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Alchemy Software Products Experience the desktop computing power and convenience of simulating and modeling chemical mechanisms with REACT for Windows, the software program for use by chemists in research laboratories and by academic institutions. |
| Summary of Features System Requirements Program Interface Mechanistic Data Page Reaction Times Page Tabulated Results Page Plot of Results Page Menu Bar Tool Bar Performing a Calculation |
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| Read
the review of REACT
for Windows in the Journal of Chemical Education (J. Chem. Educ.) |
| Summary of Features | Top of page | |
| REACT for Windows is composed of three main parts: the chemical mechanism editor, integration algorithm, and calculated results tabulator and plotter. The mechanism editor facilitates the entry and editing of mechanistic and reaction time data. The mechanistic data includes the title of the mechanism and any additional descriptive information, the set of chemical reactions, their respective forward and reverse rate coefficients, and the initial concentration of each species involved in the mechanism. The reaction times are the time points where the integrator reports the concentration data and the time derivative of the concentration data for each species. There is considerable flexibility available in the selection of reaction times. The reaction times can be any combination of as many as 1000 geometrically or linearly spaced values and any number of specific values. |
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The integration algorithm is the heart of any kinetics simulation program and the one in REACT for Windows is a proven and efficient integrator adept at handling stiff differential equations. Once the integration calculation has been successfully completed, the program displays the concentration results for all species in a tabular format. The program provides considerable flexibility in the presentation and viewing of both the concentration data and its time derivative for each species. Specific sets of data can then be exported to an ASCII file for importing into other software applications such as Microsoft Excel for further analysis. Finally, any set of data type, species concentration or its time derivative, can be plotted for a graphical summary view of trends in the data for that species. Reports, which can include any combination of data sets, can be printed and printed copies of plots also can be readily obtained, provided a printer is available. |
| System Requirements | Top of page | |
In order to use REACT for Windows you need:
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| Program Interface | Top of page | |
| The program interface is composed of four pages. Each page has a tab with its title. The titles of the four pages are Mechanistic Data, Reaction Times, Tabulated Results, and Plot of Results. Upon starting the program, the Mechanistic Data page is initially exposed and the latter two titles are dimmed to indicate that they are currently inaccessible since there are no results to display as shown below. By simply clicking on its tab with the mouse each page is accessed, but only one page is exposed at a time. | ||
| Mechanistic Data Page | Top of page | |
| The Mechanistic Data page (shown below) is used to enter and edit the chemical mechanism and related information. The chemical mechanism is composed of the reaction equations and the associated rate coefficients for the forward and reverse reactions. A list of mechanism species is automatically maintained and displayed in the components list on the Mechanistic Data Page. It is used to select species for entering or editing initial concentration values. A title for the mechanism and any ancillary information about the mechanism is also entered. | ||
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| Reaction Times Page | Top of page | |
| The Reaction Times page is used to enter and edit the reaction time values. These values are the times used by the integration algorithm to report the calculated results for the species concentration and its time derivative. The calculated data sets are the results of the integration calculation, which can be displayed in tabular or plotted format. There is considerable flexibility in choosing the reaction times. The allowable error value for the integration is also displayed and edited on this page in addition to the Begin Calculation command button to begin the integration calculation. | ||
| Tabulated Results Page | Top of page | |
| The Tabulated Results page is used to display the calculated results in a tabular format. This page is initially inaccessible upon starting the program since there are no results to display. However, the page is automatically displayed upon the successful completion of an integration calculation. The ability to select the displayed data is accessed on this page using the Display Options command button. The ability to quickly print the displayed data in a report is accessed using the Print Results command button. The ability to export selected data to an ASCII file for use in other programs is also accessed on this page using the Export Results command button. | ||
| Plot of Results Page | Top of page | |
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The Plot of Results page is used to display plots of the calculated results. This page is also inaccessible after the program is initially started and until there are results to plot. Once there are results to plot, the ability to select the data to be plotted is accessed on this page using the Plot Options command button. Once a plot is displayed, it can be sent to the printer for printing by pressing the Print Plot command button. The Plot of Results page is accessed by clicking on its tab. If a plot is not currently displayed, the Plot Options dialog box is immediately opened so that you can choose which data to plot. The component data you wish to plot is selected in the same way as data displayed in the Display Options dialog box. The difference is that only five data sets can be plotted at one time. The Plot Options control monitors the data as it is selected and determines the default Y-axis range and parameters. The X-axis range and parameters are also determined based on the type of time progression series. The program may advise you that the data you wish to plot changes by several orders of magnitude and you might want to use a logarithmic scale for the Y-axis. You have complete control over the display of the data and can manually change the axes parameters to suit your needs. Once all the data has been selected and added to the plot list, the plot can be displayed by clicking the OK command button. In our example, the results for the example2 mechanism are shown below. In this mechanism, an intermediate AB* is produced which links the reactants and products. This type of mechanism is common to many important industrial and biochemical reaction mechanisms including the Michaelis-Menten mechanism and any mechanism involving a pre-equilibrium. The plot of the data is shown below on the Plot of Results page. The plot includes a title and a legend that identifies the individual curves. Additional data can be plotted using the Plot Options by clicking on the Plot Options command button. The plot can be sent to a printer for printing by clicking the Print Plot command button. |
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| Menu Bar | Top of page | |
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Like other Windows programs, REACT for Windows has a menu bar for the easy access of various program functions via the menu feature. The menu bar located near the top of the program window includes the File, Options, Calculate and Help menu lists. These menu lists are available with each page view. The File menu
list contains many familiar features to manipulate your mechanistic data, calculated results and files. A list of the five most recent files is listed under the File menu and can be readily accessed by clicking on the desired file. By clicking on the example2.rxn mechanism file, one of the example files installed with the program, the mechanistic data is loaded into the program. Once the mechanistic data is loaded, the Mechanistic Data page now looks like the one shown
earlier. A mechanism description identifies the mechanism being modeled. The example mechanism is a simple one consisting of two reversible consecutive second-order reactions. This mechanism contains an intermediate species AB* and depending on the rate coefficients for the reactions can lead to a pre-equilibrium condition in the mechanism.
