Synthesis, experimental and DFT studies on crystal structure, FT-IR, 1H, and 13C NMR spectra, and evaluation of aromaticity of three derivatives of xanthens

Article abstract of DOI:10.1134/S107036321312027X

Several derivatives of xanthenes are prepared by the condensation of aldehydes and dimedone in H₂O in the presence of a catalytic amount of trichlorotriazine. The crystalline products were characterized by FTIR, ¹H, and ¹³

Full text of DOI:10.1134/S107036321312027X

ISSN 1070-3632, Russian Journal of General Chemistry, 2013, Vol. 83, No. 12, pp. 2352–2360. © Pleiades Publishing, Ltd., 2013.
Synthesis, Experimental and DFT Studies on Crystal Structure,
FT–IR, 1H, and 13C NMR Spectra, and Evaluation of Aromaticity
of Three Derivatives of Xanthens1
L. Zare Fekria, M. Nikpassandb, and M. Goldoosta
a Department of Chemistry, Payame Noor University, PO Box 19395-3697 Tehran, Iran
email: chem_zare@pnu.ac.ir; chem_zare@yahoo.com
b Department of Chemistry, Rasht Branch, Islamic Azad University, Rasht, Iran
Received July 22, 2013
Abstract—Several derivatives of xanthenes are prepared by the condensation of aldehydes and dimedone in
H2O in the presence of a catalytic amount of trichlorotriazine. The crystalline products were characterized by
FTIR, 1H, and 13C NMR spectra. Density Functional Theory (DFT) calculations on the B3LYP level were used
1
to optimize the geometry and calculate the crystal structure, FTIR, H NMR and 13C NMR spectra of the
selected synthesized compounds. We found that the values of FTIR, 1H, and 13C NMR spectra obtained by the
B3LYP method are in accordance with experimental data. The calculated NICS indicate that the six-membered
rings in xanthenes are essentially homoaromatic.
DOI: 10.1134/S107036321312027X
INTRODUCTION
shift (NICS) calculated at the ring center is a good
criterion for aromaticity in such molecules.
Xanthene derivatives are important heterocyclic
compounds because of their useful biological and
pharmacological properties like antiviral, antibacterial
and antiinflammatory activities [1]. These compounds
are also used as dyes [2], as luminescent sensors [3], in
laser technologies [4], in fluorescent materials for the
visualization of biomolecules [5], and in photodynamic
therapy [6].
EXPERIMENTAL
IR spectra were determined on a Shimadzu IR-470
1
spectrometer. H NMR spectra were obtained on a
Bruker DRX 500, and 13C NMR spectra, on a Bruker
DRX 125 Avance spectrometer, in CDCl3 as solvent
and with TMS as internal reference. Chemicals were
purchased from Merck and Fluka. All used solvents
were dried and distilled according to standard
procedures.
In recent years, density functional theory (DFT)
calculations have been used extensively for calculating
a wide variety of molecular properties such as
equilibrium structure, charge distribution, FTIR and
NMR spectra, and have provided reliable results which
are in agreement with experimental data [7]. In this
research, Beck’s three-parameter exchange functional
[8] with Lee, Yang and Parr’s [9] correlation
functional (B3LYP) developed by Truhlar et al. [10]
have been used to perform theoretical calculations on
A mixture of aldehyde (1 mmol), dimedone
(2 mmol), and 0.03 g of trichlorotriazine (TCT) in
10 mL of H2O were refluxed for the required reaction
time (2–6 min). The progress of the reaction was
monitored by TLC (EtOAc:petroleum ether 1 : 4).
After completion of the reaction, the mixture was
filtered. The product was recrystallized from ethanol to
produce xanthene derivatives IIIa–IIIc as pure
crystalline products.
1
the structure, FTIR, H, and 13C NMR spectra, and
some additional properties of the title compounds.
3,4,6,7-tetrahydro-9-(4-methoxyphenyl)-3,3,6,6-
In 1996, Schleyer [11] proposed the nucleus
independent chemical shifts (NICS) as a reliable crite-
rion of aromaticity. The nucleus independent chemical
tetramethyl-2H-xanthene-1,8-(5H,9H)-dione (IIIa).
