Introduction of an electron push-pull system yields a planar Red Kaede fluorescence protein chromophore analogue stabilized by a C = O...π interaction

Article abstract of DOI:10.1007/s12039-015-0855-5

Abstract Crystal structures of four red kaede fluorescence protein chromophore analogues are reported here. Molecules I-III adopt a non-planar geometry stabilized by π...π stacking and hydrogen bonding. Introduction of an electron push-pull system induces

Full text of DOI:10.1007/s12039-015-0855-5

c
J. Chem. Sci. Vol. 127, No. 5, May 2015, pp. 941–948. ꢀ Indian Academy of Sciences.
DOI 10.1007/s12039-015-0855-5
Introduction of an electron push-pull system yields a planar Red Kaede
fluorescence protein chromophore analogue stabilized by a C = O . . . π
interaction
ASHISH SINGH, BASANTA KUMAR RAJBONGSHI and GURUNATH RAMANATHAN∗
Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India 208 016
e-mail: gurunath@iitk.ac.in
MS received 10 November 2014; revised 15 January 2015; accepted 25 January 2015
Abstract. Crystal structures of four red kaede fluorescence protein chromophore analogues are reported here.
Molecules I-III adopt a non-planar geometry stabilized by π . . . π stacking and hydrogen bonding. Introduction
of an electron push-pull system induces molecule IV to be planar and a C = O . . . π supramolecular interaction
is observed as well. Strong electron withdrawing and donating groups also ensure formation of a higher order
two and three dimensional supramolecular architecture through hydrogen bonds in molecules I and IV. All the
analogues exhibit good photoluminescence properties and emit in the red region with excellent quantum yields.
Keywords. Imidazolin-5-one; RFP chromophore; C = O . . . π stacking; planar polyenes; supramolecular
interactions.
stacking facilitate the formation of pyramids,6 layers,8
sheets9 and other supramolecular structures.10 A donor-
acceptor type of C=O· · · C short contact in one of the
imidazolin-5-one derivatives was reported by our group
previously.9a Here, in this communication, we show that
supramolecular architecture and crystal packing of four
RFP chromophore analogues (figure 1) can be tailored
by appropriate substitutions. These molecules are not
planar despite being π- conjugated systems. Confor-
mation of conjugated molecules is a delicate interplay
between eclipsing strains of groups around the double
bonds, steric effects of the substituents and the coun-
terbalancing electron transfer through the conjugated
π bonds. If the former is the stabilizing factor, then
the molecule twists out of plane to become curved.6
Creation of an electron push-pull system forces weak
C=O....π11 supramolecular interaction in molecule IV,
that in turn, stabilizes planarity and also assists in higher
order supramolecular assembly. This interaction was
supported by theoretical studies as well. We have also
analyzed the photoluminescence properties of all ana-
logues and found good quantum yields with emission in
the red region.
1. Introduction
Red kaede fluorescence protein (RFP) belongs to the
family of green fluorescent proteins (GFP) that were
isolated from the stony coral trachyphyllia geoffroyi.1
Kaede proteins contain a GFP like imidazolin-5-one
chromophore. However, on absorption of UV or vio-
let light (350–420nm), the protein backbone between
Nα and Cα of His62 breaks and forms the red kaede
fluorescent protein chromophore2 (figure 1). This chro-
mophore is 2000 times more fluorescent in comparison
to the wild type GFP chromophore. Due to its impor-
tance as a fluorescent marker3 and use in application
such as ultra-high resolution fluorescence imaging,4
this chromophore and its analogues were synthesized
and investigated by us. The kaede chromophore has
also been studied as an organic photovoltaic material.5
The crystal structures of kaede chromophores or its
analogues have not yet been studied systematically.
The first crystal structure of a red kaede protein chro-
mophore analogue was reported by our group in 2012,
wherein we observed a deviation from planarity with
two distinct orientations of the N−phenyl ring in the
molecule that resulted in chiral conformations giving
rise to an interesting concomitant polymorphism.6
In crystals of RFP and many of the GFP chro-
mophore analogues, intermolecular interactions, such
as O. . .H/C-H· · · π hydrogen bonding7 and π · · · π
2. Experimental
2.1 Materials
Column chromatography was done in 60–120 and 100–
200 mesh particle size silica gel and in neutral alumina.
