Mechanism of alkene isomerization by bifunctional ruthenium catalyst: A theoretical study

Article abstract of DOI:10.1016/j.jorganchem.2011.08.034

The molecular mechanism of the isomerization of 1-pentene to form (E)-2-pentene catalyzed by the bifunctional ruthenium catalyst has been investigated using density functional theory calculations. The reaction is likely to proceed through the following steps: 1) the β-H elimination to generate the ruthenium hydride intermediate; 2) the reductive elimination of the hydride intermediate to generate the nitrogen-protonated allyl intermediate; 3) the transportation of the hydrogen by the dihedral rotation with Ru-P bond acting as axis; 4) the oxidative addition to afford another hydride complex; 5) the reductive elimination of the hydride intermediate to form the C ₂-C₃ π-coordinated agostic intermediate; 6) the coordination of the nitrogen to the ruthenium center to give the final product. The rate-determining step is the oxidative addition step (the process of the hydrogen moves to ruthenium center from the nitrogen atom) with the free energy of 31.2 kcal/mol in the acetone solvent. And the N-heterocyclic ligand in the catalyst mainly functions in the two aspects: affords an important internal-basic center (nitrogen atom) and works as a transporter of hydrogen. Our results would be helpful for experimentalists to design more effective bifunctional catalysts for isomerization of a variety of heterofunctionalized alkene derivatives.

Full text of DOI:10.1016/j.jorganchem.2011.08.034

Journal of Organometallic Chemistry 698 (2012) 1e6
Contents lists available at SciVerse ScienceDirect
Journal of Organometallic Chemistry
journal homepage: www.elsevier.com/locate/jorganchem
Mechanism of alkene isomerization by bifunctional ruthenium catalyst:
A theoretical study
*
Jingcong Tao , Fengshen Sun, Tao Fang
Department of Information Engineering, Laiwu Vocational and Technical College, Laiwu, 271100, PR China
a r t i c l e i n f o
a b s t r a c t
Article history:
The molecular mechanism of the isomerization of 1-pentene to form (E)-2-pentene catalyzed by the
bifunctional ruthenium catalyst has been investigated using density functional theory calculations. The
Received 10 May 2011
Received in revised form
18 August 2011
reaction is likely to proceed through the following steps: 1) the
b-H elimination to generate the
ruthenium hydride intermediate; 2) the reductive elimination of the hydride intermediate to generate
the nitrogen-protonated allyl intermediate; 3) the transportation of the hydrogen by the dihedral
rotation with RueP bond acting as axis; 4) the oxidative addition to afford another hydride complex; 5)
Accepted 23 August 2011
Keywords:
the reductive elimination of the hydride intermediate to form the C2-C3
p-coordinated agostic inter-
Reaction mechanism
Alkene isomerization
Bifunctional ruthenium catalyst
Density functional theory
mediate; 6) the coordination of the nitrogen to the ruthenium center to give the final product. The rate-
determining step is the oxidative addition step (the process of the hydrogen moves to ruthenium center
from the nitrogen atom) with the free energy of 31.2 kcal/mol in the acetone solvent. And the N-
heterocyclic ligand in the catalyst mainly functions in the two aspects: affords an important internal-
basic center (nitrogen atom) and works as a transporter of hydrogen. Our results would be helpful for
experimentalists to design more effective bifunctional catalysts for isomerization of a variety of heter-
ofunctionalized alkene derivatives.
Ó 2011 Elsevier B.V. All rights reserved.
1. Introduction
mechanism of this isomerization process has been proposed by
Grotjahn et al (Scheme 1). The catalytic cycle is initiated by the
Isomerization of the double bond of an unsaturated compound is
an important reaction in organic chemistry [1e10]. And transition-
metal-catalyzed isomerization of the carbonecarbon double bond
of alkene has been a considerable-interest area [11e17]. Recently,
Grotjahn and co-workers reported an attractive ruthenium catalyst
to catalyze the extensive isomerization of alkenes [18]. This ruthe-
nium catalyst is a mono-metallic catalyst with an N-heterocyclic
ligand (as shown in Scheme 1S), which has been confirmed by NMR.
