This section reviews the features and functions available under the Setup menu. These include preparation of input for ab initio, and semi-empirical molecular orbital calculations, density functional calculations, as well as for molecular mechanics calculations, for evaluation of properties based on quantum chemical wavefunctions and for calculation of graphical surfaces and volumes for later display. Spartan's interface to Gaussian 94 is described. Finally, provision for storing and retrieving calculation and graphics selections is described.

Selection of Setup results in display of the following menu:

Lists

Ab Initio

Density Functional

Semi-Empirical

Mechanics

External

Properties

Surfaces

Volumes

Standard

Submit Ctrl+X

(Keystroke equivalents are given by the underlined letter in the menu entry).

The first entry in the Setup menu (Lists) allows selection of whether or not specific list operations (conformation searching, coordinate driving, and similarity analysis) are actually to be invoked upon execution. This entry is available only if one or more of these list operations has previously been requested (under the Build menu); otherwise Lists is dehighlighted.

Specification of input required for an ab initio molecular orbital calculation is by way of Ab Initio under the Setup menu. Similarly, the required input to specify a density functional calculation is constructed using Density Functional, a semi-empirical molecular orbital calculation using Semi-Empirical, and a molecular mechanics calculation using Mechanics. Electronic structure calculations may also be performed using the Gaussian 94 program by way of External.

The Setup menu also invokes dialogs needed to specify the calculation of properties based on quantum chemical wavefunctions (Properties), and for generation of isosurfaces and 2D slices derived from wavefunctions at either ab initio or density functional levels (including from Gaussian 94), or from semi-empirical levels for later display (Surfaces and Volumes). Finally, the Setup menu is also used to actually launch calculations for the appropriate wavefunctions and/or properties or graphical objects (Submit).

Specific settings for the selected calculation module and for the properties and graphics modules may be stored and later retrieved using Create and Apply, respectively, under Standard.

Selection of Lists under the Setup menu (available only if one or more list operations have previously been requested) results in display of the following dialog.

Conformer Search will be "on" if a conformer search has previously been requested (see Section 7.2), and Coordinate Driving will be "on" if coordinate driving has previously been requested (see Section 7.5). Only one of these may be "on", and in case both have previously been requested, only the last request will be recognized. The user can alter this by clicking on one of the entries from among the available choices: Conformer Search and Coordinate Driving. Clicking on Save exits the dialog with the appropriate selection activated; clicking on Cancel exits the dialog with no further action.

Ab Initio molecular orbital models, in particular Hartree-Fock models and second-order Møller Plesset perturbation models (MP2) for treatment of electron correlation, remain a mainstay in computational investigations, in particular for organic systems. Hartree-Fock models are extensively documented and are routinely applicable to molecules comprising twenty or more heavy (non-hydrogen) atoms, and MP2 methods to molecules containing up to approximately ten heavy atoms. This opens up a considerable part of organic chemistry to scrutiny.

Hartree-Fock models are "expensive" in that they scale (formally) as the fourth power of the number of basis functions used to describe the system. Although modern programs such as Spartan exhibit a much smaller limiting size dependence (at or below the third power of the total number of basis functions), applications to systems comprising more than fifty heavy atoms still represent a considerable challenge. This remains the domain for semi-empirical treatments, and perhaps as well for density functional models.

Hartree-Fock models generally provide a good account of equilibrium geometries of molecules incorporating main-group elements, and of the energetics of reactions in which there is no net bond making or bond breaking. On the other hand, Hartree-Fock models provide a poor account of the energetics of reactions which do involve bond making or breaking, for example, homolytic bond dissociation reactions, as well as absolute activation energies. In these cases, significant correlation effects are associated with a change in total number of electron pairs, and procedures such as MP2, which take explicit account of electron correlation, are required although density functional models, in particular, non-local density functional models, may provide a satisfactory alternative. Finally, Hartree-Fock models are unreliable in their description of the structures of transition metal inorganics and organometallics. Semi-empirical methods appear to show promise here, as do density functional models.

