Prerequisites: GL (if possible, z buffer) or X11 (X window),
licence.
Information:
Online (menu Help); printed and online:
Manual (Spartan User's Guide),
Tutorial.
Start: spartan5 {$\hookleftarrow$},
Possible option at X terminals (slow!): spartan5 -x11autoshade {$\hookleftarrow$}.
theory: HF, UHF, MP2, UMP2
basis: STO-3G, 3-21G(*), 6-31G*, 6-31G**, 6-311G**, Custom
theory: SVWN (Local Spin Density Approximation),
BP (Becke-Perdew), pBP
basis: DN, DN*, DN**
MNDO, MNDO/d, AM1, PM3, PM3(tm)
Merck Molecular Force Field (MMFF), Sybyl (Allinger's MM2 and MM3 are no longer offered in version 5.0)
About Spartan: version number, copyright
Colors: colors for screen background and models
(e.g. .7,.7,.7)
Preferences: display modes (perspective, tumble, box,
...)
Print Setup: printer setup (selection and characteristics of
printers for the output of pictures or text, optionally as
PostScript or RGB file)
Monitor: job control
Periodic Table: availability of quantum-chemical methods
for the elements
Calculator: pocket calculator
New: construction of a new molecule with the model builder
Open: opens a new file
Close: closes the current file
Save: saves the molecule as shown on screen
Save As: saves the file with a new name
Merge As: merges two or more molecules
Group As
Delete: deletes a molecule
Import: reads a file in an external format
-- (Sybyl MOL, Sybyl MOL2, MacroModel, PDB)
Export: saves a molecule in an external file format
-- (Sybyl MOL, Sybyl MOL2, MacroModel, PDB)
Print
Quit: terminates spartan
Wire: wireframe model
Ball and Wire: ball-and-wire model
Tube: cylinder (tube) model
Ball and Spoke: ball-and-stick (spoke) model
Space Filling: CPK model
Hide: hides the model
Hydrogens: hydrogen atoms are shown if checked
Labels: display of atom symbols
Edit Labels
Box: draws a box around the molecule
Distance: measurement of distances between atoms
(also distance from a plane)
Angle: measurement of bond angles
Dihedral: measurement of dihedral angles
Freeze Center: freeze a center (in minimization)
Constrain Distance: set a distance (in minimization)
Constrain Angle: set an angle (in minimization)
Constrain Dihedral: set a dihedral angle (in minimization)
Define Point: definition of a central point
Define Plane: definition of a plane
Surface Area: output of the surface area of the space-filling
model in Å2
Volume output of the volume area of the space-filling
model in Å3
Report Symmetry: show the point group
Edit Structure: modify the structure by means of the molecule editor
Conformer Search: (setup or display, respectively)
Transition Search: generates an intermediate from reactant und product
Vibration Sequence: generates a sequence of pictures from a vibration
Coordinate Driving: variation of a distance, an angle or
a dihedral angle
Combinatorial Study: construction of a series of substituted
molecules from a parent compound
Isotopes: isotopic labeling
Lists: Conformer Search, Coordinate Driving
Ab Initio: dialogue for ab-initio calculations
Density Functional: dialogue for density functional (DFT) calculations
Semi-Empirical: dialogue for semi-empirical calculations
Mechanics: dialogue for force-field calculations
External: Gaussian 94
Properties: (orbitals, frequencies, charges)
Surfaces: (electron densities, HOMO, LUMO, spin)
Volumes: volume representations
Standard
Submit: submit a job for execution
Output: text output of a calculation
Properties: total energy (in Hartree, kcal/mol or kJ/mol),
dipol moment, energy HOMO/LUMO, molecular weight, charges, surfaces
Surfaces: display of surfaces
Slices: (Create, Edit, Delete) 2D slices from a 3D volume
Isosurfaces: (Create, Edit, Delete) isosurfaces
from a 3D volume
Vibrations: animation of normal-mode vibrations
Use of the Mouse
Keystroke Equivalents shortcuts for entering commands from the keyboard
Ab Initio Options
Density Functional Options
Semi-Empirical Options
Mechanics Options
Properties Options
Graphics Options
Conformer Search Options
Available Elements (restrictions)
"File Import/File Export": Alchemy MOL or MDL MOL are not implemented
"Save [As]" creates a new subdirectory
display quality: on systems with limited
graphics capabilities (such as X terminals), first a sketchy
outline drawing is shown, unless spartan was started with the option
"-x11autoshade". A better graphics quality
can be obtained by pressing the key "1".
Pressing the key "3" (on SGI workstations!) yields a
3D representation (color coding red/blue).
