This section reviews the features and functions available under the Setup
menu. These include preparation of input for ab initio, and semiempirical 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 
SemiEmpirical 
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 semiempirical molecular orbital calculation using
SemiEmpirical, 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
semiempirical 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.
Section 8.1: Lists
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.
Section 8.2: Ab Initio
Ab Initio molecular orbital models, in particular HartreeFock models and
secondorder Møller Plesset perturbation models (MP2) for treatment of
electron correlation, remain a mainstay in computational investigations, in particular
for organic systems. HartreeFock models are extensively documented and
are routinely applicable to molecules comprising twenty or more heavy
(nonhydrogen) atoms, and MP2 methods to molecules containing up to
approximately ten heavy atoms. This opens up a considerable part of organic chemistry to scrutiny.
HartreeFock 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 semiempirical
treatments, and perhaps as well for density functional models.
HartreeFock models generally provide a good account of equilibrium
geometries of molecules incorporating maingroup elements, and of the energetics
of reactions in which there is no net bond making or bond breaking. On the
other hand, HartreeFock 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, nonlocal density functional models, may provide a satisfactory
alternative. Finally, HartreeFock models are unreliable in their description of the
structures of transition metal inorganics and organometallics. Semiempirical
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, pulldown menus and buttons which
together direct input into Spartan's ab
initio module.
 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).
 Task
Available tasks appear in a menu to the right of
Task:
Task:

Single Point Energy
Geometry Optimization
Transition Structure
 
 Theory
Available ab initio levels appear in a menu to the right of
Theory:
HF implies restricted HartreeFock theory for closedshell molecules
and unrestricted HartreeFock theory for openshell molecules.
Unrestricted HartreeFock 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 secondorder MøllerPlesset theory
for closedshell molecules and unrestricted secondorder
MøllerPlesset theory for openshell molecules. Openshell MøllerPlesset theory
can be "forced" by selecting UMP2.
 Direct
If checked, signifies use of direct (HartreeFock and secondorder
MøllerPlesset) methods. Except for very small molecules,
ab initio jobs should always be carried out using direct methods.
 Basis
Available basis sets appear in a menu to the right of
Basis:
Basis:

STO3G
321G(*)
631G*
631G**
6311G**
Custom:
 
321G(*) here refers to use of the 321G representation for
first row, maingroup elements as well as for transition metals,
but use of the 321G(*) basis set for secondrow and heavier
maingroup elements. Use of the 321G basis set without
supplementary d functions on secondrow and heavier maingroup elements
may be specified by entering "321G" 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 
STO3G 
H  Xe 
STO3G* 
H  Ar 
321G(*) 
H  Xe, except He and Ne 
631G*, 631G**, 631G (nd,mp) 
H  Ar, except He and Ne 
6311G**, 6311G (nd,mp) 
H  Ne, except He 
Information regarding availability for the more commonlyused
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).
 Total Charge
Total molecular charge (an integer). The default value
(0) may be changed.
 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.
 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).
 Constraints
If checked, signifies introduction of constraints on distances, angles
and dihedral angles into geometry optimization, transitionstate
optimization, conformation searching and coordinate driving at
ab initio levels. Does not apply to singlepoint energy calculations. See
Sections 6.5 to 6.7 for information on constraining geometrical parameters.
 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
singlepoint energy calculations. See Section
6.4 for information of freezing atoms.
 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.
 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 floatingpoint 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 HartreeFock, RHF for
closedshell molecules, UHF for openshell molecules.)

