Spartan 5.1 User's Guide

Chapter 8: The Setup Menu

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.


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 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.


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 Hartree-Fock 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 Hartree-Fock models (which scale as the fourth power of the number of basis functions). The crossover point between Hartree-Fock and density functional models depends on many factors, not least among them the program. For Spartan's modules, it is typically around 50-70 basis functions.

Density functional models require large underlying basis sets, including functions with higher angular quantum number than occupied in the ground-state atom (p functions on hydrogen and d functions on main-group 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 Hartree-Fock schemes. Such a requirement greatly favors a strict numerical implementation of density functional methods, as opposed to an alternative implementation in which the Hartree-Fock 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 main-group elements as well as for molecules incorporating transition metals. The latter is especially important, because Hartree-Fock methods do not generally provide reliable descriptions of the structures of transition-metal 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 Hartree-Fock models. On the other hand, so-called non-local or gradient corrected density functional models, such as the Becke-Perdew 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, pull-down menus and buttons which together direct input into Spartan's density functional 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 density functional levels appear in a menu to the right of Theory:

    Theory:


    SVWN
    BP
    pBP

    SVWN gives the local density model while BP and pBP provide self-consistent and perturbative implementations of the non-local Becke-Perdew model, respectively.

  4. Basis

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

    Basis:


    DN
    DN*
    DN**

    The DN, DN* and DN** basis sets are roughly the same "size" as the
    6-31G, 6-31G* and 6-31G** 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.

  5. Total Charge

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

  6. 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.

  7. 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).

  8. 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 density functional levels. Does not apply to single-point energy calculations. See Sections 6.5 to 6.7 for information on constraining geometrical parameters.

  9. 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 density functional levels. Does not apply to single-point energy calculations. See Section 6.4 for information on freezing atoms.

  10. 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 floating-point argument.


    Run Type
    OPT Optimize the molecular geometry.

    TSOPT Optimize a transition state geometry.


    Functional
    SVWN Use the local exchange-correlation potential.

    BP Introduce non-local corrections according to the method of Becke and Perdew in a self-consistent manner.

    pBP Introduce non-local corrections according to the method of Becke and Perdew in a perturbative manner.


    Basis Set
    DN Use DN numerical split-valence 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 = 1.0E-05 for single point energy calculations and 1.0E-06 for geometry and transition structure optimizations).

    DAMP=F Set SCF damping factor to be F (P'=(1-F)*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 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=6.0E-03 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 transition-state 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 (extra-fine) (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 (extra-fine) (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


  11. Start Using

    Spartan allows a density functional 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 density functional calculation. At the present time, this feature applies only to equilibrium geometry (and not transition-state geometry calculation).

  12. 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 "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 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 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 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: Semi-Empirical

Semi-empirical 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 Hartree-Fock 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, semi-empirical 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 present-generation semi-empirical 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, semi-empirical methods, rather than looked at as "stand-alone" 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 semi-empirical repertoire, and now implemented inside Spartan, include the MNDO/d method of Thiel, and transition-metal parameterizations for use in conjunction with PM3. The former offers slightly improved quality for molecules incorporating heavy main-group 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 Semi-Empirical 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 Semi-Empirical module.

  1. 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).

  2. Task

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

    Task:


    Single Point Energy
    Geometry Optimization
    Transition Structure

  3. Model

    Available semi-empirical 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) semi-empirical models.

    Semi-Empirical Model Atoms by Available Parameters
    MNDO H, Li-F, Mg, Si-Cl, Zn, Ge, Br, Sn, Sb, Te, I.
    MNDO/d Si, P, S, Cl, Br, I (used in conjunction with
    MNDO for H and first-row elements).
    AM1 H, B-F, Al-Cl, Zn, Ge, Se, Br, Sn, I.
    PM3 H, Li-F, Mg-Cl, Ca, Zn-Br, Cd, In-I, 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 non-transition metals).

    Current information regarding availability of semi-empirical 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 semi-empirical 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).

  4. Solvent

    Semi-empirical 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 (C-T)). 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 open-shell 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
      a) AM1aq only.

    Current information regarding availability of semi-empirical models for solvated systems appears under Available Elements in the Help menu (see Section 10.10).

  5. Total Charge

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

  6. 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.

  7. 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 semi-empirical 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).

  8. Constraints

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

  9. 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 semi-empirical levels. Does not apply to single-point energy calculations. See Section 6.4 for information on freezing atoms.

  10. 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 transition-metal inorganics and organometallics, sometimes present convergence problems.

  11. Options

    The above features as well as many other options available to Spartan's semi-empirical 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 floating-point argument.

    Wherever possible, keywords for Spartan's semi-empirical module are the same as those providing analogous functions in the ab initio module.


    Run Type (Default is a single-point 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 semi-empirical method.

    AM1 AM1 semi-empirical 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 H----H repulsions in PM3 (default for PM3 with transition metals).

    HHOFF Turn off H----H repulsions in PM3.

    Wavefunction (Default is Hartree-Fock, RHF for closed-shell molecules, UHF for open-shell 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=1.0E-5 for single point energies; varies between 1.0E-5 and 1.0E-7 for optimizations, 1.0E-10 for numerical frequencies).

    DAMP=F Set SCF damping factor to be F (P' = (1-F)*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 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 (default=1.0E-3 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.


  12. Start Using

    Spartan allows a semi-empirical 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:

    Geometry:

    Sybyl
    Merck

    The mechanics method selected will correspond to the geometry input to the semi-empirical calculation. At the present time, this feature applies only to equilibrium geometry (and not transition-state geometry calculation).

  13. 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:

    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 using one semi-empirical model on the basis of a previous calculation using a different semi-empirical model. Ab initio wavefunctions and/or Hessians may not be used as starting guesses for calculations at semi-empirical 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 Semi-Empirical 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 (semi-empirical) level of calculation is accomplished in a similar manner (following successful completion of the initial calculation): by adjusting the parameters in the Semi-Empirical 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 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 Semi-Empirical 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 Semi-Empirical dialog) exits the dialog without saving any information.


Section 8.4.1: Semi-Empirical Parameters

Spartan's Semi-Empirical 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.


Chapter 8, Continued


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