∗For correspondence
941

942
Ashish Singh et al.
Figure 1. Conversion of the green fluorescent protein chromophore to a red kaede
fluorescent protein chromophore (left). The four red kaede fluorescent protein chro-
mophore analogues reported here are shown inside the box.
by solvent-free vinylogous condensation reaction13a
with aldehydes (p-tolualdehyde, cinnamaldehyde and
terephthaldehyde).
Melting point of all (I-IV) compounds was recorded in
a JSGWꢀ melting point apparatus. For TLC analysis,
MERCKꢀ Kieselgel 60 F254 plates were used. 1H NMR
spectra were recorded using JEOLꢀ 500 (500 MHz)
and JEOLꢀ 400 (400 MHz) NMR spectrometer in
CDCl3 as a solvent. Proton decoupled 13C NMR spectra
was taken in JEOLꢀ 500 (125 MHz) NMR spectrom-
eter. For recording mass spectra, a Waterꢀ ESI-Qtof
instrument was used.
AllsolventswerepurchasedfromSDFine Chemicals.
These were purified by literature procedures.12 Anhy-
drous sodium acetate and anhydrous zinc chloride were
used as such. p-methoxybenzaldehyde, p-methyl benz-
aldehyde, Methylamine, pN,N-dimethylaminobenzal-
dehyde, trans cinnamaldehyde and terephthalaldehyde
were purchased from Sigma-Aldrich and used as such.
Distilled acetic anhydride was used. Synthesis of Red
Kaede protein chromophore analogues (I–IV) is shown
in supporting information (scheme 1 and 2)
2.3 Spectroscopic characterization
2.3a (4Z)-4-(4-Hydroxybenzylidene)-1-phenyl-2-((1E,
3E)-4-phenylbuta-1,3-dienyl)-1,4-dihydro-5H-imidazolin-
5-one (I): Needle-shaped deep red crystals. Isolated
yield: 80%; M.p. 213–214◦C; Rf 0.5 (45% Ethyl
acetate-Petroleum ether).IR (KBr) νmax/cm−1: 3064,
1
1668, 1593, 1500, 1442, 1385. H NMR (500 MHz,
CDCl3+ DMSO-D6): δ 6.18 (d, J = 14.9 Hz, 1H), 6.86
(d, J = 8.6 Hz, 2H), 7.01 (s, 1H), 7.01–7.16 (m, 2H),
7.26–7.28 (m, 1H), 7.32–7.35 (m, 4H), 7.47–7.57 (m,
5H), 7.74 (dd, J1 = 15.2 Hz, J2 = 10.3 Hz, 1H), 8.18
(d, J = 8.6 Hz, 2H). 13C NMR (CDCl3+ DMSO-D6,
125 MHz): δ 115.9, 116.9, 125.7, 126.6, 127.0, 127.5,
127.6, 127.7, 128.3, 128.6, 128.7, 129.3, 133.3, 134.4,
136.1, 139.3, 140.3, 156.8, 160.0, 169.0. ESI-MS+
m/z Calcd. for C26H21N2O2 393.1603 [M+H], found
393.1604.
