AMPAC™ GUI Examples

Manage Orbital Occupancy 3D Reaction Surfaces
Transition Metals-Copper Surface DNA Display from pdb file
Building Structures Charge Display
Electrostatic Charge Surface Gaussian™ ONIOM Setup
Display of MO Surfaces Display of Vibrational Modes
Determine Stereochemistry 2D Property Contours
Manage Molecular Orbitals Graphically
This dialog box shows the molecular orbital energy management dialog box showing the MOs of benzene.  The MO displayed is one of the HOMOs (see the checked red box.)  The HOMO/LUMO orbitals are highlighted in yellow.  Electrons can be dragged and dropped between orbitals to arrange occupancy and spin state.
3D Reaction Surface Plot
A potential energy surface from a 2-coordinate reaction pathway is displayed here.  This calculation can be set up within AGUI using its intuitive tools.
Transition Metals-Copper Surface
This image shows a small segment of a 34-atom copper elemental surface with a formate molecule adsorbed on the top layer.  The three white dots are dummy atoms that are being used to aid in defining the geometry of the formate.
pdb Files-DNA Segment
This image shows am AMPAC GUI visualization of a short segment of DNA loaded from a pdb file.  Note that AGUI completed the valences by adding hydrogen atoms to those places that were needed.
Building Structures
This image is a spiro-ortho carbonate that was constructed using both fragment and atom-by atom methods.  The builder in AMPAC's GUI builds molecules like chemists think.
  Charge Display
The atoms in this image are colored by charge, where green atoms are positive and red atoms are negative.  The intensity of the color shows the magnitude of the charge.  Numerical values can also be displayed.  An image of this screen can be captured and inserted in a publication or presentation.
Electrostatic Charge on a Surface
Here is shown a colored display of the electrostatic charge computed by AMPAC has been superimposed on an electron isodensity surface.  The positive and negative regions of the molecule show where polar reactions might be more or less likely.
  ONIOM Setup for Gaussian03™
This image shows a DNA polymerase with an included substrate.  AGUI can define low, middle and high layers for the MM/QM treatment of this system.
Display of Molecular Orbitals
This image shows a molecular orbital superimposed on the structure of a molecule.  Any MO can be displayed.  Difference between MOs and other plotted properties can also be plotted.
Display of Vibrational Modes
The arrows attached to the atoms in this display indicated the directions and magnitudes of a particular vibrational mode.  The modes can also be animated and simulated spectra produced.
AGUI will determine the absolute stereochemical configuration of each chiral center in the molecule at the push of a button!.
2D Property Contours
This image shows a 2D plot of total electron density projected onto the plane of this aromatic system.