Synthesis, characterization and theoretical studies of 5-(benzylthio)-1- cylopentyl-1H-tetrazole

Article abstract of DOI:10.1016/j.saa.2014.07.071

In this study, 5-(benzylthio)-1-cylopentyl-1H-tetrazole (5B1C1HT) have been synthesized. Boiling points of the obtained compound have been determined and it has been characterized by FT-IR, ¹H NMR, ¹³C-APT and LC-MS spectroscopy techniques. The FT-IR, ¹H NMR and ¹³C-APT spectral measurements of the 5B1C1HT compound and complete assignment of the vibrational bands observed in spectra has been discussed. The spectra were interpreted with the aid of normal coordinate analysis following full structure optimization and force field calculations based on Density Functional Theory (DFT) at 6-311++G^**, cc-pVDZ and cc-pVTZ basis sets. The optimized geometry with 6-311++G ^** basis sets were used to determine the total energy distribution, harmonic vibrational frequencies, IR intensities.

Full text of DOI:10.1016/j.saa.2014.07.071

Accepted Manuscript
Synthesis, Characterization and Theoretical Studies of 5-(benzylthio)-1-cylo-
pentyl-1H-tetrazole
S. Saglam, A. Disli, Y. Erdogdu, M.K. Marchewka, N. Kanagathara, B. Bay,
M.T. Güllüoğlu
PII:
S1386-1425(14)01152-4
http://dx.doi.org/10.1016/j.saa.2014.07.071
SAA 12491
DOI:
Reference:
Spectrochimica Acta Part A: Molecular and Biomo-
lecular Spectroscopy
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Revised Date:
Accepted Date:
5 December 2013
11 July 2014
28 July 2014
Please cite this article as: S. Saglam, A. Disli, Y. Erdogdu, M.K. Marchewka, N. Kanagathara, B. Bay, M.T.
Güllüoğlu, Synthesis, Characterization and Theoretical Studies of 5-(benzylthio)-1-cylopentyl-1H-tetrazole,
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy (2014), doi: http://dx.doi.org/10.1016/j.saa.
2014.07.071
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Synthesis, Characterization and Theoretical Studies of 5-(benzylthio)-1-
cylopentyl-1H-tetrazole
S. Saglam1, A. Disli2, Y. Erdogdu3, M.K. Marchewka4,*, N.Kanagathara5, B. Bay2, M.T.
Güllüoğlu3,
1Department of Physics, Gazi University, Besevler, 06500, Ankara, Turkey
2Department of Chemistry, Gazi University, Besevler, 06500, Ankara, Turkey
3Department of Physics, Ahi Evran University, 40040, Kirsehir, Turkey
4Institute of Low Temperature and Structure Research,Polish Academy of Sciences,
50-950, Wroclaw 2, P.O. Box 937, Poland
5Department of Physics, Vel Tech Dr. RR & Dr. SR Technical University, Chennai-62, India
Corresponding author E-mail id: marchewka.mariusz578@gmail.com
ABSTRACT
In this study, 5-(Benzylthio)-1-cylopentyl-1H-tetrazole (5B1C1HT) have been synthesized.
Boiling points of the obtained compound have been determined and it has been characterized
by FT-IR, 1H-NMR, 13C-APT and LC-MS spectroscopy techniques. The FT-IR, 1H-NMR and
13C-APT spectral measurements of the 5B1C1HT compound and complete assignment of the
vibrational bands observed in spectra has been discussed. The spectra were interpreted with
the aid of normal coordinate analysis following full structure optimization and force field
calculations based on density functional theory (DFT) at 6-311++G**, cc-pVDZ and cc-
pVTZ basis sets. The optimized geometry with 6-311++G** basis sets were used to determine
the total energy distribution, harmonic vibrational frequencies, IR intensities.
Keywords: Alkyl tetrazole, Thiotetrazole, Sulphur, Alkylation, DFT, Conformational analysis
1

1. INTRODUCTION
During the last few years tetrazoles have a great attention by the researchers and so many new
synthetic methods are getting progress day by day. Due to the carboxylic acids bioisoster,
tetrazoles take part in many pharmacological agents. Although having close acidity, tetrazoles
are more liphofilic than corresponding carboxylate and ionized at physiological pH [1].
Because of all these properties tetrazoles have a wide range of applications and they have
various biological activities. In a study, it has been show that tetrazoles have effective both on
the microorganisms and DNA. In that study, either observing DNA damages or being
important changes in DNA conformation have been showed [2].
As well as synthetic organic chemistry, tetrazoles are used in polimer science,
nanotechnology, biosensor, molecular identification [3-6]. As we mentioned above tetrazoles
are high biological agent such as antibacterial, antifungal, antienflamatuar, antineoplastic,
antiviral, antitumor agents [7]. Just a couple of decades ago especially thiotetrazoles and
derivative compounds begin to used in cancer and AIDS treatment [8,9]. Furthermore, these
compounds are used in synthesis of HIV-proteaz inhibitor for AIDS treatment and angiotensin
II receptor blockers for hypertansion treatment [10, 11]. Tetrazole derivative compounds also
effect the central nervous system [12, 13]. Therefore, the researchers synthesized central
nervous system stimulating compounds such as Cardiazole.
In this work, we synthesized a new tetrazole derivative: 5-(benzylthio)-1-cylopentyl-1H-
tetrazole, this compound is characterized by FT-IR, 1H-NMR, 13C-APT and LC-MS
spectroscopy techniques. In addition, we were performed the conformational analysis,
structural and vibrational properties of the 5B1C1HT molecule by means of DFT calculations
using the B3LYP functional with 6-311++G**, cc-pVDZ and cc-pVTZ basis sets. In the
2