HF 
Calculate HartreeFock energy (RHF for
closedshell molecules, UHF for openshell molecules). 
RHF 
Calculate RHF energy and wavefunction for
singlet spin states. 
UHF 
Calculate UHF energy and wavefunction for
nonsinglet spin states; can also be used for singlet states. 
MP2, MP2=C 
Calculate the MP2 correction to the HF energy
(RMP2 for closedshell molecules, UMP2 for openshell 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

STO3G 
Use STO3G basis (possible extensions: * ). 
631G 
Use 321G basis (possible extensions: +,++, (*), *). 
321G 
Use 631G basis (possible extensions: +,++, *, **, (nd,mp)). 
6311G 
Use 6311G 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 (STO3G and 321G only). 
XBASIS 
Input custom basis set. Basis functions for all
different elements which comprise the molecule need to be
input. Input is on an elementbyelement basis and not on
an atombyatom 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 6.176690E02
2.591090E+01 3.587940E01
5.533350E+00 7.007130E01
SP 2 [sp shell with 2 gaussians]
3.664980E+00 3.958970E01 2.364550E01
7.705450E01 1.215840E+00 8.606190E01
SP 1 [sp shell with 1 gaussian]
1.958570E01 1.000000E+00 1.000000E+00
H 2 [hydrogen, 2 shells]
S 2 [s shell with 2 gaussians]
5.447178E+00 1.562850E01
8.245472E01 9.046910E01
S 1 [s shell with 1 gaussian]
3.664980E+00 3.958970E01 2.364550E01
F 3 [fluorine, 3 shells]
S 3 [s shell with 3 gaussians]
4.138010E+02 5.854830E02
6.224460E+01 3.493080E01
1.343400E+01 7.096320E01
SP 2 [sp shell with 2 gaussians]
9.777590E+00 4.073270E01 2.466800E01
2.086170E+00 1.223140E+00 8.523210E01
SP 1 [sp shell with 1 gaussian]
4.823830E01 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, semiempirical
AM1 molecular orbital guess (default for molecules
comprising first and secondrow elements only);
GUESS=MNDO, MNDO semiempirical molecular orbital guess (with
d orbitals if appropriate); GUESS=PM3, PM3 semiempirical molecular orbital guess;
GUESS=HUCKEL, HUCKEL molecular orbital guess (STO3G 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 = ____HOMOLUMO_____
(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 = 1.0E06 for
single point energy calculations and 1.0E08 for geometry
and transition structure optimizations). 
ENERGY=F 
Set SCF energy convergence criterion to be F
(default =1.0E5 for single point energy calculations, 1.0E7
for geometry and transitionstate optimizations and 1.0E10
for frequency calculations). Normally used for direct SCF only. 
ENERGY=F 
Set SCF energy convergence criterion to be F
(default =1.0E5 for single point energy calculations, 1.0E7
for geometry and transitionstate optimizations and 1.0E10
for frequency calculations). Normally used for direct SCF only. 
DAMP=F 
Set SCF damping factor to be F (P' = (1F)*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
transitionstate optimization cycles to be N (default=20 +
number of independent geometrical parameters for
geometry optimization and 18 + 3* number of
independent geometrical parameters for transitionstate optimization). 
TOLG=F 
Set convergence criterion for the max gradient
component to be F (in a.u.) (default = 1.0E04 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 eigenvalues 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 incore 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 DacreElder
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 DacreElder 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


