The Importance of Intermolecular Interaction in Solid-state

X-ray Crystal Structures (Ed.: Saikat Kumar Seth)

Published by New Academic Publishers, New Delhi (2016), ISBN: 9788186772898

Chapter - 1

QUANTITATIVE CRYSTAL STRUCTURE

ANALYSIS OF NAPHTHO[2,1-B]FURAN-2-
YLMETHANOL: INPUTS FROM PIXEL, AIMALL
AND HIRSHFELD ANALYSIS
Dhananjay Deya, Prakash .Vb, Vasuc, Shet Prakash M d,e, Deepak Chopra*a
a
Crystallography and Crystal Chemistry Laboratory, Department of Chemistry,
Indian Institute of Science Education and Research Bhopal, Bhopal-462066,
Madhya Pradesh, India.
b
Shirdi Sai Engineering College, Anekal, Bangalore-562106
c
Vivekananda Degree College, Malleshwaram West, Bangalore-560055
d
Department of Chemistry, University College of Science, Tumkur University,
Tumkur, India.
e
Centre for Advanced Materials, Tumkur University, Tumkur, India.

1.1 INTRODUCTION
The study of crystal structures containing more than one independent
molecule in the asymmetric unit is of interest in crystal engineering [1]. It
is of interest to investigate whether the second independent molecule is
significantly different or not from the first molecule [2]. Brock has performed
such studies on alcohols and phenols and has provided an explanation
for –OH containing organic compounds which have crystallized with Z’
> 1 compared to other organic molecular crystals [3]. According to their
studies, the interaction between the crystallographically independent
molecules occurs mainly via the formation of cooperative hydrogen bonded
O–H∙∙∙O chains, O–H∙∙∙O rings or a O–H∙∙∙O dimer. In such a case, it is
difficult to achieve a structure with Z’ = 1 to pack and hence Z’ > 1 is the
alternative option for the –OH containing organic compounds. In 2006, some
research groups have nicely explained the presence of multiple molecules
in the asymmetric unit (Z’) [4]. Crystals which were obtained from melt
crystallization or sublimation have higher propensity to achieve crystal
structures with Z’ > 1 [5]. It has been demonstrated that crystal structures
with high Z’ have a loose packing but important interactions (replace) [6].
Brock et. al. have shown that biphenyls containing a hydroxyl group are
prone to exhibit high Z’ behaviour as the tendency to form a strong O–H∙∙∙O
hydrogen bond needs to be balanced with the difficulties of packing twisted
biphenyl fragments in the crystal [7].
2 Dhananjay Dey, Prakash V, Vasu, Shet Prakash M and Deepak Chopra

Naphthofurans are an important class of oxygen-containing π-rich

heteroaromatic compounds that are found in biologically active compounds
[8] and in organic functional materials [9]. These compounds have been
known to regulate hepatocyte nuclear factor 4α which is associated
with proliferation, progression and metastasis of HCC (hepatocellular
carcinoma is the most common type of liver cancer) [10]. HNF 4α is a
nuclear transcription factor that binds DNA as a homodimer, control the
expression of several genes which play a role in the development of liver
and kidney [11]. Naphthofurans are used widely in heterocyclic chemistry
[12]. Naphtho [1,2-b] furan derivatives are used in treatment and prevention
of glaucoma [13].