1
Colorless solid; mp: 146–148°C; H NMR (500 MHz,
CDCl3), δ, ppm: 0.99 s (6H); 1.1 s (6H); 2.2 q (J =
16.4 Hz, 4H); 2.45 s (4H); 3.73 s (3H); 4.7 s (1H), 6.73
d (J = 8.62 Hz, 2H), 7.18 d (J = 8.6 Hz, 2H). 13C NMR
1
The text was submitted by the authors in English.
2352

SYNTHESIS, EXPERIMENTAL AND DFT STUDIES ON CRYSTAL STRUCTURE
2353
Table 1. Effect of catalyst amount on the synthesis of com-
pound IIIa
X
CHO
Run no. Catalyst amount, g
Time, min
Yield, %
O
O
O
O
TCT
+ 2
1
2
–
180
30
52
83
0.01
X
O
3
4
0.03
0.05
5
5
96
94
I
II
III
Scheme 1. Pathway to xanthenes synthesis.
(500 MHz, CDCl3), δ; ppm: 28.47, 30.44, 32.97,
33.36, 42.00, 116.79, 127.45, 129.19, 129.52, 145.25,
164.47, 193.22. IR (KBr), ν, cm–1: 3014, 2873, 1667,
1624, 1510, 1360, 1215.
2H). 13C NMR (125 MHz, CDCl3), δ, ppm: 191.35,
147.0, 146.54, 130.9, 128.1, 123.9, 115.3, 47.4, 33.7,
31.9, 29.9, 27.9 IR (KBr), ν, cm−1: 3100, 2920, 1680,
1600, 1540, 1510, 1340, 1200.
3,4,6,7-tetrahydro-3,3,6,6-tetramethyl-9-phenyl-
2H-xanthene-1,8(-5H,9H)-dione (IIIb). White solid;
mp: 202–203°C; 1H NMR (500 MHz, CDCl3), δ, ppm:
1.03 s (6H); 1.14 s (6H); 2.24 q (J = 15.70 Hz, 4H);
2.50 s (4H); 4.79 s (1H); 7.24 m (5H). 13C NMR (500
MHz, CDCl3), δ, ppm: 27.29, 29.30, 31.47, 32.28,
40.84, 50.69, 115.26, 128.23, 129.78, 132.03, 142.71,
162.44, 196.00. IR (KBr), ν, cm−1: 3019, 2964, 1667,
1625, 1464, 1215.
The other products were characterized by compari-
son of their spectroscopic and physical data with those
of samples synthesized by reported procedures.
Computational details. All molecular structures
were completely optimized at the B3LYP level of
theory along with standard 6-31G(d) basis set. Har-
monic vibration frequencies were calculated for all
optimized structures to prove that true stationary points
had been found. The gauge-independent atomic orbital
(GIAO) NMR calculations were carried out at the
B3LYP level using 6-31G(d) basis set. To study the
aromaticity of the hetrocycles, the NICS at the center
of all rings was calculated using the gauge independent
atomic orbital (GIAO) method at the B3LYP level
3,4,6,7-tetrahydro-3,3,6,6-tetramethyl-9-(4-nitro-
phenyl)-2H-xanthene-1,8-(5H,9H)-dione (IIIc). White
solid; mp: 220–222°C; 1H NMR (500 MHz, CDCl3), δ,
ppm: 1.15 s (6H), 1.28 s (6H), 2.35–2.54 m (8H), 5.58
s (1H), 7.29 d (J = 8.8 Hz, 2H), 8.17 d (J = 8.8 Hz,
Table 2. Synthesis of xanthenes using TCT
Run no.