2.2 Synthesis of Compounds (I–IV)
Imidazolin-5-ones (I–IV) were synthesized by proce-
dures reported previously6,8b,9,13 (see supplementary 2.3b (4Z)-4-(4-methoxybenzylidene)-1-methyl-2-((1E,
information). Briefly acetyl glycine was refluxed with 3E)-4-phenylbuta-1,3-dienyl)-1,4-dihydro-5H-imidazolin-
a para-substituted aromatic aldehyde in acetic anhy- 5-one (II): Needle-shaped red crystals. Isolated yield:
dride in presence of sodium acetate to get an oxa- 40%; M.p. 140–145◦C; Rf 0.5 (40% Ethyl acetate-
zolone. In the next step the column purified oxazolones Petroleum ether).IR (KBr) νmax/cm−1: 3023, 2930,
1
were converted into imidazolin-5-ones by solvent 2837, 1700, 1663, 1595, 1506, 1449. H NMR (500
free Lewis acid catalysed reaction14 with primary MHz, CDCl3): δ 3.28 (s, 3H, NCH3), 3.87 (s, 3H,
amines (methylamine, aniline). The column purified OCH3), 6.40 (d, J = 15.3 Hz, 1H, CH=CH), 6.98 (d,
2-methylimidazolin-5-ones were further converted to J = 8.9 Hz, 2H, ArH), 7.04 (d, J = 5.8 Hz, 2H, ArH),
imidazolin-5-ones with extended conjugation (I–IV) 7.12 (s, 1H, =CHAr), 7.31–7.40 (m, 3H), 7.51 (d, J =

C = O . . . π interaction in rfp chromophore analogue
943
8.2 Hz, 2H, ArH), 7.88 (m, 1H), 8.21 (d, J = 8.5 Hz, M.p. 165–170◦C; Rf 0.5 (50% ethyl acetate-petroleum
2H). 13C NMR (CDCl3, 125 MHz): δ 26.6, 55.4, 114.3, ether). IR (KBr) νmax/cm−1: 3451, 2933, 1688, 1627,
114.4, 116.0, 127.2, 127.3, 127.4, 127.8, 128.9, 129.1, 1598, 1463. 1H NMR (500 MHz, CDCl3): 3.34 (s, 3H,
134.4, 136.3, 140.2, 141.2, 158.6, 161.3, 170.8. ESI- NCH3), 3.87 (s, 3H, OCH3), 6.96 (d, J = 16.03 Hz,
MS+ m/z Calcd. for C22H20N2O2345.1524 [M+H], 1H, CH=CH), 6.98 (d, J = 9.12 Hz, 2H, ArH), 7.19 (s,
found 345.1609.
1H, =CHAr), 7.78 (d, J = 8.015 Hz, 2H, ArH), 7.93
(d, J = 8.015Hz, 2H, ArH), 8.10 (d, J = 16.03 Hz, 1H,
CH=CH), 8.21 (d, J = 8.5 Hz, 2H, ArH), 10.04 (s,
1H, CHO).13C NMR (CDCl3, 125 MHz): δ 26.8, 55.5,
114.5, 116.0, 127.5, 128.4, 128.7, 130.3, 134.6, 137.0,
137.4, 138.9, 140.9, 158.0, 161.7, 170.6, 191.4. ESI-
MS+ m/z Calcd.for C28H38N3O: 347.13510 [M+H],
found 347.1390
2.3c (4Z)-4-(4-methoxybenzylidene)-1-methyl-2-(4-
methylstyryl)-1H-imidazol-5(4H)-one (III): Rod-shaped
yellow crystals. Isolated yield: 30%; M.p. 125–130◦C;
Rf 0.5 (40% Ethyl acetate-Petroleum ether). IR (KBr)
νmax/cm−1: 2935, 2839, 1698, 1598, 1510, 1436. H
1
NMR (500 MHz, CDCl3): 2.39 (s, 3H, ArCH3), 3.32
(s, 3H, NCH3), 3.87 (s, 3H, OCH3), 6.78 (d, J = 15.5
Hz, 1H, CH=CH), 6.97 (d, J = 8.5 Hz, 2H, ArH), 7.13
(s, 1H, =CHAr), 7.23 (d, J = 7.95 Hz, 2H, ArH), 7.53
(d, J = 7.95 Hz, 2H, ArH), 8.06 (d, J = 15.9 Hz, 1H,
CH=CH), 8.21 (d, J = 8.5 Hz, 2H, ArH). 13C NMR
(CDCl3, 125 MHz): 21.6, 26.7, 55.4, 111.8, 114.4,
127.1, 127.8, 128.0, 129.8, 132.6, 134.3, 137.8, 140.7,
140.8, 158.9, 161.3, 171.0. ESI-MS+ m/z Calcd. for
C21H20N2O2 333.1524 [M+H], found 333.1605.
2.4 X-ray crystallography
Single crystal X-ray data were collected at 298 K on
a Bruker AXS SMART APEX CCD diffractometer
equipped with a molybdenum sealed tube (λ = 0.71073
Å) and highly oriented graphite monochromator. The
data integration and reduction were processed with
SAINT+.15 The collected reflection data were cor-
rected by empirical absorption correction method with
SADABS.16 The structures were solved using WinGX
2.3d 4-((E)-2-((Z)-4-(4-methoxybenzylidene)-1-methyl- version 1.70.01 package. Direct method using SHELX
5-oxo-4,5-dihydro-1H-imidazol-2-yl)vinyl)benzaldehyde 9717 was used for solving the structures. The structures
(IV): Red needle-shape crystals. Isolated yield: 60%; were further refined using full matrix least square
Table 1. Summary of x-ray structure parameters of molecules I–IV.
