CASPiE (Biodiesel II): Stereoselective Ni-Catalyzed Hydrogenation

Rosemarie Dawn Tagare

July 30, 2013
Methods and Background

The purpose of this lab was to reduce the internal alkyne of ethyl oct-3-ynoate, synthesized in the
previous lab session, to the cis-alkene ethyl (Z)-oct-3-enoate through Ni-catalyzed hydrogenation
(Figure 1). During this reaction, a thin-layer chromatography plate was obtained in order to track
the progress of product formation. Rotary evaporation and vacuum filtration were used in order
to isolate the product obtained. Then, infrared spectroscopy was used to determine whether or
not the desired cis-alkene was formed. This experiment was considered a success because the
TLC plate indicated different retention factors for ethyl oct-3-ynoate and ethyl (Z)-oct-3-ynoate,
suggesting that the product had a significantly different polarity than the starting material.
Additionally, the IR spectrum of the isolated product indicated the presence of an alkene, a
carbonyl group, and two methyl groups, which are all characteristic of ethyl (Z)-oct-3-enoate.


Figure 1. Ni-Catalyzed Hydrogenation Reaction of Ethyl Oct-3-ynoate to Ethyl (Z)-oct-3-enoate.

This weeks lab is the second of a two-part series developed by the Center for Authentic Science
Practice in Education (CASPiE). Its focus is biodiesel, a renewable fuel produced by the
transesterification of triglycerides into their respective esters of fatty acids. In addition to being
renewable, biodiesel is preferable over petroleum diesel because its negative impact on the
environment is substantially smaller. Of the benefits to the environment, one of the most
important is that biodiesel does not contribute to the increase of global warming gases since it
mainly releases CO
2
and H
2
O upon burning. However, biodiesels pitfall is its relatively high
level of nitrogen oxide (NO
x
) emissions in comparison to petroleum diesel. The hypothesis
examined in this module states that biodiesels high level of NO
x
emissions is attributed to
unsaturated carbon side chains found on the ester. In order to investigate this claim, this module
aims to develop an efficient method of synthesizing fatty acid surrogatessuch as ethyl (Z)-oct-3-
enoatefor lab testing. Additionally, sufficient amounts of these surrogates must be made so that
they can be analyzed though shock pyrolysis. These surrogates are needed because the fatty acids
produced by biodiesel combustion have relatively low equilibrium vapor pressures, making them
impractical for shock tube pyrolysis. As mentioned earlier, the specific goal of this lab was to
synthesize ethyl (Z)-oct-3-enoate from ethyl oct-3-ynoate. Ethyl (Z)-oct-3-enoate is a fatty acid
surrogate that would be helpful in determining the effects of unsaturation of esters carbon side
chains on biodiesels levels of nitrogen oxide emission.

In this lab, a nickel-catalyzed hydrogenation was employed in order to reduce an internal alkyne
to a cis-alkene. Hydrogenation is considered a reduction reaction. These types of reactions are
characterized by increased bonding to hydrogen atoms, decreased bonding to oxygen atoms,
and/or decreased oxidation number caused by a gain in electron density on carbon. In order to
calculate oxidation number, three rules are used: each bond to an atom less electronegative than
carbon is counted as -1, each bond to an atom more electronegative than carbon is counted as +1
and each carbon-carbon bond is counted as 0. These values are calculated for an entire
compound and added together in order to determine the overall oxidation number of the
molecule. During this experiment, hydrogenation added hydrogen to unsaturated carbons,
causing the oxidation number to decrease. This indicated an increased electron density around
carbon because it is more electronegative than hydrogen.

In order to perform hydrogenation, transition metal catalysts, such as palladium, are utilized to
carry out the reaction at a reasonable rate and low temperature. During this lab, Ni(OAc)
2
reacted
with NaBH
4
to form Ni
2
B, which acted as a catalyst for the hydrogenation reaction. This method
was used rather than Pd/C because the latter reaction would have reduced the alkyne to an alkane
rather than the desired alkene. To prevent a complete reduction to an alkane, ethylenediamine
was utilized to poison the nickel catalyst and reduce its activity. Ethylenediamine works in a
way comparable to how lead acetate and quinoline poison palladium and lower the activity of
Lindlars catalyst, thus preventing the complete saturation of an alkyne to an alkane.

