REACTION KINETICS

Presented by Ray Johnson with notes from

Pierre Glynn and Alex Blum, March 2011
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Outline

Why look at kinetics?

Things that control kinetics
Various reaction rate laws
Class examples
Optional examples (good reference,
have digital copy of example K1)
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Thermodynamics vs. Kinetics

Thermodynamics predicts equilibrium
dissolution/precipitation concentrations
Probably OK for reactive minerals
(Mondays useful minerals list) and
groundwater
Need kinetics for slow reactions and/or
fast moving water
3

Kinetics is
Concentration versus Time

Dissolution half-life

Appelo and Postma, 2005

Half-life

(pH 5 dissolution of the solid phase)

Gypsum hours
Calcite days
Dolomite years
Biotite, kaolinite, quartz millions of
years
If half-life is << residence time then
equilibrium conditions can be used
If half-life is >> residence time then
kinetics will need to be considered

Factors that affect kinetics

Concentration
pH
Light
Temperature
Organics
Catalysts
Surface area
Diffusion
Biogeochemistry
And more
6

General Concepts
Transport vs. Reaction Control
Elementary vs. Overall Reactions
Detailed Balancing
Microscopic Reversibility

Temperature Dependence
Surface Area
Silicate mineral dissolution kinetics & weathering
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Transport vs. Reaction Control

a) Transport control
b) Surface reaction control
c) Mixed Transport and surface-reaction control
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Transport limitations:
diffusion in solution
solid-state diffusion

Reaction limitations:
surface reaction control
surface characteristics
crystal defects
impurities
crystal morphology

Elementary vs. overall reactions

Reactions are the result of molecular collisions; & almost
invariably depend on the collision of no more than 2
molecular species at a time.
Overall reactions, such as:
2 KAlSi 3O8 + 2H + + 9H 2O
Al 2Si 2O 5 (OH) 4 + 4H 4SiO 4 + 2K +

do not reveal the sequential, and possibly parallel, sets of

molecular interactions, i.e. elementary reactions, that are
actually involved.

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Example of fast reactions (only 1 elementary step):

Ag + + Cl - AgCl (s)
CO 2,aq + OH - HCO3-

Example of a two step reaction:

&
O3 O 2 + O
&+ O 2 O
O
3

_____________
2 O3 3 O 2

Overall reaction:

The reaction rate requires knowledge of the rate-limiting

elementary reaction (usually only one).
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Principle of Detailed Balancing:

The net rate of a reaction is the difference between the
forward and the backward microscopic rates (eg.
microscopic dissolution vs. precipitation).

Principle of Microscopic Reversibility:

The forward and the backward reactions have the same
molecular mechanism.

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Activation Energies and Temperature Dependence

Reaction rates are often exponentially dependent on
temperature, and are also highly depend on the activation
energy EA required for a molecular reaction.
E A

RT

Rate A exp

or log Rate

1
T

The pre-exponential factor A may depend on pH, solution

chemistry, surface characteristics, and many other factors
including temperature.

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Activation Energy (EA)

1) Reaction rates are exponentially dependent on EA
2) EA depends on the direction of a reaction
3) Catalysis lowers the EA required for a reaction (note
activated complex)
Exothermic reaction

Endothermic reaction

EA

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from http://www.ucdsb.on.ca/tiss/stretton/chem2/rate03

Note log scale for rates

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Surface Area
Critical to rate calculations and predictions
Geometric area estimation (often requires
averaging or stochastic theory)
BET measurements, usually w/ N2 (4
compared to 3 for H2O)

Surface roughness (BET/Geometric):

SR = 5 - 12 for fresh ground silicate
SR = 300 - 2000 for deeply weathered
natural silicates

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17

Silicate dissolution kinetics

and pH

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19

20

Silicate weathering
reaction rates

21

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What model to use?

