NMR study, theoretical calculations for assignment of the Z- and E-isomers, and kinetics investigation of stable phosphorus ylides involving a 2-mercapto-4,6-dimethyl pyrimidine

Article abstract of DOI:10.1002/hc.20632

In the present work, NMR, theoretical, kinetics, and mechanism investigations were undertaken for a one-pot condensation reaction between 2-mercapto-4,6-dimethyl pyrimidine and dialkyl acetylenedicarboxylates in the presence of triphenyphosphine containing novel stable phosphorus ylides 4a-c. Herein, theoretical calculations have been employed for assignment of the most stable isomers (Z or E) of phosphorus ylides 4a,c by natural population analysis, atoms in molecules methods, and CHelpG keyword, in which E-4(a, c) are more stable forms as the majors. The ¹H, ¹³C, and ³¹P NMR data of these ylides are consistent with results obtained from theoretical calculations. In addition, kinetic investigation of new ylides was undertaken by ultraviolet spectrophotometry. Useful information was obtained from studies of the effect of solvent, structure of reactants (different alkyl groups within the dialkyl acetylenedicarboxylates), and also the concentration of reactants on the rate of reactions. The proposed mechanism was confirmed according to the obtained results and a steady-state approximation, and the first step (k₂) of the reaction was recognized as a rate-determining step on the basis of the experimental data.

Full text of DOI:10.1002/hc.20632

Heteroatom Chemistry
Volume 21, Number 7, 2010
NMR Study, Theoretical Calculations for
Assignment of the Z- and E-Isomers, and
Kinetics Investigation of Stable Phosphorus
Ylides Involving a 2-Mercapto-4,6-dimethyl
Pyrimidine
Mohammad Zakarianezhad, Sayyed Mostafa Habibi-Khorassani,
Ali Ebrahimi, Malek Taher Maghsoodlou, and Hojjat Ghasempour
Department of Chemistry, University of Sistan and Baluchestan, P.O. Box 98135-674,
Zahedan, Iran
Received 11 March 2010; revised 12 June 2010
ꢀ
C
step on the basis of the experimental data. 2010 Wi-
ABSTRACT: In the present work, NMR, theoret-
ley Periodicals, Inc. Heteroatom Chem 21:462–474, 2010;
ical, kinetics, and mechanism investigations were
View this article online at wileyonlinelibrary.com. DOI
undertaken for a one-pot condensation reaction be-
10.1002/hc.20632
tween 2-mercapto-4,6-dimethyl pyrimidine and di-
alkyl acetylenedicarboxylates in the presence of triph-
enyphosphine containing novel stable phosphorus
INTRODUCTION
ylides 4a–c. Herein, theoretical calculations have been
employed for assignment of the most stable isomers
(Z or E) of phosphorus ylides 4a,c by natural pop-
ulation analysis, atoms in molecules methods, and
CHelpG keyword, in which E-4(a, c) are more stable
forms as the majors. The 1H, 13C, and 31P NMR data of
these ylides are consistent with results obtained from
theoretical calculations. In addition, kinetic investiga-
tion of new ylides was undertaken by ultraviolet spec-
trophotometry. Useful information was obtained from
studies of the effect of solvent, structure of reactants
(different alkyl groups within the dialkyl acetylenedi-
carboxylates), and also the concentration of reactants
on the rate of reactions. The proposed mechanism
was confirmed according to the obtained results and
a steady-state approximation, and the first step (k2)
of the reaction was recognized as a rate-determining
The synthesis of phosphorus ylides is an important
reaction in organic chemistry because of the appli-
cation of these compounds in the synthesis of or-
ganic products [1–29]. Several methods have been
developed for the preparation of phosphorus ylides
[10,11]. These ylides are usually prepared by treat-
ment of a phosphonium salt with a base, and phos-
phonium salts are usually prepared from the phos-
phine and alkyl halide [2,3]. Phosphonium salts are
also prepared by Michael addition of phosphorus
to activated olefins [1]. The phosphonium salts are
most often converted to the ylides by treatment with
a strong base, though weaker bases can be used if
the salt is acidic enough. Michael addition of phos-
phorus(III) compounds such as triphenylphosphine
to acetylenic esters leads to reactive 1,3-dipolar in-
termediate betaines, which are not detected even at
low temperatures [14]. These unstable species can be
trapped by a protic reagent, ZH, such as methanol,
amide, or imide, to produce various compounds, for
example, ylides [4–29].
Correspondence to: Sayyed Mostafa Habibi-Khorassani; e-mail:
smhabibius@yahoo.com.
Contract grant sponsor: University of Sistan and Baluchestan.
c
ꢀ
2010 Wiley Periodicals, Inc.
462

