Chemical Kinetics COVID
Chemical Kinetics COVID
org/jchemeduc Article
■ INTRODUCTION
The global outbreak of the COVID-19 disease (caused by the
concepts has been widely used in textbooks, including those
employed to teach chemical kinetics.5−7
SARS-CoV-2 coronavirus strain) is undoubtedly a new Students often encounter difficulties when studying differ-
experience for humanity, which has impacted people’s lives ential equations used to understand the dynamics of a chemical
worldwide. Concepts such as epidemics, viruses, and virus spread system.8 Also, fitting of experimental data to complex kinetic
are now explained everywhere and became part of the daily news models (e.g., beyond simple first- and second-order reactions) is
and accessible knowledge. A way to connect, in a positive way, rarely discussed in standard chemistry curricula.9 In this regard,
the global COVID-19 experience with chemistry is to use the complex kinetic schemes are often simplified employing the
recently acquired knowledge about virus spread as an analogy to steady-state approximation, a concept commonly taught in
explain chemical kinetics in the classroom using an experience- introductory physical chemistry courses.10 Herein, we present
based learning (EBL) approach based on a simple epidemio- a general, analytical approach to the learning of chemical kinetics
logical model. EBL refers to teaching practices that take where such approximations are not needed, teaching the
previous, current, or arising experiences of the learner as the students how to deal directly with the kinetic models per se,
core of the teaching−learning process.1 This approach has the using numerical integration methods to solve them. Previous
advantage of being more participative and engaging, providing reports in this Journal9,11 have illustrated both the importance of
the students with a real-life event that relates to a new concept.2
developing coding skills, as well as going beyond the steady-state
This leads to building new knowledge connected to previously
learned ideas, which helps to understand the meaning of those
ideas beyond memorization.3 Special Issue: Insights Gained While Teaching Chem-
One way to link previous and current knowledge is by using istry in the Time of COVID-19
analogies. In this way, while comparing new notions with Received: June 16, 2020
familiar and relatable experiences, the students have the Revised: July 9, 2020
opportunity to give meaning to abstract ideas and remember Published: July 22, 2020
them more easily.4 The power of analogies to understand
© 2020 American Chemical Society and
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approximation in the analysis of kinetic models in the study of Here, A and B are the reactants. Y is an intermediate; C is the
chemical reactions. product, and a, b, c, and y are the coefficients for the elementary
A full understanding “beyond-paper” of the meaning and steps of the mechanism. The rate laws for the elementary steps of
behavior of the mathematically described system is desired, but this system can then be expressed as follows:
it is sometimes challenging to achieve in the classroom due to
d[A] d[B]
the abstract character of differential equations. The analogy = = −k1[A]a [B]b
between simple epidemiological models and mechanistic dt dt (2.a)
equations in chemical kinetics has been pointed out recently
d[Y]
in ref 12. Among the simplest epidemiological models, one of the = k1[A]a [B]b − k 2[Y] y
most popular is the susceptible−infected−removed (SIR) dt (2.b)
model, proposed by Kermack and Mc Kendrick in 1927.13
d[C]
This model explains the time evolution of populations belonging = k 2[Y] y
to these three “compartments” similarly as a mechanism of dt (2.c)
consecutive reactions. Here, k1 and k2 are the kinetic constants for the first and second
In this work, we present a new approach to the teaching of elementary steps of the mechanism.
chemical kinetics, offering the students the possibility to relate Note that eqs 2.a−2.c are coupled: that is, they need to be
their own experience during the worldwide outbreak of the solved as a system since the kinetic evolution of one chemical
COVID-19 pandemic with chemical kinetics. By creating an species affects that of all other species. The solution of this
analogy between the virus spread and the simulation of a second- system of ordinary differential equations yields the concen-
order autocatalytic chemical system in a programming language tration of the reactant, intermediate, and product at any given
of choice (in this paper, we present implementations in Python time, describing the evolution of the reaction, as the reactants are
and MATLAB), students can connect a real-life application of a consumed and the products formed. For further information, the
model. Students can also fit the available experimental data for interested reader can refer to ref 10.
