Spartan 5.1 User's Guide

Chapter 8 (Con't): The Setup Menu


Section 8.5: Mechanics

Molecular mechanics methods, based on empirical force fields, represent the simplest class of techniques applicable to the description of molecular equilibrium geometry. At the one extreme, there are very simple force fields such as SYBYL which have been developed to encompass a wide variety of diverse molecular systems but which often lead to unacceptable errors. At the other end, there are force fields such as MMFF (Merck Molecular Force Field) with much more detailed parameterization. These typically give very good results but only for molecular systems within their narrow range of parameterization.

Aside from the obvious difference in cost of application, molecular mechanics techniques differ from quantum chemical structure methods in two fundamental ways. For one, they are limited to the description of molecular equilibrium geometry and conformation and vibrational frequencies. The geometries of non-equilibrium structures, for example, transition states are not accessible, at least with present-generation functional forms and parameterizations. Needless to say, information about the electronic structures of molecules is unavailable. On the other hand, quantum chemical methods are applicable both to equilibrium and non-equilibrium systems, and are able to furnish information, not only about geometry, but also about other properties which may be related to electronic character.

Because molecular mechanics techniques are based on force fields parameterized against (experimental or high-level calculated) data for specific compounds, it is to be expected that they will perform better for these, or closely related compounds, than they will for systems which are fundamentally different. Non-empirical (ab initio) quantum chemical structure techniques, on the other hand, make no explicit use of experimental data, and their overall performance would not be expected to be highly sensitive to the details of the systems at hand.

Selection occurs by clicking on Mechanics, and results in display of the following dialog.

  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

  3. Force Field

    Available molecular mechanics force fields appear in a menu to the right of Force Field:

    Force Field:

    SYBYL
    Merck

  4. 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).

  5. Constraints

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

  6. Freeze

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

  7. Options

    The above features as well as many other options available to Spartan's Mechanics module may be designated by way of keywords. These are entered directly into the Options box. A complete listing of keywords is provided below. These are separated by category: run type, model, optimization, miscellaneous and printing, and control all aspects of the molecular mechanics calculation. 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.


Run Type
OPT Optimize the molecular geometry.

FREQ Generate a Hessian and associated normal modes of vibration and vibrational frequencies.


Model
SYBYL SYBYL force field. Default is mixture of SYBYL and Wavefunction's X force field to account of atom types not accomodated in SYBYL. To restrict to "pure" SYBYL use PURE keyword.

MMFF Merck molecular force field (MMFF 94). Default does not allow user extension. Use EXTEND keyword if this is desired.

PURE Use with SYBYL to not incorporate Wavefunction's X force field extensions.

EXTEND Use with MMFF to allow user defined extensions.


Optimization
OPTCYCLE=N Set maximum number of geometry optimization cycles to be N (default=20 + number of independent geometrical parameters).

TOLG=F Specify the max gradient convergence criterion (this overrides the Spartan preferences file).

TOLBOND=F Specify the max displacement convergence criterion (this overrides the Spartan preferences file).

TOLE=F Specify the energy convergence criterion (this overrides the Spartan preferences file).

CONSTRAIN Use predefined constraints in optimization.


Miscellaneous
NOSYMTRY Do not attempt to maintain symmetry.

DEFZERO Set all missing force field parameters to zero.

ZEROD Set all missing dihedral parameters to zero.

NOMOVE Do not reorient coordinate system. Use of this option invokes NOSYMTRY.

FMISSING Freeze in place any unknown atoms.

MAINTAINZERO Freeze all bond angles around high-coordination
(>6 atoms) centers.

FREEDZERO Allow angle relaxation around high-coordination
(>6 atoms) centers (default).

MAXSYMATOMS=N Turn symmetry off if molecule contains more than N atoms (default =50).

VDW=F Distance to begin "turning off" van der Waals forces.

VDW2=F Distance at which van der Waals forces are set to zero.


Printing
PRINTLEV=N

Set the print level.
N=1 default
N=2 verbose
N=3 debug


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 Mechanics 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 the File menu (see Section 4.5). After a file 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 Mechanics dialog) exits the dialog without saving any information.


Section 8.5.1: Molecular Mechanics Parameters

Spartan's Mechanics module reads parameters from a set of files:

         params.SYBYL         SYBYL parameters
         params.MMFF          MMFF 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.


Section 8.6: External

External under the Setup menu provides access to other programs by way of Spartan's graphical user interface.


Section 8.6.1: Gaussian 94

Gaussian 94 is an electronic structure program supporting a wide variety of
ab initio and density functional calculation types. It is the latest members in the Gaussian series of programs begun in John Pople's group at Carnegie-Mellon University in 1970, and now distributed by Gaussian, Inc.

Gaussian 94 provides access to several capabilities which are not presently available in Spartan's ab initio and density functional modules, including the following:

  1. Basis sets including f functions.

  2. Analytical Hartree-Fock and MP2 second derivatives for calculating vibrational frequencies and thermochemical properties.

