simulateCA {eChem}

Simulate a Chronoamperometry Experiment

Description

Simulates either a single pulse or a double pulse chronoamperometry experiment using either an E, EC, or CE mechanism, where E is a redox reaction and where C is a chemical reaction that either precedes or follows the redox reaction.

Usage

simulateCA(e.start = 0, e.pulse = -0.5, e.form = -0.25,
  mechanism = c("E", "EC", "CE"), ko = 1, kcf = 0, kcr = 0,
  pulses = c("single", "double"), t.1 = 10, t.2 = 0, t.end = 30,
  n = 1, alpha = 0.5, d = 1e-05, area = 0.01, temp = 298.15,
  conc.bulk = 0.001, t.units = 2000, x.units = 180, sd.noise = 0)

Arguments

e.start

Initial potential (in volts).

e.pulse

Potential after applying the initial pulse (in volts).

e.form

Formal potential for the redox reaction (in volts).

mechanism

Mechanism for the electrochemical system; one of E for redox reaction only, EC for redox reaction with a following chemical reaction, or CE for redox reaction with a preceding chemical reaction. Default is E.

ko

Standard heterogeneous electron transfer rate constant for the redox reaction (in cm/s).

kcf

Homogeneous first-order rate constant for the forward chemical reaction (in s^-1).

kcr

Homogeneous first-order rate constant for the reverse chemical reaction (in s^-1).

pulses

Either single or double. For a single pulse experiment, the initial potential is e.start and the final potential is e.pulse, and for a double pulse potential, the initial potential is e.start, the intermediate potential is e.pulse, and the final potential is e.start; the default is a single pulse experiment.

t.1

The time at which the first pulse is applied (in s).

t.2

The time at which the second pulse is applied (in s).

t.end

The time at which the experiment ends (in s).

n

Number of electrons in the redox reaction.

alpha

Transfer coefficient.

d

Diffusion coefficient for Ox and Red (in cm^2 s^-1).

area

Surface area of the electrode (in cm^2).

temp

Temperature (in K).

conc.bulk

Initial bulk concentration of Ox or Red for an E or an EC mechanism, or the combined initial concentrations of Ox and Z, or of Red and Z for a CE mechanism (in mol/L).

t.units

The number of increments in time for the diffusion grids.

x.units

The number of increments in distance for the diffusion grids.

sd.noise

The standard deviation for noise as a percent of maximum current (in \muA).

Value

Returns a list with the following components

expt

type of experiment; defaults to CA for a chronoamperometry simulation

mechanism

type of mechanism used for the simulation

file_type

value that indicates whether the output includes all data (full) or a subset of data (reduced); defaults to full for caSim

current

vector giving the current as a function of time

potential

vector giving the potential as a function of time

time

vector giving the times used for the diffusion grids

distance

vector giving the distances from electrode surface used for the diffusion grids

oxdata

diffusion grid, as a matrix, giving the concentration of Ox

reddata

diffusion grid, as a matrix, giving the concentrations of Red

chemdata

diffusion grid, as a matrix, giving the concentrations of Z

formalE

formal potential for the redox reaction

initialE

initial potential

pulseE

potential after apply the initial pulse

electrons

number of electrons, n, in the redox reaction

ko

standard heterogeneous electron transfer rate constant

kcf

homogeneous first-order rate constant for forward chemical reaction

kcr

homogeneous first-order rate constant for reverse chemical reaction

alpha

transfer coefficient

diffcoef

diffusion coefficient for Ox and Red

area

surface area for electrode

temperature

temperature

conc.bulk

initial concentration of Ox or Red for an E or EC mechanism, or the combined initial concentrations of Ox and Z, or of Red and Z for a CE mechanism

tunits

the number of increments in time for the diffusion grids

xunits

the number of increments in distance for the diffusion grids

sdnoise

standard deviation, as percent of maximum current, used to add noise to simulated data

direction

-1 for an initial reduction reaction of Ox to Red; +1 for an initial oxidation reaction of Red to Ox

pulses

number of pulses: either single or double

time_pulse1

time when first pulse is applied

time_pulse2

time when second pulse is applied

time_end

time when experiment ends

k_f

vector of forward electron transfer rate constant as a function of potential

k_b

vector of reverse electron transfer rate constant as a function of potential

jox

vector giving the flux of Ox to the electrode surface as a function of potential

jred

vector giving the flux of Red to the electrode surface as a function of potential

Examples

ex_ca = simulateCA(e.start = 0.25, e.pulse = -0.25, e.form = 0,
  pulses = "double", t.2 = 20, x.units = 100, t.units = 1000)
str(ex_ca)