Kinetics and mechanism of the reaction between 2,3,4,5,6-pentafluorophenylacetonitrile and guanidine-like bases and the structure of the products

Article abstract of DOI:10.1016/j.molstruc.2006.02.015

The reactions between the 2,3,4,5,6-pentafluorophenylacetonitrile (PFPA) and such strong N-bases as 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene (MTBD) and 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) have been studied by UV-vis kinetic, high-resolution LSIMS, ¹⁹F NMR and FT-IR methods. The products of these reactions (compounds 1 and 2 and oligomers) have been isolated and their structures have been studied using the methods mentioned. They have been identified as ortho or para substituted dimers and a mixture of trimers, tetramers and pentamers of PFPA. All the products are formed in a relatively slow processes described by various low equilibrium constants. The structures of the ortho or para substituted dimers have been visualized by PM5 semiempirical calculations.

Full text of DOI:10.1016/j.molstruc.2006.02.015

Journal of Molecular Structure 794 (2006) 230–236
www.elsevier.com/locate/molstruc
Kinetics and mechanism of the reaction between 2,3,4,5,6-pentafluoro
phenylacetonitrile and guanidine-like bases and the structure of the products
*
Błaz˙ej Gierczyk, Grzegorz Schroeder, Piotr Przybylski, Bogumil Brzezinski
´
Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland
Received 17 January 2006; accepted 13 February 2006
Available online 27 March 2006
Abstract
The reactions between the 2,3,4,5,6-pentafluorophenylacetonitrile (PFPA) and such strong N-bases as 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-
5-ene (MTBD) and 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) have been studied by UV–vis kinetic, high-resolution LSIMS, 19F NMR and FT-IR
methods. The products of these reactions (compounds 1 and 2 and oligomers) have been isolated and their structures have been studied using the
methods mentioned. They have been identified as ortho or para substituted dimers and a mixture of trimers, tetramers and pentamers of PFPA. All
the products are formed in a relatively slow processes described by various low equilibrium constants. The structures of the ortho or para
substituted dimers have been visualized by PM5 semiempirical calculations.
q 2006 Elsevier B.V. All rights reserved.
Keywords: N-base; Guanidines; Fluorinated compounds; Carbanions; Nucleophilic substitution; 1H NMR; 19F NMR; FT-IR; Mass spectrometry; PM5
semiempirical calculations
1. Introduction
In our previous papers, we have also studied the reactions of
fluoronitrobenzenes, fluorochlorobenzenes and fluorobenzoic
acids with strong nitrogen bases [26–29]. As a further
contribution to these studies in this paper we demonstrate the
influence of strong bases (TBD and MTBD) on the generation
of carbanion by the abstraction of one proton from the
methylene group of 2,3,4,5,6-pentafluorophenylacetonitrile
(PFPA) followed by intermolecular nucleophilic substitution
of fluorine atom yielded various products. The mechanism of
the formation of these products as well as their structures are
discussed.
Fluoroorganic compounds, because of their unique chemical,
physicochemical and biological properties have been widely
studied and used [1,2].
Amidines such as 1,8-diazabicyclo[5.4.0]undec-7-ene
(DBU) or 1,5-diazabicyclo[4.3.0]non-5-ene (DBN) and guani-
dines such as 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD),
7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene (MTBD) belong
to very strong N-bases with small nucleophilicity [3–8]. DBU,
DBN, TBD and MTBD molecules as a very strong N-bases are
very important agents in the deprotonation reactions of weak
O–H [8–13], N–H [14–16] and C–H [17–19] acids, whereas
when protonated they, except for MTBD, can form homo-
conjugated complexes [20]. Furthermore, in our previous
papers, we have demonstrated that MTBD can form hydrogen-
bonded chains with phenols, biphenols and N–H acids in non-
polar aprotic solvents as well as in the solid state [9–13,21,22].
The same is true for TBD but the respective complexes have
much more complicated structures, both in the solutions and in
the solid state [23–25].
2. Experimental
2,3,4,5,6-Pentafluorophenylacetonitrile and guanidine
bases: 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD), 7-methyl-
1,5,7-triazabicyclo[4.4.0]dec-5-ene (MTBD), and 2,3,4,5,6-
pentafluorophenylacetonitrile (PFPA) were commercial
products of Fluka and were used without any purification.
The structures of these compounds are presented in Scheme 1.
2.1. Synthesis
*
Corresponding author. Tel.: C48 61 829 1330; fax: C48 61 865 8008.
E-mail address: bbrzez@main.amu.edu.pl (B. Brzezinski).
To a vigorously stirred solution of PFPA (10 mmol) in dry
diethyl ether (100 cm3) a solution of MTBD (5 mmol) in the
same solvent (25 cm3) was added. The dark violet mixture was
heated and stirred for 2 h. After then the solvent was
0022-2860/$ - see front matter q 2006 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2006.02.015