  3. Electron correlation methods beyond MP2, including MP3, MP4 and QCISD(T).

  4. Excited state calculations using the CI singles (CIS) method.

  5. Density functional models using hybrid functionals.

Spartan's builders may be employed, molecular models displayed and manipulated, and input may be constructed, as with any of Spartan's own modules, with convenient dialogs. Text output from Gaussian 94 may be accessed from Spartan using the Output entry from the Display menu (see Section 9.1). A number of properties can be calculated based on Hartree-Fock or correlated density matrices, e.g., charges based on electrostatic potentials. Molecular orbitals and Hartree-Fock and correlated electron densities from Gaussian 94 may be displayed either as isosurfaces (see Sections 9.3 and 9.4), or as 2D slices (see Section 9.4). Electron densities from Gaussian 94 may also be used to calculate electrostatic potentials for graphical display. Finally, second derivatives calculated using Gaussian 94 may be used to construct normal mode vibrations for animation within Spartan.

While the interface attempts to provide access to Spartan's full range of graphical capabilities to the Gaussian user, there are presently some limitations:

  1. Inability to provide input to Gaussian 94 other than that supplied from Spartan's graphical user interface. There is no way to specify atomic masses and to perform certain types of NBO analyses. Also, the GVB method requires additional input and may not be directly invoked at present.

    This restriction may be overcome by "hand editing" the input file produced by Spartan's graphical user interface.

  2. While any text output from Gaussian 94 may be examined from Spartan's graphical interface, certain graphics and properties calculations cannot be processed. Perhaps the most important are calculations involving f-type basis functions.

Selection of Gaussian 94 results in display of the following dialog.

  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
    Other

    Selection of Other results in display of a box alongside of the menu. The desired task (the Gaussian keyword) needs to be entered. Acceptable keywords are enumerated in the documentation to Gaussian 94.

  3. Theory

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

    Theory:







    HF
    MP2
    MP4
    CISD
    QCISD
    QCISD(T)
    CIS
    Other

    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 explicitly specifying UHF. In a similar way, the various correlation schemes enumerated above refer to restricted methods for closed-shell systems and unrestricted methods for open-shell systems. Unrestricted methods for closed-shell systems may be forced by explicitly specifying them.

    Selection of Other results in display of a box alongside of the menu. The desired level of calculation (the Gaussian keyword) needs to be entered. Acceptable keywords are enumerated in the documentation for Gaussian 94. Use of Other is not only for specification of methods not included in the Theory menu, but also for forcing unrestricted methods for closed-shell systems. Density functional models need to be specified using Other (or using program options; see below).

  4. Basis

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

    Basis:







    STO-3G
    3-21G(*)
    6-31G(d)
    6-31+G(d)
    6-311+G(2d,p)
    D95(d,p)
    LANL2DZ
    Custom

    Note that only a few basis sets are included in the menu. Specification of other basis sets built into Gaussian 94 is accomplished by selection of Custom followed by entering the appropriate basis set name in the box. Available (built in) basis sets are enumerated in the documentation for Gaussian 94.

  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. Memory

    Specifies the memory (in mwords) available to Gaussian 94. The default value (2.0 mwords) may be changed.

  8. Direct

    Turns on the direct keyword in Gaussian. The default setting is "on", meaning that direct methods are to be employed.

  9. 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).

  10. Options

    The above features as well as many other options available to Gaussian 94 may be designated by way of keywords. These are entered directly into the Options box. A complete listing of acceptable keywords is found in the documentation for Gaussian 94.

  11. Restart

    At the center of the Gaussian dialog box are two switches which permit the use of a wavefunction and/or Hessian from a previous calculation as initial to the present calculation.

If the present molecule is a member of a group, 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 group; turned "off", the operations apply only to the present molecule.

The Gaussian 94 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 the File menu (see Section 4.5). After a file 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 Gaussian 94 dialog) exits the dialog without saving any information.


Section 8.7: Properties

Spartan's ab initio, density functional and semi-empirical modules not only provide geometry and energy, but also a wavefunction from which other "properties" such as dipole moments and atomic charges may be obtained. These modules, together with the mechanics module, also provide the Hessian (the matrix of second derivatives with regard to coordinate displacements) from which normal-mode vibrational frequencies and thermodynamic quantities such as entropies and free energies may be calculated. Processing and printing of this information is the function of Spartan's properties module, which is also used to process wavefunctions from the Gaussian 94 program.

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

The dialog is divided into four sections: Print, Solvation, LogP and Population, with each section containing one or more entries. Selection signifies that specific printing is to be carried and/or a particular property is to be evaluated the next time the job is submitted. These functions are independent of level of calculation, i.e., ab initio, density functional, semi-empirical or molecular mechanics, and will be carried out using the appropriate wavefunction.

Additional printing, other solvation models and population options as well as control over temperature and pressure (in evaluation of thermodynamic properties) may be accessed from the Options box (see below).

  1. Print: MOs

    Print molecular orbitals in the text output as column vectors along with the corresponding orbital energies. Not applicable to molecular mechanics calculations.

  2. Print: Dipole

    Print the dipole moment in the text output. Dipole moments are automatically obtained following an ab initio, density functional,
    semi-empirical or MMFF molecular mechanics calculation, and are available from the Display menu (see Section 9.2.4) or from the spreadsheet (see Section 11.2.3). Not applicable to SYBYL molecular mechanics calculations.