1.2 Experimental Procedure

1.2.1 Synthesis
To a mixture of Lithium aluminum hydride (40 mmol) in tetrahydrofuran
(10 ml), the solution of ethyl naphtho[2,1-b]furan-2-carboxylate (10 mmol)
in THF (10 ml) was added slowly with continuous stirring at 00C for 2h.
The completion of the reaction was monitored by TLC. The reaction mixture
was quenched in ammonium chloride solution. The product (Naphtho[2,1-b]
furan-2-ylmethanol) was extracted in ethyl acetate and purified through silica
gel column chromatography. Finally, the compound has been characterized
by 1H-NMR, and FTIR spectroscopy. The IR spectrum of this compound has
shown an absorption band at 3225cm-1 due to stretching frequency of the
–O-H group. FTIR (KBr pellet, cm-1):- Bulk: 3225 (-OH) in cm-1, 1H-NMR
(CDCl3, 400 MHz): δ 8.09 (d, J = 8.12 Hz, 1H), 7.93 (d, J = 8.09 Hz, 1H), 7.71
(d, J = 8.96 Hz, 1H), 7.59 (m, 2H), 7.47 (t, J = 7.44 Hz, 1H), 7.24 (s, 1H), 7.16
(s, 1H), 4.86 (s, 2H).

Scheme 1.1 Preparation of Naphtho[2,1-b]furan-2-ylmethanol

1.2.2 Crystal growth and structure refinement

The synthesized compound has been crystallized from solvent methanol
at room temperature via slow evaporation. Low temperature [100(2) K]
crystallographic data was collected on Bruker D8 venture PHOTON 100
CMOS diffractometer using Mo-Kα radiation (λ = 0.71073Å) in phi (ϕ) and
Quantitative Crystal Structure Analysis of Naphtho[2,1- b] furan-2-ylmethanol 3

omega (ω) scan. Empirical absorption corrections were made using SADABS
[14]. The unit cell measurement, data collection, integration, scaling and
absorption correction was performed using Bruker Apex II software [15].
The crystal structure was solved by direct methods using SIR 92 [16] and
refined by the full matrix least squares method using SHELXL97 [17] present
in the program suite WinGX (version 1.80.05)[18]. The non-hydrogen atoms
are refined anisotropically and the hydrogen atoms bonded to C atom, were
positioned geometrically and refined using a riding model with Uiso (H)
=1.2Ueq. The hydrogen atom connected with the oxygen atom was located
and then refined isotropically. The molecular connectivity and the crystal
packing diagrams were generated using Mercury 3.5.1 (CCDC) program
[19]. Geometrical calculations were done using PARST [20] and PLATON
[21]. The details of the data collection and the crystal structure refinement
are shown in Table 1.1.

1.2.3 Calculations of the Intermolecular Energies for the Molecular Pairs

In order to evaluate the energies associated with various non-covalent
interactions present in the crystal, PIXEL calculations have been performed.
The pairing energy of the dimer is divided into the corresponding Coulombic,
polarization, dispersion and repulsion energies [22]. The Hirshfeld surface
associated with the fingerprint plots were performed using CrystalExplorer
3.1 [23]. This method suggests a facile way of obtaining information on
trends in crystal packing. 2D fingerprint-plots [24] provide a convenient
mean of quantifying the interactions within the crystal structures to identify
the similarities and dissimilarities between independent molecules present
in the asymmetric unit.

1.2.4 Topological analysis

The AIMALL ab initio calculations for some selected dimers at the
crystal geometry (with the hydrogen atoms moved to their neutral value)
were performed at the DFT-B3LYP/6-311++G** level using Gaussian 09. The
formatted checkpoint file (fchk) was used as an input file for calculations
using AIMALL (version 13.05.06) [25]. The electron density features at the
bond critical points, which are computed, is as follows: (i) electron density
(ρb), (ii) Laplacian (∇2ρb) and (iii) the kinetic energy density (Gb). Eint=
0.429 Gb (in au) [26].

1.3 Results and Discussion

The single crystal X-ray diffraction revealed that the title compound
crystallizes in the centrosymmetric monoclinic space group P21/c with
three independent molecules (Z’ = 3) in the asymmetric unit. ORTEP has
4 Dhananjay Dey, Prakash V, Vasu, Shet Prakash M and Deepak Chopra

Table 1.1 Single Crystal Data Collection and Refinement.