COVID-19 with the SIR model, expanding their understanding The rate of the reaction can be changed by a catalyst, a species
of the different concepts involved in chemical kinetics. that participates in the reaction by increasing the reaction rate,
We provide a generally applicable framework for the without being consumed (i.e., the catalyst is recovered at the end
implementation, solution, and analysis of complex kinetic of the catalytic cycle).10
schemes in these programming languages, meaning the students Autocatalysis exists when a reactant, an intermediate or a
can later adopt these programs to their own needs. In this regard, product catalyzes a reaction.14 The simplest such example is a
we emphasize the importance of the development of coding second-order (or quadratic) autocatalytic reaction,15−18 where
skills and the use of scientific computing software for the two reactants, A and X, yield two molecules of X (eq 3a):
students in the chemical sciences to remain competitive with
other disciplines. k1
■
A + X → 2X (3a)
d [I ] β
a = [S ][I ] − γ[I ]
Part a was adapted with permission from ref 26. Copyright 1996 dt N (8.b)
American Chemical Society.
d [R ]
= γ [I ]
dt (8.c)
Here, the rate of consumption of S (eq 8.a) depends on the
product of S and I species (resembling a second-order reaction),
and the rate of production of R is described by a first-order decay
Figure 1. Graphical scheme of a second-order autocatalytic reaction,
showing the pathways (arrows) and states (boxes) through which the
of I (eq 8.c). The constants β and γ represent, respectively, the
chemical system evolves. per-capita transmission rate and the removed rate (“product
formation”). The units for β/N are [population−1 time−1], which
SIR Model
are equivalent to the units of a second-order rate constant [M−1
s−1]; and the units for γ are [time−1], which are equivalent to the
The SIR model divides a host population (N) into three units of a first-order kinetic constant [s−1]. The inverse of γ has
sections: susceptible (individuals that are prompt to acquire the the units of time, and it is known as the mean infectious period, μ,
disease upon contact with sick individuals, S), infected the period during which an infected person can spread the
(individuals that are currently affected and can spread the disease.
virus to healthy individuals that they come across, I), and The system of ordinary differential equations (ODEs)
removed (individuals who are no longer able to contract the associated with the SIR model does not have an analytical
disease and spread it, R). Figure 2 summarizes the relationship solution in terms of elementary functions.27 Still, approxima-
between S, I, and R. tions and iterative solutions have been previously reported.28 It
is often the case that realistic chemical systems lead to systems of
ODEs which do not have analytical solutions. In such cases, the
recommended approach is to numerically integrate the ODE
system using the methods available in several software packages,
such as MATLAB29 or Python.30,31 Some of us have adapted this
Figure 2. Graphical scheme of the SIR model, showing the approach in the examination of realistic, more complex kinetic
interconversion pathways (arrows) between the three different schemes involved in proton-coupled electron transfer,32 and
compartments (boxes). See the text for further details. photocatalytic water splitting.33 Other numerical methods can
be used to solve kinetic models in spreadsheet software like
Microsoft Excel, as exemplified in ref 34.
In essence, numerical integration of differential equations
Through Figure 2, we can establish the analogy between the consists of calculating the time-dependent functions, in our
SIR model and the second-order autocatalytic process described system, S(t), I(t), and R(t), which evolve from the initial state at
earlier (cf., Figure 1). Altogether, these three categories t = 0, based on discrete changes in successive, small-time
comprise the entire host population, N: intervals (as given by the differential equations themselves). The
S+I+R=N (5) interested reader can refer to more specialized literature reports
on the topic for further details.35−38 Nevertheless, this approach
This model assumes that the host population remains constant is straightforward to implement and is illustrative of more
(no deaths or births take place), leading to a population that general situations, and the code presented here can be adapted
does not change in time (eq 6): accordingly.
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■
pubs.acs.org/jchemeduc Article
γ i S(∞) yzz
numerically.
S(∞) − N lnjjjj
kinetic models described herein, using the inbuilt ode23t29 and
z = S(0) + I(0)
β k S(0) z{
odeint30,31 routines, respectively.
We divided the code into two sets: the first one used as a (9)
“testing” routine to evaluate the effects of changing different
parameters in the evolution of the kinetic model. The second From this, we conclude that the ratio between the two kinetic
part contains a routine used to fit the SIR model to the current constants is significant in determining the global evolution of the
COVID-19 cases. Both routines can be easily adapted to more system, as will be discussed in the following. The ratio β/γ, often
general cases where data gathered in a laboratory experiment denoted 0 , represents the reproductive number of an epidemy.
following a different kinetic scheme can be analyzed and/or As can be observed, setting β constant and changing γ (Figure
simulated. The code is provided in the Supporting Information, 4a,b) affect both the infected and removed sub-populations.
along with detailed explanations on its implementation, use, and Turning to the plots shown in Figure 4, we shall now discuss the
adaptation. Throughout this paper, we have used the SIR model effect of varying the ratio between β and γ, as well as their
(eqs 8.a−8.c) as the kinetic scheme of choice. absolute values.