conformational analysis, the minimum energy conformational geometries were performed
with the help of potential energy surface scan. The complete assignment of the bands
observed in the vibrational spectra were performed taking into account the natural internal
coordinates for the more stable structures by using the harmonic force field with the Pulay´s
Scaled Quantum Mechanics Force Field (SQMFF) methodology [14].
1. EXPERIMENTAL
All chemicals and solvents used were reagent grade (Merck or Aldrich or Sigma) and were
used without additional purification. Reactions were monitored by thin layer chromatography
(TLC) on precoated silica gel 60 F254 plates from Merck and plates were visualized by UV
light. Column chromatography was performed using Merck Silica Gel 60 F254 (particle size:
0.63–0.200 mm; 70–230 mesh ASTM). Melting points were determined with an
Electrothermal 9100 melting point apparatus and were uncorrected. IR spectrum (4000–400
cm-1) was recorded using KBr disk on a Mattson 1000 FT-IR spectrometer and reported in
cm-1 units. Fig.1. shows the FT-IR spectrum of 5B1C1HT.
• Position of Figure 1
1H and 13C-NMR spectra were recorded on a Bruker spectrometer (300 MHz for 1H-NMR and
75 MHz for 13C-NMR). Chemical shifts were reported in δ ppm units with respect to
tetramethylsilane (TMS) as an internal reference in DMSO-d6 or CDCl3 and coupling
constants (J) were reported in Hz units. Mass spectra measurements were recorded on a
Waters ACQUITY ultra performance liquid chromatography combined with Micromass LCT
Premier TM XE TOF–MS. (see Fig.2SM and 3SM in supplementary material)
• Position of Figure 2SM
• Position of Figure 3SM
3

1.1.
Synthesis of benzyl thiocyanate
Initially, benzyl bromide (1.26 g, 0.01mol) and potassium thiocyanate (1.16 g, 0.012 mol) in
methanol (25 mL) were stirred at reflux for 2h. Obtained KBr salt was removed by filtration
at the end of the reaction and methanol was evaporated. Then (50 mL) distilled water added to
the remaining slightly yellow colored benzyl thiocyanate for removing excess potassium
thiocyanate. After the filtration, benzyl thiocyanate crystallized from ethanol and dried in the
O
vacuum. Yield 85 % ,mp 39-41 C , IR (KBr) υ: 3034 (aromatic -C=C–H); 2991 (aliphatic –
1
C–H); 2153 (–SCN); 1493,1486 (aromatic –C=C). H NMR (300 MHz, CDCl3) δ: 7.40 (s,
5H, Ar–H), 4.20 (s, 2H –S–CH2)
1.2.
Synthesis of 5-(benzylthio)-1H-tetrazole
Suspension of triethylammonium chloride (0.69 g, 0.005 mol) in toluene (50 mL) was
prepared in a 250-mL two-necked flask equipped with a reflux condenser. Then, sodium azide
(0.33 g, 0.005mol) was slowly added portion-wise with stirring. A solution of benzyl
thiocyanate (3) (0.745 g, 0.005 mol) in toluene (50 mL) was slowly added, stirred for 10 min,
and then heated to gentle reflux for 18 h. After cooling the reaction mixture, distilled water
(20 mL) was added and the aqueous layer was separated. Then the toluene layer was washed
with water (3 × 5 mL) and aqueous extracts were collected (white coloured). Then the
aqueous layer was cooled to room temperature and acidified to pH 3-4 using dilute HCl while
stirring for 10 min. The formed solid precipitate was collected and washed with water and
crystallized from ethanol and dried in the vacuum. Yield 85 % , mp 136-138 oC , IR (KBr) υ:
3453 (–N–H), 3027 (aromatic –C=C–H), 2899 (aliphatic –C–H), 1635, 1543 (–C=C), 1493 (–
1
N=N), 1457 (aromatic –C=C), H NMR (300 MHz, CDCl3) δ: 13.38-11.49 (s, 1H –N–H),
7.45-7.30 (m, 5H Ar–H), 4.52 (s, 1H –S–CH2)
4

1.3.Synthesis of 5-(benzylthio)-1-cylopentyl-1H-tetrazole
A mixture of (5-benzylthio)-1H-tetrazole (1.53 g, 0.008 mol), K2CO3 (2.21 g, 0.016 mol) and
cyclopentyl bromide (1.78 g, 0.012 mol) in DMF ( 25 mL ) were stirred at 100 oC for 3 hours.
The reactionwas monitored by TLC. Reaction mixture was cooled to room temperature and
work-up was made with ethyl acetate and iced-water for removing the DMF and organic was
collected. After evaporation of the solvent the reaction mixture was separated by column
chromatography, using a mixture of hexane-ethyl acetate (9:1) as the eluent. Yield 48 % , bp
o
215 C ,HR-MS for C13H17N4S+ ([M-H]+) Calc: 261.1174; Found: 261.1172. Scheme 1 is
given in the supplementary material.
•
Position of Scheme 1
2. COMPUTATIONAL DETAILS
The Density Functional Theory calculations were carried out by means of Gaussian 09 [15]
software; invoking gradient geometry optimization [16. 17]. To find the stable conformers,
the potential energy surface of 5B1C1HT molecule was scanned with MMFF simulations.
Conformational analysis calculation carried out with the Spartan 10 program [18] and then all
conformational geometry optimized by using B3LYP/6-31G(d,p) basis set in the Gaussian 09
program package. We are determined the most stable geometry of the 5B1C1HT molecule.
The optimized geometry of the most stable conformer was used in the Nuclear Magnetic
Rezonans, Vibrational frequency calculations and other structural and electronic properties at
the DFT level. In the present work, the DFT method B3LYP with 6-311++G(d,p), cc-pVDZ
and cc-pVTZ basis sets were used for the computation of all molecular properties of
optimized structures. The vibrational modes were assigned on the basis of TED analysis for
B3LYP/6-311++G(d,p) using SQM program [19].
5