Formula C13H10O2
Formula weight 198.21
Temperature/K 100(2)
Wavelength (Å) 0.71073
Solvent system Methanol, RT
CCDC number 1062581
Crystal system Monoclinic
Space group P21/c
a (Å) 19.4639(16)
b (Å) 17.2656(12)
c (Å) 8.7750(8)
α (˚) 90
β (˚) 101.397(3)
l (˚) 90
V(Å3) 2890.7(4)
Z’, Z 3, 12
Density(g cm-3) 1.366
μ (mm-1) 0.092
F (000) 1248
θ (min, max) 2.36, 29.57
Treatement of hydrogens Mixed
hmin, max, kmin, max, lmin, max (-27, 27), (-23, 23), (-12, 12)
No. of ref. 74411
No. of unique ref./ obs. Ref. 8092, 6127
No. parameters 162
Rall, Robs 0.0696, 0.0482
wR2all, wR2obs 0.1365, 0.1225
Δρmin, max (eÅ-3) -0.249, 0.462
G. O. F. 1.025
been shown in Figure 1.1 with different colours code (molecule A: olive,
molecule B: purple and molecule C: saddle brown). The molecule contains
a naptho[2,1-b]furan moiety and a –CH2OH group is attached with the
furan ring. The overall conformation of the molecule is planar excluding
the –OH group. The molecule has one flexible part around the C–C single
bond. Table 1.2 lists some selected bond and torsion angles. The torsion
angle (C11-C12-C13-O2) of molecule A is 110.2(2)º wherein for molecule B
Quantitative Crystal Structure Analysis of Naphtho[2,1- b] furan-2-ylmethanol 5

(C24-C25-C26-O4) and molecule C (C37-C38-C39-O6) the values are 121.1(1)

º and 122.7(2)º respectively. The naptho[2,1-b]furan moiety of molecule A
is aligned parallel with the molecule B. The molecule B and molecule C are
connected via the strong O4–H4∙∙∙O6 intermolecular hydrogen bond with
short H∙∙∙O distance (1.92Å) and high directionality (156º). Table 1.3 lists
the molecular pairs with intermolecular interactions involved along with
the geometrical parameters. The geometrical restrictions placed on the
intermolecular H-bonds are the sum of the van der Waals radi +0.4 Å and
the directionality is greater than 110º [27].

Figure 1.1 ORTEP view of the molecular structure having three molecules (Z’
= 3) in the asymmetric unit. Thermal ellipsoids are drawn at 50% probability.
Bending arrows are showing the torsion angle in the asymmetric unit.
Table 1.2 Some selected bond angles and torsion angles (º).
Molecule A Molecule B Molecule C
O2-C13-C12 112.3(1) O4-C26-C25 111.8(1) O6-C39-C38 115.0(1)
C11-C12-C13-O2 110.7(2) C24-C25-C26-O4
121.1(1) C37-C38-C39-O6 122.7(2)
In Figure 1.2, we have shown the molecular pairs (represented with
decreasing stabilization energy) extracted from the crystal packing
performed using calculations obtained from PIXEL. The crystallographically
independent molecules (A, B and C) lead to the formation of a strong O–
H∙∙∙O zigzag chain down the bc plane (Figure 1.3). In addition, the crystal
packing is with weak C–H∙∙∙O and C–H∙∙∙π intermolecular interactions. In
the crystal, the strongest interaction was formed via the adjacent 21 screw
related molecules (between A and C) which are connected together with
O–H∙∙∙O hydrogen bond (involving H6 with O2) and a C–H∙∙∙π (involving
6 Dhananjay Dey, Prakash V, Vasu, Shet Prakash M and Deepak Chopra