Aldehyde
mp (observed) mp (reported)
References
[17]
Time, min
Yield, %a,b
1
5
6
2
2
5
3
4
3
5
5
3
96
94
98
93
92
97
92
95
90
91
93
242–243
202–203
220–222
231–233
210–212
171–173
250–251
248–249
225–226
225–227
222–224
242–243
204–206
221–223
229–230
210–211
170–172
248–249
247–248
225–227
226–229
–
4-Methoxybenzaldehyde
Benzaldehyde
2
[17]
3
[17]
4-Nitrobenzaldehyde
4-Chlorobenzaldehyde
4-Methylbenzaldehyde
3-Nitrobenzaldehyde
2-Nitrobenzaldehyde
4-Hydroxybenzaldehyde
2-Chlorobenzaldehyde
2-Bromobenzaldehyde
4-Fluorobenzaldehyde
4
[17]
5
[17]
6
[17]
7
[17]
8
[17]
9
[17]
10
11
[17]
[17]
a
b
Isolated yield. The products were characterized by comparison of their spectroscopic and physical data with those of samples
synthesized by published.
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 83 No. 12 2013

2354
ZARE FEKRI et al.
OH
O
O
HO
Cl
N
OH
Cl
HCl
N
N
N
Ar
H
OH
N
O
H+
OH
Ar
N
Cl
O
H
+
H2O
O
O
H
O
Ar
H
Ar
H+
I
O−H
O
O
Ar
O O
Ar
OH HO
Ar
H2O
O
O
O
Scheme 2. Proposed mechanism of the TCT catalyzed synthesis of xanthenes.
using 6-31G(d) basis set. Calculations of geometry
optimizations, vibration frequencies, and NMR
parameters were carried out with GAUSSIAN 98
program [12].
efficient and environmentally friendly procedure for
the synthesis of pharmaceutical compounds [13–16]
prompted us to synthesize of derivatives of xanthenes
1
and to calculate the FT-IR, H, and 13C NMR spectra
of selected compounds at the B3LYP level.
RESULTS AND DISCUSSION
Recent developments in the xanthes chemistry and
our continued interest in the development of an
Initially, the optimization of catalyst amount to use
in the synthesis of compound IIIa was performed
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SYNTHESIS, EXPERIMENTAL AND DFT STUDIES ON CRYSTAL STRUCTURE
2355
IIIa
IIIb
IIIc
Fig. 1. Geometry optimization of IIIa–IIIc.
(Table 1). The optimized amount of TCT to carry out
this reaction is 0.03 g. The higher amount of TCT does
not have any significamt effect on the reaction yield
and time.
rings correspond to sp2-hybridized bond angles (120°)
as shown in Table 3.
The observed and calculated frequencies using DFT
B3LYP/6-31G and probable assignments for IIIa–IIIc
are summarized in Table 4. The C=C stretching bands
appear at 1464–1625 cm−1 in the infrared spectrum.
The bands occurring in the IR spectra at 1215 and
1360, 1215 and 1200 cm−1 in IIIa–IIIc, respectively
are assigned to the C–O stretching vibrations. The
C=O stretching bands are observed at 1667, 1667, and
1680 cm−1 in IIIa–IIIc, respectively.
With the best catalyst in hand, several aromatic
aldehydes were converted to correspounding xanthenes
by the treatment with two equivalents of dimedones.
The results are summerized in Table 2.
The possible mechanism of the synthesis of
compounds III in the presence of TCT as a catalyst is
shown in Scheme 2. On the basis of this mechanism,
TCT catalyzes this reaction by conversion itself to HCl
in situ and activating the aldehyde by making the
carbonyl group susceptible to the nucleophilic attack
by dimedone followed by the nucleophilic attack of the
second molecule of dimedone on the α,β-unsaturated
compound in Micheal addition reaction, enolization
and dehydration giving product III as a result.
The aromatic C–H stretching vibrations in IIIa–
IIIc are observed at 3014, 3019, and 3100 cm–1,
respectively. The asymmetric and symmetric stretching
vibrations of the nitro group are the most intense bands
of the spectrum. The frequencies observed at 1510 cm−1
in the infrared spectrum are assigned to the –NO2
asymmetric stretching modes of IIIc. The very strong
symmetric stretching vibration of nitro group of the
compound is assigned to the wave number 1340 cm−1
in the infrared spectra. The correction factors used to
correlate the experimentally observed and theoretically
computed frequencies for each vibration mode of IIIa–
The geometries were optimized at the B3LYP level
of theory with standard 6-31G(d) basis set as shown in
Fig. 1. The harmonic vibration frequencies were cal-
culated by this method and the results were compared
with experimental FTIR spectrum. The most widely
used technique for calculating NMR shielding tensors
is the GIAO (Gauge Including Atomic Orbital) method.
