Metal directed assemblies of a dipeptide: Formation of β-pleated sheets

Article abstract of DOI:10.1002/ejic.200600219

The crystal structure of N-phthaloylglycylglycine and its complexes with copper(II) and zinc(II) are studied. The N-phthaloylglycylglycinato copper(II) complex has a polymeric structure formed by bridging carboxylates. The corresponding N-phthaloylglycylglycinato zinc(II) complex is monomeric. Both the metal complexes have self-assembled hydrogen-bonded structures in which dipeptide ligand adopt β-pleated conformations. Wiley-VCH Verlag GmbH & Co. KGaA, 2006.

Full text of DOI:10.1002/ejic.200600219

SHORT COMMUNICATION
DOI: 10.1002/ejic.200600219
Metal Directed Assemblies of a Dipeptide: Formation of β-Pleated Sheets
Nilotpal Barooah,[a] Rupam J. Sarma,[a] and Jubaraj B. Baruah*[a]
Keywords: Hydrogen bonding / Self-assembly / Dipeptide / β-Sheets / Coordination polymer
The crystal structure of N-phthaloylglycylglycine and its
complexes with copper(II) and zinc(II) are studied. The N-
phthaloylglycylglycinato copper(II) complex has a polymeric
structure formed by bridging carboxylates. The correspond-
ing N-phthaloylglycylglycinato zinc(II) complex is mono-
meric. Both the metal complexes have self-assembled hydro-
gen-bonded structures in which dipeptide ligand adopt β-
pleated conformations.
(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim,
Germany, 2006)
Directed assembly of molecules through noncovalent in- ture to the intermolecular N–H···O interactions observed in
teractions and metal coordination is a fundamental process case of amides, which have a dominating effect on the self-
in nature.[1] Self-organization and molecular recognition of assembly process.[10] Crystal structure shows that the self-
biomolecules[1e] using peptides are rationalized by taking assembly of the dipeptide L in the solid state is governed
into account a host of weak interactions[2] that include hy- by intermolecular hydrogen-bonding interactions; the mole-
drogen bonding, aromatic π interactions, and hydrophobic cule adopts a puckered conformation as shown in Figure 1.
interactions. The ability of peptides to adopt various sec- The amide N–H is involved in the formation of hydrogen
ondary structures has been a subject of extensive study,[3] bonds with the carbonyl oxygen atom of the phthalimide
and in this regard the effects of metal ions in stabilizing unit (dN2···O4 3.04 Å; Є D–H···A 156.0°), which extends
particular conformations of peptides have immense impor- along crystallographic a axis. Moreover, the amide carbonyl
tance.[4] The β-sheet assembly of peptide chains is particu- is strongly hydrogen-bonded to the oxygen atom of the car-
larly important in case of globular proteins and various boxylic acid group (dO1···O3 2.59 Å; Є D–H···A 165.1°) as
template-directed strategies to assemble natural or non-nat- shown in Figure 1. Thus, intermolecular hydrogen-bonding
ural peptides and synthetic peptide analogs into similar as- interactions in L leads to the formation of two-dimensional
semblies have been investigated.[5] Coordination of the pep- sheets, wherein the individual molecules adopt folded con-
tide to a particular metal ion predominantly governs the formations; however, the structure does not correspond to
local structure of the active site in metalloenzymes.[6] Even β-pleated sheet structure. The torsion angle for rotation
though attempts have been made to rationalize the interac- about the C–N bond (φ) is 70.9° while the corresponding
tion of metal ions with peptides,[7] the structural elucidation angle for the C–C bond rotation (ψ) is 19.9°. The important
of such assemblies with regard to tuning the secondary in- hydrogen bond angles and bond lengths of L in the hydro-
teractions in the peptide[5b,8] is scarce. Given this back- gen-bonded assembly are listed in Table 1. It is important to
ground, we report the solid-state structures of the N-pro- note that the interplanar distance between the phthalimide
tected dipeptide derived from glycylglycine, and sub- groups of L is ca. 3.34 Å, which could indicate the presence
sequently rationalize the effect of metal-ion templating on of weak aromatic π interactions.
