Synthesis, vibrational, electrostatic potential and NMR studies of (E and Z) 1-(4-chloro-3-nitrophenyl)-3-(2-methoxyphenyl)triazene: Combined experimental and DFT approaches

Article abstract of DOI:10.1016/j.molstruc.2016.06.053

Using new experimental methods, 1-(4-chloro-3-nitrophenyl)-3-(2-methoxyphenyl) triazene, (CNPMPT) structure was synthesized in the laboratory. The structure has two E and Z conformational states that E is a more stable state than the Z. After synthesis of

Full text of DOI:10.1016/j.molstruc.2016.06.053

Accepted Manuscript
Synthesis, vibrational, electrostatic potential and NMR studies of (E and Z) 1-(4-
chloro-3-nitrophenyl)-3-(2-methoxyphenyl)triaz-1-ene: Combined experimental and
DFT approaches
Mohammad Kazem Rofouei, Reza Soleymani, Abolfazl Aghaei, Mahmoud Mirzaei
PII:
S0022-2860(16)30639-1
10.1016/j.molstruc.2016.06.053
MOLSTR 22672
DOI:
Reference:
To appear in: Journal of Molecular Structure
Received Date: 24 February 2016
Revised Date: 20 June 2016
Accepted Date: 20 June 2016
Please cite this article as: M.K. Rofouei, R. Soleymani, A. Aghaei, M. Mirzaei, Synthesis,
vibrational, electrostatic potential and NMR studies of (E and Z) 1-(4-chloro-3-nitrophenyl)-3-(2-
methoxyphenyl)triaz-1-ene: Combined experimental and DFT approaches, Journal of Molecular
Structure (2016), doi: 10.1016/j.molstruc.2016.06.053.
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Graphical Abstract (Pictogram)

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Synthesis, vibrational, electrostatic potential and NMR studies of (E
and Z)1-(4-chloro-3-nitrophenyl)-3-(2-methoxyphenyl)triaz-1-ene:
Combined experimental and DFT approaches
Mohammad Kazem Rofouei 1, Reza Soleymani 2, *, Abolfazl Aghaei 3 and Mahmoud Mirzaei 4
1Faculty of Chemistry, Kharazmi University, Tehran, Iran.
2Young Researchers and Elite Club, Shahre-Rey Branch, Islamic Azad University, Tehran, Iran.
3Faculty of Chemistry, Tarbiat Moallem University, Tehran, Iran.
4Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan
University of Medical Sciences, Isfahan, Iran.
* Corresponding author e-mail address: reza.soleymani@hotmail.com
Tel: +98 2633350468- Mob: +98 9123782899
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Abstract
Using new experimental methods, 1-(4-chloro-3-nitrophenyl)-3-(2-methoxyphenyl) triaz-1-ene,
(CNPMPT) structure was synthesized in the laboratory. The structure has two E and Z
conformational states that E is a more stable state than the Z. After synthesis of the structure,
crystallization process was carried out and its chemical properties were investigated using
experimental and theoretical methods. The structure has orthorhombic crystal system with space
group equal to Pbca and its unit cell parameters comprise a= 7.0723 (9), b= 7.5333 (9), and c=
13.7138 (15).To further study and identify the structure, in addition to X-Ray diffraction, NMR
and FT-IR analyses were also done on the structure. Then, the structure was discussed and
studied using density functional theory (DFT) at the theory level B3LYP, B3PW91 and
PBEPBE. The structural and thermodynamic parameters, electrostatic potential,
corresponding Hirshfield surface, electrophilicity (ω), chemical potential (ꢀ), chemical hardness
(η) and max amount of electronic charge transfer (ꢁNmax) were examined for this structure. The
results showed that the experimental and theoretical results were very consistent.
Keywords: Synthesis, DFT, Single crystal, Electrophilicity.
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1. Introduction
Triazenes are colorful compounds with strong bad smell that normally exist as gases. The
compounds also have density and boiling point higher than diazene compounds. These
compounds have unsaturated molecular formula R1 R2 N-N = NR3 consisting of three nitrogen
atoms and three substituted groups. [1] Since the substituted group can be consisted of hydrogen,
halogen atoms as well as cyclic compounds, it makes up lots of derivatives. Triazenes have many
applications and properties. [2-4] Derivatives of these compounds can be used as various drugs
like anti-cancers. [5] However, many derivatives of these compounds are used in paint industry
as color indicators. [6] Due to strong electron transportπ-π×,group N = N-N can act as ligands
for various metals and make up complex with the metals. [7, 8] One method of producing
triazenes is the spontaneous decomposition of Tetrazenes. In this study, it is tried to show a
different and modern method for synthesizing these compounds.Triazene compounds have been
used for the preparation of several sensors for determination of heavy metals, [9, 10] and also
used in solid-phase extraction. [11, 12] They have been studied for their anorectic activity and
potency against specific tumor cell lines, [13–17] as well as they have been applied as protecting
groups in natural product synthesis [18, 19] or used to form heterocycles. [20, 21] Various
compounds have been prepared from these compounds, because of linkage ability of them to
carbonic nano tubes that have important abilities especially in man’s body metabolism. [22] A
kind of these compounds applied in agronomy chemistry for insecticides and weeds synthesis.
However, they have been used in pigments synthesis. [23, 24]
HOMO and LUMO are two parameters that can be calculated through density functional theory
(DFT). Through these two parameters, we can calculate and examine the electrophilicity
values, chemical hardness, chemical potential and the maximum amount of electronic charge
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transferred. [25-27] Electrophilicity is in fact a factor to demonstrate the reactivity for organic
and inorganic compounds and it is also evaluated and reported for many systems. In fact, high
chemical potential and low chemical hardness indicates
a
system with good
electrophone species. Electrophilicity values are different for various compounds based on
HOMO and LUMO and accordingly the structure performance in chemical reactions will be
different.