H11 with Cg2ʹʹ) intermolecular interaction. The corresponding interaction

energy is -10.9 kcal/mol wherein the Coulombic contribution (46%) is more
significant than the polarization (21%) and dispersion (33%) contributions
The second molecular pair formed via weak C–H∙∙∙O (H26A involving
with O4) and C–H∙∙∙π(H24 interacts with Cg2ʹ) intermolecular interaction,
the stabilization energy being -8.3 kcal/mol. In this case, the dispersion
contribution (63%) is more than the Coulombic (26%) and polarization (11%)
contributions. Another molecular pair formed via strong O–H∙∙∙O hydrogen
bond (involving H4A with O6) with -6.7 kcal/mol stabilization energy
where Coulombic (57%) contribution is more than polarization (22%) and
dispersion (21%) contribution. In addition to that, H2A interacts with O4
leads to the formation of a strong O–H∙∙∙O hydrogen bond, the interaction
energy being -5.7kcal/mol. Furthermore, other molecular pairs (from VI to
XII) having interaction energies in the range of -5.2 kcal/mol to -1.5 kcal/
mol, also contribute towards the crystal packing.
Table 1.3 Interaction energy (in kcal/mol) of the molecular pairs and related
intermolecular interactions along with their geometry.
Motifs Symmetry Centroid- ECoul EPol EDisp ERep ETot Possible Geometry
centroid interactions (Å/ º)
distance
(Å)
I -x+1, y-1/2, 4.858 -13.9 -6.5 -10.0 19.5 -10.9 O6-H6...O2 1.79, 173
-z+1/2 C11-H11...Cg2’’ 2.66, 142
II x, -y+1/2, 4.822 -4.1 -1.8 -9.7 7.3 -8.3 C26-H26A∙∙∙O4 2.68, 132
z+1/2 C24-H24∙∙∙Cg2’ 2.68, 130
C17-H17∙∙∙π(C14) 2.96, 145
III x, y, z 11.300 -10.4 -3.9 -3.8 11.4 -6.7 O4-H4A∙∙∙O6 1.92, 156
IV -x+1, y-1/2, 5.193 -2.3 -1.1 -8.6 5.5 -6.6 C39-H39B∙∙∙O1 2.51, 145
-z+3/2 C30-H30∙∙∙Cg1 3.00, 137
C37-H37∙∙∙Cg2 2.65, 150
V -x+1, -y+1, 9.953 -12.1 -5.6 -3.3 15.3 -5.7 O2-H2A∙∙∙O4 1.78, 173
-z+1
VI x, -y+3/2, 5.438 -2.4 -1.1 -7.5 5.8 -5.2 C8-H8∙∙∙O2 2.67 166
z-1/2 C7-H7∙∙∙π(C10) 2.64, 128
VII -x+1, y-1/2, 5.565 -2.3 -1.3 -7.5 6.2 -5.1 C34-H34∙∙∙O3 2.82, 133
-z+1/2 C33-H33∙∙∙Cg2’ 2.77, 124
VIII -x+1, -y+1, 5.663 -1.7 -0.5 -5.7 3.0 -4.9 Molecular 3.360(2)
-z+1 stacking
IX -x+1, y-1/2, 5.762 -1.0 -0.7 -6.2 4.0 -3.9 C21-H21∙∙∙π(C38) 2.92, 131
-z+3/2 C20-H20∙∙∙π(C36) 2.72, 131
X -x+1, -y, -z+1 10.114 -1.3 -0.5 -2.3 2.1 -2.1 C39-H39A∙∙∙O6 2.75 162
XI -x+1, y-1/2, 9.268 -0.3 -0.2 -1.8 0.6 -1.7 C26-H26A∙∙∙O1 2.82, 145
-z+3/2
XII x, -y+1/2, 9.309 -0.2 -0.1 -1.4 0.3 -1.5 C13-H13A∙∙∙O5 2.87, 152
z+1/2
Quantitative Crystal Structure Analysis of Naphtho[2,1- b] furan-2-ylmethanol 7

Figure 1.2 Molecular pairs in order of decreasing stabilization energies.

