4
0
.70ꢂ0.05ꢂ0.05 mm, orthorhombic, P2 2 2 , T¼298 K,
1
˚ ˚ ˚
1 1
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˚
3
ꢀ3
1
911.5(7) A , Z¼4, d
¼1.308 g cm , 2202 reflections
calcd
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(
(
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