The templating effect of CuII and ZnII ions, two of the
biologically important metal ions, on the self-assembly of
the dipeptide L has been studied by preparing the corre-
sponding Cu2L4(H2O)4·2H2O and ZnL2(H2O)4 complexes.
Reaction of L with copper acetate mono hydrate results in
the formation of the complex 1 which possess the molecular
formula CuL2(H2O)2·2H2O. The crystal structure of 1
shows that each of the copper center is coordinated to L
through the oxygen atoms of the carboxylate group; the co-
ordinated water molecules are trans to each other in a ne-
arly square-planar geometry with Cu1···O1 and Cu1···O6
bond lengths of 1.9471(10) and 1.9445(13) Å, respectively.
The carbonyl oxygen of another adjacent glycinato unit
leads to a weak Cu1···O2 (dCu1···O2 2.650 Å) coordination,
the self-assembly of this dipeptide.
Condensation of glycylglycine with phthalic anhydride
under hydrothermal conditions and subsequent recrystalli-
zation from aqueous ethanol afforded the N-protected di-
peptide, N-phthaloylglycylglycine (L) as colorless needles.
The introduction of the phthaloyl group was expected to
stabilize the two-dimensional assembly of the molecules in
the solid state through intermolecular aromatic interac-
tions.[9] These π interactions can be complementary in na-
[a] Department of Chemistry, Indian Institute of Technology,
Guwahati, 781 039, India
E-mail: juba@iitg.ernet.in
Supporting information for this article is available on the
WWW under http://www.eurjic.org or from the author.
2942
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Metal Directed Assemblies of a Dipeptide: Formation of β-Pleated Sheets
SHORT COMMUNICATION
here that metal-directed self-assembled systems also give
rise to porous metal-organic frameworks as well as coordi-
nation polymers.[11]
In the case of complex 1, the water molecules included
inside the lattice probably underlines the importance of
water in stabilizing the β-sheets,[2] formed by the dipeptide
units connected to the CuII center. We have found that the
ligand organization in this complex is governed by weak
hydrogen-bonding interactions between the amide groups
of the dipeptide and the interstitial water molecules. In this
complex, intermolecular hydrogen bonding between the
amide N–H groups and the amide carbonyl groups (dN1···O3
2.94 Å; Є D–H···A 157.8°) is complemented by weak C–
H···O interaction involving C4–H as donor and O3 as ac-
ceptor (dC4···O3 3.05 Å). This weak C–H···O interaction is
well within the range reported elsewhere.[2b] These two weak
interactions assemble the N-phthaloylglycylglycinato li-
gands leading to a parallel β-pleated sheet conformation as
shown in the Figure 2 (a). The torsion angle for rotation
about the C–N bond (φ) is –135.3°, while the corresponding
angle for the C–C bond rotation (ψ) is 169.2° which is
within the limit of β-sheet structure.[3a–3b] This corresponds
to a trans conformation about the C–C bond.[3b] The hydro-
gen-bond donor···acceptor distances and angles of complex
1 are listed in Table 2.
Figure 1. 2D Molecular sheets arising from intermolecular hydro-
gen bonding in L; (Inset) The hydrogen-bonded molecular sheets
viewed parallel to bc plane.
Table 1. Hydrogen-bonding geometry (distances and angles) in N-
phthaloylglycylglycine (L).
D–H···A
N2–H···O4#[a] 0.85
O1–H···O3##
0.89
dD–H [Å] dH···A [Å] dD···A [Å] Є D–H···A[°]
2.24
1.71
3.044
2.593
157.03
164.82
#
[a] Symmetry transformations used to generate atoms: x–1, y, z,
##
–x+3/2, y+1/2, –z+1/2.