B. Gierczyk et al. / Journal of Molecular Structure 794 (2006) 230–236
231
Table 1
Elementary analysis and high resolution MS data for negative ions of
compounds 1, 2 and a mixture of oligomers
Compound
Elemental analysis
MS
Calc. (%)
C-48.75
Found (%)
Calc.
Found
C-48.73
394.0152
393.0079
C16H3F9N2
1
H-0.77
N-7.11
C-48.75
H-0.79
N-7.10
C-48.73
Scheme 1. Structures of substrates.
394.0152
393.0062
evaporated and the dark, oily residue was dissolved in
dichloromethane. This solution was washed twice with
50 cm3 of 1 mol dmK3 HCl and the organic layer was
separated and dried over Na2SO4. The solvent was evaporated
in vacuum. The products were separated by column chroma-
tography on silica gel using diethyl ether as eluent. Three
fractions were collected: the first (compound 1), the second
(compound 2) and the third (mixture of oligomers). After
solvent evaporation the semisolid products were obtained.
C16H3F9N2
2
H-0.77
N-7.11
H-0.80
N-7.09
Oligomers
580.0119
580.0110
767.0174
954.0199
C24H3F13N3
767.0165
C32H4F17N4
954.0209
C40H5F21N5
2.2. UV–vis spectra
peak matching technique and m-nitrobenzyl alcohol as solvent.
Elemental compositions of the ions discussed were determined
with an error less than 10 ppm in relation to perfluorokerosene
at a resolving power of 10,000.
The UV–vis spectra were recorded in CH3CN on an Agilent
8453 spectrometer using a 1 cm cell thick and the samples of
the concentration 5!10K5 mol dmK3. The data of these
spectra are collected in Table 1.
2.6. Kinetic measurements
2.3. NMR measurements
The kinetic runs were carried out using a stop Agilent
8453 spectrophotometer with the cell block thermostated to
G0.1 8C. The kinetic runs were completed under pseudo-first-
order conditions with the base concentration in large excess
(0.01–0.05 mol dmK3). The base solutions were prepared
directly before starting the kinetic measurements. The
observed rate constants (kobs) were calculated from the traces
of absorbance vs. time using two methods: intermediate decay
(Guggenheim’s method) and the formation of the respective
newest intermediates (initial rate method). The second-order
rate constants for forward (k) reaction were calculated by linear
least-squares fit of the variation of kobs vs. base concentration
(kobsZk[B]Cint).
1H and 19F NMR spectra were recorded on Varian-Gemini
300 spectrometer at 300.075 and 282.352 MHz, respectively.
The 0.01 M solutions of products in CDCl3 were used for all
measurements. The chemical shifts were measured to an
1
internal standard (TMS for H spectra; CFCl3 for 19F NMR
1
spectra; dZ0.000 ppm). For H NMR spectra 608 pulse width
4500 Hz spectral width; 2 s acquisition time; 32k FT-size. The
19F NMR spectra were measured as follows: spectral width
128k, 608 pulse width and 0.64 s acquisition time.
2.4. FT-IR measurements
The FT-IR spectra of 2,3,4,5,6-pentafluorophenylacetonitrile
(PFPA) with MTBD were recorded in acetonitrile
(0.10 mol dmK3) at 300 K on a Bruker IFS 113v spectrometer.
2.7. PM5 calculations
˚
Acetonitrile spectral-grade was stored over 3 A molecular sieves
PM5 semiempirical calculations were performed using the
WIN MOPAC 2003 program [30]. The full geometry optimization
was carried out without any symmetry constraints [31].
for several days. All manipulations with the substances were
performed in a carefully dried and CO2-free glove box.
A cell with Si windows and wedge-shaped layers was used to
avoid interferences (mean layer thickness 176 mm). The spectra
were taken with an IFS 113v FT-IR spectrophotometer (Bruker,
2.8. Elementary analysis
Karlsruhe) equipped with a DTGS detector; resolution 2 cmK1
,
The elementary analysis was carried out on Vario ELIII
(Elementar, USA).
NSSZ125. The Happ-Genzel apodization function was used.
2.5. Mass spectrometry
3. Results and discussion
High-resolution LSIMS spectra were obtained on two sector
mass spectrometer (AMD-604) of the B/E geometry using a
The formulae and the atoms numbering in the compounds
obtained (1 and 2 and oligomers) are shown in Scheme 2.