Selection of Ab Initio under the Setup menu results in display of the
following dialog.

This contains a number of boxes, pull-down menus and buttons which together direct input into Spartan's ab initio module.

1. Title

   Any text information fitting on a single line may be entered into the Title box. This will be reproduced in the text output file (accessible under Output in the Display menu; see Section 9.1).

2. Task

   Available tasks appear in a menu to the right of Task:

   Task:

   Single Point Energy Geometry Optimization Transition Structure

3. Theory

   Available ab initio levels appear in a menu to the right of Theory:

   Theory:

   HF UHF MP2 UMP2

   HF implies restricted Hartree-Fock theory for closed-shell molecules and unrestricted Hartree-Fock theory for open-shell molecules. Unrestricted Hartree-Fock theory may be desirable for calculations on singlet diradicals and related species, and can be "forced" by selecting UHF. In a similar way, MP2 implies restricted second-order Møller-Plesset theory for closed-shell molecules and unrestricted second-order Møller-Plesset theory for open-shell molecules. Open-shell Møller-Plesset theory can be "forced" by selecting UMP2.

4. Direct

   If checked, signifies use of direct (Hartree-Fock and second-order Møller-Plesset) methods. Except for very small molecules, ab initio jobs should always be carried out using direct methods.

5. Basis

   Available basis sets appear in a menu to the right of Basis:

   Basis:

   STO-3G 3-21G(*) 6-31G* 6-31G** 6-311G** Custom:

   3-21G(*) here refers to use of the 3-21G representation for first row, main-group elements as well as for transition metals, but use of the 3-21G(*) basis set for second-row and heavier main-group elements. Use of the 3-21G basis set without supplementary d functions on second-row and heavier main-group elements may be specified by entering "3-21G" in the box resulting from selection of Custom. This is not advised.

   Note that only a few of the more popular basis sets are included in the menu. Specification of other standard (built in) basis sets is accomplished by selection of Custom from the menu, followed by entering the appropriate basis set name in the box which will then appear. Available (built in) basis sets are enumerated below.

   Basis Set	Atoms by Available Basis Set
   STO-3G	H - Xe
   STO-3G*	H - Ar
   3-21G(*)	H - Xe, except He and Ne
   6-31G*, 6-31G**, 6-31G (nd,mp)	H - Ar, except He and Ne
   6-311G**, 6-311G (nd,mp)	H - Ne, except He

   Information regarding availability for the more commonly-used basis sets appears under Periodic Table in the Logo menu (see Section 3.6), and under Available Elements in the Help menu (see Section 10.10).

   Gaussian basis sets other than the standard representations stored internally may be employed by Spartan. Specification of the XBASIS keyword (see Options).

6. Total Charge

   Total molecular charge (an integer). The default value (0) may be changed.

7. Multiplicity

   Spin multiplicity. The default setting "singlet" may be changed either by clicking on t to the right of the box, and selecting instead "doublet" or "triplet" from the menu which appears, or by entering a numerical value into the box to the right of Multiplicity. Multiplicity is 1 for singlets, 2 for doublets, 3 for triplets, 4 for quartets, etc.

8. Frequencies

   If checked, signifies calculation of vibrational frequencies and corresponding normal modes of vibration. These are then available in the text output (Output under the Display menu Section 9.1) along with selected thermodynamic properties (entropies and free energies). Vibrational modes may be animated using Vibrations under the Display menu (see Section 9.6).

   Frequency evaluation requires calculation of the complete matrix of second derivatives of the energy with respect to coordinate displacements. Spartan's ab initio module accomplishes this by numerical differentiation of analytical first derivatives using symmetry coordinates. The procedure is very costly (especially for molecules without symmetry), and should only be performed when absolutely necessary, i.e., to calculate an infrared spectrum (see Section 9.6) or to verify that a transition state smoothly connects reactants and products (see Section 7.3).