When the N-heterocyclic group on the phosphorus is replaced by
phenyl group, the reaction rate of the isomerization of 1-pentene
and pent-4-en-1-ol are 330 and 10,000 times slower than using
the N-heterocyclic ligand, respectively. Thus, this evidence can
elucidate the important role of the heterocycle in the catalyst. Using
this catalyst, a variety of heterofunctionalized alkene derivatives can
isomerize to the high-purity (E)-isomer products (61e97%), just at
low loading (2e5%) in many cases. As a bifunctional catalyst, in
which the Lewis acid and Lewis base are ruthenium and nitrogen
(directly bound to ruthenium), respectively, it can move an alkene
double bond over 30 positions along an alkene chain. The possible
exchange of acetonitrile for alkene. Then, the deprotonation takes
place at an allylic position with the assistance of the basic
ruthenium-bound nitrogen on the heterocyclic ligand. Finally, the
proton goes back to either end of the allyl moiety from the nitrogen
atom and promotes isomerization. To our knowledge, no computa-
tional study has been carried out to investigate the mechanistic
details of alkene isomerization catalyzed by the bifunctional
ruthenium catalyst.
In this work, we will perform density functional theory calcu-
lations to explore the mechanistic details of alkene isomerization
catalyzed by the bifunctional ruthenium catalyst and to find how
the catalyst operated in this isomerization process. A prototype
reaction, the isomerization of 1-pentene to (E)-2-pentene (95%)
required only 15 min at room temperature in acetone using 2 mol%
catalyst (as shown in Scheme 2), is chosen for study. The results
provide a general picture on the mechanism of the isomerization of
alkenes, and a molecular level picture on how the bifunctional
ruthenium catalyst function in the isomerization process. The
information revealed in this study may be useful to experimen-
talists for inventing more effective bifunctional catalysts for isom-
erization of alkenes and a variety of heterofunctionalized alkene
derivatives.
* Corresponding author. Tel.: þ86 634 6427328; fax: þ86 634 6270706.
E-mail addresses: jingcongtao@gmail.com, lzytjc@163.com (J. Tao).
0022-328X/$ e see front matter Ó 2011 Elsevier B.V. All rights reserved.
doi:10.1016/j.jorganchem.2011.08.034

2
J. Tao et al. / Journal of Organometallic Chemistry 698 (2012) 1e6
N
N
NH
P
[Ru]
P
NH
N
P
N
N
P
[Ru]
P
P
N
P
P
P
N
H
[Ru]
[Ru]
[Ru]
H
H
[Ru]
H
H
[Ru]
H
H
[Ru]
H
[Ru]
H
H
H
H
H
+
+
R
3
R
+
R
R
CH3CN
2
3
5
R
4
N
P
[Ru]
Scheme 1. Mechanistic hypothesis proposed by Grotjahn et al.
P
P
1
N
H
P
P
N
H
HN
N
2. Computational methods
[Ru]
[Ru]
[Ru]
[Ru]
H
H
H
H
All calculations are carried out using the Gaussian03 package
[19]. Two basis sets are used. The geometries of all stationary points
are fully optimized with the B3LYP density functional [20,21] with
the basis set 1 (BS1). In BS1, relativistic effective core potential (ECP)
[22,23] is employed for ruthenium and phosphorus. The basis set
for Ru is a modified LANL2DZ plus an f-type polarization function
[24], in which the two 5p functions of the standard LANL2DZ are
replaced by the optimized 5p functions from Couty and Hall [25].
For phosphorus, the standard LANL2DZ augmented by a d-type
function with the exponent of 0.387 is used [26]. For the catalyst 1,
the five-membered N-heterocyclic atoms, a 6-31G (d, p) basis set is
employed, and all of the other atoms in the ligands (heterocyclic
ligand and cyclopentadienyl group) are described with the 3-21G
basis set. For all atoms in 1-pentene, a 6-31G (d, p) basis set is used.