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Figure 4. Effect of the kinetic constants β and γ in the simulated evolution of the susceptible (S), infected (I), and removed (R) subpopulations. (A) β =
1; γ = 0.01; (B) β = 1; γ = 0.01; (C) β = 0.01; γ = 0.01; (C) β = 0.05; γ = 0.01. In all cases, N = 10−6; S(O) = 106 − 1; I(O) = 1; and R(O) = 1.
Figure 5. Number of active cases and fit results for several countries using the SIR model as discussed in the text. The raw data is shown as empty
circles, and the fits are denoted with solid red lines.
If β ≤ γ (0 ≤ 1), the system will not show a significant evidenced by a faster decay of I(t) for the case in Figure 4b. This
evolution over time, and the number of infected individuals will is analogous to a situation where, in a quadratic autocatalytic
always be very close to I(0). In kinetic terms, this means that the chemical mechanism (as mentioned above), the first step
autocatalytic species decomposes faster than it is produced, (second-order autocatalysis) is fast and the second one (catalyst
leading to a negligible intermediate (catalyst) population, and deactivation) is slow, so we can say that the second step of the
essentially indicating that the reaction never proceeds SIR mechanism (eq 7.b) is the rate-determining step of the entire
significantly beyond the initial conditions. process.
We now turn to more realistic cases with β > γ (0 > 1), The kinetic constant γ (and hence its inverse, μ) is disease-
analyzing the first two cases with identical β but different γ values specific, and the only way it can be altered is by the introduction
(Figure 4a,b). In Figure 4a, with β = 100γ, the conversion from I of a medical treatment, which accelerates the recovery.
to R is not as efficient as in case Figure 4b (where β = 10γ), which Analogously, in our simplified autocatalytic model, the
causes I to accumulate. The quantity μ = 1/γ, as previously decomposition rate of the autocatalytic species depends on
defined, represents the mean infectious period. In Figure 4a, μ = the chemical nature of the substance itself. In this way, by
100 days, while in Figure 4b, μ = 10 days. This change in μ can be keeping γ constant but changing β (Figure 4c,d), it is possible to
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observe that the two processes in the mechanism are affected. If A graphical summary of the obtained results is given in Figure
we follow the mechanism, one infected person “reacts” with a 6. We observe that the values of β and μ are within the same
susceptible person and spreads the infection, as in an order of magnitude in a comparison across the studied countries.
autocatalytic process, in which the autocatalytic species (Y in
eqs 2.a−2.c, or I in eqs 8.a−8.c) is regenerated. In addition, the
time at which the maximum of I(t) occurs is very sensitive to
changes in β. From this, we conclude that the value of β is critical
for the development of the epidemy. If we analyze the meaning
of the constants β and γ in the context of an epidemy, the real
value of γ depends on the main characteristics of the disease
(duration of the sickness, duration of the infection period, and
lethality). In contrast, as the β value is related to the spread of the
disease, the measures of quarantine and social distancing, which
can reduce this value, are certainly capable of “f lattening the
(infected) curve”, as observed in the case of Figure 4c when
compared to Figure 4d. Moreover, as noted in Figure 4c, if the
spread is not so efficient, not all of the population will catch the
disease (in this example, ca. 200,000 people remained healthy at
the end), analogous to the chemical situation where not all of the
reactant S produces the intermediate I. This can be quantified by
using eq 9, yielding the expected number of remaining
susceptible individuals at infinite time. Figure 6. Constants β and μ (= 1/γ) from the fits of the studied
If we move to our chemical analogy, we started with an excess countries to the SIR model.
of the reactant S and an almost negligible quantity of I (a
“catalytic” amount), which in all the cases shown is enough to
start the reaction. Nevertheless, if β ≤ γ, the production of I (the The students can note that the model fits better with some
catalyst) is not enough to considerably accelerate the reaction. experimental data than with other data, leading to higher relative
When β is large enough to ensure the formation of I in a errors in a few cases. Nevertheless, the limitations of the model
reasonable time (β > γ, or equivalently 0 > 1), the rate of the have to be taken into account to evaluate the results of any
fitting: in our case, the SIR model does not consider the change
first reaction (eq 7.a) certainly affects the performance of the
in the conditions before and after the quarantine and social
entire reaction: if we increase the rate of the autocatalytic distancing measures, that results in a time-dependent β(t) and
reaction, more I will be produced, and it will continue to γ(t), which is beyond the scope of this paper.
accelerate the reaction, up to a point in which all the equivalent This last aspect of the pandemic data contrasts with what one
reactant S will be consumed and transformed into I (cases a, b, would expect from a chemical system, where the kinetic
and d, when compared to c in Figure 4). At this point, the constants are only dependent on the temperature according to
concentration of I will reach a maximum, and the rate of the the Arrhenius equation.10 When encountering a similar
deactivation of the catalyst will depend on the magnitude of the situation, in which the given kinetic model does not fit the
kinetic constant for the second reaction (γ), the rate- data to an acceptable level, the chemical researcher can refine the
determining step. initial guess parameters or evaluate the limitations of the model.