Cis/trans isomerism is a type of stereoisomerism that describes the relative orientation
of functional groups within a molecule. Generally, these isomers contain double bonds, which
have restricted rotation due to the -bond (electron overlap above and below the plane of the
atoms). When the substituents are located adjacent to each other, the diastereomer is referred to
as cis (Latin: on the same side), whereas, when the substituents are located across from each
other, the diastereomer is referred to as trans (Latin: on the other side). One simple molecule
displaying cis/trans isomerism is 2-butene (Figure 2). The cis/trans system for naming isomers
should generally only be used when there are only two different substituents on a double bond.
E/Z notation describes absolute orientation, and it is the IUPAC standard for tri- and
tetrasubstituted alkenes. Each substituent is assigned a priority (higher atomic numbers get
higher priority). If the two groups with the higher priorities are on the same side of the double
bond, it is described as the (Z)-isomer. If the two groups with the higher priorities are on
opposite sides of the double bond, then this is the (E)-isomer. An example of this can be seen
with the isomers of 1-bromo-2-chloro-1-fluoroethene (Figure 3).


Figure 2. Cis/trans isomerism in 2-butene. Figure 3. E/Z notation of 1-bromo-2-chloro-1-fluoroethene.

Hydrogenation works by bringing H
2
in close proximity to an alkyne and coordinating them to
the metal, which reduces the activation energy of the reaction. Trans and cis-alkenes are both
possible products of this type of reaction, but in this lab, the reaction is completely
stereoselective and only isolated cis-alkenes. This stereoselectivity can be explained by the way
H
2
and the substrate were bound to the surface of the metal catalyst; a hydrogen atom was added
to the face of the substrate facing the metal and since the substrate remained attached to the
surface during this process, a second hydrogen atom was added to the same face. This syn
addition (addition to the same face of a -bond) resulted in a cis-alkene product. Trans-alkenes
were not formed using this mechanism because hydrogen and the substrate were not
simultaneously bound to the metal catalyst. Thus, anti addition was not possible.

As mentioned earlier, in this specific lab, thin-layer chromatography was used in order to
determine whether or not the hydrogenation reaction had come to completion. If the TLC plate
indicated the presence of the starting product, ethyl oct-3-ynoate, in the reaction product, it
would suggest that the reaction had not gone to completion. In other words, not all of the ethyl
oct-3-ynoate alkyne was converted into the expected ethyl (Z)-oct-3-enoate alkene product.
However, if the TLC plate indicated that there was no ethyl oct-3-ynoate in the reaction product,
it would suggest that the reaction reached completion (all of the reactant was converted into ethyl
(Z)-oct-3-enoate).

Thin-layer chromatography (TLC) uses differences in polarity in order to separate pigments
within a compound utilizes the presence of functional groups within a compound and allows
them to bind with the mobile phase. This, in turn, separates compounds according to the polarity
of functional groups it contains. Compounds that are highly polar have lower retention factors
because they remain within the stationary phase for longer periods of time in comparison to their
less polar counterparts. This means that these highly polar pigments will be appear at lower
positions on the TLC plate in comparison to those that are less polar.

During this lab, rotary evaporation was utilized twice: once to remove the ethanol and once to
remove a diethyl ether from the product. Rotary evaporators are designed to rapidly evaporate
solvents without the risk of bumping. It works by using a variable-speed motor to rotate a
reaction flask containing an unwanted solvent. At the same time, a vacuum is applied to the
flask, which lowers the boiling point of the solvent (Heat may also be applied via water bath in
order to quicken the reaction). The rotation causes a thin film of the solution to spread over the
inside of the flask, which accelerates the evaporation rate. Additionally, this process prevents
bumping by agitating the mixture within the flask. Vacuum strength, water bath temperature, and
rotation speed can be adjusted in to achieve a desired rate of evaporation. This method of solvent
removal was used during lab because it was more time-efficient than vacuum distillation.

As in many of our lab experiments, IR spectroscopy was used in order to identify functional
groups present within the compound isolated after rotary evaporation. This technique measures
the absorption of radiation corresponding to transitional vibrations of the chemical bonds within
functional groups. Each particular functional group has a different dipole with characteristic
energy levels because specific bonds within each group vibrate at unique frequencies. These
frequencies can range from 4000-500 cm
-1
, and they are measured as wavenumbers in cm
-1

(Figure 4). Since each functional group vibrates at a unique frequency, it is possible to identify
the functional groups within molecules using methods such as Fourier Transform Infrared
Spectroscopy (FTIR).