Another parameter to be measured is electrostatic potential. In fact the map presented by which
shows the charge distribution in the chemical structure. This is available as a three-dimensional
map that is composed of red color showing the relative frequency of number of electrons and
blue representing the relative lack of electron. [27-28] Once examined the distribution of
electrons in the structure, the structure performance in various reactions can be
predicted. Usually, yellow and green represent the relative average values of the electrostatic
potential. The electrostatic potential is directly related to electronegativity values and the
electronegativity difference is a determinatekey in the nature of chemical bonding.
Hirshfield surface is a parameter showing the distribution of electron and the electron density in
a crystal structure and to obtain it, crystal structure file (CIF) should be available. In fact, it is
constructed by partitioning space in the crystal into regions where the electron distribution of a
sum of spherical atoms for the molecule dominates the corresponding sum over the crystal.
Surface properties are displayed with two parameters de and di. In fact, we can obtain
information on the environment around the crystal structure in the unit cell using this map. De
is the distance from the Hirshfeld surface to the nearest nucleus outside the surface. Di is the
corresponding distance to the nearest nucleus inside the surface. [29, 30]
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2. Experimental details
2.1. General method
All chemicals were of analytical grade and were used as commercially obtained without further
1
purification. H NMR and 13C NMR spectra were recorded on BrukerAvance 300 MHz
spectrometer in DMSO solvents, and all chemical shifts were reported in d unit downfield from
Tetramethylsilane (TMS). FT-IR spectra were recorded using Perkin–Elmer RXI spectrometer
using KBr disks. Elemental analysis was carried out using a Perkin–Elmer 2,400(II) CHNS/O
analyzer.
2.2. Synthesis
The synthetic route is shown in scheme 1. The 0.01 mol (1.72 g) of 4-Chloro-3-nitroaniline was
dissolved in 200 mL of acidic solution (6N HCl, d=1.18 Kg/L), and the solution was cooled to 0
◦C. It was slowly diazotized within 5 min by adding 0.01mol (0.69 g) of sodium nitrite in 10 mL
of water under vigorous stirring. After further stirring for 10 min, 0.01mol (1.10 g) of ortho
Anisidine in 5 mL methanol was slowly added to the resulting solution under stirring for a period
of 10 min. The mixture was maintained at pH 7–8 by adding appropriate amount of aqueous
sodium acetate and stirred at room temperature for half an hour. The mixture was filtered out,
washed with cold water, and dried in vacuum overnight at room temperature. The brown product
(Yield 90%) was dissolved in 30 ml pure acetonitrile (stored in a freezer). Needle like crystals
1
was obtained by slow evaporation of the solvent in a week. H-NMR (300 MHz, DMSO-d6) δ
7.29–7.66 (7H, m, phenyl protons), 12.97 (1H, s, NH), 3.83 (3H, s, methyl).13C-NMR (300 MHz,
DMSO-d6) δ 55.86, 113.14, 124.52, 125.70, 125.82, 130.80, 131.08, 134.19, 137.48, 138.08,
155.95, 157.26, 159.90. IR (KBr, ν cm-1): 3305.73 (N-H), 3013.56 (C-H, sp2), 1422.73-1599.31
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(C=C), 1027.06 (C-Cl), 1342.93, 1514.79 (N=O), 1256.63 (C-N), 1042.98, 1256.63 (C-O)
1218.94 (N-N). Elemental Anal. Calc. for C15H15N3O (306.7 g mol-1): C, 50.91; H, 3.61; N,
18.27. Found: C, 50.97; H, 3.24; N, 18.23%.
3. Computational details
For further comparison, the experimental results of the structure were discussed and studied
using DFT at three theory levels, B3LYP, B3PW91 and PBEPBE and basic mode 6-311G (d,
p). For this purpose, Gaussian 03 was used. [31] To do so,the structure was preliminary designed
using Gauss view 03 and subsequently, the structure was optimized. For all calculations, the
standard conditions of the gas phase of 1 atmospheric pressure and 298 Kelvin temperature was
considered. To do the calculation, Pentium 4 with RAM memory 4 GB and processor 2.4 Giga
Hertz core i7 along with the Windows XP has been used. GIAO method was used to calculate
the amount of chemical shift in atoms of carbon and hydrogen. For more consistency of
experimental and theoretical results, Tetramethylsilane (TMS) standard was considered to
calculate the values of chemical shifts. For this purpose, the structure was initially optimized and
then the chemical shift values were calculated. Veda 4 was used for evaluationof the vibrational
parameters as well as analysis of structure PED. [32] This application will help to examine the
vibrational parameters for each bond based on the intensity of the vibration. For consistency of
vibrational parameters obtained experimentally with theoretically obtained values, a different
scale facture was used. Values considered for scale factures were intended 0.967 for theory
B3LYP, 0.963 for B3PW91 and 0.991 for PBEPBE method. [33] Fingerprint plots and
corresponding Hirshfield surface coverage were also examined using CrystalExplorer 3.1. [34]
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To investigate the placement of the structure in the unit cell, Mercury 3.6 [35] and to assess and
calculate the electrostatic potential values determined for different parts of the structure Molekel
software were used. [36]
4. Result and discussion
4.1. Description of the crystal structure
1- (4-chloro-3-nitrophenyl)-3-(2-methoxyphenyl)triaz -1-ene structure (CNPMPT) was examined
using X-Ray diffraction and its crystallography and structural parameters were assessed. This
structure has an empirical formula as C13H11ClN4O3 (Fig 1). The molecular weight is 306.7. The
structure has an Orthorhombic and Space Group Pbca crystal system. Orthorhombic crystal
system is one of the 7 crystal systems known with three vectors in which the three vectors are
unequal and all angles are 90 degree. All data obtained from X-Ray diffraction analysis have
been reported in Table 1. As Table 1 shows, the unit cell dimensions in the structure are obtained
as a = 7.0723 (9), b = 7.5333 (9), and c = 13.7138 (15), respectively. The placement of structure
in the unit cell and the formation of hydrogen bonds are shown in Figure 2. The amount
of absorption coefficient for the structure is also obtained 0.292 mm-1.
