Synthesis and conformational analysis of [3-(6-Chloropyridazin-3-YL)-3,4- Dihydropyridazino-[4,5-b]Quinoxalin-2(1I)-YL](Phenyl)Methanone

Article abstract of DOI:10.1007/s10593-014-1489-0

[3-(6-Chloropyridazin-3-yl)-3,4-dihydropyridazino[4,5-b]quinoxalin-2(1H) -yl](phenyl)methanone has been synthesized and its two stable forms were isolated. For the establishment of their structures, B3LYP geometry and energy and GIAO/B3LYP NMR calculation

Full text of DOI:10.1007/s10593-014-1489-0

Chemistry of Heterocyclic Compounds, Vol. 50, No. 3, June, 2014 (Russian Original Vol. 50, No. 3, March, 2014)
SYNTHESIS AND CONFORMATIONAL ANALYSIS OF
[3-(6-CHLOROPYRIDAZIN-3-YL)-3,4-DIHYDROPYRIDAZINO-
[4,5-b]QUINOXALIN-2(1Н)-YL](PHENYL)METHANONE
1
1
1
2
*
A. I. Karkhut , K. B. Bolibrukh , S. V. Polovkovych , O. Khoumeri ,
O. S. Solovyov3, T. Terme2, P. Vanelle2, and V. P. Novikov1
[3-(6-Chloropyridazin-3-yl)-3,4-dihydropyridazino[4,5-b]quinoxalin-2(1H)-yl](phenyl)methanone has
been synthesized and its two stable forms were isolated. For the establishment of their structures,
B3LYP geometry and energy and GIAO/B3LYP NMR calculations of possible conformers using the
polarizable continuum model were performed. The differences in calculated spectra allow attributing
calculated structures and obtained substances by their 1H and 13C NMR. The conformer ratio correlates
with their calculated Gibbs energies.
1
Keywords: cyclic hydrazine, quinoxaline, conformational analysis, density functional theory, GIAO H
NMR calculation.
Nitrogen-containing heterocycles are widespread and important building blocks of natural molecular
structures and in synthetic chemistry. The quinoxaline ring very often appears as a part of many products with a
wide range of applications.
Substituted quinoxalines are an important class of benzo-fused heterocycles that constitute a scaffold of
a large variety of pharmacologically active compounds that have antibacterial [1, 2], antifungal [3], anticancer
[4], antituberculosis [5] and antimalarial [6] activities. Also, some quinoxalin-2-ones and quinoxaline-2,3-di-
ones exhibit antimicrobial [7] and potential antithrombotic [8] activities. The quinoxaline fragment is the basis
of different insecticides, fungicides, herbicides, and receptor antagonists [9]. Synthetic quinoxalines are
fragments of such antibiotics as echinomycin, levomycin, and actinomycin that are known to be inhibitors of
gram-positive bacteria growth and that show activity against various tumor tissues [10].
_______
*To whom correspondence should be addressed, e-mail: vnovikov@polynet.lviv.ua.
1National University "Lviv Polytechnic", 12 Bandera St., Lviv 79013, Ukraine.
2Aix-Marseille Univ., CNRS, Institut de Chimie Radicalaire ICR, UMR 7273, 27 Bd J. Moulin, Marseille
Cedex 05 13385, France; e-mail: patrice.vanelle@univ-amu.fr.
3Shupyk National Medical Academy of Postgraduate Education, 9 Dorohozhyts'ka St., Kyiv 04112, Ukraine;
e-mail: office@nmapo.edu.ua.
_________________________________________________________________________________________
Published in Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 453-458, 2014. Original article
submitted February 2, 2014.
0009-3122/14/5003-0415©2014 Springer Science+Business Media New York
415