Figure 4. Sample IR Spectrum.
While IR spectroscopy is able to differentiate between constitutional isomers and other types of
compounds that differ in connectivity and structure, it is not capable of distinguishing between
enantiomers because they are contain the same functional groups and share the same molecular
formula. Conversely, IR spectroscopy is able to distinguish between cis and trans-alkenes
because the substituent orientation around the double bond yields different energy levels. While
trans-alkenes produce a peak around 960-980 cm
-1
, cis-alkenes produce a peak around 665-730
cm
-1
. This difference is observed because cis-alkenes are less symmetrical than trans-alkenes.

In order to determine if the desired product ethyl (Z)-oct-3-enoatewas synthesized during this
lab, the IR spectrum was analyzed. The presence of a carbonyl group and a cis-alkene indicated
that the correct product was formed.

Nuclear magnetic resonance (NMR) can also distinguish between cis and trans-alkenes. By
using
1
H-NMR coupling constants (J-values), one can determine which type of alkene is
produced.

Figure 5.
1
H-NMR Coupling Constants for Cis and Trans Alkenes (image via. chadlandrie.com).
In trans-alkenes, substituents are on opposite sides of a -bond. For this reason, peaks are more
separated, which produces J-values are in the range of 14-19 Hz. In contrast, cis-alkenes range
from 4-12 Hz because their substituents are on the same side of a -bond, so peaks are located
closer together (Figure 5).

Experimental Procedures

I. Ni-Catalyzed Hydrogenation Reaction

Two drops of ethyl oct-3-ynoate synthesized in the previous lab were placed in a small test tube
and diluted with 1 mL of methylene chloride. Parafilm was placed over the top of the tube, and it
was set aside for later use in thin-layer chromatography. A 0.402-g sample of crystalline blue
nickel acetate tetrahydride was added to a 250-mL round-bottom flask, along with 10 mL of 95%
ethanol. (The Ni(OAc)
2
H
2
O did not dissolve in the EtOH.) A rubber septum was then placed
over the top of the top of the flask. Using the balloon assembly pictured below (Figure 6), the
flask was flushed with nitrogen gas (N
2
) and vented with a needle in order to replace the
displaced gas.

Figure 6. Balloon Assembly.

After all the N
2
had deflated from the balloon, the balloon was filled with hydrogen gas (H
2
), and
the flask was flushed with this gas, venting with a needle. After the H
2
had deflated from the
balloon, it was refilled once more with hydrogen gas. However, when the flask was flushed, the
venting needle was removed in order to maintain a positive pressure during the reaction.

Using a needle and 1-mL syringe, 1.617 mL of 1.0M NaBH
4
in ethanol was added to the flask
through the septum. The solution turned a dark purplish-black color and began to form small
bubbles. After bubbling ceased, a 0.216-mL sample of ethylenediamine was then added to the
flask using another needle and 1-mL syringe, as well. In a 50-mL beaker, the sample of ethyl oct-
3-ynoate synthesized during the previous lab was dissolved in 10 mL of ethanol. This solution
was then added to the reaction flask through the septum using a needle and 5-mL syringe. The
flask was then gently swirled for 30 minutes.

As the reaction took place, a TLC plate was obtained after 30 minutes elapsed. This was done by
threading a thin capillary tube through a needle, piercing the septum with the needle, and
obtaining a sample of the reaction mixture in the long capillary tube. On the TLC plate, three
spots were made 1 cm above the bottom: one of the starting material (ethyl oct-3-ynoate
previously set aside in the test tube), one co-spot of the starting material and reaction product,
and one of the reaction product. Then it was placed in a 100-mL beaker containing 5 mL of a 1:9
diethyl ether/hexanes mixture used as the eluting solvent (Figure 7).

Figure 7. TLC Plate Setup.

The plate was given a sufficient amount of time to develop then it was viewed under a UV light
and stained with KMnO
4
so that the TLC spots could be visualized.

II. Workup 1: Vacuum Filtration through Celite

The hydrogen balloon was carefully removed from the flask and the remaining H
2
was vented in
the hood. The flask was then flushed with a balloon of N
2
and vented with a needle, which
prevented the Ni(OAc)
2
4H
2
O catalyst from igniting. When the balloon completely deflated, the
septum was removed and the reaction flask was set aside.

In order to remove nickel acetate tetrahydride (Ni(OAc)
2
4H
2
O) from the reaction solution,
vacuum filtration was performed. The apparatus for this separation method was constructed
using a 250-mL Erlenmeyer flask with a vacuum sidearm, a filter adapter, a Bchner funnel, and
rubber pressure tubing (Figure 8). The flask was then clamped to a ring stand and the pressure
tubing was connected to a water aspirator.