9. Constraints

   If checked, signifies introduction of constraints on distances, angles and dihedral angles into geometry optimization, transition-state optimization, conformation searching and coordinate driving at ab initio levels. Does not apply to single-point energy calculations. See Sections 6.5 to 6.7 for information on constraining geometrical parameters.

10. Freeze

    If checked, signifies that the coordinates of any "frozen" atoms will not be moved during geometry optimization, transition state optimization or conformation search at ab initio levels. Does not apply to single-point energy calculations. See Section 6.4 for information of freezing atoms.

11. Converge

    If checked, invokes the following keyword (see discussion under Options below for complete explanation) used to assist convergence in the
    scf procedure.

    DAMP = 0.75

    Converge should normally be selected only in response to experiencing convergence difficulties.

12. Options

    The above features as well as many other options available to Spartan's ab initio module may be designated by way of keywords. These are directly entered into the Options box. A complete listing of keywords is provided below. These are divided into categories: run type, wavefunction, basis set, initial guess, SCF, optimization, properties, miscellaneous and printing, and control all aspects of the calculation. Keywords are either selected from existing menus or are entered directly as text. Keywords may be either single words or expressions. Keyword=N indicates an integer argument, keyword=C indicates a character argument, and keyword=F indicates a floating-point argument.

    Run Type
    OPT, OPT = C	Optimize the molecular geometry. OPT=NUMERICAL signified use of numerical rather than analytical gradients.
    TSOPT, TSOPT= C	Optimize a transition state geometry. TSOPT = NUMERICAL signifies use of numerical rather than analytical gradients.
    GRADIENT	Calculate the gradient of the energy with respect to geometrical distortions.

    Wavefunction (Default is Hartree-Fock, RHF for closed-shell molecules, UHF for open-shell molecules.)
    HF	Calculate Hartree-Fock energy (RHF for closed-shell molecules, UHF for open-shell molecules).
    RHF	Calculate RHF energy and wavefunction for singlet spin states.
    UHF	Calculate UHF energy and wavefunction for non-singlet spin states; can also be used for singlet states.
    MP2, MP2=C	Calculate the MP2 correction to the HF energy (RMP2 for closed-shell molecules, UMP2 for open-shell molecules). MP2 or MP2=FC invokes frozen core approximation which involves excitations from valence molecular orbitals only; MP2=FU involves excitations from all filled molecular orbitals.
    UMP2, UMP2=C	Calculate the MP2 correction to the HF energy for non singlet spin states; can also be used for singlet states. UMP2=FC and FU as described above.

    Basis Set
    STO-3G	Use STO-3G basis (possible extensions: * ).
    6-31G	Use 3-21G basis (possible extensions: +,++, (*), *).
    3-21G	Use 6-31G basis (possible extensions: +,++, *, **, (nd,mp)).
    6-311G	Use 6-311G basis (possible extensions: +, ++, *, **, (nd,mp)). Note: d shells are always pure with this basis.
    PURED	Use five spherical d functions instead of six Cartesian d functions.
    SONLY	Use the s function only of transition metal valence sp shells (STO-3G and 3-21G only).
    XBASIS	Input custom basis set. Basis functions for all different elements which comprise the molecule need to be input. Input is on an element-by-element basis and not on an atom-by-atom basis. Required input (free format) for each different element is as follows: (a) For each different atomic number, a single line containing the atomic symbol (character variable) and the number of shells which comprise the representation for that atomic number (integer variable). (b) For each shell (set of atomic orbitals of the same principal quantum number), the shell type (character variable s, p, sp or d) and the number of Gaussians which comprise the shell (integer variable). There is presently a limit of six Gaussians per shell. (c) For each Gaussian, the exponent and s, p and d coefficients (floating point variables). Elements follow each other in any order, the mnemonic ENDBAS is used to signify the end of input. The table below provides an example of input of a general basis set. Text enclosed by "[ ]" are comments and are not included in the input.