For each stationary point, vibrational frequencies are calculated to
obtain zero-point vibrational energies (ZPVE) and verify whether it
is a minimum or a transition state. Intrinsic reaction coordinates
(IRC) [27,28] calculations are performed from each transition state
to verify whether the reactant and the product are really connected
by the transition state.
9
7
8
6
Scheme 3. The reaction pathway supposed for the catalyzed isomerization.
3.1. The formation of the active catalyst
In experiment, [CpRu(II)(CH3CN)3]þ PF6- (217.1 mg,0.49 mmol)
and the required phosphine ligand (125.9 mg, 0.51 mmol) were
mixed in acetone to generate the yellowish brown powder. Finally,
the 18e precatalyst [CpRu(II)(CH3CN)L]þ PF6- (a, Scheme 1S) was
confirmed by the NMR and elemental analysis. And the initial
dissociation of an acetonitrile (CH3CN) ligand is found to be much
more facile, with the free energy change of 6.9 and -0.2 kcal/mol, in
gas phase and in the solution phase, respectively.
½CpRuðCH3CNÞLꢀþ/½CpRuLꢀþþCH3CN
Therefore, a 16e complex, [CpRu(II)L]þ PF6ꢁ, is to be formed. And in
this work, the cation [CpRu(II)L]þ (c, Scheme 1S) is the active
catalyst.
More accurate relative energies of all species are obtained by
subsequent single point calculations with a larger basis set (BS2) at
the geometries optimized with BS1, denoted as B3LYP/BS2//B3LYP/
BS1. In BS2, for the catalyst 1, a 6-311þþG(d,p) basis set is employed
for the phosphorus and the five-membered N-heterocyclic atoms,
a 6-31G(d, p) basis set is employed for all of the other atoms in the
ligands (heterocyclic ligand and cyclopentadienyl group). For all
atoms in 1-pentene, a 6-311þþG (d,p) basis set is used. For all
stationary points, free energies of solvation are computed as the
energy difference between single point B3LYP/BS2 calculations in
acetone calculated with the PCM model [29] and those in the gas
phase at the B3LYP/BS1 gas-phase geometries.
3.2. The allyl mechanism
According to the pathway shown in Scheme 3, the initial step of
the reaction is the coordination of 1-pentene to the ruthenium
center to produce the
p-bound intermediate 2. Then, the agostic
intermediate 3 is obtained by the positional adjustment of 1-
pentene on the metal. Thus, the CeH bond, at the activated allylic
position (i.e. b-H) of the 1-pentene, is oxidatively added to generate
the s3-allyl hydride 4. Next, the Ru-bound hydrogen moves to the
basic nitrogen to produce the intermediate 5. Subsequently, the N-
bound hydrogen is transported to the side of the terminal allylic
carbon to give 6. And another s3-allyl hydride 7 is obtained by an
oxidative addition reaction. Then, the agostic species 8 is formed by
the reductive elimination. Finally, the final product dissociates from
3. Results and discussion
the p-bound intermediate 9, and the active catalyst is regenerated.
In this section, we will explore the potential energy surface of
the isomerization of 1-pentene catalyzed by the bifunctional
cationic ruthenium catalyst 1 (as shown in Scheme 3), and in the
next subsection, how this catalyst function in the isomerization
process will be elucidated. The optimized structures of all
stationary points are collected in Figs.1 and 2, and their relative free
energies are provided in Fig. 3.
Due to two possible geometric isomers for 2-pentene, E or Z,
there should be two possible reaction pathways to generate the
products of (E)-2-pentene and (Z)-2-pentene, respectively. The
reaction pathway for producing the 2-pentene with E or Z config-
uration should be similar. In the experiments with the ruthenium
catalyst, the main product is of E configuration. Thus, only the
process for the formation of the (E)-2-pentene is discussed in this
work.
