Experiment 1: Analysis of the Error in a Linear Treatment of the

Arrhenius Equation

Error analysis is an essential component of experimental work. Typical error analyses may
involve analyzing the fit of experimental data to some model, and/or estimating the error that is
propagated through a mathematical treatment of the results. In this “experiment” you will gain some
experience with both types of analyses: in Part A, you will develop a spreadsheet to perform a linear
least squares fit of temperature-dependent kinetic data to a linear form of the Arrhenius equation.
This spreadsheet will be used as a template for similar analyses in future experiments. In Part B, you
will use differential error analysis to determine the error in the activation energy and pre-exponential
factor using values based on your least squares fits to the data.
The spreadsheet program that we are using in this course is Microsoft Excel, version 8.0
(MSOffice98). The section in this lab manual on using Excel (Appendix A) contains some useful
information that you are expected to know by the end of this experiment about using this software.
One set of hardcopy manuals is also available in the computer lab, and the entire manual is available
using the Help keys within Excel. All error analysis equations have been discussed in the “Treatment
of Error” section of the laboratory manual.
One important hint: save early and save often! Networked computers crash often, resulting in a
loss of unsaved data. Be sure to save your work on the hard drive in your own folder inside the
Student Files folder on the desktop. It is a good idea to also save your work on a floppy diskette.
However, you should work from the copy that is saved on the hard drive to reduce the probability
of a system crash.
You must keep a good notebook on this exercise just as any other experiment. See the
section “Notebooks and Reports” for more information on keeping a good notebook.

The Objective:
Obtain 95% confidence intervals for the Activation Energy and Pre-exponential factor for
the H-D exchange reaction in a peptide using the kinetic data in Table 1.

Table 1: Kinetic data for the exchange of an amide H for D in a peptide.

Temperature (K) Rate constant (1/Ms)

303.0 6.12 x 10-4
308.0 9.53 x 10-4
313.0 2.05 x 10-3
318.0 3.35 x 10-3
328.0 1.41 x 10-2

The data in Table 1 describes the dependence of the rate constant, k, on temperature, T, for the
reaction of an amide proton with deuterated methanol:
H D
C N + CD3OD C N + CD3OH
O O

This occurs in peptides and proteins when they are exposed to deuterated methanol. The kinetics of
such reactions can reveal information on the three-dimensional structures of peptides and proteins.

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1. Error Analysis Experimental Physical Chemistry

In this experiment, we will model the dependence of the rate constant for this reaction on
temperature using the Arrhenius equation:
RT
k = A e −Ea (1)

where A is the frequency factor, E a is the activation energy for the reaction, and R is the gas constant.
The frequency factor describes the probability of the reaction occurring, while the activation energy
is a measure of the energy needed to get the reaction started. Both A and E a are very useful physical
quantities to know because the rate constant can be calculated for any temperature once these two
parameters are known. Both parameters also reveal other interesting information on the
thermodynamics of the reaction, as we shall see later.

In order to determine the 95% confidence intervals for A and E a, you will ultimately need to
complete the following tasks:

A. Use a linear least squares analysis to fit the data to a linear version of equation (1). To
do this, you will first need to recast the Arrhenius equation so that it is in a linear form:
y=α + βx (2)
where y is a function only of k, and x is a function only of T (this is called linearizing the
equation). In so doing, you will determine the forms of α and β. Preferably, A will appear in
only one term, and Ea will appear in the other term. In the process of performing the fit of the
data to equation (2), you will obtain 95% confidence intervals for α and β.

B. Use differential error analysis to calculate the 95% confidence intervals for Ea and A from
the 95% confidence intervals for α and β.

C. Evaluate the quality of the fit. A general rule of thumb in analyzing data is: Never use the
results without interpreting the error. You will need to briefly discuss the quality of the fit based
on the errors in α and β, and based on the errors in Ea and A.

Part A: The Linear Least Squares (LLS) Fit

1. Getting started.

 Do this section in your notebook before you come to lab.