4.2. Geometrical parameters
4.2.1. Bond length
For better study and results, the chemical and structural parameters of the
structure were compared with some similar compounds. The reason to choose these compounds
is the structural and chemical similarity, crystallography analysis, and theoretical calculations on
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the structures. Surveyed structures include ADQF, [37] TBH derivatives, [38] DMPF,
[39] DPTF, [40] and BH complexes. [41] The structural parameters were studied using
experimental methods, crystallography method and also using density functional theory at three
different levels, B3LYP, B3PW91 and PBEPBE. The results have been reported in Table 2. As
Table 2 shows, the bond N=N was obtained 1.261 Å using the experimental method, and 1.262,
1.260 and 1.282 Å, respectively using B3LYP, B3PW91 and PBEPBE methods. However, for
N-N bond using experimental method, it is obtained 1.328
Å
and using
B3LYP, B3PW91 and PBEPBE methods, 1.324, 1.318 and 1.328 Å, respectively. Results of
other bonds’ length suggest the top consistency of the theoretical and experimental results. As
shown in Table 2 and supplementary dataS1, the experimental and theoretical results are highly
consistent.In the structure TBH derivatives, [38] the N-N bond length was reported 1.328 to
1.387 Å using experimental methods and 1.315 to 1.351 Å using theoretical method. However,
N-N bond in the structure of BH complexes were obtained 1.310 to 1.384 Å using the theory
method that is highly consistent with results obtained for the CNPMPT. [41] Also, if the
bonds C-C, C = C and C-N in CNPMPT structure are compared with other structures, you will
see that the results are highly consistent with similar structures. [37-41]
4.2.2. Bond angle and dihedral angle
The results of the bond and planar angles in CNPMPT structure are quite close to the results
obtained for the length of bonds with similar structures. The obtained experimental and
theoretical results are also quite close to each other. For example, the experimental results for
N22-N21-N20 was 112.4 degrees that based on B3LYP, B3PW91 and PBEPBE methods, it is
obtained 112.5, 112.3 and 111 degrees, respectively. Also, the bond angle for N21-N20-C3 was
obtained 121.2 degrees using the experimental results and 123.8, 123.9 and 126.9 degrees,
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respectively using theory methods based on B3LYP, B3PW91 and PBEPBE methods. Of course,
depending on the type of substitution orientation and conformational state used by the structure,
the bond and planar angles will have different values. Space congestion in the substituent groups
will affect the results.
4.3. Vibrational assignments
Comparing the infrared spectrum of two substances, they are believed to be similar, one can
discover whether they really are equal or not. If all the adsorptions in the spectrum of two
molecules are coincided, then almost certainly the two are the same. The second use of the
infrared spectrum that is more important than the first is that it gives information about the
structure of a molecule. Adsorptions associated with each bond can be found in a small part of
infrared vibrational area. CNPMPT structure contains 32 atoms and 90 normal vibration
parameters. FT-IR analysis on the structure were obtained using experimental and theoretical
methods (Fig 3). To calculate the vibrating parameters of CNPMPT structure, DFT method at
three levels of theory B3LYP, B3PW91 and PBEPBE and the basic state 6-311G (d, p) was used.
For more consistent results with experimental results, the conversion factor 0.967, 0.963 and
0.991 were used respectively. [33] As shown in Table 3, the experimental and theoretical results
are highly consistent. Comparing experimental method with DFT method at B3LYP theory level
showed linear equation Y= 1.0165x- 15.643 with R²= 0.9997, comparison with the theoretical
level B3PW91 showed linear equation Y= 1.0171x- 14.58 with R²= 0.9997 and then comparison
with theoretical level PBEPBE showed linear equation Y= 1.0171x- 22.004 with R²= 0.9995
(Supplementary dataS2.).
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4.3.1. C-H vibrations
C-H vibration parameter is entirely dependent on the type of hybridization. CH vibration
parameter with SP3 hybridization appears below 3000 and with SP2 hybridization in the range of
3100 and with SP hybridization upper than 3200. Stretching vibration usually appear in the range
of 2850 to 3200. Depending on the type of hybridization, bending vibrations are expected to be
appeared in the range of 1000 to 1300 cm-1. But for CNPMPT structure, C-H stretching vibration
appeared in the range of 3090, 3013, 2977, 2944 and 2840 cm-1 with various intensities using the
experimental FT-IR. But using DFT method at B3LYP theory level, CH stretching vibrations
appear in the range of 2907 to 3117 cm-1 and at B3PW91 theory level in the range of 2902 to
3111 cm-1 and for PBEPBE theory level in the range of 2912 to 3123 cm-1. But comparing
CNPMPT structure with other structures shows similar results from the vibration amplitude. For
structure DPTF was observed in the range of 2978 to 3212 cm-1 using the experimental method,
in the range of 3155 to 3281 cm-1 using DFT at B3LYP theory level [40]. In the BH structure,
[41] complexes appear in the range of 2700 to 3180 cm-1 using experimental methods of
vibration amplitude based on the type of vibration and using theory in the range of 2800 to 3012.
However, in the structure [37] ADQF, C-H stretching vibration amplitude was observed in the
range of 2916 cm-1 using the experimental method and in the range of 2854 to 3063 cm-1 using
theoretical method. But bending vibration C-H using the experimental method was observed in
the range of 1145 and 1157 and through DFT method at three levels of theory B3LYP, B3PW91
and PBEPBE in the range of 1127 to 1165 and 1120 to 1160 cm-1 as well as 1115 to 1145 cm-1.
