CompuChem Distribution:
GaussView 5.0 
2000 XP+Vista
Interface mit Moleküleditor für Gaussian Windows
GaussView ist ein erschwingliches, vollausgestattes
graphisches Interface
GaussView - Features at a Glance Build and Examine Molecules in 3 Dimensions Specify and Save User Preferences Powerful Molecule Building and Viewing
Capabilities
Setting up Gaussian Jobs Features for Setting Up
ONIOM Jobs Visualizing Gaussian Results Gauss View can graphically display a variety of Gaussian calculation
results, including the following: Presentation and Publication-Quality
Output GaussView can produce graphical output containing any of the
images that it generates. PostScript,
JPEG and TIFF formats are supported. You can
send such images to a printer for an immediate
hard copy or export them to an external file
for subsequent inclusion in documents or modification with graphical editing software. Studying Magnetic Properties
mit integriertem Moleküleditor für Gaussian Windows.
Die neuen Möglichkeiten
der Version 05:
Gaussian Quick Launch & Job Schemes: Launch Gaussian without saving
the molecule first, and save commonly-used calculation types as templates.
3D Scan Plots: Results from Scan calculations over 2 variables are displayed
as a 3D plot.
Greatly expanded plot features for Spectra: Support for UV/Visual spectra
and the ability to customize all spectrum plots,including frequency scaling.
Enhanced Fragment Library support.
Contour plots: Display surface slices. Also, much faster surface generation.
Movie files: Generate animations of geometry optimizations, IRCs and
other calculation types as well as molecular vibrations from frequency jobs.
With GaussView you can construct molecular systems of interest
quickly and efficiently using its molecule building facility. You can also set up and run Gaussian calculations right from the interface, and monitor their progress as they run. When a calculation has completed,
you can use GaussView to examine a variety of results graphically via its advanced visualization facilities.
GaussView's Builder palette makes constructing molecules simple and fast.
The molecule in the illustration is a platinum-olefin complex. This class of compounds are interesting in that
the PtR2group has the ability to stabilize strained olefins upon formation of the complex. Here, we are in the
process of completing the molecule by adding a benzene ring to the phosphorous atom on the right. We do so by selecting
the desired ring from GaussView's Rings
palette and then clicking on the existing hydrogen
atom. We can then adjust the angle of the ring using other facilities on the Builder palette.
Build structures by atom, functional group, ring, amino acid (central fragment, amino-terminated and carboxyl-terminated
forms) or nucleoside (central fragment, C3’-terminated, C5’-terminated and free nucleoside forms).
Show or hide as many builder panels as desired.
Define custom fragment libraries.
Open PDB files and other standard molecule file formats.
Optionally add hydrogens to structures automatically, with excellent accuracy.
Graphically examine & modify all structural parameters.
Rotate even large molecules in 3 dimension: translation, 3D rotation and zooming are all accomplished via simple
mouse operations.
Move multiple molecules in the same window individually or as a group.
Adjust the orientation of any molecule display.
View molecules in several display modes: wire frame, tubes, ball and stick or space fill style.
Display multiple views of the same structure.
Customize element colors and window backgrounds.
Use the advanced Clean function to rationalize sketched-in structures
Constrain molecular structure to a specific symmetry (point group).
Recompute bonding on demand.
Build unit cells for 1, 2 and 3 dimensional periodic boundary conditions calculations (including constraining to
a specific space group symmetry).
Specify ONIOM layer assignments in several simple, intuitive ways: by clicking on the desired atoms, by bond attachment
proximity to a specified atom, by absolute distance from a specified atom, and by PDB file residue.
Bacteriorhodopsin, set up for an
ONIOM calculation (stylized).
See T. Vreven and K. Morokuma, “Investigation of the S0->S1 excitation in bacteriorhodopsin with the
ONIOM(MO:MM) hybrid method,” Theor. Chem. Acc. (2003).
Set Up Gaussian Calculations
Molecule specification input is set up automatically.
Specify additional redundant internal coordinates by clicking on the appropriate atoms and optionally setting the
value.
Specify the input for any Gaussian 03 calculation type.
Select the job from a pop-up menu. Related options automatically appear in the dialog.
Select any method and basis set from pop-up menus.
Set up calculations for systems in solution. Select the desired solvent from a pop-up menu.
Set up calculations for solids using the periodic boundary conditions method. GaussView specifies the translation
vectors automatically.
Set up molecule specifications for QST2 and QST3 transition state searches using the Builder’s molecule group feature
to transform one structure into the reactants, products and/or transition state guess.
Select orbitals for CASSCF calculations using a graphical MO editor, rearranging the order and occupations with
the mouse.
Start and monitor local Gaussian jobs.
Start remote jobs via a custom script.
Visualize Gaussian Results
Show calculation results summary.
Examine atomic changes: display numerical values or color atoms by charge (optionally selecting custom colors).
Create surfaces for molecular orbitals, electron density, electrostatic potential, spin density, or NMR shielding
density from Gaussian job results.
Display as solid, translucent or wire mesh.
Color surfaces by a separate property.
Load and display any cube created by Gaussian.
Animate normal modes associated with vibrational frequencies (or indicate the motion with vectors).
Display spectra: IR, Raman, NMR, VCD.
The observed (yellow) and computed
(blue) hyperfine spectra for H2C6N (N=4-3).