Kinetics Investigation of Stable Phosphorus Ylides Involving a 2-Mercapto-4,6-dimethyl Pyrimidine 463
FIGURE 1 (a) The reaction between triphenylphosphine 1, dialkyl acetylenedicarboxylate 2 (2a, 2b, or 2c), and 2-mercapto-
4,6-dimethyl pyrimidine 3 for generation of stable phosphorus ylides 4 (4a, 4b, or 4c). (b) The two geometrical isomers Z-4a
and E-4a (minor and major, respectively) of ylide 4a.
These ylides usually exist as a mixture of the two
geometrical isomers, although some ylides exhibit
one geometrical isomer. Assignment of the stability
of the two Z- and E- isomers is possible in phos-
phorus ylides by experimental methods, such as 1H,
13C NMR, IR spectroscopy, mass spectrometry, and
elemental data analysis. For this reason, quantum
mechanical calculation has been performed to gain
a better understanding of the most important ge-
ometrical parameters and also relative energies of
both the geometrical isomers.
volving the two geometrical isomers such as Z- and
E-isomers. The reaction is shown in Fig. 1. For
assignment of the two Z and E isomers as a mi-
nor or major form in phosphorus ylides 4a,c con-
taining a 2-mercapto-4,6-dimethyl pyrimidine, first
the Z- and the E-isomers were optimized for all
ylide structures at the HF/6-31G(d,p) level of the-
ory [31] by the Gaussian98 package program [32].
The relative stabilization energies in both geomet-
rical isomers were calculated at the HF/6-31G(d,p)
and B3LYP/6-311++G∗∗ levels. Atoms in molecules
(AIM) [33], natural population analysis (NPA) meth-
ods, and CHelpG keyword at the HF/6-31G(d,p) level
of theory were employed to gain a better understand-
ing of the most geometrical parameters in both the
E-4(a, c) and the Z-4(a, c) of phosphorus ylides. The
theoretical results for ylide 4b are nearly the same
as those that were obtained for ylide 4a, because
the ylides 4a and 4b have very similar alkyl groups
(methyl and ethyl, respectively); for this reason, cal-
culations have been reported for just ylides 4a and
4c. The numbers of critical points and intramolecu-
lar hydrogen bonds have been recognized as well as
the atoms that existed on the Z- and E-isomers. The
results altogether reveal the effective factors on the
stability of Z and E ylide isomers. The relative sta-
bilization energies for the two [Z-4(a, c) and E-4(a,
c)] isomers (see Figs. 2 and 3) are reported in Ta-
ble 1; as can be seen, the E-4a and E-4c isomers are
more stable than the Z-4a and Z-4c forms (1.00 and
1.27 kcal/mol, respectively) at the B3LYP level. In
addition, Jx−y, the values of proton and carbon cou-
MATERIALS AND METHODS
Quantum mechanical calculation has been per-
formed by the Gaussian98 program and using the
AIM2000 program packages. Di-tert-butylacetylene-
dicarboxylate, triphenylphosphine, and 2-mercapto-
4,6-dimethyl pyrimidine were purchased from Fulka
(Buchs, Switzerland) and used without further pu-
rification. All extra-pure solvents including 1,4-
dioxane and ethyl acetate were obtained from Merck
(Darmstadt, Germany). A Cary UV–vis spectropho-
tometer model Bio-300 with a 10-mm-light-path
black quartz spectrophotometer cell was employed
throughout the current work.
RESULTS AND DISCUSSION
Calculations
A facile synthesis of the reaction between triph-
enylphosphine 1, dialkyl acetylenedicarboxylates 2,
and 2-mercapto-4,6-dimethyl pyrimidine 3 (as a SH-
heterocyclic compound) was reported earlier [30]
for the generation of phosphorus ylides 4a–c, in-
pling constants, and also chemical shifts (δHiso, δiCso
)
have been calculated at the mentioned level using
SPINSPIN keyword.
Heteroatom Chemistry DOI 10.1002/hc

464 Zakarianezhad et al.
FIGURE 2 (a) Intramolecular hydrogen bonds (dotted lines) in the two E-4a and Z-4a geometrical isomers of stable ylide 4a.
(b) Partial molecular graphs, including intramolecular hydrogen bond critical points (BCPS) for the two rotational isomers such
as E-4a and Z-4a. Small red spheres and lines correspond to BCPS bond paths, respectively.
Further investigation was undertaken to deter-
mine more effective factors in the stability of the two
Z- and E- isomers, on the basis of AIM calculations
at the HF/6-31G(d,p) level of theory by the AIM2000
program package [34]. In recent years, AIM theory
has often been applied in the analysis of H bonds. In
this theory, the topological properties of the electron
density distribution are derived from the gradient
vector field of the electron density ∇ρ(r) and on the
called the bond critical point (BCP). The values of
the charge density and its Laplacian at these critical
points give useful information regarding the strength
2
of the H bonds [34]. The ranges of ρ(r) and ∇ ρ(r)
are 0.002–0.035 e/a03 and 0.024–0.139 e/a50, respec-
tively, if H bonds exist [35]. The AIM calculation in-
dicates intramolecular hydrogen bond critical points
(H-BCP) for the two Z-4(a, c) and E-4(a, c) isomers.
Intramolecular H-BCPs along with partial molecular
graphs for the two rotational isomers are shown in
Figs. 2 and 3 (dotted lines). The most important geo-
metrical parameters involving some H bonds (bond
length and their relevant bond angle) are reported in
Table 2. The electron densities (ρ) × 103, Laplacian
2
Laplacian of the electron density ∇ ρ(r). The Lapla-
2
cian of the electron density, ∇ ρ(r), identifies regions
of space wherein the electronic charge is locally de-
2
2
pleted [∇ ρ(r) > 0] or built up [∇ ρ(r) < 0] [33].
Two interacting atoms in a molecule form a criti-
cal point in the electron density, where ∇ρ (r) = 0,
2
of electron density ∇ ρ(r) × 103, and energy density
Heteroatom Chemistry DOI 10.1002/hc

