Polar For Windows: Electrochemical simulation

Polar 4 For Windows

Electrochemical simulation and data analysis

DrHuang Pty Ltd

124 Eastern Avenue, Kingsford, Sydney, NSW 2032, Australia

Phone: (61 2) 9662 0516

mailto:polarography@bigFoot.com
mailto:showing@biFoot.com

www.electrochem.net

www.DrHuang.net

www.electroanal.com

2/12/1999

Contents

1. Introduction
2. Features
3. Menu
4. Input
5. Playing Around

5.1 Running Simulation
5.2 Comparing Curves
5.3 Analyzing Data
5.4 Extracting Parameters by Curve Fitting
5.5 Stripping Voltammetry

6. Frequently Asked Questions (FAQ)
7. References

Chapter 1
Introduction

It analytically and digitally simulates voltammograms (polarograms) on any mechanism at 8 electrode geometry (planar, spherical, semi-spherical, cylindrical, semi-cylindrical, microdisc, thin film, and rotating electrodes) in over 5 techniques (linear sweep and CV, DC, normal pulse, differential pulse, and square wave voltammetries). It outputs current, resistance, conductivity, and surface concentration. It also simulates effects of charge current, resistance, noise, electrolyte, stripping time, stripping potential, etc. User can type in his mechanism.

It analyses any ASCII x-y data for detecting peak location, peak value, semi-derivative, derivative, integral, semi-integral, curve fitting, and separating overlapped peaks.

It shows tip when the user put mouse cursor over a label. The program can separate overlapped voltammograms into individuals, and extract real peak from voltammogram with noise and baseline. It outputs the theoretical peak values, the peak current and potential and current-potential data, which can be imported into other program (e.g. Lotus 123). User can copy-and-paste the voltammogram into his document.

It has been successfully applied to fit experimental polarograms (voltammograms) of In(III), Cd(II), Pb(II), Tl(I), Cr(III), Zn(II), and binuclear copper complex in aqueous and non-aqueous media at mercury, solid metal and non-metal electrodes (specifically the dropping mercury, hanging mercury drop, gold, platinum and glassy carbon electrodes) by various electrochemical techniques (differential pulse, square wave, and pseudo-derivative normal pulse polarographies) [1-5].

It is available from the author or download from my Web site. If you have any question, please read FAQ in its document.

Chapter 2
Features

Digital simulation
Flexible for any mechanism up to second-order chemical reaction. User can type in his mechanism.

Analytical simulation
No divergence problem in simulation. No overflow problem in simulation. Fast simulation.

Over 5 techniques
Linear sweep, CV, DC, normal pulse, differential pulse, square wave voltammetries. Multi-cyclic voltammetry, cyclic differential pulse voltammetry.

4 Outputs
It outputs current, resistance, conductivity and surface concentration.

Theoretical peak
You can compare your data with theoretical peak values to see if your experimental conditions reach theoretical limit or not.

Simulating effect of noise, charge current, resistance, electrolyte, stripping time, stripping potential, etc.

Separating overlapped peaks
It manually and auto separates overlapped peaks into individuals, and extract real peak from voltammogram with noise and baseline. So you can exactly determine peaks.

Preconcentration
You can change preconcentration conditions for stripping voltammetry.

Pre-equilibration

Curve fitting
It manually and auto fits the simulated voltammograms into experimental data, and extracts kinetic parameters from experimental data.

Import and export data
You can export simulated data into your favor program (e.g. MS Excel). You can copy-n-paste the voltammogram into your document.

Derivative, integral, semi-derivative, semi-integral
Semi-derivative is useful for CV. It can change a shape of reversible CV into symmetric peak so easy to determine peak.

8 electrode geometry
planar, spherical, semi-spherical, cylindrical, semi-cylindrical, microdisk, thin film, and rotating electrodes.

Tip
It shows tip for help when you put mouse cursor over a label.