Conformational analysis is an actively developing area of organic chemistry. The ability of a molecule
to change its conformation under the influence of intermolecular interactions is a fundamental property of many
biologically active, especially nitrogen-containing, compounds and is the basis of their functioning [11].
Experimental study of these changes using physicochemical methods faces methodological difficulties related to
the fact that energetically disfavored conformers [12-15], which are not detected in experiment but may be
biologically significant, are neglected. Therefore, in some cases application of efficient, modern methods of
computational chemistry is the only way to get such information. But even when experimental data are
sufficiently complete, these calculations could give very useful information for their interpretation. Density
functional theory (DFT) is widely used for molecule conformation analysis due to its low computational
complexity (compared with post-Hartree–Fock methods) and good results in comparative analysis of a series of
similar molecules. It is one of the most attractive methods for predicting NMR shifts and coupling constants of
organic molecules [16, 17]. In most cases good matching between calculated and obtained data gives correct
information on the spatial structure of the investigated molecules [18, 19]. This method is attractive also because
it allows investigating even unstable conformers that cannot be obtained in pure form.
The investigated compound contains a 6-membered hydrazine ring. The biological activity and
1
conformational studies in solution using H NMR at different temperatures of similar cyclic hydrazines are
reported, e.g., in [20], and at room temperature in the case of the C-unsubstituted saturated ring, equilibrium
between rotamer forms is observed. In our case, rotamer stability would have to be greater due to the higher
cycle rigidity caused by fusion with the aromatic ring and greater obstruction of the benzoyl fragment rotation.
[3-(6-Chloropyridazin-3-yl)-3,4-dihydropyridazino[4,5-b]quinoxalin-2(1H)-yl](phenyl)methanone (1)
was obtained by the interaction of 2,3-bis(bromomethyl)quinoxaline and N'-(6-chloropyridazin-3-yl)benzo-
hydrazide.
O
O
N
N
N
N
K2CO3
HN
HN
Ph
N
Br
Br
N
N
Ph
N
+
DMF, room temp., 5 h
N
N
Cl
Cl
1
As the result of the reaction, a mixture of products was obtained. After separation by liquid
chromatography, two compounds with ratio 3:4 with the same element composition and some differences in 1H
NMR spectra were obtained; therefore, the formation of stable rotamers was assumed.
In order to determine the structures of these rotamers, conformational analysis was performed using the
B3LYP/6-31(d,p) method implemented in the Gaussian 09 package [21]. Relaxed scan of the potential energy
surface in vacuum in regard to dihedral angles of the substituents and nitrogen inversion found two minima,
corresponding to rotation of the benzoyl moiety at ~180° with almost planar structure of the O=C–N system
with a minimum rotation barrier of 50 kJ/mol. The relaxed scan of the pyridazine ring rotation for both positions
of the benzoyl fragment showed two minima, one of which, corresponding to ~180° rotation, is of high energy
and is not detected due to the small exit barrier. The calculated benzoyl fragment rotation barrier is not very
high, but we did not observe the conversion of one form to another under normal conditions – the NMR spectra
showed the presence of discrete compounds. This can be explained by the fact that it is not a transition between
flexible conformations but the rotation of a bulky substituent in a rather rigid cycle.
Zero-point energy and thermal corrections were obtained after B3LYP/6-31+(d,p) optimization of both
forms in vacuum followed by vibrational frequency calculations. Since we were interested in the relative energy
of two similar forms, such a method was recognized as sufficient. The difference in Gibbs energy of these forms
is 8.86 kJ/mol in favor of form I with a more convenient trans configuration of the O=C–N–N fragment.
According to NBO analysis [22], both forms are stabilized by weak hydrogen bonds, forming 5-membered
416

cycles – two for form I (O(2)···H(37)–C(18) 2.27 Å, energy of bonding E(2) 4.98 kJ/mol; N(5)···H(39)–C(19) 2.31
Å, E(2) 7.36 kJ/mol), and one for form II (N(5)···H(39)–C(19) 2.30 Å, E(2) 8.28 kJ/mol).
The obtained two forms were reoptimized by the B3LYP/6-31G(d,p) method using the polarizable
continuum model (PCM) [23] with chloroform as solvent. The optimized geometry is shown in Figure 1.
Fig 1. Molecular structure of rotamers optimized by the B3LYP/6-31G(d,p) method.
1
13
For attributing the calculated structures to the obtained compounds, H and C NMR calculations were
carried out at the B3LYP/6-311G(2d,p)//6-31G(d,p) level of theory using the GIAO method in chloroform
(PCM). Results of the calculations and comparison with experimental spectra obtained in CDCl3 are shown in
Table 1. Spin-spin coupling constants were not calculated because their difference in two forms is not
1
significant. Good concordance between calculations and experiment was achieved in both H and 13C NMR
spectra.
The main difference between both 1H and 13C NMR spectra of the two forms is the quinoxaline system
shielding asymmetry in form II as compared to form I, as is seen in Table 1, which makes possible an easy
conformer attribution based on even one of these spectra. Some distinctions in the shifts of the benzene and
pyridazine proton signals may be caused by their magnetic mutual influence in form I, and the difference
between forms of methylene group signals is caused by the significant difference in hydrazine cycle structural
nonrigidity, which vibrational analysis also indicates.
417