Molecule
I
II
III
IV
Empirical Formula
Molecular Weight
Temperature/K
Crystal system
Space group
a/Å
C26H20N2O2
392.44
298(2)
Monoclinic
P21
6.691(2)
19.642(4)
7.719(3)
90
92.123(2)
90
1013.8(5)
2
1.286
0.082
C22H20N2O2
344.40
298(2)
Monoclinic
P21/n
14.121(5)
10.361(4)
14.130(5)
90
117.632(7)
90
1831.5(12)
4
1.249
0.081
C22H24N2O2.5
356.43
298(2)
Triclinic
P-1
7.0564(17)
7.4268(17)
18.270(4)
90.823(5)
91.860(5)
109.877(3)
899.6(4)
2
C21H18N2O3
346.37
298(2)
Monoclinic
Pn
4.9084(17)
14.926(5)
12.013(4)
90
99.761(7)
90
867.4(5)
2
1.326
0.090
b/Å
c/Å
α/0
β/0
γ /0
Volume/Å3
Z
Dx/Mgcm−3
μ /mm−1
1.316
0.086
F (000)
412
728
380
364
Crystal size / Mm
θ range for data collection/0
Reflectionscollected
Independentreflections
Data/restraints/ parameters
Goodness-of-fit on F2
Final R indices [I >2Sigma (I)]
0.27×0.22×0.20
2.1–28.4
6471
3803
3803/1/ 271
0.24×0.21×0.19
2.5–28.3
11792
4499
4499/0/ 235
0.22×0.19×0.18
3.1–25.5
4916
3277
3277/1/ 249
0.16×0.14×0.13
2.2–26
7682
2880
2880/2/ 235
1.028
R1 = 0.0536
wR2 = 0.1565
951959
1.056
0.954
1.022
R1 = 0.0936
wR2 = 0.2105
951962
R1 = 0.0626
wR2 = 0.2079
951960
R1= 0.0769
wR2 = 0.2519
951961
CCDC No.

944
Ashish Singh et al.
◦
Table 2. Significant intermolecular interactions (interatomic distances in Å and bond angles in ) observed in the crystal
structures of imidazolin-5-ones I–IV.
Molecule
I
D-H···A
D-H (Å)
H···A (Å)
D···A (Å)
<D-H···A(◦)
Symmetry codes
O(2)-H(2)···O(1)
C(17)-H(17)···O(2)
C(16)-H(16)···O(1)
C(4)-H(4)···O(1)
C22-H(22A)···O(1)
C(21)-H(21C)···π
C(3)-H(3)···O(2)
0.82
0.93
0.93
0.93
0.96
0.96
0.93
1.91(40)
2.67(47)
2.67 (18)
2.41(30)
2.14(27)
2.68(5)
2.671(60)
3.231(80)
3.557(32)
3.257(45)
2.877(32)
3.562(32)
3.315(5)
153(33)
119(41)
159(18)
152(21)
169(33)
152(22)
168(12)
−x, −0.5+y, 2−z
2−x, 1/2+y, 1−z
0.5−x, 0.5+y, 1.5−z
1−x, −y, 1−z
1−x,−y,1−z
II
III
1+x, 1+y, z
IV
2.40 (26)
−2+x,y,1+z
on F2 (SHELX 97).17 All the non-hydrogen atoms
were refined anisotropically. The hydrogen atoms were
refined isotropically and treated as riding atoms by
using SHELXL default parameters. The structures
reported here have been deposited in CCDC database
and have the accession numbers 951959-62.
information (figure S1). Crystallographic parameters
of molecule I–IV are given in table 1 and signifi-
cant intermolecular interactions are summarized in the
table 2.