 Start Using
Spartan allows an ab initio calculation to be preceded by
calculation of equilibrium geometry using either molecular mechanics or
semiempirical 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:
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 transitionstate geometry) calculations.
 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:
 To restart a calculation which has not converged either in the SCF or
in the optimization of equilibrium or transitionstate geometry. In
the former case, the wavefunction from the previous
(nonconverged) calculation may be input, while in the latter the Hessian from the
previous calculation (and perhaps as well the wavefunction) may be used.
 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 semiempirical calculation of equilibrium
or transitionstate 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 "highlevel" calculation (or by entering it for the first time
in the case that the initial calculation was performed at a
semiempirical 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 righthand 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.
Section 8.3: Density Functional
Density functional theory represents an alternative to conventional
correlated methods for improved energy and property descriptions over that available
from HartreeFock models. Density functional methods (formally) scale as the
square of the number of basis functions times the number of points used for
numerical integration (which itself scales in proportion to the number of atoms). In
practice, even better scaling is observed for sufficiently large molecules. Thus,
density functional models should be superior computationally to HartreeFock
models (which scale as the fourth power of the number of basis functions). The
crossover point between HartreeFock and density functional models depends on
many factors, not least among them the program. For
Spartan's modules, it is typically around 5070 basis functions.
Density functional models require large underlying basis sets, including
functions with higher angular quantum number than occupied in the groundstate atom
(p functions on hydrogen and d functions on maingroup elements) in order
to achieve acceptable results. This is a property of correlated methods in
general, and is one of the factors which makes "equivalent" conventional
approaches, e.g., MP2, very expensive relative to HartreeFock schemes. Such a
requirement greatly favors a strict numerical implementation of density functional
methods, as opposed to an alternative implementation in which the HartreeFock
Coulomb contribution and (optionally) part of the exchange contribution is
utilized. Spartan's implementation is strictly numerical.
Density functional models provide a good account of equilibrium
geometries (assuming a large underlying basis set), both for compounds with
maingroup elements as well as for molecules incorporating transition metals. The latter
is especially important, because HartreeFock methods do not generally
provide reliable descriptions of the structures of transitionmetal inorganic
and organometallic systems.
Local density models are not successful in their description of reaction
energetics, except for processes which compare very similar "chemical environments".
This pattern of behavior is similar to that exhibited by HartreeFock models. On
the other hand, socalled nonlocal or gradient corrected density functional
models, such as the BeckePerdew model incorporated into
Spartan, have proven to be quite successful for a variety of energetic comparisons, including
comparisons in which bonds are broken or formed. Overall, these methods typically
yield energetic results of "MP2 quality" at a small fraction of the cost.
Selection of Density Functional under the
Setup menu results in display of the following dialog.
This contains a number of boxes, pulldown menus and buttons which
together direct input into Spartan's density functional
module.
 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).
 Task
Available tasks appear in a menu to the right of
Task :
Task:

Single Point Energy
Geometry Optimization
Transition Structure
 
 Theory
Available density functional levels appear in a menu to the right of Theory:
SVWN gives the local density model while BP and pBP provide
selfconsistent and perturbative implementations of the nonlocal
BeckePerdew model, respectively.
 Basis
Available basis sets appear in a menu to the right of
Basis:
The DN, DN* and DN** basis sets are roughly the same "size" as the
631G, 631G* and 631G** Gaussian basis sets, respectively.
However, because they are derived from "numerical" atomic solutions, they
are expected to be superior in "quality" to the corresponding Gaussian
basis sets. DN* and DN** representations which incorporate
polarization functions on heavy atoms only and on all atoms, respectively, are
likely to be more suitable for density functional calculations than the DN
basis set which does not incorporate such functions. DN, DN* and DN**
basis sets are available for the first 54 elements of the Periodic Table.
 Total Charge
Total molecular charge (an integer). The default value
(0) may be changed.
 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.
 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 density functional module does this numerically. As
frequency calculation is likely to be very costly, it 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).
 Constraints
If checked, signifies introduction of constraints on distances, angles
and dihedral angles into geometry optimization, transitionstate
optimization, conformation searching and coordinate driving at density
functional levels. Does not apply to singlepoint energy calculations. See
Sections 6.5 to 6.7 for information on constraining geometrical parameters.
 Freeze
If checked, signifies that the coordinates of any "frozen" atoms
will not be moved during geometry optimization,
transitionstate optimization or conformation search at density functional levels.
Does not apply to singlepoint energy calculations. See
Section 6.4 for information on freezing atoms.
 Options
The above features as well as many other options available to
Spartan's Density Functional 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, functional, basis set,
scf, initial guess, optimization, 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 floatingpoint argument.
Run Type

OPT 
Optimize the molecular geometry. 
TSOPT 
Optimize a transition state geometry. 
Functional

SVWN 
Use the local exchangecorrelation potential. 
BP 
Introduce nonlocal corrections according to the
method of Becke and Perdew in a selfconsistent manner. 
pBP 
Introduce nonlocal corrections according to the
method of Becke and Perdew in a perturbative manner. 
Basis Set