Kinetics Investigation of Stable Phosphorus Ylides Involving a 2-Mercapto-4,6-dimethyl Pyrimidine 465
FIGURE 3 (a) Intramolecular hydrogen bonds (dotted lines) in the two E-4c and Z-4c geometrical isomers of stable ylide 4c.
(b) Partial molecular graphs, including intramolecular hydrogen bond critical points (BCPS) for the two rotational isomers such
as E-4c and Z-4c. Small red spheres and lines correspond to BCPS bond paths, respectively.
−H(r) × 104 are also reported in Tables 3 and 4.
is less than in Z-4a (88.6 au), an important factor
in the instability of E-4a (Table 5). It seems that the
E-4a stability stems from the two opposite factors
(dipole moment and total Hamiltonian) in which the
influence of dipole moment is superior to that of to-
tal Hamiltonian, resulting in a slight relative stabil-
ity in E-4a (1 kcal/mol in comparison with the Z-4a
isomers). This is in good agreement with the exper-
A negative total energy density at the BCP reflects
a dominance of potential energy density, which is
the consequence of an accumulated stabilizing elec-
tronic charge [36]. The numbers of hydrogen bonds
in both categories (E-4a and Z-4a) and (E-4c and
Z-4c) are 5 and 6 and 12 and 12, and the values
2
of ρ and ∇ ρ(r) × 103 for them are in the ranges
1
imental results [30] based upon the H, 13C, and 31P
0.003–0.012 and 0.006–0.013 e/a30, 0.002–0.014 and
0.002–0.013 e/a30, 14.56–45.48 and 26.36–57.76 e/a50,
and 7.60–58.84 and 8.88–57.16 e/a50, respectively. In
addition, the Hamiltonians [−H(r) × 104] are in the
ranges 8.60–17.80 and 5.80–22.60 au and 5.00–21.30
and 4.80–21.40 au, respectively (see Tables 3 and 4).
NMR data with a slightly more experimental abun-
dance percentage of 59 for E-4a. The total value of
ꢀ
the total Hamiltonian (−H (= −H(r) × 104)) in
tot
both the E-4c and Z-4c isomers is approximately the
same (153 and 152 au, respectively) but the dipole
moment in E-4c (5.55 D) is less than in Z-4c (6.96
D); in fact the latter factor accounts as a lone factor
on relative stability of E-4c (1.27 kcal/mol in com-
parison with Z-4c). This difference in stabilization
energy is also too low in which the observation of
two E-4c and Z-4c is reasonable. Herein, there is a
2
These HBs show ∇ ρ(r) > 0 and H(r) < 0, which ac-
cording to the classification of Rozas et al. [37] are
medium-strength hydrogen bonds. Although dipole
moment in E-4a (5.42 D) is less than that in Z-4a
(7.00 D) and appears to be an effective factor of
E-4a stability, the value of −H in E-4a (67.9 au)
tot
Heteroatom Chemistry DOI 10.1002/hc

466 Zakarianezhad et al.
2
TABLE 3 Values of a = ρ × 103, b = ∇ ρ × 103, and c =
TABLE 1 Relative Energy (kcal/mol) for the Z- and E-
Isomers of Ylides 4a and 4c, Obtained at HF/6-31G (d,p)
and B3LYP/6-311++G(d,p) Levels
−H(r) × 104 for the Z-4a and E-4a Isomers of Ylide 4a Cal-
culated at the Hydrogen Bond Critical Points
Geometrical Isomer
HF
B3LYP
E
a
b
c
Z
a
b
c
Z-4a
E-4a
Z-4c
E-4c
1.50
0.00
0.47
0.00
1.00
0.00
1.27
0.00
1
2
3
4
5
12.15 45.48
9.50
1
2
3
4
5
6
6.90 26.36
5.80
9.22 32.08 15.10
9.60 36.80 17.80
11.89 42.00 16.90
13.41 57.76 22.60
8.99 32.12 15.50
10.65 39.04 17.20
6.73 28.92 12.60
9.71 34.16 14.90
3.30 14.56
8.60
good agreement between the results obtained from
the 1H, 13C,31P NMR data with a slightly more exper-
imental abundance percentage of 56 for E-4c.
Also, the charges on different atoms, which are
calculated by AIM, NPA methods, and CHelpG key-
word at HF/6–31G(d,p) level, are reported in Table 6
for the two Z- and E-isomers of ylides 4a and 4c.
There is a good agreement among the results in the
three methods.
The individual chemical shifts have been char-
acterized by NMR calculations at the mentioned
level. The total spin–spin coupling constant is the
sum of four components: the paramagnetic spin-
orbit (PSO), diamagnetic spin-orbit (DSO), Fermi-
contact (FC), and spin-dipole (SD) terms. The value
All values are in atomic units.
TABLE 4 Values of a = ρ ×103, b = ∇ ρ ×103, and c =
−H(r) × 104 for the Z-4c and E-4c Isomers of Ylide 4c Cal-
culated at the Hydrogen Bond Critical Points
2
E
A
b
C
Z
a
b
c
1
2
3
12.05 46.60 13.00
12.34 47.68 13.00
14.29 58.84 21.30
1
11.85 46.32 13.50
11.75 45.28 12.50
6.31 25.48
13.72 57.16 21.40
3.15 13.92 7.90
13.13 49.76 11.90
12.67 48.36 12.40
6.98 29.92 12.80
9.72 34.48 15.00
2
3
4
5
6
7
8
9
6.70
4
5
2.50
2.14
8.88
7.60
5.90
5.00
6
7
8
9
13.05 49.64 12.10
12.89 48.96 12.20
11.60 44.36 10.70
11.90 42.20 16.80
10
11
12
5.65 22.84 10.10 10
9.78 36.96 17.60 11
9.16 31.68 14.90 12 11.07 40.36 17.30
2.74
8.88
4.80
of chemical shifts (δ) and coupling constants (Jx−y
)
9.12 33.48 16.20
are reported in Tables 7–10. As can be seen, there is a
good agreement between both the experimental [30]
and theoretical chemical shifts (δ) and coupling con-
stants (Jx−y). In the present work, molecular struc-
tures of ylides 4a–c involving four large atoms such
as sulfur, phosphorus, and two nitrogen atoms are
huge, with large numbers of other atoms (C, H); for
this reason, a basis set higher than HF/6-31G(d, p)
is impossible in a higher performance for obtaining
more accurate calculations. This limitation results
in a difference between both the experimental and
theoretical coupling constants and chemical shifts
in some functional groups.
All values are in atomic units.
Kinetics Studies
To gain further insight into the reaction mechanism
between triphenylphosphine 1, dialkyl acetylenedi-
carboxylates 2, and 2-mercapto-4,6-dimethyl pyrim-
idine 3 (as a SH-heterocyclic compound) for the gen-
eration of phosphorus ylides 4a–c, a kinetic study of
the reactions was undertaken by the UV spectropho-
tometric technique. The synthesis of these reactions
TABLE 2 Most Important Geometrical Parameters Corresponding to H Bonds (Bond Lengths and Their Relevant Angles) for
the Two Z and E Isomers in Ylides 4a and 4c
E-4a
Z-4a
E-4c
Z-4c
C31H34 · · ·O43
2.98a (129.46)b
2.39 (124.91)
2.53 (118.17)
C10 14
H
· · ·Oc3(4)
2.74 (109.33)
2.60 (114.47)
2.48 (101.46)
2.42 (121.98)
C7H42 · · ·C30
C7H42 · · ·N58
C
62H64 · · ·O3
2.42 (110.97)
2.43 (111.70)
2.43 (111.56)
2.41 (112.03)
2.47 (111.19)
C66H67 · · ·O3
C78H80 · · ·O43
Bond lengths are in angstroms, and bond angles are in degrees.
aBond length.
bBond angle.
cIt is relevant to the Z isomer.
Heteroatom Chemistry DOI 10.1002/hc

