Fluorescence studies of selected 2-alkylaminopyrimidines

Article abstract of DOI:10.3390/90700520

The reactions of 2-chloropyrimidine with methylamine, ethylamine and piperidine gave the corresponding 2-N-methylamino-, 2-N-ethylamino- and 2N-piperidinopyrimidines, respectively. The fluorescence properties of these alkylamino derivatives in chloroform, ethyl acetate, carbon tetrachloride, acetone, ether, ethanol and methanol were studied. All the alkylamino derivatives showed the highest fluorescence intensity in polar protic solvents; thus 2-N-methylaminopyrimidine (highest fluorescence intensity at 377 nm when excited at 282 nm) and 2-N-ethylaminopyrimidine (highest fluorescence intensity at 375 nm, when excited at 286 nm) showed the highest fluorescence in methanol. In ethanol, 2-N-piperidinopyrimidine showed a fluorescence peak at 403 nm when excited at 360 nm and in chloroform it fluoresced at 392 nm when excited at 356 nm.

Full text of DOI:10.3390/90700520

Molecules 2004, 9, 520-526
molecules
ISSN 1420-3049
http://www.mdpi.org
Fluorescence Studies of Selected 2-Alkylaminopyrimidines
Z. Abdullah 1,*, N. Mohd Tahir 2, M. R Abas 1 , Z. Aiyub 1 and B.K Low 3
1
Department of Chemistry, Faculty of Science, Univ. of Malaya, 50603, Kuala Lumpur, Malaysia.
Department of Chemical Sciences, Kolej Universiti Sains dan Teknologi, Mengabang Telipot, 21030
2
Kuala Terengganu, Terengganu, Malaysia.
Lot 15, Jalan 1B, Kg. Cheras Baru, 56100, Kuala Lumpur, Malaysia.
3
* Author to whom correspondence should be addressed: zana@um.edu.my; Tel: (+60)-03-79674240;
Fax: (+60)-03-79674193
Received: 2 March 2004 / Accepted: 15 March 2004 / Published: 30 June 2004
Abstract: The reactions of 2-chloropyrimidine with methylamine, ethylamine and
piperidine gave the corresponding 2-N-methylamino-, 2-N-ethylamino- and 2N-
piperidinopyrimidines, respectively. The fluorescence properties of these alkylamino
derivatives in chloroform, ethyl acetate, carbon tetrachloride, acetone, ether, ethanol and
methanol were studied. All the alkylamino derivatives showed the highest fluorescence
intensity in polar protic solvents; thus 2-N-methylaminopyrimidine (highest fluorescence
intensity at 377 nm when excited at 282 nm) and 2-N-ethylaminopyrimidine (highest
fluorescence intensity at 375 nm, when excited at 286 nm) showed the highest
fluorescence in methanol. In ethanol, 2-N-piperidinopyrimidine showed a fluorescence
peak at 403 nm when excited at 360 nm and in chloroform it fluoresced at 392 nm when
excited at 356 nm.
Keywords: Fluorescence spectroscopy, alkylaminopyrimidines, fluorometry, fluorogenic
reagents

Molecules 2004, 9
521
Introduction
Science and technology are progressing very fast but advances in science, especially in the fields of
biology, chemistry and medicine, are sometimes limited by the availability of suitable extremely
sensitive analytical techniques. For example, analytical techniques are needed to examine mechanisms
as well as for investigating the behaviour of certain analytical reagents at very low concentrations. In
environmental science, a very sensitive technique is needed to detect chemical pollutants such as
phenols, amines and aromatic hydrocarbons.
The fluorescence technique has been used extensively for the detection of amino acids [1-3]. For
non-fluorescent amino acids, structural modifications can be carried out to give fluorescent products,
which are then detected fluorometrically. Thus, for example, tryamine, found in animal urine and
tissues, can be determined by first condensing it with formaldehyde, followed by oxidation to give a
fluorescent product [4], which is then estimated by this technique. Obviously, fluorescent amines can
also be detected fluorometrically. For example, serotine (hydroxyindole) is a very highly fluorescent
compound and therefore can be easily detected using fluorescence spectroscopy [5].
Aliphatic amines are non-fluorescent compounds. Currently, the detection of individual aliphatic
amines is done by first separating them using various chromatographic techniques, followed by
identification, either by comparing the retention time on a chromatogram or using mass spectroscopy.
When aliphatic amines are treated with a selected heterocyclic compounds, fluorescent products were
obtained [6]. These results have been the starting point of a preliminary study towards detecting
aliphatic amines using a fluorescence technique.
Results and Discussion
The secondary 2-alkylaminopyrimidines were obtained by reacting 2-chloropyrimidine with the
respective primary alkylamines. Thus, 2-N-methylaminopyrimidine and 2-N-ethylaminopyrimidine
were obtained when an ethanolic solution of 2-chloropyrimidine was treated with methylamine or
ethylamine, respectively, as shown in Scheme 1.
Scheme 1
EtOH
N
N
+
R NH2
reflux
N
Cl
N
NHR
2-chloropyrimidine
R = CH3 (2-N-methylpyrimidine)
R = CH2-CH3 (2-N-ethylpyrimidine)