Figure 1.3 Packing network showing the strong O–H∙∙∙O and C–H∙∙∙O chain
along the c axis.
8 Dhananjay Dey, Prakash V, Vasu, Shet Prakash M and Deepak Chopra

Figure 1.4 Molecular graphs of the molecular pairs involving different

independent molecules present in the asymmetric unit, depicting the bond
critical points represented with red colour. The dotted lines indicate the bond
paths between the interacting atoms.
Table 1.4 Topological parameters at the bond critical point (BCP’s) of selected
intermolecular interactions.
Pair Interaction d(Å) Rij(Å) ρBCP D2ρBCP Vb (a.u.) Gb (a.u.) D.EG
(e/Å3) (e/Å5) (kcal/
mol)
I O6-H6∙∙∙O2 1.74 1.76 0.260 3.333 -0.035766 0.035169 9.12
C11-H11∙∙∙C34 2.71 2.81 0.052 0.523 -0.003574 0.004499 1.17
III O4-H4A∙∙∙O6 1.88 1.90 0.210 2.541 -0.025337 0.025847 6.69
IV C30-H30∙∙∙C1 2.90 2.93 0.036 0.339 -0.002436 0.002979 0.77
C37-H37∙∙∙C7 3.00 3.40 0.032 0.346 -0.002495 0.003042 0.79
C37-H37∙∙∙C9-C10 2.92 3.52 0.034 0.380 -0.002578 0.003258 0.84
C39-H39B∙∙∙O1 2.51 2.52 0.061 0.686 -0.005563 0.006342 1.64
VII C33-H33∙∙∙C23 2.51 2.54 0.072 0.780 -0.005444 0.003588 0.93
C34-H34∙∙∙O3 2.82 2.85 0.031 0.405 -0.002970 0.003588 0.93
IX C21-H21∙∙∙C38 2.92 2.98 0.034 0.342 -0.002369 0.002962 0.77
C20-H20∙∙∙C36 2.72 2.79 0.052 0.561 -0.003785 0.004802 1.24
XI C26-H26A∙∙∙O1 2.82 2.84 0.030 0.359 -0.002629 0.003160 0.82

In order to obtain quantitative insights into the nature of the weak

and strong interactions for the molecular pairs associated with different
independent molecules present in the asymmetric unit, we have performed
the topological analysis using QTAIM [28] method. It is of interest to evaluate
whether it can be deemed to be a “hydrogen bond” in accordance with the
rules of IUPAC [29]. Table 1.4 lists all the topological parameters obtained
from the AIMALL calculation for the strong O–H∙∙∙O hydrogen bond and
weak C–H∙∙∙C, C–H∙∙∙O intermolecular interactions. For the strong O–H∙∙∙O
hydrogen bond in molecular pair I (A & C), the electron density and the
Laplacian at the bond critical point were observed to be 0.260 e/Å3 and 3.333
Quantitative Crystal Structure Analysis of Naphtho[2,1- b] furan-2-ylmethanol 9

e/Å5 and the corresponding bond dissociation energy is 9.12 kcal/mol. But
in case of III, the electron density and the Laplacian at the bond critical point
were observed to be 0.210 e/Å3 and 2.541 e/Å5 and the corresponding bond
dissociation energy is 6.69 kcal/mol. For the weak C–H∙∙∙C intermolecular
interactions the electron density and the Laplacian at the BCP were observed
in the range of 0.032 - 0.072 e/Å3 and 0.339 - 0.780 e/Å5 respectively and the
corresponding bond dissociation energies were observed in the range of 0.77
to 1.24 kcal/mol. The electron density and the Laplacian at the BCP for the
weak C–H∙∙∙O interactions were observed in the range of 0.030 - 0.061 e/Å3
and 0.359 - 0.686 e/Å5 respectively and the corresponding bond dissociation
energy was observed in the range of 0.93 to 1.64 kcal/mol.
In Figure 1.5, the fingerprint plots of all the three molecules (A, B and
C) present in the asymmetric unit, have been shown. All the molecules
have a sharp double-spike feature. These spikes are associated with the
O∙∙∙H contacts. The plot of percentage contribution (Figure 1.6) of various
atom∙∙∙atom contacts gives us an idea about the most common intermolecular

