Synthesis, crystal structure, Hirshfeld surface analysis, electronic structure through DFT study and fluorescence properties of a new anthracene based organic tecton

Article abstract of DOI:10.1016/j.molstruc.2017.05.074

A new organic molecule 9,10-bis((2-(pyridin-2-yl)-1H-imidazol-1-yl)methyl)anthracene (APIM) has been synthesized. Crystal structure analysis of the molecular solid reveals that CH?π and π?π interactions are the molecular packing forces in the solid state. Thermal analysis of the molecular solid shows relatively higher decomposition temperature of the crystalline molecular solid that correlates well with the cooperative nature of CH?π and π?π interactions. Density Functional Theory (DFT) optimized structure of the molecule closely correlates with that found in the crystal. DFT optimizations also lead to the similar CH?π and π?π interaction motifs that are found within the crystal. Hirshfeld surface analysis provides detailed insight into the relative importance of various weak forces in the molecular packing. Study of the fluorescence behavior of the molecules shows quenching in the presence of metal ions.

Full text of DOI:10.1016/j.molstruc.2017.05.074

Accepted Manuscript
Synthesis, crystal structure, Hirshfeld surface analysis, electronic structure through
DFT study and fluorescence properties of a new anthracene based organic tecton
Nilasish Pal, Debabrata Singha, Atish Dipankar Jana
PII:
S0022-2860(17)30684-1
10.1016/j.molstruc.2017.05.074
MOLSTR 23815
DOI:
Reference:
To appear in: Journal of Molecular Structure
Received Date: 28 February 2017
Revised Date: 8 May 2017
Accepted Date: 16 May 2017
Please cite this article as: N. Pal, D. Singha, A.D. Jana, Synthesis, crystal structure, Hirshfeld surface
analysis, electronic structure through DFT study and fluorescence properties of a new anthracene based
organic tecton, Journal of Molecular Structure (2017), doi: 10.1016/j.molstruc.2017.05.074.
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ACCEPTED MANUSCRIPT
Synthesis, crystal structure, Hirshfeld surface analysis, electronic structure through DFT
study and fluorescence properties of a new anthracene based organic tecton
Nilasish Pal,*a Debabrata Singha,a Atish Dipankar Jana*b
aDepartment of Chemistry, Seth Anandaram Jaipuria College, 10, Raja Nabakrishna Street,
Kolkata – 700005, West Bengal, India, e-Mail: nilasishpal@gmail.com
bDepartment of Physics, Behala College, Parnashree, Kolkata-700060, West Bengal, India, e-
Mail: atishdipankarjana@yahoo.in
Graphical Abstract:
A new Z-shaped molecular tecton self-assembles through cooperative C-H···π and π···π
interaction leading to hierarchical assembly of molecular rectangle, molecular tape and 2D
supramolecular layer.
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Synthesis, crystal structure, Hirshfeld surface analysis, electronic structure through DFT
study and fluorescence properties of a new anthracene based organic tecton
Nilasish Pal,*a Debabrata Singha,a Atish Dipankar Jana*b
aDepartment of Chemistry, Seth Anandaram Jaipuria College, 10, Raja Nabakrishna Street,
Kolkata – 700005, West Bengal, India, e-Mail: nilasishpal@gmail.com
bDepartment of Physics, Behala College, Parnashree, Kolkata-700060, West Bengal, India, e-
Mail: atishdipankarjana@yahoo.in
*Corresponding Author: Nilasish Pal, e-Mail: nilasishpal@gmail.com and Atish Dipankar Jana,
e-Mail: atishdipankarjana@yahoo.in
Abstract:
A new organic molecule 9,10-bis((2-(pyridin-2-yl)-1H-imidazol-1-yl)methyl)anthracene (APIM)
has been synthesized. Crystal structure analysis of the molecular solid reveals that CH···π and
π···π interactions are the molecular packing forces in the solid state. Thermal analysis of the
molecular solid shows relatively higher decomposition temperature of the crystalline molecular
solid that correlates well with the cooperative nature of CH···π and π···π interactions. Density
Functional Theory (DFT) optimized structure of the molecule closely correlates with that found
in the crystal. DFT optimizations also lead to the similar CH···π and π···π interaction motifs that
are found within the crystal. Hirshfeld surface analysis provides detailed insight into the relative
importance of various weak forces in the molecular packing. Study of the fluorescence behavior
of the molecules shows quenching in the presence of metal ions.