Having discussed the general effects of the variation in the In the first case, it is important to note that the solutions found
kinetic constants, we now move on to a real-life application of through the fitting routine are obtained according to the
the SIR model to fit the data of the COVID-19 pandemic. imposed degrees of freedom of the model. Depending on the
Fitting of COVID-19 Case Data initial conditions, one can encounter different solutions.
To choose the best initial guess for a given system, the
The results of the fits of the number of active cases (defined as researcher should refer to previously reported similar results in
total confirmed cases − recoveries − deaths) for the selected the literature, or experiment using different initial guesses
countries are shown in Figure 5. Note that, despite the fact that spanning a range of acceptable values. Notice that if a given
the SIR model defined previously does not account for deaths, initial guess for a parameter is several orders of magnitude
we consider the deaths and recoveries as part of the “removed” different from the optimal value (predicted by the model), more
population group, since they are unable to contract the disease. iterations will be needed to converge to a reasonable value. If not
We fitted the number of active cases (corresponding to I(t) in enough iterations are allowed in the fitting routine (or
the SIR model) because it is the experimental observable that inappropriate convergence criteria are used), the results
contains the most information (i.e., I(t) depends explicitly on obtained from a suboptimal solution could lead to the wrong
both β and γ). In this regard, when evaluating the kinetics of a impression that the data does not adjust to the model at all.
chemical system, it is preferred and recommended to monitor When evaluating the limitations of the model, the researcher
the species linked with the highest number of parameters. can even propose a new reasonable mechanism to achieve a
Ideally, a global fit, including all the species, is preferred but better fitting, using an improved description of the observed
often precluded by the technique used to monitor the reaction. kinetics. In this regard, the SIR model discussed throughout this
As illustrated in Figure 5, we observe an excellent agreement paper assumes that no deaths or births take place (N is
between the data and the fits to the SIR model. The kinetic constant), which is clearly not the case in a real-life pandemic
constants and their errors can be found in the Supporting such as COVID-19. To overcome this limitation, the kinetic
Information (Table S1). model (eqs 8.a−8.c) can be modified to include deaths and
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births, which enter as additional terms in the equations for S and Lorenzo Echevarría − Department of Chemistry, University of
I. The number of removed individuals (R) is then back- Central Florida, Orlando, Florida 32816, United States;
calculated from N, the total population (using the relation S + I + ́
Departamento de Quimica, ́ Caracas
Universidad Simón Bolivar,
R = N), which is now time-dependent, including both birth and 1080-A, Venezuela
death rates. These models, however, are mathematically much Complete contact information is available at:
more complex and outside of the scope of this work. The https://pubs.acs.org/10.1021/acs.jchemed.0c00698
interested reader can refer to refs 27 and 28 for a more in-depth
treatment of these systems. Author Contributions
In any case, in our chemical analogy, no reactants/products ∇
escape the reaction vessel, and thus, the SIR model with constant E.S.-R. and R.F.-T. contributed equally to this work.
population best serves the purpose of an analogy between Notes
chemical kinetics and epidemiological models. The authors declare no competing financial interest.
■ CONCLUSIONS
Following Kolb’s cycle, we present an engaging approach to
■ ACKNOWLEDGMENTS
We thank our students for being our source of inspiration,
teaching a chemical kinetics class that uses the experience of the
through their insight and valuable questions during our
students with the COVID-19 outbreak to establish an analogy
experiences while teaching chemical kinetics and related topics.
between the kinetics of a chemical system that follows second-
We gratefully acknowledge the contribution of Melania
order autocatalysis with subsequent catalyst deactivation. As
Mazzaglia in the design of the TOC graphic.