This method was used for calculating 1H NMR and 13C
NMR chemical shifts at the B3LYP/6-31G(d) level.
All the calculations were carried out with the Gaussian
03 software.
X
10
H17
9
H15
H14
11
A
12H18
H13 O28
52H
51H
50H
49H
48H
47H
7
4
O 27
H29
3
5
H30
19
26
H 35
H 36
H 37
20
21
25
B
33
34
31
32
24
23
The structure and the scheme of atoms numbering
in IIIa–IIIc are shown in Fig. 2.
22
2
6
O
1
H
H
H
42
H
H
H
41
44
H
43
H
Evaluation of data on bond distances, bond angles,
and dihederal angles indicates the presence of
resonance in pyran rings, since (a) the bond distances
C–O in pyran rings are shorter than the standard value
(C–O 1.43 Å) and (b) the bond angles C–O–C in pyran
40
38
H
39
45
46
IIIa, X = OCH3; IIIb, X = H; IIIc, X = NO2;.
Fig. 2. Structure and atom numbering of IIIa–IIIc.
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 83 No. 12 2013

2356
ZARE FEKRI et al.
Table 3. Selected structural parameters calculated for IIIa–IIIc by DFT/B3LYP method with a 6-31G basis sets
Parameter
Parameter
IIIa
Bond length
IIIb
IIIc
IIIa
IIIb
IIIc
Bond angle
118.1703
111.7056
107.9273
O1–C2
C2–C3
C3–C19
1.3764
1.3764
1.4323
1.3764
1.3764
1.4671
1.3761
1.3764
1.4135
C2–O –C6
C5–C4–C7
C5–C4–H13
118.1243
111.5515
108.0078
118.2373
111.2752
108.1880
C3–C4,
C4–C5
C4–C7
1.5237
1.5237
1.5377
1.5237
1.5236
1.5382
1.5234
1.5234
1.5373
C7–C4–H13
C4–C7–C8
107.2043
121.2660
107.3702
121.0132
107.3716
120.9553
C4–H13
C5–C6
C7–C8
1.0930
1.3764
1.3996
1.0927
1.3764
1.3967
1.0925
1.3764
1.3984
Dihederal angle
C8–C9
1.3881
1.3949
1.3909
C4–C7–C8–H14
C4–C7–C12–H18
C5–C4–C7–C8
0.0004
0.0003
–118.0281
–0.006
0.0031
–118.1448 –118.2126
0.0000
0.0002
C19–O27
1.2345
1.2453
1.2146
C5–C4–C7–C12
H13–C4–C7–C8
61.9711
0.0108
61.8501
0.0071
61.787
0.0027
Table 4. Observed FTIR and frequencies calculated using B3LYP/6-31G(d) force field
IIIa
IIIb
IIIc
Assignment
calculated
1213.65
1378.89
–
experimental calculated experimental
calculated
experimental
1200
ν(C–O)
1215
1360
–
1213.13
1215
–
1213.55
–
ν(C–O)
ν(NO2)
ν(NO2)
ν(C=C)
ν(C=C)
ν(C=O)
–
–
–
–
1366.06
1550.30
1573.07
1712.05
1732.22
1340
–
–
–
–
1510
1540.00
1648.60
1710.56
1510
1624
1667
1450.3
1710.77
1732.14
1464
1625
1667
1540
1600
1680
ν(C–H) aliphatic
ν(C–H) aromatic
2999.45
3016.85
2873
3014
3017.26
3089.13
2964
3019
3009.85
3095.37
2920
3100
IIIc under DFT-B3LYP method are similar. The linear
regression between the experimental and theoretical
wave numbers of IIIa–IIIc are shown in Figs. 3 and 4.