Table 2.1 Features

-----------------------------------------------------------------------------
version                 Public	Student       Standard	Full	competitor

digital simulation	y	y		y	y	y
analytical simulation	y	y		y	y	n
theoretical peak 	y	y		y	y	n

Techniques:
LSV, CV                	y       y               y	y	y
DC			y	y		y	y	n
normal pulse            y       y               y	y	n
differential pulse      y       y               y	y	n
cyclic DPV	        y       y               y	y	n
square wave             y       y               y	y	n

Output:
current 		y	y		y	y	y
resistance		y	y		y	y	n
conductivity 		y	y		y	y	n
surface concentration 	y	y		y	y	y

Effect:
chemical mechanisms     y       y               y	y	y
noise                   y       y               y	y	y
charge current          y       y               y	y	y
resistance		y	y		y	y	y
electrolyte		y	y		y	y	n
preconcentration	y	y		y	y	n
pre-equilibration	y	y		y	y	y
conductivity		y	y		y	y	n

Analysis:
derivative              y       y               y	y	n
integral               	y       y               y	y	n
semi-derivative         y       y               y	y	n
semi-integral           y       y               y	y	n
manual fit     	        n       y               y	y	y
auto fit              	n	n               y	y	y
manual separate		n	n		n	y	n	
auto separate		n	n		n	y	n

Electrode:
planar                  y       y               y	y	y
(micro)spherical        y       y               y	y	y
(micro)hemispherical	y	y		y	y	y
(micro)cylindrical      y       y               y	y	y
(micro)hemicylindrical	y	y		y	y	y
microdisc		y	y		y	y	n
thin film		y	y		y	y	y
rotating disc		y	y		y	y	y

tip			y	y		y	y	n
import data             n       y               y	y	y
export data             n       y               y	y	n
-----------------------------------------------------------------------------
note: y = yes, n = no. price may be changed.

Chapter 3
Menu

File menu

Save submenu
It saves experimental parameters.
Import Data submenu
It imports data file into Polar.
Export Data submenu
It export data to other program as data file. e.g. if you export data as the .csv file, you open it into MS Excel by double-clicking it.
Copy To Clipboard
It copy graph into clipboard, so you can paste graph into your document.
Print
It prints graph.
Exit

Input menu

Technique submenu
Mechanism submenu
Instrument submenu
Chemicals submenu

Run menu

Simulate submenu
It runs simulation.
Manual Fit submenu
It fit simulated curve into experimental curve as you manually change parameter value.
Auto Fit submenu
It auto fit simulated curve into experimental curve.
Manual Separate submenu
It separate overlapped peaks into individuals as you manually change parameter value.
Auto Separate submenu
It auto separate overlapped peaks into individuals.

Display menu

Option submenu
It is to change plot options.
Plot submenu
It plots curve without run simulation.
Next submenu
It plots next curve.

Analysis menu

Find Peak submenu
Find halfwave E submenu
Semi-derivative submenu
Semi-integral submenu
Derivative submenu
Integral submenu

Help menu

Logon submenu
You logon to activate menus by input of password.
About submenu
It displays info about author.

Some menus will be activated only after you click the Simulate submenu or load data because they require data.

Chapter 4
Input

4.1 Techniques window

1) Linear sweep and cyclic voltammetry
2) DC voltammetry
3) Normal pulse voltammetry
4) Differential pulse voltammetry
5) Square wave voltammetry

The shapes of DC and normal pulse polarogram are S-shape. The shapes of differential pulse and square wave voltammograms usually are peak-shape. But there is effect of the DC term on differential pulse voltammogram.

4.2 Mechanism window

User can type in his mechanism in Digital Simulation section. In order to faster computation, you should type in reactants only without products if chemical reaction is irreversible.

4.3 Instrument Window
Instrumental Parameters Section:

E start: starting potential (V).
E end: ending potential (V).
E step: step potential (V).
v: scan rate (V/s). For square wave voltammetry, v=E step/t pulse.
E pulse: pulse potential (V).
T: temperature (°C).
t pulse: pulse time or pulse width for pulse voltammetry (s).
t drop: mercury dropping time or pulse length for pulse voltammetry (s).
Noise: ratio of noise to maximum signal (%).
C dl: double layer capacitor for charge current (F).
R: resistance (Ohm).

Scan:
Single: single scan.
Cycles: cyclic scan, e.g. cyclic voltammetry (CV).
2 Cycles: 2-cycle scan.

Electrode Section:

Planar: planar electrode.
(Micro)Spherical: spherical electrode or micro spherical electrode.
(Micro)Hemispherical: hemispherical electrode or micro hemispherical electrode.
(Micro)Cylindric: cylindrical electrode or micro cylindrical electrode.
Microdisc: microdisc electrode, radius <1e-4 cm
Thin film: thin film electrode
Rotating disc: rotating disc electrode
Area: electrode area (cm²).
Radius: electrode radius (cm).
Length: electrode length for cylindrical electrode or micro cylindrical electrode, or mercury film thickness for stripping voltammetry (cm).