Molecule I crystallized in a monoclinic system with
chiral space group P 21 (table 1). The mono-substituted
benzene ring and p-disubstituted benzene ring twist
out of the imidazolin-5-one plane by 2◦ and 8◦ respec-
tively. The crystal structure of molecule I exhibits a
strong hydrogen bond between O(2)-H(2)···O(1) of the
imidazolin-5-one ring with a distance of 1.91 Å and
3. Results and Discussion
3.1 Crystallographic studies
All crystals were grown by slow evaporation from a associated bond angle is 152.8◦. A stable π···π stack-
3:1 mixture of methanol and dichloromethane at room ing18 with a distance of 3.58 Å between imidazolin-
temperature. Molecules I, II and IV crystallized in 5-one and mono-substituted benzene ring is also
monoclinic system, while molecule III crystallized present. The hydrogen bonding interaction and π···π
in a triclinic crystal system. The ortep diagrams of stacking assembles into a two-dimensional sheet-like
all the reported molecules are shown in supporting supramolecular architecture in molecule I (figure 2).
Figure 2. Two dimensional sheet in molecule I formed by O(2)-H(2)···O(1)
hydrogen bond (1.91 Å, dotted violet line) and π···π stacking (3.58 Å, dotted
green line). Some of the hydrogen atoms are omitted for clarity. Colour code:
carbon: yellow; oxygen: red; nitrogen: blue; hydrogen: black.

C = O . . . π interaction in rfp chromophore analogue
945
Molecule II was also crystallized in monoclinic crys-
tal system but in achiral space group P 21/n. The unit
cell contains four molecules. Molecule II also devi-
ates significantly from planarity. The two benzene rings
are rotated by 8◦ and 5◦ from the imidazolinone-
5-one ring plane respectively. The crystal structure
shows a weak π···π stacking between the electron
deficient imidazolin-5-one heterocyclic ring and the
mono-substituted benzene ring with a distance 3.61 Å
(figure 3). A weak intermolecular hydrogen bond is
formed between imidazolinone oxygen O(1) and aro-
matic hydrogen C(16)-H(16) (2.67Å), which is shorter
than the sum of the van der Waals radii of the inter-
acting atoms. This weak hydrogen bond makes the
molecules arrange themselves in a zig-zag fashion to
form a one-dimensional chain-like structure (figure S2).
Molecule III crystallized in a triclinic crystal system
with centrosymmetric space group P -1. The asymmet-
ric unit of molecule III contains two solvent (methanol)
molecules. Both the methanol molecules appear at the
edge of the unit cell (figure S3) and have a statistical
Figure 3. A π···π stacking between imidazolin-5-one and
monosubstituted benzene ring (green dotted line) in molecule
II. Colour code: carbon: yellow; oxygen: red; nitrogen: blue;
hydrogen: black.
Figure 4. (a) Layer structure of molecule III formed by C(4)-H(4)···O(1)
and C(22)-H(22A)···O(1) hydrogen bonds (dotted green lines); (b) C(21)-
H(21C)···π hydrogen bonds (dotted orange lines) and π···π stacking (green
dotted line) between molecules. Some of the hydrogen atoms are omitted for
clarity. Colour code: carbon: yellow; oxygen: red; nitrogen: blue; hydrogen:
black.

946
Ashish Singh et al.
C(21)-O(2)···π with the distance of 3.35Å (figure 5).
This distance is shorter than the sum of van der Waals
radii of the interacting atoms.19 The nature of the
C=O···π interaction is most likely a lone pair···π inter-
action. The hydrogen bonds and C=O···π interactions
holds this molecule in three dimensions and forms a
supramolecular network of molecule IV. The C=O···π
interaction thus mandates planarity as a stereoelectronic
requirement.The C=O···π interactions thus play a signifi-
cant role in stabilizing the planarity in molecule IV.
