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Submit as a single PDF to the course website by 8:59 pm on 2/24. Late assignments not accepted.

==========================================================

1. A reaction is carried out with 1-cyclohexenyl allyl malonitrile at 409 K. Calculate the first order rate

constant from the data below. What is the half life?

t [min]

0

5

10

% reaction

19.8

34.2

46.7

2. The reaction 2A (gas) = B (gas) is second order in A and has a half life of 1 hour. If the initial pressure

of A is 1 atm, what are PA and PB at t=1 hour and t = 2 hour?

3. The growth of a bacterial colony can be modeled as a first-order process in which the probability of

cell division is linear with respect to time such that dN/N = dt, where dN is the number of cells that

divide in the time interval dt, and is a constant.

a. Use the preceding expression to show that the number of cells in the colony is given by

N=Noexp(t), where N is the number of cell colonies and No is the number of colonies

present at t=0.

b. The generation time is the amount of time it takes for the number of cells to double. Using

the answer to part (a), derive an expression for the generation time.

c. In milk at 310 K, the bacterium Lactobacillus acidophilus has a generation time of about 75

min. Construct a plot of the acidophilus concentration as a function of time for time

intervals of 15, 30, 45, 60, 90, 120, and 150 min after a colony of size No is introduced into a

container of milk.

4. Bacteriorhodopsin is a protein found in Halobacterium halobium that converts light energy into a

transmembrane proton gradient that is used for ATP synthesis. After light is absorbed by the

protein, the following initial reaction sequence occurs, with k1=2 x 1012 sec-1 and k2=3.3 x 1011 sec-1.

k1

k2

BJ K

a. At what time will the maximum concentration of the intermediate J occur?

b. Construct plots of the concentration of each species versus time.

k1

B , find [A(t)] given that [A(0)]=[Ao] and [B(0)]=0. Derive the solution yourself,

k2

consulting the notes as necessary. Both the forward and reverse reactions are first order.

6. (Oxtoby 18.5) Nitrogen oxide reacts with hydrogen at elevated temperatures according to the

chemical reaction 2NO(g) + 2H2(g) N2(g) + 2H2O(g). It is observed that, when the concentration of

H2 is cut in half, the rate of the reaction is also cut in half. When the concentration of NO is

multiplied by 10, the rate of the reaction increases by a factor of 100.

a. Write the rate expression for this reaction and give the units of the rate constant k.

b. If [NO] were multiplied by 3 and [H2] by 2, what change in the rate would be observed?

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7. Chemical kinetics is a tool that working scientists use frequently, including me. In this problem we

will work out some kinetics relationships I used in a paper. In the paper I showed that the dye Cy5

(left) can react with the molecule TCEP (middle) to form a new species (right). We can treat this like

A B

k1

k2

C where A is Cy5, B is TCEP, and C is the new species (a covalent adduct between Cy5

and TCEP). Assume the reaction is first order with respect to all species. (Note that the topic of the

paper is related to the topic of the 2014 Chemistry Nobel Prize.)

a. Write an expression for the concentration of [Aeq] as a function of [B], Keq, and [A0]. You can

assume [C0]=0.

b. Look at the equilibrium data in panel B), below, to estimate Keq. It will be helpful to know

that the blue dots are at 0, 0.125, 0.25, 0.5, 1, 2, 4, 8, 16, 32, 64 mM (left to right).

c. Derive an expression for [A(t)] for an initial condition of nonzero [A0] and [B0], but [C0]=0.

The exact solution is messy, so we will simplify by assuming that [B] is constant (I also did

this in the paper). This is reasonable since in the experiment [B]>15[A] for all measurements.

d. Using your expression from part c), write out an equation for the total decay rate kdecay in

terms of k1, k2, and [B]. It follows a line.

e. I measured the decay rates, and one example is shown in panel C). The decay rates observed

for a range of concentrations of [B] are shown in panel D). Now, look at panel D) to estimate

k1 and k2. The blue dots there are 1, 2, 4, 6, 8, and 10 mM.

f. Use these values of k1 and k2 to estimate the expected equilibrium constant based on your

equation in part a). Does the equilibrium constant from the rates match the equilibrium

constant you got from the data in panel B)?

g. In the paper I reported Keq=0.9 mM-1, k1=0.031 mM-1 s-1, and k2=0.03 s-1. How well do your

estimates match? (Note that for our first principles problems we emphasize use of a

unitless Keq but in practice many scientists still use Keq values bearing units.)

h. In panel D), if you extrapolate the line to zero TCEP concentration, you get a nonzero decay

rate. However, when there is no TCEP present there should be no quenching reaction. How

do you explain this apparent contradiction? (I got asked this during a presentation.)

2/3

Figure from Phosphine quenching of cyanine dyes as a versatile tool for fluorescence microscopy, J Am

Chem Soc, 135, 1197-2000 (2013). Measurements in panels A) and B) are done at equilibrium (after the

concentrations no longer change) while in panel C) the dynamics are measured and in panel D) the

observed decay rates are summarized. See the URL below if you want to check out the paper.

https://sites.google.com/a/uw.edu/the-vaughan-group/publications

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