Thus, vibration frequencies calculated by using the
B3LYP functional with 6-31G basis sets can be
utilized to eliminate the uncertainties in the funda-
mental assignments in infrared vibration spectra.
spectrum, with chemical shift values from 100 to
1
150 ppm in 13C NMR, and 6–8.5 ppm in H NMR
spectra of IIIa–IIIc.
Due to the influence of electronegative atom, the
chemical shift value of C2 in IIIa–IIIc differ signi-
ficantly in the shift positions, and the corresponding
values of chemical shifts related to C2 are 163.42 in
IIIa, 162.44 in IIIb, and 164.53 ppm in IIIc,
respectively. A downfield shift is observed for C2
compared with C3 in IIIa–IIIc. That is due to the
mesomeric effect between C2–C3–C19–O27. The cal-
culated and experimental chemical shift values given
1
The H and 13C theoretical and experimental che-
mical shifts, isotropic shielding tensors, and as-
signments of signals in the NMR spectra of IIIa–IIIc
are presented in Tables 5 and 6, respectively. Aromatic
carbons give signals in overlapped areas of the
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SYNTHESIS, EXPERIMENTAL AND DFT STUDIES ON CRYSTAL STRUCTURE
2357
(a)
Experimental wave number
Calculated chemical shift, ppm
Fig. 4. A plot of correlation between experimental and
theoretical IR spectrum of IIIc at the B3LYP/6-31G(d)
level.
Calculated wave number
(b)
(a)
0.518x + 0.962y
R2 = 0.974
Experimental wave number
Calculated chemical shift, ppm
(b)
0.102x + 1.002y
R2 = 0.999
Calculated wave number
Fig. 3. A plot of correlation between experimental and
theoretical IR spectra of (a) IIIa and (b) IIIb at the
B3LYP/6-31G(d) level.
in Tables 5 and 6 show a good agreement. The linear
1
regressions of the experimental and theoretical H and
13C NMR Chemical shifts of IIIa–IIIc are presented in
Calculated chemical shift, ppm
Figs. 5–7.
Fig. 5. A plot of correlation between experimental and
1
theoretical (a) H NMR and (b) 13C NMR chemical shifts
Aromaticity is a central concept in explaining the
structure, stability, and reactivity of certain molecules.
It is commonly explained by the ring current theory
that attributes the unique properties shared by aromatic
molecules to a special electron delocalization in which
the geometry allows the electrons a cyclic path for
delocalization. NICS has been used as a reliable
of IIIa calculated at the B3LYP/6-31G(d) level.
criterion of aromaticity since it has been proposed by
Schleyer et al. in 1996.
According to the definition of NICS, which has
been explained in the introduction part, the more
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2358
ZARE FEKRI et al.
Table 5. Experimental and calculated 1H NMR isotropic chemical shifts (ppm) with respect to TMS in the spectra of IIIa–IIIc
IIIa
IIIb
IIIc
experimental
Assignment
H50, H49, H48
calculated
0.38
experimental calculated experimental
calculated
0.27
0.99
0.38
1.03
1.15
H47, H46, H45
H44, H43
H51, H52
X16
H13
H17
1.37
1.71
2.95
1.77
3.99
6.28
7.07
1.1
2.2
1.36
1.77
1.72
7.16
4.06
7.16
7.16
1.14
2.5 0
2.24
7.24
4.79
7.24
7.24
0.45
1.84
2.34
–
1.28
2.45
2.94
–
3.73
2.45
4.7 0
6.73
7.18
4.13
7.7
4.58
8.17
7.29
H18
7.36
Table 6. Experimental and calculated 13C NMR isotropic chemical shifts (ppm) with respect to TMS in the spectra of IIIa–IIIc
IIIa
IIIb
IIIc
experimental
Assignment
calculated
28.02
32.45
32.82
34.08
39.53
–
experimental calculated experimental
calculated
28.23
28.40
33.44
34.33
48.98
–
C33
C21
C22
C4
C20
X16
C3
28.47
30.44
32.97
33.36
42.00
–
27.81
28.04
32.09
32.59
39.62
49.65
117.46
128.02
27.29
29.30
31.47
32.28
40.84
50.69
115.26
128.23
27.90
29.90
31.90
33.70
47.40
–
118.32
127.63
116.79
129.52
117.51
123.76
115.3
123.92
C11
C12
C7
127.46
148.03
127.45
164.47
193.22
129.19
145.25
127.51
163.42
196.66
128.48
134.44
141.65
164.73
193.25
129.78
132.03
142.71
162.44
196.01
127.74
148.56
135.07
168.23
194.70
128.07
146.99
130.9
C10
C2
164.53
191.35
C19
Table 7. Data for NICS calculation of IIIa–IIIc
negative the value of NICS the more aromatic is the
molecule. The calculated NICSs of IIIa–IIIc are listed
in Table 7. Comparison of the NICSs of ring A with
that of ring B indicates that all of rings A are more
aromatic than rings B.
