How to run Spartan

Spartan is a commercial software from Wavefunction, Inc. (http://www.wavefun.com).
It contains a number of quantum chemical and molecular mechanical methods together with a user-friendly graphical interface.

There are two different versions of this program, which are quite different and are described separately.

• Spartan Pro 1.0.6 for PC (at computer room Centrum)
• Spartan 5.0 for IRIX (at the department; only on tjaste, user id sgibio; bio password)

Manuals (books) are available at the department and in the computer room.

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PC Spartan Pro 1.0.6 on Windows

 Getting started and building structures

1. Start Spartan by pointing at the Start button - Departments - MNF - Spartan
2. Wait for the Spartan screen to appear.
3. Select `New' under the pull-down menu `File' to invoke the "Builder screen". Build your molecule using the mouse. All unfilled bonds are assumed to end with a hydrogen atom. With Expert, you get the full periodic table and more geometries.
4. Save your molecule (under `File') when it is built under 'Up One Level' - 'My Computer' - 'nn on Lukemi\Usr\Stud'.
5. Orient the molecule using the mouse according to the table below and select the appearance you prefer under `Model'.

 

Keyboard	Left button	Right button
-	picking; X/Y rotate	X/Y translate
shift	Z rotate	scale up/down

1. Open the appropriate files, if necessary.
2. Orient the molecule.
3. Select `Calculations' under `Setup' and set desired values (Task, Method, Basis set, Charge, Multiplicity, etc.).  Also select the properties you want to compute (note that frequencies are expensive) and what you want to print.
4. Press the 'OK' button when you are finished.
5. Select `Surfaces' under `Setup'. Here you can select (`Add') to show the electron density, the occupied orbitals (counting down from the highest occupied molecular orbital, HOMO), or the unoccupied orbitals (counting up from the lowest unoccupied molecular orbital, LUMO). In addition, you can choose to map the electrostatic potential or any molecular orbital onto any surface (`Property'). You first select the `Surface', then the `Property', and then press the `OK' button. Several surfaces can be selected (more 'Add') before you close the menu with cross at the upper right corner.

Note that the normal density (isosurface of 0.002 e/au³) gives the size surface, whereas density (bond) (0.08 e/au³) gives the bond surface.
6. Submit the job by choosing `Submit' under `Setup'. A small window appears to confirm that you have submitted the job (you must press OK before the job starts) and another one appears when the calculation has completed.

• Select `Measure Distance' under `Geometry', and click on two atoms (or a bond) to get the distance (there is also a botton shortcut for this). Similarly, you can get other geometry data (Measure Angle and Dihedral). You deselect an atom by clicking on it again. You can change an angle by writing in a new value in the distance box and then hit return.
• Select `Properties' under `Display'. Note that the result of this depens on what you have selected (a molecule, an atom, a bond, a surface, a constraint, etc.). Note that if you write down the energy in au (atomic units), you will need five decimals.
• 'Display' `Vibrations' will allow you to see the frequencies and to animate the corresponding vibrations. The animation is stopped by deselecting the vibration.
• The selected surfaces can be visualised by selecting `Surface' under `Display'. Click on the desired surface  You must turn off old surfaces before visualising a new one, otherwise you will see two surfaces at the same time. You can change the surface properties (e.g. the iso-level by selecting the surface and then select t'Display' - 'Properties').

• Energy: Mark the molecule and select properties.
• Solvation energy: Mark the molecule and select properties; look for the enetry Energy(aq) or Energy + SM5.4/P. You have to check the E. solvation box in the calculations dialog.
• Homo energy: Mark the molecule and select properties
• Lumo energy: Mark the molecule and select properties.
• Dipole moment: Mark the molecule and select properties.
• Volume: Mark the molecule and select properties.
• Area: Mark the molecule and select properties.
• Mulliken and ESP charges: Select an atom and select properties. To get the ESP charges, you have to check the Elect. Charges box in the Calculations dialog. If you also check the Atomic Charges box, you will get a list of all ESP charges in the output (Display). Likewise you will get a list of the Mulliken and NPA (natural population analysis; similar to, but better than, Mulliken) charges in the output.
• Bond length: Select Measure Distance under Geometry or select the measure distance button.
• Angle: Select Measure Angle under Geometry or select the measure angle button.
• Dihedral (torsion) angle: Select Measure Dihedral under Geometry or select the measure dihedral button.
• Cpu time: Select Output under Display. Note that there are separate timings for the energy calculation / geometry optimisation / frequency calculation and the properties calculations (the first is most interesting).
• Zero-point energy: In the ouput (under Display), at the end of the print frequency section. It is written only if you check the Frequency and Thermodonamic correction boxes in the Calculations menu.
• Thermodynamic corrections: In the ouput (under Display), at the end of the frequency section. They are written only if you check the Frequency and Thermodonamic correction boxes in the Calculations dialog.
• Number of basis functions: In the output (under Display), almost at the beginning (typically ~12th line).
• Orbital coefficients: In the output (under Display) if the print orbitals & energies box in the Calculations dialog is checked.
• Orbital energies: In the output (under Display) if the print orbitals & energies box in the Calculations dialog is checked.
• Orbitals: Surfaces under Display, but you have to request them first with Add.
• Potential: Surfaces under Display, but you have to request them first with Add..
• Electron density: Surfaces under Display, but you have to request them first with Add..
• Spin density: Surfurces under Display, but you have to request them first with Add. It can also be found in output (if print orbitals & energies is checked).
• Chirality: Mark an atom and select properties. You can also select Configure Labbels under Model, select chirality and then select Labels (also under Model). Note that you will only see the labels if you have a ball and wire or a wire model (change it under Model).
• Frequencies: Vibrations under Display, but they have to be requested first by checking the Frequencies and Vibrational Modes in the Calculations dialog. You will see both the frequency and the symmetry of each vibration and you may animate each vibration by checking the box. A list of all frequencies and normal modes are also available in the Output (under Display). Note that there is a bug in the program so that the frequencies in Vibrations are not updated if you rerun the calculation - you have to close and open the file to get them updated.

