|
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.
- Title
Any text information fitting on a single line may be entered into
the Title box. This will be reproduced in the text output file (accessible
under Output in the Display menu; see
Section 9.1).
- Task
Available tasks appear in a menu to the right of Task:
Task:
|
Single Point Energy
Geometry Optimization
| |
- Force Field
Available molecular mechanics force fields appear in a menu to the
right of Force Field:
- 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).
- 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.
- 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.
- 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:
- Basis sets including f functions.
- Analytical Hartree-Fock and MP2 second derivatives for
calculating vibrational frequencies and thermochemical properties.
- Electron correlation methods beyond MP2, including MP3, MP4
and QCISD(T).
- Excited state calculations using the CI singles (CIS) method.
- 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:
- 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.
- 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.
- Title
Any text information fitting on a single line may be entered into
the Title box. This will be reproduced in the text output file (accessible
under Output in the Display menu; see
Section 9.1).
- Task
Available tasks appear in a menu to the right of
Task:
Task:
|
Single Point Energy
Geometry Optimization
Transition Structure
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.
- 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).
- 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.
- Total Charge
Total molecular charge (an integer). The default value
(0) may be changed.
- Multiplicity
Spin multiplicity. The default setting "singlet" may be changed either
by clicking on t to the right of the box, and selecting instead "doublet"
or "triplet" from the menu which appears, or by entering a numerical
value into the box to the right of
Multiplicity. Multiplicity is 1 for singlets,
2 for doublets, 3 for triplets, 4 for quartets, etc.
- Memory
Specifies the memory (in mwords) available to Gaussian 94. The
default value (2.0 mwords) may be changed.
- Direct
Turns on the direct keyword in Gaussian. The default setting is
"on", meaning that direct methods are to be employed.
- 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).
- 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.
- 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).
- Print: MOs
Print molecular orbitals in the text output as column vectors along
with the corresponding orbital energies. Not applicable to
molecular mechanics calculations.
- 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.
- 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.
- 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.
- Print: Bond Order
Print bond orders in the text output. Not applicable to molecular
mechanics calculations.
- 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).
- Print Thermodynamics
If a Hessian is available, print thermodynamic properties in the text output.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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:
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.
- 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.
- 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.
- 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.
- Resolution
Selection of surface resolution is from the menu to the right of
Resolution:
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.
- 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.
- 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.
- 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!
- 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
|
|
|---|
- 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
- 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.
- Resolution
Selection of resolution is from the menu to the right of
Resolution:
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.
- 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.
- 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.
- 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!
- 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
|
|
|---|
- 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:
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.
|