Keywords: Anthracene-2-(2ꞌ-Pyridyl)imidazole tecton, CH···π interaction, π···π interaction,
DFT study, Hirshfeld surface analysis, fluorescence quenching
Highlights:
•
•
•
•
•
•
Synthesis of a new Anthracene-2-(2ꞌ-Pyridyl)imidazole molecular tecton.
Cooperative CH···π, π···π interaction in crystal packing.
DFT study of the π-stacking interactions.
Prominent Hirshfeld fingerprint region.
Relatively higher thermal stability of the compound.
Fluorescence quenching by the metal ions.
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1.
Introduction:
Designed synthesis of molecular materials with interesting physico-chemical properties is
being pursued vigorously throughout the world. In the area of organic molecular materials
various weak intermolecular forces such as hydrogen bonding [1–3], π···π interaction [4–7],
CH···π interaction [8,9] etc., are generally utilized to control the molecular organization in the
solid state and to steer properties of the crystalline solid materials [10–13]. At present it has
become an art to judiciously combine different functional units into a single molecule to steer the
molecular reactivity [14,15], rigidity/flexibility [16–18] and self/mutual interaction [19–21]. This
can be done by manipulating various weak forces like hydrogen bonding, aromatic π-stacking
interactions etc. In this regard designing molecular units or tectons having desired shape and size
with the placement of functional groups at suitable locations on the molecule is the ultimate
influencing factors that govern how the molecules unite into super molecules. Through this
methodology various supramolecular architectures like molecular rectangle [22,23], molecular
cages and containers [24,25] etc. have been designed which are often utilized as nano-scale
functional units in nano-devices [26,27].
We report here the design of a new organic molecular tecton based on three different π-
stacking units – namely anthracene, pyridine and imidazole. Anthracene moiety posses strong
aromaticity and its π-electron system is attractive for the design of luminescent materials [11,28–
30]. Pyridyl unit on the other hand is a very versatile one, generally having strong affinity
towards metal ions and there are innumerable pyridine based ligands designed with an aim to
efficiently bind metal nodes [31,32] producing metal-organic frameworks (MOFs). Imidazole
molecule is a biologically important one and is capable of coordination to metal center together
with hydrogen bonding capability through the -NH group[33–35]. With an aim to combine the
above mentioned functionalities simultaneously into a single molecule we have attempted to
synthesize a new organic molecular tecton by combining anthracene, pyridine and imidazole
groups and have successfully designed a symmetric, semi-rigid and relatively long molecular
tecton (Scheme 1). It is expected that the molecular self-assembly of such a molecule should be
governed by π-stacking interactions which is indeed the case as revealed by X-ray crystal
structure. CH···π and π···π interactions cooperatively act in unison resulting supramolecular 2D
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layers that are stacked inside the solid. A computational study was undertaken to better
understand the electronic nature of the molecule and its intermolecular interactions. DFT study
reveals that molecule adopts the lowest energy conformation in the solid state and the optimized
geometry is in close agreement with the computed one. Geometries of the CH···π and π···π
motifs have also been computed and the corresponding interaction energies have been estimated.
Thermal stability analysis of the crystalline solid reveals a moderately high thermal
decomposition temperature correlating with the strong binding of the crystalline solid resulting
from cooperative CH···π and π···π forces. A fluorescence study has been carried out with a set
of metal ions which shows quenching of fluorescence activity in the presence of metal ions.
Scheme 1: Reagent and conditions: i) Paraformaldehyde, Anh. ZnCl2, Conc. HCl, 1,4-Dioxane
ii) 40% Glyoxal, Conc. NH3, stirring, 1h, 0°C, iii) NaOH, PhCl/H2O, Bu4NBr, reflux.
2.
Experimental Section:
2.1. Material and methods
All solvents and reagents were obtained commercially and used without further purification.
Infrared (IR) spectroscopic studies have been carried out with Perkin-Elmer Spectrum one using
1
KBr pellet. H NMR and 13C NMR were recorded with Bruker 400 MHz NMR spectrometer.