  3. Print: Mulliken

    Print the results of a Mulliken population analysis in the text output. Mulliken atomic charges are automatically obtained following an ab initio, density functional or semi-empirical calculation, and are available from the Display menu (see Section 9.2.7).Not applicable to molecular mechanics calculations.

  4. Print: Natural

    Print the results of a natural population analysis in the text output. Natural (NBO) atomic charges are automatically obtained following an ab initio or density functional or calculation, and are available from the Display menu (see Section 9.2.7). Note that Mulliken and NBO charges are identical for semi-empirical calculations. Not applicable to molecular mechanics calculations.

  5. Print: Bond Order

    Print bond orders in the text output. Not applicable to molecular mechanics calculations.

  6. Print: Frequencies

    If a Hessian is available, print normal-mode frequencies and the corresponding vibrational modes in the text output. The latter are also available for animation using Vibrations under the Display menu (see Section 9.6).

  7. Print Thermodynamics

    If a Hessian is available, print thermodynamic properties in the text output.

  8. Solvation: AM1-SM2

    Evaluate aqueous solvation energy according to the AM1-SM2 model of Cramer and Truhlar (J. Computer Aided Molecular Design, 6, 69 (1992)), and print in the text output. Also made available to the spreadsheet.

  9. Solvation: AM1aq

    Evaluate aqueous solvation energy according to the AM1aq model of Dixon, Leonard and Hehre (Israel J. Chem., 33, 427 (1993)), and print in the text output. Also made available to the spreadsheet.

  10. Solvation: AM1hd

    Evaluate solvation energy in hexadecane according to the AM1hd model of Dixon and Hehre (unpublished), and print in the text output. Also made available to the spreadsheet.

  11. Solvation: AM1oct

    Evaluate solvation energy in octanol according to the AM1oct model
    of Dixon and Hehre (unpublished), and print in the text output. Also made available to the spreadsheet.

  12. LogP: Ghose-Crippen

    Evaluate LogP according to the method of Ghose, Pritchett and Crippen (J. Computational Chem., 9, 80 (1988)), and print in the text output. Also made available to the spreadsheet.

  13. LogP: Villar

    Evaluate LogP according to the method of Villar (J. Computational Chem., 6, 681 (1991); Int. J. Quantum Chem., 44, 203 (1992)), and print in the text output. Also made available to the spreadsheet.

  14. LogP: Dixon-Hehre

    Evaluate LogP according to the method of Dixon and Hehre (unpublished), and print in the text ouput. This involves explicit evaluation of AM1oct and AM1aq solvation models (see above). Also made available to the spreadsheet.

  15. Population: Electrostatic Charges

    Calculate atomic charges based on fits to the electrostatic potential and print in the text output. The method used is based on a uniform sampling of data points extending outward from the van der Waals (contact) surface. Not applicable to molecular mechanics calculations.

  16. Population: Hybrid

    Compute and print atomic hybridizations associated with a natural population analysis. Available selections are provided in a menu to the right of Hybrid:

    Hybrid:


    Normal
    Ionic
    3-Center

    Normal indicates that the molecule under consideration is properly described in terms of a conventional valence structure. Ionic indicates formal charges are required for proper description. 3-Center specifies description in terms of 3-center bonds. Not applicable to molecular mechanics calculations.

  17. Options

    At the bottom of the dialog is a box into which any of the options listed in the table below can be entered directly into the Options box. 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.


Keyword Description

NOSYMTRY Do not use symmetry during the calculation of molecular properties.

PRINTMO Print the molecular orbitals plus symmetry labels where known; also prints orbital energies.

NBO=C Do and print natural bond order hybridization analysis:

NBO=IONIC,

NBO=NORMAL (default),

NBO=3C (three center).

POP Print natural population analysis for atomic charges.

MULPOP Print Mulliken population analysis.

BONDORDER Print out Mulliken and Löwdin bond order matrix plus atomic valences and free valences for UHF.

DEORTHOG Deorthogonalizes semi-empirical MOs before calculating properties.

POSTHF Do population analysis using density matrix from post Hartree-Fock procedure; requires MP2DEN keyword on ab initio job before doing population analysis. Also applied to jobs run using Gaussian 94.

DIPOLE Calculate dipole moment.

FREQ Print vibrational frequencies and normal modes together with symmetry labels where known. Calculate thermodynamic properties (entropy and enthalpy at standard temperature and pressure and zero point vibrational energy).

ELCHARGE=N Obtains charge from electrostati potential using a grid of N points per atomic unit (default=1 point per atomic unit).

TEMPERATURE=F Temperature used in calculation of thermodynamic properties (default=298°K).

PRESSURE=F Pressure used in calculation of thermodynamic properties (default=1 atm).

MOMENTS Calculates and prints principal moments of inertia.