    Methyl Flouride

    C 3 [carbon, 3 shells] S 3 [s shell with 3 gaussians] 1.722560E+02 6.176690E-02 2.591090E+01 3.587940E-01 5.533350E+00 7.007130E-01 SP 2 [sp shell with 2 gaussians] 3.664980E+00 -3.958970E-01 2.364550E-01 7.705450E-01 1.215840E+00 8.606190E-01 SP 1 [sp shell with 1 gaussian] 1.958570E-01 1.000000E+00 1.000000E+00 H 2 [hydrogen, 2 shells] S 2 [s shell with 2 gaussians] 5.447178E+00 1.562850E-01 8.245472E-01 9.046910E-01 S 1 [s shell with 1 gaussian] 3.664980E+00 -3.958970E-01 2.364550E-01 F 3 [fluorine, 3 shells] S 3 [s shell with 3 gaussians] 4.138010E+02 5.854830E-02 6.224460E+01 3.493080E-01 1.343400E+01 7.096320E-01 SP 2 [sp shell with 2 gaussians] 9.777590E+00 -4.073270E-01 2.466800E-01 2.086170E+00 1.223140E+00 8.523210E-01 SP 1 [sp shell with 1 gaussian] 4.823830E-01 1.000000E+00 1.000000E+00 ENDBAS [indicates the end of general basis set input]

    Initial Guess
    GUESS=C	Initial guess for SCF. GUESS=SE, semi-empirical AM1 molecular orbital guess (default for molecules comprising first- and second-row elements only); GUESS=MNDO, MNDO semi-empirical molecular orbital guess (with d orbitals if appropriate); GUESS=PM3, PM3 semi-empirical molecular orbital guess; GUESS=HUCKEL, HUCKEL molecular orbital guess (STO-3G basis set only); GUESS=CORE, core Hamiltonian guess; GUESS=READ, read wavefunction guess from archive; GUESS=ALL, provide initial guess (one of the types specified above) at each cycle in an optimization.
    EXCHANGE, EXCHANGE=C	Exchanges the HOMO and LUMO (default a orbitals only): A only a HOMO and LUMO are exchanged B only b HOMO and LUMO are exchanged AB both a and b orbitals exchanged
    MIX	Specifies that the a and b HOMO's in the guess wavefunction should be constructed according to, HOMOa = ____HOMO+LUMO_____ (Square root of 2) HOMOb = ____HOMO-LUMO_____ (Square root of 2) This is useful in generating a guess wavefunction for singlet diradicals, or in cases where the degeneracy in HOMOa and HOMOb needs to be broken.

    SCF
    DIRECTSCF, DIRECT	Direct HF and MP2 energies; direct HF gradients only.
    MEMORY=N	Requests N mbytes of additional memory for the direct MP2 (default=16 mbytes). The more memory available, the more electrons can be correlated per pass and the quicker the job.
    MAXCYCLE=N	Set maximum number of SCF iterations to be N (default N = 50).
    CONVERGE=F	Set SCF density convergence criterion (rms change in the density matrix) to be F (default F = 1.0E-06 for single point energy calculations and 1.0E-08 for geometry and transition structure optimizations).
    ENERGY=F	Set SCF energy convergence criterion to be F (default =1.0E-5 for single point energy calculations, 1.0E-7 for geometry and transition-state optimizations and 1.0E-10 for frequency calculations). Normally used for direct SCF only.
    ENERGY=F	Set SCF energy convergence criterion to be F (default =1.0E-5 for single point energy calculations, 1.0E-7 for geometry and transition-state optimizations and 1.0E-10 for frequency calculations). Normally used for direct SCF only.
    DAMP=F	Set SCF damping factor to be F (P' = (1-F)*P+F*Pold), (default F=0.5 for GUESS=CORE and 0.00 (no damping) for all other initial guesses). Damping is turned off once the density matrix has converged to .005.
    NODAMP	Turn off SCF damping, i.e., set F = 0.0.
    NODIIS	Turn off the use of Pulay's DIIS convergence accelerator. By default, DIIS is used.
    DIIS=N	Switch on DIIS all the time. N is the size of the iterative subspace; it should be an integer between 2 and 10 (default=5).

