Chemistry 245: Computational Chemistry
Syllabus
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Instructor: |
Benjamin Gherman |
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Office Hours: |
Mondays, 2:00p.m. – 3:30p.m. and by appointment (appointments must be made 24 hours ahead) |
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Office: |
Sequoia Hall 416-C |
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Phone: |
916-278-6600 |
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E-mail: |
ghermanb@csus.edu (please include “Chem245” in the subject line) |
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Website: |
Brief introduction/background in computational theory, with emphasis
on chemical/biochemical applications.
Demonstration/instruction of widely used modeling/computational
software. Covering techniques including
molecular mechanics, semi-empirical methods, and ab initio methods. Application of computational methods to
thermodynamics, kinetics, spectra, electrochemistry, molecular properties.
· Understanding of the basic theory behind standard computational chemistry methods (molecular mechanics, semi-empirical theory, ab initio theories, density functional theory, and solvation models) as well as these methods’ strengths and weaknesses.
· Use of these methods to extract chemical information (molecular properties and thermodynamic and kinetic quantities) pertinent to a chemical system.
· Effectively utilize computational chemistry software (especially Spartan ‘08).
· Learn to design molecular models and optimally match computational methods to problems.
· Be able to critically assess the application of computational methods in journal articles.
C. J. Cramer, “Essentials of Computational Chemistry: Theories and Models.” 2nd edition, Wiley, John & Sons, Inc., 2004. (ISBN 0-470-09182-7)
Miscellaneous journal articles (see detailed class schedule). PDF files will be available electronically on the course website.
o F. Jensen, “Introduction to computational chemistry,” 2nd edition, Wiley, John & Sons, Inc., 2007. (ISBN 0-470-01187-4)
o W. Hehre, “A Guide to Molecular Mechanics and Quantum Chemical Calculations,” Wavefunction, Inc., 2003.
o “Spartan ’08 Tutorial and User’s Guide,” Wavefunction, Inc., 2006-2009.
The course website is www.csus.edu/indiv/g/ghermanb/F11_245.htm. The main page of the website will show announcements, and have links to the syllabus, course calendar, homework assignments, and readings. Any material presented in PowerPoint in lectures will also be posted.
Four homeworks will be assigned during the semester. These will primarily be completed using Spartan in the computational computer lab (SQU 536).
Considering that these homeworks will require running calculations, it is highly recommended to start them early. This will provide time to seek help if you have questions about running the software and allow greater flexibility in using the computer resources.
The roster for the class will be randomly divided into two groups. One will follow the homework “(a)” schedule; the other, the homework “(b)” schedule. This is being done in order to alleviate bottlenecks in the usage of the computational computer lab.
Late
work will not be accepted. UIf
you miss a homework, your score on that homework will be 0.
During the course of the semester, there will periodically be in-class assignments/activities to complete. In such cases, the first half of the class period will be devoted to a lecture, while the second half will be devoted to working on the activity. These activities will be accompanied by detailed procedures and will focus on a single aspect from that day’s lecture. The goal of the activity is to gain immediate hands-on experience in working with the day’s lecture topic.
The completed activities will be due at the end of that class or at the beginning of the next session. Late work will not be accepted. UIf you miss an assignment, your score on that assignment will be 0.U Your lowest two assignment scores will be dropped.
Four
quizzes will be given during the semester at the start of a class session. Your lowest quiz score will be dropped. UThere will be no make-up
quizzes; if you miss a quiz, your score on that quiz will be 0.
Each week before a quiz, a journal article will be posted to the course website. You will be responsible for reading that article prior to the next class and the quiz will test your comprehension of that article. You will be permitted to bring the article to the quiz as well as to make notes on the article itself.
Questions you should consider as you read the articles:
· What was the goal of this particular research? How does this relate to any long-term goal or big-picture questions?
· What theoretical methods were used and what answers were the authors trying to obtain from these methods?
· What assumptions were made in the theoretical model? Consider both explicit and implicit assumptions.
· Was theory successful in obtaining the answers the authors sought? Discuss the comparison to experimental data. Were there failures or inabilities of theory in the paper?
· What improvements might have been made to the calculations in the paper? How practical would it be to implement them?
There will be one mid-term exam and a final exam according to the following schedule:
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Mid-term Exam |
Tuesday, October 25 |
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Final Exam |
Tuesday, December 13, 5:15p.m.-7:15p.m. |
There will be no make-up exams. UIf you miss the mid-term examination, your score will zeroU. Exceptions regarding missed mid-term exams will be made only in legitimate cases, in which case the final exam score will be weighted double.