The C=O...π interaction in RFP chromophore
(molecule IV) was further investigated by electronic
structure theory. The wave functions were generated
by applying B3LYP approximations using 6-31G(d,p)20
basis set for the supramolecular interactions of the crys-
tal structure of molecule IV. These calculations were
analyzed by AIMALL software21 in light of Bader’s
theory22 of atom in molecules. The electron density dis-
tribution in the crystal environment supports the pres-
ence of C=O...π interactions. A bond critical point of
spatial electron density of (3, -1) nature is found in
molecule IV between oxygen of free CHO and the elec-
tron deficient benzene ring (figure S4). Also the positive
value for the laplacian22 ( ρbcp) supports a closed shell
C=O...π interaction (figure S4)
disorder. The p−methyl substituted benzene ring is sig-
nificantly twisted and results in a 44◦ deviation from
the plane of imidazolin-5-one ring. The dihedral angle
between p-methoxy substituted benzene and imidazoli-
none ring is 4◦. The molecules form a sheet like struc-
ture with the help of intermolecular C(4)-H(4)···O(1)
(2.41 Å) hydrogen bonds while the methanol molecules
form individual C(22A)-H(22A)···O(1) (2.14 Å) hydro-
gen bonds between the sheets, thus connecting the layers
(figure 4b). A weak π···π stacking (3.91Å) is observed
between the two para substituted benzene rings. Apart
from π···π stacking, two C-H···π hydrogen bonds (C-
H(20B)···π (2.798Å) and C-H(21C)···π (2.681Å)) are also
present which stabilize the molecular packing (figure 4b).
Molecule IV, which has a free aldehyde group at
the para position of the benzene ring, adopted a planar
π-skeleton. The molecule IV crystallized with the P n
space group. The dihedral angle of the aldehyde con-
taining benzene and para methoxy substituted benzene
ring with imidazolinone ring is 1◦ and 3◦ respectively.
The molecular architecture is stabilized by two inter-
molecular hydrogen bonds (between C(3)-H(3)···O(2)
(2.40 Å, 167.5◦) and C(17)-H(17)···O(3) (2.63 Å,
133.5◦)). Moreover, apart from hydrogen bonds, a
striking C=O···π interaction is observed between
Figure 5. (a) Three dimensional arrangement of molecule IV stabilized by
C-H···O hydrogen bonding and C=O···π interactions. (b) A close view of
C=O···π interactions. Other hydrogen atoms are free from short contact and are
omitted for clarity. Colour code: carbon: yellow; oxygen: red; nitrogen: blue;
hydrogen: black.

C = O . . . π interaction in rfp chromophore analogue
947
supramolecular interaction is present in molecule IV
that facilitates electron donation from the methoxy
group across the π-skeleton of the molecule to the
aldehyde group. In all the molecules, π...π stacking is
present while a strong hydrogen bonding is observed
in molecule I to stabilize the crystal packing. We also
noticed that the presence of strong electron donating
groups (-OH in molecule I) and electron withdraw-
ing group (-CHO in molecule IV) leading to two and
three dimensional supramolecular architecture respec-
tively. This creation of electron pushpull systems forces
the molecule to become planar in order to ensure that
the p-orbitals are aligned to facilitate electron transfer
across the molecule which is also supported by pho-
tophysical studies. Further investigations in this regard
are under way.
1.0
0.8
0.6
0.4
0.2
0.0
I
II
III
IV
500
600
700
800
Wavelength(nm)
Figure 6. Normalized emission spectra of molecule I–IV
at room temperature in methanol solvent (Excitation wave-
length: 441 nm for I and II, 426 nm and 431 nm for molecule
III and IV respectively).
Supplementary Information
Supplementary information contains spectra of all com-
pounds and are available at www.ias.ac.in/chemsci.
The RFP chromophore analogues are supposed to
have a planar structure due to the sp2 hybridized
skeleton. However molecules I–III and the previously
reported N-phenyl analogue6 adopted a non-planar
geometry, stabilized by hydrogen bonding, π···π stack-
ing and C-H···π hydrogen bonds type of supramolec-
ular interaction. Molecule IV, where a strong electron
withdrawing group (-CHO) is present adopted a planar
structure stabilized only through the hydrogen bond and
C=O···π interactions. Among all the known RFP chro-
mophore analogues till date, molecule IV is the first
example having the C=O···π interaction and a planar
structure.
Acknowledgements
We are thankful to IIT, Kanpur, India for the finan-
cial assistance and Mr. Khalid Badi-Uz-Zama for assis-
ting us in computational study. A.S. and B.K.R. thank
UGC and CSIR, India for junior and senior research
fellowship (JRF & SRF). Compound I was synthesized
and solved by B.K.R. and has been reported only in
his thesis previously. At present, B.K.R. is an assistant
professor at Cotton College State University, Assam.
Anonymous referees are thanked for their comments.
The photophysical properties of molecule I-IV have
been investigated in methanol in 10 μ M concentra-
tions and data is presented in table S1. All molecules
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