Molecule, Sybyl and other graphics programs, such as Spartan, can be used to input structures into quantum mechanical software programs like Ampac and Gaussian. To get the symmetry of a molecule correct in Gaussian sometimes requires inputting the structure manually using a "z-matrix" that describes the molecule in terms of bond lengths, bond angles and dihedral angles. The input (ch2o3.com)and output (ch2o3.log)files from such a calculation are contained on the class web page. The z-matrix file can be written using the jot editor on the SGI's (see the UNIX/SGI page) or another file editor by following the principles for writing them on the z-matrix page. Look on the Gaussian 98 page for details on how to run jobs specified in the .com file, and how to tell when a job in the queue has completed successfully. When the job is done, it writes a ".log" file with the results. The ch2o3.log file contains a condensation of the output from calculations in which the geometry of the molecule formaldehydehas been optimized and then its infrared vibrational frequencies calculated by taking second derivatives of the energy of the molecule with respect to all of the 3N-6 possible vibrational modes within the molecule, where N is the number of atoms. The theoretical calculation was carried out at the Hartree-Fock level with a 3-21G basis set that includes 2s and 2p valence orbitals (inner and outer) on each C and O and 1s orbitals on the H's.
1) Write a z-matrix for the input file for a calculation on acrolein, transoid propenal, OCHCH=CH2 , in a manner similar to that on the web page for formaldehyde, also at the HF/3-21G level with an fopt and freq calculation using reasonable initial values for the bond lengths and angles. Fix the dihedral angles at appropriate values of 0.0 or 180.0 degrees to force the molecule to remain planar, Cs symmetry, by entering the actual values 0.0 or 180.0 (be sure to use the decimal points), into the z-matrix rather than letters for the variables. For this exercise, include pop=reg on the command line, to be able to visualize the molecular orbitals. To get an archive file (filename.a) to be "punched", written to the disk when the job finishes you need to type "punch=archive" on the command line as well.
**Note: Immediately after you submit a Gaussian job, you can check to see if the job is being executed by typing top. This will bring an active table of all the ongoing processes and the %CPU each process uses, in the computer you are logged on to. The top table gets updated once every few seconds. To quit top, simply type q. For Gaussian jobs the processes are named l###.exe link in the program you are in.
NQS is a queue software program installed on the CCL computers. Its function is to put batch jobs in line and execute one job at a time, on a given computer. If you submit several Gaussian jobs, NQS runs the first one submitted. All the other jobs will be placed in a queue and will be executed automatically in turn. To monitor the NQS queue, type qstat -ad and a list of jobs will appear. The job running will have an R (i.e, running) and the job(s) waiting will show a W (i.e, waiting) as the job status.
**Note: If your job is taking much longer than 5 CPU minutes (not clock time) (use qstat to show how how much CPU time has been used), then you may need to look to see if your z-matrix is miswritten to give a wierd geometry that does not optimize properly. To look at the geometry that you input in your z-matrix, you can use Molden, even for a job that is running, to see if the optimization is going astray.. When using Molden, geometry first displayed is the initial geometry in the optimization. To see the subsequent geometries use Next until you reach the lst geoemtry. The Molden screen can not be printed. The display of vibrational frequencies works, but the display of orbitals does not work properly. Printing can be done from Molecule on a Mac, and the orbitals can be printed.
This calculation should take less than 5 minutes of cpu time to complete. Use "ls -l" in order to look for the log file in your directory and then look at the end of the file to see if it completed successfully (it should have some random quote) or alternatively for some error message.
Normally, after the Gaussian jobs are completed successfully, 4 files should be displayed for each job when you type ls, or ls -l.
3. Checkpoint file: (Displayed as filename.chk) A binary file containing the current geometry, force constants, and wavefunctions. The checpoint file is generated for the first job, and overwritten (updated) after each subsequent job.