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24

25

Solute
accumulation
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Conclusions: silicate weathering

1) Natural weathering rates in soils are 102 to 105
slower than experimental rates
2) Weathering rates in aquifers depend on (water
chemistry)/(residence time)/(extent of reaction)??
3) Accumulation of solutes retards dissolution rates??
4) Discrepancies between natural and experimental
rates are consistent w/ models of solute
accumulation in pores
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Putting kinetics into a

geochemical model
Use rate laws
Hopefully have some experimental
and/or real world data references
Give it a try, dont let the equations and
mathematics make you sweat
First, understand the rate law and then
convert into PHREEQC command
lines
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Rate Laws
Mathematically describes the change in
concentration with time (derivative)
Simple if constant rate (zero order linear)
Complex if rate constant changes with
time due to multiple factors (i.e.,
concentration, temperature, pH, etc.),
thus higher order, non-linear
Remember that experimental data may
not represent real world conditions
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30

Appelo and Postma, 2005

Oxidation of Fe2+
Look at example on p. 156 of Appelo
and Postma, 2005
With multiple species (iron, pH, and
oxygen), we can have different rate
orders
Note pH to OH- calculation and second
order rate dependence
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Appelo and Postma, 200532

Reaction Kinetics in PHREEQC

PHREEQC can simulate irreversible reactions with either the:
REACTION keyword for specified amounts of
stoichiometric reactions.
KINETICS keyword, where the reaction rate is
determined by a mathematical expression taking into
account the composition and other pertinent information for
the reacting phases.

Using the KINETICS keyword also means that at least one

RATE keyword must be entered to define the rate law for a
particular reaction. Multiple RATE definitions can be entered
for a given KINETICS keyword.
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Explore in PHREEQC

Find the rate icon (d/dt) and open

What does this screen do for us?
Open the help on RATES
Explore this page together

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35

Explore in PHREEQC
Find the kinetics icon (K) and open
What do these three screens do for us?
Note Runge-Kutta (faster) and CVODE
(more robust for multiple interacting rates)
for ordinary differential equations

Select pyrite as a defined rate and hit

OK. What happened?
Find pyrite in the RATES block in
phreeqc.dat database

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37

Would have to
add parms

#######
#Pyrite
#######
#
# Williamson, M.A. and Rimstidt, J.D., 1994,
# Geochimica et Cosmochimica Acta, v. 58, p. 5443-5454.
#
# Example of KINETICS data block for pyrite rate:
#
KINETICS 1
#
Pyrite
#
-tol 1e-8
#
-m0 5.e-4
#
-m
5.e-4
#
-parms 2.0 0.67 .5
-0.11
Pyrite
-start
1 rem
Williamson and Rimstidt, 1994
2 rem
parm(1) = log10(A/V, 1/dm)
parm(2) = exp for (m/m0)
3 rem
parm(3) = exp for O2
parm(4) = exp for H+
10 if (m <= 0) then goto 200
20 if (si("Pyrite") >= 0) then goto 200
25 rate = -10.19 + parm(1) + parm(3)*lm("O2") + parm(4)*lm("H+") + parm(2)*log10(m/m0)
30 moles = 10^rate * time
40 if (moles > m) then moles = m
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200 save moles
-end

Book Example
Work through Example 4.15 together on
page 164 in Appelo and Postma, 2005.
Start with understanding the rate
expression equation 4.66 and go from
there.

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General Rate Law

R = overall reaction rate (mol/L/s)

k = specific rate (mol/m2/s)
A0 = initial surface area of solid (m2)
V = volume of solution (m3)
m = moles of solid at a given time
m0 = initial moles of solid
(m/mo)n accounts for changes in reactive surface sites during
dissolution
g(C) = function for things in the solution composition that can influence
the rate (i.e., pH, distance from equilibrium, catalysis, etc.)