Before you even sit down at the computer, you need to set up the problem and your goals
in your notebook. Remember that your notebook should contain enough information so that
someone else could reproduce the experiment without any other handouts (see the Example
Notebook Record for ideas). This includes understanding what you are doing and why. Write a brief
description of the problem and the goals and copy the data from Table 1 into your notebook.
Now that you have established the background for your experiment, you need to linearize
equation (1). In this case, you should find that there is a simple mathematical manipulation that will
transform equation (1) into a linear equation. Write out the transformation of equation (1) clearly, and
define all of the variables in equation (2) in terms of variables in equation (1).

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Example: Linearizing the equation z = r cos θ + t

We wish to transform this equation into something of the form in equation (2). If we were
interested in the dependence of z on θ, we could linearize the equation by squaring both
sides, so that

z 2 = r cos θ + t
Now we have a linear equation of the form (2) where y=z2, x=cosθ, α=t, and β=r. That is, a
function of z is linearly dependent on a function of θ. (Notice that the original equation
cannot be identified as one of the form (2) since a function of z is not linearly dependent on
a function of θ.) This is a nice transformation because r and t appear separately in α and β,
which means that we can determine their values using a LLS analysis.
If instead we were interested in the dependence of z on t, the same transformation would
yield y=z2, x=t, α=rcosθ, and β=0. While this is also linear, it is less useful because r and θ
could not be determined from the LLS values of α and β alone.

2. Creating the LLS worksheet.

 Do this section during lab. Be sure to keep a good notebook record as you go.

If you are working on one of the PowerMacs, create a folder labeled with your name within
the Student Files folder. All of your work throughout the semester should be saved in this folder.
Stray files are often deleted, so please be sure to keep track of where your files are saved! If you are
working on a PC, create a temporary folder labeled with your name in the "My Documents" folder.
You will be constructing a large table to calculate the best fit (LLS) values of α and β. (If you
are unfamiliar with Excel, you should take a few minutes to read through the section on Using Excel
(Appendix A)). Your worksheet should be labeled and easy to follow, just like your notebook.
Your first task is to set up the worksheet using the format in Figure 1. Column A contains
the values of the index n , which keeps track of how many data points you have. Columns B and C
contain the experimental data. Enter the experimental data from Table 1 into the worksheet in
columns B and C. The syntax for entering numbers in scientific notation in Excel is Ae-B (for
example, 3.12 x 10-5 is entered as 3.12e-5).

Figure 1: Format for a Linear Least Squares Analysis Spreadsheet

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Columns D and E contain the transformed (linearized) data. Use the function editor or look
in the function library to find the syntax for the functions that transform your (k, T) data into (x, y)
data. Take advantage of the copy and paste abilities in Excel to make this process quicker. (See Using
Excel, section III and the example below for more explicit instructions.)
Example: Transforming (θ, z) data into (x, y)= (cosθ , z2) data
Suppose that columns B3:B5 contain θ data, and columns C3:C5 contain z data. To
calculate the values of y=z2 in column E, you would first enter =B3^2 in cell E3, then copy
the contents of cell E3 into cells E4 and E5. A similar process would lead to values of
x=cosθ in column D, using instead =cos(C3) in cell D3.

Save your worksheet in your folder using the Save As... command in the File menu.
(All later saves may be done using the Save command under the File menu, or by
using the diskette icon on the toolbar.)