NMR analysis has been performed by using Gauge Independent Atomic Orbital (GIAO)
method. Theoretical chemical shifts are compared with experimental results for the
1
identification and characterization of 5B1C1HT molecule. The H and 13C NMR chemical
shifts calculations of the most stable conformer of the 5B1C1HT molecule were made by
using B3LYP functional with 6-311++G(d,p) basis set. The calculations were performed in
DMSO solution using IEF-PCM model. Theoretical chemical shifts are agreement with
experimental ones in DMSO solution [20-24].
3. RESULTS AND DISCUSSION
3.1.
Conformational analysis
To find stable conformers, a detailed conformational analysis was carried out for the
5B1C1HT molecule. Rotating 10 each degree intervals around the free rotation bonds,
potential energy surface of the 5B1C1HT molecule was scanned by MMFF simulations. And
then full geometry optimizations of these structures were performed by B3LYP/6-31G(d,p)
method. The ground state conformer of the 5B1C1HTmolecule have been optimized at
B3LYP levels at 6-311G++(d,p) level are shown in Fig. 4SM. The optimized energies and
zero point corrected optimized energies of conformers are given in the Table 1. The optimized
energy of other conformers is higher than those of conformer 1. As a result, the energy
obtained for conformer 1 of the 5B1C1HTmolecule was found to be the global minimum.
• Position of Figure 4SM
• Position of Table 1
3.2.
Molecular structure
The ground state conformer of the 5B1C1HTcompound belongs to C1 point group symmetry.
The optimized molecular geometry of the 5B1C1HTcompound is shown in Fig.4SM.
Optimized bond lengths, bond angles and dihedral angles of the molecule are predicted using
B3LYP6-311++G(d,p), cc-pVDZ and cc-pVTZ levels and it is mentioned in Table 2.
6

• Position of Table 2
3.3.
Vibrational spectral analysis
Table 3 lists the results of three DFT calculations of the normal modes of vibration that were
performed using the Gaussian 09 [15] program package. These results were obtained using
the B3LYP functional with the 6-311++G(d,p), cc-pVDZ and cc-pVTZ basis set. The
5B1C1HT molecule has 34 atoms, which possess 96 normal modes of vibrations. All
vibrations are active in infrared spectra. The recorded FT-IR spectral data, calculated
wavenumbers and IR intensities are given in Table 3. The total energy distributions for all
fundamental vibrations were calculated using scaled quantum mechanics (SQM) method at
B3LYP/ 6-311++G(d,p) level. The assignments were presented in terms of the percent TED
of the internal motions in the modes. When relating the experimental frequencies with the
calculated ones, we also considered the calculated IR intensities (Fig. 1).
• Position of Table 3
CH2/3 stretching vibrations appear between 2900 and 3000 cm-1 as expected [24-27]. As seen
in Table 3, there are 16 Carbon–Hydrogen stretching vibrations where the five stretches of the
benzyl group are predicted to range from a low value of 3012 cm-1 to a high of 3052 cm-1, the
nine stretching modes of the cyclopentyl group in the range from 2886 to 2973 cm-1, and the
two CH stretch vibration for the carbon attached to the sulfur atom predicted at 2939 cm-1 and
3002 cm-1. According to the FT-Infrared spectral data, 3063 and 3086 cm-1peaks are assigned
to the CH stretching vibrations of the Benzyl group in the FT-IR spectra. Symmetric CH
stretching vibrations of the cyclopentyl group are monitored at 2873 and 2959 cm-1 in the
Infrared spectra. 3028 cm-1 is determined as the asymmetric stretching vibrations of the
7

cyclopentyl group in the FT-IR spectra.Also in the IR spectra of the compounds, the aromatic
-C=C-H stretching bands are larger than those of aliphatic -C-H stretching bands.
In the 2500 cm-1 region, we were measured at 2146 cm-1 in the FT-IR spectra of benzyl
thiocyanide. This peak belongs to the –CN group. In the next step synthesis, we were obtained
the 5-(benzylthio)-1H-tetrazole compound. In this compound, this sharp peak was
disappeared as we hoped when the aromatic tetrazole ring was obtained. This was a crucial
proof of tetrazole formation in our synthesis.
In the fingerprint region, the biggest peak is the CC stretching vibrations. The stretching
vibrations of Carbon-Carbon bond in the benzyl group are measured at 1173 cm-1, 1585 cm-1
and 1600 cm-1 in the Infrared spectra. These vibrations are predicted at 1185 cm-1, 1569 cm-1
and 1588 cm-1 in the DFT calculations (6-311+G(d,p) basis sets). These modes are mixing
mode with CCH in plane bending modes. Pure CC stretching mode is calculated at 1296 cm-1
(6-311++G(d,p) basis set). This vibration is not experimentally observed in the FT-IR spectra.
In the fingerprint region, the most intensities peaks are experimentally appeared at 697 cm-1
and 1369 cm-1 in the FT-IR spectra. We are assigned νNC stretching τCCCH as very strong peaks.
Similarly, these vibrations are calculated at 686 cm-1 and 1372 cm-1 in the DFT calculations.
Infrared intensities of those are 92.89 (for 686 cm-1) and 100 (for 1369 cm-1) by using
theoretical methods. In the present work, relative absorption intensities normalised with
highest peak absorbance equal to 100.
In general, due to the band is of variable intensity, the assignment of band due to the Carbon-
Sulfur stretching vibration in different compounds is difficult in the FT-IR spectra. These
peaks may be found over the wide region 1035-245 cm-1 [28]. There are four C-S stretches for
8