Molecules 2004, 9
522
The starting materials 2-chloropyrimidine, ethylamine and methylamine did not show any
fluorescence properties in ethanol. Table 1 shows the fluorescence intensity of 2-N-methylpyrimidine
and Table 2 shows the fluorescence intensity of 2-N-ethylaminopyrimidine in various solvents.
Table 1. Fluorescence peaks of 2-N-methylaminopyrimidine in various solvents
Excitation
wavelength (nm)
Fluorescence
peak (nm)
361
Relative
intensity*
0.0942
0.0822
0.0079
0.0315
0.0356
0.4271
0.4843
Solvents
Chloroform
Ethyl acetate
Carbon tetrachloride
Acetone
Ether
Ethanol
278
280
286
335
282
282
283
366
351
370
359
377
351
Methanol
* Phenol was used as standard
2-N-Methylaminopyrimidine showed the highest fluorescence peak in methanol followed by
ethanol, as shown in Table 1. The same phenomenon was also observed with 2-N-ethylamino-
pyrimidine, as indicated in Table 2. The fluorescence intensity of both compounds decreased markedly
in non-polar solvents.
Table 2. Fluorescence peaks of 2-N-ethylaminopyrimidine in various solvents
Excitation
wavelength (nm)
Fluorescence
peak (nm)
360
Relative
intensity*
0.1540
0.0712
0.0720
0.0400
0.0365
0.4401
0.4672
Solvents
Chloroform
Ethyl acetate
Carbon tetrachloride
Acetone
Ether
Ethanol
290
282
286
335
289
286
285
365
359
370
358
375
378
Methanol
*Phenol was used as standard
The high fluorescence intensity observed in ethanol and methanol is probably due to hydrogen
bonding by the solvents. The maximum intensity observed in these two solvents is due to the non-
bonding electron of the solute, that is 2-N-methylaminopyrimidine and 2-N-ethylaminopyrimidine,
which is bonded to the hydrogen atom of the solvent, forming a stable hydrogen-bonded complex as
shown in Figure 1.

Molecules 2004, 9
523
Figure 1
H
O
H
H
C
H
R
N
O
N
N CH2CH3
H
C
H
H
R
Hydrogen bond
complex
This complex stabilizes the ground state as well as the excited state of the n → π* transition.
However, the ground state of 2-N-methylaminopyrimidine and 2-N-ethylaminopyrimidine has two
electrons in the non-bonding orbital whereas the excited state has only one, therefore the stabilisation
of the ground state is greater. As the result, the energy of n → π* transition increases, thus favouring
the low laying π → π* transition which is responsible for the higher fluorescence intensity.
2-N-Piperidinopyrimidine was obtained when 2-chloropyrimidine is treated with an alcoholic
solution of piperidine as shown below (Scheme 2). Like the other amines, piperidine itself showed no
fluorescence properties. Table 3 shows the fluorescence intensity of 2-N-piperidinopyrimidine in
various solvents.
Scheme 2
EtOH
N
N
+
reflux
N
H
N
Cl
N
N
piperidine
2-chloropyrimidine
2-N-piperidinopyrimidine
Table 3. Fluorescence peak of 2-N-piperidinopyrimidine in various solvents
Excitation
wavelength (nm)
Fluorescence
peak (nm)
392
Relative
intensity*
0.3657
0.1710
0.2041
0.1082
0.3514
0.2852
Solvents
Chloroform
Ethyl acetate
Acetone
Ether
Ethanol
356
354
356
350
360
358
391
397
380
403
Methanol
407
*Phenol was used as standard

Molecules 2004, 9
524
The lower fluorescence intensity observed with 2-N-piperidinopyrimidine in ethanol compared to
either 2-N-methylamino or 2-N-ethylaminopyrimidine is believed to be due to the piperidino ring
flipping from one conformation to another, thus losing energy during the process (Figure 2). As the
result, the energy emitted when the excited molecules fall to the ground state is less and consequently a
low fluorescence intensity is observed. The highest fluorescence intensity observed in polar solvents
such as ethanol and methanol is believed to be for the same reason as in the case of 2-N-methylamino-
and 2-N-ethylaminopyrimidine.
Figure 2. Flipping of the piperidino ring in 2-N-piperidinopyrimidine
N
N
N
N
N
N
2-N-Piperidinopyrimidine also showed high fluorescence intensity in chloroform. There is no clear
explanation for this observation because typically, when establishing a solvent-fluorescence
relationship, hydrogen bonding, the dielectric constant of the solvent and its viscosity are frequently
invoked to explain these relationships [7-8]. However, sometimes these effects may cancel each other
out and as a result the solvent-fluorescence relationship is largely unpredictable. In the case of the 2-N-
piperidino derivative, further work is in progress to understand the above phenomena.
Conclusions
2-Chloropyrimidine is a non-fluorescent compound, but when it reacts with selected aliphatic
amines, fluorescent compounds are formed. Their fluorescence intensity was observed to be at
maximum when the polar solvents are used.
Acknowledgements
Financial support of this work by the University of Malaya is gratefully acknowledged.
Experimental
General
The substituted pyrimidines were obtained as described below by treatment of 2-chloropyrimidine
with piperidine, methylamine and ethylamine, respectively [9-10]. The fluorescence studies of the
starting materials in ethanol and the studies of the 2-alkylaminopyrimidines in chloroform, carbon