1. Start with one reactant.
2. Select 'Reaction' under 'Build'.
3. Show the program how bonds (electrons) will move by clicking on bonds that will move (e.g. from a double bond to a C-O bond; then click first on the double bond and then on the C-O bond). An arrow will appear for each moved electron.
4. An atom may be moved by first clicking on the bond to be removed, the Shift-clicking on the atom to move, and finally on the atom that will receive the atom.
5. When all arrows are drawn, click on the double arrow box at the lower right corner of the window and you will see the guess for the transition structure.
6. When you are satisfied with the transition structure guess, select 'Calculations' under 'Setup'. First run a single-point energy calculation, computing 'Frequencies' and printing 'Vibrational modes'. Check that you get one single imaginary (negative) frequency and that it represent the desired reaction coordinate (animate it).
7. Then run the full optimisation of the transition state. Select 'Calculations' under 'Setup', and choose to 'Calculate' 'Transition State Geometry'. It is always good to Compute 'Frequencies' and Print 'Vibrational modes'. Now, you probably also want to Print 'Thermodynamics'. Again, check that you get one single imaginary (negative) frequency and that it represent the desired reaction coordinate (animate it).

Spredsheet

• To add a distance/angel/dihedral into the spredsheet:

Open Spreadsheet (under Display).
Select Measure Distance/Angle/Dihedral (under Geometry)
Select the atoms involved
Press the P button at the lower right corner of the window.
The distance/angle/dihedral will then automatically be included in the spreadsheet.

1. Select `Save As' under `File'.
2. Select Brookhaven (*.pdb) under 'Save as type'
3. Enter the file name.

Monitor running jobs

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Getting nice plots after energy profile calculations in Spartan on windows:

1. Choose "Display - Spreadsheet" in the menu
2. Add "E" column
3. Select a cell in the first empty column
4. Choose "Geometry - measure xxx" in the menu (where xxx is bond, angle or dihedral depending on the dynamic constraint you have used)
5. Select the constraint on the molecule
6. Click the "P" button in the bottom right corner of the screen.
7. If you have used a dihedral constraint select the dihedral column in the spreadsheet and click the "sort" button on the spreadsheet
8. Choose "Display - plots" in the menu
9. Choose x-axis "xxx as above" and y-axis "E"

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Fitting of plots in Spartan on Windows:

1. Make sure you are in view mode ("Build - view" in the menu)
2. Click on the y-axis label (most often "E kcal/mole")
3. Choose "Display - properties" in the menu
4. Choose Fit:Quadratic LSQ (or whatever you need)

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Spartan 5.0 for IRIX

This version is present on at one single computer, tjaste (SGI); user id sgibio; bio password.
At present only three builder sessions are allowed simultaneously.

You must run spartan -X11 on the linux machines.

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Getting started and building structures

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Start a job

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Coordinate driving

1. Select Coordinate driving under Build.
2. Select a bond, angle, or dihedral to constrain.
3. Select starting and final values, as well as step size
4. Possibly, select more coordinates
5. Select Save, SaveAs, or Quit under File
6. Select the method under Set up and use Coordinate Driving as the task.
7. Submit the job and wait until it has finished.
8. You can now plot the relative energies by selecting Column Add Rel. E and then Plot, Create.

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If you are using more programs than Spartan, you may need to transfer coordinates between these programs. Then, we must write the coordinates in a format that all programs can read. The format we will use is called PDB (Protein Data Bank), a format originally designed for protein X-ray crystallography data. It contains a number of fields that must be in certain columns in the file. However, we are only interested in two fields, the atom name (element) and the coordinates.

In order to import coordinates in PDB format into Spartan, you simply do the following.

To write coordinates in PDB format from Spartan, you do this.

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