title compound. The normal modes no’s are ν17, ν18, ν19 and ν24. The ν24 mode is pure C-S
stretching mode. 24th mode’s is predicted at 630 cm-1 for B3LYP/6-311++G(d,p) level of
theory. Other stretching modes are mixing with bending and stretching vibrations. CS
vibrations with mixing other bending and stretching are determined in 438-468 cm-1 region in
the DFT (6-311++G(d,p) basis sets) calculation. We are not measured these peaks in the
FT-IR spectra.
Characteristic vibration peaks are generally observed in Infrared spectra at 1640-1335 and
1200-900 cm-1 for free Tetrazole groups [28, 29]. Due to the interaction of С = С, С = N, and
N = N vibrations in the compound, the assignment of vibrations to the individual bonds could
not be determined. The absorption bands at 1640-1335 cm-1 are characteristic of stretching
and at 1200-900 cm-1 of skeletal vibrations of a cycle. In the present work, 1369 cm-1 peak is
belongs to the -C=N double bonds stretching of this group in the FT-IR spectra. The skeletal
vibration of the Tetrazole group is appeared at 1072 cm-1 in the FT-IR spectra. This peak is
predicted at 1066 cm-1 by using the DFT computations.
The obtained TED results show that the NN stretching vibrations are calculated at 1284, 1275,
1032 and 978 cm-1 by DFT computations. According to the TED results, 1032 and 1284 pure
NN stretching modes. Other of them are mixing modes with tetrazole group vibrations. In the
experimental data, only one mode is monitored in the FT-IR spectra. This peak is determined
at 1296 cm-1. Other modes is not determined in the experimental spectra.
The CH2 scissoring vibrations are measured at 1453 cm-1 in the Infrared spectra. These
vibrations are predicted at 1438-1464 cm-1 region. Other CH2 scissoring vibration is obtained
at 1400 cm-1 in the FT-IR spectra. This peak possess to the scissoring vibrations of the S-CH2
9

group. The predicted vibrational frequencies have been compared with the experimental FT-
IR spectra. The observed and the calculated frequencies are found to be in good agreement.
3.4.
NMR spectra
1
The measured 13C and H NMR spectra are shown in Figs. 2SM-3SM. The computed and
1
observed 13C NMR and H NMR chemical shift values are tabulated in Table 4. The
calculated values of 13C and 1H chemical shifts by B3LYP/6- 311++G(d, p) level of theory in
DMSO environment are summarized.
• Position of Table 4
The 1H NMR spectra of the title compound, the lowest NMR signals belongs to the methylene
group of cyclopentyl ring. These signals were showed in the range 2.29-1.67 ppm. These
peaks are appeared in the region 1.60-2.40 ppm by DFT computations. The 1H NMR spectra
of the cyclopentyl thiotetrazole compounds showed the singlet peaks belong to protons of the
methylene groups between aromatic benzene ring and sulphur atom at the 4.42 ppm. These
chemical shifts are predicted at 4.13 ppm (H13) and 5.17 ppm (H14) by means of DFT
computations.
Multiple peaks were showed in the range 5.23-4.56 ppm for the -CH group protons of the
cyclopentyl bounded tetrazole ring. This signal of H24 proton is calculated at 4.60 ppm by
1
DFT. In the pentyl group, it has the larger H NMR signals in both experimental and
1
theoretical spectra The H NMR signals of the phenyl group for the aromatic protons in the
range 7.38-7.24 ppm. These signals are observed at 7.24 ppm (H10), 7.29 ppm (H11), 7.35 ppm
(H7), 7.37 ppm (H8) and 7.38 ppm (H9) by experimental methods. We are calculated at 7.38
ppm (H10), 7.48 ppm (H11), 7.60 ppm (H7), 7.71 ppm (H8) and 8.02 ppm (H9) in the
theoretical method. Moreover, at the compound 5-(benzylthio)-1H-tetrazole we monitored an
10

N-H signal about 12.43 ppm belongs to the tetrazole ring as weak and broad. This data also
prove the tetrazole formation.
In the previously work [30-31], it note that the range of 13C NMR chemical shifts for a typical
organic molecule usually is bigger than 100 ppm, the accuracy ensures reliable interpretation
of spectroscopic parameters. In the present paper, 13C NMR chemical shifts of the pentyl and
tetrazole group for the title compound are larger than 100 ppm. These signals are observed in
the region 127.15-163.0 ppm in the experimental spectra. We are performed at the 132.7 (C5),
132.9 (C6), 133.8 (C1), 134.9 (C2), 135.3 (C4), 146.2 (C3) and 163.3 (C16) by using the
theoretical calculations. As seen in Table 4, the observed and the calculated 13C NMR signals
are found to be in good agreement. 163.3 ppm signal posses to the tetrazole group and are
higher signal in the 13C NMR spectra. Other peaks belong to the carbon atoms of the phenyl
group.
According to 13C NMR signal of the phenyl and tetrazole group, the chemical shifts of
1
obtained and calculated for the H atoms of cyclopentyl group are lower than those. All
signals are smaller than 100 ppm. The bigger signal is that of C21 atom. This peak observed
experimentally at 65.19 ppm and theoretically at 65.23 ppm. Other signals are calculated in
the region 30.09-44.19 ppm and measured in the 24.27-37.86 ppm. According to the NMR
spectra, the observed and the calculated NMR signals are found to be in good agreement.
3.5.
Molecular Electrostatic Potential Maps (MEP)
MEP that is occurred by the nuclei and the electrons is a very useful property for analyzing
and predicting molecular reactive behavior. MEP mapping is very useful in the investigation
11

of the molecular structure with its physiochemical property relationship. The potential has
been particularly useful as an indicator of the sites or regions of a molecule to which an
approaching electrophile is initially attracted, and it has also been applied successfully to the
study of interactions that involve a certain optimum relative orientation of the reactants.
• Position of Figure 5SM
• Position of Figure 6SM
3.6.
Electronic properties
The evolvement of the electronic structure can be by calculating the highest occupied
molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) as well as the
energy gap (EGAP) between HOMO and LUMO. Both HOMO and LUMO are the main orbital
taking part in chemical reaction. (See HOMO-LUMO plot in supplementary materials). The
HOMO energy characterizes the ability of electron giving, the LUMO characterizes the ability
of electron accepting, and the gap between HOMO and LUMO characterizes the molecular
chemical stability. The energy gap between the HOMO’s and LUMO’s is the most important
parameter in determining molecular electrical transport properties because it is a measure of
electron conductivity. The values of LUMO and HOMO and their energy gap consider the
chemical activity of the molecule. The decrease in the HOMO and LUMO energy gap shows
the eventual charge transfer interaction taking place within the molecule which is responsible
for the activity of the molecule.
• Position of Figure 7SM
• Position of Figure 8SM
4. CONCLUSION
Firstly, we have been synthesized the 5-(Benzylthio)-1-cylopentyl-1H-tetrazole (5B1C1HT)
1
compound. The FT-IR, H-NMR, 13C-APT and LC-MS spectra for 5B1C1HT have been
recorded and interpreted. Theoretical conformational, structural, vibrational and Nuclear
12