SOLVENT=C Corrects the total energy (ab initio and density functional calculations or heat of formation (semi-empirical calculations) for the effect of solvent. The following solvent models are supported. For water:
    MNDOaq    C=MNDOAQ
    AM1aq     C=AM1AQ          
    PM3aq     C=PM3AQ
    SM2       C=AM1-SM2
    SM3       C=PM3-SM3
    SM5.4a    C=SM54A
    SM5.4p    C=SM54P

for hexadecane:

    MNDOhd    C=MNDOHD
    AM1hd     C=AM1HD
    PM3hd     C=PM3HD 

LOGP=C Calculates and prints LogP. (Also made available to the spreadsheet).
    C=GHOSE     method of Ghose and Crippen
    C=VILLAR     method of Villar
    C=DIXON     method of Dixon and Hehre

NOMOVE Do not reorient the input molecular coordinates (also sets NOSYMTRY).

ORBE Print molecular orbital energies

EXCHANGE, Exchanges the HOMO and LUMO (default a orbitals only):
EXCHANGE=C 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)

HOMOa = ___HOMO + LUMO___
        (Square root of 2)

PRINTLEV=N Specify the print level:
N=1 default
N=2 verbose
N=3 debug

PRINTNBO Print AO to NBO transformation matrix.

FSCALE=F Scale the frequencies by the specified factor.

WT Alter the isotope mass for an atom:
WT = X ~ Y
Sets the isotope of atom number X to Y

BTABLE=C Generate a summary of geometric information:
B interactomic distances
A interactomic angles
D interactomic dihedrals
BTABLE=AB requests both distance and angles.

NEAREST=F Specify the multiplication factor (applied to nearest-neighbor distances) when generating the geometric information (default=1.2).

ELP Specify that the elpot + polpot grid will be used to
generate atomic charges (this is valid for closed-shell,
HF-only molecules).

SYMTHRESH=F Set the symmetry threshold (default=0.00001).

PRINTFREQ Specify that the IR frequencies are to be printed.


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

Clicking on Save exits the dialog with all selections recorded; clicking on Cancel exits the dialog but any selections are lost.


Section 8.8: Surfaces and Volumes

Spartan provides for graphical display of quantities resulting from semi-empirical and ab initio molecular orbital calculations as well as density functional calculations. These quantities include the molecular orbitals, the electron density, the electrostatic and polarization potentials (or sum of the two) and, for open-shell systems, the difference in electron densities arising from the a and b spin manifolds (the spin density). There are two different graphical display modes. The first, accessed from Surfaces under the Setup menu, results in isosurfaces with or without a specific properly mapped onto the surface. The second, accessed from Volumes under the Setup menu, results in data being generated inside a
specific volume from which either isosurfaces and/or slices may later be obtained in real time. While the former display mode is somewhat easier to use, the latter is much more flexible.

Several different surfaces (or several copies of same surfaces with different properties mapped) and/or several different slices may be simultaneous displayed. This allows visual comparison of different graphical quantities. In addition,
any of the usual structural representations (skeletal, ball-and-stick, tube, ball-and-spoke and space-filling models) may be displayed along with the surfaces, mapped surfaces and/or slices. The total graphical display can become very complex, and selective use of meshes and/or translucent solids (as opposed to opaque solids) may facilitate visualization of such composite images. Experimentation is advised!*

    *A brief discussion of graphical models available in Spartan and examples of their use in
    elucidating molecular structure and chemical reactivity is available: W.J. Hehre, W.W. Huang and J.E. Nelson, A Guide to Graphical Models and Graphical Modeling in Spartan, Wavefunction, Inc., Irvine, CA , 1997.


Section 8.8.1: Surfaces

Isosurfaces of molecular orbitals, electron and spin densities and electrostatic and polarization potentials are easily constructed using Spartan's graphics module for later display as an "arrangement of dots", a mesh or a fully-lighted opaque or translucent solid. Examples of graphical output in orthogonal projection are reproduced here in grayscale in Figure 8.1. Surfaces (like other graphical objects) may also be rendered in perspective and, with the aid of color filtration techniques, in stereo.

Additionally, any one of the quantities listed above may be mapped onto an isosurface. For example, the value of the electrostatic potential may be mapped onto a surface of constant electron density, yielding an image portraying both steric and electrostatic characteristics. Mapping involves the use of color; colors toward the blue represent one extreme value of a property and colors toward the red represent the other extreme. The resulting surface may be viewed as conveying four dimensions of information, three dimensions required to portray the geometry of the surface and the fourth dimension to portray the value of the property. Maps may either be presented in terms of continuous gradations of color, or in terms of a set number of color bands, so-called texture-mapped surfaces.

Table 8.1: Typical Surfaces Generated by SPARTAN

Frontier orbitals for a symmetry-allowed Diels-Alder reaction, showing interaction of the HOMO of 1,3-butadiene and the LUMO of ehtylene.

Space-filling model and electron density surface (0.002 electrons/au3) of cycoloheanone, showing overall molecular size and shape.

Electron density surface for (0.08 electrons/au3) of transition surface for pyrolysis of ethyl formate, showing bonding in the transition state.

Electrostatic potential surfaces (-10 kcal/mol) of trimethylalamine (left) and dimethyl ether (right), showing the lone pairs on nitrogen and oxygen, respectively.

Spin density surface (0.002 electrons/au3) of allyl radical, showing spin density on terminal carbons.