Kinetics Investigation of Stable Phosphorus Ylides Involving a 2-Mercapto-4,6-dimethyl Pyrimidine 467
TABLE 7 Selected 1H NMR Chemical Shift (δ in ppm) and
Coupling Constants (J in Hz) for Some Functional Groups in
the E-4a Isomer as a Major Form
TABLE 5 Most Important Geometrical Parameters Involving
the Value of −Htot (in au), Dipole Moment (in D), and the
Number of Hydrogen Bonds for the Two Z- and E-Isomers of
Ylides 4a and 4c
Groups
δH (ppm)
JPH (Hz)
Geometrical
Isomer
Dipole
Number of
6H, 2s, 2 CO2Me 3.76a and 3.81a
(3.50 and 3.53)b
−Htot (au) Moment (D) Hydrogen Bonds
E-4a
Z-4a
E-4c
Z-4c
67.9
88.6
153
152
5.42
7.00
5.55
9.96
5
6
12
12
6H, s, ArMe2
1H, s, Ar-H57
15H, m, 3C6H5
2.15 (2.24)
6.68 (6.25)
7.31–7.75 (7.24–7.82)
1H, d, P C CH 4.88 (3.89)
19.70a (19.69)b
aExperimental data in accord with the results reported in the literature
[30].
bTheoretical data.
has been reported earlier [30]. First, it was necessary
to find the appropriate wavelength to follow the ki-
netic study of the reaction. For this purpose, in the
first experiment, 3 × 10−3 M solution of compounds
1, 2c, and 3 was prepared in 1,4-dioxane as solvent.
An approximately 3-mL aliquot from each reactant
was pipetted into a 10-mm-light-path quartz spec-
trophotometer cell, and the relevant spectra were
recorded over the wavelength range 190–400 nm.
Figures 4–6 show the UV spectra of compounds 1,
2c, and 3, respectively. In a second experiment, a
1-mL aliquot from the 3 × 10−3 M solutions of each
compound of 1 and 3 was pipetted first into a quartz
spectrophotometer cell (as there is no reaction be-
TABLE 8 Selected 1H NMR Chemical Shift (δ in ppm) and
Coupling Constants (J in Hz) for Some Functional Groups in
the Z-4a Isomer as a Minor Form
Groups
δH (ppm)
2.31a (2.36)b
JPH (Hz)
6H, s, ArMe2
6H, 2s, 2 CO2Me 3.67 and 3.74
(3.32 and 3.64)
1H, s, Ar-H57
6.75 (6.23)
7.31–7.75 (7.36–7.92)
15H, m, 3C6H5
1H, d, P C CH 4.96 (3.85)
18.10a (17.67)b
aExperimental data in accord with the results reported in the literature
[30].
bTheoretical data.
tween them); later a 1-mL aliquot of the 3 × 10−3
M
solution of reactant 2c was added to the mixture, and
the reaction was monitored by recording scans of the
entire spectra every 10 min over the whole reaction
time at ambient temperature. The UV spectra shown
in Fig. 7 are typical. From this, the appropriate
wavelength was found to be 410 nm (corresponding
mainly to 2-mercapto-4,6-dimethyl pyrimidine 3).
At this wavelength, compounds 4, 2c, and 1 have
relatively no absorbance value. This then provided
the opportunity to fully investigate the kinetics of
the reaction between triphenylphosphine 1, di-tert-
butyl acetylenedicarboxylate 2c, and 2-mercapto-
4,6-dimethyl pyrimidine 3 at 410 nm in the presence
of 1,4-dioxane as solvent. Since the spectrophotome-
ter cell of the UV instrument had a 10-mm-light-
path cuvette, the UV–vis spectra of compound 4c
were measured over the concentration range 2 ×
10−4M ≤ M4c ≤ 10−3 M to check for a linear re-
lationship between absorbance values and concen-
trations. With the suitable concentration range and
wavelength identified, the following procedure was
employed.
For each kinetic experiment, first a 1-mL aliquot
from each freshly made 3 × 10−3 M solution of
TABLE 6 Charges on Different Atoms for the Two E- and Z-Isomers in Ylides 4a and 4c, Calculated at HF/6-31G(d,p)
Theoretical Level
Number of Atoms
Z-4a
E-4a
Z-4c
E-4c
C1
C2
C7
O3
O4
P6
−0.80a (−0.37)b (−0.89)c
1.85 (0.92) (0.96)
0.26 (−0.04) (−0.45)
−1.39 (−0.66) (−0.76)
−1.29 (−0.48) (−0.66)
3.25 (0.04) (1.87)
−0.73 (−0.52) (−0.87)
1.86 (0.93) (0.95)
−0.78 (−0.36) (−0.89)
1.87 (0.89) (0.96)
0.29 (0.06) (−0.44)
−0.74 (−0.56) (−0.87)
1.86 (0.94) (0.96)
0.28 (0.24) (−0.45)
−1.41 (−0.73) (−0.81)
−1.24 (−0.57) (−0.67)
3.24 (0.14) (1.88)
0.24 (−0.01) (−0.45)
−1.41 (−0.73) (−0.80) −1.41 (−0.63) (−0.78)
−1.26 (−0.34) (−0.64) −1.28 (−0.63) (−0.69)
3.24 (0.18) (1.88)
3.24 (0.06) (1.87)
aCalculated by the AIM method.
bCalculated by the CHelpG Keyword.
cCalculated by the NPA method.
Heteroatom Chemistry DOI 10.1002/hc