Magnetic Rezonans Spectral analyses of 5B1C1HT molecule were performed by Gaussian 09
and Spartan 10 software. The NMR and FT-IR spectral experimental results were compared
with the theoretical values. The NMR chemical shifts and the peaks of FT-IR spectra
experimentally showed good agreement with the theoretical values. In addition, we plotted the
Molecular Electrostatic Potential Maps and HOMO-LUMO of the title compound.
ACKNOWLEDGEMENT
One of the Authors (Y. Erdogdu) thanks to Ahi Evran University Research Fund for its
financial support. Project Numbers: FEN.4003.12.007. Computing resources used in this
work were provided by the National Center for High Performance Computing of Ahi Evran
University in Turkey (AHILAB).
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Yurdakul, Opt. Spectrosc. 114 (2013) 46-57.
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14

26. S.H.Bayari, B.Seymen, H.Ozisik, S.Saglam, J. Mol. Struc. THEOCHEM
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15

Fig. 1
16

17

18

19

20

21

22

23

Table 1 Energetic of the nine conformers calculated at the B3LYP/6-31G(d,p) level.
Conformers
E (Hartree)
∆E (kcal/mol)
∆E0 (kcal/mol)
-1122.18758401
-1122.18673242
-1122.18536105
-1122.18533564
-1122.18511016
-1122.18424734
-1122.18373654
-1122.18337209
-1122.18317819
0.000
0.534
1.394
1.410
1.552
2.093
2.413
2.642
2.763
0.000
0.532
1.369
1.333
1.371
1.984
2.472
2.652
2.613
Conformer-1
Conformer-2
Conformer-3
Conformer-4
Conformer-5
Conformer-6
Conformer-7
Conformer-8
Conformer-9
∆E0: Zero point corrected energy
24