The results obtained for C-H bending vibration in CNPMPT structure are consistent with the
results obtained for other compounds. [37-41]
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4.3.2. NO2 vibrations
The experimental results obtained for CNPMPT structure shows the symmetric stretching
vibration of NO2 within the range of 1599, 1569, 1523 cm-1 and asymmetric stretching vibration
in the range of 1342 cm-1. However, theoretical calculations using DFT method at three levels of
theory B3LYP, B3PW91 and PBEPBE show symmetric and asymmetric stretching vibration in
different areas. At B3LYP level, it shows the asymmetric stretching vibration in the range of
1339 cm-1 and symmetric stretching vibration in districts 1540, 1567 and 1591 cm-1. At B3PW91
level, the symmetric stretching vibration is shown in the range of 1550, 1582 and 1612 cm-1 as
well as asymmetric stretching vibration in the range of 1364 cm-1. PBEPBE also shows
symmetric stretching vibration in the area 1528, 1549 and 1583 cm-1 and asymmetric stretching
vibration in the range of 1351 cm-1. NO2 group gives two strong bonds in the infrared spectrum.
In these compounds, asymmetric stretching vibration is appeared in 1500 to 1600 cm-1 and
asymmetric stretching vibration in the range of 1300 to 1400 cm-1, because of the resonance in
the functional group NO2.
4.3.3. C-C and C=C vibrations
C-C and C=C stretching vibration is within the circular structure. Using the experimental
approach, the vibration amplitude for the structure CNPMPT is observed in 1523 cm-1 and using
the theory method, the vibration amplitude using DFT at three theoretical level B3LYP,
B3PW91 and PBEPBE was in the 1410-1591, 1404-1612 and 1394-1583 cm-1,respectively.
Tension ring adsorptions are usually appeared in pairs in the range of 1575 to 1600cm-1, and
Everton/Hybrid strips are expected to be appeared in the range of 1600 to 2000 cm-1. However,
the amplitude of stretching and bending vibrations changes depending on the type and number of
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substitutions. In similar structures such as DPTF, [40] the amplitude of stretching vibrations of
C-C appear from 1413 to 1492 cm-1, while appears in the region of 1482 to 1550 cm-1 by using
DFT method. In TBH derivatives, [38] using the theory of revealed that vibration amplitude of
C=C and C-C bonds, which have resonance, appear from 1251 to 1613 cm-1, which
experimentally appeared in the range of 1239 to 1621 cm-1. Moreover, in DMPF structure, [39]
the experimental results indicated that the amplitude of stretching vibration of C-C appear in the
region of 1516, 1323, and 1300 cm-1. The theoretical results for this structure match perfectly
with experimental results. The bending vibration of C-C-C group appear in region less than 1050
cm-1. In CNPMPT structure, the bending vibration of C-C-C group appear in the regions of
673,747, 783, and 1027 cm-1 using experimental method. The theoretical results using DFT
method also shows the bending vibration of C-C-C in three regions of 568-1099, 567-1027, and
564-1011 cm-1 in three theoretical levels of B3LYP, B3PW91, and PBEPBE, respectively. The
amplitude of bending vibration were also in the same range for similar components. [37-41]
4.3.4. N-H vibrations
In DMPF structure, N-H stretching vibration was in the range of 3301 cm-1 by experimental
method, while appeared in the range of 3448 and 3436 cm-1 using theoretical method. In BH
complexes, [41] the N-H stretching vibration was in the range of 3428 to 3691 cm-1 by
experimental method, while appeared in the range of 3579 and 3583 cm-1 using theoretical
method. In ADQF structure, [37] it was in the range of 3173 and 3367 cm-1 by experimental
method, and in the region of 3367 to 3503 cm-1 by theoretical method. The first and second types
of amines and also amides have the stretching and bending vibrations of NH groups. The
amplitude of stretching vibrations of this group is between 3100 and 3500 cm-1 with medium to
high peak intensity, and its bending vibration is in the range of 1500 to 1700 cm-1. But in
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CNPMPT structure, the amplitude of N-H stretching vibration is about 3305 cm-1 by
experimental method, while appears in 3351, 3353, and 3290 cm-1 by using DFT method in three
theoretical level of B3LYP, B3PW91, and PBEPBE, respectively. The bending vibration for
CNPMPT structure was in the range of 1476 and 1514 cm-1 by experimental method, while
appeared in three regions of 1498-1500, 1488-1508, and 1480-1500 cm-1 by using DFT method
in three theoretical level of B3LYP, B3PW91, and PBEPBE, respectively. Investigating similar
structures also showed N-H group bending vibrations in the range of 1530 to 1670 cm-1.
4.3.5. C-N vibrations
In ADQF structure, [37] C-N stretching vibration appeared in the region of 1208 cm-1 by
experimental results, and in the range of 1208 and 1296 cm-1 by theoretical method. The
stretching vibration of C=N was appeared in the region of 1479 cm-1 by theoretical method. [41]
In TBH derivatives, [38] the stretching vibration of C=N was in the range of 1179 to 1571 cm-1
by experimental method, and was appeared in the range of 1126 to 1542 cm-1 by theoretical
method. However, this range of changes are due to presence of resonance and aromatic mode. In
amine groups and aromatic amines, the stretching vibration of aromatic C-N appears in the range
of 1000 to 1350 cm-1, and the stretching vibration of C=N appears in the range of 1500 to 1650
cm-1. Moreover, the bending vibration associated with C-N and C=N usually appear in the region
of 400 to 800 cm-1 with rather medium intensities. In CNPMPT structure, there should be no
vibration for C=N. but presence of resonance between nitrogen and carbon atoms increases the
absorption range of this bond and the rank of bond increases from 1 to 2 in some cases. In this
structure, the stretching vibration of C-N group was in the region of 1218 cm-1 by experimental
method, while appeared in three levels of 1220-1243, 1227-1243, and 1223-1237 cm-1 by DFT
method in three theoretical level of B3LYP, B3PW91, and PBEPBE, respectively. For C=N
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bond, the liberation was also in the region of 1514 cm-1 by experimental method, and in three
regions of 1500, 1508, and 1500 cm-1 by DFT method in three theoretical level of B3LYP,
B3PW91, and PBEPBE, respectively. As Table 3 indicates, the bending vibration of C-N group
also appears in regions less than 750 cm-1.
