Unraveling SN2 Reaction Kinetics: A Study on Activation Energy Variation

Introduction

In 1935 Sir Christopher KelkIngold and Edward D. Hughes were studying two competitive mechanism that alkylhalides were involved in, today we know them as Nucleophilic substitution whereby it’s a reaction of an electron pair donor with an electron pair acceptor. The discovery of the mechanism had a profound effect on the chemistry industry and resonated into the pharmaceutical industry many years later. The pharmaceutical industry as we know of today is fighting a major crisis that is the result of excessive usage of antibiotics leading to wide spread development of antibiotic resistance in bacteria.

Many intermittent solutions had been proposed to curb the crisis as we know of today. One of the many solutions besides coupling the antibiotics with other drugs in order to improve the efficacy of the antibiotics will be the modification of the antibiotics in order to reduce the chances in which the bacteria’s enzymes such as penicillinase can recognize and break down the antibiotics penicillin before it can perform its task to kill the bacteria from the inside.

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The modification as mentioned is executed on the R side chain of the antibiotic shown in figure 1. By switching the side R groups of the antibiotics, it renders the enzyme penicillinase ineffective as explained using the Induced fit hypothesis of enzymes whereby a mismatch of the 3d configuration of the substrate penicillin (modified) will not fit the active site of the enzyme penicillinase well and thus wont be broken down easily. The modification as we know of today is namely through the nucleophilic acyl substitution of the R groups (FutureLearn, 2019).

Knowing the importance of this simple mechanism, it is thus worthwhile for us to study the kinetics of the mechanisms in depth through a simpler reaction set up such as chlorobutane and ethanol as it demonstrates the mechanism of the nucleophilic substation mechanism in detail. Thus, this investigation aims to find out the activation energy of SN2 reaction by varying the temperatures of the reactions and employing basic manipulation of the Arrhenius equation. Figure 1: Chemical structure of penicillin with boxed up area showing the substitution site where R1 side chain can be replace with other groups to lower antibiotic resistance.

Background Information

Nucleophilic substitution is when the reaction involves a nucleophile replacing a leaving group. It is a reaction of the halogenoalkane involves breaking the bond (Chemistry LibreTexts, 2019). All the halogens are more electronegative than carbon. The SN2 reaction is a bimolecular reaction, which means that the rate depends on the concentration of two reactants. The choices of solvent are important for proceeding SN2 reaction. Polar aprotic solvent is suitable for SN2 mechanism involving transition state.

Since chlorobutane is a primary halogenoalkane, this reaction will follow SN2 mechanism. Hydroxide ion is attracted to the electron deficient carbon in the halogenoalkane, which leads to a reaction where substitution of the halogen occurs. When the chlorobutane reacts with a solution silver nitrate in a mixture of ethanol and water, the chlorine is replaced by that exist in the aqueous reaction medium (Chemguide.co.uk, 2019). Resulting products are butanol and chloride ion. The arrow represents the motion of an electron pair. The dotted line shows that the bond is weakening.

Next, the chloride ion reacts with silver ion and produce silver chloride, which is the white precipitate of this reaction.

k: Rate constant

Ea: Activation energy

T: Temperature in Kelvin

R: Gas constant

A: Arrhenius constant

In order to find the activation energy, which is the minimum energy, required for reaction to occur for this SN2 reaction, Arrhenius equation and rate law will be used. The rate equation would be stated as below.

We will need to vary the temperature at which the reactions are conducted, by doing so the rate will change and the rate constant will also change accordingly. Rate increases; rate constant increases. By linearizing Arrhenius equation, we can plot against in Kelvin by doing so the activation energy is equal to .

Hypothesis

Intuitively, I believed that when the temperature increases, the rate of reaction would increase due to the increase in frequency of collision. Based on collision theory the proportion of reactant particles with higher kinetic energy that satisfy the activation energy will increase. Thus, increasing rate of reaction and rate constant. By using rate law and Arrhenius equation, activation energy would be found and the value is (Chemgapedia.de, 2019)

Procedure

1. Prepare 5 test tubes, label them trial 1,2,3,4,5 and label 1 additional test tube of silver nitrate.
2. Set temperature of water bath to 30.
3. Use a dropper and add 1 of 100% ethanol into test tube label trial 1 to 5.
4. Use a dropper and add 1 of chlorobutane into test tube label trial 1 to 5 and cover test tube with the stopper to prevent evaporation.
5. Use a dropper and add 5 of Silver nitrate into test tube label Silver nitrate and close with the stopper.
6. Put all six-test tubes into the water bath for at least 3 minutes to ensure that the reagents reach equilibrium with the temperature of the water bath.
7. Use a clean dropper to take out 1 of silver nitrate and put it into test tube trial 1, shake the test tube for three times and start the stop watch, stop the timer when the white precipitate obscure the test tube fully.
8. Repeat the step 7 for the remaining test tube trial 2 to 5 and record the time taken for white ppt to obscure the test tube fully.
9. Repeat the step 1 to 8 for temperatures 35.

Safety

Prevention:

• Wear safety glasses and a lab coat.
• Keep the containers tightly closed
• If it contacted with skin or eyes, rinse immediately with water.
• Use safety gloves.

Disposal:

• Disposal of chemicals must be done in the chemical waste bin within the lab

Ethanol

• Causes severe eye irritation.
• Flammable liquid and vapour.
• Causes respiratory tract irritation.

Silver nitrate

• Contact with other material may cause a fire.
• Causes burns by all exposure routes.
• Toxic to aquatic organisms, may cause long-term adverse effects in the aquatic environment

Qualitative data

• The reaction mixtures colour change from transparent to opaque white due to the formation of white precipitate
• The white precipitate form settles down to the bottom of the test tube
• As the temperature increases the rate of obscuring seem to become faster

Data Processing

Sample calculation of data processing and error propagation using data values at :

Table 2: Processed data table

Arrhenius plot of SN2 reaction between chlorobutane and hydroxide

Arrhenius plot of SN2 reaction between chlorobutane and hydroxide

In order to find the uncertainty of activation energy, maximum and minimum gradients are required. The equation of uncertainty would be . On the graph 2, yellow line represents maximum gradient, red line represents minimum gradient and blue line represents best-fit line.

Conclusion

In conclusion, during this SN2 reaction, as temperature increase, the rate of reaction also increases. Through out the data process and graph, the activation energy of chlorobutane is found as . This will be my experimental value and theoretical value is 102.6 (Chemgapedia.de, 2019). The total experimental error is calculated below.

According to this calculation, the total experimental error of 29.2% is equals to random and systematic error edit together therefore if you take the Total experimental error off to 29.2% if you deduct the 118% random error from above activation energy uncertainty calculation, you will be able to get a negative systematic error. A negative systematic error means that method that I have applied, led to a huge negative error that cannot be salvaged with equipment change. The negative systematic error could be due to the heat loss or the reaction endpoint that it was unable to decide clearly due to the lack of usage of machines such as spectrophotometer. And this is highly inaccurate leading to the excessively high systematic error

The major error in this experiment can be said as heat loss to surroundings and equipment error. Firstly, equipment such as dropper had 25-percentage error, which affected the uncertainty of . This eventually led to create huge gap between maximum activation energy and minimum activation energy. Secondly, heat lost to surroundings and equipment can affect the activation energy. When the temperature changes, it also changes the gradient of the graph to be steeper or flatter. Thus, this can affect the activation energy of the SN2 reaction of chlorobutane.