Synthesis, Crystal Structure and Dft Studies of 8-chloro-3-((3-chlorobenzyl)thio)-[1,2,4]triazolo[4,3-a]pyridine

8-chloro-3-((3-chlorobenzyl)thio)-[1,2,4]triazolo[4,3-a]pyridine was synthesized and recrystallized from EtOH. The compound was characterized by 1H NMR, 13C NMR, FTIR, MS, elemental analysis and X-ray diffraction. The compound was crystallized in the monoclinic space group P2(1)/c with a = 8.1992(5), b = 21.7731(12), c = 7.8454(6) A, α = 90, β = 108.421(7), γ = 90°, V = 1328.81 (15)A3, Z = 4 and R = 0.0351. Theoretical calculation of the title compound was carried out with B3LYP/6-31G. The full geometry optimization was carried out by using the 6-31G basis set. The frontier orbital energy and atomic net charges were discussed. The experimental results of the compound have been compared with theoretical results and it was found that the experimental data shows good agreement with the calculated values.


Synthesis and Spectra Analysis
The synthetic procedure for the title compound is shown in Scheme 1.The starting material 3-chloro-2-hydrazinylpyridine was synthesized according to the method in our previous papers [14,15].The key intermediate 8-chloro- [1,2,4]triazolo [4,3-a]pyridine-3(2H)-thione was obtained according to the method which was reported by Chen [25].3-Chloro-2-hydrazinylpyridine was used to react with thiourea under microwave irradiation to afford the key intermediate.The target compound 2 was obtained by the reaction between intermediate 1 and 1-chloro-3-(chloromethyl)benzene under microwave irradiation at the alkaline condition.The thioamide (-NH-C(=S)) structure showed in the key intermeadiate can exist either as the thione, or thiol tautomeric form.The 1 H NMR of intermediate and the final compound indicated that the substitution of 8-chloro- [1,2,4]triazolo [4,3-a]pyridin-3(2H)-thione occurred at the sulfur atom instead of the nitrogen atom, as expected for thiol.With regard to the mass spectra, the title compound showed an M-H signal.

Frontier Orbital Energy Analysis and Molecular Total Energies
Molecular total energy and frontier orbital energy levels are listed in Table 1.The energy gap between HOMO and LUMO was calculated by B3LYP.According to the frontier molecular orbital theory, HOMO and LUMO are the most important factors that affect the bioactivity.HOMO has the priority to provide electrons, while LUMO can accept electrons first.Thus, the study on the frontier orbital energy can provide useful information about the biological mechanism.As shown in Figure 1, the geometry of title compound was optimized by using DFT method.The LUMO of the title compound is mainly located on the 1,2,4-triazolo[4,3-a]pyridine ring.However, the HOMO of the title compound is located on the1,2,4-triazolo[4,3-a]pyridine ring, benzene ring and thioether group.Therefore, the electrons transit from the benzene ring to the 1,2,4-triazolo[4,3-a]pyridine ring via thioether bridge, while the energy gap between the HOMO and LUMO is 0.17985 Hartree.

Crystal Structure
The selected bond lengths, bond angles and torsion angles are shown in Table 2.The molecular structure of the title compound is shown in Figure 2. The title compound consists of pyridine ring, 1,2,4-triazole ring and benzene ring according to X-ray single-crystal structure determination.Generally, the average bond lengths and bond angles of these rings are in normal ranges [26][27][28][29].In 1,2,4-triazole and pyridine ring system, the C5-N1, C1-N1 and C6-N3 bonds are significantly longer than C=N bond (1.28 Å) [30], which indicates significant electron delocalization in the fused ring system.The torsion angle of C6-S1-C7-C8 is 176.69(18)°, which indicates that the two rings are co-planar.The experimental values correlate with the theoretical values.As it shown in Figure 2, the 1,2,4-triazolo[4,3-a]pyridine ring is nearly parallel with benzene ring in a quite small dihedral angle (θ) of 14.7°.The 1,2,4-triazolo[4,3-a]pyridine ring (C1, C2, C3, C4, C5, N2, N3, C6, N1) and benzene ring (C8, C9, C10, C11, C12, C13) are fairly co-planar according to plane equation −0.586x + 8.623y + 6.991z = 9.2949 and −0.617x + 3.270y + 7.524z = 5.8229, and the largest deviation from the least squares plane are 0.0067 nm and 0.0046 nm.The title compound has an extensive network of hydrogen bonds.The parameters of intramolecular and intermolecular bonds are given in Table 3.They are linked together by C-H•••N hydrogen bonds (Figure 3).The hydrogen bonds strengthen the integration of the 3D networks.Taking DFT as an example again (Figure 4), all the nitrogen atoms are the most negatively charged ones, which can easily interact with the positively charged part of the receptor.Therefore, we supposed that this compound can combine with the amino-acid residue on its surface by interacting with the 1,2,4-triazolo[4,3-a]pyridine ring, which may be responsible for the bioactivity.

Instruments
Melting points were determined by using an X-4 apparatus and were uncorrected. 1H NMR and 13 C NMR spectra were measured on a Bruker AV-400 or ANANCE III (500 M) instrument by using TMS as an internal standard and CDCl3 or DMSO-d6 as the solvent.FT-IR was determined on a Nicolet AVATAR instrument.Elemental analyses were performed on a Vario EL elemental analyzer.Crystallographic data of the compound was collected on a Rigaku Saturn diffractometer.All the reagents are of analytical grade or freshly prepared before using.

Therotical Calculations
According to the above crystal structure, a crystal unit was selected as the initial structure, while DFT-B3LYP/6-31G methods in Gaussian 03 package [31] were used to optimize the structure of the title compound.Vibration analysis showed that the optimized structures were in accordance with the minimum points on the potential energy surfaces, which means no virtual frequencies.It proved that the optimized structures were stable.All the convergent precisions were the system default values, and all the calculations were carried out on a DELL computer.

Figure 2 .
Figure 2. The molecular structure of the title compound.

Figure 3 .
Figure 3.The pack of title compound.

Table 1 .
Total energy and frontier orbital energy.