Table 2 Optimized geometric parameters of the title compounds
Bond Lengths ()
C1-C2
C1-C6
C1-H7
C2-C3
C2-H8
C3-C4
C3-C12
C4-C5
C4-H9
6-311++G(d,p) cc-pVDZ
cc-pVTZ
1.387
1.391
1.081
1.396
1.083
1.395
1.500
1.390
1.081
1.389
1.081
1.081
1.088
1.085
1.857
1.751
1.320
1.349
1.355
1.283
1.353
1.463
1.549
1.555
1.087
1.533
1.090
1.089
1.536
1.087
1.090
1.533
1.093
1.089
1.089
1.091
Bond Angles ()
C2-C1-C6
C2-C1-H7
C6-C1-H7
C1-C2-C3
C1-C2-H8
C3-C2-H8
C2-C3-C4
C2-C3-C12
C4-C3-C12
C3-C4-C5
C3-C4-H9
C5-C4-H9
6-311++G(d,p) cc-pVDZ
cc-pVTZ
120.0
119.8
120.1
120.7
119.6
119.6
118.9
120.4
120.6
120.3
119.3
120.3
120.2
119.6
120.0
119.7
120.1
120.1
111.4
112.3
114.6
108.8
102.4
106.3
100.5
127.5
123.8
108.5
105.7
111.1
106.9
107.5
130.8
121.6
112.3
112.9
104.8
105.9
110.8
110.0
104.7
108.5
112.1
109.6
113.7
107.7
105.6
111.4
108.7
113.1
110.2
107.5
103.1
110.4
112.3
110.1
113.3
107.3
103.7
112.5
109.8
113.2
109.6
107.6
Dihedral Angles ()
C6-C1-C2-C3
C6-C1-C2-H8
C7-C1-C2-C3
C7-C1-C2-H8
C2-C1-C6-C5
C2-C1-C6-H11
H7-C1-C6-C5
H7-C1-C6-H11
C1-C2-C3-C4
C1-C2-C3-C12
H8-C2-C3-C4
H8-C2-C3-C12
C2-C3-C4-C5
C2-C3-C4-H9
C12-C3-C4-C5
C12-C3-C4-H9
C2-C3-C12-H13
C2-C3-C12-H14
C2-C3-C12-S15
C4-C3-C12-H13
C4-C3-C12-H14
C4-C3-C12-S15
C3-C4-C5-C6
C3-C4-C5-H10
H9-C4-C5-C6
H9-C4-C5-H10
C4-C5-C6-C1
C4-C5-C6-H11
H10-C5-C6-C1
H10-C5-C6-H11
C3-C12-S15-C16
H13-C12-S15-C16
H14-C12-S15-C16
C12-S15-C16-N17
C12-S15-C16-N20
S15-C16-N17-N18
N20-C16-N17-N18
S15-C16-N20-N19
S15-C16-N20-C21
N17-C16-N20-N19
N17-C16-N20-C21
C16-N17-N18-N19
N17-N18-N19-N20
N18-N19-N20-C16
N18-N19-N20-C21
C16-N20-C21-C22
C16-N20-C21-C23
C16-N20-C21-H24
N19-N20-C21-C22
N19-N20-C21-C23
N19-N20-C21-H24
N20-C21-C22-C25
N20-C21-C22-H26
N20-C21-C22-H27
C23-C21-C22-C25
C23-C21-C22-H26
C23-C21-C22-H27
H24-C21-C22-C25
H24-C21-C22-H26
H24-C21-C22-H27
N20-C21-C23-C28
N20-C21-C23-H29
N20-C21-C23-H30
C22-C21-C23-C28
C22-C21-C23-H29
C22-C21-C23-H30
H24-C21-C23-C28
H24-C21-C23-H29
H24-C21-C23-H30
C21-C22-C25-C28
C21-C22-C25-H31
C21-C22-C25-H32
6-311++G(d,p) cc-pVDZ
cc-pVTZ
0.025
-179.8
179.7
-0.170
0.073
179.8
-179.6
0.167
-0.127
-179.4
179.7
0.471
0.133
179.5
179.4
-1.196
33.49
156.0
-82.31
-145.7
-23.22
98.40
-0.036
-179.9
-179.4
0.699
-0.067
-179.8
179.8
0.032
-82.87
156.1
41.98
-15.82
165.9
-178.3
0.136
178.0
-1.019
-0.525
-179.5
0.330
-0.652
0.718
179.8
110.9
-129.2
-9.436
-67.95
51.81
171.6
141.6
24.51
-94.45
17.90
-99.22
141.8
-101.4
141.3
22.43
-115.9
7.246
125.6
7.361
130.5
-111.0
127.2
-109.5
8.864
-36.42
81.27
-158.8
1.391
1.395
1.084
1.400
1.085
1.399
1.500
1.394
1.083
1.393
1.084
1.084
1.091
1.088
1.863
1.755
1.322
1.352
1.356
1.287
1.356
1.468
1.554
1.557
1.090
1.538
1.092
1.091
1.538
1.089
1.093
1.536
1.096
1.092
1.092
1.094
1.396
1.398
1.092
1.403
1.093
1.404
1.505
1.397
1.091
1.398
1.092
1.092
1.099
1.096
1.868
1.759
1.327
1.355
1.359
1.289
1.358
1.467
1.556
1.556
1.098
1.538
1.100
1.100
1.537
1.098
1.102
1.536
1.104
1.100
1.100
1.102
120.0
119.8
120.1
120.6
119.6
119.6
118.9
120.4
120.5
120.3
119.3
120.3
120.2
119.6
120.0
119.7
120.0
120.1
111.6
112.4
114.4
108.8
102.4
106.4
100.1
127.3
124.0
108.5
105.8
111.2
106.8
107.5
130.8
121.6
112.2
112.6
104.7
106.0
111.0
110.2
104.9
108.6
112.0
109.7
113.6
107.7
105.4
111.6
108.5
113.4
110.1
107.5
103.3
110.4
112.2
110.0
113.3
107.3
103.4
112.5
109.9
113.2
109.8
107.7
120.0
119.8
120.1
120.7
119.6
119.6
118.9
120.3
120.6
120.2
119.2
120.5
120.3
119.5
120.0
119.6
120.1
120.1
111.5
112.5
114.5
109.1
102.5
105.8
99.93
127.7
123.7
108.5
105.7
111.3
106.8
107.5
130.9
121.4
111.9
112.4
104.8
105.8
111.4
110.4
105.1
108.2
112.2
109.7
113.7
107.6
105.3
111.6
108.5
113.6
109.9
107.6
103.2
110.4
112.3
109.9
113.5
107.3
103.1
112.7
109.7
113.4
109.8
107.9
0.008
179.8
179.6
-0.160
0.102
179.8
179.5
0.193
-0.16
0.041
-179.8
179.7
-0.091
0.043
179.8
-179.6
0.126
-0.121
-179.5
179.7
0.317
0.117
179.5
179.5
-1.084
28.81
151.9
-87.11
-150.5
-27.47
93.48
-0.034
-179.8
-179.4
0.747
-0.047
-179.8
179.7
-0.009
-86.19
152.7
38.43
-10.34
171.3
-178.3
0.214
178.0
-0.359
-0.576
-178.9
0.249
-0.603
0.718
179.2
109.6
-131.3
-11.30
-68.53
50.46
170.5
136.5
19.36
-99.3
C5-C6
-179.4
179.6
0.374
0.219
179.6
179.5
-1.071
33.37
156.0
-82.35
-145.9
-23.25
98.34
-0.111
-179.9
179.5
0.661
-0.051
-179.8
179.7
0.006
-80.36
158.6
44.44
-20.08
161.6
-178.3
0.073
178.0
-1.99
-0.490
179.4
0.401
-0.701
0.726
-179.2
112.7
-127.6
-7.869
-67.32
52.32
172.1
138.6
21.26
-97.6
C5-H10
C6-H11
C12-H13
C12-H14
C12-S15
S15-C16
C16-N17
C16-N20
N17-N18
N18-N19
N19-N20
N20-C21
C21-C22
C21-C23
C21-H24
C22-C25
C22-H26
C22-H27
C23-C28
C23-H29
C23-H30
C25-C28
C25-H31
C25-H32
C28-H33
C28-H34
C4-C5-C6
C4-C5-H10
C6-C5-H10
C1-C6-C5
C1-C6-H11
C5-C6-H11
C3-C12-H13
C3-C12-H14
C3-C12-S15
H13-C12-H14
H13-C12-S15
H14-C12-S15
C12-S15-C16
S15-C16-N17
S15-C16-N20
N17-C16-N20
C16-N17-N18
N17-N18-N19
N18-N19-N20
C16-N20-N19
C16-N20-C21
N19-N20-C21
N20-C21-C22
N20-C21-C23
N20-C21-H24
C22-C21-C23
C22-C21-H24
C23-C21-H24
C21-C22-C25
C21-C22-H26
C21-C22-H27
C25-C22-H26
C25-C22-H27
H26-C22-H27
C21-C23-C28
C21-C23-H29
C21-C23-H30
C28-C23-H29
C28-C23-H30
H29-C23-H30
C22-C25-C28
C22-C25-H31
C22-C25-H32
C28-C25-H31
C28-C25-H32
H31-C25-H32
C23-C28-C25
C23-C28-H33
C23-C28-H34
C25-C28-H33
C25-C28-H34
H33-C28-H34
15.18
-102.6
138.9
-104.5
138.0
19.18
-112.9
10.70
129.0
10.20
133.8
-107.7
130.5
-105.8
12.52
-34.87
82.81
-157.3
13.70
-103.4
137.7
-106.3
136.4
17.70
-110.2
13.52
131.9
12.24
136.0
-105.5
132.9
-103.2
15.22
-34.47
83.03
-157.1
25