Simulaneous display of the LUMO and the electron density surfaces of cyclohexanone, showing accessibility for nucleophilic attack.

Selection of Surfaces from the Setup menu results in display of a dialog.


The box at the top of the Surfaces dialog is used to store command lines for execution by Spartan's graphics module. Individual entries are selected by clicking on them.

Pull-down menus in the middle of the dialog allow specification of a number of common surfaces and properties to be mapped onto these surfaces as well as designation of resolution.

  1. Surface

    Available surfaces are accessed from the menu to the right of Surfaces:

    Surface:










    density
    density(bond)
    HOMO-
    HOMO
    LUMO
    LUMO+
    SOMO
    spin
    elpot
    polpot
    elpot+polpot

    These include the electron density at isosurface values which provide indication of overall molecular size (density) and of location of chemical bonds (density (bond)), the molecular orbitals (HOMO-, HOMO, LUMO, LUMO+, SOMO), the spin density (spin), the electrostatic potential (elpot), the polarization potential (polpot) and the sum of the two (elpot+polpot). Other isosurfaces may be requested using "expert mode" (see below).

    At the present time, evaluation of the polarization potential requires one or two orders of magnitude more computation than evaluation of the electrostatic potential.

    SOMO (singly-occupied molecular orbital) and spin are accessible only if the molecule under consideration involves unpaired electrons (multiplicity >1 or if open shell methods have been explicitely requested). Otherwise, the menu entries are dehighlighted.

    Selection of two of the entries, "HOMO-" and "LUMO+", results in display of box alongside of the entry, e.g.,

    This contains a number providing a decrement value from the HOMO and increment value from the LUMO, and so allows specification of any molecular orbital. This value may be changed.

    Specification of HOMO-, HOMO, LUMO or LUMO+ for a molecule with unpaired electron requires selecting the spin of the orbital. In this case, a toggle appears.

    Isosurface displays for several of the entries are sensitive to the isosurface value, and the default values (see table below) may be changed.

    isosurface default isosurface value
    density 0.002 electrons/au3
    density (bond) 0.08 electrons/au3
    spin 0.002 electrons/au3
    elpot -10 kcal/mol
    polpot -10 kcal/mol
    elpot+polpot -10 kcal/mol

    Selection of any of these will result in a Value box, the contents of which may be changed.

  2. Property

    Available properties are accessed from the menu to the right of Property:

    Surface:









    none
    HOMO-
    HOMO
    LUMO
    LUMO+
    SOMO
    spin
    elpot
    polpot
    elpot+polpot

    Available properties are the molecular orbitals (HOMO-, HOMO, LUMO, LUMO+, SOMO), the spin density (spin), the electrostatic potential (elpot), the polarization potential (polpot) and the sum of the two (elpot+polpot). As with surfaces, HOMO- and LUMO+ entries carry decrement and increment values, respectively. Additional properties may be requested in "expert mode". Finally, selection of none indicates that no property is to be mapped onto the surface.

  3. Resolution

    Selection of surface resolution is from the menu to the right of Resolution:

    Resolution:


    low
    med
    high

    Medium resolution generally is of sufficient quality for routine work, low resolution is used to get rough images very quickly, while high resolution may be employed to obtain graphics suitable for publication. The time to produce an image as well as disk storage requirements for that image increase significantly with increasing resolution.

  4. Add

    Clicking on Add creates a line in the box at the top of the dialog based on the contents of the three menus.

     surface=text1  property=text2  resolution=text3  pending

    "text1", "text2" and "text3" are text strings, and the entry "property = text2" is optional. The contents of the menus are not changed.

  5. Replace

    Clicking on Replace replaces the highlighted entry in the box at the top of the dialog with an entry based on the contents of the three menus. The contents of the menus are not changed.

  6. Delete

    Clicking on Delete removes the highlighted entry from the box. Following deletion, the next entry up in the list becomes highlighted. If the highlighted entry corresponds to one in which a graphics file has previously been generated (marked "completed"), this command actually removes the graphics file; repeated clicking on Delete rapidly removes all graphics files. No warnings are provided. Be careful!

  7. Expert Mode

    While the above procedure is adequate for setting up some of the most common graphics surfaces, certain features are accessible only through expert mode. Expert mode is reached by clicking on Expert at the top left corner of the dialog. (It is turned "off" by clicking a second time.) Note that Expert is visible only if Expert in the Preferences dialog under the Logo menu (see Section 3.3) has been turned "on". A new dialog appears.

    Here, the previous Surface, Property and Resolution menus have been replaced by a box into which the commands listed below may be directly entered. These are divided according to category: Surface type, property and miscellaneous. Entries may either be single words or expressions. Keyword=C indicates a character argument and keyword = F indicates a floating-point argument.