232
B. Gierczyk et al. / Journal of Molecular Structure 794 (2006) 230–236
Scheme 2. Structures and atom numbering of compounds 1 and 2 as well as a tetrahedral and linear forms of para substituted trimers.
In the reaction, of PFPA with the TBD or MTBD strong
3.1. Kinetic studies
bases two dimeric (compounds 1 and 2) and a mixture of
oligomeric products were isolated. The analytical and LSIMS
data of these compounds are collected in Table 1. The LSIMS
data in this table indicate directly that compounds 1 and 2 are
dimers and the other one are mixture of tri-, tetra- and penta-
mers as indicated in Scheme 2.
In the UV spectrum, of PFPA in acetonitrile a band at
lmaxZ242 nm is observed. After addition of TBD or MTBD,
the intensity of this band decreases an a new one arises with
lmaxZ310 nm. This process is very fast but it is characterized
by a relatively low equilibrium constant. With time the
concentration of this intermediate decreases and a new one
characterized by lmaxZ440 nm appears. The newly formed
intermediate converts into another (lmaxZ390 nm) and finally
into a product with lmaxZ250 nm. It is interesting to note that
an addition of HCl to neutralize the solution containing the
intermediate, for which lmaxZ390 nm is observed, changes the
direction of all reactions with the formation of the substrate
(lmaxZ242 nm) indicating that all these reactions are
reversible. The reaction pathway and the structures of the
intermediates characterized by respective lmax are shown in
The structures of compounds 1 and 2 can be deduced from
their 19F NMR spectra. The spectrum of compound 1 shows
three signals originated from C6F5– group and two from para-
substituted –C6F4– group. In the spectrum of compound 2,
besides the three signals originated from C6F5– group, the
ortho-substitution is indicated by the presence of four signals
attributed to non-equivalent fluorine atoms. Furthermore, all of
these signals show the spin–spin coupling with one or two
fluorine atoms via three bonds, which is only possible for
ortho-substituted isomer (Table 2).
Table 2
Spectral data for compounds obtained
Compound HR-MS
neg. ion
1H NMR (ppm)
19F NMR (ppm)
1
10 20
2
3
4
5
6
–
7
–
1
2
393.0079
393.0062
4.52; 1H s 3.89; 2H s K143.7; 2F d; 22 Hz
K165.8;
2F t;
K170.5;
1F t;
K145.7;
2F d;
K148.2;
2F d;
22 Hz
K166.3;
2F t;
22 Hz
K170.2;
1F t;
21 Hz
21 Hz
K168.4;
1F t;
4.61; 1H s 3.85; 2H s K142.7; 2F d; 22 Hz
K146.3;
1F d;
K168.9;
1F t;
K147.4;
1F d;
22 Hz
22 Hz
20 Hz
20 Hz
20 Hz
20 Hz
Oligomers 580.0110; 4.6; b
3.8–3.9; b K142.7; K143.9; K144.5;
K145.5; K147.4; K147.9;
K165.0; K166.4; K166.9;
K167.3; K168.5; K170.3;
K170.7b
(mixture)
767.0174;
954.0199a
s, singlet, d, doublet; t, triplet; b, broad signal.
a
Only main peaks were noted.
b
All signal were broadened.