4.3.6. N=N and N–N vibrations
In BH complexes, [41] the stretching vibration of N=N was in the range of 1056 to 1257 cm-1 by
experimental method, and in the range of 1045 to 1267 cm-1 by theoretical method. The
stretching and bending vibrations are usually visible for N-N and N=N bonds in treasons. In
CNPMPT structure, the amplitude of N-N bond vibration is in the range of 1218 and 1256 cm-1
by experimental method, and in the range of 1184-1255, 1192-1259, and 1183-1258 cm-1 by
DFT method in three theoretical level of B3LYP, B3PW91, and PBEPBE, respectively. The
amplitude of vibration for N=N bond is also in the range of 1463 and 1514 cm-1 by experimental
method, and in the range of 1453-1500, 1449-1508, and 1437-1500 cm-1 by DFT method in three
theoretical level of B3LYP, B3PW91, and PBEPBE, respectively. Furthermore, the amplitude of
bending vibration of N-N-N is below 1000 cm-1.
4.3.7. C-O vibrations
The vibration of C-O group in CNPMPT is in the range of 1027, 1218, and 1256 cm-1 by
experimental method, and in the range of 1017-1269, 1020-1269, and 1009-1262 cm-1 by DFT
method in three theoretical level of B3LYP, B3PW91, and PBEPBE, respectively. The methoxy
group attached to the aromatic ring includes C-O bond, where two different types of carbon are
attached to oxygen. Therefore, the stretching vibration of C-O group is visible in two different
regions. It is usually expected that the stretching vibration of C-O appears in the range of 950 to
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1300 cm-1. In DMPF structure, [39] the stretching vibration of C-O group is reported in two
regions of 1990 and 1213 cm-1 by experimental method.
4.3.8. C-Cl vibrations
The stretching vibration of C-Cl in CNPMPT structure was appeared to be in the region of 1027
cm-1 by experimental method, and in the range of 1019-1093, 1027-1097, and 1011-1084 1262
cm-1 by DFT method in three theoretical level of B3LYP, B3PW91, and PBEPBE, respectively.
It has to be noted that aryl chlorines are expected to be appeared in the range of 1100 to 1305 cm-
1. The bending movement occurs easier than stretching movement and the constant force
coefficient, K, is smaller for it. Moreover, the bonds between atoms with higher weights vibrate
in lower frequencies compared to the bonds between atoms with lower weights. The trend of
C─H> C─C> C─O> C─Cl> C─Br> C─I is based on increasing vibration frequency.
4.4. NMR spectra
Nuclear magnetic resonance was first discovered in 1946, by Felix Bloch from Stanford
University and Edward Parcel from Harvard University, independently. [42] They showed
absorption of electromagnetic radiation resulted from transfer of nucleus energy levels occurred
in a strong magnetic field. These two physicists achieved the Nobel Prize of 1952 for their work.
[43] In the first five years after discovery of nuclear magnetic resonance method, chemists found
out that the molecular environment of objects affects the absorption of radiation by nucleons in
presence of a magnetic field, and this effect could be attributed to the molecular structure. The
development of nuclear magnetic resonance spectroscopy method was remarkable since then,
and this method has had a significant effect on development of organic chemistry, inorganic
chemistry and biochemistry. For further characterization of CNPMPT structure, besides FT-IR
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investigation, the amounts of chemical shifts for carbon and hydrogen atoms are also discussed
by utilizing the experimental and theoretical method of density function (Supplementary dataS3).
As the obtained results in tables 4 and supplementary dataS4 show, the results of chemical shift
of carbon atoms are highly consistent with each other. However, the results of hydrogen atoms
are a little different in some cases which could be attributed to solvent effects on hydrogen atoms
in empirical mode. The theoretical calculations are performed in gas phase and the solvent
effects are neglected. But the values of chemical shift are different depending on the type of
nucleon and chemical environment of atoms. The gauge including atomic orbitals (GIAO)
method was used to carry out calculations in three theoretical levels of B3LYP, B3PW91, and
PBEPBE. This method is applicable to calculate chemical shifts of many components and gives
precise results consistent with chemical shifts obtained experimentally. [43-45] The base mode
of 6-311G(d,P) was utilized for all theoretical levels. The results are TMS chemical shifts are
used as reference. First, the structure was optimized and the amounts of chemical shift was
13
calculated for different atoms. The consistency is rather high in C-NMR results. But there is a
1
high discrepancy between theoretical and experimental results for H-NMR, especially in H19,
which is due to solvent effects in experimental results, as mentioned earlier.
4.5. Molecular electronic potential maps
As the electrostatic potential map in Fig. 4 shows, charge distribution is different for different
parts of CNPMPT molecule in three theoretical levels of B3LYP, B3PW91, and PBEPBE. The
hydrogen atoms in this map have the lowest electrostatic potential, while the oxygen atoms have
the highest electrostatic potential. The chlorine atom is also shown in green and is within the
middle range of electrostatic potential. The obtained results for three theoretical levels are almost
similar. Furthermore, nitrogen atoms belonging to treason group are shown in yellow and almost
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have a more negative value compared to chlorine. The electrostatic potential actually represents
charge distribution of molecules in three dimensions. This map actually enables one to identify
and investigate the charge distribution and atomic charges in different parts of molecules.
Predicting the behavior and function of molecules in chemical reactions is also possible via this
this. In order to compute and present this map, first, the corresponding structure is optimized by
utilizing density functional theory, then the electrostatic potential map is calculated and recorded
using Molkele software. As shown in Fig. 4, the range of electrostatic potential changes for
CNPMPT structure in three theoretical levels of B3LYP, B3PW91, and PBEPBE is -0.0835-
0.0553, -0.0864-0.0597, and -0.0818-0.0592, respectively.