HRMS was recorded on a XEVO-G2QTOF#YA288 spectrometer. Thermal study has been
carried out with Perkin Elmer STA 6000 Simultaneous Thermal Analyzer.
2.2. Synthesis of APIM:
The desired molecule (APIM) has been synthesized easily by the phase transfer catalyst
mediated coupling of 2-(2ꞌ-Pyridyl)imidazole and 9,10-bis(chloromethyl)anthracene as
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illustrated in Scheme-1. 2-(2ꞌ-Pyridyl)imidazole and 9,10-bis(chloromethyl)anthracene were
synthesized in the first stage according to the previously published procedure[36–39].
Next to a solution of 9,10-bis(chloromethyl)anthracene (1g, 3.63 mmol) and 2-(2ꞌ-
Pyridyl)imidazole (1.2 g, 7.27 mmol) in chlorobenzene (20 ml), aqueous NaOH (7.5 M, 20 ml)
was added. Catalytic amount of tetra butyl ammonium bromide (TBAB) was added to the
mixture. The mixture was then refluxed for 6 h. Upon cooling to room temperature a yellow
solid precipitate was formed which was collected by filtration and washed with water. The
organic layer was washed with water for 2-3 times and dried over Na2SO4 and then solvent was
removed by rotary evaporator and the combined solid was crystallized from methanol. Good
quality light yellow coloured crystals suitable for single crystal XRD obtained upon slow
evaporation of methanol solution.
1H NMR (400 MHz, CDCl3) : 8.774 (dd, J = 4.8 & 0.8 Hz, 1H), 8.452 - 8.413 (m, 2H), 8.387
(d, J = 8.0 Hz, 1H), 7.917 (td, J = 7.6 & 1.6 Hz, 1H), 7.571 – 7.533 (m, 2H), 7.390 – 7.357 (m,
1H), 6.967 (s, 2H), 6.958 (d, J = 1.2 Hz, 1H), 6.431 (d, J = 1.2 Hz, 1H)
13C NMR (400 MHz, CDCl3): δ 151.29, 148.40, 144.42, 136.99, 131.05, 129.01, 128.33, 126.94,
124.84, 123.14, 122.71, 121.90
IR (cm-1): 3011 (w), 1673 (m), 1587 (s), 1480 (s), 1453 (s), 1249 (s), 1089 (m), 785 (s), 701 (s).
HRMS (ESI/QTOF) m/z: [M + H]+ Calcd for C32H25N6 493.2141; Found 493.2152
2.3. X-ray Crystallography:
Diffraction intensities for the compounds were collected at 293(2) K on a Bruker Kappa
Apex-II CCD area-detector diffractometer (MoKα, λ=0.71073 Å). The structures were solved by
the direct method and refined with full-matrix least-squares technique using the SHELXL-2014
program package[40]. Anisotropic thermal parameters were applied to all the non-hydrogen
atoms. The hydrogen atoms were generated using riding atom model. Crystal data as well as
details of data collection and refinement for the compound has been summarized in Table 1.
Selected bond distances and bond angles are listed in Table 2, π···π interaction data in Table 3
and C-H···π interaction data in Table 4.
2.4. Hirshfeld surface analysis:
Molecular Hirshfeld surfaces [41,42] in the crystal structure are constructed based on the
electron distribution calculated as the sum of spherical atom electron densities [43]. For a given
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crystal structure and set of spherical atomic electron densities, the Hirshfeld surface is unique.
The normalized contact distance (dnorm) based on both de (the distance from the point to the
nearest nucleus external to the surface) and di (the distance to the nearest nucleus internal to the
surface), and the van der Waals (vdW) radii of the atom, given by equation (1) enables
identification of the regions of particular importance to intermolecular interactions [44,45]. The
value of the dnorm is negative or positive when intermolecular contacts are shorter or longer than
vdW separations, respectively. The combination of de and di in the form of a two-dimensional
(2D) fingerprint plot provides a summary of intermolecular contacts in the crystal [41]. The
Hirshfeld surfaces are mapped with dnorm and 2D fingerprint plots presented in this paper were
generated using Crystal-Explorer 2.1. [46] Graphical plots of the molecular Hirshfeld surfaces
mapped with dnorm used a red, white, blue color scheme, where red highlights shorter contacts,
white is used for contacts around the vdW separation, and blue is for longer contacts. Moreover,
two further colored properties (shape index and curvedness) based on the local curvature of the
surface can be specified.