The predicted spectrum allows spectral assignments to be made for the observed peaks,
a task which is often difficult or impossible from the experimental data alone due to spectral overlap.
Experimental data provided by S. E. Novick, W. Chen, M. C. McCarthy and P. Thaddeu
Display absolute NMR results or results with respect to an available reference compound.
Animate geometry optimizations, IRC reaction path following, potential energy surface scans, and BOMD and ADMP
trajectories.
Produce web graphics and publication quality graphics files and printouts.
Save/print images at arbitrary size and resolution.
Create TIFF, JPEG, PNG, BMP and vector graphics EPS files.
Customize element, surface, charge and background colors, or select high quality gray scale output.
Customize many aspects of GaussView functionality:
How the Builder operates: atom and fragment join methods, adding hydrogens when needed, automated full or partial
clean operations, and the like.
Default Gaussian calculation settings.
Gaussian job execution methods.
Default display modes, vibrational mode animation, color settings, and similar items.
Window placement and visibility.
Default folder locations (including defaulting to the current working directory).
Image capture and printing defaults.
Clean function parameters.
Short Reference:
GaussView incorporates an excellent molecule builder which
enables even very large molecules to be rapidly sketched in and then examined in three dimensions.
GaussView includes the following features:
GaussView's Gaussian Calculation Setup window allows you to specify any type of Gaussian calculation
in a simple, straightforward manner. All
of the features of Gaussian are supported by the GaussView interface.
Appropriate Link 0 Commands are generated automatically by GaussView, and you can add to or modify them as desired.
When the desired job type is selected from this pop-up menu, the appropriate options appear automatically in the
area below it.
The Solvation area allows you to select and specify parameters for any of Gaussian's
available SCRF models.
For advanced users, the Additional
Keywords area allows you to place any Gaussian
keyword into the route section of your job. Once the form is filled out, you can use the Edit button to open the
generated input file in a text editor for further customization, and the Submit button to begin execution of the
job.
GaussView fills in the charge
and spin multiplicity for you.
The Method area allows you to specify the desired model chemistry-basis set and theoretical method-for the job.
In this example, we are setting up an three-layer ONIOM calculation (selected via the corresponding check box).
Here, we specify the model chemistry for the high accuracy layer. The General Options area gives you quick access
to several commonly-used general purpose options via a single mouse click.
GaussView makes defining the various layers of an ONIOM calculation straightforward. Atoms can be assigned to layers via the normal graphical molecule builder interface, and layers defined
in existing Gaussian command files are recognized and preserved.
Atoms can be selected for layer inclusion in several ways, including by bond attachment proximity to a specified
atom, absolute distance from a specified atom and placement within a defined group within the originating PDB file.
In this example, we are in the process of assigning the selected ring and attached groups to the low accuracy layer
via the Layer Selection dialog.
GaussView displays the atoms assigned to each layer using a different molecule display mode, in this case, ball
and stick for the high layer and tubes for the medium layer.
Optimized molecular structures
Molecular orbitals
Atomic charges
Electron density surfaces from any computed density
Electrostatic potential surfaces
NMR shielding density
Animation of the normal modes corresponding to vibrational frequencies
Surfaces may be displayed in solid, translucent and wire-mesh modes. Surfaces can also be colored by a separate
property. For example the illustrations below show the electrostatic potential-painted charge density surface for
chloroform in both the solid (left) and translucent (right) display modes:
Here we present a small study using Gaussian and GaussView illustrating how the two may be used in combination
to investigate molecular systems.
The NMR shielding density for the methine proton of in-[3(4,10)] [7] metacyclophane is shown below (surface on
the right), plotted on an isosurface of current density magnitude. (The molecule itself is pictured at the left.)
Shielding density increases from red (deshielding) to blue (shielding). It was computed using Gaussian's NMR facility
and visualized in GaussView.
The current density, which determines
NMR shieldings by the Biot-Savart law, is induced by an external magnetic field parallel to the C3 axis and leads
to an unusually large shielding of the methine proton. In accord with the classic ring current model, this result
is primarily due to the strong diamagnetic phenyl ring currents and the location of the methine proton, which is
calculated to be only 1.70 Angstroms above the phenyl ring. The calculated shielding anisotropy for the methine
proton is 23.9 ppm while the calculated isotropic chemical shift is -4.4 ppm relative to TMS, in good agreement
with the experimental value of -4.0 ppm.
We can compare these shielding densities to those for a phenyl proton in the same compound, shown in the illustration
on the left. As before, the shielding density increases from red (deshielding) to blue (shielding). The current
density is induced by an external magnetic filed parallel to the C3 axis and leads to a -3 ppm deshielding contribution
to the phenyl proton from the bonded carbon and the two neighboring carbons.
The phenyl proton shielding is in sharp contrast to that for
the methine proton (left the phenyl ring, along the C3 axis), where the shielding contribution from its own atom
is the same as that for the phenyl proton. However, the bonded carbon shields the methine proton by over 5 ppm,
and each phenyl ring carbon shields the methine proton by over 3 ppm, leading to a very large shielding of the
methine proton. Once again, in accord with the classic ring current model, these results are primarily due to the
strong diamagnetic phenyl ring currents and the location of the phenyl and methine protons.
Computed results and images for
the NMR study were generated by James R. Cheeseman (Lorentzian, Inc.) and Roy Dennington and Todd Keith (Semichem,
Inc.).