Comp. no. Ring
NICS0
–9.1716
0.4442
NICS0.5
–10.1449
–1.4045
NICS 1
–9.8130
–2.4810
A
B
IIIa
IIIb
The NICS calculated at 0, 0.5, and 1 Å indicates
that the data will increase as the result of increasing
distances from the centers of rings.
A
B
A
B
–8.4391
0.8206
–9.1781
1.0328
–10.0818
–0.9743
–10.5063
–0.6805
–10.3662
–1.7438
–10.2512
–1.3901
On the other hand, we found B ring has negative
calculated NICS1 and is relatively stable. We realize it
has a homoaromatic structure as shown in Fig. 8.
IIIc
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SYNTHESIS, EXPERIMENTAL AND DFT STUDIES ON CRYSTAL STRUCTURE
2359
(a)
(a)
0.501x + 0.982y
R2 = 0.978
Calculated chemical shift, ppm
(b)
Calculated chemical shift, ppm
(b)
0.154x + 0.985y
R2 = 0.996
Calculated chemical shift, ppm
Fig. 7. A plot of correlation between experimental and
1
theoretical (a) H NMR and (b) 13C NMR chemical shifts
of IIIc calculated at the B3LYP/6-31G(d) level.
Calculated chemical shift, ppm
Fig. 6. A plot of correlation between experimental and
1
theoretical (a) H NMR and (b) 13C NMR chemical shifts
of IIIb calculated at the B3LYP/6-31G(d) level.
CONCLUSIONS
The geometries of IIIa–IIIc were optimized with
DFT-B3LYP using 6–31G basis sets. The selected
molecular structural parameters of the optimized
geometries of the compounds have been obtained from
DFT calculations. The vibration frequencies of the funda-
mental modes of the compound have been precisely
assigned and analyzed and the theoretical results were
compared with the experimental vibrations. 1H and 13C
NMR isotropic chemical shifts were calculated and the
assignments made were compared with the experi-
Fig. 8. Representation of homoaromaticity in xanthene ring.
mental values. Thus the present investigation provides
complete vibration assignments, structural information,
and chemical shifts of the compounds. Finally, we
present the calculated NICS values for all molecules
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2360
ZARE FEKRI et al.
10. Zhao, Y., Gonzalez-Garcia, N., and Truhlar, D.G.,
J. Phys. Chem. A, 2005, vol. 109, no. 9, pp. 2012–2018.
11. Schleyer, P.V.R., Chem. Rev., 2001, vol.101, no. 5,
and discuss the change in their aromaticity associated
with the structural modifications. The calculated NICS
indicate that the xanthene ring is essentially
homoaromatic with NICS values falling within the
range from –1 to –2 ppm.
pp. 1115–1118.
12. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E.,
Robb, M.A., Cheeseman, J.R., Montgomery, J.A.,
Vreven, T., Kudin, K.N., Burant, J.C., Millam, J.M.,
Iyengar, S.S., Tomasi, J., Barone, V., Mennucci, B.,
Cossi, M., Scalmani, G., Rega, N., Petersson, G.A.,
Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R.,
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ACKNOWLEDGMENTS
We thank the Research Committee of Islamic Azad
University of Rasht Branch for partial support given to
this study.
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