DN 
Use DN numerical splitvalence basis set. 
DN* 
Use DN* numerical polarization basis set. 
DN** 
Use DN** numerical polarization basis set;
polarization functions on all atoms. 
SCF

MAXCYCLE=N 
Set maximum number of SCF iterations to be N (default N=50). 
CONVERGE=F 
Set SCF density convergence criterion to be F (rms
change in the density matrix) (default F = 1.0E05 for single
point energy calculations and 1.0E06 for geometry
and transition structure optimizations). 
DAMP=F 
Set SCF damping factor to be F
(P'=(1F)*P+F*Pold) (default F=0.7). 
BADSTEPS=N 
Number of "bad" steps allowed in SCF procedure. 
Optimization

OPTCYCLE=N 
Set maximum number of geometry or
transitionstate optimization cycles to be N (default=20 + number
of independent geometrical parameters for geometry optimization and 18 + 3* number of
independent geometrical parameters for transitionstate optimization). 
TOLG=F 
Set convergence criterion for the max gradient
component to be F (in a.u.) (default=6.0E03 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= 0.001Å). Due to numerical uncertainties,
TOLBOND should not be set below 0.0005Å. 
TOLDIH=F 
Similar to TOLBOND except for dihedral
angles (default=0.05°). 
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). 
HESS=C 
Guess at Hessian in geometry and
transitionstate optimization. HESS=UNIT, Hessian is unit
matrix; HESS=ARCH, read Hessian from archive file. 
EIGMIN=F 
Sets minimum value allowed for magnitude of
Hessian eigenvalues during optimization (default=0.0001).
This option attempts to limit motion in floppy molecules. 
CONSTRAIN 
Constrained optimization in Cartesian coordinates
(applies also to conformation search). 
PARTIAL 
Carry out optimization with some atoms frozen. 
Miscellaneous

NOSYMTRY 
Do not use molecular symmetry to speed up the calculation. 
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. 
GRID=C 
Resolution of grid used in numerical integration. GRID=XF (extrafine)
(same as MESH=XF). 
MESH=C 
Resolution of mesh used in numerical integration.
 MESH=C (coarse).
 MESH=M (medium).
 MESH=F (fine) (default is fine).
 MESH=XF (extrafine) (same as GRID=XF).

NOARC 
Suppresses writing of an archive file. 
Printing

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



 Start Using
Spartan allows a density functional calculation to be preceded
by calculation of equilibrium geometry using either molecular
mechanics or semiempirical 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:
The level of theory selected will correspond to the geometry input to
the density functional calculation. At the present time, this feature applies
only to equilibrium geometry (and not transitionstate geometry calculation).
 Restart Using
This permits use of a Hessian and/or potential from a previous
calculation as initial output to the present calculation. This facility is analogous
to that already described for ab initio calculations and has similar uses.
In practice, restart of a job following initial execution which has
not successfully completed is accomplished by reentering the
Density Functional dialog and switching on
Restart Hessian and/or Restart
Potential as appropriate, followed by resubmitting the job
(Submit under the Setup menu, see following). Use of information from one
calculation (at a lower 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
Density Functional dialog to reflect dialog to reflect the desired "highlevel" calculation
(or by entering it for the first time in the case that the initial calculation
was performed at a semiempirical level), switching to
Restart Hessian and/or Restart
Potential as appropriate and then resubmitting the job.
If the present molecule is a member of a list, a
Global button appears in the top righthand 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 Density Functional dialog may be exited either by
clicking on Save or Save As. (These 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 Density Functional
dialog) exits the dialog without saving any information.
Section 8.4: SemiEmpirical
Semiempirical molecular orbital methods were originally formulated (in
the late 1960's and early 1970's) to allow routine applications to organic
chemistry. At the time only qualitative schemes such as extended Hückel theory
were available and HartreeFock models were limited by high cost to very
small systems. In the last two decades, and largely through the work of Dewar and
his coworkers, semiempirical techniques have evolved into a powerful
alternative to ab initio methods for computational organic chemistry, even though the
latter is now routinely applicable to fairly complex systems.
The favorable performance of presentgeneration semiempirical
models (MNDO, AM1 and PM3) with regard to organic structure determination is
well documented. Less well known is their generally poor performance for
the description of reaction energetics. Thus, semiempirical methods, rather
than looked at as "standalone" techniques, might better be positioned in the
important role of "structure getters", leaving the calculation of energetics and
other properties to ab initio and/or density functional techniques.
Recent additions to the semiempirical repertoire, and now implemented
inside Spartan, include the MNDO/d method of Thiel, and
transitionmetal parameterizations for use in conjunction with PM3. The former
offers slightly improved quality for molecules incorporating heavy maingroup elements,
while the latter provides the first consistent parameterization for transition metals,
and should now permit routine applications to inorganic and organometallic chemistry.
Selection of SemiEmpirical under the
Setup menu results in display of the following dialog.
This contains a number of boxes, pulldown menus and buttons which
together direct input into Spartan's SemiEmpirical
module.
 Title
Any text information fitting on single line may be input into the
Title box. This will be reproduced in the text output file (accessible
under Output in the Display menu see
Section 9.1).
 Task
Available tasks appear in a menu to the right of
Task:
Task:

