Welcome!

This course is designed to acquaint you with some of the tools afforded by modern computational modeling programs.  We will be discussing the theoretical basis behind several different computational methods, examining how these methods can be implemented, critically assessing the results, and exploring visualization tools.  You should have a good background in quantum chemistry at the level of undergraduate physical chemistry.  We will emphasize hands-on use of programs such as Spartan, Macromodel, Jaguar, Gaussian and/or Hyperchem.

News will be posted here throughout the term.

• 1/11:  I have added some tips in case you are experiencing sluggish performance of the remote desktop.  See the "Remote Access" page.  If you are satisfied with performance, you need not fiddle with these!
• 1/13:  Monday is a University holiday, and there will be no class meeting.
• 1/16:  Because of the "Mouse locking" issue that we've been having difficulty with, I'd like to replace the VNC binary on Wngr343d with a newer one that I hope will avoid this problem.  However, that requires me to kill everyone's desktop.  I will plan on this Wednesday after class.  
• 1/17:  I have revised the Mac instructions for how to move files over the net.
• 1/25:  Since I miscalculated the impact of the MLK holiday on my lecture schedule, the paper-and-pencil component of HW 3 will be postponed and will be part of HW 4.  The Homework page has been updated to reflect this.
• 2/3:  The Midterm Exam will be during class on Wednesday, Feb. 15.  Coverage will include Molecular Mechanics and force fields, the simple Hückel MO method, perturbation MO theory, and semiempirical methods.  (Cramer, Ch's 1,2,4,5.)
• 2/7:  I've added a note about solvation energy options for Experiment 9 to the Homework page.
• 2/15:  Here are links to the Exam and to the Key.  Both are PDF files and will require the Acrobat reader.  Stats:  High 94, Avg. 76.
• 3/7:  I have increased the limit for the number of simultaneous jobs to 5, while keeping the per-user limit at 2.  I hope this helps cycle through some of the job queue a little more efficiently.
• 3/7:  Because of my departure for the ACS meeting, I will need to have any written form of the term papers by noon on Wednesday, March 22.  However, you may submit them via email or by placing in your Linux directory in any common word processing format (Word, OpenDocument, PDF, etc.); 6 p.m. on March 22 will be the deadline.
• 3/9:  Schedule for oral presentations:
• Friday, March 11:  Selena, May and Jie
• Monday, March 14:  Heath, Mark and Mike
• Wednesday, March 16:  Lauren, Yu-Chieh and Li
• Friday, March 18:  Somnath, Jun and Jay
• 3/16:  As is common at the end of the course, we are experiencing computational bottlenecks.  I have some recommendations:
• If you cannot see the monitor, look at the file /var/spartan/queue.  This lists all jobs and their users, as well as whether it is running (1) or not (0).  If you need me to kill any jobs, please let me know which ones and I will do so.
• I can show folks how to use Gaussian on the lab computers in GbAd314.  You can save the structures from Spartan in a Gaussian-compatible format, and open and run them on the Windows box.  Also, if you have your own Windows computer, I can install the University-licensed version of Gaussian.  Particularly for semiempirical jobs, this may be useful.
• Be conscious of the fact that there is competition for the resources right now in choosing what level is necessary for the term paper.  I'm not making the grade dependent on having everything done, but more on the quality of your experimental design and interpretation of (even preliminary) results.  If you will need a month more to finish everything at the MP2 level, it's OK to say so.
• 3/30:  I have passed the graded reports back to your mailboxes.  You are welcome to continue these (or other!) projects using the resources available for the course.  However, if you have jobs going that you no longer wish to continue, please let me know so I can free resources for others.

Course Information

Meeting time:  MWF 11-11:50 BAT 250
Instructor:  Kevin P. Gable
Weniger 341, phone 737-6744
Office hour: 11-12 TR, but anytime by appointment.

Email:  kevin.gable@oregonstate.edu

Course text and other materials:

"A Laboratory Book of Computational Organic Chemistry" (Hehre, Shusterman & Huang) will be used for assigned exercises. An additional text, Cramer's "Essentials of Computational Chemistry: Theories and Models" provides background discussion of all methods that will be discussed.

Each student will be given an account on the Linux workstation located in Weniger 343 (IP: 128.193.222.22).  This will be necessary to use Spartan and Jaguar computational packages. You may also use Hyperchem, available on any PC hooked up to the Department network (several computers in Gilbert Addition 311 are set up to use this) or Gaussian03 (on some of the GbAd PCs; we have a campus license and I can lend you the install disk).  Comparatively inexpensive versions of Spartan are available to you as students from Wavefunction, Inc., but they do lack some high-end features.  ChemOffice has the capacity to perform molecular mechanics minimizations; this may be a useful method for generating structures for submission to other programs.  Lectures will use Spartan primarily, but we will do some exercises with Gaussian and/or Jaguar. 

Schedule of topics:

Grading:

There will be three components of the final grade.  Each will be treated equally; the letter grade will be based on the total score out of 300 points possible.

Midterm exam (100 points):  coverage will be on HMO theory and applications, and on the principles behind semiempirical methods.

Weekly exercises(6 X 10 points + 2 X 20 points; 8 total):  Problems from Hehre, Shusterman and Huang will be assigned.  You may work these in any package you are comfortable with, but you must submit electronic versions of your input and output files that includes information on when the job was run, what package and method was used, and either a set of coordinates for the optimized molecule or its energy (or both), depending on what is appropriate for the exercise.  Finally, a text or word-processed file with answers to questions posed by the text must be submitted.  You must leave the graded output file(s) in an identifiable location on the wngr343d workstation by Friday at 5 p.m.  Files with timestamps after the deadline will be assessed a late penalty.

Final project (75 points written part; 25 points oral part):  You must complete a final project that involves application of the tools you have learned to a chemical problem.  Several suggestions are provided below, but you are encouraged to consider projects related to your research.  Each student should get a project approved by the end of Week 6.  You will write a 5-10 page paper describing the problem, your approach, the results and your interpretation.  You will also make a brief (10 minute) presentation to the class.

"Students with documented disabilities who may need accommodations, who have any emergency medical information the instructor should know of, or who need special arrangements in the event of evacuation, should make an appointment with the instructor as early as possible, no later than the first week of the term."

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