3.2.1. The formation of the s3-allyl hydride
Initially, 1-pentene is M-coordinated to the ruthenium to form
an 18e complex 2. In 2, the C1eC2 bond is elongated to 1.396 Å
(from 1.333 Å in free 1-pentene), indicating that the CeC double
bond activation by ruthenium has been significantly achieved. The
free energy change of this coordination step is 10.8 kcal/mol above
the reactants (as shown in Fig. 3). Next, there will be two possible
modes for the allylic-positional hydrogen transfer. The first one is
that the proton directly moves to the basic nitrogen (N1) from the
allylic position (C3). Much endeavor has been done to find the
transition state of this
responding structure could be located. The second one is that the
-H adds to the ruthenium center to produce the s3-allyl hydride.
b-H elimination step, but none of the cor-
b
Initially, the agostic intermediate 3 is formed via the transition
state TS1. In TS1, the RueH distance is getting shorter (from
3.370 Å in 2 to 2.372 Å), but the RueN1 bond is breaking (from
2.324 Å in 2 to 3.123 Å). The free energy barrier of this agostic
(a), 2 mol%
Acetone
25
15 min
1-pentene
(E)-2-pentene
95 %
intermediate-formation step is 11.0 kcal/mol. Subsequently, the
b-
Scheme 2. The isomerization of 1-pentene.
H elimination affords the s3-allyl hydride 4 via the transition state

J. Tao et al. / Journal of Organometallic Chemistry 698 (2012) 1e6
3
Fig. 1. Optimized geometries of the stationary points along the reaction pathway of isomerization. All H atoms (except those involved in isomerization process) are omitted for
clarity.
TS2. In TS2, the RueH bond is forming (from 1.901 Å in 3 to
1.623 Å), and the C3eH bond is breaking (from 1.188 Å in 3 to
1.676 Å). The free energy barrier of this b-H elimination step is
The first mode is the positional adjustment of the Ru-bound
hydrogen. In this way, the hydrogen can shift to the side of the
terminal allyl carbon (C1). However, this adjustment must over-
come a very high free energy barrier (45.1 kcal/mol, relative to 1
and 1-pentene). Hence, it is impossible for the isomerization to go
along in this mode.
3.0 kcal/mol with respect to 3.
3.2.2. The reductive elimination
In order to achieve the isomerization, the Ru-bound hydrogen
must migrate to the terminal allyl carbon (C1). For the intermediate
4, there will be three modes for the hydrogen transfer.
For the second mode, the Ru-bound hydrogen may initially add
to the carbon of the cyclopentadienyl (Cp) ligand (the corre-
sponding transition state is TS30) to generate the intermediate 50,

4
J. Tao et al. / Journal of Organometallic Chemistry 698 (2012) 1e6
Fig. 2. Optimized geometries of the stationary points along the reaction pathway of isomerization. All H atoms (except those involved in isomerization process) are omitted for
clarity.
and then the hydrogen was migrated to the side of the terminal allyl
carbon (C1) by the rotation of Cp group. And the subsequent steps
will be the oxidative addition following the reductive elimination.
The free energy of TS30 is 35.3 kcal/mol (relative to 1 and 1-
pentene). Therefore, it is difficult for this mode to take place
under the experimental conditions.
this rotational step is only 3.6 kcal/mol. Therefore, the rotation is
facile under the experimental environment to generate the inter-
mediate 6.
3.2.4. The oxidative addition and the subsequent steps to produce
the final product
For the last mode, the hydrogen migrates to the nitrogen atom
(N1) to generate the intermediate 5 via the transition state TS3. In
TS3, the Ru-H bond is breaking (from 1.594 Å in 4 to 1.778 Å), but
the HeN1 bond is forming (from 1.951 Å in 4 to 1.453 Å). The free
energy of TS3 is 25.0 kcal/mol (relative to 1 and 1-pentene).
Comparison of the above three modes, one can find that the
third one is the most possible pathway for the isomerization
reaction to undergo through. The subsequent steps, after the
formation of 5 by the reductive elimination step, will be discussed
in the next subsection in detail.
