Links to download Zoom Lab Videos and PDF files

  • Lecture Date: Monday, August 31, 2020

    Today was our introductory lecture. We discussed possible structure of the course and options for the curriculum moving forward. We went over the syllabus, grading scheme, and what I think the laboratory course is going to look like in a virtual realm. No notes were taken today.

  • Lecture Date: Wednesday, September 2, 2020

    We looked at the three different types of computational packages and discussed what they are generally used for. In addition we focused our attention on the file format used for Mopac, the Z-Matrix.

  • Lecture Date: Wednesday, September 9, 2020

    Today we attempted to take a deeper look at the Z-Matrix file used by MOPAC to relate the starting geometry of a job file. We then attempted to show how to use WebMO to modify the Z-Matrix through the Z-Matrix editor. We looked at the issues MOPAC has when the dihedral angle of a molecule becomes undefined and how to use dummy atoms to help define the geometry resolving the dihedral angle issue. Unfortunately the Z-Matrix editor can'apos;t handle dummy atoms and the Z-Matrix occasionally needs to be written by hand.

  • Lecture Date: Monday, September 14, 2020

    We covered the basics of how to calculate and verify transition states from performing transition state searches, saddle calculations, using coordinate scans to get close to transition state geometries, and force calculations. We looked specifically as SN2 transition states.

  • Lecture Date: Wednesday, September 16, 2020

    Today was a doing day. The video may be choppy and hard to watch as an instructional video. Mostly what we did today was to have students use notes that I emailed out to the class to try and reproduce the calculations. Today we focused on the calculation of methylbromide as a substrate, followed by a reaction path calculation with choride and methylbromide varying the bond length between the chloride and carbon of the methylbromide. We used a dummy atom to help constring the reaction path calculation, though this substantially increased the complexity of setting up the reaction. I'apos;ll post the files emailed out here as well to use a guide once they are completed.

  • Lecture Date: Monday, September 21, 2020

    After a computer software update over the weekend we ran into technical difficulties. Lecture and lab were scrapped for Monday.

  • Lecture Date: Wednesday, September 23, 2020

    Having recovered from Monday's technical difficulties, we are back at it again. Today we completed the transition state search calculation and the force calculation to verify the transition state. As homework over the weekend you are asked to calculate the transition state for the SN2

    reaction of ethylbromide with chloride ion. This is the same process that you have just completed, only adding one more carbon to the substrate.

  • Lecture Date: Monday, September 28, 2020

    Today we did further work on the SN2 calculations of the ethyl substrate and the isopropyl substrate. No notes were taken during this lab session. All the work was done with screen share and active participation.

  • Lecture Date: Wednesday, September 30, 2020

    Two main topics today were the use of the IRC calculation to find both the starting material and product locations from the transition state, and the normalization of the energies so that the activation energy of the reactions can be directly compared. We also assigned a new compound asking you guys to calculation the transition state for a tertiary-butyl bromide with chloride ion for Monday.

  • Lecture Date: Monday, October 5, 2020

    We took a break from computational chemistry today to exam the Grignard reaction. We covered the Grignard reaction of benzyl bromide reacting with magnesium metal to produce phenyl magnesium bromide. We then looked at reacting the Grignard reagent with benzophenone to produce triphenylmethanol (also called triphenylcarbinol).

  • Lecture Date: Wednesday, October 7, 2020

    We borrowed a bit of lab time today to review some of the synthesis concepts from lecture. We looked at a few synthesis problems and discussed some key concepts in these synthesis problems.

  • Lecture Date: Monday, October 12, 2020

    Today we wrapped up the SN2 calculations lab with an overview of how to handle the data workup in excel. We walked through the calculations and how to handle the data. An excel spreadsheet template was developed and emailed out. The excel spreadsheet will also be attached below.

  • Lecture Date: Wednesday, October 14, 2020

    We are stealing a bit of time from lab again to do some review and practice problems for lecture. We did a couple of retrosynthesis problems starting from alkanes, but also review some common patterns to look for in synthesis problems.