Single Point Energy
Geometry Optimization
Transition Structure
 
 Model
Available semiempirical models are selected from a menu to the
right of Model:
Model:

MNDO
MNDO/d
AM1
PM3
PM3(tm)
 
At the present time, the following elements are supported for the
MNDO, MNDO/d, AM1, PM3 and PM3(tm) semiempirical models.
SemiEmpirical Model 
Atoms by Available Parameters 
MNDO 
H, LiF, Mg, SiCl, Zn, Ge, Br, Sn, Sb, Te, I. 
MNDO/d 
Si, P, S, Cl, Br, I (used in conjunction with MNDO for H and firstrow elements). 
AM1 
H, BF, AlCl, Zn, Ge, Se, Br, Sn, I. 
PM3 
H, LiF, MgCl, Ca, ZnBr, Cd, InI, Hg. 
PM3(tm)  Ti, Zr, Hf, Ta, Cr, Mo, W, Mn, Fe, Ru, Co,
Rh, Ni, Pd, Cu, Gd (used in conjunction
with PM3 for nontransition metals). 
Current information regarding availability of semiempirical
models appears under Periodic Table in the
Logo menu (see Section 3.6), and under
Available Elements in the Help menu (see
Section 10.10).
As semiempirical parameterizations are developed, in particular
for MNDO/d and PM3 (tm), they can easily be added to the existing
data files (see Section 8.4.1).
 Solvent
Semiempirical calculations can, if desired, be performed in the
presence of a static electric field representing a solvent. Available solvent
models appear in a menu to the right of
Solvent:
Solvent:

None
Water
Hexadecane
Water
 
Models available from this dialog include the
MNDOaq, AM1aq, PM3aq (Water) and MNDOhd,
AM1hd, PM3hd (Hexadecane) models for water and hexadecane, respectively, developed by Dixon, Leonard and
Hehre and based closely on the earlier SM2 model of Cramer and Truhlar
(for water only) which, along with the SM3 model, is also available
(Water (CT)). Specification of the former set is automatic (selecting
Water and AM1 will automatically provide the
AM1aq model), while the Cramer/Truhlar SM2 model applies to the AM1 method and the SM3 model
to the PM3 method. SM1 and SM1a models of Cramer and Truhlar are
also available, but need to be specified as options (see table below). At
the present time, only the AM1aq and the Cramer/Truhlar models are
available for ions, and the former only to protonated amine and carboxylic
acid functionality. Also, none of the solvation models are presently
available for openshell molecules.
Solvation 
Atoms by Available Parameters 
MNDOaq, AM1aq, PM3aq 
H, C, N, O, F, S, Cl, Br, NR3+ a, CO2 a 
MNDOhd, AM1hd, PM3hd 
H, C, N, O, F, S, Cl, Br 
SM1 
H, C, N, O, F, P, S, Cl, Br 
SM1a 
H, C, N, O, F, P, S, Cl, Br 
SM2 
H, C, N, O, F, P, S, Cl, Br 
SM3 
H, C, N, O, F, P, S, Cl, Br 

