74
P. Panwaria and A. Das
of the cyclic aromatic trimer of the binding energy of about −20 kcal/mol in the
experiment demonstrates that the aromatic trimeric interactions present in the side
chains of proteins contribute significantly to the stability of proteins [174].
3.1.3 Indole…Furan and Indole…Thiophene Complexes
The T-shaped geometry of the aromatic dimers is one of the common structural
motifs observed in biomolecules and materials [178, 179]. Benzene dimer is the most
extensively studied aromatic dimer from both experimental and theoretical point of
view [180–185]. Interestingly, the experimentally observed benzene dimer has a Tshaped geometry [183]. However, both parallel-displaced and T-shaped structures of
the dimer are almost isoenergetic according to the CCSD(T)/CBS level calculation
[178, 186]. It is further intriguing to note that the observed benzene dimer is not
perfectly T-shaped, but the planes of the two benzene moieties are tilted with respect
to each other to include secondary π-π interaction [184, 185]. It is also found that
the benzene units in the crystal structure are oriented in a similar tilted T-shaped
or herringbone geometry. Thus, it is again evident that the subtle interplay between
various non-covalent interactions is the key to the optimum structure of any molecular
system. The tilted T-shaped structure of the benzene dimer is an effect of the fine
balance between the C-H…π hydrogen bonding and π…π interactions [184, 185].
Aromatic dimers comprising heterocyclic compounds are of special importance
due to their prevalence in a wide range of molecular assemblies. The simplest Nheterocyclic compound, which replaces benzene, is pyridine. It has been reported
from theoretical calculations that the preferred structure of the pyridine dimer and
pyridine…benzene complex is parallel-displaced π-stacked [187]. The substitution
of the nitrogen atom in the pyridine ring significantly reduces the π-electron density
in the center of the ring. Hence, pyridine favors π-stacking configuration of the
dimer instead of the T-shaped geometry through π-hydrogen bonding interaction.
Thus, Sherrill and co-workers concluded that aromatic heterocycles are very poor
π-hydrogen bond acceptors [26, 185, 187]. Das and co-workers have investigated
the effect of heteroatoms (O, S) other than nitrogen present in the aromatic ring on
the strength of the π-hydrogen bonding interaction [144, 188].
Figure 8A shows mass-selected electronic spectra of the indole monomer,
indole…furan, and indole…(furan) 2 complexes measured using 1C-R2PI spectroscopy by Das and co-workers[144]. The spectra of the dimer and trimer show a
broad background, which is mostly due to the fragmentation of higher-order clusters
of indole and furan into the mass channels of smaller clusters. The IR spectrum of the
indole…furan dimer measured using RIDIR spectroscopy is presented in Fig. 8Bb.
Theoretical IR spectra of a few possible low energy conformers of indole…furan
dimer designated as T
/ (N-H…π), HB (N-H…O), Syn-PD
/ , Anti-PD are provided
in Fig. 8B. The T
/ conformer, which is the global minimum, has a tilted T-shaped
structure held primarily by N-H…π hydrogen bonding interaction. The HB is the
N-H…O hydrogen-bonded structure with V-shaped geometry, which gets additional
P. Panwaria and A. Das
of the cyclic aromatic trimer of the binding energy of about −20 kcal/mol in the
experiment demonstrates that the aromatic trimeric interactions present in the side
chains of proteins contribute significantly to the stability of proteins [174].
3.1.3 Indole…Furan and Indole…Thiophene Complexes
The T-shaped geometry of the aromatic dimers is one of the common structural
motifs observed in biomolecules and materials [178, 179]. Benzene dimer is the most
extensively studied aromatic dimer from both experimental and theoretical point of
view [180–185]. Interestingly, the experimentally observed benzene dimer has a Tshaped geometry [183]. However, both parallel-displaced and T-shaped structures of
the dimer are almost isoenergetic according to the CCSD(T)/CBS level calculation
[178, 186]. It is further intriguing to note that the observed benzene dimer is not
perfectly T-shaped, but the planes of the two benzene moieties are tilted with respect
to each other to include secondary π-π interaction [184, 185]. It is also found that
the benzene units in the crystal structure are oriented in a similar tilted T-shaped
or herringbone geometry. Thus, it is again evident that the subtle interplay between
various non-covalent interactions is the key to the optimum structure of any molecular
system. The tilted T-shaped structure of the benzene dimer is an effect of the fine
balance between the C-H…π hydrogen bonding and π…π interactions [184, 185].
Aromatic dimers comprising heterocyclic compounds are of special importance
due to their prevalence in a wide range of molecular assemblies. The simplest Nheterocyclic compound, which replaces benzene, is pyridine. It has been reported
from theoretical calculations that the preferred structure of the pyridine dimer and
pyridine…benzene complex is parallel-displaced π-stacked [187]. The substitution
of the nitrogen atom in the pyridine ring significantly reduces the π-electron density
in the center of the ring. Hence, pyridine favors π-stacking configuration of the
dimer instead of the T-shaped geometry through π-hydrogen bonding interaction.
Thus, Sherrill and co-workers concluded that aromatic heterocycles are very poor
π-hydrogen bond acceptors [26, 185, 187]. Das and co-workers have investigated
the effect of heteroatoms (O, S) other than nitrogen present in the aromatic ring on
the strength of the π-hydrogen bonding interaction [144, 188].
Figure 8A shows mass-selected electronic spectra of the indole monomer,
indole…furan, and indole…(furan) 2 complexes measured using 1C-R2PI spectroscopy by Das and co-workers[144]. The spectra of the dimer and trimer show a
broad background, which is mostly due to the fragmentation of higher-order clusters
of indole and furan into the mass channels of smaller clusters. The IR spectrum of the
indole…furan dimer measured using RIDIR spectroscopy is presented in Fig. 8Bb.
Theoretical IR spectra of a few possible low energy conformers of indole…furan
dimer designated as T
/ (N-H…π), HB (N-H…O), Syn-PD
/ , Anti-PD are provided
in Fig. 8B. The T
/ conformer, which is the global minimum, has a tilted T-shaped
structure held primarily by N-H…π hydrogen bonding interaction. The HB is the
N-H…O hydrogen-bonded structure with V-shaped geometry, which gets additional