How to Model a Molecule Using Avogadro Software
Download the program., Run the program., Pick a chemical molecule to model., Pick your settings., De-select the "Adjust Hydrogens" option., In the element section, click the drop down menu and select Carbon., Repeat the lsat step, but choose Oxygen...
Step-by-Step Guide
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Step 1: Download the program.
When downloading the program, just follow the regular downloading methods that are used on each computer's operating system (Macintosh or Windows).
You can download the software from https://sourceforge.net/projects/avogadro/files/latest/download. -
Step 2: Run the program.
After downloading, click and open the program.
It might take a minute or two to load, but do not worry or get frustrated and give it time. , For these instructions we'll start with something simple, a carbon dioxide molecule., In this program, you are allowed to pick the what you want to see on the model.
For example, if you want each element to be labeled in the molecule, select the "Label" option in the left hand side menu titled "Display Types".
Or, if you wanted the dipole moment to be displayed, select the "Dipole" option in the same menu.
However, always make sure that the "Ball and Stick" option is always selected so that your elements show up on the software. , The "Adjust Hydrogens" option adds hydrogens to any molecule added, and so it is not needed when making a Carbon dioxide molecule.
Also, it is better to always de-select this option because adding the hydrogens yourself gives you more control over the position and their order in the molecule as opposed to the software adding it by default. , This drop-down menu is the one we will be using to add any elements we need throughout this process.
Once you have selected carbon, click anywhere in the black drawing area for the element to show up. , Then click on the black drawing area and drag towards the carbon until both elements are connected and have a bond connecting them.
Repeat this step for the second oxygen atom. , A CO2 molecule has a double bond, and to change the bonds, just click on the Bond Order drop down menu and choose "Double".
Then just click and drag between the elements that have the double bond between them.
In the CO2 case, click and drag from the oxygen to the carbon and the bonds will change from single to double. , This features conforms your molecule into the best molecular shape based on chemical properties of your model according to VSEPR theory.
Once you select that feature, the model will take the preferred and standard chemical structure, which is a linear. , To view important information about the molecule, from the "View" drop down menu, select "Properties" and then select "Molecule Properties..." This will give you weight of the molecule, dipole moment, and other important information that you would otherwise need to calculate to find. , This option will be more helpful with more complicated molecules where more elements are involved.
From the same menu as Step 10, select "Properties" and then select "Angle Properties" which will give you all the angles in degrees and give you the vertex.
This, however, will only be accurate if you made sure that you have optimized the geometry after finishing building the molecule. , You have now built a very simple molecule.
However, with this software, chemistry homework will be easy when you have all the information you need at your fingertips.
The most important thing to remember is to make sure that the geometry of your model is optimized to ensure that all the properties are accurate.
As you get more advanced, you can manipulate the molecules to add forces, have dipole moments, find the Van Der Waal interactions, and other cool chemical processes. -
Step 3: Pick a chemical molecule to model.
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Step 4: Pick your settings.
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Step 5: De-select the "Adjust Hydrogens" option.
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Step 6: In the element section
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Step 7: click the drop down menu and select Carbon.
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Step 8: Repeat the lsat step
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Step 9: but choose Oxygen from the menu.
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Step 10: Change "Bond Order".
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Step 11: From the extensions menu
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Step 12: select Optimize Geometry.
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Step 13: From the View menu
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Step 14: find the properties of the molecule.
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Step 15: From the View menu
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Step 16: find the angle properties.
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Step 17: That's it!
Detailed Guide
When downloading the program, just follow the regular downloading methods that are used on each computer's operating system (Macintosh or Windows).
You can download the software from https://sourceforge.net/projects/avogadro/files/latest/download.
After downloading, click and open the program.
It might take a minute or two to load, but do not worry or get frustrated and give it time. , For these instructions we'll start with something simple, a carbon dioxide molecule., In this program, you are allowed to pick the what you want to see on the model.
For example, if you want each element to be labeled in the molecule, select the "Label" option in the left hand side menu titled "Display Types".
Or, if you wanted the dipole moment to be displayed, select the "Dipole" option in the same menu.
However, always make sure that the "Ball and Stick" option is always selected so that your elements show up on the software. , The "Adjust Hydrogens" option adds hydrogens to any molecule added, and so it is not needed when making a Carbon dioxide molecule.
Also, it is better to always de-select this option because adding the hydrogens yourself gives you more control over the position and their order in the molecule as opposed to the software adding it by default. , This drop-down menu is the one we will be using to add any elements we need throughout this process.
Once you have selected carbon, click anywhere in the black drawing area for the element to show up. , Then click on the black drawing area and drag towards the carbon until both elements are connected and have a bond connecting them.
Repeat this step for the second oxygen atom. , A CO2 molecule has a double bond, and to change the bonds, just click on the Bond Order drop down menu and choose "Double".
Then just click and drag between the elements that have the double bond between them.
In the CO2 case, click and drag from the oxygen to the carbon and the bonds will change from single to double. , This features conforms your molecule into the best molecular shape based on chemical properties of your model according to VSEPR theory.
Once you select that feature, the model will take the preferred and standard chemical structure, which is a linear. , To view important information about the molecule, from the "View" drop down menu, select "Properties" and then select "Molecule Properties..." This will give you weight of the molecule, dipole moment, and other important information that you would otherwise need to calculate to find. , This option will be more helpful with more complicated molecules where more elements are involved.
From the same menu as Step 10, select "Properties" and then select "Angle Properties" which will give you all the angles in degrees and give you the vertex.
This, however, will only be accurate if you made sure that you have optimized the geometry after finishing building the molecule. , You have now built a very simple molecule.
However, with this software, chemistry homework will be easy when you have all the information you need at your fingertips.
The most important thing to remember is to make sure that the geometry of your model is optimized to ensure that all the properties are accurate.
As you get more advanced, you can manipulate the molecules to add forces, have dipole moments, find the Van Der Waal interactions, and other cool chemical processes.
About the Author
Brenda Cox
Enthusiastic about teaching creative arts techniques through clear, step-by-step guides.
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