B. Gierczyk et al. / Journal of Molecular Structure 794 (2006) 230–236
233
Scheme 3. Proposed mechanism of the reaction of PFPA with N-bases (para substitution is shown as an example).
Scheme 3 and the rate constants determined are collected in
Table 3. Except for the reaction of the formation of the
intermediate with lmaxZ310 nm all the reactions are rather
slow.
Fig. 1(a–c) shows the FT-IR spectra in the region 4000–
400 cmK1 of the acetonitrile mixtures of PFPA and MTBD
with different ratios. For comparison, the spectrum of MTBD is
also given. In Fig. 2(a–c), the regions of the Bohlmann bands,
the stretching vibrations of cyano groups n (C^N) and the n
(C]N) vibrations are given on extended scale.
3.2. FT-IR studies
In the spectrum of the 1:1 mixture of PFPA with MTBD in
comparison with that of MTBD the Bohlmann band intensity
decreases and instead new bands arise. First of all, a band at
3377 cmK1 of a weak intensity as well as a shoulder
at 1627 cmK1 indicate the presence of protonated and non-
hydrogen bonded MTBD molecules. Furthermore, the new
band at 2143 cmK1 assigned to the n (C^N) vibrations
indicates that the cyano group is bonded in the arrangement in
which the electron density strongly increases, i.e. in the
respective carbanion (intermediate with lmaxZ310 nm,
Recently, we have discussed the FT-IR spectra of MTBD
and its protonated forms in acetonitrile [10]. The spectrum of
MTBD is characterised by the so-called Bohlmann band at
2846 cmK1 and the n (C]N) vibrations at 1609 cmK1. When
MTBD is protonated, the band assigned to the n (NCH)
vibration arises at 3377 cmK1 and the n (C]N) vibrations
appear as an intense doublet with maxima at 1627 and
1602 cmK1 if the protonated MTBD cation is non-hydrogen
bonded.
Table 3
Second order rate constants at 25 8C [kGSD (MK1 sK1)] for the reactions of PFPA with TBD and MTBD
Kind of rate constant
TBD
MTBD
Product decay lZ310 nm
Formation product lZ440 nm
Product decay lZ440 nm
Formation product lZ390 nm
0.0632G0.0003
0.0638G0.0004
0.0327G0.0003
0.0318G0.0002
0.0055G0.0003
0.0056G0.0004
0.0021G0.0002
0.0021G0.0003

234
B. Gierczyk et al. / Journal of Molecular Structure 794 (2006) 230–236
Scheme 3). It is interesting to note that in the spectrum of the
acetonitrile solution of PFPA the respective n (C^N)
vibrations are masked by the cyano group of the solvent. In
the spectrum of the 2:1 mixture of PFPA with MTBD, the
intensity of the band of n (C^N) vibrations at 2143 cmK1
slightly increases due to the shift of the equilibrium reaction
with the formation of the carbanion toward the right hand side.
In contrast to the last spectrum, in the spectrum of the 1:2
mixture of PFPA with MTBD, the intensity of the band at
2143 cmK1 slightly decreases and a new one much stronger
than the first one arises at 2198 cmK1. The position of this new
band demonstrates the decrease in the electron density in the
arrangement of the cyano group. This observation can be
explained by the further reaction of the carbanion with
formation of the intermediate with lmaxZ390 nm (Scheme
3). It is interesting to note that comparable shifts of the cyano
group band position in the FT-IR spectra were earlier observed
for the hydrogen bonded complexes of 4-cyanophenol with
strong N-bases [9,32]. The structure of intermediate with
lmaxZ390 nm is further confirmed by the band with a
maximum at about 2500 cmK1 in the spectrum of 1:2 mixture
Fig. 1. FT-IR spectra of the mixtures in acetonitrile of PFPA with MTBD (—)
and for comparison of MTBD (– – –): (a) mixture 1:1, (b) mixture 2:1, and (c)
mixture 1:2.
Fig. 2. FT-IR spectra with the extended scales of the mixtures in acetonitrile of
PFPA with MTBD of the mixtures: ($ $-$ $-$ $-) 1:1, ( ) 2:1, (-$-$-$-) mixture
1:2 (—), and for comparison of MTBD (– – –) and its protonated form by
HAuCl4 (/).
Scheme 4. The energetically favorable structures of: (a) compound 1 and (b)
compound 2.