4. Command file: (Displayed as filename.com) Is the input file.
a) Tabulate the optimized bond lengths in Angstroms and the total energy in atomic units. One atomic unit = 627.51 kcal/mole.
b) Tabulate the Mullikan charges on each atom and discuss whether the charges are in accord with what you expected from resonance forms of acrolein.
c) Tabulate the experimental IR/Raman frequencies, grouped by symmetry, from J. Phys. Chem. Ref. Data, 1977, 6, No. 3 (see Table below) and compare with your calculated vibrational frequencies. See if there is a multiplicative empirical scaling factor that would consistently bring the calculated frequencies into better agreement with experiment. This should be done with Excel and a least squares regression analysis to get the slope, as in the QSAR exercise.
d) Tabulate the experimental ionization potentials in electron volts (in eV), grouped by symmetry, from the table below from K. Kimura, Handbook of He I Photoelectron Spectra, 1981. Compare these with the calculated orbital energies in accord with Koopmans' Theorem, again using the Excel linear regression analysis to get a slope and intercept. Give the equation for the fit with the calculated slope and intercept in your report. The conversion factor is 1 atomic unit = 27.212 eV.
Total Energy: The total electronic energy can be found in the closely spaced set of numbers at the end of the .log file. It will be found as HF=-nnn.nnnnnn for a Hartree-Fock calculation. This closely spaced set of numbers, which is delimited by forward slashes (/), represents an archive or summary of the calculation and is found at the end of a successfully completed .log file. Because this archive is slash delimited, you need to follow from 'HF=' to the next forward slash and include all of the digits to that point which may be on the next line. Of course, some of these digits are outside the range of significant figures. Normally, the energy should be quoted in reports to six decimal places.
Molecular Orbital Energies: In order to obtain the molecular orbital energies to compare with experimental ionization potentials, look in the Population Analysis section of the .log file where the Eigenvalues (which are the orbital energies) are tabulated in units of Hartrees. 27.212 eV = 1 Hartree. The output lists the symmetries of all of the occupied orbitals and the virtual, or antibonding, orbitals followed by a list of the orbital energies in order of increasing energy. For a planar molecule, such as acrolein, the A' orbitals are sigma orbitals and the A" orbitals are of pi symmetry. Using the pop=regular keywords in the command, or route, section of the input file will include a table of the molecular orbital coefficients for the five highest occupied molecular orbitals and the five lowest unoccupied molecular orbitals. The coefficients are tabulated in columns with the appropriate molecular orbital energy and symmetry at the top of the column. The rows below the molecular orbital energy are the contributions from the atomic orbitals in the basis set arranged in order of the atom number scheme used in the z-matrix, or Cartesian coordinates, used to describe the molecule in the input file. From the coefficients, the shape of each orbital can be derived. Molden and Molecule are both programs which can be used to display them graphically.
Table of experimental values of fundamental IR frequencies for acrolein in cm-1.
A' 3103 1360 A" 993
3028 1275 980
3000 1158 959
2800 912 593
1724 564 157
1625 327
1420
Table of experimental ionization potentials from photoelectron spectroscopy of acrolein in eV.
A", pi C=C 10.10
A', lone pair O 10.92
A", pi C=O 13.7
A', pi type CH2 14.6
A', sigma C-O 14.6
A', sigma C-C 16.3
A', sigma C-C 16.3
DO NOT print your entire .log file to the printer. It takes far too much space, wasting paper and expensive toner. You can cut and paste what you want to a jot window for your report, using more and tail commands to display the parts of the .log file that are most important. See the edited formaldehyde(output) example from the Gaussian 98 page, to see how to read the output and what parts of the output are important fo rincorporation in your report: The z-matrix you used, the final geometry as optimized parameters, the population analysis with eigenvalues and eigenvectors for the details, the Mulliken charges for all atoms and with hydrogens groured on the cerbons (heavy atoms), and the final archive entry (found at the end of the .log file).