Figure 8. Vacuum Filtration Setup.
In a 100-mL beaker, a 20-mL sample of ethanol was combined with Celite in order to form a
slurry (a thick, yet wet consistency). The water aspirator was turned on at the maximum level
and filter paper was added to the Bchner funnel. The filter paper was wet using a small portion
of ethanol then the slurry was poured into the funnel, creating a 0.5-inch layer of the mixture.
Before the Celite dried, the rubber tubing was removed. Filtrate in the flask was discarded, then
the apparatus was reassembled. Again, the water aspirator was turned on at the maximum level.
The round-bottom flask containing the reaction mixture was swirled and all of its contents were
poured onto the Celite bed in the Bchner funnel. A blackened layer of powder was left on top of
the plug. The reaction flask was then washed with 10 mL of ethanol, and the mixture was also
poured onto the Celite. The plug was also rinsed with one 10-mL portion of ethanol. This process
of vacuum filtration was able to remove the Ni(OAc)
2
4H
2
O catalyst from the reaction mixture
because it is not soluble. The remaining liquid was light brown in color.

III. Workup 2: Rotary Evaporation of Ethanol

In order to remove approximately 80% of ethanol from the solution, a rotary evaporator was used
(Figure 9). The round-bottom reaction flask (evaporation flask) was attached to the rotary
evaporator, and a Keck clip was added to secure the glassware. The evaporator was then run for
5-10 minutes so that the ethanol had sufficient time to boil off. This process left light brown
liquid in the reaction flask.

Figure 9. Rotary Evaporator.

IV. Workup 3: Aqueous Extraction of Nickel Salts and Ethylenediamine

After rotary evaporation was performed, a 50-mL sample of diethyl ether was added to the
reaction flask. This solution was then decanted into a separatory funnel. A 50-mL sample of
water was then added to the funnel before a stopper was inserted. The funnel was then gently
shaken and vented occasionally to release pressure. Layers were allowed to settle (Figure 10)
then the bottom, water layer was drained into a beaker.


Figure 10. Aqueous Extraction Setup.

Another 50-mL sample of water was then added to the funnel and the extraction process was
repeated once more. The top, diethyl ether-containing layer was then decanted into a 125-mL
Erlenmeyer flask and dried using Na
2
SO
4
until no additional clumping occurred. This aqueous
extraction was needed in order to remove water-soluble impurities (nickel salts and
ethylenediamine) from the product.

V. Workup 4: Rotary Evaporation of Diethyl Ether

A dry, 250-mL round-bottom flask was weighed and its mass was recorded before the filtrate
from the previous step was decanted into it. A pipette was used to extract as much liquid as
possible. In order to remove diethyl ether from the reaction product, a rotary evaporator was used
(Figure 9). The round-bottom reaction flask was attached to the rotary evaporator, and a Keck
clip was added to secure the glassware. The evaporator was then run for 5-10 minutes so that the
diethyl ether had sufficient time to boil off. This process left an oily yellow liquid in the flask.
The flask was then weighed and its mass was recorded.

VI. IR Spectroscopy

A pipette was capped with a rubber bulb and used to transfer a drop of the isolated product to the
infrared spectroscopy machine. An IR spectrum was obtained for the sample and possible
functional groups were identified. (Refer to the attached data sheet for complete peak data.)

Data Acquisition/Presentation

Thin-Layer Chromatography

One TLC plate was obtained during the Ni-catalyzed hydrogenation reaction (Figure 11).

Figure 11. TLC Plate Obtained.

R
f
Calculations
R
f
=

starting material = ethyl oct-3-ynoate
reaction product = ethyl (Z)-oct-3-enoate

R
f
starting material =


= 0.28
R
f
co-spot =


= 0.60
R
f
reaction product =


= 0.60

Table 1. Thin-Layer Chromatography Data.
TLC plate
(30 minute reaction)
D
solvent
5.0 cm
D
starting material
1.4 cm
R
f
starting material 0.28
D
co-spot
3.0 cm
R
f
co-spot 0.60
D
reaction product
3.0 cm
R
f
reaction product 0.60
In the TLC plate we obtained, the R
f
of the co-spot and R
f
of the reaction product were
significantly higher than the R
f
of the starting product.