H26-C22-C25-C28
H26-C22-C25-H31
H26-C22-C25-H32
H27-C22-C25-C28
H27-C22-C25-H31
H27-C22-C25-H32
C21-C23-C28-C25
C21-C23-C28-H33
C21-C23-C28-H34
H29-C23-C28-C25
H29-C23-C28-H33
H29-C23-C28-H34
H30-C23-C28-C25
H30-C23-C28-H33
H30-C23-C28-H34
C22-C25-C28-C23
C22-C25-C28-H33
C22-C25-C28-H34
H31-C25-C28-C23
H31-C25-C28-H33
H31-C25-C28-H34
H32-C25-C28-C23
H32-C25-C28-H33
H32-C25-C28-H34
81.69
-160.6
-40.81
-157.5
-39.90
79.89
-31.73
-154.3
85.56
-154.2
83.22
-36.91
85.20
-37.36
-157.5
41.33
163.4
-76.03
-76.62
45.47
166.0
163.1
-74.77
45.75
81.75
-160.7
-40.91
-157.6
-40.09
79.77
-33.54
-156.2
83.43
-156.0
81.20
-39.08
83.19
-39.53
-159.8
42.16
164.4
-74.74
-75.69
46.57
167.3
164.0
-73.64
47.17
79.92
-162.3
-42.51
-159.2
-41.56
78.30
-29.82
-152.6
87.38
-152.0
85.19
-34.80
87.52
-35.27
-155.2
41.10
163.4
-76.22
-76.83
45.48
165.8
162.8
-74.78
45.56
26

Table 3 Calculated (B3LYP) vibrational wavenumbers (cm−1), measured FT-IR bands and
assignments for the title compound
6-311++G,p
Freqa
cc-pVDZ cc-pVTZ Exp.IR
TEDc (%)
Freqa
Freqa
0
22
27
31
0.838
0.087
2.449
0.313
2.906
1.637
4.453
4.014
2.994
0.672
3.267
2.266
1.170
3.332
0.014
0.823
1.953
1.928
9.772
1.107
15.08
1.576
0.746
81.45
13.83
4.017
92.89
0.590
29.11
8.060
12.38
1.234
2.743
2.181
13.41
5.070
4.914
4.529
6.101
0.789
0.393
14.59
0.256
2.317
10.71
7.746
34.82
2.758
19.30
13
26
28
36
12
24
31
44
ν1
τNCSC(42%)+τCCNC(29%)
ν2
τNCSC(28%)+τCSCH(13%)+τHCCC(10%)+τCSCC(10%)+τCCNN(10%)
τCSCH(19%)+τHCCC(18%)+τCSCC(16%)+τNCSC(12%)
τHCCN(35%)+τCCCN(26%)+τCCCH(10%)
τSCCC(47%)+τCSCC(17%)+τCSCH(10%)
τCCCC(25%)+δSCC(22%)+τCCCH(22%)
τCNCN(18%)+τCNNN(15%)+τCNCS(14%)+τNCSC(13%)
δNCS(40%)+δCNC(14%)+δCNN(10%)+δCSC(10%)
δCSC(44%)+δCNC(10%)+δCNN(10%)
τNNCS(36%)+τCNCS(11%)
τHCCC(33%)+τCCCC(16%)
τHCCC(22%)+τCCCC(10%)
δSCC(15%)+τCCCC(10%)+
δCCC(66%)
ν3
ν4
ν5
51
55
52
ν6
107
115
118
159
221
245
261
288
328
400
405
438
465
468
524
552
614
615
630
664
677
686
700
752
793
803
829
836
856
875
880
893
905
919
955
971
978
984
992
1008
1016
1032
1056
1065
106
115
123
163
228
245
270
287
335
404
411
442
467
473
523
552
612
619
633
667
688
695
704
761
797
804
838
843
850
885
890
898
914
921
961
982
985
988
995
1012
1020
1043
1064
1066
109
116
120
161
226
249
259
289
331
403
406
439
467
470
525
554
612
615
633
670
693
697
708
759
794
804
835
837
853
873
879
895
914
921
960
974
979
988
992
1009
1018
1026
1052
1061
ν7
ν8
ν9
ν10
ν11
ν12
ν13
ν14
ν15
ν16
ν17
ν18
ν19
ν20
ν21
ν22
ν23
ν24
ν25
ν26
ν27
ν28
ν29
ν30
ν31
ν32
ν33
ν34
ν35
ν36
ν37
ν38
ν39
ν40
ν41
ν42
ν43
ν44
ν45
ν46
ν47
ν48
ν49
τCCCC(63%)+τCCCH(33%)+
δCCN(26%)+τHCCN(25%)+τCCCN(11%)
νCS(14%)+δNCS(11%)+νCN(10%)
νCS(34%)+δNCS(14%)+δCSC(11%)
νSC(20%)+τCCCH(11%)+τCCCC(10%)
δCCC(27%)+τHCCC(22%)+δHCC(10%)
δCCC(34%)+δSCC(10%)
δCCC(57%)+δCCH(18%)
δCCC(16%)+τCCCH(10%)
νSC(62%)
τNNCN(19%)+νCN(16%)
τNNCN(22%)+τCNNN(13%)+τNCSC(10%)
τCCCH(55%)+τCCCC(33%)
τNNNC(43%)+τNNNN(26%)+τNNCN(16%)
τCCCH(53%)+τCCCC(10%)
νCC(53%)+δCCC(15%)
νCC(14%)+τHCCH(13%)+τHCCC(12%)
τCCCH(81%)+τHCCH(17%)
νCC(27%)+τHCCC(20%)+δHCC(19%)
τHCCC(26%)+δHCC(14%)+τCSCH(12%)+τSCCC(10%)+δHCS(10%)
νCC(77%)
νCC(60%)
νCC(40%)+δCCH(12%)
τCCCH(55%)+τHCCH(32%)
δCCH(18%)+τHCCH(15%)+νCC(14%)
τHCCH(54%)+τCCCH(33%)
τHCCH(65%)+τHCCC(16%)
νNN(38%)+δNNC(17%)+νNC(14%)
νCC(39%)+δCCC(39%)
νCC(38%)+τHCCH(10%)
νCC(49%)+τHCCH(10%)
δCCH(26%)+νCC(24%)+νCC(23%)+δCCC(14%)
νNN(71%)
νCC(23%)+νNN(11%)
562
620
697
728
766
803
814
840
863
913
941
1014
1029
1052
νCC(29%)+δHCC(18%)+δNNN(14%)
27