Table 2. Hydrogen bonding geometry (distances and angles) in
complex 1[a]
.
which gives the CuII center axially distorted octahedral ge-
ometry as shown in Figure 2 (a). The unusual bridging
mode of the carboxylate group in this coordination motif
leads to a one-dimensional coordination network of CuII
D–H···A
dD–H [Å] dH···A [Å] dD···A [Å] Є D–H···A[°]
N1–H···O3#[b]
O6–H···O7##
O6–H···O2
0.79
0.81
0.81
2.18
1.89
1.88
2.11
2.944
2.668
2.650
2.851
162.3
158.5
157.7
170.5
ions along crystallographic b axis with CuII···CuII distance O7–H···O2+### 0.74
of 4.71 Å. The two O1···Cu1···O6 and O1···Cu1···O2 bond
angles are 93.40° and 86.85°, respectively. The distorted oc-
tahedral geometry (Figure 2, b) of the CuII center in com-
plex 1 is also obvious from its ESR spectra. At room tem-
perature, the ESR spectrum of the solid complex 1 shows a
[a] O6 is from coordinated water; O7 is from interstitial water.
[b] Symmetry transformations used to generate atoms: # x, y+1, z;
##
###
x–1, y+1, z+1,
–x+1, y, –z+3/2.
In a similar way, the ZnII complex ZnL2(H2O)4 (2) was
strong signal with center field at 3177.6 G (g = 2.124), synthesized and structurally characterized. Each ZnII ion is
which is an indication for the axially distorted octahedral coordinated to two monodentate carboxylic groups of L
geometry around the CuII center. It may be pointed out and four water molecules; which results in an octahedral
Figure 2. (a) Structure of the hydrogen-bonded sheets in complex 1 (interstitial water molecules are excluded for clarity); (b) Coordination
environment of CuII centers in the complex (thermal ellipsoids drawn to 30% probability).
Eur. J. Inorg. Chem. 2006, 2942–2946
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N. Barooah, R. J. Sarma, J. B. Baruah
SHORT COMMUNICATION
coordination environment around each ZnII center as Table 3. Hydrogen bonding geometry (distances and angles) in
complex 2.
shown in Figure 3. The Zn1···O1, Zn1···O6 and Zn1···O7
bond lengths are 2.0921(15), 2.0586(16), 2.1429(16) Å,
respectively. The crystal structure of 2 also reveals that the
N-phthaloyl-protected dipeptide residues assemble through
intermolecular N1–H···O3 hydrogen bonds (dN1···O3 O7–H···O1 [x, y+1, z] 0.80
3.04 Å; Є D–H···A 157.8°) along with weak C4–H···O3 in-
D–H···A
N1–H···O3 [x, y+1, z] 0.86
O6–H···O2 1.03
dD–H [Å] dH···A [Å] dD···A [Å] Є D–H···A[°]
2.23
1.65
1.88
3.044
2.652
2.672
157.8
159.7
170.4
teractions (dC4···O3 3.11 Å). These two weak interactions
lead to the formation of parallel β-pleated sheets as shown
in Figure 3.
The presence of two interstitial water molecules per for-
mula unit in complex 1 has a structural role to play, as they
hold the hydrogen-bonded dipeptide β-sheets (Figure 4, a)
through intermolecular O7–H···O2 (dO7···O2 2.85 Å; Є D–
H···A 170.5°) and O7–H···O5 (dO7···O5 2.99 Å; Є D–H···A
165.7°) interactions. Furthermore, each interstitial water
molecule is bound to a coordinated water molecule through
intermolecular O6–H···O7 (dO6···O7 2.66 Å; Є D–H···A
158.5°) hydrogen bonds. The presence two interstitial water
molecules in the lattice is reflected in the thermogram of
the compound, which shows 8.9% weight loss in the tem-
perature range 75–120 °C corresponding to loss of three
water molecules (theoretical weight loss 8.2%) correspond-
ing to interstitial and coordinated water molecules. In the
case of 2, the coordinated water molecules are involved in
intramolecular O6–H···O7 (dO6···O7 2.91 Å; Є D–H···A
149.9°) and intermolecular O7–H···O4 (dO7···O4 3.02 Å;
Figure 3. Ligand organization around the ZnII centers of the com-
plex 2.