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Start with calculating surface volume factor (A0/V)

density

porosity

Surface area (A0) = 22.6 m2/kg

Volume of water in contact with 1 kg of soil =
0.162 L (do unit conversion)

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m = calculated
m0 is given as 103 mol/L
IAP/K = SR(Quartz) = calculated in PHREEQC

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Now use PHREEQC

Example 4.15
Appelo and
Postma, 2005
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Exercise KA
1) Using the rate and kinetic blocks for pyrite dissolution in
the phreeqc.dat file, write out and explain the rate laws and
equations used.
2) Simulate the reaction of pyrite (use 2% pyrite and the
phreeqc.dat rate expression) with an oxygen-equilibrated
water such as the Oklahoma recharge water (used in
sorption exercise S3). How long does it take to react away
the oxygen dissolved in one unit volume of water? Given
the initial concentration of pyrite specified, how many
volumes of recharge water would it take to consume all the
pyrite?

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Exercise KB
1) Enter the two Sierra Spring waters from Garrels & Christ into a
PHREEQC input file. Assume a temperature of 25 C for both.
Units are mmol/L.
Description
Ephemeral Spring
Perennial Spring

Number
Temp
pH
6.2
6.8

Ca
0.078
0.26

Mg
0.029
0.071

Na
0.134
0.259

K
0.028
0.04

Alk.
0.328
0.895

Cl
0.014
0.03

S(6)
0.01
0.025

Si
0.273
0.41

2) Using the most dilute water, add the RATE laws and suggested
KINETICS blocks that are present in the phreeqc.dat file to
simulate the kinetic reaction of the water with albite and K-spar.
3) Ignoring other possible reactions, how long would it take to
obtain a water with Si, Na and K concentrations similar to
those in the Perennial Spring?
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Exercise KB (part 2)
4) Using the rate and kinetic blocks for K-spar and albite
dissolution. Write out and explain the rate laws and equations
used.

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Exercise K1 (optional if time)

1) Enter the 2 waters from the Norman, OK, landfill into a
PHREEQC input file. Assume a temperature of 16.6 C for
both. Units are mg/L. Do not enter DOC. Which water is
contaminated? How did you specify redox conditions?
-units mg/L
Description

pH

MLSNPD -6 7.01
MLS38-6
6.78

Ca

Mg

166 52.6
514 232

Na
91.8
606

Alk.
as HCO3
2.5
626
14.4
2642

Cl

S(6)

181 113.6
1027
0.1

Br

Si

Fe(2)

Mn

0.79 18.60 0.13 1.94

7.54 35.90 19.30 0.90

Sr

Ba

1.06 0.14
9.87 7.12

N(5) N(-3) DOC

as NO3as NH4
0.05
2.1
2.9
3.48
15.0 159

2) (Ulrich et al., 2003) used field and lab techniques to identify the
biogeochemical factors affecting the rate of sulfate reduction in
the leachate contaminated water. They obtained a MichaelisMenten type relationship with KM & Vmax values of 80 M SO4
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and 0.83 M SO4/day, resp.

Michaelis-Menten kinetics
1) Based on enzyme kinetics
k1

k2

E + S ES EP E + P
k1

2) Similar to transition state theory; based on the

idea of an activated complex, or an enzymesubstrate (ES) compound, whose
concentration controls the rate of reaction
3) Assumes that the concentration of ES is at
steady-state (d(ES)/dt = 0)
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1) Measurements needed are:

the total amount of enzyme, ET = E + ES

the concentration of substrate, S
the measured steady state velocity: V = k2 (ES)

2) The maximal velocity is measured, Vmax = k2 (ET), using the

highest substrate concentration
3) The Michaelis-Menten constant, KM = (k-1 + k2)/k1, is simply
the substrate concentration that gives a reaction velocity
half of Vmax. Also, for a slow reaction, k2 << k-1, KM = k-1/k1
= Keq
4) The Michaelis-Menten equation is:

V Vmax

(S )
KM (S )

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50

Norman landfill

51

Norman landfill

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Exercise K1 (cont)
3) Enter the RATES keyword in PHREEQC to describe the
Michaelis-Menten type rate law for SO4 reduction using the
constants determined by Ulrich et al. (2003). Note that
PHREEQC uses seconds and moles and adjust the KM & Vmax
constants accordingly. Call the rate law Sulfate_reduction.
4) Sulfate will be the limiting substrate. Notice that KM is high
compared to the initial SO4 concentrations. Nevertheless, as
a first step, assume a zero-order reaction where the rate is
simply equal to VMAX.