Current information regarding availability of semiempirical
models for solvated systems appears under Available
Elements in the Help menu (see Section
10.10).
 Total Charge
Total molecular charge (an integer). The default value
(0) may be changed.
 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.
 Frequencies
If checked, signifies calculation of vibrational frequencies
and corresponding normalmodes 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 semiempirical module does this numerically. As
frequency calculation is likely to be very costly, it should be performed only
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).
 Constraints
If checked, signifies introduction of constraints on distances, angles
and dihedral angles into geometry optimization, transition state
optimization and conformation searching at semiempirical levels. Does not apply
to singlepoint energy calculations. See Sections
6.5 to 6.7 for information on constraining geometrical parameters.
 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 semiempirical levels. Does not apply to
singlepoint energy calculations. See Section
6.4 for information on freezing atoms.
 Converge
If checked, invokes the following keywords (see discussion
under Options below for complete explanations) used to assist convergence
in the SCF procedure.
DAMP = 0.75 DIIS = 5 GUESS = CORE NOPSEUDO
Converge should normally be invoked only in response to
experiencing convergence difficulties. Experience suggests that aromatic and
other delocalized molecules, as well as transitionmetal inorganics
and organometallics, sometimes present convergence problems.
 Options
The above features as well as many other options available to
Spartan's semiempirical 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,
model, wavefunction, solvent, initial guess, SCF, optimization,
properties, configuration interaction, miscellaneous and printing, and control
all aspects of the electronic structure calculation. Keywords are
either selected from existing menus or are entered directly as text.
Keywords may either be single words or expressions. Keyword=N indicates
an integer argument, keyword = C indicates a character argument
and keyword = F indicates a floatingpoint argument.
Wherever possible, keywords for Spartan's
semiempirical module are the same as those providing analogous functions in the
ab initio module.
Run Type (Default is a singlepoint energy calculation)

OPT 
Optimize the molecular geometry. 
TSOPT 
Optimize a transition state geometry. 
GRADIENT 
Calculate the gradient of the energy with respect
to geometrical distortions. 
Model

MNDO 
MNDO semiempirical method. 
AM1 
AM1 semiempirical method 
PM3 
PM3 semiempirical method 
DFUNCTION 
MNDO becomes MNDO/d, PM3 becomes PM3(tm) 
MMOK 
Include the molecular mechanics amide correction
in semiempirical energy calculations 
HHON 
Turn on HH repulsions in PM3 (default for PM3
with transition metals). 
HHOFF 
Turn off HH repulsions in PM3. 
Wavefunction (Default is HartreeFock, RHF for closedshell
molecules, UHF for openshell molecules.)

HF 
Calculate HartreeFock energy (RHF for closedshell molecules, UHF for openshell molecules). 
RHF 
Calculate RHF energy and wavefunction for singlet spin states. 
UHF 
Calculate UHF energy and wavefunction for nonsinglet spin states; can also be used for single states. 
Solvent

SOLVENT=C 
SOLVENT=NONE, no solvent (default); 
SOLVENT=C 
SOLVENT=NONE, no solvent (default);
SOLVENT=AQ, MNDOaq, AM1aq, PM3aq models;
SOLVENT=HD, MNDOhd, AM1hd, PM3hd models;
SOLVENT=SM1, Cramer/Truhlar SM1 model;
SOLVENT=SM1A, Cramer/Truhlar SM1a model;
SOLVENT=SM2, Cramer/Truhlar SM2 model;
SOLVENT=SM3, Cramer/Truhlar SM3 model;
SOLVENT=SM54, Chambers/Hawkins/Cramer/Truhlar SM5.4 model. 
IONICGROUPS 
Looks for ionic groups for the purpose of
MNDOaq, AM1aq and PM3aq solvation models even though the molecule
is not charged. 
Initial Guess

GUESS=C 
GUESS=HUCKEL, HUCKEL molecular orbital
guess (default); GUESS=CORE, core Hamiltonian
guess; GUESS=READ, read from archive. GUESS=ALL, do
a Hückel guess at every optimization cycle. 
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 particularly useful in generating a
guess wavefunction for singlet diradicals, or in cases where
the degeneracy in HOMOa and HOMOb needs to be broken.