Preconcentration Section:

E pre: preconcentration potential (V).
R stir: stirring rate (rpm). Stirring solution
t pre: preconcentration time (s).
t pre const: preconcentration time constant (/s).
P const: electrode constant. It only related to electrode.

4.3 Chemicals Window
Species Section:

D: diffusion coefficient (cm²/s).
C anal: analytical concentration (M).
C init: initial concentration for simulation (M).
C fitted: fitted value of concentration (M).
C min: minimum concentration for fitting (M).
C max: maximum concentration for fitting (M).

Heterogeneous Reaction Section:

ks: heterogeneous standard rate constant (cm/s).
a: electron transfer coefficient.
n: electron number.
E°: standard electrode potential (V).

Homogeneous Reaction Section:

kf: forward chemical reaction rate constant.
kb: backward chemical reaction rate constant.
Kq: chemical equilibrium constant, Kq = kf/kb.

Chapter 5
Playing Around

5.1 Running Simulation

A simplest way to play simulation is just to click the Simulate submenu under the Run menu. It uses the default values to simulate a linear sweep voltammogram.

Notice that some menu (e.g. the Display menu and the Analysis menu) will be activated only after run simulation or load data because they require data.

5.1.1 Effect of Electrode Size - Microelectrode

Simulation technology for microelectrode is the same as for macro electrode, but the electrode size is very small, e.g. electrode radius is 1e-4 cm. A shape of voltammogram will be changed. Note that the planar electrode geometry is not available for microelectrode.

5.2 Comparing Curves

After run first simulation, click the Display menu, and click the Option submenu. Select the Overlap choice, then run second simulation.

5.3 Analyzing Data

Semi-derivative is useful for CV. It can change a shape of CV into symmetric peak if CV is reversible.

5.4 Extracting Parameters by Curve Fitting

5.4.1 Fitting to Simulation Curve

In order to extract kinetic parameters, you can fit a simulation curve to another simulated or experimental curve. You should manual fit before auto fit. The manual fit shows how well your initial guess values work. It can retrieve any of 20 parameters (concentration C, standard electrode potential E°, and the heterogeneous standard rate constant ks) from voltammogram by curve fitting. If it diverged, you should change their initial values, then try again.

e.g. run simulation with all default values, then change the C value from 1e-3 to 2e-3 in the Species section, click the Auto Fit menu. You will see the fitted value of 0.001 in the C fitted field next to the C text field.

5.4.2 Fitting to Experimental Curve

It is similar to fit simulated curve. But you should input your experimental values of E start, E end, E step, etc. into the Experimental section. Polar requires data are in SI unit and first peak is positive value. If your experimental data are not, please convert your experimental data.

5.5 Stripping Voltammetry

Select the Preconcentration in the Experiential Parameters window. Change the preconcentration potential value in the E pre text field, and preconcentration time in the t pre text field. The preconcentration potential value usually is -0.2/n V to specie’s standard electrode potential. The preconcentration time usually is a number of minutes. You should enter your electrode constant into the P cont text field, and your mercury film thickness into the Length field in the Electrode section of the Experimental window if you use a planar mercury film electrode.

Chapter 6
Frequently Asked Questions (FAQ)

Q: Which platforms can Polar run on?
A: Its 32-bit version Polar32 runs on IBM PC under Windows 95/98/NT while its 16-bit version Polar32b runs under Windows 3/3.1/3.11/95/98/NT.

The 32-bit version needs Microsoft Visual Basic 6 runtime DLL files (e.g. msvbvm60.dll, comdlg32.ocx) in the same directory as Polar or in the directory \windows\system for Windows 3.11 or 95, or in the directory \winnt\system32 for Windows NT.

The 16-bit version needs Microsoft Visual Basic 4 runtime DLL files (e.g. vb40016.dll and oc25.dll) in the same directory as Polar or in the directory \windows\system for Windows 3.1, or in the directory \winnt\system for Windows NT.

Q: Where can I download these dll?