    Surface Type
    SURFACE = C

    Specifies generation of a surface. C is one of the following designators:

    density            electron density
    density_alpha      a density
    density_beta       b density
    density_MP2        MP2 density
    density_alpha_MP2  a MP2 density
    density_beta_MP2   b MP2 density
    
    homo(-n)         molecular orbital 
    lumo(+n)         (closedshell systems only)
    mon          
      
    ahomo(-n)         a molecular orbitals
    alumo(+n)         (openshell systems only)
    amon       
    somo(-n)       
    
    bhomo(-n)         b molecular orbitals
    blumo(+n)         (openshell systems only)
    bmon            
    
    elpot             electrostatic potential
    elpot_MP2         electrostatic potential
                      from MP2 density
    elpot_Mulliken    electrostatic potential
                      from Mulliken charges
    elpot_nbo         electrostatic potential 
                      from NBO charges
    
    elpot_elcharge    electrostatic potential
                      based on charges read
                      from input file
    
    polpot            polarization potential
    
    elpot+polpot      sum of electrostatic and      
                      polarization potentials
    
    spin              spin density (openshell
                      systems only)
    

    Here n is a positive integer, indicating the number of the molecular orbital to be generated, either in terms of an offset from the number of the highestoccupied or lowestunoccupied molecular orbitals or in absolute terms (mon). a and b preceding orbital designation correspond to a and b spin manifolds in the case of calculations with unpaired electrons (openshell calculations), homo and lumo for open-shell systems are taken as ahomo and alumo, respectively. somo is the same as ahomo. In addition, C may be an expression adding or subtracting any of the quantities above. This is described below.


    Property
    PROPERTY = C Specifies that a property is to be mapped onto a surface. C is either one of the quantities given under Surface (above) or "none" (no property to be mapped). A property cannot be mapped onto the surface of a molecular orbital. In addition, C may be an expression adding or subtracting any of the quantities above. This is described below.


    Miscellaneous
    RESOLUTION=C
    or

    RESOLUTION=F
    Specifies the resolution at which the surface is to be generated. Acceptable specifications are floating-point values (F) corresponding to the distances (in Ångstroms) between grid points or the character strings "low", "med" or "high" (corresponding to distances of 0.7, 0.5 and 0.25Å, respectively).

    VALUE = F Specifies the value of the surface (only). Default values have been provided above.

    EXACT Calculate the surface normals exactly rather than approximately. This is significantly slower but may lead to slight improvements in graphics appearance.

    DUAL Generate simultaneous positive and negative isovalue surfaces. This is enforced for molecular orbitals

    POSTHF Use post HartreeFock density matrix for plotting or for calculation of electrostatic potential; requires MP2DEN keyword on ab initio jobs before requesting graphics calculations. Also applies to jobs run using Gaussian 94.

    WRITESURFACE
    or

    WRITESURFACE=C

    Specific that a file is to be created containing the surface, with or without an encoded property. The file name is C.

    EADD = C
    EDEL = C

    Add and delete an electron from a density matrix.

    Acceptable character strings are:

          homo(-n)        EDEL only
          lumo(+n)        EADD only
          mon
          ahomo(-n)       EDEL only
          alumo(+n)       EADD only
          amon
          somo(-n)
          bhomo(-n)       EDEL only
          blumo(+n)       EADD only
          bmon      
    


  8. Expressions

    Surfaces and properties can either be single entities (as defined above), or expressions of the form:

    SURFACE = surface1.operand.surface2.operand....
    PROPERTY = property1.operand.property2.operand....

    surface1, surface2,.... can be any of the surfaces listed above and property1, property2,.... can be any of the properties listed above. Two of the surfaces (properties), density and elpot, may be modified by the EADD and EDEL options, to indicate that the underlying density matrix has been altered. The form of modifications is as follows:

    density [EADD = xx, EDEL = yy]
    elpot [EADD = xx, EDEL = yy]

    where xx and yy are expressions (see below). The only operands permitted are " + ", " - " and " * ".

    A number of examples of expressions follow.

    surface = density property = elpot.-.elpot_mulliken
    The difference between the full electrostatic potential and the electrostatic potential based on Mulliken charges encoded on the electron density surface.
    surface = density.-.density [EDEL=homo, EADD=lumo]
    The difference between the electron density based on the original density matrix and that formed by exciting an electron from the highest-occupied to lowest-unoccupied molecular orbital.

    As in the operation of non-expert mode, entries are added by clicking on Add. An existing entry may be replaced by first clicking on it and then clicking on Replace.

An alternative to typing in the complete text required for a graphics entry is to modify an existing entry. Text in the Surface, Value, and Resolution menus prior to clicking on Expert will automatically appear in the lower box upon selection of expert mode. Alternatively, clicking on an entry in the upper box copies it to the lower box, where it may then be modified.

If the present molecule is a member of a list, the 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.

Clicking on Save exits the dialog with all selections recorded; clicking on Cancel exits the dialog but any selections are lost.


Section 8.8.2: Volumes

Another way of storing information for later graphical display is in terms of a volume, that is, a three-dimensional array of values of some property. This makes it possible not only to construct isosurfaces as those previously described in Section 8.8.1, but also a variety of two-dimensional cuts (slices) into the volume. Further, the value of the isosurface and the position of the slice in the volume may be varied in real time. Finally, volume data, unlike surface data, readily lends itself to graphical comparisons revealing similarities or differences between systems. In summary, volumes present an alternative and more flexible way of presenting information for visual consumption.