    Optimization
    OPTCYCLE=N	Set maximum number of geometry or transition-state optimization cycles to be N (default=20 + number of independent geometrical parameters for geometry optimization and 18 + 3* number of independent geometrical parameters for transition-state optimization).
    TOLG=F	Set convergence criterion for the max gradient component to be F (in a.u.) (default = 1.0E-04 a.u.).
    TOLBOND=F	Set convergence criterion for the max change in a bond length. This option is also used to establish maximum displacements in Cartesian optimizations (default=0.0003Å).
    TOLANG=F	Similar to TOLBOND except for bond angles (default=0.05°).
    TOLDIH=F	Similar to TOLBOND except for dihedral angles (default=0.05°).
    TOLE=F	Set convergence on energy to F. This criterion will override all other convergence criteria provided that the RMS gradient is below TOLG.
    MAXSTEP=F	Longest step that the optimization can make in a single cycle. Step size is measured as a distance in parameter space where bond lengths are given in a.u. and angles in radians (default=0.3).
    GDIIS=F, GDIIS=C	Use DIIS procedure for geometry and transition state optimizations. GDIIS will be switched on when the RMS gradient (in a.u.) falls below F (default=0.1). GDIIS=ALL, use DIIS procedure for all iterations.
    HESS=C	Guess at Hessian in geometry optimization. HESS=UNIT, Hessian is unit matrix; HESS=SYBYL, Hessian from SYBYL force field; HESS=MMFF, Hessian from MMFF force field; HESS=ARCH, read Hessian from archive file; HESS=SE or HESS=AM1, Hessian from AM1 calculation; HESS=MNDO, Hessian from MNDO calculation (with d orbitals if appropriate); HESS=PM3, Hessian from PM3 calculation.
    EIGMIN=F	Sets minimum value allowed for magnitude of Hessian eigen-values during optimization (default=0.0001). This option attempts to limit motion in floppy molecules.
    PREOPT=C	Preoptimizes geometry before commencing geometry optimization. PREOPT=SYBYL, use SYBYL force field; PREOPT=MMFF, use MMFF force field (reverts to SYBYL if MMFF not available); PREOPT=MNDO, use MNDO (with d orbitals if appropriate); PREOPT=AM1, use AM1; PREOPT=PM3.
    STEP=C	C=LINE, do a line search during a minimization if the energy rises; C=REDUCE, reduce the stepsize during a TS optimization if the energy change is the opposite sign to that predicted before the step is taken. Neither of the above are available for MP2 optimizations using analytical gradients.
    CONSTRAIN	Constrained optimization in Cartesian coordinates (applies also to conformation search).
    MODE=N	Follow mode N in a transition structure optimization.
    PARTIAL	Carry out optimization with some atoms frozen.

    Properties
    FREQ=C	Calculate frequencies by numerical differentiation of analytical gradients. Default is use of central differences (FREQ=CD). FREQ=FD, use forward instead of central differences (reduces time by approximately 50% but is less accurate). The step size is 0.005 au for central differences and 0.0025 au for forward differences.
    FD=F	Sets step size for numerical differentiation (default=0.005 au for central differences and 0.0025 au for backward differences).
    MP2DEN	Write the MP2 density correction to the archive file (currently available for in-core MP2 only).
    Miscellaneous
    NOSYMTRY	Do not use molecular symmetry to speed up the calculation. (By default, molecular symmetry is used to the maximum extent possible. The Dacre-Elder method is used to reduce integral computation. For most point groups, Fock matrix diagonalization is assisted by transforming to a symmetry orbital basis). For MP2 calculations, the Dacre-Elder method cannot be used, so unique integrals are directly transformed into the full set using the point group operations of Abelian subgroups.
    ABEL	Limits symmetry to that of Abelian point groups. This option is automatically enabled for MP2 calculations.
    NOMOVE	Do not reorient coordinates (to center of mass and along symmetry axes, etc.). The use of this option forces elimination of the use of symmetry (sets NOSYMTRY).
    UNITS=C	Geometry is given in atomic units (UNITS=AU) or Ångstroms (UNITS=ANG, default). Ordinarily, this keyword would be used in conjunction with Cartesian input of the molecular geometry.
    CHECK	Processes job input only. This option is intended to be used to check job input (geometry, symmetry, size of basis set, etc.).
    NOARC	Suppresses writing of an archive file.
    LST	Estimate initial transition structure using linear synchronous transit.
    QST	Estimate initial transition structure using quadratic synchronous transit.
    ACCEPT	Accepts archive with different symmetry than current molecule.