4.6. Fingerprint plots and corresponding Hirshfield surface coverage for CNPMPTstructure
3D shapes of Hirshfield surface coverage and 2D images of Fingerprint plots showed the share of
each atom in molecular interactions. Hydrogen atom had the highest share of 51.5% in
Fingerprint plots. On the other hand, nitrogen atoms had the lowest share of 8.1% in Fingerprint
plots and molecular interactions. Hirshfield surface analysis actually shows the molecular
interactions in 3D. The share of each molecular interactions is shown in Fig. 5.
4.7. Other molecular properties
The thermodynamic parameters, HOMO and LUMO values are discussed and investigated
through DFT results in three theoretical levels of B3LYP, B3PW91, and PBEPBE (Table 5). By
extracting these values, the electrophilicity, chemical hardness, chemical potential, dipole
moment, zero-point vibrational energy, entropy, and heat capacity of this structure is examined
and reported. The obtained results indicate the stability of structure in conformational state of E
(Supplementary dataS5). Although after conformational drawing of Z for this structure and
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optimization, because state E is more stable that state Z, again the optimized structure would
choose the conformational state of E with the lower energy level as the spatial interactions are
lower in this state.Further comparisons were done using GaussSum software, and DOS Spectrum
for all cases is reported in supplementary dataS6.
Crystallographic data for structural analysis reported in this paper have been deposited with the
Cambridge Crystallographic Data Centre and allocated the deposition number CCDC 1433072.
These data can be obtained free of charge via www.ccdc.cam.ac.uk/conts/retrieving.html (or
from the Cambridge Crystallographic Data Centre, 12, Union Road, Cambridge CB2 1EZ, UK;
Fax: +44 1223 336033, e-mail: deposit@ccdc. cam.ac.uk].
5. Conclusions
CNPMPT structure is unique and has many applications in various chemical, medical, painting,
industries etc. This compound is able to form complexes with different metals and can act as
multi-denticity ligand in different complexes. Furthermore, this structure is capable of having a
specific medicinal or antibacterial properties due to having two conformations of E and Z, which
is can be investigated by other researchers in future. This structure in synthesized by a new
1
method is investigated and characterized by FT-IR, Absorbance electron spectrum, H-NMR,
13C-NMR, and X-ray single crystal diffraction. The theoretical calculations for this structure are
discussed in the following using DFT method in three levels of B3LYP, B3PW91, and PBEPBE.
CNPMPT structure has orthorhombic structure with Pbca space group and wavelength of
0.71073. The DFT results in B3LYP theoretical level showed that this structure has a total
energy of -882733.1034 KCal/mol. Total entropy of this structure is 146.169 Cal/Mol-Kelvin,
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and its heat capacity is 69.157 Cal/Mol-Kelvin. This structure has the ability of forming polymer
and can form hydrogen bonds with the atoms in its neighborhood.
Acknowledgements
The authors are indebted to Ms. Esfandyar and Mr. Ehsan Fereyduni, for their interest in this
work and many helpful discussions.
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References
[1] D.B. Kimball, M.M. Haley, Triazenes: A versatile tool in organic synthesis. Angew Chem Int
Ed Engl. 41 (2002) 3338-3351.
[2] R. Lazny, J. Poplawski, J. Köbberling, D. Enders, S. Bräse, Triazenes: A useful protecting
strategy for sensitive secondary amines. Synlett. 8 (1999) 1304-1306.
[3] M. Kazem-Rostami, A. Khazaei, A.R. Moosavi-Zare, M. Bayat, S.Saednia, Novel one-pot
synthesis of thiophenols from related triazenes under mild conditions. Synlett, 23 (2012) 1893-
1896.
[4] A. Goeminne, P.J. Scammells, S.M. Devine, B.L. Flynn, Richter cyclization and co-
cyclization reactions of triazene-masked diazonium ions. Tetrahedron Lett. 51 (2010) 6882-
6885.
[5] D. Ionescu, V.Neagu, V. Dobre, I. Niculescu-Duvaz, Potential anticancer agents. XXII.
Pharmacological properties of some new triazene derivatives. Neoplasma.28 (1981)19-26.
[6] W.B. Chen, W.X. Ma, X.Y. Xu, Synthesis of 1-(4-antipyrine)-3-(3-nitroaniline)-triazene and
its color reaction with Mercury(II). Adv. Mater. Res. 455-456 (2012) 895-900.
[7] H. Tavallali, H. Shafiekhani, M.K. Rofouei, M. Payehghadr, A new triazene ligand
immobilized on triacetylcellulose membrane for selective determination of Mercury ion. J. Braz.
Chem. Soc. 25 (2014) 861-866.
[8] M.K. Rofouei, M.R. Melardi, M. Barkhi, H.R.K. Ghaydar, Synthesis and crystal structure of
Bis[1,3-bis(2-methoxyphenyl)triazene]mercury(II). Japan Soc. Anal. Chem. 24 (2008) X81-X82.
[9] M.B. Gholivand, M. Mohammadi, M. Khodadadian, M.K. Rofouei, Novel platinum(II)
selective membrane electrode based on 1,3-bis(2-cyanobenzene)triazene. Talanta, 78 (2009) 922-
928.
20

ACCEPTED MANUSCRIPT
[10] M.B. Gholivand, M. Mohammadi, M.K. Rofouei, Optical sensor based on 1,3-di(2-
methoxyphenyl)triazene for monitoring trace amounts of mercury(II) in water samplesa. Mater.
Sci. Eng. C 30 (2010) 847-852.
[11] M.K. Rofouei, M. Payehghadr, M. Shamsipur, A. Ahmadalinezhad, Solid phase extraction
of ultra traces silver(I) using octadecyl silica membrane disks modified by 1,3-bis(2-
cyanobenzene) triazene (CBT) ligand prior to determination by flame atomic absorption. J.
Hazard. Mater, 168 (2009) 1184-1187.