Spartan allows for construction of graphical volumes of arbitrary size and use of these volumes both for display as isosurfaces (see Section 9.5) and as a variety of two-dimensional slices (see Section 9.4). Slices may be planar, cylindrical or spherical, and be represented in terms of simple contour lines, as continuous gradations of color, or as a series of color bands. Different slices and different isosurfaces (relating either to the same quantity or to different quantities) may be simultaneously displayed. In addition, any one of the usual structure representations (skeletal, ball-and-stick, tube, ball-and-spoke and space-filling) may accompany the graphics.

Isosurfaces and two-dimensional slices are calculated at the time of display from property values previously obtained throughout a volume of fixed size. This is in terms of a three-dimensional box associated with a particular molecule, the location and dimensions of which can be user modified (see Section 5.10). Indeed, to save computation time, the box can be constructed to enclose only that part of a molecule which may be of particular interest.

Selection of Volumes from the Setup menu results in display of a dialog.

The large box at the top of the Volumes dialog is used to store command lines for execution by the graphics module. Individual entries are selected by clicking on them.

Pull-down menus in the middle of the dialog allow specification of a number

  1. Volume

    Available volumes are accessed from the menu to the right of Volume:

    Volume:









    density
    HOMO-
    HOMO
    LUMO
    LUMO+
    SOMO
    spin
    elpot
    polpot
    elpot+polpot

    These include the electron density (density), the molecular orbitals (HOMO-, HOMO, LUMO, LUMO+, SOMO), the spin density (spin), the electrostatic potential (elpot), the polarization potential (polpot), and the sum of the two (elpot+polpot). Other volumes may be requested using "expert mode" (see below).

    SOMO (singly-occupied molecular orbital) and spin are accessible only if the molecule under consideration involves unpaired electrons (multiplicity >1 or if open shell methods have been explicitely requested). Otherwise, the menu entries are dehighlighted.

    Selection of two of the entries, "HOMO-" and "LUMO+", results in display of text box alongside of the entry, e.g.

    This contains a number providing a decrement value from the HOMO and increment value from the LUMO, and so allows specification of any molecular orbital. This value may be changed.

    Specification of HOMO-, HOMO, LUMO or LUMO+ for a molecule with unpaired electron requires selecting the spin of the orbital. In this case, a toggle appears.

  2. Resolution

    Selection of resolution is from the menu to the right of Resolution:

    Resolution:


    low
    med
    high

    Medium resolution generally is of sufficient quality for routine work, low resolution is used to get rough images very quickly, while high resolution may be employed to obtain graphics suitable for publication. The time to produce an image as well as disk storage requirements for that image increase significantly with increasing resolution.

  3. Add

    Clicking on Add creates a line in the box at the top of the dialog based on the contents of the two menus.

       volume = text1   resolution = text2   pending
    

    "text1" and "text2" are text strings. The contents of the menus are not changed.

  4. Replace

    Clicking on Replace replaces the highlighted entry in the box at the top of the dialog with an entry based on the contents of the two menus. The contents of the menus are not changed.

  5. Delete

    Clicking on Delete removes the highlighted entry from the box. Following deletion, the next entry up in the list becomes highlighted. If the highlighted entry corresponds to one in which a graphics file has previously been generated (marked "completed"), this command actually removes the graphics file from the file system; repeated clicking on Delete rapidly removes all graphics files. No warnings are provided. Be careful!

  6. Expert Mode

    While the above procedure is adequate for setting up some of the most common graphics requests, certain features are accessible only through expert mode. Expert mode is reached by clicking on Expert at the top left corner of the dialog. (It is turned "off" by clicking a second time.) Note, that Expert is visible only if Expert in the Preferences dialog under the Logo menu (see Section 3.3) has been turned "on". A new dialog appears.

    Here the previous Volume and Resolution menus have been replaced by a box into which the commands listed below may be directly entered. These are divided according to category: volume and miscellaneous. Entries may either be single words or expressions. Keyword=C indicates a character argument and keyword = F indicates a floating-point argument.


    Volume Type
    VOLUME= C Specifies generation of a volume. C is one of the following designators:

    density            electron density
    density_alpha      a density
    density_beta       b density
    density_MP2        MP2 density
    density_alpha_MP2  a MP2 density
    density_beta_MP2   b MP2 density
    
    homo(-n)           molecular orbital (closed-
    lumo(+n)           shell systems only)
    mon            
    
    ahomo(-n)          a molecular orbitals
    alumo(+n)          (openshell systems only)
    amon       
    somo(-n)       
    
    bhomo(-n)          b molecular orbitals
    blumo(+n)          (openshell systems only)
    bmon            
    
    elpot              electrostatic potential
    elpot_MP2          electrostatic potential
    		   from MP2 density
    elpot_Mulliken     electrostatic potential
    		   from Mulliken charges
    elpot_nbo          electrostatic potential
    		   from NBO charges
    
    elpot_elcharge     electrostatic potential 
    		   based on charges read 
    		   from input file
    
    polpot             polarization potential
    
    elpot+polpot       sum of electrostatic and      
                       polarization potentials
    
    spin               spin density (openshell
    		   systems only)
    

    Here n is a positive integer, indicating the number of the molecular orbital to be generated, either in terms of an offset from the number of the highestoccupied or lowestunoccupied molecular orbitals or in absolute terms (mon). a and b preceding orbital designation correspond to a and b spin manifolds in the case of calculations with unpaired electrons (openshell calculations), homo and lumo for open-shell systems are taken as ahomo and alumo, respectively. somo is the same as ahomo. In addition, C may be an expression adding or subtracting any of the quantities above. This is described below.


