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An affordable, full-featured graphical user interface for Gaussian 03
GaussView 3.0 makes using Gaussian 03 simple and straightforward:
| • | Sketch in molecules using its advanced 3D Structure Builder, or load in molecules from standard files. |
| • | Set up and submit Gaussian 03 jobs right from the interface, and monitor their progress as they run. |
| • | Examine calculation results graphically via state-of-the-art visualization features: display molecular orbitals and other surfaces, view spectra, animate normal modes, geometry optimizations and reaction paths. |
GaussView supports all Gaussian 03 features, and it includes graphical facilities for generating keywords and options, molecule specifications and other input sections for even the most advanced calculation types. GaussView makes it simple to set up ONIOM layers, unit cells for Periodic Boundary Conditions jobs, CASSCF active spaces, molecule specifications for transition structure optimizations using the STQN method, and so on. We’ll look at many of them in the following pages.
| 1. | Here, we are preparing an ONIOM calculation on a HIV protease fragment with an inhibitor. We need to assign atoms to ONIOM layers and then specify Gaussian keywords and options. |
| 2. | Setting up the input file for an ONIOM job is very simple in GaussView. You simply click the ONIOM check box and then specify the method and basis set for each layer using the corresponding tab on the Method panel. The job type and other options are set using the various tabs in this dialog. |
| 3. | Atoms are assigned to layers using the Layer Selection Tool (and layers defined in existing job files are recognized and preserved). We have already placed the inhibitor in the High layer. These atoms are displayed in ball and stick mode, and ones in the Low layer appear as tubes. |
| 4. | Currently, the atoms in residue number 50 in both chains are selected (highlighted). We selected then in a single step using the Select PDB Group dialog (reached by clicking the Layer Selection Tool’s Select PDB Group button). Once selected, atoms can be assigned to the desired layer using the controls in the Layer Selection Tool dialog. |
Building Molecules
GaussView includes an advanced Molecule Builder. You can use it to rapidly sketch in molecules and examine them in three dimensions. You can build molecules by atom, ring, group, amino acid and nucleoside, and you can also open PDB and other standard molecule files (hydrogen atoms can be added automatically with excellent accuracy and reliability).
| 1. | Here, we are building spiroselenurane. This window shows the completed molecule. |
| 2. | We have already placed an iso-indene ring into the Builder window and changed the appropriate atoms from carbon to oxygen and selenium. We are about to add a second iso-indene ring to the structure at the selenium atom. When we click on it, the second ring will appear, and the selenium atom will become part of both rings. Afterwards, we will adjust the angle of the two rings and then add the methyl groups. |
| 3. | The current fragment appears in the Builder’s display area. We have selected the connection point as the selenium atom by moving the hot spot in the iso-indene ring. |
| 4. | Although we are adding a ring to our structure, we can also display other Builder palettes as desired. |
Setting Up Gaussian 03 Calculations
GaussView’s Gaussian Calculation Setup window allows you to set up Gaussian 03 jobs in a simple and straightforward manner. All of the features of Gaussian 03 are supported by the interface, enabling you to prepare input for any job type.
Visualizing Gaussian Results
GaussView can graphically display a variety of Gaussian calculation results, including the following:
| • | Molecular orbitals |
| • | Atomic charges |
| • | Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties. Surfaces may be displayed in solid, translucent and wire mesh modes. |
| • | Surfaces can be colored by a separate property. |
| • | Animation of the normal modes corresponding to vibrational frequencies. |
| • | Animation of the steps in geometry optimizations, potential energy surface scans, intrinsic reaction coordinate (IRC) paths, and molecular dynamics trajectories from BOMD and ADMP calculations. |
Displaying Surfaces
Software chimica
Programma chimica
Sistema molecolare
Struttura molecolare
Orbitale molecolare
Molecole
Spettro
Atomo
Shielding density increases from red (deshielding) to blue (shielding).
The molecule itself is displayed to the right. See R. A. Pascal Jr., C. G. Winans and D. Van Engen, J. Am. Chem. Soc., 111, 3007 (1989).
Using a translucent surface makes it easier to correlate structure and properties.
GaussView can display a variety of computed spectra, including IR, Raman, NMR and VCD. Here we see the VCD spectra for two conformations of spiropentyl acetate, a chiral derivative of spiropentane. See F. J. Devlin, P. J. Stephens, C. Österle, K. B. Wiberg, J. R. Cheeseman, and M. J. Frisch, J. Org. Chem. 67, 8090 (2002).
Visualizing and Manipulating Molecular Orbitals
The MO Editor (right) allows you to reorder orbitals. We are using this dialog to select orbitals for a CASSCF calculation. Clicking on an orbital highlights it and makes it part of the active space. Electrons may also be moved between orbitals by dragging them. For example, we have moved an electron from the HOMO (orbital 66) to the (new) LUMO (orbital 68). GaussView automatically adjusts the spin multiplicity as necessary. The Gaussian Calculation Setup window can receive information from the MO Editor and add the corresponding keywords and input to the Gaussian job file.
