• Optimized molecular structures.
• Molecular orbitals.
• Electron density surfaces from any computed density.
• Electrostatic potential surfaces.
• Surfaces for magnetic properties.
• Surfaces may also be viewed as contours.
• Atomic charges and dipole moments.
• Animation of the normal modes corresponding to vibrational frequencies.
• IR, Raman, NMR, VCD and other spectra.
• Molecular stereochemistry information.
• Animation of geometry optimizations, IRC reaction path following, potential energy surface scans, and ADMP and BOMD trajectories. Two variable scans can also be displayed as 3D plots.
• Plots of the total energy and other data from the same job types as in the previous item.

1. Start a new file by selecting the New=>Create Molecule Group option from the File menu in the main window.
2. Click on the Rings icon on the Builder window; this makes Rings your "current fragment" as a ring structure appears in the main window.
3. Click on the Rings icon again; this opens the Ring Fragment palette. Select benzene from the ring fragments; a benzene molecule appears in the Current Fragment window. (Alternatively, you can select benzene from the drop-down list in the main window.)
4. Return to the View window. Click once: benzene displays.
5. Double-click on Element on the Builder window to open the Element Fragment palette. Click on nitrogen to select it.
6. Click on the "hot" atom in the Current Fragment display; a nitrogen atom appears.
   Do not select one of the hybridizations. It is usually easier to use untyped atoms.
7. In the View window, click on the carbon atom you want to change to nitrogen.
8. Select the Delete Atom button on the Builder window.
9. On the View window, delete the hydrogen attached to the nitrogen by clicking on it.
10. Click on the Rebond button on the Builder window, then click on the Clean button.
    You will often want to rebond before cleaning.
    Pyridine is now complete. Save your work.

1. Start a new file by selecting the New=>Create Molecule Group option from the File menu in theView window. Select the element iron and then choose the trigonal bipyramidal iron template:
   
2. Return to the View window. Click once: the iron molecule displays.
3. Double-click on R-Group on the Builder window to open the R-Group Fragment palette. Select the linear C-N template and place this group on each bond to the iron atom. Note that we select this template rather than one of the C-O groups because the former is linear.
4. Change the nitrogen atoms to oxygen atoms: select the element oxygen and then the free atom template (using either the choices at the bottom of the Element Fragment palette or the drop-down list on the main screen).
   The molecule is now complete

Features new to GaussView 5 are in scarlet; features enhanced in GaussView 5 are in teal.

Examine Molecular Structures

• Rotate, translate and zoom in 3D with:
  • Mouse operations
  • Precision positioning toolbar
  • Available in every graphical display
• View numeric value for any structural parameter
• Use multiple synchronized or independent views of same structure
  • Customize display layout
• Manipulate multiple structures individually or as an ensemble
• Display formats: wire frame, tubes, ball & stick/bond type, space fill (CPK) style
• View per-atom labels for element, serial number, NMR shielding (when available)
• Visualize depth with fog feature
• Display stereochemistry info
• Highlight, display or hide atoms based on rich selection capabilities
  • Persistent highlighting available

Building/Modifying Molecules

• Convenient palettes:
  • Atoms (including hybridization)
  • Functional groups
  • Rings
  • Amino acids (central fragment, amino- or carboxyl-terminated)
  • Nucleosides (central fragment, C3’-, C5’-terminated, free forms)
  • Custom fragment libraries
• Import standard molecule file formats:
  • PDB
  • Gaussian input, output, checkpoint and cubes files
  • Sybyl files: .mol2, .ml2
  • MDL files: .mol, .rxn, .sdf
  • Crystallographic Information files: .cif
  • Optionally include intermediate structures from optimizations etc.
  • Multi-structure .sdf and .mol2 files
  • Accurately add hydrogens automatically or manually
  • Include/discard waters on PDF import
  • Optionally apply standard residue bonding on PDF import
  • Include/convert lone pairs for .mol2
• Modify bond type/length, bond angles, dihedral angles
• Rationalize structures with an advanced Clean function
• Recompute bonding on demand
• Constrain structure to specific point group symmetry
• Mirror invert structure
• Invert structure about selected atom
• Place atom/fragment at centroid position of selected atoms
• Define named groups of atoms via:
  • Click and marquee selection modes (customizable)
  • Complex filters combining atom type, number, MM settings, ONIOM layer
  • Select by PDB resuide and/or secondary structure (e.g., chain)
  • Expand selections by bond or proximity
  • Use groups for display purposes and in Gaussian input
• Specify nonstandard isotopes
• Customize fragment placement behavior