A: Microsoft Visual Basic 6 runtime DLL files are from http://www.simtel.net/simtel.net/win95/dll.html, where msvbvm60.dll is inside simvb6-3.zip. Microsoft Visual Basic 4 16-bit runtime DLL files are from http://www.simtel.net/simtel.net/win3/dll.html.

Q: When I click the Simulate menu, I got error: No data.
A: I guess you are running it under non-English version of Windows. Please change language setting to English in the Regional Setting of the Control Panel, and restart Polar. Or try it under English version of Windows. Some non-English versions of Windows have problem to run English version program.

Q: I cannot save a file.

A: You miss the Microsoft Visual Basic 6 runtime DLL file comdlg32.ocx.

Q: When I installed to run setup.exe, an error occured:
while registering the file
>c:\windows\system\MSRD2x35.dll
Shall I (Abort, Retry, Ignore)?
A: Ignore. Do not worry about MSRD2x35.dll. Running Polar did not use it, setup.exe check it only.

Q: Still have install problem?
A: I suggest you close all programs (include Office, Mail) before install Polar. If you still have problem, try to register file msvbvm60.dll by double click or type following command in DOS:

Cd \windows\system
Regsvr32 msvbvm60.dll
then start Polar.

Q: Why are some menus grey?
A: Some menus will be activated only after you click the Simulate menu or load data because they need data.

Q: I cannot see any chemical reaction in Public version. Is this part of the program not finished yet or is it only available in the registered version?
A: There is only one chemical reaction available in the Public version. You can change chemical reaction rate kf, e.g. 10¹⁰. The registered versions include common mechanisms. Please read document for details.

Q: Does it include my mechanism?
A: If your mechanism is missing, please send your requirement into author. Author may add your mechanism into new version special for you.

Q: Can it fit data by curve fitting?
A: Yes. As easy as just point and click.

Q: Can I change graph into other program Lotus 123 or Excel?
A: Yes. You export data in text file, then read data into Lotus 123 or Excel.

Q: Some submenus semi-derivative, semi-integral, derivative, and integral, seem to not work sometime. How can I do?
A: You should first click the Next submenu under the Plot menu, then try semi-derivative submenu.

Q: How much does registration cost?
A: About $100.

Q: How can I get registered version?
A: You will receive it if you send author register fee by check or money order.

Q: What are difference among Public, Standard and Professional, and Full versions?
A: The Public version is for teaching, the Standard version is for average users, the Professional version is for professionals, and the Full version is for special users.

Q: When I run the SWV with default conditions as a digital simulation, it does not appear to give the correct curve. Why?
Because default conditions are for linear sweep and CV only. For SWV, DC, NPV and DPV, you should change scan rate v to 0.01. For SWV you should calculate correct scan rate by v=E step/t pulse before run digital simulation.

Q: Is it possible to click on a point and then have displayed both the current and potential for the point? Also, does it have any zoom features?
A: You can import any ASCII x-y data from Polar to my software VisualMath For Java. In VisualMath For Java, you click on a point and then have displayed both the current and potential for the point. Also, it has zoom features.

Q: How does it compare to competitors?
A: Polar has advantages over competitors:

Competitor simulates a single technique CV only, while Polar has more features, e.g. simulate over 5 techniques (see details on the table in Chapter 2 Features and Prices).
Competitor cannot separate overlapped peaks, while Polar does.
Competitor does not support Windows 95 features, e.g. long filename, while Polar does.
Competitor cannot simulate multi-electron reaction in one step, while Polar does.
You download and try Polar free.
Polar is much cheaper.
You do not worry about if you lose the Dongle. Competitor is copy-protected by the Dongle, but Polar is not.

Chapter 7
References

[1] W. Huang, T. Henderson, A.M. Bond and K.B. Oldham, Curve fitting to resolve overlapping voltammetric peaks: model and examples, Anal. Chim. Acta, 1995, 304, 1-15.

[2] W. Huang and B. Hibbert, Computers & Chem., 1995, 19(4), 433.

[3] W. Huang and B. Hibbert, Computers & Chem., 1995, 19(4), 435.

[4] W. Huang and B. Hibbert, Polar 2.0 for Windows: simulator of voltammogram, Chem. in Aus., 1996, 131.

[5] J. Mo, P. Cai, W. Huang and F. Yun, Theory and application on multiple semidifferential electrochemical stripping analysis with thin mercury film formed in situ, Acta Chimica Sinica, 1984, 42(6), 556-561, CA 101: 162712.