Animating Optimizations and Reaction Paths
GaussView 3.0 introduces several new animation capabilities in addition to displaying molecular vibrations corresponding to normal modes present in earlier versions. These new animation sequences can be viewed with GaussView, and the individual frames can be saved for import into animation/movie editing software.
Steps from a geometry optimization of benzene. We began with a distorted, nonplanar, nonsymmetric structure which optimized quickly to the actual geometry. The entire optimization sequence can be animated in GaussView when the calculation is complete.
This sequence displays a series structures from an Intrinsic Reaction Path (IRC) calculation of the 1,2 hydrogen shift reaction in which formaldehyde transforms into trans hydroxycarbene. This job type begins at a transition structure and follows the potential energy surface path down to the reactants and products. In this case, the first (leftmost) frame shows a structure that is close to formaldehyde, structures very similar to the transition structure appear in frames 4 and 5, and a structure tending toward the product appears in the final frame. Animating the reaction path from an IRC calculation makes it easy to identify the specific reactants and products that are connected by a given transition state structure.
Setting Up Jobs for Periodic Systems
Gaussian 03 can perform Periodic Boundary Conditions (PBC) calculations in order to model periodic systems in condensed phases such as polymers, surfaces and crystals. GaussView 3.0 provides a rich PBC facility for creating the molecule specifications for such calculations, and the program takes care of creating the appropriate Gaussian 03 input from your graphically defined unit cell.
GaussViewW is an affordable, full-featured graphical user interface for Gaussian. With GaussViewW you can construct molecular systems of interest quickly and efficiently using its molecule building facility. You can also use it to set up and run Gaussian calculations and to visualize a variety of results.
GaussViewW incorporates an excellent molecule builder for rapidly building even very large molecules:
| • | Build molecules by atom, ring, group and amino acid. |
| • | Import molecules from other sources by simply opening them. |
| • | You can also add hydrogens automatically to structures orig-inating from PDB files with excellent reliability. |
| • | Rotate even very large molecules in three dimensions. |
GaussViewW includes easy-to-use graphical interfaces for even the most complicated Gaussian 03 input types: defining ONIOM layers, specifying unit cells for Periodic Boundary Conditions calculations, selecting orbitals for CASSCF calculations (see the lower left dialog in the illustration), and the like.
Gaussian jobs can be launched from within the user interface, and the calculation results can be examined when it finishes.
GaussViewW can visualize a variety of different Gaussian results, including:
| • | Optimized structures. |
| • | Molecular orbitals. |
| • | Electron densities, electrostatic potentials and other surfaces. |
| • | IR and Raman spectra and the associated normal modes. |
| • | Animated geometry optimization, IRC and trajectory results. |
GaussViewM is an affordable, full-featured graphical user interface for Gaussian. With GaussViewM you can construct molecular systems of interest quickly and efficiently using its molecule building facility. You can also use it to set up and run Gaussian calculations and to visualize a variety of results.
GaussViewM incorporates an excellent molecule builder for rapidly building even very large molecules:
| • | Build molecules by atom, ring, group and amino acid. |
| • | Import molecules from other sources by simply opening them. |
| • | You can also add hydrogens automatically to structures orig-inating from PDB files with excellent reliability. |
| • | Rotate even very large molecules in three dimensions. |
GaussViewM includes easy-to-use graphical interfaces for even the most complicated Gaussian 03 input types: defining ONIOM layers, specifying unit cells for Periodic Boundary Conditions calculations, selecting orbitals for CASSCF calculations (see the lower left dialog in the illustration), and the like.
Gaussian jobs can be launched from within the user interface, and the calculation results can be examined when it finishes.
GaussViewM can visualize a variety of different Gaussian results, including:
| • | Optimized structures. |
| • | Molecular orbitals. |
| • | Electron densities, electrostatic potentials and other surfaces. |
| • | IR and Raman spectra and the associated normal modes. |
| • | Animated geometry optimization, IRC and trajectory results. |
Build and Examine Molecules in 3 Dimensions
| • | 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).
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| • | 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.
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| • | View molecules in several display modes: wire frame, tubes, ball and stick or space fill style.
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| • | 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. |
Set Up Gaussian 03 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.
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| • | Start and monitor local Gaussian jobs. | ||||||||||||
| • | Start remote jobs via a custom script. |
Visualize Gaussian 03 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.
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| • | Animate normal modes associated with vibrational frequencies (or indicate the motion with vectors). | ||||||
| • | Display spectra: IR, Raman, NMR, VCD.
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| • | 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.
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Specify and Save User Preferences
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 03 calculation settings. |
| • | Gaussian 03 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. |