Chemistry 145/245: Applications of Computational Chemistry

 

Fall 2013

Wednesdays 5:00 – 7:30 PM

Sequoia Hall 456

 

Benjamin Gherman

Office Hours: Mondays, 3:00 PM – 4:30 PM

(and by appointment, made 24 hrs ahead)

E-mail: ghermanb@csus.edu

Office: Sequoia Hall 416-C

 

 

 


Announcements

        7/11/13:  The course textbook is “Essentials of Computational Chemistry,” 2nd edition, by Cramer (ISBN: 0-470-09182-7).

        7/11/13:  A tentative course schedule is now available.

        8/6/13: A tentative version of the syllabus has now been posted.

 

 

 


Course Information

        Syllabus (click here for PDF version)

        Lecture Schedule

        Powerpoint content from lectures, listed by day.

        Handouts from lectures, listed by day.

 

Resources from Spartan ‘10

        A Guide to Molecular Mechanics and Quantum Chemical Calculations

        Spartan ’10 Tutorial and User’s Guide

 

 

 


In-Class Exercises

         In-class exercise 1 (assignment – PDF) due by Wednesday, 9/11/13

(solutions – PDF)

        In-class exercise 2 (assignment – PDF) due by Wednesday, 9/18/13

(solutions – PDF)

        In-class exercise 3 (assignment – PDF) due by Wednesday, 9/25/13

(solutions – PDF, Excel spreadsheet)

        In-class exercise 4 (assignment – PDF) due by Wednesday, 10/2/13

(solutions – PDF)

        In-class exercise 5 (assignment – PDF) due by Wednesday, 10/9/13

 (solutions – PDF)

        In-class exercise 6 (assignment – PDF) due by Wednesday, 10/16/13

(solutions – PDF)

        In-class exercise 7 (assignment – PDF) due by Wednesday, 10/23/13

(solutions – PDF)

        In-class exercise 8 (assignment – PDF) due by Wednesday, 11/6/13

(solutions – PDF)

        In-class exercise 9 (assignment – PDF) due by Wednesday, 11/27/13

(solutions – PDF)

        In-class exercise 10 (assignment – PDF) due by Wednesday, 12/4/13

(solutions – PDF, Excel spreadsheet)

 

 


Homework Assignments

        Homework 1a (assignment – PDF) due Wednesday, 9/18/13

(solutions – PDF)

        Homework 1b (assignment – PDF) due Wednesday, 9/25/13

(solutions – PDF)

        Homework 2a (assignment – PDF) due Wednesday, 10/16/13

(solutions – PDF)

        Homework 2b (assignment – PDF) due Wednesday, 10/9/13

(solutions – PDF)

        Homework 3 (assignment – PDF) due Wednesday, 11/13/13

(solutions – PDF)

        Homework 4 (assignment – PDF) due Wednesday, 12/4/13

(solutions – PDF)

 

 


Readings (to be completed prior to the class session)

        Reading for quiz #1 on Wednesday, 9/18/13 - J. Phys. Chem. B, 2005, 109, 5884-5890

o       quiz #1 PDF; quiz #1 answers PDF

        Reading for quiz #2 on Wednesday, 10/9/13 – Chem. Phys. Lett., 1994, 231, 325-330

o       quiz #2 PDF; quiz #2 answers PDF

        Reading for quiz #3 on Wednesday, 11/13/13 - Phys. Chem. Chem. Phys., 2005, 7, 2701-2705

o       quiz #3 PDF; quiz #3 answers PDF

        Reading for quiz #4 on Wednesday, 12/4/13 - J. Org. Chem., 2003, 68, 6375-6386

o       quiz #4 PDF; quiz #4 answers PDF

 

 

        Additional reading for Wednesday, 9/18/13 – New supercomputer enables MD calculations on proteins

        For Wednesday 11/6/13 - J. Phys. Chem. A, 2004, 108, 5479-5483

        For Wednesday 11/20/13 – J. Phys. Chem. A, 2006, 110, 2493-2499

        For Wednesday 11/27/13 – J. Chem. Theory Comput., 2006, 2, 1085-1092

        Additional reading for Tuesday 12/4/13 - J. Am. Chem. Soc., 2004, 126, 7652-7664 and J. Am. Chem. Soc., 2005, 127, 1025-1037

 

 

Additional Interesting Reading (not required, but recommended)

        MMFF94 force field -  J. Comp. Chem., 1996, 17, 490-519.

        C&E News, June 30, 2008 -  “Battle of the Functionals”

        Popularity poll density functionals 2012

        Perspective articles on computational chemistry and density functional theory.

        A good review of density functional theory: Phys. Chem. Chem. Phys., 2009, 11, 10757-10816.

        Two good reviews of QM/MM:  Angew. Chem. Int. Ed., 2009, 48, 1198-1229 and Top. Curr. Chem., 2007, 268, 173-290.

 

 

Related Resources

        Vibrational frequency scale factors:  from the CCCBDB and from the Truhlar group at UMN

        NMR chemical shift linear regression correction parameters:  from CHESHIRE  

 

 

 


Exams

 

        Mid-term Exam – (Exam, Solutions) on Wednesday, 10/30/13

o       Practice exam and practice exam solutions.

        Final Exam  - Wednesday, 12/18/13  5:15p.m.-7:15p.m.

 

 

 


Final Project (Chem 245 only)

        Paper and oral presentation – (assignment PDF)  due Wednesday, 12/11/13