On SGI workstations also the option blur
may be available, provided that spartan had been started
as follows: spartan5 -blur; pressing the key "2"
then yields a particularly attractive presentation.
About Spartan: version number, copyright
Colors: colors for screen background and models
Preferences: display modes (perspective, tumble, box)
Save: saves the molecule
Save As: saves the file with a new name
Quit: terminates the molecule editor, optionally with saving
Undo / Redo
Add: add a fragment to a free valence
New: place a new fragment separately
Bond: make a bond
Break: break a bond
Delete: delete atoms
Minimize: geometry optimization by means of a force-field calculation
Move: shift or rotate fragments
Clear: delete a molecule from screen
Wire
Ball and Wire
Labels
Distance: measurement of distances between atoms
Angle: measurement of bond angles
Dihedral: measurement of dihedral angles
Freeze Center: freeze a center (in minimization)
Constrain Distance: set a distance (in minimization)
Constrain Angle: set an angle (in minimization)
Constrain Dihedral: set a dihedral angle (in minimization)
Define Ligand Point
Define Point: define a central point
Define Plane: define a plane
Report Symmetry: display a point group
left mouse button for selections (menus, atoms, bonds)
middle mouse button [+Shift] for rotations
right mouse button [+Shift] for shifting (translations)/zooming (resizing)
In the molecule editor, fragments can be rotated about a selected bond (dashed; if necessary, first click with the left mouse button) by pressing the space bar and the middle mouse button simultaneously and moving the mouse pointer up or down.
| keyboard | left mouse button | middle mouse button | right mouse button |
|
| |||
| - | selection | xy rotation | xy translation |
| shift | - | z rotation | zoom |
| space bar | - | rotation about a bond | - |
| (only in builder) | |||
| + control | - | global rotation | global translation |
The molecule editor works similarly to a molecule construction set. Building blocks are atoms with appropriate hybridization, functional groups or rings, as well as fragments from a library. After selecting an atom (or a larger building block) in the Fragment Panel, click into the main window. Connection to a fragment is achieved by clicking a free valence, which is the tip of a yellow vector. Hydrogen atoms need not be added explicitly.
The bond which was formed last is shown dashed, it is activated. A fragment can be rotated about this bond by simultaneously pressing the space bar and the middle mouse button while moving the mouse up or down. An arbitrary bond can be selected by clicking with the left mouse button.
An atom can be replaced by another one (with the same hybridization) if the replacement atom is clicked in the Fragment Panel followed by a double click (with the left mouse button) at the atom to be replaced. Ring closures can be achieved by selecting "Bond" and then clicking the respective free valences. Analogously, double bonds can be introduced by clicking free valences at neighboring atoms.
In general it is a good idea to optimize the raw construction of the molecule by means of "Minimize". Here a force-field calculation according to the preselected model (Merck or Sybyl, see Preferences) is performed. For special purposes it is possible to make constraints, see the menu Geometry).
There are four variants of the molecule editor: Entry,
Expert, Peptide and Nucleotide,
furthermore, a library is available.
In the entry editor, valence rules have to be obeyed strictly,
but in the expert editor not, so that e.g. complicated organometallic
compounds can be built. In the peptide editor, the 20 proteinogenic
amino acids are available, which can be assembled easily
(Build Sequence) to form an 
helix or a
sheet. The nucleotide editor allows the construction of
DNA or RNA strands from the respective four bases.
Note: Bond types are meaningful only in force-field calculations but not in quantum-chemical calculations.
In the following a few applications of the program "spartan" are outlined. More detailed descriptions can be found in the printed tutorial.
LMB = left mouse button, MMB = middle mouse button.
Menu File New. Builder: atoms are specified by atom type and hybridization; click a tetrahedral carbon atom (LMB), click into the main window; click a linear carbon atom, then the tip of a free valence; click a linear nitrogen atom, then the tip of the free triple bond. Menu File Quit Yes, enter a name for the molecule. Rotations of the molecule (with MMB pressed), models (menu Model); X terminals: a better graphics quality can be achieved by pressing `1'.
Question: Where will a nucleophilic attack occur preferentially? The LUMO (Lowest Unoccupied Molecular Orbital) should give a clue.
Build the molecule (a rotation about the central single bond might be necessary: click, space bar+MMB). Setup Semi-Empirical, (Title,) Task Geometry Optimization, Model AM1, Solvent None (Charge 0, Multiplicity 1), Save.
