Spartan Primer

Spartan Primer - Working with Spartan When you start...

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Working with Spartan When you start Spartan, the Spartan window appears. This is a standard Windows interface with menus, toolbars, and a working area. The File and Edit menus are standard windows menus. The other menus are unique to Spartan. Model : allows you to change the display of the molecule. Geometry : Used to measure angles and lengths and to constrain angles and lengths. Build : Add or remove atoms and bonds Setup : Choose calculation method and variations Display : Output from calculations, surfaces, animated vibrations Search : Transition states and tautomers The toolbar lists some of the more common menu items. If you hold the mouse over the toolbar item, a tooltip will appear to tell you what that tool does. Menus Toolbar Working area
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Let’s Build a Molecule Building a simple molecule is easy if you follow these steps: Click the new page icon. The builder window will appear. The standard window is the entry- level window with common atom types listed. Click on the atom type that you want. If we wanted to build ethane, we choose the sp 3 carbon. Click in the working area and you carbon will be deposited. Notice the four valences on the atom. We can attach other atoms or groups to these positions. To make ethane, click the sp 3 carbon again and click any of the valences. The molecule is built using standard bond angles and lengths. Click the minimize button and Spartan performs a quick energy minimization on the structure. The energy is given in the small window (the message window) that appears on the lower right of the screen. That’s it. Your simple molecule is finished. Save is if you want. Common atoms and hybridizations The highlighted carbon is an sp 3 carbon. Note the currently selected item is in the preview window. Common functional groups and rings to save you the trouble of creating them. Always check here first before building a complex molecule. Message window appears here
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Mousing Around In Spartan, the right mouse button typically moves the molecule while the left button rotates. The left button will rotate in the x-y directions; holding the SHIFT key and the left button rotates around the z-axis. To rotate around a bond, use ALT left button. Measuring Lengths and Angles Under the Geometry menu, choose measure distance . The energy window disappears and a distance window replaces it. Click on any two atoms; they do not have to be bonded. For example, the distance between a carbon and any hydrogen on an adjacent carbon is 2.15Å. Spartan uses Angstroms as the unit for length. 1 Å = 0.1 nm = 100 pm. Angles are measured by choosing three atoms or two bonds that define the angle. Under the Geometry menu, choose measure angle . Click any three atoms or two bonds. To select a bond, click in the center of the bond. Dihedral angles require four bonds or three atoms.
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Calculations To perform a calculation, choose Setup , Calculations and a new window will appear. You set the parameters for the calculation here. At this stage, we will not discuss everything in this
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This note was uploaded on 11/18/2011 for the course CHEM lab1 taught by Professor Tajik during the Spring '11 term at UC Irvine.

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Spartan Primer - Working with Spartan When you start...

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