After the formation of 6, the hydrogen will migrate to the
terminal carbon (C1) to generate the final product. Firstly, the
directly transfer of the hydrogen from the N1 atom to the C1 atom is
taken into account. But it is similar to the above mentioned that
none of the transition state is to be located. Herein, the oxidative
addition initially takes place to generate the s3-allyl hydride 7 via
the transition state TS5. In TS5, the RueH bond is forming (from
2.615 Å in 6 to 1.766 Å), but the HeN1 bond is breaking (from
1.032 Å in 6 to 1.463 Å). And this oxidative addition step is the rate-
determining step with the free energy of 27.2 kcal/mol (relative to 1
and 1-pentene). Subsequently, the hydrogen adds to the terminal
allyl carbon (C1) via the transition state TS6. In TS6, the RueH bond
is breaking (from 1.583 Å in 7 to 1.614 Å), but the HeC1 bond is
forming (from 2.134 Å in 7 to 1.6723 Å). And the C1eC2 bond is
elongated to 1.436 Å (from 1.419 Å in 7). The free energy barrier of
this reductive elimination step is only 0.3 kcal/mol with respect to
7. Hence, another agostic intermediate 8, in which the RueN1 bond
distance is 3.370 Å, is afforded. Next, the basic nitrogen (N1) will
3.2.3. The transportation of the hydrogen
To ensure the successful progress of the isomerization reaction,
the hydrogen on the nitrogen atom (N1) must be transported to the
side of the terminal allyl carbon (C1). For 5, the most possible mode
for the transportation of the hydrogen (on the N1 atom) is the
dihedral rotation with the RueP bond acting as axis, the corre-
sponding transition state is TS4 (Fig. 2). The free energy barrier of

J. Tao et al. / Journal of Organometallic Chemistry 698 (2012) 1e6
5
a
(38.5)
35.3
G298 (kcal/mol)
(33.8)
29.6
TS3'
5'
(25.6)
22.8
TS3
(26.1)
21.8
(24.0)
21.1
(23.2)
19.8
25.0
5
TS2
(28.9)
TS1
4
20.9
(24.2)
3
N
(14.6)
10.8
P
N
H
P
H
NH
[Ru]
P
H
[Ru]
H
[Ru]
2
H
N
P
(0.0)
0.0
H
[Ru]
H
1 +
1-pentene
N
P
[Ru]
Reaction coordinate
b
G298 (kcal/mol)
(31.2)
27.2
(27.5)
24.5
(28.1)
25.0
(28.0)
24.7
(26.9)
22.2
(23.8)
20.7
TS5
(23.4)
19.5
TS6
TS4
5
7
P
TS7
20.9
6
N
H
8
(24.2)
(16.7)
12.6
P
HN
[Ru]
P
H
[Ru]
N
H
H
[Ru]
9
H
P
N
(0.0)
0.0
[Ru]
H
H
(- 4.1)
-3.1
1 + 1-pentene
1 +(E)-2-pentene
Reaction coordinate
Fig. 3. Free energy profiles of the isomerization of 1-pentene in gas phase and in the solution phase (values in parentheses).
