# Molecular Structure Displays using the Immersadesk©.

SC '97, San Jose, CA

Ken Flurchick*, Lee Bartolotti** and Theresa L. Windus*+
*Ohio Supercomputer Center |  | **North Carolina Supercomputing Center |  | +Aeronautical Systems Center
OSC |  | NCSC |  | MSRC PET
1224 Kinnear Rd. |  | 3021 Cornwallis Rd. |  | 2435 Fifth Street, Bldg. 676
Columbus, OH 43212 |  | RTP, NC 27709 |  | WPAFB, OH 45433

Scientific visualization is a powerful method to display the results of computer simulations and/or experimental measurements. We have ported the functionality of the Application Visualization System (AVS) from Advanced Visual Systems, Inc. module we have written called coord_to_geom to the Immersadesk© environment from Pyramid Systems, Inc.

Navigation throughout the molecule is accomplished by:

1. Button 1: Toggle between rotation on or off (initially off). This follows the position of the wand.
2. Button 2: Toggle between scale and translation (initially scale). The actual functionality is controlled only by the joystick.
3. Button 3: Reset to initial configuration.

For these displays, the visualization process begins by reading the structural information and other output data from the calculation. The data is currently displayed using traditional ball and stick models. The size of the atom is determined from the van der Waals radii, taken from Emsley ["The Elements" John Emsley, Oxford Molecular Press, 1989 ISBN 0-19-855237-8], and one can input coordinates in either Bohrs or Angstroms.

The program can read structural information from the following types of files:

1. Plain XYZ Coordinates called PlainCoord. Atom types specified by numerical entry in periodic table.
2. XYZ Coordinates called coord. Atom types specified by atomic name as a character string.
3. Gaussian© Cube Files called Cube.
4. Brookhaven Protein Data Bank called pdb.
5. GAMESS Coordinates via a PERL script called PGamess.
6. GAMESS Plotting Option called Gamess Cube.
7. MSI DCAR called Dcar.
8. DMOL XYZ called DMOL_XYZ.
9. Mopac Electrostatic Potential called Mopac ESP.
10. Mopac coordinates called Mopac XYZ.
11. MOL2 called mol2.
12. MOL called mol.
13. CHEM3D called Chem3d.
14. Molecular Mechanics Code MM3 called mm3.

In this demonstration, we will show several examples using the IMMERSADESK to display molecular structure.

- DoD Challenge Application: Materials for Laser Hardening

  Authors P. N. Day, Z. Wang, and R. Pachter
  Materials Directorate, Wright Laboratory
  WL/MLPJ
  Wright-Patterson AFB, OH
  VRML Display

  The objective of this effort is to explore and design novel materials with controlled properties for laser hardening applications at the Materials Directorate, AFRL, applying newly developed methods, algorithms and scalable advanced software. In particular, we study materials with fast nonlinear optical (NLO) response over broad spectral band-widths such as reverse saturable absorbers, as well as polymer dispersed liquid crystals and advance absorbing dyes, which are critical for laser eye and sensor protection.

- Lithium Intercalated Graphite

  Author Dr. Lawrence Scanlon
  Air Force Research Lab
  Wright-Patterson, AFB OH

  Computational chemistry has been used to investigate the nature of lithium bonding within a C60 [Fullerene] carbon lattice. Two lithium-C60 systems were investigated. A trilithium-C60 system with a charge and multiplicity of (0,4) is shown. Optimized geometries for these systems suggest two types of lithium within the C60 lattice. An ionic lithium is obtained for the dilithium-C60 system and a lithium with covalent character is obtained for the trilithium-C60 system. In both cases the lithium-lithium separation of 2.96 Angstroms or less is consistent with that required in order to achieve ampere-hour capacities greater than that obtained in a stage 1 lithium intercalated graphite.

- Calculation of the Heats of Formation of Prospective Rocket Fuels

  Authors Jeff Mills and Jerry Boatz
  Air Force Research Laboratory
  Propulsion Directorate
  Edwards AFB, CA

  tetra(nitromethyl)spirotriskadecane | 2,2,6,6-tetra(nitromethyl)-spiro[3.3] heptane | 2,6-bisoxetane

  VRML Display

  The heat of formation of a chemical substance, the energy required to assemble it from its component elements, provides an important measure of its intrinsic energy content. Thus, prediction of this parameter plays an important role in the search for new energetic molecules. Accurate theoretical calculations enable evaluation of prospective high-energy rocket fuels and propellant additives in support of experimental investigators.

  These calculations provide critical parameters necessary for the evaluation of a specific set of proposed rocket fuels and also help to justify a means of efficiently screening prospective molecules in the future. Theoretical investigations of this sort, in tandem with experimental research, are part of the effort to reduce the time and expense required to develop and deploy new propellants capable of higher performance and increased payload.

- Design of New High Energy Species

  Authors Mark S. Gordon and Takako Kudo
  Department of Chemistry
  Iowa State University
  Ames, IA
  VRML Display

  Polyhedral Oligomeric Silsesquioxanes (POSS) hold great promise as lubricants and protective coatings for space vehicles, among many other uses. At present, however, little is known about the mechanism of formation of these species, or about the role of solvent, catalysts, or pendant chemical groups. The objective of this research is to use computational chemistry to determine plausible routes to the POSS and then to propose new synthetic routes and new species.