Weekly Assignments on "Computational Chemistry"
(Created: 05/31/16; Updated: 10/27/16)

Assignment #0 (08/20/16): GaussView & G09W Basics (Un-Scored Exercises)
Learning Goals: Building Molecular Models. Setting-Up and Running G09W. Reading Output. Input (GJF) and Output (LOG, CHK) Files.
Tasks: Opt+Freq RHF/6-31G* for simple donor-acceptor substituted (hetero)arene (i.e., para-nitroaniline)

Assignment #1 (updated 09/07/16; 08/20/16): Geometry Definition: Cartesian & Internal Coordinates, Symmetry Constraints
Learning Goals: Construction of GJF files for simple structures with GaussView and from scratch. Symmetry constraints. Step-by-step internal coordinate scanning.
Tasks: Opt+Freq RHF/6-31G* for YH3(n-) (n = 0, Y = N, P; n = -1, Y = C, Si) in C3v and D3h Symmetry. Inversion scan in C3v symmetry.
Rubric (08/20/16). Sample as PDF and as XLSX.

Assignment #2 (updated 09/13/16; 08/20/16): Geometry Definition: File Formats, Redundant Coordinates, PES Scans
Learning Goals: Construction of GJF files for more complicated structures. From CIF (Mercury) & PDB files.
Tasks: Opt+Freq RHF/6-31G* (a) of a dimeric molecular aggregate starting from the crystal structure and (b) of an active site transition metal complex starting from a crystal structure of an enzyme.
Molecular Crystal Sample as CIF file (ASCII).
Enzyme Sample 5CJH: Crystal Structure of Eukaryotic Oxoiron MagKatG2 at pH 8.5 (PDF).
Rubric (08/20/16). Sample as PDF and as DOCX.

Assignment #3 (updated 09/13/16; 08/25/16; 08/23/16): Basis Sets: Exponents and Contraction Coefficients
Learning Goals: Basis Sets, Augmentation, Modification, General Basis Sets.
Tasks: Minima, TS, and IRC for a simple reaction (isomerization, nucleophilic substitution, or polar addition) at several RHF levels.
Rubrics for isomerizations, nucleophilic substitutions and polar additions differ slightly (08/25/16). Sample for addition reaction as PDF and as DOCX. Sample for rearrangement reaction as PDF and as DOCX.

Assignment #4 (updated 09/13/16; 08/26/16): Molecular Orbitals & Configuration Interaction (CI) Methods.
Learning Goals: MOs, Active Space, CI Methods and Approximations, Correlation Energy.
Tasks: Electron correlation effects on structures, reaction energies and activation energies for a simple reaction (isomerization, nucleophilic substitution, or polar addition)
Rubric (08/26/16). Sample as PDF parts 1, 2, and 3, and as DOCX.

Assignment #5 (updated 10/08/16; 10/03/16): Vibrational Analysis in Spectroscopy and Thermochemistry.
Learning Goals: Intra- & Intermolecular Interactions. Molecular vibrations, IR & Raman Spectra, and Thermochemistry.
Tasks: Binding energies of lithium cation hydrate, water dimer, and benzene dimer using RHF, MP2, and DFT theory.
Rubric (10/03/16). Sample as PDF and as DOCX.

Assignment #6 (updated 10/18/16; 10/08/16): Properties & Visualization (ED, SD, Populations, Moments, ESP, NMR).
Learning Goals: Electron and Spin Density Distributions, Electron and Spin Populations, Electric Moments, and Magnetic Shielding Tensors.
Tasks: Ethanol (DM, MC, ED, ESP, H-NMR) and Ozone Singlet (RHF: DM, MC; UHF: DM, MC, MSP, SD).
Rubric (10/08/16). Sample as PDF and as DOCX.

Assignment #7 (updated 10/18/16; 10/15/16): Solvation Methods & Approaches to High-Precision Energies.
Learning Goals: Estimation of Solvation Effects (SCRF) and Multi-Level Methods (G4, CBS).
Tasks: Solvent Effects on Methyl Cation Affinity of N2. Multi-Level Methods.

Rubric (10/15/16). Sample as PDF (1, 2, 3) and as DOCX.

Assignment #8 (updated (f) 11/02/16; 10/13/16): Semi-empirical Methods (SEM) and Layer Methods (LM).
Learning Goals: Modeling of large systems with SEM. Inclusion of environment effects on "active site" with LM.
Tasks: Model 3-Base Pair ds-DNA with SEM (AM1). Study property in H-bonding region of central AT pair with LM (ONIOM).
Source of ds-DNA Geometry: From Double-Stranded DNA Topology, download the file IRx0pdb.txt and rename it to IRx0.pdb. Or download the local version of IRx0.pdb.
Rubric (10/13/16). Sample as PDF (1, 2) and as DOCX.

Assignment #9 (10/25/16): Project Proposal with Preliminary Results. 1. Specific Aims, Cast & PESA
Learning Goals: Enhance your Research with Methods of Electronic Structure Theory.
Tasks for A09 & A10: Define an original problem, construct a research plan, and compute preliminary results. In A09, formulate specific aims, define your "cast" of systems to study, and obtain preliminary results from PES analysis.
Rubric (10/26/16). Sample as PDF and as DOCX.

Assignment #10 (10/25/16): Project Proposal with Preliminary Results. 2. A09 plus Background & Significance, Properties, and Proposal
Learning Goals: Enhance your Research with Methods of Electronic Structure Theory.
Tasks for A09 & A10: Define an original problem, construct a research plan, and compute preliminary results. In A10, complete your work in A09 by addition of section on background & significance, addition of preliminary results on properties, project description and time line.
Peer Review of A10 Submissions (10/25/16) involves three-fold, constructive, and un-scored scientific peer review. Samples of peer reviews R10 as PDF and as DOCX.

Assignment #11 (updated 10/26/16; 08/20/16): Oral Presentations of A10 Projects.
Learning Goals: Presentation and Defense of Project Proposal (A10).
Tasks: Construct, present and defend arguments in oral presentation.
Rubric (08/20/16).

Presentation Awards (based on R11 peer review scores): Gold (PPSM), Silver (PPSM), Bronze (PPSM).

Assignment #12 (10/27/16): Revision of A10 Projects.
Learning Goals: Revise Project Proposal Using Feedback from R10 and R11.
Tasks: Construct, present and defend arguments in scientific writing. Approaches to constructive criticism, revision and rebuttal.
Rubric (10/27/16).

Project Awards (based on R12 peer review scores): Gold (PDF), Gold (PDF), Bronze (PDF).

Course Wordle: Images 1, 2, 3, 4, & 5.