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GaussView 5  量子化學計算軟體

• 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

• 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 to an entire molecule or to selected residues or secondary structures
  • 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

• 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

• 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

• 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

• 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