[12] M.K. Rofouei, A. Sabouri, A. Ahmadalinezhad, H. Ferdowsi, Solid phase extraction of ultra
traces mercury (II) using octadecyl silica membrane disks modified by 1,3-bis(2-
ethoxyphenyl)triazene (EPT) ligand and determination by cold vapor atomic absorption
spectrometry. J. Hazard. Mater. 192 (2011) 1358-1363.
[13] D.T. Hill, K.G. Stanley, J.E. Williams, B. Love, P.J. Fowler, J.P. McCafferty, E. Macko,
C.E. Berkoff, C.B. Ladd, 1,3-Diaryltriazenes: a new class of anorectic agents. J. Med. Chem. 26
(1983) 865-869.
[14] F. Brahimi, Z. Rachid, J.P. McNamee, M.A. Alaoui-Jamali, A.M. Tari, B.J. Jean-Claude,
Mechanism of action of a novel “combi-triazene” engineered to possess a polar functional group
on the alkylating moiety: Evidence for enhancement of potency. Biochem. Pharmacol, 70 (2005)
511-519.
[15] H. Adibi, M. B. Majnooni, A. Mostafaie, K. Mansouri and M. Mohammadi, Synthesis, and
in-vitro cytotoxicity studies of a series of triazene derivatives on human cancer cell lines. Iran. J.
Pharm. Res. 12 (2013) 695-703.
[16] H.S. Friedman, T. Kerby, H. Calvert, Temozolomide and treatment of malignant glioma.
Clin. Cancer Res. 6 (2000) 2585-2597.
21

ACCEPTED MANUSCRIPT
[17] S.S. Agarwala, J.M. Kirkwood, Temozolomide, a novel alkylating agent with activity in the
central nervous system, may improve the treatment of advanced metastatic melanoma.
Oncologist, 5 (2000) 144-151.
[18] K.C. Nicolaou, C.N.C. Boddy, H. Li, A.E. Koumbis, R. Hughes, S. Natarajan, N.F. Jain,
J.M. Ramanjulu, S. Bräse, M.E. Solomon, Total synthesis of vancomycin—part 2:
Retrosynthetic analysis, synthesis of amino acid building blocks and strategy evaluations. Chem.
Eur. J. 5 (1999) 2602-2621.
[19] P. Lazny, M. Sienkiewicz, S. Brase, Application of triazenes for protection of secondary
amines. Tetrahedron. 57 (2001) 5825-5832.
[20] P. Knochel, C.Y. Liu, Preparation of polyfunctional arylmagnesium reagents bearing a
triazene moiety. A new carbazole synthesis. Org. Lett. 7 (2005) 2543-2546.
[21] D.B. Kimball, T.J.R. Weakley, R. Herges, M.M. Haley, Deciphering the mechanistic
dichotomy in the cyclization of 1-(2-Ethynylphenyl)-3,3-dialkyltriazenes:ꢂ Competition between
pericyclic and pseudocoarctate pathways. J. Am. Chem. Soc. 124 (2002) 13463-13473.
[22] H.A. Dabbagh, A. Teimouri, A. Najafi, R. Shiasi, DFT and ab initio calculations of the
vibrational frequencies and visible spectra of triazenes derived from cyclic amines. Spectrochim.
Acta Part A 67 (2007) 437-443.
[23] A. Zarei, L. Khazdooz, H. Aghaei, G. Azizi, A.N.Chermahinie, A. R. Hajipour, Synthesis of
triazenes by using aryl diazonium silica sulfates under mild conditions. Dyes and Pigments
101(2014) 295-302.
[24] B.A. Iglesias, M. Hörner, H.E. Toma, K. Araki, 5-(1-(4-phenyl)-3-(4-nitrophenyl)triazene)-
10,15,20-triphenylporphyrin: a new triazene-porphyrin dye and its spectroelectrochemical
properties. J. Porphyrins Phthalocyan. 16 (2012) 200-209.
22

ACCEPTED MANUSCRIPT
[25] R.G. Parr, L.V. Szentpály, S. Liu, Electrophilicity index. J. Am. Chem. Soc. 121 (1999)
1922-1924.
[26] R. Ahmadi, R. Soleymani, The influence of tyrozine on energetic property in graphene
oxide: A DFT studies. Orient. J. Chem. 30 (2014) 57-62.
[27] R. Soleymani, R.D. Dijvejin, A.F.G.A.Hesar, E. Sobhanie, Synthesis 4-(4/-methylphenyl)-
2-mercaptothiazole structure with NMR, vibrational, Mass spectroscopy and DFT studies.
Oriental Journal of Chemistry. 28 (2012) 1291-1304.
[28] R. Soleymani, Y. Mohammad Salehi, T. Yousofzad, M. Karimi-Cheshmeh Ali, Synthesis,
NMR, vibrational and Mass Spectroscopy with DFT/HF studies of 4-(4/-Bromophenyl)-2-
mercaptothiazole structure. Orient. J. Chem. 28 (2012) 627-638.
[29] J.J. McKinnon, D. Jayatilaka, M.A. Spackman, ChemCommun.37 (2007) 3814-3816.
[30] J.J. Koenderink, Solid Shape,Cambridge MA, MIT Press.(1990).
[31] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman,
J.A. Montgomery, T. Vreven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V.
Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada,
M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H.
Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, C. Adamo, J. Jaramillo, R.
Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochter ski, P.Y.
Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich,
A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B.
Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A.
Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y.
23

ACCEPTED MANUSCRIPT
Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C.
Gonzalez, J.A. Pople, Gaussian 03 Revision C.02, Gaussian Inc., Pittsburgh, PA, (2003).
[32] M.H Jamroz, Vibrational Energy Distribution Analysis VEDA 4, Warsaw.(2004).
[33] Computational Chemistry Comparison and Benchmark DataBase, Release 17b, September,
NIST Standard Reference Database 10 (2015).
[34] S.K.Wolff,D.J.Grimwood,J.J.McKinnon,D.Jayatilaka,and M. A. Spackman,
CrystalExplorer, Version 1. 5, University of Western Australia, Perth, Australia, (2007).