Columns F-L contain quantities that will be needed to actually calculate the LLS fit of the data
in columns D and E to equation (2). These quantities come from expressions within equations 22, 25,
and 27 in the Treatment of Error section of this lab manual:
2 )
(xi − x), (y i − y), (xi − x) , (xi − x)(yi − y ), x2i , ri , ri2 , yi (3)
In this notation, x1 is the first x value, x2 is the second x value, and so on (so that xi is the i th x value -
thus the usefulness of the first column on the left.) In order to calculate these values, you will need
to calculate average values of x and y, which should be placed at the bottom of each column. For
example, if your x data is in cells D3:D5, you would enter =AVERAGE(D3:D5) into cell D7 in order
to calculate x.
Now you can fill in the body of the spreadsheet by entering the appropriate formulas in
columns F-L in the spreadsheet. For all of the functions in row 3, use absolute addressing for
constants (i.e. the average of a column) and relative addressing for variables (xi for example); see
Using Excel, Part III if you don’t know what these terms mean. Avoiding the use of absolute
addressing now will cause you serious headaches later in the semester (we will use this spreadsheet
again!), so take the time now to “do it right”. Note that once you have prepared the column for (x1-
x) in column F, you only need to enter = F3^2 in cell H3 to calculate the value of (x1 - x)2.
Keep your calculator handy and check some of the calculations
yourself to make sure that your spreadsheet is working properly
(document these checks in your notebook).

Fill in the remaining rows or columns by copying and pasting cells or columns that have similar
formulas, but check to be sure that the addresses are correct afterwards. Also, enter the formulas for
the sums of the expressions in (3) in the row below the averages row. The syntax for sum is the
same as for average, except that the function is named SUM.

Have you been saving your worksheet?

You now have all the information in your spreadsheet that you need in order to calculate the
) )
best fit values of the least squares parameters, α and β. Enter the formulas for α and β from the

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Treatment of Error section into cells B15 and B16. You will again need to use both relative and absolute
addressing when you write these formulas.
) )
Enter the formulas for the errors in α and β using the expressions for the standard
) )
deviations in α and β in the Treatment of Error section. To do so, you will first need to calculate a
value for D, the denominator of equations (27a,b). Use the appropriate value of tν,0.95 (the Student-t
value) to obtain the 95% confidence intervals. (Note that we cannot use Z tables because we only
have 5 measurements.)
Some approximate values of selected quantities are given in Figure 2. Check to make sure
that all of your values make sense before you go on! SAVE YOUR WORKSHEET (this is your final
reminder). Also, record your results in your notebook. You may simply print out a copy of your
spreadsheet and tape it into your notebook. In any case, you will ultimately need to include a copy
of the spreadsheet (one version each of formulas and numbers – see Appendix A, section IV) with
your lab report.

Figure 2: Values of selected quantities for LLS analysis

Finally, it is always a good idea to get a visual check on your fit. To do this, first plot your x,y
data using a scatter plot (do not use the connect-the-dots version!). Be sure to remove the gray background on
)
the plot. Then, calculate the values of y in column M using equation (2). (Note that if you want
copy and paste to work for this column, you needed to use absolute addressing correctly in referring
) ) )
to α and β .) Click on your plot, and append the y data to the plot (see Using Excel or click on the
Help menu for help). Double click on the newly appended data and use No Symbols, Automatic
Line options to show the best fit data as a line. Print out this plot and include it in your notebook.

Part B: Differential Error Analysis (DEA)

3. Calculating the 95% confidence intervals for A and Ea.

 Most of the work in this section can be done at home, in your notebook. Record all of
your work clearly as you go!

In order to calculate the 95% confidence intervals for the physically interesting parameters A
and Ea, you need to obtain expressions for A and Ea in terms of α and β (i.e.: in our example above,
we had the trivial case where α=t, so that now t=α. Your transformations should be slightly more
interesting.) Show your transformations in a clear, organized way in your notebook.

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Once you have expressions for A and Ea in terms of α and β, you can use differential error
analysis to propagate the errors in α and β (in the form of 95% confidence intervals) into errors in A
and Ea (also in the form of 95% confidence limits). The master equation that you need to work from
is equation 20 in the Treatment of Error section. You will use two separate DEA expressions to do
this: one for F=A and one for F=Ea.
Example: Propagating the error in α into an error in t.
Using our trivial example above, we have the following expression for our original variable (t)
in terms of the LLS best fit parameter α:

t=α

From LLS, we know the error (as a 95% confidence interval) in α is λα. The master DEA
equation is (equation 19 from Treatment of Error):
2 2
 ∂F  2  ∂F  2
λ =
2
F λ +  λ
 ∂x  x  ∂y  y
In this case, F=t, x=α, and there is no y variable (t is a function only of x). Therefore, to
determine λt we only need (∂t/∂α)=1. Therefore, the 95% confidence limit in t is given by:
2
λt = (1) λ 2
α = λα
which should seem reasonable: since in this trivial example, t and α are equal! (In general
this is not the case).