468 Zakarianezhad et al.
TABLE 9 Selected 13C NMR Chemical Shift (δ in ppm) and
Coupling Constants (J in Hz) for Some Functional Groups in
the E-4a Isomer as a Major Form
Groups
d, C41
d, Cortho
d, Cipso
S, ArMe2
d, Cmeta
d, Cpara
2s, 2Ome
δC (ppm)
JPC (Hz)
O
169.31a (169.32)b
132.49 (134.11)
124.77 (127.76)
22.41 (23.53)
127.38 (126.26)
130.61 (132.15)
49.35 and 51.28
(46.10 and 46.99)
171.93 (167.32)
164.84 (169.54)
48.44 (44.55)
9.90a (10.34)b
92.20 (91.10)
12.00 (8.52)
d, P C C2
s, 2Cme
10.70 (10.12)
d, P C C7H
CH57
113.45 (107.57)
FIGURE 4 UV spectrum of 10−3 M of triphenylphosphine 1
in 1,4-dioxane.
aExperimental data in accord with the results reported in the literature
[30].
bTheoretical data.
TABLE 10 Selected 13C NMR Chemical Shift (δ in ppm) and
Coupling Constants (J in Hz) for Some Functional Groups in
the Z-4a Isomer as a Minor Form
Groups
d, C41
d, Cortho
d, Cmeta
d, Cipso
d, Cpara
S, ArMe2
2s, 2Ome
δH (ppm)
JPHz (Hz)
O
168.14a (169.42)b
132.49 (132.79)
127.27 (126.71)
125.44 (127.04)
130.70 (132.12)
22.41 (23.55)
47.89 and 51.28
(45.31 and 47.10)
49.27 (45.74)
9.90a (10.64)b
10.80 (8.40)
91.90 (90.55)
d, P C C7H
CH57
FIGURE
acetylenedicarboxylate 2c in 1,4-dioxane.
5 M of di-tert-butyl
UV spectrum of 10−3
113.31 (107.38)
171.79 (164.00)
164.77 (169.27)
d, P C C2
s, 2Cme
10.50 (6.88)
aExperimental data in accord with the results reported in the literature
[30].
bTheoretical data.
compounds 1 and 3 in 1,4-dioxane was pipetted into
a quartz cell, and then a 1-mL aliquot of the 3 ×
10−3 M of solution of the reactant 2c was added
to the mixture, keeping the temperature at 15.0◦C.
The reaction kinetics was followed by plotting UV
absorbance against time. Figure 8 shows the ab-
sorbance change (dotted line) versus time for the
1:1:1 addition reaction between compounds 1, 2c,
and 3 at 15.0◦C. The infinity absorbance (A∞), that
is, the absorbance at reaction completion, can be ob-
served from Fig. 8 at t = 200 min. With respect to
this value, zero, first, or second curve fitting could be
drawn automatically for the reaction by the software
[38] associated with the UV instrument. Using the
original experimental absorbance versus time data
FIGURE 6 UV spectrum of 10−3 M of 2-mercapto-4,6-
dimethyl pyrimidine 3 in 1,4-dioxane.
provided a second-order fit curve (full line) that fits
exactly the experimental curve (dotted line) as shown
in Fig. 9. Thus, the reaction between triphenylphos-
phine 1, di-tert-butyl acetylenedicarboxylate 2c, and
Heteroatom Chemistry DOI 10.1002/hc

Kinetics Investigation of Stable Phosphorus Ylides Involving a 2-Mercapto-4,6-dimethyl Pyrimidine 469
FIGURE 7 (a) UV spectra of the reaction between 1, 2c, and 3 with 10−3 M concentration of each compound as reaction
proceeds in 1,4-dioxane with 10-mm-light-path cell. (b) Expanded section of the UV spectra over the wavelength range 310–
500 nm.
3 follows second-order kinetics. The second-order
rate constant (k2) is then automatically calculated
using a standard equation [38] within the program
at 15.0◦C. It is reported in Table 11.
Furthermore, kinetic studies were carried out us-
ing the same concentration of each reactant in the
continuation of experiments with concentrations of
5 × 10−3 M and 7 × 10−3 M, respectively. As expected,
the second-order rate constant was independent of
the concentration and its value was the same as in
the previous experiment. In addition, the overall or-
der of reaction was also 2.
ferent temperatures and solvent polarities but other-
wise under the same conditions as for the previous
experiment. For this purpose, ethyl acetate with 6
dielectric constant was chosen as a suitable solvent
because it not only could dissolve all compounds but
also did not react with them. The effects of solvents
and temperature on the rate constant are presented
in Table 11. The results show that the rate of reac-
tion in each case was increased at higher tempera-
tures. In addition, the rate of reaction between 1, 2c,
and 3 was accelerated in a higher dielectric constant
environment (ethyl acetate) in comparison with a
lower dielectric constant environment (1,4-dioxane)
at all temperatures investigated. In the temperature
range studied, the dependence of the second-order
rate constant (ln k2) of the reactions on the reciprocal
temperature is consistent with the Arrhenius equa-
tion, giving activation energy of reaction between
Effect of Solvents and Temperature
To determine the effect of change in temperature
and solvent environment on the rate of reaction, it
was elected to perform various experiments at dif-
FIGURE 9 Second-order fit curve (solid line) accompanied
by the original experimental curve (circles) for the reaction
between compounds 1, 2c, and 3 at 410 nm and 15.0◦C in
1,4-dioxane.
FIGURE 8 Experimental absorbance changes against time
at 410 nm for the reaction between compounds 1, 2c, and 3
at 15.0◦C in 1,4-dioxane.
Heteroatom Chemistry DOI 10.1002/hc