It is noteworthy that in both the structures of complexes Є D–H···A 150.2°) hydrogen-bonding interactions. These
1 and 2, the presence of coordinated water as well as the interactions stabilize the formation of individual β-pleated
interstitial water molecules (in case of 1) is crucial in stabi- sheets in 1 and 2 as shown in Figure 4, parts a and b,
lizing the self-assembled β-pleated sheets. The hydrogen respectively. Thermogravimetric analysis of complex 2 (ple-
bond lengths and bond angles that are involved in the for- ase refer to supporting information, for supporting infor-
mation in complex 2 are listed in Table 3. The torsion angle mation see also the footnote on the first page of this article)
for rotation about the C–N bond (φ) in this case is –153.6° shows that the four-coordinated water molecules are lost
and for the C–C bond rotation (ψ) is 165.7°, which are sim- between 70–135 °C, which corresponding to about 9.3%
ilar to those in the complex 1 and is indicative of β-pleated weight loss (theoretically calculated weight loss for such
sheets.[2b]
process corresponds to 10.9%).
Figure 4. (a) Packing pattern of 1 (viewed along b axis); (b) packing pattern of 2 (viewed along b axis).
2944 Eur. J. Inorg. Chem. 2006, 2942–2946
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Metal Directed Assemblies of a Dipeptide: Formation of β-Pleated Sheets
SHORT COMMUNICATION
precipitate was filtered and washed with ethanol. The precipitate
was redissolved in 20 mL of distilled water, concentrated to 10 mL,
and left undisturbed. After three days light blue needle-like crystals
of the product were collected by filtration and dried in air. Yield
for the crystalline product: 0.067 g (20% based on Cu). IR (KBr):
Thus, we have structurally characterized the solid-state
assemblies of N-phthaloylglycylglycine that are formed
through intermolecular hydrogen bonding, and shown that
the self-assembly of this molecule can be tuned to adopt a
β-sheet conformation by introduction of metal ions, in this
case CuII and ZnII. It is found that the parallel β-pleated
sheet assembly of the dipeptide leads to a one-dimensional
CuII carboxylate coordination polymer through carboxylate
bridging in a different manner over conventional paddle-
wheel-type of structures.[12] Currently, we are studying the
different motifs that are crucial in the metal template as-
sembly of similar dipeptides and higher analogs.
ν = 3590 (s), 3309 (s) 3094 (br. s), 1772 (w), 1726 (s), 1658 (s), 1562
˜
(s), 1409 (s), 1322 (w), 1265 (w), 1122 (w), 958 (s), 758 (s), 723 (s)
cm–1.
Synthesis of Complex 2: A solution of zinc(II) acetate dihydrate
(0.110 g, 0.5 mmol) in 20 mL ethanol was added dropwise to a
homogeneous stirred solution of L (0.263 g, 1 mmol) in ethanol/
water (20 mL, 1:1, v/v) at room temperature. Off-white precipitate
had started appearing within 15 minutes of addition. The solution
was stirred for another two hours, and the resulting precipitate was
filtered and washed with ethanol. The precipitate was redissolved
in 20 mL of distilled water, concentrated to 10 mL and left undis-
turbed. After five days light colorless plate-like crystals of the prod-
uct were collected by filtration and dried in air. Yield for the crys-
Experimental Section
The X-ray diffraction data were collected at room temperature with
a Bruker 3-circle diffractometer (Bruker Nonius SMART APEX 2)
equipped with CCD area detectors, and using graphite-monochro-
mated Mo-Kα radiation (λ = 0.71073 Å) from 60W microfocus Sie-
mens Microsource with glass polycapillary optics. X-ray diffraction
data for all the crystals were collected with Bruker SMART soft-
ware. This software was also used for indexing and determining the
unit cell parameters. The structures were solved by direct methods
and refined by full-matrix least-squares against F2 for all data using
SHELXTL software.[14] All non-H atoms were refined by full-ma-
trix least-squares in the anisotropic approximation and the hydro-
gen atoms attached to these atoms were treated as “riding” in cal-
culated positions in the case of complex 2; with L and complex 1
the hydrogen atoms were located on the difference Fourier maps.