SCF

MAXCYCLE=N 
Set maximum number of SCF iterations to be N
(default N=200). 
CONVERGE=F 
Set SCF convergence criterion to be F (rms change in
the density matrix). Will only be used if requested. 
ENERGY=F 
Set SCF energy convergence (default F=1.0E5 for
single point energies; varies between 1.0E5 and 1.0E7
for optimizations, 1.0E10 for numerical frequencies). 
DAMP=F 
Set SCF damping factor to be F (P' = (1F)*P+F*Pold)
(default=0.5 for GUESS=CORE and 0.0 (no damping)
for all other initial guesses). Damping is gradually switched
off when the largest change in density matrix is below 0.01;
it is switched off entirely when largest change is below 0.005. 
NODAMP 
Turn off SCF damping, i.e., set F = 0. 
NODIIS 
Turn off DIIS. By default DIIS is used, but only if
the energy increases during the SCF procedure. 
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). 
NOPSEUDO 
Switch off pseudodiagonalization. By
default, pseudodiagonalization is switched on when the
largest change in the density matrix is below 0.01. 
LEVSHIFT=F 
Set level shift factor. Shifts energies of virtual orbitals
by F (default=0.0, i.e., no level shifting). Only switched
on if energy increases. 
GRADUAL 
Be less aggressive in turning off damping and
switching to pseudodiagonalization. This can help in cases of
poor SCF convergence. 
Optimization

NUMERICAL 
Eliminate default use of analytical gradients. 
OPTCYCLE=N 
Set maximum number of geometry or
transitionstate optimization cycles to be N (default=20 + number
of independent geometrical parameters for geometry optimization and 18 + 3* number of
independent geometrical parameters for transitionstate optimization). 
TOLG=F 
Set convergence criterion for the max gradient
component to be F (in a.u.) (default=1.0E04 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 (default=1.0E3 on the
heat of formation in kcal/mol). Note that the
energy convergence criterion will override all other
convergence criteria provided 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. 
GDIIS=F 
Use DIIS procedure for geometry and transition
state optimizations. GDIIS will be switched. 
NOGDIIS 
Turn of DIIS procedure in geometry and transition
state optimizations. 
MODE=N 
Follow mode N in a transition structure optimization. 
HESS=C 
Guess at Hessian in geometry optimization.
Hess=Unit, Hessian is unit matrix; HESS=SYBYL, Hessian
derived from SYBYL force field. 
EIGMIN=F 
Sets minimum value allowed for magnitude of
Hessian eigenvalues during optimization (default=0.0001).
This option attempts to limit motion in floppy molecules. 
PREOPT 
Preoptimizes geometry using SYBYL force field
before commencing geometry optimization. 
SEMIGRAD=F 
Set the step size, for the numerical gradient
during optimization (default=0.0005). 
GRADSCF 
Perform full SCF/CI calculation during gradient
calculation 
GRADSCF=F 
during geometry optimization. GRADSCF = HF, use
SCF (default), GRADSCF=CI, use SCF+CI. 
NOSUFF 
Prevent optimizations in solvent from terminating
with "sufficient conditions met" which occurs when only 2
of 3 convergence criteria are met. 
CONSTRAIN 
Constrained optimization in Cartesian coordinates
(also applies to conformation search). 
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).
 FREQ=ANALYTICAL, use second derivatives and analytical methods
irrespective of available memory. BE CAREFUL.

