The Extensions Menu is a catalog of computational plugins equipped with Avogadro. These plugins can interact with molecules, generate input file dialogs for quantum codes, and create molecule property dialogs.
Animation
Selecting “Animation” will open the animate trajectory dialog box shown below. From here you can load a file, view and edit the animation, as well as save the file in a PC compatible format.
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
Optimize Geometry
- The Avogadro Exam is designed for Grade 11 high school students in their first high school chemistry course. Topics include: structure of matter, bonding, reactions, solutions, and gases. The test includes a few probing and demanding questions on some of the main topics of high school chemistry. Avogadro Exam date: Thursday, May 20, 2021.
- Avogadro's gas law states the volume of a gas is proportional to the number of moles of gas present when the temperature and pressure are held constant. This example problem demonstrates how to use Avogadro's law to determine the volume of a gas when more gas is added to the system.
- Avogadro's number, 6.022. 10 23 is the number of things in one mole. The question indicates that there is 1 mole of H 2. Thus there are 6.022. 10 23 molecules of H 2. However the question is asking for the amount of atoms in 1 mole of H 2.
- Avogadro's number, 6.022. 10 23 is the number of things in one mole. The question indicates that there is 1 mole of H 2. Thus there are 6.022. 10 23 molecules of H 2. However the question is asking for the amount of atoms in 1 mole of H 2.
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“Optimize Geometry” provides a quick, realistic rendition of a molecule using molecular mechanics.
Molecular Mechanics
“Molecular Mechanics” allows you to edit the geometry optimization of a molecule, so that it best suits your purposes.
Setup Force Field…
A dialog box will open when “Setup Force Field…” is selected. This dialog box provides you with the ability to choose the type of force field, and algorithm that can best optimize your molecular parameters, and preferences.
Calculate Energy
“Calculate Energy” determines the amount of energy per the amount of material (kJ/mol), and displays this number in a pop up dialog box.
Conformer Search
“Conformer Search” is a way to easily search for conformers within a molecule (dialog box shown below). A more detailed outline on how to perform a conformer search is found in the “Optimizing Geometry” section of this manual. Avogadro only renders staggered conformations, and does not calculate ring conformers.
Constraints
“Constraints” is a way to ensure atom stability in various selections (dialog box depicted below). The constraints that can be applied to a molecule include Ignore Atom, Fix Atom, Fix Atom X, Fix Atom Y, Fix Atom Z, Distance, Angle, and Torsion Angle. A detailed outline on how to use the constraints feature is found in the “Optimizing Geometry” section of this manual.
Ignore Selection
“Ignore Selection” allows you to select a specific part of a molecule to omit during a geometry optimization.
Fix Selected Atoms
“Fix Selected Atoms” also allows you to set a certain part of a molecule to fix during optimization.
Avogadro Extensions–Plugins
Avogadro's Number Example Problems
Avogadro provides you with the ability to interface your molecules with other dialog based plugins. These extensions interact with a molecule to provide further molecular information, and additional computation abilities. These plugins include but aren’t limited to GAMESS, Abinit, Dalton, GAMESS-UK, Gaussian, MOLPRO, MOPAC, NWChem, PSI4, Q-Chem, and LAMMPS.
General “How To” for Plugins
Avogadro (as you will see below) can be used to display molecular orbitals, QTAIM, spectra, as well as create surfaces. However, many of these features can not be used to their full potential without first running one of the plugins listed in the section above. Gaussian is one of the most common plugins used, due to it’s wide range of basis sets/functions.
Running Gaussian
After selecting “Gaussian” from the Extensions menu, the dialog box depicted below will appear. You can edit the dialog box and add specific keywords to utilize these features in Avogadro. For example, typing “freq” in the dialog box will compute force constants and vibrational frequencies. More information on keywords for Gaussian can be found at the Gaussian website (http://www.gaussian.com/g_tech/g_ur/l_keywords09.htm). Then clicking generate will let you save the file to your computer, so you can run the file in external software.
Once the file has been run through the external software, you will have a .g03 or .g09 file that will open the keyword selection in a toolbar on the right hand side of the screen. “Freq” will open the vibrations toolbar shown below.
Molecular Orbitals
The “Molecular Orbitals” selection will display the molecular orbitals for orbitals with full status bars. The quality of the orbitals can be adjusted an reconfigured if need be. This feature only works by running gaussian extension files (.fchk, .g03, .g09, etc.).
QTAIM (Quantum Theory of Atoms in Molecules)
QTAIM displays the implicit bonding that is theorized to take place between the hydrogens of organic crystals (the implicit bonding is conveyed through dots). This display type is utilized by importing a .wfn file from the “QTAIM”, “Molecular Graph” selection under the “Extensions” menu. Selecting “Molecular Graph with Lone Pairs” or “Atomic Charge” will provide concurrent information about the molecule. More information can be found on this process in the Tutorial section of this manual.
Spectra…
Clicking on “Spectra…” will create a spectra visualization of a .g03, or .g09 file that has been run with the keyword “freq”. A spectral visualization can also be created through the vibrations toolbar by selecting “Show Spectra…”.
Create Surfaces…
“Create Surfaces…” allows you to view the Van der Waals, Electrostatic Potential, Electron Density, and Molecular Orbital Surfaces. The surface type options for viewing depend on what type of calculations have previously been run on the molecule. The type of file you open/create allows for more or less surface viewing options (generally discussed under Avogadro Extensions–Plugins). This feature also allows you to edit the color, resolution, and iso value to further enhance your surface.
Avogadro is a “molecular editor,” designed to be easy to use to construct and view molecules and materials in 3D. It runs on Windows, Linux, and Mac.
This manual was largely made on a Mac, but the interface should be very similar on any computer.
When you initially open Avogadro you will be presented with a screen such as the one shown below.
Opening a File
The first thing you will probably want to do is open a file and navigate around the molecule. To do this click on the File menu and select Open....
You can then look through the files on your disk and find an appropriate chemical file. Thanks to Open Babel, a large number of file types are supported including CML, XYZ, SDF, Mol2, PDB etc. Several example molecules are supplied with Avogadro.
The screen shot above shows the ethanol.cml file opened up and displayed using the default Ball and Stick display type. Notice that when a new file is opened Avogadro switches from the Draw Tool to the Navigate Tool, which allows you to view the molecule without editing it.
Navigation
Avogadro Constant Example
You can zoom in/out using the scroll wheel on your mouse or holding down the middle mouse button and moving the mouse cursor up/down. You can rotate the view by holding down the left mouse button and moving the mouse cursor. You can also translate the view by holding down the right mouse button and moving the mouse cursor.
Avogadro Exam
Note: if your mouse only has one or two buttons you can also use the modifier keys (shift and control) along with the left mouse button to perform actions where you would normally use the middle or right mouse buttons respectively.