=
+
(1)
2.5. Methodology of DFT study:
For understanding the stability of the APIM molecule and its various π-stacked motifs have been
explored through DFT computations. All calculations were performed using the GAUSSIAN
package [47]. Initial geometries of the APIM molecule and its π-stacked dimeric C-H···π, π···π
motifs were adopted from the crystal structure and geometry optimizations for each one has been
carried out at the DFT 6-311G level of theory with B3LYP hybrid density functional. The
binding energy for these motifs have estimated according to the formula, B.E. = (Energy of the
motif) – 2*(Energy of a single molecule). The torsional rotational barrier potential of the pyridyl
ring with respect to the imidazole ring around the imidazole pyriyl C3-C4 bond (Fig. 1) has been
computed at the same level of theory.
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3.
Table 1: Crystal data and Refinement parameters
Crystal Data
Result and discussion
Formula
C32 H24 N6
492.57
triclinic
Formula Weight
Crystal System
Space group
1
P (No. 2)
a, b, c [Å]
7.8590(6) 8.2822(6) 10.0540(8)
alpha, beta, gamma [◦]
79.983(4) 72.232(5) 83.858(5)
612.68(8)
V [Å3]
Z
1
D(calc) [g/cm3]
Mu(MoKα) [ /mm ]
F(000)
1.335
0.082
258
Crystal Size [mm]
0.12 x 0.15 x 0.17
Data Collection
Temperature (K)
Radiation [Å]
Theta Min-Max [◦]
Dataset
Tot., Uniq. Data, R(int)
Observed data [I > 2.0 σ(I)]
293
MoKα 0.71073
2.5, 27.5
-10: 10 ; -10: 10 ; -11: 11
10648, 2674, 0.041
2018
Refinement
Nref, Npar
2674, 172
R, wR2, S
0.0396, 0.1073, 1.04
0.00, 0.00
Max. and Av. Shift/Error
Min. and Max. Resd. Dens. [e/Å3]
-0.13, 0.19
2
2
w = 1/[σ(Fo )+(
0.0465P)2+0.0837P] where P=( Fo +2Fc2)/3
3.1. X-ray crystal structure:
The ORTEP view of APIM has been shown in Fig. 1 which shows that imidazolyl-N and
Pyridyl-N are in trans geometry on either side of the central anthracene moiety.
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Fig. 1: The ORTEP diagram (30% ellipsoidal probability) with atom numbering scheme.
Symmetry equivalent atoms has symmetry code *=-x,1-y,1-z.
The molecule is centrosymmetric with the centre of inversion at the middle of the central
phenyl ring of the anthracene moiety. On each side of the central anthracene moiety, two pyridyl
imidazole units are attached through C-N bond. The N1-C9-C10 angle is 113.25◦. The linear
extension of the ligand across two N atoms (N2 and N2*) of two imidazole ring is 11.754Å. The
imidazole ring plane is inclined by 45.18◦ with respect to the perpendicular plane of the
anthracene moiety passing through the C9-C9* axial direction. The farthest hydrogen atom (H )
attached to the imidazole ring is at a distance 4.12Å above and below the anthracene mean plane
and the centroid of this ring is 2.09 Å above the anthracene mean plane. The centroid of the
pyridyl ring is just 0.75 Å away from the anthracene mean plane. The linear extension of the
molecule across the pyridyl ring is 17.99 Å. The dihedral angle between the pyridyl and the
imidazole ring plane is 19.13◦. Two donor N atoms, N1 and N3 attached respectively to the
imidazole ring and the pyridyl ring respectively are rotate by 158.50◦ with respect to each other.