coordinate to the ruthenium accompanying the elimination of the
3.4. The role of the N-heterocyclic ligand in the ruthenium catalyst
agostic structure, the corresponding transition state is TS7. In TS7,
the RueN1 bond distance is shortened to 3.049 Å, and the RueH
bond distance is elongated to 2.622 Å (from 1.919 Å in 8). The free
energy barrier of this coordination step is 2.7 kcal/mol (relative to
8). Therefore, the intermediate 8 can easily convert into 9, in which
As mentioned above, for the intermediate 4, when the nitrogen
atom on heterocyclic ligand does not operate in the catalyst cycle,
there are mainly two channels for the reaction to progress. The first
one is the positional adjustment of the hydrogen on the ruthenium
center, but with a very high free energy (45.1 kcal/mol, relative to 1
and 1-pentene). For the second, the hydrogen initially adds to the
carbon of cyclopentadienyl (Cp) ligand (the corresponding transi-
tion state is TS30), and then undergoes through the rotation of Cp
group to transfer the hydrogen to the same side of the terminal allyl
carbon (C1). The free energy of TS30 is 35.3 kcal/mol (relative to 1 and
1-pentene). Therefore, it is difficult for the isomerization reaction to
take place through these two channels under the experimental
conditions. And this result is in agreement with the experimental
evidence, which is that when the phenyl group is used to substitute
for the N-heterocyclic group on the phosphorus, the reaction rate of
the isomerization of 1-pentene is 330 times slower than that using
the N-heterocyclic ligand. However, when the hydrogen adds to the
nitrogen (N1), the free energy of the elimination step from 4 to 5 is
reduced to 25.0 kcal/mol (relative to 1 and 1-pentene). In a similar
way, the free energy of the oxidative addition step from 6 to 7, which
the C2eC3 double bond
p-coordinated to the ruthenium. Ulti-
mately, the product, (E)-2-pentene, can be released from the
species 9, and the active catalyst 1 is regenerated.
3.3. The solvent effect on the reaction
In the preceding subsections, the free energy profiles of the
whole reaction in gas phase have been discussed. When the solvent
effect is taken into account, the relative energies of the interme-
diates and transition states are increased to different extent (as
shown in Fig. 3), but the qualitative trend of the free energy profile
remains the same (as in gas phase).
For example, the rate-determining step on the whole reaction
pathway is the oxidative addition step from 6 to 7 in both gas phase
and the solution phase, which with the free energies of 27.2 (gas
phase) and 31.2 kcal/mol (solvent), respectively.

6
J. Tao et al. / Journal of Organometallic Chemistry 698 (2012) 1e6
is the rate-determining step, is 27.2 kcal/mol (gas phase). Therefore,
this can elucidate that the N-heterocyclic ligand in the catalyst
affords an important internal-basic nitrogen atom (act as a Lewis
base). Thus, the nitrogen atom (as the Lewis base) and the ruthe-
nium atom (as the Lewis acid) in this bifunctional catalyst can work
cooperatively to promote the isomerization reaction.
Appendix. Supplementary Information
Supplementary Information associated with this article can be
found, in the online version, at doi:10.1016/j.jorganchem.2011.08.
034.
After the formation of 5, it is the dihedral rotation with the RueP
bond acting as axis that transport the hydrogen (on the N1 atom) to
the side of the terminal allyl carbon, the corresponding transition
state is TS4. The free energy barrier of this rotational step is only
3.6 kcal/mol. Therefore, the N-heterocyclic ligand in the catalyst
also works as a transporter of hydrogen.
In general, the N-heterocyclic ligand in the bifunctional catalyst
mainly functions in the two aspects: affords an important internal-
basic center (nitrogen atom) and works as a transporterof hydrogen.
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4. Conclusions
In this paper, we have carried out detailed density function
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hydride intermediate to form the C2eC3
p-coordinated agostic
intermediate; 6) the coordination of the nitrogen to the ruthenium
center to produce the final product. For the whole reaction, the
rate-determining step is the oxidative addition step (the process of
the hydrogen moves to ruthenium atom from the nitrogen atom)
with the free energy of 31.2 kcal/mol in the acetone solvent. And
the N-heterocyclic ligand in the bifunctional ruthenium catalyst
mainly functions in the two aspects: affords an important internal-
basic center (nitrogen atom) and works as a transporter of
hydrogen. The mechanism proposed here for the isomerization of
1-pentene is expected to be general for isomerization of many other
alkene derivatives, and thus would be helpful for experimentalists
to design more effective bifunctional catalysts for isomerization of
a variety of heterofunctionalized alkene derivatives.
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Acknowledgments
The calculations were performed at the Institute of Theoretical
and Computational Chemistry Nanjing University. And I will
express my gratitude to Prof. Shuhua Li for his help.