1072
1133
1066
1126
1143
1148
1152
1166
1185
1192
1198
1219
1234
1264
1275
1284
1296
1297
1303
1309
1319
1345
1372
1413
1417
1436
1438
1442
1446
1464
1476
1569
1588
2886
2905
2909
2917
2939
2942
2949
2951
2965
2973
3002
3012
3023
3033
3043
3050
20.62
65.47
0.218
0.387
9.031
2.724
7.565
3.791
27.59
6.295
56.83
0.034
5.599
24.90
0.731
15.99
3.323
1.114
2.472
42.75
100
62.41
58.70
10.19
2.686
13.66
11.68
11.23
14.95
1.351
2.502
58.11
36.31
34.59
26.44
16.42
65.21
18.03
48.50
31.16
39.77
0.080
11.09
2.330
32.13
25.45
14.79
1074
1125
1135
1138
1151
1160
1187
1189
1203
1218
1220
1254
1272
1292
1301
1304
1306
1307
1319
1346
1389
1395
1406
1414
1420
1424
1438
1443
1479
1586
1605
2936
2955
2957
2968
2989
2996
3001
3007
3020
3029
3058
3068
3079
3090
3101
3108
1066
1128
1141
1146
1153
1167
1184
1195
1197
1222
1227
1268
1277
1285
1293
1298
1304
1310
1324
1344
1368
1411
1415
1438
1441
1442
1447
1464
1481
1570
1589
2918
2937
2943
2949
2969
2974
2979
2983
2996
3007
3032
3046
3057
3067
3077
3084
ν50
ν51
ν52
ν53
ν54
ν55
ν56
ν57
ν58
ν59
ν60
ν61
ν62
ν63
ν64
ν65
ν66
ν67
ν68
ν69
ν70
ν71
ν72
ν73
ν74
ν75
ν76
ν77
ν78
ν79
ν80
ν81
ν82
ν83
ν84
ν85
ν86
ν87
ν88
ν89
ν90
ν91
ν92
ν93
ν94
ν95
ν96
δNNN(23%)+νCC(16%)+νNN(10%)
δHCC(15%)+δNNN(10%)
δCCH(59%)+νCC(17%)
δHCC(39%)+δHCS(26%)
δHCC(20%)+τHCCH(17%)
δCCH(76%)+νCC(16%)
νCC(64%)+δHCC(14%)
δCCH(25%)+τCCCH(11%)
νNC(27%)+δNNC(10%)
δCCH(39%)+τCCCH(10%)
δHCS(37%)+δHCC(22%)+τHCCC(33%)
δCCH(28%)+τHCCH(14%)
νNN(26%)+δHCC(23%)
νNN(40%)
1173
1199
1242
1296
νCC(67%)
δHCC(26%)+τHCCC(25%)
δCCH(36%)+τHCCH(28%)+τHCCC(12%)
δHCC(42%)
1316
1369
1400
δCCH(87%)
νNC(31%)+τHCCH(13%)+τCCCH(10%)
νNC(62%)+τNNC(12%)+νNN(10%)
νNC(25%)+τHCCH(11%)
δHCH(35%)+τCSCH(19%)+τHCCC(16%)+δHCC(12%)
δCCH(54%)+νCC(29%)
δHCH(24%)+τHCCH(23%)+τCCCH(12%)
δHCH(27%)+τHCCH(25%)
δHCH(29%)+τHCCH(29%)
δHCH(34%)+τHCCH(27%)
δCCH(62%)+νCC(33%)
νCC(70%)+δCCH(12%)
νCC(67%)+δCCH(16%)
νHC(96%)
νHC(100%)
νHC(97%)
νHC(99%)
νHC(100%)
νHC(95%)
νHC(97%)
νHC(99%)
νHC(95%)
1453
1473
1585
1600
2873
2959
3028
νHC(91%)
νHC(100%)
νHC(98%)
νHC(99%)
νHC(100%)
νHC(9(6%)
νHC(98%)
3063
3086
aObtained from the wave numbers calculated at 0.967 for 6-311++G(d,p)), 0.970 for cc-pVDZ, 0.965 for cc-pVTZ.
ν: stretching, δ: bending, τ: torsion
bRelative absorption intensities normalized with highest peak absorption equal to 100.
cTotal energy distribution calculated B3LYP/6-311++G(d,p) level of theory. Only contributions 10% are listed.
28

Table 4 The observed and predicted 1H and 13C NMR isotropic chemical shifts (with respect
to TMS, all values in ppm) f
Atom Numbering
Theoretical
30.09
31.71
37.73
39.27
44.19
62.37
132.7
132.9
133.8
134.9
135.3
146.2
163.3
Experimental
24.27
24.27
32.79
32.79
37.86
65.19
127.5
127.5
128.8
128.8
129.0
136.8
163.0
C28
C25
C23
C22
C12
C21
C5
C6
C1
C2
C4
C3
C16
H31
H29
H33
H26
H34
H32
H30
H27
H24
H13
H14
H10
H11
H7
1.60
1.71
1.75
1.75
1.95
1.98
2.01
2.40
4.60
4.13
5.17
7.38
7.48
7.60
7.71
8.02
1.67
1.67
1.67
1.67
2.20
2.20
2.20
2.29
5.23-4.56
4.42
4.42
7.24
7.29
7.35
7.37
7.38
H8
H9
29