TABLE 1. Calculated and Experimental Spectral Data of Compound 1
Chemical shifts, δ, ppm
Proton
number*
GIAO calculated 1H NMR spectrum
Form I Form II
1H NMR spectrum in CDCl3
Form I
Form II
44
41
42, 43
32, 36
30
31
33–35
39
8.34
8.34
8.12; 8.12
7.63; 8.14
7.60
8.47
8.39
8.18; 8.22
7.34; 8.11
7.40
8.09-7.95 (2H, m)
–
7.80-7.76 (2H, m)
7.67 (2H, d)
7.33 (1H, d)
7.48 (1H, d)
8.19-8.13 (1H, m)
8.06-7.99 (1H, m)
7.83-7.69 (2H, m)
8.04 (2H, d)
7.62 (1H, d)
7.31 (1H, d)
7.56-7.40 (3H, m)
5.65 (2H, s)
7.71
7.06
7.51; 7.85; 7.80 7.61; 7.69; 7.87 7.47-7.35 (3H, m)
6.47
6.86
6.18 (1H, d)
37
38, 40
6.30
4.54; 4.33
5.45
4.86; 4.97
5.88 (1H, br. d)
4.72 (2H, br. ps. t)
–
5.60 (2H, s)
Δδ, ppm, GIAO calculated / found from spectra
Atom number*
Form I
Form II
H-41 – H-44
H-42 – H-43
H-30 – H-31
C-20 – C-21
C-24 – C-25
0.00 / 0.00
0.00 / 0.00
0.11 / 0.15
0.35 / 0.98
0.06 / 0.09
0.12 / 0.08
0.04 / 0.02
0.34 / 0.31
2.48 / 1.25
1.00 / 1.22
_______
*Numbering of protons and atoms as in Figure 1.
The population of the conformers correlates with their calculated Gibbs energies – the more
energetically favorable conformer is the major one.
It should be noted that both obtained compounds must be chiral, but we did not try to isolate the optical
isomers at this stage.
Thus, a novel compound, [3-(6-chloropyridazin-3-yl)-3,4-dihydropyridazino[4,5-b]quinoxalin-2(1H)-
yl](phenyl)methanone, was synthesized by the reaction of 2,3-bis(bromomethyl)quinoxaline and N'-(6-chloro-
pyridazin-3-yl)benzohydrazide, and its two stable rotamers were isolated by liquid chromatography. Their
1
structure was determined using H and 13C NMR spectral data and DFT calculations. Application of the
polarized continuum model significantly improved the agreement between calculated and experimental spectra –
in the case of calculations in vacuum a sufficiently large error in methylene proton shifts was observed. The
results of geometric, spectral, and thermochemical calculations at the DFT level of theory were recognized as
sufficiently adequate.
EXPERIMENTAL
1H and 13C NMR spectra were recorded on a Bruker AC 200 spectrometer (200 and 50 MHz,
respectively) in CDCl3, internal standard TMS. Elemental analyses were performed by the Center of
Microanalyse of Aix-Marseille University. Melting points were determined on a Büchi capillary melting point
apparatus and are uncorrected. Column chromatography was performed on silica gel 60 (Merck, particle size
0.063-0.200 mm, 70-230 mesh ASTM). TLC was performed on 5×10 cm aluminum plates coated with silica gel
60 F254 (Merck), eluent Et2O–CH2Cl2, 1:20. 2,3-Bis(bromomethyl)quinoxaline was synthesized by the method
of [24], N'-(6-chloropyridazin-3-yl)benzohydrazide was synthesized by a method similar to that reported in [25].
418