470 Zakarianezhad et al.
TABLE 11 Values of Overall Second-Order Rate Constant
for the Reaction Between 1, 2c, and 3 in the Presence of Sol-
vents Such As 1,4-Dioxane and Ethyl Acetate, Respectively,
at All Temperatures Investigated
k2(M−1 min−1
)
Solvent
ε
15.0◦C
20.0◦C
25.0◦C
30.0◦C
1,4-Dioxane
Ethyl acetate
2
6
73.5
114.9
92.7
131.2
109.9
156.4
131.9
184.6
1, 2c, and 3 (27.9 kJ/mol) from the slope shown in
Fig. 10.
Effect of Concentration
FIGURE 11 Pseudo-first-order fit curve (solid line) for the
reaction between 3 and 2c in the presence of an excess of 1
(10−2 M) at 410 nm and 15.0◦C in 1,4-dioxane.
To determine the reaction order with respect
to triphenylphosphine 1 and dialkyl acetylene-
dicarboxylate 2 (2c) in the next experiments, all ki-
netic studies were carried out in the presence of ex-
cess 3. Under this condition, the rate equation may
therefore be expressed as
equal to the second-order rate constant (k2); this is
possible when γ is zero in Eq. (1). It appears, there-
fore, that the reaction is zero and second order with
respect to 3 (SH-acid) and the sum of 1 and 2 (2a)
(α + β = 2), respectively.
α
β
γ
Rate = kobs [1] [2] kobs = k2 [3] or
(1)
ln kobs = ln k2 + γ ln [3]
In this case, 3 × 10−2 M of 3 instead of 3 × 10−3
M
To determine the reaction order with respect to
dialkyl acetylenedicarboxylate 2 (2c), the next exper-
iment was performed in the presence of an excess of
1 (rate = koꢁ bs [3]γ [2]β, koꢁ bs = k2 [1]α (Eq. 2)). The
original experimental absorbance versus time data
provides a pseudo-first-order fit curve at 410 nm,
which exactly fits the experimental curve (circles)
as shown in Fig. 11.
using the original experimental absorbance versus
time data provides a second-order fit curve (solid
line) against time at 410 nm, which exactly fits the
experimental curve. The value of rate constant was
the same as that obtained from the previous exper-
iment (3 × 10−3 M). Repetition of the experiments
with 5 × 10−2 M and 7 × 10−2 M of 3 gave, sepa-
rately, the same fitted curve and rate constant. In
fact, the experimental data indicated that the ob-
served pseudo-second-order rate constant (kobs) was
As a result, since γ = 0 (as determined previ-
ously), it is reasonable to accept that the reaction
is first order with respect to compound 2 (2c) (β =
1). Because the overall order of reaction is 2 (α +
β + γ = 2), it is obvious that α = 1 and the order of
triphenylphosphine 1 must be equal to one. This ob-
servation was also obtained for reactions between 1,
2b, and 3 and 1, 2a, and 3. On the basis of the above
results, a simplified proposed reaction mechanism is
shown in Fig. 12.
The experimental results indicate that the third
step (rate constant k3) is possibly fast. In contrast,
it may be assumed that the third step is the rate-
determining step for the proposed mechanism. In
this case, the rate law can be expressed as follows:
Rate = k3[I1][3]
(3)
The steady-state assumption can be employed for
[I1], which is generated by the following equation:
FIGURE 10 Dependence of the second-order rate constant
(ln k2) on reciprocal temperature for the reaction between
compounds 1, 2c, and 3 measured at wavelength 410 nm in
1,4-dioxane in accordance with the Arrhenius equation.
k2[1][2]
[I1] =
k−2 + k3[3]
Heteroatom Chemistry DOI 10.1002/hc