  • Lecture Date: Monday, October 19, 2020

    So I totally messed up today. We did a problem solving session this morning and I just sort of jumped in and forgot to record the entire thing. I'apos;m sorry. And the thing is these are sort of dynamic. They are really hard to go back in and redo a lecture from scratch. I'apos;m attaching the notes from today, which are pretty good. Even better, I'apos;m going to attach some studie guides and practice problem sets to the lecture notes and video. It makes more sense to post them over there. So no video today, just the notes. Sorry.

    UPDATE - Thanks to Fernanda who asked me to go over these notes in office hours, and had the wherewithal to ask me to record the session, we now have a video review of this problem session. Updated notes and video posted below.

  • Lecture Date: Wednesday, October 21, 2020

    More problem solving sessions today, but this time I remembered to hit the record button!

  • Lecture Date: Monday, October 26, 2020

    Today we looked at some different problem types. It is important to remember that the synthesis is not the whole exam. There are individual skill sets like regioselective reactions and predicting the products. There are also puzzle type problems where you need to work backwards. All of these problem types serve to work your brain in different ways, stretching and expanding your problem solving skills and the stretching and expanding the creative ways you can look at problems!

  • Lecture Date: Wednesday, October 28, 2020

    Today we went back to more synthesis problems and a closer look at the study guide that was posted in the Lecture videos from the 19th that was the big picture common synthesis themes. I'll repost that study guide below. We went through most of the first set of problems using the epoxide pattern, but we also looked at the other patterns. This is an excellent study guide and one that you guys should really spend some time with.

  • Lecture Date: Monday, November 2, 2020

    We used today as an open session to deal with questions from the exam. Recordings and notes below.

  • Lecture Date: Wednesday, November 4, 2020

    In lab today we looked the process of doing a literature search with Web of Science. We utilized a VPN to connect to UCSC and the Science Library. We covered the basics of conducting a literature search and how to narrow down the field by sorting the articles by the number of citations a journal article has acquired.

  • Lecture Date: Monday, November 9, 2020

    Today we used lab to do NMR practice problems looking at using the number of chemical environments to match spectra to structure.

  • Lecture Date: Monday, November 16, 2020

    Today we did more NMR practice looking at spin-spin coupling and how to organize the shear amount of data that we need to handle in NMR problems.

  • Lecture Date: Wednesday, November 18, 2020

    We did NMR practice from the WebSpectra website. These spectra are the main ones that I point students towards for practice problems, but the quality of the spectra is lower and absolute integration values are missing. We show how to deal with all those problems in this session.

  • Lecture Date: Monday, November 23, 2020

    We covered the introduction to mass spectrometry today. We described who the instrument works, sensitivity, and introduction to how mass spectrometry is used with other spectra to deduce the structure and formula for a previously unknown compound.

  • Lecture Date: Wednesday, November 25, 2020

    Today we went over the mass spec practice materials available at Linda Breci's website "Introduction to Mass Spectrometry." This is where you should go for Mass Spec problems and practice.

  • Lecture Date: Monday, November 30, 2020

    Today we looked at the first example of how to put it all together - mass spectrometry to find the molecular formula, IR for some functional groups, NMR for functional groups and connectivity. We also used the spectroscopy rubric as a guide and checklist to keep track of all the parts to the problem.

  • Lecture Date: Wednesday, December 2, 2020

    Today we finished up mass spec with some more mass spectrometry problems. We focused on halogen and ketone problems in this lecture.

  • Lecture Date: Monday, December 7, 2020

    Last couple of lectures. We used today to introduce aromaticity. We discussed where aromaticity comes from, a bit of molecular orbital theory, Huckel's Rule, and he use of Frost's Circle to predict the relative energy levels of the pi system.

  • Lecture Date: Wednesday, December 9, 2020

    Alright, this does it. This is our last lab lecture. This was actually a really good session where we looked at two spectroscopy problems that I put together as a study problems. I work through both problems and highlight the non-linear nature of the way that I often attack these problems. As you work through problems you often find that you need to reconsider previous assumptions as new information comes in. These two should be helpful in working through the final problem on the exam.

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