    Miscellaneous
    RESOLUTION=C
    or

    RESOLUTION=F

    Specifies the resolution at which the volume is to be generated. Acceptable specifications are floating-point values (F) corresponding to the distances (in Ångstroms) between grid points or the character strings "low", "med" or "high" (corresponding to distances of 0.7, 0.5 and 0.25Å, respectively).

    POSTHF Use post HartreeFock density matrix for plotting or for calculation of electrostatic potential; requires MP2DEN keyword on ab initio jobs before requesting graphics calculations. Also applies to jobs run using Gaussian 94.

    WRITEVOLUME
    or

    WRITEVOLUME=C

    Specific that a file is to be created containing the volume. The file name is C.

    EADD = C
    EDEL = C

    Add and delete an electron from a density matrix.
    Acceptable character strings are:

         homo(-n)          EDEL only
         lumo(+n)          EADD only
         mon
         ahomo(-n)         EDEL only
         alumo(+n)         EADD only
         amon
         somo(-n)
         bhomo(-n)         EDEL only
         blumo(+n)         EADD only
         bmon     
    


  7. Expressions

    These follow the same form as expressions already detailed for surfaces and properties.

    As in the operation of non-expert mode, entries are added by clicking on Add. An existing entry may be replaced by first clicking on it and then clicking on Replace.

    An alternative to typing in the complete text required for a graphics entry is to modify an existing entry. Text in the Volume and Resolution menus prior to clicking on Expert will automatically appear in the lower text box upon selection of expert mode. Alternatively, clicking on an entry in the upper box copies it to the lower box, where it may then be modified.

    If the present molecule is a member of a list, the 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.

    Clicking on Save exits the dialog with all selections recorded; clicking on Cancel exits the dialog, but any selections are lost.


Section 8.9: Standard

Allows settings for the selected computational dialog (from among Ab Initio, Density Functional, Semi-Empirical, Mechanics or External), the Properties dialog and the Surfaces and Volumes dialogs to be stored under a user defined name for later retrieval and use. It is particularly useful for performing repetitive series of calculations (at the same level of theory and requesting the same information), as well as for facilitating standards. Selection of Standard under the Setup menu results in display of a sub-menu:

Standard:

Create
Apply


Section 8.9.1: Create

Saves selected calculation level and requests for properties, surfaces and volumes. Selection leads to the usual file browser, the only entries in which are further directories and previously created standards, and request for a name. Clicking on Standardize exits the dialog with this name saved. Clicking on Cancel also exits the dialog, but no information is saved. No changes to the selection of the calculation level or to the contents of any of the dialogs is made.


Section 8.9.2: Apply

Applies a previously saved standard (selection of calculation level and settings to the appropriate dialogs). Selection results in the usual file browser, the only entries in which are further directories and previously saved "standards". Clicking on the selected standard, followed by clicking on Apply (or double clicking on the selected standard) exits the dialog, with the calculation level and the contents of the appropriate dialogs set. Any previous dialog selections and/or settings are lost. Clicking on Cancel also exits the dialog, but no changes to existing calculation choice or dialog contents is made.


Section 8.10: Submit

Following setup of a molecular mechanics, ab initio, density functional or semi-empirical calculation, and/or request for properties and/or for generation of graphics files, the required calculations are actually performed following Submit under the Setup menu. A Gaussian 94 job is also requested in this manner. In the case of single workstation usage, selection of Submit requires no further action and leads directly to a dialog indicating that the job has actually been submitted.

Submission of a job to Gaussian 94 results in a different dialog. If Gaussian 94 is not installed, an informative dialog is provided instead.

In the time between job submission and actual completion of execution, the user is free to perform other tasks. Molecules which are executing may be examined but may not be altered. The user may also exit Spartan or even log off (but not shut down) the workstation. Spartan will hold any messages until the user returns to the program.

When a job has finished executing (or, in the case of the user exiting Spartan, upon the first reentry following completion of the job), a dialog appears on screen.

If for some reason a job fails to complete normally, an informative dialog will appear on screen.

Reason for the failure should be provided in the text output file (see Section 9.1).

Spartan allows job submission to a machine other than the workstation on which the graphical user interface resides. A list of machines on which Spartan's compute modules reside must be provided in the file hosts in the .spartanrc directory (see Appendix B). The hosts file supplied with Spartan does not contain any entries. If this file is not edited, local submission will occur without further involvement. If, on the other hand, the file contains additional entries, selection of submit will result in a dialog displayed on screen.

Selection of a machine follows by clicking on the appropriate entry in the text box, followed by clicking on Submit. If local submission is also desired, the entry "localhost" must be added to the hosts file. Omission of "localhost" will prevent the submission of local jobs.


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