Kinetics Investigation of Stable Phosphorus Ylides Involving a 2-Mercapto-4,6-dimethyl Pyrimidine 471
the reaction between two ions carries a dispersed
charge, which here is divided between the attacking
2-mercapto-4,6-dimethyl pyrimidine and the phos-
phonium ions. Bonding of solvent (ethyl acetate)
to this dispersed charge would be much weaker
than to the concentrated charge of 2-mercapto-4,6-
dimethyl pyrimidine and phosphonium ions. The
solvent, thus, stabilizes the species ions more than
it would the transition state, and therefore Ea would
be higher, slowing down the reaction. However, in
practice, ethyl acetate speeds up the reaction and for
this reason, the fourth step, which is independent of
the change in the solvent medium, could not be the
rate-determining step. Furthermore, the rate law of
formation of the product (fourth step) for a proposed
reaction mechanism with application of steady-state
assumption can be expressed by
Rate = k4[I2][Z−]
By application of steady state for [I−] and [Z−],
and the replacement of their values in the above-
mentioned equation, the following equation is
obtained:
FIGURE 12 Proposed mechanism for the reaction between
1, 2 (2a, 2b, or 2c), and 3 for the generation of phosphorus
ylides 4a–c.
The value of [I1] can be replaced in Eq. (3) to obtain
the equation
k2 k3 [1] [2] [3]
Rate =
(4)
k−2 + k3 [3]
k2k3[1][2][3]
Rate =
This equation is independent of the rate constant
for the fourth step (k4) and shows why the fourth
step would not be affected by a change in the solvent
medium. In addition, it has been suggested earlier
that the kinetics of ionic species’ phenomena (e.g.,
the fourth step) is very fast [39–41]. If the first step
(rate constant k2) were the rate-determining step, in
this case, two reactants (triphenylphosphine 1 and
dialkyl acetylenedicarboxylate 2), as we have seen in
Fig. 12, have no charge and could not form strong
ion–dipole bonds to the high dielectric constant sol-
vent, ethyl acetate. However, the transition state car-
ries a dispersed charge, which here is divided be-
tween the attacking 1 and 2 and, hence, bonding
of solvent to this dispersed charge is much stronger
than the reactants, which lack charge. The solvent,
thus, stabilizes the transition state more than it does
the reactants and, therefore, Ea is reduced, which
speeds up the reaction. Our experimental results
show that the solvent with higher dielectric con-
stant exerts a powerful effect on the rate of reac-
tion (in fact, the first step has the rate constant k2
in the proposed mechanism), but the opposite oc-
curs with the solvent of lower dielectric constant (see
Tables 11–13). The results of the current work (ef-
fects of solvent and concentration of compounds)
have provided useful evidence for steps 1 (k2), 3 (k3),
and 4 (k4) of the reactions between triphenylphos-
phine 1, dialkyl acetylenedicarboxylate 2 (2a, 2b,
k−2 + k3[3]
Since it was assumed that k3 is relevant to the rate-
determining step, it is reasonable to make the fol-
lowing assumption:
k−2
k3 [3]
So the rate law becomes
k2 k3 [1] [2] [3]
Rate =
k−2
The final equation indicates that the overall order
of reaction is three, which is not compatible with
the experimental overall order of reaction (=two).
In addition, according to this equation, the order
of reaction with respect to 2-mercapto-4,6-dimethyl
pyrimidine 3 is one, whereas it was actually shown
to be equal to zero. For this reason, it appeared
that the third step is fast. If we assume that the
fourth step (rate constant k4) is the rate-determining
step for the proposed mechanism, in this case,
there are two ionic species to consider in the rate-
determining step, namely phosphonium ion (I2) and
2-mercapto-4,6-dimethyl pyrimidine (Z−). The phos-
phonium and 2-mercapto-4,6-dimethyl pyrimidine
ions, as we have seen in Fig. 12, have full positive
and negative charges and form very powerful ion-
dipole bonds to the ethyl acetate, the high dielectric
constant solvent. However, the transition state for
Heteroatom Chemistry DOI 10.1002/hc

472 Zakarianezhad et al.
TABLE 14 Activation Parameters Involving ꢀG#, ꢀS#, and
ꢀH# for the Reactions Between 1, 2a, and 3, 1, 2b, and 3
and also 1, 2c, and 3 at 15.0◦C in 1,4-Dioxane on the Basis
of the Eyring Equation
TABLE 12 Values of Overall Second-Order Rate Constant
for the Reaction Between 1, 2b, and 3 in the Presence of Sol-
vents Such As 1,4-Dioxane and Ethyl Acetate, Respectively,
at All Temperatures Investigated
k2(M−1 min−1
)
ꢀG#
ꢀH#
ꢀS#
Reactions
(kJ mol−1
)
(kJ mol−1
)
(J mol−1K−1
)
Solvent
ε
15.0◦C
20.0◦C
25.0◦C
30.0◦C
1, 2a, and 3
1, 2b, and 3
1, 2c, and 3
103
103
107
10.4
12.5
23.1
−321
−314
−292
1,4-Dioxane
Ethyl acetate
2
6
417.5
641.9
464.3
702.6
520.3
781.4
599.1
876.3
TABLE 13 Values of Overall Second-Order Rate Constant
for the Reaction Between 1, 2a, and 3 in the Presence of
Solvents Such As 1,4-Dioxan and Ethyl Acetate, Respectively,
at All Temperatures Investigated
d[I1]
k2[1] [2]
= 0,
[I1] =
(7)
dt
k−2 + k3 [3]
We can now replace [I1] in Eq. (6) to obtain the equa-
tion
k2(M−1 min−1
)
Solvent
ε
15.0◦C
20.0◦C
25.0◦C
30.0◦C
k2 k3 [1] [2] [3]
k4 [Z−] k−2 + k3 [3]
ꢂ
ꢃ
[I2] =
1,4-Dioxane
Ethyl acetate
2
6
483.1
706.2
531.3
768.1
592.6
843.4
660.2
917.3
The value of [I2] can be put into Eq. (5) to obtain the
rate Eq. (8) for the proposed mechanism:
k2 k3 k4 [1] [2] [3] [Z−]
k4 [Z−] k−2 + k3 [3]
ꢂ
ꢃ
Rate =
Rate =
or
or 2c), and 2-mercapto-4,6-dimethyl pyrimidine 3.
Two steps involving 3 and 4 are not determin-
ing, although the discussed effects, taken altogether,
are compatible with the first step (k2) of the pro-
posed mechanism and would allow it to be the rate-
determining step. However, a good kinetic descrip-
tion of the experimental result using a mechanis-
tic scheme based upon the steady-state approxima-
tion is frequently taken as evidence of its validity. By
application of this, the rate formation of product 4
from the reaction mechanism (Fig. 12) is given by
k2 k3 [1] [2] [3]
ꢂ
ꢃ
(8)
k−2 + k3 [3]
Since experimental data indicated that steps 3 (k3)
and 4 (k4) are fast but step 1 (k2) is slow, it is, there-
fore, reasonable to make the following assumption:
k3 [3]
So the rate equation becomes
Rate = k2 [1] [2]
This equation, which was obtained from a mech-
anistic scheme (shown in Fig. 12) by applying the
steady-state approximation, is compatible with the
results obtained by UV spectrophotometry. With re-
spect to Eq. (9), which shows the overall rate con-
stant (k2), the activation parameters involving ꢀG#,
ꢀS#, and ꢀH# for three reactions (1, 2a and 3, 1,
2b, and 3, and also 1, 2c, and 3) can now be calcu-
lated by using the Eyring equation for the first step
(k2, rate-determining step, Fig. 1) as an elementary
reaction; the results are reported in Table 14.
k−2
(9)
d[4]
d[ylide]
=
= rate = k4 [I2] [Z−]
(5)
dt
dt
We can apply the steady-state approximation to [I1]
and [I2]:
d[I1]
= k2 [1] [2] − k−2 [I1] − k3 [I1] [3]
dt
d[I2]
= k3 [I1] [3] − k4 [I2] [Z−]
dt
To obtain a suitable expression for [I2] to put into
Eq. (5), we can assume that, after an initial brief
period, the concentration of [I1] and [I2] achieves a
steady state with their rates of formation and rates
Further Kinetic Investigations
ꢁ
of disappearance just balanced. Therefore, d[I1] dt
ꢁ
Effect of Structure of Dialkyl Acetylenedicar-
boxylates. To confirm the above observations, fur-
ther experiments were performed with diethyl
acetylenedicarboxylate 2b and dimethyl acetylenedi-
carboxylate 2a, respectively, under the same
and d[I2] dt are zero and we can obtain expressions
for [I2] and [I1] as follows:
d[I2]
dt
k3[I1] [3]
k4 [Z−]
= 0,
[I2] =
(6)
Heteroatom Chemistry DOI 10.1002/hc