[35] C. F. Macrae, I. J. Bruno, J. A. Chisholm, P. R. Edgington, P. McCabe, E. Pidcock, L.
Rodriguez-Monge, R. Taylor, J. van de Streek and P. A. Wood, Mercury CSD 2.0 – new features
for the visualization and investigation of crystal structures. J. Appl. Cryst. 41 (2008) 466-470.
[36] P. Flükinger, H. P. Lüthi, S. Portmann, and J. Weber, Molekel 4.3, Swiss Center for
Scientific Computing, Manno.(2000).
[37] D.M. Suresh, M. Amalanathan, S. Sebastian, D. Sajan, I. Hubert Joe, V. BenaJothy, Ivan
Nemec, Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical
compound 7-Amino-2,4-dimethylquinolinium formate – DFT approach. Spectrochim. Acta Part
A. 115 (2013) 595-602.
[38] M. NadeemArshad, A. Bibi, T. Mahmood, A. M. Asiri, and K. Ayub, Synthesis, crystal
structures and spectroscopic properties of triazine-based hydrazone derivatives; A comparative
experimental-theoretical study. Molecules 20 (2015) 5851-5874.
[39] M.K. Rofouei, N. Sohrabi, M. Shamsipur, E. Fereyduni, S. Ayyappan, N. Sundaraganesan,
X-ray crystallography characterization, vibrational spectroscopy, NMR spectra and quantum
chemical DFT/HF study of N,N′-di(2-methoxyphenyl)formamidine. Spectrochim. Acta Part A 76
(2010) 182-190.
24

ACCEPTED MANUSCRIPT
[40] M.K. Rofouei, E. Fereyduni, N. Sohrabi, M. Shamsipur, J. Attar Gharamaleki, N. Sundaraganesan,
Synthesis, X-ray crystallography characterization, vibrational spectroscopic, molecular electrostatic
potential maps, thermodynamic properties studies of N,N
Part A 78 (2011) 88-95.
′-di(p-thiazole)formamidine. Spectrochim. Acta
[41] A.A. Soayed, H.M. Refaat, L. Sinha, Syntheses, structural elucidation, thermal properties, theoretical
quantum chemical studies (DFT) and biological studies of barbituric–hydrazone complexes. J. Saudi
Chem. Soc. 19 (2015) 217-226.
[42] M. Wainwright, Background and Theory Page of Nuclear Magnetic Resonance Facility, Analytical
Centre - University of Southern Wales Sydney (2014).
[43] N. Shah, A. Sattar, M. Benanti, S. Hollander, L. Cheuck, Magnetic resonance spectroscopy as an
imaging tool for cancer: A review of the literature. J. Am. Osteopathic Assoc. 106 (2006) 23-27.
[44] R. D. Dejvejen, G. Zarei, R. Soleymani, NMR, aromaticity and energetic property in C6H4O2M
(M=C, S, O and N) dicarbaldehyde derivatives: A computational study. Orient. J. Chem. 28 (2012) 1229-
1240.
[45] R. Soleymani, M. Karimi-Cheshmeh Ali, N. Niakan, NMR Studies of BH3-attaching in the zigzag
and armchair BN nanotubes: A DFT study. Orient. J. Chem. 28 (2012)815-827.
25

ACCEPTED MANUSCRIPT
Table Captions:
Table 1. Crystal data and structure refinement.
Table 2. Computed and experimental bond distances (A), bond angles (◦), torsion angles (◦) for
(CNPMPT) structure.
Table 3. Vibrational wavenumbers obtained for (CNPMPT) structure at B3LYP, B3PW91 and
PBEPBE levels of theory with 6-311G (d,p) basis set [harmonic frequency (cm−1), IRint
(Kmmol−1)].
Table 4.Theoretical and experimental 1H and 13C isotropic chemical shifts (with respect to
TMS, all values in ppm) for (CNPMPT) structure.
Table 5. Theoretically computed energies (kcal.mol−1), zero-point vibrational
energies(kcal.mol−1), rotational constants (GHz), heat capacities (cal.mol-1.K-1),
entropies(cal.mol-1.K-1), dipole moment (Debye), molecular orbitals energies (
ε
HOMOand εLUMO
,
eV), electronic chemical potential, ꢀ (eV), chemical hardness, η (eV), electrophilicity, ω (eV)
and maximum amount of electronic charge transfer for (CNPMPT) structure.
Scheme Captions:
Scheme 1. Synthetic route for the new compound (CNPMPT).
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Figure Captions:
Fig. 1. Serial number of atom and optimized structure of (CNPMPT) structure performed by
B3LYP/6-311G (d, p) method (a), different conformations of the title compound (b).
Fig. 2. A view of the hydrogenbonds are shown as dashed lines (a) and crystal packing down the
α-axis for the title compound (b).
Fig. 3. FT-IR spectrum obtained by experimental (a) in terms of percentage transmission and
DFT method (b) in terms of intensity for (CNPMPT) structure.
Fig. 4. B3LYP/6-311G (d, p) calculated 3D molecular electrostatic potential of CNPMPT
(isosurfacevalue 0.01 a.u.).
Fig. 5. Show 3D and 2D images of fingerprint plots and corresponding Hirshfield surface
coverage for CNPMPT structure.
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Supplementary Data Captions:
S1. Correlation between bond length obtained by experimental (X-Ray diffraction) and
theoretical value (DFT method) for the title compound.
S2. Correlation between DFT and experimental frequenciesfor the title compound.
1
S3. Show 13C (a) and H (b) NMR spectrum obtained by experimental methods for the title
compound.
S4. Correlation between theoretical and experimental methods for NMR property in (CNPMPT)
structure.
S5. Show E (a) and Z (b) conformation of (CNPMPT) structure.
S6. Show density of spectrum (Dos) and HOMO-LUMO highlight obtained by B3LYP level of
theoryfor CNPMPT structure.
28