    Printing
    PRINTMO	Print molecular orbital energies and coefficients.
    PRINTLEV=N	Set the print level: N = 1 default N = 2 verbose N = 3 debug

13. Start Using

    Spartan allows an ab initio calculation to be preceded by calculation of equilibrium geometry using either molecular mechanics or semi-empirical molecular orbital methods without the user having to deal with the intermediate result. Geometry choices are given in a menu to the right of Geometry:

    Geometry:

    Sybyl Merck MNDO AM1 PM3

    The level of theory selected will correspond to the geometry input to the ab initio calculation. At the present time, this feature applies only to equilibrium geometry (and not transition-state geometry) calculations.

14. Restart Using

    This permits use of a Hessian and/or wavefunction from a previous calculation as initial input to the present calculation. There are two important uses:

    1. To restart a calculation which has not converged either in the SCF or in the optimization of equilibrium or transition-state geometry. In the former case, the wavefunction from the previous (non-converged) calculation may be input, while in the latter the Hessian from the previous calculation (and perhaps as well the wavefunction) may be used.

    2. To provide a starting guess either at the wavefunction and/or Hessian (as well as the geometry) for a calculation at a higher level of theory on the basis of a previous calculation at a lower level of theory. The most common case will be use of the wavefunction and/or the Hessian resulting from a semi-empirical calculation of equilibrium or transition-state geometry to initiate an ab initio calculation. Such a tactic will often lead to significant overall time savings.

    In both of the above scenarios, the "restart" feature operates using the archive file produced by the previous calculation. In this regard, access to previous information is predicated on it actually being in the archive. If it is not, then the appropriate restart switch will be deactivated. In practice, restart of a job following initial execution which has not successfully completed is accomplished by reentering the Ab Initio dialog and switching on Restart Hessian and/or Restart Wavefunction as appropriate, followed by resubmitting the job (Submit under the Setup menu, see Section 8.10). Use of information from one calculation (at a low level of theory) to another (at a higher level) is accomplished in a similar manner (following successful completion of the initial "low level" calculation) by adjusting the parameters in the Ab Initio dialog to reflect the desired "high-level" calculation (or by entering it for the first time in the case that the initial calculation was performed at a semi-empirical level), switching on Restart Hessian, and/or Restart Wavefunction as appropriate and then resubmitting the job.

If the present molecule is a member of a list, Global appears in the top right-hand corner of the dialog. Turned "on", this indicates that setup operations are to be applied to all members of the list; turned "off", the operations apply only to the present molecule.

The Ab Initio dialog may be exited either by clicking on either Save or Save As. (These buttons will be deactivated (dehighlighted) if the job is already executing.) Exit from the dialog by clicking on Save overwrites any previous information whether or not any changes or additions were made. If the prior information is to be kept, click instead on Save As, which will create a copy under a new name (and not alter the original). The user is presented with a file browser identical to that described under Save As in the File menu (see Section 4.5). After a name has been supplied, clicking on Save saves the information and exits the dialog. The file on screen is renamed and the original file is closed. Clicking on Cancel exits the dialog without saving the file.

Clicking on Cancel (in the Ab Initio dialog), exits the dialog without saving any information.

         params.MNDO       MNDO parameters
         params.AM1        AM1 parameters
         params.PM3        PM3 parameters
         params.MNDOD      MNDO/d parameters
         params.PM3D       PM3(tm) parameters