Computational Chemistry

(under construction)

We utilize several computational approaches to aid our experimental structure determination of weakly bound complexes or stable molecules. There are many different levels of calculation available to us, ranging from relatively simple, semi-empirical calculations (which can take from a few seconds to a few minutes to complete) to fully fledged ab initio calculations (which can take several days or sometimes even several weeks to complete). The laboratory desktop computer and the Chemistry department Tru64 Unix workstation both have the Gaussian 98 ab initio suite of programs installed which allow us to carry out ab initio calculations into the structure and properties of the systems we wish to study. We can calculate the lowest energy (most stable) arrangement of the atoms for these species and hence predict what the rotational spectrum should look like. In addition to Gaussian 98, the PC runs the Spartan molecular modeling program. This program does much the same as Gaussian although calculation of energy profiles is much simpler on this package. The packages provide not only structural predictions but also furnish additional properties such as dipole moment, electronic charge distribution, electric field gradients at certain nuclei (which can be useful to interpret hyperfine splittings within rotational spectra), and barriers to internal rotation.

Semi-empirical programs (such as the ORIENT program of Anthony Stone) are much less computationally expensive than the ab initio software and provide a relatively fast way to examine a large number of possible conformations. The relative stabilities of these geometries can be explored using semi-empirical techniques and then the lowest energy structures may be further explored using ab initio techniques, using the optimized semi-empirical structures as starting points.

Computational Resources

  • Gateway E6000 - A single processor 2.8 GHz Pentium 4 PC with 2GB of RAM (and the Windows XP operating system). This machine is used to run the Gaussian 03W suite of ab initio programs and also Spartan 04 for Windows molecular modeling software. These packages are used in the initial investigations into the possible structures and properties of the molecules or complexes under study. Much less computationally expensive semi-empirical models are also available on this machine which allow us to explore possible structures and to gain insight into the relative stabilities of different geometries. This computer also runs the spectral fitting programs used in the prediction, analysis and assigment of the rotational spectra, including the ubiquitous SPFIT program written by Herb Pickett at JPL. Finally, C/C++ and Fortran code can be compiled and run using the Absoft Pro Fortran v. 8.2 software, giving us the ability to write and compile new code for tackling problems for which programs do not already exist.
  • Compaq AlphaPC 264DP Workstation - A dual processor (two 500MHz Alpha EV6 cpu's) workstation running Tru64 Unix, providing a stable platform for the calculations too large for the PC to handle. This machine has 1GB RAM and also runs the Gaussian 98 software (although it is not set up for parallel processing with this software package). OpenPBS (Portable Batch System) software has recently been installed on this workstation allowing multiple users to submit their jobs to various queues, thus ensuring optimum utilization of the system's resources. This workstation belongs to the Department of Chemistry and is also used in the teaching of upper level Chemistry courses that involve computational chemistry or molecular spectroscopy (such as CHM3915, CHM3920, CHM4770 or CHM5300). This workstation died in December 2006 and has since been replaced with a Penguin Computing workstation - details below.
  • Penguin Computing Tempest 2150 Workstation.
    - Two dual-core AMD Opteron 285 CPU's
    - 16 GB RAM
    - Operating System: RedHat Enterprise Linux 4
    - Software: Gaussian 03/GaussView and GAMESS
  • Department PC lab - The Chemistry Department also has a dedicated PC lab with 10 PC's was set up for use by Chemistry majors; this lab currently has 5 machines running an older version of the Spartan software. 5 new, much faster PC's were purchased in Summer 2005 to replace the oldest 5 machines and the new machines will run the latest, full version of Spartan 04, which allows access to many new features, such as the implementation of correlated levels of theory and the ability to calculate UV/vis spectra, NMR properties and enable potential energy surfaces to be plotted via scans of geometrical coordinates.

    Computational Links

  • SuSE Linux
  • Red Hat Linux
  • Mozilla - is an open source web browser. This software is freely available for a number of platforms including Linux, Unix, Windows and Mac
  • Gaussian Inc. - providers of the Gaussian 98 suite of programs
  • Wavefunction Inc. - providers of Spartan software
  • GAMESS - the General Atomic and Molecular Electronic Structure System (GAMESS) ab intio quantum chemistry package
  • CADPAC - the Cambridge Analytic Derivatives Package

    • Contact information Email sapeebles@eiu.edu or call me at (217) 581-2679.

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