The supramolecular assembly of the ligand in the solid state is governed by the π-
stacking interactions. Molecules assemble into a stacked array along crystallogrphic b-axis by
CH···π interaction (Table 4). C2 atom of the imidazole ring acts as hydrogen donor to the
peripheral phenyl rings of the anthracene moiety. The symmetric nature and step like shape (Z-
shape) of the molecule is amenable for this self-complementary assembly leading to the
formation of molecular rectangle and susequently to a molecular tape (Fig. 2). Adjacent tapes
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are joined into a 2D sheet [(110) planes] by π···π inteaction among the imidazole rings of
adjacent tapes. The centroid to centroid distance between the interacting imidazole rings is
3.5355(9) Å (Table 3). Successive (110) planes are stacked along c-axis (Fig. 3) through π-
stacking interactions involving pyridyl rings (centroid to centroid distance 3.8399(10) Å (Table
3)) which protrude out on both sides of the mean plane of (110) sheets.
Fig. 2: Supramolecular assembly of the molecules into a 2D sheet through π···π and C-
H···π interaction.
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Fig. 3: 3D packing of 2D layers in the crystal
Table 2: Bond Distance and Bond Angle table (Ǻ, °)
Bond Distances
N1-C1
N1-C3
N1-C9
N2-C2
N2-C3
N3-C4
N3-C8
C1-C2
C3-C4
C4-C5
C5-C6
1.3669(18)
1.3721(17)
1.4728(16)
1.369(2)
1.3254(17)
1.3436(18)
1.3363(19)
1.354(2)
C6-C7
C7-C8
C9-C10
1.361(2)
1.373(2)
1.5169(18)
1.4114(17)
1.4068(18)
1.4331(19)
1.4428(18)
1.355(2)
1.412(2)
1.354(2)
1.4340(18)
C10-C11
C10-C16
C11-C12
C11 -C16*
C12 -C13
C13 -C14
C14 -C15
C15 -C16*
1.4762(19)
1.387(2)
1.377(2)
Bond Angles
C1-N1 -C3
C1-N1 -C9
106.62(11)
123.93(11)
C10 -C16 -C11*
C10 -C16 -C15*
120.44(11)
121.58(12)
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C3-N1 -C9
C2-N2 -C3
C4-N3 -C8
N1-C1 -C2
N2-C2 -C1
N1-C3 -N2
N1-C3 -C4
N2-C3 -C4
N3-C4 -C3
N3-C4 -C5
C3-C4 -C5
C4-C5 -C6
C5-C6 -C7
C6 -C7 -C8
N3 -C8 -C7
N1 -C9 -C10
C9 -C10 -C11
C9 -C10 -C16
C11 -C10 -C16
C10 -C11 -C12
C10 -C11 -C16*
C12 -C11 -C16*
C11 -C12 -C13
C12 -C13 -C14
C13 -C14 -C15
C14 -C15 -C16*
*=-x,1-y,1-z
128.46(11)
C11*-C16 -C15*
N1 -C1 -H1
C2 -C1 -H1
N2 -C2 -H2
C1 -C2 -H2
C4 -C5 -H5
C6 -C5 -H5
C5 -C6 -H6
C7 -C6 -H6
C6 -C7 -H7
C8 -C7 -H7
N3 -C8 -H8
C7 -C8 -H8
N1 -C9 -H9A
N1 -C9 -H9B
C10 -C9 -H9A
C10 -C9 -H9B
H9A -C9 -H9B
C11 -C12 -H12
C13 -C12 -H12
C12 -C13 -H13
C14 -C13 -H13
C13 -C14 -H14
C15 -C14 -H14
C14 -C15 -H15
C16* -C15 -H15
117.97(12)
127
127
125
125
120
120
120
120
121
121
118
118
109
109
109
109
108
119
119
120
120
120
120
119
119
105.20(11)
117.48(13)
106.36(12)
110.75(13)
111.07(12)
126.50(11)
122.41(12)
118.49(12)
121.62(13)
119.84(12)
119.14(14)
119.68(16)
117.97(16)
124.10(15)
113.25(11)
120.53(12)
119.11(11)
120.28(11)
122.95(12)
119.25(12)
117.80(11)
121.59(13)
120.51(14)
120.37(13)
121.61(13)
Table-3: Geometrical parameters (Å, °) for the face to face π-stacking interactions in the
crystalline compound.