Molecules 2004, 9
525
tetrachloride, ethyl acetate, dichloromethane, acetone, ether, ethanol and methanol were carried out at
room temperature in a quartz cell using a Hitachi Model 200 Fluorescence Spectrometer. Phenol was
used as the standard. 1H-NMR and 13C-NMR spectra were recorded for CDCl3 solutions using a JEOL
JNM-GSX 270 FT NMR instrument. Mass spectra were recorded using a VG Prospec (Fisons
Instruments) and infrared spectra were recorded using a Perkin-Elmer FTIR Model 1650
Spectrophotometer.
Alkylaminopyrimidine Syntheses
2-N-Methylaminopyrimidine. 2-Chloropyrimidine (0.16 g) was added to methylamine (5 mL) and the
mixture heated under reflux in an oil bath at 120-140oC for four hours, then cooled and extracted with
ether (2 x 10 mL). The ethereal layer was washed with water and dried over anhydrous sodium
sulphate. Filtration and evaporation of solvent gave crude product which was then recrystallised from
hexane-acetone (10:1) to give colourless, transparent, plate-like crystals. Yield: 65%; m.p. 56-58oC (lit.
[12] 58-59oC); IR (cm-1): 3458.5; 1H-NMR (δ): 8.27 (d, 2H, C4 and C6 of pyrimidine ring), 6.52 (t, 1H,
13
pyrimidine ring C5), 5.26 (b, 1H, N-H group), 2.98 (d, 3H, CH3); C-NMR (δ): 162.90 (pyrimidine
ring C2), 157.99 (pyrimidine ring C4 and C6), 110.36 (pyrimidine ring C5), 28.33 (C methyl); MS:
M+= 109.1559 (C5H7N3 requires M+ = 109.0640).
2-N-Ethylaminopyrimidine. 2-Chloropyrimidine (0.15 g) was added to ethylamine (3 mL) and the
mixture was heated under reflux in an oil bath at 120-140oC for four hours and then cooled. The
organic product was extracted with ether (2 x 15mL). The ethereal extracts were washed with water
and dried over anhydrous sodium sulphate. Filtration and evaporation of solvent gave the crude
product which was then recrystallised from hexane-chloroform to give white crystals. Yield: 60%; m.p.
1
49-53oC. IR (cm-1): 3443.8; H-NMR (δ): 8.26 (d, 2H, pyrimidine ring C4 and C6), 6.51 (t, 1H,
pyrimidine ring C5), 5.11 (b, 1H, N-H group), 3.46 (q, 2H, ethyl group Cα), 1.24 (t, 3H, ethyl group
Cβ); 13C-NMR (δ): 162.29 (pyrimidine ring C2), 158.01 (pyrimidine ring C4 and C6), 110.37
(pyrimidine ring C5), 36.23 (ethyl group Cα), 14.89 (ethyl group Cβ); MS: M+ = 123.2055 (C6H9N3
requires M+ = 123.0796).
2-N-Piperidinopyrimidine. 2-Chloropyrimidine (0.5 g), piperidine (5 mL) and ethanol (5 mL) were
refluxed for two hours. The mixture was evaporated and the residue was extracted with ether (3 x 10
mL). The ether extracts were washed with water and dried over anhydrous sodium sulphate.
o
Evaporation of the solvent gave a yellowish liquid. Yield: 48%; b.p. 120oC/16mmHg (120 C/
1
16mmHg [11]); H-NMR (δ): 8.27 (d, 2H, pyrimidine ring C4 and C6), 6.14 (t, 1H, pyrimidine ring
C5), 3.77 (m, 4H, piperidine ring C2’ and C6’), 1.65 (m, 6H, piperidine ring C3’, C4’ and C5’); 13C-NMR
(δ): 161.62 (pyrimidine ring C2), 157.63 (pyrimidine ring C4 and C6), 108.99 (pyrimidine ring C5),
44.70 (piperidine ring C2’ and C6’), 25.68 (piperidine ring C3’ and C5’), 24.82 (piperidine ring C4’); MS:
M+ = 163.2464 (C9H13N3 requires M+ = 163.1109).

Molecules 2004, 9
526
General Procedure for Fluorescence Measurements: 2-N-Piperidinopyrimidine
2-N-Piperidinopyrimidine (5.1 mg) was dissolved in ethanol (25.0 mL) and the fluorescence
measurements were taken at room temperature using an instrument sensitivity of 2.00. The same
concentrations of 2-N-piperidinopyrimidine in chloroform, carbon tetrachloride, ethyl acetate,
dichloromethane, acetone, ether and methanol were prepared and the measurements recorded under
identical conditions. This procedure was repeated with 2-N-ethylamino and 2-N-methylamino-
pyrimidine, using the same concentrations in the various solvents and the same instrument settings.
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