Figure 1.5: Fingerprint plots for the three independent molecules: full (left
column) and resolved into C∙∙∙H (second column), H∙∙∙H (third column), O∙∙∙H
(right) contacts showing the percentages of contacts contributed to the total
Hirshfeld surface area for the molecules.
10 Dhananjay Dey, Prakash V, Vasu, Shet Prakash M and Deepak Chopra

interactions present in the crystal. The molecule C contains 2% more C∙∙∙H

contacts compared to the others (molecule A and molecule B). Molecule A
and molecule B have similar O∙∙∙H contribution (~17.4%) but molecule C
has slightly less O···H contribution (16.6%) from the other two molecules.
H∙∙∙H contribution is almost similar for the three molecules.

Figure 1.6: Relative contribution of various atom∙∙∙atom contacts to the crystal

packing of the different isomers.

Scheme 1.2: CSD search with three independent molecules in the asymmetric
unit.
We have performed an evaluation of the Cambridge Structural Database
(CSD) with three independent molecules (Z’ = 3) in the asymmetric unit
(Scheme 1.2). A total of 18 hits (100%) were obtained with some constraints
(R factor < = 0.1, not disordered, not polymeric, no errors, no ions, no
powder structures, only organics). Amongst all the observed hits, only one
hit matched with the space group P21/c with Z’ = 3 and Z = 12 [30].
Table 1.5 lists some selected crystal structures (from Cambridge
Structural Database) which contains naphthofuran moiety having different
functional groups. In all crystal structures, naphthofuran moiety is planar.
Yorimitsu et. al. have synthesized a library of naphthofuran derivative
Quantitative Crystal Structure Analysis of Naphtho[2,1- b] furan-2-ylmethanol 11

compounds and investigated their photophysical properties (absorption,

emission and fluorescence) in the solid state as well as in solution state
[36]. The crystal packing of BAGVAH, GITLIF and WIZZUB have been
stabilized via the formation of R22(8) supramolecular synthon utilizing
the strong O–H∙∙∙O hydrogen bond. In DAVQUO, a molecular dimer was
formed via R12(5) synthon using weak C–H∙∙∙O interaction wherein C–H
acts as a bifurcated donor. In most of the cases, the molecular stacking
between two naphthofuran moieties contributes toeards the stabilization
of the crystal packing.
Table 1.5: Cambridge Structural Database (CSD) search for the compounds
having naphthofuran moiety.
Refcode Structure Refcode Structure
DAVQUO BAGVAH
[31] [37]

XAZWIG GITLIF
[32] [38]

LERXEN GENPEV
[33] [39]

CUHQEC MEQLOK
[34] [40]

WOBBAR LUZXUA
[35] [41]

WIZZUB COMGEQ
[36] [42]

HEJRAR BERHEL
[36] [43]

- CADFAQ
[44]
12 Dhananjay Dey, Prakash V, Vasu, Shet Prakash M and Deepak Chopra

1.4 CONCLUSIONS
In this study, we have analyzed the crystal structure of synthesized
Naphtho[2,1-b]furan-2-ylmethanol compound in terms of the nature and
energetics of various intermolecular interactions involving in the crystal
packing. The strong O–H∙∙∙O hydrogen bonded chains provides maximum
stabilization alongwith other weak C–H∙∙∙O and C–H∙∙∙π intermolecular
interactions in the packing. PIXEL calculations suggest the presence
of molecular pairs and provide quantitative information about their
contribution towards the crystal packing. Furthermore, QTAIM studies also
give the information about the topological parameters at the bond critical
points. Hirshfeld surface associated fingerprint plots also contribute for
understanding the individual type of atom∙∙∙atom contacts. It is of interest to
study and investigate this molecule further for existence of more polymorphs
with reduced number of molecules (Z’ < 3) in the asymmetric unit.

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