Interacting rings Distance between Dihedral Slip
centroid of R(i) and angle angle
Perpendicular distance of
R(i) centroid from R(j)
ring plane
centroid of R(j)
(Å)
3.5355(9)
3.8399(10)
(°)
(°)
(Å)
R1→R1i
5.8
5.8
3.5177(6)
-3.5995(6)
R2→ R2j
20.4
20.4
i=1-X,-Y,-Z
j=1-X,-Y,1-Z
R1: N1→C1→C2→N2→C3→
R2: N3→C4→C5→C6→C7→C8→
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Table-4: Geometrical parameters (Å, °) for the edge to face C-H···π interactions in the
crystalline compound.
X-H→ ring(j)
X-H···R(j)
Distance
X···centroid ring
angle(°)
between H atom (j) distance(Å)
and ring centroid
(j) (Å)
2.63
-2.63
C2-H2→ R4i
C2-H2→ R4ii
i= X,-1+Y,Z
ii=-X,-Y,1-Z
174
174
3.5670(16)
3.5670(16)
R4: C11→C12→C13→ C14→C15→C16*→
*= -x,1-y,1-z
3.2. Hirshfeld surface analysis:
Hirshfeld surface analysis has become a popular tool to understand the relative
importance of various atom···atom interactions in a crystalline solid. The dnorm surface,
curvedness and shape index for APIM has been depicted in Fig. 4. dnorm range is between -0.14
Å to 1.2 Å; shaped index range is -1.0Å to 1.0Å and curvedness range is -4.0 Å to 0.4 Å. Two
sets of complementary deep red spots (a, a′) and (b,b′) and two relatively lighter red spots (c and
d) are clearly visible on the dnorm surface. Red regions on the molecule indicate region of contacts
on the molecule which are shorter than the van der Waal’s distances of interacting atoms. Blue
regions are at a distance greater than the van der Waal’s distance and white regions are those
where distances are comparable to van der Waal’s distances. Region marked ‘a’ is on one of the
peripheral rings of anthracene and its complementary region ‘a′’ is situated on the imidazole
group of APIM. These two self-complementary regions of APIM are responsible for C-H···π
interactions between successive APIM molecules that lead to their assembly in the ab-plane. ‘b’
and ‘b′’ correspond to π···π interaction regions where imidazole groups come in close contact
with each other. Intra molecular hydrogen bonding (CH···N) contact regions are marked by c
and d on dnorm surface. The curvedness surface shows regions over the molecule are separated
from each other by blue boundaries and also correspond to regions which are involved in similar
nature of interactions. In the shape index curve blue regions are convex and red regions are
concave.
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Fig. 4: dnorm , curvedness and shape index surfaces of APIM
The fingerprint plot has been depicted in Fig. 5. C···H interactions and C···C interactions
contribute respectively 31.7% and 4.2% of total interactions. In the C···H fingerprint plot two
symmetric broad peaks are visible with di+de >
̴
3.4 Å. The π···π interactions in the C···C
3.4 Å to 4.0 Å. The C···H
fingerprint plot are the broad green region with di+de in-between
̴
fingerprint plot mainly corresponds to C-H···π interactions and C···C fingerprint plot mainly
correspond to π···π interactions. As C···H interactions are overwhelmingly greater than C···C
interactions (31.7% and 4.2% respectively) it can be concluded that C-H···π interactions play
more important role than π···π interactions in the crystal. As overall C···all interaction is 39.2%,
it is obvious that CH···π and π···π are the two main contributors where carbon atoms are
involved. The other small (3.3%) share of C···all interaction is between nitrogen atoms and
carbon atoms. The overall importance of nitrogen atoms in the molecular interactions is just
14.0%, depicted in the N···all fingerprint plot this shows two sharp spikes corresponding to intra-
molecular CH···N interaction responsible for twist of the pyridyl moiety with respect to the
imidazole moiety. The major share of interactions is due to H···H interactions which is 50.1% of
total interactions. In H···H fingerprint plot the triangular shaped broad green region over blue
background is again clustered around two regions. These are the close contact regions of H
atoms to C atoms and N atoms due respectively to C-H···π interactions and C-H···N hydrogen
bonding interactions. The N···N interactions correspond a negligible 0.1% of all atom-atom
interactions in the crystal. Hirshfeld surface analysis thus clearly indicates that in the present
crystal, directional assembly of APIM molecules is governed mainly by C-H···π and π···π
interactions.