LUMO surface: Setup, Surfaces, Surface LUMO, Property None, Resolution med, Add, Save; Setup Submit (localhost, Submit). When done: Display Surfaces, click selection, Display Surface, possibly select style, OK.
Alternatively: Surface density, Property LUMO; Submit. Display Surfaces, deactivate LUMO surface, activate new surface, Map Property (red: minimum, here zero, blue: maximum, here positive), possibly Legend On.
Setup Ab initio, Task Geometry Optimization, Theory HF, Basis 3-21G(*), activate "Frequencies", Save; Setup Submit (localhost, Submit). When done: Display Vibration, click a frequency, Display. 6 frequencies are to be assigned. (The calculated frequencies are systematically about 10% too high.)
In functional groups, the active free valence can be switched by clicking if necessary.
Pyridine: "Rings" phenyl, click into the main window, click N(aromatic), double-click a carbon atom.
Cyclohexene: "Rings" cyclohexyl, click into the main window, Bond, click the tips of the free valences at two neighboring carbon atoms, Minimize.
It is usually economical to pre-optimize the geometry by
means of a semi-empirical calculation. Wavefunction and
Hessian (for Geometry Optimization) can be reused by clicking
the respective button.
(Caution: t 
nbase4.)
Conversion of energy units: 1 Hartree = 627.5 kcal/mol (thermochemical calories).
MP2 takes electron correlation into account; MP4 does that even more rigorously, but is only available in Gaussian-94.
Setup Semi-Empirical, AM1 Geometry Optimization, Multiplicity 2.
Setup Surfaces: surface=spin; surface=density, property=spin;
surface=aHOMO (for spin!); Submit.
(Example: cis and trans cyclodecene.)
First the molecule is built as usual.
Build Conformer Search: double-click one of the single bonds (in an open-chain compound, it may be necessary to select several single bonds successively, but note that the total number of conformers increases multiplicatively), Method: Osawa, Quit, Save Yes. Setup Mechanics, Task Geometry Optimization, Force Field Merck, Save; Setup Submit (localhost, Submit). When the calculation has successfully terminated, a series of generated conformations is obtained.
First, build and optimize a (monomeric) molecule of acetic acid. Then put together two molecules in a reasonable arrangement and store with "Merge As", finally optimize the dimer (e.g., PM3, Solvent None or Solvent Water, respectively).
Preliminary remark: Transition states are saddle points on the energy hypersurface, i.e., they are minima with the exception of just one coordinate which characterizes the reaction pathway (like a pass in the mountains). For this reaction coordinate, a normal vibration with an imaginary frequency is obtained. Force-field calculations are completely unsuitable for the calculation of transition states, semi-empirical calculations usually give poor results because of their parameterization.
For the calculation of a transition state (or activated complex), it is first necessary to build a structure which can serve as a reasonable starting point. For that purpose, the following three strategies are at disposal: (1) one might start with an already known transition state of a closely related system; (2) one creates an "average" from reactant and product structures; (3) one makes an educated guess of the geometry by means of "chemical intuition".
Method "averaging" of reactant/product ("linear synchronous transition"): First the reactant and the product molecule are built. (Both must have the same number of atoms.) Then both molecules are brought on the screen. Click the reactant, select the menu Build Transition Search, click the product, make a pairwise assignment of the atoms, Edit Generate, Quit and Save. (Example: acetone, keto-enol tautomerism in the gas phase.)
Calculation of the transition state: Setup Ab Initio, Task Transition Structure, Theory HF, Basis STO-3G (it might be necessary to increase the limit for optimization cycles, Options: OPTCYCLE=..., e.g., OPTCYCLE=200), Save; Setup Properties Frequencies; Setup Submit. When done: Display Vibration; the imaginary frequency indicates the reaction pathway.
Method "Chemical Intuition": Starting from a similar structure (e.g. intermediate or product), the geometry is distorted (bond lengths, bond angles, dihedral angles) so that it resembles the assumed geometry of the transition state. For that purpose, restrictions are introduced in the Builder; menu Geometry Constrain Distance (or Angle, Dihedral, respectively); Minimize. (Example: Diels-Alder reaction. If necessary, atom positions can be frozen by "Freeze Center".)
Examples from the library:
Fragment_Library
reaction_archive
07_pericycleelectrocycliccyclobutene_to_butadiene_AM1
07_pericycleDiels-Aldercyclopentadiene+acrylonitrile_AM1
02_substitutionSN1-SN2SN2_CH3Cl+F_AM1
(charge: -1, nosymtry!)
Peptide with "Peptide" Builder, Build sequence, click the amino acids one after the other, finally fix the end groups (ionic or neutral).