The Options menu lists provide program functions to control the displaying, plotting and printing of data and setting the program options. The rate coefficient calculator can be accessed from the Calculate menu as can the integration calculation. The Help menu provides access to the Help function and how best to obtain technical support. |
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| Tool Bar | Top of page | |
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The tool bar, which is located directly beneath the menu bar, contains a set of icons that provides convenient access to frequently used program features. It also has a control that indicates the current editor typing mode and a drop down list of available typing modes for entering reaction equations. The Begin Calculation command button is also located on the tool bar for ready access to begin an integration calculation. Status Bar The status bar, located at the bottom of the program window, contains information about the status of the program. This information includes instructions on what to do next or the result of a recent action, the name and path of the current working file, the time and date, and the status of the Caps Lock and Num Lock keys. This bar should be monitored when you are uncertain about what to do next. |
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| Performing a Calculation | Top of page | |
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Once a mechanism file, such as Example2.rxn, has been loaded into the program or you have entered a new mechanism, you can perform a calculation. The program will check to ensure that you have sufficient data entered before beginning a calculation. As an example, let review what the program looks like when the Example2 mechanism is loaded. The Mechanistic Data page
contains the mechanism title, descriptive information about the mechanism
and a list of the reactions and the species in the mechanism. A reaction can be edited by selecting a reaction in the mechanism and clicking on the Edit command button. The reaction and its forward and reverse rate coefficients are then displayed. Once all the changes have been completed, the Edit command button is clicked again to accept the changes. Reactions can be added and inserted into the mechanism list. They can also be deleted and hidden from the list, which means that the reaction is not included in any subsequent calculations until it is re-activated. |
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| The Rate Coefficient Calculator, shown here, can be accessed when needed to help determine the rate coefficients for reactions within the mechanism. |  |
| Once the mechanism data has been entered, the initial concentrations of components can be entered. This is accomplished by selecting a component from the components list and entering its concentration in the Initial Concentration text box. Once the initial concentration data has been entered, we can now proceed to entering the reactions times where we would like the calculated results reported. Pressing the Tab key or clicking on the Reaction Times page tab will expose the Reaction Times page. There is considerable flexibility in selecting these reaction times. One can choose from either a linear or geometric progression for the time series. The linear progression has each pair of times differing by a constant additive value while a geometric progression has each pair differing by a constant multiplicative value. Choosing a geometric progression will cause the time scale in any subsequent plot to be logarithmic and allow you to investigate decades of time while maintaining the same number of data points in each decade. This will be illustrated later. One can also choose to have any specific time value also included provided it doesn't already exist in the above progression series. The initial and final time values are entered and depending on the type of progression, the linear interval or the total number of time points in the series can be entered. Entering one of these values causes the program to calculate the other. For the geometric series, you can only enter the number of time points. The program will determine the geometric multiplicative constant. Once all the reaction times have been entered, a calculation can begin. The Begin Calculation command button on the Reaction Times page or on the tool bar can be clicked to start the integration calculation. The program checks the mechanistic data to ensure that there is sufficient data to perform a calculation and if an error occurs, reports it to you with information about the data deficiency, e.g. an initial concentration may be missing. The integration calculation begins if no errors are found and the algorithm will keep you informed of its progress. The integration algorithm currently can accommodate up to 85 species in the mechanism and as many reactions as your computer memory will allow. Upon the successful completion of the integration calculation, the Tabulated Results page is displayed, and the time it took for the integrator to complete the calculation is momentarily displayed in the status bar. The concentration results for all the species are available for inspection as well. The concentration data for the first five species and the first twenty reaction times are displayed if required, i.e. there could be fewer of course. Additional data if present can be viewed by navigating to various regions of the display table using the vertical and horizontal slide bars and arrows or shortcut keys. The data can be displayed in any arbitrary order using the Display Options control which is accessed by clicking on the Display Options command button. The Display Options control how the calculated results are displayed in the results table. The component and its data type is selected and then the data is added to the display list. The calculated results can be displayed in any order and can even be repeated if desired. Component data can be displayed next to each other for easy comparison and evaluation using the Display Options. When comparing experimental data with calculated results, the reaction times can be limited to just specific times that equal experimental reaction times. This will allow you to readily fit your calculated results to experimental data by adjusting the appropriate rate coefficients. The displayed results can be printed in a report by clicking on the Print Results command button and exported to an ASCII file by clicking on the Export Results command button. More comprehensive reports with their options can be obtained using the File/Print menu option or the print report icon on the tool bar. |
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| REACT
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