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Fig. 5: Finger print plot of intermolecular interactions present in the crystal of compound APIM
3.3. Results of DFT study:
The minimum energy optimized structure of the APIM molecule has nearly the same
bond lengths and bond angles (Table S1) as that has been observed in the crystal structures. The
standard deviations of bond length and bond angles of APIM molecule between crystallographic
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and DFT computational results are 0.02 Å and 1.58◦ respectively (Table S2). The computed
molecular dipole moment is nearly zero (0.0000005, 0.000000, 0.0000003) Debye. In the
optimized geometry the pyridyl and the imidazole rings are also trans to each other like crystal
structure. The dihedral angle between the pyridyl and the imidazole ring plane in the optimized
single molecule is 11.80◦ (which is 19.13◦ in crystal) (Fig. S1). Imidazolyl nitrogen (N2) and
pyridyl nitrogen (N3) are rotate by 167.03◦ (crystal: 158.50◦) with respect to each other. The
linear extension of the ligand across two N atoms (N2 and N2*) of two imidazole ring is 11.69Å
(crystal: 11.754Å). To assess the potentiality of APIM as a plausible ligand for metal chelation,
we have attempted to estimate the rotational potential barrier across the connecting bond (C3-
C4) between imiazole and pyridyl moiety. The DFT calculation reveals that this energy barrier is
quite high (28.8072 kcal/mole) [Fig. S2]. This correlated well with fact that pyridyl forms
intramolecular hydrogen bond (C15-H15···N3) with the central anthracene moiety of APIM
which is also present in the crystal structure (Table S3). HOMO, LUMO, HOMO -1 and
electrostatic potential (ESP) of the optimized structure have been depicted in Fig. 6. HOMO and
LUMO both are mainly localized over the anthracene moiety whereas HOMO-1 is localized over
the pyridyl imidazole part of the molecule. Highest negative charge concentration is over the
pyridyl and imidazole N-atoms, whereas the hydrogen atoms attached to the bridging carbon
atoms between central anthracene moiety and pyridyl-imidazole uints are highest electro
positive.
We have also optimized the C-H···π and π···π motifs starting with the similar initial
geometry as has been observed in the crystal. These motifs also nicely converge to their
respective minimum energy configuration. The H to (ring centriod) distance in the C-H···π
optimized geometry is 3.116 Ǻ (Fig. S3) and the centroid to centroid distance in the π···π motif is
3.874 Ǻ (Fig. S4). The corrected binding energy for these motifs is 0.885kcal/mole (for C-H···π)
and 3.240 kcal/mole (for π···π). So the cohesive force generated the cooperative action C-H···π
and π···π interaction can be approximated to be 4.125 kcal/mole.
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Fig. 6: HOMO, LUMO, HOMO -1and electrostatic potential(ESP) surface of APIM
3.4. Thermal-Study:
Thermal study of the molecular compound (Fig. 7) reveals a quite high decomposition
temperature (320°C) which is rarely seen in case of organic compounds. Starting from 50°C up
to 320°C mass loss is very slow (~ only 4.5 %) and then within 350°C 29 % mass is lost. The
mass loss behavior beyond 320°C is more or less exponential in nature. One can clearly observe
two small isotherms one at 275°C and the other one at 330°C. These clearly indicate the
molecular rearrangement (phase change) within the solid. These two peaks can be assigned to
two different intermolecular forces responsible for crystal packing – the CH···π and the π···π
interactions. The separation between these peaks (~55°C) indicates the differing strength of these
interactions. The DFT study of intermolecular CH···π and π···π interactions reveal that CH···π
interaction is stronger than π···π interactions in this system. One can estimate approximately the
differing strength of these interactions to be ~kBT = 55 kB = 32.62 kcal/mole.
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Fig. 7: TG curve of the compound (Heating rate 10°C/min., Nitrogen atmosphere)
3.5. Photo Physical Study:
Anthracene moiety is a well known fluorophore and the designing of the new molecular tecton
utilizing anthracene at the core was with an aim to study the possible modulation of fluorescence
property of the newly synthesized molecule. Fluorescence study of this molecule with various
metal ions like Zn2+, Co2+, Ni2+,Mn2+,Fe2+,Al3+, Tb2+ have been carried out. Experimental
fluorescence spectra have been depicted in Fig. 8 and Fig. S5 to Fig. S10. The general trend of
the fluorescence spectra is a significant quenching of the fluorescence intensity of the 427 nm
peak with the increase of metal ion concentration. Fig. 8 shows the change in the fluorescence
intensity of anthracene emission at 450 nm in APIM in the presence of increasing amounts of
Zn2+ ion concentration. A possible cause of quenching of fluorescence is that the molecule binds
with the metal ions resulting a photo-induced electron transfer (PET) from the binding sites to
the excited state of anthracene.