For the final project, students will give 15-minute oral presentations and write a 5-page report on a selected computational chemistry topic. Full details on the final project as well as a list of possible topics will be distributed later in the semester. Students will work in pairs on this assignment. The last day of instruction will be devoted to the oral presentations.
For both Chem 145 and Chem 245, the presentations will also form the basis for one question on the final exam.
Regrade
Requests
All regrade requests must be made in writing Uwithin 1 week of when the paper is returnedU. Your attached note must make clear why you think an error exists. Any requests beyond this point will be not be considered.
Grades in the course will be based on the total number of points received on homeworks, quizzes, exams, and final project:
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Chem 145 |
Chem 245 |
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3 best quizzes (out of 4) |
x 20 pts each |
= 60 points |
= 60 points |
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4 homeworks |
x 40 pts each |
= 160 points |
= 160 points |
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8 best in-class assignments (out of 10) |
x 15 pts each |
= 120 points |
= 120 points |
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1 mid-term exam |
x 150 pts each |
= 150 points |
= 150 points |
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1 final exam |
x 150 pts each |
= 150 points |
= 150 points |
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1 final project oral presentation |
x 50 pts each |
n/a |
= 50 points |
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1 final project written report |
x 100 pts each |
n/a |
= 100 points |
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----------------- |
----------------- |
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640 points |
790 points |
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A to A- |
100-90% |
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B to B- |
89-80% |
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C to C- |
79-70% |
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D to D- |
69-60% |
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F |
<60% |
Class sessions will typically involve a mix of lecture, demonstrations, in-class exercises, and discussion of applications from journal articles. Lectures will not repeat the content of the assigned readings and will be used to highlight key points and concepts. Exams will be based upon both the material from class and the readings. Activities in class should facilitate completion of homework assignments and provide guidance for quizzes. Thus, Uattendance is highly encouragedU.
Academic integrity is essential to a positive teaching and learning environment. All students enrolled in University courses are expected to complete coursework responsibilities with fairness and honesty. Failure to do so by seeking unfair advantage over others or misrepresenting someone else's work as your own can result in disciplinary action. The University policy on academic honesty can be found at http://www.csus.edu/admbus/umanual/UMA00150.htm.
Students with special needs should contact the office of Services to Students with Disabilities (http://www.csus.edu/sswd/sswd.html, Lassen Hall 1008, 916-278-6955) and be prepared to provide them with disability documentation. Please then discuss accommodation needs with me after class or during my office hours early in the semester.
Please silence all cell phones during class. You may use an audio recorder if you wish.
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topic |
reading |
assignment |
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Tues 8/30 |
course introduction; introduction to theory; introduction to software |
Chapter 1 |
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Tues 9/6 |
classical mechanics; force fields |
Chapter 2 |
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Tues 9/13 |
classical dynamics |
Chapter 3 |
HW #1(a) due quiz #1 |
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Tues 9/20 |
Hartree-Fock theory; Hückel theory |
Chapter 4 |
HW #1(b) due |
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Tues 9/27 |
semi-empirical theory; geometry representations |
Chapter 5 |
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Tues 10/4 |
ab initio Hartree-Fock theory; basis sets |
Chapter 6 (and review Section 4.5) |
HW #2(b) due quiz #2 |
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Tues 10/11 |
molecular properties: partial charges; IR spectra; etc. |
Chapter 9 (sections 1-3) |
HW #2(a) due |
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Tues 10/18 |
thermodynamic properties and transition states |
Chapters 10, 15.1-15.3, 15.6 |
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Tues 10/25 |
MIDTERM EXAM |
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Tues 11/1 |
density functional theory |
Chapter 8 |
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Tues 11/8 |
implicit solvation models (1) |
Chapter 11, 12.5.4 |
HW #3 due quiz #3 |
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Tues 11/15 |
implicit solvation models (2) |
Section 10.5.4 |
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Tues 11/22 |
spectra: NMR, UV-Vis open-shell molecules |
Sections 9.4, 14.3.2 Section 6.3.3 |
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Tues 11/29 |
hybrid quantum mechanics/molecular mechanics (QM/MM) methods |
Chapter 13 |
HW #4 due quiz #4 |
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Tues 12/6 |
final project oral presentations |
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Tues 12/13 5:15p.m.-7:15p.m. |
FINAL EXAM |
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Notes:
This schedule is tentative and subject to change. However, the dates of the exams will remain fixed.