1
13
Calculated values for the H and C chemical shifts were referenced to the corresponding values for
TMS, calculated at the same level of theory.
[3-(6-Chloropyridazin-3-yl)-3,4-dihydropyridazino[4,5-b]quinoxalin-2(1H)-yl](phenyl)methanone (1).
2,3-Bis(bromomethyl)quinoxaline (0.784 g, 2.5 mmol), N'-(6-chloropyridazin-3-yl)benzohydrazide (0.618 g,
2.5 mmol), K2CO3 (0.685 g, 5.0 mmol), and DMF (25 ml) were added into a two-necked flask equipped with a
nitrogen inlet. The reaction mixture was stirred and maintained at room temperature for 5 h. After this time,
TLC analysis showed that the starting products were totally consumed. The reaction mixture was treated with
ice water and extracted three times with CH2Cl2. The organic phase was washed with H2O and then dried over
Na2SO4. After evaporation, the products were separated and purified by silica gel chromatography (eluent
CH2Cl2) to give rotamers I and II with a total yield of 47%. Also, a mixture of slightly different soluble
polycondensation products was obtained.
Form I. Yield 27%, white precipitate, mp 222-225°C, Rf 0.31. 1H NMR spectrum, δ, ppm (J, Hz): 8.09-
7.95 (2H, m, H-6,9); 7.80-7.76 (2H, m, H-7,8); 7.67 (2H, d, J = 7.2, H-2,6 Ph); 7.48 (1H, d, J = 9.4, H-5
pyridazine); 7.47-7.35 (3H, m, H-3,4,5 Ph); 7.33 (1H, d, J = 9.4, H-4 pyridazine); 6.18 (1H, d, J = 17.1, H(39));
13
5.88 (1H, br. d, J ~ 16, H(37)); 4.72 (2H, br. ps. t, J ~ 17, H(38), H(40)). C NMR spectrum, δ, ppm: 172.3
(CO); 158.4 (C-3 pyridazine); 150.7 (C-6 pyridazine); 147.3 (C-4a); 146.3 (C-10a); 141.2 (C-5a); 141.1 (C-9a);
131.9 (CH); 130.8 (2CH); 130.6 (2CH); 128.9 (CH); 128.6 (2CH); 128.3 (CH); 127.5 (2CH); 116.1 (C-4
pyridazine); 76.2 (4-CH2); 49.9 (1-CH2). Found, %: C 62.54; H 3.79; N 20.72. C21H15ClN6O. Calculated, %:
C 62.61; H 3.75; N 20.86.
1
Form II. Yield 20%, light-brown precipitate, mp 211-213°C, Rf 0.51. H NMR spectrum, δ, ppm
(J, Hz): 8.19-8.13 (1H, m, H-9); 8.06-7.99 (3H, m, H-6, H-2,6 Ph); 7.83-7.69 (2H, m, H-7,8); 7.62 (1H, d,
J = 9.3, H-4 pyridazine); 7.56-7.40 (3H, m, H-3,4,5 Ph); 7.31 (1H, d, J = 9.3, H-5 pyridazine); 5.65 (2H, s) and
13
5.60 (2H, s, 1,4-CH2). C NMR spectrum, δ, ppm: 159.1 (CO); 158.4 (C-3 pyridazine); 150.9 (C-4a); 149.7
(C-10a); 149.3 (C-6 pyridazine); 142.0 (C-5a); 140.8 (C-9a); 131.5 (CH); 131.3 (2CH); 130.1 (2CH); 129.3
(CH); 129.1 (CH); 128.6 (2CH); 127.3 (2CH); 117.3 (C-4 pyridazine); 74.5 (1-CH2); 58.0 (4-CH2). Found, %:
C 62.49; H 3.77; N 20.81. C21H15ClN6O. Calculated, %: C 62.61; H 3.75; N 20.86.
The authors express their deep gratitude to the SSI "Institute for Single Crystals" of National Academy
of Sciences of Ukraine for software and computational facilities.
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