Setup Features for Specific Job Types
Specify input for complex calculations via simple mouse/spreadsheet operations:

• Build unit cells for polymers, 2D surfaces and crystals (periodic boundary conditions)
  • Constrain to specific space group symmetry
• Assign atoms to ONIOM layers by:
  • Direct selection
  • Bond proximity to specified atom
  • Absolute distance from specified atom
  • PDB file residue, secondary structure
  • Complex selection criteria
• View/specify MM atom types and charges
• Add/redefine redundant internal coordinates
• Specify frozen atoms/coordinates during geometry optimizations
• Specify atom equivalences for QST2/QST3 transition state optimizations
• Manipulate MOs: Select, rearrange and/or reoccupy orbitals for CASSCF etc
• Define fragments for fragment guess/counterpoise calculations
  • Assign fragment-specific charges and spin multiplicities
• Include PDB data in molecule specification
• Select normal modes for frequency calculations
• Specify atoms for NMR spin-spin coupling

Prepare and Run Gaussian Calculations

• Create input files via a straightforward menu-driven interface:
  • Select job/method/basis from pop-up menu; related options appear automatically
  • Supports all Gaussian 09 features
  • Convenient access to commonly-used general options (e.g., SCF-QC)
  • Extra input sections in imported files are retained
• Select solvent and specify other parameters for calculations in solution
• Specify any Link 0 command
  • Specify setting for multiprocessor and cluster/network parallel jobs
• Use calculation schemes to set up jobs from templates
• “Quick launch” Gaussian jobs with a single mouse click
• Molecule specification created automatically
  • Optional connectivity section
• Monitor/control local Gaussian and utility processes
• Stream log files in a text-searchable window
• Initiate remote jobs via a customizable script
• Generate job-specific input automatically
  • PBC translation vector for periodic structures like polymers and crystals
  • Orbital alterations
  • Multiple molecule specifications for QST2/QST3 transition state searches
  • Fragment guess and counterpoise per-fragment charge and spin multiplicity

Visualize Gaussian Results

• Show calculation results summary
• Examine atomic changes: numerical values, color atoms by charge, dipole moment vector
• Create surfaces and contours for molecular orbitals, electron density, electrostatic potential, spin density, NMR shielding density
  • Display formats: solid, translucent or wire mesh
  • Color surfaces by a separate property
  • Specify desired contour plane
  • Load any cube created by Gaussian
  • Save computed cubes for future reuse
  • Perform operations on cubes (e.g., subtract for a difference density).
  • Save computed cubes to files for reuse
• Animate normal modes associated with vibrational frequencies
  • Indicate motion via displacement vector, dipole derivative unit vector
  • Displace structures any specified distance along normal mode
  • Select subset of modes for display
  • Save generated normal modes back to checkpoint file
  • Substitute isotopes in frequency analysis/normal modes
• Display spectra: IR, Raman, NMR, VCD, ROA, UV-Visible, etc.
• Specify incident light frequency for frequency-dependent calculations.
• NMR Results:
  • Report absolute NMR chemical shifts or relative to reference compound
  • Export NMR summary data as text
• Animate structure sequences: geometry optimizations, IRC reaction paths, potential energy surface scans, BOMD and ADMP trajectories
  • Single play or continuous looping
  • Play in reverse
  • Plots of related data are also produced
• Display 3D surface plots for 2-variable scan calculations
• Customize plot and spectra displays by zooming, scaling, inverting, etc.
  • Add molecular properties to plots
• Save any image to a file (including customizations)
  • Produce web graphics: JPEG, PNG and other formats
  • Produce publication quality graphics files and printouts: TIFF, JPEG, vector graphics EPS and other formats
  • Create images at arbitrary size and resolution
  • Select full color or high quality grey scale formats
  • Specify custom colors and/or background
• Save plots as images or textual data files
• Save animations in GIF or MNG format or as individual frames

Customize GaussView
Set/save preferences for most aspects of GaussView functionality:

• Control building toolbars individually
• Colors: per-element, molecule window background, surfaces, transparency
• Builder operation: atom and fragment join methods, adding hydrogens when needed, automated full or partial clean operations, etc.
• Gaussian 09 calculation settings
• Gaussian job execution methods
• Display modes
• Window placement and visibility
• Icon sizes
• File/directory locations
• Image capture and printing defaults
• Animation settings and movie defaults
• Clean function parameters
• Charge distribution display defaults
• GaussView Tips facility
• Windows file extension associations