Table 2. Reaction Table of Ni-Catalyzed Hydrogenation Reaction.
ethyl oct-3-
ynoate
Ni(OAc)
2

4H
2
O
ethanol NaBH
4
in
ethanol
ethylenediamine
molar mass 168.23 g/mol 248.86 g/mol 46.07 g/mol 37.83 g/mol 60.10 g/mol
reaction
weight or
volume

2.72 g

0.402 g

20 mL

1.617 mL

0.216 mL
density --- --- 0.789 g/mL 1.0 mol/L 0.90 g/mL
mmol 16.17 1.617 --- 1.617 3.234
equivalents 1.0 0.10 --- 0.10 0.20

Mass Calculation of Ethyl (Z)-oct-3-enoate

mass of sample = (mass of round-bottom flask + mass of sample) mass of round-bottom flask
(M
round-bottom flask + ethyl (Z)-oct-3-enoate
) M
round-bottom flask
= (92.66 g) 90.36 g = 2.30 g
= empirical mass of product
Calculation of Percent Yield

Using the initial amount of ethyl oct-3-ynoate used in the nickel-catalyzed hydrogenation
reaction, as well as known data about the compound (Table 2), we calculated the theoretical
yield of ethyl (Z)-oct-3-enoate.

= moles


= 0.01617 mol of ethyl oct-3-ynoate
(0.01617 mol*10
3

= 16.17 mmol of ethyl oct-3-ynoate)

0.01617 mol of ethyl oct-3-ynoate used = 0.01617 mol of ethyl (Z)-oct-3-enoate produced

molar mass of ethyl (Z)-oct-3-enoate = 170.25 g/mol
0.01617 mol*170.25

= 2.75 g of ethyl (Z)-oct-3-enoate produced

= theoretical mass of product
% yield =


*100%
% yield
ethyl (Z)-oct-3-enoate
=


*100% = 83.64%


Infrared Spectroscopy Analysis

IR spectroscopy was performed on the isolated ethyl (Z)-oct-3-enoate in order to identify
functional groups present. Refer to attached sheet for full peak data.

Table 3. IR Spectroscopy Data of Ethyl (Z)-oct-3-enoate.
Peak Frequency (cm
-1
) Bond Indicated
786.89 cis C=C
1600.90 C=C
1719.02 C=O
2956.02 sp
3
C-H
2928.88 sp
3
C-H

In the IR spectrum for the isolated compound indicated the presence of three functional groups:
cis-alkene (C=C), alkene (C=C), carbonyl (C=O), and methyl (sp
3
C-H) (Table 3). All of these
groups are characteristic of ethyl (Z)-oct-3-enoate.


Conclusion

The purpose of this lab was to synthesize the cis-alkene, ethyl (Z)-oct-3-enoate, through a nickel-
catalyzed hydrogenation reaction. This experiment was considered a success because the TLC
plates obtained during the experiment indicated substantially different retention factors for the
starting material and the isolated hydrogenation product. In the TLC plate obtained, it was
observed that the retention factor for the starting material was lower than that of the product. The
R
f
value of the starting material was 0.28 in comparison to the reaction products R
f
of

0.60.
These differences indicate that the ethyl oct-3-ynoate synthesized in the previous lab was
transformed into a product with a significantly different polarity.

Additionally, the IR spectrum of the isolated reaction product indicated the presence of
functional groups characteristic of ethyl oct-3-ynoate. A peak at 786.89 cm
-1
indicated the
presence of a cis-alkene, while a peak at 1600.90 cm
-1
indicated the presence of a general alkene.
A peak at 1719.02 cm
-1
indicated the presence of a carbonyl group. Finally, peaks at 2928.88
cm
-1
and 2956.02 cm
-1
indicated the presence of two sp
3
C-H groups (methyl groups).

Although this experiment was considered a success, the yield for this experiment (83.64%) was
lower than it should have been. Only 2.30 g of ethyl (Z)-oct-3-enoate were formed, while it was
expected that 2.75 g would be produced by the hydrogenation reaction. Even though this was a
very good yield, numerous workups that were performed could have contributed to the loss of
the desired product. During these filtrations and separations, some of the desired alkene product
may have lingered on the apparatus being used (i.e. vacuum filtration flask, Bchner funnel,
etc.), rather than being collected in the final round-bottom flask. For future lab sessions, it should
be noted that smaller sizes of glassware should be used when possible in order to minimize the
surface area on which residue of the desired product would adhere.