4
Y. Liu et al. / Journal of Molecular Structure 1208 (2020) 127869
0
0
0
ꢁ
ꢁ
C(6 ) and C(6)-C(5)-C(5 )-C(4 ) (0.1(4) and ꢀ0.1(4) respectively)
0
are different from the reported torsion angles of 2,2 -bipyridine
N(1)-C(5)-C(6)-N(2) and C(4)-C(5)-C(6)-C(7)(26.13 and 33.39
ꢁ
ꢁ
respectively) [21].
Hydrogen bonding plays an important role in the stability of the
crystal structure. The molecules of 1 are linked by two intermo-
0
lecular C(4)eH(4) … N(1 ) (2.527 Å), C(6)eH(6) … N(1) (2.539 Å)
hydrogen bondings, as shown in Table 3. It is worth noting that the
crystal packing is further stabilized by weak
p-p interactions. The
perpendicular distance between two pyridine rings of different
molecules is 3.887 Å, as shown in Fig. 2. In general, the crystal
structure of 1 shows that the intermolecular packing is stabilized by
hydrogen bondings,
.3. Conformational determination
The conformation of a molecule seriously influences its physical
p-p interactions, as shown in Fig. 2.
3
and chemical properties. Therefore, reliable conformational anal-
ysis plays a key role in the understanding of structure. Initial
conformational searching of the title compound 1 was performed
by Spartan 08 program [22] with MMFF [23,24] molecular me-
chanics force field. Then, geometry optimizations and frequency
calculation of all the possible conformers were performed by using
DFT/B3LYP/6-311G** in Gaussian 09 package [15,25]. Based on the
relative free energies, the percentage of each conformer in the
equilibrium mixture at room temperature (T ¼ 295.15 K) can be
predicted. The Gibbs free energy (G), relative Gibbs free energy
Fig. 2. Crystal structure stacking diagram and hydrogen bonding diagram of com-
pound 1.
ꢀ1
(
D
G ¼ expð ꢀ Gi =RTÞ, gas constant R ¼ 8.314 J (mol K) ) and
Boltzmann distribution (Boltzmann weighting factor Pi ¼
expðꢀGi=RTÞ
ꢂ 100%) for different conformers of compound 1 are
S
f
expðꢀGj=RTÞ
Table 4
shown in Table 4.
The eight conformers of compound 1 are given in Fig. 3. The
difference between the eight conformers is mainly caused by the
a
Gibbs free energy (G), relative Gibbs free energy (
D
G) , and Boltzmann weighting
factor (Pi %)b of the conformers of compound 1.
Conformer
G (kcal molꢀ1)
△G (kcal mol
ꢀ1
)
Pi %
rotation of the C(5)-C(5 ) bond connecting the two pyridine rings.
0
One of the pyridine rings was immobilized, and the other pyridine
1
1
1
1
1
1
1
1
e1
e2
e3
e4
e5
e6
e7
e8
ꢀ734073.6589
ꢀ734073.6538
ꢀ734073.5089
ꢀ734073.5039
ꢀ734071.8146
ꢀ734071.8058
ꢀ734071.6565
ꢀ734071.4795
0
27.20
26.97
21.06
20.88
1.17
1.15
0.89
0.66
ꢁ
0
ring was rotated 360 with the C(5)-C(5 ) bond as a spin bond while
scanning the potential energy surface of the molecule, as shown in
Fig. 4. Compound 1 was detected to have four relatively stable
conformers 1e1 (27.20%), 1e2 (26.97%), 1e3 (21.06%), 1e4 (20.88%)
and four relatively unstable conformers 1e5 (11.70%), 1e6 (11.52%),
1e7 (0.89%), 1e8 (0.66%). The energy barriers for the transitions
from stable conformers 1e1, 1e2, 1e3, 1e4 to corresponding un-
stable conformers 1e6, 1e7, 1e5, 1e8 are 2.0024, 1.6893, 2.0294,
0.0050
0.1500
0.1550
1.8442
1.8530
2.0024
2.1793
a
Related to the most stable conformer.
Boltzmann weighting factor (Pi %) based on △G.
b
1.8480 kcal/mol, respectively.
The crystal structure of 1 was compared to the DFT optimized
structure. The conformational isomers 1e7 calculated by DFT are
most similar to the crystal conformation obtained by X-ray
diffraction, but there are also some differences. The main reason for
NMR and MS spectroscopies, as shown in Supplementary Material
Figs. S1eS5.
the conjecture is the result of the inter-molecular
p
-
p
bond action,
3
.2. Crystallographic analysis
0
as shown in Fig. 1. For the selected torsion angles C(4)-C(5)-C(5 )-
0 0 0 0 0
In order to further investigate the structural characteristics of
C(4 ), C(4)-C(5)-C(5 )-C(6 ), C(6)-C(5)-C(5 )-C(4 ) and C(6)-C(5)-
0
0
ꢁ
ꢁ
ꢁ
the synthesized compound, the title compound 1 was subjected to
X-ray diffraction crystal structure analysis. The measured values
reveal that 1 possess monoclinic crystal system having P2
C(5 )-C(6 ), the values of crystal structure 1 are ꢀ180.0 , 0.1 , ꢀ0.1
ꢁ
and ꢀ180.0 , respectively, which are highly similar to the values of
ꢁ
ꢁ
ꢁ
ꢁ
1
/c space
conformer 1e7 with ꢀ179.82 , 0.13 , 0.23 and ꢀ179.82 . Some
geometric parameters of the experimental values of crystal 1 and
the calculated values of conformer 1e7 are listed in Table 2. As
expected, most of the calculated geometry parameters of the
compound 1 are close to the X-ray data.
group [unit cell dimensions: a ¼ 10.1672(14) Å, b ¼ 4.6017(7) Å,
ꢁ
3
c ¼ 12.1004(18) Å,
b
¼ 94.343 , V ¼ 564.51 Å , Z ¼ 2,
ꢀ1
m
¼ 0.174 mm ]. ORTEP diagram of the crystal structure of 1 is
shown in Fig. 1. The main crystallographic data are summarized in
Table 1.
All bond lengths, bond angles and torsion angles in the crystal
structure are within the normal range, as shown in Table 2. In
compound 1, the CeC bond length between the two pyridine rings
3.4. Molecular electrostatic potential (MEP)
In order to understand the information of the intermolecular
interaction region of the title compound 1, the molecular electro-
static potential of the conformer 1e7 (same as the crystal structure)
0
is 1.489(5) Å, which is similar to the CeC bond length of the 4,4 -
0
bipyridine ligand, 1.48 Å [20]. The torsion angle C(4)-C(5)-C(5 )-