GaussView 6 is the latest iteration of a graphical interface used with Gaussian. It aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instruction, and helps in the interpretation of Gaussian output (e.g., you can use it to plot properties, animate vibrations, visualize computed spectra, etc.).
 
Examine Molecular Structures

•  •  Rotate, translate and zoom in 3D with:
  •    º  Mouse operations
  •    º  Precision positioning toolbar
  •    º  Available in every graphical display
•  •  View numeric value for any structural parameter
•  •  Use multiple synchronized or independent views of same structure
  •    º  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
  •    º  Persistent highlighting available

Building/Modifying Molecules

•  •  Convenient palettes:
  •    º  Atoms (including hybridization)
  •    º  Functional groups
  •    º  Rings
  •    º  Amino acids (central fragment, amino- or carboxyl-terminated)
  •    º  Nucleosides (central fragment, C3’-, C5’-terminated, free forms)
  •    º  Custom fragment libraries
•  •  Import standard molecule file formats:
  •    º  PDB
  •    º  Gaussian input, output, checkpoint and cubes files
  •    º  Sybyl files: .mol2, .ml2
  •    º  MDL files: .mol, .rxn, .sdf
  •    º  Crystallographic Information files: .cif
  •    º  Optionally include intermediate structures from optimizations etc.
  •    º  Multi-structure .sdf and .mol2 files
  •    º  Accurately add hydrogens automatically or manually to an entire molecule or to selected residues or secondary structures
  •    º  Include/discard waters on PDF import
  •    º  Optionally apply standard residue bonding on PDF import
  •    º  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:
  •    º  Click and marquee selection modes (customizable)
  •    º  Complex filters combining atom type, number, MM settings, ONIOM layer
  •    º  Select by PDB resuide and/or secondary structure (e.g., chain)
  •    º  Expand selections by bond or proximity
  •    º  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)
  •    º  Constrain to specific space group symmetry
•  •  Assign atoms to ONIOM layers by:
  •    º  Direct selection
  •    º  Bond proximity to specified atom
  •    º  Absolute distance from specified atom
  •    º  PDB file residue, secondary structure
  •    º  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
  •    º  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:
  •    º  Select job/method/basis from pop-up menu; related options appear automatically
  •    º  Supports all Gaussian 09 features
  •    º  Convenient access to commonly-used general options (e.g., SCF-QC)
  •    º  Extra input sections in imported files are retained
•  •  Select solvent and specify other parameters for calculations in solution
•  •  Specify any Link 0 command
  •    º  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
  •    º  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
  •    º  PBC translation vector for periodic structures like polymers and crystals
  •    º  Orbital alterations
  •    º  Multiple molecule specifications for QST2/QST3 transition state searches
  •    º  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
  •    º  Display formats: solid, translucent or wire mesh
  •    º  Color surfaces by a separate property
  •    º  Specify desired contour plane
  •    º  Load any cube created by Gaussian
  •    º  Save computed cubes for future reuse
  •    º  Perform operations on cubes (e.g., subtract for a difference density).
  •  º  Save computed cubes to files for reuse
•  •  Animate normal modes associated with vibrational frequencies
  •    º  Indicate motion via displacement vector, dipole derivative unit vector
  •    º  Displace structures any specified distance along normal mode
  •    º  Select subset of modes for display
  •    º  Save generated normal modes back to checkpoint file
  •    º  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:
  •    º  Report absolute NMR chemical shifts or relative to reference compound
  •    º  Export NMR summary data as text
•  •  Animate structure sequences: geometry optimizations, IRC reaction paths, potential energy surface scans, BOMD and ADMP trajectories
  •    º  Single play or continuous looping
  •    º  Play in reverse
  •    º  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.
  •    º  Add molecular properties to plots
•  •  Save any image to a file (including customizations)
  •    º  Produce web graphics: JPEG, PNG and other formats
  •    º  Produce publication quality graphics files and printouts: TIFF, JPEG, vector graphics EPS and other formats
  •    º  Create images at arbitrary size and resolution
  •    º  Select full color or high quality grey scale formats
  •    º  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