■
active learning, we provided the students with tools to
understand how to predict the behavior of a kinetic system
and fit experimental data to a “kinetic” model (in our case, the REFERENCES
SIR model for virus spread), and discuss the goodness of the (1) Daus, K.; Rigsby, R. The Power of Experiential Learning:
fitting. We analyzed the behavior of the system when changing Leveraging Your General Education Curriculum To Invigorate Your
the constants of the process (as an analogy with kinetic Chemistry Courses. In The Promise of Chemical Education: Addressing
constants) and related the obtained results with the con- our Students’ Needs; American Chemical Society, 2015; Vol. 1193, pp
101−113.
sequences of following the stay at home and quarantine orders to (2) Foley, G. Understanding Adult Education and Training, 2nd ed.;
“flatten the curve” of the infection. We are positive that the Allen & Unwin: St. Leonards, New South Wales, 2000.
abilities acquired through this approach will enable future (3) Ausubel, D. P. A subsumption theory of meaningful verbal learning
generations of students of chemical sciences to gain an in-depth and retention. J. Gen Psychol 1962, 66, 213−24.
understanding of the modeling and analysis of complex, realistic (4) Cox, C.; Schatzberg, W. E. International Perspectives on Chemistry
kinetic schemes with the help of robust and efficient computer Education, Research, and Practice; ACS Symposium Series 1293;
codes. American Chemical Society: Washington, DC, 2018.
■
(5) Cortés-Figueroa, J. E.; Pérez, W. I.; López, J. R.; Moore-Russo, D.
ASSOCIATED CONTENT A. An Analogy Using Pennies and Dimes To Explain Chemical Kinetics
Concepts. J. Chem. Educ. 2011, 88 (7), 932−936.
* Supporting Information
sı
(6) Rodriguez, J.-M. G.; Towns, M. H. Catalyzing Student Learning:
The Supporting Information is available at https://pubs.ac- Using Analogies To Teach Enzyme Kinetics. J. Chem. Educ. 2019, 96
s.org/doi/10.1021/acs.jchemed.0c00698. (7), 1401−1406.
(7) Schultz, E. Dice Shaking as an Analogy for Radioactive Decay and
Table of fitted parameters, detailed description of the First Order Kinetics. J. Chem. Educ. 1997, 74 (5), 505.
MATLAB code, and detailed description of the Python (8) Winkel, B. Parameter estimates in differential equation models for
code (PDF) chemical kinetics. International Journal of Mathematical Education in
Science and Technology 2011, 42 (1), 37−51.
MATLAB code and database files (ZIP) (9) Pavlis, R. R. Kinetics without Steady State Approximations. J.
Python code and database files (ZIP) Chem. Educ. 1997, 74 (9), 1139.
■
(10) Atkins, P. W. A.; De Paula, J. A.; Keeler, J. A. Atkins’ Physical
Chemistry, 11th ed., international ed.; Oxford University Press, 2018.
AUTHOR INFORMATION (11) Fisher, A. A. E. Developing the Chemist’s Inner Coder: A
Corresponding Author MATLAB Tutorial on the Stochastic Simulation of a Pseudo-First-
Order Reaction. J. Chem. Educ. 2020, 97 (5), 1476−1480.
Florencio E. Hernández − Department of Chemistry and (12) Simon, C., The SIR dynamic model of infectious disease
CREOL/The College of Optics and Photonics, University of transmission and its analogy with chemical kinetics. ChemRxiv preprint,
Central Florida, Orlando, Florida 32816, United States; 2020.
orcid.org/0000-0001-7753-6995; (13) Kermack, W. O.; McKendrick, A. G. Contributions to the
Email: [email protected] mathematical theory of epidemicsI. Bull. Math. Biol. 1991, 53 (1),
33−55.
Authors (14) Schuster, P. What is special about autocatalysis? Monatsh. Chem.
Estefanía Sucre-Rosales − Department of Chemistry, University 2019, 150 (5), 763−775.
(15) Lavabre, D.; Pimienta, V.; Levy, G.; Micheau, J. C. Reversible,
of Central Florida, Orlando, Florida 32816, United States mixed first- and second-order and autocatalytic reactions as particular
Ricardo Fernández-Terán − Department of Chemistry, cases of a single kinetic rate law. J. Phys. Chem. 1993, 97 (20), 5321−
University of Zurich, CH-8057 Zurich, Switzerland; 5326.
orcid.org/0000-0002-4665-3520 (16) Scott, S. K. Reversible autocatalytic reactions in an isothermal
David Carvajal − Institute of Advanced Materials (INAM), CSTR: Multiplicity, stability and relaxation times. Chem. Eng. Sci. 1983,
Universitat Jaume I, 12006 Castelló, Spain 38 (10), 1701−1708.
2604 https://dx.doi.org/10.1021/acs.jchemed.0c00698
J. Chem. Educ. 2020, 97, 2598−2605
Journal of Chemical Education pubs.acs.org/jchemeduc Article
2605 https://dx.doi.org/10.1021/acs.jchemed.0c00698
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