Kinetics Investigation of Stable Phosphorus Ylides Involving a 2-Mercapto-4,6-dimethyl Pyrimidine 473
under the same condition are approximately 5.5–
7.00 times more than for the reaction with di-tert-
butyl acetylenedicarboxylate 2c (see Tables 11–13).
It seems that both inductive and steric factors for the
bulky alkyl groups in 2c tend to reduce the overall
reaction rate (see Eq. (9)). In the case of dimethyl
acetylenedicarboxylate 2a, the lower steric and in-
ductive effects of the dimethyl groups exert a pow-
erful effect on the rate of the reaction.
CONCLUSIONS
The assignment of the Z- and E-isomers as a mi-
FIGURE 13 Second-order fit curve (solid line) accompanied
nor or major form in both the ylides 4a and 4c
was undertaken by AIM, NPA methods, and CHelpG
keyword. Quantum mechanical calculation clarified
how the ylides 4a and 4c exist in solution as a mix-
ture of the two geometrical isomers. This result was
in good agreement with the experimental data. In
addition, the NMR study on the basis of theoreti-
cal calculations was employed for determination of
chemical shifts and coupling constants of the two
major E-4(a, c) and minor Z-4(a, c) geometrical iso-
mers. In addition, kinetic investigation of these reac-
tions was undertaken using UV spectrophotometry.
The results can be summarized as follow: (1) The
appropriate wavelengths and concentrations were
determined to follow the reaction kinetics. (2) The
overall reaction order followed second-order kinet-
ics, and the reaction orders with respect to tri-
phenylphosphine, dialkyl acetylenedicarboxylate,
and 2-mercapto-4,6-dimethyl pyrimidine were one,
one, and zero, respectively. (3) The values of the
second-order rate constants of all reactions were
calculated automatically with respect to the stan-
dard equation, using the software associated with
the Cary-300 UV equipment. (4) The rates of all
reactions were accelerated at higher temperatures.
Under the same conditions, the activation energy
of the reaction with di-tert-butyl acetylenedicar-
boxylate 2c (27.9 kJ/mol) was higher than that for
the two reactions, which were followed by the di-
ethyl acetylenedicarboxylate 2b (17.3 kJ/mol) and
dimethyl acetylenedicarboxylate 2a (15.2 kJ/mol) in
1,4-dioxane. (5) The rates of all reactions were in-
creased in solvents of higher dielectric constant, and
this can be related to differences in stabilization by
the solvent of the reactants and the activated com-
plex in the transition state. (6) Increased steric bulk
in the alkyl groups of the dialkyl acetylenedicarboxy-
lates, accompanied by the correspondingly greater
inductive effect, reduced the overall reaction rate.
(7) With respect to the experimental data, the first
step of the proposed mechanism was recognized
by the original experimental curve (circles) for the reaction
between compounds 1, 2b, and 3 at 410 nm and 15.0◦C in
1,4-dioxane.
conditions as used in the previous experiments. The
values of the second-order rate constant (k2) for the
reactions between 1, 2b, and 3 and 1, 2a, and 3 are
reported in Tables 12 and 13, respectively, for all sol-
vents and temperatures investigated. The original ex-
perimental absorbance curves (circles) accompanied
by the second-order fitted curves (solid line), which
exactly fit experimental curves (circles) (Figs. 13 and
14), confirm the previous observations again for both
reactions at 15.0◦C and 410 nm.
As can be seen from Tables 12 and 13, the
behavior of diethyl acetylenedicarboxylate 2b and
dimethyl acetylenedicarboxylate 2a is the same for
the di-tert-butyl acetylenedicarboxylate 2c (Table 11)
with respect to the reaction with triphenylphos-
phine 1 and 2-mercapto-4,6-dimethyl pyrimidine 3.
The rate of the former reactions was also accel-
erated in a higher dielectric constant environment
and with higher temperatures; however, these rates
FIGURE 14 Second-order fit curve (solid line) accompanied
by the original experimental curve (circles) for the reaction
between compounds 1, 2a, and 3 at 410 nm and 15.0◦C in
1,4-dioxane.
Heteroatom Chemistry DOI 10.1002/hc

474 Zakarianezhad et al.
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Heteroatom Chemistry DOI 10.1002/hc