POLAR 
Calculate polarizabilities and hyperpolarizabilities. 
FD=F 
Sets step size for numerical differentiation
(default=0.005 au for central differences and 0.0025 au for
forward differences). 
INTENSITY 
Obtain IR intensities 
RESTART 
Restart a frequency calculation using the data in
an intermediate file. 
Configuration Interaction

CI or CISD 
Perform a singles and doubles CI, and obtain UV/visible 
CI=N 
spectrum. CI=N; use N orbitals (N/2 occupied and N/2 
CI=F 
unoccupied).Default=6 (3/3); CI=F, include orbital within 
CI=C 
F eV of HOMO; CI=SP, number of occupied
and unoccupied orbitals to be specified. 
CIS 
Perform a singles CI, and obtain UV/visible spectrum. 
CIS=N 
Argument conventions as above. 
CIS=F, CIS=C 

CID 
Perform a doubles CI, and obtain UV/visible spectrum. 
CID=N 
Argument conventions as above. 
CID=F, CIF=C 

OCCUPIED=N 
Set number of occupied orbitals to be included. 
UNOCCUPIED=N 
Set number of unoccupied orbitals to be included. 
The maximum number of orbitals (occupied or unoccupied) in a CI
calculation is 30, although memory limitations will likely reduce this number in practice. 
Miscellaneous

UNITS=AU or UNITS=ANG 
Geometry is given in atomic units or angstroms (default).
Ordinarily, this keyword would be used in
conjunction with Cartesian input of the molecular geometry. 
NOARC 
Suppresses writing of an archive file. 
NOSYMTRY 
Do not use symmetry. 
CHECK 
Stop after checking input file. 
NOMOVE 
Do not reorient coordinates. This option forces
elimination of the use of symmetry, (sets NOSYMTRY). 
WRITEARCH =N 
Set the number of optimization cycles between
writing an archive file (default=5 cycles). 
Printing

PRINTMO 
Print molecular orbital energies and coefficients. 
PRINTLEV=N 
Set the print level.
N=1 default N=2 verbose N=3 debug 
CIPRINT=N 
Print dipole moment, charges
and bond orders for state N. 



 Start Using
Spartan allows a semiempirical calculation to be preceded by
calculation of equilibrium geometry using molecular mechanics methods,
without the user having to deal with the intermediate result. Geometry
choices are given in a menu to the right of
Geometry:
The mechanics method selected will correspond to the geometry input
to the semiempirical calculation. At the present time, this feature
applies only to equilibrium geometry (and not transitionstate geometry calculation).
 Restart Using
This provides facilities which permit use of a Hessian and/or
wavefunction from a previous calculation as initial input to the present
calculation. This facility, which closely parallels that associated with the
Ab Initio dialog, has two different functions:
 To restart a calculation which has not converged either in
the SCF or in the optimization of equilibrium or
transitionstate geometry. In the former case, the wavefunction from the
previous (nonconverged) calculation may be input, while in the latter
the Hessian from the previous calculation (and perhaps as well
the wavefunction) may be used.
 To provide a starting guess either at the wavefunction
and/or Hessian (as well as the geometry) for a calculation using
one semiempirical model on the basis of a previous calculation
using a different semiempirical model. Ab
initio wavefunctions and/or Hessians may not be used as starting guesses for
calculations at semiempirical levels; an error message will be provided.
In both 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
SemiEmpirical 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 level of calculation to
another (semiempirical) level of calculation is accomplished in a similar
manner (following successful completion of the initial calculation): by
adjusting the parameters in the
SemiEmpirical dialog to reflect the
desired calculation, 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 righthand 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 SemiEmpirical dialog may be exited either by
clicking on the Save or Save As
buttons. (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 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
SemiEmpirical dialog) exits the dialog without saving any
information.
Section 8.4.1: SemiEmpirical Parameters
Spartan's SemiEmpirical module reads parameters from a set of files:
params.MNDO MNDO parameters
params.AM1 AM1 parameters
params.PM3 PM3 parameters
params.MNDOD MNDO/d parameters
params.PM3D PM3(tm) parameters
The program "looks first" in the current molecule directory, then in the
user's home directory, and only then in the directory containing
Spartan. New parameters may be added or existing parameters modified if desired.