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1.5x106
1.0x106
5.0x105
0.0
400
450
500
550
600
Wavelength (nm)
Fig. 8. Change in emission spectra of APIM (c = 2.5 X 10-5 M) upon addition of Zn2+ (c = 1.00
X 10-3 M, as perchlorate salt) in CH3CN (λ ex = 370 nm).
4. Conclusion
A new 2-(2ꞌ-Pyridyl)imidazole based symmetric organic molecule with anthracene fluorophore at
its core has been synthesized. In the design of the molecule it was easy to foresee that
π···π/CH···π interactions along with possible weak CH···N interaction could be possible
cohesive forces for molecular self-assembly. Even in the presence of very few structure-directing
interactions, predicting a crystal structure is a challenging task in crystal engineering [48] - so it
was essential to obtain crystal structure to explore the specific manner in which π···π/CH···π
forces operate in self-assembling APIM. The X-ray crystallographic analysis indeed revealed
the simultaneous presence of both π···π/CH···π interactions in the molecular packing. The Z-
shape of the molecule facilitates a rectangular assembly of two molecules through CH···π
interaction having a calculated cohesion energy of 0.885kcal/mole. Due to symmetric nature of
the designed molecule with respect to the anthracene core this assembly self-propagates along
the crystallographic b-axis. It has often been observed that when more than one structure
directing inter molecular forces are responsible for crystal packing, the forces generally
propagates molecular assembly in mutually exclusive directions[45,46]. In a similar manner
π···π interaction in the present crystal structure is responsible for molecular assembly along the
crystallographic a-axis and CH···π interactions along crystallographic b-axis and thus both the
interactions cooperate and coexist together in the present crystal. Successive supramolecular
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chains formed by CH···π interactions are further united into 2D supramolecular sheet by π···π
interactions. The calculated π···π interaction energy of the molecule is 3.240 kcal/mole. Though
the crystal has been assembled through weak forces only, it shows a moderately high thermal
stability (320°C) due to cooperative action of CH···π and π···π forces. The fluorescence study
reveals that a series of metal ions act as efficient quencher for the fluorescence activity of the
newly designed molecule. This new semi-rigid molecular tecton would possibly be an efficient
ligand for metal coordination and might come out to be a good spacer for the design of porous
and other functional materials. Efforts towards this are currently underway in our laboratory.
5. Supplementary data
CCDC 1532214 contains the supplementary crystallographic data for compound APIM. This
data can be obtained free of charge via http://www.ccdc.cam.ac.uk/conts/retrieving.html, or from
the Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax:
+44 1223 336 033; or e-mail: deposit@ccdc.cam.ac.uk. Supplementary file contains additional
results from DFT computation, Hirshfeld analysis and fluorescence study.
Acknowledgements
This work is supported by the SERB-DST, New Delhi (Sanction No. SB/FT/CS-170/2012) and
UGC Minor Research Project Grant (PSW-105/13-14(ERO)). A. D. Jana thanks UGC (New
Delhi) for financial support under Minor Research Project, Grant no F.No.PSW-41/14-15 (ERO).
Thanks to Prof. K. Ghosh, Department of Chemistry, University of Kalyani for using
Fluorimeter in his DST funded project. We also thank Department of Chemistry, Assam
University, Silchar, India, for providing us TG-DTA facility.
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Highlights:
•
•
•
•
•
•
Synthesis of a new Anthracene-2-(2ꞌ-Pyridyl)imidazole molecular tecton.
Cooperative CH···π, π···π interaction in crystal packing.
DFT study of the π-stacking interactions.
Prominent Hirshfeld fingerprint region.
Relatively higher thermal stability of the compound.
Fluorescence quenching by the metal ions.
1