Once you have obtained expressions for A and Ea and their confidence limits, you can either
perform the calculations for A, Ea and their errors in your notebook, or perform the calculations on
your spreadsheet and enter the results into your notebook. In any case, don’t forget to include units
in all reported values, even for α and β.
You must also report a reasonable number of significant figures. The number of significant
figures in your reported result will depend on both the number of SF in your original data, and on
the size of the error estimates.
Example: Determining the appropriate number of SF in a reported value.
Suppose that our original data was known to 3 SF, and that we determined that:

z = 90.22 ± 0.0423

Our first inclination would be to report z and λz to 3 SF (our original number of SF), so that:

z = 90.2 ± 0.0423
but this is not a reasonable answer. By writing the above equation, we imply that we know
that z lies in the range 90.1577 to 90.2423. However, 3 SF in z only specifies z to 1
decimal place, so clearly we cannot make this statement. Neither can we insist that we
have only one decimal place in both z and in λz, because this would mean reporting an error
of 0.0. Instead, we must compromise and report both z and the error to the smallest
number of decimal places so that the error is non-zero:

z = 90.22 ± 0.04

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Part C: Evaluation of the Fit

Your notebook should include a summary of your results, as well as a short discussion of
the goodness of the fit. In order to evaluate the goodness of the fit, you will need to present several
pieces of data:
A. Two versions of your spreadsheet: one with numbers, and one with formulas. Both copies
must have row and column numbers labeled (see Using Excel, section V). You may have
already pasted these into your notebook.
B. A summary of results, in a table, including:
• The equation that you used to fit the data (the linearized form).
• The definitions of α and β in terms of A and Ea.
• The best-fit values of α and β, with 95% confidence limits, to the correct number
of significant figures, with units.
• The best-fit values of A and Ea, with 95% confidence limits, to the correct number
of significant figures, with units.
• Relative (%) errors in all four parameters (α, β, A, Ea) for evaluation of the fit.
C. Two plots of the fits of your data to the model.
• The linear plot (y vs. x) showing your best fit line (data as points, the fit as a line).
• An exponential plot (k vs. T) (data as points, the fit as a line).
For the exponential plot, insert a best-fit "trendline", which is a fit calculated internally by
Excel. To do this, plot your data using a scatter plot. Click on the data points, then pull
down the chart menu and select "insert trendline". Click on the options tab and check the
options for displaying the equation for the line, and the R2 value.

Using these data (A-C), evaluate the quality of the fit by discussing (briefly):
• the relative and absolute errors in α and β
• the relative and absolute errors in A and Ea
• the relative errors in the two sets of parameters.
• the look of the linear fit
Try to avoid making vague statements like “the fit was good”. Rather, discuss how well the data
appears to conform to the model that we imposed upon it. Remember that we can write any
equation that we want, but that doesn’t mean that the data will obey that equation. For example, the
Arrhenius equation does sometimes fail to accurately model the temperature dependence of kinetic
data.
Finally, compare the values that Excel obtained using the linear model and exponential
model to your LLS results. It is a commonly accepted fact that fitting data directly to an exponential
function is far more difficult (more error ridden) than fitting data to a linear function. Do your
results support this fact? Why might this be? Are all of the errors associated with the linear fit
small?
Before you decide that you have finished, be sure that your notebook contains all of the
information necessary to repeat the experiment. Hand it to someone who is not taking CHM313
and ask them to tell you what they think you did!

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