Reading posted for a given day should be completed prior to that class period.
[Notes: This schedule is tentative and subject to change. However, the dates of the exams will remain fixed.
Reading posted for a given day should be completed prior to that class period.]
1) course introduction; syllabus
2) introduction to theory; examples of applications
3) in-class exercise: introduction to Spartan ‘08 (in-class assignment #1)
1) classical mechanics overview
2) force field terms
3) comparison of different force fields
4) in-class exercise: molecular mechanics in Spartan (in-class assignment #2)
* HW #1(a) assigned
1) quiz #1 and literature application discussion (J. Phys. Chem. A, 2004, 108, 621-627)
2) classical dynamics overview
3) MD and Monte Carlo simulations
4) applications: protein folding, NMR determination of protein structure
5) in-class exercise: simulating MD in Excel (in-class assignment #3)
* HW #1(a) due; HW #1(b) assigned
1) Schrödinger equation, Born-Oppenheimer approximation
2) LCAO approach
3) Hückel theory
4) in-class exercise: Hückel theory (in-class assignment #4)
5) Hartree-Fock theory introduction and Self-consistent field method
* HW #1(b) due
1) finish Hartree-Fock theory
2) semi-empirical methods overview
3) comparison of CNDO, INDO, NDDO formalisms and performance
4) geometry representations: Cartesian coordinates, z-matrices, symmetry
5) in-class exercise: writing z-matrices (in-class assignment #5)
* HW #2(b) assigned
1) quiz #2 and literature application discussion (J. Am. Chem. Soc., 1996, 118, 8920-8924)
2) basis sets (Gaussian functions, polarization & diffuse functions, effective core potentials)
3) practical issues: SCF convergence, symmetry
4) Hartree-Fock theory accuracy
5) in-class exercise: electrophilic aromatic substitution of toluene and nitrobenzene – verification of
substitution patterns via semi-empirical and Hartree-Fock calculations (in-class assignment #6)
* HW #2(b) due; HW #2(a) assigned
Molecular properties:
1) multipole moments and molecular electrostatic potential
2) partial atomic charges and atomic spin
3) ionization potentials; electron affinities
4) infrared spectra
5) in-class exercise: organometallic metal-carbonyl half-sandwich complexes (in-class assignment #7)
1) computing enthalpy, entropy, and free energy changes for reactions
2) isodesmic reactions
3) application: calculating heats of formation and relative stability of species
4) determining transition states
5) transition state theory, rate constants
6) kinetic isotope effects, transmission coefficients
7) in-class exercise: hydrogen atom transfer between organic molecules (in-class assignment #8)
* group sign-up for final project; HW #3 assigned
1) density functional theory overview
2) Hohenberg-Kohn theorems, Kohn-Sham methodology
3) exchange & correlation functionals
4) DFT performance and comparison with MO theory
5) application discussion: transition metal complexes (J. Phys. Chem. A, 2004, 108, 5479-5483)
1) quiz #3 and literature application discussion (Phys. Chem. Chem. Phys., 2005, 7, 2701-2705)
2) the process of solvation and solvation effects on reactions
3) continuum solvation models
4) mixed explicit/implicit solvation models
5) standard-state corrections
* HW #3 due; HW #4 assigned
1) calculation of pKa values and reduction potentials
2) calculation of partition coefficients
3) application discussion: pKa values with different solvation models (J. Phys. Chem. A, 2006, 110, 2493-
2499)
4) in-class exercise: determining pKa values with different solvation models (in-class assignment #9)
2) application discussion: empirical corrections to computed NMR spectra (J. Chem. Theory Comput.,
2006, 2, 1085-1092)
3) UV-Vis spectra and TD-DFT methods
4) open-shell molecules and unrestricted wave functions
5) in-class exercise: NMR spectra at different levels of theory (in-class assignment #10)
1) quiz #4 and literature application discussion (J. Org. Chem., 2003, 68, 6375-6386)
2) overview of QM/MM methods
3) QM/MM boundaries between space and atoms
4) application discussions (J. Am. Chem. Soc., 2004, 126, 7652-7664;
J. Am. Chem. Soc., 2005, 127, 1025-1037)
* HW #4 due