B. Gierczyk et al. / Journal of Molecular Structure 794 (2006) 230–236
235
of PFPA with MTBD indicating the abstraction of the FK anion
from the 2,3,4,5,6-pentafluorophenyl ring and the formation of
an asymmetric MTBD-HC/FK intermolecular hydrogen
bond. Furthermore, the presence in the spectrum of the band
assigned to the n (NCH) vibration at 3377 cmK1 indicates that
this FK anion abstraction process is very slow and it is
described by a further equilibrium reaction.
In the spectra of PFPA with MTBD at different ratios in the
region 1700–1450 cmK1 (Fig. 2(c)) the bands assigned to the n
(CaC) aromatic ring vibrations at 1662, 1526, 1513 cmK1
,
characteristic of PFPA molecule, are still observed. Besides
these bands, a new bands arise at 1650 cmK1 and in the range
1500–1475 cmK1, indicating only partial deprotonation of the
PFPA molecule. This also means that the equilibrium constants
of the reactions are very low.
3.3. PM5 calculations
The visualized structures of compounds 1 and 2 are shown
in Scheme 4. The calculated heats of formation of these
favourable structures are K272.82 and K269.34 kcal/mol,
respectively. These values demonstrate that both structures are
energetically comparable and this can be the reason for their
formation under experimental conditions. The structures of
isomeric trimers are shown in Scheme 5. The heats of
formation of the linear and tetrahedral structures are
K390.43 and K384.23 kcal/mol, respectively, indicating that
the first one is energetically more favourable. This difference
can be probably a result of the stereochemical reason between
Scheme 5. The energetically favorable structures of trimers: (a) linear and (b)
tetrahedral.
Scheme 6. The structure of calculated dendrimer by PM5 method (WinMopac 2003).

236
B. Gierczyk et al. / Journal of Molecular Structure 794 (2006) 230–236
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both structures. The MS spectra detected the formation of other
oligomers. With the time, however, the formation of very
complex, due to the ortho and para substitution, dendrimeric
polymers is quite possible, because the oligomers can reacts
with monomers or with each other if an excess of the strong
base is used, i.e. that these oligomers are so-called
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Because of high acidity of the C–H hydrogen atoms (pKaZ
15.8; DMSO [33]) in PFPA molecule an addition of a strong
N-base causes its deprotonation with formation of a carbanion.
The carbanions attack a carbon atoms in the aromatic ring in
ortho or para positions of PFPA second molecule with the
formation of Meisenheimer complexes and a further elimin-
ation FK anion, which form a hydrogen bonded complex with a
protonated MTBD molecule. First, the reaction yields the
dimers and with the time also oligomers. The formation of such
compounds is confirmed by the high-resolution LSIMS spectra.
The FT-IR spectra indicate the formation of carbanions,
protonated MTBD molecules as well as the abstraction of the
FK anion in the reaction with formation of asymmetrical
intermolecular hydrogen bonds. The structures of 1–2
compounds are confirmed by 19F NMR spectra and visualized
by PM5 semiempirical calculations. It is interesting to note that
the use of the TBD or MTBD in the reactions with PFPA yield
products different from those observed in the reaction of PFPA
and NaOH in water/CCl4 mixture discussed previously by
Nakayama et al. [33].
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