Class Day

Topics Covered

BATs

Class #1

08/27

Syllabus, expectations

Potential energy surfaces

Class #2

08/29

Potential energy surfaces, calculable properties, how molecular modeling works, units, resources

Calculate degrees of freedom in a system. Given a PES indicate the locations of the local and global minima and the transition states. Know relation to rate and equilibrium.

Know difference between constructed and actual properties. Don't be confused by atomic units. Know what CPU speed, memory, and disk space are and what I mean by expensive

Class #3

09/03

Basic overview of MM, SE, and ab Initio

MM: empirical forcefield, atom types, functional forms of terms in Estrain

Begin to know which model is appropriate for a particular system and calculation. Know basic differences between MM, SE, and ab Initio

Explain concept of atom types and why they are used. Identify the energy terms that contribute to Estrain, the functional forms that are often used, and the parameters that are needed for a given functional form.

Class #4

09/05

1st lab day

Lab #1

Class #5

09/10

Class #6

09/12

Review

Non-bonded potentials

Given a small molecule, identify the minimum atom types and parameters for Estrain. Discuss the advantages and disadvantages of having a larger number of atom types

Draw the van der Waals potential for non-bonded interactions. Write the Lennard-Jones potential and know what eAB and sAB are and how to get them from eAA, eBB, sAA, and sBB.

Class #7

09/17

Know that electrostatic terms are important. Discuss how you assign charges to the atoms (by atom type, for each atom in a group, for each atom in your molecule) (fit to dipoles, fit to ab initio)

Give a brief discussion of how parameter values are determined by the forcefield creators. Discuss what factors you would consider when choosing a forcefield and what you would do if you had an atom type for whichthere were no parameters

Class #8

09/19

heats of formation, What can we do with molecular mechanics

HW #1

Break down the molecular mechanics total energy into each of its components and describe what those components are. Explain why you cannot compare the forcefield energy of molecules with different bonds you must compare the total energy

Discuss some of the things that molecular mechanics is well suited for. Explain why you must be careful about starting a geometry minimization from a planar geometry

Class #9

09/25

Discuss advantages and disadvantages of molecular mechanics (questions that molecular mechanics cannot address)

Define wavefunction, operator, expectation value, probability distribution

Class #10

09/27

Lab day

Class #11

10/01

Given the unlabeled quantities, and , write the Hamiltonian for a system of 5 or fewer charged particles.

Define and discuss the variational principle. Define and discuss the Born-Oppenheimer approximation.

Class #12

10/03

Exam

Class #13

10/08

Define and briefly discuss LCAO. From the picture of two atomic orbitals predict sign and relative magnitude of the overlap matrix. Define secular determinant and briefly discuss how it is used to find the MOs in LCAO formalism. Define the SCF method; Discuss why it is needed and how it works.

Class #14

10/10

Lab #3

HOMOs, LUMOs and FMO theory

Class #15

10/15

Lab #3

HOMOs, LUMOs and FMO theory

Class #16

10/17

Finish MO theory; Fock operator, one and two electron integrals

See classes 11 and 13, Briefly define the electronic wavefunction and how it is found. In words describe each of the four terms in the fock operator. Know which are one electron integrals and which are two electron integrals. Explain Figure 4.3

Class #17

10/22

NDDO Semi-empirical methods

List and discuss some of the approximations made in NDDO methods. Which integrals are set to zero, set equal to an optimizable parameter, or approximated by the interactions of point charges. How does this decrease the computational cost while either increasing the accuracy or not hurting it too much

Class #18

10/24

Lab #4, HW #3

Class #19

10/29

Class #20

10/31

Using graphs/sketches if necessary, describe the difference between Slater-type atomic orbitals and Gaussian function. Answer why Gaussian functions are used to describe atomic orbitals even though they are so different than the accurate Slater-type orbitals.

Describe the differences between the following basis sets: STO-3G, 3-21G, 6-31G, and 6-311G. Define single-zeta, double-zeta, and triple-zeta basis sets

Class #21

11/05

Discuss what polarization and diffuse functions are and why (in general terms) they may be needed. Given the name of a basis set (6-311G or 6-31+G or 3-21G* or aug-cc-pVDZ or 6-311G(2df,2pd)), tell whether or not it includes polarization or diffuse functions.

Discuss bootstrapping as it relates to SCF convergence or geometry convergence.

Class #22

11/07

Class #23

11/12

Class #24

11/14

From the name of a calculation, know which method beyond (or other than) HF is being used. (ie MP2/6-31+G* or CCSD/cc-pVDZ or B3LYP/3-21G)

For systems that don't need MCSCF, know which method of including correlations effects is the best balance of accuracy vs cost and which is the gold-standard in single reference. List two correlations methods that you can use in conjuction with MCSCF.

From the name recognize when a DFT calculation is being done. For any future work - know that DFT does well for most systems - know where to find clues to exceptions in your textbook.