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Exercise K1 (cont)
5) Your RATE block (for the 0-order case) should look something
like this, where you have substituted the correct value for
Vmax:
RATES
Sulfate_reduction
-start
10 if (m <= 0) then goto 100
30 rate = Vmax
40 moles = rate * time
50 if (moles > m) then moles = m
100 save moles
-end
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Exercise K1 (cont)
6) The sulfate reduction is simulated as a kinetic reaction adding
organic matter (formula is CH2O) to the solution. The
reduction of sulfate takes place as a consequence of the
addition of CH2O. The amount of CH2O is not a limiting factor.
To properly define the kinetics block you will need to
determine how many moles n of CH2O get oxidized per mole
of SO4 reduced. The number of moles of CH2O available (i.e.
the DOC value) will define the current concentration available
m. Your kinetics block should start like this, with numerical
values substituted:
KINETICS 1
Sulfate_reduction
-formula CH2O n
-m
DOC value in moles/kgw

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Exercise K1 (cont)
7) Use the SELECTED_OUTPUT keyword to have PHREEQC
output total concentrations on S(6), S(-2), S, C(4), and
information on the kinetics of Sulfate_reduction.
8) Specify output steps at 0 seconds, and 0.1, 0.2, 0.4, 0.6, 0.8,
1, 2, 4, 6, 8, 10, and 20 years.
9) Graph the decay of SO4, the increase in S(-2), and the
decrease in the number of moles of reactant available (CH2O)
w/ time.

56

Exercise K1 (cont)
10) What happens to TDIC?
11) Calculate or estimate how long it would takes to oxidize all the
dissolved organic carbon?
12) What are the final concentrations of SO4, S(-2), and DOC after
20 years?

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Exercise K1 (cont)
13) Examine the SO4 concentration (the limiting substrate) in the
initial water and compare it to the Michaelis-Menten constant,
Km. Which one is significantly smaller? What is the actual
limiting rate law?
14) Re-run the exercise with the full Michaelis-Menten expression
described in the RATES block, with SO4 as the limiting
substrate. Add some additional time steps to carry out the
simulation to 200 years.

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Michaelis-Menten kinetics for sulfate reduction

(constants from Ulrich et al., ES&T, 2003)

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Exercise K1 (part 2)
15) Ulrich et al. claim that barite dissolution provides the source of
most of the S(6) in the Norman waters. In a new simulation,
use the background water from near the Norman landfill.
Maintain equilibrium with barite. Use the rate law and the
kinetics keywords previously defined in part 1.
16)Specify output steps at 0 second, 0.1, 0.2, 0.4, 0.6, 0.8, 1, 2, 4,
6, 8, 10 and 20 years.
17) Graph the decay of SO4, and the increase in S(-2) and Ba
with time.
18) How do the values compare with those observed in the
leachate-contaminated water?

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Exercise K2 (optional if time)

1) Examine the rate and kinetic blocks for Organic carbon
reaction, using Monod kinetics, present in the phreeqc.dat file.
Write out, and explain the rate laws and equations used.
2) Simulate the kinetic reaction specified using a water
equilibrated with atmospheric O2 and and a log pCO2 of 1.5.
What is the initial organic carbon concentration specified?
How long does it take for the reactants to disappear?
3) Repeat the problem using the background water from the
Norman landfill
4) Repeat the problem using the contaminated water from the
Norman landfill

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