In all cases, the hydrogen atoms attached to polar atoms such as
O and N were located on the difference Fourier maps and refined
in the final structure in isotropic approximation.
talline product: 0.078 g (23% based on Zn). IR (KBr): ν = 3534
˜
(s), 3319 (s) 3075 (br. s), 1770 (w), 1722 (s), 1650 (s), 1551 (s), 1411
1
(s), 1311 (w), 1246 (w), 1116 (w), 955 (s), 755 (s), 715 (s) cm–1. H
NMR ([D6]DMSO): δ = 8.3 (s, 1 H–NH), 7.8 (m, 4 H), 4.2 (s, 2 H),
3.6 (d, J = 4.4 Hz, 2 H) ppm.
Supporting Information (see also the footnote on the first page of
this article) is available for selected crystallographic data, FT-IR
spectra of the dipeptide and complex 1, the ESR spectrum of 1 and
1H HOMOCOSY spectra of complex 2.
Acknowledgments
The authors thank DST (India) for financial support.
CCDC-297186 (for 1), -297187 (for 2) and -299730 (for L) contain
the supplementary crystallographic data for this paper. These data
can be obtained free of charge from The Cambridge Crystallo-
graphic Data Centre via www.ccdc.cam.ac.uk/data_request/cif.
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Glycylglycine, phthalic anhydride, copper(II) acetate dihydrate and
zinc(II) acetate dihydrate were procured from Fluka and used as
received. The NMR spectra were recorded with a Varian 400 MHz
spectrophotometer at room temperature while the FT-IR spectra
were recorded with Nicolet Impact–410 spectrometer using
OMNIC software.
Synthesis of N-Phthaloylglycylglycine (L): A finely ground mixture
of phthalic anhydride (0.444 g, 3 mmol) and glycylglycine (0.396 g,
3 mmol) was heated to approximately 175 °C in a 50-mL round-
bottomed flask. The molten mixture was cooled to room tempera-
ture, and the resulting solid was purified by recrystallization from
ethanol/water (1:9, v/v) mixture to obtain the product. Yield: 0.30 g
(39%). IR (KBr): ν = 3363 (s), 2935 (br. s), 2873 (br. s), 2597 (s),
˜
1737 (s), 1701 (s), 1621 (s), 1543 (s), 1419 (s), 1393 (s), 1332 (w),
1
1230 (s), 1107 (w), 953 (s), 728 (w) cm–1. H NMR ([D6]DMSO):
δ = 12.8 (br. s, 1 H–COOH), 8.5 (s, 1 H–NH), 7.8 (m, 4 H), 4.2 (s, 2
H), 3.7 (d, J = 5.6 Hz, 2 H) ppm. 13C NMR ([D6]DMSO): δ =
176.1,172.7, 171.7, 139.9, 137.1, 128.5, 46.2, 45.7 ppm.
Synthesis of Complex 1: A solution of copper(II) acetate dihydrate
(0.100 g, 0.5 mmol) in ethanol (20 mL) was added dropwise to a
homogeneous stirred solution of L (0.263 g, 1 mmol) in ethanol/
water (20 mL, 1:9, v/v) at room temperature. Light blue precipitate
had started appearing within 15 minutes of addition of the ligand.
The solution was stirred for another two hours, and the resulting
Eur. J. Inorg. Chem. 2006, 2942–2946
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N. Barooah, R. J. Sarma, J. B. Baruah
SHORT COMMUNICATION
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Received: March 10, 2006
Published Online: June 14, 2006
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Eur. J. Inorg. Chem. 2006, 2942–2946